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Aquatic ecosystems are regarded as a hub of antibiotic and metal resistance genes. River Ganges is a unique riverine system in India with socio-cultural and economic significance. However, it remains underexplored for its microbiome and associated resistomes along its anthropogenically impacted course. The present study utilized a nanopore sequencing approach to depict the microbial community structure in the sediments of the river Ganges harboring antibiotic and metal resistance genes (A/MRGs) in lower stretches known for anthropogenic impact. Comprehensive microbiome analyses revealed resistance genes against 23 different types of metals and 28 classes of antibiotics. The most dominant ARG category was multidrug resistance, while the most prevalent MRGs conferred resistance against copper and zinc. Seasonal differences dismally affected the microbiota of the Ganges. However, resistance genes for fosmidomycin and tetracycline varied with season ANOVA, p < 0.05. Interestingly, 333 and 334 ARG subtypes were observed at all the locations in pre-monsoon and post-monsoon, respectively. The taxa associated with the dominant ARGs and MRGs were Pseudomonas and Burkholderia, which are important nosocomial pathogens. A substantial phage diversity for pathogenic and putrefying bacteria at all locations attracts attention for its use to tackle the dissemination of antibiotic and metal-resistant bacteria. This study suggests the accumulation of antibiotics and metals as the driving force for the emergence of resistance genes and the affiliated bacteria trafficking them. The present metagenomic assessment highlights the need for comprehensive, long-term biological and physicochemical monitoring and mitigation strategies toward the contaminants associated with ARGs and MRGs in this nationally important river.

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Microbial carbohydrate-active enzymes (CAZyme) can be harnessed for valorization of Lignocellulosic biomass (LCB) to value-added chemicals/products. The two Indian Rivers Ganges and the Yamuna having different origins and flow, face accumulation of carbon-rich substrates due to the discharge of wastewater from adjoining paper and pulp industries, which could potentially contribute to the natural enrichment of LCB utilizing genes, especially at their confluence. We analyzed CAZyme diversity in metagenomic datasets across the sacred confluence of the Rivers Ganges and Yamuna. Functional annotation using CAZyme database identified a total of 77,815 putative genes with functional domains involved in the catalysis of carbohydrate degradation or synthesis of glycosidic bonds. The metagenomic analysis detected ~ 41% CAZymes catalyzing the hydrolysis of lignocellulosic biomass polymers- cellulose, hemicellulose, lignin, and pectin. The Beta diversity analysis suggested higher CAZyme diversity at downstream region of the river confluence, which could be useful niche for culture-based studies. Taxonomic origin for CAZymes revealed the predominance of bacteria (97%), followed by archaea (1.67%), Eukaryota (0.63%), and viruses (0.7%). Metagenome guided CAZyme diversity of the microflora spanning across the confluence of Ganges-Yamuna River, could be harnessed for biomass and bioenergy applications. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-022-03190-7.

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Large river systems, such as the River Ganges (Ganga), provide crucial water resources for the environment and society, yet often face significant challenges associated with cumulative impacts arising from upstream environmental and anthropogenic influences. Understanding the complex dynamics of such systems remains a major challenge, especially given accelerating environmental stressors including climate change and urbanization, and due to limitations in data and process understanding across scales. An integrated approach is required which robustly enables the hydrogeochemical dynamics and underpinning processes impacting water quality in large river systems to be explored. Here we develop a systematic approach for improving the understanding of hydrogeochemical dynamics and processes in large river systems, and apply this to a longitudinal survey (> 2500 km) of the River Ganges (Ganga) and key tributaries in the Indo-Gangetic basin. This framework enables us to succinctly interpret downstream water quality trends in response to the underpinning processes controlling major element hydrogeochemistry across the basin, based on conceptual water source signatures and dynamics. Informed by a 2019 post-monsoonal survey of 81 river bank-side sampling locations, the spatial distribution of a suite of selected physico-chemical and inorganic parameters, combined with segmented linear regression, reveals minor and major downstream hydrogeochemical transitions. We use this information to identify five major hydrogeochemical zones, characterized, in part, by the inputs of key tributaries, urban and agricultural areas, and estuarine inputs near the Bay of Bengal. Dominant trends are further explored by investigating geochemical relationships (e.g. Na:Cl, Ca:Na, Mg:Na, Sr:Ca and NO3:Cl), and how water source signatures and dynamics are modified by key processes, to assess the relative importance of controls such as dilution, evaporation, water-rock interactions (including carbonate and silicate weathering) and anthropogenic inputs. Mixing/dilution between sources and water-rock interactions explain most regional trends in major ion chemistry, although localized controls plausibly linked to anthropogenic activities are also evident in some locations. Temporal and spatial representativeness of river bank-side sampling are considered by supplementary sampling across the river at selected locations and via comparison to historical records. Limitations of such large-scale longitudinal sampling programs are discussed, as well as approaches to address some of these inherent challenges. This approach brings new, systematic insight into the basin-wide controls on the dominant geochemistry of the River Ganga, and provides a framework for characterising dominant hydrogeochemical zones, processes and controls, with utility to be transferable to other large river systems.

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The Ganga River is facing mounting environmental pressures due to rapidly increasing human population, urbanisation, industrialisation and agricultural intensification, resulting in worsening water quality, ecological status and impacts on human health. A combined inorganic chemical, algal and bacterial survey (using flow cytometry and 16S rRNA gene sequencing) along the upper and middle Ganga (from the Himalayan foothills to Kanpur) was conducted under pre-monsoon conditions. The upper Ganga had total phosphorus (TP) and total dissolved nitrogen concentrations of less than 100 µg l-1 and 1.0 mg l-1, but water quality declined at Kannauj (TP = 420 µg l-1) due to major nutrient pollution inputs from human-impacted tributaries (principally the Ramganga and Kali Rivers). The phosphorus and nitrogen loads in these two tributaries and the Yamuna were dominated by soluble reactive phosphorus and ammonium, with high bacterial loads and large numbers of taxa indicative of pathogen and faecal organisms, strongly suggesting sewage pollution sources. The high nutrient concentrations, low flows, warm water and high solar radiation resulted in major algal blooms in the Kali and Ramganga, which greatly impacted the Ganga. Microbial communities were dominated by members of the Phylum Proteobacteria, Bacteriodetes and Cyanobacteria, with communities showing a clear upstream to downstream transition in community composition. To improve the water quality of the middle Ganga, and decrease ecological and human health risks, future mitigation must reduce urban wastewater inputs in the urbanised tributaries of the Ramganga, Kali and Yamuna Rivers.

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River confluences are interesting ecological niche with limited information in respect of the structure and the functions of diverse microbial communities. Fungi are gaining global attention as promising biological spectacles for defining the trophic status of riverine systems. We condense existing knowledge in confluence diversity in two Indian rivers (i.e. Ganges and Yamuna), by combining sediment metagenomics using long read aided MinION nanopore sequencing. A total of 63 OTU's were observed, of which top 20 OTU's were considered based on relative abundance of each OTU at a particular location. Fungal genera such as Aspergillus, Penicillium, Kluveromyces, Lodderomyces, and Nakaseomyces were deciphered as potential bio indicators of river pollution and eutrophication in the confluent zone. In silico functional gene analysis uncovered hits for neurodegenerative diseases and xenobiotic degradation potential, supporting bioindication of river pollution in wake of anthropogenic intervention.

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The river Ganges, the National Heritage, and the lifeline of millions of Indians, unfortunately, ranked the second most polluted rivers of the world in 2017. This review reveals the current trends of the water quality of the Ganges assessed around 36 stretches during 2012-2016, to indicate an improvement around 6 (16.7%), deterioration around 14 (38.9%), and non-significant changes around 16 (44.4%) stretches. An increase in dissolved oxygen and a decrease in biochemical oxygen demand were observed at six stretches (Devprayag [S5], Rishikesh upstream [S7], Varanasi upstream [S19], Mokama upstream [S25], Mokama downstream [S26], and Munger [S27]). The total and fecal coliform contamination decreased at seven stretches (Rudraprayag [S2 and S3], Devprayag [S5 and S6], Rishikesh [S7], Varanasi upstream [S19], and Munger [S27]) due to improved hygienic conditions, but it increased subsequently at eight stretches (Haridwar [S8], Kanpur [S15], Raibareili [S16], Prayagraj [S17 and S18], Patna [S24], Berhampore [S30], and Serampore [S31]) due to improper defecation and mass bathing during 2007-2016. Dissolved oxygen level declined significantly, and biochemical oxygen demand increased (> 3 ppm), alarmingly at places receiving heavy untreated sewage water. The water quality of the Ganges was good up to Rishikesh, because of an undisrupted flow of the uncontaminated water from the higher altitudes (≥ 372 m) with higher forest cover, lower temperatures (< 21 °C), and higher dissolved oxygen (≥ 8.5 ppm) and due to the dissolution of antipathogenic chemical constituents of the medicinal herbs, pollutant degrading alkaline phosphatase, and bacteriophages. The present review is a systematic collection of data on river pollution, its scientific analyses, and its relationship with 6Ps (namely population, poverty, pollution, precipitation, plantation, and periodicity). Not only that, but the river water restoration measures have also suggested through the novel interlinked water working groups for implementing integrated water management strategies.

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Two new species of the genus Trichodina Ehrenberg, 1838, T. silondiata sp. nov. and T. pangasi sp. nov. from the gills of freshwater fish Silonia silondia (Hamilton 1822) and Pangasius pangasius (Hamilton-Buchanan) respectively from the river Ganges of West Bengal are described here. Wet smears of gills and skins were prepared in the field, air dried and impregnated with Klein's dry silver method. In case of S. silondia (Hamilton 1822) 24 out of 146 host fishes were parasitized on the gills. Infestation rate in case of P. pangasius (Hamilton-Buchanan) was not significant. From a total of 86 examined host fish, only seven were parasitized on the gills. The mean diameters of the body of the specimens of T. silondiata sp. nov. and T. pangasi sp. nov. were 32.7-60.6 (46.4 ± 6.3) µm and 38.9-54.1 (44.9 ± 3.0) µm respectively. Taxonomic and morphometric data for these ectoparasitic trichodinids based on wet silver nitrate impregnated specimens are presented.