Experimental Evidence for Manure-Borne Bacteria Invasion in Soil During a Coalescent Event: Influence of the Antibiotic Sulfamethazine.

The fertilization of agricultural soil by organic amendment that may contain antibiotics, like manure, can transfer bacterial pathogens and antibiotic-resistant bacteria to soil communities. However, the invasion by manure-borne bacteria in amended soil remains poorly understood. We hypothesized that this kind of process is both influenced by the soil properties (and those of its microbial communities) and by the presence of contaminants such as antibiotics used in veterinary care. To test that, we performed a microcosm experiment in which four different soils were amended or not with manure at an agronomical dose and exposed or not to the antibiotic sulfamethazine (SMZ). After 1 month of incubation, the diversity, structure, and composition of bacterial communities of the soils were assessed by 16S rDNA sequencing. The invasion of manure-borne bacteria was still perceptible 1 month after the soil amendment. The results obtained with the soil already amended in situ with manure 6 months prior to the experiment suggest that some of the bacterial invaders were established in the community over the long term. Even if differences were observed between soils, the invasion was mainly attributable to some of the most abundant OTUs of manure (mainly Firmicutes). SMZ exposure had a limited influence on soil microorganisms but our results suggest that this kind of contaminant can enhance the invasion ability of some manure-borne invaders.

Role of Biofilms in Contaminant Bioaccumulation and Trophic Transfer in Aquatic Ecosystems: Current State of Knowledge and Future Challenges.

In freshwater environments, microbial assemblages attached to submerged substrates play an essential role in ecosystem processes such as primary production, supported by periphyton, or organic matter decomposition, supported by microbial communities attached to leaf litter or sediments. These microbial assemblages, also called biofilms, are not only involved in nutrients fluxes but also in contaminants dynamics. Biofilms can accumulate metals and organic contaminants transported by the water flow and/or adsorbed onto substrates. Furthermore, due to their high metabolic activity and their role in aquatic food webs, microbial biofilms are also likely to influence contaminant fate in aquatic ecosystems. In this review, we provide (1) a critical overview of the analytical methods currently in use for detecting and quantifying metals and organic micropollutants in microbial biofilms attached to benthic substrata (rocks, sediments, leaf litter); (2) a review of the distribution of those contaminants within aquatic biofilms and the role of these benthic microbial communities in contaminant fate; (3) a set of future challenges concerning the role of biofilms in contaminant accumulation and trophic transfers in the aquatic food web. This literature review highlighted that most knowledge on the interaction between biofilm and contaminants is focused on contaminants dynamics in periphyton while technical limitations are still preventing a thorough estimation of contaminants accumulation in biofilms attached to leaf litter or sediments. In addition, microbial biofilms represent an important food resource in freshwater ecosystems, yet their role in dietary contaminant exposure has been neglected for a long time, and the importance of biofilms in trophic transfer of contaminants is still understudied.

Interfacial photochemistry of biogenic surfactants: a major source of abiotic volatile organic compounds.

Films of biogenic compounds exposed to the atmosphere are ubiquitously found on the surfaces of cloud droplets, aerosol particles, buildings, plants, soils and the ocean. These air/water interfaces host countless amphiphilic compounds concentrated there with respect to in bulk water, leading to a unique chemical environment. Here, photochemical processes at the air/water interface of biofilm-containing solutions were studied, demonstrating abiotic VOC production from authentic biogenic surfactants under ambient conditions. Using a combination of online-APCI-HRMS and PTR-ToF-MS, unsaturated and functionalized VOCs were identified and quantified, giving emission fluxes comparable to previous field and laboratory observations. Interestingly, VOC fluxes increased with the decay of microbial cells in the samples, indicating that cell lysis due to cell death was the main source for surfactants and VOC production. In particular, irradiation of samples containing solely biofilm cells without matrix components exhibited the strongest VOC production upon irradiation. In agreement with previous studies, LC-MS measurements of the liquid phase suggested the presence of fatty acids and known photosensitizers, possibly inducing the observed VOC production via peroxy radical chemistry. Up to now, such VOC emissions were directly accounted to high biological activity in surface waters. However, the results obtained suggest that abiotic photochemistry can lead to similar emissions into the atmosphere, especially in less biologically-active regions. Furthermore, chamber experiments suggest that oxidation (O3/OH radicals) of the photochemically-produced VOCs leads to aerosol formation and growth, possibly affecting atmospheric chemistry and climate-related processes, such as cloud formation or the Earth's radiation budget.

The use of copper as plant protection product contributes to environmental contamination and resulting impacts on terrestrial and aquatic biodiversity and ecosystem functions.

Copper-based plant protection products (PPPs) are widely used in both conventional and organic farming, and to a lesser extent for non-agricultural maintenance of gardens, greenspaces, and infrastructures. The use of copper PPPs adds to environmental contamination by this trace element. This paper aims to review the contribution of these PPPs to the contamination of soils and waters by copper in the context of France (which can be extrapolated to most of the European countries), and the resulting impacts on terrestrial and aquatic biodiversity, as well as on ecosystem functions. It was produced in the framework of a collective scientific assessment on the impacts of PPPs on biodiversity and ecosystem services in France. Current science shows that copper, which persists in soils, can partially transfer to adjacent aquatic environments (surface water and sediment) and ultimately to the marine environment. This widespread contamination impacts biodiversity and ecosystem functions, chiefly through its effects on phototrophic and heterotrophic microbial communities, and terrestrial and aquatic invertebrates. Its effects on other biological groups and biotic interactions remain relatively under-documented.

Response of a diuron-degrading community to diuron exposure assessed by real-time quantitative PCR monitoring of phenylurea hydrolase A and B encoding genes.

A real-time quantitative PCR method was developed to detect and quantify phenlylurea hydrolase genes' (puhA and puhB) sequences from environmental DNA samples to assess diuron-degrading genetic potential in some soil and sediment microbial communities. In the soil communities, mineralization rates (determined with [ring-¹4C]-labeled diuron) were linked to diuron-degrading genetic potentials estimated from puhB number copies, which increased following repeated diuron treatments. In the sediment communities, mineralization potential did not depend solely on the quantity of puhB copies, underlining the need to assess gene expression. In the sediment samples, both puhB copy numbers and mineralization capacities were highly conditioned by whether or not diuron-treated soil was added. This points to transfers of degradative potential from soils to sediments. No puhA gene was detected in soil and sediment DNA extracts. Moreover, some sediments exhibited high diuron mineralization potential even though puhB genes were not detected, suggesting the existence of alternative diuron degradation pathways.

The effect of temperature and a herbicide mixture on freshwater periphytic algae.

Temperature is a strong driver of biofilm formation and of the dynamics of microalgae in freshwater. Moreover, exposure to herbicides is a well-known stressor of periphytic communities in anthropized aquatic environments. We tested these two environmental factors on periphytic communities that had been sampled from the littoral zone of Lake Geneva and acclimatized in the lab for 3 weeks at 18, 21, 24 and 28 °C. After this acclimation period, differences in the composition of the diatom community and decreases in cell density were observed corresponding to the temperature gradient. These acclimated communities were then exposed to 23 and 140 nM of a mixture composed of equitoxic quantities of atrazine, terbutryn, diuron and isoproturon. The periphytic community was more sensitive to the herbicide mixture at 18 °C than at higher temperatures, suggesting that higher temperature reduced its toxicity. Small and pioneer diatom species known to be promoted by contamination also appeared to benefit from higher temperatures. Temperature therefore appears to condition the herbicide sensitivity of periphytic communities.

Recommendations to reduce the streetlight effect and gray areas limiting the knowledge of the effects of plant protection products on biodiversity.

Preserving biodiversity against the adverse effects of plant protection products (PPPs) is a major environmental and societal issue. However, despite intensive investigation into the ecotoxicological effects of PPPs, the knowledge produced remains fragmented given the sheer diversity of PPPs. This is due, at least in part, to a strong streetlight effect in the field of ecotoxicology. Indeed, while some PPPs have been investigated in numerous ecotoxicological studies, there are many for which the scientific literature still has little or no information on their ecotoxicological risks and effects. The PPPs under the streetlight include a large variety of legacy substances and a more limited number of more recent or currently-in-use substances, such as the herbicide glyphosate and the neonicotinoid insecticides. Furthermore, many of the most recent PPPs (including those used in biocontrol) and PPP transformation products (TPs) resulting from abiotic and/or biotic degradation are rarely addressed in the international literature in the field of ecotoxicology. Here, based on a recent collective scientific assessment of the effects of PPPs on biodiversity and ecosystem services in the French and European contexts, this article sets out to illustrate the limitations and biases caused by the streetlight effect and numbers of gray areas, and issue recommendations on how to overcome them.

Improved assessment of the impacts of plant protection products on certain soil ecosystem services requires better consideration of terrestrial microalgae and cyanobacteria.

There is growing scientific and societal consciousness that the environmental risks and impacts of plant protection products (PPPs) cannot be properly assessed without considering ecosystem services. However, the science on this issue remains incomplete and fragmented, as recently illustrated in a collective scientific assessment that pointed out the limited knowledge on the risks and impacts of PPPs on soil ecosystem services, which are clearly overlooked. Beside soil ecosystem services, certain key players involved in these services are largely overlooked in the scientific literature on the risks and impacts of PPPs, namely soil microbial photosynthetic communities. Here, we followed the principles of evidence-based logic chain approaches to show the importance of considering these microorganisms when studying the impacts of PPPs on certain services provided by soil ecosystems, with a focus on regulating and maintenance services that play a role in the regulation of baseline flows and extreme events. Terrestrial microalgae and cyanobacteria are ubiquitous photosynthetic microorganisms that, together with other soil micro- and macro-organisms, play key roles in the ecosystem functions that underpin these ecosystem services. There is an extensive literature on the ecotoxicological effects of PPPs on different organisms including soil microorganisms, but studies concerning soil microbial photosynthetic communities are very scarce. However, there is scientific evidence that herbicides can have both direct and indirect impacts on these microbial photosynthetic communities. Given that they play key functional roles, we argue that soil microbial photosynthetic communities warrant greater attention in efforts to assess the environmental risks and impacts of PPPs and, ultimately, help preserve or restore the regulating and maintenance services provided by soil ecosystems.

Linking ecotoxicological effects on biodiversity and ecosystem functions to impairment of ecosystem services is a challenge: an illustration with the case of plant protection products.

There is growing interest in using the ecosystem services framework for environmental risk assessments of chemicals, including plant protection products (PPPs). Although this topic is increasingly discussed in the recent scientific literature, there is still a substantial gap between most ecotoxicological studies and a solid evaluation of potential ecotoxicological consequences on ecosystem services. This was recently highlighted by a collective scientific assessment (CSA) performed by 46 scientific experts who analyzed the international science on the impacts of PPPs on biodiversity, ecosystem functions, and ecosystem services. Here, we first point out the main obstacles to better linking knowledge on the ecotoxicological effects of PPPs on biodiversity and ecological processes with ecosystem functions and services. Then, we go on to propose and discuss possible pathways for related improvements. We describe the main processes governing the relationships between biodiversity, ecological processes, and ecosystem functions in response to effects of PPP, and we define categories of ecosystem functions that could be directly linked with the ecological processes used as functional endpoints in investigations on the ecotoxicology of PPPs. We then explore perceptions on the possible links between these categories of ecosystem functions and ecosystem services among a sub-panel of the scientific experts from various fields of environmental science. We find that these direct and indirect linkages still need clarification. This paper, which reflects the difficulties faced by the multidisciplinary group of researchers involved in the CSA, suggests that the current gap between most ecotoxicological studies and a solid potential evaluation of ecotoxicological consequences on ecosystem services could be partially addressed if concepts and definitions related to ecological processes, ecosystem functions, and ecosystem services were more widely accepted and shared within the ecotoxicology community. Narrowing this gap would help harmonize and extend the science that informs decision-making and policy-making, and ultimately help to better address the trade-off between social benefits and environmental losses caused by the use of PPPs.

Impacts of neonicotinoids on biodiversity: a critical review.

Neonicotinoids are the most widely used class of insecticides in the world, but they have raised numerous concerns regarding their effects on biodiversity. Thus, the objective of this work was to do a critical review of the contamination of the environment (soil, water, air, biota) by neonicotinoids (acetamiprid, clothianidin, imidacloprid, thiacloprid, thiamethoxam) and of their impacts on terrestrial and aquatic biodiversity. Neonicotinoids are very frequently detected in soils and in freshwater, and they are also found in the air. They have only been recently monitored in coastal and marine environments, but some studies already reported the presence of imidacloprid and thiamethoxam in transitional or semi-enclosed ecosystems (lagoons, bays, and estuaries). The contamination of the environment leads to the exposure and to the contamination of non-target organisms and to negative effects on biodiversity. Direct impacts of neonicotinoids are mainly reported on terrestrial invertebrates (e.g., pollinators, natural enemies, earthworms) and vertebrates (e.g., birds) and on aquatic invertebrates (e.g., arthropods). Impacts on aquatic vertebrate populations and communities, as well as on microorganisms, are less documented. In addition to their toxicity to directly exposed organisms, neonicotinoid induce indirect effects via trophic cascades as demonstrated in several species (terrestrial and aquatic invertebrates). However, more data are needed to reach firmer conclusions and to get a clearer picture of such indirect effects. Finally, we identified specific knowledge gaps that need to be filled to better understand the effects of neonicotinoids on terrestrial, freshwater, and marine organisms, as well as on ecosystem services associated with these biotas.

Main conclusions and perspectives from the collective scientific assessment of the effects of plant protection products on biodiversity and ecosystem services along the land-sea continuum in France and French overseas territories.

Preservation of biodiversity and ecosystem services is critical for sustainable development and human well-being. However, an unprecedented erosion of biodiversity is observed and the use of plant protection products (PPP) has been identified as one of its main causes. In this context, at the request of the French Ministries responsible for the Environment, for Agriculture and for Research, a panel of 46 scientific experts ran a nearly 2-year-long (2020-2022) collective scientific assessment (CSA) of international scientific knowledge relating to the impacts of PPP on biodiversity and ecosystem services. The scope of this CSA covered the terrestrial, atmospheric, freshwater, and marine environments (with the exception of groundwater) in their continuity from the site of PPP application to the ocean, in France and French overseas territories, based on international knowledge produced on or transposable to this type of context (climate, PPP used, biodiversity present, etc.). Here, we provide a brief summary of the CSA's main conclusions, which were drawn from about 4500 international publications. Our analysis finds that PPP contaminate all environmental matrices, including biota, and cause direct and indirect ecotoxicological effects that unequivocally contribute to the decline of certain biological groups and alter certain ecosystem functions and services. Levers for action to limit PPP-driven pollution and effects on environmental compartments include local measures from plot to landscape scales and regulatory improvements. However, there are still significant gaps in knowledge regarding environmental contamination by PPPs and its effect on biodiversity and ecosystem functions and services. Perspectives and research needs are proposed to address these gaps.

Use of polar organic chemical integrative samplers to assess the effects of chronic pesticide exposure on biofilms.

The responses of aquatic organisms to chronic exposure to environmental concentrations of toxicants, often found in mixtures, are poorly documented. Here passive sampler extracts were used in experimental contamination of laboratory channels, to investigate their effects on natural biofilm communities. A realistic mixture of pesticides extracted from Polar Organic Chemical Integrative Samplers was used to expose biofilms in laboratory channels to total pesticide concentrations averaging 0.5 ± 0.1 µg l⁻¹. The level of exposure was representative of field conditions in terms of relative proportions of the substances but the exposure concentration was not maintained (decreasing concentrations between contamination occasions). The impact on the structural as well as the functional characteristics of the autotrophic and heterotrophic components was determined, using biofilm grown in uncontaminated conditions (reference site) and in sites exposed to pesticides (contaminated site). The exposure imposed did not significantly modify the structure or functions of reference biofilms, nor did it modify tolerance as measured by mixture EC50 (EC50 mix). In contrast, the communities from the more contaminated downstream section lost tolerance following decreased dose exposure, but community composition remained fairly stable. Overall, these results indicate that low levels of contamination did not lead to strong changes in community structure, and 14-day changes in tolerance seemed to depend mainly on physiological adaptation, suggesting that other environmental factors or longer-lasting processes prevailed. This study reports the first attempt to use passive sampler extracts as a realistic composite contaminant for experimental exposure of biofilms, with promising perspectives in further ecotoxicology studies.

Effects of organic herbicides on phototrophic microbial communities in freshwater ecosystems.

Over the past 15 years, significant research efforts have been channeled into assessing the effects of organic herbicides on freshwater phototrophic microbial communities. The results of this research are reviewed herein. The main conclusions we have reached after performing this review can be summarized into five points: · Most relevant assessments have dealt with the effects of triazine and phenylurea herbicides. Herbicides from these chemical classes are often considered to be model compounds when photosystem-II inhibitors are studied. · Until the early 2000s, the vast majority of investigations conducted to evaluate herbicide effects on phototropic microbes were performed in microcosms or mesocosms. In such studies, herbicides were usually applied alone, and often at concentrations much higher than those detected in the environment. More recently, the trend has been toward more realistic and relevant studies, in which lower herbicide concentrations were considered, and compound mixtures or successive treatments were tested. Increasingly, in situ studies are being designed to directly evaluate microbial community responses, following chemical exposures in contaminated aquatic environments. · Several biological end points are used to evaluate how organisms in the phototrophic microbial community respond to herbicide exposure. These end points allow the detection of quantitative changes, such as chl a concentrations, total cell counts or periphytic biomass, qualitative changes such as community structure to algal diversity, or functional changes such as photosynthesis and respiration, among others. They may give different and complementary information concerning the responses of microbial communities. · PICT approaches, which have generally combined functional and structural measurements, may prove to be valuable for assessing both an immediate impact, and for factoring in the contamination history of an ecosystem at the community level. · Finally, any relevant assessment of pesticide effects should incorporate a detailed environmental characterization that would include abiotic parameters (light, flow speed, nutrient content), or biotic parameters (diversity and structure of biofilms), because these control the bioavailability of pesticides, and thereby the exposure of microbial communities. To improve the value of ecotoxicological risk assessments, future research is needed in two key areas: first, more information on the effects of pollutants at the community level must be obtained (new tools and new end points), and second, more effort must be directed to reinforce the ecological relevance of toxicological investigations.

A pilot experiment to assess the efficiency of pharmaceutical plant wastewater treatment and the decreasing effluent toxicity to periphytic biofilms.

Pharmaceutical industry effluents are complex and highly variable in time. Assessing the efficiency of a pharmaceutical industry wastewater treatment plant (WWTP) and the resulting decrease in effluent toxicity and ecological risk is thus not straightforward. We set up an original in situ pilot directly connected to a pharmaceutical WWTP to monitor the chronic toxicity of successive effluents using natural periphytic biofilms. Their structural and functional responses to effluent exposure were assessed by combining (i) a molecular approach to characterize the bacterial and diatom diversity and (ii) functional measurements of photosynthetic and enzyme activities. Effluent contamination by pharmaceuticals strongly decreased after the quaternary treatment (activated carbon). Most of the structural biological characteristics improved with cumulative WWTP treatment (bacterial diversity, microbial genetic structure, and biological diatom index), showing community recovery along the treatment process. However, functional parameters did not show clear links with treatment steps, suggesting that microbial activities were not solely driven by pharmaceuticals produced during the experimental period. Operationally, this type of pilot system offers a useful tool for biomonitoring approaches and offers new approaches for industrial managers to assess the ecological risk of production effluents in receiving water.

Contrasting Effects of Environmental Concentrations of Sulfonamides on Microbial Heterotrophic Activities in Freshwater Sediments.

The sulfonamide antibiotics sulfamethoxazole (SMX) and sulfamethazine (SMZ) are regularly detected in surface sediments of contaminated hydrosystems, with maximum concentrations that can reach tens of µg kg-1 in stream and river sediments. Little is known about the resulting effects on the exposed benthic organisms. Here we investigated the functional response of stream sediment microbial communities exposed for 4 weeks to two levels of environmentally relevant concentrations of SMX and SMZ, tested individually. To this end, we developed a laboratory channel experiment where natural stream sediments were immersed in water contaminated with nominal environmental concentrations of 500 and 5,000 ng L-1 of SMX or SMZ, causing their accumulation in surface sediments. The mean maximum concentrations measured in the sediment (about 2.1 µg SMX kg-1 dw and 4.5 µg SMZ kg-1 dw) were consistent with those reported in contaminated rivers. The resulting chronic exposure had various effects on the functional potential of the sediment microbial communities, according to the substance (SMX or SMZ), the type of treatment (high or low) and the measured activity, with a strong influence of temporal dynamics. Whereas the SMZ treatments resulted in only transient effects on the five microbial activities investigated, we observed a significant stimulation of the ß-glucosidase activity over the 28 days in the communities exposed to the high concentration of SMX. Together with the stimulation of aerobic respiration at low SMX concentrations and the reduced concentration observed in the last days, our results suggest a potential biodegradation of sulfonamides by microbial communities from sediments. Given the key functional role of surface sediment microbial communities in streams and rivers, our findings suggest that the frequently reported contamination of sediments by sulfonamides is likely to affect biogeochemical cycles, with possible impact on ecosystem functioning.

Diversity, Functions and Antibiotic Resistance of Sediment Microbial Communities From Lake Geneva Are Driven by the Spatial Distribution of Anthropogenic Contamination.

Lake sediments are natural receptors for a wide range of anthropogenic contaminants including organic matter and toxicants such as trace metals, polycyclic aromatic hydrocarbons, polychlorinated biphenyls that accumulate over time. This contamination can impact benthic communities, including microorganisms which play a crucial role in biogeochemical cycling and food-webs. The present survey aimed at exploring whether anthropogenic contamination, at a large lake scale, can influence the diversity, structure and functions of microbial communities associated to surface sediment, as well as their genetic potential for resistance to metals and antibiotics. Changes in the characteristics of these communities were assessed in surface sediments collected in Lake Geneva from eight sampling sites in October 2017 and May 2018. These sampling sites were characterized by a large concentration range of metal and organic compound contamination. Variation between the two sampling periods were very limited for all sampling sites and measured microbial parameters. In contrast, spatial variations were observed, with two sites being distinct from each other, and from the other six sites. Benthic communities from the most contaminated sampling site (Vidy Bay, near the city of Lausanne) were characterized by the lowest bacterial and archaeal diversity, a distinct community composition, the highest abundance of antibiotic resistance genes and functional (respiration, denitrification, methanogenesis, phosphatase, and beta-glucosidase) activity levels. The second sampling site which is highly influenced by inputs from the Rhône River, exhibited low levels of diversity, a distinct community composition, high abundance of antibiotic resistance genes and the highest bacterial abundance. Overall, our results suggest that local anthropogenic contamination, including organic matter and toxicants, is a major driver of the diversity and functioning of sediment-microbial communities in Lake Geneva. This highlights the need to consider benthic microbial communities and a suite of complementary ecotoxicological endpoints for more effective environmental risk assessments of contaminants in lake sediments.

Collective scientific assessment as a relevant tool to inform public debate and policymaking: an illustration about the effects of plant protection products on biodiversity and ecosystem services.

Several sustainable development goals cannot be achieved without implementing a new generation of environmental measures to better preserve or restore biodiversity and ecosystem services. However, understanding and addressing biodiversity loss and ecosystem degradation is a challenging problem that is not solvable without integrating the best and latest science. It is crucial to enhance the legibility of this knowledge for decision-makers and policymakers following good-practice standards of scientific assessment. This is the main objective of collective scientific assessments (CSAs), as carried out by the French National Research Institute for Agriculture, Food and the Environment (INRAE) since the early 2000s following a documented procedure to inform public policy and foster public debate on complex interdisciplinary issues. This article describes the main steps of the CSA procedure designed by INRAE's Directorate for Collective Scientific Assessment, Foresight and Advanced Studies, from formulation of the initial question asked by public or para-public bodies (typically ministry divisions or environmental agencies) to wider dissemination of the results and conclusions. This process description is then illustrated through the example of a CSA recently commissioned by three French Ministries (for Ecology, for Research, and for Agriculture) regarding (i) contamination of terrestrial, freshwater, and marine ecosystems by plant protection products (PPPs); (ii) the resulting effects on biodiversity and ecosystem services; and (iii) possible prevention and mitigation strategies. The capacity of this kind of CSA to inform public debate and policymaking is then exemplified through a description of the main outcomes generated by the latest CSA dealing with the adverse effects of PPPs. We also provide a short overview of some key expectations from the current CSA, with a focus on the recent development of the ecosystem service approach in ecological risk assessments of PPPs in the European Union. This illustration demonstrates that CSAs, which are applicable to a wide variety of complex interdisciplinary questions that are not limited to environmental issues, are a relevant tool to inform public debate and policymaking.

Antibiotrophy: Key Function for Antibiotic-Resistant Bacteria to Colonize Soils-Case of Sulfamethazine-Degrading Microbacterium sp. C448.

Chronic and repeated exposure of environmental bacterial communities to anthropogenic antibiotics have recently driven some antibiotic-resistant bacteria to acquire catabolic functions, enabling them to use antibiotics as nutritive sources (antibiotrophy). Antibiotrophy might confer a selective advantage facilitating the implantation and dispersion of antibiotrophs in contaminated environments. A microcosm experiment was conducted to test this hypothesis in an agroecosystem context. The sulfonamide-degrading and resistant bacterium Microbacterium sp. C448 was inoculated in four different soil types with and without added sulfamethazine and/or swine manure. After 1 month of incubation, Microbacterium sp. (and its antibiotrophic gene sadA) was detected only in the sulfamethazine-treated soils, suggesting a low competitiveness of the strain without antibiotic selection pressure. In the absence of manure and despite the presence of Microbacterium sp. C448, only one of the four sulfamethazine-treated soils exhibited mineralization capacities, which were low (inferior to 5.5 ± 0.3%). By contrast, manure addition significantly enhanced sulfamethazine mineralization in all the soil types (at least double, comprised between 5.6 ± 0.7% and 19.5 ± 1.2%). These results, which confirm that the presence of functional genes does not necessarily ensure functionality, suggest that sulfamethazine does not necessarily confer a selective advantage on the degrading strain as a nutritional source. 16S rDNA sequencing analyses strongly suggest that sulfamethazine released trophic niches by biocidal action. Accordingly, manure-originating bacteria and/or Microbacterium sp. C448 could gain access to low-competition or competition-free ecological niches. However, simultaneous inputs of manure and of the strain could induce competition detrimental for Microbacterium sp. C448, forcing it to use sulfamethazine as a nutritional source. Altogether, these results suggest that the antibiotrophic strain studied can modulate its sulfamethazine-degrading function depending on microbial competition and resource accessibility, to become established in an agricultural soil. Most importantly, this work highlights an increased dispersal potential of antibiotrophs in antibiotic-polluted environments, as antibiotics can not only release existing trophic niches but also form new ones.

Environmental Concentrations of Sulfonamides Can Alter Bacterial Structure and Induce Diatom Deformities in Freshwater Biofilm Communities.

Since the early 1920s, the intensive use of antibiotics has led to the contamination of the aquatic environment through diffuse sources and wastewater effluents. The antibiotics commonly found in surface waters include sulfamethoxazole (SMX) and sulfamethazine (SMZ), which belong to the class of sulfonamides, the oldest antibiotic class still in use. These antibiotics have been detected in all European surface waters with median concentrations of around 50 ng L-1 and peak concentrations of up to 4-6 µg L-1. Sulfonamides are known to inhibit bacterial growth by altering microbial production of folic acid, but sub-lethal doses may trigger antimicrobial resistance, with unknown consequences for exposed microbial communities. We investigated the effects of two environmentally relevant concentrations (500 and 5,000 ng L-1) of SMZ and SMX on microbial activity and structure of periphytic biofilms in stream mesocosms for 28 days. Measurement of sulfonamides in the mesocosms revealed contamination levels of about half the nominal concentrations. Exposure to sulfonamides led to slight, transitory effects on heterotrophic functions, but persistent effects were observed on the bacterial structure. After 4 weeks of exposure, sulfonamides also altered the autotrophs in periphyton and particularly the diversity, viability and cell integrity of the diatom community. The higher concentration of SMX tested decreased both diversity (Shannon index) and evenness of the diatom community. Exposure to SMZ reduced diatom species richness and diversity. The mortality of diatoms in biofilms exposed to sulfonamides was twice that in non-exposed biofilms. SMZ also induced an increase in diatom teratologies from 1.1% in non-exposed biofilms up to 3% in biofilms exposed to SMZ. To our knowledge, this is the first report on the teratological effects of sulfonamides on diatoms within periphyton. The increase of both diatom growth rate and mortality suggests a high renewal of diatoms under sulfonamide exposure. In conclusion, our study shows that sulfonamides can alter microbial community structures and diversity at concentrations currently present in the environment, with unknown consequences for the ecosystem. The experimental set-up presented here emphasizes the interest of using natural communities to increase the ecological realism of ecotoxicological studies and to detect potential toxic effects on non-target species.

Changes in sediment microbial diversity following chronic copper-exposure induce community copper-tolerance without increasing sensitivity to arsenic.

Sediment microbial communities were exposed for 21 days to an environmental concentration of copper to assess Cu-induced composition changes and resulting effects on microbial sensitivity to acute Cu and As toxicity. Chronic Cu exposure reduced the diversity of the bacterial and archaeal communities from Day 0 to Day 21. The pollution-induced community tolerance concept (PICT) predicts that loss of the most sensitive taxa and gain of more tolerant ones should increase the capacity of Cu-exposed communities to tolerate acute Cu toxicity. Although diversity loss and functional costs of adaptation could have increased their sensitivity to subsequent toxic stress, no increased sensitivity to As was observed. PICT responses varied according to heterotrophic activity, selected as the functional endpoint for toxicity testing, with different results for Cu and As. This suggests that induced tolerance to Cu and As was supported by different species with different metabolic capacities. Ecological risk assessment of contaminants would gain accuracy from further research on the relative contribution of tolerance acquisition and co-tolerance processes on the functional response of microbial communities.