Metagenomic insights unveil the dominance of undescribed Actinobacteria in pond ecosystem of an Indian shrine

Actinobacteria have been an excellent source of novel antibiotics for several decades. However, their community remains unexplored in the pond sediments. The metagenomic analysis holds immense potential for identifying rare and uncharacterized microorganisms from many ecological habitats. The present study was designed to delineate and understand the bacterial diversity with special focus on Actinobacteria in pond sediment collected from Sanjeeviraya Hanuman Temple, Tamil Nadu, India. The sediment had an average temperature (25.32%), pH (7.13), salinity (0.960 Mmhos/cm) and high organic content (10.7%) posing minimal stress on growth condition of the microbial community. Subsequent molecular manipulations, sequencing and metagenomics analysis of 16S rRNA confirmed the presence of 40 phyla, 100 classes, 223 orders, 319 families and 308 genera in the sediment sample dominated by Acidobacteria (18.14%), Proteobacteria (15.13%), Chloroflexi (12.34), Actinobacteria (10.84%), and, Cyanobacteria (5.58%). Within the Actinobacteria phylum, Acidothermus (29.68%) was the predominant genus followed by Actinospica (17.65%), Streptomyces (14.64%), Nocardia (4.55%) and Sinomonas (2.9%). At the species level, only 15.2% within the Actinobacterial phylum were assigned to cultured species. This study reveals the huge unexplored diversity of Actinobacterial community indicating that the microbial ecology of pond sediment is a neglected field which needs attention and also illustrates the highly enriched bioactivity with potential pharmaceutical and industrial significance. •This study is the first microbial metagenomic work on pond ecosystem of Indian Shrine.•Metagenomic results evidenced the existence of rare uncultured forms of actinobacteria in pond ecosystem of Indian Shrine.•This data is used to understand the ecology, taxonomy and anthropogenic impact of unexplored environments such as oldest ponds.•Rare actinobacteria present in the pond ecosystem is a promising resource for bioprospecting applications.