Bacterial assemblages of urban microbiomes mobilized by runoff waters match land use typologies and harbor core species involved in pollutant degradation and opportunistic human infections

Effects of snowmelt runoff on bacterial communities and antimicrobial resistance gene concentrations in an urban river in a cold climate region

Urban rivers are essential for human activities and ecosystems. Urban runoff is a major source of various pollutants in urban rivers. In this study, we investigated the effect of rainfall and snowmelt subsequently causing urban runoff in a cold climate region on bacterial community structures and antimicrobial resistance gene concentrations in an urban river in Sapporo city, Japan, which has an average snowfall of 4.8 m. Bacterial community structures of the river water were analyzed by next generation sequencing of bacterial 16S rRNA genes. The antimicrobial resistance genes, mphA and blaIMP, were determined using quantitative polymerase chain reaction. Rainfall and snowmelt increased the effluent discharge rate of treated wastewater, and river water depth. Rainfall and snowmelt also increased Escherichia coli concentrations by 4-20 folds in the river, probably because of combined sewer overflows, urban runoff, or increased effluent discharge rate of treated wastewater to the river. Urban runoff and the subsequent discharge of treated wastewater decreased the bacterial alpha diversity and increased the species evenness of bacteria. Bacterial beta diversity analysis showed that the discharge of treated wastewater caused by rainfall and snowmelt changed the structure and diversity of the bacterial community in the river. The concentrations of the antimicrobial resistance gene mphA were related to the discharge of treated wastewater. In contrast, the antimicrobial resistance gene blaIMP appeared to be present in the upstream pristine environment. Results of this study should be informative for challenge to reduce the antimicrobial resistance bacteria due to combined sewer overflows by wastewater management authorities.

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.

Runoff microbiome quality assessment of a city center rainwater harvesting zone shows a differentiation of pathogen loads according to human mobility patterns

The hygienic quality of urban surfaces can be impaired by multiple sources of microbiological contaminants. These surfaces can trigger the development of multiple bacterial taxa and favor their spread during rain events through the circulation of runoff waters. These runoff waters are commonly directed toward sewer networks, stormwater infiltration systems or detention tanks prior a release into natural water ways. With water scarcity becoming a major worldwide issue, these runoffs are representing an alternative supply for some usage like street cleaning and plant watering. Microbiological hazards associated with these urban runoffs, and surveillance guidelines must be defined to favor these uses. Runoff microbiological quality from a recently implemented city center rainwater harvesting zone was evaluated through classical fecal indicator bacteria (FIB) assays, quantitative PCR and DNA meta-barcoding analyses. The incidence of socio-urbanistic patterns on the organization of these urban microbiomes were investigated. FIB and DNA from Human-specific Bacteroidales and pathogens such as Staphylococcus aureus were detected from most runoffs and showed broad distribution patterns. 16S rRNA DNA meta-barcoding profilings further identified core recurrent taxa of health concerns like Acinetobacter, Mycobacterium, Aeromonas and Pseudomonas, and divided these communities according to two main groups of socio-urbanistic patterns. One of these was highly impacted by heavy traffic, and showed recurrent correlation networks involving bacterial hydrocarbon degraders harboring significant virulence properties. The tpm-based meta-barcoding approach identified some of these taxa at the species level for more than 30 genera. Among these, recurrent pathogens were recorded such as P. aeruginosa, P. paraeruginosa, and Aeromonas caviae. P. aeruginosa and A. caviae tpm reads were found evenly distributed over the study site but those of P. paraeruginosa were higher among sub-catchments impacted by heavy traffic. Health risks associated with these runoff P. paraeruginosa emerging pathogens were high and associated with strong cytotoxicity on A549 lung cells. Recurrent detections of pathogens in runoff waters highlight the need of a microbiological surveillance prior allowing their use. Good microbiological quality can be obtained for certain typologies of sub-catchments with good hygienic practices but not all. A reorganization of Human mobility and behaviors would likely trigger changes in these bacterial diversity patterns and reduce the occurrences of the most hazardous groups.

Ecological assessment of combined sewer overflow management practices through the analysis of benthic and hyporheic sediment bacterial assemblages from an intermittent stream

Combined sewer overflows (CSO) are used to avoid overloading unitary sewers and wastewater treatment plants. Following the European Council Directive on Urban Wastewater Treatment (UWT), CSO discharges are regulated using guidelines that aim to reduce their ecological impact on aquatic systems. A model CSO, which is part of a long-term experimental field observatory, was modified according to these guidelines and used to evaluate the benefits of compliance through analyses of the bacteriological and chemical states of the receiving intermittent stream. The benthic and hyporheic sediments of similar geomorphic units located upstream and downstream of a monitored CSO outlet were compared before and after changes in CSO regimes. Hydrological, pollutants (Metal Trace Elements, MTE; Polycyclic Aromatic Hydrocarbons, PAH; fecal indicator bacteria, FIB), and tpm-based DNA meta-barcoding datasets resolving the occurrences of >700 bacterial species of nearly 200 genera were studied. The frequency of overflow was confirmed to have significantly decreased following the application of the UWT guidelines. Overflows became almost limited to periods of heavy summer thunderstorm events. These changes were not associated with a significant decrease in most of the surveyed MTE, PAH, and FIB among stream sediments, except for chromium. Ecological benefits were highlighted by significant changes in tpm-based meta-barcoding community patterns between the UWT compliant sampling period and the previous one. Bacterial community change point analyses confirmed this segregation in the meta-barcoding dataset according to hydrological indices such as the number of CSO events and discharged volumes. A significant decline in CSO bacterial taxa in the benthic and hyporheic sediments was observed. Thirty-four CSO indicator species were identified, including Aeromonas caviae, Aeromonas media, and Pseudomonas oleovorans. These indicators, often documented as opportunistic pathogens (to humans, animals or plants) and/or pollutant degraders, were proposed as ecological sentinels for the assessment of CSO impacts.

Microbe-sediment interactions in Great Lakes recreational waters: Implications for human health risk

Microbial assessments of recreational water have traditionally focused on culturing or DNA-based approaches of the planktonic water column, omitting influence from microbe-sediment relationships. Sediment (bed and suspended) has been shown to often harbour levels of bacteria higher than the planktonic phase. The fate of suspended sediment (SS) bacteria is extensively related to transport dynamics (e.g., deposition) of the associated sediment/floc. When hydraulic energy allows, SS will settle, introducing new (potentially pathogenic) organisms to the bed. With turbulence, including waves, currents and swimmers, the risk of human ingestion is elevated due to resuspension of bed sediment and associated microbes. This research used multiplex nanofluidic reverse transcriptase quantitative PCR on RNA of bacteria associated with bed and SS to explore the active bacteria in freshwater shorelines. Bacterial genes of human health concern regarding recreational water use were targeted, such as faecal indicator bacteria (FIB), microbial source tracking genes and virulence factors from waterborne pathogens. Results indicate avian sources (i.e., gulls, geese) to be the largest nonpoint source of FIB associated with sediment in Great Lakes shorelines. This research introduces a novel approach to microbial water quality assessments and enhances our understanding of microbe-sediment dynamics and the quality of freshwater beaches.

Evidence of Bacterial Community Coalescence between Freshwater and Discharged tpm-Harboring Bacterial Taxa from Hospital and Domestic Wastewater Treatment Plants among Epilithic Biofilms

The ability of WWTP outflow bacteria at colonizing rock surfaces and contributing to the formation of river epilithic biofilms was investigated. Bacterial community structures of biofilms (b-) developing on rocks exposed to treated wastewaters (TWW) of a hospital (HTWW) and a domestic (DTWW) clarifier, and to surface waters of the stream located at 10 m, 500 m, and 8 km from the WWTP outlet, were compared. Biofilm bacterial contents were analyzed by cultural approaches and a tpm-based DNA metabarcoding analytical scheme. Co-occurrence distribution pattern analyses between bacterial datasets and eighteen monitored pharmaceuticals were performed. Higher concentrations of iohexol, ranitidine, levofloxacin, and roxithromycin were observed in the b-HTWW while atenolol, diclofenac, propranolol, and trimethoprim were higher in the b-DTWW. MPN growth assays showed recurrent occurrences of Pseudomonas aeruginosa and Aeromonas caviae among these biofilms. An enrichment of multi-resistant P. aeruginosa cells was observed in the hospital sewer line. P. aeruginosa MPN values were negatively correlated to roxithromycin concentrations. The tpm DNA metabarcoding analyses confirmed these trends and allowed an additional tracking of more than 90 species from 24 genera. Among the recorded 3082 tpm ASV (amplicon sequence variants), 41% were allocated to the Pseudomonas. Significant differences through ANOSIM and DESeq2 statistical tests were observed between ASV recovered from b-HTWW, b-DTWW, and epilithic river biofilms. More than 500 ASV were found restricted to a single sewer line such as those allocated to Aeromonas popoffii and Stenotrophomonas humi being strictly found in the b-HTWW file. Several significant correlations between tpm ASV counts per species and pharmaceutical concentrations in biofilms were recorded such as those of Lamprocystis purpurea being positively correlated with trimethoprim concentrations. A tpm source tracking analysis showed the b-DTWW and b-HTWW tpm ASV to have contributed, respectively, at up to 35% and 2.5% of the epilithic river biofilm tpm-taxa recovered downstream from the WWTP outlet. Higher contributions of TWW taxa among epilithic biofilms were recorded closer to the WWTP outlet. These analyses demonstrated a coalescence of WWTP sewer communities with river freshwater taxa among epilithic biofilms developing downstream of a WWTP outlet.