Impact of a wastewater treatment plant on microbial community composition and function in a hyporheic zone of a eutrophic river

Metagenomics insights into bacterial diversity and antibiotic resistome of the sewage in the city of Belém, Pará, Brazil

Introduction

The advancement of antimicrobial resistance is a significant public health issue today. With the spread of resistant bacterial strains in water resources, especially in urban sewage, metagenomic studies enable the investigation of the microbial composition and resistance genes present in these locations. This study characterized the bacterial community and antibiotic resistance genes in a sewage system that receives effluents from various sources through metagenomics.

Methods

One liter of surface water was collected at four points of a sewage channel, and after filtration, the total DNA was extracted and then sequenced on an NGS platform (Illumina® NextSeq). The sequenced data were trimmed, and the microbiome was predicted using the Kraken software, while the resistome was analyzed on the CARD webserver. All ecological and statistical analyses were performed using the. RStudio tool.

Results and discussion

The complete metagenome results showed a community with high diversity at the beginning and more restricted diversity at the end of the sampling, with a predominance of the phyla Bacteroidetes, Actinobacteria, Firmicutes, and Proteobacteria. Most species were considered pathogenic, with an emphasis on those belonging to the Enterobacteriaceae family. It was possible to identify bacterial groups of different threat levels to human health according to a report by the U.S. Centers for Disease Control and Prevention. The resistome analysis predominantly revealed genes that confer resistance to multiple drugs, followed by aminoglycosides and macrolides, with efflux pumps and drug inactivation being the most prevalent resistance mechanisms. This work was pioneering in characterizing resistance in a sanitary environment in the Amazon region and reinforces that sanitation measures for urban sewage are necessary to prevent the advancement of antibiotic resistance and the contamination of water resources, as evidenced by the process of eutrophication.

Wastewater-effluent discharge and incomplete denitrification drive riverine CO2, CH4 and N2O emissions

Rivers are well-known sources of the greenhouse gasses (GHG) carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O). These emissions from rivers can increase because of anthropogenic activities, such as agricultural fertilizer input or the discharge of treated wastewater, as these often contain elevated nutrient concentrations. Yet, the specific effects of wastewater effluent discharge on river GHG emissions remain poorly understood. Here, we studied two lowland rivers which both receive municipal wastewater effluent: river Linge and river Kromme Rijn. Dissolved concentrations and fluxes of CH4, N2O and CO2 were measured upstream, downstream and at discharge locations, alongside water column properties and sediment composition. Microbial communities in the sediment and water column were analysed using 16S rRNA gene sequencing. In general, observed GHG emissions from Linge and Kromme Rijn were comparable to eutrophic rivers in urban and agricultural environments. CO2 emissions peaked at most discharge locations, likely resulting from dissolved CO2 present in the effluent. CH4 emission was highest 2 km downstream, suggesting biological production by methanogenic activity stimulated by the effluents' carbon and nutrient supply. Dissolved N2O concentrations were strongly related to NO3- content of the water column which points towards incomplete riverine denitrification. Notably, methanogenic archaea were more abundant downstream of effluent discharge locations. However, overall microbial community composition remained relatively unaffected in both rivers. In conclusion, we demonstrate a clear link between wastewater effluent discharge and enhanced downstream GHG emission of two rivers. Mitigating the impact of wastewater effluent on receiving rivers will be crucial to reduce riverine GHG contributions.

Variability of Biodegradation Rates of Commercial Chemicals in Rivers in Different Regions of Europe

Biodegradation is one of the most important processes influencing the fate of organic contaminants in the environment. Quantitative understanding of the spatial variability in environmental biodegradation is still largely uncharted territory. Here, we conducted modified OECD 309 tests to determine first-order biodegradation rate constants for 97 compounds in 18 freshwater river segments in five European countries: Sweden, Germany, Switzerland, Spain, and Greece. All but two of the compounds showed significant spatial variability in rate constants across European rivers (ANOVA, P < 0.05). The median standard deviation of the biodegradation rate constant between rivers was a factor of 3. The spatial variability was similar between pristine and contaminated river segments. The longitude, total organic carbon, and clay content of sediment were the three most significant explanatory variables for the spatial variability (redundancy analysis, P < 0.05). Similarities in the spatial pattern of biodegradation rates were observed for some groups of compounds sharing a given functional group. The pronounced spatial variability presents challenges for the use of biodegradation simulation tests to assess chemical persistence. To reflect the variability in the biodegradation rate, the modified OECD 309 test would have to be repeated with water and sediment from multiple sites.

High-proportions of tailwater discharge alter microbial community composition and assembly in receiving sediments

The tailwater from wastewater treatment plants serves as an important water resource in arid regions, alleviating the conflict between supply and demand. However, the effects of different tailwater discharge proportions on microbial community dynamics remain unclear. In this study, we investigated the effects of different tailwater discharge proportions on the water quality and microbial community characteristics of sediments in receiving water bodies under controlled conditions (WF-1, WF-2, WF-3, WF-4, and WF-5, containing 0% tailwater + 100% natural water, 25% tailwater + 75% natural water, 50% tailwater + 50% natural water, 75% tailwater + 25% natural water, and 100% tailwater + 0% natural water, respectively). Microbial co-occurrence networks and structural equation model were used to unveil the relationship between microbial communities and their shaping factors. Results showed that distinct microbial community compositions were found in the sediments with low- (< 50%) and high- (> 50%) proportions of tailwater. Specifically, WCHB1-41 and g_4-29-1, which are involved in organic degradation-related functions, were the key genera in the high-proportion cluster. A total of 21 taxa were more abundant in the low-proportion (< 50%) cluster than that in high-proportion (> 50%). Moreover, higher modularity was observed in the low-proportion. Total phosphorus directly affected while ammonia nitrogen indirectly affected the microbial community structure. Our findings support the distinct heterogeneity of microbial communities driven by tailwater discharge in receiving water bodies, and further confirmed that high-proportion tailwater depletes sensitive microbial communities, which may be avoided through scientific management.

Spatial and temporal distribution of the microbial community structure in the receiving rivers of the middle and lower reaches of the Yangtze River under the influence of different wastewater types

The gradual intensification of human activity has caused severe negative impacts on the ecosystems of the Yangtze River Basin. Treated effluents still affect the environment and health of receiving rivers, particularly in terms of microbial community structure. However, relatively few studies have been conducted on the differences in the effects of wastewater types on microbial community structure. Three sampling campaigns (237 samples) were conducted in the Nanjing and Wuhan sections of the Yangtze River Basin. Our results showed that the microbial community structure differed significantly among the water periods and could recover to its original state at > 500 m downstream of the outfall. The diversity of the receiving rivers under the influence of industrial wastewater was higher than that of the other wastewater types, although the number of taxa was lower than that of other wastewater types. Cyanobium_PCC-6307 and Rhodoferax were screened for biomarkers in samples affected by domestic and industrial wastewater, respectively. Although different kinds of wastewater influenced the microbial community structure, environmental factors, and geographical distance were still the main drivers. This study suggests that treated wastewater still poses a risk to ecosystems and highlights the importance of effective management strategies for assessing ecosystem health.

River Sediments Downstream of Villages in a Karstic Watershed Exhibited Increased Numbers and Higher Diversity of Nontuberculous Mycobacteria

The impact of residential villages on the nontuberculous mycobacteria (NTM) in streams flowing through them has not been studied in detail. Water and sediments of streams are highly susceptible to anthropogenic inputs such as surface water flows. This study investigated the impact of seven residential villages in a karst watershed on the prevalence and species spectrum of NTM in water and sediments. Higher NTM species diversity (i.e., 19 out of 28 detected) was recorded downstream of the villages and wastewater treatment plants (WWTPs) compared to sampling sites upstream (i.e., 5). Significantly, higher Zn and lower silicon concentrations were detected in sediments inside the village and downstream of the WWTP's effluents. Higher phosphorus concentration in sediment was downstream of WWTPs compared to other sampling sites. The effluent from the WWTPs had a substantial impact on water quality parameters with significant increases in total phosphorus, anions (Cl-and N-NH3-), and cations (Na+ and K+). The results provide insights into NTM numbers and species diversity distribution in a karst watershed and the impact of urban areas. Although in this report the focus is on the NTM, it is likely that other water and sediment microbes will be influenced as well.

Phylogenetic and ecophysiological novelty of subsurface mercury methylators in mangrove sediments

Mangrove sediment is a crucial component in the global mercury (Hg) cycling and acts as a hotspot for methylmercury (MeHg) production. Early evidence has documented the ubiquity of well-studied Hg methylators in mangrove superficial sediments; however, their diversity and metabolic adaptation in the more anoxic and highly reduced subsurface sediments are lacking. Through MeHg biogeochemical assay and metagenomic sequencing, we found that mangrove subsurface sediments (20-100 cm) showed a less hgcA gene abundance but higher diversity of Hg methylators than superficial sediments (0-20 cm). Regional-scale investigation of mangrove subsurface sediments spanning over 1500 km demonstrated a prevalence and family-level novelty of Hg-methylating microbial lineages (i.e., those affiliated to Anaerolineae, Phycisphaerae, and Desulfobacterales). We proposed the candidate phylum Zixibacteria lineage with sulfate-reducing capacity as a currently understudied Hg methylator across anoxic environments. Unlike other Hg methylators, the Zixibacteria lineage does not use the Wood-Ljungdahl pathway but has unique capabilities of performing methionine synthesis to donate methyl groups. The absence of cobalamin biosynthesis pathway suggests that this Hg-methylating lineage may depend on its syntrophic partners (i.e., Syntrophobacterales members) for energy in subsurface sediments. Our results expand the diversity of subsurface Hg methylators and uncover their unique ecophysiological adaptations in mangrove sediments.

Impact of wastewater treatment upgrade and nitrogen removal on bacterial communities and their interactions in eutrophic prairie streams

Eutrophication can impact bacteria by altering fluxes and processing of nutrients and organic matter. However, relatively little is known of how bacterial communities, diversity, and interactions with phytoplankton might respond to nutrient management. We used 16S rRNA amplicon sequencing to compare bacterial assemblages in the water column upstream (control) and downstream (impact) of a wastewater treatment plant (WWTP) located on a eutrophic prairie stream. Sampling occurred before (2012) and after (2018) the 2016 biological nutrient removal (BNR) upgrade that removed >90% of nitrogen (N, mainly NH4+). Multivariate ordination suggested that effluent-impacted bacterial communities were associated mainly with elevated NH4+ concentrations before the upgrade, whereas those after BNR were characteristic of reference systems (low NO3-, diverse regulation). Genera such as Betaproteobacteria and Rhodocyclacea were abundant at impacted sites in 2012, whereas Flavobacterium and a potential pathogen (Legionella) were common at impacted sites in 2018. Nitrifier bacteria (Nitrospira and Nitrosomonas) were present but rare at all sites in 2012, but recorded only downstream of the WWTP in 2018. Generalized additive models showed that BNR reduced bacterial diversity, with ∼70% of the deviance in diversity explained by hydrology, pH, nutrients, and phytoplankton abundance. Overall, NH4+ removal reduced symptoms of cultural eutrophication in microbe assemblages.

Wastewater treatment plant effluent discharge decreases bacterial community diversity and network complexity in urbanized coastal sediment

The wastewater treatment plant (WWTP) effluent discharge affects the microorganisms in the receiving water bodies. Despite the ecological significance of microbial communities in pollutant degradation and element cycling, how the community diversity is affected by effluent remains obscure. Here, we compared the sediment bacterial communities exposed to different intensities of WWTP effluent discharge in Hangzhou Bay, China: i) a severely polluted area that receives effluent from an industrial WWTP, ii) a moderately polluted area that receives effluent from a municipal WWTP, and iii) less affected area that inner the bay. We found that the sediment bacterial diversity decreased dramatically with pollution levels of inorganic nutrients, heavy metals, and organic halogens. Microbial community assembly model analysis revealed increased environmental selection and decreased species migration rate in the severely polluted area, resulting in high phylogenetic clustering of the bacterial communities. The ecological networks were less complex in the two WWTP effluent receiving areas than in the inner bay area, as suggested by the smaller network size and lower modularity. Fewer negative network associations were detected in the severely (6.7%) and moderately (8.3%) polluted areas than in the less affected area (16.7%), indicating more collaborative inter-species behaviors are required under stressful environmental conditions. Overall, our results reveal the fundamental impacts of WWTP effluents on the ecological processes shaping coastal microbial communities and point to the potential adverse effects of diversity loss on ecosystem functions.

Differences in Carbon and Nitrogen Migration and Transformation Driven by Cyanobacteria and Macrophyte Activities in Taihu Lake

The metabolic activities of primary producers play an important role in the migration and transformation of carbon (C) and nitrogen (N) in aquatic environments. This study selected two typical areas in Taihu Lake, a cyanobacteria-dominant area (Meiliang Bay) and a macrophyte-dominant area (in the east area of the lake), to study the effects of cyanobacteria and macrophyte activities on C and N migration and transformation in aquatic environments. The results showed that total N and total particulate N concentrations in the water of the cyanobacteria-dominant area were much higher than those in the macrophyte-dominant area, which was mainly due to the assimilated intracellular N in cyanobacteria. Macrophyte activity drove a significantly higher release of dissolved organic C (DOC) in the water than that driven by cyanobacteria activity, and the DOC contents in the water of the macrophyte-dominant area were 2.4~4.6 times the DOC contents in the cyanobacteria-dominant area. In terms of the sediments, organic matter (OM), sediment total N and N species had positive correlations and their contents were higher in the macrophyte-dominant area than in the cyanobacteria-dominant area. Sediment OM contents in the macrophyte-dominant area increased from 4.19% to 9.33% as the sediment deepened (0~10 cm), while the opposite trend was presented in the sediments of the cyanobacteria-dominant area. Sediment OM in the macrophyte-dominant area may contain a relatively high proportion of recalcitrant OC species, while sediment OM in the cyanobacteria-dominant area may contain a relatively high proportion of labile OC species. Compared with the macrophyte-dominant area, there was a relatively high richness and diversity observed in the bacterial community in the sediments in the cyanobacteria-dominant area, which may be related to the high proportion of labile OC in the OM composition in its sediments. The relative abundances of most OC-decomposing bacteria, denitrifying bacteria, Nitrosomonas and Nitrospira were higher in the sediments of the cyanobacteria-dominant area than in the macrophyte-dominant area. These bacteria in the sediments of the cyanobacteria-dominant area potentially accelerated the migration and transformation of C and N, which may supply nutrients to overlying water for the demands of cyanobacteria growth. This study enhances the understanding of the migration and transformation of C and N and the potential effects of bacterial community structures under the different primary producer habitats.

Geography, taxonomy, and ecological guild: Factors impacting freshwater macroinvertebrate gut microbiomes

Despite their diversity, global distribution, and apparent effects on host biology, the rules of life that govern variation in microbiomes among host species remain unclear, particularly in freshwater organisms. In this study, we sought to assess whether geographic location, taxonomy (order, family, and genus), or functional feeding group (FFG) designations would best explain differences in the gut microbiome composition among macroinvertebrates sampled across 10 National Ecological Observatory Network's (NEON) freshwater stream sites in the United States. Subsequently, we compared the beta diversity of microbiomes among locations, taxonomy (order, family, and genus), and FFGs in a single statistical model to account for variation within the source microbial community and the types of macroinvertebrates sampled across locations. We determined significant differences in community composition among macroinvertebrate orders, families, genera, and FFGs. Differences in microbiome compositions were underscored by different bacterial ASVs that were differentially abundant among variables (four bacterial ASVs across the 10 NEON sites, 43 ASVs among the macroinvertebrate orders, and 18 bacterial ASVs differing among the five FFGs). Analyses of variations in microbiome composition using the Bray-Curtis distance matric revealed FFGs as the dominant source of variation (mean standard deviation of 0.8), followed by stream site (mean standard deviation of 0.5), and finally family and genus (mean standard deviation of 0.3 each). Our findings revealed a principal role for FFG classification in insect gut microbiome beta diversity with additional roles for geographic distribution and taxonomy.

Endospores associated with deep seabed geofluid features in the eastern Gulf of Mexico

Recent studies have reported up to 1.9 × 10²⁹ bacterial endospores in the upper kilometre of deep subseafloor marine sediments, however, little is understood about their origin and dispersal. In cold ocean environments, the presence of thermospores (endospores produced by thermophilic bacteria) suggests that distribution is governed by passive migration from warm anoxic sources possibly facilitated by geofluid flow, such as advective hydrocarbon seepage sourced from petroleum deposits deeper in the subsurface. This study assesses this hypothesis by measuring endospore abundance and distribution across 60 sites in Eastern Gulf of Mexico (EGM) sediments using a combination of the endospore biomarker 2,6-pyridine dicarboxylic acid or 'dipicolinic acid' (DPA), sequencing 16S rRNA genes of thermospores germinated in 50°C sediment incubations, petroleum geochemistry in the sediments and acoustic seabed data from sub-bottom profiling. High endospore abundance is associated with geologically active conduit features (mud volcanoes, pockmarks, escarpments and fault systems), consistent with subsurface fluid flow dispersing endospores from deep warm sources up into the cold ocean. Thermospores identified at conduit sites were most closely related to bacteria associated with the deep biosphere habitats including hydrocarbon systems. The high endospore abundance at geological seep features demonstrated here suggests that recalcitrant endospores and their chemical components (such as DPA) can be used in concert with geochemical and geophysical analyses to locate discharging seafloor features. This multiproxy approach can be used to better understand patterns of advective fluid flow in regions with complex geology like the EGM basin.

The microbial diversity in industrial effluents makes high-throughput sequencing-based source tracking of the effluents possible

In order to explore the microbial diversity in industrial effluents, and on this basis, to verify the feasibility of tracking industrial effluents in sewer networks based on sequencing data, we collected 28 sewage samples from the industrial effluents relative to four factories in Shenzhen, China, and sequenced the 16S rRNA genes to profile the microbial compositions. We identified 5413 operational taxonomic units (OTUs) in total, and found that microbial compositions were highly diverse among samples from different locations in the sewer system, with only 107 OTUs shared by 90% of the samples. These shared OTUs were enriched in the phylum of Proteobacteria, the families of Comamonadaceae and Pseudomonadaceae, as well as the genus of Pseudomonas, with both degradation related and pathogenic bacteria. More importantly, we found differences in microbial composition among samples relevant to different factories, and identified microbial markers differentiating effluents from these factories, which can be used to track the sources of the effluents. This study improved our understanding of microbial diversity in industrial effluents, proved the feasibility of industrial effluent source tracking based on sequencing data, and provided an alternative technique solution for environmental surveillance and management.

Insights into the microbial community of treated wastewater, its year-round variability and impact on the receiver, using cultivation, microscopy and amplicon-based methods

Apart from chemical constituents, wastewater treatment plant (WWTP) effluents also release microorganisms that can be important to the receiving water bodies either from a sanitary point of view, or taking to the account the biogeochemical potential of the recipients. However, little is known about the treated wastewater microbial community, its composition, seasonal changes, functions and fate in the waters of the receiver. Thus, this study presents a synergistic approach coupling new and traditional methods: analytical chemistry, classical microbiology (cultivation- and microscopy-based methods), as well as Next Generation Sequencing and a quantitative real-time polymerase chain reaction (qPCR). The results show that in terms of bacterial community composition, treated wastewater differed from the environmental samples, irrespectively if they were related or unrelated to the WWTP effluent discharge. The canonical correspondence analysis (CCA) taking into account chemical parameters and taxonomical biodiversity indirectly confirmed the seasonal deterioration of the treated wastewater quality as a result of temperature-driven change of activated sludge community structure and biomass washout (observed also by DAPI staining). Despite seasonal fluctuations of total suspended solids and inter-related parameters (such as COD, BOD, TN, TP), the treated wastewater quality remained within current discharge limits. It was due to treatment processes intensively adjusted by WWTP operators, particularly those necessary to maintain an appropriate rate of autotrophic processes of nitrification and to support biological phosphorus removal. This can explain the observed microbiome composition similarity among WWTP effluents at high taxonomic levels. Obtained data also suggest that besides wastewater treatment efficiency, WWTP effluents are still sources of both human-related microorganisms as well as bacteria equipped in genes involved in N-cycling. Their potential of participation in nutrients cycling in the receivers is widely unknown and require critical attention and better understanding.

River Biofilms Microbiome and Resistome Responses to Wastewater Treatment Plant Effluents Containing Antibiotics

Continuous exposure to low concentrations of antibiotics (sub-minimal inhibitory concentration: sub-MIC) is thought to lead to the development of antimicrobial resistance (AMR) in the environmental microbiota. However, the relationship between antibiotic exposure and resistance selection in environmental bacterial communities is still poorly understood and unproven. Therefore, we measured the concentration of twenty antibiotics, resistome quality, and analyzed the taxonomic composition of microorganisms in river biofilms collected upstream (UPS) and downstream (DWS) (at the point of discharge) from the wastewater treatment plant (WWTP) of Poitiers (France). The results of statistical analysis showed that the antibiotic content, resistome, and microbiome composition in biofilms collected UPS were statistically different from that collected DWS. According to Procrustes analysis, microbial community composition and antibiotics content may be determinants of antibiotic resistance genes (ARGs) composition in samples collected DWS. However, network analysis showed that the occurrence and concentration of antibiotics measured in biofilms did not correlate with the occurrence and abundance of antibiotic resistance genes and mobile genetic elements. In addition, network analysis suggested patterns of co-occurrence between several ARGs and three classes of bacteria/algae: Bacteroidetes incertae sedis, Cyanobacteria/Chloroplast, and Nitrospira, in biofilm collected UPS. The absence of a direct effect of antibiotics on the selection of resistance genes in the collected samples suggests that the emergence of antibiotic resistance is probably not only due to the presence of antibiotics but is a more complex process involving the cumulative effect of the interaction between the bacterial communities (biotic) and the abiotic matrix. Nevertheless, this study confirms that WWTP is an important reservoir of various ARGs, and additional efforts and legislation with clearly defined concentration limits for antibiotics and resistance determinants in WWTP effluents are needed to prevent their spread and persistence in the environment.

Impacts of municipal wastewater treatment plant discharge on microbial community structure and function of the receiving river in Northwest Tibetan Plateau

Wastewater treatment plant (WWTP) effluents carrying plenty of nutrients and micropollutants pose serious threats to receiving rivers, however, the response of microbial community structure and function to WWTP effluents discharge is still poorly understood. To address this knowledge gap, paired water and sediment samples from 17 sites of the Huangshui River, and effluents from 6 WWTPs were collected to investigate the effect of WWTP discharge on riverine microbial communities. Our results revealed that WWTP effluents exerted significant effects on planktonic rather than sedimentary microorganisms in the receiving river. Notably, lower diversity and richness of planktonic communities were observed in the effluent-influenced section (WRW) than other river sections (RW) along the urban river. Meanwhile, network analysis potentially revealed lower stability of co-occurrence patterns of microbial communities in WRW. The remarkably higher antibiotics, nitrate-nitrogen, and water temperature in WRW samples caused by WWTPs played essential roles in shaping the structure and function of planktonic microbial communities. This study suggested the enrichment of multiple-drug resistance genes and destruction of energy metabolisms were caused by sewage effluents, and highlighted the importance of effective management strategies for protecting the ecological health of the receiving river.

Bacterial Indicators Are Ubiquitous Members of Pelagic Microbiome in Anthropogenically Impacted Coastal Ecosystem

Coastal zones are exposed to various anthropogenic impacts, such as different types of wastewater pollution, e.g., treated wastewater discharges, leakage from sewage systems, and agricultural and urban runoff. These various inputs can introduce allochthonous organic matter and microbes, including pathogens, into the coastal marine environment. The presence of fecal bacterial indicators in the coastal environment is usually monitored using traditional culture-based methods that, however, fail to detect their uncultured representatives. We have conducted a year-around in situ survey of the pelagic microbiome of the dynamic coastal ecosystem, subjected to different anthropogenic pressures to depict the seasonal and spatial dynamics of traditional and alternative fecal bacterial indicators. To provide an insight into the environmental conditions under which bacterial indicators thrive, a suite of environmental factors and bacterial community dynamics were analyzed concurrently. Analyses of 16S rRNA amplicon sequences revealed that the coastal microbiome was primarily structured by seasonal changes regardless of the distance from the wastewater pollution sources. On the other hand, fecal bacterial indicators were not affected by seasons and accounted for up to 34% of the sequence proportion for a given sample. Even more so, traditional fecal indicator bacteria (Enterobacteriaceae) and alternative wastewater-associated bacteria (Lachnospiraceae, Ruminococcaceae, Arcobacteraceae, Pseudomonadaceae and Vibrionaceae) were part of the core coastal microbiome, i.e., present at all sampling stations. Microbial source tracking and Lagrangian particle tracking, which we employed to assess the potential pollution source, revealed the importance of riverine water as a vector for transmission of allochthonous microbes into the marine system. Further phylogenetic analysis showed that the Arcobacteraceae in our data set was affiliated with the pathogenic Arcobacter cryaerophilus, suggesting that a potential exposure risk for bacterial pathogens in anthropogenically impacted coastal zones remains. We emphasize that molecular analyses combined with statistical and oceanographic models may provide new insights for environmental health assessment and reveal the potential source and presence of microbial indicators, which are otherwise overlooked by a cultivation approach.

Irrigation suitability of White River in Indiana, Midwestern USA

Climate change models consistently project future precipitation reduction and temperature increase during the crop growing season in the US Midwest, which may exacerbate surface water scarcity issues confronting regional agriculture. To maintain consistent crop yields under the risk of increased droughts, farmers may shift from rain-fed agriculture to irrigation agriculture, particularly during drought periods. There is an urgent need to understand whether surface water in the Midwest is suitable for irrigation. In this study, irrigation water quality was comprehensively analyzed for commonly used parameters regarding salt content including sodium adsorption ratio (SAR), adjusted sodium adsorption ratio (SAR_adj), soluble sodium percentage (SSP), electrical conductivity (EC), total dissolved solids (TDS), residual sodium bicarbonate (RSBC), magnesium adsorption ratio (MAR), permeability index (PI), Kelley's ratio (KR), synthetic harmful coefficient (SHC), and salinity. Results indicate that water in the White River at Muncie was rated mostly in excellent to good condition with regard to irrigation quality. However, the irrigation suitability level exhibited two distinct patterns between May-July and August-October. Specifically, an average of 7.8% of the samples from May to July were unsuitable for irrigation, and an average of 24.5% of samples from August to October were unsuitable for irrigation considering all parameters. Flow rate change over time and the release of pollutants from wastewater treatment plants and combine sewage outflows to the White River impacted on the irrigation water quality variations of the river. This study showed that there are higher risks during the fall season for farmers to use surface water as an irrigation source, and this risk might be greater if extended or more frequent drought events occur in the future. To our best knowledge, this is the first peer-reviewed study on irrigation water quality assessment in the Midwest and provides useful information for farmers and decision makers to consider while formulating applications for irrigation.

Deciphering the black box of microbial community of common effluent treatment plant through integrated metagenomics: Tackling industrial effluent

Identifying the microbial community and their functional potential from different stages of common effluent treatment plants (CETP) can enhance the efficiency of wastewater treatment systems. In this study, wastewater metagenomes from 8 stages of CETP were screened for microbial diversity and gene profiling along with their corresponding degradation activities. The microbial community displayed 98.46% of bacterial species, followed by Eukarya (0.10%) and Archaea 0.02%. At the Phylum level, Proteobacteria (28.8%) was dominant, followed by Bacteroidetes (16.1%), Firmicutes (11.7%), and Fusobacteria (6.9%) which are mainly capable of degrading the aromatic compounds. Klebsiella pneumoniae, Wolinella succinogenes, Pseudomonas stutzeri, Desulfovibrio vulgaris, and Clostridium sticklandii were the most prevalent species. The functional analysis further demonstrated the presence of enzymes linked with genes/pathways known to be involved in the degradation/metabolization of aromatic compounds like benzoate, bisphenol, 1,2-dichloroethane phenylalanine. This information was further validated with the whole genome analysis of the bacteria isolated from the CETP. We anticipate that integrating both shotgun and whole-genome analyses can reveal the rich reservoir for novel enzymes and genes present in CETP effluent that can contribute to designing efficient bioremediation strategies for the environment in general CETP system, in particular.

Monitoring Microbial Populations and Antibiotic Resistance Gene Enrichment Associated with Arctic Waste Stabilization Ponds

Given that the microbial communities of Arctic waste stabilization ponds (WSPs) are poorly studied to date, our characterization of multiple WSP systems and time points provides important baseline data that will assist with ongoing monitoring of effluent impacts on downstream aquatic ecosystems in the Arctic. This research also identifies indicator amplicon sequence variants (ASVs) of WSPs that will be helpful for future monitoring for WSP effluent attenuation and demonstrates that WSP microbial communities are enriched in antibiotic resistance genes.

Wastewater management in the Canadian Arctic is challenging due to climate extremes, small population sizes, and lack of conventional infrastructure for wastewater treatment. Although many northern communities use waste stabilization ponds (WSPs) as their primary form of wastewater treatment, few studies have explored WSP microbial communities and assessed effluent impacts on receiving waters from a microbiological perspective. Here, we used 16S rRNA gene and metagenome sequencing to characterize WSP and receiving water microbial communities for two time points bracketing the spring WSP thaw in Baker Lake (Nunavut) and compared these results to other Nunavut WSPs in Cambridge Bay and Kugluktuk. Most amplicon sequence variants (ASVs) recovered from these WSP samples belonged to the phylum Proteobacteria, with considerable variation between the three locations and only six ASVs shared among the WSPs at >0.2% relative abundance. Wastewater indicator ASVs for the Baker Lake WSP were identified, and few indicator ASVs were detected in samples originating from other upstream or downstream sites. The metagenomic data revealed a strong enrichment of antibiotic resistance genes for WSP samples relative to downstream and reference samples, especially for genes associated with macrolide resistance. Together, our results provide a baseline characterization for WSP microbial communities, demonstrate how indicator ASVs can be used to monitor attenuation and dilution of effluent microorganisms, and reveal that WSPs can serve as hot spots for antibiotic resistance genes.

IMPORTANCE Given that the microbial communities of Arctic waste stabilization ponds (WSPs) are poorly studied to date, our characterization of multiple WSP systems and time points provides important baseline data that will assist with ongoing monitoring of effluent impacts on downstream aquatic ecosystems in the Arctic. This research also identifies indicator amplicon sequence variants (ASVs) of WSPs that will be helpful for future monitoring for WSP effluent attenuation and demonstrates that WSP microbial communities are enriched in antibiotic resistance genes. Given operational and infrastructure changes anticipated for wastewater treatment systems in the Arctic, baseline data such as these are essential for further development of safe and effective wastewater treatment systems.

Contrasting community assembly processes structure lotic bacteria metacommunities along the river continuum

The heterogeneous nature of lotic habitats plays an important role in the complex ecological and evolutionary processes that structure the microbial communities within them. Due to such complexity, our understanding of lotic microbial ecology still lacks conceptual frameworks for the ecological processes that shape these communities. We explored how bacterial community composition and underlying ecological assembly processes differ between lotic habitats by examining community composition and inferring community assembly processes across four major habitat types (free-living, particle-associated, biofilm on benthic stones and rocks, and sediment). This was conducted at 12 river sites from headwater streams to the main river in the River Thames, UK. Our results indicate that there are distinct differences in the bacterial communities between four major habitat types, with contrasting ecological processes shaping their community assembly processes. While the mobile free-living and particle-associated communities were consistently less diverse than the fixed sediment and biofilm communities, the latter two communities displayed higher homogeneity across the sampling sites. This indicates that the relative influence of deterministic environmental filtering is elevated in sediment and biofilm communities compared with free-living and particle-associated communities, where stochastic processes play a larger role.

Fate of Trace Organic Compounds in Hyporheic Zone Sediments of Contrasting Organic Carbon Content and Impact on the Microbiome

The organic carbon in streambed sediments drives multiple biogeochemical reactions, including the attenuation of organic micropollutants. An attenuation assay using sediment microcosms differing in the initial total organic carbon (TOC) revealed higher microbiome and sorption associated removal efficiencies of trace organic compounds (TrOCs) in the high-TOC compared to the low-TOC sediments. Overall, the combined microbial and sorption associated removal efficiencies of the micropollutants were generally higher than by sorption alone for all compounds tested except propranolol whose removal efficiency was similar via both mechanisms. Quantitative real-time PCR and time-resolved 16S rRNA gene amplicon sequencing revealed that higher bacterial abundance and diversity in the high-TOC sediments correlated with higher microbial removal efficiencies of most TrOCs. The bacterial community in the high-TOC sediment samples remained relatively stable against the stressor effects of TrOC amendment compared to the low-TOC sediment community that was characterized by a decline in the relative abundance of most phyla except Proteobacteria. Bacterial genera that were significantly more abundant in amended relative to unamended sediment samples and thus associated with biodegradation of the TrOCs included Xanthobacter, Hyphomicrobium, Novosphingobium, Reyranella and Terrimonas. The collective results indicated that the TOC content influences the microbial community dynamics and associated biotransformation of TrOCs as well as the sorption potential of the hyporheic zone sediments.

Chemometric Assessment of Bulgarian Wastewater Treatment Plants' Effluents

Surface water quality strongly depends on anthropogenic activity. Among the main anthropogenic sources of this activity are the wastewater treatment plant (WWTP) effluents. The discharged loads of nutrients and suspended solids could provoke serious problems for receiving water bodies and significantly alter the surface water quality. This study presents inventory analysis and chemometric assessment of WWTP effluents based on the mandatory monitoring data. The comparison between the Bulgarian WWTPs and previously reported data from other countries reveals that discharged loads from investigated WWTPs are lower. This is particularly valid for total suspended solids (TSS). The low TSS loads are the reason for the deviations of the typical calculated WWTP effluent ratios of Bulgarian WWTPs compared to the WWTPs worldwide. The performed multivariate analysis reveals the hidden factors that determine the content of WWTP effluents. The source apportioning based on multivariate curve resolution analysis provides detailed information for source contribution profiles of the investigated WWTP effluent loads and elucidate the difference between WWTPs included in this study.

BALOs Improved Gut Microbiota Health in Postlarval Shrimp (Litopenaeus vannamei) After Being Subjected to Salinity Reduction Treatment

White shrimp, Litopenaeus vannamei, is a widely farmed species. In China, shrimp postlarvae (PL) are frequently subjected to salinity reduction treatment to meet end growers' needs. However, although this treatment effectively reduces vibrio counts, its impact on gut microbiota health is still unknown. In this study, we applied a euryhaline strain of BALOs, BDN-1F2 (BD), and Bacillus subtilis (SD) to the rearing of second-generation shrimp PL after salinity reduction treatment so as to determine if they could impact PL gut microbiota by using high-throughput sequencing analysis. Results show that PL gut microbiota, both compositionally and functionally, have been badly wrecked after salinity reduction treatment with the generally recognized as opportunistic pathogens Gammaproteobacteria being the only dominant class at day 1 of test, viz., 99.43, 85.61, and 83.28% in BD, SD, and control (CD) groups, respectively. At day 7, Gammaproteobacteria was still the only dominant class in the SD and CD groups with relative abundance of 99.77 and 99.87% correspondingly, whereas in the BD group, its value dropped to 8.44%. Regarding biodiversity parameter the Shannon index, over the 7-day test period, while the SD group was unchanged (0.98-0.93), the CD group dropped to 0.94 from 2.94, and the BD group was raised to 7.14 from 0.93. Functionally, compared to control, the SD group displayed similar strength of various predicted community functions, but the BD group had hugely enhanced its various capabilities (p < 0.05). These results demonstrated that the addition of BDN-1F2 had exceedingly improved PL gut microbiota health by raising its biodiversities and strengthening its functionalities. On reviewing data derived from this as well as relevant studies, a Shannon index cutoff value was tentatively suggested so as to differentiate microbiota-healthy PL7-15 from the unhealthy ones. Furthermore, a conceptual mechanism of BALOs in the rectification/improvement of the microbial community health has also been proposed.

Dynamics of coastal bacterial community average ribosomal RNA operon copy number reflect its response and sensitivity to ammonium and phosphate

The nutrient-rich effluent from wastewater treatment plants (WWTPs) constitutes a significant disturbance to coastal microbial communities, which in turn affect ecosystem functioning. However, little is known about how such disturbance could affect the community's stability, an important knowledge gap for predicting community response to future disturbances. Here, we examined dynamics of coastal sediment microbial communities with and without a history of WWTP's disturbances (named H1 and H0 hereafter) after simulated nutrient input loading at the low level (5 mg L^-1 NH₄⁺-N and 0.5 mg L^-1 PO₄^3--P) or high level (50 mg L^-1 NH₄⁺-N and 5.0 mg L^-1 PO₄^3--P) for 28 days. H0 community was highly sensitive to both low and high nutrient loading, showing a faster community turnover than H1 community. In contrast, H1 community was more efficient in nutrient removal. To explain it, we found that H1 community constituted more abundant and diversified r-strategists, known to be copiotrophic and fast in growth and reproduction, than H0 community. As nutrient was gradually consumed, both communities showed a succession of decreasing r-strategists. Accordingly, there was a decrease in community average ribosomal RNA operon (rrn) copy number, a recently established functional trait of r-strategists. Remarkably, the average rrn copy number of H0 communities was strongly correlated with NH₄⁺-N (R² = 0.515, P = 0.009 for low nutrient loading; R² = 0.749, P = 0.001 for high nutrient loading) and PO₄^3--P (R² = 0.378, P = 0.034 for low nutrient loading; R² = 0.772, P = 0.001 for high nutrient loading) concentrations, while that of H1 communities was only correlated with NH₄⁺-N at high nutrient loading (R² = 0.864, P = 0.001). Our results reveal the potential of using rrn copy number to evaluate the community sensitivity to nutrient disturbances, but community's historical contingency need to be taken in account.

Functional Analysis of a Polluted River Microbiome Reveals a Metabolic Potential for Bioremediation

The objective of this study is to understand the functional and metabolic potential of the microbial communities along the Apatlaco River and highlight activities related to bioremediation and its relationship with the Apatlaco’s pollutants, to enhance future design of more accurate bioremediation processes. Water samples were collected at four sampling sites along the Apatlaco River (S1–S4) and a whole metagenome shotgun sequencing was performed to survey and understand the microbial metabolic functions with potential for bioremediation. A HMMER search was used to detect sequence homologs related to polyethylene terephthalate (PET) and polystyrene biodegradation, along with bacterial metal tolerance in Apatlaco River metagenomes. Our results suggest that pollution is a selective pressure which enriches microorganisms at polluted sites, displaying metabolic capacities to tolerate and transform the contamination. According to KEGG annotation, all sites along the river have bacteria with genes related to xenobiotic biodegradation. In particular, functions such as environmental processing, xenobiotic biodegradation and glycan biosynthesis are over-represented in polluted samples, in comparison to those in the clean water site. This suggests a functional specialization in the communities that inhabit each perturbated point. Our results can contribute to the determination of the partition in a metabolic niche among different Apatlaco River prokaryotic communities, that help to contend with and understand the effect of anthropogenic contamination.

Impact of wastewater effluent pollution on stream functioning: A whole-ecosystem manipulation experiment

The ecological effects of wastewater treatment plant (WWTP) effluents on stream ecosystems cause growing concern. However, it is difficult to assess these effects as most streams receiving WWTP effluents are also affected by other stressors. We performed a whole-ecosystem manipulation experiment following a BACI design (Before-After/Control-Impact) in order to exclude the influence of other potentially confounding factors. We diverted part of the effluent of a large tertiary urban WWTP into a small, unpolluted stream, and studied its effects on ecosystem structure and functioning over two years (i.e., one year before and one year after the effluent diversion). Although highly diluted (final concentration in the receiving stream averaged 3%), the effluent promoted biofilm chlorophyll-a and biomass (2.3 and 2.1 times, respectively), exo-enzymatic activities (phosphatase 2.2 and glucosidase 4.2 times) and invertebrate-mediated organic matter decomposition (1.4 times), but reduced phosphorus uptake capacity of the epilithic biofilm down to 0.5 of the initial values. Biofilm metabolism, reach-scale nutrient uptake and microbially-mediated organic matter decomposition were not affected. Our results indicate that even well treated and highly diluted WWTP effluents can also affect the structure of the biofilm community and stream ecosystem functioning.

Decay of elevated antibiotic resistance genes in natural river sediments after sedimentation of wastewater particles

Large-scale wastewater treatment plants (WWTPs) discharge hundreds of tons of total suspended solids (TSS) into surface waters every year. Additionally, a comparable amount is released by sewer overflows during heavy rain events in case of combined sewer systems. Along with sedimentation, particle-attached microorganisms and their antibiotic resistance genes (ARGs) are herewith transported to the riverbed of the receiving water. To better understand the dynamics of this process, a particulate wastewater fraction was added into batch reactors, which were previously filled with natural river sediments and tap water. In parallel, antibiotics (ABs) (erythromycin, tetracycline, ciprofloxacin, roxithromycin, penicillin V, and sulfamethoxazole) were spiked to investigate their capability to select for resistance. The abundance of six ARGs (ermB, tetM, bla_TEM, sul1, CTX-M-32, and qnrS) as well as total bacteria (16S rDNA) was monitored in waters and in sediments for a duration of two months using quantitative PCR. Despite a continuous exposure to ABs (5 μg/L each), the abundance of ARGs remained unaffected. Addition of wastewater particles resulted in a sudden and strong increase of ARGs in waters (3-5 log units) and sediments (1-4 log units), however, elevated ARGs underwent a particular and complete decay. Our results indicate that the increased ARG abundances in receiving rivers are the result of a continuous import of ARGs from WWTP discharges or sewer overflow events. They further imply that elevated ARGs do not persist in receiving rivers, if this continuous import is removed. This seems to be the case merely for ARGs introduced by wastewater, given that a stable background concentration of ARGs was observed for the native population.

From Genes to Nitrogen Removal: Determining the Impacts of Poultry Industry Wastewater on Tidal Creek Denitrification

The intensification of the poultry industry in the last decades has led to a sharp increase in the number of animal processing plants discharging wastewater to water bodies. These discharges may have a significant effect on environmental quality and on important ecosystem functions, such as denitrification. We conducted a seasonal survey and a microcosm experiment in an impacted and a reference tidal creek to investigate the impacts of wastewater discharge from a poultry processing plant on sedimentary microbial communities, denitrification activity, and nitrate removal. Denitrification potential was measured using slurry incubations, and the microbial community was examined with 16S rDNA MiSeq sequencing and quantitative polymerase chain reaction of denitrification genes. The lowest denitrification rates were observed in the impacted creek, especially near the wastewater discharge, and denitrification inhibition by impacted creek water was clearly observed in the microcosm experiment. Denitrification rates were associated with changes in the microbial community composition and gene abundance. Estimated nitrate removal was lower in the impacted creek, and higher chlorophyll levels were observed in a downstream coastal bay through remote sensing. This study demonstrates denitrification inhibition by wastewater discharge from a poultry processing plant with potential consequences to coastal eutrophication.

Application of a novel molecular technique to characterise the effect of settling on microbial community composition of activated sludge

Activated sludge (AS) and return activated sludge (RAS) microbial communities from three full-scale municipal wastewater treatment plants (denoted plant A, B and C) were compared to assess the impact of sludge settling (i.e. gravity thickening in the clarifier) and profile microorganisms responsible for nutrient removal and reactor foaming. The results show that all three plants were dominated with microbes in the phyla of Proteobacteria, Bacteroidetes, Verrucomicrobia, Actinobacteria, Chloroflexi, Firmicutes, Nitrospirae, Spirochaetae, Acidobacteria and Saccharibacteria. AS and RAS shared above 80% similarity in the microbial community composition, indicating that sludge thickening does not significantly alter the microbial composition. Autotrophic and heterotrophic nitrifiers were present in the AS. However, the abundance of autotrophic nitrifiers was significantly lower than that of the heterotrophic nitrifiers. Thus, ammonium removal at these plants was achieved mostly by heterotrophic nitrification. Microbes that can cause foaming were at 3.2% abundance, and this result is well corroborated with occasional aerobic biological reactor foaming. By contrast, these microbes were not abundant (<2.1%) at plant A and C, where aerobic biological reactor foaming has not been reported.

Physiological characteristics and toxin production of Microcystis aeruginosa (Cyanobacterium) in response to DOM in anaerobic digestion effluent

The ecological implications of livestock production intensification have received sustained attention across the globe. Anaerobic digestion is the main process for livestock waste treatment. However, the ecological consequences of dissolved organic matter originating from anaerobic digestion (AD-DOM) in eutrophic water bodies remain elusive. In this study, the physiological responses of a bloom-forming cyanobacterium, Microcystis aeruginosa, to AD-DOM were investigated. Moreover, the composition of AD-DOM was identified by using thermochemolysis followed by gas chromatography-mass spectrometry (GC-MS) analysis. The growth of M. aeruginosa FACHB905 was not sensitive to low levels (0.625-1.25%, V/V) of AD-DOM but was inhibited by high levels (2.5-5%, V/V) of AD-DOM, resulting from photoinhibition damage to photosystem II (PSII). The main target of AD-DOM in PSII was the electron accepting side (ψ₀) or the electron donor side (φ P₀), depending on time variables. The reactive oxygen species (ROS) level showed a positive correlation with AD-DOM addition; however, it was higher than that of the control for 3.75-5% AD-DOM on the 6th day. The intracellular microcystin contents (including MC-LR and Dha⁷-MC-LR) decreased in response to AD-DOM addition, but extracellular microcystin increased after 6 days of exposure. In addition, GC-MS detection showed that AD-DOM is mainly composed of lignin-derived aromatic compounds, alkanes/alkene, nitrogen-containing compounds, and sterols. The results presented in this study suggested that AD-DOM released from the livestock industry may play a subtle role in affecting harmful algal blooms through level-dependent variables. In addition, the ecological consequences of microcystin released by toxin-producing species under AD-DOM stress are still worth considering.

Revealing chlorinated ethene transformation hotspots in a nitrate-impacted hyporheic zone

Hyporheic zones are increasingly thought of as natural bioreactors, capable of transforming and attenuating groundwater pollutants present in diffuse baseflow. An underappreciated scenario in the understanding of contaminant fate in hyporheic zones is the interaction between point-source trichloroethene (TCE) plumes and ubiquitous, non-point source pollutants such as nitrate. This study aims to conceptualise critical biogeochemical gradients in the hyporheic zone which govern the export potential of these redox-sensitive pollutants from carbon-poor, oxic aquifers. Within the TCE plume discharge zone, discrete vertical profiling of the upper 100 cm of sediment pore water chemistry revealed an 80% increase in dissolved organic carbon (DOC) concentrations and 20-60 cm thick hypoxic zones (<2 mg O₂ L^-1) within which most reactive transport was observed. A 33% reduction of nitrate concentrations coincided with elevated pore water nitrous oxide concentrations as well as the appearance of manganese and the TCE metabolite cis-1,2-dichloroethene (cDCE). Elevated groundwater nitrate concentrations (>50 mg L^-1) create a large stoichiometric demand for bioavailable DOC in discharging groundwater. With the benefit of a high-resolution grid of pore water samplers investigating the shallowest 30 cm of hypoxic groundwater flow paths, we identified DOC-rich hotspots associated with submerged vegetation (Ranunculus spp.), where low-energy metabolic processes such as mineral dissolution/reduction, methanogenesis and ammonification dominate. Using a chlorine index metric, we show that enhanced TCE to cDCE transformation takes place within these biogeochemical hotspots, highlighting their relevance for natural plume attenuation.

Effect of River Ecological Restoration on Biofilm Microbial Community Composition

Across the world, there have been increasing attempts to restore good ecological condition to degraded rivers through habitat restoration. Microbial communities developing as biofilms play an important role in river ecosystem functioning by driving organic matter decomposition and ecosystem respiration. However, little is known about the structure and function of microbial communities in riverine systems and how these change when habitat restoration is implemented. Here, we compared the biofilm bacterial community composition using 16S rRNA genes targeted high-throughput Illumina Miseq sequencing in three river types, degraded urban rivers, urban rivers undergoing habitat restoration and forested rivers (our reference conditions). We aimed to determine: (i) the biofilm bacterial community composition affected by habitat restoration (ii) the difference in bacterial diversity in restored rivers, and (iii) correlations between environmental variables and bacterial community composition. The results showed that both water quality and biofilm bacterial community structure were changed by habitat restoration. In rivers where habitat had been restored, there was an increase in dissolved oxygen, a reduction in organic pollutants, a reduction in bacterial diversity and a related developing pattern of microbial communities, which is moving towards that of the reference conditions (forested rivers). River habitat management stimulated the processing of organic pollutants through the variation in microbial community composition, however, a big difference in bacterial structure still existed between the restored rivers and the reference forest rivers. Thus, habitat restoration is an efficient way of modifying the biofilm microbial community composition for sustainable freshwater management. It will, however, take a much longer time for degraded rivers to attain a similar ecosystem quality as the “pristine” forest sites than the seven years of restoration studied here.

Evaluating the Impact of Wastewater Effluent on Microbial Communities in the Panke, an Urban River

Pharmaceuticals are consumed in high amounts and can enter as emerging organic compounds in surface waters as they are only partially retained in wastewater treatment plants (WWTPs). Receiving pharmaceuticals may burden the aquatic environment, as they are designed to be bioactive even at low concentrations. Sediment biofilm populations were analyzed in river sediments due to the exposure of an inflow of WWTP effluents. Illumina MiSeq 16S rRNA gene amplicon sequencing was performed of 108 sediment samples, which were taken from multiple cores within three sampling locations in the Panke River, with one sampling site located downstream of the inflow. Sequencing data were processed to infer microbial community structure in samples concerning the environmental variables, such as micropollutants and physicochemical parameters measured for each core. More than 25 different micropollutants were measured in pore water samples, in which bezafibrate, clofibric acid, carbamazepine, and diclofenac were detected at high concentrations. Bacterial 16S rRNA gene amplicons revealed Nitrospirae, Proteobacteria, Chloroflexi, Actinobacteria, Acidobacteria, Bacteroidetes, and Ignavibacteriae as the most abundant groups in the samples. Differences in microbial community composition were observed with respect to micropollutants. However, our findings revealed that the composition of the microbial community was not only governed by the effluent. The significant changes in the alpha- and beta-diversity were explained by phenobarbital and SO42−, which did not originate from the WWTP indicating that more unobserved factors are also likely to play a role in affecting the biofilm community’s composition.

Antimicrobial-Resistant Escherichia coli from Environmental Waters in Northern Colorado

Waterborne Escherichia coli are a major reservoir of antimicrobial resistance (AMR), including but not limited to extended-spectrum beta-lactamase (ESBL) and Klebsiella pneumoniae carbapenemase (KPC) mechanisms. This study quantified and described ESBL- and KPC-producing E. coli in Northern Colorado from sewer water, surface water, and influent and effluent wastewater treatment sources. Total detected bacteria and E. coli abundances, and the percentages that contain ESBL and/or KPC, were compared between water sources. Seventy E. coli isolates from the various waters had drug resistance validated with a panel of 17 antibiotics using a broth microdilution assay. The diverse drug resistance observed across E. coli isolates was further documented by polymerase chain reaction of common ESBL genes and functional relatedness by PhenePlate assay-generated dendrograms (n=70). The total E. coli abundance decreased through the water treatment process as expected, yet the percentages of E. coli harboring ESBL resistance were increased (1.70%) in surface water. Whole-genome sequencing analysis was completed for 185 AMR genes in wastewater E. coli isolates and confirmed the presence of diverse AMR gene classes (e.g., beta-lactams and efflux pumps) in isolate genomes. This study completed surveillance of AMR patterns in E. coli that reside in environmental water systems and suggests a role for integrating both phenotypic and genotypic profiling beyond ESBL and KPC mechanisms. AMR screening via multiple approaches may assist in the prevention of drug-resistant E. coli spread from waters to animals and humans.

Profiling microbial communities in a watershed undergoing intensive anthropogenic activities

In lotic ecosystems highly susceptible to anthropogenic activities, the influences of environmental variables on microbial communities and their functions remain poorly understood, despite our rapidly increasing sequencing ability. In this study, we profiled the microbial communities in the hyporheic sediments of a watershed undergoing intensive anthropogenic activities via next-generation sequencing of 16S rRNA V4-V5 hypervariable regions on Illumina MiSeq platform. Tidal impacts on microbial communities were investigated via co-occurrence networks. In addition, the influences of physicochemical variables including salinity, and the concentrations of nutrients, organic matter and heavy metals on the microbial communities were explored via canonical correspondence analyses. The sediment samples were collected from 19 sites covering the whole main river stem of the target watershed (n = 19; Maozhou river watershed, Shenzhen, China). The samples were sub-divided in the field for microbiological analyses and measurements of physicochemical variables. The results indicated that core microbiome was associated with archaea methanogens and bacteria members from Proteobacteria, Chloroflexi, Bacteroidetes, Acidobacteria, Synergistetes and Firmicutes, among which, gram-negative and anaerobic bacteria genera contributing to the cycling of carbon, nitrogen and sulfur were predominant. Site-specific microbiomes were revealed that may serve as indicators of local environmental conditions (e.g., members affiliated to Oceanospirillales were abundant at sites with salt intrusion). Distinct microbial co-occurrence networks were identified for non-tidal, inter-tidal and tidal sites. Major environmental factors influencing microbial community composition included the concentrations of nitrate and bicarbonate in river water, pore water concentrations of sulfate, dissolved organic carbon and electrical conductivity, as well as manganese concentrations associated with the solid sediment. Collectively, the results of this study provide fundamental insights into the influence of environmental perturbations on microbial community composition in a lotic system, which may aid in the design of effective remediation and/or restoration strategies in the target watershed and beyond.

Inherent bacterial community response to multiple heavy metals in sediment from river-lake systems in the Poyang Lake, China

Sediment is the one of most important storage of heavy metal. Microbiotas in sediment can be used as the effective indicators of heavy metals. The goal of this study was to understand the bacterial communities responding to heavy metal enrichment in sediments and prioritize some factors that affected significantly to bacterial community. Sediments were sampled from five river-lake systems in the Poyang Lake in dry season, and the bacterial community was analyzed using Illumina high-throughput sequencing. Relationships between sediment environment and the diversity and structure of bacterial communities were determined by correlation analysis and redundancy analysis (RDA). The result indicated that Cd and Sb were identified as the heavy metals of the great risk in sediments. Sediments from five river-lake systems shared 31.83% core operational taxonomic units (OTUs) of bacterial communities. Proteobacteria (33.54% of total sequences) and Actinobacteria (15.04%) were the dominant phyla across all sites. High enrichment of heavy metals (MRI and mC_d) resulted in low diversity of bacterial communities (Simpson index). The RDA revealed pH, OC, mCd, and Efs of As, Pb, Cd were major factors related to bacterial community structure changes. The dominant phylum Actinobacteria was regarded as tolerant bacteria, while the dominant phylum Proteobacteria was named as resistant bacteria in sediment with high anthropogenic Cd enrichment.

Identification of Degradation Pathways of Chlorohydrocarbons in Saturated Low-Permeability Sediments Using Compound-Specific Isotope Analysis

This study aims to investigate whether compound-specific carbon isotope analysis (CSIA) can be used to differentiate the degradation pathways of chlorohydrocarbons in saturated low-permeability sediments. For that purpose, a site was selected, where a complex mixture of chlorohydrocarbons contaminated an aquifer-aquitard system. Almost 50 years after contaminant releases, high-resolution concentration, CSIA, and microbial profiles were determined. The CSIA profiles showed that in the aquitard cis-dichloroethene (cDCE), first considered as a degradation product of trichloroethene (TCE), is produced by the dichloroelimination of 1,1,2,2-tetrachloroethane (TeCA). In contrast, TeCA degrades to TCE via dehydrohalogenation in the aquifer, indicating that the aquifer-aquitard interface separates two different degradation pathways for TeCA. Moreover, the CSIA profiles showed that chloroform (CF) is degraded to dichloromethane (DCM) via hydrogenolysis in the aquitard and, to a minor degree, produced by the degradation of carbon tetrachloride (CT). Several microorganisms capable of degrading chlorohydrocarbons were detected in the aquitard, suggesting that aquitard degradation is microbially mediated. Furthermore, numerical simulations reproduced the aquitard concentration and CSIA profiles well, which allowed the determination of degradation rates for each transformation pathway. This improves the prediction of contaminant fate in the aquitard and potential magnitude of impacts on the adjacent aquifer due to back-diffusion.

Sewage Sludge Microbial Structures and Relations to Their Sources, Treatments, and Chemical Attributes

Sewage sludges generation and their disposal have become one of the greatest challenges of the 21st century. They have great microbial diversity that may impact wastewater treatment plant (WWTP) efficiency and soil quality whether used as fertilizers. Therefore, this research aimed to characterize microbial community diversity and structure of 19 sewage sludges from São Paulo, Brazil, as well as to draw their relations to sludge sources [domestic and mixed (domestic+industrial)], biological treatments (redox conditions and liming), and chemical attributes, using molecular biology as a tool. All sludges revealed high bacterial diversity, but their sources and redox operating conditions as well as liming did not consistently affect bacterial community structures. Proteobacteria was the dominant phylum followed by Bacteroidetes and Firmicutes; whereas Clostridium was the dominant genus followed by Treponema, Propionibacterium, Syntrophus, and Desulfobulbus. The sludge samples could be clustered into six groups (C1 to C6) according their microbial structure similarities. Very high pH (≥11.9) was the main sludge attribute segregating C6, that presented very distinct microbial structure from the others. Its most dominant genera were Propionibacterium > > Comamonas > Brevundimonas > Methylobacterium ∼Stenotrophomonas ∼Cloacibacterium. The other clusters' dominant genera were Clostridium > > Treponema > Desulfobulbus ∼Syntrophus. Moreover, high Fe and S were important modulators of microbial structure in certain sludges undertaking anaerobic treatment and having relatively low N-Kj, B, and P contents (C5). However, high N-Kj, B, P, and low Fe and Al contents were typical of domestic, unlimed, and aerobically treated sludges (C1). In general, heavy metals had little impact on microbial community structure of the sludges. However, our sludges shared a common core of 77 bacteria, mostly Clostridium, Treponema, Syntrophus, and Comamonas. They should dictate microbial functioning within WWTPs, except by SS12 and SS13.

River biofilm community changes related to pharmaceutical loads emitted by a wastewater treatment plant

Wastewater treatment plants (WWTP) are the main sources of a broad spectrum of pharmaceuticals found in freshwater ecosystems. These pollutants raise environmental health concerns because of their highly bioactive nature and their chronic releases. Despite this, pharmaceuticals' effects on aquatic environments are poorly defined. Biofilms represent a major part of the microbial life in rivers and streams. They can drive key metabolic cycles and their organizations reflect exposures to changing chemical, physical, and biological constraints. This study estimated the concentrations, over a 3-year period, of ten pharmaceuticals and five nutrients in a river contaminated by a conventional WWTP fed by urban and hospital wastewaters. Variations in these concentrations were related to biofilm bacterial community dynamics. Rock biofilms had developed over defined periods and were harvested at four locations in the river from the up- and downstream WWTP discharge point. Pharmaceuticals were found in all locations in concentrations ranging from not being detected to 192 ng L^-1. Despite the high dilution factor of the WWTP effluents by the receiving river, pharmaceuticals were found more concentrated downstream than upstream the WWTP. Shifts in bacterial community structures linked to the environmental emission of pharmaceuticals were superior to seasonal community changes. A community structure from a site located downstream but close to the WWTP was more strongly associated with high pharmaceutical loads and different from those of biofilm samples from the WWTP upstream or far downstream sites. These latter sites were more strongly associated with high nutrient contents. Low environmental concentrations of pharmaceuticals can thus be transferred from WWTP effluents to a connected stream and induce bacterial aquatic community changes over time.

Long-term industrial metal contamination unexpectedly shaped diversity and activity response of sediment microbiome

Metal contamination poses serious biotoxicity and bioaccumulation issues, affecting both abiotic conditions and biological activity in ecosystem trophic levels, especially sediments. The MetalEurop foundry released metals directly into the French river "la Deûle" during a century, contaminating sediments with a 30-fold increase compared to upstream unpolluted areas (Férin, Sensée canal). Previous metaproteogenomic work revealed phylogenetically analogous, but functionally different microbial communities between the two locations. However, their potential activity status in situ remains unknown. The present study respectively compares the structures of both total and active fractions of sediment prokaryotic microbiomes by coupling DNA and RNA-based sequencing approaches at the polluted MetalEurop site and its upstream control. We applied the innovative ecological concept of Functional Response Groups (FRGs) to decipher the adaptive tolerance range of the communities through characterization of microbial lifestyles and strategists. The complementing use of DNA and RNA sequencing revealed indications that metals selected for mechanisms such as microbial facilitation via "public-good" providing bacteria, Horizontal Gene Transfer (HGT) and community coalescence, overall resulting in an unexpected higher microbial diversity at the polluted site.

Toxicity evaluation of textile effluents and role of native soil bacterium in biodegradation of a textile dye

Water pollution caused by the discharge of hazardous textile effluents is a serious environmental problem worldwide. In order to assess the pollution level of the textile effluents, various physico-chemical parameters were analyzed in the textile wastewater and agricultural soil irrigated with the wastewater (contaminated soil) using atomic absorption spectrophotometer and gas chromatography-mass spectrometry (GC-MS) analysis that demonstrated the presence of several toxic heavy metals (Ni, Cu, Cr, Pb, Cd, and Zn) and a large number of organic compounds. Further, in order to get a comprehensive idea about the toxicity exerted by the textile effluent, mung bean seed germination test was performed that indicated the reduction in percent seed germination and radicle-plumule growth. The culturable microbial populations were also enumerated and found to be significantly lower in the wastewater and contaminated soil than the ground water irrigated soil, thus indicating the biotic homogenization of indigenous microflora. Therefore, the study was aimed to develop a cost effective and ecofriendly method of textile waste treatment using native soil bacterium, identified as Arthrobacter soli BS5 by 16S rDNA sequencing that showed remarkable ability to degrade a textile dye reactive black 5 with maximum degradation of 98% at 37 °C and pH in the range of 5-9 after 120 h of incubation.

Natural attenuation of chlorinated ethenes in hyporheic zones: A review of key biogeochemical processes and in-situ transformation potential

Chlorinated ethenes (CEs) are legacy contaminants whose chemical footprint is expected to persist in aquifers around the world for many decades to come. These organohalides have been reported in river systems with concerning prevalence and are thought to be significant chemical stressors in urban water ecosystems. The aquifer-river interface (known as the hyporheic zone) is a critical pathway for CE discharge to surface water bodies in groundwater baseflow. This pore water system may represent a natural bioreactor where anoxic and oxic biotransformation process act in synergy to reduce or even eliminate contaminant fluxes to surface water. Here, we critically review current process understanding of anaerobic CE respiration in the competitive framework of hyporheic zone biogeochemical cycling fuelled by in-situ fermentation of natural organic matter. We conceptualise anoxic-oxic interface development for metabolic and co-metabolic mineralisation by a range of aerobic bacteria with a focus on vinyl chloride degradation pathways. The superimposition of microbial metabolic processes occurring in sediment biofilms and bulk solute transport delivering reactants produces a scale dependence in contaminant transformation rates. Process interpretation is often confounded by the natural geological heterogeneity typical of most riverbed environments. We discuss insights from recent field experience of CE plumes discharging to surface water and present a range of practical monitoring technologies which address this inherent complexity at different spatial scales. Future research must address key dynamics which link supply of limiting reactants, residence times and microbial ecophysiology to better understand the natural attenuation capacity of hyporheic systems.

The role of microbial diversity and composition in minimizing sludge production in the oxic-settling-anoxic process

The oxic-settling-anoxic (OSA) process, which involves an aerobic tank attached to oxygen- and substrate-deficient external anoxic reactors, minimizes sludge production in biological wastewater treatment. In this study, the microbial community structure of OSA was determined. Principal coordinate analysis showed that among the three operational factors, i.e., (i) redox condition, (ii) external reactor sludge retention time (SRT_ext), and (iii) sludge interchange between aerobic and anoxic reactors, redox condition had the greatest impact on microbial diversity. Generally, reactors with lower oxidation-reduction potential had higher microbial diversity. The main aerobic sequencing batch reactor of OSA (SBR_OSA) that interchanged sludge with an external anoxic reactor had greater microbial diversity than SBR_control which did not have sludge interchange. SBR_OSA sustained high abundance of the slow-growing nitrifying bacteria (e.g., Nitrospirales and Nitrosomondales) and consequently exhibited reduced sludge yield. Specific groups of bacteria facilitated sludge autolysis in the external reactors. Hydrolyzing (e.g., Bacteroidetes and Chloroflexi) and fermentative (e.g., Firmicutes) bacteria, which can break down cellular matter, proliferated in both the external aerobic/anoxic and anoxic reactors. Sludge autolysis in the anoxic reactor was enhanced with the increase of predatory bacteria (e.g., order Myxobacteriales and genus Bdellovibrio) that can contribute to biomass decay. Furthermore, β- and γ-Proteobacteria were identified as the bacterial phyla that primarily underwent decay in the external reactors.

Dehalococcoides as a Potential Biomarker Evidence for Uncharacterized Organohalides in Environmental Samples

The massive production and improper disposal of organohalides resulted in worldwide contamination in soil and water. However, their environmental survey based on chromatographic methods was hindered by challenges in testing the extremely wide variety of organohalides. Dehalococcoides as obligate organohalide-respiring bacteria exclusively use organohalides as electron acceptors to support their growth, of which the presence could be coupled with organohalides and, therefore, could be employed as a biomarker of the organohalide pollution. In this study, Dehalococcoides was screened in various samples of bioreactors and subsurface environments, showing the wide distribution of Dehalococcoides in sludge and sediment. Further laboratory cultivation confirmed the dechlorination activities of those Dehalococcoides. Among those samples, Dehalococcoides accounting for 1.8% of the total microbial community was found in an anaerobic granular sludge sample collected from a full-scale bioreactor treating petroleum wastewater. Experimental evidence suggested that the influent wastewater in the bioreactor contained bromomethane which support the growth of Dehalococcoides. This study demonstrated that Dehalococcoides could be employed as a promising biomarker to test the present of organohalides in wastestreams or other environmental samples.

Microbial Community Response on Wastewater Discharge in Boreal Lake Sediments

Despite high performance, municipal wastewater treatment plants (WWTPs) still discharge significant amounts of organic material and nitrogen and even microbes into the receiving water bodies, altering physico-chemical conditions and microbial functions. In this study, we examined how nitrified wastewater affects the microbiology of boreal lake sediments. Microbial community compositions were assessed with next generation sequencing of the 16S rRNA gene, and a more detailed view on nitrogen transformation processes was gained with qPCR targeting on functional genes (nirS, nirK, nosZ_I, nosZ_II, amoA_archaea, and amoA_bacteria). In both of the two studied lake sites, the microbial community composition differed significantly between control point and wastewater discharge point, and a gradual shift toward natural community composition was seen downstream following the wastewater gradient. SourceTracker analysis predicted that ∼2% of sediment microbes were of WWTP-origin on the study site where wastewater was freely mixed with the lake water, while when wastewater was specially discharged to the sediment surface, ∼6% of microbes originated from WWTP, but the wastewater-influenced area was more limited. In nitrogen transformation processes, the ratio between nitrifying archaea (AOA) and bacteria (AOB) was affected by wastewater effluent, as the AOA abundance decreased from the control point (AOA:AOB 28:1 in Keuruu, 11:1 in Petäjävesi) to the wastewater-influenced sampling points, where AOB dominated (AOA:AOB 1:2–1:15 in Keuruu, 1:3–1:19 in Petäjävesi). The study showed that wastewater can affect sediment microbial community through importing nutrients and organic material and altering habitat characteristics, but also through bringing wastewater-originated microbes to the sediment, and may thus have significant impact on the freshwater biogeochemistry, especially in the nutrient-poor boreal ecosystems.