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Bacterial Diversity in a Sri Lankan Geothermal Spring Assessed by Culture-Dependent and Culture-Independent Approaches

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Abstract

Hot springs harbour diverse and interesting groups of microorganisms adapted to extreme conditions. However, due to limitations in the culture-dependent approach, most of such thermophiles remain uncultured and unexplored. Hence, this study was conducted to gain a comprehensive understanding of the bacterial diversity of Mahapelessa hot spring, Sri Lanka using both culture-dependent and culture-independent approaches. The in situ temperature of the water sample was 44.5 °C and the pH was 8.14. 16S rRNA Sanger sequencing of DNA extracted from the 18 bacterial isolates revealed the presence of eight genera belonging to two phyla: Proteobacteria (84%) and Firmicutes (16%) and the most abundant genus being Klebsiella. A total of 23 bacterial phyla representing 80 classes, 43 orders, 123 families, 205 genera and 83 species were detected by 16S rRNA V3-V4 region by amplicon metagenome sequencing of DNA extracted from water samples, where the most abundant phylum was the Proteobacteria (57.39%), followed by Firmicutes (23.7%) and Chloroflexi (4.14%). The three phyla Actinobacteria, Planctomycetes and Bacteroidetes were also detected less than 3% in abundance while 4.48% of bacteria could not be fit into any known phylum. The most abundant genera were Burkholderia (14.87%), Desulfotomaculum (7.23%) and Stenotrophomonas (6.1%). Four strictly anaerobic bacteria, Anaerosolibacter carboniphilus (0.71%), Bellilinea caldifistulae (0.04%), Salimesophilobacter vulgaris (0.1%), Anaerobacterium chartisolvens (0.12%); two potential plant growth-promoting bacteria, Azospirillum halopraeferens (0.04%) and Bradyrhizobium liaoningense (0.16%) and one potential alkali tolerant and sulphate-reducing bacterium, Desulfovibrio alkalitolerans (0.45%) were recorded. Pigmentiphaga sp. was isolated from Mahapelessa hot spring and to the best of our knowledge, this is the first record of this genus from a hot spring. This study gives insight into the vast bacterial diversity present in the Mahapelessa hot spring from the culture-independent approach which could not be identified using standard culturing techniques.

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Funding

National Institute of Fundamental Studies, Hantana Road, Kandy, Sri Lanka.

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Authors and Affiliations

  1. Molecular Microbiology and Human Diseases Research Group, National Institute of Fundamental Studies, Hantana Road, Kandy, Sri Lanka

    Supun N. Samarasinghe & Dhammika N. Magana-Arachchi

  2. Department of Plant and Molecular Biology, University of Kelaniya, Kelaniya, Sri Lanka

    Rasika P. Wanigatunge

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  1. Supun N. Samarasinghe
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  2. Rasika P. Wanigatunge
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All authors contributed to the study conception and design. Material preparation, data collection and analysis were performed by SNS, RPW and DNM-A. The first draft of the manuscript was written by SNS and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

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Correspondence to Dhammika N. Magana-Arachchi.

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Samarasinghe, S.N., Wanigatunge, R.P. & Magana-Arachchi, D.N. Bacterial Diversity in a Sri Lankan Geothermal Spring Assessed by Culture-Dependent and Culture-Independent Approaches. Curr Microbiol 78, 3439–3452 (2021). https://doi.org/10.1007/s00284-021-02608-4

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