title: Global Isotope Metabolomics Reveals Adaptive Strategies for Nitrogen Assimilation.
abstract: Nitrogen cycling is a microbial metabolic process essential for global ecological/agricultural balance. To investigate the link between the well-established ammonium and the alternative nitrate assimilation metabolic pathways, global isotope metabolomics was employed to examine three nitrate reducing bacteria using (15)NO3 as a nitrogen source. In contrast to a control (Pseudomonas stutzeri RCH2), the results show that two of the isolates from Oak Ridge, Tennessee (Pseudomonas N2A2 and N2E2) utilize nitrate and ammonia for assimilation concurrently with differential labeling observed across multiple classes of metabolites including amino acids and nucleotides. The data reveal that the N2A2 and N2E2 strains conserve nitrogen-containing metabolites, indicating that the nitrate assimilation pathway is a conservation mechanism for the assimilation of nitrogen. Co-utilization of nitrate and ammonia is likely an adaption to manage higher levels of nitrite since the denitrification pathways utilized by the N2A2 and N2E2 strains from the Oak Ridge site are predisposed to the accumulation of the toxic nitrite. The use of global isotope metabolomics allowed for this adaptive strategy to be investigated, which would otherwise not have been possible to decipher.
authors.affiliation: Scripps Center for Metabolomics, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States.
authors.forename: Michael E
authors.initials: ME
authors.lastname: Kurczy
authors.affiliation: Scripps Center for Metabolomics, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States.
authors.forename: Erica M
authors.initials: EM
authors.lastname: Forsberg
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Georgia , Athens, Georgia 30602, United States.
authors.forename: Michael P
authors.initials: MP
authors.lastname: Thorgersen
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Georgia , Athens, Georgia 30602, United States.
authors.forename: Farris L
authors.initials: FL
authors.lastname: Poole
authors.affiliation: Scripps Center for Metabolomics, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States.
authors.forename: H Paul
authors.initials: HP
authors.lastname: Benton
authors.affiliation: Metabolomics Platform, Faculty of Biology and Medicine, University of Lausanne , Rue du Bugnon 19, 1011 Lausanne, Switzerland.
authors.forename: Julijana
authors.initials: J
authors.lastname: Ivanisevic
authors.affiliation: Scripps Center for Metabolomics, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States.
authors.forename: Minerva L
authors.initials: ML
authors.lastname: Tran
authors.affiliation: Department of Biochemistry, University of Missouri , Columbia, Missouri 65211, United States.
authors.forename: Judy D
authors.initials: JD
authors.lastname: Wall
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States.
authors.forename: Dwayne A
authors.initials: DA
authors.lastname: Elias
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Georgia , Athens, Georgia 30602, United States.
authors.forename: Michael W W
authors.initials: MW
authors.lastname: Adams
authors.affiliation: Scripps Center for Metabolomics, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States.|Departments of Chemistry, Molecular, and Computational Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States.
authors.forename: Gary
authors.initials: G
authors.lastname: Siuzdak
mesh_terms: D000596:Amino Acids / Q000378:metabolism; D000641:Ammonia / Q000378:metabolism*; D019295:Computational Biology; D058440:Denitrification; D055432:Metabolomics; D009566:Nitrates / Q000378:metabolism*; D009586:Nitrogen Fixation; D009590:Nitrogen Radioisotopes; D009711:Nucleotides / Q000096:biosynthesis; D011549:Pseudomonas / Q000378:metabolism*; D011687:Purines / Q000096:biosynthesis / Q000378:metabolism; D011743:Pyrimidines / Q000096:biosynthesis / Q000378:metabolism
chemical_list: D000596:Amino Acids; D009566:Nitrates; D009590:Nitrogen Radioisotopes; D009711:Nucleotides; D011687:Purines; D011743:Pyrimidines; D000641:Ammonia