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.

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Abstract
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.
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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.
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.
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3 Citations in Europe PMC

Data provided by Europe PubMed Central.

Stark contrast in denitrification and anammox across the deep Norwegian trench in the Skagerrak.
Trimmer M, Engstrom P, Thamdrup B., Appl. Environ. Microbiol. 79(23), 2013
PMID: 24056465

44 References

Data provided by Europe PubMed Central.

A comparison of various Gibbs energy dissipation correlations for predicting microbial growth yields
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

Madigan, 2003
Diurnal variation of denitrification and nitrification in sediments colonized by benthic microphytes
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
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
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
Big bacteria.
Schulz HN, Jorgensen BB., Annu. Rev. Microbiol. 55(), 2001
PMID: 11544351
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
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
Growth yields in bacterial denitrification and nitrate ammonification.
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
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
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

Tiedje, 1988
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
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

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