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.

Elemental Sulfur and Organic Matter Amendment Drive Alkaline pH Neutralization and Mineral Weathering in Iron Ore Tailings Through Inducing Sulfur Oxidizing Bacteria

Mineral weathering and alkaline pH neutralization are prerequisites to the ecoengineering of alkaline Fe-ore tailings into soil-like growth media (i.e., Technosols). These processes can be accelerated by the growth and physiological functions of tolerant sulfur oxidizing bacteria (SOB) in tailings. The present study characterized an indigenous SOB community enriched in the tailings, in response to the addition of elemental sulfur (S0) and organic matter (OM), as well as resultant S0oxidation, pH neutralization, and mineral weathering in a glasshouse experiment. The addition of S0 was found to have stimulated the growth of indigenous SOB, such as acidophilic Alicyclobacillaceae, Bacillaceae, and Hydrogenophilaceae in tailings. The OM amendment favored the growth of heterotrophic/mixotrophic SOB (e.g., class Alphaproteobacteria and Gammaproteobacteria). The resultant S0 oxidation neutralized the alkaline pH and enhanced the weathering of biotite-like minerals and formation of secondary minerals, such as ferrihydrite- and jarosite-like minerals. The improved physicochemical properties and secondary mineral formation facilitated organo-mineral associations that are critical to soil aggregate formation. From these findings, co-amendments of S0 and plant biomass (OM) can be applied to enhance the abundance of the indigenous SOB community in tailings and accelerate mineral weathering and geochemical changes for eco-engineered soil formation, as a sustainable option for rehabilitation of Fe ore tailings.

Structure and Chemical Composition of Soil C-Rich Al-Si-Fe Coprecipitates at Nanometer Scale

Soil carbon stabilization is mainly driven by organo-mineral interactions. Coprecipitates, of organic matter with short-range order minerals, detected through indirect chemical extraction methods, are increasingly recognized as key carbon sequestration phases. Yet the atomic structure of these coprecipitates is still rather conceptual. We used transmission electron microscopy imaging combined with energy-dispersive X-ray and electron energy loss spectroscopy chemical mappings, which enabled direct nanoscale characterization of coprecipitates from Andosols. A comparison with reference synthetic coprecipitates showed that the natural coprecipitates were structured by an amorphous Al, Si, and Fe inorganic skeleton associated with C and were therefore even less organized than short-range order minerals usually described. These amorphous types of coprecipitates resembled previously conceptualized nanosized coprecipitates of inorganic oligomers with organics (nanoCLICs) with heterogeneous elemental proportions (of C, Al, Si, and Fe) at nanoscale. These results mark a new step in the high-resolution imaging of organo-mineral associations, while shedding further light on the mechanisms that control carbon stabilization in soil and more broadly in aquatic colloid, sediment, and extraterrestrial samples.

Impact of Silicon on Plant Nutrition and Significance of Silicon Mobilizing Bacteria in Agronomic Practices

Globally, rejuvenation of soil health is a major concern due to the continuous loss of soil fertility and productivity. Soil degradation decreases crop yields and threatens global food security. Improper use of chemical fertilizers coupled with intensive cultivation further reduces both soil health and crop yields. Plants require several nutrients in varying ratios that are essential for the plant to complete a healthy growth and development cycle. Soil, water, and air are the sources of these essential macro- and micro-nutrients needed to complete plant vegetative and reproductive cycles. Among the essential macro-nutrients, nitrogen (N) plays a significant in non-legume species and without sufficient plant access to N lower yields result. While silicon (Si) is the 2nd most abundant element in the Earth’s crust and is the backbone of soil silicate minerals, it is an essential micro-nutrient for some plants. Silicon is just beginning to be recognized as an important micronutrient to some plant species and, while it is quite abundant, Si is often not readily available for plant uptake. The manufacturing cost of synthetic silica-based fertilizers is high, while absorption of silica is quite slow in soil for many plants. Rhizosphere biological weathering processes includes microbial solubilization processes that increase the dissolution of minerals and increases Si availability for plant uptake. Therefore, an important strategy to improve plant silicon uptake could be field application of Si-solubilizing bacteria. In this review, we evaluate the role of Si in seed germination, growth, and morphological development and crop yield under various biotic and abiotic stresses, different pools and fluxes of silicon (Si) in soil, and the bacterial genera of the silicon solubilizing microorganisms. We also elaborate on the detailed mechanisms of Si-solubilizing/mobilizing bacteria involved in silicate dissolution and uptake by a plant in soil. Last, we discuss the potential of silicon and silicon solubilizing/mobilizing to achieve environmentally friendly and sustainable crop production.

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.

Epilithic Microbial Community Functionality in Deep Oligotrophic Continental Bedrock

The deep terrestrial biosphere hosts vast sessile rock surface communities and biofilms, but thus far, mostly planktic communities have been studied. We enriched deep subsurface microbial communities on mica schist in microcosms containing bedrock groundwater from the depth of 500 m from Outokumpu, Finland. The biofilms were visualized using scanning electron microscopy, revealing numerous different microbial cell morphologies and attachment strategies on the mica schist surface, e.g., bacteria with outer membrane vesicle-like structures, hair-like extracellular extensions, and long tubular cell structures expanding over hundreds of micrometers over mica schist surfaces. Bacterial communities were analyzed with amplicon sequencing showing that Pseudomonas, Desulfosporosinus, Hydrogenophaga, and Brevundimonas genera dominated communities after 8–40 months of incubation. A total of 21 metagenome assembled genomes from sessile rock surface metagenomes identified genes involved in biofilm formation, as well as a wide variety of metabolic traits indicating a high degree of environmental adaptivity to oligotrophic environment and potential for shifting between multiple energy or carbon sources. In addition, we detected ubiquitous organic carbon oxidation and capacity for arsenate and selenate reduction within our rocky MAGs. Our results agree with the previously suggested interaction between the deep subsurface microbial communities and the rock surfaces, and that this interaction could be crucial for sustaining life in the harsh anoxic and oligotrophic deep subsurface of crystalline bedrock environment.

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.

Acidophilic Iron- and Sulfur-Oxidizing Bacteria, Acidithiobacillus ferrooxidans, Drives Alkaline pH Neutralization and Mineral Weathering in Fe Ore Tailings

The neutralization of strongly alkaline pH conditions and acceleration of mineral weathering in alkaline Fe ore tailings have been identified as key prerequisites for eco-engineering tailings-soil formation for sustainable mine site rehabilitation. Acidithiobacillus ferrooxidans has great potential in neutralizing alkaline pH and accelerating primary mineral weathering in the tailings but little information is available. This study aimed to investigate the colonization of A. ferrooxidans in alkaline Fe ore tailings and its role in elemental sulfur (S⁰) oxidation, tailings neutralization, and Fe-bearing mineral weathering through a microcosm experiment. The effects of biological S⁰ oxidation on the weathering of alkaline Fe ore tailings were examined via various microspectroscopic analyses. It is found that (1) the A. ferrooxidans inoculum combined with the S⁰ amendment rapidly neutralized the alkaline Fe ore tailings; (2) A. ferrooxidans activities induced Fe-bearing primary mineral (e.g., biotite) weathering and secondary mineral (e.g., ferrihydrite and jarosite) formation; and (3) the association between bacterial cells and tailings minerals were likely facilitated by extracellular polymeric substances (EPS). The behavior and biogeochemical functionality of A. ferrooxidans in the tailings provide a fundamental basis for developing microbial-based technologies toward eco-engineering soil formation in Fe ore tailings.

Local Geomorphological Gradients and Land Use Patterns Play Key Role on the Soil Bacterial Community Diversity and Dynamics in the Highly Endemic Indigenous Afrotemperate Coastal Scarp Forest Biome

Southern Afrotemperate forests are small multi-layered and highly fragmented biodiversity rich biomes that support unique flora and fauna endemism. However, little is known about the microbial community and their contribution to these ecosystems. In this study, high throughput sequencing analysis was used to investigate the soil bacterial community structure and function, and understand the effect of local topography/geomorphological formations and land use patterns on a coastal scarp forest. Soil samples were collected from three forest topography sites: upper (steeper gradients, 30-55°; open canopy cover, <30%), mid (less steep, 15-30°; continuous forest canopy, >80%), and lower (flatter gradient, <15°; open canopy cover, 20-65%), and from the adjacent sugarcane farms. Results indicated that forest soils were dominated by members of phyla Proteobacteria (mainly members of α-proteobacteria), Actinobacteria, Acidobacteria, Firmicutes, and Planctomycetes, while Actinobacteria and to a lesser extent β-proteobacteria and γ-proteobacteria dominated SC soils. The core bacterial community clustered by habitat (forest vs. sugarcane farm) and differed significantly between the forest topography sites. The Rhizobiales (genera Variibacter, Bradyrhizobium, and unclassified Rhizobiales) and Rhodospirallales (unclassified Rhodospirillum DA111) were more abundant in forest mid and lower topographies. Steeper forest topography (forest_upper) characterized by the highly leached sandy/stony acidic soils, low in organic nutrients (C and N) and plant densities correlated to significant reduction of bacterial diversity and richness, associating significantly with members of order Burkholderiales (Burkholderia-Paraburkholderia, Delftia, and Massilia) as the key indicator taxa. In contrast, changes in the total nitrogen (TN), soil organic matter (SOM), and high acidity (low pH) significantly influenced bacterial community structure in sugarcane farm soils, with genus Acidothermus (Frankiales) and uncultured Solirubrobacterales YNFP111 were the most abundant indicator taxa. Availability of soil nutrients (TN and SOM) was the strongest driver of metabolic functions related to C fixation and metabolism, N and S cycling; these processes being significantly abundant in forest than sugarcane farm soils. Overall, these results revealed that the local topographical/geomorphological gradients and sugarcane farming affect both soil characteristics and forest vegetation (canopy coverage), that indirectly drives the structure and composition of bacterial communities in scarp forest soils.

Bio-imaging with the helium-ion microscope: A review

Scanning helium-ion microscopy (HIM) is an imaging technique with sub-nanometre resolution and is a powerful tool to resolve some of the tiniest structures in biology. In many aspects, the HIM resembles a field-emission scanning electron microscope (FE-SEM), but the use of helium ions rather than electrons provides several advantages, including higher surface sensitivity, larger depth of field, and a straightforward charge-compensating electron flood gun, which enables imaging of non-conductive samples, rendering HIM a promising high-resolution imaging technique for biological samples. Starting with studies focused on medical research, the last decade has seen some particularly spectacular high-resolution images in studies focused on plants, microbiology, virology, and geomicrobiology. However, HIM is not just an imaging technique. The ability to use the instrument for milling biological objects as small as viruses offers unique opportunities which are not possible with more conventional focused ion beams, such as gallium. Several pioneering technical developments, such as methods to couple secondary ion mass spectrometry (SIMS) or ionoluminescence with the HIM, also offer the possibility for new and exciting research on biological materials. In this review, we present a comprehensive overview of almost all currently published literature which has demonstrated the application of HIM for imaging of biological specimens. We also discuss some technical features of this unique type of instrument and highlight some of the new advances which will likely become more widely used in the years to come.

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.