A hydration-based biophysical index for the onset of soil microbial coexistence

Characterization of bacterial diversity between two coastal regions with heterogeneous soil texture

Studying microbial diversity and the effects of external factors on the microbiome could expand our understanding of environmental alterations. Silt and sand are mineral particles that form soil texture and even though most of the soils on earth contain a fraction of them and some other soils form almost by them, their effects on the microbiome remained to elucidate. In this study, the bacterial biodiversity of sand and silt clay soils was investigated. Furthermore, their effects on plant growth have been determined. Our data showed that biodiversity and biomass of microbiome are higher in silt-based soil. It is interesting that the pseudomonas genera only exist in silt-based soil while it is in the absence of sand-based soil. In contrast, B. thuringiensis could be found in sand-based soil while it is not found in silt texture. Our data also demonstrated that there are no significant changes in stress response between the two groups however, differential physiological changes in plants inoculated with silt and sand based bacterial isolates have been observed. This data could indicate that smaller size particles could contain more bacteria with higher biodiversity due to providing more surfaces for bacteria to grow.

Artificial Soils Reveal Individual Factor Controls on Microbial Processes

Soil matrix properties influence microbial behaviors that underlie nutrient cycling, greenhouse gas production, and soil formation. However, the dynamic and heterogeneous nature of soils makes it challenging to untangle the effects of different matrix properties on microbial behaviors. To address this challenge, we developed a tunable artificial soil recipe and used these materials to study the abiotic mechanisms driving soil microbial growth and communication. When we used standardized matrices with varying textures to culture gas-reporting biosensors, we found that a Gram-negative bacterium (Escherichia coli) grew best in synthetic silt soils, remaining active over a wide range of soil matric potentials, while a Gram-positive bacterium (Bacillus subtilis) preferred sandy soils, sporulating at low water potentials. Soil texture, mineralogy, and alkalinity all attenuated the bioavailability of an acyl-homoserine lactone (AHL) signaling molecule that controls community-level microbial behaviors. Texture controlled the timing of AHL sensing, while AHL bioavailability was decreased ~10⁵-fold by mineralogy and ~10³-fold by alkalinity. Finally, we built artificial soils with a range of complexities that converge on the properties of one Mollisol. As artificial soil complexity increased to more closely resemble the Mollisol, microbial behaviors approached those occurring in the natural soil, with the notable exception of organic matter. IMPORTANCE Understanding environmental controls on soil microbes is difficult because many abiotic parameters vary simultaneously and uncontrollably when different natural soils are compared, preventing mechanistic determination of any individual soil parameter's effect on microbial behaviors. We describe how soil texture, mineralogy, pH, and organic matter content can be varied individually within artificial soils to study their effects on soil microbes. Using microbial biosensors that report by producing a rare indicator gas, we identify soil properties that control microbial growth and attenuate the bioavailability of a diffusible chemical used to control community-level behaviors. We find that artificial soils differentially affect signal bioavailability and the growth of Gram-negative (Escherichia coli) and Gram-positive (Bacillus subtilis) microbes. These artificial soils are useful for studying the mechanisms that underlie soil controls on microbial fitness, signaling, and gene transfer.

The chosen few-variations in common and rare soil bacteria across biomes

Soil bacterial communities are dominated by a few abundant species, while their richness is associated with rare species with largely unknown ecological roles and biogeography. Analyses of previously published soil bacterial community data using a novel classification of common and rare bacteria indicate that only 0.4% of bacterial species can be considered common and are prevalent across biomes. The remaining bacterial species designated as rare are endemic with low relative abundances. Observations coupled with mechanistic models highlight the central role of soil wetness in shaping bacterial rarity. An individual-based model reveals systematic shifts in community composition induced by low carbon inputs in drier soils that deprive common species of exhibiting physiological advantages relative to other species. We find that only a "chosen few" common species shape bacterial communities across biomes; however, their contributions are curtailed in resource-limited environments where a larger number of rare species constitutes the soil microbiome.

Root-mediated bacterial accessibility and cometabolism of pyrene in soil

Partial transformation of pollutants and mobilization of the produced metabolites may contribute significantly to the risks resulting from biological treatment of soils polluted by hydrophobic chemicals such as polycyclic aromatic hydrocarbons (PAHs). Pyrene, a four-ringed PAH, was selected here as a model pollutant to study the effects of sunflower plants on the bacterial accessibility and cometabolism of this pollutant when located at a spatially distant source within soil. We compared the transformation of passively dosed ¹⁴C-labeled pyrene in soil slurries and planted pots that were inoculated with the bacterium Pseudomonas putida G7. This bacterium combines flagellar cell motility with the ability to cometabolically transform pyrene. Cometabolism of this PAH occurred immediately in the inoculated and shaken soil slurries, where the bacteria had full access to the passive dosing devices (silicone O-rings). Root exudates did not enhance the survival of P. putida G7 cells in soil slurries, but doubled their transport in column tests. In greenhouse-incubated soil pots with the same pyrene sources instead located centimeters from the soil surface, the inoculated bacteria transformed ¹⁴C-labeled pyrene only when the pots were planted with sunflowers. Bacterial inoculation caused mobilization of ¹⁴C-labeled pyrene metabolites into the leachates of the planted pots at concentrations of approximately 1 mg L^-1, ten times greater than the water solubility of the parent compound. This mobilization resulted in a doubled specific root uptake rate of ¹⁴C-labeled pyrene equivalents and a significantly decreased root-to-fruit transfer rate. Our results show that the plants facilitated bacterial access to the distant pollutant source, possibly by increasing bacterial dispersal in the soil; this increased bacterial access was associated with cometabolism, which contributed to the risks of biodegradation.

Soil bacterial diversity mediated by microscale aqueous-phase processes across biomes

Soil bacterial diversity varies across biomes with potential impacts on soil ecological functioning. Here, we incorporate key factors that affect soil bacterial abundance and diversity across spatial scales into a mechanistic modeling framework considering soil type, carbon inputs and climate towards predicting soil bacterial diversity. The soil aqueous-phase content and connectivity exert strong influence on bacterial diversity for each soil type and rainfall pattern. Biome-specific carbon inputs deduced from net primary productivity provide constraints on soil bacterial abundance independent from diversity. The proposed heuristic model captures observed global trends of bacterial diversity in good agreement with predictions by an individual-based mechanistic model. Bacterial diversity is highest at intermediate water contents where the aqueous phase forms numerous disconnected habitats and soil carrying capacity determines level of occupancy. The framework delineates global soil bacterial diversity hotspots; located mainly in climatic transition zones that are sensitive to potential climate and land use changes.

Spatial heterogeneity stabilizes predator-prey interactions at the microscale while patch connectivity controls their outcome

Natural landscapes are both fragmented and heterogeneous, affecting the distribution of organisms, and their interactions. While predation in homogeneous environments increases the probability of population extinction, fragmentation/heterogeneity promotes coexistence and enhances community stability as shown by experimentation with animals and microorganisms, and supported by theory. Patch connectivity can modulate such effects but how microbial predatory interactions are affected by water-driven connectivity is unknown. In soil, patch habitability by microorganisms, and their connectivity depend upon the water saturation degree (SD). Here, using the obligate bacterial predator Bdellovibrio bacteriovorus, and a Burkholderia prey, we show that soil spatial heterogeneity profoundly affects predatory dynamics, enhancing long-term co-existence of predator and prey in a SD-threshold dependent-manner. However, as patches and connectors cannot be distinguished in these soil matrices, metapopulations cannot be invoked to explain the dynamics of increased persistence. Using a set of experiments combined with statistical and physical models we demonstrate and quantify how under full connectivity, predation is independent of water content but depends on soil microstructure characteristics. In contrast, the SD below which predation is largely impaired corresponds to a threshold below which the water network collapses and water connectivity breaks down, preventing the bacteria to move within the soil matrix.

A hierarchy of environmental covariates control the global biogeography of soil bacterial richness

Soil bacterial communities are central to ecosystem functioning and services, yet spatial variations in their composition and diversity across biomes and climatic regions remain largely unknown. We employ multivariate general additive modeling of recent global soil bacterial datasets to elucidate dependencies of bacterial richness on key soil and climatic attributes. Although results support the well-known association between bacterial richness and soil pH, a hierarchy of novel covariates offers surprising new insights. Defining climatic soil water content explains both, the extent and connectivity of aqueous micro-habitats for bacterial diversity and soil pH, thus providing a better causal attribution. Results show that globally rare and abundant soil bacterial phylotypes exhibit different levels of dependency on environmental attributes. Surprisingly, the strong sensitivity of rare bacteria to certain environmental conditions improves their predictability relative to more abundant phylotypes that are often indifferent to variations in environmental drivers.

Cell-to-cell bacterial interactions promoted by drier conditions on soil surfaces

Bacterial cell-to-cell interactions are in the core of evolutionary and ecological processes in soil and other environments. Under most conditions, natural soils are unsaturated where the fragmented aqueous habitats and thin liquid films confine bacterial cells within small volumes and close proximity for prolonged periods. We report effects of a range of hydration conditions on bacterial cell-level interactions that are marked by plasmid transfer between donor and recipient cells within populations of the soil bacterium Pseudomonas putida Using hydration-controlled sand microcosms, we demonstrate that the frequency of cell-to-cell contacts under prescribed hydration increases with lowering water potential values (i.e., under drier conditions where the aqueous phase shrinks and fragments). These observations were supported using a mechanistic individual-based model for linking macroscopic soil water potential to microscopic distribution of liquid phase and explicit bacterial cell interactions in a simplified porous medium. Model results are in good agreement with observations and inspire confidence in the underlying mechanisms. The study highlights important physical factors that control short-range bacterial cell interactions in soil and on surfaces, specifically, the central role of the aqueous phase in mediating bacterial interactions and conditions that promote genetic information transfer in support of soil microbial diversity.

Synthetic microbial ecology and the dynamic interplay between microbial genotypes

Assemblages of microbial genotypes growing together can display surprisingly complex and unexpected dynamics and result in community-level functions and behaviors that are not readily expected from analyzing each genotype in isolation. This complexity has, at least in part, inspired a discipline of synthetic microbial ecology. Synthetic microbial ecology focuses on designing, building and analyzing the dynamic behavior of ‘ecological circuits’ (i.e. a set of interacting microbial genotypes) and understanding how community-level properties emerge as a consequence of those interactions. In this review, we discuss typical objectives of synthetic microbial ecology and the main advantages and rationales of using synthetic microbial assemblages. We then summarize recent findings of current synthetic microbial ecology investigations. In particular, we focus on the causes and consequences of the interplay between different microbial genotypes and illustrate how simple interactions can create complex dynamics and promote unexpected community-level properties. We finally propose that distinguishing between active and passive interactions and accounting for the pervasiveness of competition can improve existing frameworks for designing and predicting the dynamics of microbial assemblages.

Biophysical processes supporting the diversity of microbial life in soil

Soil, the living terrestrial skin of the Earth, plays a central role in supporting life and is home to an unimaginable diversity of microorganisms. This review explores key drivers for microbial life in soils under different climates and land-use practices at scales ranging from soil pores to landscapes. We delineate special features of soil as a microbial habitat (focusing on bacteria) and the consequences for microbial communities. This review covers recent modeling advances that link soil physical processes with microbial life (termed biophysical processes). Readers are introduced to concepts governing water organization in soil pores and associated transport properties and microbial dispersion ranges often determined by the spatial organization of a highly dynamic soil aqueous phase. The narrow hydrological windows of wetting and aqueous phase connectedness are crucial for resource distribution and longer range transport of microorganisms. Feedbacks between microbial activity and their immediate environment are responsible for emergence and stabilization of soil structure-the scaffolding for soil ecological functioning. We synthesize insights from historical and contemporary studies to provide an outlook for the challenges and opportunities for developing a quantitative ecological framework to delineate and predict the microbial component of soil functioning.

High Temporal and Spatial Variability of Atmospheric-Methane Oxidation in Alpine Glacier Forefield Soils

Glacier forefield soils can provide a substantial sink for atmospheric CH₄, facilitated by aerobic methane-oxidizing bacteria (MOB). However, MOB activity, abundance, and community structure may be affected by soil age, MOB location in different forefield landforms, and temporal fluctuations in soil physical parameters. We assessed the spatial and temporal variability of atmospheric-CH₄ oxidation in an Alpine glacier forefield during the snow-free season of 2013. We quantified CH₄ flux in soils of increasing age and in different landforms (sandhill, terrace, and floodplain forms) by using soil gas profile and static flux chamber methods. To determine MOB abundance and community structure, we employed pmoA gene-based quantitative PCR and targeted amplicon sequencing. Uptake of CH₄ increased in magnitude and decreased in variability with increasing soil age. Sandhill soils exhibited CH₄ uptake rates ranging from -3.7 to -0.03 mg CH₄ m^-2 day^-1 Floodplain and terrace soils exhibited lower uptake rates and even intermittent CH₄ emissions. Linear mixed-effects models indicated that soil age and landform were the dominating factors shaping CH₄ flux, followed by cumulative rainfall (weighted sum ≤4 days prior to sampling). Of 31 MOB operational taxonomic units retrieved, ∼30% were potentially novel, and ∼50% were affiliated with upland soil clusters gamma and alpha. The MOB community structures in floodplain and terrace soils were nearly identical but differed significantly from the highly variable sandhill soil communities. We concluded that soil age and landform modulate the soil CH₄ sink strength in glacier forefields and that recent rainfall affects its short-term variability. This should be taken into account when including this environment in future CH₄ inventories.IMPORTANCE Oxidation of methane (CH₄) in well-drained, "upland" soils is an important mechanism for the removal of this potent greenhouse gas from the atmosphere. It is largely mediated by aerobic, methane-oxidizing bacteria (MOB). Whereas there is abundant information on atmospheric-CH₄ oxidation in mature upland soils, little is known about this important function in young, developing soils, such as those found in glacier forefields, where new sediments are continuously exposed to the atmosphere as a result of glacial retreat. In this field-based study, we investigated the spatial and temporal variability of atmospheric-CH₄ oxidation and associated MOB communities in Alpine glacier forefield soils, aiming at better understanding the factors that shape the sink for atmospheric CH₄ in this young soil ecosystem. This study contributes to the knowledge on the dynamics of atmospheric-CH₄ oxidation in developing upland soils and represents a further step toward the inclusion of Alpine glacier forefield soils in global CH₄ inventories.

The Impact of Hydration and Temperature on Bacterial Diversity in Arid Soil Mesocosms

Hot desert ecosystems experience rare and unpredictable rainfall events that resuscitate the arid flora and fauna. However, the effect of this sudden abundance of water on soil microbial communities is still under debate. We modeled varying rainfall amounts and temperatures in desert soil mesocosms and monitored the microbial community response over a period of 21 days. We studied two different wetting events, simulating heavy (50 mm) and light (10 mm) rain, as well as three different temperature regimes: constant 25° or 36°C, or a temperature diurnal cycle alternating between 36 and 10 °C. Amplicon sequencing of the bacterial ribosomal RNA revealed that rain intensity affects the soil bacterial community, but the effects are mitigated by temperature. The combination of water-pulse intensity with lower temperature had the greatest effect on the bacterial community. These experiments demonstrated that the soil microbial response to rain events is dependent not only on the intensity of the water pulse but also on the ambient temperature, thus emphasizing the complexity of bacterial responses to highly unpredictable environments.

Individual-Based Model of Microbial Life on Hydrated Rough Soil Surfaces

Microbial life in soil is perceived as one of the most interesting ecological systems, with microbial communities exhibiting remarkable adaptability to vast dynamic environmental conditions. At the same time, it is a notoriously challenging system to understand due to its complexity including physical, chemical, and biological factors in synchrony. This study presents a spatially-resolved model of microbial dynamics on idealised rough soil surfaces represented as patches with different (roughness) properties that preserve the salient hydration physics of real surfaces. Cell level microbial interactions are considered within an individual-based formulation including dispersion and various forms of trophic dependencies (competition, mutualism). The model provides new insights into mechanisms affecting microbial community dynamics and gives rise to spontaneous formation of microbial community spatial patterns. The framework is capable of representing many interacting species and provides diversity metrics reflecting surface conditions and their evolution over time. A key feature of the model is its spatial scalability that permits representation of microbial processes from cell-level (micro-metric scales) to soil representative volumes at sub-metre scales. Several illustrative examples of microbial trophic interactions and population dynamics highlight the potential of the proposed modelling framework to quantitatively study soil microbial processes. The model is highly applicable in a wide range spanning from quantifying spatial organisation of multiple species under various hydration conditions to predicting microbial diversity residing in different soils.

Bacterial flagellar motility on hydrated rough surfaces controlled by aqueous film thickness and connectedness

Recent studies have shown that rates of bacterial dispersion in soils are controlled by hydration conditions that define size and connectivity of the retained aqueous phase. Despite the ecological implications of such constraints, microscale observations of this phenomenon remain scarce. Here, we quantified aqueous film characteristics and bacterial flagellated motility in response to systematic variations in microhydrological conditions on porous ceramic surfaces that mimic unsaturated soils. We directly measured aqueous film thickness and documented its microscale heterogeneity. Flagellar motility was controlled by surface hydration conditions, as cell velocity decreased and dispersion practically ceased at water potentials exceeding –2 kPa (resulting in thinner and disconnected liquid films). The fragmentation of aquatic habitats was delineated indirectly through bacterial dispersal distances within connected aqueous clusters. We documented bacterial dispersal radii ranging from 100 to 10 μm as the water potential varied from 0 to –7 kPa, respectively. The observed decrease of flagellated velocity and dispersal ranges at lower matric potentials were in good agreement with mechanistic model predictions. Hydration-restricted habitats thus play significant role in bacterial motility and dispersal, which has potentially important impact on soil microbial ecology and diversity.

Exometabolite niche partitioning among sympatric soil bacteria

Soils are arguably the most microbially diverse ecosystems. Physicochemical properties have been associated with the maintenance of this diversity. Yet, the role of microbial substrate specialization is largely unexplored since substrate utilization studies have focused on simple substrates, not the complex mixtures representative of the soil environment. Here we examine the exometabolite composition of desert biological soil crusts (biocrusts) and the substrate preferences of seven biocrust isolates. The biocrust's main primary producer releases a diverse array of metabolites, and isolates of physically associated taxa use unique subsets of the complex metabolite pool. Individual isolates use only 13−26% of available metabolites, with only 2 out of 470 used by all and 40% not used by any. An extension of this approach to a mesophilic soil environment also reveals high levels of microbial substrate specialization. These results suggest that exometabolite niche partitioning may be an important factor in the maintenance of microbial diversity.

Production and consumption of metabolites by soil microorganisms are important for nutrient cycling and maintenance of microbial diversity. Here, Baran et al. study metabolite uptake and release by desert soil microorganisms, showing that coexisting microbes can have divergent substrate preferences.

Trophic interactions induce spatial self-organization of microbial consortia on rough surfaces

The spatial context of microbial interactions common in natural systems is largely absent in traditional pure culture-based microbiology. The understanding of how interdependent microbial communities assemble and coexist in limited spatial domains remains sketchy. A mechanistic model of cell-level interactions among multispecies microbial populations grown on hydrated rough surfaces facilitated systematic evaluation of how trophic dependencies shape spatial self-organization of microbial consortia in complex diffusion fields. The emerging patterns were persistent irrespective of initial conditions and resilient to spatial and temporal perturbations. Surprisingly, the hydration conditions conducive for self-assembly are extremely narrow and last only while microbial cells remain motile within thin aqueous films. The resulting self-organized microbial consortia patterns could represent optimal ecological templates for the architecture that underlie sessile microbial colonies on natural surfaces. Understanding microbial spatial self-organization offers new insights into mechanisms that sustain small-scale soil microbial diversity; and may guide the engineering of functional artificial microbial consortia.