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Microbial communities in semi-consolidated carbonate sediments of the Southwest Indian Ridge

  • Microbial Ecology and Environmental Microbiology
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Abstract

White semi-consolidated carbonate sediments attached to black ferromanganese oxide films were collected approximately 50 km west of a newly discovered hydrothermal field near the Southwest Indian Ridge (SWIR). The biodiversity of the prokaryotic communities within the field was examined using clone library-based culture-independent analysis of the exterior black oxides and the interior white carbonates. Subsequent 16S rRNA gene analysis suggested that Gamma-proteobacteria, Acidobacteria, and Thaumarchaeota members dominated the bacterial and archaeal clone libraries. To further characterize the metabolic processes within the microbial community, analyses of the amoA (coding the alpha subunit of the ammonia monooxygenase for Archaea) and aprA (coding the alpha subunit of the dissimilatory adenosine-5′-phosphosulfate reductase for the sulfate-reducing and sulfur-oxidizing prokaryotes) functional genes were conducted. The functional gene analysis results suggested that Thaumarchaeota and Alphaproteobacteria members were the potential players that participated in N and S cycles in this marine carbonate sedimentary environment. This paper is the first to describe the microbial communities and their potential metabolic pathways within the semi-consolidated carbonate sediments of the SWIR.

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References

  • Arakawa, S., Sato, T., Yoshida, Y., Usami, R., and Kato, C. 2006. Comparison of the microbial diversity in cold-seep sediments from different depths in the Nankai Trough. J. Gen. Appl. Microbiol. 52, 47–54.

    Article  CAS  PubMed  Google Scholar 

  • Barns, S.M., Delwiche, C.F., Palmer, J.D., and Pace, N.R. 1996. Perspectives on archaeal diversity, thermophily and monophyly from environmental rRNA sequences. Proc. Natl. Acad. Sci. USA 93, 9188–9193.

    Article  CAS  PubMed  Google Scholar 

  • Batch, W., Banerjee, N.R., Dick, H.J.B., and Baker, E.T. 2002. Discovery of ancient and active hydrothermal systems along the ultra-slow spreading Southwest Indian Ridge 10-16°E. Geochem. Geophys. Geosyst. 3, 10.1029/2001GC000279.

  • Becker, P.T., Samadi, S., Zbinden, M., Hoyoux, C., Compère, P., and Ridder, C.D.E. 2009. First insights into the gut microflora associated with an echinoid from wood falls environments. Cah. Biol. Mar. 50, 343–352.

    Google Scholar 

  • Blazejak, A., Kuever, J., Erseus, C., Amann, R., and Dubilier, N. 2006. Phylogeny of 16S rRNA, ribulose 1,5-bisphosphate carboxylase/oxygenase, and adenosine 5-phosphosulfate reductase genes from gamma- and alpha-proteobacterial symbionts in gutless marine worms (oligochaeta) from Bermuda and the Bahamas. Appl. Environ. Microbiol. 72, 5527–5536.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Boström, K. and Peterson, M.N.A. 1969. The origin of aluminum-poor ferromanganoan sediments of high heat flow on the East Pacific Rise. Marine Geol. 7, 427–447.

    Article  Google Scholar 

  • Bowman, J.P. and McCuaig, R.D. 2003. Biodiversity, community structural shifts, and biogeography of prokaryotes within Antarctic continental shelf sediment. Appl. Environ. Microbiol. 69, 2463–2483.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Cave, R.R., German, C.R., Thomson, J., and Nesbitt, R.W. 2002. Fluxes to sediments underlying the Rainbow hydrothermal plume at 36° 14 N on the Mid-Atlantic Ridge. Geochimica et Cosmochimica Acta. 66, 1905–1923.

    Article  CAS  Google Scholar 

  • Curtis, T.P., Sloan, W.T., and Scannell, J.W. 2002. Estimating prokaryotic diversity and its limits. Proc. Natl. Acad. Sci. USA 99, 10494–10499.

    Article  CAS  PubMed  Google Scholar 

  • Dang, H.Y., Zhang, X.X., Sun, J., Li, T.G., Zhang, Z.N., and Yang, G.P. 2008. Diversity and spatial distribution of sediment ammonia-oxidizing crenarchaeota in response to estuarine and environmental gradients in the Changjiang Estuary and East China Sea. Microbiology 154, 2084–2095.

    Article  CAS  PubMed  Google Scholar 

  • Delong, E.F. 1992. Archaea in coastal marine environments. Proc. Natl. Acad. Sci. USA 89, 5685–5689.

    Article  CAS  PubMed  Google Scholar 

  • Dojka, M.A., Hugenholtz, P., Haack, S.K., and Pace, N.R. 1998. Microbial diversity in a hydrocarbon- and chlorinated-solvent contaminated aquifer undergoing intrinsic bioremediation. Appl. Environ. Microbiol. 64, 3869–3877.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Dong, C., Lai, Q., Chen, L., Sun F., Shao, Z., and Yu, Z. 2010. Oceanibaculum pacificum sp. nov., isolated from hydrothermal field sediment of the south-west Pacific Ocean. Int. J. Syst. Evol. Microbiol. 60, 219–222.

    Article  CAS  PubMed  Google Scholar 

  • Edwards, K.J., Rogers, D.R., Wirsen, C.O., and McCollom, T.M. 2003. Isolation and characterization of novel psychrophilic, neutrophilic, Fe-oxidizing, chemolithoautotrohic α- and γ-Proteobacteria from the deep sea. Appl. Environ. Microbiol. 69, 2906–2913.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Ehrhardt, C.J., Haymon, R.M., Lamontagne, M.G., and Holden, P.A. 2007. Evidence for hydrothermal Archaea within the basaltic flanks of the East Pacific Rise. Environ. Microbiol. 9, 900–912.

    Article  CAS  PubMed  Google Scholar 

  • Ehrich, S., Behrens, D., Lebedeva, E., Ludwig, W., and Bock, E. 1995. A new obligately chemolithoautotrophic, nitriteoxidizing bacterium, Nitrospira moscoviensis sp. nov. and its phylogenetic relationship. Arch. Microbiol. 164, 16–23.

    Article  CAS  PubMed  Google Scholar 

  • Fierer, N., Bradford, M.A., and Jackson, R.B. 2007. Toward an ecological classification of soil bacteria. Ecology 88, 1354–1364.

    Article  PubMed  Google Scholar 

  • Francis, C.A., Beman, J.M., and Kuypers, M.M.M. 2007. New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation. ISME J. 1, 19–27.

    Article  CAS  PubMed  Google Scholar 

  • Fuhrman, J.A. and Davis, A.A. 1997. Widespread Archaea and novel Bacteria from the deep sea as shown by 16S rRNA gene sequences. Mar. Ecol. Prog. Ser. 150, 275–285.

    Article  Google Scholar 

  • German, R., Baker, E.T., Mevel, C., Tamaki, K., the FUJI Science Team. 1998. Hydrothermal activity along the southwest Indian ridge. Nature 395, 490–493.

    Article  CAS  Google Scholar 

  • Gillan, D. and Danis, B. 2007. The archaebacterial communities in Antarctic bathypelagic sediments. Deep-Sea Research II. 54, 1682–1690.

    Article  Google Scholar 

  • Good, I.J. 1953. The population frequencies of species and the estimation of population parameters. Biometrika 40, 237–264.

    Google Scholar 

  • Hagstrom, A., Pommier, T., Rohwer, F., Simu, K., Stolte, W., Svensson, D., and Zweifel, U.L. 2002. Use of 16S ribosomal DNA for delineation of marine bacterioplankton species. Appl. Environ. Microbiol. 68, 3628–3633.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Hammer, Ø., Harper, D.A.T., and Ryan, P.D. 2001. PAST: Paleontological statistics software package for education and data analysis. Palaeontologia Electronica 4, 1–9.

    Google Scholar 

  • Herndl, G.J., Reinthaler, T., Teira, E., van Aken, H., Veth, C., Pernthaler, A., and Pernthaler, J. 2005. Contribution of Archaea to total prokaryotic production in the deep Atlantic Ocean. Appl. Environ. Microbiol. 71, 2303–2309.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Hugenholtz, P., Goebel, B.M., and Pace, N.R. 1998. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J. Bacteriol. 180, 4765–4774.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Kato, S., Kobayashi, C., Kakegawa, T., and Yamagishi, A. 2009. Microbial communities in iron-silica-rich microbial mats at deep-sea hydrothermal fields of the Southern Mariana Trough. Environ. Microbiol. 11, 2094–2111.

    Article  CAS  PubMed  Google Scholar 

  • Kato, C., Li, L., Tamaoka, J., and Horikoshi, K. 1997. Molecular analyses of the sediment of the 11000-m deep Mariana Trench. Extremophiles 1, 117–123.

    Article  CAS  PubMed  Google Scholar 

  • Knoblauch, C., Jørgensen, B.B., and Harder, J. 1999. Community size and metabolic rates of psychrophilic sulfate-reducing bacteria in Arctic marine sediments. Appl. Environ. Microbiol. 65, 4230–4233.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Könneke, M., Bernhard, A.E., de la Torre, J.R., Walker, C.B., Waterbury, J.B., and Stahl, D.A. 2005. Isolation of an autotrophic ammonia-oxidizing marine archaeon. Nature 437, 543–546.

    Article  PubMed  Google Scholar 

  • Lane, D.J. 1991. 16S/23S rRNA sequencing, pp. 115–175. In Stackebrandt, E. and Goodfellow, M. (eds.), Nucleic acid techniques in bacterial systematics. Wiley, Chichester, UK.

    Google Scholar 

  • Li, L., Kato, C., and Horikoshi, K. 1999. Microbial diversity in sediments collected from the deepest cold-seep area, the Japan trench. Mar. Biotechnol. 1, 391–400.

    Article  CAS  PubMed  Google Scholar 

  • Li, J.W., Peng, X.T., Zhou, H.Y., Li, J.T., and Sun, Z.L. 2013. Molecular evidence for microorganisms participating in Fe, Mn, and S biogeochemical cycling in two low-temperature hydrothermal fields at the Southwest Indian Ridge. J. Geophys. Res. 118, doi: 10.1002/jgrg.20057.

  • Li, H.R., Yu, Y., Luo, W., Zeng, Y.X., and Chen, B. 2009. Bacterial diversity in surface sediments from the Pacific Arctic Ocean. Extremophiles 13, 233–246.

    Article  CAS  PubMed  Google Scholar 

  • Liao, L., Xu, X.W., Jiang, X.W., Wang, C.S., Zhang, D.S., Ni, J.Y., and Wu, M. 2011. Microbial diversity in deep-sea sediment from the cobalt-rich crust deposit region in the Pacific Ocean. FEMS Microbiol. Ecol. 78, 565–585.

    Article  CAS  PubMed  Google Scholar 

  • Little, B.J., Wagner, P.A., and Lewandowski, Z. 1997. Spatial relationships between bacteria and mineral surface, pp. 123–159. Geomicrobiology: Interactions Between Microbe and Minerals. In Banfield, J.F. and Nelason, K.H. (eds). Mineralolgical Society of America Washington, DC, USA.

    Google Scholar 

  • López-García, P., Duperron, S., Philippot, P., Foriel, J., Susini, J., and Moreira, D. 2003. Bacterial diversity in hydrothermal sediment and epsilonproteobacterial dominance in experimental microcolonizers at the Mid-Atlantic Ridge. Environ. Microbiol. 5, 961–976.

    Article  PubMed  Google Scholar 

  • Maidak, B.L., Cole, J.R., Lilburn, T.G., Parker, C.T., Saxman, P.R., Farris, R.J., Garrity, G.M., Olsen, G.L., Schmidt, T.M., and Tiedje, J.M. 2001. The RDP-II (Ribosomal Database Project). Nucleic Acids Res. 29, 173–174.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Mason, O.U., Di Meo-Savoie, C.A., Van Nostrand, J.D., Zhou, J., Fisk, M.R., and Giovannoni, S.J. 2009. Prokaryotic diversity, distribution, and insights into their role in biogeochemical cycling in marine basalts. ISME J. 3, 231–242.

    Article  CAS  PubMed  Google Scholar 

  • Meyer, B. and Kuever, J. 2007. Molecular analysis of the diversity of sulfate-reducing and sulfur-oxidizing prokaryotes in the environment, using aprA as functional marker gene. Appl. Environ. Microbiol. 73, 7664–7679.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Mincer, T.J., Church, M.J., Taylor, L.T., Preston, C., Karl, D.M., and DeLong, E.F. 2007. Quantitative distribution of presumptive archaeal and bacterial nitrifiers in Monterey Bay and the North Pacific subtropical gyre. Environ. Microbiol. 9, 1162–1175.

    Article  CAS  PubMed  Google Scholar 

  • Mitra, N.G., Sachidanand, B., Agarwal, G.D., and Upadhyay, A. 1998. Microbial transformations of iron, manganese and copper in soil. Acta. Botanica. Indica. 26, 71–81.

    Google Scholar 

  • Munch, U., Lalou, C., Halbach, P., and Fujimoto, H. 2001. Relict hydrothermal events along the super-slow Southwest Indian spreading ridge near 63°56 E — Mineralogy, chemistry and chronology of sulfide samples. Chem. Geol. 177, 341–349.

    Article  CAS  Google Scholar 

  • Muller, M.R., Minshull, T.A., and White, R.S. 1999. Segmentation and melt supply at the Southwest Indian Ridge. Geol. 27, 867–870.

    Article  Google Scholar 

  • Newberry, C.J., Webster, G., Cragg, B.A., Parkes, R.J., Weightman, A.J., and Fry, J.C. 2004. Diversity of prokaryotes and methanogenesis in deep subsurface sediments from the Nankai Trough, Ocean Drilling Program Leg 190. Environ. Microbiol. 6, 274–287.

    Article  PubMed  Google Scholar 

  • Patriat, P. and Segoufin, J. 1988. Reconstruction of the central Indian Ocean. Tectonophysics 155, 211–234.

    Article  Google Scholar 

  • Peng, X.T., Chen, S., Zhou, H.Y., Zhang, L.X., Wu, Z.J., Li, J.T., Li, J.W., and Xu, H.C. 2011. Diversity of biogenic minerals in low-temperature Si-rich deposits from a newly discovered hydrothermal field on the ultraslow spreading Southwest Indian Ridge. J. Geophys. Res. 116, G03030, doi:10.1029/2011JG001691.

    Google Scholar 

  • Polymenakou, P.N., Lampadariou, N., Mandalakis, M., and Tselepides, A. 2009. Phylogenetic diversity of sediment bacteria from the southern Cretan margin, Eastern Mediterranean Sea. Syst. Appl. Microbiol. 32, 17–26.

    Article  CAS  PubMed  Google Scholar 

  • Quaiser, A., López-García, P., ZIvanovic, Y., Henn, M., Rodríguez-Valera, F., and Moreira, D. 2007. Comparative analysis of genome fragments of Acidobacteria from deep Mediterranean plankton. Environ. Microbiol. 10, 2704–2717.

    Article  Google Scholar 

  • Quaiser, A., Ochsenreiter, T., Lanz, C., Schuster, S.C., Treusch, A.H., Eck, J., and Schleper, C. 2004. Acidobacteria forms a coherent but highly diverse group within the bacterial domain: evidence from environmental genomics. Mol. Microbiol. 50, 563–575.

    Article  Google Scholar 

  • Ravenschlag, K., Sahm, K., Knoblauch, C., Jørgensen, B.B., and Amann, R. 2000. Community structure, cellular rRNA content and activity of sulfate reducing bacteria in marine arctic sediments. Appl. Environ. Microbiol. 66, 3592–3602.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Ravenschlag, K., Sahm, K., and Amann, R. 2001. Quantitative molecular analysis of the microbial community in marine arctic sediments (Svalbard). Appl. Environ. Microbiol. 67, 387–395.

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Ravenschlag, K., Sahm, K., Pernthaler, J., and Amann, R. 1999. High bacterial diversity in permanently cold marine sediments. Appl Environ. Microbiol. 65, 3982–3989.

    CAS  PubMed Central  PubMed  Google Scholar 

  • Reed, A.J., Lutz, R.A., and Vetriani, C. 2006. Vertical distribution and diversity of bacteria and archaea in sulfide and methane-rich cold seep sediments located at the base of the Florida Escarpment. Extremophiles 10, 199–211.

    Article  CAS  PubMed  Google Scholar 

  • Ruehland, C., Blazejak, A., Lott, C., Loy, A., Erseus, C., and Dubilier, N. 2008. Multiple bacterial symbionts in two species of co-occurring gutless oligochaete worms from Mediterranean Sea grass sediments. Environ. Microbiol. 10, 3404–3416.

    Article  CAS  PubMed  Google Scholar 

  • Sahm, K., MacGregor, B.J., Jørgensen, B.B., and Stahl, D.A. 1999. Sulphate reduction and vertical distribution of sulphate-reducing bacteria quantified by rRNA slot-blot hybridization in a coastal marine sediment. Environ. Microbiol. 1, 65–74.

    Article  CAS  PubMed  Google Scholar 

  • Sánchez-Peinado, M., González-López, J., Martínez-Toledo, M., Pozo, C., and Rodelas, B. 2010. Influence of linear alkylbenzene sulfonate (LAS) on the structure of Alphaproteobacteria, Actinobacteria, and Acidobacteria communities in a soil microcosm. Environ. Sci. Pollut. Res. 17, 779–790.

    Article  Google Scholar 

  • Santelli, C.M., Orcutt, B.N., Banning, E., Bach, W., Moyer, C.L., Sogin, M.L., Staudigel, H., and Edwards, K.J. 2008. Abundance and diversity of microbial life in ocean crust. Nature 453, 653–656.

    Article  CAS  PubMed  Google Scholar 

  • Scheirer, D.S., Baker, E.T., and Johnson, K.T.M. 1998. Detection of hydrothermal plumes along the Southeast Indian Ridge near the Amsterdam-St Paul Plateau. Geophys. Res. Lett. 25, 97–100.

    Article  Google Scholar 

  • Sohrin, Y., Gamo, T., the Shipboard Science Party of the INDOYO. 1999. CTD observations to search for hydrothermal activity on the Southwest Indian Ridge and the Central Indian Ridge just north of the Rodriguez Triple Junction: the Yokosuka/Shinkai MODE ′98 Leg 3 INDOYO cruise. JAMSTEC J. Deep-sea Res. 15, 7–11.

    Google Scholar 

  • Stein, L.Y., La Duc, M.T., Grundl, T.J., and Nealson, K.H. 2001. Bacterial and archaeal populations associated with freshwater ferromanganous micronodules and sediments. Environ. Microbiol. 3, 10–18.

    Article  CAS  PubMed  Google Scholar 

  • Tao, C., Lin, J., Guo, S., Chen, Y.J., Wu, G., Han, X., German, C.R., Yoerger, D.R., Zhu, J., Zhou, N., and et al. 2007. First discovery and investigation of a high-temperature hydrothermal vent field on the ultraslow spreading Southwest Indian Ridge, AGU Fall Meeting, Abstract #T52B-07.

    Google Scholar 

  • Tao, C.H., Wu, G.H., Su, X., Egorov, I.V., Dobretsova, I.G., Zhao, H.Q., Chen, J., Zhou, N., Yang, J.Y., Chen, Z.G., and et al. 2008. Inactive hydrothermal vent field discovered at the Southwest Indian Ridge 50.5°E. Inter Ridge News. http://www.interridge.org/zh-hans/node/55706.

    Google Scholar 

  • Teske, A., Hinrichs, K.U., Edgcomb, V., de Vera Gomez, A., Kysela, D., Sylva, S.P., Sogin, M.L., and Jannasch, H.W. 2002. Microbial diversity of hydrothermal sediments in the Guaymas Basin: evidence for anaerobic methanotrophic communities. Appl. Environ. Microbiol. 68, 1994–2007

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Xu, M., Wang, P., Wang, F., and Xiao, X. 2005. Microbial diversity at a deep-sea station of the Pacific nodule province. Biodivers. Conserv. 14, 3363–3380.

    Article  Google Scholar 

  • Yoon, J., Yasumoto-Hirose, M., Katsuta, A., Sekiguchi, H., Matsuda, S., Kasai, H., and Yokota, A. 2007. Coraliomargarita akajimensis gen. nov., sp. nov., a novel member of the phylum ‘Verrucomicrobia’ isolated from seawater in Japan. Int. J. Syst. Evol. Microbiol. 57, 959–963.

    Article  CAS  PubMed  Google Scholar 

  • Zhang, W., Ki, J.S., and Qian, P.Y. 2008. Microbial diversity in polluted harbor sediments I: Bacterial community assessment based on four clone libraries of 16S rDNA. Estuar. Coast Shelf Sci. 76, 668–681.

    Article  Google Scholar 

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Authors and Affiliations

  1. Sanya Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, P. R. China

    Jiwei Li & Xiaotong Peng

  2. Southwest Jiaotong University, Chengdu, 610031, P. R. China

    Jiwei Li

  3. State Key Laboratory of Marine Geology, Tongji University, Shanghai, 200092, P. R. China

    Xiaotong Peng, Huaiyang Zhou, Jiangtao Li & Shun Chen

  4. Qingdao Institute of Marine Geology, Qingdao, 266071, P. R. China

    Zhilei Sun

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  1. Jiwei Li
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Li, J., Peng, X., Zhou, H. et al. Microbial communities in semi-consolidated carbonate sediments of the Southwest Indian Ridge. J Microbiol. 52, 111–119 (2014). https://doi.org/10.1007/s12275-014-3133-1

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