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

Soil organic matter dynamics mediated by arbuscular mycorrhizal fungi - an updated conceptual framework

Arbuscular mycorrhizal (AM) fungi play an important role in soil organic matter (SOM) formation and stabilization. Previous studies have emphasized organic compounds produced by AM fungi as persistent binding agents for aggregate formation and SOM storage. This concept overlooks the multiple biogeochemical processes mediated by AM fungal activities, which drive SOM generation, reprocessing, reorganization, and stabilization. Here, we propose an updated conceptual framework to facilitate a mechanistic understanding of the role of AM fungi in SOM dynamics. In this framework, four pathways for AM fungi-mediated SOM dynamics are included: 'Generating', AM fungal exudates and biomass serve as key sources of SOM chemodiversity; 'Reprocessing', hyphosphere microorganisms drive SOM decomposition and resynthesis; 'Reorganizing', AM fungi mediate soil physical changes and influence SOM transport, redistribution, transformation, and storage; and 'Stabilizing', AM fungi drive mineral weathering and organo-mineral interactions for SOM stabilization. Moreover, we discuss the AM fungal role in SOM dynamics at different scales, especially when translating results from small scales to complex larger scales. We believe that working with this conceptual framework can allow a better understanding of AM fungal role in SOM dynamics, therefore facilitating the development of mycorrhiza-based technologies toward soil health and global change mitigation.

Exploring the potential: Can arsenic (As) resistant silicate-solubilizing bacteria manage the dual effects of silicon on As accumulation in rice?

Rice (Oryza sativa L.) cultivation in regions marked by elevated arsenic (As) concentrations poses significant health concerns due to As uptake by the plant and its subsequent entry into the human food chain. With rice serving as a staple crop for a substantial share of the global population, addressing this issue is critical for food security. In flooded paddy soils, where As availability is pronounced, innovative strategies to reduce As uptake and enhance agricultural sustainability are mandatory. Silicon (Si) and Si nanoparticles have emerged as potential candidates to mitigate As accumulation in rice. However, their effects on As uptake exhibit complexity, influenced by initial Si levels in the soil and the amount of Si introduced through fertilization. While low Si additions may inadvertently increase As uptake, higher Si concentrations may alleviate As uptake and toxicity. The interplay among existing Si and As availability, Si supplementation, and soil biogeochemistry collectively shapes the outcome. Adding water-soluble Si fertilizers (e.g., Na2SiO3 and K2SiO3) has demonstrated efficacy in mitigating As toxicity stress in rice. Nonetheless, the expense associated with these fertilizers underscores the necessity for low cost innovative solutions. Silicate-solubilizing bacteria (SSB) resilient to As hold promise by enhancing Si availability by accelerating mineral dissolution within the rhizosphere, thereby regulating the Si biogeochemical cycle in paddy soils. Promoting SSB could make cost-effective Si sources more soluble and, consequently, managing the intricate interplay of Si's dual effects on As accumulation in rice. This review paper offers a comprehensive exploration of Si's nuanced role in modulating As uptake by rice, emphasizing the potential synergy between As-resistant SSB and Si availability enhancement. By shedding light on this interplay, we aspire to shed light on an innovative attempt for reducing As accumulation in rice while advancing agricultural sustainability.

Management of Plant Beneficial Fungal Endophytes to Improve the Performance of Agroecological Practices

By dint of the development of agroecological practices and organic farming, stakeholders are becoming more and more aware of the importance of soil life and banning a growing number of pesticide molecules, promoting the use of plant bio-stimulants. To justify and promote the use of microbes in agroecological practices and sustainable agriculture, a number of functions or services often are invoked: (i) soil health, (ii) plant growth promotion, (iii) biocontrol, (iv) nutrient acquiring, (v) soil carbon storage, etc. In this paper, a review and a hierarchical classification of plant fungal partners according to their ecosystemic potential with regard to the available technologies aiming at field uses will be discussed with a particular focus on interactive microbial associations and functions such as Mycorrhiza Helper Bacteria (MHB) and nurse plants.

Under the canopy: disentangling the role of stemflow in shaping spatial patterns of soil microbial community structure underneath trees

Stemflow is a spatially concentrated input of rainwater at the base of trees, resulting from precipitation draining down tree branches to the stem. Depending on tree shape, stemflow can represent a significant fraction of the total rainfall that contacts the tree's canopy area, and can become chemically enriched along its drainage path. As a result, stemflow has been hypothesized to influence microbial communities in the receiving soil proximal to the stem. However, previous studies have (i) yielded conflicting results on the significance of stemflow as a driver in bacterial community composition, and (ii) not directly compared communities in soils with and without stemflow receipt. In this study, a stemflow diversion system was employed on Quercus virginiana trees in Skidaway Island (Georgia, USA) to directly compare soil bacterial communities receiving no stemflow to those beneath trees with no diversion system in place. In both treatments, sample distance from the stem significantly influenced bacterial community structure. However, the absence of stemflow resulted in increased bacterial community diversity across all samples. Stemflow diversion also significantly altered longitudinal patterns in the abundance of multiple taxonomic groups. These results support the hypothesis that Q. virginiana stemflow has a significant impact on bacterial soil inhabitants and is a key factor in taxon selection in stem-proximal communities.

The potential of mineral weathering of halophilic-endophytic bacteria isolated from Suaeda salsa and Spartina anglica

Bacteria have the abilities of salt tolerant, mineral weathering and plant growth promoting can promote the growth of plants in saline lands. However, few reports of the mineral weathering capacity of halophilic-endophytic bacteria, raising the question of whether the halophilic-endophytic weathering bacteria are fundamentally distinct from those in plants communities. In this study, we isolated and characterized halophilic bacterial strains from the roots and leaves of Suaeda salsa and Spartina anglica with respect to their mineral weathering pattern, role in the promoting plant growth, community structure, and their changes in these two plants. Using improved Gibbson medium, we obtained 156 halophilic bacterial strains, among which 92 and 64 strains were isolated from the S. salsa and S. anglica samples, respectively. The rock weathering patterns of the isolates were characterized using batch cultures that measure the quantity of Si, Al, K, and Fe released from crystal biotite under aerobic conditions. Significantly, the biomass and capacity of the mineral weathering of the halophilic-endophytic bacteria were different in the plants. The abundance of the halophilic-endophytic bacterials in the Suaeda salsa was significantly greater than Spartina anglica, whereas the mineral weathering bacterial in the Suaeda salsa was similar to the Spartina anglica. Furthermore, the proportion of plant growth-promoting bacteria in the Suaeda salsa was higher than Spartina anglica. Phylogenetic analyses show that the weathered minerals were inhabited by specific functional groups of bacteria (Halomonas, Acinetobacter, Burkholderia, Alcaligenes, Sphingobium, Arthrobacter, Chryseobacterium, Paenibacillus, Microbacterium, Ensifer, Ralstonia and Enterobacter) that contribute to the mineral weathering. The changes in halophilic endophytes weathering communities between the two plants were attributable not only to major bacterial groups but also to a change in the minor population structure.

Fungal and Bacterial Communities in Tuber melanosporum Plantations from Northern Spain

Tuber melanosporum (Ascomycota, Pezizales) is an ectomycorrhizal fungus that produces highly appreciated hypogeous fruiting bodies called black truffles. The aim of this paper was to research the composition of ectomycorrhiza-associated fungal and bacterial communities in T. melanosporum oak plantations. Results of this paper showed the competitive effect of T. melanosporum on other fungal species, especially other mycorrhizal and pathogenic species. T. melanosporum was shown to be associated mainly with bacteria, some of them important for their properties as mycorrhizal helper bacteria. A dendrogram analysis of co-occurrence showed that T. melanosporum tended to co-occur with the following bacteria species: Singulisphaera limicola, Nannocistis excedens and Sporosarcina globispora. In addition, it was linked to fungal species such as Mortierella elongata, M. minutissima, Cryptococcus uzbekistanensis, C. chernovii and C. aerius. This study provides an exhaustive analysis of the diversity, structure and composition of fungal and bacterial communities associated with T. melanosporum to enhance understanding of the biology, composition and role of these communities in truffle plantations.

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.

Enhanced diversity and rock-weathering potential of bacterial communities inhabiting potash trachyte surface beneath mosses and lichens - A case study in Nanjing, China

Mosses and lichens have been shown to play an important role in enhancing global chemical weathering of the surface rock. However, there are no studies concerning the effects of mosses and lichens on the microbial communities inhabiting rock surfaces. In this study, culture-dependent and culture-independent analyses were employed to compare the diversity, composition, and rock-weathering activity of bacterial communities inhabiting potash trachyte surfaces covered by mosses (MR) and lichens (LR) with those inhabiting surrounding bare rock surfaces (BR). Analyses of 16S rRNA gene Miseq sequencing revealed that the order of alpha (α) diversity indices, in terms of the number of unique operational taxonomic units (OTUs) and Faith's index of phylogenetic diversity, was MR > LR > BR. Moreover, α-diveristy indices were positively correlated with the content of available phosphorus (AP) in rock samples (r = 0.87-0.92), and this explained 70% of the variation in bacterial community structure. The culture-dependent analyses revealed that 100% of the culturable bacterial strains could enhance potash trachyte weathering, and the order of rock-weathering acitivity of bacterial strains was MR > LR > BR. Acidolysis was found to be the major mechanism involved in the bacteria-mediated weathering of potash trachyte. Moreover, bacterial strians related to the genera Dyella and Ralstonia showed the highest rock-weatheirng activity, and both Dyella and Ralstonia were enriched in MR. The results of this study enhance our understanding of the roles of bacteria facilitated by mosses and lichens in rock weathering, element cycling, and soil formation, and provide new insights into the interaction between non-vascular plants and the bacteria on rock surfaces.

Contribution of Arbuscular Mycorrhizal Fungi, Phosphate-Solubilizing Bacteria, and Silicon to P Uptake by Plant

Phosphorus (P) availability is usually low in soils around the globe. Most soils have a deficiency of available P; if they are not fertilized, they will not be able to satisfy the P requirement of plants. P fertilization is generally recommended to manage soil P deficiency; however, the low efficacy of P fertilizers in acidic and in calcareous soils restricts P availability. Moreover, the overuse of P fertilizers is a cause of significant environmental concerns. However, the use of arbuscular mycorrhizal fungi (AMF), phosphate-solubilizing bacteria (PSB), and the addition of silicon (Si) are effective and economical ways to improve the availability and efficacy of P. In this review the contributions of Si, PSB, and AMF in improving the P availability is discussed. Based on what is known about them, the combined strategy of using Si along with AMF and PSB may be highly useful in improving the P availability and as a result, its uptake by plants compared to using either of them alone. A better understanding how the two microorganism groups and Si interact is crucial to preserving soil fertility and improving the economic and environmental sustainability of crop production in P deficient soils. This review summarizes and discusses the current knowledge concerning the interactions among AMF, PSB, and Si in enhancing P availability and its uptake by plants in sustainable agriculture.

Successional trajectory of bacterial communities in soil are shaped by plant-driven changes during secondary succession

This study investigated the potential role of a nitrogen-fixing early-coloniser Alnus Nepalensis D. Don (alder) in driving the changes in soil bacterial communities during secondary succession. We found that bacterial diversity was positively associated with alder growth during course of ecosystem development. Alder development elicited multiple changes in bacterial community composition and ecological networks. For example, the initial dominance of actinobacteria within bacterial community transitioned to the dominance of proteobacteria with stand development. Ecological networks approximating species associations tend to stabilize with alder growth. Janthinobacterium lividum, Candidatus Xiphinematobacter and Rhodoplanes were indicator species of different growth stages of alder. While the growth stages of alder has a major independent contribution to the bacterial diversity, its influence on the community composition was explained conjointly by the changes in soil properties with alder. Alder growth increased trace mineral element concentrations in the soil and explained 63% of variance in the Shannon-diversity. We also found positive association of alder with late-successional Quercus leucotrichophora (Oak). Together, the changes in soil bacterial community shaped by early-coloniser alder and its positive association with late-successional oak suggests a crucial role played by alder in ecosystem recovery of degraded habitats.

Effects of mineral substrate on ectomycorrhizal fungal colonization and bacterial community structure

Ectomycorrhizal (ECM) fungi can promote the nutrient uptake of plants from soil minerals by bioweathering. However, effects of different minerals on ECM fungal colonization and bacterial community structures in the soil remains poorly documented. Here, we investigated ECM fungal composition and bacterial communities in different mineral-filled mesh bags buried in forest soil. Control (filled with quartz, which has little nutrients for plants) and mineral (apatite, potash feldspar and serpentine) -filled mesh bags were buried in E-horizon soil for six months. After incubation, the contents of available elements in bags were determined, bacterial population sizes were quantified by quantitative PCR, and bacterial and ECM fungal community structures in mesh bags were assessed using high-throughput sequencing. The results showed that dozens of ECM fungal species colonized in different mesh bags, of which 17, 54 and 47 ECM species were observed in apatite-, potash feldspar- and serpentine-filled bags, respectively. Ectomycorrhizal fungal composition and bacterial community structure are affected significantly by mineral types. Pseudomonas, Sphingomonas, Bacillus and Paenibacillus, known for high weathering potential, were the preponderant bacteria in mineral-filled bags compared to the control. Ectomycorrhizal fungi are able to selectively colonize mesh bags based on mineral types, and may have a certain influence on the formation of bacterial community structure, implying a possible cooperation of ECM fungi and bacteria in soil mineral weathering.

Challenging Global Waste Management - Bioremediation to Detoxify Asbestos

As the 21st century uncovers ever-increasing volumes of asbestos and asbestos-contaminated waste, we need a new way to stop 'grandfather's problem' from becoming that of our future generations. The production of inexpensive, mechanically strong, heat resistant building materials containing asbestos has inevitably led to its use in many public and residential buildings globally. It is therefore not surprising that since the asbestos boom in the 1970s, some 30 years later, the true extent of this hidden danger was exposed. Yet, this severely toxic material continues to be produced and used in some countries, and in others the disposal options for historic uses - generally landfill - are at best unwieldy and at worst insecure. We illustrate the global scale of the asbestos problem via three case studies which describe various removal and/or end disposal issues. These case studies from both industrialised and island nations demonstrate the potential for the generation of massive amounts of asbestos contaminated soil. In each case, the final outcome of the project was influenced by factors such as cost and land availability, both increasing issues, worldwide. The reduction in the generation of asbestos containing materials will not absolve us from the necessity of handling and disposal of contaminated land. Waste treatment which relies on physico-chemical processes is expensive and does not contribute to a circular model economy ideal. Although asbestos is a mineral substance, there are naturally occurring biological-mediated processes capable of degradation (such as bioweathering). Therefore, low energy options, such as bioremediation, for the treatment for asbestos contaminated soils are worth exploring. We outline evidence pointing to the ability of microbe and plant communities to remove from asbestos the iron that contributes to its carcinogenicity. Finally, we describe the potential for a novel concept of creating ecosystems over asbestos landfills ('activated landfills') that utilize nature's chelating ability to degrade this toxic product effectively.

A microcosm approach highlights the response of soil mineral weathering bacterial communities to an increase of K and Mg availability

The access and recycling of the base cations are essential processes for the long-lasting functioning of forest ecosystems. While the role of soil bacterial communities has been demonstrated in mineral weathering and tree nutrition, our understanding of the link between the availability of base cations and the functioning of these communities remains limited. To fill this gap, we developed a microcosm approach to investigate how an increase in key base cations (potassium or magnesium) impacted the taxonomic and functional structures of the bacterial communities. During a 2-month period after fertilization with available potassium or magnesium, soil properties, global functions (metabolic potentials and respiration) as well as mineral weathering bioassays and 16S rRNA amplicon pyrosequencing were monitored. Our analyses showed no or small variations in the taxonomic structure, total densities and global functions between the treatments. In contrast, a decrease in the frequency and effectiveness of mineral weathering bacteria was observed in the fertilized treatments. Notably, quantitative PCR targeting specific genera known for their mineral weathering ability (i.e., Burkholderia and Collimonas) confirmed this decrease. These new results suggest that K and Mg cation availability drives the distribution of the mineral weathering bacterial communities in forest soil.

Transcriptome Analysis Provides Novel Insights into the Capacity of the Ectomycorrhizal Fungus Amanita pantherina To Weather K-Containing Feldspar and Apatite

Ectomycorrhizal (ECM) fungi, symbiotically associated with woody plants, markedly improve the uptake of mineral nutrients such as potassium (K) and phosphorus (P) by their host trees. Although it is well known that ECM fungi can obtain K and P from soil minerals through biological weathering, the mechanisms regulating this process are still poorly understood at the molecular level. Here, we investigated the transcriptional regulation of the ECM fungus Amanita pantherina in weathering K-containing feldspar and apatite using transcriptome sequencing (RNA-seq) and validated these results for differentially expressed genes using real-time quantitative PCR. The results showed that A. pantherina was able to improve relevant metabolic processes, such as promoting the biosynthesis of unsaturated fatty acids and steroids in the weathering of K-containing feldspar and apatite. The expression of genes encoding ion transporters was markedly enhanced during exposure to solid K-containing feldspar and apatite, and transcripts of the high-affinity K transporter ApHAK1, belonging to the HAK family, were significantly upregulated. The results also demonstrated that there was no upregulation of organic acid biosynthesis, reflecting the weak weathering capacity of the A. pantherina isolate used in this study, especially its inability to utilize P in apatite. Our findings suggest that under natural conditions in forests, some ECM fungi with low weathering potential of their own may instead enhance the uptake of mineral nutrients using their high-affinity ion transporter systems.IMPORTANCE In this study, we revealed the molecular mechanism and possible strategies of A. pantherina with weak weathering potential in the uptake of insoluble mineral nutrients by using transcriptome sequencing (RNA-seq) technology and found that ApHAK1, a K transporter gene of this fungus, plays a very important role in the acquisition of K and P. Ectomycorrhizal (ECM) fungi play critical roles in the uptake of woody plant nutrients in forests that are usually characterized by nutrient limitation and in maintaining the stability of forest ecosystems. However, the regulatory mechanisms of ECM fungi in acquiring nutrients from minerals/rocks are poorly understood. This study investigated the transcriptional regulation of A. pantherina weathering K-containing feldspar and apatite and improves the understanding of fungal-plant interactions in promoting plant nutrition enabling increased productivity in sustainable forestry.

Mycorrhizosphere Bacterial Communities and their Sensitivity to Antibacterial Activity of Ectomycorrhizal Fungi

We investigated whether ectomycorrhizal (ECM) fungal species exhibit antibacterial activity towards culturable bacterial communities in mycorrhizospheres. Four hundred and thirty bacterial strains were isolated from the ECM root tips of Pinus densiflora and bulk soil, and 21 were co-cultured with six ECM fungal species. Three hundred and twenty-nine bacterial 16S rDNA sequences were identified in ECM roots (n=185) and bulk soil (n=144). Mycorrhizosphere isolates were dominated by Gram-negative Proteobacteria from 16 genera, including Burkholderia, Collimonas, Paraburkholderia, and Rhizobium. Paraburkholderia accounted for approximately 60%. In contrast, bulk soil isolates contained a high number of Gram-positive Firmicutes, particularly from Bacillus. Paraburkholderia accounted for ≤20% of the bacterial isolates from bulk soil, which was significantly lower than its percentage in ECM root tips. Co-cultures of six ECM fungal species with the 21 bacterial strains revealed that eight strains of three Gram-positive genera-Arthrobacter, Bacillus, and Lysinibacillus-were sensitive to the antibacterial activity of the fungi. In contrast, the Gram-negative strains, including five Paraburkholderia strains, two Burkholderia strains, and a Rhizobium sp., were not sensitive. The strength of fungal antibacterial activity varied in a species-dependent manner, but consistently affected Gram-positive bacteria. These results suggest that Gram-positive bacteria are excluded from the mycorrhizosphere by the antibacterial activity of ECM fungi, which develops specific soil bacterial communities in the mycorrhizosphere.

Isolation and characterization of mineral-dissolving bacteria from different levels of altered mica schist surfaces and the adjacent soil

Microorganisms play important role in mineral weathering. However, little is known about rock-associated mineral-dissolving bacteria. In this study, 129 bacterial isolates were obtained from the less and more weathered mica schist surfaces and the adjacent soil and characterized for mineral dissolving activity, population, and the linkage of rock weathering level and distribution of the bacteria. Among the 129 isolates, 112 isolates could dissolve biotite. The relative abundance of the highly effective Fe solubilizers was significantly higher on the more altered rock surface (89.6%) than in the soil (51.2%) and on the less altered rock surface (22.5%), while the relative abundance of the highly effective Si solubilizers was significantly higher in the soil (65.9%) than on the more (41.7%) and less (12.5%) altered rock surfaces. Furthermore, 17.5-42.5%, 87.5%, and 60.9-90.2% of the highly effective acid- and siderophore-producing isolates were obtained in the less and more weathered rocks and the soil, respectively. The mineral-dissolving bacteria belonged to 18 genera and Burkholderia, Bacillus, and Paenibacillus were the dominant and highly effective mineral-dissolving bacteria. Phylogenetic analysis found 2, 9, and 5 bacterial species in the highly effective mineral-dissolving bacteria on the less and more altered rock surfaces and in the soil, respectively. The results showed the abundant and diverse mineral-dissolving bacterial populations on the more weathered rock surfaces. The results also suggested distinct mineral-dissolving activities and mechanisms of the bacteria and highlighted the possibility for the development of bacterial inocula for plant nutrition improvement in silicate mineral-rich soils.

Impact of soil pedogenesis on the diversity and composition of fungal communities across the California soil chronosequence of Mendocino

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.

Differences in weathering pattern, stress resistance and community structure of culturable rock-weathering bacteria between altered rocks and soils

In this study, we isolated and characterized rock-weathering bacteria from the surfaces of less and more altered tuffs, along with the adjacent soils, with respect to their rock weathering pattern, stress resistance, community structure, and the changes in these rocks and soils. Using a moderate-nutrition medium, we obtained 150 isolates from the rocks and soils. The rock-weathering patterns of the isolates were characterized using batch cultures that measure the quantity of Si, Al, and Fe released from tuff under aerobic conditions. Based on the potential of the bacterial influence on the element releases, the isolates could be grouped into highly, moderately, and least effective element solubilizers, respectively. Significantly more highly effective Al and Fe solubilizers were observed in the altered rocks, while the soils had more highly effective Si solubilizers. Furthermore, more isolates from the altered rocks significantly acidified the culture medium in the rock weathering process. Dynamic changes in the element release showed the distinct element releasing patterns of three selected isolates. More isolates from the altered rocks could grow at 4 °C or at 55 °C or at pH 4. Some isolates from the altered rocks could grow at pH 10 and with 10–15% (w/v) NaCl. The altered rocks and the soils existed in diverse and different highly weathering-specific culturable rock-weathering community structures. The changes in the culturable weathering communities between the altered rocks and the soils were attributable not only to major bacterial groups but also to a change in the minor population structure.

Rock-weathering bacteria from the surfaces of less and more altered tuffs were isolated and characterized, along with the adjacent soils, with respect to their rock weathering pattern, stress resistance, community structure, and the changes in the rocks and soils.

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.

Location-Related Differences in Weathering Behaviors and Populations of Culturable Rock-Weathering Bacteria Along a Hillside of a Rock Mountain

Bacteria play important roles in rock weathering, elemental cycling, and soil formation. However, little is known about the weathering potential and population of bacteria inhabiting surfaces of rocks. In this study, we isolated bacteria from the top, middle, and bottom rock samples along a hillside of a rock (trachyte) mountain as well as adjacent soils and characterized rock-weathering behaviors and populations of the bacteria. Per gram of rock or surface soil, 10⁶-10⁷ colony forming units were obtained and total 192 bacteria were isolated. Laboratory rock dissolution experiments indicated that the proportions of the highly effective Fe (ranging from 67 to 92 %), Al (ranging from 40 to 48 %), and Cu (ranging from 54 to 81 %) solubilizers were significantly higher in the top rock and soil samples, while the proportion of the highly effective Si (56 %) solubilizers was significantly higher in the middle rock samples. Furthermore, 78, 96, and 6 % of bacteria from the top rocks, soils, and middle rocks, respectively, significantly acidified the culture medium (pH < 4.0) in the rock dissolution process. Most rock-weathering bacteria (79 %) from the rocks were different to those from the soils and most of them (species level) have not been previously reported. Furthermore, location-specific rock-weathering bacterial populations were found and Bacillus species were the most (66 %) frequently isolated rock-weathering bacteria in the rocks based on cultivation methods. Notably, the top rocks and soils had the highest and lowest diversity of rock-weathering bacterial populations, respectively. The results suggested location-related differences in element (Si, Al, Fe, and Cu) releasing effectiveness and communities of rock-weathering bacteria along the hillside of the rock mountain.

Mineral Types and Tree Species Determine the Functional and Taxonomic Structures of Forest Soil Bacterial Communities

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.

Biofilm adaptation to iron availability in the presence of biotite and consequences for chemical weathering

Bacteria in nature often live within biofilms, exopolymeric matrices that provide a favorable environment that can differ markedly from their surroundings. Biofilms have been found growing on mineral surfaces and are expected to play a role in weathering those surfaces, but a clear understanding of how environmental factors, such as trace-nutrient limitation, influence this role is lacking. Here, we examine biofilm development by Pseudomonas putida in media either deficient or sufficient in Fe during growth on biotite, an Fe rich mineral, or on glass. We hypothesized that the bacteria would respond to Fe deficiency by enhancing biotite dissolution and by the formation of binding sites to inhibit Fe leaching from the system. Glass coupons acted as a no-Fe control to investigate whether biofilm response depended on the presence of Fe in the supporting solid. Biofilms grown on biotite, as compared to glass, had significantly greater biofilm biomass, specific numbers of viable cells (SNVC), and biofilm cation concentrations of K, Mg, and Fe, and these differences were greater when Fe was deficient in the medium. Scanning electron microscopy (SEM) confirmed that biofilm growth altered the biotite surface, smoothing the rough, jagged edges of channels scratched by hand on the biotite, and dissolving away small, easy-to-access particles scattered across the planar surface. High-resolution magic angle spinning proton nuclear magnetic resonance (HRMAS ¹ H NMR) spectroscopy showed that, in the Fe-deficient medium, the relative amount of polysaccharide nearly doubled relative to that in biofilms grown in the medium amended with Fe. The results imply that the bacteria responded to the Fe deficiency by obtaining Fe from biotite and used the biofilm matrix to enhance weathering and as a sink for released cation nutrients. These results demonstrate one mechanism by which biofilms may help soil microbes overcome nutrient deficiencies in oligotrophic systems.

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

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.

Temporal changes of bacterial communities in the Tuber melanosporum ectomycorrhizosphere during ascocarp development

Ectomycorrhizae create a multitrophic ecosystem formed by the association between tree roots, mycelium of the ectomycorrhizal fungus, and a complex microbiome. Despite their importance in the host tree's physiology and in the functioning of the ectomycorrhizal symbiosis, detailed studies on ectomycorrhiza-associated bacterial community composition and their temporal dynamics are rare. Our objective was to investigate the composition and dynamics of Tuber melanosporum ectomycorrhiza-associated bacterial communities from summer to winter seasons in a Corylus avellana tree plantation. We used 16S ribosomal RNA (rRNA)-based pyrosequencing to compare the bacterial community structure and the richness in T. melanosporum's ectomycorrhizae with those of the bulk soil. The T. melanosporum ectomycorrhizae harbored distinct bacterial communities from those of the bulk soil, with an enrichment in Alpha- and Gamma-proteobacteria. In contrast to the bacterial communities of truffle ascocarps that vastly varies in composition and richness during the maturation of the fruiting body and to those from the bulk soil, T. melanosporum ectomycorrhiza-associated bacterial community composition stayed rather stable from September to January. Our results fit with a recent finding from the same experimental site at the same period that a continuous supply of carbohydrates and nitrogen occurs from ectomycorrhizae to the fruiting bodies during the maturation of the ascocarps. We propose that this creates a stable niche in the ectomycorrhizosphere although the phenology of the tree changes.

Specific impacts of beech and Norway spruce on the structure and diversity of the rhizosphere and soil microbial communities

The impacts of plant species on the microbial communities and physico-chemical characteristics of soil are well documented for many herbs, grasses and legumes but much less so for tree species. Here, we investigate by rRNA and ITS amplicon sequencing the diversity of microorganisms from the three domains of life (Archaea, Bacteria and Eukaryota:Fungi) in soil samples taken from the forest experimental site of Breuil-Chenue (France). We discovered significant differences in the abundance, composition and structure of the microbial communities associated with two phylogenetically distant tree species of the same age, deciduous European beech (Fagus sylvatica) and coniferous Norway spruce (Picea abies Karst), planted in the same soil. Our results suggest a significant effect of tree species on soil microbiota though in different ways for each of the three microbial groups. Fungal and archaeal community structures and compositions are mainly determined according to tree species, whereas bacterial communities differ to a great degree between rhizosphere and bulk soils, regardless of the tree species. These results were confirmed by quantitative PCR, which revealed significant enrichment of specific bacterial genera, such as Burkholderia and Collimonas, known for their ability to weather minerals within the tree root vicinity.

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

Soil 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.

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

We 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).

Pioneer microbial communities of the Fimmvörðuháls lava flow, Eyjafjallajökull, Iceland

Little is understood regarding the phylogeny and metabolic capabilities of the earliest colonists of volcanic rocks, yet these data are essential for understanding how life becomes established in and interacts with the planetary crust, ultimately contributing to critical zone processes and soil formation. Here, we report the use of molecular and culture-dependent methods to determine the composition of pioneer microbial communities colonising the basaltic Fimmvörðuháls lava flow at Eyjafjallajökull, Iceland, formed in 2010. Our data show that 3 to 5 months post eruption, the lava was colonised by a low-diversity microbial community dominated by Betaproteobacteria, primarily taxa related to non-phototrophic diazotrophs such as Herbaspirillum spp. and chemolithotrophs such as Thiobacillus. Although successfully cultured following enrichment, phototrophs were not abundant members of the Fimmvörðuháls communities, as revealed by molecular analysis, and phototrophy is therefore not likely to be a dominant biogeochemical process in these early successional basalt communities. These results contrast with older Icelandic lava of comparable mineralogy, in which phototrophs comprised a significant fraction of microbial communities, and the non-phototrophic community fractions were dominated by Acidobacteria and Actinobacteria.

Depth-related changes in community structure of culturable mineral weathering bacteria and in weathering patterns caused by them along two contrasting soil profiles

Bacteria play important roles in mineral weathering and soil formation. However, few reports of mineral weathering bacteria inhabiting subsurfaces of soil profiles have been published, raising the question of whether the subsurface weathering bacteria are fundamentally distinct from those in surface communities. To address this question, we isolated and characterized mineral weathering bacteria from two contrasting soil profiles with respect to their role in the weathering pattern evolution, their place in the community structure, and their depth-related changes in these two soil profiles. The effectiveness and pattern of bacterial mineral weathering were different in the two profiles and among the horizons within the respective profiles. The abundance of highly effective mineral weathering bacteria in the Changshu profile was significantly greater in the deepest horizon than in the upper horizons, whereas in the Yanting profile it was significantly greater in the upper horizons than in the deeper horizons. Most of the mineral weathering bacteria from the upper horizons of the Changshu profile and from the deeper horizons of the Yanting profile significantly acidified the culture media in the mineral weathering process. The proportion of siderophore-producing bacteria in the Changshu profile was similar in all horizons except in the Bg2 horizon, whereas the proportion of siderophore-producing bacteria in the Yanting profile was higher in the upper horizons than in the deeper horizons. Both profiles existed in different highly depth-specific culturable mineral weathering community structures. The depth-related changes in culturable weathering communities were primarily attributable to minor bacterial groups rather than to a change in the major population structure.

Functional profiling and distribution of the forest soil bacterial communities along the soil mycorrhizosphere continuum

An ectomycorrhiza is a multitrophic association between a tree root, an ectomycorrhizal fungus, free-living fungi and the associated bacterial communities. Enzymatic activities of ectomycorrhizal root tips are therefore result of the contribution from different partners of the symbiotic organ. However, the functional potential of the fungus-associated bacterial communities remains unknown. In this study, a collection of 80 bacterial strains randomly selected and isolated from a soil-ectomycorrhiza continuum (oak-Scleroderma citrinum ectomycorrhizas, the ectomycorrhizosphere and the surrounding bulk soil) were characterized. All the bacterial isolates were identified by partial 16S rRNA gene sequences as members of the genera Burkholderia, Collimonas, Dyella, Mesorhizobium, Pseudomonas, Rhizobium and Sphingomonas. The bacterial strains were then assayed for β-xylosidase, β-glucosidase, N-acetyl-hexosaminidase, β-glucuronidase, cellobiohydrolase, phosphomonoesterase, leucine-aminopeptidase and laccase activities, chitin solubilization and auxin production. Using these bioassays, we demonstrated significant differences in the functional distribution of the bacterial communities living in the different compartments of the soil-ectomycorrhiza continuum. The surrounding bulk soil was significantly enriched in bacterial isolates capable of hydrolysing cellobiose and N-acetylglucosamine. In contrast, the ectomycorrhizosphere appeared significantly enriched in bacterial isolates capable of hydrolysing glucopyranoside and chitin. Notably, chitinase and laccase activities were found only in bacterial isolates belonging to the Collimonas and Pseudomonas genera. Overall, the results suggest that the ectomycorrhizal fungi favour specific bacterial communities with contrasting functional characteristics from the surrounding soil.

A short-term mineral amendment impacts the mineral weathering bacterial communities in an acidic forest soil

Mineral amendment (i.e. calcium, phosphorous, potassium and/or magnesium) is a management practice used in forestry to improve nutrient availability and recover soil fertility, especially in nutrient-poor forest ecosystems. However, whether this amendment can lead to modifications of the soil characteristics and an improvement in tree growth, and its impact on the soil bacterial communities, especially the mineral weathering bacterial communities, remains poorly documented. In this study, we investigated the short-term impact of a mineral amendment on the taxonomic and functional structure of the mineral weathering bacterial communities. To do this, a plantation of four-year old oak (Quercus petraea) trees amended with or without dolomite [CaMg(CO3)2] was established in the experimental forest site of Breuil-Chenue, which is characterized by an acidic soil and a low availability of calcium and magnesium. Three years after amendment, soil samples were used to isolate bacteria as well as to determine the soil characteristics and the metabolic potentials of these soil microbial communities. Based on a bioassay for quantifying the solubilisation of inorganic phosphorous, we demonstrate that the bacterial isolates coming from the non-amended bulk soil were significantly more efficient than those from the amended bulk soil. No difference was observed between the bacterial isolates coming from the amended and non-amended rhizospheres. Notably, the taxonomic analyses revealed a dominance of bacterial isolates belonging to the Burkholderia genus in both samples. Overall, our results suggest that the bioavailability of nutritive cations into soil impacts the distribution and the efficacy of mineral weathering bacterial communities coming from the soil but not those coming from the rhizosphere.

Functional assays and metagenomic analyses reveals differences between the microbial communities inhabiting the soil horizons of a Norway spruce plantation

In temperate ecosystems, acidic forest soils are among the most nutrient-poor terrestrial environments. In this context, the long-term differentiation of the forest soils into horizons may impact the assembly and the functions of the soil microbial communities. To gain a more comprehensive understanding of the ecology and functional potentials of these microbial communities, a suite of analyses including comparative metagenomics was applied on independent soil samples from a spruce plantation (Breuil-Chenue, France). The objectives were to assess whether the decreasing nutrient bioavailability and pH variations that naturally occurs between the organic and mineral horizons affects the soil microbial functional biodiversity. The 14 Gbp of pyrosequencing and Illumina sequences generated in this study revealed complex microbial communities dominated by bacteria. Detailed analyses showed that the organic soil horizon was significantly enriched in sequences related to Bacteria, Chordata, Arthropoda and Ascomycota. On the contrary the mineral horizon was significantly enriched in sequences related to Archaea. Our analyses also highlighted that the microbial communities inhabiting the two soil horizons differed significantly in their functional potentials according to functional assays and MG-RAST analyses, suggesting a functional specialisation of these microbial communities. Consistent with this specialisation, our shotgun metagenomic approach revealed a significant increase in the relative abundance of sequences related glycoside hydrolases in the organic horizon compared to the mineral horizon that was significantly enriched in glycoside transferases. This functional stratification according to the soil horizon was also confirmed by a significant correlation between the functional assays performed in this study and the functional metagenomic analyses. Together, our results suggest that the soil stratification and particularly the soil resource availability impact the functional diversity and to a lesser extent the taxonomic diversity of the bacterial communities.

Correlation of the abundance of betaproteobacteria on mineral surfaces with mineral weathering in forest soils

Pyrosequencing-based analysis of 16S rRNA gene sequences revealed a significant correlation between apatite dissolution and the abundance of betaproteobacteria on apatite surfaces, suggesting a role for the bacteria belonging to this phylum in mineral weathering. Notably, the cultivation-dependent approach demonstrated that the most efficient mineral-weathering bacteria belonged to the betaproteobacterial genus Burhkolderia.

Distinct ectomycorrhizospheres share similar bacterial communities as revealed by pyrosequencing-based analysis of 16S rRNA genes

Analysis of the 16S rRNA gene sequences generated from Xerocomus pruinatus and Scleroderma citrinum ectomycorrhizospheres revealed that similar bacterial communities inhabited the two ectomycorrhizospheres in terms of phyla and genera, with an enrichment of the Burkholderia genus. Compared to the bulk soil habitat, ectomycorrhizospheres hosted significantly more Alpha-, Beta-, and Gammaproteobacteria.

Mineral-microbe interactions: biotechnological potential of bioweathering

Mineral-microbe interaction has been a key factor shaping the lithosphere of our planet since the Precambrian. Detailed investigation has been mainly focused on the role of bioweathering in biomining processes, leading to the selection of highly efficient microbial inoculants for the recovery of metals. Here we expand this scenario, presenting additional applications of bacteria and fungi in mineral dissolution, a process with novel biotechnological potential that has been poorly investigated. The ability of microorganisms to trigger soil formation and to sustain plant establishment and growth are suggested as invaluable tools to counteract the expansion of arid lands and to increase crop productivity. Furthermore, interesting exploitations of mineral weathering microbes are represented by biorestoration and bioremediation technologies, innovative and competitive solutions characterized by economical and environmental advantages. Overall, in the future the study and application of the metabolic properties of microbial communities capable of weathering can represent a driving force in the expanding sector of environmental biotechnology.