Soil networks become more connected and take up more carbon as nature restoration progresses

Soil organisms have an important role in aboveground community dynamics and ecosystem functioning in terrestrial ecosystems. However, most studies have considered soil biota as a black box or focussed on specific groups, whereas little is known about entire soil networks. Here we show that during the course of nature restoration on abandoned arable land a compositional shift in soil biota, preceded by tightening of the belowground networks, corresponds with enhanced efficiency of carbon uptake. In mid- and long-term abandoned field soil, carbon uptake by fungi increases without an increase in fungal biomass or shift in bacterial-to-fungal ratio. The implication of our findings is that during nature restoration the efficiency of nutrient cycling and carbon uptake can increase by a shift in fungal composition and/or fungal activity. Therefore, we propose that relationships between soil food web structure and carbon cycling in soils need to be reconsidered

Draft Genome Sequence of Burkholderia sp. Strain PML1(12), an Ectomycorrhizosphere-Inhabiting Bacterium with Effective Mineral-Weathering Ability

International audienceWe report the draft genome sequence of Burkholderia sp. PML1(12), a soil bacterium isolated from the Oak-Scleroderma citrinum ectomycorrhizosphere in the experimental forest site of Breuil-Chenue (France)

Identification of a novel type of glucose dehydrogenase involved in the mineral weathering ability of Collimonas pratensis strain PMB3(1)

International audienceThe exact molecular mechanisms as well as the genes involved in the mineral weathering (MW) process by bacteria remain poorly characterized. To date, a single type of glucose dehydrogenase (GDH) depending on a particular co-factor named pyrroloquinoline quinone (PQQ) is known. These enzymes allow the production of gluconic acid through the oxidation of glucose. However, it remains to be determined how bacteria missing PQQ-dependent GDH and/or the related pqq biogenesis genes weather minerals. In this study, we considered the very effective mineral weathering bacterial strain PMB3(1) of Collimonas pratensis. Genome analysis revealed that it does not possess the PQQ based system. The use of random mutagenesis, gene complementation and functional assays allowed us to identify mutants impacted in their ability to weather mineral. Among them, three mutants were strongly altered on their acidification and biotite weathering abilities (58 to 75% of reduction compared to WT) and did not produce gluconic acid. The characterization of the genomic regions allowed noticeably to the identification of a Glucose/Methanol/Choline oxidoreductase. This region appeared very conserved among collimonads and related genera. This study represents the first demonstration of the implication of a PQQ-independent GDH in the mineral weathering process and explains how Collimonas weather minerals

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

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

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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

Dual transcriptomics and proteomics analyses of the early stage of interaction between Caballeronia mineralivorans PML1(12) and mineral

International audienceMinerals and rocks represent essential reservoirs of nutritive elements for the long‐lasting functioning of forest ecosystems developed on nutrient‐poor soils. While the presence of effective mineral weathering bacteria was evidenced in the rhizosphere of different plants, the molecular mechanisms involved remain uncharacterized. To fill this gap, we combined transcriptomic, proteomics, geo‐chemical and physiological analyses to decipher the potential molecular mechanisms explaining the mineral weathering effectiveness of strain PML1(12) of Caballeronia mineralivorans . Considering the early‐stage of the interaction between mineral and bacteria, we identified the genes and proteins differentially expressed when: i) the environment is depleted of certain essential nutrients (i.e ., Mg and Fe), ii) a mineral is added and iii) the carbon source (i.e ., glucose or mannitol) differs. The integration of these data demonstrates that strain PML1(12) is capable of i) mobilizing iron through the production of a NRPS‐independent siderophore, ii) inducing chemotaxis and motility in response to nutrient availability and iii) strongly acidifying its environment in presence of glucose using a suite of GMC oxidoreductases to weather mineral. These results provide new insights into the molecular mechanisms involved in mineral weathering and their regulation, and highlight the complex sequence of events triggered by bacteria to weather minerals

Increase of apatite dissolution rate by Scots pine roots associated or not with Burkholderia glathei PML1(12)Rp in open-system flow microcosms

The release of nutritive elements through apatite dissolution represents the main source of phosphorus, calcium, and several micronutrients (e.g., Zn, Cu) for organisms in non-fertilized forest ecosystems. The aim of this study was to quantify, for the first time, the dissolution rate of apatite grains by tree roots that were or were not associated with a mineral weathering bacterial strain, and by various acids known to be produced by tree roots and soil bacterial strains in open-system flow microcosms. In addition, we explored whether the mobilization of trace elements (including rare earth elements) upon apatite dissolution was affected by the presence of trees and associated microorganisms. The dissolution rate of apatite by Scots pine plants that were or were not inoculated with the strain Burkholderia glathei PML1(12)Rp, and by inorganic (nitric) and organic (citric, oxalic and gluconic) acids at pH 5.5, 4.8, 3.8, 3.5, 3.0, and 2.0 was monitored in two controlled experiments: “plant–bacteria interaction” and “inorganic and organic acids”. Analyses of the outlet solutions in the “plant–bacteria interaction” experiment showed that Scots pine roots and B. glathei PML1(12)Rp produced protons and organic acids such as gluconate, oxalate, acetate, and lactate. The weathering budget alculation revealed that Scots pines (with or without PML1(12)Rp) significantly increased (factor > 10) the release of Ca, P, As, Sr, Zn, U, Y, and rare earth elements such as Ce, La, Nd from apatite, compared to control abiotic treatment. Scanning electron microscopy observation confirmed traces of apatite dissolution in contact of roots. Most dissolved elements were taken up by Scots pine roots, i.e., approximately 50% of Ca, 70% of P, 30% of As, 70% of Sr, 90% of Zn, and 100% of U, Y, and rare earth elements. Interestingly, no significant additional effect due to the bacterial strain PML1(12)Rp on apatite dissolution and Scots pine nutrition and growth was observed. The “inorganic and organic acids” experiment demonstrated that the apatite dissolution efficacy of organic acids was higher than for the inorganic acid and varied in function of the acids: oxalic acid > citric acid > gluconic acid > nitric acid for pH 63.5. In addition, apatite dissolution increased with increasing acidity for each acid. Only oxalic acid generated non-stoichiometric release of calcium and phosphorus from apatite in the solution at pH 63.5, due to the precipitation of Ca-oxalate crystals at apatite surfaces. Comparison of the experiments revealed that the apatite dissolution rate by Scots pines supplied with nutritive solution at pH 5.5 reached 2.0 10 13 mol cm 2 s 1 and Altogether our results highlight that, through the production of weathering agents, notably protons and organic acids, tree roots and root-associated microorganisms are able to significantly increase the release of macro- and micro-nutrients from apatite, thus maintaining high-nutrient conditions to support their growth