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. 2009 Jun 10;49(2):169–187. doi: 10.1007/s12088-009-0034-9

Phylogenetic profiling of bacterial community from two intimately located sites in Balramgari, North-East coast of India

Arvind Kumar Gupta 1, Ashraf Yusuf Rangrez 1, Pankaj Verma 1, Anil Chatterji 2, Yogesh S Shouche 1,✉
PMCID: PMC3450138  PMID: 23100766

Abstract

Microbial communities in coastal subsurface sediments play an important role in biogeochemical cycles. In this study microbial communities in tidal subsurface sediments of Balramgari in the state of Orissa, India were investigated using a culture independent approach. Two 16S rDNA cloned libraries were prepared from the closely located (100 m along the coast) subsurface sediment samples. Library I sediment samples had higher organic carbon content but lower sand percentage in comparison to Library II. A total of 310 clone sequences were used for DOTUR analysis which revealed 51 unique phylotypes or operational taxonomic units (OTUs) for both libraries. The OTUs were affiliated with 13 major lineages of domain bacteria including Proteobacteria (α, β, δ and λ), Acidobacteria, Actinobacteria, Cyanobacteria, Chloroflexi, Firmicutes, Verrucomicrobia, Bacteroidetes, Gemmatimonadetes and TM7. We encountered few pathogenic bacteria such as Aeromonas hydrophila and Ochrobactrum intermedium, in sediment from Library I. ∫-LIBSHUFF comparison depicts that the two libraries were significantly different communities. Most of the OTUs from both libraries possessed ≥85% to <97% similarity to RDP database sequences depicting the putative presence of new species, genera and phylum. This work revealed the complex and unique bacterial diversity from coastal habitat of Balramgari and shows that, in coastal habitat a variability of physical and chemical parameter has a prominent impact on the microbial community structure.

Keywords: Ecosystem, Microbial diversity, Marine sediment, 16S rDNA

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References

  • 1.Delong E.F. Ecology Archaea in coastal marine environments. Proc Natl Acad Sci USA. 1992;89:5685–5689. doi: 10.1073/pnas.89.12.5685. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 2.Hugenholtz P., Goebel B.M., Pace N.R. Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol. 1998;180:4765–4774. doi: 10.1128/jb.180.18.4765-4774.1998. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 3.Pace N.R. A molecular view of microbial diversity and the biosphere. Science. 1997;276:734–740. doi: 10.1126/science.276.5313.734. [DOI] [PubMed] [Google Scholar]
  • 4.Qasim S.Z. The Indian Ocean: Images and Realities. New Delhi: Oxford and IBH; 1999. pp. 57–90. [Google Scholar]
  • 5.Amann R.I., Ludwig W., Schleifer K.H. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev. 1995;59:143–169. doi: 10.1128/mr.59.1.143-169.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 6.Schauer M., Hahn M.W. Diversity and phylogenetic affiliations of morphologically conspicuous large filamentous bacteria occurring in the pelagic zones of a broad spectrum of freshwater habitats. Appl Environ Microbiol. 2005;71(4):1931–1940. doi: 10.1128/AEM.71.4.1931-1940.2005. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 7.Chatterji A (1994) The Indian Horseshoe Crab — A Living Fossil. A Project Swarajya Publication. p. 157
  • 8.Chauhan O.S. Laminae and grain size measures in beach sediments, east coast beaches. Ind J Coast Res. 1992;8:172–182. [Google Scholar]
  • 9.Wakeel S.K., Riley J.P. The determination of organic carbon in marine muds. Journal de Consel permanent international l’exploration de la mer. 1956;22:180–193. [Google Scholar]
  • 10.Weisburg W.G., Barns S.M., Pelletier D.A., Lane D.J. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol. 1991;173:697–703. doi: 10.1128/jb.173.2.697-703.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 11.Ashelford K.E., Chuzhanova N.A., Fry J.C., Jones A.J., Weightman A.J. New screening software shows that most recent large 16S rRNA gene clone libraries contain chimeras. Appl Environ Microbiol. 2006;72:5734–5741. doi: 10.1128/AEM.00556-06. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 12.Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search program. Nucleic Acids Res. 1997;25:3389–3402. doi: 10.1093/nar/25.17.3389. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 13.Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positionspecific gap penalties and weight matrix choice. Nucleic Acid Res. 1994;22:4673–4680. doi: 10.1093/nar/22.22.4673. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 14.Xie C.H., Yokota A. Phylogenetic analyses of the nitrogen-fixing genus Derxia. J Gen Appl Microbiol. 2004;50:129–135. doi: 10.2323/jgam.50.129. [DOI] [PubMed] [Google Scholar]
  • 15.Felsenstein J (1993) PHYLIP (phylogenetic inference package) version 3.61 University of Washington, Seattle, USA
  • 16.Schloss P.D., Handelsman J. Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol. 2005;71:1501–1506. doi: 10.1128/AEM.71.3.1501-1506.2005. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 17.Stackebrandt E., Goebel B.M. Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol. 1994;44:846–849. [Google Scholar]
  • 18.Huelsenbeck J.P., Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics. 2001;17:754–7555. doi: 10.1093/bioinformatics/17.8.754. [DOI] [PubMed] [Google Scholar]
  • 19.Good I.J. The population frequencies of species and the estimation of the population parameters. Biometrika. 1953;40:237–264. [Google Scholar]
  • 20.Hurlbert S.H. The non-concept of species diversity: a critique and alternative parameters. Ecology. 1971;52:577–586. doi: 10.2307/1934145. [DOI] [PubMed] [Google Scholar]
  • 21.Schloss P.D., Larget B.R., Handelsman J. Integration of microbial ecology and statistics: a test to compare gene libraries. Appl Environ Microbiol. 2004;70:5485–5492. doi: 10.1128/AEM.70.9.5485-5492.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 22.Buckley D.H., Graber J.R., Schmidt T.M. Phylogenetic analysis of nonthermophilic members of the kingdom Crenarchaeota and their diversity and abundance in soils. Appl Environ Microbiol. 1998;64:4333–4339. doi: 10.1128/aem.64.11.4333-4339.1998. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 23.Blattner F.R., Plunkett G., Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. The complete genome sequence of Escherichia coli K-12. Science. 1997;277:1453–1474. doi: 10.1126/science.277.5331.1453. [DOI] [PubMed] [Google Scholar]
  • 24.Wang G.C.Y., Wang Y. Frequency of formation of chimeric molecules is a consequence of PCR coamplification of 16S rRNA genes from mixed bacterial genomes. Appl Environ Microbiol. 1997;63:4645–4650. doi: 10.1128/aem.63.12.4645-4650.1997. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 25.Green D.H., Llewellyn L.E., Negri A.P., Blackburn S.I., Bolch C.J. Phylogenetic and functional diversity of the cultivable bacterial community associated with the paralytic shellfish poisoning dinoflagellate Gymnodinium catenatum. FEMS Microbiol Ecol. 2004;47:345–357. doi: 10.1016/S0168-6496(03)00298-8. [DOI] [PubMed] [Google Scholar]
  • 26.Yurkov V., Jappe J., Vermeglio A. Tellurite resistance and reduction by obligately aerobic photosynthetic bacteria. Appl Environ Microbiol. 1996;62:4195–4198. doi: 10.1128/aem.62.11.4195-4198.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 27.Apisarnthanarak A., Kiratisin P., Mundy L.M. Evaluation of Ochrobactrum intermedium bacteremia in a patient with bladder cancer. Diagn Microbiol Infect Dis. 2005;53:153–155. doi: 10.1016/j.diagmicrobio.2005.05.014. [DOI] [PubMed] [Google Scholar]
  • 28.Urbance J.W., Bratina B.J., Stoddard S.F., Schmidt T.M. Taxonomic characterization of Ketogulonigenium vulgare gen. nov., sp. nov. and Ketogulonigenium robustum sp. nov., which oxidize L-sorbose to 2-keto-L-gulonic acid. Int J Syst Evol Microbiol. 2001;51:1059–1070. doi: 10.1099/00207713-51-3-1059. [DOI] [PubMed] [Google Scholar]
  • 29.Maturrano L., Santos F., Rossello-Mora R., Anton J. Microbial diversity in maras salterns, a hypersaline environment in the peruvian andes. Appl Environ Microbiol. 2006;72:3887–3895. doi: 10.1128/AEM.02214-05. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 30.Wang D.L., Xiao M., Qian W., Han B. Screening and identification of a photosynthetic bacterium reducing selenite to red elemental selenium. Wei Sheng Wu Xue Bao. 2007;47:44–47. [PubMed] [Google Scholar]
  • 31.Srinivas T.N.R., Anil-Kumar P., Sasikala C., Ramana C.V., Süling J., Imhoff J.F. Rhodovulum marinum sp. nov., a novel phototrophic purple non-sulfur alphaproteobacterium from marine tides of Visakhapatnam. India Int J Syst Evol Microbiol. 2006;56:1651–1656. doi: 10.1099/ijs.0.64005-0. [DOI] [PubMed] [Google Scholar]
  • 32.Brettar I., Christen R., Botel J., Lunsdorf H., Hofle M.G. Anderseniella baltica gen. nov.,sp. nov., a novel marine bacterium of the Alphaproteobacteria isolated from sediment in the central Baltic Sea. Int J Syst Evol Microbiol. 2007;57:2399–2405. doi: 10.1099/ijs.0.65007-0. [DOI] [PubMed] [Google Scholar]
  • 33.Xie C.H., Yokota A. Phylogenetic analyses of the nitrogen-fixing genus Derxia. J Gen Appl Microbiol. 2004;50:129–135. doi: 10.2323/jgam.50.129. [DOI] [PubMed] [Google Scholar]
  • 34.Iizuka T., Tokura M., Jojima Y., Hiraishi A., Yamanaka S., Fudou R. Enrichment and phylogenetic analysis of moderately thermophilic myxobacteria from hot springs in Japan. Microbes Environ. 2006;21:189–199. doi: 10.1264/jsme2.21.189. [DOI] [Google Scholar]
  • 35.Hippe H., Vainshtein M., Gogotova G.I., Stackebrandt E. Reclassification of Desulfobacterium macestii as Desulfomicrobium macestii comb. Nov Int J Syst Evol Microbiol. 2003;53:1127–1130. doi: 10.1099/ijs.0.02574-0. [DOI] [PubMed] [Google Scholar]
  • 36.Schnell S., Bak F., Pfennig N. Anaerobic degradation of aniline and dihydroxybenzenes by newly isolated sulfate-reducing bacteria and description of Desulfobacterium aniline. Arch Microbiol. 1989;152:556–563. doi: 10.1007/BF00425486. [DOI] [PubMed] [Google Scholar]
  • 37.Ellner G., Busman A., Rainey F.A., Diekman H. A syntrophic propionate-oxidizing, sulfate-reducing bacterium from a fluidized bed reactor. Syst Appl Microbiol. 1996;19:414–420. [Google Scholar]
  • 38.Blazejak A., Erseus C., Amann R., Dubilier N. Coexistence of bacterial sulfide oxidizers, sulfate reducers, and spirochetes in a gutless worm (Oligochaeta) from the Peru margin. Appl Environ Microbiol. 2005;71:1553–1561. doi: 10.1128/AEM.71.3.1553-1561.2005. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 39.Thamdrup B., Rossello-Mora R., Amann R. Microbial manganese and sulfate reduction in Black Sea shelf ediments. Appl Environ Microbiol. 2000;66:2888–2897. doi: 10.1128/AEM.66.7.2888-2897.2000. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 40.Oremland R.S., Hoeft S.E., Santini J.M., Bano N., Hollibaugh R.A., Hollibaugh J.T. Anaerobic oxidation of arsenite in monolake water by a facultative arsenite-oxidizing chemoautotroph, strain MLHE-1. Appl Environ Microbiol. 2002;68:4795–4802. doi: 10.1128/AEM.68.10.4795-4802.2002. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 41.Ulledge J., Ahmad A., Steudler P.A., Pomerantz W.J., Cavanaugh C.M. Family- and genus-level 16S rRNA-targeted oligonucleotide probes for ecological studies of methanotrophic bacteria. Appl Environ Microbiol. 2001;67:4726–4733. doi: 10.1128/AEM.67.10.4726-4733.2001. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 42.Schäfer H. Isolation of Methylophaga spp. from Marine dimethylsulfide-degrading enrichment cultures and identification of polypeptides induced during growth on dimethylsulfide. Appl Environ Microbiol. 2007;73:2580–2591. doi: 10.1128/AEM.02074-06. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 43.Ruimy R., Breittmayer V., Elbaze P., Lafay B., Boussemart O., Gauthier M., Christen R. Phylogenetic analysis and assessment of the genera Vibrio, Photobacterium, Aeromonas, and Plesiomonas deduced from small-subunit rRNA sequences. Int J Syst Bacteriol. 1994;44:416–426. doi: 10.1099/00207713-44-3-416. [DOI] [PubMed] [Google Scholar]
  • 44.Syutsubo K., Kishira H., Harayama S. Development of specific oligonucleotide probes for the identification and in situ detection of hydrocarbon-degrading Alcanivorax strains. Environ Microbiol. 2001;3:371–379. doi: 10.1046/j.1462-2920.2001.00204.x. [DOI] [PubMed] [Google Scholar]
  • 45.Meo C.A., Wilbur A.E., Holben W.E., Feldman R.A., Vrijenhoek R.C., Cary S.C. Genetic variation among endosymbionts of widely distributed vestimentiferan tubeworms. Appl Environ Microbiol. 2000;66:651–658. doi: 10.1128/AEM.66.2.651-658.2000. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 46.Dubilier N., Mulders C., Ferdelman T., Beer D., Pernthaler A., Klein M., Wagner M., Erseus C., Thiermann F., Krieger J., Giere O., Amann R. Endosymbiotic sulphatereducing and sulphide-oxidizing bacteria in an oligochaete worm. Nature. 2001;411:298–302. doi: 10.1038/35077067. [DOI] [PubMed] [Google Scholar]
  • 47.Goto K., Omura T., Hara Y., Sadaie Y. Application of the partial 16S rDNA sequence as an index for rapid identification of species in the genus Bacillus. J Gen Appl Microbiol. 2000;46:1–8. doi: 10.2323/jgam.46.1. [DOI] [PubMed] [Google Scholar]
  • 48.Kowallik K.V., Stoebe B., Schaffran I., Kroth-Pancic P., Freier U. The chloroplast genome of a chlorophyll a+c- containing alga, Odontella sinensis. Plant Mol Biol Rep. 1995;13:336–342. doi: 10.1007/BF02669188. [DOI] [Google Scholar]
  • 49.Das S., Lyla P.S., Khan S.A. Marine microbial diversity and ecology: importance and future perspectives. Cur Science. 2006;90:1325–1335. [Google Scholar]
  • 50.More M.I., Herrick J.B., Silva M.C., Ghiorse W.C., Madsen E.L. Quantitative cell lysis of indigenous microorganisms and rapid extraction of microbial DNA from sediment. Appl Environ Microbiol. 1994;60:1572–1580. doi: 10.1128/aem.60.5.1572-1580.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 51.Wilson K.H., Blitchington R.B. Human colonic biota studied by ribosomal DNA sequence analysis. Appl Environ Microbiol. 1996;62:2273–2278. doi: 10.1128/aem.62.7.2273-2278.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 52.Kerkhof L., Speck M. Ribosomal RNA gene dosage in marine bacteria. Mol Mar Biol Biotechnol. 1997;6:260–267. [PubMed] [Google Scholar]
  • 53.Chandler D.P., Fredrickson J.K., Brockman F.J. Effect of PCR template concentration on the composition and distribution of total community 16S rDNA clone libraries. Mol Ecol. 1997;6:475–482. doi: 10.1046/j.1365-294X.1997.00205.x. [DOI] [PubMed] [Google Scholar]
  • 54.Farrelly V., Rainey F.A., Stackebrandt E. Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species. Appl Environ Microbiol. 1995;61:2798–2801. doi: 10.1128/aem.61.7.2798-2801.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]

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