title: Nitrobacter winogradskyi transcriptomic response to low and high ammonium concentrations.
abstract: Nitrobacter winogradskyi Nb-255 is a nitrite-oxidizing bacterium that can grow solely on nitrite (NO2(-)) as a source of energy and nitrogen. In most natural situations, NO2(-) oxidation is coupled closely to ammonium (NH4(+)) oxidation by bacteria and archaea and, conceptually, N. winogradskyi can save energy using NH4(+) to meet its N-biosynthetic requirements. Interestingly, NH4(+) delayed the growth of N. winogradskyi when at concentrations higher than 35 mM, but grew well at concentrations below 25 mM NH4(+) while adjusting the expression of 24% of its genes. Notable genes that changed in expression included those with roles in nitrogen and carbon assimilation. Contrary to expectations, higher expression of glutamate synthase (GOGAT), instead of glutamate dehydrogenase, was detected at higher NH4(+) concentration. Genes in assimilatory NO2(-) metabolism and the degradation of glycogen and biofilm/motility were downregulated when N. winogradskyi was grown in the presence of NH4(+). Nitrobacter winogradskyi grown in medium with 25 mM NH4(+) upregulated genes in post-translational modification, protein turnover, biogenesis and chaperons. The data suggest that N. winogradskyi physiology is modified in the presence of NH4(+) and is likely to be modified during coupled nitrification with NH3 oxidizers.
authors: Botany and Plant Pathology, Microbiology Oregon State University, Corvallis, OR 97331-2902, USA sayavedl@science.oregonstate.edu.
authors: Luis
authors: L
authors: Sayavedra-Soto
authors: Department of Biology, Metropolitan State University of Denver, Denver CO 80217-3362, USA.
authors: Rebecca
authors: R
authors: Ferrell
authors: Botany and Plant Pathology, Microbiology Oregon State University, Corvallis, OR 97331-2902, USA.
authors: Michael
authors: M
authors: Dobie
authors: Botany and Plant Pathology, Microbiology Oregon State University, Corvallis, OR 97331-2902, USA.
authors: Brett
authors: B
authors: Mellbye
authors: Biological and Ecological Engineering, Oregon State University, Corvallis, OR 97331, USA.
authors: Frank
authors: F
authors: Chaplen
authors: Botany and Plant Pathology, Microbiology Oregon State University, Corvallis, OR 97331-2902, USA.
authors: Alex
authors: A
authors: Buchanan
authors: Botany and Plant Pathology, Microbiology Oregon State University, Corvallis, OR 97331-2902, USA.
authors: Jeffrey
authors: J
authors: Chang
authors: Microbiology Oregon State University, Corvallis, OR 97331, USA.
authors: Peter
authors: P
authors: Bottomley
authors: Botany and Plant Pathology, Microbiology Oregon State University, Corvallis, OR 97331-2902, USA.
authors: Daniel
authors: D
authors: Arp
mesh_terms: D064751:Ammonium Compounds / Q000378:metabolism*; D018441:Biofilms; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D005969:Glutamate Dehydrogenase / Q000235:genetics; D005970:Glutamate Synthase / Q000235:genetics; D006003:Glycogen / Q000378:metabolism; D018832:Molecular Chaperones / Q000235:genetics; D058465:Nitrification / Q000235:genetics; D009573:Nitrites / Q000378:metabolism; D009576:Nitrobacter / Q000235:genetics* / Q000254:growth & development* / Q000378:metabolism; D010084:Oxidation-Reduction; D011499:Protein Processing, Post-Translational; D059467:Transcriptome
chemical_list: D064751:Ammonium Compounds; D018832:Molecular Chaperones; D009573:Nitrites; D006003:Glycogen; D005970:Glutamate Synthase; D005969:Glutamate Dehydrogenase
keywords: Nitrobacter; ammonia; transcriptome