In situ development of a methanotrophic microbiome in deep-sea sediments.
Journal
The ISME journal
ISSN: 1751-7370
Titre abrégé: ISME J
Pays: England
ID NLM: 101301086
Informations de publication
Date de publication:
01 2019
01 2019
Historique:
received:
13
02
2018
accepted:
04
08
2018
revised:
06
07
2018
pubmed:
30
8
2018
medline:
1
8
2019
entrez:
30
8
2018
Statut:
ppublish
Résumé
Emission of the greenhouse gas methane from the seabed is globally controlled by marine aerobic and anaerobic methanotrophs gaining energy via methane oxidation. However, the processes involved in the assembly and dynamics of methanotrophic populations in complex natural microbial communities remain unclear. Here we investigated the development of a methanotrophic microbiome following subsurface mud eruptions at Håkon Mosby mud volcano (1250 m water depth). Freshly erupted muds hosted deep-subsurface communities that were dominated by Bathyarchaeota, Atribacteria and Chloroflexi. Methanotrophy was initially limited to a thin surface layer of Methylococcales populations consuming methane aerobically. With increasing distance to the eruptive center, anaerobic methanotrophic archaea, sulfate-reducing Desulfobacterales and thiotrophic Beggiatoaceae developed, and their respective metabolic capabilities dominated the biogeochemical functions of the community. Microbial richness, evenness, and cell numbers of the entire microbial community increased up to tenfold within a few years downstream of the mud flow from the eruptive center. The increasing diversity was accompanied by an up to fourfold increase in sequence abundance of relevant metabolic genes of the anaerobic methanotrophic and thiotrophic guilds. The communities fundamentally changed in their structure and functions as reflected in the metagenome turnover with distance from the eruptive center, and this was reflected in the biogeochemical zonation across the mud volcano caldera. The observed functional succession provides a framework for the response time and recovery of complex methanotrophic communities after disturbances of the deep-sea bed.
Identifiants
pubmed: 30154496
doi: 10.1038/s41396-018-0263-1
pii: 10.1038/s41396-018-0263-1
pmc: PMC6298960
doi:
Substances chimiques
RNA, Ribosomal, 16S
0
Methane
OP0UW79H66
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Pagination
197-213Références
Reeburgh W. Oceanic methane biogeochemistry. Chem Rev. 2007;107:486–513.
pubmed: 17261072
doi: 10.1021/cr050362v
Ruff SE, Biddle JF, Teske AP, Knittel K, Boetius A, Ramette A. Global dispersion and local diversification of the methane seep microbiome. Proc Natl Acad Sci USA. 2015;112:4015–20.
pubmed: 25775520
doi: 10.1073/pnas.1421865112
pmcid: 4386351
Tavormina PL, Ussler W III, Orphan VJ. Planktonic and sediment-associated aerobic methanotrophs in two seep systems along the North American margin. Appl Environ Microbiol. 2008;74:3985–95.
pubmed: 18487407
pmcid: 2446507
doi: 10.1128/AEM.00069-08
Bessette S, Moalic Y, Gautey S, Lesongeur F, Godfroy A, Toffin L. Relative abundance and diversity of bacterial methanotrophs at the oxic–anoxic interface of the Congo deep-sea fan. Front Microbiol. 2017;8:715.
pubmed: 28487684
pmcid: 5403828
doi: 10.3389/fmicb.2017.00715
Paul BG, Ding H, Bagby SC, Kellermann MY, Redmond MC, Andersen GL, et al. Methane-oxidizing bacteria shunt carbon to microbial mats at a marine hydrocarbon seep. Front Microbiol. 2017;8:186.
pubmed: 28289403
pmcid: 5326789
doi: 10.3389/fmicb.2017.00186
Knittel K, Boetius A. Anaerobic oxidation of methane: progress with an unknown process. Annu Rev Microbiol. 2009;63:311–34.
pubmed: 19575572
doi: 10.1146/annurev.micro.61.080706.093130
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.
pubmed: 12032340
doi: 10.1073/pnas.072210299
pmcid: 124316
Bhattarai S, Cassarini C, Gonzalez-Gil G, Egger M, Slomp CP, Zhang Y, et al. Anaerobic methane-oxidizing microbial community in a coastal marine sediment: anaerobic methanotrophy dominated by ANME-3. Microb Ecol. 2017;74:608–22.
pubmed: 28389729
doi: 10.1007/s00248-017-0978-y
Winkel M, Mitzscherling J, Overduin PP, Horn F, Winterfeld M, Rijkers R, et al. Anaerobic methanotrophic communities thrive in deep submarine permafrost. Sci Rep. 2018;8:1291.
pubmed: 29358665
pmcid: 5778128
doi: 10.1038/s41598-018-19505-9
Ruff SE, Kuhfuss H, Wegener G, Lott C, Ramette A, Wiedling J, et al. Methane seep in shallow-water permeable sediment harbors high diversity of anaerobic methanotrophic communities, Elba, Italy. Front Microbiol. 2016;7:374.
pubmed: 27065954
pmcid: 4814501
doi: 10.3389/fmicb.2016.00374
Wasmund K, Kurtböke DI, Burns KA, Bourne DG. Microbial diversity in sediments associated with a shallow methane seep in the tropical Timor Sea of Australia reveals a novel aerobic methanotroph diversity. FEMS Microbiol Ecol. 2009;68:142–51.
pubmed: 19573197
doi: 10.1111/j.1574-6941.2009.00667.x
Boetius A, Wenzhöfer F. Seafloor oxygen consumption fuelled by methane from cold seeps. Nat Geosci. 2013;6:725–34.
doi: 10.1038/ngeo1926
Joye SB, Bowles MW, Samarkin VA, Hunter KS, Niemann H. Biogeochemical signatures and microbial activity of different cold-seep habitats along the Gulf of Mexico deep slope. Deep Res Part II Top Stud Oceanogr. 2010;57:1990–2001.
doi: 10.1016/j.dsr2.2010.06.001
Niemann H, Lösekann T, de Beer D, Elvert M, Nadalig T, Knittel K, et al. Novel microbial communities of the Haakon Mosby mud volcano and their role as a methane sink. Nature. 2006;443:854–8.
pubmed: 17051217
doi: 10.1038/nature05227
Felden J, Wenzhöfer F, Feseker T, Boetius A. Transport and consumption of oxygen and methane in different habitats of the Håkon Mosby Mud Volcano (HMMV). Limnol Oceanogr. 2010;55:2366–80.
doi: 10.4319/lo.2010.55.6.2366
Andreassen K, Hubbard A, Winsborrow M, Patton H, Vadakkepuliyambatta S, Plaza-Faverola A, et al. Massive blow-out craters formed by hydrate-controlled methane expulsion from the Arctic seafloor. Science (80-). 2017;356:948–53.
doi: 10.1126/science.aal4500
Dickens GR. Rethinking the global carbon cycle with a large, dynamic and microbially mediated gas hydrate capacitor. Earth Planet Sci Lett. 2003;213:169–83.
doi: 10.1016/S0012-821X(03)00325-X
Kessler JD, Valentine DL, Redmond MC, Du M, Chan EW, Mendes SD, et al. A persistent oxygen anomaly reveals the fate of spilled methane in the Deep Gulf of Mexico. Science (80-). 2011;331:312–5.
doi: 10.1126/science.1199697
Crespo-Medina M, Meile CD, Hunter KS, Diercks A-R, Asper VL, Orphan VJ, et al. The rise and fall of methanotrophy following a deepwater oil-well blowout. Nat Geosci. 2014;7:423–7.
doi: 10.1038/ngeo2156
Joye SB, Teske AP, Kostka JE. Microbial dynamics following the Macondo Oil Well blowout across Gulf of Mexico environments. Bioscience. 2014;64:766–77.
doi: 10.1093/biosci/biu121
Kopf AJ. Significance of mud volcanism. Rev Geophys. 2002;40:1005.
doi: 10.1029/2000RG000093
Milkov AV, Sassen R, Apanasovich TV, Dadashev FG. Global gas flux from mud volcanoes: a significant source of fossil methane in the atmosphere and the ocean. Geophys Res Lett. 2003;30:1037.
doi: 10.1029/2002GL016358
De Beer D, Sauter E, Niemann H, Kaul N, Foucher J-P, Witte U, et al. In situ fluxes and zonation of microbial activity in surface sediments of the Håkon Mosby mud volcano. Limnol Oceanogr. 2006;51:1315–31.
doi: 10.4319/lo.2006.51.3.1315
Felden J, Lichtschlag A, Wenzhöfer F, de Beer D, Feseker T, Pop Ristova P, et al. Limitations of microbial hydrocarbon degradation at the Amon mud volcano (Nile deep-sea fan). Biogeosciences. 2013;10:3269–83.
doi: 10.5194/bg-10-3269-2013
Feseker T, Boetius A, Wenzhöfer F, Blandin J, Olu K, Yoerger DR, et al. Eruption of a deep-sea mud volcano triggers rapid sediment movement. Nat Commun. 2014;5:5385.
pubmed: 25384354
doi: 10.1038/ncomms6385
Pickett STA. Space-for-time substitution as an alternative to long-term studies. In: Likens GE, editor. Long-term studies in ecology: approaches and alternatives. New York, NY: Springer; 1989 .
doi: 10.1007/978-1-4615-7358-6_5
Marcon Y. Georeferenced photomosaic of the Håkon Mosby mud volcano during Maria S. Merian cruise MSM16/2 (LOOME), link to GeoTIFF archive (32 GB). 2016. https://doi.org/10.1594/PANGAEA.864702
Milkov AV, Vogt PR, Crane K, Lein AY, Sassen R, Cherkashev GA. Geological, geochemical, and microbial processes at the hydrate-bearing Haakon Mosby mud volcano: a review. Chem Geol. 2004;205:347–66.
doi: 10.1016/j.chemgeo.2003.12.030
Vogt RP, Gardner J, Crane K. The Norwegian–Barents–Svalbard (NBS) continental margin: introducing a natural laboratory of mass wasting, hydrates, and ascent of sediment, pore water, and methane. Geo-Mar Lett. 1999;19:2–21.
doi: 10.1007/s003670050088
Foucher J-P, Dupré S, Scalabrin C, Feseker T, Harmegnies F, Nouzé H. Changes in seabed morphology, mud temperature and free gas venting at the Håkon Mosby mud volcano, offshore northern Norway, over the time period 2003-6. Geo-Mar Lett. 2010;30:157–67.
doi: 10.1007/s00367-010-0193-z
Perez-Garcia C, Feseker T, Mienert J, Berndt C. The Håkon Mosby mud volcano: 330 000 years of focused fluid flow activity at the SW Barents Sea slope. Mar Geol. 2009;262:105–15.
doi: 10.1016/j.margeo.2009.03.022
Lein A, Vogt P, Crane K, Egorov A, Ivanov M. Chemical and isotopic evidence for the nature of the fluid in CH4-containing sediments of the Håkon Mosby Mud Volcano. Geo-Mar Lett. 1999;19:76–83.
doi: 10.1007/s003670050095
Luff R, Wallmann K. Fluid flow, methane fluxes, carbonate precipitation and biogeochemical turnover in gas hydrate-bearing sediments at Hydrate Ridge, Cascadia Margin: numerical modeling and mass balances. Geochim Cosmochim Acta. 2003;67:3403–21.
doi: 10.1016/S0016-7037(03)00127-3
Joye SB, Boetius A, Orcutt BN, Montoya JP, Schulz HN, Erickson MJ, et al. The anaerobic oxidation of methane and sulfate reduction in sediments from Gulf of Mexico cold seeps. Chem Geol. 2004;205:219–38.
doi: 10.1016/j.chemgeo.2003.12.019
Bowles MW, Mogollón JM, Kasten S, Zabel M, Hinrichs K-U. Global rates of marine sulfate reduction and implications for sub-sea-floor metabolic activities. Science (80-). 2014;344:889–91.
pubmed: 24812207
doi: 10.1126/science.1249213
Feseker T, Foucher JP, Harmegnies F. Fluid flow or mud eruptions? Sediment temperature distributions on Håkon Mosby mud volcano, SW Barents Sea slope. Mar Geol. 2008;247:194–207.
doi: 10.1016/j.margeo.2007.09.005
Parkes RJ, Cragg B, Roussel E, Webster G, Weightman A, Sass H. A review of prokaryotic populations and processes in sub-seafloor sediments, including biosphere:geosphere interactions. Mar Geol. 2014;352:409–25.
doi: 10.1016/j.margeo.2014.02.009
Blazejak A, Schippers A. High abundance of JS-1- and Chloroflexi-related Bacteria in deeply buried marine sediments revealed by quantitative, real-time PCR. FEMS Microbiol Ecol. 2010;72:198–207.
pubmed: 20180854
doi: 10.1111/j.1574-6941.2010.00838.x
Nobu MK, Narihiro T, Rinke C, Kamagata Y, Tringe SG, Woyke T, et al. Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor. ISME J. 2015;9:1710–22.
pubmed: 25615435
pmcid: 4511927
doi: 10.1038/ismej.2014.256
Lloyd KG, Schreiber L, Petersen DG, Kjeldsen KU, Lever MA, Steen AD, et al. Predominant archaea in marine sediments degrade detrital proteins. Nature. 2013;496:215–8.
doi: 10.1038/nature12033
pubmed: 23535597
Hoshino T, Toki T, Ijiri A, Morono Y, Machiyama H, Ashi J, et al. Atribacteria from the subseafloor sedimentary biosphere disperse to the hydrosphere through submarine mud volcanoes. Front Microbiol. 2017;8:1135.
pubmed: 28676800
pmcid: 5476839
doi: 10.3389/fmicb.2017.01135
Durbin AM, Teske A. Microbial diversity and stratification of South Pacific abyssal marine sediments. Environ Microbiol. 2011;13:3219–34.
pubmed: 21895908
doi: 10.1111/j.1462-2920.2011.02544.x
Braun S, Mhatre SS, Jaussi M, Røy H, Kjeldsen KU, Pearce C, et al. Microbial turnover times in the deep seabed studied by amino acid racemization modelling. Sci Rep. 2017;7:5680.
pubmed: 28720809
pmcid: 5516024
doi: 10.1038/s41598-017-05972-z
Starnawski P, Bataillon T, Ettema TJG, Jochum LM, Schreiber L, Chen X, et al. Microbial community assembly and evolution in subseafloor sediment. Proc Natl Acad Sci USA. 2017;114:2940–5.
doi: 10.1073/pnas.1614190114
pubmed: 28242677
pmcid: 5358386
Trembath-Reichert E, Morono Y, Ijiri A, Hoshino T, Dawson KS, Inagaki F, et al. Methyl-compound use and slow growth characterize microbial life in 2-km-deep subseafloor coal and shale beds. Proc Natl Acad Sci USA. 2017;114:E9206–E9215.
doi: 10.1073/pnas.1707525114
pubmed: 29078310
pmcid: 5676895
Lichtschlag A, Felden J, Brüchert V, Boetius A, de Beer D. Geochemical processes and chemosynthetic primary production in different thiotrophic mats of the Haakon Mosby Mud Volcano (Barents Sea). Limnol Oceanogr. 2010;55:931–49.
doi: 10.4319/lo.2010.55.2.0931
Lösekann T, Knittel K, Nadalig T, Fuchs B, Niemann H, Boetius A, et al. Diversity and abundance of aerobic and anaerobic methane oxidizers at the Haakon Mosby Mud Volcano, Barents Sea. Appl Environ Microbiol. 2007;73:3348–62.
pubmed: 17369343
pmcid: 1907091
doi: 10.1128/AEM.00016-07
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.
pubmed: 17227423
doi: 10.1111/j.1462-2920.2006.01127.x
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.
pubmed: 27357680
doi: 10.1073/pnas.1603757113
pmcid: 4948357
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.
pubmed: 16000782
pmcid: 1169053
doi: 10.1128/AEM.71.7.3725-3733.2005
Marlow J, Skennerton CT, Li Z, Chourey K, Hettich R, Pan C, et al. Proteomic stable isotope probing reveals biosynthesis dynamics of slow growing methane based microbial communities. Front Microbiol. 2016;7:1–21.
doi: 10.3389/fmicb.2016.00563
Tavormina PL, Ussler W, Joye SB, Harrison BK, Orphan VJ. Distributions of putative aerobic methanotrophs in diverse pelagic marine environments. ISME J. 2010;4:700–10.
pubmed: 20147984
doi: 10.1038/ismej.2009.155
Dedysh SN, Panikov NS, Liesack W, Grosskopf R, Zhou J, Tiedje JM. Isolation of acidophilic methane-oxidizing bacteria from northern peat wetlands. Science (80-). 1998;282:281–4.
doi: 10.1126/science.282.5387.281
Ruff SE, Arnds J, Knittel K, Amann R, Wegener G, Ramette A, et al. Microbial communities of deep-sea methane seeps at Hikurangi Continental Margin (New Zealand). PLoS ONE. 2013;8:e72627.
pubmed: 24098632
pmcid: 3787109
doi: 10.1371/journal.pone.0072627
Sommer S, Linke P, Pfannkuche O, Niemann H, Treude T. Benthic respiration in a seep habitat dominated by dense beds of ampharetid polychaetes at the Hikurangi Margin (New Zealand). Mar Geol. 2010;272:223–32.
doi: 10.1016/j.margeo.2009.06.003
Galand PE, Casamayor EO, Kirchman DL, Lovejoy C. Ecology of the rare microbial biosphere of the Arctic Ocean. Proc Natl Acad Sci USA. 2009;106:22427–32.
pubmed: 20018741
doi: 10.1073/pnas.0908284106
pmcid: 2796907
Jousset A, Bienhold C, Chatzinotas A, Gallien L, Gobet A, Kurm V, et al. Where less may be more: how the rare biosphere pulls ecosystems strings. ISME J. 2017;11:853.
pubmed: 28072420
pmcid: 5364357
doi: 10.1038/ismej.2016.174
Goffredi SK, Wilpiszeski R, Lee R, Orphan VJ. Temporal evolution of methane cycling and phylogenetic diversity of archaea in sediments from a deep-sea whale-fall in Monterey Canyon, California. ISME J. 2008;2:204–20.
pubmed: 18219285
doi: 10.1038/ismej.2007.103
Bienhold C, Pop Ristova P, Wenzhöfer F, Dittmar T, Boetius A. How deep-sea Wood Falls sustain chemosynthetic life. PLoS ONE. 2013;8:e53590.
pubmed: 23301092
pmcid: 3534711
doi: 10.1371/journal.pone.0053590
Pop Ristova P, Bienhold C, Wenzhöfer F, Rossel PE, Boetius A. Temporal and spatial variations of bacterial and faunal communities associated with deep-sea Wood Falls. PLoS ONE. 2017;12:e0169906
pubmed: 28122036
pmcid: 5266260
doi: 10.1371/journal.pone.0169906
Ruff SE, Felden J, Marcon Y, Ramette A, Boetius A. Development of bacterial and archaeal communities in erupted subsurface muds at the Håkon Mosby mud volcano. 2016. https://doi.pangaea.de/10.1594/PANGAEA.861266
Felden J, Ruff SE, Ertefai T, Inagaki F, Hinrichs K-U, Wenzhöfer F. Anaerobic methanotrophic community of a 5346-m-deep vesicomyid clam colony in the Japan Trench. Geobiology. 2014;12:183–99.
pubmed: 24593671
pmcid: 4237546
doi: 10.1111/gbi.12078
Cline JD. Spectrophotometric determination of hydrogen sulfide in natural waters. Limnol Oceanogr. 1969;14:454–8.
doi: 10.4319/lo.1969.14.3.0454
Hall POJ, Aller RC. Rapid, small-volume, flow injection analysis for ΣCO2 and NH4+in marine and freshwaters. Limnol Oceanogr. 1992;37:1113–9.
doi: 10.4319/lo.1992.37.5.1113
Grasshoff K, Kremling K, Ehrhardt M. Methods of seawater analysis. 3rd edn. Weinheim, Germany: WILEY-VCH; 1999.
doi: 10.1002/9783527613984
Jørgensen BB. A comparison of methods for the quantification of bacterial sulfate reduction in coastal marine sediments. Geomicrobiol J. 1978;1:11–27.
doi: 10.1080/01490457809377721
Treude T, Boetius A, Knittel K, Wallmann K, Jørgensen BB. Anaerobic oxidation of methane above gas hydrates at Hydrate Ridge, NE Pacific Ocean. Mar Ecol Prog Ser. 2003;264:1–14.
doi: 10.3354/meps264001
Kallmeyer J, Ferdelman TG, Weber A, Fossing H, Jørgensen BB. A cold chromium distillation procedure for radiolabeled sulfide applied to sulfate reduction measurements. Limnol Oceanogr Methods. 2004;2:171–80.
doi: 10.4319/lom.2004.2.171
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009;75:7537–41.
pubmed: 19801464
pmcid: 2786419
doi: 10.1128/AEM.01541-09
Schloss PD, Gevers D, Westcott SL. Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS ONE. 2011;6:e27310.
pubmed: 22194782
pmcid: 3237409
doi: 10.1371/journal.pone.0027310
Quince C, Lanzen A, Curtis TP, Davenport RJ, Hall N, Head IM, et al. Accurate determination of microbial diversity from 454 pyrosequencing data. Nat Methods. 2009;6:639–41.
pubmed: 19668203
doi: 10.1038/nmeth.1361
Huse SM, Welch DM, Morrison HG, Sogin ML. Ironing out the wrinkles in the rare biosphere through improved OTU clustering. Environ Microbiol. 2010;12:1889–98.
pubmed: 20236171
pmcid: 2909393
doi: 10.1111/j.1462-2920.2010.02193.x
Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics. 2011;27:2194–2200.
pubmed: 21700674
pmcid: 3150044
doi: 10.1093/bioinformatics/btr381
Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W, Schleifer K-H, et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol. 2014;12:635–45.
pubmed: 25118885
doi: 10.1038/nrmicro3330
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–D596.
pubmed: 23193283
doi: 10.1093/nar/gks1219
Chao A. Nonparametric estimation of the number of classes in a population. Scand J Stat. 1984;11:265–70.
Bray JR, Curtis JT. An ordination of the Upland forest communities of Southern Wisconsin. Ecol Monogr. 1957;27:326–49.
doi: 10.2307/1942268
Kruskal JB. Nonmetric multidimensional scaling: a numerical method. Psychometrika. 1964;29:115–29.
doi: 10.1007/BF02289694
Oksanen J, Blanchet FG, Kindt R, Legendre P, Minchin PR, O´Hara RB, et al. vegan: Community Ecology Package. 2012. https://CRAN.R-project.org/package=vegan
Roberts DW labdsv: Ordination and multivariate analysis for ecology. 2012. https://CRAN.R-project.org/package=labdsv
Zhou J, Bruns MA, Tiedje JM. DNA recovery from soils of diverse composition. Appl Environ Microbiol. 1996;62:316–22.
pubmed: 8593035
pmcid: 167800
doi: 10.1128/aem.62.2.316-322.1996
Ruff SE, Ramette A, Boetius A. Metadata und statistical analysis of archaeal and bacterial sequences originating from sediments of the Håkon Mosby mud volcano. 2016. https://doi.pangaea.de/10.1594/PANGAEA.861873
Müller AL, Kjeldsen KU, Rattei T, Pester M, Loy A. Phylogenetic and environmental diversity of DsrAB-type dissimilatory (bi)sulfite reductases. ISME J. 2015;9:1152–65.
pubmed: 25343514
doi: 10.1038/ismej.2014.208
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19:455–77.
pubmed: 22506599
pmcid: 3342519
doi: 10.1089/cmb.2012.0021
Miller CS, Baker BJ, Thomas BC, Singer SW, Banfield JF. EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data. Genome Biol. 2011;12:R44.
pubmed: 21595876
pmcid: 3219967
doi: 10.1186/gb-2011-12-5-r44
Bushnell B, Rood J, Singer E. BBMerge—accurate paired shotgun read merging via overlap. PLoS ONE. 2017;12:e0185056.
pubmed: 29073143
pmcid: 5657622
doi: 10.1371/journal.pone.0185056
Abubucker S, Segata N, Goll J, Schubert AM, Izard J, Cantarel BL, et al. Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput Biol. 2012;8:e1002358.
pubmed: 22719234
pmcid: 3374609
doi: 10.1371/journal.pcbi.1002358
Suzek BE, Wang Y, Huang H, McGarvey PB, Wu CH, Consortium the U. UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches. Bioinformatics. 2015;31:926–32.
pubmed: 25398609
doi: 10.1093/bioinformatics/btu739
Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2014;12:59.
pubmed: 25402007
doi: 10.1038/nmeth.3176
Conway JR, Lex A, Gehlenborg N. UpSetR: an R package for the visualization of intersecting sets and their properties. bioRxiv. 2017;33:2938–40.
Meyer-Reil LA. Benthic response to sedimentation events during autumn to spring at a shallow water station in the Western Kiel Bight. Mar Biol. 1983;77:247–56.
doi: 10.1007/BF00395813