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Deep sequencing analysis of bacterial community structure of Soldhar hot spring, India

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Abstract

We investigated the bacterial community structure of Soldhar hot spring with extreme high temperature 95°C located in Uttarakhand, India using high throughput sequencing. Bacterial phyla Proteobacteria (88.8%), Deinococcus-Thermus (7.5%), Actinobacteria (2.3%), and Firmicutes (1.07%) were predominated in the sequencing survey, whereas Bacteroidetes, Verrucomicrobia, Aquificae and Acidobacteria were detected in relatively lower abundance in Soldhar hot spring. At the family level, Comamonadaceae (52.5%), Alteromonadaceae (15.9%), and Thermaceae (7.5%) were mostly dominated in the ecosystem followed by Chromatiaceae, Microbacteriaceae, and Cyclobacteriaceae. Besides, members of Rhodobacteraceae, Moraxellaceae, Xanthomonadaceae, Aquificaceae, Enterobacteriaceae, Bacillaceae, Methylophilaceae, etc. were detected as a relatively lower abundance. In the present study we discuss the overall microbial community structure and their relevance to the ecology of the Soldhar hot spring environment.

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References

  • Blank, C.E., Cady, S.L., and Pace, N.R., Microbial composition of near-boiling silica-depositing thermal springs throughout Yellowstone National Park, Appl. Environ. Microbiol., 2002, vol. 68, pp. 5123–5135.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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., et al., QIIME allows analysis of high-throughput community sequencing data, Nat. Methods, 2010, vol. 7, no. 5, pp. 335–336.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Edgar, R.C., Haas, B.J., Clemente, J.C., Quince, C., and Knight, R., UCHIME improves sensitivity and speed of chimera detection, Bioinformatics, 2011, vol. 27, no. 16, pp. 2194–2200.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Elshahed, M.S., Senko, J.M., Najar, F.Z., Kenton, S.M., Roe, B.A., Dewers, T.A., Spear, J.R., and Krumholz, L.R., Bacterial diversity and sulfur cycling in a mesophilic sulfide-rich spring, Appl. Environ. Microbiol., 2003, vol. 69, no. 9, pp. 5609–5612.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ghelani, A., Patel, R., Mangrola, A., and Dudhagara, P., Cultivation-independent comprehensive survey of bacterial diversity in Tulsi Shyam Hot Springs, India, Genomics Data, 2015, vol. 4, pp. 54–56.

    Article  Google Scholar 

  • Jackson, T.J., Ramaley, R.F., and Meinschein, W.G., Thermomicrobium, a new genus of extremely thermophilic bacteria, Int. J. Syst. Evol. Microbiol., 1973, vol. 23, no. 1, pp. 28–36.

    Article  Google Scholar 

  • Jünemann, S., Prior, K., Szczepanowski, R., Harks, I., Ehmke, B., Goesmann, A., Stoye, J., and Harmsen, D., Bacterial community shift in treated periodontitis patients revealed by ion torrent 16S rRNA gene amplicon sequencing, PLoS One, 2012, vol. 7, no. 8, e41606.

    Article  PubMed  PubMed Central  Google Scholar 

  • Kumbhare, S.V., Dhotre, D.P., Dhar, S.K., Jani, K., Apte, D.A., Shouche, Y.S., and Sharma, A., Insights into diversity and imputed metabolic potential of bacterial communities in the continental shelf of Agatti Island, PLoS One, 2015, vol. 10, no. 6, e0129864.

    Article  PubMed  PubMed Central  Google Scholar 

  • Kumar, B., Trivedi, P., Mishra, A.K., Pandey, A., and Palni, L.M.S., Microbial diversity of soil from two hot springs in Uttaranchal Himalaya, Microbiol. Res., 2004, vol. 159, no. 2, pp. 141–146.

    Article  CAS  PubMed  Google Scholar 

  • Kambura, A.K., Mwirichia, R.K., Kasili, R.W., Karanja, E.N., Makonde, H.M., and Boga, H.I., Bacteria and Archaea diversity within the hot springs of Lake Magadi and Little Magadi in Kenya, BMC Microbiol., 2016, vol. 16, p. 136.

    Article  PubMed  PubMed Central  Google Scholar 

  • Mangrola, A., Dudhagara, P., Koringa, P., Joshi, C.G., Parmar, M., and Patel, R., Deciphering the microbiota of Tuwa hot spring, India using shotgun metagenomic sequencing approach, Genomics Data, 2015, vol. 4, pp. 153–155.

    PubMed  Google Scholar 

  • Munson, M.A., Banerjee, A., Watson, T.F., and Wade, W.G., Molecular analysis of the microflora associated with dental caries, J. Clin. Microbiol., 2004, vol. 42, no. 7, pp. 3023–3029.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pandey, A., Dhakar, K., Sati, P., Sharma, A., Kumar, B., and Palni, L.M.S., Geobacillus stearothermophilus (GBPI_16): a resilient hyperthermophile isolated from an autoclaved sediment sample, Proc. Natl. Acad. Sci. India, 2014, vol. B84, no. 2, pp. 349–356.

    Google Scholar 

  • Pandey, A., Dhakar, K., Sharma, A., Payal, P., Sati, P., and Kumar, B., Thermophilic bacteria that tolerate wide temperature and pH range colonize the Soldhar (95°C) and Ringigad (80°C) hot springs of Uttarakhand, India, Ann. Microbiol., 2015, vol. 65, pp. 809–816.

    Article  CAS  Google Scholar 

  • Preuesse, E., Quast, C., Knittel, K., Fuchs, B., Ludwig, W., Peplies, J., and Glöckner, F.O., SILVA a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB, Nucleic Acids Res., 2007, vol. 35, no. 21, pp. 7188–7196.

    Article  Google Scholar 

  • Purcell, D., Sompong, U., Yim, L.C., Barraclough, T.G., Peerapornpisal, Y., and Pointing, S.B., The effects of temperature, pH and sulphide on the community structure of hyperthermophilic streamers in hot springs of northern Thailand, FEMS Microbiol. Ecol., 2007, vol. 60, no. 3, pp. 456–466.

    CAS  Google Scholar 

  • Rondon, M.R., August, P.R., Bettermann, A.D., Brady, S.F., Grossman, T.H., Liles, M.R., Loiacono, K.A., Lynch, B.A., MacNeil, I.A., Minor, C., Tiong, C.L., Gilman, M., Osburne, M.S., Clardy, J., Handelsman, J., and Goodman, R.M., Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms, Appl. Environ. Microbiol., 2000, vol. 66, no. 6, pp. 2541–2547.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Saha, P., Mondal, A.K., Mayilraj, S., Krishnamurthi, S., Bhattacharya, A., and Chakrabarti, T., Paenibacillus assamensis sp. nov., a novel bacterium isolated from a warm spring in Assam, India, Int. J. Syst. Evol. Microbiol., 2005, vol. 55, no. 6, pp. 2577–2581.

    CAS  Google Scholar 

  • Sangwan, N., Lambert, C., Sharma, A., Gupta, V., Khurana, P., Khurana, J.P., Sockett, R.E., Gilbert, J.A., and Lal, R., Arsenic rich Himalayan hot spring metagenomics reveal genetically novel predator–prey genotypes, Environ. Microbiol. Rep., 2015, vol. 7, no. 6, pp. 812–823.

    Article  CAS  PubMed  Google Scholar 

  • 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., and Weber, C.F., Introducing mothur: open-source,platform-independent,community-supported software for describing and comparing microbial communities, Appl. Environ. Microbiol., 2009, vol. 75, no. 23, pp. 7537–7541.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sharma, A., Jani, K., Shouche, Y.S., and Pandey, A., Microbial diversity of the Soldhar hot spring,India,assessed by analyzing 16S rRNA and protein-coding genes, Ann. Microbiol., 2015, vol. 65, no. 3, pp. 1323–1332.

    Article  CAS  Google Scholar 

  • Sharma, A., Pandey, A., Shouche, Y.S., Kumar, B., and Kulkarni, G., Characterization and identification of Geobacillus spp. isolated from Soldhar hot spring site of Garhwal Himalaya,India, J. Bas. Microbiol., 2009, vol. 49, no. 2, pp. 187–194.

    Article  CAS  Google Scholar 

  • Shivaji, S., Chaturvedi, P., Begum, Z., Pindi, P.K., Manorama, R., Padmanaban, D.A., Shouche, Y.S., Pawar, S., Vaishampayan, P., Dutt, C.B., Datta, G.N., Manchanda, R.K., Rao, U.R., Bhargava, P.M., and Narlikar, J.V., Janibacter hoylei sp. nov., Bacillus isronensis sp. nov. and Bacillus aryabhattai sp. nov., isolated from cryotubes used for collecting air from the upper atmosphere, Int. J. Syst. Evol. Microbiol., 2009, vol. 59, no. 12, pp. 2977–2986.

    CAS  PubMed  Google Scholar 

  • Singh, A. and Subudhi, E., Structural insights of microbial community of Deulajhari (India) hot spring using 16SrRNA based metagenomic sequencing, Genomics Data, 2016, vol. 7, pp. 101–102.

    Article  PubMed  Google Scholar 

  • Tekere, M., Lötter, A., Olivier, J., Jonker, N., and Venter, S., Metagenomic analysis of bacterial diversity of Siloam hot water spring, Limpopo, South Africa, Afr. J. Biotechnol., 2011, vol. 10, no. 78, pp. 18005–18012.

    Google Scholar 

  • Tekere, M., Prinsloo, A., Olivier, J., Jonker, N., and Stephanus, V., An evaluation of the bacterial diversity at Tshipise, Mphephu and Sagole hot water springs, Limpopo Province, South Africa, Afr. J. Microbiol., 2012, vol. 6, no. 23, pp. 4993–5004.

    CAS  Google Scholar 

  • Trivedi, P., Kumar, B., and Pandey, A., Conservation of soil microbial diversity associated with two hot springs in Uttaranchal Himalaya, Natl. Acad. Sci. Lett., 2006, vol. 29, nos. 5–6, pp. 185–188.

    Google Scholar 

  • Vasileiadis, S., Puglisi, E., Arena, M., Cappa, F., Cocconcelli, P.S., and Trevisan, M., Soil bacterial diversity screening using single 16S rRNA gene V regions coupled with multi-million read generating sequencing technologies, PLoS One, 2012, vol. 7, no. 8, e42671.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang, Q., Garrity, G.M., Tiedje, J.M., and Cole, J.R., Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy, Appl. Environ. Microbiol., 2007, vol. 73, no. 16, pp. 5261–5267.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Weltzer, M.L., and Miller, S.R., Division-specific differences in bacterial community assembly of two alkaline hot spring ecosystems from Yellowstone National Park, Microb. Ecol., 2013, vol. 65, no. 3, pp. 537–540.

    Article  PubMed  Google Scholar 

  • Whiteley, A.S., Jenkins, S., Waite, I., Kresoje, N., Payne, H., Mullan, B., Allcock, R., and O’Donnell, A., Microbial 16S rRNA ion tag and community metagenome sequencing using the ion torrent (PGM) platform, J. Microbiol. Methods., 2012, vol. 91, no. 1, pp. 80–88.

    Article  CAS  PubMed  Google Scholar 

  • Xie, W., Wang, F., Guo, L., Chen, Z., Sievert, S.M., Meng, J., Huang, G., Li, Y., Yan, Q., Wu, S., Wang, X., Chen, S., He, G., Xiao, X., and Xu, A., Comparative metagenomics of microbial communities inhabiting deep-sea hydrothermal vent chimneys with contrasting chemistries, ISME J., 2011, vol. 5, no. 3, pp. 414–426.

    Article  PubMed  Google Scholar 

  • Zhou, H., Li, J., Peng, X., Meng, J., Wang, F., and Ai, Y., Microbial diversity of a sulphide black smoker in main endeavour hydrothermal vent field,Juan de Fuca Ridge, J. Microbiol., 2009, vol. 47, no. 3, pp. 235–247.

    Article  CAS  PubMed  Google Scholar 

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Authors and Affiliations

  1. Microbial Culture Collection, National Centre for Cell Science, Pune, Maharashtra, 411007, India

    A. Sharma, D. Paul, D. Dhotre, K. Jani & Y. S. Shouche

  2. Biotechnological Applications, G.B. Pant National Institute of Himalayan Environment and Sustainable Development, Kosi-Katarmal, Uttakrakhand, Almora, 263643, India

    A. Pandey

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  1. A. Sharma
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  6. Y. S. Shouche
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Sharma, A., Paul, D., Dhotre, D. et al. Deep sequencing analysis of bacterial community structure of Soldhar hot spring, India. Microbiology 86, 136–142 (2017). https://doi.org/10.1134/S0026261717010118

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