Vapor flux induced by temperature gradient is responsible for providing liquid water to hypoliths.

Commonly comprised of cyanobacteria, algae, bacteria and fungi, hypolithic communities inhabit the underside of cobblestones and pebbles in diverse desert biomes. Notwithstanding their abundance and widespread geographic distribution and their growth in the driest regions on Earth, the source of water supporting these communities remains puzzling. Adding to the puzzle is the presence of cyanobacteria that require liquid water for net photosynthesis. Here we report results from six-year monitoring in the Negev Desert (with average annual precipitation of ~ 90 mm) during which periodical measurements of the water content of cobblestone undersides were carried out. We show that while no effective wetting took place following direct rain, dew or fog, high vapor flux, induced by a sharp temperature gradient, took place from the wet subsurface soil after rain, resulting in wet-dry cycles and wetting of the cobblestone undersides. Up to 12 wet-dry cycles were recorded following a single rain event, which resulted in vapor condensation on the undersides of the cobblestones, with the daily wet phase lasting for several hours during daylight. This 'concealed mechanism' expands the distribution of photoautotrophic organisms into hostile regions where the abiotic conditions limit their growth, and provides the driving force for important evolutionary processes not yet fully explored.

Aqueous habitats and carbon inputs shape the microscale geography and interaction ranges of soil bacteria.

Earth's diverse soil microbiomes host bacteria within dynamic and fragmented aqueous habitats that occupy complex pore spaces and restrict the spatial range of ecological interactions. Yet, the spatial distributions of bacterial cells in soil communities remain underexplored. Here, we propose a modelling framework representing submillimeter-scale distributions of soil bacteria based on physical constraints supported by individual-based model results and direct observations. The spatial distribution of bacterial cell clusters modulates various metabolic interactions and soil microbiome functioning. Dry soils with long diffusion times limit localized interactions of the sparse communities. Frequently wet soils enable long-range trophic interactions between dense cell clusters through connected aqueous pathways. Biomes with high carbon inputs promote large and dense cell clusters where anoxic microsites form even in aerated soils. Micro-geographic considerations of difficult-to-observe microbial processes can improve the interpretation of data from bulk soil samples.

Global Soil Hydraulic Properties dataset based on legacy site observations and robust parameterization.

The representation of land surface processes in hydrological and climatic models critically depends on the soil water characteristics curve (SWCC) that defines the plant availability and water storage in the vadose zone. Despite the availability of SWCC datasets in the literature, significant efforts are required to harmonize reported data before SWCC parameters can be determined and implemented in modeling applications. In this work, a total of 15,259 SWCCs from 2,702 sites were assembled from published literature, harmonized, and quality-checked. The assembled SWCC data provide a global soil hydraulic properties (GSHP) database. Parameters of the van Genuchten (vG) SWCC model were estimated from the data using the R package 'soilhypfit'. In many cases, information on the wet- or dry-end of the SWCC measurements were missing, and we used pedotransfer functions (PTFs) to estimate saturated and residual water contents. The new database quantifies the differences of SWCCs across climatic regions and can be used to create global maps of soil hydraulic properties.

Farm vehicles approaching weights of sauropods exceed safe mechanical limits for soil functioning.

Mechanization has greatly contributed to the success of modern agriculture, with vastly expanded food production capabilities achieved by the higher capacity of farm machinery. However, the increase in capacity has been accompanied by higher vehicle weights that increase risks of subsoil compaction. We show here that while surface contact stresses remained nearly constant over the course of modern mechanization, subsoil stresses have propagated into deeper soil layers and now exceed safe mechanical limits for soil ecological functioning. We developed a global map for delineating subsoil compaction susceptibility based on estimates of mechanization level, mean tractor size, soil texture, and climatic conditions. The alarming trend of chronic subsoil compaction risk over 20% of arable land, with potential loss of productivity, calls for a more stringent design of farm machinery that considers intrinsic subsoil mechanical limits. As the total weight of modern harvesters is now approaching that of the largest animals that walked Earth, the sauropods, a paradox emerges of potential prehistoric subsoil compaction. We hypothesize that unconstrained roaming of sauropods would have had similar adverse effects on land productivity as modern farm vehicles, suggesting that ecological strategies for reducing subsoil compaction, including fixed foraging trails, must have guided these prehistoric giants.

Dielectric Measurement of Agricultural Grain Moisture-Theory and Applications.

Moisture content is a critical variable for the harvesting, processing, storing and marketing of cereal grains, oilseeds and legumes. Efficient and accurate determination of grain moisture content even with advanced nondestructive techniques, remains a challenge due to complex water-retaining biological structures and hierarchical composition and geometry of grains that affect measurement interpretation and require specific grain-dependent calibration. We review (1) the primary factors affecting permittivity measurements used in practice for inferring moisture content in grains; (2) develop novel methods for estimating critical parameters for permittivity modeling including packing density, porosity, water binding surface area and water phase permittivity and (3) represent the permittivity of packs of grains using dielectric mixture theory as a function of moisture content applied to high moisture corn (as a model grain). Grain permittivity measurements are affected by their free and bound water contents, chemical composition, temperature, constituent shape, phase configuration and measurement frequency. A large fraction of grain water is bound exhibiting reduced permittivity compared to that of free water. The reduced mixture permittivity and attributed to hydrophilic surfaces in starches, proteins and other high surface area grain constituents. The hierarchal grain structure (i.e., kernel, starch grain, lamella, molecule) and the different constituents influence permittivity measurements due to their layering, geometry (i.e., kernel or starch grain), configuration and water-binding surface area. Dielectric mixture theory offers a physically-based approach for modeling permittivity of agricultural grains and similar granular media.

Controlling pore-scale processes to tame subsurface biomineralization.

Microorganisms capable of biomineralization can catalyze mineral precipitation by modifying local physical and chemical conditions. In porous media, such as soil and rock, these microorganisms live and function in highly heterogeneous physical, chemical and ecological microenvironments, with strong local gradients created by both microbial activity and the pore-scale structure of the subsurface. Here, we focus on extracellular bacterial biomineralization, which is sensitive to external heterogeneity, and review the pore-scale processes controlling microbial biomineralization in natural and engineered porous media. We discuss how individual physical, chemical and ecological factors integrate to affect the spatial and temporal control of biomineralization, and how each of these factors contributes to a quantitative understanding of biomineralization in porous media. We find that an improved understanding of microbial behavior in heterogeneous microenvironments would promote understanding of natural systems and output in diverse technological applications, including improved representation and control of fluid mixing from pore to field scales. We suggest a range of directions by which future work can build from existing tools to advance each of these areas to improve understanding and predictability of biomineralization science and technology.

Bacterial age distribution in soil - Generational gaps in adjacent hot and cold spots.

Resource patchiness and aqueous phase fragmentation in soil may induce large differences local growth conditions at submillimeter scales. These are translated to vast differences in bacterial age from cells dividing every thirty minutes in close proximity to plant roots to very old cells experiencing negligible growth in adjacent nutrient poor patches. In this study, we link bacterial population demographics with localized soil and hydration conditions to predict emerging generation time distributions and estimate mean bacterial cell ages using mechanistic and heuristic models of bacterial life in soil. Results show heavy-tailed distributions of generation times that resemble a power law for certain conditions, suggesting that we may find bacterial cells of vastly different ages living side by side within small soil volumes. Our results imply that individual bacteria may exist concurrently with all of their ancestors, resulting in an archive of bacterial cells with traits that have been gained (and lost) throughout time-a feature unique to microbial life. This reservoir of bacterial strains and the potential for the reemergence of rare strains with specific functions may be critical for ecosystem stability and function.

Rare and localized events stabilize microbial community composition and patterns of spatial self-organization in a fluctuating environment.

Spatial self-organization is a hallmark of surface-associated microbial communities that is governed by local environmental conditions and further modified by interspecific interactions. Here, we hypothesize that spatial patterns of microbial cell-types can stabilize the composition of cross-feeding microbial communities under fluctuating environmental conditions. We tested this hypothesis by studying the growth and spatial self-organization of microbial co-cultures consisting of two metabolically interacting strains of the bacterium Pseudomonas stutzeri. We inoculated the co-cultures onto agar surfaces and allowed them to expand (i.e. range expansion) while fluctuating environmental conditions that alter the dependency between the two strains. We alternated between anoxic conditions that induce a mutualistic interaction and oxic conditions that induce a competitive interaction. We observed co-occurrence of both strains in rare and highly localized clusters (referred to as "spatial jackpot events") that persist during environmental fluctuations. To resolve the underlying mechanisms for the emergence of spatial jackpot events, we used a mechanistic agent-based mathematical model that resolves growth and dispersal at the scale relevant to individual cells. While co-culture composition varied with the strength of the mutualistic interaction and across environmental fluctuations, the model provides insights into the formation of spatially resolved substrate landscapes with localized niches that support the co-occurrence of the two strains and secure co-culture function. This study highlights that in addition to spatial patterns that emerge in response to environmental fluctuations, localized spatial jackpot events ensure persistence of strains across dynamic conditions.

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.

Global earthworm distribution and activity windows based on soil hydromechanical constraints.

Earthworm activity modifies soil structure and promotes important hydrological ecosystem functions for agricultural systems. Earthworms use their flexible hydroskeleton to burrow and expand biopores. Hence, their activity is constrained by soil hydromechanical conditions that permit deformation at earthworm's maximal hydroskeletal pressure (≈200kPa). A mechanistic biophysical model is developed here to link the biomechanical limits of earthworm burrowing with soil moisture and texture to predict soil conditions that permit bioturbation across biomes. We include additional constraints that exclude earthworm activity such as freezing temperatures, low soil pH, and high sand content to develop the first predictive global map of earthworm habitats in good agreement with observed earthworm occurrence patterns. Earthworm activity is strongly constrained by seasonal dynamics that vary across latitudes largely due to soil hydromechanical status. The mechanistic model delineates the potential for earthworm migration via connectivity of hospitable sites and highlights regions sensitive to climate.

Spatiotemporal metabolic modeling of bacterial life in complex habitats.

The combination of genome-scale metabolic networks with spatially explicit representation of microbial habitats (spatiotemporal metabolic network modeling) paves the way to predict complex metabolic landscapes to a hitherto unparalleled detail, thus providing new insights into trophic interactions occurring at different scales. Placing detailed bacterial metabolism in realistic physical environment highlights the roles of physical barriers and diffusional bottlenecks on bacterial community interactions, structure and stability. We review recent advances in spatiotemporal metabolic network modeling using a few illustrative examples that highlight the immense potential of these novel approaches to interpret and design metabolic mediated interactions in structures (natural and engineered) environments.

Persistent decay of fresh xylem hydraulic conductivity varies with pressure gradient and marks plant responses to injury.

Defining plant hydraulic traits is central to the quantification of ecohydrological processes ranging from land-atmosphere interactions, to tree mortality and water-carbon budgets. A key plant trait is the xylem specific hydraulic conductivity (Kx ), that describes the plant's vascular system capacity to transport water. While xylem's vessels and tracheids are dead upon maturity, the xylem is neither inert nor deadwood, various components of the sapwood and surrounding tissue remaining alive and functional. Moreover, the established definition of Kx assumes linear relations between water flux and pressure gradient by tacitly considering the xylem as a "passive conduit". Here, we re-examine this notion of an inert xylem by systematically characterizing xylem flow in several woody plants using Kx measurements under constant and cyclic pressure gradients. Results show a temporal and pressure gradient dependence of Kx . Additionally, microscopic features in "living branches" are irreversibly modified upon drying of the xylem, thus differentiating the macroscopic definition of Kx for living and dead xylem. The findings highlight the picture of the xylem as a complex and delicate conductive system whose hydraulic behaviour transcends a passive gradient-based flow. The study sheds new light on xylem conceptualization, conductivity measurement protocols, in situ long-distance water transport and ecosystem modelling.

Spatial organization in microbial range expansion emerges from trophic dependencies and successful lineages.

Evidence suggests that bacterial community spatial organization affects their ecological function, yet details of the mechanisms that promote spatial patterns remain difficult to resolve experimentally. In contrast to bacterial communities in liquid cultures, surface-attached range expansion fosters genetic segregation of the growing population with preferential access to nutrients and reduced mechanical restrictions for cells at the expanding periphery. Here we elucidate how localized conditions in cross-feeding bacterial communities shape community spatial organization. We combine experiments with an individual based mathematical model to resolve how trophic dependencies affect localized growth rates and nucleate successful cell lineages. The model tracks individual cell lineages and attributes these with trophic dependencies that promote counterintuitive reproductive advantages and result in lasting influences on the community structure, and potentially, on its functioning. We examine persistence of lucky lineages in structured habitats where expansion is interrupted by physical obstacles to gain insights into patterns in porous domains.

A framework for modelling soil structure dynamics induced by biological activity.

Soil degradation is a worsening global phenomenon driven by socio-economic pressures, poor land management practices and climate change. A deterioration of soil structure at timescales ranging from seconds to centuries is implicated in most forms of soil degradation including the depletion of nutrients and organic matter, erosion and compaction. New soil-crop models that could account for soil structure dynamics at decadal to centennial timescales would provide insights into the relative importance of the various underlying physical (e.g. tillage, traffic compaction, swell/shrink and freeze/thaw) and biological (e.g. plant root growth, soil microbial and faunal activity) mechanisms, their impacts on soil hydrological processes and plant growth, as well as the relevant timescales of soil degradation and recovery. However, the development of such a model remains a challenge due to the enormous complexity of the interactions in the soil-plant system. In this paper, we focus on the impacts of biological processes on soil structure dynamics, especially the growth of plant roots and the activity of soil fauna and microorganisms. We first define what we mean by soil structure and then review current understanding of how these biological agents impact soil structure. We then develop a new framework for modelling soil structure dynamics, which is designed to be compatible with soil-crop models that operate at the soil profile scale and for long temporal scales (i.e. decades, centuries). We illustrate the modelling concept with a case study on the role of root growth and earthworm bioturbation in restoring the structure of a severely compacted soil.

Reduced gravity promotes bacterially mediated anoxic hotspots in unsaturated porous media.

Human endeavours into deep space exploration and the prospects of establishing colonies on nearby planets would invariably involve components of bioregenerative life support for food production, cabin atmosphere renewal, and waste recycling. Growing plants and their microbiomes in porous media under different gravitational fields may present new challenges due to effects of liquid distribution on gaseous exchange with roots and microorganisms. We provide the first direct evidence that capillary driven liquid reconfiguration in porous media under reduced gravity conditions reduces oxygen diffusion pathways and enhances anoxic conditions within bacterial hotspots. Parabolic flight experiments using model porous media inoculated with aerobic and facultative anaerobic bacteria reveal the systematic enhancement of anoxic conditions during the reduced gravity periods in the presence but not in the absence of bacterial activity. The promotion of anoxic conditions under reduced gravity may lead to higher nitrous oxide and methane emissions relative to Earth conditions, on the other hand, anoxic conditions could be beneficial for perchlorate bioremediation of Martian soil. The results highlight changes in soil bacterial microhabitats under reduced gravity and the challenges of managing bioregenerative life support systems in space.

Soil structure is an important omission in Earth System Models.

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.

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.

The engineering of spatially linked microbial consortia - potential and perspectives.

Traditional biotechnological applications of microorganisms employ mono-cultivation or co-cultivation in well-mixed vessels disregarding the potential of spatially organized cultures. Metabolic specialization and guided species interactions facilitated through spatial isolation would enable consortia of microbes to accomplish more complex functions than currently possible, for bioproduction as well as biodegradation processes. Here, we review concepts of spatially linked microbial consortia in which spatial arrangement is optimized to increase control and facilitate new species combinations. We highlight that genome-scale metabolic network models can inform the design and tuning of synthetic microbial consortia and suggest that a standardized assembly of such systems allows the combination of 'incompatibles', potentially leading to countless novel applications.

Rapid Shifts in Bacterial Community Assembly under Static and Dynamic Hydration Conditions in Porous Media.

The complexity of natural soils presents a challenge to the systematic identification and disentanglement of governing processes that shape natural bacterial communities. Studies have highlighted the critical role of the soil aqueous phase in shaping interactions among soil bacterial communities. To quantify and improve the attributability of soil aqueous-phase effects, we introduced a synthetic and traceable bacterial community to simple porous microcosms and subjected the community to constant or dynamic hydration conditions. The results were expressed in terms of absolute abundance and show species-specific responses to hydration and nutrient conditions. Hydration dynamics exerted a significant influence on the fraction of less-abundant species, especially after extended incubation periods. Phylogenetic relationships did not explain the group of most abundant species. The ability to quantify species-level dynamics in a bacterial community offers an important step toward deciphering the links between community composition and functions in dynamic terrestrial environments.IMPORTANCE The composition and activity of soil bacteria are central to various ecosystem services and soil biogeochemical cycles. A key factor for soil bacterial activity is soil hydration, which is in a constant state of change due to rainfall, drainage, plant water uptake, and evaporation. These dynamic changes in soil hydration state affect the structure and function of soil bacterial communities in complex ways often unobservable in natural soil. We designed an experimental system that retains the salient features of hydrated soil yet enables systematic evaluation of changes in a representative bacterial community in response to cycles of wetting and drying. The study shows that hydration cycles affect community abundance, yet most changes in composition occur with the less-abundant species (while the successful ones remain dominant). This research offers a new path for an improved understanding of bacterial community assembly in natural environments, including bacterial growth, maintenance, and death, with a special focus on the role of hydrological factors.

Microscale pH variations during drying of soils and desert biocrusts affect HONO and NH3 emissions.

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 (NH3) 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 NH3 emission dynamics. Additionally, we predict strong effects of atmospheric NH3 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.