Current production by non-methanotrophic bacteria enriched from an anaerobic methane-oxidizing microbial community

Lovley, 2017, Syntrophy goes electric: direct interspecies electron transfer, Annu Rev Microbiol, 71, 643, 10.1146/annurev-micro-030117-020420 McInerney, 2009, Syntrophy in anaerobic global carbon cycles, Curr Opin Biotechnol, 20, 623, 10.1016/j.copbio.2009.10.001 Boetius, 2000, A marine microbial consortium apparently mediating anaerobic oxidation of methane, Nature, 407, 623, 10.1038/35036572 Hinrichs, 1999, Methane-consuming archaebacteria in marine sediments, Nature, 398, 802, 10.1038/19751 Hoehler, 1994, Field and laboratory studies of methane oxidation in an anoxic marine sediment: evidence for a methanogen-sulfate reducer consortium, Global Biogeochem Cycles, 8, 451, 10.1029/94GB01800 Orphan, 2002, Multiple archaeal groups mediate methane oxidation in anoxic cold seep sediments, Proc Natl Acad Sci U S A, 99, 7663, 10.1073/pnas.072210299 Reeburgh, 1977, Microbial methane consumption reactions and their effect on methane distributions in freshwater and marine environments, Limnol Oceanogr, 22, 1, 10.4319/lo.1977.22.1.0001 Raghoebarsing, 2006, A microbial consortium couples anaerobic methane oxidation to denitrification, Nature, 440, 918, 10.1038/nature04617 Ettwig, 2008, Denitrifying bacteria anaerobically oxidize methane in the absence of Archaea, Environ Microbiol, 10, 3164, 10.1111/j.1462-2920.2008.01724.x Cai, 2019, Acetate production from anaerobic oxidation of methane via intracellular storage compounds, Environ Sci Technol, 10.1021/acs.est.9b00077 Xin, 2009, Production of methanol from methane by methanotrophic bacteria, Biocatal Biotransform, 22, 225, 10.1080/10242420412331283305 Sydow, 2014, Electroactive bacteria - molecular mechanisms and genetic tools, Appl Environ Microbiol, 98, 8481 Yilmazel, 2018, Electrical current generation in microbial electrolysis cells by hyperthermophilic archaea Ferroglobus placidus and Geoglobus ahangari, Bioelectrochemistry, 119, 142, 10.1016/j.bioelechem.2017.09.012 Wegener, 2015, Intercellular wiring enables electron transfer between methanotrophic archaea and bacteria, Nature, 526, 587, 10.1038/nature15733 McGlynn, 2015, Single cell activity reveals direct electron transfer in methanotrophic consortia, Nature, 526, 7574, 10.1038/nature15512 Scheller, 2016, Artificial electron acceptors decouple archaeal methane oxidation from sulfate reduction, Science, 351, 703, 10.1126/science.aad7154 Bai, 2019, Humic substances as electron acceptors for anaerobic oxidation of methane driven by ANME-2d, Water Res, 164, 10.1016/j.watres.2019.114935 Beal, 2009, Manganese- and iron-dependent marine methane oxidation, Science, 325, 10.1126/science.1169984 Weber, 2017, Anaerobic methanotrophic archaea of the ANME-2d cluster Are active in a low-sulfate, iron-rich freshwater sediment, Front Microbiol, 8, 619, 10.3389/fmicb.2017.00619 Zhang, 2019, Biochar-Mediated anaerobic oxidation of methane, Environ Sci Technol, 53, 6660, 10.1021/acs.est.9b01345 Cai, 2018, A methanotrophic archaeon couples anaerobic oxidation of methane to Fe(III) reduction, ISME J, 10.1038/s41396-018-0109-x Leu, 2020, Anaerobic methane oxidation coupled to manganese reduction by members of the Methanoperedenaceae, ISME J, 14, 1030, 10.1038/s41396-020-0590-x Ettwig, 2016, Archaea catalyze iron-dependent anaerobic oxidation of methane, Proc Natl Acad Sci U S A, 113, 10.1073/pnas.1609534113 Shi, 2016, Extracellular electron transfer mechanisms between microorganisms and minerals, Nat Rev Microbiol, 14, 651, 10.1038/nrmicro.2016.93 Kletzin, 2015, Cytochromes c in Archaea: distribution, maturation, cell architecture, and the special case of Ignicoccus hospitalis, Front Microbiol, 6, 439, 10.3389/fmicb.2015.00439 Zheng, 2020, Methane-dependent mineral reduction by aerobic methanotrophs under hypoxia, Environ Sci Technol, 7, 606 Tanaka, 2018, Extracellular electron transfer via outer membrane cytochromes in a methanotrophic bacterium Methylococcus capsulatus (bath), Front Microbiol, 9, 2905, 10.3389/fmicb.2018.02905 Bretschger, 2007, Current production and metal oxide reduction by Shewanella oneidensis MR-1 wild type and mutants, Appl Environ Microbiol, 73, 7003, 10.1128/AEM.01087-07 Bond, 2003, Electricity production by Geobacter sulfurreducens attached to electrodes, Appl Environ Microbiol, 69, 1548, 10.1128/AEM.69.3.1548-1555.2003 Caccavo, 1994, Geobacter sulfurreducens sp. nov., a hydrogen- and acetate-oxidizing dissimilatory metal-reducing microorganism, Appl Environ Microbiol, 60, 10.1128/aem.60.10.3752-3759.1994 Coates, 1996, Isolation of geobacter species from diverse sedimentary environments, Appl Environ Microbiol, 62, 10.1128/aem.62.5.1531-1536.1996 Marsili, 2008, Shewanella secretes flavins that mediate extracellular electron transfer, Proc Natl Acad Sci U S A, 105, 10.1073/pnas.0710525105 Li, 2013, Electron transfer capacity dependence of quinone-mediated Fe(III) reduction and current generation by Klebsiella pneumoniae L17, Chemosphere, 92, 218, 10.1016/j.chemosphere.2013.01.098 Huang, 2015, Exoelectrogenic bacterium phylogenetically related to Citrobacter freundii, isolated from anodic biofilm of a microbial fuel cell, Appl Biochem Biotechnol, 175, 1879, 10.1007/s12010-014-1418-9 Mehta-Kolte, 2012, Geothrix fermentans secretes two different redox-active compounds to utilize electron acceptors across a wide range of redox potentials, Appl Environ Microbiol, 78, 6987, 10.1128/AEM.01460-12 Salas, 2010, Reduction of graphene oxide via bacterial respiration, ACS Nano, 4, 4852, 10.1021/nn101081t Shaw, 2020, Extracellular electron transfer-dependent anaerobic oxidation of ammonium by anammox bacteria, Nat Commun, 11, 2058, 10.1038/s41467-020-16016-y Kalathil, 2019, Bioinspired synthesis of reduced graphene oxide-wrapped geobacter sulfurreducens as a hybrid electrocatalyst for efficient oxygen evolution reaction, Chem Mater, 31, 3686, 10.1021/acs.chemmater.9b00394 Kurth, 2019, Anaerobic methanotrophic archaea of the ANME-2d clade feature lipid composition that differs from other ANME archaea, FEMS Microbiol Ecol, 95, 10.1093/femsec/fiz082 Berks, 1995, Enzymes and associated electron transport systems that catalyse the respiratory reduction of nitrogen oxides and oxyanions, Biochim Biophys Acta, 1232, 10.1016/0005-2728(95)00092-5 Chaumeil, 2019 Vaksmaa, 2017, Enrichment of anaerobic nitrate-dependent methanotrophic ‘Candidatus Methanoperedens nitroreducens’ archaea from an Italian paddy field soil, Appl Microbiol Biotechnol, 10.1007/s00253-017-8416-0 Ettwig, 2009, Enrichment and molecular detection of denitrifying methanotrophic bacteria of the NC10 phylum, Appl Environ Microbiol, 75, 3656, 10.1128/AEM.00067-09 de Graaf, 1996, Comparison of acetate turnover in methanogenic and sulfate-reducing sediments by radiolabeling and stable isotope labeling and by use of specific inhibitors: evidence for isotopic exchange, Appl Environ Microbiol, 62, 772, 10.1128/aem.62.3.772-777.1996 Finke, 2007, Acetate, lactate, propionate, and isobutyrate as electron donors for iron and sulfate reduction in Arctic marine sediments, Svalbard, FEMS Microbiol Ecol, 59, 10, 10.1111/j.1574-6941.2006.00214.x Zhuang, 2019, Significance of acetate as a microbial carbon and energy source in the water column of Gulf of Mexico: implications for marine carbon cycling, Global Biogeochem Cycles, 33, 223, 10.1029/2018GB006129 Speers, 2012, Electron donors supporting growth and electroactivity of Geobacter sulfurreducens anode biofilms, Appl Environ Microbiol, 78, 437, 10.1128/AEM.06782-11 Szeinbaum, 2017, Microbial manganese(III) reduction fuelled by anaerobic acetate oxidation, Environ Microbiol, 19, 3475, 10.1111/1462-2920.13829 Shi, 2012, Mtr extracellular electron-transfer pathways in Fe(III)-reducing or Fe(II)-oxidizing bacteria: a genomic perspective, Biochem Soc Trans, 40, 1261, 10.1042/BST20120098 Edwards, 2018, Structural modeling of an outer membrane electron conduit from a metal-reducing bacterium suggests electron transfer via periplasmic redox partners, J Biol Chem, 293, 8103, 10.1074/jbc.RA118.001850 Hayat, 2012, BOCTOPUS: improved topology prediction of transmembrane beta barrel proteins, Bioinformatics, 28, 516, 10.1093/bioinformatics/btr710 Gralnick, 2006, Extracellular respiration of dimethyl sulfoxide by Shewanella oneidensis strain MR-1, Proc Natl Acad Sci U S A, 103, 4469, 10.1073/pnas.0505959103 Armenteros, 2019, SignalP 5.0 improves signal peptide predictions using deep neural networks, Nat Biotechnol, 37, 420, 10.1038/s41587-019-0036-z Krogh, 2001, Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes, J Mol Biol, 305, 567, 10.1006/jmbi.2000.4315 Holmes, 2016, The electrically conductive pili of Geobacter species are a recently evolved feature for extracellular electron transfer, Microb Genom, 2 Ru, 2019, Assessing possible mechanisms of micrometer-scale electron transfer in heme-free geobacter sulfurreducens pili, J Phys Chem B, 123, 5035, 10.1021/acs.jpcb.9b01086 Tan, 2017, Expressing the geobacter metallireducens PilA in geobacter sulfurreducens yields pili with exceptional conductivity, mBio, 8, 10.1128/mBio.02203-16 Haroon, 2013, Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage, Nature, 500, 567, 10.1038/nature12375 Yang, 2020, Genomic and enzymatic evidence of acetogenesis by anaerobic methanotrophic archaea, Nat Commun, 11, 3941, 10.1038/s41467-020-17860-8 Ding, 2017, Decoupling of DAMO archaea from DAMO bacteria in a methane-driven microbial fuel cell, Water Res, 110, 112, 10.1016/j.watres.2016.12.006 McAnulty, 2017, Electricity from methane by reversing methanogenesis, Nat Commun, 8, 15419, 10.1038/ncomms15419 Reguera, 2018, Microbial nanowires and electroactive biofilms, FEMS Microbiol Ecol, 94, 10.1093/femsec/fiy086 Fortney, 2018, Stable isotope probing for microbial iron reduction in chocolate pots hot spring, yellowstone national park, Appl Environ Microbiol, 84, 10.1128/AEM.02894-17 Nauhaus, 2002, In vitro demonstration of anaerobic oxidation of methane coupled to sulphate reduction in sediment from a marine gas hydrate area, Environ Microbiol, 4, 296, 10.1046/j.1462-2920.2002.00299.x Coates, 1998, Recovery of humic-reducing bacteria from a diversity of environments, Appl Environ Microbiol, 64, 1504, 10.1128/AEM.64.4.1504-1509.1998 Lyautey, 2011, Electroactivity of phototrophic river biofilms and constitutive cultivable bacteria, Appl Environ Microbiol, 77, 5394, 10.1128/AEM.00500-11 Chakraborty, 2013, Neutrophilic, nitrate-dependent, Fe(II) oxidation by a Dechloromonas species, World J Microbiol Biotechnol, 29, 617, 10.1007/s11274-012-1217-9 Szeinbaum, 2019, Expression of extracellular multiheme cytochromes discovered in a betaproteobacterium during Mn(III) reduction, Preprint He, 2019, Extracellular electron transfer may Be an overlooked contribution to pelagic respiration in humic-rich freshwater lakes, mSphere, 4, 10.1128/mSphere.00436-18 Kan, 2011, Diverse bacterial groups are associated with corrosive lesions at a Granite Mountain Record Vault (GMRV), J Appl Microbiol, 111, 329, 10.1111/j.1365-2672.2011.05055.x Uria, 2017, Electrochemical performance and microbial community profiles in microbial fuel cells in relation to electron transfer mechanisms, BMC Microbiol, 17, 10.1186/s12866-017-1115-2 Engel, 2019, Long-term behavior of defined mixed cultures of geobacter sulfurreducens and Shewanella oneidensis in bioelectrochemical systems, Front Bioeng Biotechnol, 7, 60, 10.3389/fbioe.2019.00060 Nevin, 2008, Power output and columbic efficiencies from biofilms of Geobacter sulfurreducens comparable to mixed community microbial fuel cells, Environ Microbiol, 10, 2505, 10.1111/j.1462-2920.2008.01675.x Nurk, 2017, metaSPAdes: a new versatile metagenomic assembler, Genome Res, 27, 824, 10.1101/gr.213959.116 Li, 2010, Fast and accurate long-read alignment with Burrows-Wheeler transform, Bioinformatics, 26, 589, 10.1093/bioinformatics/btp698 Li, 2009, The sequence alignment/map format and SAMtools, Bioinformatics, 25, 2078, 10.1093/bioinformatics/btp352 Graham, 2017, BinSanity: unsupervised clustering of environmental microbial assemblies using coverage and affinity propagation, PeerJ, 5, 10.7717/peerj.3035 Wu, 2014, MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm, Microbiome, 2, 26, 10.1186/2049-2618-2-26 Kang, 2015, MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities, PeerJ, 3 Sieber, 2018, Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy, Nat Microbiol, 3, 836, 10.1038/s41564-018-0171-1 Parks, 2018, A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life, Nat Biotechnol, 10.1038/nbt.4229 Parks, 2015, CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes, Genome Res, 25, 1043, 10.1101/gr.186072.114 Seemann, 2014, Prokka: rapid prokaryotic genome annotation, Bioinformatics, 30, 2068, 10.1093/bioinformatics/btu153 Huerta-Cepas, 2019, eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses, Nucleic Acids Res, 47, D309, 10.1093/nar/gky1085 Huerta-Cepas, 2017, Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper, Mol Biol Evol, 34, 2115, 10.1093/molbev/msx148 Cai, 2019, Acetate production from anaerobic oxidation of methane via intracellular storage compounds, Environ Sci Technol, 10.1021/acs.est.9b00077 Huang, 2015, Nitrogen removal characteristics of a newly isolated indigenous aerobic denitrifier from oligotrophic drinking water reservoir, Zoogloea sp. N299, Int J Mol Sci, 16, 10038, 10.3390/ijms160510038