An Integrated Culture and Metagenomic Based Study of Microbial Diversity and Role of Potentially Opportunistic Microbial Flora in a Carcass Dumping Site in Keru, Jodhpur

Vultures are natural scavengers of the environment which can remove animal carcasses and help in retarding the growth of microorganisms associated with decomposition. In the present study, carcass dumping sites of Keru, Jodhpur (Rajasthan, India) were used to study microbial diversity, community structure and functional potential. 16S rRNA gene sequencing amplicon and shotgun metagenomic analysis confirmed the various forms of microbes are associated with the carcass. Studies confirmed that the dominated microflora of sites are Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes, which are prominently associated with organic matter degradation. Samples DL, D9, and T9 represented higher PD values, representing higher phylogenetic relationships with CL-2 and TL which showed comparatively lesser PD values, indicating more phylogenetically related communities. A significant value of variation was described by the ordination axes (PC1: 24.1%, PC2: 18.0%, and PC3: 14.9%), showing that significant community-level differences were observed within low-dimensional space. The spatial heterogeneity of carcass waste prominent habitats confirmed that where organic inputs and microhabitat conditions vary between sites, data showed OTU richness and ranged from 1,089 to 1,721 OTUs per sample, with the highest richness in T9 and the lowest in CL-2 samples. The current work demonstrated that diverse, functionally adaptive microbial communities are interlinked environmental compartments supported by extended corpse persistence in the absence of effective scavenger-mediated clearance.