Trait-Based Representation of Biological Nitrification: Model Development, Testing, and Predicted Community Composition

Bouskill, Nicholas J.; Tang, Jinyun; Riley, William J.; Brodie, Eoin L.

doi:10.3389/fmicb.2012.00364

Title: Trait-Based Representation of Biological Nitrification: Model Development, Testing, and Predicted Community Composition

Abstract

Trait-based microbial models show clear promise as tools to represent the diversity and activity of microorganisms across ecosystem gradients. These models parameterize specific traits that determine the relative fitness of an “organism” in a given environment, and represent the complexity of biological systems across temporal and spatial scales. In this study we introduce a microbial community trait-based modeling framework (MicroTrait) focused on nitrification (MicroTrait-N) that represents the ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) and nitrite-oxidizing bacteria (NOB) using traits related to enzyme kinetics and physiological properties.We used this model to predict nitrifier diversity, ammonia (NH3) oxidation rates, and nitrous oxide (N2O) production across pH, temperature, and substrate gradients. Predicted nitrifier diversity was predominantly determined by temperature and substrate availability, the latter was strongly influenced by pH. The model predicted that transient N2O production rates are maximized by a decoupling of the AOB and NOB communities, resulting in an accumulation and detoxification of nitrite to N2O by AOB. However, cumulative N2O production (over 6 month simulations) is maximized in a system where the relationship between AOB and NOB is maintained.When the reactions uncouple, the AOB become unstable and biomass declines rapidly, resulting in decreased NH3 oxidation and N2O production. Wemore »« less

Authors:

Bouskill, Nicholas J. ^[1]; Tang, Jinyun ^[2]; Riley, William J. ^[2]; Brodie, Eoin L. ^[1]

Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Earth Sciences Division. Ecology Dept.
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Earth Sciences Division. Climate Science Dept.

Publication Date:: Sun Jan 01 00:00:00 EST 2012

Research Org.:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Org.:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

OSTI Identifier:: 1628074

Grant/Contract Number:: AC02-05CH11231

Resource Type:: Accepted Manuscript

Journal Name:: Frontiers in Microbiology

Additional Journal Information:: Journal Volume: 3; Journal ID: ISSN 1664-302X

Publisher:: Frontiers Research Foundation

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES; Microbiology; nitrogen cycle; models; biological; geochemistry; mathematical modeling; nitrification

Citation Formats


                    Bouskill, Nicholas J., Tang, Jinyun, Riley, William J., and Brodie, Eoin L. Trait-Based Representation of Biological Nitrification: Model Development, Testing, and Predicted Community Composition.  United States: N. p., 2012. 
Web.  doi:10.3389/fmicb.2012.00364.

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                    Bouskill, Nicholas J., Tang, Jinyun, Riley, William J., & Brodie, Eoin L. Trait-Based Representation of Biological Nitrification: Model Development, Testing, and Predicted Community Composition.  United States.  https://doi.org/10.3389/fmicb.2012.00364

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                    Bouskill, Nicholas J., Tang, Jinyun, Riley, William J., and Brodie, Eoin L. Sun .  
"Trait-Based Representation of Biological Nitrification: Model Development, Testing, and Predicted Community Composition".  United States.  https://doi.org/10.3389/fmicb.2012.00364.  https://www.osti.gov/servlets/purl/1628074.

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@article{osti_1628074,

  title        = {Trait-Based Representation of Biological Nitrification: Model Development, Testing, and Predicted Community Composition},

  author       = {Bouskill, Nicholas J. and Tang, Jinyun and Riley, William J. and Brodie, Eoin L.},

  abstractNote = {Trait-based microbial models show clear promise as tools to represent the diversity and activity of microorganisms across ecosystem gradients. These models parameterize specific traits that determine the relative fitness of an “organism” in a given environment, and represent the complexity of biological systems across temporal and spatial scales. In this study we introduce a microbial community trait-based modeling framework (MicroTrait) focused on nitrification (MicroTrait-N) that represents the ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) and nitrite-oxidizing bacteria (NOB) using traits related to enzyme kinetics and physiological properties.We used this model to predict nitrifier diversity, ammonia (NH3) oxidation rates, and nitrous oxide (N2O) production across pH, temperature, and substrate gradients. Predicted nitrifier diversity was predominantly determined by temperature and substrate availability, the latter was strongly influenced by pH. The model predicted that transient N2O production rates are maximized by a decoupling of the AOB and NOB communities, resulting in an accumulation and detoxification of nitrite to N2O by AOB. However, cumulative N2O production (over 6 month simulations) is maximized in a system where the relationship between AOB and NOB is maintained.When the reactions uncouple, the AOB become unstable and biomass declines rapidly, resulting in decreased NH3 oxidation and N2O production. We evaluated this model against site level chemical datasets from the interior of Alaska and accurately simulated NH3 oxidation rates and the relative ratio of AOA:AOB biomass. The predicted community structure and activity indicate (a) parameterization of a small number of traits may be sufficient to broadly characterize nitrifying community structure and (b) changing decadal trends in climate and edaphic conditions could impact nitrification rates in ways that are not captured by extant biogeochemical models.},

  doi          = {10.3389/fmicb.2012.00364},

  journal      = {Frontiers in Microbiology},

  number       = ,

  volume       = 3,

  place        = {United States},

  year         = {Sun Jan 01 00:00:00 EST 2012},

  month        = {Sun Jan 01 00:00:00 EST 2012}

}

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Works referenced in this record:

Competition for limiting amounts of oxygen between Nitrosomonas europaea and Nitrobacter winogradskyi grown in mixed continuous cultures
journal, May 1993

Laanbroek, Hendrikus J.; Gerards, Saskia
Archives of Microbiology, Vol. 159, Issue 5
DOI: 10.1007/bf00288593

Steady state and transient growth of autotrophic nitrifying bacteria
journal, January 1987

Keen, G. A.; Prosser, J. I.
Archives of Microbiology, Vol. 147, Issue 1
DOI: 10.1007/bf00492908

Energy coupling and respiration inNitrosomonas europaea
journal, November 1976

Drozd, Jan William
Archives of Microbiology, Vol. 110, Issue 2-3
DOI: 10.1007/bf00690236

Linking Microbial and Ecosystem Ecology Using Ecological Stoichiometry: A Synthesis of Conceptual and Empirical Approaches
journal, December 2010

Hall, E. K.; Maixner, F.; Franklin, O.
Ecosystems, Vol. 14, Issue 2
DOI: 10.1007/s10021-010-9408-4

Kinetics of nitrification of various amounts of ammonium added to soils
journal, January 1990

Nishio, T.; Fujimoto, T.
Soil Biology and Biochemistry, Vol. 22, Issue 1
DOI: 10.1016/0038-0717(90)90059-9

Ammonia oxidation in nitrosomonas at NH3 concentrations near km: Effects of pH and temperature
journal, December 1994

Groeneweg, Joost; Sellner, Beate; Tappe, Wolfgang
Water Research, Vol. 28, Issue 12
DOI: 10.1016/0043-1354(94)90074-4

Ammonium stability and nitrogen isotope fractionations for –NH3(aq)–NH3(gas) systems at 20–70°C and pH of 2–13: Applications to habitability and nitrogen cycling in low-temperature hydrothermal systems
journal, May 2012

Li, Long; Lollar, Barbara Sherwood; Li, Hong
Geochimica et Cosmochimica Acta, Vol. 84
DOI: 10.1016/j.gca.2012.01.040

Unifying temperature effects on the growth rate of bacteria and the stability of globular proteins
journal, April 2005

Ratkowsky, David A.; Olley, June; Ross, Tom
Journal of Theoretical Biology, Vol. 233, Issue 3
DOI: 10.1016/j.jtbi.2004.10.016

Soil carbon and nitrogen mineralization: Theory and models across scales
journal, July 2009

Manzoni, Stefano; Porporato, Amilcare
Soil Biology and Biochemistry, Vol. 41, Issue 7
DOI: 10.1016/j.soilbio.2009.02.031

Oxygen exchange with water alters the oxygen isotopic signature of nitrate in soil ecosystems
journal, June 2011

Kool, Dorien M.; Wrage, Nicole; Oenema, Oene
Soil Biology and Biochemistry, Vol. 43, Issue 6
DOI: 10.1016/j.soilbio.2011.02.006

The phylogeny of the genus Nitrobacter based on comparative rep-PCR, 16S rRNA and nitrite oxidoreductase gene sequence analysis
journal, June 2007

Vanparys, Bram; Spieck, Eva; Heylen, Kim
Systematic and Applied Microbiology, Vol. 30, Issue 4
DOI: 10.1016/j.syapm.2006.11.006

Response to Kearney and Porter: Both functional and community ecologists need to do more for each other
journal, September 2006

McGill, Brian J.; Enquist, Brian J.; Weiher, Evan
Trends in Ecology & Evolution, Vol. 21, Issue 9
DOI: 10.1016/j.tree.2006.06.020

Nitrification in acid soils: micro-organisms and mechanisms
journal, June 2001

De Boer, W.; Kowalchuk, G. A.
Soil Biology and Biochemistry, Vol. 33, Issue 7-8
DOI: 10.1016/s0038-0717(00)00247-9

Diversity peaks at intermediate productivity in a laboratory microcosm
journal, August 2000

Kassen, Rees; Buckling, Angus; Bell, Graham
Nature, Vol. 406, Issue 6795
DOI: 10.1038/35020060

Productivity and sustainability influenced by biodiversity in grassland ecosystems
journal, February 1996

Tilman, David; Wedin, David; Knops, Johannes
Nature, Vol. 379, Issue 6567
DOI: 10.1038/379718a0

Experimental demonstration of chaotic instability in biological nitrification
journal, July 2007

Graham, David W.; Knapp, Charles W.; Van Vleck, Erik S.
The ISME Journal, Vol. 1, Issue 5
DOI: 10.1038/ismej.2007.45

Toward a mechanistic understanding of how natural bacterial communities respond to changes in temperature in aquatic ecosystems
journal, February 2008

Hall, Edward K.; Neuhauser, Claudia; Cotner, James B.
The ISME Journal, Vol. 2, Issue 5
DOI: 10.1038/ismej.2008.9

Ammonia concentration determines differential growth of ammonia-oxidising archaea and bacteria in soil microcosms
journal, January 2011

Verhamme, Daniel T.; Prosser, James I.; Nicol, Graeme W.
The ISME Journal, Vol. 5, Issue 6
DOI: 10.1038/ismej.2010.191

The Western English Channel contains a persistent microbial seed bank
journal, November 2011

Caporaso, J. Gregory; Paszkiewicz, Konrad; Field, Dawn
The ISME Journal, Vol. 6, Issue 6
DOI: 10.1038/ismej.2011.162

Who is who in litter decomposition? Metaproteomics reveals major microbial players and their biogeochemical functions
journal, March 2012

Schneider, Thomas; Keiblinger, Katharina M.; Schmid, Emanuel
The ISME Journal, Vol. 6, Issue 9
DOI: 10.1038/ismej.2012.11

Sizing up metatranscriptomics
journal, August 2012

Moran, Mary Ann; Satinsky, Brandon; Gifford, Scott M.
The ISME Journal, Vol. 7, Issue 2
DOI: 10.1038/ismej.2012.94

Isolation of an autotrophic ammonia-oxidizing marine archaeon
journal, September 2005

Könneke, Martin; Bernhard, Anne E.; de la Torre, José R.
Nature, Vol. 437, Issue 7058
DOI: 10.1038/nature03911

Archaea predominate among ammonia-oxidizing prokaryotes in soils
journal, August 2006

Leininger, S.; Urich, T.; Schloter, M.
Nature, Vol. 442, Issue 7104
DOI: 10.1038/nature04983

Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria
journal, September 2009

Martens-Habbena, Willm; Berube, Paul M.; Urakawa, Hidetoshi
Nature, Vol. 461, Issue 7266
DOI: 10.1038/nature08465

Nitrification driven by bacteria and not archaea in nitrogen-rich grassland soils
journal, August 2009

Di, H. J.; Cameron, K. C.; Shen, J. P.
Nature Geoscience, Vol. 2, Issue 9
DOI: 10.1038/ngeo613

Erratum: High nitrous oxide production from thawing permafrost
journal, July 2010

Elberling, Bo; Christiansen, Hanne H.; Hansen, Birger U.
Nature Geoscience, Vol. 3, Issue 7
DOI: 10.1038/ngeo893

The role of ecological theory in microbial ecology
journal, May 2007

Prosser, James I.; Bohannan, Brendan J. M.; Curtis, Tom P.
Nature Reviews Microbiology, Vol. 5, Issue 5
DOI: 10.1038/nrmicro1643

Nitrifying and denitrifying pathways of methanotrophic bacteria
journal, November 2011

Stein, Lisa Y.; Klotz, Martin G.
Biochemical Society Transactions, Vol. 39, Issue 6
DOI: 10.1042/bst20110712

Benefits of plant diversity to ecosystems: immediate, filter and founder effects
journal, December 1998

Grime, J. P.
Journal of Ecology, Vol. 86, Issue 6
DOI: 10.1046/j.1365-2745.1998.00306.x

Altered soil microbial community at elevated CO2 leads to loss of soil carbon
journal, March 2007

Carney, K. M.; Hungate, B. A.; Drake, B. G.
Proceedings of the National Academy of Sciences, Vol. 104, Issue 12
DOI: 10.1073/pnas.0610045104

The genomic basis of trophic strategy in marine bacteria
journal, September 2009

Lauro, F. M.; McDougald, D.; Thomas, T.
Proceedings of the National Academy of Sciences, Vol. 106, Issue 37, p. 15527-15533
DOI: 10.1073/pnas.0903507106

Thaumarchaeotes abundant in refinery nitrifying sludges express amoA but are not obligate autotrophic ammonia oxidizers
journal, September 2011

Mussmann, M.; Brito, I.; Pitcher, A.
Proceedings of the National Academy of Sciences, Vol. 108, Issue 40
DOI: 10.1073/pnas.1106427108

Cultivation of an obligate acidophilic ammonia oxidizer from a nitrifying acid soil
journal, September 2011

Lehtovirta-Morley, L. E.; Stoecker, K.; Vilcinskas, A.
Proceedings of the National Academy of Sciences, Vol. 108, Issue 38
DOI: 10.1073/pnas.1107196108

Niche specialization of terrestrial archaeal ammonia oxidizers
journal, December 2011

Gubry-Rangin, C.; Hai, B.; Quince, C.
Proceedings of the National Academy of Sciences, Vol. 108, Issue 52
DOI: 10.1073/pnas.1109000108

The Paradox of the Plankton
journal, May 1961

Hutchinson, G. E.
The American Naturalist, Vol. 95, Issue 882
DOI: 10.1086/282171

The Influence of Metal Ion Concentrations and pH Value on the Growth of a Nitrosomonas Strain Isolated from Activated Sludge
journal, June 1968

Loveless, J. E.; Painter, H. A.
Journal of General Microbiology, Vol. 52, Issue 1
DOI: 10.1099/00221287-52-1-1

Species evenness and productivity in experimental plant communities
journal, October 2004

Mulder, C. P. H.; Bazeley-White, E.; Dimitrakopoulos, P. G.
Oikos, Vol. 107, Issue 1
DOI: 10.1111/j.0030-1299.2004.13110.x

The turnover of organic carbon in subsoils. Part 1. Natural and bomb radiocarbon in soil profiles from the Rothamsted long-term field experiments
journal, April 2008

Jenkinson, D. S.; Poulton, P. R.; Bryant, C.
European Journal of Soil Science, Vol. 59, Issue 2
DOI: 10.1111/j.1365-2389.2008.01025.x

N ₂ O emission rates in a California meadow soil are influenced by fertilizer level, soil moisture and the community structure of ammonia-oxidizing bacteria
journal, March 2009

Avrahami, Sharon; Bohannan, Brendan J. M.
Global Change Biology, Vol. 15, Issue 3
DOI: 10.1111/j.1365-2486.2008.01727.x

Climatic constraints on trait-based forest assembly: Climatic constraints on forest assembly
journal, September 2011

Laughlin, Daniel C.; Fulé, Peter Z.; Huffman, David W.
Journal of Ecology, Vol. 99, Issue 6
DOI: 10.1111/j.1365-2745.2011.01885.x

The role of functional traits and trade-offs in structuring phytoplankton communities: scaling from cellular to ecosystem level
journal, December 2007

Litchman, Elena; Klausmeier, Christopher A.; Schofield, Oscar M.
Ecology Letters, Vol. 10, Issue 12
DOI: 10.1111/j.1461-0248.2007.01117.x

A structured and dynamic framework to advance traits-based theory and prediction in ecology
journal, March 2010

Webb, Colleen T.; Hoeting, Jennifer A.; Ames, Gregory M.
Ecology Letters, Vol. 13, Issue 3
DOI: 10.1111/j.1461-0248.2010.01444.x

A trait-based approach for modelling microbial litter decomposition
journal, May 2012

Allison, S. D.
Ecology Letters, Vol. 15, Issue 9
DOI: 10.1111/j.1461-0248.2012.01807.x

Quantitative analyses of the abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea of a Chinese upland red soil under long-term fertilization practices
journal, September 2007

He, Ji-zheng; Shen, Ju-pei; Zhang, Li-mei
Environmental Microbiology, Vol. 9, Issue 9
DOI: 10.1111/j.1462-2920.2007.01358.x

The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria
journal, November 2008

Nicol, Graeme W.; Leininger, Sven; Schleper, Christa
Environmental Microbiology, Vol. 10, Issue 11
DOI: 10.1111/j.1462-2920.2008.01701.x

Relative abundance and diversity of ammonia-oxidizing archaea and bacteria in the San Francisco Bay estuary
journal, November 2008

Mosier, Annika C.; Francis, Christopher A.
Environmental Microbiology, Vol. 10, Issue 11
DOI: 10.1111/j.1462-2920.2008.01764.x

Bacteria rather than Archaea dominate microbial ammonia oxidation in an agricultural soil
journal, July 2009

Jia, Zhongjun; Conrad, Ralf
Environmental Microbiology, Vol. 11, Issue 7
DOI: 10.1111/j.1462-2920.2009.01891.x

TheEscherichia coliO157:H7 EhaB autotransporter protein binds to laminin and collagen I and induces a serum IgA response in O157:H7 challenged cattle
journal, July 2009

Wells, Timothy J.; McNeilly, Tom N.; Totsika, Makrina
Environmental Microbiology, Vol. 11, Issue 7
DOI: 10.1111/j.1462-2920.2009.01905.x

Some Thoughts on Nutrient Limitation in Algae
journal, September 1973

Droop, M. R.
Journal of Phycology, Vol. 9, Issue 3
DOI: 10.1111/j.1529-8817.1973.tb04092.x

Distribution and ecophysiology of the nitrifying bacteria emphasizing cultured species
journal, August 2001

Koops, Hans-Peter; Pommerening-RÃ¶ser, Andreas
FEMS Microbiology Ecology, Vol. 37, Issue 1
DOI: 10.1111/j.1574-6941.2001.tb00847.x

Comparison of PCR primer-based strategies for characterization of ammonia oxidizer communities in environmental samples
journal, June 2006

Mahmood, Shahid; Freitag, Thomas E.; Prosser, James I.
FEMS Microbiology Ecology, Vol. 56, Issue 3
DOI: 10.1111/j.1574-6941.2006.00080.x

Archaea rather than bacteria control nitrification in two agricultural acidic soils: Archaeal nitrification in acidic soils
journal, October 2010

Gubry-Rangin, Cécile; Nicol, Graeme W.; Prosser, James I.
FEMS Microbiology Ecology, Vol. 74, Issue 3
DOI: 10.1111/j.1574-6941.2010.00971.x

Environmental factors shaping the ecological niches of ammonia-oxidizing archaea
journal, September 2009

Erguder, Tuba H.; Boon, Nico; Wittebolle, Lieven
FEMS Microbiology Reviews, Vol. 33, Issue 5
DOI: 10.1111/j.1574-6976.2009.00179.x

Computational Improvements Reveal Great Bacterial Diversity and High Metal Toxicity in Soil
journal, August 2005

Gans, J.
Science, Vol. 309, Issue 5739
DOI: 10.1126/science.1112665

Community Genomics Among Stratified Microbial Assemblages in the Ocean's Interior
journal, January 2006

DeLong, E. F.
Science, Vol. 311, Issue 5760
DOI: 10.1126/science.1120250

Emergent Biogeography of Microbial Communities in a Model Ocean
journal, March 2007

Follows, M. J.; Dutkiewicz, S.; Grant, S.
Science, Vol. 315, Issue 5820
DOI: 10.1126/science.1138544

Microbial Biogeography: From Taxonomy to Traits
journal, May 2008

Green, J. L.; Bohannan, B. J. M.; Whitaker, R. J.
Science, Vol. 320, Issue 5879
DOI: 10.1126/science.1153475

Isotopic Signature of N2O Produced by Marine Ammonia-Oxidizing Archaea
journal, July 2011

Santoro, A. E.; Buchwald, C.; McIlvin, M. R.
Science, Vol. 333, Issue 6047
DOI: 10.1126/science.1208239

Response of Nitrosospira sp. Strain AF-Like Ammonia Oxidizers to Changes in Temperature, Soil Moisture Content, and Fertilizer Concentration
journal, February 2007

Avrahami, Sharon; Bohannan, Brendan J. M.
Applied and Environmental Microbiology, Vol. 73, Issue 4
DOI: 10.1128/aem.01803-06

Serological Diversity Within a Terrestrial Ammonia-Oxidizing Population
journal, October 1978

Belser, L. W.; Schmidt, E. L.
Applied and Environmental Microbiology, Vol. 36, Issue 4
DOI: 10.1128/aem.36.4.589-593.1978

Identification of Heterotrophic Nitrification in a Sierran Forest Soil
journal, October 1984

Schimel, Joshua P.; Firestone, Mary K.; Killham, Kenneth S.
Applied and Environmental Microbiology, Vol. 48, Issue 4
DOI: 10.1128/aem.48.4.802-806.1984

Competition for Ammonium between Nitrifying and Heterotrophic Bacteria in Dual Energy-Limited Chemostats
journal, January 1991

Verhagen, Frank J. M.; Laanbroek, Hendrikus J.
Applied and Environmental Microbiology, Vol. 57, Issue 11
DOI: 10.1128/aem.57.11.3255-3263.1991

Nitrous Oxide Production and Methane Oxidation by Different Ammonia-Oxidizing Bacteria
journal, June 1999

Jiang, Qing-Qiao; Bakken, Lars R.
Applied and Environmental Microbiology, Vol. 65, Issue 6
DOI: 10.1128/aem.65.6.2679-2684.1999

In Situ Analysis of Nitrifying Biofilms as Determined by In Situ Hybridization and the Use of Microelectrodes
journal, July 1999

Okabe, Satoshi; Satoh, Hisashi; Watanabe, Yoshimasa
Applied and Environmental Microbiology, Vol. 65, Issue 7
DOI: 10.1128/aem.65.7.3182-3191.1999

Community Structure and Activity Dynamics of Nitrifying Bacteria in a Phosphate-Removing Biofilm
journal, March 2001

Gieseke, Armin; Purkhold, Ulrike; Wagner, Michael
Applied and Environmental Microbiology, Vol. 67, Issue 3
DOI: 10.1128/aem.67.3.1351-1362.2001

Nitrification and Nitrifying Bacteria in the LowerSeine River and Estuary(France)
journal, December 2003

Cébron, Aurélie; Berthe, Thierry; Garnier, Josette
Applied and Environmental Microbiology, Vol. 69, Issue 12
DOI: 10.1128/aem.69.12.7091-7100.2003

Ammonia or Ammonium Ion as Substrate for Oxidation by Nitrosomonas europaea Cells and Extracts
journal, January 1974

Suzuki, Isamu; Dular, Usha; Kwok, S. C.
Journal of Bacteriology, Vol. 120, Issue 1
DOI: 10.1128/jb.120.1.556-558.1974

Model for bacterial culture growth rate throughout the entire biokinetic temperature range.
journal, January 1983

Ratkowsky, D. A.; Lowry, R. K.; McMeekin, T. A.
Journal of Bacteriology, Vol. 154, Issue 3
DOI: 10.1128/jb.154.3.1222-1226.1983

The Impact of Microbial Metabolism on Marine Dissolved Organic Matter
journal, January 2011

Kujawinski, Elizabeth B.
Annual Review of Marine Science, Vol. 3, Issue 1
DOI: 10.1146/annurev-marine-120308-081003

Modeling Diverse Communities of Marine Microbes
journal, January 2011

Follows, Michael J.; Dutkiewicz, Stephanie
Annual Review of Marine Science, Vol. 3, Issue 1
DOI: 10.1146/annurev-marine-120709-142848

Trait-Based Community Ecology of Phytoplankton
journal, December 2008

Litchman, Elena; Klausmeier, Christopher A.
Annual Review of Ecology, Evolution, and Systematics, Vol. 39, Issue 1
DOI: 10.1146/annurev.ecolsys.39.110707.173549

Mechanisms of Inorganic Oxidation and Energy Coupling
journal, October 1974

Suzuki, I.
Annual Review of Microbiology, Vol. 28, Issue 1
DOI: 10.1146/annurev.mi.28.100174.000505

Population Ecology of Nitrifying Bacteria
journal, October 1979

Belser, L. W.
Annual Review of Microbiology, Vol. 33, Issue 1
DOI: 10.1146/annurev.mi.33.100179.001521

Ammonia-Oxidizing Bacteria: A Model for Molecular Microbial Ecology
journal, October 2001

Kowalchuk, George A.; Stephen, John R.
Annual Review of Microbiology, Vol. 55, Issue 1
DOI: 10.1146/annurev.micro.55.1.485

Controls on Nitrogen Cycling in Terrestrial Ecosystems: a Synthetic Analysis of Literature data
journal, May 2005

Booth, Mary S.; Stark, John M.; Rastetter, Edward
Ecological Monographs, Vol. 75, Issue 2
DOI: 10.1890/04-0988

Analysis of Factors Controlling Soil Organic Matter Levels in Great Plains Grasslands1
journal, January 1987

Parton, W. J.; Schimel, D. S.; Cole, C. V.
Soil Science Society of America Journal, Vol. 51, Issue 5
DOI: 10.2136/sssaj1987.03615995005100050015x

On the Origin of the Theory of Mineral Nutrition of Plants and the Law of the Minimum
journal, January 1999

van der Ploeg, R. R.; Bo¨hm, W.; Kirkham, M. B.
Soil Science Society of America Journal, Vol. 63, Issue 5
DOI: 10.2136/sssaj1999.6351055x

Biogeochemical controls and isotopic signatures of nitrous oxide production by a marine ammonia-oxidizing bacterium
journal, January 2010

Frame, C. H.; Casciotti, K. L.
Biogeosciences, Vol. 7, Issue 9
DOI: 10.5194/bg-7-2695-2010

Multi-nutrient, multi-group model of present and future oceanic phytoplankton communities
journal, January 2010

Litchman, E.; Klausmeier, C. A.; Miller, J. R.
Biogeosciences Discussions
DOI: 10.5194/bgd-3-607-2006

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journal, September 2017

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Journal of Geophysical Research: Biogeosciences, Vol. 122, Issue 9
DOI: 10.1002/2017jg003871

Realizing the potential of trait-based aquatic ecology: New tools and collaborative approaches: Challenges of trait-based aquatic ecology
journal, October 2016

Kremer, Colin T.; Williams, Alicia K.; Finiguerra, Michael
Limnology and Oceanography, Vol. 62, Issue 1
DOI: 10.1002/lno.10392

Engineering microbial consortia for controllable outputs
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The ISME Journal, Vol. 10, Issue 9
DOI: 10.1038/ismej.2016.26

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DOI: 10.1038/ismej.2017.115

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journal, October 2016

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DOI: 10.1038/s41467-017-01116-z

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DOI: 10.1093/femsec/fiv113

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DOI: 10.1126/science.aan5712

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DOI: 10.3389/fmicb.2016.00214

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DOI: 10.3390/pr2040711

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DOI: 10.5194/bg-10-8329-2013

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DOI: 10.5194/gmd-10-3277-2017

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Title: Trait-Based Representation of Biological Nitrification: Model Development, Testing, and Predicted Community Composition

Abstract

Citation Formats

Competition for limiting amounts of oxygen between Nitrosomonas europaea and Nitrobacter winogradskyi grown in mixed continuous cultures journal, May 1993

Steady state and transient growth of autotrophic nitrifying bacteria journal, January 1987

Energy coupling and respiration inNitrosomonas europaea journal, November 1976

Linking Microbial and Ecosystem Ecology Using Ecological Stoichiometry: A Synthesis of Conceptual and Empirical Approaches journal, December 2010

Kinetics of nitrification of various amounts of ammonium added to soils journal, January 1990

Ammonia oxidation in nitrosomonas at NH3 concentrations near km: Effects of pH and temperature journal, December 1994

Ammonium stability and nitrogen isotope fractionations for –NH3(aq)–NH3(gas) systems at 20–70°C and pH of 2–13: Applications to habitability and nitrogen cycling in low-temperature hydrothermal systems journal, May 2012

Unifying temperature effects on the growth rate of bacteria and the stability of globular proteins journal, April 2005

Soil carbon and nitrogen mineralization: Theory and models across scales journal, July 2009

Oxygen exchange with water alters the oxygen isotopic signature of nitrate in soil ecosystems journal, June 2011

The phylogeny of the genus Nitrobacter based on comparative rep-PCR, 16S rRNA and nitrite oxidoreductase gene sequence analysis journal, June 2007

Response to Kearney and Porter: Both functional and community ecologists need to do more for each other journal, September 2006

Nitrification in acid soils: micro-organisms and mechanisms journal, June 2001

Diversity peaks at intermediate productivity in a laboratory microcosm journal, August 2000

Productivity and sustainability influenced by biodiversity in grassland ecosystems journal, February 1996

Experimental demonstration of chaotic instability in biological nitrification journal, July 2007

Toward a mechanistic understanding of how natural bacterial communities respond to changes in temperature in aquatic ecosystems journal, February 2008

Ammonia concentration determines differential growth of ammonia-oxidising archaea and bacteria in soil microcosms journal, January 2011

The Western English Channel contains a persistent microbial seed bank journal, November 2011

Who is who in litter decomposition? Metaproteomics reveals major microbial players and their biogeochemical functions journal, March 2012

Sizing up metatranscriptomics journal, August 2012

Isolation of an autotrophic ammonia-oxidizing marine archaeon journal, September 2005

Archaea predominate among ammonia-oxidizing prokaryotes in soils journal, August 2006

Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria journal, September 2009

Nitrification driven by bacteria and not archaea in nitrogen-rich grassland soils journal, August 2009

Erratum: High nitrous oxide production from thawing permafrost journal, July 2010

The role of ecological theory in microbial ecology journal, May 2007

Nitrifying and denitrifying pathways of methanotrophic bacteria journal, November 2011

Benefits of plant diversity to ecosystems: immediate, filter and founder effects journal, December 1998

Altered soil microbial community at elevated CO2 leads to loss of soil carbon journal, March 2007

The genomic basis of trophic strategy in marine bacteria journal, September 2009

Thaumarchaeotes abundant in refinery nitrifying sludges express amoA but are not obligate autotrophic ammonia oxidizers journal, September 2011

Cultivation of an obligate acidophilic ammonia oxidizer from a nitrifying acid soil journal, September 2011

Niche specialization of terrestrial archaeal ammonia oxidizers journal, December 2011

The Paradox of the Plankton journal, May 1961

The Influence of Metal Ion Concentrations and pH Value on the Growth of a Nitrosomonas Strain Isolated from Activated Sludge journal, June 1968

Species evenness and productivity in experimental plant communities journal, October 2004

The turnover of organic carbon in subsoils. Part 1. Natural and bomb radiocarbon in soil profiles from the Rothamsted long-term field experiments journal, April 2008

N 2 O emission rates in a California meadow soil are influenced by fertilizer level, soil moisture and the community structure of ammonia-oxidizing bacteria journal, March 2009

Climatic constraints on trait-based forest assembly: Climatic constraints on forest assembly journal, September 2011

The role of functional traits and trade-offs in structuring phytoplankton communities: scaling from cellular to ecosystem level journal, December 2007

A structured and dynamic framework to advance traits-based theory and prediction in ecology journal, March 2010

A trait-based approach for modelling microbial litter decomposition journal, May 2012

Quantitative analyses of the abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea of a Chinese upland red soil under long-term fertilization practices journal, September 2007

The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria journal, November 2008

Relative abundance and diversity of ammonia-oxidizing archaea and bacteria in the San Francisco Bay estuary journal, November 2008

Bacteria rather than Archaea dominate microbial ammonia oxidation in an agricultural soil journal, July 2009

TheEscherichia coliO157:H7 EhaB autotransporter protein binds to laminin and collagen I and induces a serum IgA response in O157:H7 challenged cattle journal, July 2009

Some Thoughts on Nutrient Limitation in Algae journal, September 1973

Distribution and ecophysiology of the nitrifying bacteria emphasizing cultured species journal, August 2001

Comparison of PCR primer-based strategies for characterization of ammonia oxidizer communities in environmental samples journal, June 2006

Archaea rather than bacteria control nitrification in two agricultural acidic soils: Archaeal nitrification in acidic soils journal, October 2010

Environmental factors shaping the ecological niches of ammonia-oxidizing archaea journal, September 2009

Computational Improvements Reveal Great Bacterial Diversity and High Metal Toxicity in Soil journal, August 2005

Community Genomics Among Stratified Microbial Assemblages in the Ocean's Interior journal, January 2006

Emergent Biogeography of Microbial Communities in a Model Ocean journal, March 2007

Microbial Biogeography: From Taxonomy to Traits journal, May 2008

Isotopic Signature of N2O Produced by Marine Ammonia-Oxidizing Archaea journal, July 2011

Response of Nitrosospira sp. Strain AF-Like Ammonia Oxidizers to Changes in Temperature, Soil Moisture Content, and Fertilizer Concentration journal, February 2007

Serological Diversity Within a Terrestrial Ammonia-Oxidizing Population journal, October 1978

Identification of Heterotrophic Nitrification in a Sierran Forest Soil journal, October 1984

Competition for Ammonium between Nitrifying and Heterotrophic Bacteria in Dual Energy-Limited Chemostats journal, January 1991

Nitrous Oxide Production and Methane Oxidation by Different Ammonia-Oxidizing Bacteria journal, June 1999

In Situ Analysis of Nitrifying Biofilms as Determined by In Situ Hybridization and the Use of Microelectrodes journal, July 1999

Community Structure and Activity Dynamics of Nitrifying Bacteria in a Phosphate-Removing Biofilm journal, March 2001

Nitrification and Nitrifying Bacteria in the LowerSeine River and Estuary(France) journal, December 2003

Ammonia or Ammonium Ion as Substrate for Oxidation by Nitrosomonas europaea Cells and Extracts journal, January 1974

Model for bacterial culture growth rate throughout the entire biokinetic temperature range. journal, January 1983

The Impact of Microbial Metabolism on Marine Dissolved Organic Matter journal, January 2011

Modeling Diverse Communities of Marine Microbes journal, January 2011

Trait-Based Community Ecology of Phytoplankton journal, December 2008

Mechanisms of Inorganic Oxidation and Energy Coupling journal, October 1974

Population Ecology of Nitrifying Bacteria journal, October 1979

Ammonia-Oxidizing Bacteria: A Model for Molecular Microbial Ecology journal, October 2001

Controls on Nitrogen Cycling in Terrestrial Ecosystems: a Synthetic Analysis of Literature data journal, May 2005

Analysis of Factors Controlling Soil Organic Matter Levels in Great Plains Grasslands1 journal, January 1987

On the Origin of the Theory of Mineral Nutrition of Plants and the Law of the Minimum journal, January 1999

Competition for limiting amounts of oxygen between Nitrosomonas europaea and Nitrobacter winogradskyi grown in mixed continuous cultures
journal, May 1993

Steady state and transient growth of autotrophic nitrifying bacteria
journal, January 1987

Energy coupling and respiration inNitrosomonas europaea
journal, November 1976

Linking Microbial and Ecosystem Ecology Using Ecological Stoichiometry: A Synthesis of Conceptual and Empirical Approaches
journal, December 2010

Kinetics of nitrification of various amounts of ammonium added to soils
journal, January 1990

Ammonia oxidation in nitrosomonas at NH3 concentrations near km: Effects of pH and temperature
journal, December 1994

Ammonium stability and nitrogen isotope fractionations for –NH3(aq)–NH3(gas) systems at 20–70°C and pH of 2–13: Applications to habitability and nitrogen cycling in low-temperature hydrothermal systems
journal, May 2012

Unifying temperature effects on the growth rate of bacteria and the stability of globular proteins
journal, April 2005

Soil carbon and nitrogen mineralization: Theory and models across scales
journal, July 2009

Oxygen exchange with water alters the oxygen isotopic signature of nitrate in soil ecosystems
journal, June 2011

The phylogeny of the genus Nitrobacter based on comparative rep-PCR, 16S rRNA and nitrite oxidoreductase gene sequence analysis
journal, June 2007

Response to Kearney and Porter: Both functional and community ecologists need to do more for each other
journal, September 2006

Nitrification in acid soils: micro-organisms and mechanisms
journal, June 2001

Diversity peaks at intermediate productivity in a laboratory microcosm
journal, August 2000

Productivity and sustainability influenced by biodiversity in grassland ecosystems
journal, February 1996

Experimental demonstration of chaotic instability in biological nitrification
journal, July 2007

Toward a mechanistic understanding of how natural bacterial communities respond to changes in temperature in aquatic ecosystems
journal, February 2008

Ammonia concentration determines differential growth of ammonia-oxidising archaea and bacteria in soil microcosms
journal, January 2011

The Western English Channel contains a persistent microbial seed bank
journal, November 2011

Who is who in litter decomposition? Metaproteomics reveals major microbial players and their biogeochemical functions
journal, March 2012

Sizing up metatranscriptomics
journal, August 2012

Isolation of an autotrophic ammonia-oxidizing marine archaeon
journal, September 2005

Archaea predominate among ammonia-oxidizing prokaryotes in soils
journal, August 2006

Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria
journal, September 2009

Nitrification driven by bacteria and not archaea in nitrogen-rich grassland soils
journal, August 2009

Erratum: High nitrous oxide production from thawing permafrost
journal, July 2010

The role of ecological theory in microbial ecology
journal, May 2007

Nitrifying and denitrifying pathways of methanotrophic bacteria
journal, November 2011

Benefits of plant diversity to ecosystems: immediate, filter and founder effects
journal, December 1998

Altered soil microbial community at elevated CO2 leads to loss of soil carbon
journal, March 2007

The genomic basis of trophic strategy in marine bacteria
journal, September 2009

Thaumarchaeotes abundant in refinery nitrifying sludges express amoA but are not obligate autotrophic ammonia oxidizers
journal, September 2011

Cultivation of an obligate acidophilic ammonia oxidizer from a nitrifying acid soil
journal, September 2011

Niche specialization of terrestrial archaeal ammonia oxidizers
journal, December 2011

The Paradox of the Plankton
journal, May 1961

The Influence of Metal Ion Concentrations and pH Value on the Growth of a Nitrosomonas Strain Isolated from Activated Sludge
journal, June 1968

Species evenness and productivity in experimental plant communities
journal, October 2004

The turnover of organic carbon in subsoils. Part 1. Natural and bomb radiocarbon in soil profiles from the Rothamsted long-term field experiments
journal, April 2008

N ₂ O emission rates in a California meadow soil are influenced by fertilizer level, soil moisture and the community structure of ammonia-oxidizing bacteria
journal, March 2009

Climatic constraints on trait-based forest assembly: Climatic constraints on forest assembly
journal, September 2011

The role of functional traits and trade-offs in structuring phytoplankton communities: scaling from cellular to ecosystem level
journal, December 2007

A structured and dynamic framework to advance traits-based theory and prediction in ecology
journal, March 2010

A trait-based approach for modelling microbial litter decomposition
journal, May 2012

Quantitative analyses of the abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea of a Chinese upland red soil under long-term fertilization practices
journal, September 2007

The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria
journal, November 2008

Relative abundance and diversity of ammonia-oxidizing archaea and bacteria in the San Francisco Bay estuary
journal, November 2008

Bacteria rather than Archaea dominate microbial ammonia oxidation in an agricultural soil
journal, July 2009

TheEscherichia coliO157:H7 EhaB autotransporter protein binds to laminin and collagen I and induces a serum IgA response in O157:H7 challenged cattle
journal, July 2009

Some Thoughts on Nutrient Limitation in Algae
journal, September 1973

Distribution and ecophysiology of the nitrifying bacteria emphasizing cultured species
journal, August 2001

Comparison of PCR primer-based strategies for characterization of ammonia oxidizer communities in environmental samples
journal, June 2006

Archaea rather than bacteria control nitrification in two agricultural acidic soils: Archaeal nitrification in acidic soils
journal, October 2010

Environmental factors shaping the ecological niches of ammonia-oxidizing archaea
journal, September 2009

Computational Improvements Reveal Great Bacterial Diversity and High Metal Toxicity in Soil
journal, August 2005

Community Genomics Among Stratified Microbial Assemblages in the Ocean's Interior
journal, January 2006

Emergent Biogeography of Microbial Communities in a Model Ocean
journal, March 2007

Microbial Biogeography: From Taxonomy to Traits
journal, May 2008

Isotopic Signature of N2O Produced by Marine Ammonia-Oxidizing Archaea
journal, July 2011

Response of Nitrosospira sp. Strain AF-Like Ammonia Oxidizers to Changes in Temperature, Soil Moisture Content, and Fertilizer Concentration
journal, February 2007

Serological Diversity Within a Terrestrial Ammonia-Oxidizing Population
journal, October 1978

Identification of Heterotrophic Nitrification in a Sierran Forest Soil
journal, October 1984

Competition for Ammonium between Nitrifying and Heterotrophic Bacteria in Dual Energy-Limited Chemostats
journal, January 1991

Nitrous Oxide Production and Methane Oxidation by Different Ammonia-Oxidizing Bacteria
journal, June 1999

In Situ Analysis of Nitrifying Biofilms as Determined by In Situ Hybridization and the Use of Microelectrodes
journal, July 1999

Community Structure and Activity Dynamics of Nitrifying Bacteria in a Phosphate-Removing Biofilm
journal, March 2001

Nitrification and Nitrifying Bacteria in the LowerSeine River and Estuary(France)
journal, December 2003

Ammonia or Ammonium Ion as Substrate for Oxidation by Nitrosomonas europaea Cells and Extracts
journal, January 1974

Model for bacterial culture growth rate throughout the entire biokinetic temperature range.
journal, January 1983

The Impact of Microbial Metabolism on Marine Dissolved Organic Matter
journal, January 2011

Modeling Diverse Communities of Marine Microbes
journal, January 2011

Trait-Based Community Ecology of Phytoplankton
journal, December 2008

Mechanisms of Inorganic Oxidation and Energy Coupling
journal, October 1974

Population Ecology of Nitrifying Bacteria
journal, October 1979

Ammonia-Oxidizing Bacteria: A Model for Molecular Microbial Ecology
journal, October 2001

Controls on Nitrogen Cycling in Terrestrial Ecosystems: a Synthetic Analysis of Literature data
journal, May 2005

Analysis of Factors Controlling Soil Organic Matter Levels in Great Plains Grasslands1
journal, January 1987

On the Origin of the Theory of Mineral Nutrition of Plants and the Law of the Minimum
journal, January 1999

Biogeochemical controls and isotopic signatures of nitrous oxide production by a marine ammonia-oxidizing bacterium
journal, January 2010

Multi-nutrient, multi-group model of present and future oceanic phytoplankton communities
journal, January 2010

Effects of temperature and particles on nitrification in a eutrophic coastal bay in southern China: Nitrification and Environmental Factors
journal, September 2017