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This work primarily emphases on evaluating the prevalence of organic micropollutants (OMPs) in the perennial Yamuna River (YR) that flow through the national capital of India, Delhi. Sixteen sampling campaigns (non-monsoon, n = 9; monsoon n = 7) were organized to understand the seasonal variations with special emphasis on monsoon. We have found fifty-five OMPs in the monsoon; while forty-seven were detected in non-monsoon. Fifty-seven screened and quantified OMPs in the most polluted stretch of River Yamuna included the pharmaceutically active compounds, pesticides, endocrine-disrupting chemicals, phthalates, personal care products, fatty acids, food additives, hormones, and trace organics present in hospital wastes. During monsoon months, compounds for which concentrations exceeded 50 µg/L were: adenine (64.6 µg/L), diethyl phthalate (62.9 µg/L), and octamethyltrisiloxane (56.9 µg/L); and the same for non-monsoon months was only for 1-dodecanethiol (52.3 µg/L). The average concentration of OMPs in non-monsoon months indicate PhACs>PCPs>Pesticides>Fatty acids>Hospital waste>Hormones>Pesticides>EDCs. In monsoon months due to surface runoff and high volume of untreated wastewater discharges few more OMPs concentrations were detected which mainly includes PhACs (clofibric acid, diclofenac sodium, gemfibrozil, ketoprofen), pesticides (aldrin, metribuzin, atrazine, simazine). Due to dilution effect in the monsoon months, average concentrations of 3-acetamido-5-bromobenzoic acid (PhACs) was reduced from 45.22 µg/L to 14.07 µg/L, whereas some EDCs such as 2,4- Di-tert-amylphenol, 3,5- di-tert-butyl-4-hydroxybenzyl alcohol, Triphenylphosphine oxide, Benzophenone were found in much higher concentrations in the monsoon months. Octamethyltrisiloxane (PCPs) was detected 50 times higher in concentration in the monsoon months. Interestingly, the concentration of about 50 % of the OMPs was more in the monsoon samples than in non-monsoon samples which is contrary to the general understanding that monsoon-induced dilution lowers the concentrations of OMPs. In RY water higher magnitude of diclofenac sodium, ibuprofen, ketoprofen, and clofibric acid was found than Europe and North America rivers. Hormones such as estriol and estrone in RY water are found 70 to 100 times higher than the maximum reported concentrations in the US streams. Finally, various OMPs responded differently to the monsoon season as evident from multivariate analyses.

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The large population residing in the northern region of India surrounding Delhi mostly depends on water of River Yamuna, a tributary of mighty Ganga for agriculture, drinking and various religious activities. However, continuous anthropogenic activities mostly due to pollution mediated by rapid urbanization and industrialization have profoundly affected river microflora and their function thus its health. In this study, potential of whole-genome metagenomics was exploited to unravel the novel consortia of microbiome and their functional potential in the polluted sediments of the river at Delhi. Analysis of high-quality metagenome data from Illumina NextSeq500 revealed substantial differences in composition of microbiota at different sites dominated by Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria and Chloroflexi phyla. The presence of highly dominant anaerobic bacteria like Dechloromonas aromatica (benzene reducing and denitrifying), Rhodopseudomonas palustris (organic matter reducing), Syntrophus aciditrophicus (fatty acid reducing) and Syntrophobacter fumaroxidans (sulphate reducing) in the polluted river Yamuna signifies the impact of unchecked pollution in declining health of the river ecosystem. A decline in abundance of phages was also noticed along the downstream river Yamuna. Mining of mycobiome reads uncovered plethora of fungal communities (i.e. Nakaseomyces, Aspergillus, Schizosaccharomyces and Lodderomyces) in the polluted stretches due to the availability of higher organic carbon and total nitrogen (%) could be decoded as promising bioindicators of river trophic status. Pathway analysis through KEGG revealed higher abundance of genes involved in energy metabolism (nitrogen and sulphur), methane metabolism, degradation of xenobiotics (Nitrotoluene, Benzoate and Atrazine), two-component system (atoB, cusA and silA) and membrane transport (ABC transporters). Catalase-peroxidase and 4-hydroxybenzoate 3-monooxygenase were the most enriched pollution degrading enzymes in the polluted study sites of river Yamuna. Overall, our results provide crucial insights into microbial dynamics and their function in response to high pollution and could be insightful to the ongoing remediation strategies to clean river Yamuna.

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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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Rivers are the lifeline of every living being, be it humans or animals. Clean water is essential for everyone. However, increased urbanization and rapid industrialization have led to rising pollution level in rivers. COVID-19 on the contrary has changed the entire ecosystem. Limited industrial activities, reduced people movement during COVID times has led to improvement in environment, be it atmosphere or hydrosphere. Present work aims to study the impact of COVID-19 on water quality index of river Yamuna as it traverses from Himalayan segment to Upper segment. Five sites are chosen between a stretch of 60+ km, and samples are collected during monsoon and post-monsoon seasons. Physico-chemical parameters (pH, Turbidity, Sulphate, Phosphate, Fluoride, Chloride, Total Hardness, Calcium, Magnesium, Dissolved Oxygen, BOD, COD, Alkalinity), water quality index and Pearson correlation coefficient were calculated for all chosen sites. Since the study was initiated during COVID, initial results show the impact of reduced industrial and urban activities in improving the overall water quality.

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The River Yamuna emerges from Saptarishi Kund, Yamunotri and merge with River Ganges at Allahabad, India. Anthropogenic stress has affected the water quality of the river Yamuna drastically in the stretch traversing Delhi and its satellite towns (National Capital Region, NCR). In the present study, effect of water quality on the microbial life in the River Yamuna was analyzed using ciliate communities (Protista, Ciliophora) as bio-indicators. Water samples were collected from six sampling sites chosen according to the levels of pollution along the river and water quality was analysed using standard physicochemical factors. As the river traverses Delhi NCR, water quality deteriorates considerably as indicated by the Water Quality Index at the selected sampling sites. Seventy-four ciliate species representing nine classes were recorded. Based on the Shannon diversity index, maximum species diversity was found at the point where the river enters Delhi. The saprobity index showed the river water was beta-mesosaprobic when the river enters Delhi and alpha-mesosaprobic at downstream sites after the first major drain outfall. Significant relationship between the spatial variation in ciliate communities and abiotic parameters indicate that ciliates can be used as effective bioindicators of pollution in the River Yamuna.

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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 present study aims to monitor the surface water quality of different regions in Delhi (India). With many physical and chemical properties, all samples had a high load of pollution in which Najafgarh drain (Nd) exhibited maximum and laboratory tap water (Ltw) minimum contamination. Water samples contained notable amounts of heavy metals including Cr, Cd, As, Cu, Pb and Hg. A total of 88 Hg-resistant bacteria were isolated from all the regions except Ltw. Among all the samples, the density of Hg-resistant bacteria was highest in sample of Nd and their morphotype heterogeneity was highest in sample collected from river Yamuna nearby Kashmiri gate (Kg). Different strains showed different patterns of resistance to different heavy metals and antibiotics. Multiple antibiotic resistance (MAR) indices were high in two samples, the highest reported in a sample taken from river Yamuna nearby Majnu ka tila (Mkt) (0.34). The 12.5% and 24.45% isolates showed ß- and α-hemolytic natures, respectively that might be of pathogenic concern. In this account, high concentrations of heavy metals and their resistant bacteria in surface water have severely damaged the quality of water and their resources and produced high risk to the associated life forms.