Functional metagenomic landscape of polluted river reveals potential genes involved in degradation of xenobiotic pollutants

Impact of Anthropogenic Activity on Community Structure and Function of Microbiomes in Polluted Stretches of River Yamuna at New Delhi, India: Insights From Shotgun Metagenomics

“…KEGG ortholog analysis revealed the presence of "Xenobiotics biodegradation and metabolism" genes in all the samples, where taxonomic classi cation informed about the presence of bacteria involved in degradation of various xenobiotic compounds (Dechloromonas aromatica: benzene reducing; Rhodopseudomonas palustris: organic matter reducing, and Syntrophus aciditrophicus: fatty acid reducing). Furthermore, benzoate, nitrotoluene, aminobenzoate, drug metabolism, and polycyclic aromatic hydrocarbons degrading genes were found in this study were similar with ndings from polluted rivers (Yadav et al, 2021a). Moreover, a good correlation between various water and sediment quality parameters and the pathways involved in degradation of end products of hexachlorocyclohexane (one of the highly toxic organochlorine xenobiotic compound) and other xenobiotic compounds indicates that under the stress of various pollutants, microbiome community develops diverse metabolic functions to adapt to the changes in habitats (Mishra et al, 2021;Zhang et al, 2020).…”

“…Presence of PDEs like peroxidases in polluted river sediment signi es their role in degradation of recalcitrant dyes and other xenobiotic compounds such as phenol (Bansal and Kanwar, 2013). Furthermore, highly abundant 4hydroxybenzoate monooxygenase, biphenyl 2,3-dioxygenase and chemotaxis protein III detected in this study implies their participation in degradation of dye, hydrocarbons, and to sense environmental cues (Sankara Subramanian et al, 2020;Yadav et al, 2021b). Overall, our study has contributed in understanding the microbiome community structure and their functions in the sediments of river Yamuna.…”

MinION Nanopore Sequencing Accelerates Progress towards Ubiquitous Genetics in Water Research

“…For the tissue of aquatic organisms, biomass concentration will be unnecessary [32,34,59]. Genetic material from biomass-rich sediment samples (0.2 to 1 g) and sludge samples (0.5 mL) can also be extracted directly [45,51,60,61,75], or after centrifugation of small to medium slurry volumes (2 to 50 mL) with collection of the pellets [52,62,69]. Zooplanktonic biomass can be harvested with meshes having 200 µm openings [36], while the biomass of algae [74] and cyanobacteria [48] can be isolated by medium to large volume centrifugation (0.05 to 1 L).…”

“…The related procedures involve sample homogenization and agitation in bead tubes with the addition of a cell lysis solution, phase separation, DNA or RNA binding, and washing steps before the purified genetic material can be obtained. Most studies working with water samples used the respective kits, while kits optimized for soil were used to extract sediment [46,49,53,60,61,67], wastewater [62,69,70,72], and algal biomass samples [59]. Enzymes like lysozymes sometimes assist with cell lysis, for example in a study of planktonic riverine microbial consortia [37] and plastic-associated species in the Mediterranean Sea [44].…”

“…As a minimum, the purified genetic material needs repair and preparation of the fragmented DNA/RNA strand ends followed by ligation (i.e., attachment) of the sequencing adaptors which interact with the flow cell nanopores. This can be done with ligation sequencing kits that were popular choices to sequence DNA [43,45,46,49,52,53,55,60,61,67,70,72,76] and derived amplicons [31,32,34,35,44,58,59,73,74], or amplicons of complementary DNA (cDNA, see below) [28]. Semmouri et al [33] evaluated the MinION potential for direct RNA nanopore sequencing using the corresponding kit.…”