Metagenomic insights to understand the role of polluted river Yamuna in shaping the gut microbial communities of two invasive fish species

Abstract

The gastrointestinal microbial community plays a crucial role in host health, immunity, protection, development and provides nutrients to the host. The rising human-induced pollution and heavy metal contamination in all aquatic systems globally has led us to explore the gut microbial diversity of two exotic invasive fish Cyprinus carpio (Linnaeus, 1858) and Oreochromis niloticus (Linnaeus,1857) from river Yamuna, India. These fishes are aquatic bioindicators with high demographic resilience. Exploring these associations would pave the way for addressing problems that inhabitant fishes are facing due to the increasing pollution load in the River Yamuna. Based on 16S rRNA gene amplicon sequencing, our results deliver comparative information on the gut microbiome of these fishes and highlight connotations between the microbiome of gut and water samples. The gut of C. carpio and O. niloticus was dominated by phyla Proteobacteria whereas Bacteroidetes dominated the water sample. Microbial communities showed predicted roles such as pathogenicity (Escherichia-Shigella, Aeromonas veronii, Vibrio cholerae, Streptococcus iniae, Flavobacterium columnare, Klebsiella pneumoniae, Mycobacterium sp.), probiotic applications (Bacillus velezensis, Lactobacillus plantarum, Enterococcus faecalis, Bifidobacterium longum, Lactococcus lactis, Leuconostoc falkenbergense) and involvement in sewage and organic matter decomposition (Nitrosomonas sp., Methanosaeta harundinacea, Dechloromonas agitata, Thauera humireducens, Zoogloea ramigera). Heavy metal degrading members (Leucobacter chromiireducens, Pseudomonas fluorescens, P. aeruginosa, Klebsiella pneumoniae, and Micrococcus luteus) were detected in gut microbiome samples thus supporting the notion that fish shapes its gut microbiota with changing ecology. Functional profiling showed that microbial communities are specialized in metabolic functions thus reflecting the dietary profile of these invasive fishes.

Keywords: Gut; Microbiome; Pollution; Yamuna.