Groundwater Isolation Governs Chemistry and Microbial Community Structure along Hydrologic Flowpaths

International audienceThis study deals with the effects of hydrodynamic functioning of hard-rock aquifers on microbial communities. In hard-rock aquifers, the heterogeneous hydrologic circulation strongly constrains groundwater residence time, hydrochemistry, and nutrient supply. Here, residence time and a wide range of environmental factors were used to test the influence of groundwater circulation on active microbial community composition, assessed by high throughput sequencing of 16S rRNA. Groundwater of different ages was sampled along hydrogeologic paths or loops, in three contrasting hard-rock aquifers in Brittany (France). Microbial community composition was driven by groundwater residence time and hydrogeologic loop position. In recent groundwater, in the upper section of the aquifers or in their recharge zone, surface water inputs caused high nitrate concentration and the predominance of putative denitrifiers. Although denitrification does not seem to fully decrease nitrate concentrations due to low dissolved organic carbon concentrations, nitrate input has a major effect on microbial communities. The occurrence of taxa possibly associated with the application of organic fertilizers was also noticed. In ancient isolated groundwater, an ecosystem based on Fe(II)/Fe(III) and S/SO4 redox cycling was observed down to several 100 of meters below the surface. In this depth section, microbial communities were dominated by iron oxidizing bacteria belonging to Gallionellaceae. The latter were associated to old groundwater with high Fe concentrations mixed to a small but not null percentage of recent groundwater inducing oxygen concentrations below 2.5 mg/L. These two types of microbial community were observed in the three sites, independently of site geology and aquifer geometry, indicating hydrogeologic circulation exercises a major control on microbial communities

Large-scale sequence-based information-novel understanding of ecology and novel avenues to test ecological hypotheses

International audienc

Large-scale sequence-based information-novel understanding of ecology and novel avenues to test ecological hypotheses

International audienc

Génotypage SNP : Protocole Hi-Plex2: Application à 5 espèces d’intérêt en écologie et évolution

International audienc

Génotypage SNP : Protocole Hi-Plex2: Application à 5 espèces d’intérêt en écologie et évolution

International audienc

Ecophylogeny of the endospheric root fungal microbiome of co-occurring Agrostis stolonifera

International audienceBACKGROUND: Within the root endosphere, fungi are known to be important for plant nutrition and resistance to stresses. However, description and understanding of the rules governing community assembly in the fungal fraction of the plant microbiome remains scarce. METHODS: We used an innovative DNA- and RNA-based analysis of co-extracted nucleic acids to reveal the complexity of the fungal community colonizing the roots of an Agrostis stolonifera population. The normalized RNA/DNA ratio, designated the 'mean expression ratio', was used as a functional trait proxy. The link between this trait and phylogenetic relatedness was measured using the Blomberg's K statistic. RESULTS: Fungal communities were highly diverse. Only ∼1.5% of the 635 OTUs detected were shared by all individuals, however these accounted for 33% of the sequence number. The endophytic fungal communities in plant roots exhibit phylogenetic clustering that can be explained by a plant host effect acting as environmental filter. The 'mean expression ratio' displayed significant but divergent phylogenetic signals between fungal phyla. DISCUSSION: These results suggest that environmental filtering by the host plant favours the co-existence of related and similar OTUs within the Basidiomycota community assembly, whereas the Ascomycota and Glomeromycota communities seem to be impacted by competitive interactions which promote the co-existence of phylogenetically related but ecologically dissimilar OTUs

A microorganisms’ journey between plant generations

Abstract Background Plants are colonized by a great diversity of microorganisms which form a microbiota and perform additional functions for their host. This microbiota can thus be considered a toolbox enabling plants to buffer local environmental changes, with a positive influence on plant fitness. In this context, the transmission of the microbiota to the progeny represent a way to ensure the presence of beneficial symbionts within the habitat. Examples of such transmission have been mainly described for seed transmission and concern a few pathogenic microorganisms. We investigated the transmission of symbiotic partners to plant progeny within clonal plant network. Methods We used the clonal plant Glechoma hederacea as plant model and forced newly emitted clonal progeny to root in separated pots while controlling the presence of microorganisms. We used an amplicon sequencing approach of 16S and 18S rRNA targeting bacteria/archaea and fungi respectively to describe the root microbiota of mother and clonal-plant offspring. Results We demonstrated the vertical transmission of a significant proportion of the mother plants’ symbiotic bacteria and fungi to the daughters. Interestingly, archaea were not transmitted to the daughter plants. Transmitted communities had lower richness, suggesting a filtration during transmission. We found that the transmitted pool of microorganisms was similar among daughters, constituting the heritability of a specific cohort of microorganisms, opening a new understanding of the plant holobiont. We also found significant effects of distance to the mother plant and of growth time on the richness of the microbiota transmitted. Conclusions In this clonal plant, microorganisms are transmitted between individuals through connections, thereby ensuring the availability of microbe partners for the newborn plants as well as the dispersion between hosts for the microorganisms. This previously undescribed ecological process allows the dispersal of microorganisms in space and across plant generations. As the vast majority of plants are clonal, this process might be therefore a strong driver of ecosystem functioning and assembly of plant and microorganism communities in a wide range of ecosystems

Genome-Wide Transcriptional Profiling and Metabolic Analysis Uncover Multiple Molecular Responses of the Grass Species Lolium perenne Under Low-Intensity Xenobiotic Stress

International audienceLolium perenne, which is a major component of pastures, lawns, and grass strips, can be exposed to xenobiotic stresses due to diffuse and residual contaminations of soil. L. perenne was recently shown to undergo metabolic adjustments in response to sub-toxic levels of xenobiotics. To gain insight in such chemical stress responses, a de novo transcriptome analysis was carried out on leaves from plants subjected at the root level to low levels of xenobiotics, glyphosate, tebuconazole, and a combination of the two, leading to no adverse physiological effect. Chemical treatments influenced significantly the relative proportions of functional categories and of transcripts related to carbohydrate processes, to signaling, to protein-kinase cascades, such as Serine/Threonine-protein kinases, to transcriptional regulations, to responses to abiotic or biotic stimuli and to responses to phytohormones. Transcriptomics-based expressions of genes encoding different types of SNF1 (sucrose non-fermenting 1)-related kinases involved in sugar and stress signaling or encoding key metabolic enzymes were in line with specific qRT-PCR analysis or with the important metabolic and regulatory changes revealed by metabolomic analysis. The effects of pesticide treatments on metabolites and gene expression strongly suggest that pesticides at low levels, as single molecule or as mixture, affect cell signaling and functioning even in the absence of major physiological impact. This global analysis of L. perenne therefore highlighted the interactions between molecular regulation of responses to xenobiotics, and also carbohydrate dynamics, energy dysfunction, phytohormones and calcium signaling

Evolution of Dopamine Receptor Genes of the D1 Class in Vertebrates.

International audienceThe receptors of the dopamine neurotransmitter belong to two unrelated classes named D(1) and D(2). For the D(1) receptor class, only two subtypes are found in mammals, the D(1A) and D(1B,) receptors, whereas additional subtypes, named D(1C), D(1D), and D(1X), have been found in other vertebrate species. Here, we analyzed molecular phylogeny, gene synteny, and gene expression pattern of the D(1) receptor subtypes in a large range of vertebrate species, which leads us to propose a new view of the evolution of D(1) dopamine receptor genes. First, we show that D(1)(C) and D(1)(D) receptor sequences are encoded by orthologous genes. Second, the previously identified Cypriniform D(1)(X) sequence is a teleost-specific paralog of the D(1)(B) sequences found in all groups of jawed vertebrates. Third, zebrafish and several sauropsid species possess an additional D(1)-like gene, which is likely to form another orthology group of vertebrate ancestral genes, which we propose to name D(1)(E). Ancestral jawed vertebrates are thus likely to have possessed four classes of D(1) receptor genes-D(1)(A), D(1)(B(X)), D(1)(C(D)), and D(1)(E)-which arose from large-scale gene duplications. The D(1)(C) receptor gene would have been secondarily lost in the mammalian lineage, whereas the D(1)(E) receptor gene would have been lost independently in several lineages of modern vertebrates. The D(1)(A) receptors are well conserved throughout jawed vertebrates, whereas sauropsid D(1)(C) receptors have rapidly diverged, to the point that they were misidentified as D(1)(D). The functional significance of the D(1)(C) receptor loss is not known. It is possible that the function may have been substituted with D(1)(A) or D(1)(B) receptors in mammals, following the disappearance of D(1)(C) receptors in these species

Organic agriculture and field edges uphold endospheric wheat microbiota at field and landscape scale

International audienceAgricultural intensification has been demonstrated to induce a loss of biodiversity. Despite the key role of symbiotic microorganisms in plant nutrition and protection, the impact of agricultural intensification on these microorganisms is not fully understood. Organic farming and field edges (as semi-natural elements) may promote a higher microbial diversity thanks to lower anthropic disturbance and higher plant diversity. We sampled wheat individuals in pairs of wheat fields (one organic and one conventional) along a distance gradient to the edges (hedgerow vs. grassy), in 20 landscape windows selected along an uncorrelated gradient of organic farming and hedgerow density. We demonstrated that organic farming shaped microbial composition and increased fungal and bacterial richness, while hedgerows had a neutral or negative effect on richness depending on the microbial phyla considered. In contrast to bacteria, fungal communities were heterogeneously distributed within fields, having a higher diversity for some phyla close to field edges. Overall we highlighted that fungi responded more to the field scale while bacteria were more affected by landscape scale. The effect of agricultural intensification on plant microbiota and therefore on the functions provided by microorganisms to the plants has to be considered at a multiple spatial scale-from field to landscape