Abstract
Microbial diversity of 1,000 m deep pelagic sediment from off Coast of Andaman Sea was analyzed by a culture independent technique, bacterial tag encoded FLX titanium amplicon pyrosequencing. The hypervariable region of small subunit ribosomal rRNA gene covering V6–V9, was amplified from the metagenomic DNA and sequenced. We obtained 19,271 reads, of which 18,206 high quality sequences were subjected to diversity analysis. A total of 305 operational taxonomic units (OTUs) were obtained corresponding to the members of firmicutes, proteobacteria, plantomycetes, actinobacteria, chloroflexi, bacteroidetes, and verucomicrobium. Firmicutes was the predominant phylum, which was largely represented with the family bacillaceae. More than 44 % of sequence reads could not be classified up to the species level and more than 14 % of the reads could not be assigned to any genus. Thus, the data indicates the possibility for the presence of uncultivable or unidentified novel bacterial species. In addition, the community structure identified in this study significantly differs with other reports from marine sediments.
Similar content being viewed by others
References
Polymenakou PN, Lampadariou N, Mandalakis M, Tselepides A (2009) Phylogenetic diversity of sediment bacteria from the Southern Cretan margin, Eastern Mediterranean Sea. Syst Appl Microbiol 32:17–26
Surajit D, Lyla PS, Ajmal Khan S (2006) Marine microbial diversity and ecology: importance and future perspectives. Curr Sci 90:1325–1337
Azam F (1998) Oceanography: microbial control of oceanic carbon flux:the plot thickens. Science 280:694–696
Wu H, Yatao Guo Y, Wang G, Dai S, Li X (2011) Composition of bacterial communities in deep-sea sediments from the South China Sea, the Andaman Sea and the Indian Ocean. Afr J Microbiol Res 5:5273–5283
Biddle JF, SylvanJB Brazelton WJ, Tully BJ, Edwards KJ, Moyer CL, Heidelberg JF, Nelson WC (2012) Prospects for the study of evolution in the deep biosphere. Frontiers Microbiol. doi:10.3389/fmicb.2011.00285
Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D et al (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66–74
Dini-Andreote F, Andreote FD, Araújo WL, Trevors JT, Van Elsas JD (2012) Bacterial genomes: habitat specificity and uncharted organisms. Microb Ecol 64:1–7
Edwards RA, Rodriguez-Brio B, Wegley L et al (2006) Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics 7:57
Roesch LF, Fulthope PR, Riva A, Casella G, Hadwin AK et al (2007) Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J 1:283–290
Huber JA, Mark Welch DB, Morrison HG, Huse SM, Neal PR (2007) Microbial population structures in the deep marine biosphere. Science 318:97–100
Kim BS, Kim BK, Lee JH, Kim M, Lim YW, Chun J (2008) Rapid phylogenetic dissection of prokaryotic community structure in tidal flat using pyrosequencing. J Microbiol 46:357–363
Keijser BJF, Zaura E, Huse SM et al (2008) Pyrosequencing analysis of the oral microflora of healthy adults. J Dent Res 87:1016–1020
Liu Z, DeSantis TZ, Andersen GL, Knight R (2008) Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers. Nucl Acid Res 36:120
Zhou J, Brunns MA, Tiedje JM (1996) DNA recovery from soil of diverse composition. Appl Environ Microbiol 62:316–322
Dowd SE, Sun Y, Secor PR, Rhoads DD, Wolcott BM, James CA, Wolcott RD (2008) Survey of bacterial diversity in chronic wounds using pyrosequencing, DGGE, and full ribosome shotgun sequencing. BMC Microbiol 8:43–58
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M et al (2009) Introducing mothur: open source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541
Zajec N, Stres B, Avgustin G (2012) Distinct approaches for the detection and removal of chimeric 16S rRNA sequences can significantly affect the outcome of between-site comparisons. Aquat Microb Ecol 66:13–21
Cole JR, Chai B, Farris RJ, Wang Q, Kulam SA, McGarrell DM, Garrity GM, Tiedje JM (2004) The ribosomal database project (RDP-II): sequences and tools for high- throughput rRNA analysis. Nucl Acids Res 33:D294–D296
Huson DH, Mitra S, Ruscheweyh HJ, Weber N, Schuster SC (2011) Integrative analysis of environmental sequences using MEGAN4. Genome Res. doi:10.1101/gr.120618.111
Mori H, Maruyama F, Kurokawa K (2010) SVofItTwareOMI: visualization tool for taxonomic compositions of microbial communities based on 16S rRNA gene sequences. BMC Bioinformatics 11:332
Schloss PD, Handelsman J (2004) Status of the microbial census. Microbiol Mol Biol Rev 68:686–691
Mitra S, Stark M, Huson DH (2011) Analysis of 16S rRNA environmental sequences using MEGAN. BMC Genomics 21:17
Schloss PD (2010) The effects of alignment quality, distance calculation method, sequence filtering and region on the analysis of 16s rRna gene-based studies. PLoS Comput Biol 6:e1000844
Briggs BR, Inagaki F, Morono Y, Futagami T, Huguet C, Rosell-Mele A, Lorenson TD, Colwell FS (2012) Bacterial dominance in subseafloor sediments characterized by methane hydrates. FEMS Microbiol Ecol 81:88–98
Andersson AF, Lindberg M, Jakobsson H, Backhed F, Nyren P, Engstrand L (2008) Comparative analysis of human gut microbiota by barcoded pyrosequencing. PLoS ONE 3:e2836
Tekere M, Prinsloo A, Olivier J, Jonker N, Venter S (2012) An evaluation of the bacterial diversity at Tshipise, Mphephu and Sagole hot water springs, Limpopo Province, South Africa. Afr J Microbiol Res 6:4993–5004
Bowman JP, McCuaig RD (2003) Biodiversity, community structural shifts, and biogeography of prokaryotes within Antarctic continental shelf sediment. Appl Environ Microbiol 69:2463–2483
Xu M, Wang P, Wang F, Xiao X (2005) Microbial diversity at a deep-sea station of the Pacific Nodule Province. Biodiversity Conserv 14:3363–3380
Ravenschlag K, Sahm K, Amann R (2000) Quantitative molecular analysis of the microbial community in marine arctic sediments (svalbard). Appl Environ Microbiol 67:387–395
Levin LA, Etter RJ, Rex MA, Gooday AJ, Smith CR, Pineda J, Stuart CT, Hessler RR, Pawson D (2001) Environmental influences on regional deep-sea species diversity. Annu Rev Ecol Syst 132:51–93
Sogin ML, Morrison HG, Huber JA, Welch DM, Huse SM, Neal PR, Arretia JM, Herndl GJ (2006) Microbial diversity in the deep sea and the underexplored “rare biosphere”. Proc Natl Acad Sci USA 103:12115–12120
Siefert JL, Larios-Sanz M, Nakamura LK, Slepecky RA, Paul JH, Moore ER, Fox GE, Jurtshuk P (2000) Phylogeny of marine Bacillus isolates from the Gulf of Mexico. Curr Microbiol 41:84–88
Miranda CA, Martins OB, Clementino MM (2008) Species-level identification of Bacillus strains isolated from marine sediments by conventional biochemical, 16S rRNA gene sequencing and inter-tRNA gene sequence lengths analysis. Antonie Van Leeuwenhock 93:297–304
Jang SK, Zhang W, Qian PY (2009) Discovery of marine Bacillus species by 16S rRNA and rpoB comparisons and their usefulness for species identification. J Microbiol Methods 77:48–57
Ivanova EP, Vysotskii MV, Svetashev VI, Nedashkovskaya OI, Gorshkova NM, Mikhailov VV, Yumoto N, Shigeri Y, Taguchi T, Yoshikawa S (1999) Characterization of Bacillus strains of marine origin. Int Microbiol 2:267–271
Nealson KH, Ford J (1980) Surface enhancement of bacterial manganese oxidation: implications for aquatic environments. Geo Microbiol J 2:21–37
Tebo BM, Ghiorse WC, Waasbergen LG, Sering PL, Caspi R (1997) Bacterially-mediated mineral formation: insights into manganese(II) oxidation from molecular genetic and biochemical studies. In: Banfield JF, Nealson KH (eds) Geomicrobiology: interactions between microbes and minerals, Washington, DC. Mineral Soc Am 35:225–266
Oh HM, Giovannoni SJ, Ferriera S, Johnson J, Cho JC (2009) Complete genome sequence of Erythrobacter litoralis HTCC2594. J Bacteriol 191:2419–2420
Sorokin DY, Tourova TP, Muyzer G, Kuenen GJ (2008) Thiohalospira halophila gen. nov., sp. nov., and T. alkaliphila sp. nov., novel obligately chemolithoautotrophic, halophilic, sulfur-oxidizing gammaproteobacteria from hypersaline habitats. Int J Syst Evol Microbiol 58:1685–1692
Acknowledgments
The authors thankfully acknowledge funding from Department of Biotechnology, New Delhi (No. BT/PR-10486/BCE/08/657/2008). The authors also thank Mr. Ravi, vessel manager, NIOT for his support. Authors also acknowledge the central facilities, CAS, CEGS, NRCBS and IPLS at MKU.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Sundarakrishnan, B., Pushpanathan, M., Jayashree, S. et al. Assessment of Microbial Richness in Pelagic Sediment of Andaman Sea by Bacterial Tag Encoded FLX Titanium Amplicon Pyrosequencing (bTEFAP). Indian J Microbiol 52, 544–550 (2012). https://doi.org/10.1007/s12088-012-0310-y
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12088-012-0310-y