Cite this paper:
ZHANG Wenyan, LIU Jia, DONG Yi, LI Xuegang, XU Cong, XIAO Tian, PAN Hongmiao, WU Long-Fei. Archaeal community structure in sediments from a seamount in the Mariana Volcanic Arc[J]. Journal of Oceanology and Limnology, 2019, 37(4): 1197-1210

Archaeal community structure in sediments from a seamount in the Mariana Volcanic Arc

ZHANG Wenyan1,2,3,6, LIU Jia1,2,3, DONG Yi1,2,6, LI Xuegang1,2,6, XU Cong1,2,3, XIAO Tian1,2,4,6, PAN Hongmiao1,2,4,6, WU Long-Fei4,5
1 Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China;
2 Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China;
3 University of Chinese Academy of Sciences, Beijing 100049, China;
4 International Associated Laboratory of Evolution and Development of Magnetotactic Multicellular Organisms (LIA-MagMC), CNRS-CAS, Marseille-Beijing-Qingdao-Sanya;
5 Aix Marseille Univ, CNRS, LCB, Marseille, 31 chemin Joseph Aiguier, F-13402, France;
6 Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
Abstract:
Seamounts are subsurface mountains in the ocean. Examination of the abundance and distribution of Archaea in seamount ecosystems may provide a better understanding of their ecological functions. Most studies of marine archaeal assemblages in seamount area have focused on hydrothermal vents or ferromanganese crusts. We investigated the archaeal communities from a seamount of the Mariana Volcanic Arc, in the tropical western Pacific Ocean by using high-throughput sequencing. Thaumarchaeota was dominant in the sediments of all sample stations. Community diversity and species richness were greatest at stations near the top of the seamount, and lowest at the deepest station. One sample station on the steep southeast slope that faced the Yap-Mariana trench had a unique composition of Archaea. In summary, depth has an important influence on archaeal community structure, and the geographic properties and sediment characteristics may explain the unique distribution patterns of Archaea in this seamount. This study provides a foundation for future research on Archaea in seamounts.
Key words:    seamount|archaeal diversity|community structure|Nitrosopumilales   
Received: 2018-03-22   Revised: 2018-05-21
Tools
PDF (4120 KB) Free
Print this page
Add to favorites
Email this article to others
Authors
Articles by ZHANG Wenyan
Articles by LIU Jia
Articles by DONG Yi
Articles by LI Xuegang
Articles by XU Cong
Articles by XIAO Tian
Articles by PAN Hongmiao
Articles by WU Long-Fei
References:
Amato K R, Yeoman C J, Kent A, Righini N, Carbonero F, Estrada A, Gaskins H R, Stumpf R M, Yildirim S, Torralba M, Gillis M, Wilson B A, Nelson K E, White B A, Leigh S R. 2013. Habitat degradation impacts black howler monkey (Alouatta pigra) gastrointestinal microbiomes.The ISME Journal, 7(7):1 344-1 353, https://doi.org/10.1038/ismej.2013.16.
Auguet J C, Barberan A, Casamayor E O. 2010. Global ecological patterns in uncultured Archaea. The ISME Journal, 4(2):182-190, https://doi.org/10.1038/ismej.2009.109.
Bano N, Ruffin S, Ransom B, Hollibaugh J T. 2004.Phylogenetic composition of Arctic Ocean archaeal assemblages and comparison with Antarctic assemblages.Applied and Environmental Microbiology, 70(2):781-789, https://doi.org/10.1128/aem.70.2.781-789.2004.
Bolger A M, Lohse M, Usadel B. 2014. Trimmomatic:a flexible trimmer for Illumina sequence data.Bioinformatics, 30(15):2 114-2 120, https://doi.org/10.1093/bioinformatics/btu170.
Bray J R, Curtis J T. 1957. An ordination of the upland forest communities of southern Wisconsin. Ecological Society of America, 27(4):325-349, https://doi.org/10.2307/1942268.
Brochier-Armanet C, Boussau B, Gribaldo S, Forterre P. 2008.Mesophilic Crenarchaeota:proposal for a third archaeal phylum, the Thaumarchaeota. Nature Reviews Microbiology, 6(3):245-252, https://doi.org/10.1038/nrmicro1852.
Caporaso J G, Kuczynski J, Stombaugh J, Bittinger K, Bushman F D, Costello E K, Fierer N, Peña A G, Goodrich J K, Gordon J I, Huttley G A, Kelley S T, Knights D, Koenig J E, Ley R E, Lozupone C A, McDonald D, Muegge B D, Pirrung M, Reeder J, Sevinsky J R, Turnbaugh P J, Walters W A, Widmann J, Yatsunenko T, Zaneveld J, Knight R. 2010. QⅡME allows analysis of high-throughput community sequencing data. Nature Methods, 7(5):335-336, https://doi.org/10.1038/nmeth.f.303.
Chao A, Lee S M. 1992. Estimating the number of classes via sample coverage. Journal of the American Statistical Association, 87(417):210-217.
Chao A, Ma M C, Yang M C K. 1993. Stopping rules and estimation for recapture debugging with unequal failure rates. Biometrika, 80(1):193-201, https://doi.org/10.1093/biomet/80.1.193.
Chao A. 1984. Nonparametric estimation of the number of classes in a population. Scandinavian Journal of Statistics, 11(4):265-270.
Clark M R, Rowden A A, Schlacher T, Williams A, Consalvey M, Stocks K I, Rogers A D, O'Hara T D, White M, Shank T M, Hall-Spencer J M. 2010. The ecology of seamounts:structure, function, and human impacts. Annual Review of Marine Science, 2:253-278, https://doi.org/10.1146/annurev-marine-120308-081109.
Danovaro R, Corinaldesi C, Luna G M, Magagnini M, Manini E, Pusceddu A. 2009. Prokaryote diversity and viral production in deep-sea sediments and seamounts. DeepSea Research Part Ⅱ:Topical Studies in Oceanography, 56(11-12):738-747, https://doi.org/10.1016/j.dsr2.2008. 10.011.
Danovaro R, Molari M, Corinaldesi C, Dell'Anno A. 2016.Macroecological drivers of archaea and bacteria in benthic deep-sea ecosystems. Science Advances, 2(4):e1500961, https://doi.org/10.1126/sciadv.1500961.
DeLong E F. 1992. Archaea in coastal marine environments.Proceedings of the National Academy of Sciences of the United States of America, 89(12):5 685-5 689.
DeSarbo W S, Hwang H, Jedidi K. 2016. Redundancy Analysis. John Wiley & Sons, Ltd.Durbin A M, Teske A. 2010. Sediment-associated microdiversity within the Marine Group I Crenarchaeota.Environmental Microbiology Reports, 2(5):693-703, https://doi.org/10.1111/j.1758-2229.2010.00163.x.
Durbin A M, Teske A. 2012. Archaea in organic-lean and organic-rich marine subsurface sediments:an environmental gradient reflected in distinct phylogenetic lineages. Frontiers in Microbiology, 3:168, https://doi.org/10.3389/fmicb.2012.00168.
Edgar R C, Haas B J, Clemente J C, Quince C, Knight R. 2011.UCHIME improves sensitivity and speed of chimera detection. Bioinformatics, 27(16):2 194-2 200, https://doi.org/10.1093/bioinformatics/btr381.
Edgar R C. 2013. UPARSE:highly accurate OTU sequences from microbial amplicon reads. Nature Methods, 10(10):996-998, https://doi.org/10.1038/nmeth.2604.
Emerson D, Moyer C L. 2010. Microbiology of seamounts:common patterns observed in community structure.Oceanography, 23(1):148-163, https://doi.org/10.5670/oceanog.2010.67.
Fuhrman J A, McCallum K, Davis A A. 1992. Novel major archaebacterial group from marine plankton. Nature, 356(6365):148-149, https://doi.org/10.1038/356148a0.
Gantner S, Andersson A F, Alonso-Sáez L, Bertilsson S. 2011.Novel primers for 16S rRNA-based archaeal community analyses in environmental samples. Journal of Microbiological Methods, 84(1):12-18, https://doi.org/10.1016/j.mimet.2010.10.001.
Gilbert J A, Field D, Swift P, Newbold L, Oliver A, Smyth T, Somerfield P J, Huse S, Joint I. 2009. The seasonal structure of microbial communities in the Western English Channel. Environmental Microbiology, 11(12):3 132-3 139, https://doi.org/10.1111/j.1462-2920.2009.02017.x.
Hara K, Kakegawa T, Yamashiro K, Maruyama A, Ishibashi J I, Marumo K, Urabe T, Yamagishi A. 2005. Analysis of the archaeal sub-seafloor community at Suiyo Seamount on the Izu-Bonin Arc. Advances in Space Research, 35(9):1 634-1 642, https://doi.org/10.1016/j.asr.2005.04.111.
He Y, Li M, Perumal V, Feng X, Fang J, Xie J, Sievert S M, Wang F. 2016. Genomic and enzymatic evidence for acetogenesis among multiple lineages of the archaeal phylum Bathyarchaeota widespread in marine sediments.Nature Microbiology, 1(6):16 035, https://doi.org/10. 1038/nmicrobiol.2016.35.
Herndl G J, Reinthaler T, Teira E, Van Aken H, Veth C, Pernthaler A, Pernthaler J. 2005. Contribution of Archaea to total prokaryotic production in the deep Atlantic Ocean.Applied and Environmental Microbiology, 71(5):2 303-2 309, https://doi.org/10.1128/AEM.71.5.2303-2309.2005.
Hill M O, Gauch Jr H G. 1980. Detrended correspondence analysis:an improved ordination technique. Vegetatio, 42(1-3):47-58, https://doi.org/10.1007/bf00048870.
Huber J A, Butterfield D A, Baross J A. 2002. Temporal changes in archaeal diversity and chemistry in a midocean ridge subseafloor habitat. Applied and Environmental Microbiology, 68(4):1 585-1 594, https://doi.org/10.1128/aem.68.4.1585-1594.2002.
Huo Y Y, Cheng H, Post A F, Wang C S, Jiang X W, Pan J, Wu M, Xu X W. 2015. Ecological functions of uncultured microorganisms in the cobalt-rich ferromanganese crust of a seamount in the central Pacific are elucidated by fosmid sequencing. Acta Oceanologica Sinica, 34(4):92-113, https://doi.org/10.1007/s13131-015-0650-7.
Jolliffe I T. 2002. Principal Component Analysis. 2nd edn.Springer-Verlag, New York.
Jorgensen S L, Hannisdal B, Lanzén A, Baumberger T, Flesland K, Fonseca R, Øvreås L, Steen I H, Thorseth I H, Pedersen R B, Schleper C. 2012. Correlating microbial community profiles with geochemical data in highly stratified sediments from the Arctic Mid-Ocean Ridge.Proceedings of the National Academy of Sciences of the United States of America, 109(42):E2 846-E2 855,https://doi.org/10.1073/pnas.1207574109.
Karner M B, DeLong E F, Karl D M. 2001. Archaeal dominance in the mesopelagic zone of the Pacific Ocean. Nature 409(6819):507-510, https://doi.org/10.1038/35054051.
Kato S, Nakawake M, Kita J, Yamanaka T, Utsumi M, Okamura K, Ishibashi J I, Ohkuma M, Yamagishi A. 2013.Characteristics of microbial communities in crustal fluids in a deep-sea hydrothermal field of the Suiyo Seamount.Frontiers in Microbiology, 4:85, https://doi.org/10.3389/fmicb.2013.00085.
Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones S J, Marra M A. 2009. Circos:an information aesthetic for comparative genomics. Genome Research, 19(9):1 639-1 645, https://doi.org/10.1101/gr. 092759.109.
Lauer A, Sorensen K B, Teske A. 2016. Phylogenetic characterization of marine benthic Archaea in organicpoor sediments of the eastern Equatorial Pacific Ocean(ODP Site 1225). Microorganisms, 4(3):32, https://doi.org/10.3390/microorganisms4030032.
Lavelle J W, Mohn C. 2010. Motion, commotion, and biophysical connections at deep ocean seamounts.Oceanography, 23(1):90-103, https://doi.org/10.5670/oceanog.2010.64.
Liao L, Xu X W, Jiang X W, Wang C S, Zhang D S, Ni J Y, Wu M. 2011. Microbial diversity in deep-sea sediment from the cobalt-rich crust deposit region in the Pacific Ocean.FEMS Microbiology Ecology, 78(3):565-585, https://doi.org/10.1111/j.1574-6941.2011.01186.x.
Liu J, Zhang W Y, Li X G, Li X G, Chen X M, Li J H, Teng Z J, Xu C, Santini C L, Zhao L, Zhao Y, Zhang H, Zhang W J, Xu K D, Li C L, Pan Y X, Xiao T, Pan H M, Wu L F. 2017. Bacterial community structure and novel species of magnetotactic bacteria in sediments from a seamount in the Mariana volcanic arc. Scientific Reports, 7(1):17 964, https://doi.org/10.1038/s41598-017-17445-4.
Magurran A E. 1988. Ecological Diversity and Its Measurement.Princeton University Press, Princeton, USA.
Massana R, DeLong E F, Pedrós-Alió C. 2000. A few cosmopolitan phylotypes dominate planktonic archaeal assemblages in widely different oceanic provinces.Applied and Environmental Microbiology, 66(5):1 777-1 787, https://doi.org/10.1128/AEM.66.5.1777-1787. 2000.
Menard H W. 1964. Marine Geology of the Pacific. McGrawHill, New York, NY.
Meng J, Xu J, Qin D, He Y, Xiao X, Wang F P. 2014. Genetic and functional properties of uncultivated MCG archaea assessed by metagenome and gene expression analyses.The ISME Journal, 8(3):650-659, https://doi.org/10.1038/ismej.2013.174.
Nakagawa T, Ishibashi J I, Maruyama A, Yamanaka T, Morimoto Y, Kimura H, Urabe T, Fukui M. 2004. Analysis of dissimilatory sulfite reductase and 16S rRNA gene fragments from deep-sea hydrothermal sites of the Suiyo Seamount, Izu-Bonin Arc, Western Pacific. Applied and Environmental Microbiology, 70(1):393-403, https://doi.org/10.1128/AEM.70.1.393-403.2004.
Nitahara S, Kato S, Urabe T, Usui A, Yamagishi A. 2011.Molecular characterization of the microbial community in hydrogenetic ferromanganese crusts of the Takuyo-Daigo Seamount, northwest Pacific. FEMS Microbiology Letters, 321(2):121-129, https://doi.org/10.1111/j.1574-6968.2011.02323.x.
Nitahara S, Kato S, Usui A, Urabe T, Suzuki K, Yamagishi A. 2017. Archaeal and bacterial communities in deep-sea hydrogenetic ferromanganese crusts on old seamounts of the northwestern Pacific. PLoS One, 12(2):e0173071, https://doi.org/10.1371/journal.pone.0173071.
O'Hara T D. 2007. Seamounts:centres of endemism or species richness for ophiuroids? Global Ecology and Biogeography, 16(6):720-732, https://doi.org/10.1111/j. 1466-8238.2007.00329.x.
Offre P, Spang A, Schleper C. 2013. Archaea in biogeochemical cycles. Annual Review of Microbiology, 67:437-457, https://doi.org/10.1146/annurev-micro-092412-155614.
Ohene-Adjei S, Teather R M, Ivan M, Forster R J. 2007.Postinoculation protozoan establishment and association patterns of methanogenic archaea in the ovine rumen.Applied and Environmental Microbiology, 73(14):4 609-4 618, https://doi.org/10.1128/AEM.02687-06.
Opatkiewicz A D, Butterfield D A, Baross J A. 2009. Individual hydrothermal vents at Axial Seamount harbor distinct subseafloor microbial communities. FEMS Microbiology Ecology, 70(3):413-424, https://doi.org/10.1111/j.1574-6941.2009.00747.x.
Qin W, Heal K R, Ramdasi R, Kobelt J N, Martens-Habbena W, Bertagnolli A D, Amin S A, Walker C B, Urakawa H, Könneke M, Devol A H, Moffett J W, Armbrust E V, Jensen G J, Ingalls A E, Stahl D A. 2017. Nitrosopumilus maritimus gen. nov., sp. nov., Nitrosopumilus cobalaminigenes sp. nov., Nitrosopumilus oxyclinae sp.nov., and Nitrosopumilus ureiphilus sp. nov., four marine ammonia-oxidizing archaea of the phylum Thaumarchaeota. International Journal of Systematic and Evolutionary Microbiology, 67(12):5 067-5 079, https://doi.org/DOI:10.1099/ijsem.0.002416.
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner F O. 2012. The SILVA ribosomal RNA gene database project:improved data processing and web-based tools. Nucleic Acids Research, 41(D1):D590-D596, https://doi.org/10.1093/nar/gks1219.
Roussel E G, Sauvadet A L, Chaduteau C, Fouquet Y, Charlou J L, Prieur D, Cambon Bonavita M A. 2009. Archaeal communities associated with shallow to deep subseafloor sediments of the New Caledonia Basin. Environmental Microbiology, 11(9):2 446-2 462, https://doi.org/10.1111/j.1462-2920.2009.01976.x.
Rowden A A, Schlacher T A, Williams A, Clark M R, Stewart R, Althaus F, Bowden D A, Consalvey M, Robinson W, Dowdney J. 2010. A test of the seamount oasis hypothesis:seamounts support higher epibenthic megafaunal biomass than adjacent slopes. Marine Ecology, 31(S1):95-106, https://doi.org/10.1111/j.1439-0485.2010.00369.x.
Schlacher T A, Rowden A A, Dower J F, Consalvey M. 2010.Seamount science scales undersea mountains:new research and outlook. Marine Ecology, 31(S1):1-13, https://doi.org/10.1111/j.1439-0485.2010.00396.x.
Schloss P D, Westcott S L, Ryabin T, Hall J R, Hartmann M, Hollister E B, Lesniewski R A, Oakley B B, Parks D H, Robinson C J, Sahl J W, Stres B, Thallinger G G, Van Horn D J, Weber C F. 2009. Introducing mothur:opensource, platform-independent, community-supported software for describing and comparing microbial communities. Applied and Environmental Microbiology, 75(23):7 537-7 541, https://doi.org/10.1128/AEM.01541-09.
Simpson J M, Kocherginskaya S A, Aminov R I, Skerlos L T, Bradley T M, Mackie R I, White B A. 2002. Comparative microbial diversity in the gastrointestinal tracts of food animal species. Integrative and Comparative Biology, 42(2):327-331, https://doi.org/10.1093/icb/42.2.327.
Šmilauer P, Lepš J. 2014. Multivariate Analysis of Ecological Data Using Canoco 5. Cambridge University Press, Cambridge.
Stahl D A, De La Torre J R. 2012. Physiology and diversity of ammonia-oxidizing archaea. Annual Review of Microbiology, 66:83-101, https://doi.org/10.1146/annurev-micro-092611-150128.
Takai K, Oida H, Suzuki Y, Hirayama H, Nakagawa S, Nunoura T, Inagaki F, Nealson K H, Horikoshi K. 2004. Spatial distribution of marine Crenarchaeota group I in the vicinity of deep-sea hydrothermal systems. Applied and Environmental Microbiology, 70(4):2 404-2 413, https://doi.org/10.1128/aem.70.4.2404-2413.2004.
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013.MEGA6:molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution, 30(12):2 725-2 729, https://doi.org/10.1093/molbev/mst197.
Thompson J D, Higgins D G, Gibson T J. 1994. CLUSTAL W:improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22(22):4 673-4 680, https://doi.org/10.1093/nar/22.22.4673.
Tourna M, Stieglmeier M, Spang A, Konneke M, Schintlmeister A, Urich T, Engel M, Schloter M, Wagner M, Richter A, Schleper C. 2011. Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil. Proceedings of the National Academy of Sciences of the United States of America, 108(20):8 420-8 425, https://doi.org/10.1073/pnas.1013488108.
Wang Q, Garrity G M, Tiedje J M, Cole J R. 2007. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology, 73(16):5 261-5 267, https://doi.org/10.1128/AEM.00062-07.
Woese C R, Fox G E. 1977. Phylogenetic structure of the prokaryotic domain:the primary kingdoms. Proceedings of the National Academy of Sciences of the United States of America, 74(11):5 088-5 090, https://doi.org/10.1073/pnas.74.11.5088.
Woese C R, Kandler O, Wheelis M L. 1990. Towards a natural system of organisms:proposal for the domains Archaea, Bacteria, and Eucarya. Proceedings of the National Academy of Sciences of the United States of America, 87(12):4 576-4 579, https://doi.org/10.1073/pnas.87.12.4576.
Wuchter C, Abbas B, Coolen M J L, Herfort L, Van Bleijswijk J, Timmers P, Strous M, Teira E, Herndl G J, Middelburg J J, Schouten S, Sinninghe Damsté J S. 2006. Archaeal nitrification in the ocean. Proceedings of the National Academy of Sciences of the United States of America, 103(33):12 317-12 322, https://doi.org/10.1073/pnas.0600756103.
Yesson C, Clark M R, Taylor M L, Rogers A D. 2011. The global distribution of seamounts based on 30 arc seconds bathymetry data. Deep Sea Research Part I:Oceanographic Research Papers, 58(4):442-453, https://doi.org/10.1016/j.dsr.2011.02.004.
Yoshioka P M. 2008. Misidentification of the Bray-Curtis similarity index. Marine Ecology Progress Series, 368:309-310, https://doi.org/10.3354/meps07728.
Zhang C L, Xie W, Martin-Cuadrado A B, Rodriguez-Valera F. 2015. Marine group Ⅱ Archaea, potentially important players in the global ocean carbon cycle. Frontiers in Microbiology, 6:1 108, https://doi.org/10.3389/fmicb. 2015.01108
Copyright © Haiyang Xuebao