The microbiome of urban waters

Identifying spatiotemporal patterns and drivers of fecal indicator bacteria in an urban lake for water quality assessment and management

The designated uses of lakes connect individuals to the natural environment, but some can expose recreational users to pathogens associated with fecal contamination that cause waterborne illnesses. Routine monitoring of fecal indicators in surface waters helps identify and track sources of fecal contamination to protect public health. We examined fecal indicators (Escherichia coli and enterococci) and factors influencing recreational freshwater quality. We collected and analyzed water samples from an urban lake for 12 months to assess water quality. Fecal indicators were detected and enumerated using IDEXX method. E. coli and enterococci were detected in nearly 100 % of all water samples, but their concentrations varied significantly among seasons and land uses. We observed high levels of E. coli and enterococci during the warmer months. The geometric means of E. coli (28.5 MPN/100 mL) and enterococci (39.3 MPN/100 mL) were below and above the recreational water quality standards, respectively. The concentrations of E. coli (7 %) and enterococci (22 %) exceeded the recommended single-sample maximum levels. Sites near urban and forested areas recorded the highest and lowest fecal indicators, respectively. Water temperature, precipitation, salinity, resistivity, DO, and hardness were significant predictors of fecal indicators. The concentrations of fecal indicators were elevated at certain times of the year, indicating the potential presence of pathogens. Overall, the measured water quality parameters of the lake were within normal ranges. This study suggests that effective lake management should focus on the warmer months and runoff from urban and open space/agricultural areas to control nonpoint source pollution.

Microbiota Composition Associates With Mosquito Productivity Outcomes in Belowground Larval Habitats

Vector mosquitoes are well-adapted to habitats in urban areas, including belowground infrastructure such as stormwater systems. As a major source of larval habitat in population centers, control of larval populations in stormwater catch basins is an important tool for control of vector-borne disease. Larval development and adult phenotypes driving vectorial capacity in mosquitoes are modulated by the larval gut microbiota, which is recruited from the aquatic environment in which larvae develop. Laboratory studies have quantified microbe-mediated impacts on individual mosquito phenotypes, but more work is needed to characterise how microbiota variation shapes population-level outcomes. Here, we evaluated the relationship between habitat microbiota variation and mosquito population dynamics by simultaneously characterising microbiota diversity, water quality, and mosquito productivity in a network of stormwater catch basins in the Chicago metropolitan area. High throughput sequencing of 16S rRNA gene amplicons from water samples collected from 60 basins over an entire mosquito breeding season detected highly diverse bacterial communities that varied with measures of water quality and over time. In situ measurements of mosquito abundance in the same basins further varied by microbiota composition and the relative abundance of specific bacterial taxa. Altogether, these results illustrate the importance of habitat microbiota in shaping ecological processes that affect mosquito populations. They also lay the foundation for future studies to characterise the mechanisms by which specific bacterial taxa impact individual and population-level phenotypes related to mosquito vectorial capacity.

One Health Threat of Treated Wastewater Discharge in Urban Ohio Rivers: Implications for Surface Water and Fish Gut Microbiome and Resistome

Wastewater treatment plants (WWTPs) are thought to be a major disseminating source of antibiotic resistance (AR) to the environment, establishing a crucial connection between human and environmental resistome. The objectives of this study were to determine how wastewater effluents impact microbiome and resistome of freshwater and fish, and identify potential AR-carrying clinically relevant pathogens in these matrices. We analyzed wastewater influent and effluent from four WWTPs in three metropolitan areas of Ohio, USA via shotgun metagenomic sequencing. We also sequenced river water and fish guts from three reaches (upstream, at the WWTP outfall, and downstream). Notably, we observed a decline in microbiome diversity and AR gene abundance from wastewater to the receiving river. We also found significant differences by reach and trophic level (diet) in beta-diversity of the fish gut microbiomes. SourceTracker revealed that 0.443 and 0.248 more of the of the fish gut microbiome was sourced from wastewater effluent in fish from the outfall and downstream locations, respectively, compared to upstream fish. Additionally, AR bacteria of public health concern were annotated in effluent and river water samples, indicating potential concern for human exposure. In summary, our findings show the continued role of wastewater as a significant AR reservoir and underscores the considerable impact of wastewater discharge on aquatic wildlife, which highlights the One Health nature of this issue.

Changes in groundwater and surface water bacterial communities under disinfection processes: Chlorination, ozonization, photo-fenton and ultraviolet radiation

Pathogenic bacteria, introduced in water sources through faecal contamination, have traditionally been investigated as individual species, leading to the establishment of microbial, sanitary, and environmental quality indicators. Recent advancements in our understanding of the microbiome and its intricate interactions within the human-microbiome-environment network advocate for a broader evaluation of the impact of disinfection on the entire microbial community. In this study, we conducted a comprehensive screening experiment involving four disinfection processes; ozone, ultraviolet radiation with wavelengths between 200 - 280 nm (UV-C), photo-Fenton, and chlorination, applied to two distinct water sources; surface (SW) and groundwater (GW). The cells that remained viable after treatment were recovered using Brain Heart Infusion (BHI) broth, and 16S rRNA gene sequencing was used for their identification. Our findings confirmed the presence of faecal contamination in the water sources and revealed distinct effects of each treatment on the recovered bacterial populations. The chlorination of groundwater samples likely had a greater impact on bacteria in a vegetative state than on spores. Consequently, this led to a higher abundance in the BHI cultures of sporulating bacteria such as Bacillus (increasing from 0.36 to 93.62 %), while ozonation led to an elevated recovery of Pseudomonas (increasing from 45.2 to 69.9 %). Conversely, in surface water, calcium hypochlorite and ozone treatments favored the selection of Staphylococcus and Bacillus, whose relative abundance in the cultures increased from 0 to 39.22 % and from 0.35 to 96.6 %, respectively. In groundwater, Pseudomonas was resistant to UV-C radiation and their relative abundance increased from 45.2 % to 93.56 %, while photo-Fenton was effective against this bacterial group decreasing its relative abundance to 0.46 %. However, other genera such as Bacteroides, Aeromonas, and Citrobacter seemed to be less injured by this disinfection process. BHI broth was successful in recovering various bacterial groups that exhibited resistance to sublethal water disinfection.

Alteration of bacterial community composition in the sediments of an urban artificial river caused by sewage discharge

Background

Urbanization has an ecological and evolutionary effect on urban microorganisms. Microorganisms are fundamental to ecosystem functions, such as global biogeochemical cycles, biodegradation and biotransformation of pollutants, and restoration and maintenance of ecosystems. Changes in microbial communities can disrupt these essential processes, leading to imbalances within ecosystems. Studying the impact of human activities on urban microbes is critical to protecting the environment, human health, and overall urban sustainability.

Methods

In this study, bacterial communities in the sediments of an urban artificial river were profiled by sequencing the 16S rRNA V3-V4 region. The samples collected from the eastern side of the Jiusha River were designated as the JHE group and were marked by persistent urban sewage discharges. The samples collected on the western side of the Jiusha River were categorized as the JHW group for comparative analysis.

Results

The calculated alpha diversity indices indicated that the bacterial community in the JHW group exhibited greater species diversity and evenness than that of the JHE group. Proteobacteria was the most dominant phylum between the two groups, followed by Bacteroidota. The relative abundance of Proteobacteria and Bacteroidota accumulated in the JHE group was higher than in the JHW group. Therefore, the estimated biomarkers in the JHE group were divided evenly between Proteobacteria and Bacteroidota, whereas the biomarkers in the JHW group mainly belonged to Proteobacteria. The Sulfuricurvum, MND1, and Thiobacillus genus were the major contributors to differences between the two groups. In contrast to JHW, JHE exhibited higher enzyme abundances related to hydrolases, oxidoreductases, and transferases, along with a prevalence of pathways associated with carbohydrate, energy, and amino acid metabolisms. Our study highlights the impact of human-induced water pollution on microorganisms in urban environments.

Inferring microbial co-occurrence networks from amplicon data: a systematic evaluation

Microbes commonly organize into communities consisting of hundreds of species involved in complex interactions with each other. 16S ribosomal RNA (16S rRNA) amplicon profiling provides snapshots that reveal the phylogenies and abundance profiles of these microbial communities. These snapshots, when collected from multiple samples, can reveal the co-occurrence of microbes, providing a glimpse into the network of associations in these communities. However, the inference of networks from 16S data involves numerous steps, each requiring specific tools and parameter choices. Moreover, the extent to which these steps affect the final network is still unclear. In this study, we perform a meticulous analysis of each step of a pipeline that can convert 16S sequencing data into a network of microbial associations. Through this process, we map how different choices of algorithms and parameters affect the co-occurrence network and identify the steps that contribute substantially to the variance. We further determine the tools and parameters that generate robust co-occurrence networks and develop consensus network algorithms based on benchmarks with mock and synthetic data sets. The Microbial Co-occurrence Network Explorer, or MiCoNE (available at https://github.com/segrelab/MiCoNE) follows these default tools and parameters and can help explore the outcome of these combinations of choices on the inferred networks. We envisage that this pipeline could be used for integrating multiple data sets and generating comparative analyses and consensus networks that can guide our understanding of microbial community assembly in different biomes. IMPORTANCE Mapping the interrelationships between different species in a microbial community is important for understanding and controlling their structure and function. The surge in the high-throughput sequencing of microbial communities has led to the creation of thousands of data sets containing information about microbial abundances. These abundances can be transformed into co-occurrence networks, providing a glimpse into the associations within microbiomes. However, processing these data sets to obtain co-occurrence information relies on several complex steps, each of which involves numerous choices of tools and corresponding parameters. These multiple options pose questions about the robustness and uniqueness of the inferred networks. In this study, we address this workflow and provide a systematic analysis of how these choices of tools affect the final network and guidelines on appropriate tool selection for a particular data set. We also develop a consensus network algorithm that helps generate more robust co-occurrence networks based on benchmark synthetic data sets.

One Health and Global Health View of Antimicrobial Susceptibility through the "Eye" of Aeromonas: Systematic Review and Meta-Analysis

Antimicrobial resistance (AMR) is one of the most pressing public health concerns; therefore, it is imperative to advance our understanding of the factors influencing AMR from Global and One Health perspectives. To address this, Aeromonas populations were identified using 16S rRNA gene libraries among human, agriculture, aquaculture, drinking water, surface water, and wastewater samples, supporting its use as indicator bacteria to study AMR. A systematic review and meta-analysis was then performed from Global and One Health perspectives, including data from 221 articles describing 15 891 isolates from 57 countries. The interconnectedness of different environments was evident as minimal differences were identified between sectors among 21 different antimicrobials. However, resistance to critically important antibiotics (aztreonam and cefepime) was significantly higher among wastewater populations compared with clinical isolates. Additionally, isolates from untreated wastewater typically exhibited increased AMR compared with those from treated wastewater. Furthermore, aquaculture was associated with increased AMR to ciprofloxacin and tetracycline compared with wild-caught seafood. Using the World Health Organization AWaRe classifications, countries with lower consumption of "Access" compared to "Watch" drugs from 2000 to 2015 demonstrated higher AMR levels. The current analysis revealed negative correlations between AMR and anthropogenic factors, such as environmental performance indices and socioeconomic standing. Environmental health and sanitation were two of the environmental factors most strongly correlated with AMR. The current analysis highlights the negative impacts of "Watch" drug overconsumption, anthropogenic activity, absence of wastewater infrastructure, and aquaculture on AMR, thus stressing the need for proper infrastructure and global regulations to combat this growing problem.

Contribution of pollution gradient to the sediment microbiome and potential pathogens in urban streams draining into Lake Victoria (Kenya)

In sub-Saharan Africa (SSA), urban rivers/streams have long been subjected to anthropogenic pollution caused by urbanization, resulting in significantly altered chemical and biological properties of surface water and sediments. However, little is known about the diversity and structure of river microbial community composition and pathogens, as well as how they respond to anthropogenic inputs. High-throughput 16S rRNA amplicon sequencing and PICRUSt predictive function profiling were used in this study to conduct a comprehensive analysis of the spatial bacterial distribution and metabolic functions in sediment of two urban streams (Kisat and Auji) flowing through Kisumu City, Kenya. Results revealed that sediment samples from the highly urbanized mid and lower stream catchment zones of both streams had significantly higher levels of total organic carbon (TOC), total nitrogen (TN), total phosphorous (TP) than the less urbanized upper catchment zone, and were severely polluted with toxic heavy metals lead (Pb), cadmium (Cd), and copper (Cu). Differential distribution of Actinobacteria, Proteobacteria, Chloroflexi, and Verrucomicrobia in sediment bacterial composition was detected along stream catchment zones. The polluted mid and lower catchment zones were rich in Actinobacteria and Proteobacteria, as well as a variety of potential pathogenic taxa such as Corynebacterium, Staphylococcus, Cutibacterium, Turicella, Acinetobacter, and Micrococcus, as well as enteric bacteria such as Faecalibacterium, Shewanella, Escherichia, Klebsiella, Enterococcus, Prevotella, Legionella, Vibrio and Salmonella. Furthermore, PICRUSt metabolic inference analysis revealed an increasing enrichment in the sediments of genes associated with carbon and nitrogen metabolism, disease pathogenesis, and virulence. Environmental factors (TOC, Pb, Cd, TN, pH) and geographical distance as significant drivers of sediment bacterial community assembly, with the environmental selection to play a dominant role. In polluted river catchment zone sediment samples, Pb content was the most influential sediment property, followed by TOC and Cd content. Given the predicted increase in urbanization in SSA, further alteration of surface water and sediment microbiome due to urban river pollution is unavoidable, with potential long-term effects on ecosystem function and potential health hazards. As a result, this study provides valuable information for ecological risk assessment and management of urban rivers impacted by diffuse and point source anthropogenic inputs, which is critical for future proactive and sustainable urban waste management, monitoring, and water pollution control in low-income countries.

Microbial community composition and function in an urban waterway with combined sewer overflows before and after implementation of a stormwater storage pipe

When the wastewater volume exceeds the sewer pipe capacity during extreme rainfall events, untreated sewage discharges directly into rivers as combined sewer overflow (CSO). To compare the impacts of CSOs and stormwater on urban waterways, we assessed physicochemical water quality, the 16S rRNA gene-based bacterial community structure, and EcoPlate-based microbial functions during rainfall periods in an urban waterway before and after a stormwater storage pipe was commissioned. A temporal variation analysis showed that CSOs have significant impacts on microbial function and bacterial community structure, while their contributions to physicochemical parameters, bacterial abundance, and chlorophyll a were not confirmed. Heat map analysis showed that the impact of CSO on the waterway bacterial community structure was temporal and the bacterial community composition in CSO is distinct from that in sewers. Hierarchical clustering analysis revealed that the waterway physicochemical water qualities, bacterial community composition, and microbial community function were distinguishable from the upper reach of the river, rather than between CSO and stormwater. Changes in the relative abundance of tetracycline resistance (tet) genes-especially tet(M)-were observed after CSOs but did not coincide with changes in the microbial community composition, suggesting that the parameters affecting the microbial community composition and relative abundance of tet genes differ. After pipe implementation, however, stormwater did not contribute to the abundance of tet genes in the waterway. These results indicate that CSO-induced acute microbial disturbances in the urban waterway were alleviated by the implementation of a stormwater storage pipe and will support the efficiency of storage pipe operation for waterway management in urban areas.

Microplastics in urban waters and its effects on microbial communities: a critical review

Microplastic (MP) pollution is one of the emerging threats to the water and terrestrial environment, forcing a new environmental challenge due to the growing trend of plastic released into the environment. Synthetic and non-synthetic plastic components can be found in rivers, lakes/reservoirs, oceans, mountains, and even remote areas, such as the Arctic and Antarctic ice sheets. MPs' main challenge is identifying, measuring, and evaluating their impacts on environmental behaviors, such as carbon and nutrient cycles, water and wastewater microbiome, and the associated side effects. However, until now, no standardized methodical protocols have been proposed for comparing the results of studies in different environments, especially in urban water and wastewater. This review briefly discusses MPs' sources, fate, and transport in urban waters and explains methodological uncertainty. The effects of MPs on urban water microbiomes, including urban runoff, sewage wastewater, stagnant water in plumbing networks, etc., are also examined in depth. Furthermore, this study highlights the pathway of MPs and their transport vectors to different parts of ecosystems and human life, particularly through mediating microbial communities, antibiotic-resistant genes, and biogeochemical cycles. Overall, we have briefly highlighted the present research gaps, the lack of appropriate policy for evaluating microplastics and their interactions with urban water microbiomes, and possible future initiatives.

Recovery of High Quality Metagenome-Assembled Genomes From Full-Scale Activated Sludge Microbial Communities in a Tropical Climate Using Longitudinal Metagenome Sampling

The analysis of metagenome data based on the recovery of draft genomes (so called metagenome-assembled genomes, or MAG) has assumed an increasingly central role in microbiome research in recent years. Microbial communities underpinning the operation of wastewater treatment plants are particularly challenging targets for MAG analysis due to their high ecological complexity, and remain important, albeit understudied, microbial communities that play ssa key role in mediating interactions between human and natural ecosystems. Here we consider strategies for recovery of MAG sequence from time series metagenome surveys of full-scale activated sludge microbial communities. We generate MAG catalogs from this set of data using several different strategies, including the use of multiple individual sample assemblies, two variations on multi-sample co-assembly and a recently published MAG recovery workflow using deep learning. We obtain a total of just under 9,100 draft genomes, which collapse to around 3,100 non-redundant genomic clusters. We examine the strengths and weaknesses of these approaches in relation to MAG yield and quality, showing that co-assembly may offer advantages over single-sample assembly in the case of metagenome data obtained from closely sampled longitudinal study designs. Around 1,000 MAGs were candidates for being considered high quality, based on single-copy marker gene occurrence statistics, however only 58 MAG formally meet the MIMAG criteria for being high quality draft genomes. These findings carry broader broader implications for performing genome-resolved metagenomics on highly complex communities, the design and implementation of genome recoverability strategies, MAG decontamination and the search for better binning methodology.

Evaluating de Novo Assembly and Binning Strategies for Time Series Drinking Water Metagenomes

Reconstructing microbial genomes from metagenomic short-read data can be challenging due to the unknown and uneven complexity of microbial communities. This complexity encompasses highly diverse populations, which often includes strain variants. Reconstructing high-quality genomes is a crucial part of the metagenomic workflow, as subsequent ecological and metabolic inferences depend on their accuracy, quality, and completeness. In contrast to microbial communities in other ecosystems, there has been no systematic assessment of genome-centric metagenomic workflows for drinking water microbiomes. In this study, we assessed the performance of a combination of assembly and binning strategies for time series drinking water metagenomes that were collected over 6 months. The goal of this study was to identify the combination of assembly and binning approaches that result in high-quality and -quantity metagenome-assembled genomes (MAGs), representing most of the sequenced metagenome. Our findings suggest that the metaSPAdes coassembly strategies had the best performance, as they resulted in larger and less fragmented assemblies, with at least 85% of the sequence data mapping to contigs greater than 1 kbp. Furthermore, a combination of metaSPAdes coassembly strategies and MetaBAT2 produced the highest number of medium-quality MAGs while capturing at least 70% of the metagenomes based on read recruitment. Utilizing different assembly/binning approaches also assists in the reconstruction of unique MAGs from closely related species that would have otherwise collapsed into a single MAG using a single workflow. Overall, our study suggests that leveraging multiple binning approaches with different metaSPAdes coassembly strategies may be required to maximize the recovery of good-quality MAGs. IMPORTANCE Drinking water contains phylogenetic diverse groups of bacteria, archaea, and eukarya that affect the esthetic quality of water, water infrastructure, and public health. Taxonomic, metabolic, and ecological inferences of the drinking water microbiome depend on the accuracy, quality, and completeness of genomes that are reconstructed through the application of genome-resolved metagenomics. Using time series metagenomic data, we present reproducible genome-centric metagenomic workflows that result in high-quality and -quantity genomes, which more accurately signifies the sequenced drinking water microbiome. These genome-centric metagenomic workflows will allow for improved taxonomic and functional potential analysis that offers enhanced insights into the stability and dynamics of drinking water microbial communities.

Unraveling the ecological processes modulating the population structure of Escherichia coli in a highly polluted urban stream network

Escherichia coli dynamics in urban watersheds are affected by a complex balance among external inputs, niche modulation and genetic variability. To explore the ecological processes influencing E. coli spatial patterns, we analyzed its abundance and phylogenetic structure in water samples from a stream network with heterogeneous urban infrastructure and environmental conditions. Our results showed that environmental and infrastructure variables, such as macrophyte coverage, DIN and sewerage density, mostly explained E. coli abundance. Moreover, main generalist phylogroups A and B1 were found in high proportion, which, together with an observed negative relationship between E. coli abundance and phylogroup diversity, suggests that their dominance might be due to competitive exclusion. Lower frequency phylogroups were associated with sites of higher ecological disturbance, mainly involving simplified habitats, higher drainage infrastructure and septic tank density. In addition to the strong negative relationship between phylogroup diversity and dominance, the occurrence of these phylogroups would be associated with increased facilitated dispersal. Nutrients also contributed to explaining phylogroup distribution. Our study proposes the differential contribution of distinct ecological processes to the patterns of E. coli in an urban watershed, which is useful for the monitoring and management of fecal pollution.

Current Trends in the Application of Nanomaterials for the Removal of Emerging Micropollutants and Pathogens from Water

Water resources contamination has a worldwide impact and is a cause of global concern. The need for provision of clean water is becoming more and more demanding. Nanotechnology may support effective strategies for the treatment, use and reuse of water and the development of next-generation water supply systems. The excellent properties and effectiveness of nanomaterials make them particularly suitable for water/wastewater treatment. This review provides a comprehensive overview of the main categories of nanomaterials used in catalytic processes (carbon nanotubes/graphitic carbon nitride (CNT/g-C₃N₄) composites/graphene-based composites, metal oxides and composites, metal–organic framework and commercially available nanomaterials). These materials have found application in the removal of different categories of pollutants, including pharmaceutically active compounds, personal care products, organic micropollutants, as well as for the disinfection of bacterial, viral and protozoa microbial targets, in water and wastewater matrices. Apart from reviewing the characteristics and efficacy of the aforementioned nanoengineered materials for the removal of different pollutants, we have also recorded performance limitations issues (e.g., toxicity, operating conditions and reuse) for their practical application in water and wastewater treatment on large scale. Research efforts and continuous production are expected to support the development of eco-friendly, economic and efficient nanomaterials for real life applications in the near future.

Aeromonas hydrophila, Bacillus thuringiensis, Escherichia coli and Pseudomonas aeruginosa utilization of Ammonium-N, Nitrate-N and Urea-N in culture

Agricultural drainage ditches represent a major source of nutrient pollution. Shifts in nitrogen source and use of animal manures have changed the bacterial composition both in species of bacteria and their abundance in agricultural ditches. This change affects how nitrogen is being cycled and potentially the final forms of available nutrients. In particular, animal manures often have bacteria such as Escherichia coli present, increasing the abundance of a bacterial species in ditches. Research has shown that the effect of different nitrogen sources is to change bacterial community composition (class, family). How this influences the role of an individual bacterial species is poorly understood. Thus, our question was how individual species would respond to different sources of nitrogen. We used Aeromonas hydrophila, Bacillus thuringiensis, Escherichia coli and Pseudomonas aeruginosa that are common in agricultural ditches and exposed them to different concentrations of nitrogen in cultures of 1 × 10⁰ and 1 × 10⁻¹ dilutions from a stock solution of bacteria. Nitrogen sources were ammonium chloride, sodium nitrate and urea. The results showed A. hydrophila and E. coli have strong similarities particularly with nitrate-N and urea-N utilization and the response was often correlated with the amount of nutrient added. P. aeruginosa while similar did not show any strong correlation with amount of nutrient added. B. thuringiensis was different from the other three bacteria in utilization or production. Research has provided insight into the role of some bacteria in nitrogen cycling and may be valuable in the future to developing management strategies to reduce nutrients.

An in silico analysis of acquired antimicrobial resistance genes in Aeromonas plasmids

Sequences of 105 Aeromonas species plasmids were probed for acquired anti-microbial resistance (AMR) genes using a bioinformatics approach. The plasmids showed no positive linear correlation between size and GC content and up to 55 acquired AMR genes were found in 39 (37%) plasmids after in silico screening for resistance against 15 antibiotic drug classes. Overall, potential multiple antibiotic resistance (p-MAR) index ranged from 0.07 to 0.53. Up to 18 plasmids were predicted to mediate multiple drug resistance (MDR). Plasmids pS121-1a (A. salmonicida), pWCX23_1 (A. hydrophila) and pASP-a58 (A. veronii) harboured 18, 15 and 14 AMR genes respectively. The five most occurring drug classes for which AMR genes were detected were aminoglycosides (27%), followed by beta-lactams (17%), sulphonamides (13%), fluoroquinolones (13%), and phenicols (10%). The most prevalent genes were a sulphonamide resistant gene Sul1, the gene aac (6')-Ib-cr (aminoglycoside 6'-N-acetyl transferase type Ib-cr) resistant to aminoglycosides and the blaKPC-2 gene, which encodes carbapenemase-production. Plasmid acquisition of AMR genes was mainly inter-genus rather than intra-genus. Eighteen plasmids showed template or host genes acquired from Pseudomonas monteilii, Salmonella enterica or Escherichia coli. The most occurring antimicrobial resistance determinants (ARDs) were beta-lactamase, followed by aminoglycosides acetyl-transferases, and then efflux pumps. Screening of new isolates in vitro and in vivo is required to ascertain the level of phenotypic expression of colistin and other acquired AMR genes detected.

Reaching a Large Urban Undergraduate Population through Microbial Ecology Course-Based Research Experiences

Traditional postsecondary education is making progress on embracing the diversity of student backgrounds and experiences while preparing them for the demands of STEM careers. Course-based undergraduate research experiences (CUREs) are effective tools to concurrently achieve many student and faculty goals: facilitating training of students, building career competencies, generating publishable research results and enabling research experiences where students apply their knowledge and interest. Georgia State University is not unique with a high student demand for research experiences and mentors that is greater than traditional research faculty labs can accommodate. Georgia State University is, however, unique in that it is a demographically diverse campus which serves minority and non-traditional students (i.e., second career and veterans) and is also rapidly growing. Therefore, to enhance the microbiology curriculum and facilitate authentic research experiences for the growing number of biology majors, a cluster of course-based research experiences in microbial ecology was developed. A former research lab space was converted to a collaborative teaching lab to serve the growth in course offerings, as well as to accommodate multiple microbial ecology research projects occurring in the same space. The courses offered appeal to students, build on the strengths of faculty experiences, and facilitate collaboration amongst students and with the greater Atlanta community. To ensure that our CUREs are accessible to the diverse students in our department, we addressed a variety of logistical and curricular challenges. Solutions to such challenges align with the goals of the university to offer research and signature experiences to ensure students are included and trained in STEM skills.

Influence of Sampling Site and other Environmental Factors on the Bacterial Community Composition of Domestic Washing Machines

Modern, mainly sustainability-driven trends, such as low-temperature washing or bleach-free liquid detergents, facilitate microbial survival of the laundry processes. Favourable growth conditions like humidity, warmth and sufficient nutrients also contribute to microbial colonization of washing machines. Such colonization might lead to negatively perceived staining, corrosion of washing machine parts and surfaces, as well as machine and laundry malodour. In this study, we characterized the bacterial community of 13 domestic washing machines at four different sampling sites (detergent drawer, door seal, sump and fibres collected from the washing solution) using 16S rRNA gene pyrosequencing and statistically analysed associations with environmental and user-dependent factors. Across 50 investigated samples, the bacterial community turned out to be significantly site-dependent with the highest alpha diversity found inside the detergent drawer, followed by sump, textile fibres isolated from the washing solution, and door seal. Surprisingly, out of all other investigated factors only the monthly number of wash cycles at temperatures ≥ 60 °C showed a significant influence on the community structure. A higher number of hot wash cycles per month increased microbial diversity, especially inside the detergent drawer. Potential reasons and the hygienic relevance of this finding need to be assessed in future studies.

Patterns of protist diversity associated with raw sewage in New York City

Protists are ubiquitous components of terrestrial and aquatic environments, as well as animal and human microbiomes. Despite this, little is known about protists in urban environments. The ~7400-mile sewer system of New York City (NYC) collects human waste from ~8 million human inhabitants as well as from animals, street runoff, and groundwater, providing an ideal system to study these microbes. We used 18S rRNA amplicon sequencing and shotgun metagenomic sequencing to profile raw sewage microbial communities. Raw sewage samples were collected over a 12-month period from 14 treatment plants of the five NYC boroughs, and compared with samples from other environments including soil, stormwater, and sediment. Sewage contained a diverse protist community dominated by free-living clades, and communities were highly differentiated across environments. Seasonal differences in protist composition were observed; however, network analysis and functional profiling demonstrated that sewage communities were robust and functionally consistent. Protists typically associated with human and animal guts or feces were frequently detected. Abundance of these parasites varied significantly both spatially and temporally, suggesting that spikes could reflect trends in the source population. This underscores sewage as a valuable model system for monitoring patterns in urban microbes and provides a baseline protist metagenome of NYC.

Characterization of bacterial communities in wastewater with enhanced taxonomic resolution by full-length 16S rRNA sequencing

Wastewater treatment is crucial to environmental hygiene in urban environments. However, wastewater treatment plants (WWTPs) collect chemicals, organic matter, and microorganisms including pathogens and multi-resistant bacteria from various sources which may be potentially released into the environment via WWTP effluent. To better understand microbial dynamics in WWTPs, we characterized and compared the bacterial community of the inflow and effluent of a WWTP in Berlin, Germany using full-length 16S rRNA gene sequences, which allowed for species level determination in many cases and generally resolved bacterial taxa. Significantly distinct bacterial communities were identified in the wastewater inflow and effluent samples. Dominant operational taxonomic units (OTUs) varied both temporally and spatially. Disease associated bacterial groups were efficiently reduced in their relative abundance from the effluent by the WWTP treatment process, except for Legionella and Leptospira species which demonstrated an increase in relative proportion from inflow to effluent. This indicates that WWTPs, while effective against enteric bacteria, may enrich and release other potentially pathogenic bacteria into the environment. The taxonomic resolution of full-length 16S rRNA genes allows for improved characterization of potential pathogenic taxa and other harmful bacteria which is required to reliably assess health risk.

The unexpected habitat in sewer pipes for the propagation of microbial communities and their imprint on urban waters

Modern urban sewer pipe infrastructure is a unique niche where microbes can thrive. Arcobacter, Acinetobacter, Aeromonas, and Trichococcus are among the organisms that dominate the microbial community of sewage influent, but are not major members of human fecal microbiome, drinking water, or groundwater. Pipe resident communities in untreated sewage are distinct from sewer biofilm communities. Because of their high biomass, these organisms likely have a role in biotransformation of waste during conveyance and could represent an important inoculum for treatment plants. Studies demonstrate stormwater systems act as direct conduits for sewage to surface waters, releasing organisms propagated in sewer pipes. Frequent occurrence of these pipe residents, in particular Arcobacter, demonstrates the extent that urban infrastructure impacts rivers, lakes, and urban coasts worldwide.

Investigating diversity of pathogenic microbes in commercial bait trade water

The recreational bait trade is a potential pathway for pathogen introduction and spread when anglers dump bait shop sourced water into aquatic systems. Despite this possibility, and previous recognition of the importance of the bait trade in the spread of aquatic invasive species (AIS), to date there has been no region wide survey documenting pathogens in retail bait shops. In this study, we analyzed 96 environmental DNA samples from retail bait shops around the Great Lakes region to identify pathogens, targeting the V4 hypervariable region of the 16S rRNA gene. Additionally, we used samples from one site in Lake Michigan as a comparison to pathogen diversity and abundance in natural aquatic systems. Our results identified nine different groups of pathogens in the bait shop samples, including those that pose risks to both humans and fish species. Compared to wild sourced samples, the bait shops had higher relative abundance and greater taxonomic diversity. These findings suggest that the bait trade represents a potentially important pathway that could introduce and spread pathogens throughout the Great Lakes region. Improving pathogen screening and angler outreach should be used in combination to aid in preventing the future spread of high risk pathogens.

Taxon-Driven Functional Shifts Associated with Storm Flow in an Urban Stream Microbial Community

Urban streams are susceptible to stormwater and sewage inputs that can impact their ecological health and water quality. Microbial communities in streams play important functional roles, and their composition and metabolic potential can help assess ecological state and water quality. Although these environments are highly heterogenous, little is known about the influence of isolated perturbations, such as those resulting from rain events on urban stream microbiota. Here, we examined the microbial community composition and diversity in an urban stream during dry and wet weather conditions with both 16S rRNA gene sequencing across multiple years and shotgun metagenomics to more deeply analyze a single storm flow event. Metagenomics was used to assess population-level dynamics as well as shifts in the microbial community taxonomic profile and functional potential before and after a substantial rainfall. The results demonstrated general trends present in the stream under storm flow versus base flow conditions and also highlighted the influence of increased effluent flow following rain in shifting the stream microbial community from abundant freshwater taxa to those more associated with urban/anthropogenic settings. Shifts in the taxonomic composition were also linked to changes in functional gene content, particularly for transmembrane transport and organic substance biosynthesis. We also observed an increase in relative abundance of genes encoding degradation of organic pollutants and antibiotic resistance after rain. Overall, this study highlighted some differences in the microbial community of an urban stream under storm flow conditions and showed the impact of a storm flow event on the microbiome from an environmental and public health perspective.IMPORTANCE Urban streams in various parts of the world are facing increased anthropogenic pressure on their water quality, and storm flow events represent one such source of complex physical, chemical, and biological perturbations. Microorganisms are important components of these streams from both ecological and public health perspectives. Analysis of the effect of perturbations on the stream microbial community can help improve current knowledge on the impact such chronic disturbances can have on these water resources. This study examines microbial community dynamics during rain-induced storm flow conditions in an urban stream of the Chicago Area Waterway System. Additionally, using shotgun metagenomics we identified significant shifts in the microbial community composition and functional gene content following a high-rainfall event, with potential environment and public health implications. Previous work in this area has focused on specific genes/organisms or has not assessed immediate storm flow impact.

Microbial Diversity and Toxin Risk in Tropical Freshwater Reservoirs of Cape Verde

The Cape Verde islands are part of the African Sahelian arid belt that possesses an erratic rain pattern prompting the need for water reservoirs, which are now critical for the country’s sustainability. Worldwide, freshwater cyanobacterial blooms are increasing in frequency due to global climate change and the eutrophication of water bodies, particularly in reservoirs. To date, there have been no risk assessments of cyanobacterial toxin production in these man-made structures. We evaluated this potential risk using 16S rRNA gene amplicon sequencing and full metagenome sequencing in freshwater reservoirs of Cape Verde. Our analysis revealed the presence of several potentially toxic cyanobacterial genera in all sampled reservoirs. Faveta potentially toxic and bloom-forming Microcystis sp., dominated our samples, while a Cryptomonas green algae and Gammaproteobacteria dominated Saquinho and Poilão reservoirs. We reconstructed and assembled the Microcystis genome, extracted from the metagenome of bulk DNA from Faveta water. Phylogenetic analysis of Microcystis cf. aeruginosa CV01’s genome revealed its close relationship with other Microcystis genomes, as well as clustering with other continental African strains, suggesting geographical coherency. In addition, it revealed several clusters of known toxin-producing genes. This survey reinforces the need to better understand the country’s microbial ecology as a whole of water reservoirs on the rise.

Partitioning of Antibiotic Resistance Genes and Fecal Indicators Varies Intra and Inter-Storm during Combined Sewer Overflows

Combined sewer overflows (CSOs) degrade water quality through the release of microbial contaminants in CSO effluent. Improved understanding of the partitioning of microbial contaminants onto settleable particles can provide insight into their fate in end-of-pipe treatment systems or following release during CSO events. Sampling was performed across the hydrograph for three storm events as well as during baseflow and wet weather in three surface waters impacted by CSO. qPCR was performed for select antibiotic resistance genes (ARG) and a marker gene for human fecal indicator organisms (BacHum) in samples processed the partitioning of microbial contaminants on settleable particles versus suspended in the aqueous phase. Amplicon sequencing was performed on both fractions of storm samples to further define the timing and partitioning of microbial contaminants released during CSO events. Samples collected at the CSO outfall exhibited microbial community signatures of wastewater at select time points early or late in the storm events. CSOs were found to be a source of ARG. In surrounding surface waters, sul1 was higher in samples from select locations during wet weather compared to baseflow. Otherwise, ARG concentrations were variable with no differences between baseflow and wet weather conditions. The majority of ARG at the CSO outfall were observed on the attached fraction of samples: 64-79% of sul1 and 59-88% of tet(G). However, the timing of peak ARG and human fecal indicator marker gene BacHum did not necessarily coincide with observation of the microbial signature of wastewater in CSO effluent. Therefore, unit processes that remove settleable particles (e.g., hydrodynamic separators) operated throughout a CSO event would achieve up to (0.5-0.9)-log removal of ARG and fecal indicators by removing the attached fraction of measured genes. Secondary treatment would be required if greater removal of these targets is needed.

Dynamic microbial populations along the Cuyahoga River

The study of the microbial communities has gained traction in recent years with the advent of next-generation sequencing with, or without, PCR-based amplification of the 16S ribosomal RNA region. Such studies have been applied to topics as diverse as human health and environmental ecology. Fewer studies have investigated taxa outside of bacteria, however. We present here data demonstrating the utility of studying taxa outside of bacteria including algae, diatoms, archaea and fungi. Here, we show how location along the Cuyahoga River as well as a transient rainfall event heavily influence the microbial composition. Our data reveal how individual OTUs vary between samples and how the patterns of OTU abundance can accurately predict sampling location. The clustering of samples reveals that these taxa are all sensitive to water conditions in unique ways and demonstrate that, for our dataset, algae was most distinctive between sample groups, surpassing bacteria. Diversity between sampling sites could allow studies investigating pollution or water quality to identify marker OTUs or patterns of OTU abundance as indicators to assess environmental conditions or the impact of human activity. We also directly compare data derived from primers amplifying distinct taxa and show that taxa besides bacteria are excellent indicators of water condition.

Aquatic urban ecology at the scale of a capital: community structure and interactions in street gutters

In most cities, streets are designed for collecting and transporting dirt, litter, debris, storm water and other wastes as a municipal sanitation system. Microbial mats can develop on street surfaces and form microbial communities that have never been described. Here, we performed the first molecular inventory of the street gutter-associated eukaryotes across the entire French capital of Paris and the non-potable waters sources. We found that the 5782 OTUs (operational taxonomic units) present in the street gutters which are dominated by diatoms (photoautotrophs), fungi (heterotrophs), Alveolata and Rhizaria, includes parasites, consumers of phototrophs and epibionts that may regulate the dynamics of gutter mat microbial communities. Network analyses demonstrated that street microbiome present many species restricted to gutters, and an overlapping composition between the water sources used for street cleaning (for example, intra-urban aquatic networks and the associated rivers) and the gutters. We propose that street gutters, which can cover a significant surface area of cities worldwide, potentially have important ecological roles in the remediation of pollutants or downstream wastewater treatments, might also be a niche for growth and dissemination of putative parasite and pathogens.

Effects of Ammonia and Density on Filtering of Commensal and Pathogenic Escherichia coli by the Cladoceran Daphnia magna

Grazing by cladocerans can reduce the survival of enteric bacteria associated with fecal pollution. This study examined the potential of Daphnia magna to filter commensal and pathogenic Escherichia coli of human origin. Grazing on commensal and pathogenic bacteria was comparable, but slightly greater at 20 compared to 15 and 25°C. Filtering activity was strongly dependent on D. magna and E. coli densities at environmentally relevant bacterial concentrations. Maximum feeding rates were >10⁷ cells h^-1 daphnid^-1, clearance rates were 1-6 mL h^-1 daphnid^-1, and filtering was independent of bacterial cell sizes between 0.7 and 1.8 µm. Filtering and ingestion of E. coli by D. magna was susceptible to acute inhibition by unionized ammonia with a 24 h EC50 of 0.18 mg L^-1 NH₃-N, and a LOEC of 0.09 mg L^-1 NH₃-N. The study indicated that biological and chemical constraints should be considered when applying Daphnia for attenuation of fecal pollution.