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MiSeq HV4 16S rRNA gene analysis of bacterial community composition among the cave sediments of Indo-Burma biodiversity hotspot

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Abstract

Caves in Mizoram, Northeast India, are potential hotspot diversity regions due to the historical significance of the formation of the Indo-Burman plateau and also because of their unexplored and unknown diversity. High-throughput paired end Illumina sequencing of the V4 region of 16S rRNA was performed to study the bacterial community of three caves situated in Champhai district of Mizoram, Northeast India. A total of 10,643 operational taxonomic units (OTUs) (based on 97 % cutoff) comprising of 21 major and 21 candidate phyla with a sequencing depth of 1,140,013 were found in this study. The overall taxonomic profile obtained by the RDP classifier and Greengenes OTU database revealed high diversity within the bacterial communities. Communities were dominated by Planctomycetes, Actinobacteria, Proteobacteria, Bacteroidetes, and Firmicutes, while members of Archaea were less varied and mostly comprising of Eukaryoarchea. Analysis revealed that Farpuk (CFP) cave sediment has low microbial diversity and is mainly dominated by Actinobacteria (80 % reads), whereas different bacterial communities were found in the caves of Murapuk (CMP) and Lamsialpuk (CLP). Analysis also revealed that a major portion of the identified OTUs was classified under rare biosphere. Importantly, all these caves recorded a high number of unclassified OTUs, which might represent new species. Further analysis with whole genome sequencing is needed to validate the unknown species as well as to determine their functional role.

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Acknowledgments

This research was supported by a grant from the State Biotech Hub and Bioinformatics Infrastructure Facility sponsored by Department of Biotechnology, Govt. of India, New Delhi.

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Authors and Affiliations

  1. Department of Biotechnology, Mizoram University, Aizawl, 796004, Mizoram, India

    Surajit De Mandal,  Zothansanga & Nachimuthu Senthil Kumar

  2. Department of Zoology, Kumaun University, Nainital, 263002, Uttarakhand, India

    Amrita Kumari Panda & Satpal Singh Bisht

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  1. Surajit De Mandal
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  2. Zothansanga
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  3. Amrita Kumari Panda
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  4. Satpal Singh Bisht
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  5. Nachimuthu Senthil Kumar
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Correspondence to Nachimuthu Senthil Kumar.

Additional information

Responsible editor: Robert Duran

Nucleotide sequence accession number

Paired end Illumina sequence data from this study were submitted to the NCBI Sequence Read Archive (SRA) under accession numbers SRA064116, SRA064118, and SRA064120.

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Table S1

Top ten bacterial genera based on OTU number among the cave samples.

Table S2

Top ten OTUs based on total read count number among the cave samples.

Table S3

Pearson’s correlation coefficient between soil characteristics and bacterial phyla.

Figure S1

Graphical representation of the relative abundance of bacterial diversity from phylum to species level of CFP using the Krona visualization tool.

Figure S2

Graphical representation of the relative abundance of bacterial diversity from phylum to species level of CLP using Krona visualization tool.

Figure S3

Graphical representation of the relative abundance of bacterial diversity from phylum to species level of CMC using the Krona visualization tool.

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De Mandal, S., Zothansanga, Panda, A.K. et al. MiSeq HV4 16S rRNA gene analysis of bacterial community composition among the cave sediments of Indo-Burma biodiversity hotspot. Environ Sci Pollut Res 23, 12216–12226 (2016). https://doi.org/10.1007/s11356-016-6423-9

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