Novel phages of unveil numerous potential auxiliary metabolic genes.

Relatively few phages that infect plant pathogens have been isolated and investigated. The species complex is present in various environments, including plants. It can cause major crop diseases, such as bacterial canker on apricot trees.

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.

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.

Unlocking secrets of microbial ecotoxicology: recent achievements and future challenges.

Environmental pollution is one of the main challenges faced by humanity. By their ubiquity and vast range of metabolic capabilities, microorganisms are affected by pollution with consequences on their host organisms and on the functioning of their environment. They also play key roles in the fate of pollutants through the degradation, transformation, and transfer of organic or inorganic compounds.

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.

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.

Soil Photosynthetic Microbial Communities Mediate Aggregate Stability: Influence of Cropping Systems and Herbicide Use in an Agricultural Soil.

Unlabelled: Edaphic cyanobacteria and algae have been extensively studied in dryland soils because they play key roles in the formation of biological soil crusts and the stabilization of soil surfaces. Yet, in temperate agricultural crop soils, little is understood about the functional significance of indigenous photosynthetic microbial communities for various soil processes. This study investigated how indigenous soil algae and cyanobacteria affected topsoil aggregate stability in cereal cropping systems.

Soil C and N statuses determine the effect of maize inoculation by plant growth-promoting rhizobacteria on nitrifying and denitrifying communities.

Maize inoculation by Azospirillum stimulates root growth, along with soil nitrogen (N) uptake and root carbon (C) exudation, thus increasing N use efficiency. However, inoculation effects on soil N-cycling microbial communities have been overlooked. We hypothesized that inoculation would (i) increase roots-nitrifiers competition for ammonium, and thus decrease nitrifier abundance; and (ii) increase roots-denitrifiers competition for nitrate and C supply to denitrifiers by root exudation, and thus limit or benefit denitrifiers depending on the resource (N or C) mostly limiting these microorganisms.

Agrifood systems and the microbial safety of fresh produce: Trade-offs in the wake of increased sustainability.

Fresh produce has been a growing cause of food borne outbreaks world-wide prompting the need for safer production practices. Yet fresh produce agrifood systems are diverse and under constraints for more sustainability. We analyze how measures taken to guarantee safety interact with other objectives for sustainability, in light of the diversity of fresh produce agrifood systems.

Pollution-induced community tolerance (PICT) as a tool for monitoring Lake Geneva long-term in situ ecotoxic restoration from herbicide contamination.

Chemical monitoring revealed a regular decrease in herbicide concentration in Lake Geneva since last decades that may be linked to an ecotoxic restoration of nontarget phytoplanktonic communities. The Pollution-induced community tolerance (PICT) approach was tested as a tool to monitor the ecotoxic restoration of Lake Geneva for herbicides from 1999 to 2011. We conducted monthly assessments in 1999 and in 2011 for the tolerance of the phytoplankton communities to two herbicides (atrazine and copper), using PICT bioassays.

Soil microbial respiration and PICT responses to an industrial and historic lead pollution: a field study.

We performed a field investigation to study the long-term impacts of Pb soil contamination on soil microbial communities and their catabolic structure in the context of an industrial site consisting of a plot of land surrounding a secondary lead smelter. Microbial biomass, catabolic profiles, and ecotoxicological responses (PICT) were monitored on soils sampled at selected locations along 110-m transects established on the site. We confirmed the high toxicity of Pb on respirations and microbial and fungal biomasses by measuring positive correlations with distance from the wall factory and negative correlation with total Pb concentrations.

The Water Cycle, a Potential Source of the Bacterial Pathogen Bacillus cereus.

The behaviour of the sporulating soil-dwelling Bacillus cereus sensu lato (B. cereus sl) which includes foodborne pathogenic strains has been extensively studied in relation to its various animal hosts. The aim of this environmental study was to investigate the water compartments (rain and soil water, as well as groundwater) closely linked to the primary B.

Enhanced co-tolerance and co-sensitivity from long-term metal exposures of heterotrophic and autotrophic components of fluvial biofilms.

Understanding the interactive effects of multiple stressors on ecosystems has started to become a major concern. The aim of our study was therefore to evaluate the consequences of a long-term exposure to environmental concentrations of Cu, Zn and As on the pollution-induced community tolerance (PICT) of lotic biofilm communities in artificial indoor channels. Moreover, the specificity of the PICT was assessed by evaluating the positive and negative co-tolerance between these metals.

In situ spatio-temporal changes in pollution-induced community tolerance to zinc in autotrophic and heterotrophic biofilm communities.

Pollution-induced community tolerance (PICT) uses increased tolerance in populations at contaminated sites as an indicator of contaminant effects. However, given the broad structural and functional complexity that characterizes biological communities, the acquisition of PICT could vary with (i) target community, (ii) intensity of toxicant exposure, (iii) the species succession stage, and (iv) the physicochemical characteristics of the studied site. To assess the spatio-temporal changes of zinc-induced tolerance in fluvial biofilm communities, we conducted an in situ study in Osor River (North-East Catalonia, Spain), which has zinc contamination.

Impact of chronic and acute pesticide exposures on periphyton communities.

Aquatic ecosystems face variable exposure to pesticides, especially during floodings which are associated with short bursts of high contaminant concentrations that influence biological systems. A study was undertaken to highlight the impact of the herbicide diuron applied in mixture with the fungicide tebuconazole on natural periphyton during flooding events. Periphyton were grown in two series of two lotic outdoor mesocosms: one series was non-contaminated while the other was exposed to chronic contamination.

Use of the MicroResp™ method to assess pollution-induced community tolerance to metals for lotic biofilms.

Understanding the ecological status of aquatic ecosystems and the impact of anthropogenic contamination requires correlating exposure to toxicants with impact on biological communities. Several tools exist for assessing the ecotoxicity of substances, but there is still a need for new tools that are ecologically relevant and easy to use. We have developed a protocol based on the substrate-induced respiration of a river biofilm community, using the MicroResp™ technique, in a pollution-induced community tolerance approach.

In situ assessment of periphyton recovery in a river contaminated by pesticides.

Recovery of bacterial and eukaryotic communities in biofilms naturally grown on stones was studied for 9 weeks after transferring them from a pesticide polluted downstream site of the river Morcille (Beaujolais, France) to a non-contaminated upstream site. Site-specific periphyton present on stones at both the down- and the upstream sampling site were collected to analyze the site-specific colonization. Throughout the experiment, structural and functional parameters were analyzed for the periphyton transferred and for the site-specific up- and downstream periphyton.

Transplantation of microbenthic algal assemblages to assess structural and functional recovery after diuron exposure.

The potential of microbenthic algal assemblages to recover after diuron exposure was investigated. Microbenthic algal assemblages (periphyton) were grown on glass slides in correspondence to a diuron-polluted and adiuron-free sampling site of a river. After 5 weeks of colonization, the impacted periphyton was transferred by translocating the colonized glass slides to the unpolluted site.

PO43- dependence of the tolerance of autotrophic and heterotrophic biofilm communities to copper and diuron.

Pollution-induced community tolerance (PICT) concept is based on the assumption that the toxicant exerts selection pressure on the biological communities when exposure reaches a critical level for a sufficient period of time and therefore sensitive species are eliminated. However, induced tolerance of microbial biofilm communities cannot be attributed solely to the presence of toxicants in rivers but also to various environmental factors, such as amount of nutrients. An experimental study was undertaken to highlight the potential impact of a phosphorus gradient on the sensitivity of periphytic microbial community to Cu and diuron.

Responses of chronically contaminated biofilms to short pulses of diuron. An experimental study simulating flooding events in a small river.

An experimental study was undertaken to highlight the potential ecotoxicological impact of the herbicide diuron on biofilms during flooding events in a small river (Morcille) in the Beaujolais vineyard area (France). We investigated the responses of chronically contaminated biofilms exposed to short-term pulses (3 h) of diuron. Biofilms were grown in indoor microcosms that were either non-contaminated or exposed to low-level chronic contamination, and not exposed, or exposed to single or double pulses of two environmental concentrations (7 and 14 microg L(-1)) of diuron.

Assessment of the effects of imidacloprid on the behavior of two earthworm species (Aporrectodea nocturna and Allolobophora icterica) using 2D terraria.

Earthworms are "ecosystem engineers" and changes in their main activities (creation of burrows and burial of organic matter) due to pollutants can have important effects on soil functions and indirectly on other components of the soil ecosystem. Using 2D terraria, we studied the behavior of two earthworm species (the endogeic Allolobophora icterica and the anecic Aporrectodea nocturna) exposed to sublethal concentrations (0.5 and 1 mg kg(-1) of dry soil) of imidacloprid, a widely used neonicotinoid insecticide.

Seasonal changes in the sensitivity of river microalgae to atrazine and isoproturon along a contamination gradient.

A study was undertaken to investigate the environmental impact of herbicides on natural communities of freshwater periphyton and phytoplankton in the river Ozanne and in related nearby water reservoirs, including both pristine and pesticide- (atrazine and isoproturon) contaminated stations. The microalgal toxicity of both herbicides was investigated by short-term studies, using the in vivo fluorescence pattern to perform dose-effect experiments. The taxonomic composition of the communities sampled was assessed by microscopy and by HPLC pigment analysis.

A risk assessment of pollution: induction of atrazine tolerance in phytoplankton communities in freshwater outdoor mesocosms, using chlorophyll fluorescence as an endpoint.

We investigated the validity and sensitivity of assessments of the induction of atrazine tolerance in freshwater outdoor mesocosmic phytoplankton communities, using the in vivo fluorescence of chlorophyll a as an endpoint, for monitoring ecotoxicology and for risk assessment programs applied to phytoplankton contaminated by photosystem II herbicides. Atrazine inhibits the photosynthetic process, and so the rise in in-vivo fluorescence could be used as a physiological manifestation of acute toxicity. Short-term tests (1 h) were used, in which increasing concentrations of the herbicide were applied to phytoplankton samples taken every two days from the mesocosms, and used to plot dose-response curves.

Toxic effects of Irgarol 1051 on phytoplankton and macrophytes in Lake Geneva.

Irgarol 1051 is a recent herbicidal compound, inhibitor of photosynthesis, used in antifouling paints. This toxic is persistent in aquatic environments, with low abiotic and biotic degradation, highly phytotoxic, and has already been detected in estuaries and coastal areas, with suspected negative impacts on non-target organisms (aquatic plants and algae). We measured the toxicity of Irgarol 1051 to macrophytes and phytoplankton from Lake Geneva (between Switzerland and France) by determining chlorophyll fluorescence yield, and phytoplankton primary production.