Rapid human pressure in semi-urban and urban areas along with increasing industrial activities has resulted in release of untreated sewage and other forms of pollutants into major rivers globally including in the Ganga. In this study, nine sites represented by 59 stations along the lower stretch of the River Ganga were monitored seasonally to understand the effect of monsoonal precipitation on environmental variables and Water Quality Index (WQI). Sampling was undertaken in pre-monsoon, monsoon and post-monsoon seasons (2019). In situ surface water temperature, dissolved oxygen, pH, total dissolved solids (TDS) and electrical conductivity (EC) were measured along with dissolved nutrients and Chlorophyll-a. Both pH and DO were strongly influenced by monsoon and affected WQI. TDS was higher in point source (PS) stations during pre-monsoon (113–538 ppm) compared to surface water (SW) stations (113–248 ppm) with strong influence of monsoon (PS-27.4-310.3 ppm; SW-27-68.9 ppm). Dissolved nutrients including nitrate and o-phosphate concentration showed significant seasonal variation and influenced monsoonal precipitation. In PS stations across studied seasons dissolved nitrate concentration varied from 26.33–646 μM while in SW the range was from 21.22–148.06 μM. In the studied sites, higher concentration of dissolved nutrients in PS stations reflected the release of untreated municipal and industrial sewage directly into the river. The effect of precipitation and resulting environmental variables was clearly evident on biological variable (concentration of Chl-a) with observed values in PS stations (0–21 mg l−1) which were lesser compared to SW stations (0–89.3 mg l−1) during monsoon. Non-metric multidimensional scaling revealed three distinct clusters with greater overlap between PS and SW stations in monsoon. The WQI values (14–52) determined for lower stretch of Ganga revealed very poor water quality in majority stations and monsoonal precipitation did not have any influence on the observed trends.

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 was monitored spatiotemporally using eDNA metagenome-based Nanopore sequencing to elucidate the 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, 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 commonly 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 and exhibited 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. A high abundance of MRGs comprising arsenic (~12%) and copper (~12%) were also identified and showed 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 in the dissemination of functional genes such as ARGs and MRGs in the lower stretch of the River Ganga.

The River Ganga is reeling from pressures of rapid urbanization and resulting anthropogenic forcings. In this study, phytoplankton community assemblages were deduced from the Dakshineswar site located in the lower stretch of River Ganga to understand the health of this river. Surface water samples were collected from six stations of Dakshineswar spanning across monsoon and post-monsoon seasons of 2019 and 2020. Stations were categorized into point source and surface water based on proximity to municipal discharges. Measurement of in situ environmental parameters showed significant differences in dissolved oxygen, total dissolved solids, electrical conductivity and suspended particulate matter between the two seasons during the study period. In particular, concentrations of dissolved nitrate and silicate were found to be higher in point source stations compared to surface water stations. The concentration of Chlorophyll-a (Chl-a) was found to be higher in post-monsoon compared to monsoon seasons. Phytoplankton communities consisted of 23 diatom taxa and 14 green algal taxa and they showed distinct seasonal and spatial variations in the study site. Phytoplankton communities were dominated by diatom taxa namely Aulacoseira, Bacillaria, Coscinodiscus, and green algal taxa such as Ulothrix, Chlorella, and Scenedesmus. There was a dramatic increase in cell abundance of Aulacoseira spp. in post-monsoon seasons indicating a bloom-like scenario. Moreover, the rapid increase in cell abundance of Aulacoseira spp. also coincided with an increase in Chl-a and a sharp fall in the concentration of dissolved silicate. Some of the encountered phytoplankton taxa such as Tetraedron, Cosmarium, Nitzschia and Scenedesmus showed strong co-occurrence patterns indicating possible association at ecological scales. Four distinct clusters were formed by nMDS ordination plot based on the influences of environmental variables on encountered phytoplankton taxa. Network analysis revealed evidence of co-occurrence patterns between several diatoms and green algal taxa.