Metagenomic insights into the functional microbial diversity of the lower stretch of the River Ganga: mapping antibiotic and metal resistance genes

Abstract

The banks of the lower stretch of River Ganga are home to several towns and megapolis representing high density of human population. A stretch of 50 km represented by prefixed stations of the lower part of Ganga (Ganga Environmental Time Series- GETS) was monitored spatiotemporally using eDNA metagenome-based Nanopore sequencing to elucidate structure of microbial communities along with mapping of antibiotic-resistant genes (ARGs), metal resistance genes (MRGs) and mobile genetic elements (MGEs). Besides, in situ environmental parameters, concentration of dissolved nutrients, metals and metalloids were measured. The concentration of dissolved oxygen ranged from 3.4–6.2 mg l−1, indicating deteriorating water quality corresponding to high population density. Dissolved nitrate concentrations were higher in some stations reflecting direct release of untreated municipal sewage into the river. In particular, concentration of metals such as Cd (2.34–38.52 ppb) and metalloids such as As (0–218.7 ppb) were found to be alarmingly high in surface water. Gammaproteobacteria was encountered ubiquitously while rare bacterioplankton represented by eleven classes showed site specificity. Several genes belonging to ARGs were identified and multidrug resistance genes (MDR) were found in all the studied stations exhibiting high abundance. The ‘hotspots’ of ARGs were widespread, possibly owing to rampant usage of personal health care products that may have contributed to observed ARG abundances. High abundance of MRGs comprising arsenic (∼12%) and copper (∼12%) were also identified showing strong correlations with the abundance of ARGs. Correlation and network analysis revealed the potential role of MGEs in the dissemination of ARGs. ANOSIM and cluster analyses supported patchy distribution patterns of microbial communities. The RDA plot showed possible influences of environmental parameters in shaping the microbial community structure and towards dissemination of functional genes such as ARGs and MRGs in the lower stretch of the River Ganga.