Emergent Properties of Microbial Activity in Heterogeneous Soil Microenvironments: Different Research Approaches Are Slowly Converging, Yet Major Challenges Remain

A voxel-based approach for simulating microbial decomposition in soil: Comparison with LBM and improvement of morphological models

This paper deals with the computational modeling of biological dynamics in soil using an exact micro-scale pore space description from 3D Computed Tomography (CT) images. Within this context, computational costs and storage requirements constitute critical factors for running simulations on large datasets over extended periods. In this research, we represent the pore space by a graph of voxels (Voxel Graph-Based Approach, VGA) and model transport in fully saturated conditions (two-phase system) using Fick's law and coupled diffusion with biodegradation processes to simulate microbial decomposition in soil. To significantly decrease the computational time of our approach, the diffusion model is solved by means of Euler discretization schemes, along with parallelization strategies. We also tested several numerical strategies, including implicit, explicit, synchronous, and asynchronous schemes. To validate our VGA, we compare it with LBioS, a 3D model that integrates diffusion (via the Lattice Boltzmann method) with biodegradation, and Mosaic, a Pore Network Geometrical Modelling (PNGM) which represents the pore space using geometrical primitives. Our method yields result similar to those of LBioS in a quarter of the computing time. While slower than Mosaic, it is more accurate and requires no calibration. Additionally, we show that our approach can improve PNGM-based simulations by using a machine-learning approach to approximate diffusional conductance coefficients.

Decoupling microbial iron reduction from anoxic microsite formation in oxic sediments: a microscale investigation through microfluidic models

Iron (Fe) reduction is one of the oldest microbial processes on Earth. After the atmosphere and ocean became oxygenated, this anaerobic process was relegated to niche anoxic environments. However, evidence of Fe reduction in oxic, partially saturated subsurface systems, such as soils and vadose zones, has been reported, with the common explanation being the formation of anoxic microsites that remain undetected by bulk measurements. To explore how microscale oxygen concentrations regulate microbial Fe reduction, we cultivated a facultative Fe-reducing bacterium using a microfluidic setup integrated with transparent planar oxygen sensors. Contrary to expectations, Fe reduction occurred under fully oxic conditions, without the formation of anoxic microsites. Our results suggest that microbially mediated Fe-reduction could be more widespread in oxic subsurface environments than previously assumed. Moreover, our mathematical modeling of oxygen dynamics around biomass-rich layers revealed that the onset of anoxia is mainly controlled by biomass spatial organization rather than the conventionally used water saturation index. This opens a new perspective on the proxies needed to predict anoxic microsite formation and Fe(III) reduction occurrence.

Microhabitat accessibility determines peptide substrate degradation by soil microbial community

Soil pore space, considered the most complex biomaterial that exists, generates a complex environment, that gives rise to a wide variety of properties, such as microbial diversity and carbon storage. Soils contain, at the same time, the largest carbon reservoir on earth and an immense amount of nutrient-limited microbial biomass. The reason why this carbon is not consumed by soil microbes is attributed to the complex nature of soil, which forms a labyrinth where carbon and microbes cannot be in direct contact. In the present study, by using microfluidics, we tested the effect of labyrinth-like structures of decreasing accessibility on the decomposing activity of soil microbial communities from a soil inoculum. The two parameters used to study the effect of microhabitat accessibility were either the turning angle in an array of channel-like pore structures or the fractal order in an array of maze-like pore structures. We found that in both cases, channels and mazes, decreasing accessibility produced a higher peptide substrate degradation. When we analyzed the degradation within the structures, we found that most of the activity is concentrated in the regions of intermediate accessibility. We think that the increased degradation activity in low accessibility mazes might be due to the reduced interactions within the microbial communities which leads to a reduction in competition. Lowered competition allows different communities with a wide range of metabolic strategies to cohabit in the structures, which resulted in a bulk increase of the peptide substrate degradation.IMPORTANCEThe role microbes have in the environment is highly influenced by the characteristics of their habitat. Here, we show that a complex habitat enhances the enzymatic activity of a soil microbial inoculum. This might occur due to a reduced competition in complex habitats, which allows a more diverse community to coexist and explore a wider variety of metabolic strategies. The different rates of enzymatic activity in different levels of complexity suggest emergent properties of microbial communities in complex microhabitats which could have important implication for microbial processes, such as soil carbon storage and nutrient cycling.

Spatially variable organic-matter-driven clogging in a stormwater infiltration pond: Isotopic, microbiological and hydrogeological evidence

Stormwater infiltration ponds (SIPs) are nature-based solutions which tend to decrease their infiltration capacity over time due to pore clogging. Organic matter (OM) is a well-known clogging driver, but how OM affects the physical and biochemical processes in a SIP remains largely unknown. An analysis encompassing soil organic carbon (SOC) stable isotopes, extracellular polymeric substances (EPS) of biofilms, DNA-based identification of microbiological communities and hydrogeological tests was carried out to elucidate the main clogging mechanisms in a large SIP in Italy. Open pits revealed a stratified soil composed of different textures and compositions, associated with artificial recharge sequences and on-site maintenance practices. A very different isotopic and microbiological signature of soil samples collected at different depths within the first meter of the soil surface was observed. Such diversity was linked to the spatially variable permeability of OM-enriched sediments limiting the infiltration. The isotopic signature beneath the more permeable (i.e., less clogged) OM-enriched layers was similar to that of the isotopic value of the biological surficial crust (δ13C → -27 ‰). Below the less permeable (i.e., more clogged) OM-enriched layers, isotopic values were more consistent with advanced degradation of organic matter (δ13C → -23 ‰). The selective hydraulic isolation of the analyzed trenches could lead to the formation of microbial microenvironments, with direct consequences on local composition of EPS and biofilm production. Based on this multidisciplinary approach, a new conceptual model could be proposed to the site managers and authorities dealing with the SIP's maintenance.

Exploring Microbial Dark Matter for the Discovery of Novel Natural Products: Characteristics, Abundance Challenges and Methods

The objective of this review is to investigate microbial dark matter (MDM) with a focus on its potential for discovering novel natural products (NPs). This first part will examine the characteristics and abundance of these previously unexplored microbial communities, as well as the challenges faced in identifying and harnessing their unique biochemical properties and novel methods in this field. MDMs are thought to hold great potential for the discovery of novel NPs, which could have significant applications in medicine, agriculture, and industry. In recent years, there has been a growing interest in exploring MDM to unlock its potential. In fact, developments in genome-sequencing technologies and sophisticated phylogenetic procedures and metagenomic techniques have contributed to drastically make important changes in our sights on the diversity of microbial life, including the very outline of the tree of life. This has led to the development of novel technologies and methodologies for studying these elusive microorganisms, such as single-cell genomics, metagenomics, and culturomics. These approaches enable researchers to isolate and analyze individual microbial cells, as well as entire communities, providing insights into their genetic and metabolic potential. By delving into the MDM, scientists hope to uncover new compounds and biotechnological advancements that could have far-reaching impacts on various fields.

DGCNN approach links metagenome-derived taxon and functional information providing insight into global soil organic carbon

Metagenomics can provide insight into the microbial taxa present in a sample and, through gene identification, the functional potential of the community. However, taxonomic and functional information are typically considered separately in downstream analyses. We develop interpretable machine learning (ML) approaches for modelling metagenomic data, combining the biological representation of species with their associated genetically encoded functions within models. We apply our methods to investigate soil organic carbon (SOC) stocks. First, we combine a diverse global set of soil microbiome samples with environmental data, improving the predictive performance of classic ML and providing new insights into the role of soil microbiomes in global carbon cycling. Our network analysis of predictive taxa identified by classical ML models provides context for their ecological significance, extending the focus beyond just the most predictive taxa to 'hidden' features within the model that might be considered less predictive using standard methods for explainability. We next develop unique graph representations for individual microbiomes, linking microbial taxa to their associated functions directly, enabling predictions of SOC via deep graph convolutional neural networks (DGCNNs). Interpretation of the DGCNNs distinguished between the importance of functions of key individual species, providing genome sequence differences, e.g., gene loss/acquisition, that associate with SOC. These approaches identify several members of the Verrucomicrobiaceae family and a range of genetically encoded functions, e.g., related to carbohydrate metabolism, as important for SOC stocks and effective global SOC predictors. These relatively understudied but widespread organisms could play an important role in SOC dynamics globally.

A review of advanced bioremediation technologies for dioxin-contaminated soil treatment: Current and future outlook

Polychlorinated dibenzo-p-dioxins (PCDD) and polychlorinated dibenzofurans (PCDF), namely known as dioxins, are persistent organic compounds with high toxicity. The presence of dioxins in soil is a major environmental issue worldwide, as it negatively impacts both ecosystems and human health. Thus, several advanced techniques have been applied to overcome this issue, offering promising treatment efficiency and cost-effectiveness. This review employs a meta-analysis strategy to provide an up-to-date assessment of the global situation of dioxin-contaminated soil. Dioxin concentrations are commonly higher in industrial and urban areas than in rural areas, primarily due to anthropogenic activities such as chemical manufacturing and waste incineration. Furthermore, several advanced bioremediation technologies for dioxin treatment, including biosurfactants, composting, and phytoremediation were highlighted and thoroughly discussed. Aerobic composting has proven to be robust in removing dioxins, achieving treatment efficiencies ranging from 65% to 85%. Whereas, phytoremediation, particularly when involving agricultural crops like zucchini, cucumber, and wheat, shows great promise in dioxin removal through various mechanisms, including root uptake and transpiration. Notably, biosurfactants such as rhamnolipids and sophorolipids have been effectively used to remediate dioxin-contaminated soil due to their significantly enhanced bioavailability of dioxins and their interaction with microbes. This review provides a comprehensive understanding of advanced biotechnologies for remediating dioxin-contaminated soil. It also addresses the technical and economic aspects of dioxin treatment and identifies future directions and research perspectives to fill knowledge gaps in this field.

An animal charcoal contaminated cottage industry soil highlighted by halophilic archaea dominance and decimation of bacteria

An animal charcoal contaminated cottage industry soil in Lagos, Nigeria (ACGT) was compared in an ex post facto study with a nearby unimpacted soil (ACGC). Hydrocarbon content was higher than regulatory limits in ACGT (180.2 mg/kg) but lower in ACGC (19.28 mg/kg). Heavy metals like nickel, cadmium, chromium and lead were below detection limit in ACGC. However, all these metals, except cadmium, were detected in ACGT, but at concentrations below regulatory limits. Furthermore, copper (253.205 mg/kg) and zinc (422.630 mg/kg) were above regulatory limits in ACGT. Next generation sequencing revealed that the procaryotic community was dominated by bacteria in ACGC (62%) while in ACGT archaea dominated (76%). Dominant phyla in ACGC were Euryarchaeota (37%), Pseudomonadota (16%) and Actinomycetota (12%). In ACGT it was Euryarchaeota (76%), Bacillota (9%), Pseudomonadota (7%) and Candidatus Nanohaloarchaeota (5%). Dominant Halobacteria genera in ACGT were Halobacterium (16%), Halorientalis (16%), unranked halophilic archaeon (13%) Salarchaeum (6%) and Candidatus Nanohalobium (5%), whereas ACGC showed greater diversity dominated by bacterial genera Salimicrobium (7%) and Halomonas (3%). Heavy metals homeostasis genes, especially for copper, were fairly represented in both soils but with bacterial taxonomic affiliations. Sites like ACGT, hitherto poorly studied and understood, could be sources of novel bioresources.

Fragmented micro-growth habitats present opportunities for alternative competitive outcomes

Bacteria in nature often thrive in fragmented environments, like soil pores, plant roots or plant leaves, leading to smaller isolated habitats, shared with fewer species. This spatial fragmentation can significantly influence bacterial interactions, affecting overall community diversity. To investigate this, we contrast paired bacterial growth in tiny picoliter droplets (1-3 cells per 35 pL up to 3-8 cells per species in 268 pL) with larger, uniform liquid cultures (about 2 million cells per 140 µl). We test four interaction scenarios using different bacterial strains: substrate competition, substrate independence, growth inhibition, and cell killing. In fragmented environments, interaction outcomes are more variable and sometimes even reverse compared to larger uniform cultures. Both experiments and simulations show that these differences stem mostly from variation in initial cell population growth phenotypes and their sizes. These effects are most significant with the smallest starting cell populations and lessen as population size increases. Simulations suggest that slower-growing species might survive competition by increasing growth variability. Our findings reveal how microhabitat fragmentation promotes diverse bacterial interaction outcomes, contributing to greater species diversity under competitive conditions.

Mobility and growth in confined spaces are important mechanisms for the establishment of Bacillus subtilis in the rhizosphere

The rhizosphere hosts complex and abundant microbiomes whose structure and composition are now well described by metagenomic studies. However, the dynamic mechanisms that enable micro-organisms to establish along a growing plant root are poorly characterized. Here, we studied how a motile bacterium utilizes the microhabitats created by soil pore space to establish in the proximity of plant roots. We have established a model system consisting of Bacillus subtilis and lettuce seedlings co-inoculated in transparent soil microcosms. We carried out live imaging experiments and developed image analysis pipelines to quantify the abundance of the bacterium as a function of time and position in the pore space. Results showed that the establishment of the bacterium in the rhizosphere follows a precise sequence of events where small islands of mobile bacteria were first seen forming near the root tip within the first 12-24 h of inoculation. Biofilm was then seen forming on the root epidermis at distances of about 700-1000 µm from the tip. Bacteria accumulated predominantly in confined pore spaces within 200 µm from the root or the surface of a particle. Using probabilistic models, we could map the complete sequence of events and propose a conceptual model of bacterial establishment in the pore space. This study therefore advances our understanding of the respective role of growth and mobility in the efficient colonization of bacteria in the rhizosphere.

Microfluidics devices for sports: A review on technology for biomedical application used in fields such as biomedicine, drug encapsulation, preparation of nanoparticles, cell targeting, analysis, diagnosis, and cell culture

Microfluidics is an interdisciplinary field that combines knowledge from various disciplines, including biology, chemistry, sports medicine, fluid dynamics, kinetic biomechanics, and microelectronics, to manipulate and control fluids and particles in micron-scale channels and chambers. These channels and chambers can be fabricated using different materials and methods to achieve various geometries and shapes. Microfluidics has numerous biomedical applications, such as drug encapsulation, nanoparticle preparation, cell targeting, analysis, diagnosis, and treatment of sports injuries in both professional and non-professional athletes. It can also be used in other fields, such as biological analysis, chemical synthesis, optics, and acceleration in the treatment of critical sports injuries. The objective of this review is to provide a comprehensive overview of microfluidic technology, including its fabrication methods, current platform materials, and its applications in sports medicine. Biocompatible, biodegradable, and semi-crystalline polymers with unique mechanical and thermal properties are one of the promising materials in microfluidic technology. Despite the numerous advantages of microfluidic technology, further research and development are necessary. Although the technology offers benefits such as ease of operation and cost efficiency, it is still in its early stages. In conclusion, this review emphasizes the potential of microfluidic technology and highlights the need for continued research to fully exploit its potential in the biomedical field and sport applications.

Elucidating fungal decomposition of organic matter at sub-micrometer spatial scales using optical photothermal infrared (O-PTIR) microspectroscopy

In microbiological studies, a common goal is to link environmental factors to microbial activities. Both environmental factors and microbial activities are typically derived from bulk samples. It is becoming increasingly clear that such bulk environmental parameters poorly represent the microscale environments microorganisms experience. Using infrared (IR) microspectroscopy, the spatial distribution of chemical compound classes can be visualized, making it a useful tool for studying the interactions between microbial cells and their microenvironments. The spatial resolution of conventional IR microspectroscopy has been limited by the diffraction limit of IR light. The recent development of optical photothermal infrared (O-PTIR) microspectroscopy has pushed the spatial resolution of IR microspectroscopy beyond this diffraction limit, allowing the distribution of chemical compound classes to be visualized at sub-micrometer spatial scales. To examine the potential and limitations of O-PTIR microspectroscopy to probe the interactions between fungal cells and their immediate environments, we imaged the decomposition of cellulose films by cells of the ectomycorrhizal fungus Paxillus involutus and compared O-PTIR results using conventional IR microspectroscopy. Whereas the data collected with conventional IR microspectroscopy indicated that P. involutus has only a very limited ability to decompose cellulose films, O-PTIR data suggested that the ability of P. involutus to decompose cellulose was substantial. Moreover, the O-PTIR method enabled the identification of a zone located outside the fungal hyphae where the cellulose was decomposed by oxidation. We conclude that O-PTIR can provide valuable new insights into the abilities and mechanisms by which microorganisms interact with their surrounding environments.IMPORTANCEInfrared (IR) microspectroscopy allows the spatial distribution of chemical compound classes to be visualized. The use of conventional IR microspectroscopy in microbiological studies has been restricted by limited spatial resolution. Recent developments in laser technology have enabled a new class of IR microspectroscopy instruments to be developed, pushing the spatial resolution beyond the diffraction limit of IR light to approximately 500 nm. This improved spatial resolution now allows microscopic observations of changes in chemical compounds to be made, making IR microspectroscopy a useful tool to investigate microscale changes in chemistry that are caused by microbial activity. We show these new possibilities using optical photothermal infrared microspectroscopy to visualize the changes in cellulose substrates caused by oxidation by the ectomycorrhizal fungus Paxillus involutus at the interface between individual fungal hyphae and cellulose substrates.

Soil as a transdisciplinary research catalyst: from bioprospecting to biorespecting

The vast microbial biodiversity of soils is beginning to be observed and understood by applying modern DNA sequencing techniques. However, ensuring this potentially valuable information is used in a fair and equitable way remains a challenge. Here, we present a public engagement project that explores this topic through collaborative research of soil microbiomes at six urban locations using nanopore-based DNA sequencing. The project brought together researchers from the disciplines of synthetic biology, environmental humanities and microbial ecology, as well as school students aged 14-16 years old, to gain a broader understanding of views on the use of data from the environment. Discussions led to the transformation of 'bioprospecting', a metaphor with extractive connotations which is often used to frame environmental DNA sequencing studies, towards a more collaborative approach-'biorespecting'. This shift in terminology acknowledges that genetic information contained in soil arises as a result of entire ecosystems, including the people involved in its creation. Therefore, any use of sequence information should be accountable to the ecosystems from which it arose. As knowledge can arise from ecosystems and communities, science and technology should acknowledge this link and reciprocate with care and benefit-sharing to help improve the wellbeing of future generations.

Soil Protists Can Actively Redistribute Beneficial Bacteria along Medicago truncatula Roots

The rhizosphere is the region of soil directly influenced by plant roots. The microbial community in the rhizosphere includes fungi, protists, and bacteria: all play significant roles in plant health. The beneficial bacterium Sinorhizobium meliloti infects growing root hairs on nitrogen-starved leguminous plants. Infection leads to the formation of a root nodule, where S. meliloti converts atmospheric nitrogen to ammonia, a bioavailable form. In soil, S. meliloti is often found in biofilms and travels slowly along the roots, leaving developing root hairs at the growing root tips uninfected. Soil protists are an important component of the rhizosphere system, able to travel quickly along roots and water films, who prey on soil bacteria and have been known to egest undigested phagosomes. We show that a soil protist, Colpoda sp., can transport S. meliloti down Medicago truncatula roots. Using model soil microcosms, we directly observed fluorescently labeled S. meliloti along M. truncatula roots and tracked the displacement of the fluorescence signal over time. Two weeks after co-inoculation, this signal extended 52 mm farther down plant roots when Colpoda sp. was also present versus treatments that contained bacteria but not protists. Direct counts also showed protists are required for viable bacteria to reach the deeper sections of our microcosms. Facilitating bacterial transport may be an important mechanism whereby soil protists promote plant health. IMPORTANCE Soil protists are an important part of the microbial community in the rhizosphere. Plants grown with protists fare better than plants grown without protists. Mechanisms through which protists support plant health include nutrient cycling, alteration of the bacterial community through selective feeding, and consumption of plant pathogens. Here, we provide data in support of an additional mechanism: protists act as transport vehicles for bacteria in soil. We show that protist-facilitated transport can deliver plant-beneficial bacteria to the growing tips of roots that may otherwise be sparsely inhabited with bacteria originating from a seed-associated inoculum. By co-inoculating Medicago truncatula roots with both S. meliloti, a nitrogen-fixing legume symbiont, and Colpoda sp., a ciliated protist, we show substantial and statistically significant transport with depth and breadth of bacteria-associated fluorescence as well as transport of viable bacteria. Co-inoculation with shelf-stable encysted soil protists may be employed as a sustainable agriculture biotechnology to better distribute beneficial bacteria and enhance the performance of inoculants.

Morphology and Size of Bacterial Colonies Control Anoxic Microenvironment Formation in Porous Media

Bacterial metabolisms using electron acceptors other than oxygen (e.g., methanogenesis and fermentation) largely contribute to element cycling and natural contaminant attenuation/mobilization, even in well-oxygenated porous environments, such as shallow aquifers. This paradox is commonly explained by the occurrence of small-scale anoxic microenvironments generated by the coupling of bacterial respiration and dissolved oxygen (O₂) transport by pore water. Such microenvironments allow facultative anaerobic bacteria to proliferate in oxic environments. Microenvironment dynamics are still poorly understood due to the challenge of directly observing biomass and O₂ distributions at the microscale within an opaque sediment matrix. To overcome these limitations, we integrated a microfluidic device with transparent O₂ planar optical sensors to measure the temporal behavior of dissolved O₂ concentrations and biomass distributions with time-lapse videomicroscopy. Our results reveal that bacterial colony morphology, which is highly variable in flowing porous systems, controls the formation of anoxic microenvironments. We rationalize our observations through a colony-scale Damköhler number comparing dissolved O₂ diffusion and a bacterial O₂ uptake rate. Our Damköhler number enables us to predict the pore space fraction occupied by anoxic microenvironments in our system for a given bacterial organization.

Keep oxygen in check: An improved in-situ zymography approach for mapping anoxic hydrolytic enzyme activities in a paddy soil

Paddy soils regularly experience redox oscillations during the wetting and draining stages, yet the effects of short-term presence of oxygen (O₂) on in-situ microbial hotspots and enzyme activities in anoxic ecosystems remain unclear. To fill this knowledge gap, we applied soil zymography to localize hotspots and activities of phosphomonoesterase (PME), β-glucosidase (BG), and leucine aminopeptidase (LAP) in three compartments of rice-planted rhizoboxes (top bulk, rooted, and bottom bulk paddy soil) under oxic (+O₂) and anoxic (O₂) conditions. Short-term (35 min) aeration decreased PME activity by 13-49 %, BG by 4-52 %, and LAP by 12-61 % as compared with O₂ in three soil compartments. The percentage of hotspot area was higher by 3-110 % for PME, by 10-60 % for BG, and by 12-158 % for LAP under +O₂ vs. O₂ conditions depending on a rice growth stage. Irrespective of the aeration conditions, the rhizosphere extent of rice plants for three enzymes was generally greater under higher moisture conditions and at earlier growth stage. Higher O₂ sensitivity for the tested enzymes at bottom bulk soil versus other compartments suggested that short-term aeration during conventional zymography may lead to underestimation of nutrient mobilization in subsoil compared to top bulk soil. The intolerance of anaerobic microorganisms against the toxicity of O₂ in the cells and the shift of microbial metabolic pathways may explain such a short-term suppression by O₂. Our findings, therefore, show that anoxic conditions and soil moisture should be kept during zymography and probably other in-situ soil imaging methods when studying anoxic systems.

Distribution of Mn Oxidation States in Grassland Soils and Their Relationships with Soil Pores

Manganese (Mn) is known to be an active contributor to processing and cycling of soil organic carbon (C), yet the exact mechanisms behind its interactions with C are poorly understood. Plant diversity in terrestrial ecosystems drives feedback links between plant C inputs and soil pores, where the latter, in turn, impact the redox environment and Mn. This study examined associations between soil pores (>36 μm Ø) and Mn within intact soils from two grassland ecosystems, after their >6-year implementation in a replicated field experiment. We used μ-XRF imaging and XANES spectroscopy to explore spatial distribution patterns of Mn oxidation states, combined with X-ray computed microtomography and 2D zymography. A high plant diversity system (restored prairie) increased soil C and modified spatial distribution patterns of soil pores as compared to a single species system (monoculture switchgrass). In switchgrass, the abundance of oxidized and reduced Mn oxidation states varied with distance from pores consistently with anticipated O₂ diffusion, while in the soil from restored prairie, the spatial patterns suggested that biological activity played a greater role in influencing Mn distributions. Based on the findings, we propose a hypothesis that Mn transformations promote C gains in soils of high plant diversity grasslands.

A workflow for segmenting soil and plant X-ray computed tomography images with deep learning in Google's Colaboratory

X-ray micro-computed tomography (X-ray μCT) has enabled the characterization of the properties and processes that take place in plants and soils at the micron scale. Despite the widespread use of this advanced technique, major limitations in both hardware and software limit the speed and accuracy of image processing and data analysis. Recent advances in machine learning, specifically the application of convolutional neural networks to image analysis, have enabled rapid and accurate segmentation of image data. Yet, challenges remain in applying convolutional neural networks to the analysis of environmentally and agriculturally relevant images. Specifically, there is a disconnect between the computer scientists and engineers, who build these AI/ML tools, and the potential end users in agricultural research, who may be unsure of how to apply these tools in their work. Additionally, the computing resources required for training and applying deep learning models are unique, more common to computer gaming systems or graphics design work, than to traditional computational systems. To navigate these challenges, we developed a modular workflow for applying convolutional neural networks to X-ray μCT images, using low-cost resources in Google's Colaboratory web application. Here we present the results of the workflow, illustrating how parameters can be optimized to achieve best results using example scans from walnut leaves, almond flower buds, and a soil aggregate. We expect that this framework will accelerate the adoption and use of emerging deep learning techniques within the plant and soil sciences.

Synthetic microbial consortia derived from rhizosphere soil protect wheat against a soilborne fungal pathogen

Synthetic microbial communities (SynComs) could potentially enhance some functions of the plant microbiome and emerge as a promising inoculant for improving crop performance. Here, we characterized a collection of bacteria, previously isolated from the wheat rhizosphere, for their antifungal activity against soilborne fungal pathogens. Ten SynComs with different compositions from 14 bacterial strains were created. Seven SynComs protected wheat from Rhizoctonia solani AG8 infection, although SynComs were not more effective than single strains in reducing wheat root rot disease. Further, the mechanisms of interaction of the tested bacteria with each other and plants were explored. We found that nine bacteria and nine SynComs impacted the root growth of Arabidopsis. Nine bacteria and four SynComs significantly inhibited the growth of AG8 by producing volatiles. The cell-free supernatants from six bacteria inhibited the growth of AG8. Together, this study provided the potential for improving crop resilience by creating SynComs.

Self-potential time series reveal emergent behavior in soil organic matter dynamics

The active cycling of carbon between soil organic matter and the atmosphere is of critical importance to global climate change. An extensive body of research exists documenting the capricious nature of soil organic matter (SOM) dynamics, which is symptomatic of an intricate network of interactions between diverse groups of heterotrophic microorganisms, complex organic substrates, and highly variable local environmental conditions. These attributes are consistent with elements of complex system theory and the temporal evolution of otherwise unpredictable patterns of behavior that emerge from long range dependency on initial conditions. Here we show that vertical depth profile of self-potential (SP) time series measurements responds in a quantitative manner to variations in soil moisture, SOM concentrations, and relative rates of microbial activity. Application of detrended fluctuation analysis (DFA) of self potential time series data is shown additionally to reveal the presence of long-range dependence and emergence of anomalous electrochemical diffusion behavior, both of which diminish with depth as SOM specific energy densities decline.

Explicit spatial modeling at the pore scale unravels the interplay of soil organic carbon storage and structure dynamics

The structure of soil aggregates plays an important role for the turnover of particulate organic matter (POM) and vice versa. Analytical approaches usually do not disentangle the continuous re-organization of soil aggregates, caught between disintegration and assemblage. This led to a lack of understanding of the mechanistic relationship between aggregation and organic matter dynamics in soils. In this study, we took advantage of a process-based mechanistic model that describes the interaction between the dynamic (re-)arrangement of soil aggregates, based on dynamic image analysis data of wet-sieved aggregates, to analyze the turnover of POM, and simultaneous soil surface interactions in a spatially and temporally explicit way. Our novel modeling approach enabled us to unravel the temporal development of aggregate sizes, organic carbon (OC) turnover of POM, and surface coverage as affected by soil texture, POM input, and POM decomposition rate comparing a low and high clay soil (18% and 33% clay content). Our results reveal the importance of the dynamic re-arrangement of soil structure on POM-related turnover of OC in soils. Firstly, aggregation was largely determined by the POM input fostering aggregates through additional gluing joints outweighing soil texture at lower decomposition rate, whereas at higher decomposition rate, soil texture had a higher influence leading to larger aggregates in the high clay soil. Secondly, the POM storage increased with clay content, showing that surface interactions may delay the turnover of OC into CO₂ . Thirdly, we observed a structural priming effect in which the increased input of POM induced increased structural re-arrangement stimulating the mineralization of old POM. This work highlights that the dynamic re-arrangement of soil aggregates has important implications for OC turnover and is driven by underlying surface interactions where temporary gluing spots stabilize larger aggregates.

Role of tactic response on the mobilization of motile bacteria through micrometer-sized pores

A major cause of high bioremediation endpoints is the limited bioaccessibility to residual contaminants resting in soil pores with diameters close to the size exclusion limit of bacterial cells. Under nongrowing conditions and in the absence of hydraulic flow, we examined how the tactic behavior of motile, contaminant-degrading Pseudomonas putida G7 cells (2 × 1 μm) influenced passage through membranes with pores ranging in size from 1 μm to 12 μm. The bacteria were spontaneously retained by the membranes - even those with the largest pore size. However, the cells were mobilized through 5 μm and 12 μm pores after the application of an attractant (salicylate). Mobilization also occurred by attraction to the common root exudate constituents γ-aminobutyric acid and citrate and repellence (or negative taxis) to zero-valent iron nanoparticles. The observed pore size threshold for tactic mobilization (5 μm) and unaltered cell fluxes and effective cell diffusion against different chemoeffector strengths and concentrations suggest that there is a physical constraint on the gradient sensing mechanism at the pores that drives the tactic response. Our results indicate that chemically mediated, small-scale tactic reactions of motile bacteria may become relevant to enhance the bioaccessibility of the residual contaminants present in micrometer-sized soil pores.

Positron-emitting radiotracers spatially resolve unexpected biogeochemical relationships linked with methane oxidation in Arctic soils

Arctic soils are marked by cryoturbic features, which impact soil-atmosphere methane (CH₄ ) dynamics vital to global climate regulation. Cryoturbic diapirism alters C/N chemistry within frost boils by introducing soluble organic carbon and nutrients, potentially influencing microbial CH₄ oxidation. CH₄ oxidation in soils, however, requires a spatio-temporal convergence of ecological factors to occur. Spatial delineation of microbial activity with respect to these key microbial and biogeochemical factors at relevant scales is experimentally challenging in inherently complex and heterogeneous natural soil matrices. This work aims to overcome this barrier by spatially linking microbial CH₄ oxidation with C/N chemistry and metagenomic characteristics. This is achieved by using positron-emitting radiotracers to visualize millimeter-scale active CH₄ uptake areas in Arctic soils with and without diapirism. X-ray absorption spectroscopic speciation of active and inactive areas shows CH₄ uptake spatially associates with greater proportions of inorganic N in diapiric frost boils. Metagenomic analyses reveal Ralstonia pickettii associates with CH₄ uptake across soils along with pertinent CH₄ and inorganic N metabolism associated genes. This study highlights the critical relationship between CH₄ and N cycles in Arctic soils, with potential implications for better understanding future climate. Furthermore, our experimental framework presents a novel, widely applicable strategy for unraveling ecological relationships underlying greenhouse gas dynamics under global change.

Harnessing belowground processes for sustainable intensification of agricultural systems

Increasing food demand coupled with climate change pose a great challenge to agricultural systems. In this review we summarize recent advances in our knowledge of how plants, together with their associated microbiota, shape rhizosphere processes. We address (molecular) mechanisms operating at the plant-microbe-soil interface and aim to link this knowledge with actual and potential avenues for intensifying agricultural systems, while at the same time reducing irrigation water, fertilizer inputs and pesticide use. Combining in-depth knowledge about above and belowground plant traits will not only significantly advance our mechanistic understanding of involved processes but also allow for more informed decisions regarding agricultural practices and plant breeding. Including belowground plant-soil-microbe interactions in our breeding efforts will help to select crops resilient to abiotic and biotic environmental stresses and ultimately enable us to produce sufficient food in a more sustainable agriculture in the upcoming decades.

Impact of Soil Sealing on Soil Carbon Sequestration, Water Storage Potentials and Biomass Productivity in Functional Urban Areas of the European Union and the United Kingdom

The negative impacts of soil sealing are numerous, from withdrawing fertile soil from biomass production to modifying the microclimate and decreasing biodiversity. Many of the processes are interrelated and propagate further undesirable consequences from local to global levels. Three issues are especially important from the viewpoint of multiscale ecological cycles and consequent environmental impacts. One is soil organic carbon (SOC), the other is soil water management and the third is biomass productivity. In this study, we assessed the lost carbon sequestration potential due to soil sealing in functional Urban Areas (FUAs) of Europe, the potential effect of soil sealing on the topsoil to hold water to its full capacity and the loss of biomass productivity potential. Findings revealed that one-fifth of the area of soil that became sealed between 2012 and 2018 was of high productivity potential, and almost two-thirds was of medium productivity potential. New soil sealing caused a loss of carbon sequestration potential estimated at 4 million tons of carbon of the FUAs and also caused an estimated potential loss of water-holding capacity of 668 million m3.

A Review of Soil Contaminated with Dioxins and Biodegradation Technologies: Current Status and Future Prospects

This article provides a comprehensive assessment of dioxins contaminating the soil and evaluates the bioremediation technology currently being widely used, and also offers recommendations for future prospects. Soil pollution containing dioxins is extremely toxic and hazardous to human health and the environment. Dioxin concentrations in soils around the world are caused by a variety of sources and outcomes, but the main sources are from the consequences of war and human activities. Bioremediation technology (bioaugmentation, biostimulation, and phytoremediation) is considered an optimal and environmentally friendly technology, with the goal of applying native microbial communities and using plant species with a high biomass to treat contaminated dioxins in soil. The powerful bioremediation system is the growth of microorganisms that contribute to the increased mutualistic and competitive relationships between different strains of microorganisms. Although biological treatment technology can thoroughly treat contaminated dioxins in soil with high efficiency, the amount of gas generated and Cl radicals dispersed after the treatment process remains high. Further research on the subject is required to provide stricter control over the outputs noted in this study.

Distribution of Burkholderia pseudomallei within a 300-cm deep soil profile: implications for environmental sampling

The environmental distribution of Burkholderia pseudomallei, the causative agent of melioidosis, remains poorly understood. B. pseudomallei is known to have the ability to occupy a variety of environmental niches, particularly in soil. This paper provides novel information about a putative association of soil biogeochemical heterogeneity and the vertical distribution of B. pseudomallei. We investigated (1) the distribution of B. pseudomallei along a 300-cm deep soil profile together with the variation of a range of soil physico-chemical properties; (2) whether correlations between the distribution of B. pseudomallei and soil physico-chemical properties exist and (3) when they exist, what such correlations indicate with regards to the environmental conditions conducive to the occurrence of B. pseudomallei in soils. Unexpectedly, the highest concentrations of B. pseudomallei were observed between 100 and 200 cm below the soil surface. Our results indicate that unravelling the environmental conditions favorable to B. pseudomallei entails considering many aspects of the actual complexity of soil. Important recommendations regarding environmental sampling for B. pseudomallei can be drawn from this work, in particular that collecting samples down to the water table is of foremost importance, as groundwater persistence appears to be a controlling factor of the occurrence of B. pseudomallei in soil.

Near-universal trends in brGDGT lipid distributions in nature

Bacterial brGDGT lipids are a prevalent tool in studies of terrestrial paleoclimate. Their distributions correlate empirically with environmental temperature and pH, and their ubiquity in terrestrial, freshwater, and marine environments gives them wide applicability. Whether correlations with temperature and pH emerge due to a physiological response of source organisms and/or a shift in bacterial community composition remains an open question with important implications for proxy development and application. We applied a newly described technique for grouping brGDGTs to a globally compiled dataset (n = 3129) consisting of all modern sample media known to host brGDGTs. We found strong resemblances in the relationships between brGDGT fractional abundances and both temperature and pH across nearly all sample types examined. We also found near-universal connections between the brGDGTs themselves. Given the markedly different bacterial communities expected to inhabit these settings, these widespread relationships may suggest physiological and/or biochemical bases for observed brGDGT distributions.

Variation in Bacterial Community Structure Under Long-Term Fertilization, Tillage, and Cover Cropping in Continuous Cotton Production

Agricultural practices alter the structure and functions of soil microbial community. However, few studies have documented the alterations of bacterial communities in soils under long-term conservation management practices for continuous crop production. In this study, we evaluated soil bacterial diversity using 16S rRNA gene sequencing and soil physical and chemical properties within 12 combinations of inorganic N fertilization, cover cropping, and tillage throughout a cotton production cycle. Soil was collected from field plots of the West Tennessee Agriculture Research and Education Center in Jackson, TN, United States. The site has been under continuous cotton production for 38 years. A total of 38,038 OTUs were detected across 171 soil samples. The dominant bacterial phyla were Proteobacteria, Acidobacteria, Actinobacteria, Verrucomicrobia, and Chloroflexi, accounting for ∼70% of the total bacterial community membership. Conventional tillage increased alpha diversity in soil samples collected in different stages of cotton production. The effects of inorganic N fertilization and conventional tillage on the structure of bacterial communities were significant at all four sampling dates (p < 0.01). However, cover cropping (p < 0.05) and soil moisture content (p < 0.05) only showed significant influence on the bacterial community structure after burn-down of the cover crops and before planting of cotton (May). Nitrate-N appeared to have a significant effect on the structure of bacterial communities after inorganic fertilization and at the peak of cotton growth (p < 0.01). Structural equation modeling revealed that the relative abundances of denitrifying and nitrifying bacteria were higher when conventional tillage and vetch cover crop practices were applied, respectively. Our results indicate that long-term tillage and fertilization are key factors increasing the diversity and restructuring the composition of bacterial communities, whereas cover cropping may have shorter-term effects on soil bacteria community structure. In this study, management practices might positively influence relative abundances of bacterial functional groups associated with N cycling. The bacteria functional groups may build a network for providing N and meet microbial N needs in the long term.

How Heterogeneous Pore Scale Distributions of Wettability Affect Infiltration into Porous Media

Wettability is an important parameter that significantly determines hydrology in porous media, and it especially controls the flow of water across the rhizosphere—the soil-plant interface. However, the influence of spatially heterogeneous distributions on the soil particles surfaces is scarcely known. Therefore, this study investigates the influence of spatially heterogeneous wettability distributions on infiltration into porous media. For this purpose, we utilize a two-phase flow model based on Lattice-Boltzmann to numerically simulate the infiltration in porous media with a simplified geometry and for various selected heterogeneous wettability coatings. Additionally, we simulated the rewetting of the dry rhizosphere of a sandy soil where dry hydrophobic mucilage depositions on the particle surface are represented via a locally increased contact angle. In particular, we can show that hydraulic dynamics and water repellency are determined by the specific location of wettability patterns within the pore space. When present at certain locations, tiny hydrophobic depositions can cause water repellency in an otherwise well-wettable soil. In this case, averaged, effective contact angle parameterizations such as the Cassie equation are unsuitable. At critical conditions, when the rhizosphere limits root water uptake, consideration of the specific microscale locations of exudate depositions may improve models of root water uptake.

Splicing Method of Micro-Nano-Scale Pore Radius Distribution in Tight Sandstone Reservoir

Accurate characterization of the micro- and nano-pore radius values in a tight sandstone reservoir is the key work to reasonably evaluate reservoir properties. The previous exploration of pore-stitching methods is mainly based on the morphological extension of similar segments. However, few scholars compare and verify the image and non-image stitching methods, so they cannot clarify the application scope of different pore-stitching methods. In this study, the pore structures of eight selected tight sandstone samples were evaluated using high-pressure mercury injection, nuclear magnetic resonance, scanning electron microscope, and the helium porosity test. Then, the C-value fitting, interpolation fitting, and morphological fitting were used to establish high-pressure mercury injection and Nuclear Magnetic Resonance (NMR) pore distribution curves to evaluate the differences among the micro-nano-scale pore radius values determined by the three fitting methods. Finally, the pore radius distribution is extracted from the binary image of Scanning Electron Microscope (SEM). After correcting the helium porosity data, the application scope of different fitting methods is evaluated by using the mean standard deviation verification method, and the optimal solution of the stitching method of pore radius distribution in each application scope is found. Compared to other studies, this research demonstrated three relatively simple methods for the determination of the full range of pore size distributions, providing a reliable method to evaluate the prerequisites of the range of application. This study provides a new idea for the micro-nano-scale pore radius splicing method of a tight sandstone reservoir, and the research results can provide a reference for the actual reservoir evaluation of oil and gas fields.

Microfluidics as an Emerging Platform for Exploring Soil Environmental Processes: A Critical Review

Investigating environmental processes, especially those occurring in soils, calls for innovative and multidisciplinary technologies that can provide insights at the microscale. The heterogeneity, opacity, and dynamics make the soil a "black box" where interactions and processes are elusive. Recently, microfluidics has emerged as a powerful research platform and experimental tool which can create artificial soil micromodels, enabling exploring soil processes on a chip. Micro/nanofabricated microfluidic devices can mimic some of the key features of soil with highly controlled physical and chemical microenvironments at the scale of pores, aggregates, and microbes. The combination of various techniques makes microfluidics an integrated approach for observation, reaction, analysis, and characterization. In this review, we systematically summarize the emerging applications of microfluidic soil platforms, from investigating soil interfacial processes and soil microbial processes to soil analysis and high-throughput screening. We highlight how innovative microfluidic devices are used to provide new insights into soil processes, mechanisms, and effects at the microscale, which contribute to an integrated interrogation of the soil systems across different scales. Critical discussions of the practical limitations of microfluidic soil platforms and perspectives of future research directions are summarized. We envisage that microfluidics will represent the technological advances toward microscopic, controllable, and in situ soil research.

Application of microfluidic systems in modelling impacts of environmental structure on stress-sensing by individual microbial cells

Environmental structure describes physical structure that can determine heterogenous spatial distribution of biotic and abiotic (nutrients, stressors etc.) components of a microorganism's microenvironment. This study investigated the impact of micrometre-scale structure on microbial stress sensing, using yeast cells exposed to copper in microfluidic devices comprising either complex soil-like architectures or simplified environmental structures. In the soil micromodels, the responses of individual cells to inflowing medium supplemented with high copper (using cells expressing a copper-responsive pCUP1-reporter fusion) could be described neither by spatial metrics developed to quantify proximity to environmental structures and surrounding space, nor by computational modelling of fluid flow in the systems. In contrast, the proximities of cells to structures did correlate with their responses to elevated copper in microfluidic chambers that contained simplified environmental structure. Here, cells within more open spaces showed the stronger responses to the copper-supplemented inflow. These insights highlight not only the importance of structure for microbial responses to their chemical environment, but also how predictive modelling of these interactions can depend on complexity of the system, even when deploying controlled laboratory conditions and microfluidics.

Interaction kinetics and accessibility of sulfadiazine in model clay-humic acid suspension: Electron spin resonance investigations with nitroxide spin label

The characterization of the interaction of sulfonamides with soil is of particular interest in environmental risk and persistence assessment. In the present work electron spin resonance spectroscopy (ESR) was used to investigate the interaction kinetics of spin labelled sulfadiazine (SL-SDZ) with model clay-humic acid suspensions. The ESR spectra showed that SL-SDZ incubated with Leonardite humic acid (LHA) and Ca-hectorite as model clay was immobilized due to covalent binding of its aniline moiety to LHA. From the immobilization kinetics measured over a period of 1200 h a pseudo-first order reaction with a time constant of 82.6 ± 25.0 h of covalent binding was determined. Additionally, SL-SDZ was strongly sorbed by LHA immediately after incubation but not durably sequestered. Compared to incubation without Ca-hectorite the covalent binding kinetics of SL-SDZ as well as its strong sorption were retarded.

Bridging Microbial Functional Traits With Localized Process Rates at Soil Interfaces

In this review, we introduce microbially-mediated soil processes, players, their functional traits, and their links to processes at biogeochemical interfaces [e.g., rhizosphere, detritusphere, (bio)-pores, and aggregate surfaces]. A conceptual view emphasizes the central role of the rhizosphere in interactions with other biogeochemical interfaces, considering biotic and abiotic dynamic drivers. We discuss the applicability of three groups of traits based on microbial physiology, activity state, and genomic functional traits to reflect microbial growth in soil. The sensitivity and credibility of modern molecular approaches to estimate microbial-specific growth rates require further development. A link between functional traits determined by physiological (e.g., respiration, biomarkers) and genomic (e.g., genome size, number of ribosomal gene copies per genome, expression of catabolic versus biosynthetic genes) approaches is strongly affected by environmental conditions such as carbon, nutrient availability, and ecosystem type. Therefore, we address the role of soil physico-chemical conditions and trophic interactions as drivers of microbially-mediated soil processes at relevant scales for process localization. The strengths and weaknesses of current approaches (destructive, non-destructive, and predictive) for assessing process localization and the corresponding estimates of process rates are linked to the challenges for modeling microbially-mediated processes in heterogeneous soil microhabitats. Finally, we introduce a conceptual self-regulatory mechanism based on the flexible structure of active microbial communities. Microbial taxa best suited to each successional stage of substrate decomposition become dominant and alter the community structure. The rates of decomposition of organic compounds, therefore, are dependent on the functional traits of dominant taxa and microbial strategies, which are selected and driven by the local environment.

Habitat geometry in artificial microstructure affects bacterial and fungal growth, interactions, and substrate degradation

Microhabitat conditions determine the magnitude and speed of microbial processes but have been challenging to investigate. In this study we used microfluidic devices to determine the effect of the spatial distortion of a pore space on fungal and bacterial growth, interactions, and substrate degradation. The devices contained channels differing in bending angles and order. Sharper angles reduced fungal and bacterial biomass, especially when angles were repeated in the same direction. Substrate degradation was only decreased by sharper angles when fungi and bacteria were grown together. Investigation at the cellular scale suggests that this was caused by fungal habitat modification, since hyphae branched in sharp and repeated turns, blocking the dispersal of bacteria and the substrate. Our results demonstrate how the geometry of microstructures can influence microbial activity. This can be transferable to soil pore spaces, where spatial occlusion and microbial feedback on microstructures is thought to explain organic matter stabilization.

Methods for Studying Bacterial–Fungal Interactions in the Microenvironments of Soil

Due to their small size, microorganisms directly experience only a tiny portion of the environmental heterogeneity manifested in the soil. The microscale variations in soil properties constrain the distribution of fungi and bacteria, and the extent to which they can interact with each other, thereby directly influencing their behavior and ecological roles. Thus, to obtain a realistic understanding of bacterial–fungal interactions, the spatiotemporal complexity of their microenvironments must be accounted for. The objective of this review is to further raise awareness of this important aspect and to discuss an overview of possible methodologies, some of easier applicability than others, that can be implemented in the experimental design in this field of research. The experimental design can be rationalized in three different scales, namely reconstructing the physicochemical complexity of the soil matrix, identifying and locating fungi and bacteria to depict their physical interactions, and, lastly, analyzing their molecular environment to describe their activity. In the long term, only relevant experimental data at the cell-to-cell level can provide the base for any solid theory or model that may serve for accurate functional prediction at the ecosystem level. The way to this level of application is still long, but we should all start small.

A walk on the dirt: soil microbial forensics from ecological theory to the crime lab

Forensics aims at using physical evidence to solve investigations with science-based principles, thus operating within a theoretical framework. This however is often rather weak, the exception being DNA-based human forensics that is well anchored in theory. Soil is a most commonly encountered, easily and unknowingly transferred evidence but it is seldom employed as soil analyses require extensive expertise. In contrast, comparative analyses of soil bacterial communities using nucleic acid technologies can efficiently and precisely locate the origin of forensic soil traces. However, this application is still in its infancy, and is very rarely used. We posit that understanding the theoretical bases and limitations of their uses is essential for soil microbial forensics to be judiciously implemented. Accordingly, we review the ecological theory and experimental evidence explaining differences between soil microbial communities, i.e. the generation of beta diversity, and propose to integrate a bottom-up approach of interactions at the microscale, reflecting historical contingencies with top-down mechanisms driven by the geographic template, providing a potential explanation as to why bacterial communities map according to soil types. Finally, we delimit the use of soil microbial forensics based on the present technologies and ecological knowledge, and propose possible venues to remove existing bottlenecks.

Soil biota shift with land use change from pristine rainforest and Savannah (Cerrado) to agriculture in southern Amazonia

Southern Amazonia is currently experiencing extensive land use change from forests to agriculture caused by increased local and global demand for agricultural products. However, little is known about the impacts of deforestation and land use change on soil biota. We investigated two regions in southern Amazonia (rainforest and Savannah/Cerrado biomes), analysing soil biota community turnover based on 16S (Archaea and Bacteria) and 18S rRNA genes (Eukaryotes, including Fungi, Protists and Animalia) and correlating them with soil chemistry and land use intensity. We found that soil biota community structure is driven by land use change in both Cerrado and rainforest. Crop fields approximatively doubled the richness of soil Archaea, Bacteria and Protists. We propose that crop systems not only increase soil pH and fertility, but also create continued disturbance (crop seasons) that stimulates soil diversity, as predicted by the dynamic equilibrium model (DEM) and the intermediate disturbance hypothesis (IDH). Even though agricultural fields had higher soil biota richness, some taxa were suppressed by agriculture (6/31 operational taxonomic units of Archaea, 245/1790 of Bacteria, 12/74 of Animalia, 20/144 of Fungi and 25/310 of Protists). Consequently, land use change in this region should proceed with caution. In the southern Amazonia region of Brazil, current laws require farmers to keep 20%-80% pristine vegetation areas on their property. Our data support the relevance of this law: since there are unique soil taxa under native vegetation, keeping these pristine areas adjacent to the agricultural fields should maximize soil biodiversity protection in these regions.

Micro on a macroscale: relating microbial-scale soil processes to global ecosystem function

Soil microorganisms play a key role in driving major biogeochemical cycles and in global responses to climate change. However, understanding and predicting the behavior and function of these microorganisms remains a grand challenge for soil ecology due in part to the microscale complexity of soils. It is becoming increasingly clear that understanding the microbial perspective is vital to accurately predicting global processes. Here, we discuss the microbial perspective including the microbial habitat as it relates to measurement and modeling of ecosystem processes. We argue that clearly defining and quantifying the size, distribution and sphere of influence of microhabitats is crucial to managing microbial activity at the ecosystem scale. This can be achieved using controlled and hierarchical sampling designs. Model microbial systems can provide key data needed to integrate microhabitats into ecosystem models, while adapting soil sampling schemes and statistical methods can allow us to collect microbially-focused data. Quantifying soil processes, like biogeochemical cycles, from a microbial perspective will allow us to more accurately predict soil functions and address long-standing unknowns in soil ecology.

Microfluidic chips provide visual access to in situ soil ecology

Microbes govern most soil functions, but investigation of these processes at the scale of their cells has been difficult to accomplish. Here we incubate microfabricated, transparent 'soil chips' with soil, or bury them directly in the field. Both soil microbes and minerals enter the chips, which enables us to investigate diverse community interdependences, such as inter-kingdom and food-web interactions, and feedbacks between microbes and the pore space microstructures. The presence of hyphae ('fungal highways') strongly and frequently increases the dispersal range and abundance of water-dwelling organisms such as bacteria and protists across air pockets. Physical forces such as water movements, but also organisms and especially fungi form new microhabitats by altering the pore space architecture and distribution of soil minerals in the chip. We show that soil chips hold a large potential for studying in-situ microbial interactions and soil functions, and to interconnect field microbial ecology with laboratory experiments.

Microbial Identification, High-Resolution Microscopy and Spectrometry of the Rhizosphere in Its Native Spatial Context

During the past decades, several stand-alone and combinatorial methods have been developed to investigate the chemistry (i.e., mapping of elemental, isotopic, and molecular composition) and the role of microbes in soil and rhizosphere. However, none of these approaches are currently applicable to characterize soil-root-microbe interactions simultaneously in their spatial arrangement. Here we present a novel approach that allows for simultaneous microbial identification and chemical analysis of the rhizosphere at micro- to nano-meter spatial resolution. Our approach includes (i) a resin embedding and sectioning method suitable for simultaneous correlative characterization of Zea mays rhizosphere, (ii) an analytical work flow that allows up to six instruments/techniques to be used correlatively, and (iii) data and image correlation. Hydrophilic, immunohistochemistry compatible, low viscosity LR white resin was used to embed the rhizosphere sample. We employed waterjet cutting and avoided polishing the surface to prevent smearing of the sample surface at nanoscale. The quality of embedding was analyzed by Helium Ion Microscopy (HIM). Bacteria in the embedded soil were identified by Catalyzed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH) to avoid interferences from high levels of autofluorescence emitted by soil particles and organic matter. Chemical mapping of the rhizosphere was done by Scanning Electron Microscopy (SEM) with Energy-dispersive X-ray analysis (SEM-EDX), Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS), nano-focused Secondary Ion mass Spectrometry (nanoSIMS), and confocal Raman spectroscopy (μ-Raman). High-resolution correlative characterization by six different techniques followed by image registration shows that this method can meet the demanding requirements of multiple characterization techniques to identify spatial organization of bacteria and chemically map the rhizosphere. Finally, we presented individual and correlative workflows for imaging and image registration to analyze data. We hope this method will be a platform to combine various 2D analytics for an improved understanding of the rhizosphere processes and their ecological significance.

Application of Nematode Community Analyses-Based Models towards Identifying Sustainable Soil Health Management Outcomes: A Review of the Concepts

Soil health connotes the balance of biological, physicochemical, nutritional, structural, and water-holding components necessary to sustain plant productivity. Despite a substantial knowledge base, achieving sustainable soil health remains a goal because it is difficult to simultaneously: (i) improve soil structure, physicochemistry, water-holding capacity, and nutrient cycling; (ii) suppress pests and diseases while increasing beneficial organisms; and (iii) improve biological functioning leading to improved biomass/crop yield. The objectives of this review are (a) to identify agricultural practices (APs) driving soil health degradations and barriers to developing sustainable soil health, and (b) to describe how the nematode community analyses-based soil food web (SFW) and fertilizer use efficiency (FUE) data visualization models can be used towards developing sustainable soil health. The SFW model considers changes in beneficial nematode population dynamics relative to food and reproduction (enrichment index, EI; y-axis) and resistance to disturbance (structure index, SI; x-axis) in order to identify best-to-worst case scenarios for nutrient cycling and agroecosystem suitability of AP-driven outcomes. The FUE model visualizes associations between beneficial and plant-parasitic nematodes (x-axis) and ecosystem services (e.g., yield or nutrients, y-axis). The x-y relationship identifies best-to-worst case scenarios of the outcomes for sustainability. Both models can serve as platforms towards developing integrated and sustainable soil health management strategies on a location-specific or a one-size-fits-all basis. Future improvements for increased implementation of these models are discussed.

Life in a Droplet: Microbial Ecology in Microscopic Surface Wetness

While many natural and artificial surfaces may appear dry, they are in fact covered by thin liquid films and microdroplets invisible to the naked eye known as microscopic surface wetness (MSW). Central to the formation and the retention of MSW are the deliquescent properties of hygroscopic salts that prevent complete drying of wet surfaces or that drive the absorption of water until dissolution when the relative humidity is above a salt-specific level. As salts are ubiquitous, MSW occurs in many microbial habitats, such as soil, rocks, plant leaf, and root surfaces, the built environment, and human and animal skin. While key properties of MSW, including very high salinity and segregation into droplets, greatly affect microbial life therein, it has been scarcely studied, and systematic studies are only in their beginnings. Based on recent findings, we propose that the harsh micro-environment that MSW imposes, which is very different from bulk liquid, affects key aspects of bacterial ecology including survival traits, antibiotic response, competition, motility, communication, and exchange of genetic material. Further research is required to uncover the fundamental principles that govern microbial life and ecology in MSW. Such research will require multidisciplinary science cutting across biology, physics, and chemistry, while incorporating approaches from microbiology, genomics, microscopy, and computational modeling. The results of such research will be critical to understand microbial ecology in vast terrestrial habitats, affecting global biogeochemical cycles, as well as plant, animal, and human health.

Translating New Synthetic Biology Advances for Biosensing Into the Earth and Environmental Sciences

The rapid diversification of synthetic biology tools holds promise in making some classically hard-to-solve environmental problems tractable. Here we review longstanding problems in the Earth and environmental sciences that could be addressed using engineered microbes as micron-scale sensors (biosensors). Biosensors can offer new perspectives on open questions, including understanding microbial behaviors in heterogeneous matrices like soils, sediments, and wastewater systems, tracking cryptic element cycling in the Earth system, and establishing the dynamics of microbe-microbe, microbe-plant, and microbe-material interactions. Before these new tools can reach their potential, however, a suite of biological parts and microbial chassis appropriate for environmental conditions must be developed by the synthetic biology community. This includes diversifying sensing modules to obtain information relevant to environmental questions, creating output signals that allow dynamic reporting from hard-to-image environmental materials, and tuning these sensors so that they reliably function long enough to be useful for environmental studies. Finally, ethical questions related to the use of synthetic biosensors in environmental applications are discussed.

The effects of long-term fertilizations on soil hydraulic properties vary with scales

Soil structure is an indicator of soil quality and its alterations following cropping system conversion or fertilization change evolve slowly. How such alterations vary with scale remains elusive. We investigated this based on the Rothamsted long-term wheat experiment (since 1843) in the UK. Triplicate cores 7 cm high and 10 cm in diameter were taken from plots that have been under different fertilizations or returned to natural woodland for more than one century for imaging using X-ray computed tomography with the voxel size being 40 µm. We then broke each core and sampled three aggregates from it to scan with the voxel size being 1.5 µm. For each core and aggregate sample, we calculated its pore size distribution, permeability and tortuosity. The results showed that the fertilization change >170 years ago reshaped the soil structure differently between the core scale and the aggregate scale. Macro-porosity of the pores (>40 µm) in the cores unfertilized or fertilized with inorganic fertilizers was low and the pores were poorly connected in the top 10 cm of soil, compared to those given farmyard manure or in the woodland. In all treatments, the pores in the core images were hydraulically anisotropic with their permeability in the horizontal direction being higher than that in the vertical direction, whereas the aggregates were comparatively isotropic. The fertilization affected image porosity and permeability at core scale more significantly than at aggregate scale, and the aggregates fertilized with farmyard manure and in the woodland were more permeable than the aggregates in other treatments. It was also found that compared to no-fertilization or fertilization with complete fertilizers, fertilizing without phosphorus over the past 20 years increased the porosity and permeability of the aggregates but not of the cores. Fertilization with inorganic fertilizers increased the tortuosity of the macropores in the cores but not of the intra-aggregate pores, compared to no-fertilization. Porosity-permeability relationship for aggregates unfertilized or fertilized with inorganic fertilisers followed a power law with R ² > 0.8. In contrast, the permeability of the aggregates in farmyard manure and in the woodland trended differently as their porosity increased. The results also revealed that the transport ability of the aggregates and cores responded differently to carbon in that with soil carbon increasing, the permeability of the aggregates increased asymptotically while the permeability of the cores, especially its horizontal component, increased exponentially.

Uncovering multi-faceted taxonomic and functional diversity of soil bacteriomes in tropical Southeast Asian countries

Environmental microbiomes encompass massive biodiversity and genetic information with a wide-ranging potential for industrial and agricultural applications. Knowledge of the relationship between microbiomes and environmental factors is crucial for translating that information into practical uses. In this study, the integrated data of Southeast Asian soil bacteriomes were used as models to assess the variation in taxonomic and functional diversity of bacterial communities. Our results demonstrated that there were differences in soil bacteriomes across different geographic locality with different soil characteristics: soil class and pH level. Such differences were observed in taxonomic diversity, interspecific association patterns, and functional diversity of soil bacteriomes. The bacterial-mediated biogeochemical cycles of nitrogen, sulfur, carbon, and phosphorus illustrated the functional relationship of soil bacteriome and soil characteristics, as well as an influence from bacterial interspecific interaction. The insights from this study reveal the importance of microbiome data integration for future microbiome research.