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Recent analyses of historical data of fish abundance and distribution have shown the importance of a long temporal perspective in the evaluation of the current status of fish populations, but pose numerous difficulties such as fragmentation and inhomogeneities in the amount of available information in space and time. Using mixed-effects models in a multiscale analysis, we identified an appropriate spatiotemporal scale of investigation of a high-quality, spatially explicit historical data set, and we reconstructed the long-term spatial dynamics of Atlantic cod (Gadus morhua) in the Kattegat-Skagerrak along the 20th century. We identified a northern and southern main aggregation of adult cod in the study area, corresponding to the Skagerrak portion of the North Sea and the Kattegat cod stocks, respectively. The stocks showed specificities in their spatial dynamics, but common extensive loss of coastal aggregations during the last decades when only 13% (Kattegat) and 35% (Skagerrak) of the estimated early century cod biomass was left. Our reconstruction showed that the collapse of the cod stocks in the area followed the peak in landings in the 1960s-1970s, suggesting that the postwar development of the industrial fisheries played a major role in the decrease of local abundances and disappearance of local adult cod aggregations. Des analyses recentes de donnees historiques sur l'abondance et la distribution de poissons ont demontre l'importance d'une perspective temporelle a long terme dans l'evaluation de l'etat actuel des populations de poissons. Ces analyses presentent toutefois de nombreuses difficultes, telles qu'une fragmentation et une heterogeneite spatiales et temporelles de la quantite d'information disponible. En utilisant des modeles a effets mixtes dans une analyse multi-echelle, nous avons cerne une echelle spatiotemporelle convenant a l'etude d'un ensemble de donnees historiques spatialement explicites de haute qualite et reconstitue la dynamique spatiale a long terme de la morue franche (Gadus morhua) dans la region du Cattegat et du Skagerrak au cours du 20e siecle. Nous avons cerne deux grandes agregations, septentrionale et meridionale, de morues adultes dans la region a l'etude, correspondant aux stocks de la region du Skagerrak de la mer du Nord et du Cattegat, respectivement. Si les deux stocks presentaient des specificites en ce qui concerne leur dynamique spatiale, ils etaient tous deux caracterises par la disparition generalisee d'agregations cotieres durant les dernieres decennies, alors qu'il ne restait que 13 % (Cattegat) et 35 % (Skagerrak) de la biomasse de morue estimee du debut du siecle. La reconstitution a demontre que l'effondrement des stocks de morue dans la region s'est produit dans la foulee de la pointe des debarquements des annees 1960-1970, portant a croire que le developpement des peches industrielles dans l'apres-guerre a joue un role majeur dans la diminution de l'abondance locale et la disparition d'agregations locales de morues adultes. [Traduit par la Redaction], Introduction There is an increasing demand for historical baselines of marine ecosystems (Pauly 1995). This is particularly relevant for the evaluation of harvested populations and to set goals for their [...]

European hake (Merluccius merluccius) is an important predator of deeper shelf-upper slope Mediterranean communities. It is a nectobenthic species distributed over a wide depth range (20-1000 m) throughout the Mediterranean [...]

Elevated levels of atmospheric CO2 lead to the increase of plant photosynthetic rates, carbon inputs into soil and root exudation. In this work, the effects of rising atmospheric CO2 levels on the metabolic active soil microbiome have been investigated at the Giessen free-air CO2 enrichment (Gi-FACE) experiment on a permanent grassland site near Giessen, Germany. The aim was to assess the effects of increased C supply into the soil, due to elevated CO2, on the active soil microbiome composition. RNA extraction and 16S rRNA (cDNA) metabarcoding sequencing were performed from bulk and rhizosphere soils, and the obtained data were processed for a compositional data analysis calculating diversity indices and differential abundance analyses. The structure of the metabolic active microbiome in the rhizospheric soil showed a clear separation between elevated and ambient CO2 (p = 0.002); increased atmospheric CO2 concentration exerted a significant influence on the microbiomes differentiation (p = 0.01). In contrast, elevated CO2 had no major influence on the structure of the bulk soil microbiome (p = 0.097). Differential abundance results demonstrated that 42 bacterial genera were stimulated under elevated CO2. The RNA-based metabarcoding approach used in this research showed that the ongoing atmospheric CO2 increase of climate change will significantly shift the microbiome structure in the rhizosphere. [ABSTRACT FROM AUTHOR]

Orchids are highly dependent on symbiotic microorganisms during their entire life cycle. Whereas an important role in orchid seed germination and early plant development is well established for mycorrhizal fungi, the influence of endophytic bacteria on orchid growth has been less investigated. Here, we report the isolation of endophytic bacteria from different organs of three terrestrial Mediterranean orchid species (Spiranthes spiralis, Serapias vomeracea and Neottia ovata), the investigation of their potential Plant Growth-Promoting (PGP) traits and their interaction with the orchid mycorrhizal (OM) fungus Tulasnella calosporain vitro. Little overlap was found among endophytic bacteria isolated from the different organs of the three orchid species. Taxonomic identification, based on the 16S rRNA gene, of fifty dereplicated bacterial isolates revealed that they belong to the genera Pseudomonas, Pantoea, Rahnella, Staphylococcus, Sphingomonas, Microbacterium, Streptomyces, Fictibacillus and Bacillus. Most bacterial isolates exhibited some potential PGP traits, such as nutrient solubilization, ACC deaminase activities and/or IAA biosynthesis. Although some Pseudomonas reduced growth of the OM fungus Tulasnella calospora, most isolates did not affect fungal growth. These results increase our understanding of the diversity and potential PGP functions of bacterial endophytes in terrestrial orchids, and suggest a role as beneficial partners in the orchid microbiota. [ABSTRACT FROM AUTHOR]

Echinacea purpurea is a plant cultivated worldwide for its pharmaceutical properties, mainly related to the stimulation of the immune system in the treatment of respiratory infections. The cypselas (fruits) of E. purpurea were examined in order to investigate the presence, localization and potential function(s) of endophytic microorganisms. Electron and confocal microscopy observations showed that three different components of microorganisms were associated to cypselas of E. purpurea: (i) one endocellular bacterial component in the cotyledons, enclosed within the host membrane; (ii) another more generic bacterial component adhering to the external side of the perianth; and (iii) a fungal component inside the porous layer of the perianth, the woody and porous modified residual of the flower, in the form of numerous hyphae able to cross the wall between adjacent cells. Isolated bacteria were affiliated to the genera Paenibacillus, Pantoea, and Sanguibacter. Plate tests showed a general resistance to six different antibiotics and also to an antimicrobial-producing Rheinheimera sp. test strain. Finally, microbiome-deprived E. purpurea seeds showed a reduced ability to germinate, suggesting an active role of the microbiome in the plant vitality. Our results suggest that the endophytic bacterial community of E. purpurea, previously found in roots and stem/leaves, might be already carried at the seed stage, hosted by the cotyledons. A further microbial fungal component is transported together with the seed in the perianth of the cypsela, whose remarkable structure may be considered as an adaptation for fungal transportation, and could influence the capability of the seed to germinate in the soil. Key Points • The fruit of Echinacea purpurea contains fungi not causing any damage to the plant. • The seed cotyledons contain endocellular bacteria. • Seed/fruit deprived of the microbiome showed a reduced ability to germinate. [ABSTRACT FROM AUTHOR]

Citrus limon (L.) Burm. F. is an important evergreen fruit crop whose rhizosphere and phyllosphere microbiota have been characterized, while seed microbiota is still unknown. Bacterial and fungal endophytes were isolated from C. limon surface-sterilized seeds. The isolated fungi—belonging to Aspergillus, Quambalaria and Bjerkandera genera—and bacteria—belonging to Staphylococcus genus—were characterized for indoleacetic acid production and phosphate solubilization. Next Generation Sequencing based approaches were then used to characterize the endophytic bacterial and fungal microbiota structures of surface-sterilized C. limon seeds and of shoots obtained under aseptic conditions from in vitro growing seedlings regenerated from surface-sterilized seeds. This analysis highlighted that Cutibacterium and Acinetobacter were the most abundant bacterial genera in both seeds and shoots, while Cladosporium and Debaryomyces were the most abundant fungal genera in seeds and shoots, respectively. The localization of bacterial endophytes in seed and shoot tissues was revealed by Fluorescence In Situ Hybridization coupled with Confocal Laser Scanning Microscopy revealing vascular bundle colonization. Thus, these results highlighted for the first time the structures of endophytic microbiota of C. limon seeds and the transmission to shoots, corroborating the idea of a vertical transmission of plant microbiota and suggesting its crucial role in seed germination and plant development. [ABSTRACT FROM AUTHOR]

Europe has a well‐established network of breeding bird monitoring that is used to produce supranational indices of population trends for many species. However, a comparison of breeding bird censuses with other methods may be beneficial to confirm the validity of such indices. The aim of this study was to assess the value of standardized capture data of migratory birds at migration bottlenecks as an indicator of the effective breeding populations. One limitation to this method is that several populations are co‐occurring at these bottlenecks and their catchment areas need to be clearly identified to allow extrapolation of population indices. Here, we used standardized trends in capture numbers of 30 species on the island of Ponza, a migration bottleneck in the central Mediterranean, and compared them to population trends estimated in the putative catchment breeding areas between 2005 and 2016. The catchment areas were identified through the analysis of ring recoveries during the breeding season of birds passing through Ponza. Our results show an agreement between the population trends observed on Ponza and those in the breeding areas in 15 out of 30 species. The correlations were strongest in species with a more robust definition of the catchment areas, that is, species with more than 10 recoveries, and for which the recoveries were most likely of breeding birds. The main reason for disagreement between the two indices in the remaining species might be related to different intensity of sampling in different areas. This issue can be solved by further developing monitoring projects in underrepresented countries, as well as by intensifying monitoring through ringing, both in the breeding grounds and at migration bottlenecks. These results show that spring migration monitoring at bottlenecks has the potential to provide a valuable complement and an independent control of breeding bird surveys, allowing raising early warnings of population declines and contributing to their conservation. [ABSTRACT FROM AUTHOR]

Banana (Musa acuminata) growth for commercial purposes requires high amounts of chemical fertilizers, generating high costs and deleterious effects on the environment. In a previous study, we demonstrated that two plant growth-promoting rhizobacteria (PGPR), Bacillus amyloliquefaciens Bs006 and Pseudomonas palleroniana Ps006, isolated in Colombia, could partially replace chemical fertilizers for banana seedling growth. In a second work, the effects of the two inoculants on banana transcripts were found to occur at different times, earlier for Bs006 and later for Ps006. This leads to the hypothesis that the two rhizobacteria have different colonization dynamics. Accordingly, the aim of this work was to analyze the dynamics of root colonization of the two PGPR, Bs006 and Ps006, on banana growth over a time frame of 30 days. We used fluorescence in situ hybridization (FISH) and confocal laser scanning microscopy (CLSM), followed by three-dimensional reconstruction and quantitative image analysis. Bacillus amyloliquefaciens Bs006 abundantly colonized banana roots earlier (from 1 to 48 h), ectophytically on the rhizoplane, and then decreased. Pseudomonas palleroniana Ps006 was initially scarce, but after 96 h it increased dramatically and became clearly endophytic. Here we identify and discuss the potential genetic factors responsible for this complementary behavior. This information is crucial for optimizing the formulation of an effective biofertilizer for banana and its inoculation strategy. [ABSTRACT FROM AUTHOR]

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