Analysis of bacterial communities and characterization of antimicrobial strains from cave microbiota

Abstract

In this study for the first-time microbial communities in the caves located in the mountain range of Hindu Kush were evaluated. The samples were analyzed using culture-independent (16S rRNA gene amplicon sequencing) and culture-dependent methods. The amplicon sequencing results revealed a broad taxonomic diversity, including 21 phyla and 20 candidate phyla. Proteobacteria were dominant in both caves, followed by Bacteroidetes, Actinobacteria, Firmicutes, Verrucomicrobia, Planctomycetes, and the archaeal phylum Euryarchaeota. Representative operational taxonomic units from Koat Maqbari Ghaar and Smasse-Rawo Ghaar were grouped into 235 and 445 different genera, respectively. Comparative analysis of the cultured bacterial isolates revealed distinct bacterial taxonomic profiles in the studied caves dominated by Proteobacteria in Koat Maqbari Ghaar and Firmicutes in Smasse-Rawo Ghaar. Majority of those isolates were associated with the genera Pseudomonas and Bacillus. Thirty strains among the identified isolates from both caves showed antimicrobial activity. Overall, the present study gave insight into the great bacterial taxonomic diversity and antimicrobial potential of the isolates from the previously uncharacterized caves located in the world's highest mountains range in the Indian sub-continent.

Keywords: 16S ribosomal RNA; Antimicrobial; Caves; Microbiota; Sediments.

Fig. 1

Distribution of microbial phyla and candidate divisions detected at relatively higher abundance in the KMG and SRG caves. Percentage abundance from KMG are shown on the x-axis and from SRG on the y-axis. The category “others” represents microbial phyla and candidate divisions that were present at <1% abundance in each cave. KMG, Koat Maqbari Ghaar; SRG, Smasse-Rawo Ghaar.

Fig. 2

Percentage distribution of the relatively dominant genera detected in the KMG and SRG caves. KMG, Koat Maqbari Ghaar; SRG, Smasse-Rawo Ghaar.

Fig. 3

Percentage distribution of relatively dominant OTUs at species level detected in ≥1% at least in one cave. KMG, Koat Maqbari Ghaar; SRG, Smasse-Rawo Ghaar.

Fig. 4

Alpha diversity of the sequence reads. (A) Rarefaction curves of the experimentally observed OTUs versus diversity (B) estimated by Chao1. (C) Boxplots of the Shannon index. KMG, Koat Maqbari Ghaar; SRG, Smasse-Rawo Ghaar.

Fig. 5

Phylogenetic analysis based on 16S rRNA gene sequences of the bacterial isolates. The neighbor-joining clustering method was used to construct the tree. Bootstrap values were calculated based on 1000 replications and are shown at branch points. The bar represents 0.01 sequence divergence. Sequences derived from the NCBI GenBank database are shown with their accession numbers. Filled circles following the experimental sequence names correspond to KMG, and non-filled circles correspond to SRG. KMG, Koat Maqbari Ghaar; SRG, Smasse-Rawo Ghaar.