Anthropogenic Activities Induce Depletion in Microbial Communities at Urban Sites of the River Ganges

Distribution of bacterial community structures and spread of antibiotic resistome at industrially polluted sites of Mini River, Vadodara, Gujarat, India

The influence of anthropogenic pollution on the distribution of bacterial diversity, antibiotic-resistant bacteria (ARBs), and antibiotic resistance genes (ARGs) was mapped at various geo-tagged sites of Mini River, Vadodara, Gujarat, India. The high-throughput 16S rRNA gene amplicon sequencing analysis revealed a higher relative abundance of Planctomycetota at the polluted sites, compared to the pristine site. Moreover, the relative abundance of Actinobacteriota increased, whereas Chloroflexi decreased in the water samples of polluted sites than the pristine site. The annotation of functional genes in the metagenome samples of Mini River sites indicated the presence of genes involved in the defence mechanisms against bacitracin, aminoglycosides, cephalosporins, chloramphenicol, streptogramin, streptomycin, methicillin, and colicin. The analysis of antibiotic resistome at the polluted sites of Mini River revealed the abundance of sulfonamide, beta-lactam, and aminoglycoside resistance. The presence of pathogens and ARB was significantly higher in water and sediment samples of polluted sites compared to the pristine site. The highest resistance of bacterial populations in the Mini River was recorded against sulfonamide (≥ 7.943 × 103 CFU/mL) and ampicillin (≥ 8.128 × 103 CFU/mL). The real-time PCR-based quantification of ARGs revealed the highest abundance of sulfonamide resistance genes sul1 and sul2 at the polluted sites of the Mini River. Additionally, the antimicrobial resistance genes aac(6')-Ib-Cr and blaTEM were also found abundantly at polluted sites of the Mini River. The findings provide insights into how anthropogenic pollution drives the ARG and ARB distribution in the riverine ecosystem, which may help with the development of antimicrobial resistance mitigation strategies.

Spatio-temporal distribution and dynamics of antibiotic resistance genes in a water-diversion lake, China

The distribution and dynamics of antibiotic resistance genes (ARGs) in water-diversion lakes are poorly understood. In this study, two comparative in situ investigations of ARG profiles targeting water diversion (DP) and non-diversion periods (NDP) were conducted in Luoma Lake, a vital transfer node for the eastern route of the South-to-North Water Diversion Project in China. The results demonstrated significant spatiotemporal variations in ARG contamination and notable differences in the co-occurrence patterns of ARGs and bacterial communities between DP and NDP. Correlations among ARGs with the 16 S rRNA, and mobile genetic elements indicate that horizontal gene transfer (HGT) and vertical gene transfer (VGT) in NDP, but only HGT in DP, were the primary mechanisms of ARG proliferation and spread, implying that water diversion could be an essential control of the transfer pattern of ARGs in a lake environment. The null model analysis indicated that stochastic processes, with predominant driver of ecological drift in the lake mainly drove the assembly of ARGs. Partial least squares structural equation modeling was developed to analyze the causal effects of the factors in shaping ARG dynamics and identify the major driving forces in the DP and NDP.

Spatial distribution of sediment bacterial communities from São Francisco River headwaters is influenced by human land-use activities and seasonal climate shifts

Riverbed sediments are dynamic freshwater environments colonized by a great diversity of microorganisms which play important roles in supporting freshwater ecosystem by performing a vast array of metabolic functions. Recent evidence generated by HTS approaches has revealed that the structure of sediment microbial communities is influenced by natural seasonal variations in water such as temperature or streamflow as well by disturbances caused by local human activities. Here, a spatiotemporal analysis of sediment microbial distribution from São Francisco River headwaters section was conducted using Illumina 16S rRNA-V4 region amplicon sequencing in order to accomplish three major goals: (i) to investigate whether the diversity and composition of bacterial communities accessed in riverbed sediments vary in response to distinct land-use activities; (ii) to estimate whether the diversity patterns vary between the dry and wet seasons; and (iii) to evaluate whether the diversity of bacterial metabolic functions, predicted by PICRUSt2 approach, varies similarly to the estimated taxonomic diversity. Our findings revealed that bacterial communities in the sediment show differences in diversity and taxonomic composition according to the anthropic activities performed in the local environment. However, the patterns in which this taxonomic diversity is spatially structured show differences between the dry and wet seasons. On the other hand, the most changes in predicted bacterial metabolic functions were verified between sediment samples accessed in portions of the river located in protected and unprotected areas. Our findings contributed with new evidence about the impact of typical land-use practices conducted in countryside landscapes from developing countries on riverbed bacterial communities, both in their taxonomic and functional structure.

Planktonic and epilithic prokaryota community compositions in a large temperate river reflect climate change related seasonal shifts

In freshwaters, microbial communities are of outstanding importance both from ecological and public health perspectives, however, they are threatened by the impact of global warming. To reveal how different prokaryotic communities in a large temperate river respond to environment conditions related to climate change, the present study provides the first detailed insight into the composition and spatial and year-round temporal variations of planktonic and epilithic prokaryotic community. Microbial diversity was studied using high-throughput next generation amplicon sequencing. Sampling was carried out monthly in the midstream and the littoral zone of the Danube, upstream and downstream from a large urban area. Result demonstrated that river habitats predominantly determine the taxonomic composition of the microbiota; diverse and well-differentiated microbial communities developed in water and epilithon, with higher variance in the latter. The composition of bacterioplankton clearly followed the prolongation of the summer resulting from climate change, while the epilithon community was less responsive. Rising water temperatures was associated with increased abundances of many taxa (such as phylum Actinobacteria, class Gammaproteobacteria and orders Synechococcales, Alteromonadales, Chitinophagales, Pseudomonadales, Rhizobiales and Xanthomonadales), and the composition of the microbiota also reflected changes of several further environmental factors (such as turbidity, TOC, electric conductivity, pH and the concentration of phosphate, sulphate, nitrate, total nitrogen and the dissolved oxygen). The results indicate that shift in microbial community responding to changing environment may be of crucial importance in the decomposition of organic compounds (including pollutants and xenobiotics), the transformation and accumulation of heavy metals and the occurrence of pathogens or antimicrobial resistant organisms.

New insights into bacterial Zn homeostasis and molecular architecture of the metal resistome in soil polluted with nano zinc oxide

Accumulation of nano ZnO (nZnO) in soils could be toxic to bacterial communities through disruption of Zn homeostasis. Under such conditions, bacterial communities strive to maintain cellular Zn levels by accentuation of appropriate cellular machinery. In this study, soil was exposed to a gradient (50-1000 mg Zn kg-1) of nZnO for evaluating their effects on genes involved in Zn homeostasis (ZHG). The responses were compared with similar levels of its bulk counterpart (bZnO). It was observed that ZnO (as nZnO or bZnO) induced a plethora of influx and efflux transporters as well as metallothioneins (MTs) and metallochaperones mediated by an array of Zn sensitive regulatory proteins. Major influx system identified was the ZnuABC transporter, while important efflux transporters identified were CzcCBA, ZntA, YiiP and the major regulator was Zur. The response of communities was dose- dependent at lower concentrations (<500 mg Zn kg-1 as nZnO or bZnO). However, at 1000 mg Zn kg-1, a size-dependent threshold of gene/gene family abundances was evident. Under nZnO, a poor adaptation to toxicity induced anaerobic conditions due to deployment of major influx and secondary detoxifying systems as well as poor chelation of free Zn ions was evident. Moreover, Zn homeostasis related link with biofilm formation and virulence were accentuated under nZnO than bZnO. While these findings were verified by PCoA and Procrustes analysis, Network analysis and taxa vs ZHG associations also substantiated that a stronger Zn shunting mechanism was induced under nZnO due to higher toxicity. Molecular crosstalks with systems governing Cu and Fe homeostasis were also evident. Expression analysis of important resistance genes by qRT-PCR showed good alignment with the predictive metagenome data, thereby validating our findings. From the study it was evident that the induction of detoxifying and resistant genes was greatly lowered under nZnO, which markedly hampered Zn homeostasis among the soil bacterial communities.

Spatio-temporal variation of the microbiome and resistome repertoire along an anthropogenically dynamic segment of the Ganges River, India

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.

Early warning of red tides using bacterial and eukaryotic communities in nearshore waters

Anthropogenic discharge activities have increased nutrient pollution in coastal areas, leading to algal blooms and microbial community changes. Particularly, microbial communities could easily be affected with variation in nutrient pollution, and thus offered a promising strategy to predict early red tides warning via microbial community-levels variation and their keystone taxa hysteretic responses to nutrient pollution. Herein high-throughput sequencing technology from 52 samples were used to explore the variation of microbial communities and find the significant tipping points with aggravating nutrient conditions in Xiaoping Island coastal area. Results indicated that bacterial and microeukaryote communities were generally spatial and seasonal heterogeneity and were influenced by the different nutrient conditions. Procrustes test results showed that the comprehensive index of organics polluting (OPI), total nitrogen (TN), inorganic nitrogen (DIN), and total phosphorus (TP) were significantly correlated with the composition of bacteria and microeukaryotes. A SEGMENTED analysis revealed that the threshold of TN, DIN, and NH₄-N for bacterial community were 0.23 ± 0.091 mg/L, 0.21 ± 0.084 mg/L, 0.09 ± 0.057 mg/L, respectively. Tipping points for TN, DIN, and NH₄-N agreed with the concentration during Ceratium tripos and Skeletonema costatum blooms. Co-occurrence network results found that Planktomarina, Acinetobacter, and Verrucomicrobiaceae were keystone and OPI-discriminatory taxa. The abundant changes of Planktomarina at station A1 were significantly correlated with the development of C. tripos blooms (r = 0.55, p < 0.05), and also significantly correlated with TN, DIN, and NO₃-N (r≥|0.55|, p < 0.05). The abundant changes of Acinetobacter and Verrucomicrobiaceae at station C1 were significantly correlated with the development of C. tripos blooms (r ≥ 0.77, p < 0.05), and also significantly correlated with PO₄-P (r ≥ 0.64, p < 0.05). The dynamic abundance of keystone taxa showed that the trend of rapid changes could be monitored 1.5 months before the occurrence of red tide. Therefore, this study provides an assessment method for early warning of red tide occurrence and factors that trigger red tide.

Microbial Population Dynamics in Lemnaceae (Duckweed)-Based Wastewater Treatment System

The dynamic microflora associated within, and in the surrounding aquatic environment, has been found to be responsible for the functional properties of many aquatic plants. The aim of the current work was to evaluate the effectiveness of Lemnaceae-based wastewater treatment system under tropical conditions and investigate the changes in the aquatic microflora upon plant growth. A biological wastewater treatment system was designed and investigated using mixed Lemnaceae culture comprising Lemna minor and Spirodela polyrhiza in a batch mode. A significant reduction in total solids (31.8%), biochemical oxygen demand (93.5%), and chemical oxygen demand (73.2%) was observed after seven days of duckweed growth using a low inoculum. A preliminary study on the change in the microbial population diversity and functionality, in the wastewater before and after treatment, revealed an increase in the denitrifying microflora in wastewater post-Lemnaceae treatment. Dominance of 10 bacterial phyla, contributing for 98.3% of the total bacterial communities, was recorded, and ~ 50.6% loss of diversity post-treatment of wastewater was revealed by the Shannon Index. Among 16 bacterial families showing relative abundance of ≥ 1% in untreated wastewater, Methylobacteriaceae, Pseudomonadaceae, Brucellaceae, Rhodobacteraceae, and Acetobacteraceae prevailed in the water post-treatment by duckweeds. This is a novel work done on the dynamics of aquatic microflora associated with Lemnaceae under tropical Indian conditions. It confirms the application of Lemnaceae-based wastewater treatment system as effective biofilter and calls for further studies on the active involvement of the endophytic and aquatic microflora in the functions of these plant.

Comparison of environmental microbiomes in an antibiotic resistance-polluted urban river highlights periphyton and fish gut communities as reservoirs of concern

Natural waterways near urban areas are heavily impacted by anthropogenic activities, including their microbial communities. A contaminant of growing public health concern in rivers is antibiotic resistant genes (ARGs), which can spread between neighboring bacteria and increase the potential for transmission of AR bacteria to animals and humans. To identify the matrices of most concern for AR, we compared ARG burdens and microbial community structures between sample types from the Scioto River Watershed, Ohio, the United States, from 2017 to 2018. Five environmental matrices (water, sediment, periphyton, detritus, and fish gut) were collected from 26 river sites. Due to our focus on clinically relevant ARGs, three carbapenem resistance genes (bla_KPC, bla_NDM, and bla_OXA-48) were quantified via DropletDigital™ PCR. At a subset of nine urbanized sites, we conducted16S rRNA gene sequencing and functional gene predictions. Carbapenem resistance genes were quantified from all matrices, with bla_KPC being the most detected (88 % of samples), followed by bla_NDM (64 %) and bla_OXA-48 (23 %). Fish gut samples showed higher concentrations of bla_KPC and bla_NDM than any other matrix, indicating potential ARG bioaccumulation, and risk of broader dissemination through aquatic and nearshore food webs. Periphyton had higher concentrations of bla_NDM than water, sediment, or detritus. Microbial community analysis identified differences by sample type in community diversity and structure. Sediment samples had the most diverse microbial communities, and detritus, the least. Spearman correlations did not reveal significant relationships between the concentrations of the monitored ARGs and microbial community diversity. However, several differentially abundant taxa and microbial functions were identified by sample type that is definitive of these matrices' roles in the river ecosystem and habitat type. In summary, the fish gut and periphyton are a concern as AR reservoirs due to their relatively high concentration of carbapenem resistance genes, diverse microbial communities, and natural functions that promote AR.

TiO2 nanoparticles exert an adverse effect on aquatic microbial communities

Titanium dioxide nanoparticle (n-TiO₂) is a widely used nanomaterial, which is inevitably released as a residue into aquatic ecosystems during material production and usage. However, the effects of n-TiO₂ on aquatic microbial communities have not been completely elucidated. This study examined the toxic effects of n-TiO₂ on eukaryotic and prokaryotic microbial communities in freshwater environments. We determined that n-TiO₂ had a greater inhibitory effect on the growth of eukaryotic algae than cyanobacteria in monocultures. A similar phenomenon was observed in a microcosm experiment, revealing that n-TiO₂ slightly reduced the content of chlorophyll-a but evidently increased the phycocyanin content. Moreover, the alpha diversity of the eukaryotic community was not affected, whereas its beta diversity increased with exposure to n-TiO₂. Although n-TiO₂ altered the composition of freshwater microbial communities, it did not change the functions of the prokaryotic community, which might be attributed to the functional redundancy of microbiota. Co-occurrence network analysis indicated that n-TiO₂ destabilized the freshwater community, especially the eukaryotic community, and potentially disturbed the aquatic ecosystem. Our study revealed that the ecological risk of n-TiO₂ on aquatic microbial communities is complex; hence, rational utilization of n-TiO₂ should be emphasized.

Bacterial communities in peat swamps reflect changes associated with catchment urbanisation

Like many peat wetlands around the world, Temperate Highland Peat Swamps on Sandstone (THPSS), located in the Sydney Basin, Australia, have been impacted by urban development. In this paper, we used Illumina 16S rRNA DNA amplicon sequencing to characterise and compare the bacterial communities of surface (top 0–2 cm) and deep (50 cm) sediments in peat swamps that occur in both urbanised and non-urbanised catchments. Proteobacteria (32.2% of reads), Acidobacteria (23.6%) and Chloroflexi (10.7%) were the most common phyla of the dataset. There were significant differences in the bacterial community structure between catchment types and depths apparent at the phyla level. Proteobacteria, Bacteroidetes, Actinobacteria and Verrucomicrobia made up a greater proportion of the reads in the surface sediments than the deeper sediments, while Chloroflexi and Nitrospirae were relatively more common in the deeper than the surface sediment. By catchment type, Acidobacteria were more common in swamps occurring in non-urbanised catchments, while Nitrospirae, Bacteroidetes and Actinobacteria were more common in those in urbanised catchments. Microbial community structure was significantly correlated with sediment pH, as was the relative abundance of several phyla, including Acidobacteria (negative correlation) and Bacteroidetes (positive correlation). As an indicator of trophic shift from oligotrophic to copiotrophic conditions associated with urbanised catchment, we found significant differences ratios of β-Proteobacteria to Acidobacteria and Bacteriodetes to Acidobacteria between the catchment types. Based on SIMPER results we suggest the relative abundance of Nitrosomonadaceae family as a potential indicator of urban degradation. As the first study to analyse the bacterial community structure of THPSS using sequencing of 16S rDNA, we reveal the utility of such analyses and show that urbanisation in the Blue Mountains is impacting the microbial ecology of these important peatland ecosystems.

Diversity and distribution of antibiotic resistance genes associated with road sediments transported in urban stormwater runoff

Recently, increasing attention has been paid to antibiotic resistance genes (ARGs) in urban stormwater runoff. However, there were little data on the diversity and distribution of ARGs associated with road sediments transported in runoff. The investigation of ARGs diversity showed that sulfonamide resistance genes (sul2 and sul3) occupied 61.7%-82.3% of total ARGs in runoff. The analysis of ARGs distribution in particulate matter (PM) implied that both tetQ and trbC existed mainly in PM with size of 150-300 μm, but other ARGs and mobile genetic elements (MGEs) were dominant in PM with size <75 μm. The discussion of potential hosts indicated that target genes (ermF, blaOXA1/blaOXA30, ermC, qnrA, sul2, tnpA-01, intI2, tetW, intI1, sul3, trbC) had the strongest subordinate relationship with Proteobacteria at phylum level and Enterobacter at genus level. The effect evaluation of ARGs distribution suggested that 13 kinds of ARGs were positively correlated with Pr/PS and Zeta potential, resulting in the more ARGs in PM with smaller size (<75 μm).

Characterization of the bacterioplankton community and the influencing factors in the upper reaches of the Han River basin

The upper reaches of the Han River are the source region of water for the Middle Route of China's South-to-North Water Diversion Project, mainly for household, industrial, and irrigation purposes. Planktonic bacteria are more sensitive than macroorganisms to water physical and chemical properties and play a critical role in biogeochemical processes in river ecosystems. In November 2017 and April 2018, a systematic and methodical survey was carried out to evaluate the water quality and bacterial communities, on the mainstem of the Han River and its five main tributaries. In this study, high-throughput sequencing technology has been employed to investigate the bacterioplankton community composition. The results indicated the following: (1) diversity increased downstream, especially in the upper reaches of the Han River. (2) The relative abundance of Actinobacteria increased with the increase of river length, while that of Bacteroidetes decreased slightly. (3) Five tributaries were found to be importance sources of taxa to the Han River; however, in both months, a large proportion of operational taxonomic units (37.84% and 36.34%, respectively) had unknown sources. (4) Finally, redundancy analysis (RDA) and Bioenv analysis showed that environmental parameters (pH, TN, Cond, NH₄⁺-N, DO, NO₂^--N, Chl-a, and T) had a great influence (p ≤ 0.05) on the bacterioplankton community. These research results are beneficial for the managing the ecological system, protecting the tributary biodiversity, and conserving the mainstem and tributaries of the Han River basin.

Easy Access to Antibiotics; Spread of Antimicrobial Resistance and Implementation of One Health Approach in India

Antimicrobial resistance (AMR) is a global public health concern because of its fast spread. India, one of the world's top consumer of antibiotics and second most populated country has its unique constraints of social, cultural and economic strata. The continual self-medication, use of antibiotics for the growth promotion in animals, and accumulation of residual antibiotics in the environment challenge the implementation of AMR containment policy. Hence, the present review attempts to delineate the influence of antibiotics abuse on the human, animal and environmental health under the realm of one health. It was based on the literature search using public databases to highlight the rapid surge in the burden of AMR in India affecting various sectors and/or ecosystems in India. It was found that the irrational and overuse of antibiotics in different sectors have led to the emergence of extended antimicrobial resistance wherein the environment acts as a reservoir of antibiotic resistance genes (ARGs); completing the cycle of contamination and recontamination. There are efforts by government policy makers to reduce the burden of AMR in the country to reduce the health risks, through the One Health approach. Parallel efforts in educating healthcare professionals, strict legislation for pharmacies and pharmaceutical companies should be prioritize. At the same time surveillance of newly emerged AMR pathogens, prioritising research focusing on AMR, and awareness camps or programs among the local population is critical while addressing the consequences of spared of AMR in India.

Metagenomic analysis of a mega-city river network reveals microbial compositional heterogeneity among urban and peri-urban river stretch

The rivers in the megacities face a constant inflow of extremely polluted wastewaters from various sources, and their influence on the connected peri-urban river is still poorly understood. The riverine system in Pune consists of Rivers Mula, Ramnadi, Pawana, Mutha, and Mula-Mutha, traversing through the urban settlements of Pune before joining River Bhima in the peri-urban region. We used MinION-based metagenomic sequencing to generate a comprehensive understanding of the microbial diversity differences between the urban and peri-urban zones, which has not been explored at the meta scale until date. The taxonomic analysis revealed significant enrichment of pollution indicators microbial taxa (Welsch's t-test, p < 0.05, Benjamini-Hochberg FDR test) such as Bacteriodetes, Firmicutes, Spirochaetes, Synergistetes, Euryarcheota in the urban waters as compared to peri-urban waters. Further, the peri-urban waters showed a significantly higher prevalence of ammonium oxidising archaeal groups such as Nitrososphaeraceae (Student's t-test p-value <0.05 with FDR correction), thereby probably suggesting the influence of agricultural runoffs. Besides, the microbial community diversity assessment also indicated the significant dissimilarity in the microbial community of urban and peri-urban waters. Overall, the analysis predicted 295 virulence genes mapping to 38 different pathogenic bacteria in the riverine system. Moreover, the higher genome coverage (at least 60%) for priority pathogens such as Pseudomonas, Klebsiella, Acinetobacter, Escherichia, Aeromonas in the sediment metagenome consolidates their dominance in this riverine system. To conclude, our investigation showed that the unrestrained anthropogenic and related activities could potentially contribute to the overall dismal conditions and influence the connected riverine stretches on the outskirts of the city.

Extended Ecological Restoration of Bacterial Communities in the Godavari River During the COVID-19 Lockdown Period: a Spatiotemporal Meta-analysis

The unprecedented COVID-19 pandemic has had major impact on human health worldwide. Whilst national and international COVID-19 lockdown and travel restriction measures have had widespread negative impact on economies and mental health, they may have beneficial effect on the environment, reducing air and water pollution. Mass bathing events (MBE) also known as Kumbh Mela are known to cause perturbations of the ecosystem affecting resilient bacterial populations within water of rivers in India. Lockdowns and travel restrictions provide a unique opportunity to evaluate the impact of minimum anthropogenic activity on the river water ecosystem and changes in bacterial populations including antibiotic-resistant strains. We performed a spatiotemporal meta-analysis of bacterial communities of the Godavari River, India. Targeted metagenomics revealed a 0.87-fold increase in the bacterial diversity during the restricted activity of lockdown. A significant increase in the resilient phyla, viz. Proteobacteria (70.6%), Bacteroidetes (22.5%), Verrucomicrobia (1.8%), Actinobacteria (1.2%) and Cyanobacteria (1.1%), was observed. There was minimal incorporation of allochthonous bacterial communities of human origin. Functional profiling using imputed metagenomics showed reduction in infection and drug resistance genes by - 0.71-fold and - 0.64-fold, respectively. These observations may collectively indicate the positive implications of COVID-19 lockdown measures which restrict MBE, allowing restoration of the river ecosystem and minimise the associated public health risk.

Exploring the allochthonous pollution influence on bacterial community and co-occurrence dynamics of River Ganga water through 16S rRNA-tagged amplicon metagenome

River Ganga is one of the largest and most sacred rivers of India. This river is largely affected by anthropogenic activities causing significant increase in water pollution. The impact of drains discharging polluted water on the bacterial community dynamics in the river remains unexplored. To elucidate this, the targeted 16S rRNA V3-V4 variable region amplicon sequencing and bioinformatic analysis were performed using water from upstream, drain, and downstream of river Ganga. Analysis revealed significant difference in relative abundances of bacterial communities. The increase in bacterial abundance and alpha diversity was detected in the downstream compared to the upstream. Environmental factors were found significantly different between upstream and downstream water. At the phyla level, highly abundant taxa such as Proteobacteria, Actinobacteria, Planctomycetes, Bacteroidetes, and Verrucomicrobia were observed. Bacterial genera like Prevotella, Bacteroides, Blautia, and Faecalibacterium (fecal indicator) had higher abundance in the downstream site. Network co-occurrence revealed that bacterial communities have a modular profile with reduced interaction in drain and downstream water. The network of co-occurring bacterial communities consists of 283 nodes with edge connectivity of 6900, 7074, and 5294 in upstream, drain, and downstream samples, respectively. Upstream communities exhibited the highest positive interaction followed by the drain and the downstream sites. Additionally, highly abundant pathogenic species such as Acinetobacter baumannii and Prevotella copri were also detected in all samples. This study suggests the drain to be allochthonous pollution vector that significantly contributes to bacterial community enrichment. From the results of this study, it is apparent that the lotic water may be used as the ecological reference to understand and monitor the variations in the bacterial communities and their co-occurrence dynamics in the fresh water ecosystems.

Nutrients and Pharmaceuticals Structure Bacterial Core Communities in Urban and Montane Stream Biofilms

Bacteria in stream biofilms contribute to stream biogeochemical processes and are potentially sensitive to the substantial levels of pollution entering urban streams. To examine the effects of contaminants on stream biofilm bacteria in situ, we exposed growing biofilms to experimental additions of nutrients [nitrogen (N), phosphorus (P), and iron (Fe)], pharmaceuticals (caffeine and diphenhydramine), nutrients plus pharmaceuticals, or no contaminants using contaminant exposure substrates (CES) in three catchments in northern Utah. We performed our study at montane and urban sites to examine the influence of existing pollution on biofilm response. We identified bacterial core communities (core) for each contaminant treatment at each land-use type (e.g., nutrient addition montane bacterial core, nutrient addition urban bacterial core, pharmaceutical addition montane bacterial core) by selecting all taxa found in at least 75% of the samples belonging to each specific grouping. Montane and urban land-use distinguished bacterial cores, while nutrients and pharmaceuticals had subtle, but nonetheless distinct effects. Nutrients enhanced the dominance of already abundant copiotrophs [i.e., Pseudomonadaceae (Gammaproteobacteria) and Comamonadaceae (Betaproteobacteria)] within bacterial cores at montane and urban sites. In contrast, pharmaceuticals fostered species-rich bacterial cores containing unique contaminant-degrading taxa within Pseudomonadaceae and Anaerolineaceae (Chloroflexi). Surprisingly, even at urban sites containing ambient pharmaceutical pollution, pharmaceutical additions increased bacterial core richness, specifically within DR-16 (Betaproteobacteria), WCHB1-32 (Bacteroidetes), and Leptotrichiaceae (Fusobacteria). Nutrients exerted greater selective force than pharmaceuticals in nutrient plus pharmaceutical addition treatments, creating bacterial cores more closely resembling those under nutrient rather than pharmaceutical addition, and promoting unique Oscillatoriales (Cyanobacteria) taxa in urban streams. Our results show that additions of N, P, and Fe intensified the dominance of already abundant copiotrophs, while additions of caffeine and diphenhydramine enabled unique taxa associated with contaminant degradation to participate in bacterial cores. Further, biofilm bacteria at urban sites remained sensitive to pharmaceuticals commonly present in waters, suggesting a dynamic interplay among pharmaceutical pollution, bacterial diversity, and contaminant degradation.

Connectivity of bacterial assemblages along the Loa River in the Atacama Desert, Chile

The Loa River is the only perennial artery that crosses the Atacama Desert in northern Chile. It plays an important role in the ecological and economic development of the most water-stressed region, revealing the impact of the mining industry, which exacerbate regional water shortages for many organisms and ecological processes. Despite this, the river system has remained understudied. To our knowledge, this study provides the first effort to attempt to compare the microbial communities at spatial scale along the Loa River, as well as investigate the physicochemical factors that could modulate this important biological component that still remains largely unexplored. The analysis of the spatial bacterial distribution and their interconnections in the water column and sediment samples from eight sites located in three sections along the river catchment (upper, middle and lower) was conducted using 16S rRNA gene-based Illumina MiSeq sequencing. Among a total of 543 ASVs identified at the family level, over 40.5% were cosmopolitan in the river and distributed within a preference pattern by the sediment substrate with 162 unique ASVs, while only 87 were specific to the column water. Bacterial diversity gradually decreased from the headwaters, where the upper section had the largest number of unique families. Distinct groupings of bacterial communities often associated with anthropogenic disturbance, including Burkholderiaceae and Flavobacteriaceae families were predominant in the less-impacted upstream section. Members of the Arcobacteraceae and Marinomonadaceae were prominent in the agriculturally and mining-impacted middle sector while Rhodobacteraceae and Coxiellaceae were most abundant families in downstream sites. Such shifts in the community structure were also related to the influence of salinity, chlorophyll, dissolved oxygen and redox potential. Network analyses corroborated the strong connectivity and modular structure of bacterial communities across this desert river, shedding light on taxonomic relatedness of co-occurring species and highlighting the need for planning the integral conservation of this basin.

Comprehensive metagenomic insights into a unique mass gathering and bathing event reveals transient influence on a riverine ecosystem

The religious mass gathering and bathing can pose a multitude of significant public health challenges and lead to severe alterations in the river microbial ecology. The Pandharpur Wari is an annual pilgrimage of Maharashtra, India, where millions of devotees carry the footprints of the saint-poets and pay their obeisance to Lord Vitthal on the 11th day of moon's waxing phase (Ashadi Ekadashi). As a part of the ritual, the engrossed devotees, walk over 250 km, take a first holy dip in a sacred river Indrayani at Alandi and secondly in Bhima River at Pandharpur. The MinION-based shotgun metagenomic approach was employed to examine the impact of spiritual mass bathing on environmental changes (concerning the river microbial community structure and functions); and public health aspects (in terms of changes in the pathogenic potential and antibiotic resistance). The analysis of bathing and post-bathing samples of both the rivers revealed alterations in the alpha and beta diversity, indicating significant spatiotemporal variations in the overall microbial structure and function. Furthermore, the analysis revealed up to 80% of differences in the abundance of virulence genes between the bathing and post bathing samples. We observed parallel increase of priority skin and enteric pathogens (ranging from 11% to 80%) such as Acinetobacter baumannii, Staphylococcus aureus, Streptococcus pyogenes, Mycobacterium tuberculosis, and Pseudomonas aeruginosa during the bathing event. Moreover, we observed a significant increase in the antibiotic resistance in the bathing samples of Bhima and Indrayani rivers respectively. Altogether, this is the first comprehensive metagenomic study unravelling the influence of religious mass-bathing on the riverine ecosystem.

Nutrient and microbial water quality of the upper Ganga River, India: identification of pollution sources

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.

Distribution of antibiotic resistance genes in an agriculturally disturbed lake in China: Their links with microbial communities, antibiotics, and water quality

In this study, six antibiotic resistance genes (ARGs), one mobile genetic element (int1), and their relation with microbial communities, antibiotics, and water quality were investigated in and around of an agriculturally disturbed lake, namely, Lake Honghu. The ARGs and int1 in the research area had a 100 % detection frequency in each sample during two sampling times. The ARGs were higher in the rivers and inlets than in Lake Honghu. Sul1 was the main ARG in this area. Antibiotics, nutrients, and dissolved oxygen were significantly, positively, and negatively correlated with nearly all of the ARGs, respectively. This finding suggests that reducing antibiotics and the eutrophication level could reduce the risk of ARGs. Microbial community shift had the most direct contribution to ARG variation. However, when the indirect effect was considered, environmental factors contributed 34 % to the ARGs' variance, the microbial community contributed 28 %, and their joint effect contributed 27 % to the ARG profiles. The abundance of Firmicutes, Gemmatimonadetes, Proteobacteria, etc. and their positive correlation with ARGs were significant, suggesting that these phyla probably carry ARGs. The study provides a systematic profile of ARG distribution and dissemination in a typical Chinese lake and new ideas to control this emerging contaminant in lakes.

Distinct responses of planktonic and sedimentary bacterial communities to anthropogenic activities: Case study of a tributary of the Three Gorges Reservoir, China

Anthropogenic activities can cause serious negative effects on ecosystems. Despite the ecological significance of bacterial communities, the integrated biogeography of planktonic and sedimentary bacterial communities in response to anthropogenic activities is not adequately understood. Here, we examined environmental parameters and the composition of planktonic and sedimentary bacteria in the Yulin River, a tributary of Three Gorges Reservoir, in response to changes in land use and dam construction. The results revealed that human-induced land use changes enhanced the nutrient concentrations in surface water and dam construction reduced the content of carbon and nitrogen in immediately downstream sediments. Intensified human-dominated land use showed a slight impact on sedimentary bacterial communities but largely reduced the diversity of planktonic bacterial communities. Moreover, human-induced land use changes increased the abundance of genes associated with denitrification, nitrification, and anammox in planktonic bacterial communities by 19.04%, 32.40% and 30.45%, respectively. In dam construction regions, the diversity and nutrient-related metabolic activity of sedimentary bacterial communities immediately downstream of the dam were decreased, whereas these changes were not observed in planktonic bacterial communities. Additionally, bacterial community composition was significantly related to nutrient concentrations variability and followed a distance-decay pattern. Furthermore, environmental effects explained more of the variation in planktonic bacterial community composition as compared with spatial effects did, whereas, sedimentary bacterial communities were more closely related to spatial effects. Our results demonstrated the distinct responses of planktonic and sedimentary bacterial communities to anthropogenic activities, and offered new insight for understanding their potential ecological influence on rivers.

In search of microbial indicator taxa: shifts in stream bacterial communities along an urbanization gradient

A majority of environmental studies describe microbiomes at coarse scales of taxonomic resolution (bacterial community, phylum), ignoring key ecological knowledge gained from finer-scales and microbial indicator taxa. Here, we characterized the distribution of 940 bacterial taxa from 41 streams along an urbanization gradient (0%-83% developed watershed area) in the Raleigh-Durham area of North Carolina (USA). Using statistical approaches derived from macro-organismal ecology, we found that more bacterial taxa were classified as intolerant than as tolerant to increasing watershed urbanization (143 vs 48 OTUs), and we identified a threshold of 12.1% developed watershed area beyond which the majority of intolerant taxa were lost from streams. Two bacterial families strongly decreased with urbanization: Acidobacteriaceae (Acidobacteria) and Xanthobacteraceae (Alphaproteobacteria). Tolerant taxa were broadly distributed throughout the bacterial phylogeny, with members of the Comamonadaceae family (Betaproteobacteria) presenting the highest number of tolerant taxa. Shifts in microbial community structure were strongly correlated with a stream biotic index, based on macroinvertebrate composition, suggesting that microbial assemblages could be used to establish biotic criteria for monitoring aquatic ecosystems. In addition, our study shows that classic methods in community ecology can be applied to microbiome datasets to identify reliable microbial indicator taxa and determine the environmental constraints on individual taxa distributions along environmental gradients.

Mass gatherings medicine: public health issues arising from mass gathering religious and sporting events

Mass gathering events are associated with major public health challenges. The 2014 Lancet Series on the new discipline of mass gatherings medicine was launched at the World Health Assembly of Ministers of Health in Geneva in May, 2014. The Series covered the planning and surveillance systems used to monitor public health risks, public health threats, and experiences of health-care providers from mass gathering events in 2012 and 2013. This follow-up Review focuses on the main public health issues arising from planned mass gathering events held between 2013 and 2018. We highlight public health and research data on transmission of infectious diseases and antibiotic-resistant bacteria, mass casualty incidents, and non-communicable diseases, including thermal disorders. In the events discussed in this Review, the combination of a large influx of people, many from countries with outbreak-prone infectious diseases, with a high degree of crowd interactions imposed substantial burdens on host countries' health systems. The detection and transmission of antibiotic-resistant bacteria in pilgrims attending the Kumbh Mela and the Hajj raise concern of possible globalisation from mass-gathering religious events. Priorities for further investments and opportunities for research into prevention, surveillance, and management of these public health issues are discussed.

Urbanization Altered Bacterial and Archaeal Composition in Tidal Freshwater Wetlands Near Washington DC, USA, and Buenos Aires, Argentina

Urban expansion causes coastal wetland loss, and environmental stressors associated with development can lead to wetland degradation and loss of ecosystem services. This study investigated the effect of urbanization on prokaryotic community composition in tidal freshwater wetlands. Sites in an urban, suburban, and rural setting were located near Buenos Aires, Argentina, and Washington D.C., USA. We sampled soil associated with two pairs of functionally similar plant species, and used Illumina sequencing of the 16S rRNA gene to examine changes in prokaryotic communities. Urban stressors included raw sewage inputs, nutrient pollution, and polycyclic aromatic hydrocarbons. Prokaryotic communities changed along the gradient (nested PerMANOVA, Buenos Aires: p = 0.005; Washington D.C.: p = 0.001), but did not differ between plant species within sites. Indicator taxa included Methanobacteria in rural sites, and nitrifying bacteria in urban sites, and we observed a decrease in methanogens and an increase in ammonia-oxidizers from rural to urban sites. Functional profiles in the Buenos Aires communities showed higher abundance of pathways related to nitrification and xenobiotic degradation in the urban site. These results suggest that changes in prokaryotic taxa across the gradient were due to surrounding stressors, and communities in urban and rural wetlands are likely carrying out different functions.

Bioaccumulation of heavy metals in Channa punctatus (Bloch) in river Ramganga (U.P.), India

Ganga is the largest riverine system of India with a fragile ecosystem. Its prone to anthropogenic disturbances because of its cultural, economic and environmental values. The contamination of river Ganga by heavy metals (HM) is due to biotic (anthropogenic sources) and abiotic (pesticides, fertilizers) sources that poses a devastating health hazard to human, plant and edible fish life. The chemical analysis with the help of atomic absorption spectrometer performed on its water samples demonstrated the accumulation of heavy metals such as Arsenic (As), Lead (Pb), Cadmium (Cd), Iron (Fe), Zinc (Zn). Moreover, the spectrophotometric analysis indicated clearly the accumulation of heavy metals in order of occurrence (Fe > As > Cd > Zn > Pb) in liver and (Zn > Fe > As > Cd > Pb) in kidney of edible fish Channa punctatus. The present study has be used to sensitively monitor the extent of heavy metals pollution in the biotic aqua life of river Ramganga system and its suggested that the bioaccumulation of heavy metal in Channa punctatus has reached above permissible limits for human consumption, indicating potential health risks. Necessary biological steps should be taken to handle such food pollution and prevent the environmental risk and food chain disruption.

World's Largest Mass Bathing Event Influences the Bacterial Communities of Godavari, a Holy River of India

Kumbh Mela is one of the largest religious mass gathering events (MGE) involving bathing in rivers. The exponential rise in the number of devotees, from around 0.4 million in 1903 to 120 million in 2013, bathing in small specified sites can have a dramatic impact on the river ecosystem. Here, we present the spatiotemporal profiling of bacterial communities in Godavari River, Nashik, India, comprising five sites during the Kumbh Mela, held in 2015. Assessment of environmental parameters indicated deterioration of water quality. Targeted amplicon sequencing demonstrates approximately 37.5% loss in microbial diversity because of anthropogenic activity during MGE. A significant decrease in phyla viz. Actinobacteria, Chloroflexi, Proteobacteria, and Bacteroidetes was observed, while we noted substantial increase in prevalence of the phylum Firmicutes (94.6%) during MGE. qPCR estimations suggested nearly 130-fold increase in bacterial load during the event. Bayesian mixing model accounted the source of enormous incorporation of bacterial load of human origin. Further, metagenomic imputations depicted increase in virulence and antibiotic resistance genes during the MGE. These observations suggest the striking impact of the mass bathing on river ecosystem. The subsequent increase in infectious diseases and drug-resistant microbes pose a critical public health concern.

Corynebacterium godavarianum sp. nov., isolated from the Godavari river, India

A Gram-stain-positive, rod-shaped, non-motile bacterium, strain PRD07^T, was isolated from Godavari river, India during the world's largest spiritual and religious mass bathing event 'Kumbh Mela'. Molecular analysis using 16S rRNA gene sequencing and phylogenetic analysis reveals the distinct phylogenetic positioning of strain PRD07^T within the genus Corynebacterium. The strain demonstrated highest sequence similarity to Corynebacterium imitans DSM 44264^T (97.9 %), Corynebacterium appendicis DSM 44531^T (97.1 %) and <96.7 % with all other members of the genus Corynebacterium. The G+C content of PRD07^T was 68.5 mol% (Tm) and the DNA-DNA hybridization depicts 61.09 % genomic relatedness with C. imitans DSM 44264^T. Chemotaxonomic assessment of strain PRD07^T suggested presence of C16 : 0 (31.6 %), C18 : 0 (3.5 %) and C18 : 1ω9c (58.6 %) as the major cellular fatty acids. The major polar lipids of strain PRD07^T were phosphatidylglycerol, diphosphatidylglycerol and glycophospholipid. Differentiating molecular, phylogenetic and chemotaxonomic characteristics of strain PRD07^T with its closest relatives necessitated the description of strain PRD07^T as a novel species of genus Corynebacterium for which the name Corynebacteriumgodavarianum sp. nov., has been proposed. The type strain is PRD07^T (=MCC 3388^T=KCTC 39803^T=LMG 29598^T).