Mineral Type and Solution Chemistry Affect the Structure and Composition of Actively Growing Bacterial Communities as Revealed by Bromodeoxyuridine Immunocapture and 16S rRNA Pyrosequencing

© 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

B and δ11B biogeochemical cycle in a beech forest developed on a calcareous soil: Pools, fluxes, and forcing parameters

International audienceRock weathering and biological cycling hold the development and sustainability of continental ecosystems, yet the interdependence of macro-and micro-nutrients biogeochemical cycles and their implications for ecosystem functioning remains unclear, despite being of particular importance in the context of global changes. This study focuses on the stocks, fluxes and processes constituting the biogeochemical cycle of boron. Vegetation, soils and solutions were monitored for a full year in a temperate beech forest developed on calcareous soil. Despite an overwhelmingly large B pool in soils, this study points to limited influence of weathering emphasizing the importance of vegetation cycling on this site. The biological imprint on the B cycle is marked by (1) a strong 11 B enrichment of solutions compared to the mineral source and (2) systematic correlations observed between B and other strongly recycled elements in all water samples. B isotopes are fractionated within the beech stand with higher values in leaves (23.5‰) and lower in fine roots (−11.7‰), suggesting that the light 10 B isotope is preferentially assimilated during plant growth. B isotopic data are consistent with a Rayleigh-like behaviour during xylem transfer leading to an 11 B enrichment in the higher parts of the trees, putting internal B transfer as the main driver of the large range of isotopic compositions between plant tissues. B apparent isotopic fractionations are observed in the annually produced biomass and total beech stand, albeit with different values: α xylem-biomass = 0.980 ± 0.009 and 0.990 ± 0.002, respectively, suggesting 11 B transfer from old to new tissue. The developed model also points to an isotopic fractionation factor during B uptake much higher than previously evaluated (0.979 < α uptake < 0.994). Overall, this study demonstrates that B isotopes appear as a promising tracer of soilplant interactions with particular emphasis on tree adaptation to B bioavailability in soil

Drought events influence nutrient canopy exchanges and green leaf partitioning during senescence in a deciduous forest

The increase in the frequency and intensity of drought events expected in the coming decades in Western Europe may disturb forest biogeochemical cycles and create nutrient deficiencies in trees. One possible origin of nutrient deficiency is the disturbance of the partitioning of the green leaf pool during the leaf senescence period between resorption, foliar leaching and senesced leaves. However, the effects of drought events on this partitioning and the consequences for the maintenance of tree nutrition are poorly documented. An experiment in a beech forest in Meuse (France) was conducted to assess the effect of drought events on nutrient canopy exchanges and on the partitioning of the green leaf pool during the leaf senescence period. The aim was to identify potential nutritional consequences of droughts for trees. Monitoring nutrient dynamics, including resorption, chemistry of green and senesced leaves, foliar absorption and leaching in mature beech stands from 2012 to 2019 allowed us to compare the nutrient exchanges for three nondry and three dry years (i.e., with an intense drought event during the growing season). During dry years, we observed a decrease by almost a third of the potassium (K) partitioning to resorption (i.e. resorption efficiency), thus reducing the K reserve in trees for the next growing season. This result suggests that with the increased drought frequency and intensity expected for the coming decades, there will be a risk of potassium deficiency in trees, as already observed in a rainfall exclusion experiment on the same study site. Reduced foliar leaching and higher parititioning to the senesced leaves for K and phosphorus (P) were also observed. In addition, a slight increase in nitrogen (N) resorption efficiency occurred during dry years which is more likely to improve tree nutrition. The calcium (Ca) negative resorption decreased, with no apparent consequence in our study site. Our results show that nutrient exchanges in the canopy and the partitioning of the green leaf pool can be modified by drought events, and may have consequences on tree nutrition

Seasons differently impact the structure of mineral weathering bacterial communities in beech and spruce stands

International audienc

Correlation of the Abundance of Betaproteobacteria on Mineral Surfaces with Mineral Weathering in Forest Soils

International audienc

Time-dependent feldspar dissolution rates resulting from surface passivation: Experimental evidence and geochemical implications

To which extent does the apparent negative correlation reported between silicate weathering rates and time result from the spontaneous physicochemical evolution of the fluid-mineral interface? To address this question, labradorite powders inserted in nylon bags and buried into two different topsoil horizons for four years were subjected to nanoscale characterization of their near-surface regions using transmission electron microscopy. These characterizations revealed the occurrence of a 30 to 70 nm-thick discontinuous amorphous silica-rich surface layer (ASSL) with a sharp crystalline-amorphous interfacial boundary between labradorite and the layer. Dissolution experiments conducted in mixed flow reactors at ambient temperature and acidic pH demonstrated that the reactivity of fresh and naturally weathered labradorite powders decreased with time, with the dissolution rate of fresh powders remaining systematically greater than that of naturally weathered powders, all over the duration of the experiments (3 weeks). In addition, the dissolution rate of all labradorite batches was noticeably lower in solutions containing elevated concentrations of SiO2(aq), which we attributed to the passivating effect of the ASSL5. This suggestion was confirmed with a simple passivation model, which enabled to capture (i) the greater reactivity of fresh powders;(ii) the dependence of the dissolution rate on [SiO2(aq)];(iii) the gradual decline of powder dissolution rate with time and (iv) the discontinuous occurrence of ASSL5. The model further supports that surface passivation could be one of the (non-exclusive) mechanisms that could account for the so-called kinetic "field-lab discrepancy". The geochemical implications of the recognition of the passivation mechanism are broad, ranging from the need to revisit the kinetic rate laws implemented in geochemical codes to the questioning of the formalism used for determining weathering rates from the study of U-series nuclides in soils and weathering profiles

Long term impact of mineral amendment on the distribution of the mineral weathering associated bacterial communities from the beech Scleroderma citrinum ectomycorrhizosphere

International audienceLiming is a known forest management procedure used to amend nutrient-poor soils such as soils of acidic forests to rectify cation deficiencies and to restore soil pH. However, although this procedure is well known for its beneficial effect on the forest trees, its relative impact on the functional and taxonomic diversity of the soil bacterial communities has been poorly investigated. In this study, we characterized the ability of the soil bacteria to weather soil minerals and to hydrolyze chitin. A collection of 80 bacterial strains was isolated from the Scleroderma citrinum ectomycorrhizosphere and the adjacent bulk soil in two stands of mature beeches (Fagus sylvatica) developed on very acidic soil and presenting two levels of calcium (Ca) availability: a control plot as well as a plot amended with Ca in 1973. All the bacterial isolates were identified by partial 16S rRNA gene sequence analysis as members of the genera Burkholderia, Bacillus, Dyella, Kitasatospora, Micrococcus, Paenibacillus, Pseudomonas, and Rhodanobacter. Using a microplate assay for quantifying the production of protons and the quantity of iron released from biotite, we demonstrated that the bacterial strains from the amended plot harbored a significant higher mineral weathering potential that the ones isolated from the control plot. Notably, the weathering efficacy of the ectomycorrhizosphere bacterial isolates was significantly greater than that of the bulk soil isolates in the control treatment but not in the amended plot. These data reveal that forest management, here mineral amendment, can strongly affect the structure of bacterial communities even over the long term

Soil Parameters Drive the Structure, Diversity and Metabolic Potentials of the Bacterial Communities Across Temperate Beech Forest Soil Sequences

International audienceSoil and climatic conditions as well as land cover and land management have been shown to strongly impact the structure and diversity of the soil bacterial communities. Here, we addressed under a same land cover the potential effect of the edaphic parameters on the soil bacterial communities, excluding potential confounding factors as climate. To do this, we characterized two natural soil sequences occurring in the Montiers experimental site. Spatially distant soil samples were collected below Fagus sylvatica tree stands to assess the effect of soil sequences on the edaphic parameters, as well as the structure and diversity of the bacterial communities. Soil analyses revealed that the two soil sequences were characterized by higher pH and calcium and magnesium contents in the lower plots. Metabolic assays based on Biolog Ecoplates highlighted higher intensity and richness in usable carbon substrates in the lower plots than in the middle and upper plots, although no significant differences occurred in the abundance of bacterial and fungal communities along the soil sequences as assessed using quantitative PCR. Pyrosequencing analysis of 16S ribosomal RNA (rRNA) gene amplicons revealed that Proteobacteria, Acidobacteria and Bacteroidetes were the most abundantly represented phyla. Acidobacteria, Proteobacteria and Chlamydiae were significantly enriched in the most acidic and nutrient-poor soils compared to the Bacteroidetes, which were significantly enriched in the soils presenting the higher pH and nutrient contents. Interestingly, aluminium, nitrogen, calcium, nutrient availability and pH appeared to be the best predictors of the bacterial community structures along the soil sequences

Effect of the Mycorrhizosphere on the Genotypic and Metabolic Diversity of the Bacterial Communities Involved in Mineral Weathering in a Forest Soil▿

To date, several bacterial species have been described as mineral-weathering agents which improve plant nutrition and growth. However, the possible relationships between mineral-weathering potential, taxonomic identity, and metabolic ability have not been investigated thus far. In this study, we characterized a collection of 61 bacterial strains isolated from Scleroderma citrinum mycorrhizae, the mycorrhizosphere, and the adjacent bulk soil in an oak forest. The ability of bacteria to weather biotite was assessed with a new microplate bioassay that measures the pH and the quantity of iron released from this mineral. We showed that weathering bacteria occurred more frequently in the vicinity of S. citrinum than in the bulk soil. Moreover, the weathering efficacy of the mycorrhizosphere bacterial isolates was significantly greater than that of the bulk soil isolates. All the bacterial isolates were identified by partial 16S rRNA gene sequence analysis as members of the genera Burkholderia, Collimonas, Pseudomonas, and Sphingomonas, and their carbon metabolism was characterized by the BIOLOG method. The most efficient isolates belonged to the genera Burkholderia and Collimonas. Multivariate analysis resulted in identification of three metabolic groups, one of which contained mainly bacterial isolates associated with S. citrinum and exhibiting high mineral-weathering potential. Therefore, our results support the hypothesis that by its carbon metabolism this fungus selects in the bulk soil reservoir a bacterial community with high weathering potential, and they also address the question of functional complementation between mycorrhizal fungi and bacteria in the ectomycorrhizal complex for the promotion of tree nutrition

Taxonomic and functional shifts in the beech rhizosphere microbiome across a natural soil toposequence.

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