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Changes in the state of rivers resulting from the activity and expansion of urban areas are likely to affect aquatic populations by increasing stress and disease, with the microbiota playing a potentially important intermediary role. Unraveling the dynamics of microbial flora is therefore essential to better apprehend the impact of anthropogenic disturbances on the health of host populations and the ecological integrity of hydrosystems. In this context, the present study simultaneously examined changes in the microbial communities associated with mucosal skin and gut tissues of eight fish species along an urbanization gradient in the Orge River (France). 16S rRNA gene metabarcoding revealed that the structure and composition of the skin microbiota varied substantially along the disturbance gradient and to a lesser extent according to fish taxonomy. Sequences affiliated with the Gammaproteobacteria, in particular the genus Aeromonas, prevailed on fish caught in the most urbanized areas, whereas they were nearly absent upstream. This rise of opportunistic taxa was concomitant with a decline in phylogenetic diversity, suggesting more constraining environmental pressures. In comparison, fish gut microbiota varied much more moderately with the degree of urbanization, possibly because this niche might be less directly exposed to environmental stressors. Co-occurrence networks further identified pairs of associated bacterial taxa, co-existing more or less often than expected at random. Few correlations could be identified between skin and gut bacterial taxa, supporting the assumption that these two microbial niches are disconnected and do not suffer from the same vulnerability to anthropic pressures.

Soil fungi play a fundamental role in the cycling of nutrients and tree nutrition in forests. As mycorrhizal fungi are closely associated with their host trees and provide them essential base cations and phosphorus, we hypothesize that they actively mine soil minerals and transfer their nutritive content to their host. Therefore, mycorrhizal fungi are expected to be important colonizers of soil mineral surfaces relative to other fungal trophic guilds. To test this hypothesis, 50 μm nylon mesh bags were filled with three different mineral types (i.e. calcite, apatite and obsidian) and buried in the same soil colonized by three forest stands (i.e. beech, Corsican pine and coppice with standards). After an in situ incubation period of 29 months in the topsoil, mineral dissolution was detectable in the mesh bags, and the analysis of the fungal communities was therefore undertaken. Minerals presented a lower fungal biomass than the surrounding bulk soil and no difference between the three mineral types tested was observed. The high-throughput sequencing (HTS) approach showed that the fungal communities differed among the three forest stands, but in each case, mineral associated fungal taxa differed significantly from those in the bulk soil. To a lesser extent, fungal communities further varied between the three mineral types. Overall, trophic inference analyses suggested that two groups of plant-associated fungi, namely the ectomycorrhizal and endophytic fungi, were the major fungal mineral colonizers. Saprophytes also appeared significantly enriched on minerals comparatively to the surrounding bulk soil. Together, our data reveal at local scale that the mineral-associated fungal communities are first determined by the forest plant cover and then by the type of mineral.

The invasion of aquifer microbial communities by aboveground microorganisms, a phenomenon known as community coalescence, is likely to be exacerbated in groundwaters fed by stormwater infiltration systems (SISs). Here, the incidence of this increased connectivity with upslope soils and impermeabilized surfaces was assessed through a meta-analysis of 16S rRNA gene libraries. Specifically, DNA sequences encoding 16S rRNA V5-V6 regions from free-living and attached aquifer bacteria (i.e., water and biofilm samples) were analysed upstream and downstream of a SIS and compared with those from bacterial communities from watershed runoffs and surface sediments from the SIS detention and infiltration basins. Significant bacterial transfers were inferred by the SourceTracker Bayesian approach, with 23 % to 57 % of the aquifer bacterial biofilms being composed of taxa from aboveground sediments and urban runoffs. Sediments from the detention basin were found more significant contributors of taxa involved in the buildup of these biofilms than soils from the infiltration basin. Inferred taxa among the coalesced biofilm community were predicted to be high in hydrocarbon degraders such as Sphingobium and Nocardia. The 16S rRNA-based bacterial community structure of the downstream-SIS aquifer waters showed lower coalescence with aboveground taxa (8 % to 38 %) than those of biofilms and higher numbers of taxa predicted to be involved in the N and S cycles. A DNA marker named tpm enabled the tracking of bacterial species from 24 genera including Pseudomonas, Aeromonas and Xanthomonas, among these communities. Several tpm sequence types were found to be shared between the aboveground and aquifer samples. Reads related to Pseudomonas were allocated to 50 species, of which 16 were found in the aquifer samples. Several of these aquifer species were found to be involved in denitrification but also hydrocarbon degradation (P. aeruginosa, P. putida and P. fluorescens). Some tpm sequence types allocated to P. umsongensis and P. chengduensis were found to be enriched among the tpm-harbouring bacteria, respectively, of the aquifer biofilms and waters. Reads related to Aeromonas were allocated to 11 species, but only those from A. caviae were recovered aboveground and in the aquifer samples. Some tpm sequence types of the X. axonopodis phytopathogen were recorded in higher proportions among the tpm-harbouring bacteria of the aquifer waters than in the aboveground samples. A significant coalescence of microbial communities from an urban watershed with those of an aquifer was thus observed, and recent aquifer biofilms were found to be significantly colonized by runoff-opportunistic taxa able to use urban C sources from aboveground compartments.

Changes in the state of rivers resulting from the activity and expansion of urban areas are likely to affect aquatic populations by increasing stress and disease, with the microbiota playing a potentially important intermediary role. Unraveling the dynamics of microbial flora is therefore essential to better apprehend the impact of anthropogenic disturbances on the health of host populations and the ecological integrity of hydrosystems. In this context, the present study simultaneously examined changes in the microbial communities associated with mucosal skin and gut tissues of eight fish species along an urbanization gradient in the Orge River (France). 16S rRNA gene metabarcoding revealed that the structure and composition of the skin microbiota varied substantially along the disturbance gradient and to a lesser extent according to fish taxonomy. Sequences affiliated with the Gammaproteobacteria, in particular the genus Aeromonas, prevailed on fish caught in the most urbanized areas, whereas they were nearly absent upstream. This rise of opportunistic taxa was concomitant with a decline in phylogenetic diversity, suggesting more constraining environmental pressures. In comparison, fish gut microbiota varied much more moderately with the degree of urbanization, possibly because this niche might be less directly exposed to environmental stressors. Co-occurrence networks further identified pairs of associated bacterial taxa, co-existing more or less often than expected at random. Few correlations could be identified between skin and gut bacterial taxa, supporting the assumption that these two microbial niches are disconnected and do not suffer from the same vulnerability to anthropic pressures.

The extension of urban and peri-urban areas and the related artificialization of soils drastically impacts the water cycle as well as biogeochemical cycles. In particular, the sealing of soils with impervious surfaces such as roads increases runoff and decreases concomitant infiltration. At the catchment scale, more significant amounts of stormwater must be collected and managed to prevent from flooding urban areas and mitigate discharge to the environment. Sustainable Urban Drainage Systems (SUDS) were developed to alleviate these problems. These systems allow the restoration of one of the main functions of urban and peri-urban soils, i.e., infiltrating stormwater. They simultaneously reduce the risk of flooding and increase groundwater recharge. Another essential service must be ensured and optimized: the removal of pollutants from infiltrating water by the soil, to avoid the degradation of the quality of the groundwater.The INFILTRON project aims to design a methodology for the assessment of infiltration and filtration of pollutants by SUDS. The project is a collaboration of many partners, with expertise in soil physics, urban hydrology, nanoparticle engineering, and modeling, to engineer a specific device for the simultaneous monitoring of water infiltration and pollutant filtration. This infiltration device both infiltrates water and injects nanoparticles (NPs) into the soil. It was sized to account for preferential flow, which is known to have a significant impact on infiltration and pollutant transfer. The engineered NPs were designed to be detectable in the ground using ground-penetrating radar (GPR) and to mimic the transfer of nano-pollutants (emerging pollutants, bacteria, etc.) commonly found in real stormwater. An infiltration-filtration model was developed to interpret the experimental data and to quantify two indicators for the assessment of water infiltration and pollutant filtration. INFILTRON will provide a very interesting toolbox for practitioners and stakeholders for the evaluation of the infiltration and filtration functions of not only SUDS within the framework of stormwater management, but also anthropized soils within the management of urban and peri-urban areas.

In soils characterized by nutrient-poor conditions trees have developed strategies to maximize the exploration of the environment through their root system. Notably, in shallow soils, trees adopt a deep-rooting strategy to access appropriate levels of water and nutrients from the bedrock. Despite the critical importance of microorganisms in nutrient access in topsoil, understanding their involvement in subsoil was rarely addressed. Our study provides the first comprehensive picture of the bacterial communities colonizing deep roots at the bedrock interface. Particularly, we aimed at deciphering if the subsoil edaphic conditions allowed the enrichment of specific bacterial communities in the rhizosphere. To answer such questioning, we focused on a shallow soil dominated by deep-rooting beech trees (Fagus sylvatica). The taxonomic and functional structures of bacterial communities were investigated through 16S rRNA-pyrosequencing analyses and in vitro bioassays on culturable representatives isolated from the saprolite, the limestone rocks and the roots penetrating those two compartments at the bedrock interface. Our taxonomic analyses revealed a rhizosphere effect, with no difference between the limestone- and saprolite-rhizosphere bacterial communities. Notably, our functional assays highlighted a significant enrichment of bacteria effective at mineral weathering in the limestone-rhizosphere compared to the surrounding environment, whereas organic matter decomposing bacteria were exclusively enriched in the saprolite-rhizosphere. Altogether our results suggest that tree roots select specific bacterial communities in subsoil as potential allies to improve nutrient availability and tree nutrition.

Co-occurrence network analysis based on amplicon sequences is increasingly used to study microbial communities. Patterns of co-existence or mutual exclusion between pairs of taxa are often interpreted as reflecting positive or negative biological interactions. However, other assembly processes can underlie these patterns, including species failure to reach distant areas (dispersal limitation) and tolerate local environmental conditions (habitat filtering). We provide a tool to quantify the relative contribution of community assembly processes to microbial co-occurrence patterns, which we applied to explore soil bacterial communities in two dry ecosystems. First, we sequenced a bacterial phylogenetic marker in soils collected across multiple plots. Second, we inferred co-occurrence networks to identify pairs of significantly associated taxa, either co-existing more (aggregated) or less often (segregated) than expected at random. Third, we assigned assembly processes to each pair: patterns explained based on spatial or environmental distance were ascribed to dispersal limitation (2%–4%) or habitat filtering (55%–77%), and the remaining to biological interactions. Finally, we calculated the phylogenetic distance between taxon pairs to test theoretical expectations on the linkages between phylogenetic patterns and assembly processes. Aggregated pairs were more closely related than segregated pairs. Furthermore, habitat-filtered aggregated pairs were closer relatives than those assigned to positive interactions, consistent with phylogenetic niche conservatism and cooperativism among distantly related taxa. Negative interactions resulted in equivocal phylogenetic signatures, probably because different competitive processes leave opposing signals. We show that microbial co-occurrence networks mainly reflect environmental tolerances and propose that incorporating measures of phylogenetic relatedness to networks might help elucidate ecologically meaningful patterns., Financial support was provided by the Spanish Ministry of Economy and Competitiveness (CGL2014‐58333‐P; CGL2017‐89751‐R) and the Generalitat Valenciana (SEJI/2017/030). MG acknowledges support by the Ramón y Cajal Programme and AGF by the FPI Programme (BES‐2015‐072580).

International audience; Les processus d'infiltration des eaux pluviales présentent un intérêt croissant dans les pays développés, car ils contribuent à réduire les phénomènes d'inondation et d'érosion, et permettent de préserver les réserves en eau. Cependant, le ruissellement des eaux pluviales en milieu urbain remobilise divers contaminants dont des microorganismes pouvant présenter un risque pour la santé humaine. Pour évaluer l'incidence des transferts bactériens sur la qualité des eaux souterraines, nous avons effectué une méta-analyse de banques de séquences codant l'ARN ribosomique 16S issus du système d'infiltration des eaux pluviales d'une zone industrielle (Chassieu, France). Les jeux de données analysés englobent plus de 100 échantillons, comprenant des eaux de ruissellement, des dépôts du bassin de rétention, des sols du bassin d'infiltration ainsi que des eaux et biofilms prélevés dans l'aquifère connecté. Une approche Bayésienne permettant le suivi des sources bactériennes avec ces données a révélé que les communautés bactériennes libres dans l'aquifère étaient peu ou modérément affectées par l'infiltration des eaux pluviales. En revanche, les eaux de ruissellement du bassin versant et les dépôts du bassin de rétention ont été identifiés comme les principaux contributeurs de bactéries formant des biofilms à la surface de billes d'argile incubées dans les eaux souterraines. Des genres bactériens potentiellement pathogènes ont été détectés à la fois en surface et dans l'aquifère. ABSTRACT Stormwater infiltration processes are of increasing interest in developed countries as they reduce urban floods and soil erosion, and alleviate water shortages. However, while flowing over impervious urban surfaces, stormwaters remobilize diverse contaminants and become a source of nonpoint pollution. Among urban contaminants, microbial pathogens reaching underground waters are one of the most serious threats to human health. To gain insights on the incidence of bacterial transfers on the quality of underground waters, a meta-analysis of bacterial 16S rRNA gene libraries from a model stormwater infiltration system (SIS) of an industrial area (Chassieu, France) was performed. The DNA datasets came from more than 100 samples, including watershed runoff, detention basin deposits, infiltration basin soils as well as waters and biofilms taken from the connected aquifer. A Bayesian bacterial source tracking approach using such DNA datasets revealed that free-living bacterial communities in groundwater were slightly affected by bacteria from the upper parts of the SIS and the watershed. In contrast, bacteria from runoffs and detention basin deposits were found to be the main groups developing as biofilms over clay beads exposed to groundwaters. Potentially pathogenic bacterial genera found in the surface samples were detected in the aquifer samples.

Plant species identity is assumed to be a major driver of belowground microbial diversity and composition. However, diagnosing which plant functional traits are responsible for shaping microbial communities remains elusive. Primary succession on barren metalliferous mining substrates was selected as the framework to study above-belowground interactions, and plant functional traits that lead the successional trajectories of soil bacterial communities were identified. The impact of the plant functional group (i.e. trees, shrubs, dwarf shrubs, perennial grasses), a trait integrating the life span and morphological structure, on the bacterial primary succession was monitored. Bacterial diversity and composition was estimated along plant size gradients including over 90 scattered patches ranging from seedlings to mature multispecific patches. Soil bacterial diversity was affected by heavy metals levels and increased towards higher resource availability underneath mature patches, with stress-tolerant heterotrophs and phototrophs being replaced by competitive heterotrophs. The plant functional group modulated these general patterns and shrubs had the greatest impact belowground by inducing the largest increase in soil fertility. Functional traits related to leaf decomposability and root architecture further determined the composition and structure of bacterial communities. These results underline the importance of plant functional traits in the assembly of soil bacterial communities, and can help guiding restoration of degraded lands., This work was supported by the I Convocatoria de ayudas de la Fundación BBVA a proyectos de investigación, the Spanish Ministerio de Economía y Competitividad (projects CGL2014-58333-P; CGL2017-89751-R) and the Generalitat Valenciana (project SEJI/2017/030). MG acknowledges support by the Ramón y Cajal programme (Ministerio de Economía y Competitividad).

cited By 0; International audience; The development of new high-throughput cultivation methods aims to increase the isolation efficiency as compared to standard techniques that often require enrichment procedures to compensate the low microbial recovery. In the current study, estuarine sulfate-reducing bacteria were isolated using an anaerobic isolation procedure in 384-well microplates. Ninety-nine strains were recovered from initial sediments. Isolates were identified according to their partial 16S rRNA sequences and clustered into 13 phylotypes. Besides, the increase in species richness obtained through enrichments or resampling was investigated. Forty-four enrichment procedures were conducted and shifts in sulfate-reducing bacterial communities were investigated through dsrAB gene fingerprinting. Despite efforts in conducting numerous enrichment conditions only few of them were statistically different from initial sample. The cultural diversity obtained from 3 of the most divergent enrichments, as well as from resampled sediments equally contributed to raise the sulfate-reducing diversity up to 22 phylotypes. Enrichments (selection of metabolism) or resampling (transient populations and micro-heterogeneity) may still be helpful to assess new microbial phylotypes. Nevertheless, all the newly cultivated strains were all representatives of minor Operational Taxonomic Units and could eventually be recovered by maintaining high-throughput isolation effort from the initial sediments.

Understanding how soil pedogenesis affects microbial communities and their in situ activities according to ecosystem functioning is a central issue in soil microbial ecology, as soils represent essential nutrient reservoirs and habitats for the biosphere. To address this question, soil chronosequences developed from a single, shared mineralogical parent material and having the same climate conditions are particularly useful, as they isolate the factor of time from other factors controlling the character of soils. In our study, we considered a natural succession of uplifted marine terraces in Mendocino, CA, ranging from highly fertile in the younger terrace (about 100,000 years old) to infertile in the older terraces (about 300,000 years old). Using ITS amplicon pyrosequencing, we analysed and compared the diversity and composition of the soil fungal communities across the first terraces (T1 to T3), with a specific focus in the forested terraces (T2 and T3) on soil samples collected below trees of the same species (Pinus muricata) and of the same age. While diversity and richness indices were highest in the grassland (youngest) terrace (T1), they were higher in the older forested terrace (T3) compared to the younger forested terrace (T2). Interestingly, the most abundant ectomycorrhizal (ECM) taxa that we found within these fungal communities showed high homology with ITS Sanger sequences obtained previously directly from ECM root tips from trees in the same study site, revealing a relative conservation of ECM diversity over time. Altogether, our results provide new information about the diversity and composition of the fungal communities as well as on the dominant ECM species in the soil chronosequence of Mendocino in relation to soil age and ecosystem development.

cited By 0; International audience; Macrophyte floating roots are considered as hotspots for methylmercury (MeHg) production in aquatic ecosystems through microbial activity. Nevertheless, very little is known about periphyton bacterial communities and mercury (Hg) methylators in such ecological niches. The ability to methylate inorganic Hg is broadly distributed among prokaryotes; however, sulfate-reducers have been reported to be the most important MeHg producers in macrophyte floating roots. In the present work, the periphyton bacterial communities colonizing Ludwigia sp. floating roots were investigated through molecular methods. Among the 244 clones investigated, anaerobic microorganisms associated with the sulfur biogeochemical cycle were identified. Notably, members of the sulfur-oxidizing prokaryotes and the anoxygenic, purple non-sulfur bacteria (Rhodobacteraceae, Comamonadaceae, Rhodocyclaceae, Hyphomicrobiaceae) and the sulfate reducers (Desulfobacteraceae, Syntrophobacteraceae, and Desulfobulbaceae) were detected. In addition, 15 sulfate-reducing strains related to the Desulfovibrionaceae family were isolated and their Hg-methylation capacity was tested using a biosensor. The overall results confirmed that Hg methylation is a strain-specific process since the four strains identified as new Hg-methylators were closely related to non-methylating isolates. This study highlights the potential involvement of periphytic bacteria in Hg methylation when favorable environmental conditions are present in such ecological micro-niches.

International audience; Mercury methylation and demethylation processes govern the fate of methylmercury in aquatic ecosystems. Under anoxic conditions, methylation activity is mainly of biological origin and is often the result of sulfate-reducing bacteria. In this study, the use of a luminescent biosensor for screening methylmercury production was validated by exposing the reporter strain to methylating or non-methylating Desulfovibrio strains. The sensitivity of the biosensor to methylmercury was shown to depend on sulfate-reducing bacterial growth conditions. Bioluminescence was measured using 1–10 mM of sulfides. As the sulfide level increased, luminescence decreased by 40–70%, respectively. Nevertheless, assuming an average of 5 mM of sulfide produced during sulfate-reducing growth, a mercury methylation potential of over 4% was detected when using 185 nM of inorganic mercury. Due to technical limitations, mercury speciation has, to date, only been investigated in a small number of bacterial strains, and no consistent phylogenetic distribution has been identified. Here, the biosensor was further used to assess the Hg methylation capacities of an additional 21 strains related to the Desulfobulbaceae. Seven of them were identified as methylmercury producers. Cultivation procedures combined with bacterial biosensors could provide innovative tools to identify new methylator clades amongst the prokaryotes.

International audience; Estuaries are highly dynamic ecosystems in which freshwater and seawater mix together. Depending on tide and river inflows, particles originating from rivers or from the remobilization of sediments accumulate in the water column. Due to the salinity gradient and the high heterotrophic activity in the estuarine plume, hypoxic and anoxic microniches may form in oxygenated waters, sustaining favorable conditions for resuspended anaerobic microorganisms. In this context, we tested the hypothesis that anaerobic sulfate-reducing prokaryotes may occur in the water column of the Adour River. Using 16S ribosomal RNA (rRNA) and dsrAB-based terminal restriction fragment length polymorphism (T-RFLP) techniques, we characterized total prokaryotic and sulfate-reducing communities along a gradient from estuarine to marine bay waters. Sulfate-reducing prokaryotes were further characterized by the description of dsrB genes and the cultivation of sulfidogenic anaerobic microorganisms. As a result, physical-chemical parameters had a significant effect on water bacterial diversity and community structure along the studied gradient. The concentration of cultured sulfidogenic microorganisms ranged from 1 to 60 × 103 cells l−1 in the water column. Sulfate-reducing prokaryotes occurring in estuarine waters were closely related to microorganisms previously detected in freshwater sediments, suggesting an estuarine origin, mainly by the remobilization of the sediments. In the marine bay station, sediment-derived sulfate-reducing prokaryotes were not cultured anymore, probably due to freshwater dilution, increasing salinity and extended oxic stress. Nevertheless, isolates related to the type strain Desulfovibrio oceani were cultured from the diluted plume and deep marine waters, indicating the occurrence of autochthonous sulfate-reducing bacteria offshore.

It has been rarely questioned as to whether the enrichment of specific bacterial taxa found in the rhizosphere of a given plant species changes with different soil types under field conditions and under similar climatic conditions. Understanding tree microbiome interactions is essential because, in contrast to annual plants, tree species require decades to grow and strongly depend on the nutritive resources of the soil. In this context, we tested using a natural toposequence the hypothesis that beech trees select specific taxa and functions in their rhizosphere based on the soil conditions and their nutritive requirements. Our 16S rRNA gene pyrosequencing analyses revealed that the soil type determines the taxa colonizing the beech rhizosphere. A rhizosphere effect was observed in each soil type, but a stronger effect was observed in the nutrient-poor soils. Although the communities varied significantly across the toposequence, we identified a core beech rhizosphere microbiome. Functionally, GeoChip analyses showed a functional redundancy across the toposequence, with genes related to nutrient cycling and to the bacterial immune system being significantly enriched in the rhizosphere. Altogether, the data suggest that, regardless of the soil conditions, trees enrich variable bacterial communities to maintain the functions necessary for their nutrition.

Although minerals represent important soil constituents, their impact on the diversity and structure of soil microbial communities remains poorly documented. In this study, pure mineral particles with various chemistries (i.e., obsidian, apatite, and calcite) were considered. Each mineral type was conditioned in mesh bags and incubated in soil below different tree stands (beech, coppice with standards, and Corsican pine) for 2.5 years to determine the relative impacts of mineralogy and mineral weatherability on the taxonomic and functional diversities of mineral-associated bacterial communities. After this incubation period, the minerals and the surrounding bulk soil were collected to determine mass loss and to perform soil analyses, enzymatic assays, and cultivation-dependent and -independent analyses. Notably, our 16S rRNA gene pyrosequencing analyses revealed that after the 2.5-year incubation period, the mineral-associated bacterial communities strongly differed from those of the surrounding bulk soil for all tree stands considered. When focusing only on minerals, our analyses showed that the bacterial communities associated with calcite, the less recalcitrant mineral type, significantly differed from those that colonized obsidian and apatite minerals. The cultivation-dependent analysis revealed significantly higher abundances of effective mineral-weathering bacteria on the most recalcitrant minerals (i.e., apatite and obsidian). Together, our data showed an enrichment of Betaproteobacteria and effective mineral-weathering bacteria related to the Burkholderia and Collimonas genera on the minerals, suggesting a key role for these taxa in mineral weathering and nutrient cycling in nutrient-poor forest ecosystems. IMPORTANCE Forests are usually developed on nutrient-poor and rocky soils, while nutrient-rich soils have been dedicated to agriculture. In this context, nutrient recycling and nutrient access are key processes in such environments. Deciphering how soil mineralogy influences the diversity, structure, and function of soil bacterial communities in relation to the soil conditions is crucial to better understanding the relative role of the soil bacterial communities in nutrient cycling and plant nutrition in nutrient-poor environments. The present study determined in detail the diversity and structure of bacterial communities associated with different mineral types incubated for 2.5 years in the soil under different tree species using cultivation-dependent and -independent analyses. Our data showed an enrichment of specific bacterial taxa on the minerals, specifically on the most weathered minerals, suggesting that they play key roles in mineral weathering and nutrient cycling in nutrient-poor forest ecosystems.

Rhizosphere represents a nutrient-rich environment and a hotspot of bacterial activities compared to the surrounding bulk soil. However, few studies have investigated how this rhizosphere effect depends on the soil conditions, and never for trees. Contrary to annual plants, trees need decades to, grow and strongly depend on the access and recycling of soil nutrients and water. In this context, we aimed at understanding if contrasted soil types impact the taxonomy and functions of bacterial communities inhabiting beech rhizosphere. To test this hypothesis, we considered the natural toposequence of Montiers, which is characterized by a same land cover dominated by beech (Fagus sylvatica) trees of the same age, growing under the same climatic conditions and under the same forestry practices. We used a combination of in vitro bioassays and 16S rRNA gene sequences analyses on a collection of 370 bacterial strains generated from beech rhizosphere and surrounding bulk soil samples collected in the organomineral horizon along the toposequence. Our study highlighted an increasing beech rhizosphere effect from the nutrient-rich to nutrient-poor soils, with specific bacterial functions related to inorganic nutrient mobilization largely and exclusively enriched in the rhizosphere of the nutrient-poor soils. This functional selection in the rhizosphere came with an enrichment of bacterial strains assigned to the Burkholderia and Collimonas genus, which appeared to be the dominant and most effective mineral weathering bacteria. Our data corroborate the hypothesis of a variable selection of specific rhizosphere bacterial communities by beech trees according to the soil conditions and the tree nutritional requirements.

International audience; The development of new high-throughput cultivation methods aims to increase the isolation efficiency as compared to standard techniques that often require enrichment procedures to compensate the low microbial recovery. In the current study, estuarine sulfate-reducing bacteria were isolated using an anaerobic isolation procedure in 384-well microplates. Ninety-nine strains were recovered from initial sediments. Isolates were identified according to their partial 16S rRNA sequences and clustered into 13 phylotypes. Besides, the increase in species richness obtained through enrichments or resampling was investigated. Forty-four enrichment procedures were conducted and shifts in sulfate-reducing bacterial communities were investigated through dsrAB gene fingerprinting. Despite efforts in conducting numerous enrichment conditions only few of them were statistically different from initial sample. The cultural diversity obtained from 3 of the most divergent enrichments, as well as from resampled sediments equally contributed to raise the sulfate-reducing diversity up to 22 phylotypes. Enrichments (selection of metabolism) or resampling (transient populations and micro-heterogeneity) may still be helpful to assess new microbial phylotypes. Nevertheless, all the newly cultivated strains were all representatives of minor Operational Taxonomic Units and could eventually be recovered by maintaining high-throughput isolation effort from the initial sediments

© 2016, Springer Science+Business Media New York. Understanding how minerals affect bacterial communities and their in situ activities in relation to environmental conditions are central issues in soil microbial ecology, as minerals represent essential reservoirs of inorganic nutrients for the biosphere. To determine the impact of mineral type and solution chemistry on soil bacterial communities, we compared the diversity, composition, and functional abilities of a soil bacterial community incubated in presence/absence of different mineral types (apatite, biotite, obsidian). Microcosms were prepared containing different liquid culture media devoid of particular essential nutrients, the nutrients provided only in the introduced minerals and therefore only available to the microbial community through mineral dissolution by biotic and/or abiotic processes. By combining functional screening of bacterial isolates and community analysis by bromodeoxyuridine DNA immunocapture and 16S rRNA gene pyrosequencing, we demonstrated that bacterial communities were mainly impacted by the solution chemistry at the taxonomic level and by the mineral type at the functional level. Metabolically active bacterial communities varied with solution chemistry and mineral type. Burkholderia were significantly enriched in the obsidian treatment compared to the biotite treatment and were the most effective isolates at solubilizing phosphorous or mobilizing iron, in all the treatments. A detailed analysis revealed that the 16S rRNA gene sequences of the OTUs or isolated strains assigned as Burkholderia in our study showed high homology with effective mineral-weathering bacteria previously recovered from the same experimental site.