Metagenomic analysis of bacterial community composition among the cave sediments of Indo-Burman biodiversity hotspot region
- Published
- Accepted
- Subject Areas
- Biodiversity, Ecology, Microbiology
- Keywords
- Indo-Burman plateau, Cave, Bacterial diversity, illumina sequencing
- Copyright
- © 2014 De Mandal et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ PrePrints) and either DOI or URL of the article must be cited.
- Cite this article
- 2014. Metagenomic analysis of bacterial community composition among the cave sediments of Indo-Burman biodiversity hotspot region. PeerJ PrePrints 2:e631v1 https://doi.org/10.7287/peerj.preprints.631v1
Abstract
Caves in Mizoram, Northeast India are potential hotspot diversity regions due to the historical significance of the formation of Indo-Burman plateau and also because of their unexplored and unknown diversity. High throughput paired end illumina sequencing of V4 region of 16S rRNA was performed to systematically evaluate the bacterial community of three caves situated in Champhai district of Mizoram, Northeast India. A total of 10,643 operational taxonomic units (based on 97% cutoff) comprising 21 bacterial phyla and 21 candidate phyla with a sequencing depth of 11, 40013 were found in this study. The overall taxonomic profile obtained by BLAST against RDP classifier and Greengene OTU database revealed high diversity within the bacterial communities, dominated by Planctomycetes, Actinobacteria, Proteobacteria, Bacteroidetes, and Firmicutes, while members of archea were less diverse and mainly comprising of eukaryoarchea. Analysis revealed that Farpuk (CFP) cave has low diversity and is mainly dominated by actinobacteria (80% reads), whereas diverse communities were found in the caves of Murapuk (CMP) and Lamsialpuk (CLP). Analysis of rare and abundant species also revealed that a major portion of the identified OTUs were falling under rare biosphere. Significantly, all these caves recorded a high number of unclassified OUTs which might represent novel species. Further, analysis with whole genome sequencing is needed to validate the novel species as well as to determine their functional significance.
Author Comment
This will be a submission to PeerJ for review.
Supplemental Information
3 Figures and 2 Tables
Table S1 Top ten bacterial genera based on OTU number among the cave samples.
Table S2 Top ten OTU’s based on total read count number among the cave samples.
Figure S1 Graphical representation of the relative abundance of bacterial diversity from phylum to species level of CFP using 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 CMP using Krona visualization tool.