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

The interplay between microbial communities and soil properties

In recent years, there has been considerable progress in determining the soil properties that influence the structure of the soil microbiome. By contrast, the effects of microorganisms on their soil habitat have received less attention with most previous studies focusing on microbial contributions to soil carbon and nitrogen dynamics. However, soil microorganisms are not only involved in nutrient cycling and organic matter transformations but also alter the soil habitat through various biochemical and biophysical mechanisms. Such microbially mediated modifications of soil properties can have local impacts on microbiome assembly with pronounced ecological ramifications. In this Review, we describe the processes by which microorganisms modify the soil environment, considering soil physics, hydrology and chemistry. We explore how microorganism-soil interactions can generate feedback loops and discuss how microbially mediated modifications of soil properties can serve as an alternative avenue for the management and manipulation of microbiomes to combat soil threats and global change.

Formation of mineral-associated organic matter in temperate soils is primarily controlled by mineral type and modified by land use and management intensity

Formation of mineral-associated organic matter (MAOM) supports the accumulation and stabilization of carbon (C) in soil, and thus, is a key factor in the global C cycle. Little is known about the interplay of mineral type, land use and management intensity in MAOM formation, especially on subdecadal time scales. We exposed mineral containers with goethite or illite, the most abundant iron oxide and phyllosilicate clay in temperate soils, for 5 years in topsoils of 150 forest and 150 grassland sites in three regions across Germany. Results show that irrespective of land use and management intensity, more C accumulated on goethite than illite (on average 0.23 ± 0.10 and 0.06 ± 0.03 mg m-2 mineral surface respectively). Carbon accumulation across regions was consistently higher in coniferous forests than in deciduous forests and grasslands. Structural equation models further showed that thinning and harvesting reduced MAOM formation in forests. Formation of MAOM in grasslands was not affected by grazing. Fertilization had opposite effects on MAOM formation, with the positive effect being mediated by enhanced plant productivity and the negative effect by reduced plant species richness. This highlights the caveat of applying fertilizers as a strategy to increase soil C stocks in temperate grasslands. Overall, we demonstrate that the rate and amount of MAOM formation in soil is primarily driven by mineral type, and can be modulated by land use and management intensity even on subdecadal time scales. Our results suggest that temperate soils dominated by oxides have a higher capacity to accumulate and store C than those dominated by phyllosilicate clays, even under circumneutral pH conditions. Therefore, adopting land use and management practices that increase C inputs into oxide-rich soils that are under their capacity to store C may offer great potential to enhance near-term soil C sequestration.

Microbial dynamics in soils of the Damma glacier forefield show succession in the functional genetic potential

Glacier retreat is a visible consequence of climate change worldwide. Although taxonomic change of the soil microbiomes in glacier forefields have been widely documented, how microbial genetic potential changes along succession is little known. Here, we used shotgun metagenomics to analyse whether the soil microbial genetic potential differed between four stages of soil development (SSD) sampled along three transects in the Damma glacier forefield (Switzerland). The SSDs were characterized by an increasing vegetation cover, from barren soil, to biological soil crust, to sparsely vegetated soil and finally to vegetated soil. Results suggested that SSD significantly influenced microbial genetic potential, with the lowest functional diversity surprisingly occurring in the vegetated soils. Overall, carbohydrate metabolism and secondary metabolite biosynthesis genes overrepresented in vegetated soils, which could be partly attributed to plant-soil feedbacks. For C degradation, glycoside hydrolase genes enriched in vegetated soils, while auxiliary activity and carbohydrate esterases genes overrepresented in barren soils, suggested high labile C degradation potential in vegetated, and high recalcitrant C degradation potential in barren soils. For N-cycling, organic N degradation and synthesis genes dominated along succession, and gene families involved in nitrification were overrepresented in barren soils. Our study provides new insights into how the microbial genetic potential changes during soil formation along the Damma glacier forefield.

Microbial pathways driving stable soil organic carbon change in abandoned Moso bamboo forests in southeast China

Mineral-associated organic carbon (MOC) is a stable component of the soil carbon (C) pool, critical to realize carbon sequestration and coping with climate change. Many Moso bamboo (Phyllostachys edulis) forests in subtropical and tropical areas that used to be intensively managed have been left unmanaged. Still, studies on MOC changes occurring during the transition from intensive management to unmanagement are lacking. Besides, the understanding of the role of microorganisms in MOC accumulation is far from satisfactory. Based on the combination of field investigation and laboratory analysis of 40 Moso bamboo forest sampling plots with different unmanaged chronosequence's in southeast China, we observed the MOC content in Moso bamboo forests left unmanaged for 2-5 years had decreased, whereas that in forests left unmanaged for 11-14 years had increased compared with that in intensively managed forests. Specifically, the MOC contents in forests left unmanaged for 11-14 years were significantly higher than in those under intensive management or unmanaged for 2-5 years. Moreover, we found that microorganisms drove MOC change through two different pathways: (i) more microorganisms led to more soil nutrients, which led to more amino sugars, ultimately resulting in the accumulation of MOC, and (ii) microorganisms promoted the accumulation of MOC by influencing the content of metal oxides (poorly crystalline aluminum oxides and free aluminum oxides). We believe that ignoring the interaction between microorganisms and metal oxides may lead to uncertainty in evaluating the relative contribution of microbial residues to MOC.

Mycorrhizae enhance reactive minerals but reduce mineral-associated carbon

Soil organic carbon (C) is the largest active C pool of Earth's surface and is thus vital in sustaining terrestrial productivity and climate stability. Arbuscular mycorrhizal fungi (AMF) form symbioses with most terrestrial plants and critically modulate soil C dynamics. Yet, it remains unclear whether and how AMF-root associations (i.e., mycorrhizae) interact with soil minerals to affect soil C cycling. Here we showed that the presence of both roots and AMF increased soil dissolved organic C and reactive Fe minerals, as well as litter decomposition and soil CO2 emissions. However, it reduced mineral-associated C. Also, high-resolution nanoscale secondary ion mass spectrometry images showed the existence of a thin coating (0.5-1.0 μm thick) of 56 Fe16 O- (Fe minerals) on the surface of 12 C14 N- (fungal biomass), illustrating the close physical association between fungal hyphae and soil Fe minerals. In addition, AMF genera were divergently related to reactive Fe minerals, with Glomus being positively but Paraglomus and Acaulospora negatively correlated with reactive Fe minerals. Moreover, the presence of roots and AMF, particularly when combined with litter addition, enhanced the abundances of several critical soil bacterial genera that are associated with the formation of reactive minerals in soils. A conceptual framework was further proposed to illustrate how AMF-root associations impact soil C cycling in the rhizosphere. Briefly, root exudates and the inoculated AMF not only stimulated the decomposition of litter and SOC and promoted the production of CO2 emission, but also drove soil C persistence by unlocking mineral elements and promoting the formation of reactive minerals. Together, these findings provide new insights into the mechanisms that underlie the formation of reactive minerals and have significant implications for understanding and managing soil C persistence.

Rhizosphere frame system enables nondestructive live-imaging of legume-rhizobium interactions in the soil

Most plants interact with various soil microorganisms as they grow through the soil. Root nodule symbiosis by legumes and rhizobia is a well-known phenomenon of plant-microbe interactions in the soil. Although microscopic observations are useful for understanding the infection processes of rhizobia, nondestructive observation methods have not been established for monitoring interactions between rhizobia and soil-grown roots. In this study, we constructed Bradyrhizobium diazoefficiens strains that constitutively express different fluorescent proteins, which allows identification of tagged rhizobia by the type of fluorophores. In addition, we constructed a plant cultivation device, Rhizosphere Frame (RhizoFrame), which is a soil-filled container made of transparent acrylic plates that allows observation of roots growing along the acrylic plates. Combining fluorescent rhizobia with RhizoFrame, we established a live imaging system, RhizoFrame system, that enabled us to track the nodulation processes with fluorescence stereomicroscope while retaining spatial information about roots, rhizobia, and soil. Mixed inoculation with different fluorescent rhizobia using RhizoFrame enabled the visualization of mixed infection of a single nodule with two strains. In addition, observation of transgenic Lotus japonicus expressing auxin-responsive reporter genes indicated that RhizoFrame system could be used for a real-time and nondestructive reporter assay. Thus, the use of RhizoFrame system is expected to enhance the study of the spatiotemporal dynamics of plant-microbe interactions in the soil.

Nitrogen-Rich Organic Matter Formation and Stabilization in Iron Ore Tailings: A Submicrometer Investigation

Organic matter (OM) formation and stabilization are critical processes in the eco-engineered pedogenesis of Fe ore tailings, but the underlying mechanisms are unclear. The present 12 month microcosm study has adopted nanoscale secondary ion mass spectrometry (NanoSIMS) and synchrotron-based scanning transmission X-ray microscopy (STXM) techniques to investigate OM formation, molecular signature, and stabilization in tailings at micro- and nanometer scales. In this system, microbial processing of exogenous isotopically labeled OM demonstrated that 13C labeled glucose and 13C/15N labeled plant biomass were decomposed, regenerated, and associated with Fe-rich minerals in a heterogeneous pattern in tailings. Particularly, when tailings were amended with plant biomass, the 15N-rich microbially derived OM was generated and bound to minerals to form an internal organo-mineral association, facilitating further OM stabilization. The organo-mineral associations were primarily underpinned by interactions of carboxyl, amide, aromatic, and/or aliphatic groups with weathered mineral products derived from biotite-like minerals in fresh tailings (i.e., with Fe2+ and Fe3+) or with Fe3+ oxyhydroxides in aged tailings. The study revealed microbial OM generation and subsequent organo-mineral association in Fe ore tailings at the submicrometer scale during early stages of eco-engineered pedogenesis, providing a basis for the development of microbial based technologies toward tailings' ecological rehabilitation.

Clay-associated microbial communities and their relevance for a nuclear waste repository in the Opalinus Clay rock formation

Microorganisms are known to be natural agents of biocorrosion and mineral transformation, thereby potentially affecting the safety of deep geological repositories used for high-level nuclear waste storage. To better understand how resident microbial communities of the deep terrestrial biosphere may act on mineralogical and geochemical characteristics of insulating clays, we analyzed their structure and potential metabolic functions, as well as site-specific mineralogy and element composition from the dedicated Mont Terri underground research laboratory, Switzerland. We found that the Opalinus Clay formation is mainly colonized by Alphaproteobacteria, Firmicutes, and Bacteroidota, which are known for corrosive biofilm formation. Potential iron-reducing bacteria were predominant in comparison to methanogenic archaea and sulfate-reducing bacteria. Despite microbial communities in Opalinus Clay being in majority homogenous, site-specific mineralogy and geochemistry conditions have selected for subcommunities that display metabolic potential for mineral dissolution and transformation. Our findings indicate that the presence of a potentially low-active mineral-associated microbial community must be further studied to prevent effects on the repository's integrity over the long term.

Deep Isolated Aquifer Brines Harbor Atypical Halophilic Microbial Communities in Quebec, Canada

The deep terrestrial subsurface, hundreds of meters to kilometers below the surface, is characterized by oligotrophic conditions, dark and often anoxic settings, with fluctuating pH, salinity, and water availability. Despite this, microbial populations are detected and active, contributing to biogeochemical cycles over geological time. Because it is extremely difficult to access the deep biosphere, little is known about the identity and metabolisms of these communities, although they likely possess unknown pathways and might interfere with deep waste deposits. Therefore, we analyzed rock and groundwater microbial communities from deep, isolated brine aquifers in two regions dating back to the Ordovician and Devonian, using amplicon and whole genome sequencing. We observed significant differences in diversity and community structure between both regions, suggesting an impact of site age and composition. The deep hypersaline groundwater did not contain typical halophilic bacteria, and genomes suggested pathways involved in protein and hydrocarbon degradation, and carbon fixation. We identified mainly one strategy to cope with osmotic stress: compatible solute uptake and biosynthesis. Finally, we detected many bacteriophage families, potentially indicating that bacteria are infected. However, we also found auxiliary metabolic genes in the viral genomes, probably conferring an advantage to the infected hosts.

Effects of Mineral on Taxonomic and Functional Structures of Microbial Community in Tengchong Hot Springs via in-situ cultivation

Diverse mineralogical compositions occur in hot spring sediments, but the impact of minerals on the diversity and structure of microbial communities remains poorly elucidated. In this study, different mineral particles with various chemistries (i.e., hematite, biotite, K-feldspar, quartz, muscovite, aragonite, serpentine, olivine, barite, apatite, and pyrite) were incubated for ten days in two Tengchong hot springs, one alkaline (pH ~ 8.34) with a high temperature (~ 82.8 °C) (Gumingquan, short as GMQ) and one acidic (pH ~ 3.63) with a relatively low temperature (~ 43.3 °C) (Wenguangting, short as WGT), to determine the impacts of minerals on the microbial communities taxonomic and functional diversities. Results showed that the mineral-associated bacterial taxa differed from those of the bulk sediment samples in the two hot springs. The relative abundance of Proteobacteria, Euryarchaeota, and Acidobacteria increased in all minerals, indicating that these microorganisms are apt to colonize on solid surfaces. The α-diversity indices of the microbial communities on the mineral surfaces in the WGT were higher than those from the bulk sediment samples (p < 0.05), which may be caused by the stochastically adhering process on the mineral surface during 10-day incubation, different from the microbial community in sediment which has experienced long-term environmental and ecological screening. Chemoheterotrophy increased with minerals incubation, which was high in most cultured minerals (the relative contents were 5.8 - 21.4%). Most notably, the sulfate respiration bacteria (mainly related to Desulfobulbaceae and Syntrophaceae) associated with aragonite in the acidic hot spring significantly differed from other minerals, possibly due to the pH buffering effect of aragonite providing more favorable conditions for their survival and proliferation. By comparison, aragonite cultured in the alkaline hot spring highly enriched denitrifying bacteria and may have promoted the nitrogen cycle within the system. Collectively, we speculated that diverse microbes stochastically adhered on the surface of minerals in the water flows, and the physicochemical properties of minerals drove the enrichment of certain microbial communities and functional groups during the short-term incubation. Taken together, these findings thereby provide novel insights into mechanisms of community assembly and element cycling in the terrestrial hydrothermal system associated with hot springs.

Effects of natural non-volcanic CO2 leakage on soil microbial community composition and diversity

Geological carbon capture and storage (CCS) can reduce anthropogenic CO₂ emissions, but questions exist about impacts at the surface if CO₂ leaks from deep storage reservoirs. To examine potential impacts on soils, previous studies have investigated the geochemistry and microbiology of volcanic soils hosting high fluxes of CO₂ rich gas. This study builds on those previous investigations by considering impacts of CO₂ leakage at a non-volcanic site, where deep geogenic CO₂ leaks from a cracked well casing. At the site, we collected 26 soil cores adjacent to soil gas monitoring wells. Based on measured CO₂ fluxes, the soil samples fall into two groups 1) high CO₂ (flux = 304.6 ± 272.1 g m^-2 d^-1, conc. = 29.1 ± 34 %) and 2) low CO₂ (flux = 15.8 ± 6.1 g m^-2 d^-1, conc. = 0.8 ± 0.9 %). Soil pH was significantly lower (p < 0.05) in high flux group samples (4.6 ± 0.3) than the low flux ones (5.3 ± 0.7). Beta diversity calculations using 16S rRNA gene sequences and redundancy analysis (RDA) revealed clear clustering of microbial communities relative to CO₂ flux and significant correlations of community composition with pH and organic carbon content. In the high flux soils, abundant microbial groups included Acidobacteriota, Ktedonobacteria, and SC-I-84 in the phylum Proteobacteria, as well as Nitrososphaeria, a genus of ammonia oxidizing archaea. Compared to volcanic sites described previously, our non-volcanic site had slight differences in soil geochemical properties and gradual shifts in community compositions between CO₂ hotspots and background locations. Moreover, the elevated abundance of SC-I-84 has not been reported in studies of volcanic sites. This study improves our ability to predict potential environmental impacts of geological CCS by expanding the range of conditions over which existing CO₂ leakage has been observed.

Current controversies on mechanisms controlling soil carbon storage: implications for interactions with practitioners and policy-makers. A review

There is currently an intense debate about the potential for additional organic carbon storage in soil, the strategies by which it may be accomplished and what the actual benefits might be for agriculture and the climate. Controversy forms an essential part of the scientific process, but on the topic of soil carbon storage, it may confuse the agricultural community and the general public and may delay actions to fight climate change. In an attempt to shed light on this topic, the originality of this article lies in its intention to provide a balanced description of contradictory scientific opinions on soil carbon storage and to examine how the scientific community can support decision-making despite the controversy. In the first part, we review and attempt to reconcile conflicting views on the mechanisms controlling organic carbon dynamics in soil. We discuss the divergent opinions about chemical recalcitrance, the microbial or plant origin of persistent soil organic matter, the contribution of particulate organic matter to additional organic carbon storage in soil, and the spatial and energetic inaccessibility of soil organic matter to decomposers. In the second part, we examine the advantages and limitations of big data management and modeling, which are essential tools to link the latest scientific theories with the actions taken by stakeholders. Finally, we show how the analysis and discussion of controversies can guide scientists in supporting stakeholders for the design of (i) appropriate trade-offs for biomass use in agriculture and forestry and (ii) climate-smart management practices, keeping in mind their still unresolved effects on soil carbon storage.

Coriander (Coriandrum sativum) Cultivation Combined with Arbuscular Mycorrhizal Fungi Inoculation and Steel Slag Application Influences Trace Elements-Polluted Soil Bacterial Functioning

The cultivation of aromatic plants for the extraction of essential oils has been presented as an innovative and economically viable alternative for the remediation of areas polluted with trace elements (TE). Therefore, this study focuses on the contribution of the cultivation of coriander and the use of arbuscular mycorrhizal fungi (AMF) in combination with mineral amendments (steel slag) on the bacterial function of the rhizosphere, an aspect that is currently poorly understood and studied. The introduction of soil amendments, such as steel slag or mycorrhizal inoculum, had no significant effect on coriander growth. However, steel slag changed the structure of the bacterial community in the rhizosphere without affecting microbial function. In fact, Actinobacteria were significantly less abundant under slag-amended conditions, while the relative proportion of Gemmatimonadota increased. On the other hand, the planting of coriander affects the bacterial community structure and significantly increased the bacterial functional richness of the amended soil. Overall, these results show that planting coriander most affected the structure and functioning of bacterial communities in the TE-polluted soils and reversed the effects of mineral amendments on rhizosphere bacterial communities and their activities. This study highlights the potential of coriander, especially in combination with steel slag, for phytomanagement of TE-polluted soils, by improving soil quality and health.

Dichotomous Role of Humic Substances in Modulating Transformation of Antibiotic Resistance Genes in Mineral Systems

Widespread antibiotic resistance genes (ARGs) have emerged as a focus of attention for public health. Transformation is essential for ARGs dissemination in soils and associated environments; however, the mechanisms of how soil components contribute to the transformation of ARGs remain elusive. Here we demonstrate that three representative mineral-humic acid (HA) composites exert contrasting influence on the transformation of plasmid-borne ARGs in Bacillus subtilis. Mineral surface-bound HA facilitated transformation in kaolinite and montmorillonite systems, while an inhibitory effect of HA was observed for goethite. The elevated transformation by HA-coated kaolinite was mainly attributed to the enhanced activity of competence-stimulating factor (CSF), while increased transformation by montmorillonite-HA composites was assigned to the weakened adsorption affinity of DNA and enhanced gene expression induced by flagella-driven cell motility. In goethite system, HA played an overriding role in suppressing transformation via alleviation of cell membrane damage. The results obtained offer insights into the divergent mechanisms of humic substances in modulating bacterial transformation by soil minerals. Our findings would help for a better understanding on the fate of ARGs in soil systems and provide potentials for the utilization of soil components, particularly organic matter, to mitigate the spread of ARGs in a range of settings.

Impact of salinity origin on microbial communities in saline springs within the Illinois Basin, USA

Saline springs within the Illinois Basin result from the discharge of deep-seated evaporated seawater (brine) and likely contain diverse and complex microbial communities that are poorly understood. In this study, seven saline/mineral springs with different geochemical characteristics and salinity origins were investigated using geochemical and molecular microbiological analyses to reveal the composition of microbial communities inhabiting springs and their key controlling factors. The 16S rRNA sequencing results demonstrated that each spring harbours a unique microbial community influenced by its geochemical properties and subsurface conditions. The microbial communities in springs that originated from Cambrian/Ordovician strata, which are deep confined units that have limited recharge from overlying formations, share a greater similarity in community composition and have a higher species richness and more overlapped taxa than those that originated from shallower Pennsylvanian strata, which are subject to extensive regional surface and groundwater recharge. The microbial distribution along the spring flow paths at the surface indicates that 59.8%-94.2% of total sequences in sedimentary samples originated from spring water, highlighting the role of springs in influencing microbiota in the immediate terrestrial environment. The results indicate that the springs introduce microbiota with a high biodiversity into surface terrestrial or aquatic ecosystems, potentially affecting microbial reservoirs in downstream ecosystems.

Nano- to Global-Scale Uncertainties in Terrestrial Enhanced Weathering

Enhanced weathering (EW) is one of the most promising negative emissions technologies urgently needed to limit global warming to at least below 2 °C, a goal recently reaffirmed at the UN Global Climate Change conference (i.e., COP26). EW relies on the accelerated dissolution of crushed silicate rocks applied to soils and is considered a sustainable solution requiring limited technology. While EW has a high theoretical potential of sequestering CO₂, research is still needed to provide accurate estimates of carbon (C) sequestration when applying different silicate materials across distinct climates and major soil types in combination with a variety of plants. Here we elaborate on fundamental advances that must be addressed before EW can be extensively adopted. These include identifying the most suitable environmental conditions, improving estimates of field dissolution rates and efficacy of CO₂ removal, and identifying alternative sources of silicate materials to meet future EW demands. We conclude with considerations on the necessity of integrated modeling-experimental approaches to better coordinate future field experiments and measurements of CO₂ removal, as well as on the importance of seamlessly coordinating EW with cropland and forest management.

Exploration of pristine plate-tectonic plains and mining exposure areas for indigenous microbial communities and its impact on the mineral-microbial geochemical weathering process in ultramafic setting

Heavy metal release from harsh ultramafic settings influences microbial diversity and function in soil ecology. This study aimed to determine how serpentine mineralosphere bacterial assemblies and their functions differed in two different plate-tectonic plains and mining exposure sites under heavy metal release conditions. The results showed that the Proteobacteria, Actinobacteria, Cyanobacteria, Planctomycetes, and Chloroflexi were the most abundant bacterial groups among all the sites. The log10-based LDA scores highlighted that some specific groups of bacterial assemblies were enriched in plate-tectonic plains and mining activity areas of the serpentine mineralosphere. Functional prediction revealed that the abundance of heavy metal (Cr and Ni) resistance and biogeochemical cycles involving functional KEGG orthology varied in samples from plate-tectonic plains and mining activity sites. The bipartite plot showed that the enrichment of the biogeochemical cycle and heavy metal resistance functional genes correlated with the abundance of serpentine mineralosphere bacterial groups at a 0.005% confidence level. The co-occurrence network plot revealed that the interconnection pattern of the indigenous bacterial assemblies changed in different plate-tectonic plains and mining exposure areas. Finally, this study concluded that due to heavy metal release, the variation in bacterial assemblies, their functioning, and intercommunity co-occurrence patterns were clarified the synergetic effect of mineral-microbial geochemical weathering process in serpentine mining areas.

Growth, biofilm formation and atrazine degrading gene (trzN) expression of Arthrobacter sp. DNS10 cultured with montmorillonite, kaolinite and goethite

The viable and degradation potential of the strains which adhered to soil minerals are essential for eliminating organic pollutants from soil. Herein, the interaction (growth, biofilm formation and survive) of Arthrobacter sp. DNS10, an atrazine degrading strain, with three kinds of typical soil minerals, such as montmorillonite, kaolinite and goethite, as well as the atrazine degradation gene (trzN) expression of the strain in the minerals system were studied. The results showed that montmorillonite had significant promotion effect on the growth of strain DNS10, followed by kaolinite, but goethite significantly inhibited the growth of strain DNS10. In contrast, goethite notably promoted the biofilm formation and there was less biofilm detected in montmorillonite containing system. The percentage of the survival bacteria in the biofilm that formed on montmorillonite, kaolinite and goethite was 53.8%, 40.8% and 28.2%. In addition, there were more reactive oxygen species (ROS) were detected in the cells that exposed to goethite than those of the cells exposed to kaolinite and montmorillonite. These results suggest that the electrostatic repulsion between kaolinite/montmorillonite and strain DNS10 prevents them from contacting each other and facilitates bacterial growth by allowing the strain to obtain more nutrients. Oppositely, the needle-like morphology of goethite might damage the strain DNS10 cell when they were combined by electrostatic attraction, and the goethite induced ROS also aggravate the cytotoxicity of goethite on strain DNS10. In addition, the relative transcription of trzN in the cells contacted with montmorillonite, kaolinite and goethite was 0.94-, 0.27- and 0.20- fold of the no mineral exposure treatment. Briefly, this research suggests that the minerals with different structure and/or physicochemical characteristics might cause various trend for the biofilm formation and degradation potential of the bacteria.

Insights into phenanthrene attenuation by hydroxyl radicals from reduced iron-bearing mineral oxygenation

The oxygenation of Fe(II)-bearing minerals for hydroxyl radicals (HO^•) formation and contaminant attenuation receive increasing attention, while the mechanisms for specific Fe(II) species in manipulating HO^• formation and contaminant attenuation are unclear. Herein, a total of four Fe(III)-bearing minerals were applied in the reduction-oxygenation processes to produce HO^•. Results showed that the total HO^• generated from the Fe-(oxyhydr)oxides were significantly higher than those from the Fe-silicates, with the order of goethite and hematite (~1500 μmol kg^-1) > Fe-montmorillonite (~550 μmol kg^-1) > chlorite (~120 μmol kg^-1). The HO^• formation was largely hinged on the reactive Fe(II) species, i.e., the surface-adsorbed/low-crystalline Fe(II) in the Fe-bearing minerals. For the co-incubation of minerals and phenanthrene, the concentrations of phenanthrene decreased from the initial 3.0 mg L^-1 to 0.7 mg L^-1 and 1.9 mg L^-1 for Fe-montmorillonite and goethite, respectively, suggesting the HO^• mediated by the Fe-montmorillonite was more conducive for phenanthrene attenuation. The goethite tended to promote the formation of free HO^•, while the Fe-montmorillonite with interlayer structure can provide attachment sites for the surface-adsorbed/low-crystalline Fe(II), resulting in high potential for surface-bound HO^• formation and phenanthrene attenuation. This study highlights the importance of Fe-bearing minerals in manipulating HO^• formation, providing new insight into the removal of contaminants in ecosystems.

Bacterial Community with Plant Growth-Promoting Potential Associated to Pioneer Plants from an Active Mexican Volcanic Complex

Microorganisms in extreme volcanic environments play an important role in the development of plants on newly exposed substrates. In this work, we studied the structure and diversity of a bacterial community associated to Andropogon glomeratus and Cheilanthes aemula at El Chichón volcano. The genetic diversity of the strains was revealed by genomic fingerprints and by 16S rDNA gene sequencing. Furthermore, a metagenomic analysis of the rhizosphere samples was carried out for pioneer plants growing inside and outside the volcano. Multifunctional biochemical tests and plant inoculation assays were evaluated to determine their potential as plant growth-promoting bacteria (PGPB). Through metagenomic analysis, a total of 33 bacterial phyla were identified from A. glomeratus and C. aemula rhizosphere samples collected inside the volcano, and outside the volcano 23 bacterial phyla were identified. For both rhizosphere samples, proteobacteria was the most abundant phylum. With a cultivable approach, 174 bacterial strains were isolated from the rhizosphere and tissue of plants growing outside the volcanic complex. Isolates were classified within the genera Acinetobacter, Arthrobacter, Bacillus, Burkholderia, Cupriavidus, Enterobacter, Klebsiella, Lysinibacillus, Pantoea, Pseudomonas, Serratia, Stenotrophomonas and Pandoraea. The evaluated strains were able to produce indole compounds, solubilize phosphate, synthesize siderophores, showed ACC deaminase and nitrogenase activity, and they had a positive effect on the growth and development of Capsicum chinense. The wide diversity of bacteria associated to pioneer plants at El Chichón volcano with PGPB qualities represent an alternative for the recovery of eroded environments, and they can be used efficiently as biofertilizers for agricultural crops growing under adverse conditions.

A critical review of mineral-microbe interaction and coevolution: mechanisms and applications

The mineral-microbe interactions play important roles in environmental change, biogeochemical cycling of elements, and formation of ore deposits. Minerals provide both beneficial (physical and chemical protection, nutrients, and energy) and detrimental (toxic substances and oxidative pressure) effects to microbes, resulting in mineral-specific microbial colonization. Microbes impact dissolution, transformation, and precipitation of minerals through their activity, resulting in either genetically-controlled or metabolism-induced biomineralization. Through these interactions minerals and microbes coevolve through Earth history. The mineral-microbe interactions typically occur at microscopic scale but the effect is often manifested at global scale. Despite advances achieved through decades of research, major questions remain. Four areas are identified for future research: integrating mineral and microbial ecology, establishing mineral biosignatures, linking laboratory mechanistic investigation to field observation, and manipulating mineral-microbe interactions for the benefit of humankind.

Neglected resistance risks: Cooperative resistance of antibiotic resistant bacteria influenced by primary soil components

Various antibiotic resistant bacteria (ARB) can thrive in soil and resist such environmental pressures as antibiotics through cooperative resistance, thereby promoting ARB retention and antibiotic resistance genes transmission. However, there has been finite knowledge in regard to the mechanisms and potential ecological risks of cooperative resistance in soil microbiome. In this study, soil minerals and organic matters were designed to treat a mixture of two Escherichia coli strains with different antibiotic resistance (E. coli DH5α/pUC19 and E. coli XL2-Blue) to determine how soil components affected cooperative resistance, and Luria-Bertani plates containing two antibiotics were used to observe dual-drug resistant bacteria (DRB) developed via cooperative resistance. Results showed quartz, humic acid, and biochar promoted E. coli XL2-Blue with high fitness costs, whereas kaolin, montmorillonite, and soot inhibited both strains. Using fluorescence microscope and PCR, it was speculated DRB could resist the antibiotic pressure via E. coli XL2-Blue coating E. coli DH5α/pUC19. E. coli DH5α/pUC19 dominated cooperative resistance. Correlation analysis and scanning electron microscope images indicated soil components influenced cooperative resistance. Biochar promoted cooperative resistance by increasing intracellular reactive oxygen species, thereby reducing the dominant strain concentration required for DRB development. Kaolin inhibited cooperative resistance the most, followed by soot and montmorillonite.

Soil minerals affect taxon-specific bacterial growth

Secondary minerals (clays and metal oxides) are important components of the soil matrix. Clay minerals affect soil carbon persistence and cycling, and they also select for distinct microbial communities. Here we show that soil mineral assemblages-particularly short-range order minerals-affect both bacterial community composition and taxon-specific growth. Three soils with different parent material and presence of short-range order minerals were collected from ecosystems with similar vegetation and climate. These three soils were provided with ¹⁸O-labeled water and incubated with or without artificial root exudates or pine needle litter. Quantitative stable isotope probing was used to determine taxon-specific growth. We found that the growth of bacteria varied among soils of different mineral assemblages but found the trend of growth suppression in the presence of short-range order minerals. Relative growth of bacteria declined with increasing concentration of short-range order minerals between 25-36% of taxa present in all soils. Carbon addition in the form of plant litter or root exudates weakly affected relative growth of taxa (p = 0.09) compared to the soil type (p < 0.01). However, both exudate and litter carbon stimulated growth for at least 34% of families in the soils with the most and least short-range order minerals. In the intermediate short-range order soil, fresh carbon reduced growth for more bacterial families than were stimulated. These results highlight how bacterial-mineral-substrate interactions are critical to soil organic carbon processing, and how growth variation in bacterial taxa in these interactions may contribute to soil carbon persistence and loss.

Shotgun Metagenomics of Deep Forest Soil Layers Show Evidence of Altered Microbial Genetic Potential for Biogeochemical Cycling

Soil microorganisms such as Bacteria and Archaea play important roles in the biogeochemical cycling of soil nutrients, because they act as decomposers or are mutualistic or antagonistic symbionts, thereby influencing plant growth and health. In the present study, we investigated the vertical distribution of soil metagenomes to a depth of 1.5 m in Swiss forests of European beech and oak species on calcareous bedrock. We explored the functional genetic potential of soil microorganisms with the aim to disentangle the effects of tree genus and soil depth on the genetic repertoire, and to gain insight into the microbial C and N cycling. The relative abundance of reads assigned to taxa at the domain level indicated a 5–10 times greater abundance of Archaea in the deep soil, while Bacteria showed no change with soil depth. In the deep soil there was an overrepresentation of genes for carbohydrate-active enzymes, which are involved in the catalyzation of the transfer of oligosaccharides, as well as in the binding of carbohydrates such as chitin or cellulose. In addition, N-cycling genes (NCyc) involved in the degradation and synthesis of N compounds, in nitrification and denitrification, and in nitrate reduction were overrepresented in the deep soil. Consequently, our results indicate that N-transformation in the deep soil is affected by soil depth and that N is used not only for assimilation but also for energy conservation, thus indicating conditions of low oxygen in the deep soil. Using shotgun metagenomics, our study provides initial findings on soil microorganisms and their functional genetic potential, and how this may change depending on soil properties, which shift with increasing soil depth. Thus, our data provide novel, deeper insight into the “dark matter” of the soil.

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.

Remineralizing soils? The agricultural usage of silicate rock powders: A review

Soil nutrient depletion threatens global food security and has been seriously underestimated for potassium (K) and several micronutrients. This is particularly the case for highly weathered soils in tropical countries, where classical soluble fertilizers are often not affordable or not accessible. One way to replenish macro- and micronutrients are ground silicate rock powders (SRPs). Rock forming silicate minerals contain most nutrients essential for higher plants, yet slow and inconsistent weathering rates have restricted their use in the past. Recent findings, however, challenge past agronomic objections which insufficiently addressed the factorial complexity of the weathering process. This review therefore first presents a framework with the most relevant factors for the weathering of SRPs through which several outcomes of prior studies can be explained. A subsequent analysis of 48 crop trials reveals the potential as alternative K source and multi-nutrient soil amendment for tropical soils, whereas the benefits for temperate soils are currently inconclusive. Beneficial results prevail for mafic and ultramafic rocks like basalts and rocks containing nepheline or glauconite. Several rock modifications are highly efficient in increasing the agronomic effectiveness of SRPs. Enhanced weathering of SRPs could additionally sequester substantial amounts of CO₂ from the atmosphere and silicon (Si) supply can induce a broad spectrum of plant biotic and abiotic stress resistance. Recycling massive amounts of rock residues from domestic mining industries could furthermore resolve serious disposal challenges and improve fertilizer self-sufficiency. In conclusion, under the right circumstances, SRPs could not only advance low-cost and regional soil sustaining crop production but contribute to various sustainable development goals.

Microbial community structure in hadal sediments: high similarity along trench axes and strong changes along redox gradients

Hadal trench sediments are hotspots of biogeochemical activity in the deep sea, but the biogeochemical and ecological factors that shape benthic hadal microbial communities remain unknown. Here, we sampled ten hadal sites from two trench regions with a vertical resolution of down to 1 cm. We sequenced 16S rRNA gene amplicons using universal and archaea-specific primer sets and compared the results to biogeochemical parameters. Despite bathymetric and depositional heterogeneity we found a high similarity of microbial communities within each of the two trench axes, while composition at the phylum level varied strongly with sediment depth in conjunction with the redox stratification into oxic, nitrogenous, and ferruginous zones. As a result, communities of a given sediment horizon were more similar to each other across a distance of hundreds of kilometers within each trench, than to those of adjacent horizons from the same sites separated only by centimeters. Total organic carbon content statistically only explained a small part of the variation within and between trenches, and did not explain the community differences observed between the hadal and adjacent shallower sites. Anaerobic taxa increased in abundance at the top of the ferruginous zone, seeded by organisms deposited at the sediment surface and surviving burial through the upper redox zones. While an influence of other potential factors such as geographic isolation, hydrostatic pressure, and non-steady state depositional regimes could not be discerned, redox stratification and diagenesis appear to be the main selective forces that structure community composition in hadal sediments.

Root Carbon Interaction with Soil Minerals Is Dynamic, Leaving a Legacy of Microbially Derived Residues

Minerals preserve the oldest, most persistent soil carbon, and mineral characteristics appear to play a critical role in the formation of soil organic matter (SOM) associations. To test the hypothesis that roots, and differences in carbon source and microbial communities, influence mineral SOM associations over short timescales, we incubated permeable mineral bags in soil microcosms with and without plants, inside a ¹³CO₂ labeling chamber. Mineral bags contained quartz, ferrihydrite, kaolinite, or soil minerals isolated via density separation. Using ¹³C-nuclear magnetic resonance, Fourier transform ion cyclotron resonance mass spectrometry, and lipidomics, we traced carbon deposition onto minerals, characterizing total carbon, ¹³C enrichment, and SOM chemistry over three growth stages of Avena barbata. Carbon accumulation was rapid and mineral-dependent but slowed with time; the accumulated amount was not significantly affected by root presence. However, plant roots strongly shaped the chemistry of mineral-associated SOM. Minerals incubated in a plant rhizosphere were associated with a more diverse array of compounds (with different functional groups-carbonyl, aromatics, carbohydrates, and lipids) than minerals incubated in an unplanted bulk soil control. We also found that many of the lipids that sorbed to minerals were microbially derived, including many fungal lipids. Together, our data suggest that diverse rhizosphere-derived compounds may represent a transient fraction of mineral SOM, rapidly exchanging with mineral surfaces.

A Taxon-Wise Insight Into Rock Weathering and Nitrogen Fixation Functional Profiles of Proglacial Systems

The Arctic environment is particularly affected by global warming, and a clear trend of the ice retreat is observed worldwide. In proglacial systems, the newly exposed terrain represents different environmental and nutrient conditions compared to later soil stages. Therefore, proglacial systems show several environmental gradients along the soil succession where microorganisms are active protagonists of the soil and carbon pool formation through nitrogen fixation and rock weathering. We studied the microbial succession of three Arctic proglacial systems located in Svalbard (Midtre Lovénbreen), Sweden (Storglaciären), and Greenland (foreland close to Kangerlussuaq). We analyzed 65 whole shotgun metagenomic soil samples for a total of more than 400 Gb of sequencing data. Microbial succession showed common trends typical of proglacial systems with increasing diversity observed along the forefield chronosequence. Microbial trends were explained by the distance from the ice edge in the Midtre Lovénbreen and Storglaciären forefields and by total nitrogen (TN) and total organic carbon (TOC) in the Greenland proglacial system. Furthermore, we focused specifically on genes associated with nitrogen fixation and biotic rock weathering processes, such as nitrogenase genes, obcA genes, and genes involved in cyanide and siderophore synthesis and transport. Whereas we confirmed the presence of these genes in known nitrogen-fixing and/or rock weathering organisms (e.g., Nostoc, Burkholderia), in this study, we also detected organisms that, even if often found in soil and proglacial systems, have never been related to nitrogen-fixing or rock weathering processes before (e.g., Fimbriiglobus, Streptomyces). The different genera showed different gene trends within and among the studied systems, indicating a community constituted by a plurality of organisms involved in nitrogen fixation and biotic rock weathering, and where the latter were driven by different organisms at different soil succession stages.

Exploration of silicate solubilizing bacteria for sustainable agriculture and silicon biogeochemical cycle

Silicon (Si), a quasi-essential element for plants, is abundant in the soil typically as insoluble silicate forms. However, plants can uptake Si only in the soluble form of monosilicic acid. Production of monosilicic acid by rock-weathering mostly depends on temperature, pH, redox-potential, water-content, and microbial activities. In the present review, approaches involved in the efficient exploration of silicate solubilizing bacteria (SSB), its potential applications, and available technological advances are discussed. Present understanding of Si uptake, deposition, and subsequent benefits to plants has also been discussed. In agricultural soils, pH is found to be one of the most critical factors deciding silicate solubilization and the formation of different Si compounds. Numerous studies have predicted the role of Indole-3-Acetic Acid (IAA) and organic acids produced by SSB in silicate solubilization. In this regard, approaches for the isolation and characterization of SSB, quantification of IAA, and subsequent Si solubilization mechanisms are addressed. Phylogenetic evaluation of previously reported SSB showed a highly diverse origin which provides an opportunity to study different mechanisms involved in Si solubilization. Soil biochemistry in concern of silicon availability, microbial activity and silicon mediated changes in plant physiology are addressed. In addition, SSB's role in Si-biogeochemical cycling is summarized. The information presented here will be helpful to explore the potential of SSB more efficiently to promote sustainable agriculture.

Temperature and microbial interactions drive the deterministic assembly processes in sediments of hot springs

Terrestrial geothermal ecosystems, as a representative of extreme environments, exhibit a variety of geochemical gradients, and their microbes are thought to be under high stress through environmental selection. However, it is still unclear how stochasticity and biotic interactions contribute to the microbial community assembly in hot springs. Here, we investigated the assembly processes and co-occurrence patterns of microbiota (i.e. bacteria and archaea) in both water and sediments sampled from fifteen hot springs in the Tengchong area, Southwestern of China, using 16S rRNA gene sequencing combined with multivariate ecological and statistical methods. These hot springs harbored more specialists than non-geothermal ecosystems, which are well-adapted to the extreme conditions, as shown by extremely high nearest-taxon index (NTI) and narrower niche width. Habitat differentiation led to the differences in microbial diversity, species-interactions, and community assembly between water and sediment communities. The sediment community showed stronger phylogenetic clustering and was primarily governed by heterogeneous selection, while undominated stochastic processes and dispersal limitation were the major assembly processes in the water community. Temperature and ferrous iron were the major factors mediating the balance of stochastic and deterministic assembly processes in sediment communities, as evidenced by how divergences in temperature and ferrous iron increased the proportion of determinism. Microbial interactions in sediments contributed to deterministic community assembly, as indicated by more complex associations and greater responsiveness to environmental change than water community. These findings uncover the ecological processes underlying microbial communities in hot springs, and provide potential insight into understanding the mechanism to maintain microbial diversity in extreme biospheres.

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.

Isolation and screening of potassium solubilizing bacteria from saxicolous habitat and their impact on tomato growth in different soil types

Bacteria that solubilize nutrients in the soil are commonly used as bio-inoculants for promoting the growth of different crop species. However, the influence of potassium (K) solubilizing bacteria (KSB) originating from saxicolous habitat (rock-dwelling) on plant growth has not been frequently examined. In this study, we isolated KSB from saxicolous habitats and estimated their ability to produce plant growth hormone, organic acids, and siderophore that may facilitate plant growth. Fifteen culturable saxicolous bacterial isolates with varied K solubilizing ability were isolated from two sites. Of these, four potential K solubilizers were selected and identified by 16S rRNA gene sequencing. The four bacterial isolates resembled Bacillus subtilis, Bacillus cereus, Bacillus licheniformis, and Burkholderia cenocepacia and produced different organic acids, indole acetic acid, and siderophore under in vitro conditions. Potassium solubilization differed among the bacterial isolates and was significantly influenced by K sources. Inoculation of KSB improved the tomato plant growth parameters like plant height, leaf area, total root length, root/shoot ratio, and tissue K content in sterilized and unsterilized Alfisol, and Vertisol soils under greenhouse conditions. We also observed higher residual K content in the KSB inoculated post-harvest soils. Among the four KSB isolates screened, B. licheniformis and B. cenocepacia presents an excellent prospect as bio-inoculants for improving tomato growth in different soil types. Besides these, the enriched K content in the post-harvest soils may help the growth of subsequent crops in sustainable agriculture.

Mineralosphere Microbiome Leading to Changed Geochemical Properties of Sedimentary Rocks from Aiqigou Mud Volcano, Northwest China

The properties of rocks can be greatly affected by seepage hydrocarbons in petroleum-related mud volcanoes. Among them, the color of sedimentary rocks can reflect the changes of sedimentary environment and weathering history. However, little is known about the microbial communities and their biogeochemical significance in these environments. In this study, contrasting rock samples were collected from the Aiqigou mud volcano on the southern margin of the Junggar Basin in Northwest China as guided by rock colors indicative of redox conditions. The physicochemical properties and mineral composition are similar under the same redox conditions. For example, the content of chlorite, muscovite, quartz, and total carbon were higher, and the total iron was lower under reduced conditions compared with oxidized environments. High-throughput sequencing of 16S rRNA gene amplicons revealed that different functional microorganisms may exist under different redox conditions; microbes in oxidized conditions have higher diversity. Statistical analysis and incubation experiments indicated that the microbial community structure is closely related to the content of iron which may be an important factor for color stratification of continental sedimentary rocks in the Aiqigou mud volcano. The interactions between organics and iron-bearing minerals mediated by microorganisms have also been hypothesized.

Distinct co-occurrence patterns of prokaryotic community between the waters and sediments in lakes with different salinity

Temporal variations and co-occurrence patterns of the prokaryotic community in saline lakes remain elusive. In this study, we investigated the temporal variations of the prokaryotic community in six lakes with different salinity by using Illumina sequencing. The results showed that prokaryotic community compositions exhibited temporal variations in all studied lakes, which may be partially caused by temporal fluctuations of environmental variables (e.g. salinity, temperature, total nitrogen). Salinity fluctuations exhibited stronger influences on temporal variations of prokaryotic community composition in the lakes with low salinity than in those with high salinity. Stochastic factors (i.e. neutral processes) also contributed to temporal variations of prokaryotic community composition, and their contributions decreased with increasing salinity in the studied saline lakes. Network analysis showed that prokaryotic co-occurrence networks of the studied lakes exhibited non-random topology. Salinity affected the phylogenetic composition of nodes in the studied networks. The topological features (e.g. average connectivity and modularity) of the studied networks significantly differed between lake waters and sediments. Collectively, these results expand our knowledge of the mechanisms underlying prokaryotic community assembly and co-occurrence relationships in saline lakes with different salinity.

The persistence of bacterial diversity and ecosystem multifunctionality along a disturbance intensity gradient in karst soil

Extensive, progressive rock emergence causes localized variations in soil biogeochemical and microbial properties that may influence the capacity for the regeneration of degraded karst ecosystems. It is likely that karst ecosystem recovery relies on the persistence of soil functions at the microbial scale, and we aimed to explored the role of interactions between soil bacterial taxa and identify keystone species that deliver key biogeochemical functions, i.e. carbon (C) and nutrient (nitrogen, N and phosphorus, P) cycling. We applied high-throughput sequencing and phylogenetic molecular ecological network approaches to topsoils sampled at rock-soil interfaces and adjacent bulk soil along an established gradient of land-use intensity in the Chinese Karst Critical Zone Observatory. Bacterial α-diversity was greater under increased perturbation and at the rock-soil interface compared to bulk soils under intensive cultivation. However, bacterial ecological networks were less intricate and connected fewer keystone taxa as human disturbance increased and at the rock-soil interface. Co-occurrence within the bacterial community in natural primary forest soils was 13% larger than cultivated soils. The relative abundances of keystone taxa Acidobacteria, Bacteroidetes and Chloroflexi increased with land-use intensity, while Proteobacteria, Actinobacteria and Verrucomicrobia decreased by up to 6%. In general, Bacteroidetes, Verrucomicrobia and Chlorobi were related to C-cycling, Proteobacteria, Actinobacteria and Chloroflexi were related to N-cycling, and Actinobacteria and Nitrospirae were related to both N- and P-cycling. Proteobacteria and Chlorobi affected C-cycling and multiple functionality indexes in the abandoned land. We conclude that increasing land-use intensity changed the soil bacterial community structure and decreased bacterial interactions. However, increases in α-diversity at the rock-soil interface in cultivated soils indicated that major soil functions related to biogeochemical cycling were maintained within keystone taxa in this microenvironment. Our study provides foundations to test the success of different regeneration practices in restoring soil microbial diversity and the multifunctionality of karst ecosystems.

Use of Mineral Weathering Bacteria to Enhance Nutrient Availability in Crops: A Review

Rock powders are low-cost potential sources of most of the nutrients required by higher plants for growth and development. However, slow dissolution rates of minerals represent an obstacle to the widespread use of rock powders in agriculture. Rhizosphere processes and biological weathering may further enhance mineral dissolution since the interaction between minerals, plants, and bacteria results in the release of macro- and micronutrients into the soil solution. Plants are important agents in this process acting directly in the mineral dissolution or sustaining a wide diversity of weathering microorganisms in the root environment. Meanwhile, root microorganisms promote mineral dissolution by producing complexing ligands (siderophores and organic acids), affecting the pH (via organic or inorganic acid production), or performing redox reactions. Besides that, a wide variety of rhizosphere bacteria and fungi could also promote plant development directly, synergistically contributing to the weathering activity performed by plants. The inoculation of weathering bacteria in soil or plants, especially combined with the use of crushed rocks, can increase soil fertility and improve crop production. This approach is more sustainable than conventional fertilization practices, which may contribute to reducing climate change linked to agricultural activity. Besides, it could decrease the dependency of developing countries on imported fertilizers, thus improving local development.

Synergistic effect of biofilm growth and cadmium adsorption via compositional changes of extracellular matrix in montmorillonite system

The interaction of bacterial biofilm and clay minerals provides great potential for heavy metal remediation in contaminated soil, yet, little is known about how heavy metal, clay minerals and their combinations affect the bacterial biofilm performance and heavy metal adsorption. In this study, the response of biofilm development as well as Cd²⁺ adsorption in the presence of Cd²⁺ and montmorillonite has been deciphered. Low concentrations of Cd²⁺ and montmorillonite or their combinations enhanced biofilm formation by increasing polysaccharides proportion in the biofilm matrix, and the maximum adsorption capacity of Cd²⁺ by biofilm was increased by 1.5 times. Furthermore, the immobilization of Cd²⁺ by soil was significantly improved when S14-biofilm was introduced. Such results could gain deeper insight into bacterial survival tactics in the complex systems which makes major contribution to microbial remediation of heavy metal polluted environments.

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.

Root morphology and exudate availability are shaped by particle size and chemistry in Brachypodium distachyon

Root morphology and exudation define a plants' sphere of influence in soils. In turn, soil characteristics influence plant growth, morphology, root microbiome, and rhizosphere chemistry. Collectively, all these parameters have significant implications on the major biogeochemical cycles, crop yield, and ecosystem health. However, how plants are shaped by the physiochemistry of soil particles is still not well understood. We explored how particle size and chemistry of growth substrates affect root morphology and exudation of a model grass. We grew Brachypodium distachyon in glass beads with various sizes (0.5, 1, 2, 3 mm), as well as in sand (0.005, 0.25, 4 mm) and in clay (4 mm) particles and in particle-free hydroponic medium. Plant morphology, root weight, and shoot weight were measured. We found that particle size significantly influenced root fresh weight and root length, whereas root number and shoot weight remained constant. Next, plant exudation profiles were analyzed with mass spectrometry imaging and liquid chromatography-mass spectrometry. Mass spectrometry imaging suggested that both, root length and number shape root exudation. Exudate profiles were comparable for plants growing in glass beads or sand with various particles sizes, but distinct for plants growing in clay for in situ exudate collection. Clay particles were found to sorb 20% of compounds exuded by clay-grown plants, and 70% of compounds from a defined exudate medium. The sorbed compounds belonged to a range of chemical classes, among them nucleosides, organic acids, sugars, and amino acids. Some of the sorbed compounds could be desorbed by a rhizobacterium (Pseudomonas fluorescens WCS415), supporting its growth. This study demonstrates the effect of different characteristics of particles on root morphology, plant exudation and availability of nutrients to microorganisms. These findings further support the critical importance of the physiochemical properties of soils when investigating plant morphology, plant chemistry, and plant-microbe interactions.

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.

Minerals play key roles in driving prokaryotic and fungal communities in the surface sediments of the Qinghai-Tibetan lakes

There is limited knowledge of the relative influences of deterministic and stochastic processes on prokaryotic and fungal communities in lake sediments. In this study, we surveyed the prokaryotic and fungal community compositions and their influencing factors in 23 surface sediments from six lakes on the Qinghai-Tibetan Plateau (QTP) with the use of Illumina sequencing. The results showed the distribution of prokaryotic and fungal communities in the studied QTP lake sediments was shaped by different assembly processes, with prokaryotes primarily governed by variable selection and homogenizing dispersal (accounting for 57.9% and 37.3% of the observed variations) and fungi being mainly regulated by variable selection, non-dominant processes and homogenizing dispersal (38.3%, 43.7% and 13.7%, respectively). Regarding the variable selection, mineralogical variables played key roles in shaping prokaryotic and fungal community structures. Collectively, these findings expand current knowledge concerning the influences of deterministic (e.g. variable selection) and stochastic processes (e.g. homogenizing dispersal and non-dominant processes) on the prokaryotic and fungal distribution in the QTP lakes.

Co-effect of minerals and Cd(II) promoted the formation of bacterial biofilm and consequently enhanced the sorption of Cd(II)

Heavy metal pollution is very common in soils. Soils are complex systems including minerals, bacteria, and various other substances. In Cd(II) contaminated soil, the combined effects of clay minerals and heavy metals on bacterial biofilm and Cd(II) adsorption are unappreciated. Our study showed that the combination of clay minerals (goethite, kaolinite, and montmorillonite) and heavy metals promoted Serratia marcescens S14 biofilm development significantly more than clay minerals or Cd(II) alone. The amount of biofilm after binary treatment with clay minerals and Cd(II) was 2.3-7.3 times than that in control. Mineral-induced cell death and the expression of the fimA, bsmA, and eps were key players in biofilm formation. Binary treatment with montmorillonite and Cd(II) significantly enhanced biofilm development and consequently increased the adsorption of Cd(II). Cd(II) removal is the result of co-adsorption of bacteria and minerals. Bacterial biofilm played an important role in Cd(II) adsorption. FTIR spectroscopy showed the components of biofilm were not affected by minerals and revealed the functional groups -OH, -NH, -CH₂, -SH, -COO participated in Cd(II) immobilization. Our findings are of fundamental significance for understanding how minerals and Cd(II) affect biofilms and thereby enhance Cd(II) adsorption and predicting the mobility and fate of heavy metals in heavy metal-contaminated soil.

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.