The non-ribosomal peptide synthetase-independent siderophore (NIS) rhizobactin produced by Caballeronia mineralivorans PML1(12) confers the ability to weather minerals.

To mobilize nutrients entrapped into minerals and rocks, heterotrophic bacteria living in nutrient-poor environments have developed different mechanisms based mainly on acidolysis and chelation. However, the genetic bases of these mechanisms remain unidentified. To fill this gap, we considered the model strain Caballeronia mineralivorans PML1(12) known to be effective at weathering. Based on its transcriptomics and proteomics responses in Fe-depleted conditions, we pointed a cluster of genes differentially expressed and putatively involved in the production of siderophores. In this study, we report the characterization of this gene region coding for the production of a non-ribosomal peptide synthetase-independent siderophore (NIS). Targeted mutagenesis associated with functional assays and liquid chromatography coupled to high-resolution tandem mass spectrometry demonstrated the production of a single siderophore, identified as rhizobactin. This siderophore represents the first NIS containing malic acid in its structure. The evidence for the implication of rhizobactin in mineral weathering was demonstrated during a hematite dissolution assay. This study provides the first demonstration of the synthesis of a NIS in the genus Caballeronia and its involvement in mineral weathering. Our conclusions reinforce the idea that strain PML1(12) is particularly well adapted to nutrient-poor environments. IMPORTANCE This work deciphers the molecular and genetic bases used by strain PML1(12) of Caballeronia mineralivorans to mobilize iron and weather minerals. Through the combination of bioinformatics, chemical, and phylogenetic analyses, we characterized the siderophore produced by strain PML1(12) and the related genes. This siderophore was identified as rhizobactin and classified as a non-ribosomal peptide synthetase-independent siderophore (NIS). Contrary to the previously identified NIS synthetases that form siderophores containing citric acid, α-ketoglutarate, or succinic acid, our analyses revealed that rhizobactin contains malic acid in its structure, representing, therefore, the first identified NIS with such an acid and probably a new NIS category. Last, this work demonstrates for the first time the effectiveness at weathering minerals of a siderophore of the NIS family. Our findings offer relevant information for different fields of research, such as environmental genomics, microbiology, chemistry, and soil sciences.

Recent progress in understanding the ecology and molecular genetics of soil mineral weathering bacteria.

Mineral weathering bacteria play essential roles in nutrient cycling and plant nutrition. However, we are far from having a comprehensive view of the factors regulating their distribution and the molecular mechanisms involved. In this review, we highlight the extrinsic factors (i.e., nutrient availability, carbon source) and the intrinsic properties of minerals explaining the distribution and functioning of these functional communities. We also present and discuss the progress made in understanding the molecular mechanisms and genes that are used by bacteria during the mineral weathering process, or regulated during their interaction with minerals, that have been recently unraveled by omics approaches.

The mineral weathering ability of Collimonas pratensis PMB3(1) involves a Malleobactin-mediated iron acquisition system.

Mineral weathering by microorganisms is considered to occur through a succession of mechanisms based on acidification and chelation. While the role of acidification is established, the role of siderophores is difficult to disentangle from the effect of the acidification. We took advantage of the ability of strain Collimonas pratensis PMB3(1) to weather minerals but not to acidify depending on the carbon source to address the role of siderophores in mineral weathering. We identified a single non-ribosomal peptide synthetase (NRPS) responsible for siderophore biosynthesis in the PMB3(1) genome. By combining iron-chelating assays, targeted mutagenesis and chemical analyses (HPLC and LC-ESI-HRMS), we identified the siderophore produced as malleobactin X and how its production depends on the concentration of available iron. Comparison with the genome sequences of other collimonads evidenced that malleobactin production seems to be a relatively conserved functional trait, though some collimonads harboured other siderophore synthesis systems. We also revealed by comparing the wild-type strain and its mutant impaired in the production of malleobactin that the ability to produce this siderophore is essential to allow the dissolution of hematite under non-acidifying conditions. This study represents the first characterization of the siderophore produced by collimonads and its role in mineral weathering.

Draft Genome Sequence of Collimonas pratensis Strain PMB3(1), an Effective Mineral-Weathering and Chitin-Hydrolyzing Bacterial Strain.

We announce the draft genome sequence of Collimonas pratensis PMB3(1), isolated from the Scleroderma citrinum mycorrhizosphere. In addition to its mineral-weathering effectiveness and antifungal activity, this strain is characterized by genomic features that give it great potential as a biocontrol and plant growth-promoting agent in nutrient-poor soils.

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

Minerals 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 vs mannitol) differs. The integration of these data demonstrates that strain PML1(12) is capable of (i) mobilizing iron through the production of a non-ribosomal peptide synthetase-independent siderophore, (ii) inducing chemotaxis and motility in response to nutrient availability and (iii) strongly acidifying its environment in the 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.

Boron Dissolved and Particulate Atmospheric Inputs to a Forest Ecosystem (Northeastern France).

Boron concentrations and isotopic compositions of atmospheric dust and dissolved depositions were monitored over a two-year period (2012-2013) in the forest ecosystem of Montiers (Northeastern France). This time series allows the determination of the boron atmospheric inputs to this forest ecosystem and contributes to refine our understanding of the sources and processes that control the boron atmospheric cycle. Mean annual dust and dissolved boron atmospheric depositions are comparable in size (13 g·ha-1·yr-1 and 16 g·ha-1·yr-1, respectively), which however show significant intra- and interannual variations. Boron isotopes in dust differ from dissolved inputs, with an annual mean value of +1 ‰ and +18 ‰ for, respectively. The notable high boron contents (190-390 µg·g-1) of the dust samples are interpreted as resulting from localized spreading of boron-rich fertilizers, thus indicating a significant local impact of regional agricultural activities. Boron isotopes in dissolved depositions show a clear seasonal trend. The absence of correlation with marine cyclic solutes contradicts a control of atmospheric boron by dissolution of seasalts. Instead, the boron data from this study are consistent with a Rayleigh-like evolution of the atmospheric gaseous boron reservoir with possible but limited anthropogenic and/or biogenic contributions.

Metal Immobilization on Wood-Derived Biochars: Distribution and Reactivity of Carbonate Phases.

Metals can be immobilized on biochars by precipitation with carbonate. The distribution of metal-carbonate phases at the surface of biochars and the conditions of their formation, however, are unknown. Electron microscopy and X-photon spectroscopy were used to characterize carbonate phases in various morphological groups of particles of a wood-derived biochar, both before and after a metal-sorption experiment. Our results showed that the distribution of metals at the surface of biochar particles depended on the corresponding wood tissues and the presence of carbonate phases. Metals were particularly concentrated (i) within calcium carbonate crystals in bark-derived particles, which originated from calcium oxalate crystals formed prior to pyrolysis, and (ii) as new phases formed by the reprecipitation of carbonate on specific tissues of biochar. The formation of biochar carbonate phases and their redistribution by dissolution-precipitation mechanisms may primarily control the localization of metals on biochar particles and the durability of metals immobilization.

The Mineralosphere Concept: Mineralogical Control of the Distribution and Function of Mineral-associated Bacterial Communities.

Soil is composed of a mosaic of different rocks and minerals, usually considered as an inert substrata for microbial colonization. However, recent findings suggest that minerals, in soils and elsewhere, favour the development of specific microbial communities according to their mineralogy, nutritive content, and weatherability. Based upon recent studies, we highlight how bacterial communities are distributed on the surface of, and in close proximity to, minerals. We also consider the potential role of the mineral-associated bacterial communities in mineral weathering and nutrient cycling in soils, with a specific focus on nutrient-poor and acidic forest ecosystems. We propose to define this microbial habitat as the mineralosphere, where key drivers of the microbial communities are the physicochemical properties of the minerals.

Atmospheric particulate deposition in temperate deciduous forest ecosystems: interactions with the canopy and nutrient inputs in two beech stands of Northeastern France.

As wood harvests are expected to increase to satisfy the need for bio-energy in Europe, quantifying atmospheric nutrient inputs in forest ecosystems is essential for forest management. Current atmospheric measurements only take into account the <0.45 µm fraction and dry deposition is generally modeled. The aims of this study were to quantify atmospheric particulate deposition (APD), the >0.45 µm fraction of atmospheric deposition, below the canopy, to study the influence of the canopy on APD, and to determine the influence of APD below canopy to nutrient input-output budgets with a focus on base cations calcium, magnesium and potassium, and phosphorus. APD was sampled every four weeks by passive collectors. We divided APD into an organic and a mineral fraction, respectively POM and MDD. MDD was divided into a soluble and a hardly soluble fraction in hydrogen peroxide, referred to as S-MDD and H-MDD, respectively. In order to better understand the influence of the canopy on APD, we studied APD in three pathways below the canopy (litterfall, stemflow and throughfall), and in open field. Our results indicated that APD in throughfall (123 ± 64 kg ha(-1)year(-1)) was significantly higher and synchronic with that in open field (33 ±9 kg ha(-1)year(-1)) in the two study sites. This concerned both POM and MDD, suggesting a large interception of APD by foliar surfaces, which is rapidly washed off by rain within four weeks. Throughfall H-MDD was the main pathway with an average of 16 ± 2 kg ha(-1)year(-1). Stemflow and litterfall were neglected. In one study site, canopy intercepted about 8 kg ha(-1)year(-1) of S-MDD. Although base cations and phosphorus inputs by APD are lower than those of <0.45 µm deposition, they contributed from 5 to 32% to atmospheric deposition and improved the nutrient budget in one of the study sites.

Taxonomic and functional diversity of Streptomyces in a forest soil.

In this work we report the isolation and the characterization of 79 Streptomyces isolates from a French forest soil. The 16S rRNA gene phylogeny indicated that a great diversity of Streptomyces was present in this soil, with at least nine different and potentially new species. Growth plate assays showed that most Streptomyces lineages exhibit cellulolytic and hemicellulolytic capacities and potentially participate in wood decomposition. Molecular screening for a specific hydrogenase also indicated a widespread potential for atmospheric H2 uptake. Co-culture experiments with representative strains showed antagonistic effects between Streptomyces of the same population and between Streptomyces and various fungi. Interestingly, in certain conditions, growth promotion of some fungi also occurred. We conclude that in forest soil, Streptomyces populations exhibit many important functions involved in different biogeochemical cycles and also influence the structure of soil microbial communities.

Chrysotile dissolution in the rhizosphere of the nickel hyperaccumulator Leptoplax emarginata.

Ni phytoextraction processes need further understanding of the interactions between Ni availability in soils and its absorption by plant roots. The large metal uptake and root exudation by hyperaccumulator species could accelerate the weathering process of Ni-bearing phases in the rhizosphere. The aim of this work was to quantify the weathering of a Ni-bearing mineral phase in the rhizosphere of the Ni-hyperaccumulator Leptoplax emarginata. The studied mineral was chrysotile which was characterized by a low Ni solubility. Column experiments were performed to assess the effect of the Ni-hyperaccumulator L. emarginata and the contribution of rhizobacteria on the dissolution rate of chrysotile. Mineral weathering was monitored by measuring Ni and Mg transferred to leachates or plants throughout the experiment. Results showed that L. emarginata increased chrysotile dissolution by more than 2-fold . The hyperaccumulator L. emarginata accumulated 88% on average of total mobilized Ni. Inoculation with Ni-resistant bacteria in the rhizosphere of L. emarginata had no significant effect on chrysotile dissolution or plant accumulation of Ni in this context. Finally, after 15 weeks of culture, 1.65% of total Ni in the system was mobilized in the planted treatments compared with 0.03% in the unplanted treatments.

Biotic and abiotic experimental identification of bacterial influence on calcium isotopic signatures.

In this study, we tested experimentally the influence of plant and bacterial activities on the calcium (Ca) isotope distribution between soil solutions and plant organs. Abiotic apatite weathering experiments were performed under two different pH conditions using mineral and organic acids. Biotic experiments were performed using either apatite or Ca-enriched biotite substrates in the presence of Scots pines, inoculated or not with the rhizosphere bacterial strain Bulkholderia glathei PML1(12), or the B. glathei PML1(12) alone. For each experiment, the percolate was collected every week and analyzed for Ca concentrations and Ca isotopic ratios. No Ca isotopic fractionation was observed for the different abiotic experimental settings. This indicates that no Ca isotopic fractionation occurs during apatite dissolution, whatever the nature of the acid (mineral or organic). The main result of the biotic experiments is the 0.22 ‰ (44)Ca enrichment recorded for a solution in contact with Scots pines grown on the bacteria-free apatite substrate. In contrast, the presence of bacteria did not cause Ca isotopic fractionation of the solution collected after 14 weeks of the experiments. These preliminary results suggest that bacteria influence the Ca isotopic signatures by dissolving Ca from apatite more efficiently. Therefore, Ca isotopes might be suitable for detecting bacteria-mediated processes in soils.

Bacterial weathering and its contribution to nutrient cycling in temperate forest ecosystems.

Unlike farmland, forests growing on acidic soils are among the terrestrial ecosystems that are the least influenced or amended by man. Forests which developed on acidic soils are characterized by an important stock of inorganic nutrients entrapped in poorly weatherable soil minerals. In this context, the mineral-weathering process is of great importance, since such minerals are not easily accessible to tree roots. To date, several bacterial genera have been noted for their ability to weather minerals and, in the case of some of them, to improve tree nutrition. Nevertheless, few studies have focused their analyses on mineral-weathering bacterial communities in relation to geochemical cycles and soil characteristics, their ecological origin, associated tree species and forest management practices. Here we discuss the heterogeneity of the mineral-weathering process in forest soils and present what is known concerning the taxonomic and functional characteristics of mineral-weathering bacteria, as well as the different locations where they have been isolated in forest soils. We also discuss the biotic and abiotic factors that may influence the distribution of these bacteria, such as the effect of tree species or forest management practices.

Influence of forest trees on the distribution of mineral weathering-associated bacterial communities of the Scleroderma citrinum mycorrhizosphere.

In acidic forest soils, availability of inorganic nutrients is a tree-growth-limiting factor. A hypothesis to explain sustainable forest development proposes that tree roots select soil microbes involved in central biogeochemical processes, such as mineral weathering, that may contribute to nutrient mobilization and tree nutrition. Here we showed, by combining soil analyses with cultivation-dependent analyses of the culturable bacterial communities associated with the widespread mycorrhizal fungus Scleroderma citrinum, a significant enrichment of bacterial isolates with efficient mineral weathering potentials around the oak and beech mycorrhizal roots compared to bulk soil. Such a difference did not exist in the rhizosphere of Norway spruce. The mineral weathering ability of the bacterial isolates was assessed using a microplaque assay that measures the pH and the amount of iron released from biotite. Using this microplate assay, we demonstrated that the bacterial isolates harboring the most efficient mineral weathering potential belonged to the Burkholderia genus. Notably, previous work revealed that oak and beech harbored very similar pHs in the 5- to 10-cm horizon in both rhizosphere and bulk soil environments. In the spruce rhizosphere, in contrast, the pH was significantly lower than that in bulk soil. Because the production of protons is one of the main mechanisms responsible for mineral weathering, our results suggest that certain tree species have developed indirect strategies for mineral weathering in nutrient-poor soils, which lie in the selection of bacterial communities with efficient mineral weathering potentials.

Mineral weathering by bacteria: ecology, actors and mechanisms.

Soil microbes play an essential role in the environment by contributing to the release of key nutrients from primary minerals that are required not only for their own nutrition but also for that of plants. Although the role of fungi in mineral weathering is beginning to be elucidated, the relative impact of bacteria in this process and the molecular mechanisms involved remain poorly understood. Here, we discuss the ecological relevance of bacterial weathering, mainly in the soil and especially in acidic forest ecosystems, which strongly depend on mineral weathering for their sustainability. We also present highlights from recent studies showing molecular mechanisms and genetic determinants involved in the dissolution of complex minerals under aerobic conditions. Finally, we consider the potential applications of genomic resources to the study of bacterial weathering.

Impact of ectomycorrhizosphere on the functional diversity of soil bacterial and fungal communities from a forest stand in relation to nutrient mobilization processes.

The ectomycorrhizal symbiosis alters the physicochemical and biological conditions in the surrounding soil, thus creating a particular environment called ectomycorrhizosphere, which selects microbial communities suspected to play a role in gross production and nutrient cycling. To assess the ectomycorrhizosphere effect on the structure of microbial communities potentially involved in the mobilization of nutrients from the soil minerals in a poor-nutrient environment, we compared the functional diversity of soil and ectomycorrhizosphere bacterial communities in a forest stand. Two hundred and sixty-four bacterial strains and 107 fungal strains were isolated from the bulk soil of an oak (Quercus petraea) stand and from oak-Scleroderma citrinum ectomycorrhizosphere and ectomycorrhizae, in two soil organo-mineral horizons (0 to 3 cm and 5 to 10 cm). They were characterized using two in vitro tests related to their capacities to mobilize iron and phosphorus. We demonstrated that the oak-S. citrinum ectomycorrhizosphere significantly structures the culturable bacterial communities in the two soil horizons by selecting very efficient strains for phosphorus and iron mobilization. This effect was also observed on the diversity of the phosphate-solubilizing fungal communities in the lower soil horizon. A previous study already demonstrated that Laccaria bicolor-Douglas fir ectomycorrhizosphere structures the functional diversity of Pseudomonas fluorescens population in a forest nursery soil. Comparing to it, our work highlights the consistency of the mycorrhizosphere effect on the functional diversity of bacterial and fungal communities in relation to the mineral weathering process, no matter the fungal symbiont, the age and species of the host tree, or the environment (nursery vs forest). We also demonstrated that the intensity of phosphorus and iron mobilization by the ectomycorrhizosphere bacteria isolated from the lower soil horizon was significantly higher compared to that which was isolated from the upper horizon. This reveals for the first time a stratification of the functional diversity of the culturable soil bacterial communities as related to phosphorus and iron mobilization.

Root-associated bacteria contribute to mineral weathering and to mineral nutrition in trees: a budgeting analysis.

The principal nutrient source for forest trees derives from the weathering of soil minerals which results from water circulation and from plant and microbial activity. The main objectives of this work were to quantify the respective effects of plant- and root-associated bacteria on mineral weathering and their consequences on tree seedling growth and nutrition. That is why we carried out two column experiments with a quartz-biotite substrate. The columns were planted with or without pine seedlings and inoculated or not with three ectomycorrhizosphere bacterial strains to quantify biotite weathering and pine growth and to determine how bacteria improve pine growth. We showed that the pine roots significantly increased biotite weathering by a factor of 1.3 for magnesium and 1.7 for potassium. We also demonstrated that the inoculation of Burkholderia glathei PML1(12) significantly increased biotite weathering by a factor of 1.4 for magnesium and 1.5 for potassium in comparison with the pine alone. In addition, we observed a significant positive effect of B. glathei PMB1(7) and PML1(12) on pine growth and on root morphology (number of lateral roots and root hairs). We demonstrated that PML1(12) improved pine growth when the seedlings were supplied with a nutrient solution which did not contain the nutrients present in the biotite. No improvement of pine growth was observed when the seedlings were supplied with all the nutrients necessary for pine growth. We therefore propose that the growth-promoting effect of B. glathei PML1(12) mainly resulted from the improved plant nutrition via increased mineral weathering.