Stormwater infiltration systems (SIS) are increasingly implemented to mitigate urban flooding and recharge groundwater but can disseminate chemical and biological contaminants, including pathogens. This study assessed the impact of six SIS, differing in vadose zone thickness and runoff transit time, on the microbial composition of the underlying aquifer. Groundwater samples and biofilms collected using passive samplers composed of 8 mm clay beads enclosed in inert pouches were analyzed via a tpm metabarcoding, enabling DNA read allocations at the species level. SIS altered groundwater tpm microbial diversity and community structure, especially in systems with shallow vadose zones and fast transit times. Downstream SIS groundwaters showed higher richness and colonization by potential pathogens such as species from Aeromonas, Pseudomonas, Stenotrophomonas, and Xanthomonas. Biofilms revealed more persistent and pronounced microbial changes than water samples, capturing bacteria with substrate-colonizing capabilities, such as Pseudomonas aeruginosa. Functional predictions from taxonomic allocations indicated a shift toward pollutant degradation and pathogenic traits in fast-transit systems. These findings indicate that SIS can promote waterborne pathogen establishment, threatening groundwater quality and public health. Transit time emerged as a critical factor modulating microbial impacts from tpm-harboring bacteria, underscoring the need to integrate microbial risk assessments into SIS design and management strategies.

Hydrograph separation using biogeochemical data is a commonly used method for the vertical decomposition of flow into surface, subsurface and groundwater contributions. However, its application to the spatial decomposition of flow remains limited, despite its potential to identify contributions linked to geological, pedological, and land use characteristics, as well as anthropogenic contaminant sources. In this study, a Bayesian mixing model was applied to the Ratier peri-urban sub-catchment of the OTHU Yzeron observatory. Eight runoff-generating sources were identified and sampled, including different land uses (e.g. forest, grassland, agricultural areas), a colluvium aquifer, and urban point discharges (e.g. sewer system, urban and road surface runoff). A wide range of biogeochemical parameters were analysed including classical (i.e., major chemical compounds, dissolved metals) and innovative tracers (i.e., characteristics of dissolved organic matter, microbial indicators). Streamwater samples collected under contrasting hydro-meteorological conditions revealed distinct source signatures and highly variable contributions, with wastewater dominating under dry weather and rapid surface runoff during summer storms. Using these results, we improved a previously designed perceptual hydrological model of the Ratier and Mercier catchments, at the hillslope scale, which highlighted the potential of spatial tracer-based decomposition in addition to classical vertical hydrological separation. More broadly, this study demonstrates the potential of such mixing model, using classical but also more innovative tracers, to provide insights for validating distributed hydrological models and to anticipate the influence of land use, urbanisation, and climate changes on runoff generation.

Road surfaces accumulate anthropogenized sediments contaminated by animal waste, soil particles, and atmospheric deposits, raising hygienic concerns. During rainfall events, these sediments can be resuspended and transported via runoff into storm and combined sewers. This study investigated the bacterial diversity and potential health hazards associated with resuspended road-deposited matter in a peri-urban area. Quantitative PCR and metabarcoding analyses of 16S rRNA and tpm genes were performed to (i) identify the sources of bacterial taxa colonizing road surfaces, (ii) define core and specific taxa and assess their capacity to survive in downstream sewer environments, and (iii) explore their functional potential. Several taxa were linked to human and animal sources, with notable occurrences of bacterial pathogen DNA signatures. Amplicon sequence variant profiling revealed that resuspended road surface communities were more similar to those in storm sewage than in combined sewage. Functional annotation suggested that road surface taxa had enhanced pollutant degradation capabilities with some representing significant health hazards. Indicator taxa were identified to support the hygienic assessment of road-deposited sediments. These findings highlight the importance of monitoring road runoff as a vector of microbial contaminants in urban water systems.

The climate crisis presents an urgent challenge for Earth's living creatures and the habitats in which they have been adapted to thrive. Climate-related stress presents risks to microorganisms, the stability of the functions they provide, and their maintenance of beneficial interactions with their hosts and ecosystems. Microbes move across the continuum of anthropogenic influence on Earth's ecosystems, from pristine to human-managed to fully urbanized environments. Because microbial feedback within and across this continuum exists at multiple, connected scales from molecules to ecosystem-level processes, predicting microbial responses to climate stress and their potentially wide-ranging consequences remains difficult. Here, we discuss the broad implications of microbial and microbiome responses to climate change as they interface with human, plant, and ecosystem health. For each section on human, plant and ecosystem health, we briefly discuss the state of knowledge for each and follow with proposed future research, including some directions that are promising but require more work to evaluate. We end by considering overarching microbial ecology research needs across these systems and microbial solutions under investigation as possible climate-resilient interventions to maintain human, plant, and ecosystem health. This work draws on diverse expertise to identify broad research directions across typically separated disciplines and builds a holistic framework for considering their interrelationships.

The distribution of two waterborne pathogens linked to global antibiotic resistance, Aeromonas caviae (Acav) and Pseudomonas aeruginosa (Paer), was examined across a mixed-use catchment. Their emission sources and impacts on water quality were assessed. A novel quantitative PCR (qPCR) assay for Acav was developed. Pathogen tracking via qPCR was compared with microbial source tracking (qMST) of fecal contamination and with land use and physicochemical data. Acav prevalence was highest in road runoff, with counts correlating with human, ruminant, and sewer MST markers and nutrient levels. Real-time in vitro assays using Caco-2 intestinal epithelial cells demonstrated the infectious potential of these freshwater Acav cells. Paer was most abundant in brooks located in forested areas. Markers from the qPCR/qMST toolbox were used to estimate the relative contribution of headwaters, road runoff, and wastewater to stream outlets during rain events. Sewer outflows and first-order brook waters draining ruminant pasture fields were identified as key sources of downstream microbial contaminants. Road runoff containing Acav and forested headwaters harboring Paer further explained the observed microbial profiles. These findings revealed the streams’ poor hygienic status and potential health risks for humans and animals. The toolbox proved effective in identifying pathogen sources and assessing their influence on water quality, delivering critical insights for enhancing the management of mixed-use catchments facing increasing pressures from climate change.

Urban river bathing is re-emerging across Europe, driven by social demand and climate change impacts. The Urban Bathing Consortium, an interdisciplinary and intersectoral consortium initiated at the University of Lyon (France), is at the forefront of studying the challenges and opportunities of creating and managing healthy, safe, and accessible river bathing spaces. Through interdisciplinary collaboration among researchers and stakeholders, the consortium proposed an analytical framework, identifying seven critical dimensions for urban river bathing: the history and revival of city-river relationships, legal and regulatory frameworks, bathing water quality, river drowning risks, river ecosystems, social perspectives, and urban planning. By examining these dimensions with state-of-the-art approaches and drawing on Lyon's experiences, the study provides scientific insights and practical recommendations for future sustainable urban river bathing development. These include revitalizing historical city-river connections, aligning local regulations with EU guidance, advancing holistic microbial water quality control, enhancing safety measures, incorporating ecological considerations, balancing competing river uses in urban planning, and addressing social needs for inclusive river governance.

Carbohydrate-protein interactions are important in cell-cell communication, signal transduction, cancer, or infection. Chemists have designed glycosylated multivalent systems to mimic these recognition phenomena and produce potent ligands of lectins with therapeutic applications. Dynamic combinatorial chemistry (DCC) provides access to libraries of glycosylated macrocycles equilibrating through reversible covalent bonds. This strategy can be applied to the rapid and efficient identification of multivalent glycoclusters by introducing a protein into the equilibrating library. This strategy allowed the identification of the best ligands for more than one lectin in a single experimental set up by using two simple 1,4-dithiophenol building blocks. Selection of the best binder by each lectin (ConA, LecA, and LecB) was accompanied by the amplification of glyco-dyn[3]arenes and glyco-dyn[4]arenes. These macrocycles could be synthesized, isolated, and displayed nanomolar dissociation constants. Furthermore, while no toxicity could be detected against human cells or bacteria, their anti-adhesive properties against Pseudomonas aeruginosa were confirmed through a virulence assay on human cells. Altogether, extremely simple 1,4-dithiophenol building blocks provided access to a large diversity of glycoconjugates that could be selected by a lectin in a simple experimental set up to identify glycoconjugates with potential anti-infectious applications, thus speeding up the discovery of potential new antibacterial treatments.

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.

Carbohydrate-protein interactions are of prime importance in cell-cell communication, signal transduction, cancer, bacterial or viral infection. Chemists have designed multivalent systems to mimick these recognition phenomena and provide potent ligands of these proteins with foreseen therapeutic applications. Dynamic combinatorial chemistry provides access to a library of chemical species in equilibrium through reversible covalent bonds. This strategy can be readily applied to the rapid and efficient identification of multivalent glycoclusters by introducing a protein into the equilibrating library for the selection of the fittest glycocluster for this protein. 1,4-Dithiophenols conjugated to monosaccharides were equilibrated into dynamic combinatorial libraries providing a diverse mixture of glycoclusters. Selection of the best ligand for different lectins (ConA, LecA and LecB from Pseudomonas aeruginosa) could increase the concentration of glyco-dyn[3]arenes and glyco-dyn[4]arenes. A key aspect of this strategy is that multiplexing can be readily achieved by using two building blocks (galactosylated and fucosylated 1,4-dithiophenols) to interrogate several lectins at once in a single experiment. These macrocyclic glycoclusters could be synthesized, isolated, then evaluated as ligands of the lectins and displayed nanomolar dissociation constants. Furthermore, while no toxicity could be detected against human cells or bacteria, their evaluation as anti-adhesive agents could be confirmed through a virulence assay on human A549 lung epithelial cells.

This study investigated the sanitary quality of digestates resulting from the mesophilic anaerobic digestion (AD) of urban and agricultural organic wastes (OWs). 40 sanitary indicators, including pathogenic bacteria, antimicrobial resistance genes, virulence factor genes, and mobile genetic elements were evaluated using real-time PCR and/or droplet digital PCR. 13 polycyclic aromatic hydrocarbons (PAHs) and 13 pharmaceutical products (PHPs) were also measured. We assessed agricultural OWs from three treatment plants to study the effect of different AD processes (feeding mode, number of stages, pH), and used three laboratory-scale reactors to study the effect of different feed-supplies (inputs). The lab-scale reactors included: Lab1 fed with 97% activated sludge (urban waste) and 3% cow manure; Lab2 fed with 85% sludge-manure mixture supplemented with 15% wheat straw (WS); and Lab3 fed with 81% sludge-manure mixture, 15% WS, and 4% zeolite powder. Activated sludge favored the survival of the food-borne pathogens Clostridium perfringens and Bacillus cereus, carrying the toxin-encoding genes cpe and ces, respectively. Globally, the reactors fed with fecal matter supplemented with straw (Lab2) or with straw and zeolite (Lab3) had a higher hygienization efficiency than the reactor fed uniquely with fecal matter (Lab1). Three pathogenic bacteria (Enterococcus faecalis, Enterococcus faecium, and Mycobacterium tuberculosis complex), a beta-lactam resistance gene (blaTEM), and three mobile genetic elements (intI1, intI2, and IS26) were significantly decreased in Lab2 and Lab3. Moreover, the concentrations of 11 PAHs and 11 PHPs were significantly lower in Lab2 and Lab3 samples than in Lab1 samples. The high concentrations of micropollutants, such as triclosan, found in Lab1, could explain the lower hygienization efficiency of this reactor. Furthermore, the batch-fed reactor had a more efficient hygienization effect than the semi-continuous reactors, with complete removal of the ybtA gene, which is involved in the production of the siderophore yersiniabactin, and significant reduction of intI2 and tetO. These data suggest that it is essential to control the level of chemical pollutants in raw OWs to optimize the sanitary quality of digestates, and that adding co-substrate, such as WS, may overcome the harmful effect of pollutants.

Water pathways and water contamination in mixed land-use catchments are complex to understand. Runoff-generating sources can be numerous and water pathways modified by anthropogenic elements. Monitoring surveys considering geochemical and microbial parameters, are often carried out on such catchment, but are often simple in terms of studied parameters. Nonetheless, they can be helpful to identify the specific signatures of the main runoff-generating sources and estimate their contribution to total runoff at the outlet of mixed land-use catchments. Based on a monthly biogeochemical monitoring program conducted between 2017 and 2019 in the Ratier catchment (19.8 km2) near Lyon (France), a step-by-step approach was developed to: (1) identify the main runoff-generating sources using a perceptual model of the Ratier catchment, (2) identify the respective biogeochemical signatures of each source using this biogeochemical dataset and hydro-meteorological indicators and (3) estimate their contribution to the stream total runoff using an End-Member Mixing Analysis method. We identified three main runoff-generating sources outside of rainy periods: a colluvium aquifer, a fractured gneiss aquifer and a saprolite layer. The monitored geochemical datasets were found divided into three groups matching these sources. Contributions of these sources were estimated based on representative tracer concentrations. Microbial parameters showed a homogeneous agricultural and anthropogenic contamination among the catchment surface water, but also deeper into the fractured gneiss groundwater. This approach showed the potential of using simple monitoring datasets to identify runoff-generating sources and estimate their contribution to total runoff. A biogeochemical dataset was used to identify three main runoff-generating sources matching the geological diversity of a peri-urban catchment. Parameters Li, Zn and Al were chosen as representative tracers of these sources to estimate their contribution to total runoff. The Human-specific HF183 and ruminant-specific rum-2-bac bacterial markers were used as tracers of respective anthropogenic and agricultural contribution to streamwater.image

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.

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.

The origin and transport of water in peri-urban catchments is complex to model as they are affected by multiple anthropogenic modifications of water pathways (surface imperviousness, sewer overflow releases…), especially in a context of fast growing urbanization. The hydrological dynamics are also impacted by natural and agricultural land use patterns. Perceptual models aim at reproducing our understanding of a catchment behaviour and can be useful to illustrate the impact of such spatial contrast and human-induced modifications on a catchment hydrological dynamics. Conservative geochemical and microbiological tracers can be linked to the hydrological processes and water pathways to enhance this understanding and to build-up the hydrological perceptual model of a catchment. From 2017 to 2019, a monthly monitoring of geochemical and microbiological tracers was conducted at the Ratier catchment (19 km²) near Lyon (France). Surface waters were collected and analysed for major chemical parameters (cations, anions, dissolved organic carbon and conductivity), dissolved metals, stable isotopes (2H et 18O), and microbial parameters (total bacterial counts, microbial source tracking DNA datasets, species – specific DNA trackings). Using these datasets, a step-by-step statistical approach was undertaken, and used to build-up the perceptual hydrological model. The main steps were: (1) group correlated biochemical parameters to reduce redundancy in the dataset, (2) compute the main indicators illustrating the hydro-climatologic dynamics during the sampling campaigns (e.g. antecedent index precipitation, average daily flow) based on the hypothesis of a two-component catchment (groundwater and subsurface flow), and (3) perform a principal component analysis to link the biogeochemical dataset to the computed hydro-climatologic indicators and the runoff processes. Results revealed a differentiation of the datasets in two groups matching groundwaters and subsurface waters. Groundwaters showed two geochemical profiles linked to the two main geological formations of the catchment. Subsurface waters showed more variable biogeochemical patterns highly influenced by land use and soil properties. This step-by-step statistical approach led to a better understanding of the dynamics of the water pathways and these insights were then used to build-up the hydrological perceptual model of the catchment. As a next step, such a model should help in the evaluation and improvement of a distributed hydrological model.

Cities are patchworks of urban catchments divided into functional units according to their commercial, residential and industrial activities, and socio-urbanistic patterns. The hypothesis of city surface microbiomes being structured by socio-urbanistic variables leading to an emergence of synurbic taxa was tested. According to the r/K microbial ecology theory, a gradient of well-adapted synurbic K-strategists and of opportunistic -r-strategists should occur over city surfaces. K-strategists would be core components while runes would be transiently detected. To resolve these patterns, sub-catchments (n = 21) of an area of high commercial and industrial activities were investigated over three time periods covering one year. The sub-catchments land use patterns and associated human behaviors were converted into socio-urbanistic variables and groupings. Bacterial cells mobilized by runoffs per sub-catchment were recovered, and analyzed by classical approaches, microbial source tracking DNA assays and DNA meta-barcoding approaches. Relationships between these datasets, the runoff physico-chemical properties, and descriptors of the socio-urbanistic groupings were investigated. 16S rRNA meta-barcoding analyses showed evidence of the occurrence of K- and r-like strategists. Twenty-eight core genera were identified, and correlation networks revealed large bacterial modules organized around actinobacterial taxa involved in hydrocarbon degradation processes. Other bacterial networks were related to the occurrences of hygienic wastes, and involved bacteria originating 1min fecal contaminations. Several r-strategists like Sulfurospirillum were recorded and found associated to point source pollutions. The tpm-metabarcoding approach deciphered these r / K strategists at the species level among more than ten genera. Nine core K-like Pseudomomas species were identified. The P. aeruginosa human opportunistic pathogen and P. syringae phytopathogens were part of these K-strategists. Other tpm-harboring bacterial pathogens showed r-like opportunistic distribution patterns. Correlation network analyses indicated a strong incidence of hygienic wastes and hydrocarbon-pollutions on tpm-harboring bacteria. These analyses demonstrated the occurrence of core synurbic bacterial K-strategists over city surfaces.

Agricultural recycling of organic waste (OW) derived from urban, agricultural and agroindustrial sources is an essential sustainable development strategy. Yet repeated application of nutrient-laden OW in crop fields can also drastically boost contaminant levels in soil. This review focuses on the consideration of three categories of OW-borne contaminants, namely trace elements, organic contaminants and pathogens (including antibiotic resistance), in environmental assessments, chiefly involving life cycle assessment (LCA) and risk assessment (RA). The in-depth discussion also focuses on gaps between empirical knowledge and the models underlying these frameworks. Potential improvements to fill the identified gaps are proposed, including novel approaches and uses of existing approaches, while also featuring various levels of "readiness." Finally, a comprehensive theoretical framework to assess OW recycling scenarios, combining complementary approaches and models, is proposed and exemplified.

The Bellecombe pilot site – SIPIBEL – was created in 2010 in order to study the characterisation, treatability and impacts of hospital effluents in an urban wastewater treatment plant. This pilot site is composed of: i) the CHAL hospital, opened in February 2012, ii) the Bellecombe wastewater treatment plant, with two separate treatment lines allowing to fully separate the hospital wastewater and the urban wastewater, and iii) the Arve River as the receiving water body and a tributary of the Rhône River and the Geneva aquifer. The data base includes in total 48 439 values measured on 961 samples (raw and treated hospital and urban wastewater, activated sludge in aeration tanks, dried sludge after dewatering, river and groundwater, and a few additional campaigns in aerobic and anaerobic sewers) with 44 455 physico-chemistry values (including 15 pharmaceuticals and 14 related transformation products, biocides compounds, metals, organic micropollutants, etc.), 2 193 bioassay values (ecotoxicity), 1 679 microbiology values (including microorganisms and antibioresistance indicators) and 112 hydrobiology values. The ZIP file available on Zenodo contains i) a PDF file describing the complete data set and its content, and ii) ten Excel files with all SIPIBEL data. Additional information is given in this Open Access paper: https://doi.org/10.1016/j.dib.2021.107726

Even though organic waste (OW) recycling via anaerobic digestion (AD) and composting are increasingly used, little is known about the impact of OW origin (fecal matters and food and vegetable wastes) on the end products’ bacterial contents. The hypothesis of a predictable bacterial community structure in the end products according to the OW origin was tested. Nine OW treatment plants were selected to assess the genetic structure of bacterial communities found in raw OW according to their content in agricultural and urban wastes and to estimate their modifications through AD and composting. Two main bacterial community structures among raw OWs were observed and matched a differentiation according to the occurrences of urban chemical pollutants. Composting led to similar 16S rRNA gene OTU profiles whatever the OW origin. With a significant shift of about 140 genera (representing 50% of the bacteria), composting was confirmed to largely shape bacterial communities toward similar structures. The enriched taxa were found to be involved in detoxification and bioremediation activities. This process was found to be highly selective and favorable for bacterial specialists. Digestates showed that OTU profiles differentiated into two groups according to their relative content in agricultural (manure) and urban wastes (mainly activated sludge). About one third of the bacterial taxa was significantly affected by AD. In digestates of urban OW, this sorting led to an enrichment of 32 out of the 50 impacted genera, while for those produced from agricultural or mixed urban/agricultural OW (called central OW), a decay of 54 genera over 60 was observed. Bacteria from activated sludge appeared more fit for AD than those of other origins. Functional inferences showed AD enriched genera from all origins to share similar functional traits, e.g., chemoheterotrophy and fermentation, while being often taxonomically distinct. The main functional traits among the dominant genera in activated sludge supported a role in AD. Raw OW content in activated sludge was found to be a critical factor for predicting digestate bacterial contents. Composting generated highly predictable and specialized community patterns whatever the OW origin. AD and composting bacterial changes were driven by functional traits selected by physicochemical factors such as temperature and chemical pollutants.

Pseudomonas aeruginosa (P.a) is one of the most critical antibiotic resistant bacteria in the world and is the most prevalent pathogen in cystic fibrosis (CF), causing chronic lung infections that are considered one of the major causes of mortality in CF patients. Although several studies have contributed to understanding P.a within-host adaptive evolution at a genomic level, it is still difficult to establish direct relationships between the observed mutations, expression of clinically relevant phenotypes, and clinical outcomes. Here, we performed a comparative untargeted LC/HRMS-based metabolomics analysis of sequential isolates from chronically infected CF patients to obtain a functional view of P.a adaptation. Metabolic profiles were integrated with expression of bacterial phenotypes and clinical measurements following multiscale analysis methods. Our results highlighted significant associations between P.a “metabotypes”, expression of antibiotic resistance and virulence phenotypes, and frequency of clinical exacerbations, thus identifying promising biomarkers and therapeutic targets for difficult-to-treat P.a infections