Predicting microbial nitrogen pathways from basic principles
van de Leemput IA, Veraart AJ, Dakos V, de Klein JJM, Strous M, Scheffer M (2011)
Environmental Microbiology 13(6): 1477-1487.
Zeitschriftenaufsatz
| Veröffentlicht | Englisch
Download
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
Autor*in
van de Leemput, Ingrid A.;
Veraart, Annelies J.;
Dakos, Vasilis;
de Klein, Jeroen J. M.;
Strous, MarcUniBi;
Scheffer, Marten
Einrichtung
Abstract / Bemerkung
Nitrogen compounds are transformed by a complicated network of competing geochemical processes or microbial pathways, each performed by a different ecological guild of microorganisms. Complete experimental unravelling of this network requires a prohibitive experimental effort. Here we present a simple model that predicts relative rates of hypothetical nitrogen pathways, based only on the stoichiometry and energy yield of the performed redox reaction, assuming competition for resources between alternative pathways. Simulating competing pathways in hypothetical freshwater and marine sediment situations, we surprisingly found that much of the variation observed in nature can simply be predicted from these basic principles. Investigating discrepancies between observations and predictions led to two important biochemical factors that may create barriers for the viability of pathways: enzymatic costs for long pathways and high ammonium activation energy. We hypothesize that some discrepancies can be explained by non-equilibrium dynamics. The model predicted a pathway that has not been discovered in nature yet: the dismutation of nitrite to the level of nitrate and dinitrogen gas.
Erscheinungsjahr
2011
Zeitschriftentitel
Environmental Microbiology
Band
13
Ausgabe
6
Seite(n)
1477-1487
ISSN
1462-2912
Page URI
https://pub.uni-bielefeld.de/record/2289586
Zitieren
van de Leemput IA, Veraart AJ, Dakos V, de Klein JJM, Strous M, Scheffer M. Predicting microbial nitrogen pathways from basic principles. Environmental Microbiology. 2011;13(6):1477-1487.
van de Leemput, I. A., Veraart, A. J., Dakos, V., de Klein, J. J. M., Strous, M., & Scheffer, M. (2011). Predicting microbial nitrogen pathways from basic principles. Environmental Microbiology, 13(6), 1477-1487. https://doi.org/10.1111/j.1462-2920.2011.02450.x
van de Leemput, Ingrid A., Veraart, Annelies J., Dakos, Vasilis, de Klein, Jeroen J. M., Strous, Marc, and Scheffer, Marten. 2011. “Predicting microbial nitrogen pathways from basic principles”. Environmental Microbiology 13 (6): 1477-1487.
van de Leemput, I. A., Veraart, A. J., Dakos, V., de Klein, J. J. M., Strous, M., and Scheffer, M. (2011). Predicting microbial nitrogen pathways from basic principles. Environmental Microbiology 13, 1477-1487.
van de Leemput, I.A., et al., 2011. Predicting microbial nitrogen pathways from basic principles. Environmental Microbiology, 13(6), p 1477-1487.
I.A. van de Leemput, et al., “Predicting microbial nitrogen pathways from basic principles”, Environmental Microbiology, vol. 13, 2011, pp. 1477-1487.
van de Leemput, I.A., Veraart, A.J., Dakos, V., de Klein, J.J.M., Strous, M., Scheffer, M.: Predicting microbial nitrogen pathways from basic principles. Environmental Microbiology. 13, 1477-1487 (2011).
van de Leemput, Ingrid A., Veraart, Annelies J., Dakos, Vasilis, de Klein, Jeroen J. M., Strous, Marc, and Scheffer, Marten. “Predicting microbial nitrogen pathways from basic principles”. Environmental Microbiology 13.6 (2011): 1477-1487.
Daten bereitgestellt von European Bioinformatics Institute (EBI)
10 Zitationen in Europe PMC
Daten bereitgestellt von Europe PubMed Central.
Complete nitrification: insights into the ecophysiology of comammox Nitrospira.
Koch H, van Kessel MAHJ, Lücker S., Appl Microbiol Biotechnol 103(1), 2019
PMID: 30415428
Koch H, van Kessel MAHJ, Lücker S., Appl Microbiol Biotechnol 103(1), 2019
PMID: 30415428
Functional Resistance to Recurrent Spatially Heterogeneous Disturbances Is Facilitated by Increased Activity of Surviving Bacteria in a Virtual Ecosystem.
König S, Worrich A, Banitz T, Harms H, Kästner M, Miltner A, Wick LY, Frank K, Thullner M, Centler F., Front Microbiol 9(), 2018
PMID: 29696013
König S, Worrich A, Banitz T, Harms H, Kästner M, Miltner A, Wick LY, Frank K, Thullner M, Centler F., Front Microbiol 9(), 2018
PMID: 29696013
Organization of biogeochemical nitrogen pathways with switch-like adjustment in fluctuating soil redox conditions.
Lamba S, Bera S, Rashid M, Medvinsky AB, Sun GQ, Acquisti C, Chakraborty A, Li BL., R Soc Open Sci 4(1), 2017
PMID: 28280580
Lamba S, Bera S, Rashid M, Medvinsky AB, Sun GQ, Acquisti C, Chakraborty A, Li BL., R Soc Open Sci 4(1), 2017
PMID: 28280580
The Thermodynamics of Marine Biogeochemical Cycles: Lotka Revisited.
Vallino JJ, Algar CK., Ann Rev Mar Sci 8(), 2016
PMID: 26515809
Vallino JJ, Algar CK., Ann Rev Mar Sci 8(), 2016
PMID: 26515809
Biotic Interactions in Microbial Communities as Modulators of Biogeochemical Processes: Methanotrophy as a Model System.
Ho A, Angel R, Veraart AJ, Daebeler A, Jia Z, Kim SY, Kerckhof FM, Boon N, Bodelier PL., Front Microbiol 7(), 2016
PMID: 27602021
Ho A, Angel R, Veraart AJ, Daebeler A, Jia Z, Kim SY, Kerckhof FM, Boon N, Bodelier PL., Front Microbiol 7(), 2016
PMID: 27602021
Microbial Mat Compositional and Functional Sensitivity to Environmental Disturbance.
Preisner EC, Fichot EB, Norman RS., Front Microbiol 7(), 2016
PMID: 27799927
Preisner EC, Fichot EB, Norman RS., Front Microbiol 7(), 2016
PMID: 27799927
Microbial catabolic activities are naturally selected by metabolic energy harvest rate.
González-Cabaleiro R, Ofiţeru ID, Lema JM, Rodríguez J., ISME J 9(12), 2015
PMID: 26161636
González-Cabaleiro R, Ofiţeru ID, Lema JM, Rodríguez J., ISME J 9(12), 2015
PMID: 26161636
Connecting the dots: linking nitrogen cycle gene expression to nitrogen fluxes in marine sediment mesocosms.
Bowen JL, Babbin AR, Kearns PJ, Ward BB., Front Microbiol 5(), 2014
PMID: 25191309
Bowen JL, Babbin AR, Kearns PJ, Ward BB., Front Microbiol 5(), 2014
PMID: 25191309
End-of-pipe denitrification using RAS effluent waste streams: Effect of C/N-ratio and hydraulic retention time
Suhr KI, Erik Arvin, Per Bovbjerg Pedersen., Aquacultural engineering. 53(), 2013
PMID: IND500617751
Suhr KI, Erik Arvin, Per Bovbjerg Pedersen., Aquacultural engineering. 53(), 2013
PMID: IND500617751
Stark contrast in denitrification and anammox across the deep Norwegian trench in the Skagerrak.
Trimmer M, Engström P, Thamdrup B., Appl Environ Microbiol 79(23), 2013
PMID: 24056465
Trimmer M, Engström P, Thamdrup B., Appl Environ Microbiol 79(23), 2013
PMID: 24056465
44 References
Daten bereitgestellt von Europe PubMed Central.
Dissimilatory nitrate reduction to ammonium (DNRA) as a nitrogen link, versus denitrification as a sink in a shallow estuary (Laguna Madre/Baffin Bay, Texas)
An, Mar Ecol Prog Ser 237(), 2002
An, Mar Ecol Prog Ser 237(), 2002
New developments in the marine nitrogen cycle.
Brandes JA, Devol AH, Deutsch C., Chem. Rev. 107(2), 2007
PMID: 17300141
Brandes JA, Devol AH, Deutsch C., Chem. Rev. 107(2), 2007
PMID: 17300141
Sulfide-induced dissimilatory nitrate reduction to ammonia in anaerobic freshwater sediments
Brunet, FEMS Microbiol Ecol 21(), 1996
Brunet, FEMS Microbiol Ecol 21(), 1996
Nitrate reduction to ammonium and organic nitrogen in an estuarine sediment.
Buresh RJ, Patrick WHJr., Soil Biol. Biochem. 13(4), 1981
PMID: IND81083855
Buresh RJ, Patrick WHJr., Soil Biol. Biochem. 13(4), 1981
PMID: IND81083855
Relationships between the denitrification capacities of soils and total, water-soluble and readily decomposable soil organic matter
Burford, Soil Biol Biochem 7(), 1975
Burford, Soil Biol Biochem 7(), 1975
Modeling nitrogen cycling in a coastal fresh water sediment
Canavan, Hydrobiologia 584(), 2007
Canavan, Hydrobiologia 584(), 2007
Partial nitrification of high ammonia concentration wastewater as a part of a shortcut biological nitrogen removal process
Ciudad, Process Biochem 40(), 2005
Ciudad, Process Biochem 40(), 2005
Why is metabolic labour divided in nitrification?
Costa E, Perez J, Kreft JU., Trends Microbiol. 14(5), 2006
PMID: 16621570
Costa E, Perez J, Kreft JU., Trends Microbiol. 14(5), 2006
PMID: 16621570
Anaerobic ammonium oxidation (anammox) in the marine environment.
Dalsgaard T, Thamdrup B, Canfield DE., Res. Microbiol. 156(4), 2005
PMID: 15862442
Dalsgaard T, Thamdrup B, Canfield DE., Res. Microbiol. 156(4), 2005
PMID: 15862442
Short- and long-term effects of temperature on the Anammox process.
Dosta J, Fernandez I, Vazquez-Padin JR, Mosquera-Corral A, Campos JL, Mata-Alvarez J, Mendez R., J. Hazard. Mater. 154(1-3), 2007
PMID: 18063297
Dosta J, Fernandez I, Vazquez-Padin JR, Mosquera-Corral A, Campos JL, Mata-Alvarez J, Mendez R., J. Hazard. Mater. 154(1-3), 2007
PMID: 18063297
An experimental study on effects of submersed macrophytes on nitrification and denitrification in ammonium-rich aquatic systems
Eriksson, Limnol Oceanogr 44(), 1999
Eriksson, Limnol Oceanogr 44(), 1999
Nitrite-driven anaerobic methane oxidation by oxygenic bacteria.
Ettwig KF, Butler MK, Le Paslier D, Pelletier E, Mangenot S, Kuypers MM, Schreiber F, Dutilh BE, Zedelius J, de Beer D, Gloerich J, Wessels HJ, van Alen T, Luesken F, Wu ML, van de Pas-Schoonen KT, Op den Camp HJ, Janssen-Megens EM, Francoijs KJ, Stunnenberg H, Weissenbach J, Jetten MS, Strous M., Nature 464(7288), 2010
PMID: 20336137
Ettwig KF, Butler MK, Le Paslier D, Pelletier E, Mangenot S, Kuypers MM, Schreiber F, Dutilh BE, Zedelius J, de Beer D, Gloerich J, Wessels HJ, van Alen T, Luesken F, Wu ML, van de Pas-Schoonen KT, Op den Camp HJ, Janssen-Megens EM, Francoijs KJ, Stunnenberg H, Weissenbach J, Jetten MS, Strous M., Nature 464(7288), 2010
PMID: 20336137
Biochemistry and molecular biology of nitrification
Ferguson, Biology of the Nitrogen Cycle (), 2007
Ferguson, Biology of the Nitrogen Cycle (), 2007
Nitrous oxide from soil denitrification: factors controlling its biological production.
Firestone MK, Firestone RB, Tiedje JM., Science 208(4445), 1980
PMID: 17771133
Firestone MK, Firestone RB, Tiedje JM., Science 208(4445), 1980
PMID: 17771133
Aerobic denitrification in permeable Wadden Sea sediments.
Gao H, Schreiber F, Collins G, Jensen MM, Svitlica O, Kostka JE, Lavik G, de Beer D, Zhou HY, Kuypers MM., ISME J 4(3), 2009
PMID: 20010631
Gao H, Schreiber F, Collins G, Jensen MM, Svitlica O, Kostka JE, Lavik G, de Beer D, Zhou HY, Kuypers MM., ISME J 4(3), 2009
PMID: 20010631
Co-occurrence of denitrification and nitrogen fixation in a meromictic lake, Lake Cadagno (Switzerland).
Halm H, Musat N, Lam P, Langlois R, Musat F, Peduzzi S, Lavik G, Schubert CJ, Sinha B, Singha B, LaRoche J, Kuypers MM., Environ. Microbiol. 11(8), 2009
PMID: 19397681
Halm H, Musat N, Lam P, Langlois R, Musat F, Peduzzi S, Lavik G, Schubert CJ, Sinha B, Singha B, LaRoche J, Kuypers MM., Environ. Microbiol. 11(8), 2009
PMID: 19397681
Hooper, 2004
Pathways, rates, and regulation of N2 production in the chemocline of an anoxic basin, Mariager Fjord, Denmark
Jensen, Mar Chem 113(), 2009
Jensen, Mar Chem 113(), 2009
Anaerobic ammonium oxidation by marine and freshwater planctomycete-like bacteria.
Jetten MS, Sliekers O, Kuypers M, Dalsgaard T, van Niftrik L, Cirpus I, van de Pas-Schoonen K, Lavik G, Thamdrup B, Le Paslier D, Op den Camp HJ, Hulth S, Nielsen LP, Abma W, Third K, Engstrom P, Kuenen JG, Jorgensen BB, Canfield DE, Sinninghe Damste JS, Revsbech NP, Fuerst J, Weissenbach J, Wagner M, Schmidt I, Schmid M, Strous M., Appl. Microbiol. Biotechnol. 63(2), 2003
PMID: 12955353
Jetten MS, Sliekers O, Kuypers M, Dalsgaard T, van Niftrik L, Cirpus I, van de Pas-Schoonen K, Lavik G, Thamdrup B, Le Paslier D, Op den Camp HJ, Hulth S, Nielsen LP, Abma W, Third K, Engstrom P, Kuenen JG, Jorgensen BB, Canfield DE, Sinninghe Damste JS, Revsbech NP, Fuerst J, Weissenbach J, Wagner M, Schmidt I, Schmid M, Strous M., Appl. Microbiol. Biotechnol. 63(2), 2003
PMID: 12955353
Annual pattern of denitrification and nitrate ammonification in estuarine sediment.
Jorgensen KS., Appl. Environ. Microbiol. 55(7), 1989
PMID: 16347979
Jorgensen KS., Appl. Environ. Microbiol. 55(7), 1989
PMID: 16347979
Dissimilatory nitrate reduction in anaerobic sediments leading to river nitrite accumulation.
Kelso B, Smith RV, Laughlin RJ, Lennox SD., Appl. Environ. Microbiol. 63(12), 1997
PMID: 16535749
Kelso B, Smith RV, Laughlin RJ, Lennox SD., Appl. Environ. Microbiol. 63(12), 1997
PMID: 16535749
Nitrifier genomics and evolution of the nitrogen cycle.
Klotz MG, Stein LY., FEMS Microbiol. Lett. 278(2), 2007
PMID: 18031536
Klotz MG, Stein LY., FEMS Microbiol. Lett. 278(2), 2007
PMID: 18031536
Evolution of an octahaem cytochrome c protein family that is key to aerobic and anaerobic ammonia oxidation by bacteria.
Klotz MG, Schmid MC, Strous M, op den Camp HJ, Jetten MS, Hooper AB., Environ. Microbiol. 10(11), 2008
PMID: 18761666
Klotz MG, Schmid MC, Strous M, op den Camp HJ, Jetten MS, Hooper AB., Environ. Microbiol. 10(11), 2008
PMID: 18761666
Anaerobic ammonium oxidation by anammox bacteria in the Black Sea.
Kuypers MM, Sliekers AO, Lavik G, Schmid M, Jorgensen BB, Kuenen JG, Sinninghe Damste JS, Strous M, Jetten MS., Nature 422(6932), 2003
PMID: 12686999
Kuypers MM, Sliekers AO, Lavik G, Schmid M, Jorgensen BB, Kuenen JG, Sinninghe Damste JS, Strous M, Jetten MS., Nature 422(6932), 2003
PMID: 12686999
A comparison of various Gibbs energy dissipation correlations for predicting microbial growth yields
Liu, Thermochimica Acta 458(), 2007
Liu, Thermochimica Acta 458(), 2007
Nitrogen transformations modeling in subsurface-flow constructed wetlands.
Liu W, Dahab MF, Surampalli RY., Water Environ. Res. 77(3), 2005
PMID: 15969290
Liu W, Dahab MF, Surampalli RY., Water Environ. Res. 77(3), 2005
PMID: 15969290
Madigan, 2003
Diurnal variation of denitrification and nitrification in sediments colonized by benthic microphytes
Risgaard-Petersen, Limnol Oceanogr 39(), 1994
Risgaard-Petersen, Limnol Oceanogr 39(), 1994
A safe operating space for humanity.
Rockstrom J, Steffen W, Noone K, Persson A, Chapin FS 3rd, Lambin EF, Lenton TM, Scheffer M, Folke C, Schellnhuber HJ, Nykvist B, de Wit CA, Hughes T, van der Leeuw S, Rodhe H, Sorlin S, Snyder PK, Costanza R, Svedin U, Falkenmark M, Karlberg L, Corell RW, Fabry VJ, Hansen J, Walker B, Liverman D, Richardson K, Crutzen P, Foley JA., Nature 461(7263), 2009
PMID: 19779433
Rockstrom J, Steffen W, Noone K, Persson A, Chapin FS 3rd, Lambin EF, Lenton TM, Scheffer M, Folke C, Schellnhuber HJ, Nykvist B, de Wit CA, Hughes T, van der Leeuw S, Rodhe H, Sorlin S, Snyder PK, Costanza R, Svedin U, Falkenmark M, Karlberg L, Corell RW, Fabry VJ, Hansen J, Walker B, Liverman D, Richardson K, Crutzen P, Foley JA., Nature 461(7263), 2009
PMID: 19779433
Anaerobic ammonium-oxidizing bacteria in marine environments: widespread occurrence but low diversity.
Schmid MC, Risgaard-Petersen N, van de Vossenberg J, Kuypers MM, Lavik G, Petersen J, Hulth S, Thamdrup B, Canfield D, Dalsgaard T, Rysgaard S, Sejr MK, Strous M, den Camp HJ, Jetten MS., Environ. Microbiol. 9(6), 2007
PMID: 17504485
Schmid MC, Risgaard-Petersen N, van de Vossenberg J, Kuypers MM, Lavik G, Petersen J, Hulth S, Thamdrup B, Canfield D, Dalsgaard T, Rysgaard S, Sejr MK, Strous M, den Camp HJ, Jetten MS., Environ. Microbiol. 9(6), 2007
PMID: 17504485
Anaerobic ammonium oxidation in a tropical freshwater system (Lake Tanganyika).
Schubert CJ, Durisch-Kaiser E, Wehrli B, Thamdrup B, Lam P, Kuypers MM., Environ. Microbiol. 8(10), 2006
PMID: 16958766
Schubert CJ, Durisch-Kaiser E, Wehrli B, Thamdrup B, Lam P, Kuypers MM., Environ. Microbiol. 8(10), 2006
PMID: 16958766
Denitrification across landscapes and waterscapes: a synthesis.
Seitzinger S, Harrison JA, Bohlke JK, Bouwman AF, Lowrance R, Peterson B, Tobias C, Van Drecht G., Ecol Appl 16(6), 2006
PMID: 17205890
Seitzinger S, Harrison JA, Bohlke JK, Bouwman AF, Lowrance R, Peterson B, Tobias C, Van Drecht G., Ecol Appl 16(6), 2006
PMID: 17205890
Completely autotrophic nitrogen removal over nitrite in one single reactor.
Sliekers AO, Derwort N, Gomez JL, Strous M, Kuenen JG, Jetten MS., Water Res. 36(10), 2002
PMID: 12153013
Sliekers AO, Derwort N, Gomez JL, Strous M, Kuenen JG, Jetten MS., Water Res. 36(10), 2002
PMID: 12153013
Online estimation of wastewater nitrifiable nitrogen, nitrification and denitrification rates, using ORP and DO dynamics.
Sperandio M, Queinnec I., Water Sci. Technol. 49(1), 2004
PMID: 14979535
Sperandio M, Queinnec I., Water Sci. Technol. 49(1), 2004
PMID: 14979535
Growth yields in bacterial denitrification and nitrate ammonification.
Strohm TO, Griffin B, Zumft WG, Schink B., Appl. Environ. Microbiol. 73(5), 2007
PMID: 17209072
Strohm TO, Griffin B, Zumft WG, Schink B., Appl. Environ. Microbiol. 73(5), 2007
PMID: 17209072
Anaerobic oxidation of methane and ammonium.
Strous M, Jetten MS., Annu. Rev. Microbiol. 58(), 2004
PMID: 15487931
Strous M, Jetten MS., Annu. Rev. Microbiol. 58(), 2004
PMID: 15487931
Missing lithotroph identified as new planctomycete.
Strous M, Fuerst JA, Kramer EH, Logemann S, Muyzer G, van de Pas-Schoonen KT, Webb R, Kuenen JG, Jetten MS., Nature 400(6743), 1999
PMID: 10440372
Strous M, Fuerst JA, Kramer EH, Logemann S, Muyzer G, van de Pas-Schoonen KT, Webb R, Kuenen JG, Jetten MS., Nature 400(6743), 1999
PMID: 10440372
Deciphering the evolution and metabolism of an anammox bacterium from a community genome.
Strous M, Pelletier E, Mangenot S, Rattei T, Lehner A, Taylor MW, Horn M, Daims H, Bartol-Mavel D, Wincker P, Barbe V, Fonknechten N, Vallenet D, Segurens B, Schenowitz-Truong C, Medigue C, Collingro A, Snel B, Dutilh BE, Op den Camp HJ, van der Drift C, Cirpus I, van de Pas-Schoonen KT, Harhangi HR, van Niftrik L, Schmid M, Keltjens J, van de Vossenberg J, Kartal B, Meier H, Frishman D, Huynen MA, Mewes HW, Weissenbach J, Jetten MS, Wagner M, Le Paslier D., Nature 440(7085), 2006
PMID: 16598256
Strous M, Pelletier E, Mangenot S, Rattei T, Lehner A, Taylor MW, Horn M, Daims H, Bartol-Mavel D, Wincker P, Barbe V, Fonknechten N, Vallenet D, Segurens B, Schenowitz-Truong C, Medigue C, Collingro A, Snel B, Dutilh BE, Op den Camp HJ, van der Drift C, Cirpus I, van de Pas-Schoonen KT, Harhangi HR, van Niftrik L, Schmid M, Keltjens J, van de Vossenberg J, Kartal B, Meier H, Frishman D, Huynen MA, Mewes HW, Weissenbach J, Jetten MS, Wagner M, Le Paslier D., Nature 440(7085), 2006
PMID: 16598256
Tiedje, 1988
A thermodynamically based correlation for maintenance gibbs energy requirements in aerobic and anaerobic chemotrophic growth.
Tijhuis L, Van Loosdrecht MC, Heijnen JJ., Biotechnol. Bioeng. 42(4), 1993
PMID: 18613056
Tijhuis L, Van Loosdrecht MC, Heijnen JJ., Biotechnol. Bioeng. 42(4), 1993
PMID: 18613056
Microbially catalyzed nitrate-dependent oxidation of biogenic solid-phase Fe(II) compounds.
Weber KA, Picardal FW, Roden EE., Environ. Sci. Technol. 35(8), 2001
PMID: 11329715
Weber KA, Picardal FW, Roden EE., Environ. Sci. Technol. 35(8), 2001
PMID: 11329715
Anaerobic redox cycling of iron by freshwater sediment microorganisms.
Weber KA, Urrutia MM, Churchill PF, Kukkadapu RK, Roden EE., Environ. Microbiol. 8(1), 2006
PMID: 16343326
Weber KA, Urrutia MM, Churchill PF, Kukkadapu RK, Roden EE., Environ. Microbiol. 8(1), 2006
PMID: 16343326
Export
Markieren/ Markierung löschen
Markierte Publikationen
Web of Science
Dieser Datensatz im Web of Science®Quellen
PMID: 21429064
PubMed | Europe PMC
Suchen in