title: Predicting microbial nitrogen pathways from basic principles.
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.
authors.affiliation: Department of Environmental Sciences, Aquatic Ecology and Water Quality Management Group, Wageningen University, Wageningen, The Netherlands. ingrid.vandeleemput@wur.nl
authors.forename: Ingrid A
authors.initials: IA
authors.lastname: van de Leemput
authors.forename: Annelies J
authors.initials: AJ
authors.lastname: Veraart
authors.forename: Vasilis
authors.initials: V
authors.lastname: Dakos
authors.forename: Jeroen J M
authors.initials: JJ
authors.lastname: de Klein
authors.forename: Marc
authors.initials: M
authors.lastname: Strous
authors.forename: Marten
authors.initials: M
authors.lastname: Scheffer
mesh_terms: D001711:Biotransformation; D019015:Geologic Sediments / Q000382:microbiology; D008954:Models, Biological; D008956:Models, Chemical; D009566:Nitrates / Q000378:metabolism; D009573:Nitrites / Q000378:metabolism; D009584:Nitrogen / Q000032:analysis / Q000378:metabolism*; D058458:Nitrogen Cycle; D010084:Oxidation-Reduction; D000644:Quaternary Ammonium Compounds / Q000378:metabolism; D012623:Seawater / Q000382:microbiology; D014871:Water Microbiology; D014874:Water Pollutants, Chemical / Q000032:analysis / Q000378:metabolism*; D014877:Water Pollution, Chemical / Q000706:statistics & numerical data
chemical_list: D009566:Nitrates; D009573:Nitrites; D000644:Quaternary Ammonium Compounds; D014874:Water Pollutants, Chemical; D009584:Nitrogen