Biogeochemical and omic evidence for paradoxical methane production via multiple co-occurring mechanisms in aquatic ecosystems

Autor: Elisabet Perez-Coronel, Beman Jm

Aquatic ecosystems are globally significant sources of the greenhouse gas methane (CH4) to the atmosphere. However, CH4is produced ‘paradoxically’ in oxygenated water via poorly understood mechanisms, fundamentally limiting our understanding of o

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https://doi.org/10.1101/2020.07.28.225276

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Substantial oxygen consumption by aerobic nitrite oxidation in oceanic oxygen minimum zones.

Autor: Beman JM; Life and Environmental Sciences, University of California, Merced, Merced, CA, USA. jmbeman@gmail.com., Vargas SM; Life and Environmental Sciences, University of California, Merced, Merced, CA, USA., Wilson JM; Life and Environmental Sciences, University of California, Merced, Merced, CA, USA.; Scripps Institution of Oceanography, University of California, San Diego, CA, USA., Perez-Coronel E; Life and Environmental Sciences, University of California, Merced, Merced, CA, USA., Karolewski JS; Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA., Vazquez S; Life and Environmental Sciences, University of California, Merced, Merced, CA, USA., Yu A; Life and Environmental Sciences, University of California, Merced, Merced, CA, USA., Cairo AE; Life and Environmental Sciences, University of California, Merced, Merced, CA, USA., White ME; Scripps Institution of Oceanography, University of California, San Diego, CA, USA., Koester I; Scripps Institution of Oceanography, University of California, San Diego, CA, USA., Aluwihare LI; Scripps Institution of Oceanography, University of California, San Diego, CA, USA., Wankel SD; Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.

Publikováno v: Nature communications [Nat Commun] 2021 Dec 02; Vol. 12 (1), pp. 7043. Date of Electronic Publication: 2021 Dec 02.

A community resource for paired genomic and metabolomic data mining.

Autor: Schorn MA; Laboratory of Microbiology, Department of Agricultural and Food Sciences, Wageningen University, Wageningen, the Netherlands.; Bioinformatics Group, Wageningen University, Wageningen, the Netherlands., Verhoeven S; Netherlands eScience Center, Amsterdam, the Netherlands., Ridder L; Netherlands eScience Center, Amsterdam, the Netherlands., Huber F; Netherlands eScience Center, Amsterdam, the Netherlands., Acharya DD; Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA., Aksenov AA; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA., Aleti G; Department of Psychiatry, University of California San Diego, San Diego, CA, USA., Moghaddam JA; Leibniz Institute for Natural Product Research and Infection Biology e.V. Hans-Knöll-Institute (HKI), Jena, Germany., Aron AT; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA., Aziz S; Pharmaceutical Biology Department, Pharmaceutical Institute, Eberhard Karls University Tübingen, Tübingen, Germany.; Microbiology Department, Biology Faculty, Jenderal Soedirman University, Purwokerto, Indonesia., Bauermeister A; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil., Bauman KD; Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA., Baunach M; University of Potsdam, Institute of Biochemistry and Biology, Potsdam-Golm, Germany., Beemelmanns C; Leibniz Institute for Natural Product Research and Infection Biology e.V. Hans-Knöll-Institute (HKI), Jena, Germany., Beman JM; Department of Life and Environmental Sciences, University of California Merced, Merced, CA, USA.; Sierra Nevada Research Institute, University of California Merced, Merced, CA, USA., Berlanga-Clavero MV; Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Microbiología, Universidad de Málaga, Málaga, Spain., Blacutt AA; Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA., Bode HB; Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany.; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany.; Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany.; Max-Planck-Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, Marburg, Germany., Boullie A; Institut Pasteur, Collection of Cyanobacteria, Paris, France., Brejnrod A; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA., Bugni TS; Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, WI, USA., Calteau A; Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France., Cao L; Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA., Carrión VJ; Microbial Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands.; Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, the Netherlands., Castelo-Branco R; Interdisciplinary Centre of Marine and Environmental Research), University of Porto, Porto, Portugal.; Faculty of Sciences, University of Porto, Porto, Portugal.; Department of Microbiology, University of Helsinki, Helsinki, Finland., Chanana S; Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA., Chase AB; Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA., Chevrette MG; Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA., Costa-Lotufo LV; Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil., Crawford JM; Department of Chemistry, Yale University, New Haven, CT, USA.; Chemical Biology Institute, Yale University, West Haven, CT, USA.; Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, USA., Currie CR; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.; Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, USA., Cuypers B; Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium.; Molecular Parasitology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium., Dang T; Technische Universität Berlin, Institut für Chemie, Berlin, Germany., de Rond T; Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA., Demko AM; Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA., Dittmann E; University of Potsdam, Institute of Biochemistry and Biology, Potsdam-Golm, Germany., Du C; Microbial Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands., Drozd C; Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA., Dujardin JC; Molecular Parasitology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium., Dutton RJ; Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA.; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA., Edlund A; J. Craig Venter Institute, Genomic Medicine Group, La Jolla, CA, USA.; Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA., Fewer DP; Department of Microbiology, University of Helsinki, Helsinki, Finland., Garg N; School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA., Gauglitz JM; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA., Gentry EC; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA., Gerwick L; Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA., Glukhov E; Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA., Gross H; Pharmaceutical Biology Department, Pharmaceutical Institute, Eberhard Karls University Tübingen, Tübingen, Germany., Gugger M; Institut Pasteur, Collection of Cyanobacteria, Paris, France., Guillén Matus DG; Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA., Helfrich EJN; Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany.; Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany.; Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland.; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, USA., Hempel BF; Technische Universität Berlin, Institut für Chemie, Berlin, Germany.; Charité, University Medicine Berlin, Berlin-Brandenburg Center for Regenerative Therapy (BCRT), Campus Virchow Klinikum, Berlin, Germany., Hur JS; Korean Lichen Research Institute, Sunchon National University, Sunchon, Republic of Korea., Iorio M; Naicons Srl, Milano, Italy., Jensen PR; Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA., Kang KB; College of Pharmacy, Sookmyung Women's University, Seoul, Korea., Kaysser L; Pharmaceutical Biology Department, Pharmaceutical Institute, Eberhard Karls University Tübingen, Tübingen, Germany.; German Centre for Infection Research (DZIF), Tübingen, Germany., Kelleher NL; Department of Chemistry, Northwestern University, Evanston, IL, USA., Kim CS; Department of Chemistry, Yale University, New Haven, CT, USA.; Chemical Biology Institute, Yale University, West Haven, CT, USA.; School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea., Kim KH; School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea., Koester I; Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA., König GM; Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany., Leao T; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA., Lee SR; School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea.; Department of Chemistry, Princeton University, Princeton, NJ, USA., Lee YY; Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA., Li X; Section of Microbiology, University of Copenhagen, Copenhagen, Denmark., Little JC; Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA., Maloney KN; Department of Chemistry, Point Loma Nazarene University, San Diego, CA, USA., Männle D; Pharmaceutical Biology Department, Pharmaceutical Institute, Eberhard Karls University Tübingen, Tübingen, Germany.; German Centre for Infection Research (DZIF), Tübingen, Germany.; Interfaculty Institute for Microbiology and Infection Medicine Tübingen, Microbiology and Biotechnology, University of Tübingen, Tübingen, Germany., Martin H C; Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología, Panama, Republic of Panama., McAvoy AC; School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA., Metcalf WW; Carl R. Woese Institute for Genomic Biology and Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA., Mohimani H; Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA., Molina-Santiago C; Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Microbiología, Universidad de Málaga, Málaga, Spain., Moore BS; Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA., Mullowney MW; Department of Chemistry, Northwestern University, Evanston, IL, USA., Muskat M; Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA., Nothias LF; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA., O'Neill EC; School of Chemistry, University of Nottingham, Nottingham, UK., Parkinson EI; Department of Chemistry and Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA., Petras D; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA., Piel J; Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland., Pierce EC; Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA., Pires K; Instituto Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil., Reher R; Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA., Romero D; Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Microbiología, Universidad de Málaga, Málaga, Spain., Roper MC; Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA., Rust M; Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland., Saad H; Pharmaceutical Biology Department, Pharmaceutical Institute, Eberhard Karls University Tübingen, Tübingen, Germany.; Phytochemistry and Plant Systematics Department, Division of Pharmaceutical Industries, National Research Centre, Cairo, Egypt., Saenz C; The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark., Sanchez LM; Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA., Sørensen SJ; Section of Microbiology, University of Copenhagen, Copenhagen, Denmark., Sosio M; Naicons Srl, Milano, Italy., Süssmuth RD; Technische Universität Berlin, Institut für Chemie, Berlin, Germany., Sweeney D; Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA., Tahlan K; Department of Biology, Memorial University of Newfoundland, St. John's, Canada., Thomson RJ; Department of Chemistry, Northwestern University, Evanston, IL, USA., Tobias NJ; Senckenberg Gesellschaft für Naturforschung, Frankfurt am Main, Germany.; LOEWE-Centre for Translational Biodiversity Genomics, Frankfurt am Main, Germany., Trindade-Silva AE; Departamento de Fisiologia e Farmacologia, Faculdade de Medicina, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil., van Wezel GP; Microbial Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands., Wang M; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA., Weldon KC; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA., Zhang F; Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, WI, USA., Ziemert N; German Centre for Infection Research (DZIF), Tübingen, Germany.; Interfaculty Institute for Microbiology and Infection Medicine Tübingen, Microbiology and Biotechnology, University of Tübingen, Tübingen, Germany., Duncan KR; University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, UK., Crüsemann M; Institute for Pharmaceutical Biology, University of Bonn, Bonn, Germany., Rogers S; School of Computing Science, University of Glasgow, Glasgow, UK., Dorrestein PC; Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA. pdorrestein@health.ucsd.edu.; Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA. pdorrestein@health.ucsd.edu.; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA. pdorrestein@health.ucsd.edu.; Department of Pharmacology and Pediatrics, University of California San Diego, La Jolla, CA, USA. pdorrestein@health.ucsd.edu., Medema MH; Bioinformatics Group, Wageningen University, Wageningen, the Netherlands. marnix.medema@wur.nl., van der Hooft JJJ; Bioinformatics Group, Wageningen University, Wageningen, the Netherlands. justin.vanderhooft@wur.nl.

Publikováno v: Nature chemical biology [Nat Chem Biol] 2021 Apr; Vol. 17 (4), pp. 363-368.

Climatic, physical, and biogeochemical changes drive rapid oxygen loss and recovery in a marine ecosystem.

Autor: Wilson J; Life and Environmental Sciences, University of California Merced, Merced, CA, 95343, USA. jessewilson13@gmail.com.; Scripps Institute of Oceanography, University of California San Diego, La Jolla, CA, 92037, USA. jessewilson13@gmail.com., Ucharm G; Coral Reef Research Foundation, Koror, 96940, Palau., Beman JM; Life and Environmental Sciences, University of California Merced, Merced, CA, 95343, USA.

Publikováno v: Scientific reports [Sci Rep] 2019 Nov 06; Vol. 9 (1), pp. 16114. Date of Electronic Publication: 2019 Nov 06.