Abstract
This study reports on the culturable microbial communities in caves from the Indian sub-continent. A high bacterial diversity and a greater bacterial taxonomic diversity is reported using MALDI-TOF spectrometry and 16S rRNA gene sequencing. This approach helped to detect a number bacterial strains from the Indian caves. The microbial diversity in the Indian caves is inadequately characterized. The study aims to expand the current understanding of bacterial diversity in the speleothems from Krem Soitan, Krem Lawbah, Krem Mawpun in Khasi Hills, Meghalaya, India. High microbial enumerations were observed on dilute nutrient agar (5.3 × 103 to 8.8 × 105) followed by M9 minimal medium (4 × 104 to 1.7 × 105) and R2A medium (1.0 × 104 to 5.7 × 105). A total of 826 bacterial isolates were selected and preserved for the study. 295 bacterial isolates were identified using MALDI-TOF spectrometry and the isolates which showed no reliable peaks were further identified by 16S rRNA gene sequencing. 91% of the total bacterial diversity was dominated by Proteobacteria and Actinobacteria. The other important phyla detected include the Firmicutes (7.45%), Deinococcus-Thermus (0.33%) and Bacteroidetes (0.67%). At the genus level, Pseudomonas (55%) and Arthrobacter (23%) were ubiquitous followed by Acinetobacter, Bacillus, Brevundimonas, Deinococcus, Flavobacterium, Paenibacillus, Pseudarthrobacter. Multivariate statistical analysis indicated that the bacterial genera formed separate clusters depending on the geochemical constituents in the spring waters suitable for their growth and metabolism. A culture-dependent approach was employed for elucidating the community structure colonizing the speleothems and wall deposits in the caves using MALDI-TOF and 16S rRNA gene sequencing. To the best of our knowledge, there are no previous geomicrobiological investigations in these caves and this study is a pioneering culture dependent study of the microbial community with many cultured isolates.
High-Throughput rRNA Gene Sequencing Reveals High and Complex Bacterial Diversity Associated with Brazilian Coffee Beans Fermentation
