Knittel K, Boetius A. Anaerobic oxidation of methane: progress with an unknown process. Annu Rev Microbiol. 2009;63:311–34.
Google Scholar
Reeburgh WS. Oceanic methane biogeochemistry. Chem Rev. 2007;107:486–513.
Google Scholar
Hatzenpichler R, Connon SA, Goudeau D, Malmstrom RR, Woyke T, Orphan VJ. Visualizing in situ translational activity for identifying and sorting slow-growing archaeal−bacterial consortia. Proc Natl Acad Sci USA. 2016;113:E4069–E4078.
Google Scholar
Skennerton CT, Chourey K, Iyer R, Hettich RL, Tyson GW, Orphan VJ. Methane-fueled syntrophy through extracellular electron transfer: uncovering the genomic traits conserved within diverse bacterial partners of anaerobic methanotrophic archaea. mBio. 2017;8:e00530–e00517.
Google Scholar
Orphan VJ, House CH, Hinrichs K-U, McKeegan KD, DeLong EF. Multiple archaeal groups mediate methane oxidation in anoxic cold seep sediments. Proc Natl Acad Sci USA. 2002;99:7663–8.
Google Scholar
Wegener G, Krukenberg V, Ruff SE, Kellermann MY, Knittel K. Metabolic capabilities of microorganisms involved in and associated with the anaerobic oxidation of methane. Front Microbiol. 2016;7:869.
Google Scholar
Metcalfe KS, Murali R, Mullin SW, Connon SA, Orphan VJ. Experimentally-validated correlation analysis reveals new anaerobic methane oxidation partnerships with consortium-level heterogeneity in diazotrophy. ISME J. 2020;15:1–20.
Krukenberg V, Riedel D, Gruber Vodicka HR, Buttigieg PL, Tegetmeyer HE, Boetius A, et al. Gene expression and ultrastructure of meso- and thermophilic methanotrophic consortia. Environ Microbiol. 2018;20:1651–6.
Milucka J, Ferdelman TG, Polerecky L, Franzke D, Wegener G, Schmid M, et al. Zero-valent sulphur is a key intermediate in marine methane oxidation. Nature. 2012;491:541–6.
Google Scholar
Schreiber L, Holler T, Knittel K, Meyerdierks A, Amann R. Identification of the dominant sulfate-reducing bacterial partner of anaerobic methanotrophs of the ANME-2 clade. Environ Microbiol. 2010;12:2327–40.
Google Scholar
Yu H, Susanti D, McGlynn SE, Skennerton CT, Chourey K, Iyer R, et al. Comparative genomics and proteomic analysis of assimilatory sulfate reduction pathways in anaerobic methanotrophic archaea. Front Microbiol. 2018;9:2917.
Scheller S, Yu H, Chadwick GL, McGlynn SE, Orphan VJ. Artificial electron acceptors decouple archaeal methane oxidation from sulfate reduction. Science. 2016;351:703–7.
Google Scholar
Wegener G, Krukenberg V, Riedel D, Tegetmeyer HE, Boetius A. Intercellular wiring enables electron transfer between methanotrophic archaea and bacteria. Nature. 2015;526:587–90.
Google Scholar
McGlynn SE, Chadwick GL, Kempes CP, Orphan VJ. Single cell activity reveals direct electron transfer in methanotrophic consortia. Nature. 2015;526:531–5.
Google Scholar
Liu Y, Beer LL, Whitman WB. Sulfur metabolism in archaea reveals novel processes. Environ Microbiol. 2012;14:2632–44.
Google Scholar
Perona JJ, Rauch BJ, Driggers CM. Sulfur assimilation and trafficking in methanogens. In: Rampelotto PH, editor. Molecular Mechanisms of Microbial Evolution. Cham: Springer International Publishing; 2018. p. 371–408.
White RH, Allen KD, Wegener G. Identification of a redox active thioquinoxalinol sulfate compound produced by an anaerobic methane-oxidizing microbial consortium. ACS Omega. 2019;4:22613–22.
Cline JD. Spectrophotometric determination of hydrogen sulfide in natural waters. Limnol Oceanogr. 1969;14:454–8.
Google Scholar
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7:335–6.
Google Scholar
Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26:2460–1.
Google Scholar
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41:D590–6.
Google Scholar
Mason OU, Case DH, Naehr TH, Lee RW, Thomas RB, Bailey JV, et al. Comparison of archaeal and bacterial diversity in methane seep carbonate nodules and host sediments, Eel River Basin and Hydrate Ridge, USA. Microb Ecol. 2015;70:766–84.
Google Scholar
Laczny CC, Sternal T, Plugaru V, Gawron P, Atashpendar A, Margossian HH, et al. VizBin – an application for reference-independent visualization and human-augmented binning of metagenomic data. Microbiome. 2015;3:1.
Google Scholar
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25:1043–55.
Google Scholar
Hyatt D, Chen G-L, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform. 2010;11:119.
Google Scholar
Chen I-MA, Chu K, Palaniappan K, Pillay M, Ratner A, Huang J, et al. IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes. Nucleic Acids Res. 2019;47:D666–D677.
Google Scholar
Agarwala R, Barrett T, Beck J, Benson DA, Bollin C, Bolton E, et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2018;46:D8–D13.
Google Scholar
Saier MH, Reddy VS, Tsu BV, Ahmed MS, Li C, Moreno-Hagelsieb G. The Transporter Classification Database (TCDB): recent advances. Nucleic Acids Res. 2016;44:D372–D379.
Google Scholar
Li H, Durbin R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics. 2009;25:1754–60.
Google Scholar
Knittel K, Losekann T, Boetius A, Kort R, Amann R. Diversity and distribution of methanotrophic archaea at cold seeps. Appl Environ Microbiol. 2005;71:467–79.
Google Scholar
Manz W, Eisenbrecher M, Neu TR, Szewzyk U. Abundance and spatial organization of Gram-negative sulfate-reducing bacteria in activated sludge investigated by in situ probing with specific 16S rRNA targeted oligonucleotides. FEMS Microbiol Ecol. 1998;25:43–61.
Google Scholar
Polerecky L, Adam B, Milucka J, Musat N, Vagner T, Kuypers MMM. Look@NanoSIMS – a tool for the analysis of nanoSIMS data in environmental microbiology. Environ Microbiol. 2012;14:1009–23.
Google Scholar
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–20.
Google Scholar
Kopylova E, Noe L, Touzet H. SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics. 2012;28:3211–7.
Google Scholar
Bray NL, Pimentel H, Melsted P, Pachter L. Near-optimal probabilistic RNA-seq quantification. Nat Biotechnol. 2016;34:525–7.
Google Scholar
Pimentel H, Bray NL, Puente S, Melsted P, Pachter L. Differential analysis of RNA-seq incorporating quantification uncertainty. Nat Methods. 2017;14:687–90.
Google Scholar
McGee WA, Pimentel H, Pachter L, Wu JY. Compositional Data Analysis is necessary for simulating and analyzing RNA-Seq data. bioRxiv 2019;564955.
Rocha DJP, Santos CS, Pacheco LGC. Bacterial reference genes for gene expression studies by RT-qPCR: survey and analysis. Antonie van Leeuwenhoek. 2015;108:685–93.
Google Scholar
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol. 2011;29:644–52.
Google Scholar
Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2015;12:59–60.
Google Scholar
Rinke C, Chuvochina M, Mussig AJ, Chaumeil P-A, Waite DW, Whitman WB, et al. A rank-normalized archaeal taxonomy based on genome phylogeny resolves widespread incomplete and uneven classifications. bioRxiv. 2020. https://doi.org/10.1101/2020.03.01.972265.
Orphan VJ, Turk KA, Green AM, House CH. Patterns of 15N assimilation and growth of methanotrophic ANME-2 archaea and sulfate-reducing bacteria within structured syntrophic consortia revealed by FISH-SIMS. Environ Microbiol. 2009;11:1777–91.
Google Scholar
Girguis PR, Cozen AE, DeLong EF. Growth and population dynamics of anaerobic methane-oxidizing archaea and sulfate-reducing bacteria in a continuous-flow bioreactor. Appl Environ Microbiol. 2005;71:3725–33.
Google Scholar
Nauhaus K, Albrecht M, Elvert M, Boetius A, Widdel F. In vitro cell growth of marine archaeal-bacterial consortia during anaerobic oxidation of methane with sulfate. Environ Microbiol. 2007;9:187–96.
Google Scholar
Meulepas RJW, Jagersma CG, Khadem AF, Buisman CJN, Stams AJM, Lens PNL. Effect of environmental conditions on sulfate reduction with methane as electron donor by an Eckernförde Bay enrichment. Environ Sci Technol. 2009;43:6553–9.
Google Scholar
McGlynn SE. Energy metabolism during anaerobic methane oxidation in ANME archaea. Microbes Environ. 2017;32:5–13.
Google Scholar
Wang F-P, Zhang Y, Chen Y, He Y, Qi J, Hinrichs K-U, et al. Methanotrophic archaea possessing diverging methane-oxidizing and electron-transporting pathways. ISME J. 2014;8:1069–78.
Google Scholar
Meyerdierks A, Kube M, Kostadinov I, Teeling H, Glöckner FO, Reinhardt R, et al. Metagenome and mRNA expression analyses of anaerobic methanotrophic archaea of the ANME-1 group. Environ Microbiol. 2010;12:422–39.
Google Scholar
Cai C, Leu AO, Xie G-J, Guo J, Feng Y, Zhao J-X, et al. A methanotrophic archaeon couples anaerobic oxidation of methane to Fe(III) reduction. ISME J. 2018;1:285.
Leu AO, Cai C, McIlroy SJ, Southam G, Orphan VJ, Yuan Z, et al. Anaerobic methane oxidation coupled to manganese reduction by members of the Methanoperedenaceae. ISME J. 2020;14:1030–41.
Google Scholar
Yanagawa K, Sunamura M, Lever MA, Morono Y, Hiruta A, Ishizaki O, et al. Niche separation of methanotrophic archaea (ANME-1 and-2) in methane-seep sediments of the eastern Japan Sea offshore Joetsu. Geomicrobiol J. 2011;28:118–29.
Google Scholar
Biddle JF, Cardman Z, Mendlovitz H, Albert DB, Lloyd KG, Boetius A, et al. Anaerobic oxidation of methane at different temperature regimes in Guaymas Basin hydrothermal sediments. ISME J. 2012;6:1018–31.
Google Scholar
Holler T, Widdel F, Knittel K, Amann R, Kellermann MY, Hinrichs K-U, et al. Thermophilic anaerobic oxidation of methane by marine microbial consortia. ISME J. 2011;5:1946–56.
Google Scholar
Roalkvam I, Jørgensen SL, Chen Y, Stokke R, Dahle H, Hocking WP, et al. New insight into stratification of anaerobic methanotrophs in cold seep sediments. FEMS Microbiol Ecol. 2011;78:233–43.
Google Scholar
Timmers PHA, Widjaja-Greefkes HCA, Ramiro-Garcia J, Plugge CM, Stams AJM. Growth and activity of ANME clades with different sulfate and sulfide concentrations in the presence of methane. Front Microbiol. 2015;6:988.
Nauhaus K, Treude T, Boetius A, Krüger M. Environmental regulation of the anaerobic oxidation of methane: a comparison of ANME-I and ANME-II communities. Environ Microbiol. 2005;7:98–106.
Google Scholar
Green-Saxena A, Dekas AE, Dalleska NF, Orphan VJ. Nitrate-based niche differentiation by distinct sulfate-reducing bacteria involved in the anaerobic oxidation of methane. ISME J. 2014;8:150–63.
Google Scholar
Wegener G, Niemann H, Elvert M, Hinrichs K-U, Boetius A. Assimilation of methane and inorganic carbon by microbial communities mediating the anaerobic oxidation of methane. Environ Microbiol. 2008;10:2287–98.
Google Scholar
Scherer P, Lippert H, Wolff G. Composition of the major elements and trace elements of 10 methanogenic bacteria determined by inductively coupled plasma emission spectrometry. Biol Trace Elem Res. 1983;5:149–63.
Google Scholar
Marsili E, Baron DB, Shikhare ID, Coursolle D, Gralnick JA, Bond DR. Shewanella secretes flavins that mediate extracellular electron transfer. Proc Natl Acad Sci USA. 2008;105:3968–73.
Google Scholar
Kotloski NJ, Gralnick JA. Flavin electron shuttles dominate extracellular electron transfer by Shewanella oneidensis. mBio 2013;4:e00553–12.
Google Scholar
Mevers E, Su L, Pishchany G, Baruch M, Cornejo J, Hobert E, et al. An elusive electron shuttle from a facultative anaerobe. eLife. 2019;8:e48054.
Google Scholar
Anderson AG, Iii FBC, Odom JM, Weimer PJ. Anthraquinones as inhibitors of sulfide production from sulfate-reducing bacteria. 1991.
Wang X, Cheng X, Ren Y, Xu G, Tang J. Humic analog AQDS can act as a selective inhibitor to enable anoxygenic photosynthetic bacteria to outcompete sulfate-reducing bacteria under microaerobic conditions. J Chem Technol Biotechnol. 2016;91:2103–10.
Google Scholar
Lee YH, Pavlostathis SG. Decolorization and toxicity of reactive anthraquinone textile dyes under methanogenic conditions. Water Res. 2004;38:1838–52.
Google Scholar
Wu Y-W, Ouyang J, Xiao X-H, Gao W-Y, Liu Y. Antimicrobial properties and toxicity of anthraquinones by microcalorimetric bioassay. Chin J Chem. 2006;24:45–50.
Google Scholar
Novotný Č, Dias N, Kapanen A, Malachová K, Vándrovcová M, Itävaara M, et al. Comparative use of bacterial, algal and protozoan tests to study toxicity of azo- and anthraquinone dyes. Chemosphere. 2006;63:1436–42.
Google Scholar
Shyu JBH, Lies DP, Newman DK. Protective role of tolC in efflux of the electron shuttle anthraquinone-2,6-disulfonate. J Bacteriol. 2002;184:1806–10.
Google Scholar
Lovley DR, Coates JD, Blunt-Harris EL, Phillips EJP, Woodward JC. Humic substances as electron acceptors for microbial respiration. Nature. 1996;382:445–8.
Google Scholar
Newman DK, Kolter R. A role for excreted quinones in extracellular electron transfer. Nature. 2000;405:94–7.
Google Scholar
Holmes DE, Ueki T, Tang H-Y, Zhou J, Smith JA, Chaput G, et al. A membrane-bound cytochrome enables Methanosarcina acetivorans to conserve energy from extracellular electron transfer. mBio. 2019;10:e00789–19.
Google Scholar
Neuberger A, Du D, Luisi BF. Structure and mechanism of bacterial tripartite efflux pumps. Res Microbiol. 2018;169:401–13.
Google Scholar
Crow A, Greene NP, Kaplan E, Koronakis V. Structure and mechanotransmission mechanism of the MacB ABC transporter superfamily. Proc Natl Acad Sci USA. 2017;114:12572–7.
Google Scholar
Jiménez-Otero F, Chan CH, Bond DR. Identification of different putative outer membrane electron conduits necessary for Fe (III) citrate, Fe (III) oxide, Mn (IV) oxide, or electrode reduction by Geobacter sulfurreducens. J Bacteriol. 2018;200:3061.
Google Scholar
Plugge CM, Scholten JCM, Culley DE, Nie L, Brockman FJ, Zhang W. Global transcriptomics analysis of the Desulfovibrio vulgaris change from syntrophic growth with Methanosarcina barkeri to sulfidogenic metabolism. Microbiology. 2010;156:2746–56.
Google Scholar
Walker CB, He Z, Yang ZK, Ringbauer JAJ, He Q, Zhou J, et al. The electron transfer system of syntrophically grown Desulfovibrio vulgaris. J Bacteriol. 2009;191:5793–801.
Google Scholar
Wenter R, Hütz K, Dibbern D, Li T, Reisinger V, Plöscher M, et al. Expression-based identification of genetic determinants of the bacterial symbiosis ‘Chlorochromatium aggregatum’. Environ Microbiol. 2010;12:2259–76.
Google Scholar
Source: Ecology - nature.com