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Metagenome Analysis of Speleothem Microbiome from Subterranean Cave Reveals Insight into Community Structure, Metabolic Potential, and BGCs Diversity

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Abstract

The Borra caves, the second largest subterranean karst cave ecosystem in the Indian sub-continent, are located at the Ananthagiri hills of Araku Valley in the Alluri district of Andhra Pradesh, India. The present investigation applied a shotgun metagenomic approach to gain insights into the microbial community structure, metabolic potential, and biosynthetic gene cluster (BGC) diversity of the microbes colonizing the surface of the speleothems from the aphotic zone of Borra caves. The taxonomic analysis of the metagenome data illustrated that the speleothem-colonizing core microbial community was dominated mainly by Alpha-, Beta-, and Gamma-Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. The key energy metabolic pathways analysis provides strong evidence of chemolithoautotrophic and chemoheterotrophic modes of nutrition in the speleothem-colonizing microbial community. Metagenome data suggests that sulfur reducers and sulfur-disproportionating microbes might play a vital role in energy generation in this ecosystem. Our metagenome data also suggest that the dissimilatory nitrifiers and nitrifying denitrifiers might play an essential role in conserving nitrogen pools in the ecosystem. Furthermore, metagenome-wide BGCs mining retrieved 451 putative BGCs; NRPS was the most abundant (24%). Phylogenetic analysis of the C domain of NRPS showed that sequences were distributed across all six function categories of the known C domain, including several novel subclades. For example, a novel subclade had been recovered within the LCL domain clade as a sister subclade of immunosuppressant cyclosporin encoding C domain sequences. Our result suggested that subterranean cave microbiomes might be a potential reservoir of novel microbial metabolites.

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Acknowledgements

This work was funded by GITAM: Research Seed Grants (F. No: 2021/0003) awarded to BS. We want to acknowledge the Andhra Pradesh State Tourism Department for allowing BS to collect the samples from Borra caves.

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Authors and Affiliations

  1. Department of Microbiology and FST, GITAM School of Science, GITAM (Deemed to Be University), Rushikonda, Visakhapatnam, Andhra Pradesh, 530045, India

    Brajogopal Samanta

  2. Bionivid Technology Private Limited, Bengaluru, Karnataka, 560043, India

    Shivasmi Sharma & Roli Budhwar

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  1. Brajogopal Samanta
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Contributions

BS: original concept, sampling, DNA work, data analysis, drafting, and editing manuscript; SS: data analysis, drafting, and editing manuscript; RB: data analysis, drafting, and editing manuscript.

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Correspondence to Brajogopal Samanta.

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Supplementary Information

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284_2023_3431_MOESM1_ESM.xlsx

Supplementary file 1: Details of taxonomic affiliations of Borra caves speleothem metagenomic contigs belonging to Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes groups. (XLSX 809 KB)

284_2023_3431_MOESM2_ESM.xlsx

Supplementary file 2: Details of taxonomic affiliations of Borra caves spring water metagenomic contigs belonging to Proteobacteria, Actinobacteria, FCB, Terrabacteria, and PVC groups. (XLSX 681 KB)

284_2023_3431_MOESM3_ESM.pdf

Supplementary file 3: Details of genes assigned to the different types of metabolism and metabolic pathways and their relative abundance. (PDF 193 KB)

284_2023_3431_MOESM4_ESM.pdf

Supplementary file 4: KEGG map for major energy metabolic pathways detected in Borra caves metagenome, including methane metabolism, carbon fixation, sulfur metabolism, and nitrogen metabolism. (PDF 194 KB)

284_2023_3431_MOESM5_ESM.xlsx

Supplementary file 5: Biosynthetic gene cluster abundance within the Borra caves speleothem metagenome contigs. BLASTP and NaPDoS analyses of C and KS domains of NRPS and PKS. BLASTP analysis of core genes of terpene biosynthetic gene clusters. (XLSX 64 KB)

284_2023_3431_MOESM6_ESM.png

Supplementary file 6: Maximum likelihood tree of Ketosynthase domains (KS domain) against the NaPDoS domain database. Natural products are color-coded according to their bioactivity. The branches of the KS domain classes were colored on the tree. Confidence values are shown on nodes. (PNG 1644 KB)

284_2023_3431_MOESM7_ESM.tif

Supplementary file 7: Relative abundance of bacterial phylum in Borra cave speleothem and spring water metagenomic libraries. (TIF 1341 KB)

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Samanta, B., Sharma, S. & Budhwar, R. Metagenome Analysis of Speleothem Microbiome from Subterranean Cave Reveals Insight into Community Structure, Metabolic Potential, and BGCs Diversity. Curr Microbiol 80, 317 (2023). https://doi.org/10.1007/s00284-023-03431-9

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