research paper about nitrogen cycle

An official website of the United States government

The .gov means it’s official. Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

The site is secure. The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Publications
Account settings

Preview improvements coming to the PMC website in October 2024. Learn More or Try it out now .

Advanced Search
Journal List
Microbes Environ
v.34(3); 2019 Sep

The Nitrogen Cycle: A Large, Fast, and Mystifying Cycle

1 Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2–15 Natsushima-cho, Yokosuka 237–0061, Japan

If a story was written entitled the “Kingdom of Microbial Ecology”, how would the characters and plot be decided? Many microbiologists will agree with the following: the primary story setting involves a magnificent castle (a habitat) in fertile land with bright sunlight (the energy source), and the king and queen are the carbon and nitrogen cycles, respectively. Although this is an unusual way to begin a research highlight article in Microbes and Environments , the nitrogen cycle is one of the most important and commonly researched topics in the field of environmental microbiology.

Nitrogen is among 6 major essential elements of CHNOPS for life and composes the building blocks and intact molecules for metabolism (amino acids and proteins), heredity (nucleotides and nucleic acids), and other important biological functions. Among the essential elements, circulating volumes of biologically available nitrogen and phosphorus are slightly limited in many biospheres of the planet, and, thus, as a whole, the biological demand for nitrogen and phosphorus and their circulation speeds are markedly greater and faster than those for carbon ( 3 ). Furthermore, although the biological transformation pathways of nitrogen compounds are less diverse than those of carbon compounds when all organic forms are taken in consideration, the complexity of the catabolic and anabolic metabolism of inorganic nitrogen compounds and their synergetic processes are beyond those for carbon and cannot be compared to those of other biologically essential elements ( 9 ). This may, at least in part, explain the great interest in as well as difficulties associated with environmental microbiology research on the nitrogen cycle, which has encouraged and motivated many scientists to study it and resulted in a greater abundance of research articles and reviews on the nitrogen cycle and metabolism than on energy, carbon, and other elemental cycles and metabolism in the last decade (a quick Google scholar search shows 3,100,000 hits for “energy cycle/metabolism”, 2,830,000 hits for “carbon cycle/metabolism”, 2,470,000 hits for “nitrogen cycle/metabolism”, and 670,000 hits for “phosphorus cycle/metabolism”).

There are two large nitrogen pools on Earth, atmospheric molecular nitrogen (N 2 ) and (biologically) reactive nitrogen (NO 3 , NH 4 , and organic nitrogens) ( 3 ). The biological nitrogen cycle mainly consists of internal interactions within the reactive nitrogen pool and in- and out-flow between reactive nitrogens and atmospheric N 2 pools. Inter-connections between the two large nitrogen pools are primarily controlled by only two biological (microbial) processes, nitrogen fixation and denitrification ( 3 ), even though the impact of anthropogenic input into the terrestrial and marine reactive nitrogen pools on the global nitrogen cycle have recently increased due to fertilization and the burning of fossil fuels.

Major catabolic and anabolic microbial nitrogen metabolic pathways are shown in Fig. 1 , the complexity of which has undoubtedly motivated scientific curiosity. In the past several years, many studies that have been published in Microbes and Environments have attempted to elucidate microbial nitrogen cycles at both the local and global scales of microbial habitats and communities.

An external file that holds a picture, illustration, etc.
Object name is 34_223_1.jpg

Microbial pathways in the nitrogen cycle. Abbreviations: AOB, ammonia-oxidizing bacteria; AOA, ammonia-oxidizing archaea; Anammox, anaerobic ammonium oxidation; DNRA, dissimilatory nitrate reduction to ammonium; NOB, nitrite-oxidizing bacteria; N-AOM, oxygenic nitrite-dependent anaerobic oxidation of methane. Key enzymes in these pathways are shown as follows: AMO, ammonia monooxygenase; HAO, hydroxylamine oxidoreductase; NirK, copper-containing nitrite reductase; NirS, cytochrome cd 1 nitrite reductase; Nrf, cytochrome c nitrite reductase; NirB, cytoplasmic nitrite reductase; NAR, membrane-bound nitrate reductase; NAP, periplasmic nitrate reductase; NXR, oxidoreductase; NOS, nitric oxide synthase; Hmp, flavohemoglobins; NorVW, flavorubredoxin; cNor, nitric oxide reductase using c-type cytochromes as an electron donor; qNor, nitric oxide reductase using quinols as an electron donor; Nos, nitrous oxide reductase; HZS, hydrazine synthase; HDH, hydrazine dehydrogenase; Nif, nitrogenase. Unknown enzymatic entities and abiotic reaction steps are shown as question marks.

Nitrogen fixation is a unique ability possessed by microorganisms called diazotrophs, and involves the conversion of very inert N 2 to reactive nitrogens (including NH 3 ) ( 2 ). The conversion of N 2 to reactive nitrogens (such as NO) always occurs with lightning, which provides reactive nitrogens to the land and ocean ( 16 ). Japanese farmers previously noted a relationship between the annual abundance of lightning and rice crop yields, and referred to this lightning as “Inazuma” (the housewife for rice crop growth). However, this abiotic nitrogen fixation input has been estimated to account for only <1/10 of biological nitrogen fixation based on theoretical calculations and only approximately 10 −5 based on laboratory experiments ( 3 , 16 ). Thus, microbial nitrogen fixation and diazotrophs are key in the global nitrogen cycle and even on various scales in biological communities ever since the Earth became a planet of life approximately 4 Ga.

Nishihara and colleagues investigated nitrogen fixation in chemolithotrophic microbial communities in a hot spring stream in Japan ( 17 – 19 ). Chemolithotrophic nitrogen fixation at high temperatures (up to 92°C) has attracted scientists researching the early evolution of life and the nitrogen cycle, and deep-sea hyperthermophilic methanogens and their nitrogen fixation processes have been extensively examined ( 12 , 20 ). The types of thermophilic diazotrophs supporting nitrogen sources for chemolithotrophic microbial communities in terrestrial geothermal environments lacking a significant reactive nitrogen input were previously unknown. A series of studies by Nishihara and colleagues revealed that nitrogen fixation occurred in thermophilic microbial mats along the hot spring stream at temperatures up to 75°C, and was not associated with the functions of thermophilic methanogenic and sulfate-reducing diazotrophs, previously known as thermophilic diazotrophs, based on activity measurements and molecular analyses ( 17 , 19 ). Nishihara and colleagues also succeeded in isolating new thermophilic chemolithoautotrophs that potentially function as primary diazotrophs in microbial mat communities and showed that they were hydrogenotrophic and/or thiotrophic diazotrophs of the genus Hydrogenobacter ( 18 ). Genetic analyses of nitrogen fixation genes and phenotypes have also been performed on ecologically important diazotrophic microbes, such as a thermophilic cyanobacterium ( 26 ) and plant-associated actinobacterium ( 8 ). Using a metatranscriptomic approach, Masuda et al. ( 11 ) found that nitrogen fixation in paddy fields was primarily driven by deltaproteobacterial populations, such as Anaeromyxobacter and Geobacter , but not by other rhizospheric Proteobacteria and Cyanobacteria that were considered to be the major diazotrophs in paddy soils. Masuda et al. ( 11 ) identified true “Inazuma”, the housewife for rice crop growth, and this study was selected for the Most Valuable Paper (MVP) award of 2017 in Microbes and Environments . It is important to note that the diversity, abundance, and function of plant-associated diazotrophs are significantly controlled by the abundance and input of other reactive nitrogens ( 14 ).

In catabolic and anabolic metabolic pathways, the significance of intermediate nitrogen metabolites, such as nitrite (NO 2 ), nitric oxide (NO) and nitrous oxide (N 2 O), has been recognized in many scientific and social contexts. Nitrification, denitrification, dissimilatory nitrate reduction to ammonium (DNRA), assimilatory ammonication, and anaerobic ammonium oxidation (Anammox) each through the transformation of these intermediate nitrogen metabolites and intermediates in natural microbial communities may be multi-directionally transformed by the complex nitrogen metabolism of various populations in response to intra- and extracellular physicochemical conditions and reaction dynamics through interspecies interactions ( Fig. 1 ). Nakagawa et al. ( 15 ) reported the diversity and abundance of a nitrous oxide reductase gene ( nosZ ) in coastal eelgrass sediments and suggested that sulfur-oxidizing Gammaproteobacteria and Bacteroidetes populations contribute to N 2 O removal in eelgrass sediment microbiomes. Siqueira et al. ( 23 ) confirmed the previously proposed hypothesis that the different denitrification pathways and functions of similar Bradyrhizobium species in the soybean rhizosphere ( e.g ., with and without nosZ ) respond to the physicochemical conditions of habitats ( e.g ., in situ O 2 concentrations). Although nitrous oxide reduction (with and without nosZ ) is not key for denitrification, the abundance of nitrate reduction (the expression of napA ) may be more important. Jang et al. ( 5 ) also isolated the novel denitrifying bacterium Bradyrhizobium nitroreducens from rice paddy soil that hosted and co-expressed two types of nitrite reductase genes ( nirK and nirS ), and the majority of denitrifiers are known to possess and use each of the two types of nitrite reductases. These are also excellent examples of the complexity of the nitrogen cycle in natural microbial communities.

Besides denitrification, DNRA is considered to play an important role in energy metabolism with the nitrates and nitrites of microbial communities occurring at relatively electron-donor-enriched and/or electron-acceptor-limiting habitats based on the thermodynamic estimation of energy efficiency. Chutivisut et al. ( 1 ) showed that the denitrifying microbial community of activated sludge from a municipal wastewater treatment plant enriched DNRA populations when it was incubated under the condition of a high donor/acceptor ratio. Furthermore, Microbes and Environments recently published a number of studies on ecologically important nitrogen catabolism by Anammox and Anammox microbial communities ( 13 , 22 ).

In many natural and anthropogenic habitats, nitrifying microbial communities are reliant on the close cooperation of two distinct groups, namely, that between ammonia- and nitrite-oxidizing metabolism (except for Comammox) ( 25 ) and also that between archaeal and bacterial populations. Ammonia-oxidizing archaea (AOA) play a significant role in natural environments and include phylogenetically and physiologically diverse members. Using a metagenomic analysis and the long-term enrichment of a thermophilic nitrifying microbial community obtained from a subsurface geothermal water stream, Kato et al. ( 6 ) demonstrated that previously uncultivated Nitrocaldus and Aigarchaeota members were enriched in the thermophilic ammonium-fed culture and may be involved in not only nitrification, but also denitrification in a long-term culture and indigenous habitats. Isoda et al. ( 4 ) and Nunoura et al. ( 21 ) reported the nitrifying archaeal phylotype diversity and potential niche separation of diverse Thaumarchaeota in Finnish and Japanese forest soils as well as in the world’s deepest Challenger Deep of the Mariana Trench. These AOA oxidize ammonia to hydroxylamine by ammonia monooxygenase (Amo); however, the enzymatic entity that catalyzes the oxidation of hydroxylamine to nitrite, corresponding to hydroxylamine dehydrogenase (Hao) in the case of ammonia-oxidizing bacteria (AOB), remains unclear ( 24 ). AOA are known to produce nitric oxide during their chemolithoautotrophic growth ( 10 ). Using the recombinant copper-containing nitrite reductase (NirK) of Nitrososhaera viennensis and enzymological characterization, Kobayashi et al. ( 7 ) confirmed that NirK is involved in the production of nitric oxide via hydroxylamine oxidation and nitrite reduction during chemolithoautotrophic growth. Under the experimental conditions described, no evidence of nitrite production from hydroxylamine by the recombinant NirK was obtained ( 7 ); however, this study provided key insights into the as-yet-unknown metabolic pathways and enzymatic entities of ammonia oxidation and nitric oxide production by AOA. This concise, but impacted study was selected for the MVP award of 2018 in Microbes and Environments .

The MVPs in Microbes and Environments in the last two years have been awarded to studies on the nitrogen cycle. Therefore, the large, fast, and complex nitrogen cycle has attracted the attention of many environmental microbiologists worldwide, and Microbes and Environments has significantly contributed to lifting the veil of secrecy surrounding “the Queen of the Kingdom of Microbial Ecology”.

Nitrogen Cycles: Past, Present, and Future

Published: September 2004
Volume 70 , pages 153–226, ( 2004 )

Cite this article

J. N. Galloway 1 ,
F. J. Dentener 2 ,
D. G. Capone 3 ,
E. W. Boyer 4 ,
R. W. Howarth 5 ,
S. P. Seitzinger 6 ,
G. P. Asner 7 ,
C. C. Cleveland 8 ,
P. A. Green 9 ,
E. A. Holland 10 ,
D. M. Karl 11 ,
A. F. Michaels 11 , 2 ,
J. H. Porter 11 , 3 ,
A. R. Townsend 11 , 4 &
C. J. Vöosmarty 11 , 5

28k Accesses

3820 Citations

61 Altmetric

Explore all metrics

This paper contrasts the natural and anthropogenic controls on the conversion of unreactive N 2 to more reactive forms of nitrogen (Nr). A variety of data sets are used to construct global N budgets for 1860 and the early 1990s and to make projections for the global N budget in 2050. Regional N budgets for Asia, North America, and other major regions for the early 1990s, as well as the marine N budget, are presented to Highlight the dominant fluxes of nitrogen in each region. Important findings are that human activities increasingly dominate the N budget at the global and at most regional scales, the terrestrial and open ocean N budgets are essentially disconnected, and the fixed forms of N are accumulating in most environmental reservoirs. The largest uncertainties in our understanding of the N budget at most scales are the rates of natural biological nitrogen fixation, the amount of Nr storage in most environmental reservoirs, and the production rates of N 2 by denitrification.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Subscribe and save.

Get 10 units per month
Download Article/Chapter or eBook
1 Unit = 1 Article or 1 Chapter
Cancel anytime

Price includes VAT (Russian Federation)

Instant access to the full article PDF.

Rent this article via DeepDyve

Institutional subscriptions

Convergent estimates of marine nitrogen fixation

Marine Nitrogen and Climate Change

Revisiting the distribution of oceanic N 2 fixation and estimating diazotrophic contribution to marine production

Explore related subjects.

Environmental Chemistry

Aber J.D., Magill A., McNulty S.G., Boone R.D., Nadelhoffer K.J., Downs M. and Hallett R. 1995. Forest biogeochemistry and primary production altered by nitrogen saturation. Water Air Soil Pollut. 85: 1665–1670.

Google Scholar

Aber J.D., McDowell W.H., Nadelhoffer K.J., Magill A., Berntson G., Kamakea M., McNulty S.G., Currie W., Rustad L. and Fernandez I. 1998. Nitrogen saturation in temperate forest ecosystems: hypotheses revisited. BioScience 48: 921–934.

Agrawal G.D., Lunkad S.K. and Malkhed T. 1999. Diffuse agricultural nitrate pollution of groundwaters in India. Water Sci. Technol. 39: 67–75.

Alexander R.B., Johnes P.J., Boyer E.W. and Smith R.A. 2002. A comparison of methods for estimating the riverine export of nitrogen from large watersheds. Biogeochemistry 57/58: 295–339.

Aller R.C., Mackin J.E., Ullman W.J., Wang C.H., Tsai S.M., Jin J.C., Sui Y.N. and Hong J.Z. 1985. Early chemical diagenesis,sediment-water solute exchange, and storage of reactive organic matter near the mouth of the Changjiang, East China Sea. Continental Shelf Res. 4(1–2): 227–251.

Altabet M.A., Francois R., Murray D.W. and Prell W.L. 1995. Climate-related variations in denitrification in the Arabian Sea from sediment 15 N/ 14 N ratios. Nature 373: 506–510.

Asner G.P., Townsend A.R., Riley W.J., Matson P.A., Neff J.C. and Cleveland C.C. 2001. Physical and biogeochemical controls over terrestrial ecosystem responses to nitrogen deposition. Biogeochemistry 54: 1–39.

Ayres R.U., Schlesinger W.H. and Socolow R.H. 1994. Human impacts on the carbon and nitrogen cycles. In: Socolow R.H., Andrews C., Berkhout R. and Thomas V. (eds), Industrial Ecology and Global Change. Cambridge University Press, New York, pp. 121–155.

Bacon P.E. and Freney J.R. 1989. Nitrogen loss from different tillage systems and the effect on cereal grain yield. Fert. Res. 20: 59–66.

Bange H., Rixen T., Johansen A., Siefert R., Ramesh R., Ittekkot V., Hoffmann M. and Andreae M. 2000. A revised nitrogen budget for the Arabian Sea. Global Biogeochem. Cycles 14: 1283–1297.

Bashkin V.N., Park S.U., Choi M.S. and Lee C.B. 2002. Nitrogen budgets for the Republic of Korea and the Yellow Sea region. Biogeochemistry 57–58: 387–403.

Behrenfeld M.and Kolber Z. 1999. Widespread iron limitation in the South Pacific Ocean. Science 283: 840–843.

Bender M., Ganning K.A., Froelich P.M., Heath G.R. and Maynard V. 1977. Interstitial nitrate profiles and oxidation of sedimentary organic matter in the eastern equatorial Atlantic. Science 198: 605–609.

Billen G. 1978. Budget of nitrogen recycling in North Sea sediments off Belgian Coast. Estuarine Coastal Marine 7(2): 127–146.

Binkley D., Cromack K. Jr. and Baker D.D. 1994. Nitrogen xation by red alder: biology, rates, and controls. In: Hibbs D.E. et al. (eds), The Biology and Management of Red Alder. Oregon State Univ. Press, Corvallis, pp. 57–72.

Blundon D.J. and Dale M.R.T 1990. Dinitrogen xation (acetylene reduction) in primary succession near Mount Robson, British Columbia, Canada. Arct. Alp Res. 22: 255–263.

Boesch D.F., Brinsfield R.B., Howarth R.W., Baker J.L., David M.B., Downsing J., Fretz A.T., Jaynes D.B., Keeney D.R., Lowarnace R., Miller K., Mitsch W.J., Nemazie D., Paerl H.W., Rabalais N.N., Randall G.W., Scavia D., Schepters J.S., Shabman L., Sharpley A.N., Simposon T.W., Staver K.W. and Townsend A. 2002. Improving water quality while maintaining agricultural production. Submitted manuscript.

Bonan G.B. 1996. A Land Surface Model (LSM Version 1.0) for Ecological, Hydrological and Atmospheric Studies: Technical Description and User 's Guide. NCAR Technical Note T.N.-417+STR. National Center for Atmospheric Research, Boulder, CO.

Boring L.R. and Swank W.T. 1984. The role of black locust (Robinia pseudo-acacia ) in forest succession. J. Ecol. 72: 749–766.

Bouwman A.F., van der Hoek K.W. and Olivier J.G.J. 1995. Uncertainty in the global source distribution of nitrous oxide. J. Geophys. Res. 100: 2785–2800.

Bouwman A.F., Lee D.S., Asman W.A.H., Dentener F.J., van der Hoek K.W. and Olivier J.G.J. 1997. A global high-resolution emission inventory for ammonia. Global Biogeochem. Cycles 11: 561–578.

Bouwman A.F., Bouman L.J.M and Batjes N.H. 2002. Estimation of global MH 3 volatilization loss from synthetic fertilizers and animal manure applied to arable lands and grasslands. Global Biogeochem. Cycles 16(2): Art. No. 1024.

Boyer E.W. and Howarth R.H. (eds) 2002. The Nitrogen Cycles at Regional to Global Scales. Kluwer, New York.

Boyer E.W., Goodale C.L., Jaworski N.A. and Howarth R.W. 2002. Anthropogenic nitrogen sources and relationships to riverine nitrogen export in the northeastern USA. Biogeochemistry 57–58: 137–169.

Bradley M.J. and Jones B.M. 2002. Reducing global NO x emissions:promoting the development of advanced energy and transportation technologies. Ambio 31: 141–149.

Brandes J.A. and Devol A.H. 2002. A global marine-fixed nitrogen isotopic budget: Implications for Holocene nitrogen cycling. Global Biogeochem. Cycles 16(4): Art. No. 1120.

Brandes J., Devol A., Yoshinari T., Jayakumar D. and Naqvi S. 1998. Isotopic composition of nitrate in the central Arabian Sea and eastern tropical North Pacific: a tracer for mixing and nitrogen cycles. Limnol. Oceanogr. 43: 1680–1689.

Brenkert A.L. (ed.) 1997. Northern Hemisphere Biome and Process Specific Forest Areas and Gross Merchantable Volumes: 1890–1990. CDIAC (Carbon Dioxide Information Analysis Center) Database DB1017 (2/1997). Oak Ridge National Laboratory, TN.

Broecker W.S. and Henderson G.M. 1998. The sequence of events surrounding termination II and their implications for the cause of glacial-interglacial CO 2 changes. Paleoceanography 13: 352–364.

Burkart M.R. and James D.E. 2003. Agricultural nitrogen trends in the Mississippi Basin, 1949–1997. In: Hellums D. (ed.), Agricultural Production Systems of the 21st Century: Challenges and Opportunities in Plant Nutrient Management. ASA Special Publication, Madison, WI.

Butterback-Bahl K., Gasche R., Willibald G. and Papen H. 2002. Exchange of N-gases at the Höglwald forest—a summary. Plant Soil 240: 117–123.

Cai G.X., Zhu Z.L., Trevitt A.C.F., Freney J.R. and Simpson J.R. 1986. Nitrogen loss from ammonium bicarbonate and urea fertilizers applied to flooded rice. Fert. Res. 10: 203–215.

Capone D.G. 1983. Benthic nitrogen xation. In: Carpenter E.J. and Capone D.G. (eds), Nitrogen in the Marine Environment. Academic Press, New York, pp.105–137.

Capone D.G. 2001. Marine nitrogen xation:what 's the fuss? Curr. Opin. Microbiol. 4: 341–348.

Capone D.G. and Carpenter E.J. 1999. Nitrogen xation by marine cyanobacteria: historical and global perspectives. Bull. Inst.Oceanogr. Monaco 19: 235–256.

Capone D.G., Zehr J., Paerl H., Bergman B. and Carpenter E.J. 1997. Trichodesmium : a globally significant marine cyanobacterium. Science 276: 1221–1229.

Capone D.G., Subramaniam A., Montoya J., Voss M., Humborg C., Johansen A., Siefert R. and Carpenter E.J. 1998. An extensive bloom of the N 2 -fixing cyanobacterium, Trichodesmiumery-thraeum , in the Central Arabian Sea. Mar. Ecol. Prog. Ser. 172: 281–292.

Capone D., Burns J.A., Montoya J.P., Michaels A.F., Subramaniam A. and Carpenter E.J. 2004. New nitrogen input to the tropical North Atlantic Ocean by nitrogen fixation by the cyano-bacterium, Trichodesmium spp. Global Biogeochemical Cycles.

Carpenter E.J. 1983a. Nitrogen xation by marine Oscillatoria ( Trichodesmium ) in the world's oceans. In: Carpenter E.J. and Capone D.G. (eds), Nitrogen in the Marine Environment. Academic Press, New York, pp. 65–103.

Carpenter E.J. 1983b. Physiology and ecology of marine Oscillatoria (Trichodesmium ). Marine Biol. Lett. 4: 69–85.

Carpenter E.J. and Capone D.G. 1992. Nitrogen fixation in Trichodesmium blooms. In: Carpenter E.J. (ed.), Marine Pelagic Cyanobacteria: Trichodesmium and other Diazotrophs. Kluwer, New York, pp. 211–217.

Carpenter E.J. and Price C.C. 1977. Nitrogen fixation, distribution, and production of Oscillatoria ( Trichodesmium ) in the northwestern Atlantic Ocean and Caribbean Sea. Limnol. Oceanog. 22: 60–72.

Carpenter E., Montoya J.P., Burns J., Mulholland M., Subramaniam A. and Capone D.G. 1999. Extensive bloom of a N 2 -fixing symbiotic association in the tropical Atlantic Ocean. Mar. Ecol. Prog. Ser. 188: 273–283.

Carpenter E.J., Subramaniam A. and Capone D.G. 2004. Biomass and primary productivity of the cyanobacterium, Trichodesmium spp., in the southwestern tropical N Atlantic Ocean. Deep-Sea Research I 51: 173–203.

Cassman K.G., Dobermann A.D. and Walters D. 2002. Agroecosystems, nitrogen management and economics. Ambio 31: 132–140.

Chameides W.L., Kasibhatla P.S., Yienger J. and Levy H. II 1994. The growth of continental-scale metro-agro-plexes, regional ozone pollution, and world food production. Science 264: 74–77.

Christensen J.P., Murray J.W., Devol A.H. and Codispoti L.A. 1987. Denitrification in continental shelf sediments has a major impact on the oceanic nitrogen budget. Global Biogeochem. Cycles 1: 97–116.

Cleveland C.C., Townsend A.R., Schimel D.S., Fisher H., Howarth R.W., Hedin L.O., Perakis S.S., Latty E.F., Von Fischer J.C., Elseroad A. and Wasson M.F. 1999. Global patterns of terrestrial biological nitrogen (N 2 )fixation in natural ecosystems. Global Biogeochem. Cycles 13: 623–645.

Codispoti L.A. and Richards F.A. 1976. Analysis of horizontal regime of denitrification in Eastern Tropical North Pacific. Limnol. Oceanog. 21: 379–388.

Codispoti L., Brandes J., Christensen J., Devol A., Naqvi S., Paerl H. and Yoshinari T. 2001. The oceanic fixed nitrogen and nitrous oxide budgets: moving targets as we enter the anthropocene? Scientia Marina 65(Supp.2): 85–105.

Conrad R. and Dentener F.J. 1999. The application of compensation point concepts in scaling of fluxes. In: Bouwman A.F. (ed.), Approaches to Scaling of Trace Gas Fluxes in Ecosystems. Elsevier, New York, pp. 203–216.

Cornell S., Rendell A. and Jickells T. 1995. Atmospheric input of dissolved organic nitrogen in the oceans. Nature 376: 243–246.

Crews T.E. 1999. The presence of nitrogen fixing legumes in terrestrial communities: evolutionary vs. ecological considerations. Biogeochemistry 46: 233–246.

Craswell E.T. and Martin A.E. 1975a. Isotopic studies of the nitrogen balance in a cracking clay. I. Recovery of added nitrogen from soil and wheat in the glasshouse and gas lysimeter. Aust. J. Soil Res. 13: 43–52.

Craswell E.T.and Martin A.E. 1975b. Isotopic studies of the nitrogen balance in a cracking clay. II. Recovery of nitrate 15 N added to columns of packed soil and microplots growing wheat in the field. Aust. J. Soil Res. 13: 53–61.

Davidson E.A. and Ackerman I.L. 1993. Changes in soil carbon inventories following cultivation of previously untilled soils. Biogeochemistry 20: 161–193.

Davidson E.A. and Kingleee W 1997. A global inventory of nitric oxide emissions from soils. Nutr. Cycl. Agroecosyst. 48: 37–50.

De Datta S.K., Trevitt A.C.F., Freney J.R., Obcemea W.N., Real J.G. and Simpson J.R. 1989. Measuring nitrogen losses from lowland rice using bulk aerodynamic and nitrogen-15 balance methods. Soil Sci. Soc. Am. J. 53: 1275–1281.

Delwiche C.C. 1970. The nitrogen cycle. Sci. Am. 223: 137–146.

Dentener F.J. and Crutzen P.J. 1994. A three-dimensional model of the global ammonia cycle. J. Atmos. Chem. 19: 331–369.

Dentener F.J. and Raes F. 2002. Greenhouse gases and atmospheric chemistry: towards integration of air pollution and climate change olicies. Third International Symposium on Non-CO 2 Greenhouse Gases (NCGG-3). Maastricht, the Netherlands.

Deutsch C., Gruber N., Key R.M., Sarmiento J.L. and Ganachaud A. 2001. Denitrification and N 2 fixation in the Pacific Ocean. Global Biogeochem. Cycles 15: 483–506.

Devol A.H. 1991. Direct measurement of nitrogen gas fluxes from continental shelf sediments. Nature 349: 319–322.

Devol A., Codispoti L. and Christensen J. 1997. Summer and winter denitrification rates in western Arctic shelf sediments. Cont. Shelf Res. 17: 1029–1050.

Dise N.B. and Wright R.F. (eds) 1992. The NITREX Project, Commission of the European Communities; Ecosystems Research Rep. No. 2. Brussels.

Dise N.B. and Wright R.F. 1995. Nitrogen leaching from European forests in relation to nitrogen deposition. For. Ecol. Manage. 71: 153–161.

Dore J.E., Brum J.R., Tupas L.M. and Karl D.M. 2002. Seasonal and interannual variability in sources of nitrogen supporting export in the oligotrophic subtropical North Pacific Ocean. Limnol. Oceanogr. 47: 1595–1607.

EDC 2000. Global Land Cover Characterization. Accessible through the Eros Data Center Distributed Active Archive Center at http://edcdaac.usgs.gov/.

Emmer E. and Thunell R.C. 2000. Nitrogen isotope variations in Santa Barbara Basin sediments: implications for denitrication in the eastern tropical North Pacific during the last 50,000 years. Paleoceanography 15(4): 377–387.

Erisman J.W., de Vries W., Kros H., Oenema O., van der Eerden L., van Zeijts H. and Smeulders S. 2001. An outlook for a national integrated nitrogen policy. Environ. Sci. Pol. 4: 87–95.

ESRI 1993. Digital Chart of the World. Environmental Systems Research Institute, Inc., Redlands, California.

Falkowski P. 1997. Evolution of the nitrogen cycle and its influence on biological sequestration of CO 2 in the oceans. Nature 387: 272–273.

Falkowski P. 2000. Rationalizing elemental ratios in unicellular algae. J. Phycol. 36: 3–6.

FAO 2000. Fertilizer requirements in 2015 and 2030. Published by Food and Agriculture Organization of the United Nations, Rome, ISBN 92-5-104450-3, pp. 29.

FAO 2002. World agriculture: towards 2015/2040, Summary Report. Published by Food and Agriculture Organization of the United Nations, Rome, ISBN 92-5-104761-8, 97 pp.

FAOSTAT 2000. FAO Statistical Databases. Accessible through the Food and Agriculture Organization of the United Nations at http://apps.fao.org.

Farrell J.W., Pedersen T.F., Calvert S.E. and Nielsen B. 1995. Glacial-interglacial changes in nutrient utilization in the equatorial Pacific Ocean. Nature 377: 514–518.

Febre Domene L. and Ayres R.U. 2001. Nitrogen's role in industrial systems. J. Indust. Ecol. 5: 77–103.

Fekete B.M., Vörösmarty C.J. and Grabs W. 2002. High-resolution fields of global runoff combining observed river discharge and simulated water balances. Global Biogeochem. Cyles 16(3): Art. No. 1042.

Fenn M.E., Poth M.A., Aber J.D., Baron J.S., Bormann B.T., Johnson D.W., Lemly A.D., McNulty S.G., Ryan D.F. and Stottlemyer R 1998. Nitrogen excess in North American ecosystems: predisposing factors, ecosystem responses and management strategies. Ecol. Appl. 8: 706–733.

Fixen P.E. and West F.B. 2002. Nitrogen fertilizers: meeting the challenge. Ambio 31: 169–176.

Follett J.R. and Follett R.F. 2001. Utilization and metabolism of nitrogen by humans. In: Follett R. and Hatfield J.L. (eds), Nitrogen in the Environment: Sources, Problems and Management. Elsevier, New York, pp. 65–92.

Freney J.R., Trevitt A.C.F, De Datta S.K., Obcemea W.N. and Real J.G. 1990. The interdependence of ammonia volatilization and denitrification as nitrogen loss processes in flooded rice in the Philippines. Biol. Fert. Soils 9: 31–36.

Freney J.R., Smith C.J. and Mosier A.R. 1992. Effect of a new nitrification inhibitor (wax coated calcium carbide) on transformations and recovery of fertilizer nitrogen by irrigated wheat. Fert. Res. 32: 1–11.

Freney J.R., Chen D.L., Mosier A.R., Rochester I.J., Constable G.A. and Chalk P.M. 1993. Use of nitrification inhibitors to increase fertilizer nitrogen recovery and lint yield in irrigated cotton. Fert. Res. 34: 37–44.

Freney J.R., Keerthisinghe D.G., Phongpan S., Chaiwanakupt P. and Harrington K. 1995. Effect of urease, nitrification and algal inhibitors on ammonia loss, and grain yield of flooded rice in Thailand. Fert. Res. 40: 225–233.

Fuhrman J.A. and Capone D.G. 1991. Possible biogeochemical consequences of ocean fertilization. Limnol. Oceanogr. 36: 1951–1959.

Galbally I.E., Freney J.R., Muirhead W.A., Simpson J.R., Trevitt A.C.F and Chalk P.M. 1987. Emission of nitrogen oxides (NO x )from a flooded soil fertilized with urea: relation to other nitrogen loss processes. J. Atmos. Chem. 5: 343–365.

Galloway J.N. 1998. The global nitrogen cycle: changes and consequences. Environ. Pollut. 102(S1): 15–24.

Galloway J.N. 2000. Nitrogen mobilization in Asia. Nutr. Cycl. Agroecosyst. 57: 1–12.

Galloway J.N. and Cowling E.B. 2002. Reactive nitrogen and the world: two hundred years of change. Ambio 31: 64–77.

Galloway J.N., Schlesinger W.H., Levy H. II, Michaels A. II and Schnoor J.L. 1995. Nitrogen fixation: anthropogenic enhancement–environmental response. Global Biogeochem. Sci. 9: 235–252.

Galloway J.N., Howarth R.W., Michaels A.F., Nixon S.W., Prospero J.M. and Dentener F.J. 1996. Nitrogen and phosphorus budgets of the North Atlantic Ocean and its watershed. Biogeochemistry 35: 3–25.

Galloway J.N., Cowling E.B., Seitzinger S.J. and Socolow R 2002. Reactive nitrogen: too much of a good thing? Ambio 31: 60–63.

Galloway J.N., Aber J.D., Erisman J.W., Seitzinger S.P., Howarth R.H., Cowling E.B. and Cosby B.J. 2003. The nitrogen cascade. BioScience 53: 341–356.

Ganeshram R.S., Pedersen T.F., Calvert S.E. and Murray J.W. 1995. Large changes in oceanic nutrient inventories from glacial to interglacial periods. Nature 376: 755–758.

Ganeshram R., Pederson T.F., Calvert S.E. and Francois R. 2002. Reduced nitrogen fixation in the glacial ocean inferred from changes in marine nitrogen inventories and phosphorus inventories. Nature 415: 156–159.

Gao Y., Kaufman J., Tanre D., Kolber D. and Falkowski P.G. 2001. Seasonal distribution of aeolian iron fluxes to the global ocean. Geophys. Res. Lett. 28: 29–32.

Goering J.J., Dugdale R.C. and Menzel D. 1966. Estimates of in situ rates of nitrogen uptake by Trichodesmium sp. in the tropical Atlantic Ocean. Limnol. Oceanogr. 11: 614–620.

Goodale C.L., Lajtha K., Nadelhoffer K.J., Boyer E.A. and Jaworski N.A. 2002. Forest nitrogen sinks in large eastern US watersheds: estimates from forest inventory and an ecosystem model. Biogeochemistry 57/58: 239–266.

Goolsby D.A., Battaglin W.A., Lawrence G.B., Artz R.S., Aulenbach B.T., Hooper R.P., Keeney D.R. and Stensland G.J. 1999. Flux and sources of nutrients in the Mississippi-Atchafalaya River Basin; Topic 3. Report for the Integrated Assessment on Hypoxia in the Gulf of Mexico. NOAA Coastal Ocean Program Decision Analysis Series No. 17. NOAA, Silver Spring, MD.

Gorham E., Vitousek P.M. and Reiners W.A. 1979. The regulation of chemical budgets over the course of terrestrial ecosystem succession. Ann. Rev. Ecol. Syst. 10: 53–84.

Green P.A., Vörösmarty C.J., Meybeck M., Galloway J.N., Peterson B.J. and Boyer E.W. 2004. Pre-industrial and contemporary fluxes of nitrogen through rivers: a global assessment based on typology. Biogeochemistry 68(1): 71–105.

Gruber N. 2004. The dynamics of the marine nitrogen cycle and its influence on atmospheric CO 2 variation. In: Follows M. and Oguz T. (eds), Carbon Climate Interactions. J. Wiley, Hoboken, NJ, in press.

Gruber N. and Sarmiento J.1997. Global patterns of marine nitrogen fixation and denitrification. Global Biogeochem. Cycles 11: 235–266.

Gundersen K., Corbin J., Hanson C., Hanson M., Hanson R., Russell D., Stollar A. and Yamada O. 1976. Structure and biological dynamics of the oligotrophic ocean photic zone off the Hawaiian Islands. Pacific Sci. 30: 45–68.

Gundersen P. 1991. Nitrogen deposition and the forest nitrogen cycle: role of denitrification. For. Ecol. Manage. 44: 15–28.

Haines J.R., Atlas R.M., Griffiths R.P. and Morita R.Y. 1981. Denitrification and nitrogen-fixation in Alaskan continental–shelf sediments. Appl. Environ. Microbiol. 41: 412–421.

Hansell D., Bates N. and Olson D. 2004. Excess nitrate and nitrogen fixation in the North Atlantic Ocean. Mar. Chem. 84: 243–265.

Haug G., Pedersen T., Sigman D., Calvert S., Nielsen B. and Peterson L. 1998. Glacial/interglacial variations in production and nitrogen fixation in the Cariaco Basin during the last 580K years. Paleoceanography 13: 427–3432.

Hedges J.I. and Keil R.G. 1995. Sedimentary organic matter preservation: an assessment and speculative synthesis. Mar. Chem. 49: 81–115.

Hedin L.O., Armesto J.J. and Johnson A.H. 1995. Patterns of nutrient loss from unpolluted, old-growth temperate forests: evaluation of biogeochemical theory. Ecology 76: 493–509.

Holland E.A., Braswell B.H., Lamarque J.F., Townsend A., Sulzman J.F., Müller J.-F., Dentener F., Brasseur G., Levy H. II, Penner J.E. and Roelofs G.J. 1997. Variations in the predicted spatial distribution of atmospheric nitrogen deposition and their impact on carbon uptake by terrestrial ecosystems. J. Geophys. Res. 102: 15849–15866.

Holland E.A., Dentener F.J., Brasswell B.H. and Sulzman J.M. 1999. Contemporary and pre-industrial global reactive nitrogen budgets. Biogeochemistry 46: 7–43.

Houghton R.A. and Hackler J.L. 2002. Carbon flux to the atmosphere from land-use changes. In: Trends: A Compendium of Data on Global Change. Carbon Dioxide Information Analysis Center, Oak Ridge National Laboratory, US Department of Energy, Oak Ridge, TN.

Howarth R.W. 1998. An assessment of human influences on fluxes of nitrogen from the terrestrial landscape to the estuaries and continental shelves of the North Atlantic Ocean. Nutr. Cycl. Agroecosyst. 52: 213–223.

Howarth R.W., Marino R., Lane J. and Cole J.J. 1988. Nitrogen fixation in freshwater, estuarine, and marine ecosystems. 2. Biogeochemical controls. Limnol. Oceanogr. 33: 688–701.

Howarth R.W., Billen G, Swaney D., Townsend A., Jaworksi N., Lajtha K., Downing J.A., Elmgren R., Caraco N., Jordan T., Berendse F., Freney J., Kudeyarov V., Murdoch P. and Zhu Zhao-Liang 1996. Regional nitrogen budgets and riverine N and P fluxes for the drainages to the North Atlantic Ocean: Natural and human influences. Biogeochemistry 35: 75–139.

Howarth R.W., Boyer E., Pabich W. and Galloway J.N. 2002. Nitrogen use in the United States from 1961–2000, and estimates of potential future trends. Ambio 31: 88–96.

Humphreys E., Freney J.R., Constable G.A., Smith J.W.B., Lilley D. and Rochester I.J. 1990. The fate of your N fertilizer. In Porch. 5th Aust. Cotton Conf., pp. 161–164.

IMAGE 2001. The IMAGE 2.2 implementation of the SRES scenarios. A comprehensive analysis of emissions, climate change and impacts in the 21st Century. CD-ROM publication 481508018. National Institute for Public Health and the Environment, Bilthoven, The Netherlands.

IPCC 1996. Climate change 1995: the science of climate change. In: Houghton J.T., Meira Filho L.G., Callander B.A., Harris N., Kattenberg A. and Maskell K. (eds), Second Assessment Report of the Intergovernmental Panel on Climate Change. Cambridge University Press, New York.

IPCC 2001. Climate change 2001: the scientific basis. In: Houghton J.T., Griggs D.J., Noguer M., van der Linden P.J., Dai X., Maskell K. and Johnson C.A. (eds), Third Assessment Report of the Intergovernmental Panel on Climate Change. Cambridge University Press, New York.

Joos F., Plattner G.K., Stocker T.F., Marchal O. and Schmittner A. 1999. Global warming and marine carbon cycle feedbacks and future atmospheric CO 2 . Science 284: 464–467.

Johnson H.B. and Mayeux H.S. 1990. Prosopis glandulosa and the nitrogen balance of rangelands: extent and occurrence of nodulation. Oecologia 84: 176–185.

Karl D.M. 1999. A sea of change:biogeochemical variability in the North Pacific subtropical gyre. Ecosystems 2: 181–214.

Karl D.M. 2002. Nutrient dynamics in the deep blue sea. Trends Microbiol. 10: 410–418.

Karl D.M., Letelier R., Hebel D.V., Bird D.F. and Winn C.D. 1992. Trichodesmium blooms and new nitrogen in the north Pacific gyre. In: Carpenter E.J., Capone D.G. and Rueter J.G. (eds), Marine Pelagic Cyanobacteria: Trichodesmium and Other Diazotrophs. Kluwer, New York, pp. 219–237.

Karl D., Letelier R., Tupas L., Dore J., Christian J. and Hebel D. 1997. The role of nitrogen xation in biogeochemical cycling in the subtropical north Pacific ocean. Nature 386: 533–538.

Karl D., Michaels A., Bergman B., Capone D., Carpenter E., Leetelier R., Lipschultz F., Paerl H., Sigman D. and Stal L. 2002. Dinitrogen fixation in the world's oceans. Biogeochemistry 57/58: 47–98.

Keerthisinghe D.G., Freney J.R. and Mosier A.R. 1993. Effect of wax-coated calcium carbide and nitrapyrin on nitrogen loss and methane emission from dry-seeded flooded rice. Biol. Fertil. Soils 16: 71–75.

Khalil M.A. and Rasmussen R.A. 1982. The global sources of nitrous oxide. J. Geophys. Res. 97: 14651–14660.

Klein Goldewijk C.G.M. and Battjes J.J. 1997. A hundred year (1890–1990) database for integrated environmental assessments (HYDE, version 1.1) Rept. 422514002, Natl. Ist. of Pub. Health and the Environment. Bilthoven, Netherlands.

Koike I. and Hattori A. 1979. Estimates of dentirification in sediments of the Bering Sea shelf. Deep Sea Res. 26(4): 409–415.

Kossinna E. 1921. Die Tiefen des Weltmeeres. Inst. Meersekunde, Veroff., Geogr.-naturwiss, 70 pp.

Kramer D.A. 1999. Minerals Yearbook. Nitrogen. US Geological Survey Minerals Information. http://minerals.usgs.gov/minerals/pubs/commodity/nitrogen/.

Kroeze C. and Seitzinger S.P. 1998. Nitrogen inputs to rivers, estuaries and continental shelves and related nitrous oxide emissions in 1990 and 2050: a global model. Nutr. Cycl. Agroecosyst. 52: 195–212.

Kroeze C., Mosier A. and Bouwman L. 1999. Closing the global N 2 O budget: a retrospective analysis 1500–1994. Global Biogeochem. Cycles 13: 1–8.

Kroeze C., Aerts R., Van Breemen N., van Dam D., van der Hoek K., Hofschreuder P., Hoosbeek M., de Klein J., Kros H., van Oene H., Oenema O., Tietema A., van der Veeren R. and de Vries W. 2003. Uncertainties in the fate of nitrogen. I: an overview of sources of uncertainty illustrated with a Dutch case study. Nutr. Cycl. Agroecosyst. 66(1): 43–69.

Laursen A.E. and Seitzinger S.P. 2002. Measurement of denitrification in rivers: an integrated, whole reach approach. Hydrobiologia 485: 67–81.

Lee K., Karl D.M., Wannikhof R. and Zhang J.-Z. 2002. Global estimate of net carbon production in the nitrate-depleted tropical and sub-tropical ocean. S. Geophys. Res. Lett. 29(19): Art. No. 1907.

Lelieveld J. and Dentener F. 2000. What controls tropospheric ozone? J. Geophys. Res. 105: 3531–3551.

Letelier R.M. and Karl D.M. 1996. Role of Trichodesmium spp. in the productivity of the sub-tropical north Pacific ocean. Mar. Ecol. Prog. Ser. 133: 263–273.

Letelier R.M. and Karl K.M. 1998. Trichodesmium spp. physiology and nutrient fluxes in the North Pacific subtropical gyre. Aquat. Microbiol. Ecol. 15: 265–276.

Levitus S., Antonov J.I., Boyer T.P. and Stephens C. 2000. Warming of the world ocean. Science 287(5461): 2225–2229.

Li C., Zhuang Y.H., Frolking S., Galloway J., Harriss R., Moore B. III, Schimel D. and Wang X.K. 2003. Modeling soil organic carbon change in croplands in China. Ecol. Appl. 13(2): 327–336.

Mackenzie F.T. 1994. Global climatic change: climatically important biogenic gases and feedbacks. In: Woodwell G. M. and Mackenzie F.T. (eds), Biotic Feedbacks in the Global Climatic System: Will the Warming Feed the Warming. Oxford University Press, UK, pp. 22–46.

Mackenzie F.T. 1998. Our Changing Planet: An Introduction to Earth System Science and Global Environmental Change, 2nd ed). Prentice-Hall, Upper Saddle River, NJ.

Martinelli L.A., Piccolo M.C., Townsend A.R., Vitousek P.M., Cuevas E., McDowell W., Robertson G.P., Santos O.C. and Treseder K. 1999. Nitrogen stable isotopic composition of leaves and soil: tropical versus temperate forests. Biogeochemistry 46: 45–65.

Matson P.A., McDowell W.H., Townsend A.R. and Vitousek P.M. 1999. The globalization of N deposition: ecosystem consequences in tropical environments. Biogeochemistry 46: 67–83.

Matson P., Lohse K. and Hall S. 2002. The globalization of nitrogen: consequences for terrestrial ecosystems. Ambio 31: 113–119.

Melillo J.M. and Cowling E.B. 2002. Reactive nitrogen and public policies for environmental protection. Ambio 31: 150–158.

Menard H. and Smith S. 1966. Hypsometry of ocean basin provinces. J. Geophys. Res. 71: 4305–4325.

Metz B., Davidson O., Swart R. and Pan J. 2001. Climate change 2001: mitigation. In: Metz B. et al. (eds), Third Assessment Report of the Intergovernmental Panel on Climate Change. Cambridge University Press, New York.

Michaels A.F., Olson D., Sarmiento J.L., Ammerman J.W., Fanning K., Jahnke R., Knap A.H., Lipschultz F. and Prospero J.M. 1996. Inputs, losses and transformations of nitrogen and phosphorus in the pelagic North Atlantic Ocean. Biogeochemistry 35: 181–226.

Michaels A., Karl D. and Capone D. 2001. Element stoichiometry, new production and nitrogen fixation. Oceanography 14: 68–77.

Middleburg J., Soetaert K., Herman P. and Heip C. 1996. Denitrification in marine sediments: a model study. Global Biogeochem. Cycles 10: 661–673.

Moomaw W.R. 2002. Energy, industry and nitrogen: strategies for reducing reactive nitrogen emissions. Ambio 31: 184–189.

Mosier A.R., Guenzi W.D. and Schweizer E.E. 1986. Soil losses of dinitrogen and nitrous oxide from irrigated crops in Northeastern Colorado. Soil Sci. Soc. Am. J. 50: 344–348.

Mosier A.R., Bleken M.A., Chaiwanakupt P., Ellis E.C., Freney J.R., Howarth R.B., Matson P.A., Minami K., Naylor R., Weeks K. and Zhu Z.-L. 2001. Policy implications of human accelerated nitrogen cycling. Biogeochemistry 52: 281–320.

Mosier A.R., Doran J.W. and Freney J.R. 2002. Managing soil denitrification. J. Soil Water Conserv. 57: 505–513.

Nadelhoffer K.J. 2001. The impacts of nitrogen deposition on forest ecosystems. In: Follett R.F. and Hatfield J.L. (eds), Nitrogen in the Environment: Sources, Problems and Management. Elsevier, New York, pp.311–331.

Nadelhoffer K.J., Aber J.D., Downs M.R., Fry B. and Melillo J.M. 1992. Biological sinks for nitrogen additions to a forested catchment. EPA/600/A-92/292.

Nadelhoffer K.J., Downs M.R., Fry B., Aber J.D., Magill A.H. and Melillo J.M. 1995. The fate of 15N-labeled nitrate additions to a northern hardwood forest in eastern Maine, USA. Oecologia 103: 292–301.

Nadelhoffer K.J., Downs M.R. and Fry B. 1999. Sinks for 15N-enriched additions to an oak forest and a red pine plantation. Ecol. Appl. 9: 72–86.

Naqvi S.W.A., Noronha R.J., Shailaja M.S., Somasundar K. and Sen Gupta R. 1992. Some aspects of the nitrogen cycle in the Arabian Sea. In: Desai B.N. (ed.), Conference Papers: Oceanography of the Indian Ocean, International Symposium, Jan. 14–16 1991. National Institute of Oceanography, Goa (India), Oxford and IBH, New Delhi, pp.285–322.

Naqvi S., Jayakumar D., Narvekar P., Naik H., Sarma V., D'Souza W., Joseph S. and George M. 2000. Increased marine production of N2O due to intensifying anoxia on the Indian continental shelf. Nature 408: 346–349.

NRC (National Research Council) 2000. Clean Coastal Waters: Understanding and Reducing the Effects of Nutrient Pollution. National Academy Press, Washington, DC.

Neff J.C., Holland E.A., Dentener F.J., McDowell W.H. and Russell K.M. 2002. The origin, composition and rates of organic nitrogen deposition. Biogeochemistry 57/58: 99–136.

Nevison C., Weiss R. and Erikson D. 1995. Global oceanic emissions of nitrous oxide. J. Geophys. Res. 100: 15809–15820.

Nixon S.W., Ammerman J.W., Atkinson P., Berounsky V.M., Billen G., Boicourt W.C., Boynton W.R., Church T.M., Ditoro D.M., Elmgren R., Garber J.H., Giblin A.E., Jahnke R.A., Owens N.J.P., Pilson M.E.Q. and Seitzinger S.P. 1996. The fate of nitrogen and phosphorus at the land-sea margin of the North Atlantic Ocean. Biogeochemistry 35: 141–180.

Oenema O. and Pietrzak S. 2002. Nutrient management in food production: achieving agronomic and environmental targets. Ambio 31: 159–168.

Orcutt K.M. et al. 2001. A seasonal study of the significance of N2 fixation by Trichodesmium spp. at the Bermuda Atlantic Time-series Study (BATS) site. Deep-Sea Res. II 48: 1583–1608.

Paerl H.W. 1993. Emerging role of atmospheric nitrogen deposition in coastal eutrophication: biogeochemical and trophic perspectives. Can. J. Fish. Aquat. Sci. 50: 2254–2269.

Paul E.A. and Clark F.E. 1997. Soil Microbiology and Biochemistry. Academic Press, New York.

Peoples M.B., Herridge D.F. and Ladha J.K. 1995. Biological nitrogen fixation: an efficient source of nitrogen for sustainable agricultural production? Plant Soil 174: 3–28.

Peterjohn W.T. and Schlesinger W.H. 1991. Factors controlling denitrification in a Chihuahuan Desert ecosystem. Soil Sci. Soc. Am. J. 55: 1694–1701.

Prather M., Ehalt D., Dentener F., Derwent R., Dlugokencky E., Holland E., Isaksen I., Katima J., Kirchho. V., Matson P., Midgley P. and Wang M. 2001. Atmospheric chemistry and greenhouse gases. In: Houghton J.T., Ding Y., Griggs D.J., Noguer M., van der Linden P.J., Dai X., Maskell K. and Johnson C.A. (eds), Climate change 2001: the scientific basis. Third Assessment Report of the Intergovernmental Panel on Climate Change. Cambridge University Press, Cambridge, NY.

Preston C.M. and Mead D.J. 1994. Growth response and recover of 15N-fertilizer one and eight growing seasons after application to lodgepole pine in British Columbia. For. Ecol. Manage. 65: 219–229.

Prospero J.M., Barrett K., Church T., Dentener F., Duce R.A., Galloway J.N., Levy H., Moody J. and Quinn P. 1996. Atmospheric deposition of nutrients to the North Atlantic Basin. Biogeochemistry 35: 27–73.

Quinn P.K., Barrett K.J., Dentener F.J., Lipschultzt F and Six K.D. 1996. Estimation of the air/sea exchange of ammonia for the North Atlantic basin. Biogeochemistry 35: 275–304.

Rabalais N. 2002. Nitrogen in aquatic ecosystems. Ambio 31: 102–112.

Rasmussen L., Beier C., Van Breemen N., De Visser P., Kreutzer K., Schierl R., Matzner E. and Farrel E.P. 1990. Study on Acid Deposition Effects by Manipulating Forest Ecosystems, New Title: EXMAN—EXperimental MANipulation of Forest Ecosystems in Europe. Air Pollution Research Report 24, Commission of the European Communities, Brussels.

Redfield A.C. 1958. The biological control of chemical factors in the environment. Am. Sci. 46: 205–221.

Ridgwell A.J., Maslin M.A. and Watson A.J. 2002. Reduced effectiveness of terrestrial carbon sequestration due to an antagonistic response of ocean productivity. Geophys. Res. Lett. 29(6): Art. No. 1095.

Robertson L.A., Dalsgaard T., Revsbech N.-P. and Kuenen J.G. 1995. Confirmation of 'aerobic denitrification 'in batch cultures, using gas chromatography and 15N mass spectrometry. FEMS Microbiol. Ecol. 18: 113–120.

Rolston D.E., Hoffman D.L. and Toy D.W. 1978. Field measurement of denitrification: I. Flux of N2 and N2O. Soil Sci. Soc. Am. J. 42: 863–869.

Rolston D.E., Sharpley A.M., Toy D.W. and Broadbent F.E. 1982. Field measurement of denitrification: III. Rates during irrigation cycles. Soil Sci. Soc. Am. J. 46: 289–296.

Roy R.N., Misra R.V. and Montanez A. 2002. Reduced reliance on mineral nitrogen, yet more food. Ambio 31: 177–183.

Sachs J.P. and Repeta D.J. 1999. Oligotrophy and nitrogen fixation during eastern Mediterranian sapropel events. Science 286: 2485–2488.

Saino T. 1977. Biological nitrogen fixation in the ocean with emphasis on the nitrogen fixing blue green alga, Trichodesmium , and its significance in the nitrogen cycle in the low latitude sea areas. Ph.D. Dissertation, Tokyo University, Japan.

Sañudo-Wilhelmy S.A., Kustka A.D., Gobler C.J., Hutchins D.A., Yang M., Lwiza K., Burns J., Capone D.G., Raven J.A. and Carpenter E.J. 2001. Phosphorus limitation of nitrogen fixation by Trichodesmium in the central Atlantic Ocean. Nature 411: 66–69.

Sarmiento J.L., Hughes T.M.C., Stouffer R.J. and Manabe S. 1998. Simulated response of the ocean carbon cycle to anthropogenic climate warming. Nature 393: 245–249.

Schlesinger W.H. 1991. Biogeochemistry: An Analysis of Global Change. Academic Press, New York.

Schlesinger W.H. and Andrews J.A. 2000. Soil respiration and the global carbon cycle. Biogeochemistry 48: 7–20.

Schlesinger W.H. and Hartley A.E. 1992. A global budget for atmospheric ammonia. Biogeochemistry 15: 191–211.

Seely B. and Lajtha K. 1997. Application of a 15N tracer to simulate and track the fate of atmospherically deposited N in the coastal forests of the Waquoit Bay Watershed, Cape Cod, Massachusetts. Oecologia 112: 393–402.

Seitzinger S.P. 1988. Denitrification in freshwater and coastal marine ecosystems: ecological and geochemical importance. Limnol. Oceanogr. 33: 702–724.

Seitzinger S.P. and Giblin A.E. 1996. Estimating denitrification in North Atlantic continental shelf sediments. Biogeochemistry 35: 235–260.

Seitzinger S.P. and Kroeze C. 1998. Global distribution of nitrous oxide production and N inputs in freshwater and coastal marine ecosystems. Global Biogeochem. Cycles 12: 93–113.

Seitzinger S.P., Kroeze C. and Styles R.V. 2000. Global distribution of N2O emissions from aquatic systems: natural emissions and anthropogenic effects. Chemosphere: Global Change Sci. 2: 267–279.

Seitzinger S.P., Styles R.V., Boyer E., Alexander R.B., Billen G., Howarth R., Mayer B. and Van Breemen N. 2002. Nitrogen retention in rivers: model development and application to water-sheds in the eastern US. Biogeochemistry 57/58: 199–237.

Shaffer G. and Ronner U. 1984. Denitrification in the Baltic Proper deep-water. Deep-Sea Res. A 31: 197–220.

Simpson J.R. and Freney J.R. 1988. Interacting processes in gaseous nitrogen loss from urea applied to flooded rice fields. In: Pushparajah E., Husin A. and Bachik A.T. (eds), Conference papers, Urea Technology and Utilization International Symposium. Malaysian Society of Soil Science, Kuala Lumpur, pp.281–290.

Simpson J.R., Freney J.R., Wetselaar R., Muirhead W.A., Leuning R. and Denmead O.T. 1984. Transformations and losses of urea nitrogen after application to flooded rice. Aust. J. Agric. Res. 35: 189–200.

Smil V. 1994. Energy in World History. Westview Press, Boulder, CO.

Smil V. 1995. Who will feed China? The China Quart. 143: 801–813.

Smil V. 1999. Nitrogen in crop production: an account of global flows. Global Biogeochem. Cycles 13: 647–662.

Smil V. 2000. Feeding the World: A Challenge for the Twenty-First Century. MIT Press, Cambridge, MA.

Smil V. 2001. Enriching the Earth. MIT Press, Cambridge, MA.

Smil V. 2002. Nitrogen and Food. Ambio 31: 126–131.

Smith B.D. 1995. The Emergence of Agriculture. Scientific American Library Series No. 24, Scientific American Library, (distributed by W.H. Freeman), New York.

Socolow R.H. 1999. Nitrogen management and the future of food: lessons from the management of energy and carbon. Proc. Natl. Acad. Sci. USA 96: 6001–6008.

Söderland R. and Rosswall T. 1982. The nitrogen cycles. In: Hutzinger O. (ed.), The Natural Environment and Biogeochemical Cycles. Springer Verlag, New York, pp.61–81.

Somasundar K., Rajendran A., Dileep Kumar M. and Sen Gupta R. 1990. Carbon and nitrogen budgets of the Arabian Sea. Mar. Chem. 30: 363–377.

Stedman D.H. and Shetter R. 1983. The global budget of atmospheric nitrogen species. In: Schwartz S.S. (ed.), Trace Atmospheric Constituents: Properties, Transformations and Fates. J. Wiley, Hoboken, NJ, pp. 411–454.

Steinhart G.S., Likens G.E. and Groffman P.M. 2000. Denitrification in stream sediments of five northeastern (USA) streams. Verh. Internat.Verein. Limnol. 27: 1331–1336.

Suthhof A., Ittekkot V. and Gaye-Haake B. 2001. Millennial-scale oscillation of denitrification intensity in the Arabian Sea during the late Quaternary and its potential influence on atmospheric N2O and global climate. Global Biogeochem. Cycles 15: 637–649.

Sverdrup H., Johnson M. and Fleming R. 1942. The Oceans. Prentice-Hall, Upper Saddle River, NJ.

Tartowski S. and Howarth R.W. 2000. Nitrogen, nitrogen cycling. Encycl. Biodiv. 4: 377–388.

Thamdrup B. and Dalsgaard T. 2002. Production of N 2 through anaerobic ammonium oxidation coupled to nitrate reduction in marine sediments. Appl. Environ. Microbiol. 68: 1312–1318.

Tilman D., Fargione J., Wol. B., D'Antonio C., Dobson A., Howarth R., Schindler D., Schlesinger W.H., Simberloff D. and Swackhamer D. 2001. Forecasting agriculturally driven global change. Science 292: 281–284.

Townsend A.R., Howarth R.H., Bazzaz F.A., Booth M.S., Cleveland C.C., Collinge S.K., Dobson A.P., Epstein P.R., Holland E.A., Keeney D.R., Mallin M.A., Rogers C.A., Wayne P. and Wolfe A.H. 2003. Human health effects of a changing global nitrogen cycle. Front Ecol. Environ. 1: 240–246.

van Aardenne J.A., Dentener F.J., Olivier J.G.J., Klijn Goldewijk C.G.M. and Lelieveld J. 2001. A 1°-1° resolution dataset of historical anthropogenic trace gas emissions for the period 1890–1990. Global Biogeochem. Cycles 15: 909–928.

Van Breemen N., Boyer E.W., Goodale C.L., Jaworski N.A., Paustian K., Seitzinger S., Lajtha L.K., Mayer B., Van Dam D., Howarth R.W., Nadelhoffer K.J., Eve M. and Billen G. 2002. Where did all the nitrogen go? Fate of nitrogen inputs to large watersheds in the northeastern USA Biogeochemistry 57/58: 267–293.

Van Drecht G., Bouwman A.F., Knoop J.M., Meinardi C. and Beusen A. 2001. Global pollution of surface waters from point and nonpoint sources of nitrogen. Sci. World 1(S2): 632–641.

van Egmond N.D., Bresser A.H.M. and Bouwman A.F. 2002. The European nitrogen case. Ambio 31: 72–78.

Vitousek P.M. 1994. Potential nitrogen fixation during primary succession in Hawaii Volcanoes National Park. Biotropica 26: 234–240.

Vitousek P.M., Howarth R.W., Likens G.E., Matson P.A., Schindler D., Schlesinger W.H. and Tilman G.D. 1997. Human alteration of the global nitrogen cycle: causes and consequences. Issue Ecol. 1: 1–17.

Vitousek P.M., Hattenschwiler S., Olander L. and Allison S. 2002. Nitrogen and nature. Ambio 31: 97–101.

Vörösmarty C.J., Fekete B.M., Meybeck M. and Lammers R.B. 2000. Geomorphometeric attributes of the global system of rivers at 30-minute spatial resolution. J. Hydrol. 237: 17–39.

Wang L. 1987. Soybeans–The miracle bean of China. In: Wittwer S., Yu Y., Sun H. and Wang L. (eds), Feeding a Billion: Frontiers of Chinese Agriculture. Michigan State University Press, East Lansing.

Whelpdale D.M., Dorling S.R., Hicks B.B. and Summers P.W. 1996. Atmospheric processes. In: Whelpdale D.M. and Kaiser M.S. (eds), Global Acid Deposition Assessment. WMO GAW Rept. No. 106, Geneva.

Whelpdale D.M., Summers P.W. and Sanhueza E. 1997. A global overview of atmospheric acid deposition flues. Environ. Monit. Assess. 48: 217–227.

Williams M.W., Baron J.S., Caine N., Sommerfeld R. and Sanford R. 1996. Nitrogen saturation in the Rocky Mountains. Environ. Sci. Technol. 30: 640–646.

Wilson T. 1978. Evidence for denitrification in aerobic pelagic sediments. Nature 274: 354–356.

Wittwer S., Yu Y., Sun H. and Wang L. 1987. Feeding a Billion: Frontiers of Chinese Agriculture. Michigan State University Press, East Lansing.

Wolfe A. and Patz J.A. 2002. Nitrogen and human health: direct and indirect impacts. Ambio 31: 120–125.

Wright R.F. and Rasmussen L. 1998. Introduction to N. I. TREX and EXMAN projects. For. Ecol. Manage. 101: 1–7.

Wu J., Sunda W., Boyle E. and Karl D. 2000. Phosphate depletion in the western North Atlantic Ocean. Science 289: 759–762.

Xing G.X. and Zhu Z.L. 2002. Regional nitrogen budgets for China and its major watersheds. Biogeochemistry 57–58: 405–427.

Yavitt J.B. and Fahey T.J. 1993. Production of methane and nitrous oxide by organic soils within a northern hardwood forest ecosystem. In: Oremland R.S. (ed.), Biogeochemistry of Global Change. Chapman and Hall, New York, pp. 261–277.

Zehr J.P., Carpenter E.J. and Villareal T.A. 2000. New perspectives on nitrogen-fixing microorganisms in subtropical and tropical open oceans. Trends Microbiol. 8: 68–73.

Zehr J. and Ward B.B. 2002. Nitrogen cycling in the ocean. New perspective on processes and paradigms. Appl. Environ. Microbiol. 68: 1015–1024.

Zehr J., Waterbury J., Turner P., Montoya J., Omoregie E., Steward G., Hansen A. and Karl D. 2001. Unicellular cyanobacteria fix N2 in the subtropical North Pacific Ocean. Nature 412: 635–638.

Zhang W.L., Tian Z.X., Zhang N. and Li X.Q. 1996. Nitrate pollution of groundwaters in northern China. Agric. Ecosyst. Environ. 59: 223–231.

Zheng X., Fu C., Xu X., Yan X., Chen G., Han S., Huang Y. and Hu F. 2002. The Asian nitrogen case. Ambio 31: 79–87.

Zhu Z.L., Cai G.X., Simpson J.R., Zhang S.L., Chen D.L., Jackson A.V. and Freney J.R. 1989. Processes of nitrogen loss from fertilizers applied to. flooded rice fields on a calcareous soil in North-Central China. Fert. Res. 18: 101–115.

Zobell C. and Anderson D.Q. 1943. Observations on the multiplication of bacteria in different volumes of stored sea water and the influence of oxygen tension and solid surfaces. J. Bacteriol. 46: 324–342.

Download references

Author information

Authors and affiliations.

Environmental Sciences Department, University of Virginia, Charlottesville, 22903, USA

J. N. Galloway

Joint Research Centre, Institute for Environment and Sustainability Climate Change Unit, Ispra, Italy

F. J. Dentener & A. F. Michaels

Wrigley Institute for Environmental Studies, University of Southern California, Los Angeles, California, USA

D. G. Capone & J. H. Porter

College of Environmental Science and Forestry, State University of New York, Syracuse, New York, USA

E. W. Boyer & A. R. Townsend

Department of Ecology & Evolutionary Biology, Cornell University, Ithaca, New York, USA

R. W. Howarth & C. J. Vöosmarty

Institute of Marine and Coastal Sciences, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, USA

S. P. Seitzinger

Department of Global Ecology, Carnegie Institution, Stanford University, Stanford, California, USA

G. P. Asner

Institute of Arctic and Alpine Research, University of Colorado, Boulder, Colorado, USA

C. C. Cleveland

Complex Systems Research Center, Institute for the Study of Earth, Oceans, and Space, University of New Hampshire, Durham, New Hampshire, USA

P. A. Green

Atmospheric Chemistry Division, National Center for Atmospheric Research, Boulder, Colorado, USA

E. A. Holland

D. M. Karl, A. F. Michaels, J. H. Porter, A. R. Townsend & C. J. Vöosmarty

You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and permissions

About this article

Galloway, J.N., Dentener, F.J., Capone, D.G. et al. Nitrogen Cycles: Past, Present, and Future. Biogeochemistry 70 , 153–226 (2004). https://doi.org/10.1007/s10533-004-0370-0

Download citation

Issue Date : September 2004

DOI : https://doi.org/10.1007/s10533-004-0370-0

Share this article

Anyone you share the following link with will be able to read this content:

Sorry, a shareable link is not currently available for this article.

Provided by the Springer Nature SharedIt content-sharing initiative

Haber-Bosch
fossil fuel combustion
denitrification
nitrogen fixation
Find a journal
Publish with us
Track your research

An official website of the United States government

The .gov means it’s official. Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

The site is secure. The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Publications
Account settings
My Bibliography
Collections
Citation manager

Save citation to file

Email citation, add to collections.

Create a new collection
Add to an existing collection

Add to My Bibliography

Your saved search, create a file for external citation management software, your rss feed.

Search in PubMed
Search in NLM Catalog
Add to Search

The Nitrogen Cycle: A Large, Fast, and Mystifying Cycle

Affiliation.

1 Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC).
PMID: 31554776
PMCID: PMC6759337
DOI: 10.1264/jsme2.ME3403rh

PubMed Disclaimer

Microbial pathways in the nitrogen…

Microbial pathways in the nitrogen cycle. Abbreviations: AOB, ammonia-oxidizing bacteria; AOA, ammonia-oxidizing archaea;…

Related information

PubChem Compound (MeSH Keyword)

LinkOut - more resources

Full text sources.

Europe PubMed Central
J-STAGE, Japan Science and Technology Information Aggregator, Electronic
PubMed Central
Citation Manager

NCBI Literature Resources

MeSH PMC Bookshelf Disclaimer

The PubMed wordmark and PubMed logo are registered trademarks of the U.S. Department of Health and Human Services (HHS). Unauthorized use of these marks is strictly prohibited.

Trending Terms:

artificial intelligence
Current Issue
First release papers
About About Science Mission & Scope Editors & Advisory Boards Editorial Policies Information for Authors Information for Reviewers Journal Metrics Staff Contact Us TOC Alerts and RSS Feeds
Submit manuscript

Transformation of the Nitrogen Cycle: Recent Trends, Questions, and Potential Solutions

Information & authors, metrics & citations, check access, get full access to this article.

View all available purchase options and get full access to this article.

Supplementary Material

References and notes, submit a response to this article, compose eletter, contributors, statement of competing interests, (0) eletters.

eLetters is a forum for ongoing peer review. eLetters are not edited, proofread, or indexed, but they are screened. eLetters should provide substantive and scholarly commentary on the article. Embedded figures cannot be submitted, and we discourage the use of figures within eLetters in general. If a figure is essential, please include a link to the figure within the text of the eLetter. Please read our Terms of Service before submitting an eLetter.

No eLetters have been published for this article yet.

Information

Published in.

Submission history

Permissions, affiliations, article usage.

Note: The article usage is presented with a three- to four-day delay and will update daily once available. Due to this delay, usage data will not appear immediately following publication.

Citation information is sourced from Crossref Cited-by service.

James N. Galloway et al.

Export citation

Select the format you want to export the citation of this publication.

Zesheng Gao,
Jianghao Zhang,
Xueyan Chen,
Xiaoxiao Qin,
Jinshui Yao,
Changbin Zhang,
Swarna Shaw,
Chiranjeeb Puthal,
Riyanka Shil,
Rudra Prasad Saha,
Rajib Majumder,
Sanmitra Ghosh,
Xue-Man Wang,
Yu-Tong Zhu,
Shi-Hui Wang,
Wen-Qian Bai,
Zhi-Fei Wang,
Wan-Qing Zeng,
Pei-Hao Peng,
Markos Daniel,
Yoseph Tarekegn,
Weiyi Tang,
Jeff Talbott,
Timothy Jones,
Bess B. Ward,
Violeta Mendoza-Martinez,
Scott L. Collins,
Jennie R. McLaren,
Cassandra J. Gaston,
Joseph M. Prospero,
Kristen Foley,
Havala O. T. Pye,
Lillian Custals,
Edmund Blades,
Peter Sealy,
James A. Christie,
Ouping Deng,
Yuanyuan Chen,
Jingze Zhao,
Dinghua Ou,
Yanyan Zhang,
Yueqiang He,
Hanqing Yang,
Rong Huang,
Sarah Albertin,
Joël Savarino,
Slimane Bekki,
Albane Barbero,
Roberto Grilli,
Quentin Fournier,
Irène Ventrillard,
Nicolas Caillon,
Naoya ADACHI,

View Options

AAAS ID LOGIN

AAAS login provides access to Science for AAAS Members, and access to other journals in the Science family to users who have purchased individual subscriptions.

Become a AAAS Member
Activate your AAAS ID
Purchase Access to Other Journals in the Science Family
Account Help

More options

Purchase digital access to this article

Download and print this article for your personal scholarly, research, and educational use.

Purchase this issue in print

Buy a single issue of Science for just $15 USD .

Restore Content Access

Restore content access for purchases made as a guest

View options

Download this article as a PDF file

Share article link

Copying failed.

Share on social media

Previous article, next article.

Get the latest news, commentary, and research, free to your inbox daily.

Your password must have 8 characters or more and contain 3 of the following:

a lower case character,
an upper case character,
a special character

Your password has been changed

Can't sign in? Forgot your password?

Enter your email address below and we will send you the reset instructions

If the address matches an existing account you will receive an email with instructions to reset your password.

Can't sign in? Forgot your username?

Enter your email address below and we will send you your username

If the address matches an existing account you will receive an email with instructions to retrieve your username

Sign in Institutional Access
This Journal

Nitrogen cycling and microbial cooperation in the terrestrial subsurface

Olivia E. Mosley 1 ,
Emilie Gios 1 ,
Murray Close 2 ,
Louise Weaver 2 ,
Chris Daughney 3 &
Kim M. Handley ORCID: orcid.org/0000-0003-0531-3009 1

The ISME Journal volume 16 , pages 2561–2573 ( 2022 ) Cite this article

13k Accesses

52 Citations

15 Altmetric

Metrics details

Microbial communities
Environmental chemistry
Freshwater ecology
Water microbiology

The nitrogen cycle plays a major role in aquatic nitrogen transformations, including in the terrestrial subsurface. However, the variety of transformations remains understudied. To determine how nitrogen cycling microorganisms respond to different aquifer chemistries, we sampled groundwater with varying nutrient and oxygen contents. Genes and transcripts involved in major nitrogen-cycling pathways were quantified from 55 and 26 sites, respectively, and metagenomes and metatranscriptomes were analyzed from a subset of oxic and dysoxic sites (0.3-1.1 mg/L bulk dissolved oxygen). Nitrogen-cycling mechanisms (e.g. ammonia oxidation, denitrification, dissimilatory nitrate reduction to ammonium) were prevalent and highly redundant, regardless of site-specific physicochemistry or nitrate availability, and present in 40% of reconstructed genomes, suggesting that nitrogen cycling is a core function of aquifer communities. Transcriptional activity for nitrification, denitrification, nitrite-dependent anaerobic methane oxidation and anaerobic ammonia oxidation (anammox) occurred simultaneously in oxic and dysoxic groundwater, indicating the availability of oxic-anoxic interfaces. Concurrent activity by these microorganisms indicates potential synergisms through metabolite exchange across these interfaces (e.g. nitrite and oxygen). Fragmented denitrification pathway encoding and transcription was widespread among groundwater bacteria, although a considerable proportion of associated transcriptional activity was driven by complete denitrifiers, especially under dysoxic conditions. Despite large differences in transcription, the capacity for the final steps of denitrification was largely invariant to aquifer conditions, and most genes and transcripts encoding N 2 O reductases were the atypical Sec-dependant type, suggesting energy-efficiency prioritization. Results provide insights into the capacity for cooperative relationships in groundwater communities, and the richness and complexity of metabolic mechanisms leading to the loss of fixed nitrogen.

Nitrogen fixation and diazotroph diversity in groundwater systems

Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater

Differential contribution of nitrifying prokaryotes to groundwater nitrification

Introduction.

Groundwater represents the largest accessible freshwater source on Earth and is stored in permeable geological units known as aquifers that are generally characterized by long water residence times, low organic matter, and slow water exchange rates [ 1 , 2 , 3 ]. Natural stores of inorganic nitrogen (nitrate, nitrite, ammonium) are typically present in low concentrations [ 4 ]. However, long residence times and close links to surface water (e.g., lakes, rivers, and wetlands) make groundwater susceptible to pollution from nitrogen-based fertilisers [ 5 ]. Nitrogen (N) contamination in the terrestrial subsurface has become a global problem [ 6 , 7 , 8 ], presenting health risks associated with nitrate in drinking water, such as methaemoglobinaemia and cancer [ 9 ], along with eutrophication of surface waters [ 10 ].

Groundwater microbial communities contain extensive phylogenetic novelty [ 11 ]. While the metabolic capabilities of many groundwater microorganisms remain to be tested in laboratory conditions, genetic evidence suggests that a diverse collection of bacteria and archaea transform nitrogen in groundwater, including novel candidate phyla [ 12 ], diverse bacterial taxa [ 11 , 13 ], archaeal ammonium oxidizers [ 13 , 14 ], and novel aquifer-adapted clades of anammox bacteria [ 15 ]. Research also suggests that numerous aquifer organisms are equipped with genes encoding partial nitrogen cycle pathways, such as nitrite reduction [ 11 , 16 ]. This has been shown to be a common feature of bacteria and archaea from other habitats [ 17 ], and suggests that cooperative interactions are commonly employed to complete individual nitrogen-cycling pathways.

The microbial nitrogen cycle comprises six distinct N-transformation processes, including ammonification, nitrogen fixation, nitrification, denitrification, anaerobic ammonium oxidation (anammox), and assimilation [ 18 , 19 ]. Microorganisms that perform these processes can be sources and sinks of nitrate. Despite distinct requirements (e.g. for oxygen), many reactions in the nitrogen cycle tend to co-occur in the environment, leading to efficient nitrogen recycling [ 19 ], competition for the same resource (e.g. by respiratory ammonifiers and denitrifiers [ 20 ]), cooperative completion of the modular denitrification pathway [ 19 ], and coupled processes, such as nitrification—denitrification [ 21 ] or nitrification—anammox [ 22 ]. Accordingly, biological processes derived from networks of microorganisms in the terrestrial subsurface play a dominant role in N-transformations [ 23 ].

Denitrification is the most studied nitrogen cycling process in groundwater to-date, due to its importance for nitrogen pollution removal [ 5 ], although operation of the truncated pathway produces less desirable forms of inorganic nitrogen - NO 2 - due to its toxicity [ 24 ], and greenhouse gases NO and N 2 O [ 5 ]. Microbial denitrification is typically linked to dissolved organic carbon concentrations in aquifers, but is also fuelled by inorganic electron donors, such as reduced forms of iron or sulfur [ 5 , 25 ]. Inorganic donors may be the primary source of electrons for nitrogen-cycling taxa given widespread organic carbon-limitation in aquifers [ 26 , 27 ]. Accordingly, nitrification and anammox appear to be typical features of shallow oxic or partially oxic aquifers [ 15 , 26 ], and carbon-limitation can create an opportunity for anammox to outcompete denitrification [ 28 ]. However, the occurrence of, or capacity for, these processes may not to be ubiquitous. A scarcity or lack of organisms capable of some processes, including nitrogen fixation, ammonia oxidation, and nitrous oxide reduction, has been reported from one low-oxygen aquifer [ 11 ]. Further work is needed to determine the distribution of nitrogen-cycling processes across different aquifers, including aquifers defined based on redox conditions and nutrient characteristics, such as pristine or N-contaminated.

This study investigates the microbial nitrogen cycle in aquifers traversing a wide range of nitrogen, organic carbon, and oxygen concentrations. We determined the metabolic capacity for each pathway in oxic and dysoxic groundwaters, and the transcriptional activity associated with these pathways (understudied in aquifers due to low cell densities) [ 29 ]. As aquifers comprise both suspended and attached communities, with distinct compositions and capacities for biogeochemical cycling [ 30 ], analyses included both groundwater (planktonic fraction) and groundwater enriched with the sediment-attached fraction. To further characterize reactions leading to nitrogen loss, we quantified ammonia monooxygenase (archaeal and bacterial ammonia oxidation), nitrous oxide reductase (final step in denitrification), and hydrazine synthase (anammox) genes in 64 groundwater samples (from 59 wells) and transcripts in 26, collected up to 860 km apart. Results give insights into environmental factors influencing the presence, co-occurrence, and transcriptional activity of nitrogen-cycling mechanisms, which determine the fate of nitrogen in aquifers.

Materials and methods

Study sites and sample collection.

Eighty samples were collected from 59 wells, spanning 10 aquifers (mostly sandy-gravel) in the Auckland, Waikato, Wellington, and Canterbury regions, New Zealand (Fig. S 1 ; Table S1 ). Wells were 4.5–114.6 m deep (18.9 m on average, Table S1 ). Wells were purged (~3–5 borehole volumes). Then, 3–90 L of groundwater (67 samples) or 0.5–15 L of attached-fraction enriched groundwater (13 samples, Canterbury sites A–D) were collected and immediately filtered on-site. The biofilm or “attached” fraction enriched groundwater (i.e combining planktonic and biofilm aquifer fractions) was collected directly following standard groundwater collection. Prior to collection of these samples, a low-frequency custom sonicator, as described by Close et al. [ 31 ] (2.43 kW) was applied for 2 min to detach biofilms and particles from the surrounding aquifer. Biomass was captured onto 142 mm diameter mixed cellulose ester membrane filters (1.2 µm pore size pre-filter over a 0.22 µm filter) using a 142 mm stainless steel filter holder (Merck Millipore Ltd, Cork, Ireland). Both filters were immediately submerged in RNAlater (ThermoFisher Scientific, Waltham, MA, USA), transported on dry ice, and stored at −80 °C. All samples were used to generate amplicon data (×80). A subset was used to quantify functional genes (×64) and transcripts (×26). A subset from Canterbury was used for metagenomics (×16) and metatranscriptomics (×6).

Dissolved oxygen (DO), water temperature, pH, oxidation-reduction potential (ORP), and specific conductance were collected on site using flow-through cell and field probes (YSI EXO sonde 2, YSI PRO+ and YSI ProDSS, Yellow Springs, OH, USA). Samples were grouped into categories based on DO concentrations: anoxic (0 mg/L), suboxic (<0.3 mg/L), dysoxic (0.3–3 mg/L or 9.4–93.8 μM), and oxic (>3 mg/L) as previously proposed for groundwater [ 32 ]. Unfiltered groundwater samples were analyzed for P, N, C, S, Fe, Cu, and alkalinity at Hill Laboratories (Hamilton, New Zealand; Supplementary Information).

Nucleic acid extraction, sequencing and genome assembly

Nucleic acid extraction for droplet digital PCR (ddPCR), 16S rRNA gene amplicons, metagenomes, metatranscriptomes, sequencing, metagenome-assembled genome generation, and transcript mapping, are as described previously [ 15 ], and detailed in the Supplementary Information. Only RNA samples with RIN ≥ 6 or DV200 > 30% (i.e. fragments >200 nucleotides) were used for downstream analyses. Metagenome-assembled genome (MAG) completeness and contamination were estimated using CheckM v1.0.12 [ 33 ], and MAGs were classified using the Genome Taxonomy Database taxonomic classification tool, GTDB-Tk v0.2.1 [ 34 ]. Metatranscriptomic reads were mapped to MAGs using Bowtie2 [ 35 ] (v2.3.5, --end-to-end --very_sensitive). Read counts were determined using featureCounts [ 36 ] (v1.6.3, -F SAF). Singleton mapped reads per gene were removed. Read counts were normalized to a modified version of transcripts per kilobase per million reads mapped (modified-TPM) [ 37 ] via (number of reads mapped to gene)*(1000/gene length)*(1000000/library size).

Quantitative PCR

Droplet digital PCR (ddPCR) of hydrazine synthase ( hzsB ), ammonia monoxygenase ( amoA ), nosZ clade I genes, and transcripts used the QX200 platform with 20 µl reactions, 10 µl 2× EvaGreen Supermix (Biorad, Hercules, CA, US), and 1 µl DNA or cDNA. RNA (24 pg–1.1 µg) was converted to cDNA using Superscript III Supermix (Invitrogen). DPEC-treated water was used for negative controls and gBlock dsDNA fragments were used as positive controls (Table S2 ; Integrated DNA Technologies, Coralville, IA, USA). Primers and PCR conditions are described in Table S2 . Data were analyzed using the QuantaSoft software package v1.0 (Bio-Rad). Positive droplet thresholds were set based on negative and positive droplet fluorescence amplitudes using the positive control as reference.

Metabolic predictions

Protein-coding gene sequences from MAGs and metagenomic reads were predicted, and annotated (Supplementary Information Table S3 ). Phylogenetic trees for HzsABC (see figure 8 in Mosley et al. [ 15 ]), AmoA, PmoA, NosZ, and NxrA were generated by aligning predicted protein (amino acid) sequences using MUSCLE with default parameters [ 38 ], and constructing trees using FastTree (for AmoA) or IQ-TREE (for others) with 1000 bootstraps [ 39 , 40 ]. IslandViewer4 [ 41 ] was used to identify genomic islands in MAG nzgw5.

Statistical analyses

Significant environmental factors were determined using R package vegan v2.5.6 functions (metaMDS, adonis, vegdist, and envfit) [ 42 ]. Bray-Curtis dissimilarities were constructed using vegan with relative abundances of MAGs or protein-coding sequences in metagenomic reads [ 42 ]. Heatmap Z-scores were calculated using Heatmap.2 from the gplots package [ 43 ]. Linear discriminant analysis and Kruskal–Wallis tests were determined using the Galaxy computational tool ( http://huttenhower.sph.harvard.edu/galaxy/ ). Adonis permutation tests were undertaken using Bray-Curtis dissimilarities. Spearman’s rank correlations ( r ) were calculated using ‘rcorr’ from the Hmisc package, and p values were adjusted using the Benjamini-Hochberg method. Statistical analyses were considered significant with p < 0.05.

Results and discussion

Distribution of nitrogen-cycling pathways in groundwater, differences in nitrogen-cycling processes based on oxygen and nitrate concentrations.

Sixteen metagenomes (Table S4 ) were obtained from duplicate wells at four sites (A–D) from two unconfined alluvial aquifers (Canterbury, Fig. S 1 ). These sites encompassed varied nitrate (0.45–12.6 g/m 3 ), DO (0.37–7.5 mg/L), and dissolved organic carbon (DOC) (0–26 g/m 3 ) concentrations (Fig. 1A ; Table S1 ). Nitrate concentrations were pristine (site C) to N-contaminated (sites A, B, D) [ 4 ]. Sites A–C were oxic and had low DOC (typical of groundwaters), whereas site D was dysoxic with relatively high DOC. Metagenomes from groundwater wells comprised pairs, representing the planktonic and sediment-attached fractions. Over 70 Gbp of raw sequence was generated per site (390 Gbp overall, 322 Gbp trimmed). However, <10% of trimmed reads per sample assembled into contigs >2Kb long and only 0.64–8.14% of reads (3.8% on average) mapped to MAGs (Table S4 ), reflecting the complexity of microbial communities in the terrestrial subsurface [ 11 ]. To capture this diversity, metagenomic reads are first used here to determine the distribution of N metabolisms.

A Bar plots showing geochemical data from groundwater samples, coloured according to site. Solid bar colour = groundwater samples. Grid lines = attached-fraction enriched groundwater. All samples from site D were characterized as dysoxic, although gwj15-16 contained 0.37 mg/L DO, which are near suboxic levels (i.e. <0.3 mg/L). For all samples shown, ammoniacal-N values were below detection. B , C Bar plots showing the abundance (average of four wells per site and standard deviation) of sequence reads encoding dissimilatory and assimilatory nitrogen-cycling proteins relative to all nitrogen-cycling processes. Predicted proteins that were statistically different between sites are bolded ( y -axis). D Schematic of the nitrogen cycle displaying statistically significant differences between sites (LEfSe, Kruskal–Wallis test, p < 0.05). Solid lines depict pathways that were significantly more abundant across the sites, whereas dashed lines indicate no significant difference. Arrows indicate the site with significantly more genes. Abbreviations: A-Amo Archaeal Amo, B-Amo Bacterial Amo, Amo ammonia monooxygenase, Pmo Particulate methane monooxygenase, Hao hydroxylamine oxidoreductase, Nxr nitrite oxidoreductase, Nar nitrate reductase (dissimilatory), Nas nitrate reductase (assimilatory), NirK copper-containing nitrite reductase, NirS cytochrome cd 1 -containing nitrite reductase, Nor nitric oxide reductase, Nos nitrous oxide reductase, Nif nitrogenase (various), Hcp hydroxylamine reductase, Nir NADPH-nitrite reductase, Nrf nitrate reductase (associated with Nap), Hdh hydrazine hydrogenase, Hzs hydrazine synthase, Hzo hydrazine oxidoreductase.

A total of 4,462,950 sequences encoding nitrogen-cycling proteins were identified from metagenomic reads (1,013,871–1,211,591/site, Table S5 ). The relative abundance of 29/68 nitrogen-cycling gene (sub)families in NCycDB [ 44 ] differed significantly among sites (Fig. 1B, C ; LEfSe, Table S6 ). Most of these encoded nitrification and anammox pathways ( p < 0.05). Sequences encoding other pathways, such as nitrogen fixation and the final steps of denitrification remained consistent across sites ( p > 0.05).

Results indicate the presence of ecologically robust mechanisms for nitrogen removal under the reduced DO conditions of dysoxic site D. In addition to the presence of metagenomic sequences encoding complete nitrification-denitrification, the relative abundances of sequences encoding anammox genes were all significantly higher at this site (LEfSe, Kruskal–Wallis test, p < 0.05). Sequences encoding genes involved in nitrate reduction to nitrite ( narGHI ), and those encoding mechanisms for nitrite reduction in the dissimilatory nitrate reduction to ammonia (DNRA) ( nrfBCD ), and denitrification ( nirS ) pathways were also higher. Anammox converts NH 4 + and NO 2 - into N 2 [ 45 ] and can be fuelled by ammonium replenished by DNRA, while anammox and denitrification (coupled to nitrification) represent alternative N 2 -generating pathways. Transcriptomic data showed a relatively high proportion of N-cycling gene expression derived from both anammox (hydrazine synthesis and oxidation) and denitrification (nitrous oxide reduction) in dysoxic groundwater (higher than that indicated by gene relative abundances), and showed that nitrifiers were transcriptionally active (Fig. 2A, B ).

A Nitrogen cycle schematics display the average abundance of nitrogen-cycling transcripts (based on modified-TPM values) per site and sample type (relative to nitrogen-cycling pathways overall (as shown). The percentage of gene transcripts associated with each pathway component is shown in black font. Coloured arrows represent pathways (purple = nitrification, green = denitrification and red = anammox). Only NrfA and not NirBD are shown for the DNRA pathway. B Heatmap shows nitrogen-cycling modified transcripts per million (modified-TPM) at each site (ordered gwj9, gwj11, gwj13-gwj16), scaled by row (Z-Score). Solid coloured blocks represent groundwater, black grid blocks represent the attached-fraction (or biomass) enriched groundwater. C Stacked bar plots display four active nitrogen-cycling genomes and the relative abundance (modified-TPM normalized to genome coverage) of their nitrogen-cycling gene transcripts across each site. Abbreviations: amo ammonia monooxygenase, pmo particulate methane monooxygenase, xmo copper-containing membrane monooxygenase, nod nitric oxide dismutase, nxr nitrite oxidoreductase, nar nitrate reductase (dissimilatory), nap periplasmic nitrate reductase, nirK copper-containing nitrite reductase, nirS cytochrome cd 1 -containing nitrite reductase, nor nitric oxide reductase, nos nitrous oxide reductase, nrf nitrate reductase, hzo hydrazine oxidoreductase, hao hydroxylamine oxidoreductase.

Oxygen availability (oxic vs suboxic/anoxic) is linked to archaeal and bacterial ammonia-oxidizer abundance or absence in aquifers [ 11 , 26 ]. As may be expected for an aerobic process, there were significantly more metagenomic sequences encoding the first step of nitrification (bacterial and archaeal amoABC ) at oxic sites A and B (LEfSe, Kruskal–Wallis test), and some of the medium-high concentrations of nitrate at these sites is likely to have been re-generated by nitrifiers [ 19 ]. Regardless, our data indicate ammonia-oxidizers were present and transcriptionally active under all conditions, including dysoxic and pristine (low N and DOC, site C). AOA and AOB can be active at DO concentrations <1 mg/L [ 46 ] comparable to, or below, those at the dysoxic site in this study, and as may be found in oxygen-depleted niches within aquifer biofilms [ 47 ]. Although, under oxygen depleted conditions such as these, AOB could instead undertake nitrite-dependent ammonia oxidation (‘nitrifier denitrification’), generating N 2 O [ 48 , 49 ].

Among non-assimilatory pathways, ammonia-oxidation prevailed in pristine groundwater. Site C contained significantly more nasA genes, which comprises part of the assimilatory nitrate reduction pathway ( p < 0.05), along with genes involved in amino acid biosynthesis such as asparagine synthetase ( asnB ) and L-asparaginase II ( ansB ) [ 50 ]. This suggests site C had enhanced potential for N uptake and storage, likely due to the large investment required to scavenge nitrogen for cellular maintenance with low nitrate and ammonia concentrations [ 51 ].

Nitrogen cycling is a core function of groundwater microbiomes, but community compositions are site-specific

To link pathways to organisms we analyzed 396 non-redundant medium-high to high-quality MAGs [ 52 ]. We reconstructed 7695 metagenome-assembled genomes (MAGs) of which 626 were non-redundant (ANI threshold of 99%), and 396 of these were estimated to be 70–100% complete, with 0–5% contamination. Nitrogen-cycling genes, specifically those involved in non-assimilatory redox reactions, such as nitrification, anammox, and complete or incomplete DNRA and denitrification (starting from nitrate reduction), were present in 40% of MAGs (Figs. 3 , 4A , and Table S7 ). The capacity for diverse nitrogen-cycling processes was again observed to be pervasive across sites, and the overall richness of taxa capable of nitrogen cycling remained comparably diverse over most sites (Fig. 5A ), regardless of large differences in measured inorganic N contents (>10-fold difference in nitrate-N, site averages 0–0.007 gm 3 nitrite-N and 0–0.018 g/m 3 ammoniacal-N). Analysis of 16S rRNA gene amplicons across 59 groundwater wells likewise shows that taxa linked through phylogenetic affiliation to nitrogen-cycling processes comprise a notable fraction (0.3–26.3%) of complex oxic to anoxic groundwater communities (Fig. S 2 ). Functional redundancy was common among N-cycling microorganisms. Multiple MAGs recovered from each sample had the collective capacity for DNRA and actively expressed genes associated with each of the major steps of nitrification and denitrification (Fig. 4B, C ).

Purple gradient (right) represents genome coverage scaled by row ( Z -Score) across sites A–D (ordered gwj01-16). Rows = MAGs; columns = samples per site (groundwater and attached-fraction enriched groundwater). Orange gradient (right) represents number of nitrogen-cycling gene copies per genome. Microorganisms are ordered based on hierarchical clustering of abundance based Bray-Curtis dissimilarity matrix with ward.D2 clustering method. Final column (labelled with asterisk) indicates genomes that were significantly more abundant at a particular site (coloured rectangle) based on LEfSe analysis.

A Number of MAGs with genes or genes expressed per pathway, with indicative genes required for each step from nitrate to ammonia or N 2 to denote complete DNRA or denitrification potential, respectively. B Number of MAGs with marker genes and marker genes overall for key N cycling processes: two steps for nitrification (purple), four steps for denitrification (dark green), DNRA (light green), and anammox (red). C Number of MAGs with at least one copy of each marker gene or marker gene expressed across groundwater samples and sites (A–D).

A Boxplots showing the median and interquartile range of richness of MAGs capable of nitrogen-cycling. Black solid circles show actual sample richness. Sites with significantly different richness are indicated by an overlying line and asterisk (Wilcoxon test, p < 0.05). B Non-metric Multi-dimensional Scaling plot showing groundwater community relatedness based on a Bray–Curtis dissimilarity matrix constructed using the relative abundance of MAGs with nitrogen-cycling genes. C Non-metric Multi-dimensional Scaling plot based on a Bray–Curtis dissimilarity matrix constructed using the relative abundance of protein-coding sequences in metagenomic reads. For ordinations environmental variables (Table S1 ) were fitted using envfit, and significant variables are indicated with an asterisk = p < 0.05. Ammoniacal-N and nitrite are not shown as >50% of values were below the detection limit and >50% of TKN values are missing.

Results suggest that nitrogen cycling is a core function of aquifer microbiomes, despite typically low levels of inorganic N in groundwater [ 4 ]. This conjecture is supported by prior evidence from ammonium- or nitrate-poor groundwater of microorganisms capable of, or actively engaged in, nitrification, anammox, or denitrification [ 25 , 26 , 28 , 53 , 54 ]. Microbial nitrogen cycling is likely to be a significant factor governing nitrogen availability in typically oligotrophic habitats, such as groundwater, the open ocean, and lakes. Indeed, in oligotrophic ocean waters with low primary production, the turnover of the dissolved inorganic nitrogen pool via microbial ammonium regeneration and nitrification is rapid [ 55 ]. Moreover, numerous microorganisms have evolved high affinities for nitrogen compounds, conferring them with competitive advantages under N-limited conditions [ 47 , 56 , 57 , 58 , 59 ].

Analysis of the spatial distributions of MAGs showed distinct site-specific compositions of bacteria and archaea capable of nitrogen cycling (Fig. 3 ), a feature also observed in groundwater microbial communities as a whole [ 13 ]. Bray–Curtis dissimilarities, calculated based on relative abundance for MAGs and metagenomic reads encoding nitrogen-cycling proteins, revealed that spatial differences significantly influenced community composition ( R 2 = 0.49 for MAGs, R 2 = 0.42 for metagenomic reads), more than DO, DOC, nitrate, and sample type (groundwater or attached-fraction enriched) (Fig. 5A, B ; Table S8 ). Most MAGs inferred to undertake nitrogen cycling (87.4%) were significantly more abundant at a specific site (22–57 MAGs/site; LEfSe, Kruskal–Wallis test). Results therefore show site-specific environmental conditions drive species selection, and the capacity for certain reactions, such as ammonia oxidation (greater in oxic groundwater) or complete denitrification (greater in dysoxic groundwater) (Fig. S 3 ).

Nitrifier diversity and activity in groundwater, and habitat specificity

Archaeal and bacterial ammonia-oxidizers exhibited distinct niche preferences, but higher similarity in transcriptional activity.

Ammonia-oxidizing archaea (AOA) and bacteria (AOB) convert ammonia to nitrite using ammonia monooxygenase (Amo) and hydroxylamine oxidoreductase (Hao), and perform the rate-limiting step in nitrification [ 60 ]. Niche differentiation between the two domains is not clearly defined [ 57 ]. However, AOA usually have a higher affinity for ammonia than AOB [ 47 , 49 , 56 ], and typically outnumber AOB in oligotrophic environments with low ammonia concentrations and salinity, consistent with groundwater in this study (mean ammoniacal-N 0.36 g/m 3 ± 1.4 SD; conductivity 220 µS/cm ± 142 SD). We found AOA and AOB exhibited distinct spatial trends in relative and absolute abundance, and activity related to various geochemical parameters in groundwater (e.g. ammonia, oxygen availability, and conductivity) (Fig. 6 ).

A Relative abundance of each MAG capable of aerobic ammonia oxidation across the sites. B Stacked barplot showing modified transcripts per million, normalized to genome coverage, of amoA , pmoA and xmoA across sites (wells SR1, SR2, E1, N3). The 7 AOA are associated with 5 genera: Nitrosotenuis (nzgw11), UBA8516 (nzgw12–14), Nitrososphaera (nzgw16), Nitrosoarchaeum (nzgw8-9) and an unclassified genus in Nitrososphaeraceae (nzgw15). The xmoA is part of a gene cluster in MAG nzgw585, recovered from the dysoxic site and classified as Gammaproteobacteria genus Nevskia , which encodes a copper-containing membrane monooxygenase (CuMMO/ xmoCAB ). The alpha subunit had best hits to Polycyclovorans sp. SAT60 and gammaproteobacterial isolate MMS_B.mb.28 (85.71% amino acid identity, NCBI NR database). CuMMO catalyzes the oxidation of short-chain alkanes, ammonia or methane [ 103 ]. C Spearman’s rank correlations between the abundance (copies/L) of nitrogen-cycling genes (DNA, samples = 64) and transcripts (RNA, samples = 26 above detection limit) determined via ddPCR and geochemical parameters (Table S11 ). Significant correlations are indicated by * are based on Bonferroni adjusted p values ( p ).

Based on metagenomic reads and MAGs, protein-coding sequences for ammonia monooxygenase (Amo) subunits were most abundant at oxic site A (Figs. 1 d, 6A ; LEfSe, Kruskal–Wallis test). This trend was mostly driven by AOA, as there were significantly more sequences encoding AOA-AmoA than AOB-AmoA overall at oxic sites (Wilcoxon rank, p < 0.05), presumably due to lower ammonia regeneration (measured ammonia/ammonium concentrations were low across all sites regardless of oxygen content, >1 gm −3 in only 6% of wells, and most below detection, Table S1 ). While not all ammonia oxidizer diversity may have been captured by the ddPCR primer sets used (e.g. the AOA primer set has a known bias against some ammonia-oxidizing Thermoproteota / Thaumarchaeota ) [ 61 ], quantification of amoA genes and transcripts demonstrated a similar relationship with oxygen across a wider set of groundwater sites (Fig. 6C ). Archaeal/bacterial amoA gene ratios were significantly and positively correlated with ORP (Spearman’s r = 0.39), and negatively correlated with borehole depth (Spearman’s r = −0.35; Table S9 ), which is expected to become increasingly oxygen-depleted with depth [ 62 ]. These gene ratios were also significantly and negatively associated with ammonia concentrations, conductivity, TDS, and pH (Spearman’s r = −0.34 to 52). Transcript ratios exhibited similar trends, albeit significant only for pH.

Taken together, results indicate that AOA and AOB abundance and activity are governed by distinct environmental niches in groundwater, as found in soils [ 63 ]. However, while AOA amoA gene concentrations were on average 40x higher than AOB genes, this difference was ten-fold less for transcripts (Table S10 ). Moreover, the deficit in significant correlations between AOA/AOB amoA transcript ratios and geochemical/physical groundwater parameters (Fig. 6 ), suggests comparatively little difference in AOA and AOB activity overall.

Ammonia-oxidizers constituted several major lineages, including a single comammox bacterium

Commensurate with a greater abundance of AOA, we reconstructed seven AOA MAGs, along with one Nitrospiraceae MAG capable of complete ammonia oxidation (comammox). All contained at least one ammonia monooxygenase gene and six contained genes encoding all AmoABC subunits (Table S7 ). AOA genomes (and their amoA genes, Figs. S 4 -S 6 ) were phylogenetically diverse, with the MAGs comprising five different genera (Fig. 6a ). Of these, nzgw14 (UBA8516) was the most abundant nitrogen cycling MAG overall (Fig. S 7 ), and was most abundant at oxic sites, along with other AOA MAGs. However, AOA MAG relative abundances did not reflect their transcriptional activity (Fig. 6B ).

Recently characterized comammox bacteria ( Nitrospira , phylum Nitrospirae ) [ 64 ] oxidize ammonia to nitrate in three steps (ammonia → hydroxylamine → nitrite → nitrate). Nitrospiraceae MAG (nzgw279) possesses genes for ammonia oxidation ( amoABC ), hydroxylamine oxidation ( haoAB ), and nitrite oxidoreductase ( nxrAB ), consistent with comammox. It also possesses a dissimilatory nitrite reductase ( nirK ) present in comammox bacteria elsewhere [ 65 , 66 ]. Based on 120 concatenated bacterial marker genes (GTDB-Tk) and the AmoA subunit, nzgw279 is closely related to clade B sublineage II comammox Nitrospira , and is most similar to Nitrospira sp. RCB obtained from an aquifer in Colorado (USA) [ 66 ] (Fig. S 5 ), indicating strong habitat driven selection, independent of geographical distance. As expected for comammox, nzgw279 relative abundance was positively correlated with ORP and DO (Spearman’s r = 0.87 and 0.63; respectively). Although comammox bacteria can be the most abundant ammonia-oxidizers in some settings (e.g. groundwater-fed sand filters, forest soils and biofilters [ 67 , 68 , 69 ]), AOA genomes were more abundant overall here (Figs. 6 , S 7 ). Nevertheless, nzgw279 was highly active in terms of nx r (although not amoA ) gene expression (Fig. 2C ).

Diverse taxa with nitrite oxidoreductase homologues, including Nitrososphaerales

In addition to comammox bacterium nzgw279, we recovered the genomes of two Nitrospiraceae that we predict are canonical nitrite oxidizers, nzgw274 (no genus designation; nxrA gene present), and nzgw276 (genus=40CM-3-62-11; nxrAB present) (Table S7 ). Neither are affiliated with known comammox bacteria ( Nitrospira spp. [ 66 ]). The nxrA from nzgw274 was expressed highest at dysoxic site D in attached-fraction enriched groundwater ( nxrA , planktonic-fraction = 0.36, attached-fraction = 8.97 TPM). MAG nzgw276 transcripts were also present, but at a much lower level. Results suggest that the well (E1) had sufficient oxygen for NOB to exist. NOB can be active at nanomolar-to-micromolar concentrations of DO [ 70 ], and thereby compete for nitrite alongside anammox and denitrifying bacteria.

Known NXR are reported to be genetically diverse [ 71 , 72 ]. The known diversity of nitrifiers continues to grow [ 73 ] and NXR has alternative uses, for example, as a nitrate reductase [ 71 , 72 ]. Here, homologues were present in a diverse range of other MAGs, including several anammox bacteria ( Planctomycetota , class Ca . Brocadiae, Table S7 ) [ 15 ], which typically use NXR to oxidize a small amount nitrite to nitrate during anammox [ 74 ], an archaeal Nitrososphaerales (nzgw5; nxrABC present), which belongs to a taxonomic group more typically associated with ammonia oxidation (this dataset, Table S7 ) [ 74 ], and various other bacterial phyla, which represent a pool of potentially novel nitrifiers (Fig. S 8a ).

To further explore NXR in the archaeal Nitrososphaerales MAG (nzgw5), we evaluated the 14,591 bp long contig (3135) on which the genes were found. The contig primarily comprises protein-coding genes with closest homology to archaea (based on the NCBI nr database) that are located on either side of a syntenous bacterial-like nxrABC gene cluster (Fig. S 8b ; Table S11 ), including chaperone-encoding torD directly adjacent to nxrC , as found in Nitrospina gracilis , which is thought to facilitate Mo cofactor maturation and insertion into NxrA [ 75 ]. To determine whether nxr genes were reproducibly present in other closely related Nitrososphaerales genomes, we searched for dereplicated MAGs sharing >99% ANI with nzgw5. We found one “replicate” Nitrososphaerales MAG (nzgw5-b) sharing 99.2% ANI, which was recovered from site B (nzgw5 derived from a co-assembly of site B samples), and that possessed a similar nxrABC gene cluster (Table S11 ).

The MAG nzgw5 shares NxrA protein sequence similarity with bacteria as phylogenetically diverse as Nitrospira defluvii , Nitrospina gracilis , and Candidatus Brocadia (Fig. S 8a ), but the highest NCBI nr database matches were to other aquifer bacteria, Candidate division Zixibacteria bacterium RBG-1 (58.56% identity) and Planctomycetes bacterium RIFCSPHIGHO2_02_FULL_52_58 (56.7% identity)—both originally recovered genomically from an aquifer in Rifle, CO, USA [ 11 , 76 ]. NxrB similarly had the highest match with other aquifer-derived genomes (also U.S.A.), including one Nitrospinae bacterium (65.97% identity), and most notably, two archaea affiliated with the Thermoproteota (previously Thaumarchaeota ) phylum—another Nitrososphaerales , and Thermoproteota bacterium (68.71–71.87% identity) [ 13 ]. While the gene cluster appears to have been horizontally acquired, we found no identifiable genomic island associated with contig 3135. However, lateral gene transfer occurs more frequently between organisms, including unrelated taxa, that share a habitat [ 77 ]. Results suggest aquifer-adapted Nitrososphaerales acquired nxr genes, and potentially also the ability for nitrite oxidation/reduction, from a co-occurring bacterium.

Nitrite-dependent methanotroph ( Ca . Methylomirabilis)

Nitrite-dependent methanotrophs were prevalent.

Analysis of metagenomic reads revealed that copper-containing, membrane-associated particulate methane monooxygenase subunit A (PmoA) sequences (a closely related AmoA homologue [ 78 ]) were ubiquitous, but significantly more abundant at oxic site A (Fig. 1C ). This protein is associated with aerobic and anaerobic nitrite-dependent methanotrophs that are able to oxidize methane to CO 2 , using methane as a sole carbon and energy source [ 79 ]. Methanotrophic bacteria can also oxidize ammonia to nitrite using particulate methane monooxygenase (pMMO) and a unique hydroxylamine oxidoreductase, HAO [ 80 ]. Interactions between methanotrophs and ammonia-oxidizers in aquifers are poorly understood. They are associated with opposite gradients of ammonia and methane, as ammonia inhibits the activity of methanotrophs and methane acts as a competitive inhibitor for ammonia oxidizers [ 81 , 82 ]. Analysis of 16S rRNA gene amplicons across a wide distribution of aquifer samples ( n = 80) showed that Ca . Methylomirabilis relative abundance was positively correlated with ammonia-oxidizers Nitrosotaleacae, Nitrosomonadaceae , and Nitrosopumilaceae (Spearman’s r = 0.42, r = 0.33 and r = 0.37, respectively). Aerobic ammonia-oxidizers consume O 2 and may provide a habitable environment for Ca . Methylomirabilis at oxic/anoxic interfaces and produce nitrite, which could potentially be directly used by these nitrite-dependent methanotrophs [ 83 ].

We recovered one nitrogen cycling methanotrophic MAG (nzgw240), related to the anaerobic methane-oxidizing genus Ca . Methylomirabilis (Figs. 6 , S 6 ) [ 84 ]. Members of Ca . Methylomirabilis perform NO 2 − dependent anaerobic methane oxidation through an intra‐aerobic pathway involving the dismutation of NO into O 2 and N 2 [ 79 , 84 ], and play an important role in controlling N 2 O and methane emissions from natural ecosystems [ 79 ]. All pmoABC subunits for methane oxidation [ 79 ] were present in nzgw240, and were closely related to those from Ca . Methylomirabilis lanthanidiphila (74.80–95.5% amino acid identity, Fig S 6 ), a methanotroph that dominated an enrichment culture after addition of rare-earth metal cerium [ 85 ]. Several genes involved in nitrogen cycling, such as nitrate oxidoreductase ( nxrAB ), nitrite reductase ( nirS ), putative NO dismutase ( nod ) and nitric oxide reductase ( norZ) were also identified in MAG nzgw240, and were expressed at the dysoxic site alongside pmoA (Figs. 2 c, 6b ), where dissolved methane was also detected [ 86 ]. The first of two nitric oxide-like reductases shares 95.6% amino acid identity with Nod (DAMO_2434) in Ca . Methylomirabilis oxyfera [ 87 ]. This enyzme is homologous to the quinol-dependent NO reductases (qNOR) [ 87 ], however experimental validation is still required to prove nitric oxide disproportionation. The second is a NO reductase sharing 88.34% amino acid identity with NorZ (DAMO_1889).

Final-step of denitrification

Atypical nosz was more common than typical nosz.

Thirty MAGs, spanning 10 bacterial phyla, contained nosZ genes (Fig. 3 ). The NosZ protein catalyzes the conversion of green-house gas N 2 O to N 2 in the last step of denitrification. Typical NosZ proteins (clade I) contain a twin-arginine translocation (Tat) signal peptide, and to date are affiliated exclusively with Proteobacteria , which usually perform complete denitrification [ 88 ]. A maximum-likelihood tree revealed that NosZ predicted protein sequences comprised both typical clade I twin-arginine (Tat) dependant N 2 O reductase with Proteobacteria (2 MAGs) and atypical clade II secretory (Sec) dependent N 2 O reductase proteins (23 MAGs) (Fig. S 9 ) [ 88 ]. The tree also shows a novel clade of Nitrospirota and Nitrospinae NosZ Sec-dependant sequences, including four NosZ sequences from this study (Fig. S 9 ) that were transcriptionally active (Fig. 7 ). Members of clade II are considered non-denitrifiers, typically performing just the final step of denitrification [ 89 ]. However, 4/7 MAGs capable of complete denitrification encode clade II NosZ, demonstrating complete denitrifiers are present across both clades. Sec-dependent protein translocation is considered more energetically favourable than Tat, requiring between 700 and 5,000 molecules (or equivalent) of ATP per protein translocation across the membrane, whereas Tat requires the equivalent of ~10,000 molecules of ATP [ 90 ]. A greater proportion of Sec signal pathways in low nutrient groundwater would be favourable for energy conservation.

A Stacked barplot shows modified-TPM of Sec- and Tat- dependent nosZ genes at each site. B Stacked barplot shows modified-TPM normalized to genome coverage of Sec- and Tat-dependent nosZ genes at each site. While complete denitrifier, Sulfuricella MAG nzgw577, contributed the most transcripts, after normalizing to MAG relative abundance, nosZ genes from two novel Nitrospinota MAGs (nzgw266-267, class UBA7883 [ 104 ]) were transcriptionally most active. c = MAGs which contain genes for the complete denitrification pathway (nzgw numbers: 271, 530, 549, 554, 561, 566, and 577).

Nitrous oxide reductase gene expression was strongly associated with oxygen availability and not limited by pathway fragmentation

Based on ddPCR, nosZ clade I genes (3 × 10 1 –6 × 10 5 copies/L) and transcripts (1 × 10 1 –7 × 10 4 copies/L) were detected across most aquifer samples tested (Table S10 ). Expression was significantly and negatively correlated with ORP (Fig. 6 ), reflecting observations elsewhere that the rate of denitrification decreases linearly with increasing ORP [ 91 ]. Accordingly, at the dysoxic site there was also a proportionally higher abundance of MAGs with nosZ genes of any type (Fig. 3 ), and of complete denitrifier MAGs, which comprised up to 42% of the nitrogen cycling community (4–31× more on average than oxic sites) (Fig. S 3 ).

N 2 O generation due to incomplete denitrification has been shown to be highest under oxic conditions in groundwater [ 92 ], comparable to sites A-C here. A fragmented denitrification pathway may explain higher N 2 O concentrations in some oxic groundwaters. Fragmented genetic potential for biogeochemical cycling processes, such as denitrification, appears to be a common trait in aquifer bacteria (Fig. 4 ) [ 11 ], necessitating metabolic handoffs among individuals to complete pathways. Our transcriptomic data points to active collaboration among incomplete denitrifiers for generation and removal of N 2 O (although in situ measurements would be required to determine the presence or absence of NO or N 2 O emissions). Transcriptional activity associated with N 2 O reduction was at least equivalent to that for generation, regardless of groundwater oxygen-content or the portion of pathway fragmentation (Fig. 2A ).

Transcriptional activity of co-occurring aerobic and anaerobic nitrogen-cycling pathways in oxic versus dysoxic groundwater

Based on transcripts mapped to MAGs, there was less nitrogen-cycling transcriptional activity at the pristine oxic site compared to the dysoxic site (average modified-TPM 69 ± 13 site C versus 359 ± 362 site D) (Fig. 2B ). This is consistent with quantification of 8x more nitrogen-cycling transcripts by ddPCR in dysoxic versus oxic groundwater, across a wider set of groundwaters (on average 7 × 10 4 transcripts/L in dysoxic and 8 × 10 3 transcripts/L in oxic groundwater; Table S11 ). The greatest proportion of mapped transcripts at the oxic site was associated with ammonia oxidation to nitrate and re-reduction to nitrite, based on ammonia monooxygenase ( amo ), nitrite oxidoreductase ( nxr ), and periplasmic nitrate reductase ( nap ) gene transcripts (Fig. 2A ). Expression of nap genes is suggestive of aerobic denitrification at this site, as nitrate reduction in the periplasm is not inhibited by oxygen [ 93 ].

At the dysoxic site, the greatest portion of gene expression in groundwater and attached-fraction enriched groundwater, based on mapped transcripts was associated with, again, nitrite oxidation ( nxr ), but also anammox ( hzo , hzs ), and denitrification ( nor and nos ) (Fig. 2A ). These genes each contributed up to 8−66% of nitrogen-cycling transcripts at site D. Hydrazine synthase hzsB transcripts (quantified by ddPCR) were also highest at the dysoxic site (April 2018), one of only seven sites in the study with detectable nitrite concentrations. Contemporaneous measurements of excess N 2 indicated active N 2 generation in dysoxic groundwater from this site (wells E1 and N3; Table S12 ) due denitrification and/or anammox [ 15 ]—the technique cannot distinguish between N 2 produced by these processes. Nitrate-based δ 18 O against δ 15 N measurements from groundwater in well N3 also indicated the occurrence of denitrification [ 86 ]. The majority of hzoA and hzsB genes were expressed by just two Planctomycetes MAGs (nzgw511–512) at this site (37% and 58%, respectively). However, when considering hzsB transcript concentrations in the wider aquifer dataset, we observed no relationship with DOC or oxygen availability (DO, ORP or borehole depth) (Fig. 6 ), indicating these bacteria are active under a wide variety of groundwater conditions, including those considered unfavourable for anammox (i.e. high DOC and DO). Ca . Brocadiae genomes recovered from Sites A–D were previously found to have a broad range of ABC transport systems and variations in substrate importation such as phosphate, cobalt, nickel, iron(III), zinc, sulfate, molybdate, lipoproteins, ribose, rhamnose, polysaccharides, and oligopeptides, suggesting that they may not just be autotrophic specialists [ 15 ]. We found evidence for greater competition among N 2 O reducers (Fig. 2B ), although most nosZ transcripts overall (81%) were expressed by a single complete denitrifier, MAG nzgw577 (genus Sulfuricella ; Fig. 7 ) at the dysoxic site (Fig. 2C ), despite it being only the third most active in terms of nosZ expression after normalizing to MAG coverage (Fig. 7 ). Members of this genus are reported to perform autotrophic denitrification coupled with the oxidation of reduced sulfur compounds [ 94 ].

Several aerobic ammonia-oxidizers, for which we recovered MAGs, were also active at the dysoxic site, contributing 5-6% of nitrogen-cycling transcripts mapped (Fig. 2B ). This suggests the potential for simultaneous nitrification and denitrification, and partial coupling of these pathways (overall modified-TPM 1:2.7 amoA : nosZ , 1:2.3 nosZ : nxrA ). Most (88%) amoA transcriptional activity at this dysoxic site was attributed to four AOA MAGs affiliated with Nitrosopumilaceae . The greatest proportion of ammonia monooxygenase transcription was associated with the attached-fraction enriched groundwater from this site (Fig. 6B ), consistent with preferences previously reported for the ammonia-oxidizing genera, Nitrososphaera and Nitrosopumilus , in groundwater [ 30 ]. Prior findings from karstic aquifers also suggest that soil-derived ammonia oxidizers may be imported into groundwater [ 26 ], which may be important for shallow aquifers that directly receive leachate from the soil zone, along with any microorganisms it carries.

The most transcribed nitrogen-cycling gene among all MAGs was nxrB from comammox Nitrospiraceae nzgw279, which showed the highest expression in attached-fraction enriched groundwater at site D. This groundwater contained more total suspended solids (Table S1 ), and therefore more sediment particles coated in biofilms [ 95 ]. Comammox Nitrospira populations have previously been found to dominate biofilms in wastewater, outnumbering all other nitrifiers [ 96 ]. As nzgw279 was associated with fewer amoA transcripts than other ammonia-oxidizers (average modified-TPM 0.77 ± 1.02 SD vs 2.01 ± 3.22 SD), and appeared to act largely as a canonical nitrifier [ 97 ], it potentially received nitrite as a by-product from the several active AOAs.

Results show methanotroph methane monooxygenase gene transcription occurred alongside gene expression associated with nitrification, anammox, and denitrification at the dysoxic site. Methanotrophs and ammonia-oxidizers share many metabolic similarities based on a common evolutionary history, and supported by the structural similarities of ammonia and methane monooxygenases [ 81 ], methanotrophs have been implicated in both methane and ammonia oxidation in groundwater [ 98 ]. In this study, Ca . Methylomirabilis (nzgw240) expressed genes, associated with concurrent methane oxidation ( pmoA ) and nitric oxide dismutation (NO 2 - reductase nirS and NO dismutase nod ) to N 2 and O 2 (Fig. 2C ) [ 84 ]. Co-occurring gene expression reveals a potential interaction among AOA, Ca . Methylomirabilis, and anammox bacteria, whereby nitrite produced from aerobic ammonia oxidation by AOA, drives anammox and nitrite-dependent anaerobic methane oxidation by Ca . Methylomirabilis . Ca . Methylomirabilis produces oxygen which could create an interface whereby AOA and comammox can co-exist. Oxygen consumption and nitrite provisioning by AOA could represent synergism with anammox in the terrestrial subsurface, as previously predicted to occur in unconfined aquifer soils [ 99 ]. Indeed, ammonia oxidizer and anammox activities, based on transcript copy numbers, were found to be tightly linked across distinct groundwater chemistries in the wider set of samples [ 15 ]. These heterogeneous reactions at the dysoxic site indicate that it likely contained mixed redox conditions in situ. This could be due to oxygen penetration from above [ 100 ], and vertical stratification of electron donors [ 101 ], geochemical gradients created by biofilm formation [ 102 ], or oxygen produced by the intra-aerobic pathway of Ca . Methylomirabilis species [ 84 ].

Results show that the capacity for non-assimilatory nitrogen-cycling reactions, such as ammonia oxidation and denitrification, was prevalent in groundwater regardless of site-specific physicochemistry, although the relative abundance of each pathway differed. Phylogenetically diverse AOA and AOB were associated with distinct environmental niches in groundwater, and AOA- amoA genes and transcripts were more abundant overall. While incomplete denitrifiers were numerous, complete denitrifiers contributed to a substantial fraction of transcriptional activity under dysoxic conditions, where activity associated with denitrification, and N-cycling transcripts was greatest. Gene expression associated with nitrification, denitrification, nitrite-dependent methane oxidation, and anammox occurred simultaneously in dysoxic groundwater, such that nitrite (or nitrate) produced by AOA or comammox could fuel anammox, denitrification, and methanotrophy by Ca . Methylomirabilis. Results provide insights into microbial N-transformations in groundwater with distinct chemical characteristics (such as oxygen availability and DOC), and potential metabolic “handoffs” among nitrogen-cycling organisms.

Data availability

Sequences are deposited with NCBI under BioProject PRJNA699054.

Taylor RG, Scanlon B, Döll P, Rodell M, Van Beek R, Wada Y, et al. Groundwater and climate change. Nat Clim Chang. 2013;3:322–9.

Article Google Scholar

Aeschbach-Hertig W, Gleeson T. Regional strategies for the accelerating global problem of groundwater depletion. Nat Geosci. 2012;5:853–61.

Article CAS Google Scholar

Alley WM, Healy RW, LaBaugh JW, Reilly TE. Flow and storage in groundwater systems. Science. 2002;296:1985–90.

Article CAS PubMed Google Scholar

Morgenstern U, Daughney CJ. Groundwater age for identification of baseline groundwater quality and impacts of land-use intensification - The National Groundwater Monitoring Programme of New Zealand. J Hydrol. 2012;456–457:79–93.

Rivett MO, Buss SR, Morgan P, Smith JWN, Bemment CD. Nitrate attenuation in groundwater: a review of biogeochemical controlling processes. Water Res. 2008;42:4215–32.

Rivett MO, Smith JWN, Buss SR, Morgan P. Nitrate occurrence and attenuation in the major aquifers of England and Wales. Q J Eng Geol Hydrogeol. 2007;40:335–52.

Yu G, Wang J, Liu L, Li Y, Zhang Y, Wang S. The analysis of groundwater nitrate pollution and health risk assessment in rural areas of Yantai, China. BMC Public Health. 2020;20:437.

Article CAS PubMed PubMed Central Google Scholar

Sundermann G, Wägner N, Cullmann A, von Hirschhausen CR, Kemfert C. Nitrate pollution of groundwater long exceeding trigger value: Fertilization practices require more transparency and oversight. DIW Wkly Rep. 2020;10:61–72.

Google Scholar

Nitrate and nitrite in drinking-water Background document for development of WHO Guidelines for Drinking-water Quality. World Health Organization; 2003. https://apps.who.int/iris/handle/10665/75380 .

Smolders AJP, Lucassen ECHET, Bobbink R, Roelofs JGM, Lamers LPM. How nitrate leaching from agricultural lands provokes phosphate eutrophication in groundwater fed wetlands: the sulphur bridge. Biogeochemistry. 2010;98:1–7.

Anantharaman K, Brown CT, Hug LA, Sharon I, Castelle CJ, Probst AJ, et al. Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nat Commun. 2016;7:13219.

Danczak RE, Johnston MD, Kenah C, Slattery M, Wrighton KC, Wilkins MJ. Members of the Candidate Phyla Radiation are functionally differentiated by carbon- and nitrogen-cycling capabilities. Microbiome. 2017;5:112 https://doi.org/10.1186/s40168-017-0331-1

He C, Keren R, Whittaker ML, Farag IF, Doudna JA, Cate JHD, et al. Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems. Nat Microbiol. 2021;3:354–65.

Cardarelli EL, Bargar JR, Francis CA. Diverse Thaumarchaeota dominate subsurface ammonia-oxidizing communities in semi-arid floodplains in the western united states. Microb Ecol. 2020;80:778–92.

Mosley OE, Gios E, Weaver L, Close M, Daughney C, Van Der Raaij R, et al. Metabolic diversity and aero-tolerance in anammox bacteria from geochemically distinct aquifers. mSystems. 2022;7:e0125521.

Article PubMed Google Scholar

Haruta S, Kato S, Yamamoto K, Igarashi Y. Intertwined interspecies relationships: approaches to untangle the microbial network. Environ Microbiol. 2009;11:2963–9. https://doi.org/10.1111/j.1462-2920.2009.01956.x

Albright MBN, Timalsina B, Martiny JBH, Dunbar J. Comparative genomics of nitrogen cycling pathways in bacteria and archaea. Microb Ecol. 2019;77:597–606.

Stein LY, Klotz MG. The nitrogen cycle. Curr Biol. 2016;26:R94–R98.

Kuypers MMM, Marchant HK, Kartal B. The microbial nitrogen-cycling network. Nat Rev Microbiol. 2018;16:263–76.

Yoon S, Cruz-García C, Sanford R, Ritalahti KM, Löffler FE. Denitrification versus respiratory ammonification: environmental controls of two competing dissimilatory NO 3 - /NO 2 - reduction pathways in Shewanella loihica strain PV-4. ISME J. 2015;9:1093–104.

Zhu W, Wang C, Hill J, He Y, Tao B, Mao Z, et al. A missing link in the estuarine nitrogen cycle? Coupled nitrification-denitrification mediated by suspended particulate matter. Sci Rep. 2018;8:2282.

Article PubMed PubMed Central Google Scholar

Lam P, Jensen MM, Lavik G, McGinnis DF, Müller B, Schubert CJ, et al. Linking crenarchaeal and bacterial nitrification to anammox in the Black Sea. Proc Natl Acad Sci USA. 2007;104:7104–9.

Huno SKM, Rene ER, Van Hullebusch ED, Annachhatre AP. Nitrate removal from groundwater: a review of natural and engineered processes. J Water Supply Res Technol - AQUA. 2018;67:885–902.

Killingstad MW, Widdowson MA, Smith RL. Modeling enhanced in situ denitrification in groundwater. J Environ Eng. 2002;128:491–504.

Handley KM, Verberkmoes NC, Steefel CI, Williams KH, Sharon I, Miller CS, et al. Biostimulation induces syntrophic interactions that impact C, S and N cycling in a sediment microbial community. ISME J. 2013;7:800–16.

Opitz S, Küsel K, Spott O, Totsche KU, Herrmann M. Oxygen availability and distance to surface environments determine community composition and abundance of ammonia-oxidizing prokaroytes in two superimposed pristine limestone aquifers in the Hainich region, Germany. FEMS Microbiol Ecol. 2014;90:39–53.

Herrmann M, Rusznyák A, Akob DM, Schulze I, Opitz S, Totsche KU, et al. Large fractions of CO 2 -fixing microorganisms in pristine limestone aquifers appear to be involved in the oxidation of reduced sulfur and nitrogen compounds. Appl Environ Microbiol. 2015;81:2384–94.

Kumar S, Herrmann M, Blohm A, Hilke I, Frosch T, Trumbore SE, et al. Thiosulfate- and hydrogen-driven autotrophic denitrification by a microbial consortium enriched from groundwater of an oligotrophic limestone aquifer. FEMS Microbiol Ecol. 2018;94:10 https://doi.org/10.1093/femsec/fiy141

Pan D, Nolan J, Williams KH, Robbins MJ, Weber KA. Abundance and distribution of microbial cells and viruses in an alluvial aquifer. Front Microbiol. 2017;8:1199.

Flynn TM, Sanford RA, Ryu H, Bethke CM, Levine AD, Ashbolt NJ, et al. Functional microbial diversity explains groundwater chemistry in a pristine aquifer. BMC Microbiol. 2013;13:146.

Close M, Abraham P, Webber J, Cowey E, Humphries B, Fenwick G, et al. Use of sonication for enhanced sampling of attached microbes from groundwater systems. Groundwater. 2020;58:901–12.

Malard F, Hervant F. Oxygen supply and the adaptations of animals in groundwater. Freshw Biol. 1999;41:1–30.

Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25:1043–55.

Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics. 2019;36:1925–7.

PubMed Central Google Scholar

Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357–9.

CAS PubMed PubMed Central Google Scholar

Liao Y, Smyth GK, Shi W. FeatureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014;30:923–30.

Wagner GP, Kin K, Lynch VJ. Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples. Theory Biosci. 2012;131:281–5.

Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinforma. 2004;5:115.

Nguyen LT, Schmidt HA, Von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015;32:268–74.

Price MN, Dehal PS, Arkin AP. FastTree 2 – approximately maximum-likelihood trees for large alignments. PLoS ONE. 2010;5:e9490.

Bertelli C, Laird MR, Williams KP, Lau BY, Hoad G, Winsor GL, et al. IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets. Nucleic Acids Res. 2017;45:W30–W35.

Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, Mcglinn D, et al. vegan: Community ecology. R Package version 25-6. 2019;2:1–297.

Warnes, GR Gplots: Various R Programming Tools for Plotting Data. 2011. http://cran.r-project.org/web/packages/gplots/index.html .

Tu Q, Lin L, Cheng L, Deng Y, He Z. NCycDB: a curated integrative database for fast and accurate metagenomic profiling of nitrogen cycling genes. Bioinformatics. 2019;35:1040–8.

Kartal B, Keltjens JT. Anammox biochemistry: a tale of heme c proteins. Trends Biochem Sci. 2016;41:998–1011.

Yu R, Chandran K. Strategies of nitrosomonas europaea 19718 to counter low dissolved oxygen and high nitrite concentrations. BMC Microbiol. 2010;10:1–11.

Straka LL, Meinhardt KA, Bollmann A, Stahl DA, Winkler MKH. Affinity informs environmental cooperation between ammonia-oxidizing archaea (AOA) and anaerobic ammonia-oxidizing (Anammox) bacteria. ISME J. 2019;13:1997–2004.

Arp DJ, Stein LY. Metabolism of inorganic n compounds by ammonia-oxidizing bacteria. Crit Rev Biochem Mol Biol. 2003;38:471–95.

Hink L, Lycus P, Gubry-Rangin C, Frostegård Å, Nicol GW, Prosser JI, et al. Kinetics of NH 3 - oxidation, NO - turnover, N 2 O-production and electron flow during oxygen depletion in model bacterial and archaeal ammonia oxidisers. Environ Microbiol. 2017;19:4882–96.

Singh SN, Tripathi RD, editors. Environmental bioremediation technologies. 1st edn. Springer-Verlag Berlin Heidelberg; 2007.

Ruan Y, Ma B, Cai C, Cai L, Gu J, Lu HF, et al. Kinetic affinity index informs the divisions of nitrate flux in aerobic denitrification. Bioresour Technol. 2020;309:123345.

Bowers RM, Kyrpides NC, Stepanauskas R, Harmon-Smith M, Doud D, Reddy TBK, et al. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nat Biotechnol. 2017;35:725–31.

Handley KM, Bartels D, O’Loughlin EJ, Williams KH, Trimble WL, Skinner K, et al. The complete genome sequence for putative H 2 - and S - oxidizer Candidatus Sulfuricurvum sp., assembled de novo from an aquifer-derived metagenome. Environ Microbiol. 2014;16:3443–62.

Bell E, Lamminmäki T, Alneberg J, Andersson AF, Qian C, Xiong W, et al. Biogeochemical cycling by a low-diversity microbial community in deep groundwater. Front Microbiol. 2018;9:2129.

Clark DR, Rees AP, Joint I. Ammonium regeneration and nitrification rates in the oligotrophic Atlantic Ocean: Implications for new production estimates. Limnol Oceanogr. 2008;53:52–62.

Martens-Habbena W, Berube PM, Urakawa H, De La Torre JR, Stahl DA. Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria. Nature. 2009;461:976–9.

Prosser JI, Nicol GW. Archaeal and bacterial ammonia-oxidisers in soil: the quest for niche specialisation and differentiation. Trends Microbiol. 2012;20:523–31.

Horak REA, Qin W, Schauer AJ, Armbrust EV, Ingalls AE, Moffett JW, et al. Ammonia oxidation kinetics and temperature sensitivity of a natural marine community dominated by Archaea. ISME J. 2013;7:2023–33.

Dimitri Kits K, Sedlacek CJ, Lebedeva EV, Han P, Bulaev A, Pjevac P, et al. Kinetic analysis of a complete nitrifier reveals an oligotrophic lifestyle. Nature. 2017;549:269–72.

Alves RJE, Wanek W, Zappe A, Richter A, Svenning MM, Schleper C, et al. Nitrification rates in Arctic soils are associated with functionally distinct populations of ammonia-oxidizing archaea. ISME J. 2013;7:1620–31.

Sintes E, Bergauer K, De Corte D, Yokokawa T, Herndl GJ. Archaeal amoA gene diversity points to distinct biogeography of ammonia-oxidizing Crenarchaeota in the ocean. Environ Microbiol. 2013;15:1647–58.

McDonough LK, Santos IR, Andersen MS, O’Carroll DM, Rutlidge H, Meredith K, et al. Changes in global groundwater organic carbon driven by climate change and urbanization. Nat Commun. 2020;11:1–10.

Bates ST, Berg-Lyons D, Caporaso JG, Walters WA, Knight R, Fierer N. Examining the global distribution of dominant archaeal populations in soil. ISME J. 2011;5:908–17.

Daims H, Lebedeva EV, Pjevac P, Han P, Herbold C, Albertsen M, et al. Complete nitrification by Nitrospira bacteria. Nature. 2015;528:504–9.

Sakoula D, Koch H, Frank J, Jetten MSM, Van Kessel MAHJ, Lücker S. Enrichment and physiological characterization of a novel comammox Nitrospira indicates ammonium inhibition of complete nitrification. ISME J. 2021;15:1010–24.

Poghosyan L, Koch H, Lavy A, Frank J, Kessel MAHJ, Jetten MSM, et al. Metagenomic recovery of two distinct comammox Nitrospira from the terrestrial subsurface. Environ Microbiol. 2019;21:3627–37.

Fowler SJ, Palomo A, Dechesne A, Mines PD, Smets BF. Comammox Nitrospira are abundant ammonia oxidizers in diverse groundwater-fed rapid sand filter communities. Environ Microbiol. 2018;20:1002–15.

Xia F, Wang JG, Zhu T, Zou B, Rhee SK, Quan ZX. Ubiquity and diversity of complete ammonia oxidizers (comammox). Appl Environ Microbiol. 2018;84:e01390–18.

Hu HW, He JZ. Comammox—a newly discovered nitrification process in the terrestrial nitrogen cycle. J Soils Sediment. 2017;17:2709–17.

Bristow LA, Dalsgaard T, Tiano L, Mills DB, Bertagnolli AD, Wright JJ, et al. Ammonium and nitrite oxidation at nanomolar oxygen concentrations in oxygen minimum zone waters. Proc Natl Acad Sci USA. 2016;113:10601–6.

Chicano TM, Dietrich L, de Almeida NM, Akram M, Hartmann E, Leidreiter F, et al. Structural and functional characterization of the intracellular filament-forming nitrite oxidoreductase multiprotein complex. Nat Microbiol. 2021;6:1129–39.

Koch H, Lücker S, Albertsen M, Kitzinger K, Herbold C, Spieck E, et al. Expanded metabolic versatility of ubiquitous nitrite-oxidizing bacteria from the genus Nitrospira . Proc Natl Acad Sci USA. 2015;112:11371–6.

Park SJ, Andrei AŞ, Bulzu PA, Kavagutti VS, Ghai R, Mosier AC. Expanded diversity and metabolic versatility of marine nitrite-oxidizing bacteria revealed by cultivation- and genomics-based approaches. Appl Environ Microbiol. 2020;86:1–17.

de Almeida NM, Wessels HJCT, de Graaf RM, Ferousi C, Jetten MSM, Keltjens JT, et al. Membrane-bound electron transport systems of an anammox bacterium: a complexome analysis. Biochim Biophys Acta Bioenergy. 2016;1857:1694–704.

Lücker S, Nowka B, Rattei T, Spieck E, Daims H. The genome of Nitrospina gracilis illuminates the metabolism and evolution of the major marine nitrite oxidizer. Front Microbiol. 2013;4:27.

Castelle CJ, Hug LA, Wrighton KC, Thomas BC, Williams KH, Wu D, et al. Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. Nat Commun. 2013;4:1–10.

Hooper SD, Mavromatis K, Kyrpides NC. Microbial co-habitation and lateral gene transfer: What transposases can tell us. Genome Biol. 2009;10:1–12.

Ricke P, Erkel C, Kube M, Reinhardt R, Liesack W. Comparative analysis of the conventional and novel pmo (particulate methane monooxygenase) operons from Methylocystis strain SC2. Appl Environ Microbiol. 2004;70:3055–63.

Ettwig KF, Butler MK, Le Paslier D, Pelletier E, Mangenot S, Kuypers MMM, et al. Nitrite-driven anaerobic methane oxidation by oxygenic bacteria. Nature. 2010;464:543–8.

Holmes AJ, Costello A, Lidstrom ME, Murrell JC. Evidence that participate methane monooxygenase and ammonia monooxygenase may be evolutionarily related. FEMS Microbiol Lett. 1995;132:203–8.

Stein LY, Roy R, Dunfield PF. Aerobic methanotrophy and nitrification: processes and connections. eLS . Chichester, UK: John Wiley & Sons, Ltd; 2012.

Nyerges G, Stein LY. Ammonia cometabolism and product inhibition vary considerably among species of methanotrophic bacteria. FEMS Microbiol Lett. 2009;297:131–6.

Welte CU, Rasigraf O, Vaksmaa A, Versantvoort W, Arshad A, Op den Camp HJM, et al. Nitrate- and nitrite-dependent anaerobic oxidation of methane. Environ Microbiol Rep. 2016;8:941–55.

Wu ML, Ettwig KF, Jetten MSM, Strous M, Keltjens JT, Van, et al. A new intra-aerobic metabolism in the nitrite-dependent anaerobic methane-oxidizing bacterium Candidatus ‘Methylomirabilis oxyfera’. Biochem Soc Trans. 2011;39:243–8.

Versantvoort W, Guerrero-Cruz S, Speth DR, Frank J, Gambelli L, Cremers G, et al. Comparative genomics of Candidatus Methylomirabilis species and description of Ca . Methylomirabilis lanthanidiphila. Front Microbiol. 2018;9:1672.

Martindale H, van der Raaij RW, Daughney CJ, Morgenstern U, Hadfield J. Measurement of neon in groundwaters for quantification of denitrification in aquifers. Lower Hutt (NZ): GNS Science. 44p. (GNS Science report; 2018/34). 2018. https://doi.org/10.21420/FR4X-J821

Ettwig KF, Speth DR, Reimann J, Wu ML, Jetten MSM, Keltjens JT. Bacterial oxygen production in the dark. Front Microbiol. 2012;3:273.

Hallin S, Philippot L, Löffler FE, Sanford RA, Jones CM. Genomics and ecology of novel N 2 O-reducing microorganisms. Trends Microbiol. 2018;26:43–55.

Conthe M, Wittorf L, Kuenen JG, Kleerebezem R, Van Loosdrecht MCM, Hallin S. Life on N 2 O: Deciphering the ecophysiology of N 2 O respiring bacterial communities in a continuous culture. ISME J. 2018;12:1142–53.

Shi LX, Theg SM. Energetic cost of protein import across the envelope membranes of chloroplasts. Proc Natl Acad Sci USA. 2013;110:930–5.

Lie E, Welander T. Influence of dissolved oxygen and oxidation-reduction potential on the denitrification rate of activated sludge. Water Sci Technol 1994;30:91–100.

McAleer EB, Coxon CE, Richards KG, Jahangir MMR, Grant J, Mellander PE. Groundwater nitrate reduction versus dissolved gas production: a tale of two catchments. Sci Total Environ. 2017;586:372–89.

Rajta A, Bhatia R, Setia H, Pathania P. Role of heterotrophic aerobic denitrifying bacteria in nitrate removal from wastewater. J Appl Microbiol. 2020;128:1261–78.

Watanabe T, Kojima H, Fukui M. Complete genomes of freshwater sulfur oxidizers Sulfuricella denitrificans skB26 and Sulfuritalea hydrogenivorans sk43H: Genetic insights into the sulfur oxidation pathway of betaproteobacteria. Syst Appl Microbiol. 2014;37:387–95.

Williamson WM, Close ME, Leonard MM, Webber JB, Lin S. Groundwater biofilm dynamics grown in situ along a nutrient gradient. Ground Water. 2012;50:690–703.

Spasov E, Tsuji JM, Hug LA, Doxey AC, Sauder LA, Parker WJ, et al. High functional diversity among Nitrospira populations that dominate rotating biological contactor microbial communities in a municipal wastewater treatment plant. ISME J. 2020;14:1857–72.

Koch H, van Kessel MAHJ, Lücker S. Complete nitrification: insights into the ecophysiology of comammox Nitrospira . Appl Microbiol Biotechnol. 2019;103:177–89.

Kutvonen H, Rajala P, Carpén L, Bomberg M. Nitrate and ammonia as nitrogen sources for deep subsurface microorganisms. Front Microbiol. 2015;6:1079.

Wang S, Radny D, Huang S, Zhuang L, Zhao S, Berg M, et al. Nitrogen loss by anaerobic ammonium oxidation in unconfined aquifer soils. Sci Rep. 2017;7:1–10.

PubMed PubMed Central Google Scholar

Schmidt CM, Fisher AT, Racz AJ, Lockwood BS, Huertos ML. Linking denitrification and infiltration rates during managed groundwater recharge. Environ Sci Technol. 2011;45:9634–40.

Kolbe T, De Dreuzy JR, Abbott BW, Aquilina L, Babey T, Green CT, et al. Stratification of reactivity determines nitrate removal in groundwater. Proc Natl Acad Sci USA. 2019;116:2494–9.

Bishop PL, Yu T. A microelectrode study of redox potential change in biofilms. Water Sci Technol. 1999;39:179–85.

Rochman FF, Kwon M, Khadka R, Tamas I, Lopez-Jauregui AA, Sheremet A, et al. Novel copper-containing membrane monooxygenases (CuMMOs) encoded by alkane-utilizing Betaproteobacteria. ISME J. 2020;14:714–26.

Parks DH, Rinke C, Chuvochina M, Chaumeil P-A, Woodcroft BJ, Evans PN, et al. Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nat Microbiol. 2017;2:1533–42.

Download references

Acknowledgements

We thank P. Abraham (ESR), H.S. Tee and J.S. Boey for help sampling wells in Canterbury and council staff in Auckland (C. Foster), Wellington (D. McQueen), Waikato (S. Herath) and Canterbury (D. Evans and R. Cressy). We thank D. Waite and J.S. Boey for bioinformatics support, and R. van der Raaij and H. Martindale for excess N 2 measurements. Computational resources were provided by New Zealand eScience Infrastructure. Research was supported by a Smart Ideas grant, from the Ministry of Business, Innovation and Employment, awarded to KMH (project UOAX1720).

Open Access funding enabled and organized by CAUL and its Member Institutions.

Author information

Authors and affiliations.

School of Biological Sciences, The University of Auckland, Auckland, New Zealand

Olivia E. Mosley, Emilie Gios & Kim M. Handley

Institute of Environmental Science and Research, Christchurch, New Zealand

Murray Close & Louise Weaver

National Institute of Water and Atmospheric Research, Wellington, New Zealand

Chris Daughney

You can also search for this author in PubMed Google Scholar

Contributions

KMH and CD conceived the study, and KMH, CD, LW, and MC obtained funding. OEM, EG and KMH collected samples. MC contributed technical expertise for in situ sonication. OEM and EG performed laboratory procedures and bioinformatic analyses. OEM led the analysis of data and writing of the manuscript with KMH. All authors reviewed the manuscript.

Corresponding author

Correspondence to Kim M. Handley .

Ethics declarations

Competing interests.

The authors declare no competing interests.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Supplementary materials, rights and permissions.

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ .

Reprints and permissions

About this article

Cite this article.

Mosley, O.E., Gios, E., Close, M. et al. Nitrogen cycling and microbial cooperation in the terrestrial subsurface. ISME J 16 , 2561–2573 (2022). https://doi.org/10.1038/s41396-022-01300-0

Download citation

Received : 19 October 2021

Revised : 19 July 2022

Accepted : 22 July 2022

Published : 08 August 2022

Issue Date : November 2022

DOI : https://doi.org/10.1038/s41396-022-01300-0

Share this article

Anyone you share the following link with will be able to read this content:

Sorry, a shareable link is not currently available for this article.

Provided by the Springer Nature SharedIt content-sharing initiative

This article is cited by

Metabolic adaptations underpin high productivity rates in relict subsurface water.

Betzabe Atencio
Eyal Geisler

Scientific Reports (2024)

Methane-dependent complete denitrification by a single Methylomirabilis bacterium

Xiangwu Yao

Nature Microbiology (2024)

High hydrostatic pressure stimulates microbial nitrate reduction in hadal trench sediments under oxic conditions

Nature Communications (2024)

Nitrogen metabolism pathways and functional microorganisms in typical karst wetlands

Environmental Science and Pollution Research (2024)

Physiological adaptation and gut microbiota changes of orange mud crab Scylla olivacea in response to increased temperature condition

Aquatic Sciences (2024)

Quick links

Explore articles by subject
Guide to authors
Editorial policies

Nitrogen cycling: A review of the processes, transformations and fluxes in coastal ecosystems

Current Science 94(11)

National Centre For Sustainable Coastal Management

This person is not on ResearchGate, or hasn't claimed this research yet.

Leibniz Centre for Tropical Marine Research (ZMT)

Abstract and Figures

Discover the world's research

25+ million members
160+ million publication pages
2.3+ billion citations
SCI TOTAL ENVIRON

Xiankui Zeng

ENVIRON SCI POLLUT R
Yingchun Dong
Xiang Zhang

Deok-Woo Kim

Youngseok Kim

Ganta Narshimulu
Sunil Jacob

ESTUAR COAST SHELF S

Mark M. Brinson

S AFR J BOT
Fiona D. Mann
T.D. Steinke

Recruit researchers
Join for free
Login Email Tip: Most researchers use their institutional email address as their ResearchGate login Password Forgot password? Keep me logged in Log in or Continue with Google Welcome back! Please log in. Email · Hint Tip: Most researchers use their institutional email address as their ResearchGate login Password Forgot password? Keep me logged in Log in or Continue with Google No account? Sign up

Information

Author Services

Initiatives

You are accessing a machine-readable page. In order to be human-readable, please install an RSS reader.

All articles published by MDPI are made immediately available worldwide under an open access license. No special permission is required to reuse all or part of the article published by MDPI, including figures and tables. For articles published under an open access Creative Common CC BY license, any part of the article may be reused without permission provided that the original article is clearly cited. For more information, please refer to https://www.mdpi.com/openaccess .

Feature papers represent the most advanced research with significant potential for high impact in the field. A Feature Paper should be a substantial original Article that involves several techniques or approaches, provides an outlook for future research directions and describes possible research applications.

Feature papers are submitted upon individual invitation or recommendation by the scientific editors and must receive positive feedback from the reviewers.

Editor’s Choice articles are based on recommendations by the scientific editors of MDPI journals from around the world. Editors select a small number of articles recently published in the journal that they believe will be particularly interesting to readers, or important in the respective research area. The aim is to provide a snapshot of some of the most exciting work published in the various research areas of the journal.

Original Submission Date Received: .

Active Journals
Find a Journal
Proceedings Series
For Authors
For Reviewers
For Editors
For Librarians
For Publishers
For Societies
For Conference Organizers
Open Access Policy
Institutional Open Access Program
Special Issues Guidelines
Editorial Process
Research and Publication Ethics
Article Processing Charges
Testimonials
Preprints.org
SciProfiles
Encyclopedia

Article Menu

Subscribe SciFeed
Recommended Articles
Google Scholar
on Google Scholar
Table of Contents

Find support for a specific problem in the support section of our website.

Please let us know what you think of our products and services.

Visit our dedicated information section to learn more about MDPI.

JSmol Viewer

Trends in the research and development of soil nitrogen mineralization in forests from 2004 to 2024.

1. Introduction

2.1. data sources, 2.2. data analysis, 3. results and discussion, 3.1. overall status of nitrogen mineralization in forest soils, 3.2. co-occurrence analysis of journals, 3.3. co-occurrence analysis of authors, 3.4. collaboration network analysis of institutions and countries, 3.5. research hotspots, 3.6. emerging trends, 3.7. future research directions and policy recommendations, 4. conclusions, 4.1. limitations, 4.2. general conclusions, supplementary materials, author contributions, data availability statement, conflicts of interest.

Arslan, H.; Güleryüz, G.; Kırmızı, S. Nitrogen mineralisation in the soil of indigenous oak and pine plantation forests in a Mediterranean environment. Eur. J. Soil Biol. 2010 , 46 , 11–17. [ Google Scholar ] [ CrossRef ]
Chen, S.; Jiang, C.; Wang, H.; Bai, Y.; Jiang, C. Trends in Research on Soil Organic Nitrogen over the Past 20 Years. Forests 2023 , 14 , 1883. [ Google Scholar ] [ CrossRef ]
An, Y.; Gao, Y.; Liu, X.; Tong, S.; Liu, B.; Song, T.; Qi, Q. Soil Organic Carbon and Nitrogen Variations with Vegetation Succession in Passively Restored Freshwater Wetlands. Wetlands 2021 , 41 , 11. [ Google Scholar ] [ CrossRef ]
Prieto-Fernández, Á.; Carballas, T. Soil organic nitrogen composition in Pinus forest acid soils: Variability and bioavailability. Biol. Fertil. Soils 2000 , 32 , 177–185. [ Google Scholar ] [ CrossRef ]
Zhang, D.; Cai, X.; Diao, L.; Wang, Y.; Wang, J.; An, S.; Cheng, X.; Yang, W. Changes in soil organic carbon and nitrogen pool sizes, dynamics, and biochemical stability during ∼160 years natural vegetation restoration on the Loess Plateau, China. Catena 2022 , 211 , 106014. [ Google Scholar ] [ CrossRef ]
Singh, G.; Mishra, D.; Singh, K.; Shukla, S.; Choudhary, G.R. Geographical settings and tree diversity influenced soil carbon storage in different forest types in Rajasthan, India. Catena 2022 , 209 , 105856. [ Google Scholar ] [ CrossRef ]
Vitousek, P.M.; Howarth, R.W. Nitrogen limitation on land and in the sea: How can it occur? Biogeochemistry 1991 , 13 , 87–115. [ Google Scholar ] [ CrossRef ]
Mitchell, M.J. Nitrate dynamics of forested watersheds: Spatial and temporal patterns in North America, Europe and Japan. J. For. Res. 2011 , 16 , 333. [ Google Scholar ] [ CrossRef ]
Keuper, F.; Dorrepaal, E.; van Bodegom, P.M.; van Logtestijn, R.; Venhuizen, G.; van Hal, J.; Aerts, R. Experimentally increased nutrient availability at the permafrost thaw front selectively enhances biomass production of deep-rooting subarctic peatland species. Glob. Change Biol. 2017 , 23 , 4257–4266. [ Google Scholar ] [ CrossRef ]
Risch, A.C.; Zimmermann, S.; Ochoa-Hueso, R.; Schütz, M.; Frey, B.; Firn, J.L.; Fay, P.A.; Hagedorn, F.; Borer, E.T.; Seabloom, E.W.; et al. Soil net nitrogen mineralisation across global grasslands. Nat. Commun. 2019 , 10 , 4981. [ Google Scholar ] [ CrossRef ]
Kuypers, M.M.M.; Marchant, H.K.; Kartal, B. The microbial nitrogen-cycling network. Nat. Rev. Microbiol. 2018 , 16 , 263–276. [ Google Scholar ] [ CrossRef ] [ PubMed ]
Dai, Z.; Yu, M.; Chen, H.; Zhao, H.; Huang, Y.; Su, W.; Xia, F.; Chang, S.X.; Brookes, P.C.; Dahlgren, R.A.; et al. Elevated temperature shifts soil N cycling from microbial immobilization to enhanced mineralization, nitrification and denitrification across global terrestrial ecosystems. Glob. Change Biol. 2020 , 26 , 5267–5276. [ Google Scholar ] [ CrossRef ] [ PubMed ]
Dawes, M.A.; Schleppi, P.; Hattenschwiler, S.; Rixen, C.; Hagedorn, F. Soil warming opens the nitrogen cycle at the alpine treeline. Glob. Change Biol. 2017 , 23 , 421–434. [ Google Scholar ] [ CrossRef ] [ PubMed ]
Elrys, A.S.; Ali, A.; Zhang, H.; Cheng, Y.; Zhang, J.; Cai, Z.C.; Müller, C.; Chang, S.X. Patterns and drivers of global gross nitrogen mineralization in soils. Glob. Change Biol. 2021 , 27 , 5950–5962. [ Google Scholar ] [ CrossRef ]
Li, Z.; Tian, D.; Wang, B.; Wang, J.; Wang, S.; Chen, H.Y.H.; Xu, X.; Wang, C.; He, N.; Niu, S. Microbes drive global soil nitrogen mineralization and availability. Glob. Change Biol. 2019 , 25 , 1078–1088. [ Google Scholar ] [ CrossRef ]
Zhu, Z.; Du, H.; Gao, K.; Fang, Y.; Wang, K.; Zhu, T.; Zhu, J.; Cheng, Y.; Li, D. Plant species diversity enhances soil gross nitrogen transformations in a subtropical forest, southwest China. J. Appl. Ecol. 2023 , 60 , 1364–1375. [ Google Scholar ] [ CrossRef ]
Zhang, M.; Liu, S.; Chen, M.; Chen, J.; Cao, X.; Xu, G.; Xing, H.; Li, F.; Shi, Z. The below-ground carbon and nitrogen cycling patterns of different mycorrhizal forests on the eastern Qinghai-Tibetan Plateau. PeerJ 2022 , 10 , e14028. [ Google Scholar ] [ CrossRef ]
Elrys, A.S.; Chen, Z.; Wang, J.; Uwiragiye, Y.; Helmy, A.M.; Desoky, E.S.M.; Cheng, Y.; Zhang, J.B.; Cai, Z.C.; Müller, C. Global patterns of soil gross immobilization of ammonium and nitrate in terrestrial ecosystems. Glob. Change Biol. 2022 , 28 , 4472–4488. [ Google Scholar ] [ CrossRef ]
Johnson, D.W.; Turner, J. Nitrogen budgets of forest ecosystems: A review. For. Ecol. Manag. 2014 , 318 , 370–379. [ Google Scholar ] [ CrossRef ]
Liu, Y.; Wang, C.; He, N.; Wen, X.; Gao, Y.; Li, S.; Niu, S.; Butterbach-Bahl, K.; Luo, Y.; Yu, G. A global synthesis of the rate and temperature sensitivity of soil nitrogen mineralization: Latitudinal patterns and mechanisms. Glob. Change Biol. 2017 , 23 , 455–464. [ Google Scholar ] [ CrossRef ]
Nederhof, A.J. Bibliometric monitoring of research performance in the Social Sciences and the Humanities: A Review. Scientometrics 2006 , 66 , 81–100. [ Google Scholar ] [ CrossRef ]
Ekundayo, T.C.; Okoh, A.I. A global bibliometric analysis of Plesiomonas-related research (1990–2017). PLoS ONE 2018 , 13 , e0207655. [ Google Scholar ] [ CrossRef ] [ PubMed ]
Wang, Z.; Zhao, Y.; Wang, B. A bibliometric analysis of climate change adaptation based on massive research literature data. J. Clean. Prod. 2018 , 199 , 1072–1082. [ Google Scholar ] [ CrossRef ]
Liu, W.; Wang, J.; Li, C.; Chen, B.; Sun, Y. Using Bibliometric Analysis to Understand the Recent Progress in Agroecosystem Services Research. Ecol. Econ. 2019 , 156 , 293–305. [ Google Scholar ] [ CrossRef ]
Liu, X.; Jiang, N.; Jing, G.; Wang, S.; Chen, Z.; Zhang, Y. Amending biochar affected enzyme activities and nitrogen turnover in Phaeozem and Luvisol. Glob. Change Biol. Bioenergy 2023 , 15 , 954–968. [ Google Scholar ] [ CrossRef ]
Hong, T.; Feng, X.; Tong, W.; Xu, W. Bibliometric analysis of research on the trends in autophagy. PeerJ 2019 , 7 , e7103. [ Google Scholar ] [ CrossRef ]
Bornmann, L.; Daniel, H.D. What do citation counts measure? A review of studies on citing behavior. J. Doc. 2008 , 64 , 45–80. [ Google Scholar ] [ CrossRef ]
Ueda, M.U.; Kachina, P.; Marod, D.; Nakashizuka, T.; Kurokawa, H. Soil properties and gross nitrogen dynamics in old growth and secondary forest in four types of tropical forest in Thailand. For. Ecol. Manag. 2017 , 398 , 130–139. [ Google Scholar ] [ CrossRef ]
Urakawa, R.; Ohte, N.; Shibata, H.; Isobe, K.; Tateno, R.; Oda, T.; Hishi, T.; Fukushima, K.; Inagaki, Y.; Hirai, K.; et al. Factors contributing to soil nitrogen mineralization and nitrification rates of forest soils in the Japanese archipelago. For. Ecol. Manag. 2016 , 361 , 382–396. [ Google Scholar ] [ CrossRef ]
Wang, Q.; Li, F.; Rong, X.; Fan, Z. Plant-soil properties associated with Nitrogen mineralization: Effect of conversion of natural secondary forests to Larch plantations in a headwater catchment in Northeast China. Forests 2018 , 9 , 386. [ Google Scholar ] [ CrossRef ]
Chen, M.; Xu, J.; Li, Z.; Li, D.; Wang, Q.; Zhou, Y.; Guo, W.; Ma, D.; Zhang, J.; Zhao, B. Long-term nitrogen fertilization-induced enhancements of acid hydrolyzable nitrogen are mainly regulated by the most vital microbial taxa of keystone species and enzyme activities. Sci. Total Environ. 2023 , 874 , 162463. [ Google Scholar ] [ CrossRef ] [ PubMed ]
Van Der Heijden, M.G.A.; Bardgett, R.D.; Van Straalen, N.M. The unseen majority: Soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. Ecol. Lett. 2008 , 11 , 296–310. [ Google Scholar ] [ CrossRef ] [ PubMed ]
Schimel, J.P.; Bennett, J. Nitrogen mineralization: Challenges of a changing paradigm. Ecology 2004 , 85 , 591–602. [ Google Scholar ] [ CrossRef ]
Schimel, J.; Balser, T.C.; Wallenstein, M. Microbial stress-response physiology and its implications for ecosystem function. Ecology 2007 , 88 , 1386–1394. [ Google Scholar ] [ CrossRef ]
Sinsabaugh, R.L. Phenol oxidase, peroxidase and organic matter dynamics of soil. Soil Biol. Biochem. 2010 , 42 , 391–404. [ Google Scholar ] [ CrossRef ]
Manzoni, S.; Trofymow, J.A.; Jackson, R.B.; Porporato, A. Stoichiometric controls on carbon, nitrogen, and phosphorus dynamics in decomposing litter. Ecol. Monogr. 2010 , 80 , 89–106. [ Google Scholar ] [ CrossRef ]
Manzoni, S.; Jackson, R.B.; Trofymow, J.A.; Porporato, A. The Global Stoichiometry of Litter Nitrogen Mineralization. Science 2008 , 321 , 684–686. [ Google Scholar ] [ CrossRef ]
Groffman, P.M.; Fisk, M.C.; Driscoll, C.T.; Likens, G.E.; Fahey, T.J.; Eagar, C.; Pardo, L.H. Calcium Additions and Microbial Nitrogen Cycle Processes in a Northern Hardwood Forest. Ecosystems 2006 , 9 , 1289–1305. [ Google Scholar ] [ CrossRef ]
Borken, W.; Matzner, E. Reappraisal of drying and wetting effects on C and N mineralization and fluxes in soils. Glob. Change Biol. 2009 , 15 , 808–824. [ Google Scholar ] [ CrossRef ]
Booth, M.S.; Stark, J.M.; Rastetter, E. Control of Nitrogen Cycling in Terrestrial Ecosystems: A Synthetic Analysis of Literature Data. Ecol. Monogr. 2005 , 75 , 139–157. [ Google Scholar ] [ CrossRef ]
Wang, Y.P.; Law, R.M.; Pak, B. A global model of carbon, nitrogen and phosphorus cycles for the terrestrial biosphere. Biogeogeoscience 2010 , 7 , 2261–2282. [ Google Scholar ] [ CrossRef ]
Vieira, R.A.; McManus, C. Bibliographic mapping of animal genetic resources and climate change in farm animals. Trop. Anim. Health Prod. 2023 , 55 , 259. [ Google Scholar ] [ CrossRef ] [ PubMed ]
Moed, H.F. Measuring contextual citation impact of scientific journals. J. Informetr. 2010 , 4 , 265–277. [ Google Scholar ] [ CrossRef ]
Zhang, F.; Liu, Y.; Zhang, Y. Bibliometric Analysis of Research Trends in Agricultural Soil Organic Carbon Mineralization from 2000 to 2022. Agriculture 2023 , 13 , 1248. [ Google Scholar ] [ CrossRef ]
Li, J.; Wang, G.; Yan, B.; Liu, G. The responses of soil nitrogen transformation to nitrogen addition are mainly related to the changes in functional gene relative abundance in artificial Pinus tabulaeformis forests. Sci. Total Environ. 2020 , 723 , 137679. [ Google Scholar ] [ CrossRef ]
Huang, Z.; Wan, X.; He, Z.; Yu, Z.; Wang, M.; Hu, Z.; Yang, Y. Soil microbial biomass, community composition and soil nitrogen cycling in relation to tree species in subtropical China. Soil Biol. Biochem. 2013 , 62 , 68–75. [ Google Scholar ] [ CrossRef ]
Zhong, Z.; Makeschin, F. Differences of soil microbial biomass and nitrogen transformation under two forest types in central Germany. Plant Soil 2006 , 283 , 287–297. [ Google Scholar ] [ CrossRef ]
Bai, J.; Xu, X.; Fu, G.; Song, M.; He, Y.; Jiang, j. Effects of temperature and nitrogen input on nitrogen mineralization in alpine soils on the Tibetan Plateau. Agric. Sci. Technol. 2011 , 12 , 1909–1912. [ Google Scholar ] [ CrossRef ]
Carmosini, N.; Devito, K.J.; Prepas, E.E. Net nitrogen mineralization and nitrification in trembling aspen forest soils on the Boreal Plain. Can. J. For. Res. 2003 , 33 , 2262–2268. [ Google Scholar ] [ CrossRef ]
Zhang, S.; Chen, D.; Sun, D.; Wang, X.; Smith, J.L.; Du, G. Impacts of altitude and position on the rates of soil nitrogen mineralization and nitrification in alpine meadows on the eastern Qinghai–Tibetan Plateau, China. Biol. Fertil. Soils 2012 , 48 , 393–400. [ Google Scholar ] [ CrossRef ]
Yan, Y.; Fang, S.; Tian, Y.; Deng, S.; Tang, L.; Dao Ngoc, C. Influence of tree spacing on soil Nitrogen mineralization and availability in Hybrid Poplar plantations. Forests 2015 , 6 , 636–649. [ Google Scholar ] [ CrossRef ]
Chen, Q.L.; Ding, J.; Li, C.Y.; Yan, Z.Z.; He, J.Z.; Hu, H.W. Microbial functional attributes, rather than taxonomic attributes, drive top soil respiration, nitrification and denitrification processes. Sci. Total Environ. 2020 , 734 , 139479. [ Google Scholar ] [ CrossRef ] [ PubMed ]
Zhang, H.; Han, G.; Huang, T.; Feng, Y.; Tian, W.; Wu, X. Mixed Forest of Larix principis-rupprechtii and Betula platyphylla Modulating Soil Fauna Diversity and Improving Faunal Effect on Litter Decomposition. Forests 2022 , 13 , 703. [ Google Scholar ] [ CrossRef ]
Xue, K.; Yuan, M.M.; Shi, Z.J.; Qin, Y.; Deng, Y.; Cheng, L.; Wu, L.; He, Z.; Van Nostrand, J.D.; Bracho, R.; et al. Tundra soil carbon is vulnerable to rapid microbial decomposition under climate warming. Nat. Clim. Change 2016 , 6 , 595–600. [ Google Scholar ] [ CrossRef ]
Bracho, R.; Natali, S.; Pegoraro, E.; Crummer, K.G.; Schädel, C.; Celis, G.; Hale, L.; Wu, L.; Yin, H.; Tiedje, J.M.; et al. Temperature sensitivity of organic matter decomposition of permafrost-region soils during laboratory incubations. Soil Biol. Biochem. 2016 , 97 , 1–14. [ Google Scholar ] [ CrossRef ]
Rousk, K.; Michelsen, A.; Rousk, J. Microbial control of soil organic matter mineralization responses to labile carbon in subarctic climate change treatments. Glob. Change Biol. 2016 , 22 , 4150–4161. [ Google Scholar ] [ CrossRef ]
Fan, B.; Yin, L.; Dijkstra, F.A.; Lu, J.; Shao, S.; Wang, P.; Wang, Q.; Cheng, W. Potential gross nitrogen mineralization and its linkage with microbial respiration along a forest transect in eastern China. Appl. Soil Ecol. 2022 , 171 , 104347. [ Google Scholar ] [ CrossRef ]
Hu, Y.; Zhang, Z.; Yang, G.; Ding, C.; Lu, X. Increases in substrate availability and decreases in soil pH drive the positive effects of nitrogen addition on soil net nitrogen mineralization in a temperate meadow steppe. Pedobiologia 2021 , 89 , 150756. [ Google Scholar ] [ CrossRef ]
Li, Y.; Tremblay, J.; Bainard, L.D.; Cade-Menun, B.; Hamel, C. Long-term effects of nitrogen and phosphorus fertilization on soil microbial community structure and function under continuous wheat production. Environ. Microbiol. 2020 , 22 , 1066–1088. [ Google Scholar ] [ CrossRef ]
Ushio, M.; Kitayama, K.; Balser, T.C. Tree species-mediated spatial patchiness of the composition of microbial community and physicochemical properties in the topsoils of a tropical montane forest. Soil Biol. Biochem. 2010 , 42 , 1588–1595. [ Google Scholar ] [ CrossRef ]
Ashraf, M.N.; Hu, C.; Wu, L.; Duan, Y.; Zhang, W.; Aziz, T.; Cai, A.; Abrar, M.M.; Xu, M. Soil and microbial biomass stoichiometry regulate soil organic carbon and nitrogen mineralization in rice-wheat rotation subjected to long-term fertilization. J. Soils Sediments 2020 , 20 , 3103–3113. [ Google Scholar ] [ CrossRef ]
Sponseller, R.A.; Gundale, M.J.; Futter, M.; Ring, E.; Nordin, A.; Näsholm, T.; Laudon, H. Nitrogen dynamics in managed boreal forests: Recent advances and future research directions. Ambio 2016 , 45 , 175–187. [ Google Scholar ] [ CrossRef ]
Ste-Marie, C.; Paré, D. Soil, pH and N availability effects on net nitrification in the forest floors of a range of boreal forest stands. Soil Biol. Biochem. 1999 , 31 , 1579–1589. [ Google Scholar ] [ CrossRef ]
Xiao, R.; Man, X.; Duan, B.; Cai, T.; Ge, Z.; Li, X.; Vesala, T. Changes in soil bacterial communities and nitrogen mineralization with understory vegetation in boreal larch forests. Soil Biol. Biochem. 2022 , 166 , 108572. [ Google Scholar ] [ CrossRef ]
Gao, L.; Smith, A.R.; Jones, D.L.; Guo, Y.; Liu, B.; Guo, Z.; Fan, C.; Zheng, J.; Cui, X.; Hill, P.W. How do tree species with different successional stages affect soil organic nitrogen transformations? Geoderma 2023 , 430 , 116319. [ Google Scholar ] [ CrossRef ]
Ilampooranan, I.; Van Meter, K.J.; Basu, N.B. Intensive agriculture, nitrogen legacies, and water quality: Intersections and implications. Environ. Res. Lett. 2022 , 17 , 035006. [ Google Scholar ] [ CrossRef ]
Gundersen, P.; Sevel, L.; Christiansen, J.R.; Vesterdal, L.; Hansen, K.; Bastrup-Birk, A. Do indicators of nitrogen retention and leaching differ between coniferous and broadleaved forests in Denmark? For. Ecol. Manag. 2009 , 258 , 1137–1146. [ Google Scholar ] [ CrossRef ]
Fierer, N.; Leff, J.W.; Adams, B.J.; Nielsen, U.N.; Bates, S.T.; Lauber, C.L.; Owens, S.; Gilbert, J.A.; Wall, D.H.; Caporaso, J.G. Cross-biome metagenomic analyses of soil microbial communities and their functional attributes. Proc. Natl. Acad. Sci. USA 2012 , 109 , 21390–21395. [ Google Scholar ] [ CrossRef ]
Petersen, D.G.; Blazewicz, S.J.; Firestone, M.; Herman, D.J.; Turetsky, M.; Waldrop, M. Abundance of microbial genes associated with nitrogen cycling as indices of biogeochemical process rates across a vegetation gradient in Alaska. Environ. Microbiol. 2012 , 14 , 993–1008. [ Google Scholar ] [ CrossRef ]
Levy-Booth, D.J.; Prescott, C.E.; Grayston, S.J. Microbial functional genes involved in nitrogen fixation, nitrification and denitrification in forest ecosystems. Soil Biol. Biochem. 2014 , 75 , 11–25. [ Google Scholar ] [ CrossRef ]
Nelson, M.B.; Martiny, A.C.; Martiny, J.B.H. Global biogeography of microbial nitrogen-cycling traits in soil. Proc. Natl. Acad. Sci. USA 2016 , 113 , 8033–8040. [ Google Scholar ] [ CrossRef ] [ PubMed ]
Zhang, K.; Li, X.; Cheng, X.; Zhang, Z.; Zhang, Q. Changes in soil properties rather than functional gene abundance control carbon and nitrogen mineralization rates during long-term natural revegetation. Plant Soil 2019 , 443 , 293–306. [ Google Scholar ] [ CrossRef ]
Zhang, X.M.; Zhang, H.Y. Modelling Microbial Nitrification and Exploring Nonlinear Mechanism by Dynamical Complexity. Chiang Mai J. Sci. 2024 , 51 , e2024001. [ Google Scholar ] [ CrossRef ]
Wang, J.; He, L.; Xu, X.; Ren, C.; Wang, J.; Guo, Y.; Zhao, F. Linkage between microbial functional genes and net N mineralisation in forest soils along an elevational gradient. Eur. J. Soil Sci. 2022 , 73 , e13276. [ Google Scholar ] [ CrossRef ]

Click here to enlarge figure

Journals	Publications	TCs/TPs	JCR	IF
Soil Biology and Biochemistry	398	65.60	Q1	9.8
Forest Ecology and Management	194	33.72	Q2	3.7
Plant and Soil	194	34.50	Q1	3.9
Biogeochemistry	138	54.41	Q2	4.0
Geoderma	120	32.18	Q1	6.1
Applied Soil Ecology	117	35.17	Q1	4.8
Science of the Total Environment	115	22.46	Q1	9.8
Global Change Biology	104	95.32	Q1	11.6
Biology and Fertility of Soils	88	39.17	Q1	6.5
Ecosystems	86	62.15	Q1	3.7
Forests	84	7.65	Q1	2.9
Soil Science Society of America Journal	69	45.08	Q2	2.9
Journal of Soils and Sediments	61	19.80	Q1	3.6
Biogeosciences	51	70.60	Q1	4.9
European Journal of Soil Biology	48	25.89	Q2	4.2
Oecologia	46	102.67	Q1	2.7
Canadian Journal of Forest Research	42	29.43	Q2	2.2
Ecology	41	161.76	Q1	4.8
Eurasian Soil Science	40	6.08	Q2	1.4
PLOS ONE	39	24.79	Q1	3.7
Journal of Geophysical Research: Biogeosciences	36	28.22	Q1	3.7
Scientific Reports	34	32.65	Q1	4.6
European Journal of Soil Science	30	30.30	Q1	4.2

	Title	Authors	Journal	Year	Citations
1	The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems	Van Der Heijden, M.G.A.; Bardgett, R.D.; Van Straalen, N.M. [ ]	Ecology Letters	2008	3045
2	Nitrogen mineralization: Challenges of a changing paradigm	Schimel, J.P.; Bennett, J. [ ]	Ecology	2004	1725
3	Microbial stress-response physiology and its implications for ecosystem function	Schimel, J.; Balser, T.C.; Wallenstein, M. [ ]	Ecology	2007	1580
4	Phenol oxidase, peroxidase and organic matter dynamics of soil	Sinsabaugh, R.L. [ ]	Soil Biology and Biochemistry	2010	911
5	Reappraisal of drying and wetting effects on C and N mineralization and fluxes in soils	Borken, W.; Matzner, E. [ ]	Global Change Biology	2009	856
6	Controls on nitrogen cycling in terrestrial ecosystems: A synthetic analysis of literature data	Booth, M.S.; Stark, J.M.; Rastetter, E. [ ]	Ecological Monographs	2005	809
7	Calcium additions and microbial nitrogen cycle processes in a northern hardwood forest	Groffman, P.M.; Fisk, M.C.; Driscoll, C.T.; Likens, G.E.; Fahey, T.J.; Eagar, C.; Pardo, L.H. [ ]	Ecosystems	2006	604
8	Stoichiometric controls on carbon, nitrogen, and phosphorus dynamics in decomposing litter	Manzoni, S.; Trofymow, J.A.; Jackson, R.B.; Porporato, A. [ ]	Ecological Monographs	2010	555
9	The global stoichiometry of litter nitrogen mineralization	Manzoni, S.; Jackson, R.B.; Trofymow, J.A.; Porporato, A. [ ]	Science	2008	493
10	A global model of carbon, nitrogen and phosphorus cycles for the terrestrial biosphere	Wang, Y.P.; Law, R.M.; Pak, B. [ ]	Biogeosciences	2010	469

Institution	Publications	Centrality	First Published Year	TCs/TPs
Chinese Acad Sci	403	0.54	2005	36.94
Cornell Univ	59	0.23	2004	68.09
Univ Alberta	72	0.18	2004	32.56
Swedish Univ Agr Sci	76	0.13	2004	60.60
Boston Univ	31	0.12	2006	74.95
US Forest Serv	78	0.11	2004	40.59
Univ Chinese Acad Sci	139	0.08	2013	34.98
Kyoto Univ	52	0.08	2004	25.32
INRA	35	0.08	2006	55.09
Univ Göttingen	33	0.08	2007	57.88

Country	Publications	Centrality	First Published Year	TCs/TPs
United States of America	1072	0.31	2004	60.06
China	987	0.1	2004	28.95
Germany	356	0.22	2004	49.69
Canada	280	0.07	2004	38.04
Australia	191	0.18	2004	46.97
Sweden	175	0.08	2004	60.97
Spain	142	0.07	2004	39.88
Japan	129	0.14	2004	22.55
France	120	0.26	2004	50.00
Brazil	114	0.01	2004	31.26

Web of Science Categories	Record Count	% of 3576
Soil science	1492	41.72
Environmental sciences	853	23.85
Ecology	787	22.01
Forestry	587	16.42
Plant sciences	427	11.94
Agronomy	310	8.67
Multidisciplinary geosciences	266	7.44
Biodiversity conservation	157	4.39
Multidisciplinary sciences	112	3.13
Microbiology	61	1.71

The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content.

Share and Cite

Zhang, X.; Zhang, H.; Wang, Z.; Tian, Y.; Liu, Z. Trends in the Research and Development of Soil Nitrogen Mineralization in Forests from 2004 to 2024. Sustainability 2024 , 16 , 7882. https://doi.org/10.3390/su16187882

Zhang X, Zhang H, Wang Z, Tian Y, Liu Z. Trends in the Research and Development of Soil Nitrogen Mineralization in Forests from 2004 to 2024. Sustainability . 2024; 16(18):7882. https://doi.org/10.3390/su16187882

Zhang, Xiumin, Huayong Zhang, Zhongyu Wang, Yonglan Tian, and Zhao Liu. 2024. "Trends in the Research and Development of Soil Nitrogen Mineralization in Forests from 2004 to 2024" Sustainability 16, no. 18: 7882. https://doi.org/10.3390/su16187882

Article Metrics

Article access statistics, supplementary material.

ZIP-Document (ZIP, 942 KiB)

Further Information

Mdpi initiatives, follow mdpi.

Subscribe to receive issue release notifications and newsletters from MDPI journals

IMAGES

Nitrogen Cycle
SOLUTION: Nitrogen cycle
What is Nitrogen Cycle? Diagram, Stages, Importance
Basic overview of the nitrogen cycle
Nitrogen Cycle: Fixation and Ammonification (A-level Biology)
Nitrogen cycle: Steps of Nitrogen cycle

VIDEO

Nitrogen Cycle 🥀💚💙#science #study #biology #youtubeshort
nitrogen cycle
Biology paper 2: Nitrogen Cycle exam revision questions and answers (Lesson)
Nitrogen Cycle: How it Works? #fishtank #aquarium #nitrogencycle
Nitrogen Cycle| Knowledge Academy
The Nitrogen Cycle #environment#scienceknowledge #facts #knowledge #shorts

COMMENTS

The nitrogen cycle
The significance of nitrogen to the biosphere and to cellular life is indisputable; however, our fundamental knowledge of the microorganisms and enzymatic processes that transform nitrogen into its various oxidation states (Figure 1) remains incomplete.Here, we outline the major microbial processes of the nitrogen cycle, the microorganisms that perform nitrogen transformations, and the ...
The Nitrogen Cycle: A Large, Fast, and Mystifying Cycle
The biological nitrogen cycle mainly consists of internal interactions within the reactive nitrogen pool and in- and out-flow between reactive nitrogens and atmospheric N 2 pools. Inter-connections between the two large nitrogen pools are primarily controlled by only two biological (microbial) processes, nitrogen fixation and denitrification (3 ...
The Evolution and Future of Earth's Nitrogen Cycle
Nitrogen's Past and Future. Microorganisms have been controlling Earth's nitrogen cycle since life originated. With life evolving around it, nitrogen became both an essential nutrient and a major regulator of climate. Canfield et al. (p. 192) review the major changes in the nitrogen cycle throughout Earth's history.
The Nitrogen Cycle: Processes, Players, and Human Impact
The process of converting N 2 into biologically available nitrogen is called nitrogen fixation. N 2 gas is a very stable compound due to the strength of the triple bond between the nitrogen atoms ...
Global Nitrogen Cycle: Critical Enzymes, Organisms, and Processes for
Nitrogen (N) is used in many of life's fundamental biomolecules, and it is also a participant in environmental redox chemistry. Biogeochemical processes control the amount and form of N available to organisms ("fixed" N). These interacting processes result in N acting as the proximate limiting nutrient in most surface environments. Here, we review the global biogeochemical cycle of N and ...
The marine nitrogen cycle: new developments and global change
Research into the marine nitrogen cycle has a long history, dating back to the late 1800s and the first scientific consideration of the role of the ocean in the global processing of nitrogen and ...
The microbial nitrogen-cycling network
Microbial transformations of nitrogen are often depicted as a cycle consisting of six distinct processes that proceed in an orderly fashion. This view of the nitrogen cycle implies that a molecule ...
The global nitrogen cycle in the twenty-first century: introduction
The final paper by Fowler et al. presents the global nitrogen cycle at the beginning of the twenty-first century, drawing major fluxes from the papers in this volume. It provides an indication of the likely changes in the major terms in future decades, the residence times for N r in terrestrial and marine ecosystems and in the atmosphere.
The Nitrogen Cycle
Abstract. Nitrogen (N) limits primary production over large areas of the earth and has a particularly complex and interesting series of biological transformations in its cycle. Human manipulation of the N cycle is intense, as large amounts of "reactive" N are needed for crop production and are produced as a by-product of fossil fuel combustion.
The global nitrogen cycle in the twenty-first century
Global nitrogen fixation contributes 413 Tg of reactive nitrogen (N r) to terrestrial and marine ecosystems annually of which anthropogenic activities are responsible for half, 210 Tg N.The majority of the transformations of anthropogenic N r are on land (240 Tg N yr −1) within soils and vegetation where reduced N r contributes most of the input through the use of fertilizer nitrogen in ...
The global nitrogen cycle in the twenty-first century: introduction
the global nitrogen cycle, including effects on climate, biodi-versity, human health as well as the importance of fertilizer nitrogen on crop yield [16]. The final paper by Fowler et al. [17] presents the global nitrogen cycle at the beginning of the twenty-first century, drawing major fluxes from the papers in this volume. It
The nitrogen cycle: Current Biology
The significance of nitrogen to the biosphere and to cellular life is indisputable; however, our fundamental knowledge of the microorganisms and enzymatic processes that transform nitrogen into its various oxidation states remains incomplete.Here, we outline the major microbial processes of the nitrogen cycle, the microorganisms that perform nitrogen transformations, and the modularity and ...
Transformation of the Nitrogen Cycle: Recent Trends ...
Humans continue to transform the global nitrogen cycle at a record pace, reflecting an increased combustion of fossil fuels, growing demand for nitrogen in agriculture and industry, and pervasive inefficiencies in its use. Much anthropogenic nitrogen is lost to air, water, and land to cause a cascade of environmental and human health problems.
Nitrogen Cycles: Past, Present, and Future
This paper contrasts the natural and anthropogenic controls on the conversion of unreactive N2 to more reactive forms of nitrogen (Nr). A variety of data sets are used to construct global N budgets for 1860 and the early 1990s and to make projections for the global N budget in 2050. Regional N budgets for Asia, North America, and other major regions for the early 1990s, as well as the marine N ...
An Earth-system perspective of the global nitrogen cycle
Perhaps the most informative record of the past activity of the global nitrogen cycle is that of atmospheric nitrous oxide (N 2 O), as its concentration is primarily determined by the magnitudes ...
The Nitrogen Cycle: A Large, Fast, and Mystifying Cycle
The Nitrogen Cycle: A Large, Fast, and Mystifying Cycle. The Nitrogen Cycle: A Large, Fast, and Mystifying Cycle ... 1 Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC). PMID: 31554776 PMCID: PMC6759337 DOI: 10.1264/jsme2.ME3403rh
Research progress of urban nitrogen cycle and metabolism
Given this nitrogen imbalance, studies of nitrogen budgets have been increasing, providing a further understanding of nitrogen cycle. As the area with the highest concentration of resource use, cities have become a hot spot for nitrogen cycle research (Zhang et al., 2021).A nitrogen study in Beijing found that fossil fuel consumption, fertilizer/feed imports, and food imports together ...
Transformation of the Nitrogen Cycle: Recent Trends ...
Abstract. Humans continue to transform the global nitrogen cycle at a record pace, reflecting an increased combustion of fossil fuels, growing demand for nitrogen in agriculture and industry, and pervasive inefficiencies in its use. Much anthropogenic nitrogen is lost to air, water, and land to cause a cascade of environmental and human health ...
(PDF) Nitrogen cycle
The nitrogen cycle is the shift between different chemical forms of nitrogen through biologic, physical, and geologic processes on. Earth. Nitrogen is an essential element for all living things ...
A chronology of human understanding of the nitrogen cycle
1976 The global nitrogen cycle. Nitrogen, phosphorus and sulphur—global cycles (eds , Svensson BH& Söderlund R), pp. 23-73. SCOPE Report 7, Ecological Bulletin (Stockholm) no. 22. Stockholm, Sweden: Swedish National Science Research Council. Google Scholar
Nitrogen cycling and microbial cooperation in the terrestrial
The nitrogen cycle plays a major role in aquatic nitrogen transformations, including in the terrestrial subsurface. However, the variety of transformations remains understudied. ... Research was ...
(PDF) Nitrogen Cycles: Past, Present, and Future
This paper contrasts the natural and anthropogenic controls on the conversion of unreactive N2 to more reactive forms of nitrogen (Nr). A variety of data sets are used to construct global N ...
(PDF) Nitrogen cycling: A review of the processes ...
PDF | The coastal and marine nitrogen cycle occupies a complex, central role within the biogeochemical cycles. Human interventions in the earth system... | Find, read and cite all the research you ...
Trends in the Research and Development of Soil Nitrogen Mineralization
Nitrogen (N) is a vital mineral nutrient for plant growth and occupies a pivotal position in biogeochemical systems. Soil nitrogen mineralization (SNM) in forests represents a significant limiting factor in terrestrial ecosystem productivity in the context of global climate change. To understand the research status and development trends of SNM in forests, 3576 articles spanning 2004 to 2024 ...

The Nitrogen Cycle: A Large, Fast, and Mystifying Cycle

Nitrogen Cycles: Past, Present, and Future

Cite this article

Access this article

Similar content being viewed by others

Convergent estimates of marine nitrogen fixation

Marine Nitrogen and Climate Change

Revisiting the distribution of oceanic N 2 fixation and estimating diazotrophic contribution to marine production

Author information

Rights and permissions

About this article

Share this article

Save citation to file

Add to My Bibliography

The Nitrogen Cycle: A Large, Fast, and Mystifying Cycle

Similar articles

Related information

LinkOut - more resources

Trending Terms:

Transformation of the Nitrogen Cycle: Recent Trends, Questions, and Potential Solutions

Supplementary Material

Information

Submission history

Export citation

View Options

More options

Restore Content Access

View options

Share article link

Share on social media

Your password must have 8 characters or more and contain 3 of the following:

Nitrogen cycling and microbial cooperation in the terrestrial subsurface

Similar content being viewed by others

Nitrogen fixation and diazotroph diversity in groundwater systems

Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater

Differential contribution of nitrifying prokaryotes to groundwater nitrification

Materials and methods

Nucleic acid extraction, sequencing and genome assembly

Quantitative PCR

Metabolic predictions

Statistical analyses

Results and discussion

Nitrogen cycling is a core function of groundwater microbiomes, but community compositions are site-specific

Nitrifier diversity and activity in groundwater, and habitat specificity

Ammonia-oxidizers constituted several major lineages, including a single comammox bacterium

Diverse taxa with nitrite oxidoreductase homologues, including Nitrososphaerales

Nitrite-dependent methanotroph ( Ca . Methylomirabilis)

Final-step of denitrification

Nitrous oxide reductase gene expression was strongly associated with oxygen availability and not limited by pathway fragmentation

Transcriptional activity of co-occurring aerobic and anaerobic nitrogen-cycling pathways in oxic versus dysoxic groundwater

Data availability

Acknowledgements

Author information

Contributions

Corresponding author

Ethics declarations

Additional information

Supplementary information

About this article

Share this article

This article is cited by

Methane-dependent complete denitrification by a single Methylomirabilis bacterium

High hydrostatic pressure stimulates microbial nitrate reduction in hadal trench sediments under oxic conditions

Nitrogen metabolism pathways and functional microorganisms in typical karst wetlands

Physiological adaptation and gut microbiota changes of orange mud crab Scylla olivacea in response to increased temperature condition

Quick links

Nitrogen cycling: A review of the processes, transformations and fluxes in coastal ecosystems

Abstract and Figures

Information

Initiatives

Article Menu

JSmol Viewer

1. Introduction

Share and Cite

Article Metrics

Further Information

IMAGES

VIDEO

COMMENTS