Habitat generalists and specialists in microbial communities across a terrestrial-freshwater gradient

Observations of distributions of microorganisms and their differences in community composition across habitats provide evidence of biogeographical patterns. However, little is known about the processes controlling transfers across habitat gradients. By analysing the overall microbial community composition (bacteria, fungi, archaea) across a terrestrial-freshwater gradient, the aim of this study was to understand the spatial distribution patterns of populations and identify taxa capable of crossing biome borders. Barcoded 454 pyrosequencing of taxonomic gene markers was used to describe the microbial communities in adjacent soil, freshwater and sediment samples and study the role of biotic and spatial factors in shaping their composition. Few habitat generalists but a high number of specialists were detected indicating that microbial community composition was mainly regulated by species sorting and niche partitioning. Biotic interactions within microbial groups based on an association network underlined the importance of Actinobacteria, Sordariomycetes, Agaricomycetes and Nitrososphaerales in connecting among biomes. Even if dispersion seemed limited, the shore of the lake represented a transition area, allowing populations to cross the biome boundaries. In finding few broadly distributed populations, our study points to biome specialization within microbial communities with limited potential for dispersal and colonization of new habitats along the terrestrial-freshwater continuum

Extracorporeal Membrane Oxygenation for Severe Acute Respiratory Distress Syndrome associated with COVID-19: An Emulated Target Trial Analysis.

RATIONALE: Whether COVID patients may benefit from extracorporeal membrane oxygenation (ECMO) compared with conventional invasive mechanical ventilation (IMV) remains unknown. OBJECTIVES: To estimate the effect of ECMO on 90-Day mortality vs IMV only Methods: Among 4,244 critically ill adult patients with COVID-19 included in a multicenter cohort study, we emulated a target trial comparing the treatment strategies of initiating ECMO vs. no ECMO within 7 days of IMV in patients with severe acute respiratory distress syndrome (PaO2/FiO2 <80 or PaCO2 ≥60 mmHg). We controlled for confounding using a multivariable Cox model based on predefined variables. MAIN RESULTS: 1,235 patients met the full eligibility criteria for the emulated trial, among whom 164 patients initiated ECMO. The ECMO strategy had a higher survival probability at Day-7 from the onset of eligibility criteria (87% vs 83%, risk difference: 4%, 95% CI 0;9%) which decreased during follow-up (survival at Day-90: 63% vs 65%, risk difference: -2%, 95% CI -10;5%). However, ECMO was associated with higher survival when performed in high-volume ECMO centers or in regions where a specific ECMO network organization was set up to handle high demand, and when initiated within the first 4 days of MV and in profoundly hypoxemic patients. CONCLUSIONS: In an emulated trial based on a nationwide COVID-19 cohort, we found differential survival over time of an ECMO compared with a no-ECMO strategy. However, ECMO was consistently associated with better outcomes when performed in high-volume centers and in regions with ECMO capacities specifically organized to handle high demand. This article is open access and distributed under the terms of the Creative Commons Attribution Non-Commercial No Derivatives License 4.0 (http://creativecommons.org/licenses/by-nc-nd/4.0/)

Biodégradation des herbicides en sols tempérés - Contrôle des communautés bactériennes dégradantes par la bioturbation du sol

During the last decades, several soil and water pollutions have been observed following intensive use of pesticides. By their high ability to adapt, soil bacteria acquired the ability to use these molecules as nutrient sources and so to degrade them. This ecological service is in situ submitted to numerous biotic interactions acting on bacteria and specially earthworm (soil engineers) bioturbation. The objectives of this study were to better understand these tight interactions between degrading soil bacteria and lumbricid macrofauna by using atrazine as a model. Two strategies were used: (i) a quantitative approach allowed us to determine the impact of earthworms on atrazine degrading bacterial abundance and activity and (ii) a qualitative approach allowed us to link diversity to function with identification of bacteria actively implied in atrazine degradation in different soil microsites produced by earthworm bioturbation.L'intensification de l'agriculture s'est accompagnée d'une utilisation importante de pesticides qui a généré une pollution généralisée des sols et des eaux, problème environnemental majeur et actuel. Sous la pression de sélection liée à l'usage régulier de pesticides (molécules xénobiotiques) des bactéries du sol se sont adaptées à ces molécules et ont acquis la capacité de les utiliser comme source nutritive et donc de les dégrader. La biodégradation constitue un service écologique majeur fournit par le sol, puisqu'elle est à la base des capacités épuratrices du sol et au-delà, de la résilience des écosystèmes. Le sol étant également un grand réservoir de biodiversité, ces bactéries dégradantes sont sous contrôle de différentes interactions biotiques et notamment celles impliquant les lombriciens, qualifiés d'organismes ingénieurs des sols de par leur action de bioturbation. Grâce à un développement méthodologique important et novateur (RT-qPCR, SIP-ARN), nous avons étudié l'impact de la bioturbation du sol par la macrofaune lombricienne sur les communautés bactériennes du sol intervenant dans la biodégradation de molécules xénobiotiques. L'atrazine a été utilisée comme molécule modèle à double titre : d'un point de vu fondamental, son utilisation pendant plus de 50 ans en France a permis aux bactéries du sol de s'adapter et au titre de l'actualité, bien qu'elle soit interdite en France depuis 2003, il s'agit toujours du principal polluant retrouvé dans les eaux souterraines et de surface. Nous avons analysé par une double approche quantitative et qualitative l'impact de la bioturbation du sol par les lombriciens sur l'abondance, l'activité et la diversité des bactéries indigènes du sol et sur celles dégradant l'atrazine. Nous avons mis en évidence que : (i) la digestion du sol par les lombriciens stimule l'activité d'une partie des bactéries du sol mais qu'une autre fraction ne résiste pas au passage dans le tube digestif des vers, (ii) la bioturbation du sol par les lombriciens génère des ‘hot spot' pour l'activité de dégradation de l'atrazine. Ainsi dans les parois de galeries les bactéries dégradantes sont sélectionnées, la dissipation de l'atrazine est rapide et les premiers acteurs du processus de dégradation ont été identifiés, (iii) la dégradation accélérée de l'atrazine dépend d'espèces bactériennes clés interagissant au sein de consortia dégradants, ainsi la diversité des bactéries dégradantes n'est pas corrélée à la fonction de dégradation. L'ensemble des résultats obtenus nous montre également que l'impact de la bioturbation par la macrofaune lombricienne sur l'activité de dégradation dépend des propriétés physico-chimiques et biologiques initiales du sol. L'ensemble de ces connaissances présente un intérêt dans un contexte de bioremédiation in situ des sols pollués puisque les lombriciens constituent une grande part de la macrofaune dans nos sols tempérés et qu'ils modifient significativement les bactéries dégradant l'atrazine au sein des microsites de sols qu'ils génèrent

Biodégradation des herbicides en sols tempérés (contrôle des communautés bactériennes dégradantes par la bioturbation du sol)

Au cours des dernières décennies, l utilisation intensive de pesticides a généré de nombreux problèmes de pollution des sols et des eaux. Grâce à leur grande capacité d adaptation, les bactéries du sol ont acquis la capacité de dégrader ces molécules en les utilisant comme source nutritive. Ce service écologique est in situ sous contrainte des nombreuses interactions biotiques auxquelles sont soumises les bactéries et notamment de la bioturbation par les lombriciens, organismes ingénieurs des sols. Ce travail de recherche a été réalisé afin de mieux comprendre ces interactions étroites entre les bactéries du sol dégradantes et la macrofaune lombricienne en utilisant l atrazine comme molécule herbicide modèle. Deux approches ont été utilisées : (i) une étude quantitative qui nous a permis de déterminer l impact des lombriciens sur l abondance et l activité des bactéries dégradant l atrazine dans le sol et (ii) une étude qualitative qui nous a permis de relier diversité et fonction en identifiant les bactéries activement impliquées dans la dégradation de l atrazine dans différents microsites de sol générés par l activité des lombriciens.During the last decades, several soil and water pollutions have been observed following intensive use of pesticides. By their high ability to adapt, soil bacteria acquired the ability to use these molecules as nutrient sources and so to degrade them. This ecological service is in situ submitted to numerous biotic interactions acting on bacteria and specially earthworm (soil engineers) bioturbation. The objectives of this study were to better understand these tight interactions between degrading soil bacteria and lumbricid macrofauna by using atrazine as a model. Two strategies were used: (i) a quantitative approach allowed us to determine the impact of earthworms on atrazine degrading bacterial abundance and activity and (ii) a qualitative approach allowed us to link diversity to function with identification of bacteria actively implied in atrazine degradation in different soil microsites produced by earthworm bioturbation.RENNES1-BU Sciences Philo (352382102) / SudocRENNES-Géosciences (352382209) / SudocSudocFranceF

Utilizing ITS1 and ITS2 to study environmental fungal diversity using pyrosequencing

International audienceThe shorter reads generated by high-throughput sequencing has led to a focus on either the ITS1 or the ITS2 sublocus in fungal diversity analyses. Our study aimed to determine how making this choice would influence the datasets obtained and our vision of environmental fungal diversity. DNA was extracted from different environmental samples (water, sediments and soil) and the total internal transcribed spacer (ITS) locus was amplified. 454-sequencing was performed targeting both ITS1 and ITS2. No significant differences in the number of sequences, operational taxonomic units (OTUs) and in the dominant OTUs were detected but less diversity was observed in the ITS2 dataset. In the soilsamples, differences in the fungal taxonomic identification were observed, with more Basidiomycota in the ITS1 dataset and more Ascomycota in the ITS2 dataset. Only one-third of the OTUs were detected in both datasets which could be due to (1) more short sequences removed in the ITS2 dataset, (2) different taxonomic affiliation depending on the sublocus used as BLASTn query and/or (3) selectivity in how a primer amplifies the true community. Although ITS1 and ITS2 datasets led to similar results at the fungal community level, for further in-depth diversity analysis this study suggests the analysis of both ITS regions, as they provided different information and were complementary

Effect of landscape management on earthworm communities in temperate grasslands

International audienceEarthworms provide a large number of ecosystem services that rely on the presence and association of specific species (Blouin et al., 2013). A better understanding of the factors ruling earthworm communities’ assembly is therefore essential. These assembly rules of earthworm communities are govern by the filter theory leading to a pool of local species (Lortie et al., 2004). Many studies focused on interactions between agriculture such as land use or management practices and earthworm communities. Landscape has already been shown to influence the distribution of various organisms, however, very few studies took into account the influence of landscape on earthworm communities (Crittenden et al., 2015; Regulska and Kolaczkowska, 2015) and to our knowledge, none were performed on grasslands. A landscape is composed of patches of habitats separated by ecological continuities. These ecological continuities (ditches, hedges, roads...) can be habitat for organisms, or can play the role of corridors or barriers for their dispersal between two environments. Dupont et al. (2015), observed population flows across the landscape leading to population diversification of A. icterica. The aim of this work was to determine the influence of landscape on earthworm communities’ assembly in grasslands by investigating a high spatial scale (250 and 500 m around each grasslands) and a finer one (within each grasslands).For the large scale, we selected 27 grasslands with a gradient of richness and diversity of the elements of landscape as well as of the hedgerow lines up to 500 m around. We sampled earthworms at 30 m from any natural or anthropogenic edge. For the fine scale, we selected 3 grasslands on which we sampled earthworms along a gradient at 1 m, 5 m, 10 m and 30 m from two borders, a hedgerow and a road. On each sampling point, earthworms were sampled with the application of formaldehyde followed by hand sorting on a square meter repeated three times. Each individual collected was identified to the species and weighed.Preliminary results showed that, at the large scale, the diversity of the landscape (richness or Shannon index) had a negative impact on the total richness of earthworm. The amount of hedges was positively correlated to the number of total and epi-anecic species but negatively related to epigeic species. At the fine scale, a specific effect of gradients on earthworm communities was observed for each of the three grasslands. For example, a positive gradient of earthworm abundance and biomass from the edge towards the centre of the grassland was observed in only one of the three grasslands. Some earthworm species such as A. caliginosa or A. chlorotica showed a negative gradient of their individual adult weight from the edge to the centre of the grassland. Overall no edge effect on the richness of earthworms was observed

Carbon-glucose use by soil bacterial communities in interaction with earthworm activities: towards a 13C SIP-RNA strategy.

Poste

Metagenomic analysis of atrazine degradation in soil.

communication oral

Carbon-glucose use by soil bacterial communities in interaction with earthworm activities: toward a C-13-SIP-RNA strategy.

communication affiché

Metagenomic analysis of atrazine degradation in soil.

communication oral