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.

Culture dependent analysis of bacterial diversity in Canada’s Raspberry Rising Cave revealed antimicrobial properties

“…Our study has revealed 94.44% of the proteobacterial community was represented by the class Gammaproteobacteria. These findings were consistent with the previous cultivation-based studies where class Gammaproteobacteria were shown to constitute the major bacterial population (Banerjee & Joshi, 2016;Yasir, 2018). For instance, bacterial diversity study on the Meghalayan caves in North-East India, exposed thirty-two different cultivable bacterial species belonging to sixteen different genera where majority belongs to Pseudomonas and Bacillus (Banerjee & Joshi, 2016).…”

“…Proteobacteria phylum was dominated by the class Gammaproteobacteria with Pseudomonas sp. observed as the major genera in accordance to previous studies (Barton et al, 2004;Banerjee & Joshi, 2016;Yasir, 2018). Proteobacterial population seldom observed to be the dominant class in most of the cave bacterial diversity studies with the majority of the bacterial population has been shown as Actinobacteria (Axenov-Gribanov et al, 2016;Ghosh et al, 2016Ghosh et al, , 2017Lavoie et al, 2017).…”

“…These findings were in consistent to a few previous cultivation-based studies on bacterial phylogenetic diversity of the karstic caves where Proteobacteria was recognized as a predominant bacterial population (Barton et al, 2004;Lu et al, International Journal of Speleology, 49 (1), 43-53. Tampa, FL (USA) January 2020 2018; Yasir, 2018). Proteobacteria phylum was dominated by the class Gammaproteobacteria with Pseudomonas sp.…”

“…Proteobacterial population seldom observed to be the dominant class in most of the cave bacterial diversity studies with the majority of the bacterial population has been shown as Actinobacteria (Axenov-Gribanov et al, 2016;Ghosh et al, 2016Ghosh et al, , 2017Lavoie et al, 2017). However, a few studies have reported Proteobacteria as the most abundant phylum (Sauro et al, 2018;Yasir, 2018;Barron et al, 2010). Our study has revealed 94.44% of the proteobacterial community was represented by the class Gammaproteobacteria.…”

Microbial biofilm community structure and composition on the lithic substrates of Herculaneum Suburban Baths

“…Heterotrophic bacteria and fungi, constitute most of the biodiversity in caves and are ubiquitous in different cave habitats [43,5]; actinobacteria involved in biomineralization processes are common [44,45,46], and Bacillus and Paenibacillus occurrence has been frequently reported [47,48].…”