Dairy cattle of different ages experience different living conditions and varied frequency of antibiotic administration that likely influence the distribution of microbiome and resistome in ways that reflect different risks of microbial transmission. To assess the degree of variance in these distributions, fecal and soil samples were collected from six distinct housing areas on commercial dairy farms (n = 7) in Washington State. 16S rRNA gene sequencing indicated that the microbiota differed between different on-farm locations in feces and soil, and in both cases, the microbiota of dairy calves was often distinct from others (P < 0.05). Thirty-two specific antibiotic resistance genes (ARGs) were widely distributed on dairies, of which several clinically relevant ARGs (including cfr, cfrB, and optrA) were identified for the first time at U.S. dairies. Overall, ARGs were observed more frequently in feces and soil from dairy calves and heifers than from hospital, fresh, lactation and dry pens. Droplet-digital PCR demonstrated that the absolute abundance of floR varied greatly across housing areas and this gene was enriched the most in calves and heifers. Furthermore, in an extended analysis with 14 dairies, environmental soils in calf pens had the most antibiotic-resistant Escherichia coli followed by heifer and hospital pens. All soil E. coli isolates (n = 1,905) are resistant to at least 4 different antibiotics, and the PFGE analysis indicated that florfenicol-resistant E. coli is probably shared across geographically-separated farms. This study identified a discrete but predictable distribution of antibiotic resistance genes and organisms, which is important for designing mitigation for higher risk areas on dairy farms.

While wastewater treatment plants have been identified as the most prominent source of emerging micropollutants in surface waters, prediction of their ambient concentrations remains a challenge. This is due to the variability of loads entering individual treatment plants and of the elimination capacity by the latter as well as potential attenuation in the river network. Although geospatially detailed models exist, they suffer from the same data input uncertainties. Here, we investigated the concentration profiles of 20 emerging pollutants in different river stretches in Luxembourg with variable sanitary pressures. Using carbamazepine as a recalcitrant wastewater indicator, the correlation of the compounds to the latter revealed source and fate variability as well as specific emitters. Relating carbamazepine to sanitary pressure, expressed as the sum of population equivalents in a catchment divided by its surface [PE ha⁻¹] allowed predicting the impact of emerging pollutants on the entire river network. The limited variability of the pollutant profiles allowed for prioritization of impacted stretches depending on the different sanitary pressures at risk quotient exceedance. The main drivers of impact were triclosan, diclofenac, clarithromycine and diuron.

Microplastic pollution within the marine environment is of pressing concern globally. Accordingly, spatial monitoring of microplastic concentrations, composition and size distribution may help to identify sources and entry pathways, and hence allow initiating focused mitigation. Spatial distribution patterns of microplastics were investigated in two compartments of the southern North Sea by collecting sublittoral sediment and surface water samples from 24 stations. Large microplastics (500−5000 μm) were detected visually and identified using attenuated total reflection (ATR) Fourier transform infrared (FTIR) spectroscopy. The remaining sample was digested enzymatically, concentrated onto filters and analyzed for small microplastics (11−500 μm) using Focal Plane Array (FPA) FTIR imaging. Microplastics were detected in all samples with concentrations ranging between 2.8 and 1188.8 particles kg−1 for sediments and 0.1–245.4 particles m−3 for surface waters. On average 98% of microplastics were <100 μm in sediments and 86% in surface waters. The most prevalent polymer types in both compartments were polypropylene, acrylates/polyurethane/varnish, and polyamide. However, polymer composition differed significantly between sediment and surface water samples as well as between the Frisian Islands and the English Channel sites. These results show that microplastics are not evenly distributed, in neither location nor size, which is illuminating regarding the development of monitoring protocols.

This study aims at quantifying and characterising microplastics (MP) distribution in the water column of the NW Mediterranean Sea as well as MP ingestion by the 2 main planktivorous fish of the area, sardine and anchovy. Debris of similar sizes were found in all water column samples and in all but 2 fish guts (out of 169). MP were found in 93% of water column samples with an average concentration of 0.23 ± 0.20 MP·m−3, but in only 12% of sardines (0.20 ± 0.69 MP·ind−1) and 11% of anchovies (0.11 ± 0.31 MP·ind−1). Fibres were the only shape of MP encountered and polyethylene terephthalate was the main polymer identified in water columns (61%), sardines (71%) and anchovies (89%). This study confirms the ubiquity of MP in the Mediterranean Sea and imparts low occurrence in fish digestive tracts.

Seafloor litter has been studied both on the continental shelves (by trawling during 24 years) and in canyons (by ROV) of the French Mediterranean sea Water (FMW). On the continental shelf, mean densities range from 49.63 to 289.01 items/km2. The most abundant categories were plastic, glass/ceramics, metals and textiles. Trend analysis shows a significant increase in plastic quantities during the study period. Plastics accumulate at all depths, with heavier items being found in deeper areas, while the continental slope-break appears as a clean area. The spatial distribution of litter revealed the influence of geomorphologic factors, anthropic activities, shipping route, river inputs. All the canyons are affected by debris but coastal canyons (Ligurian Sea and Corsica) were more impacted than offshore canyons in the Gulf of Lion. The FMW appears to be highly polluted with regard to values found in other areas, but lower than those observed in the Eastern Mediterranean.

Harmful algal blooms are a threat to aquatic organisms and coastal ecosystems. Among harmful species, the widespread distributed genus Alexandrium is of global importance. This genus is well-known for the synthesis of paralytic shellfish toxins which are toxic for humans through the consumption of contaminated shellfish. While the effects of Alexandrium species upon the physiology of bivalves are now well documented, consequences on reproduction remain poorly studied. In France, Alexandrium minutum blooms have been recurrent for the last decades, generally appearing during the reproduction season of most bivalves including the oyster Crassostrea gigas. These blooms could not only affect gametogenesis but also spawning, larval development or juvenile recruitment. This study assesses the effect of toxic A. minutum blooms on C. gigas reproduction. Adult oysters were experimentally exposed to A. minutum, at environmentally realistic concentrations (102 to 103 cells mL−1) for two months during their gametogenesis and a control group, not exposed to A. minutum was fed with a non-toxic dinoflagellate. To determine both consequences to next generation and direct effects of A. minutum exposure on larvae, the embryo-larval development of subsequent offspring was conducted with and without A. minutum exposure at 102 cells mL−1. Effects at each stage of the reproduction were investigated on ecophysiological parameters, cellular responses, and offspring development. Broodstock exposed to A. minutum produced spermatozoa with decreased motility and larvae of smaller size which showed higher mortalities during settlement. Embryo-larval exposure to A. minutum significantly reduced growth and settlement of larvae compared to non-exposed offspring. This detrimental consequence on larval growth was stronger in larvae derived from control parents compared to offspring from exposed parents. This study provides evidence that A. minutum blooms, whether they occur during gametogenesis, spawning or larval development, can either affect gamete quality and/or larval development of C. gigas, thus potentially impacting oyster recruitment.

The Deepwater Horizon (DWH) disaster released crude oil in the Gulf of Mexico for 87 days, overlapping with the reproductive season and recruitment of the oyster Crassostrea virginica. The pelagic larval life stages of C. virginica are particularly vulnerable to contaminants such as polycyclic aromatic hydrocarbons (PAHs) and oil droplets. Based on their lipophilic properties, PAHs and oil droplets can adsorb onto phytoplankton and filter-feeding C. virginica larvae may be exposed to these contaminants bound to suspended sediment, adsorbed onto algal and other particles, or in solution. This study examined the effects of exposure of C. virginica larvae to algae mixed with DWH oil. In a 14-day laboratory exposure, 5 day-old C. virginica larvae were exposed to Tisochrysis lutea mixed with four concentrations of unfiltered DWH oil (HEWAF) in a static renewal system. Larval growth, feeding capacity, abnormality and mortality were monitored throughout the exposure. Total PAH (n = 50) content of the water medium, in which larvae were grown, were quantified by GC/MS-SIM. Oil droplets were observed bound to algae, resulting in particles in the size-range of food ingested by oyster larvae (1–30 μm). After 14 days of exposure, larval growth and survival were negatively affected at concentrations of tPAH50 as low as 1.6 μg L−1. GC/MS-SIM analysis of the exposure medium confirmed that certain PAHs were also adsorbed by T. lutea and taken up by oyster larvae via ingestion of oil droplets and/or contaminated algae. Long-term exposure to chronic levels of PAH (1.6–78 μg tPAH50 L−1) was shown to negatively affect larval survival. This study demonstrates that dietary exposure of oyster larvae to DWH oil is a realistic route of crude oil toxicity and may have serious implications on the planktonic community and the food chain.

MicroRNAs (miRNAs) are a class of small non-coding RNA that control multiple biological processes through negative post-transcriptional regulation of gene expression. Recently a role of miRNAs in the response of aquatic organisms to environmental toxicants emerged. Toxicant-induced changes in miRNA expression might then represent novel biomarkers to evaluate the health status of these organisms. In this study, we aimed to identify the miRNA repertoire in the liver of the European eel Anguilla anguilla and to compare their differential expression between a polluted site located in the Gironde Estuary and a pristine site in Arcachon Bay (France). A total of 299 mature miRNAs were identified. In polluted water, 19 miRNAs were up-regulated and 22 were down-regulated. We predicted that these differentially expressed miRNAs could target 490 genes that were involved in ribosome biogenesis, response to hormones, response to chemical and chromatin modification. Moreover, we observed only few examples (29) of negative correlation between the expression levels of miRNAs and their targets suggesting that, in the system studied, miRNAs might not only regulate gene expression directly by degrading mRNA but also by inhibiting protein translation or by regulating other epigenetic processes. This study is the first example of in situ investigation of the role of miRNAs in the response of a fish species to water quality. Our findings provide new insights into the involvement of epigenetic mechanisms in the response of animals chronically exposed to pollution and pave the way for the utilization of miRNAs in aquatic ecotoxicology.

International audience | Today, the environmental awareness is leading to the recovery of the solid organic waste and the use of fossil fuels. Methanisation, or anaerobic digestion, is a solution. This process is the transformation of organic matter by bacteria in the absence of oxygen. It allows both the treatment of organic waste and provides two main products biogas and digestate. Digestate is an improved fertilizer that can be used by spreading or composting. Biogas can be used to produce heat or electricity. Biogas production is currently supported by governments of developed countries. In France, the number of installations is gradually increasing (Club Biogaz ATEE, 2011). However, waste used as raw material can potentially be rich in microorganisms. Currently, some questions arise about the potential spread of micro-organisms by this type of process. Among the among the dispersal pathways, the airborne mode of spread is often poorly explored. During the anaerobic process, a few phases seem to be able to cause the aerosolization of microorganisms, for example, the stock of raw materials or digestate handling. In this context, the EMAMET project was realised to provide data on atmospheric emissions from these processes (Bayle et al, 2016). The objectives of this study are to enumerate and describe the airborne microbial community on anaerobic digestor site caracterized by molecular approach. On a quarterly basis, over a one-year period, of the anaerobic digestion of waste water activated sludge has been monitored. For each campaign, four sampling locations have been investigated; the storage area for raw materials, the raw material preparation area, the digestion reactor and the phase separation zone of the digestate. A fifth simple, an outdoor control sampling point was also included.

Microplastic pollution has received considerable attention in marine systems, but recent work shows substantial plastic pollution also occurs in freshwater ecosystems. Most freshwater research has focused on large rivers and lakes, but small streams are the primary interface between land, where plastic is used, and drainage networks. We examined variation in the amount and form of plastic occurring in small streams spanning an urbanisation gradient. All streams contained microplastics with concentrations similar to that found in larger systems (up to 303 particles m−3 in water and 80 particles kg−1 in sediment). The most abundant types were fragments and small particles (63–500 μm). Chemical types of plastic were quite variable and often not predictable based on size, form and colour. Variation in microplastic abundance across streams was high, but only partially explained by catchment scale parameters. There was no relationship between human population density or combined stormwater overflows and microplastic abundance. Residential land cover was related to microplastic abundance, but explanatory power was low. Our results suggest local-scale factors may be more important than catchment-scale processes in determining microplastic pollution in small streams.