Reconstructing Draft Genomes Using Genome Resolved Metagenomics Reveal Arsenic Metabolizing Genes and Secondary Metabolites in Fresh Water Lake in Eastern India

Abstract

Rabindra Sarovar lake is an artificial freshwater lake in the arsenic infested eastern region of India. In this study, using the genome resolved metagenomics approach; we have deciphered the taxonomic diversity as well as the functional insights of the gene pools specific to this region. Initially, a total of 113 Metagenome Assembled Genomes (MAGs) were recovered from the two predominant seasons, that is, rainy (n = 50) and winter (n = 63). After bin refinement and de-replication, 27 MAGs (18 from Winter season and 9 from Rainy season) were reconstructed. These MAGs were either of high-quality (n = 10) or of medium quality (n = 17) that was determined based on genome completeness and contamination. These 27 MAGs spanning across 6 bacterial phyla and the most predominant ones were Proteobacteria, Bacteroidetes, and Cyanobacteria regardless of the season. Functional annotation across the MAGs suggested the existence of all known types of arsenic resistance and metabolism genes. Besides, important secondary metabolites such as zoocin_A, prochlorosin, and microcin were also abundantly present in these genomes. The metagenomic study of this lake provides the first insights into the microbiome composition and functional classification of the gene pools in two predominant seasons. The presence of arsenic metabolism and resistance genes in the recovered genomes is a sign of adaptation of the microbes to the arsenic contamination in this region. The presence of secondary metabolite genes in the lake microbiome has several implications including the potential use of these for the pharmaceutical industry.

Uncovering the diversity and distribution of biosynthetic gene clusters of prochlorosins and other putative RiPPs in marine Synechococcus strains

“…1C ) ( 3 ). Similarly, a recent metagenomic study in freshwater samples detected prochlorosin ORF sequences ( 25 ). Furthermore, in laboratory conditions, the expression of procA reaches its maximum level during the exponential phase of Prochlorococcus MIT9313 ( 10 ).…”

Bacterial diversity in the aquatic system in India based on metagenome analysis—a critical review

“…The Rabindra Sarovar lake is an artificial freshwater lake were cyanobacterial blooms occur regularly due to anthropogenic pressures which are known to be toxic, especially in freshwater. The presence of arsenic metabolism and MRGs in the retrieved genomes indicates that the microorganisms have adapted to this contamination (Ghosh et al 2021 ) (Table 3 ). Ahmad et al ( 2021 ) reported a metagenomics study from Dal lake an urban freshwater lake, highlighted the functional activities of the microbial populations are altered due to variations in environmental temperature and anthropogenic pressures that were higher in the summer period.…”

“…In most of the metagenomic studies from lake water systems in India revealed the dominance of Proteobacteria, Bacteroidetes, Chloroflexi Firmicutes, Actinobacteria, Cyanobacteria, Verrucomicrobia, and Planctomycetes (Ahmad et al 2021 ; Ghosh et al 2021 ; Rathur et al 2017; Raina et al 2019 ; Chakraborty et al 2020a ; b; 2021 ). Similar results were reported from different countries lake ecosystems such as Wadi Namar Lake from Riyadh, Saudi Arabia (Alotaibi et al 2022 ), Keenjhar, Rawal and Saif-ul-Muluk lakes in Pakistan (Saleem et al 2019 ), and Lake Meyghan, Iran (Naghoni et al 2017 ).…”