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.
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.
Trophic interactions play a vital role in soil functioning and are increasingly considered as important drivers of the soil microbiome and biogeochemical cycles. In the last decade, novel tools to ...decipher the structure of soil food webs have provided unprecedent advance in describing complex trophic interactions. Yet, the major challenge remains to understand the drivers of the trophic interactions. Evidence suggests that small scale soil physical structure may offer a unifying framework for understanding the nature and patterns of trophic interactions in soils. Here, we review the current knowledge of how restrictions on soil organisms’ ability to sense and access food resources/prey inherent to soil physical structure essentially shape trophic interactions. We focus primarily on organisms unable to deform the soil and create pores themselves, such as bacteria, fungi, protists, nematodes and microarthropods, and consider pore geometry, connectivity and hydration status as main descriptors of the soil physical structure. We point that the soil physical structure appears to mostly limit the sensing and accessibility to food resources/prey, with negative effects on bottom up controls. The main mechanisms are (i) the reduced transport of sensing molecules, notably volatiles, through the soil matrix and (ii) the wide presence of refuges leading to pore size segregation of consumer/predators and food sources/prey in pores of contrasting size. In addition, variations in the connectivity of the soil pores and the water film is suggested as a central aspect driving encounter probability between consumers/predator and food source/prey and hence locally decrease or increase top-down controls. Constraints imposed by the soil physical structure on trophic interactions are thought to be major drivers of the soil diversity and local community assemblage, notably by favoring a variety of adaptations to feed in this dark labyrinth (food specialists/flexible/generalists) and by limiting competitive exclusion through limited encounter probability of consumers. We conclude with possible future ways for an interdisciplinary and more quantitative research merging soil physics and soil food web ecology.
•Soil physical structure constrains sensing and accessibility of food resources.•Size segregation of consumers limits access to resources/prey in small pores.•Limited mobility in soil reduces opportunities of consumer - resource interactions.•Constrained trophic interactions drive the co-existence of the diverse biota in soil.•Future work merging soil physics and soil food web ecology is needed.
Microbial communities inhabiting soil aggregates dynamically adjust their activity and composition in response to variations in hydration and other external conditions. These rapid dynamics shape ...signatures of biogeochemical activity and gas fluxes emitted from soil profiles. Recent mechanistic models of microbial processes in unsaturated aggregate‐like pore networks revealed a highly dynamic interplay between oxic and anoxic microsites jointly shaped by hydration conditions and by aerobic and anaerobic microbial community abundance and self‐organization. The spatial extent of anoxic niches (hotspots) flicker in time (hot moments) and support substantial anaerobic microbial activity even in aerated soil profiles. We employed an individual‐based model for microbial community life in soil aggregate assemblies represented by 3D angular pore networks. Model aggregates of different sizes were subjected to variable water, carbon and oxygen contents that varied with soil depth as boundary conditions. The study integrates microbial activity within aggregates of different sizes and soil depth to obtain estimates of biogeochemical fluxes from the soil profile. The results quantify impacts of dynamic shifts in microbial community composition on CO2 and N2O production rates in soil profiles in good agreement with experimental data. Aggregate size distribution and the shape of resource profiles in a soil determine how hydration dynamics shape denitrification and carbon utilization rates. Results from the mechanistic model for microbial activity in aggregates of different sizes were used to derive parameters for analytical representation of soil biogeochemical processes across large scales of practical interest for hydrological and climate models.
Abstract
Microscale interactions in soil may give rise to highly localised conditions that disproportionally affect soil nitrogen transformations. We report mechanistic modelling of coupled biotic ...and abiotic processes during drying of soil surfaces and biocrusts. The model links localised microbial activity with pH variations within thin aqueous films that jointly enhance emissions of nitrous acid (HONO) and ammonia (NH
3
) during soil drying well above what would be predicted from mean hydration conditions and bulk soil pH. We compared model predictions with case studies in which reactive nitrogen gaseous fluxes from drying biocrusts were measured. Soil and biocrust drying rates affect HONO and NH
3
emission dynamics. Additionally, we predict strong effects of atmospheric NH
3
levels on reactive nitrogen gas losses. Laboratory measurements confirm the onset of microscale pH localisation and highlight the critical role of micro-environments in the resulting biogeochemical fluxes from terrestrial ecosystems.
Across many soil types and conditions, post wetting soil internal drainage exhibits predictable dynamics that lead to a stable and repeatable hydration state termed “field capacity” (FC). Soil ...regulation of internal drainage toward FC has long been recognized as producing a useful hydrologic benchmark for modeling and for estimation of plant available soil water. To overcome ambiguities and inconsistencies in various ad hoc definitions of FC, we propose using a soil intrinsic characteristic length (a matric potential value derived from drainable soil pore size distribution) to characterize the loss of hydraulic continuity associated with the attainment of FC. The resulting static criterion for FC was extended to formulate a self‐consistent dynamic criterion based on soil internal drainage dynamics. A systematic evaluation of the proposed definitions of FC using numerical simulations and experimental data reveals remarkable consistency and predictability across a wide range of soil types. The new metrics add definitiveness and robustness of this widely used concept with potential expansion to additional agronomic, hydrologic, ecological, and climatic applications.
Key Points
A soil intrinsic characteristic length defines attainment of field capacity
This static criterion was extended to define a self‐consistent dynamic one
Field capacity is characterized by a constant relative flux
Microbial activity in soil is spatially heterogeneous often forming spatial hotspots that contribute disproportionally to biogeochemical processes. Evidence suggests that bacterial spatial ...organization contributes to the persistence of anoxic hotspots even in unsaturated soils. Such processes are difficult to observe in situ at the microscale, hence mechanisms and time scales relevant for bacterial spatial organization remain largely qualitative. Here we develop an experimental platform based on glass-etched micrometric pore networks that mimics resource gradients postulated in soil aggregates to observe spatial organization of fluorescently tagged aerobic and facultative anaerobic bacteria. Two initially intermixed bacterial species, Pseudomonas putida and Pseudomonas veronii, segregate into preferential regions promoted by opposing gradients of carbon and oxygen (such persistent coexistence is not possible in well-mixed cultures). The study provides quantitative visualization and modeling of bacterial spatial organization within aggregate-like hotspots, a key step towards developing a mechanistic representation of bacterial community organization in soil pores.
Most soil hydraulic information used in Earth System Models (ESMs) is derived from pedo-transfer functions that use easy-to-measure soil attributes to estimate hydraulic parameters. This ...parameterization relies heavily on soil texture, but overlooks the critical role of soil structure originated by soil biophysical activity. Soil structure omission is pervasive also in sampling and measurement methods used to train pedotransfer functions. Here we show how systematic inclusion of salient soil structural features of biophysical origin affect local and global hydrologic and climatic responses. Locally, including soil structure in models significantly alters infiltration-runoff partitioning and recharge in wet and vegetated regions. Globally, the coarse spatial resolution of ESMs and their inability to simulate intense and short rainfall events mask effects of soil structure on surface fluxes and climate. Results suggest that although soil structure affects local hydrologic response, its implications on global-scale climate remains elusive in current ESMs.
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.
A general theoretical framework for quantifying the stomatal clustering effects on leaf gaseous diffusive conductance was developed and tested. The theory accounts for stomatal spacing and ...interactions among ‘gaseous concentration shells’. The theory was tested using the unique measurements of Dow et al. (2014) that have shown lower leaf diffusive conductance for a genotype of Arabidopsis thaliana with clustered stomata relative to uniformly distributed stomata of similar size and density.
The model accounts for gaseous diffusion: through stomatal pores; via concentration shells forming at pore apertures that vary with stomata spacing and are thus altered by clustering; and across the adjacent air boundary layer. Analytical approximations were derived and validated using a numerical model for 3D diffusion equation.
Stomata clustering increases the interactions among concentration shells resulting in larger diffusive resistance that may reduce fluxes by 5–15%. A similar reduction in conductance was found for clusters formed by networks of veins. The study resolves ambiguities found in the literature concerning stomata end-corrections and stomatal shape, and provides a new stomata density threshold for diffusive interactions of overlapping vapor shells.
The predicted reduction in gaseous exchange due to clustering, suggests that guard cell function is impaired, limiting stomatal aperture opening.
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