Anaerobic oxidation of ethane by archaea from a marine hydrocarbon seep.
Anaerobiosis
Aquatic Organisms
/ metabolism
Archaea
/ classification
Deltaproteobacteria
/ metabolism
Ethane
/ chemistry
Gases
/ chemistry
Gulf of Mexico
Methane
/ biosynthesis
Oxidation-Reduction
Oxidoreductases
/ genetics
Phylogeny
RNA, Ribosomal, 16S
/ genetics
Sulfates
/ metabolism
Sulfides
/ metabolism
Journal
Nature
ISSN: 1476-4687
Titre abrégé: Nature
Pays: England
ID NLM: 0410462
Informations de publication
Date de publication:
04 2019
04 2019
Historique:
received:
19
10
2018
accepted:
27
02
2019
pubmed:
29
3
2019
medline:
20
8
2019
entrez:
29
3
2019
Statut:
ppublish
Résumé
Ethane is the second most abundant component of natural gas in addition to methane, and-similar to methane-is chemically unreactive. The biological consumption of ethane under anoxic conditions was suggested by geochemical profiles at marine hydrocarbon seeps
Identifiants
pubmed: 30918404
doi: 10.1038/s41586-019-1063-0
pii: 10.1038/s41586-019-1063-0
doi:
Substances chimiques
Gases
0
RNA, Ribosomal, 16S
0
Sulfates
0
Sulfides
0
Oxidoreductases
EC 1.-
methyl coenzyme M reductase
EC 2.8.4.1
Ethane
L99N5N533T
Methane
OP0UW79H66
Types de publication
Journal Article
Langues
eng
Pagination
108-111Commentaires et corrections
Type : CommentIn
Références
Stadnitskaia, A. et al. Molecular and carbon isotopic variability of hydrocarbon gases from mud volcanoes in the Gulf of Cadiz, NE Atlantic. Mar. Pet. Geol. 23, 281–296 (2006).
Mastalerz, V., de Lange, G. J. & Dahlmann, A. Differential aerobic and anaerobic oxidation of hydrocarbon gases discharged at mud volcanoes in the Nile deep-sea fan. Geochim. Cosmochim. Acta 73, 3849–3863 (2009).
Sassen, R. et al. Free hydrocarbon gas, gas hydrate, and authigenic minerals in chemosynthetic communities of the northern Gulf of Mexico continental slope: relation to microbial processes. Chem. Geol. 205, 195–217 (2004).
Adams, M. M., Hoarfrost, A. L., Bose, A., Joye, S. B. & Girguis, P. R. Anaerobic oxidation of short-chain alkanes in hydrothermal sediments: potential influences on sulfur cycling and microbial diversity. Front. Microbiol. 4, 110 (2013).
pubmed: 23717305
pmcid: 3653109
Bose, A., Rogers, D. R., Adams, M. M., Joye, S. B. & Girguis, P. R. Geomicrobiological linkages between short-chain alkane consumption and sulfate reduction rates in seep sediments. Front. Microbiol. 4, 386 (2013).
pubmed: 24376442
pmcid: 3860272
Kniemeyer, O. et al. Anaerobic oxidation of short-chain hydrocarbons by marine sulphate-reducing bacteria. Nature 449, 898–901 (2007).
pubmed: 17882164
Suarez-Zuluaga, D. A., Weijma, J., Timmers, P. H. A. & Buisman, C. J. N. High rates of anaerobic oxidation of methane, ethane and propane coupled to thiosulphate reduction. Environ. Sci. Pollut. Res. Int. 22, 3697–3704 (2015).
pubmed: 25256585
Singh, R., Guzman, M. S. & Bose, A. Anaerobic oxidation of ethane, propane, and butane by marine microbes: a mini review. Front. Microbiol. 8, 2056 (2017).
pubmed: 29109712
pmcid: 5660070
Laso-Pérez, R. et al. Thermophilic archaea activate butane via alkyl-coenzyme M formation. Nature 539, 396–401 (2016).
pubmed: 27749816
Dombrowski, N., Seitz, K. W., Teske, A. P. & Baker, B. J. Genomic insights into potential interdependencies in microbial hydrocarbon and nutrient cycling in hydrothermal sediments. Microbiome 5, 106 (2017).
pubmed: 28835260
pmcid: 5569505
Evans, P. N. et al. Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics. Science 350, 434–438 (2015).
pubmed: 26494757
McKay, L. et al. Thermal and geochemical influences on microbial biogeography in the hydrothermal sediments of Guaymas Basin, Gulf of California. Environ. Microbiol. Rep. 8, 150–161 (2016).
pubmed: 26637109
Bowles, M. W., Samarkin, V. A., Bowles, K. M. & Joye, S. B. Weak coupling between sulfate reduction and the anaerobic oxidation of methane in methane-rich seafloor sediments during ex situ incubation. Geochim. Cosmochim. Acta 75, 500–519 (2011).
Boetius, A. et al. A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature 407, 623–626 (2000).
pubmed: 11034209
Knittel, K. & Boetius, A. Anaerobic oxidation of methane: progress with an unknown process. Annu. Rev. Microbiol. 63, 311–334 (2009).
pubmed: 19575572
Milucka, J. et al. Zero-valent sulphur is a key intermediate in marine methane oxidation. Nature 491, 541–546 (2012).
pubmed: 23135396
Jaekel, U. et al. Anaerobic degradation of propane and butane by sulfate-reducing bacteria enriched from marine hydrocarbon cold seeps. ISME J. 7, 885–895 (2013).
pubmed: 23254512
Savage, K. N. et al. Biodegradation of low-molecular-weight alkanes under mesophilic, sulfate-reducing conditions: metabolic intermediates and community patterns. FEMS Microbiol. Ecol. 72, 485–495 (2010).
pubmed: 20402777
McGlynn, S. E., Chadwick, G. L., Kempes, C. P. & Orphan, V. J. Single cell activity reveals direct electron transfer in methanotrophic consortia. Nature 526, 531–535 (2015).
pubmed: 26375009
Wegener, G., Krukenberg, V., Riedel, D., Tegetmeyer, H. E. & Boetius, A. Intercellular wiring enables electron transfer between methanotrophic archaea and bacteria. Nature 526, 587–590 (2015).
pubmed: 26490622
Scheller, S., Goenrich, M., Boecher, R., Thauer, R. K. & Jaun, B. The key nickel enzyme of methanogenesis catalyses the anaerobic oxidation of methane. Nature 465, 606–608 (2010).
pubmed: 20520712
Thauer, R. K. Anaerobic oxidation of methane with sulfate: on the reversibility of the reactions that are catalyzed by enzymes also involved in methanogenesis from CO
pubmed: 21489863
Callaghan, A. V. Metabolomic investigations of anaerobic hydrocarbon-impacted environments. Curr. Opin. Biotechnol. 24, 506–515 (2013).
pubmed: 22999828
Milkov, A. V. & Etiope, G. Revised genetic diagrams for natural gases based on a global dataset of >20,000 samples. Org. Geochem. 125, 109–120 (2018).
Nauhaus, K., Boetius, A., Krüger, M. & Widdel, F. In vitro demonstration of anaerobic oxidation of methane coupled to sulphate reduction in sediment from a marine gas hydrate area. Environ. Microbiol. 4, 296–305 (2002).
pubmed: 12080959
Makarova, K. S., Yutin, N., Bell, S. D. & Koonin, E. V. Evolution of diverse cell division and vesicle formation systems in Archaea. Nat. Rev. Microbiol. 8, 731–741 (2010).
pubmed: 20818414
pmcid: 3293450
Thauer, R. K. Biochemistry of methanogenesis: a tribute to Marjory Stephenson. 1998 Marjory Stephenson Prize Lecture. Microbiology 144, 2377–2406 (1998).
pubmed: 9782487
Scheller, S., Goenrich, M., Thauer, R. K. & Jaun, B. Methyl-coenzyme M reductase from methanogenic archaea: isotope effects on label exchange and ethane formation with the homologous substrate ethyl-coenzyme M. J. Am. Chem. Soc. 135, 14985–14995 (2013).
pubmed: 24003767
Ermler, U., Grabarse, W., Shima, S., Goubeaud, M. & Thauer, R. K. Crystal structure of methyl-coenzyme M reductase: the key enzyme of biological methane formation. Science 278, 1457–1462 (1997).
pubmed: 9367957
Adam, P. S., Borrel, G. & Gribaldo, S. Evolutionary history of carbon monoxide dehydrogenase/acetyl-CoA synthase, one of the oldest enzymatic complexes. Proc. Natl Acad. Sci. USA 115, E1166–E1173 (2018).
pubmed: 29358391
Widdel, F. in Handbook of Hydrocarbon and Lipid Microbiology Ch. 298 (ed. Timmis, K. N.) 3787–3798 (Springer, Berlin Heidelberg, 2010).
Laso-Pérez, R., Krukenberg, V., Musat, F. & Wegener, G. Establishing anaerobic hydrocarbon-degrading enrichment cultures of microorganisms under strictly anoxic conditions. Nat. Protoc. 13, 1310–1330 (2018).
pubmed: 29773905
Cord-Ruwisch, R. A quick method for the determination of dissolved and precipitated sulfides in cultures of sulfate-reducing bacteria. J. Microbiol. Methods 4, 33–36 (1985).
Jaekel, U., Vogt, C., Fischer, A., Richnow, H. H. & Musat, F. Carbon and hydrogen stable isotope fractionation associated with the anaerobic degradation of propane and butane by marine sulfate-reducing bacteria. Environ. Microbiol. 16, 130–140 (2014).
pubmed: 24028539
Pruesse, E., Peplies, J. & Glöckner, F. O. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28, 1823–1829 (2012).
pubmed: 22556368
pmcid: 22556368
Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 41, D590–D596 (2013).
doi: 10.1093/nar/gks1219
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).
pubmed: 4103590
pmcid: 4103590
Nurk, S., Meleshko, D., Korobeynikov, A. & Pevzner, P. A. metaSPAdes: a new versatile metagenomic assembler. Genome Res. 27, 824–834 (2017).
pubmed: 28298430
pmcid: 5411777
Mikheenko, A., Saveliev, V. & Gurevich, A. MetaQUAST: evaluation of metagenome assemblies. Bioinformatics 32, 1088–1090 (2016).
pubmed: 26614127
Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797 (2004).
pubmed: 15034147
pmcid: 15034147
Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014).
doi: 10.1093/bioinformatics/btu033
Wu, Y. W., Simmons, B. A. & Singer, S. W. MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics 32, 605–607 (2016).
pubmed: 26515820
Lagesen, K. et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35, 3100–3108 (2007).
pubmed: 17452365
pmcid: 1888812
Westram, R. et al. in Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches (ed. de Bruijn, F. J.) 399–406 (Wiley-Blackwell, New Jersey, 2011).
Cao, M. D. et al. Scaffolding and completing genome assemblies in real-time with nanopore sequencing. Nat. Commun. 8, 14515 (2017).
pubmed: 28218240
pmcid: 5321748
Walker, B. J. et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE 9, e112963 (2014).
pubmed: 25409509
pmcid: 4237348
Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25, 1043–1055 (2015).
pubmed: 25977477
pmcid: 4484387
Wu, M. & Scott, A. J. Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. Bioinformatics 28, 1033–1034 (2012).
pubmed: 22332237
Overbeek, R. et al. The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res. 42, D206–D214 (2014).
pubmed: 24293654
Kanehisa, M., Furumichi, M., Tanabe, M., Sato, Y. & Morishima, K. KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res. 45, D353–D361 (2017).
pubmed: 27899662
pmcid: 27899662
Finn, R. D. et al. The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res. 44, D279–D285 (2016).
pubmed: 26673716
Huerta-Cepas, J. et al. Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper. Mol. Biol. Evol. 34, 2115–2122 (2017).
pubmed: 28460117
pmcid: 5850834
Lowe, T. M. & Chan, P. P. tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res. 44, W54–W57 (2016).
pubmed: 27174935
pmcid: 4987944
Capella-Gutiérrez, S., Silla-Martínez, J. M. & Gabaldón, T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972–1973 (2009).
pubmed: 19505945
pmcid: 2712344
Ludwig, W. et al. ARB: a software environment for sequence data. Nucleic Acids Res. 32, 1363–1371 (2004).
pubmed: 14985472
pmcid: 390282
Pruesse, E. et al. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 35, 7188–7196 (2007).
pubmed: 17947321
pmcid: 2175337
Maidak, B. L. et al. The RDP (Ribosomal Database Project) continues. Nucleic Acids Res. 28, 173–174 (2000).
pubmed: 10592216
pmcid: 102428
Pernthaler, A., Pernthaler, J. & Amann, R. Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria. Appl. Environ. Microbiol. 68, 3094–3101 (2002).
pubmed: 12039771
pmcid: 123953
Pernthaler, A. & Pernthaler, J. Fluorescence in situ hybridization for the identification of environmental microbes. Methods Mol. Biol. 353, 153–164 (2007).
pubmed: 17332640
Yang, C., Kublik, A., Weidauer, C., Seiwert, B. & Adrian, L. Reductive dehalogenation of oligocyclic phenolic bromoaromatics by Dehalococcoides mccartyi strain CBDB1. Environ. Sci. Technol. 49, 8497–8505 (2015).
pubmed: 26101958
Vizcaíno, J. A. et al. 2016 update of the PRIDE database and its related tools. Nucleic Acids Res. 44, D447–D456 (2016).
pubmed: 26527722
Jariwala, F. B., Wood, R. E., Nishshanka, U. & Attygalle, A. B. Formation of the bisulfite anion (HSO
pubmed: 22689630
Waterhouse, A. et al. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 46, W296–W303 (2018).
pubmed: 29788355
pmcid: 6030848
Benkert, P., Tosatto, S. C. E. & Schomburg, D. QMEAN: a comprehensive scoring function for model quality assessment. Proteins 71, 261–277 (2008).
pubmed: 17932912
Stryhanyuk, H. et al. Calculation of single cell assimilation rates from SIP-NanoSIMS-derived isotope ratios: a comprehensive approach. Front. Microbiol. 9, 2342 (2018).
pubmed: 30337916
pmcid: 6178922
Polerecky, L. et al. Look@NanoSIMS—a tool for the analysis of nanoSIMS data in environmental microbiology. Environ. Microbiol. 14, 1009–1023 (2012).
pubmed: 22221878
Musat, N. et al. The effect of FISH and CARD–FISH on the isotopic composition of
pubmed: 24702905
Dowell, F. et al. Microbial communities in methane- and short chain alkane-rich hydrothermal sediments of Guaymas Basin. Front. Microbiol. 7, 17 (2016).
pubmed: 26858698
pmcid: 4731509
Welhan, J. A. & Lupton, J. E. Light hydrocarbon gases in Guaymas Basin hydrothermal fluids: thermogenic versus abiogenic origin. Bull. Am. Assoc. Petrol. Geol. 71, 215–223 (1987).
Orcutt, B. N. et al. Impact of natural oil and higher hydrocarbons on microbial diversity, distribution, and activity in Gulf of Mexico cold-seep sediments. Deep Sea Res. II Top. Stud. Oceanogr. 57, 2008–2021 (2010).
Pachiadaki, M. G., Kallionaki, A., Dählmann, A., De Lange, G. J. & Kormas, K. A. Diversity and spatial distribution of prokaryotic communities along a sediment vertical profile of a deep-sea mud volcano. Microb. Ecol. 62, 655–668 (2011).
pubmed: 21538105
Pape, T. et al. Gas hydrates in shallow deposits of the Amsterdam mud volcano, Anaximander Mountains, Northeastern Mediterranean Sea. Geo-Mar. Lett. 30, 187–206 (2010).
Heijs, S. K., Laverman, A. M., Forney, L. J., Hardoim, P. R. & van Elsas, J. D. Comparison of deep-sea sediment microbial communities in the Eastern Mediterranean. FEMS Microbiol. Ecol. 64, 362–377 (2008).
pubmed: 18422633
Egorov, A. V. & Ivanov, M. K. Hydrocarbon gases in sediments and mud breccia from the central and eastern part of the Mediterranean Ridge. Geo-Mar. Lett. 18, 127–138 (1998).
Robertson, A. H. F. et al. Collision-related break-up of a carbonate platform (Eratosthenes Seamount) and mud volcanism on the Mediterranean Ridge: preliminary synthesis and implications of tectonic results of ODP Leg 160 in the Eastern Mediterranean Sea. Geol. Soc. Spec. Publ. 131, 243–271 (1998).
Lloyd, K. G., Lapham, L. & Teske, A. An anaerobic methane-oxidizing community of ANME-1b archaea in hypersaline Gulf of Mexico sediments. Appl. Environ. Microbiol. 72, 7218–7230 (2006).
pubmed: 16980428
pmcid: 1636178
Brooks, J. M. et al. Association of gas hydrates and oil seepage in the Gulf of Mexico. Org. Geochem. 10, 221–234 (1986).
Maignien, L. et al. Anaerobic oxidation of methane in hypersaline cold seep sediments. FEMS Microbiol. Ecol. 83, 214–231 (2013).
pubmed: 22882187
Nuzzo, M. et al. Origin of light volatile hydrocarbon gases in mud volcano fluids, Gulf of Cadiz — evidence for multiple sources and transport mechanisms in active sedimentary wedges. Chem. Geol. 266, 350–363 (2009).
Roalkvam, I. et al. New insight into stratification of anaerobic methanotrophs in cold seep sediments. FEMS Microbiol. Ecol. 78, 233–243 (2011).
pubmed: 21676010
Vaular, E. N., Barth, T. & Haflidason, H. The geochemical characteristics of the hydrate-bound gases from the Nyegga pockmark field, Norwegian Sea. Org. Geochem. 41, 437–444 (2010).
Cruaud, P. et al. Comparative study of Guaymas Basin microbiomes: cold seeps vs. hydrothermal vents sediments. Front. Mar. Sci. 4, 417 (2017).
Simoneit, B. R. T., Lonsdale, P. F., Edmond, J. M. & Shanks, W. C. Deep-water hydrocarbon seeps in Guaymas Basin, Gulf of California. Appl. Geochem. 5, 41–49 (1990).
Case, D. H. et al. Methane seep carbonates host distinct, diverse, and dynamic microbial assemblages. MBio 6, e01348-15 (2015).
pubmed: 26695630
pmcid: 4701829
Milkov, A. V. et al. Co-existence of gas hydrate, free gas, and brine within the regional gas hydrate stability zone at Hydrate Ridge (Oregon margin): evidence from prolonged degassing of a pressurized core. Earth Planet. Sci. Lett. 222, 829–843 (2004).
Pop Ristova, P., Wenzhöfer, F., Ramette, A., Felden, J. & Boetius, A. Spatial scales of bacterial community diversity at cold seeps (Eastern Mediterranean Sea). ISME J. 9, 1306–1318 (2015).
pubmed: 25500510
Zaikova, E. et al. Microbial community dynamics in a seasonally anoxic fjord: Saanich Inlet, British Columbia. Environ. Microbiol. 12, 172–191 (2010).
pubmed: 19788414