Effets de la bioturbation sur la diversité des communautés bactériennes du sédiment : approches expérimentale et in-situ : de Melinna palmata aux communautés de la vasière Ouest-Gironde.

The link between benthic macrofauna and bacterial communities was assessed with two different approaches: (1) an experimental approach at the individual scale, focused on the effects of behaviour and bioturbation of the deposit feeder polychaete Melinna palmata on the bacteria lcommunity distribution on the very sediment-water interface; (2) an in situ approach at the scale of the community, focused on the correlation between spatial distribution patterns of the two biological compartments. Melinna palmata belongs to a new functional group of bioturbation described for the first time: surface conveyor. Its use allowed determining that prospection and egestion induced a significant change of bacterial communities on the sediment-water interface. This link was influenced by organic matter enrichment while influencing its fate. In a second part, the link between spatial distribution patterns of the communities was assessed in situ in the West-Gironde mud patch. Both macrofauna and bacteria changed along a gradient of organic matter quantity and quality and of particles size described in this system. However, the correlation between matrices was not statistically significant and needs to be more developed.Le lien entre la macrofaune et les communautés bactériennes benthiques a été déterminé selon deux approches : (1) une approche expérimentale à l’échelle de l’individu ciblée sur les effets de l’activité et de la bioturbation du polychète déposivore de surface Melinna palmata sur la distribution des communautés bactériennes des premiers millimètres de l’interface eau-sédiment ; (2) une approche in situ à l’échelle de la communauté de mise en corrélation des patrons spatiaux de distribution des communautés de macrofaune et de bactéries.Melinna palmata appartient à un nouveau groupe fonctionnel de bioturbation décrit pour la première fois, convoyeur de surface. L’utilisation de ce nouveau modèle biologique a permis de mettre en évidence que les activités de prospection et d’égestions modifient significativement la distribution des communautés bactériennes de la couche oxique de l’interface eau-sédiment. Ce lien est à la fois influencé par l’apport de matière organique de différentes qualités, et impacte la consommation et la minéralisation de cette matière organique.Le lien entre les patrons spatiaux de distribution des communautés de macrofaune et de bactéries a été étudié in situ, dans la vasière Ouest-Gironde. Les deux compartiments ont évolué le long d’un gradient avéré de teneur en matière organique et de taille des particules dans cette vasière.La corrélation des matrices biologiques n’a cependant pas été statistiquement significative et nécessite d’être approfondi

First record of Monocorophium uenoi (Stephenson, 1932) (Crustacea: Amphipoda: Corophiidae) in the Bay of Biscay, French Atlantic coast

International audienc

An Invasive Mussel (Arcuatula senhousia, Benson 1842) Interacts with Resident Biota in Controlling Benthic Ecosystem Functioning

The invasive mussel Arcuatula senhousia has successfully colonized shallow soft sediments worldwide. This filter feeding mussel modifies sedimentary habitats while forming dense populations and efficiently contributes to nutrient cycling. In the present study, the density of A. senhousia was manipulated in intact sediment cores taken within an intertidal Zostera noltei seagrass meadow in Arcachon Bay (French Atlantic coast), where the species currently occurs at levels corresponding to an early invasion stage. It aimed at testing the effects of a future invasion on (1) bioturbation (bioirrigation and sediment mixing) as well as on (2) total benthic solute fluxes across the sediment–water interface. Results showed that increasing densities of A. senhousia clearly enhanced phosphate and ammonium effluxes, but conversely did not significantly affect community bioturbation rates, highlighting the ability of A. senhousia to control nutrient cycling through strong excretion rates with potential important consequences for nutrient cycling and benthic–pelagic coupling at a broader scale. However, it appears that the variability in the different measured solute fluxes were underpinned by different interactions between the manipulated density of A. senhousia and several faunal and/or environmental drivers, therefore underlining the complexity of anticipating the effects of an invasion process on ecosystem functioning within a realistic context

An Invasive Mussel (Arcuatula senhousia, Benson 1842) Interacts with Resident Biota in Controlling Benthic Ecosystem Functioning

The invasive mussel Arcuatula senhousia has successfully colonized shallow soft sediments worldwide. This filter feeding mussel modifies sedimentary habitats while forming dense populations and efficiently contributes to nutrient cycling. In the present study, the density of A. senhousia was manipulated in intact sediment cores taken within an intertidal Zostera noltei seagrass meadow in Arcachon Bay (French Atlantic coast), where the species currently occurs at levels corresponding to an early invasion stage. It aimed at testing the effects of a future invasion on (1) bioturbation (bioirrigation and sediment mixing) as well as on (2) total benthic solute fluxes across the sediment–water interface. Results showed that increasing densities of A. senhousia clearly enhanced phosphate and ammonium effluxes, but conversely did not significantly affect community bioturbation rates, highlighting the ability of A. senhousia to control nutrient cycling through strong excretion rates with potential important consequences for nutrient cycling and benthic–pelagic coupling at a broader scale. However, it appears that the variability in the different measured solute fluxes were underpinned by different interactions between the manipulated density of A. senhousia and several faunal and/or environmental drivers, therefore underlining the complexity of anticipating the effects of an invasion process on ecosystem functioning within a realistic context

Clonal and plasmidic dissemination of critical antimicrobial resistance genes through clinically relevant ExPEC and APEC-like lineages (ST) in the dairy cattle population of Québec, Canada

Antimicrobial resistance can be effectively limited by improving the judicious use of antimicrobials in food production. However, its effect on the spread of AMR genes in animal populations is not well described. In the province of Québec, Canada, a new legislation implemented in 2019 has led to an unprecedented reduction in the use of critical antimicrobials in dairy production. We aimed to investigate the potential link between ESBL/AmpC E. coli isolated before and after legislation and to determine the presence of plasmids carrying genes responsible for critical AMR. We collected fecal samples from calves, cows, and manure pit from 87 Québec dairy farms approximately 2 years before and 2 years after the legislation came into effect. The whole genomes of 183 presumptive ESBL/AmpC E. coli isolated after cefotaxime enrichment were sequenced. Their phylogenetic characteristics (MLST, serogroup, cgMLST) and the presence of virulence and resistance genes and replicons were examined. A maximum likelihood phylogenetic tree was constructed based on single nucleotide polymorphism (SNPs). We identified 10 clonal lineages (same cgMLST) and 7 clones (SNPs ≤ 52). Isolates belonging to these clones could be found on different farms before and after the legislation, strongly suggesting a clonal spread of AMR genes in the population during this 4-year period. All isolates were multidrug resistant (MDR), with clone 2 being notable for the presence of macrolide, fluoroquinolone, and third-generation cephalosporin resistance genes. We also identified clinically relevant ExPEC (ST10) and APEC-like lineages (ST117, ST58, ST88) associated with the presence of ExPEC and APEC virulence genes, respectively. Our data also suggests the presence of one epidemic plasmid belonging to the IncY incompatibility group and carrying qnrs1 and blaCTX–M–15. We demonstrated that AMR genes spread through farms and can persist over a 4-year period in the dairy cattle population through both plasmids and E. coli clones, despite the restriction of critical antimicrobial use. MDR ExPEC and APEC-like STs are present in the normal microbiota of cattle (more frequently in calves). These data increase our knowledge on gene dissemination dynamics and highlight the fact that biosecurity measures should be enhanced in this industry to limit such dissemination

Marine Strategy Framework Directive - Descriptor 2, Non-Indigenous Species, Delivering solid recommendations for setting threshold values for non-indigenous species pressure on European seas

Marine Non-Indigenous Species (NIS) are animals and plants introduced accidently or deliberately into the European seas, originating from other seas of the globe. About 800 marine non-indigenous species (NIS) currently occur in the European Union national marine waters, several of which have negative impacts on marine ecosystem services and biodiversity. Under the Marine Strategy Framework Directive (MSFD) Descriptor 2 (D2), EU Member States (MSs) need to consider NIS in their marine management strategies. The Descriptor D2 includes one primary criterion (D2C1: new NIS introductions), and two secondary criteria (D2C2 and D2C3). The D2 implementation is characterized by a number of issues and uncertainties which can be applicable to the Descriptor level (e.g. geographical unit of assessment, assessment period, phytoplanktonic, parasitic, oligohaline NIS, etc.), to the primary criterion D2C1 level (e.g. threshold values, cryptogenic, questionable species, etc), and to the secondary criteria D2C2 and D2C3. The current report tackles these issues and provides practical recommendations aiming at a smoother and more efficient implementation of D2 and its criteria at EU level. They constitute a solid operational output which can result in more comparable D2 assessments among MSs and MSFD regions/subregions. When it comes to the policy-side, the current report calls for a number of different categories of NIS to be reported in D2 assessments, pointing the need for the species to be labelled/categorised appropriately in the MSFD reporting by the MSs. These suggestions are proposed to be communicated to the MSFD Working Group of Good Environmental Status (GES) and subsequently to the Marine Strategy Coordination Group (MSCG) of MSFD. Moreover, they can serve as an input for revising the Art. 8 Guidelines

Non-indigenous species refined national baseline inventories : A synthesis in the context of the European Union's Marine Strategy Framework Directive

Refined baseline inventories of non-indigenous species (NIS) are set per European Union Member State (MS), in the context of the Marine Strategy Framework Directive (MSFD). The inventories are based on the initial assessment of the MSFD (2012) and the updated data of the European Alien Species Information Network, in collaboration with NIS experts appointed by the MSs. The analysis revealed that a large number of NIS was not reported from the initial assessments. Moreover, several NIS initially listed are currently considered as native in Europe or were proven to be historical misreportings. The refined baseline inventories constitute a milestone for the MSFD Descriptor 2 implementation, providing an improved basis for reporting new NIS introductions, facilitating the MSFD D2 assessment. In addition, the inventories can help MSs in the establishment of monitoring systems of targeted NIS, and foster cooperation on monitoring of NIS across or within shared marine subregions. Highlights • Refined MSFD baseline inventories of non-indigenous species (NIS) are set in EU. • The inventories are given per EU Member State (MS) and MSFD subregion up to 2012. • The NIS lists provide a basis for reporting new NIS introductions in EU after 2012. • Our work constitutes a milestone for the MSFD Descriptor 2 implementation

Non-indigenous species refined national baseline inventories: A synthesis in the context of the European Union's Marine Strategy Framework Directive

Refined baseline inventories of non-indigenous species (NIS) are set per European Union Member State (MS), in the context of the Marine Strategy Framework Directive (MSFD). The inventories are based on the initial assessment of the MSFD (2012) and the updated data of the European Alien Species Information Network, in collaboration with NIS experts appointed by the MSs. The analysis revealed that a large number of NIS was not reported from the initial assessments. Moreover, several NIS initially listed are currently considered as native in Europe or were proven to be historical misreportings. The refined baseline inventories constitute a milestone for the MSFD Descriptor 2 implementation, providing an improved basis for reporting new NIS introductions, facilitating the MSFD D2 assessment. In addition, the inventories can help MSs in the establishment of monitoring systems of targeted NIS, and foster cooperation on monitoring of NIS across or within shared marine subregions.Henn Ojaveer and Maiju Lehtiniemi wish to acknowledge the project COMPLETE (Completing management options in the Baltic Sea region to reduce risk of invasive species introduction by shipping), co-financed by the European Union's funding Programme Interreg Baltic Sea Region (European Regional Development Fund). João Canning-Clode was supported by a starting grant in the framework of the 2014 FCT Investigator Programme (IF/01606/2014/CP1230/CT0001) and wish to acknowledge the support of Fundação para a Ciência e Tecnologia (FCT), through the strategic project UID/MAR/04292/2019 granted to MARE

Effects of bioturbation on the diversity of bacterial communities in the sediment : experimental and in situ approaches : from Melina palmata to the West Gironde mud patch.

Le lien entre la macrofaune et les communautés bactériennes benthiques a été déterminé selon deux approches : (1) une approche expérimentale à l’échelle de l’individu ciblée sur les effets de l’activité et de la bioturbation du polychète déposivore de surface Melinna palmata sur la distribution des communautés bactériennes des premiers millimètres de l’interface eau-sédiment ; (2) une approche in situ à l’échelle de la communauté de mise en corrélation des patrons spatiaux de distribution des communautés de macrofaune et de bactéries.Melinna palmata appartient à un nouveau groupe fonctionnel de bioturbation décrit pour la première fois, convoyeur de surface. L’utilisation de ce nouveau modèle biologique a permis de mettre en évidence que les activités de prospection et d’égestions modifient significativement la distribution des communautés bactériennes de la couche oxique de l’interface eau-sédiment. Ce lien est à la fois influencé par l’apport de matière organique de différentes qualités, et impacte la consommation et la minéralisation de cette matière organique.Le lien entre les patrons spatiaux de distribution des communautés de macrofaune et de bactéries a été étudié in situ, dans la vasière Ouest-Gironde. Les deux compartiments ont évolué le long d’un gradient avéré de teneur en matière organique et de taille des particules dans cette vasière.La corrélation des matrices biologiques n’a cependant pas été statistiquement significative et nécessite d’être approfondi.The link between benthic macrofauna and bacterial communities was assessed with two different approaches: (1) an experimental approach at the individual scale, focused on the effects of behaviour and bioturbation of the deposit feeder polychaete Melinna palmata on the bacteria lcommunity distribution on the very sediment-water interface; (2) an in situ approach at the scale of the community, focused on the correlation between spatial distribution patterns of the two biological compartments. Melinna palmata belongs to a new functional group of bioturbation described for the first time: surface conveyor. Its use allowed determining that prospection and egestion induced a significant change of bacterial communities on the sediment-water interface. This link was influenced by organic matter enrichment while influencing its fate. In a second part, the link between spatial distribution patterns of the communities was assessed in situ in the West-Gironde mud patch. Both macrofauna and bacteria changed along a gradient of organic matter quantity and quality and of particles size described in this system. However, the correlation between matrices was not statistically significant and needs to be more developed

Invasion along the French Atlantic coast by the non-native, carnivorous planktonic comb jelly Mnemiopsis leidyi: can an impact on shellfish farming be expected?

The distribution range of the American comb jelly Mnemiopsis leidyi has expanded across Europe for several decades, particularly in the eastern Atlantic and Mediterranean Sea. This study aims to assess its expansion along the French Atlantic coast, mainly in the Bay of Biscay and Iroise Sea, since the first record in 2014. Mnemiopsis leidyi is now clearly established along 500 km of coastline, from the coast of Lorient to Arcachon Bay, which is the southernmost colonised area in the eastern Atlantic to date. It will likely colonise the Spanish Gulf coast in the near future through natural dispersal via currents, as has occurred between the Gironde estuary and Arcachon Bay. We quantify that this species now colonises nearly 45% of the French coastline. The invaded area includes the main estuaries of the Seine, Loire, Gironde and Rhône rivers, where M. leidyi populations may constitute reservoirs for colonising other harbours through merchant vessel traffic via ballast water. Finally, the Marennes- Oléron Bay and Arcachon Bay are the two main spat-producing regions for the Pacific oyster Magallana gigas in France. As M. leidyi consumes bivalve larvae, the potential economic and ecological impacts on this shellfish industry are discussed