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The intensification of arable agriculture has resulted in an increase in vehicle wheel load and the intensity of field operations, which has increased the risk and incidence of degradation in physical properties of the uncultivated subsoil layer. Biopores generated by the long-term, repeated use of specific cover crops within an arable rotation has been suggested as an approach to improve subsoil physical properties. Therefore, this paper aimed to determine the impact of long-term repeated cover cropping and the interaction of rotation treatments with different cultivation approaches on subsoil physical properties. Data was collected at the NIAB ‘Sustainable Trial for Arable Rotations’ long-term, rotation and cultivation field experiment established in 2006. Rotation treatments comprised a brassica cover crop alternated annually with winter wheat (ALTCC) compared to continuous winter wheat (CWW). Cultivation treatments comprised PLOUGH (250 mm depth), and non-inversion cultivation at 250 mm (DEEP) and 100 mm (SHALLOW) depths. Penetration resistance and volumetric soil moisture were collected at bi-monthly intervals during the 2018/19 growing season. Undisturbed soil cores were collected for laboratory analyses of soil water retention, water stable aggregates, root morphology digital scanning and biomass, and X-ray computed tomography (CT). Results showed that treatment ALTCC combined with SHALLOW, resulted in lower penetration resistance and increased moisture in the subsoil. This increased subsoil moisture persisted later into the season compared to the control. SHALLOW increased subsoil water retention, improved subsoil root morphology and increased subsoil porosity. Benefits from treatment ALTCC were not observed where combined with higher intensity, deeper cultivation. Overall, the combination of treatments ALTCC with SHALLOW, produced significant benefits to subsoil physical properties.

Calcareous grasslands are some of Europe’s most species-rich plant communities and important biodiversity sites. These habitats are, however, threatened; many in the UK were lost to changing land use during the 20th century and pressure continues on the remaining (often scarce and fragmented) sites. Habitat restoration and rewilding are increasingly important both in the public consciousness and in governmental policy, and the ecological value and threatened nature of calcareous grasslands make them a prime target for restoration efforts. A growing number of projects are therefore working to restore or re-create chalk grassland ecosystems. An under-explored aspect of this, however, is how by-products from land development projects might be re-purposed to create the specialised soil environment needed to support calcareous grassland communities. This has the potential to combine sustainable re-use of construction materials with novel ways to create or restore calcareous grassland habitats and thus ensure infrastructure projects contribute to net biodiversity gain. In this study we investigate how to optimise the design of soil profiles to support calcareous grassland ecosystems. The study site is located in within the Central 1 section of the HS2 (High Speed 2) Phase One rail development in the Colne Valley (England) being delivered by the Align joint venture. The aim is to create a large area of calcareous grassland as part of a broader (127 hectare) mosaic habitat creation including calcareous grassland, wood pasture and wetland in land that is currently used for construction but was previously arable land. The ‘Colne Valley Western Slopes’ will, when complete, be the largest single area of habitat creation along the HS2 route and will significantly contribute to the project’s commitment to deliver ‘No Net Loss’ in biodiversity. The properties of underlying soils are critical for the establishment, development and health of this internationally important chalk grassland ecosystem. Physical, chemical and biological properties such as soil structure, drainage and restricted nutrient availability are essential for supporting the diverse plant assemblages found in calcareous grasslands. In this project, we are testing through a combination of controlled environment studies and field trials four constructed soil profiles using different configurations of site-derived materials/construction by-products, using both controlled environment studies and field trials. The site-won materials include: 2.6 M m3 of excavated chalk from 16 km of tunnel construction, crushed limestone and concrete from decommissioned compounds/haul roads, and subsoils (stripped during site clearance) that contain highly variable percentages of CaCO3. Here we present results from a large-scale mesocosm trial alongside initial field trial data to assess how these constructed soil profiles affect key factors for habitat creation, including soil hydrology, soil microbial dynamics, nutrient cycling, and vegetation establishment and diversity. The findings for this project will inform and effectively complete the earthworks design for the creation of 88 hectares of calcareous grassland in the Colne Valley, as well as providing insights for other chalk grassland restoration projects elsewhere.

Soil erosion is a result of detachment and transport of particles or small aggregates from the soil surface. Previous research has predominantly focused on studying the effects of either rainfall or wind on soil erosion processes as separate erosive agents. To date, there have been only few studies into the simultaneous effect of both agents operating at the same time on soil erosion and hydrological processes. In this research, the effect of wind velocities on the erosivity of rainfall was studied, comparing windless rain (WLR) and wind-driven rain (WDR) events when applied to a sandy loam soil. A moderate slope gradient of 11%, a simulated rainfall intensity of 90 mm hr-1, a rainfall duration of 30 minutes and wind velocities up to 9 m s-1 were used. The runoff, infiltrate and soil loss (including splash erosion measured at different heights) were compared between the different events and treatments. The soil surface roughness was measured before and after the rainfall event, using a hand-held laser scanner, to evaluate the effect of WLR and WDR on the surface morphology. The outcome of this study shows that, for the smooth surface under WDR, infiltrate volumes were less than under WLR and decreased with increasing wind velocity, while the runoff volumes increased under WDR compared with WLR. The rate of rainsplash erosion increased under the WDR event compared to the WLR event at all heights. The amount of splash-eroded particles decreased with height above the soil surface. We conclude that wind has an effect on the erosivity of rainfall; therefore, it should be considered in erosion studies.Acknowledgments: This work was funded by OCP group, Morocco

Soils contain the largest terrestrial reservoir of organic carbon, and dynamics in soil organic carbon turnover will drive carbon-climate feedbacks over the coming century. To date, most SOC dynamics have been simulated with pool-based models, which assume homogeneous physical properties in soil. However, there is increasing evidence which suggests that soil carbon turnover is not just determined by carbon inputs, but by restrictions on microbial access to organic matter in a spatially heterogeneous soil environment. Pore geometry is a critical factor in affecting the accessibility of organic matter for microorganisms, but this accessibility has not been explicitly considered in models. Therefore, we have a challenge to mechanistically predict how environmental change will impact on the balance between soil stored in soil and in the atmosphere.We will exemplify the impact of pore-connectivity on organic matter turn-over by modelling fungal mediated processes in soil. The fungal model includes important fungal processes such as growth, death and spread, secretion of enzymes to degrade soil organic matter, and translocation of dissolved organic matter through its hyphal structure. For such a complex system the question of what constitutes a connected habitat and how this affects soil processes may not be as easy to address and needs to consider more than the pore connectivity often highlighted. For example, for these fungal mediated processes, habitat connectivity may be determined by various characteristics, namely: (i) the total volume of the connected pore space; (ii) the connected air-filled pore volume, through which fungal spread predominantly occurs and gasses diffuse, (iii) the connected water phase volume, through which dissolved C diffuses, (iv) the distribution of particulate organic matter that fuels fungal growth, and (v) biological traits such as those enabling translocation through for example fungal hyphal networks. We demonstrate how various aspects of habitat connectivity differentially impact on two contrasting fungal species, representing e.g. R and K strategists. The results suggest that: i) connectivity of the water phase is critical as it regulates diffusion of dissolved organic matter; this is even so for fungi that preferentially spread through air-filled pores, and ii) whether fungi behave as R or K strategists is not just determined by fungal traits but to a large extend depends on the physical environment. Consequently, selective pressures can be exerted by physical conditions. It was however not possible to identify a key physical driver as the dynamics were mostly determined by interactions between the various types of connectivity. These different pathways tend to compensate each other, enhancing stability of the function. We argue that the fact that multiple connected pathways underpin a soil function leads to resilience of soils to perturbations and underpins soil health.

Over the last decades, a new generation of microscale models has been developed to simulate soil microbial activity. An earlier article (Pot et al., 2021) presented a detailed review of the description of soil architecture and microbial dynamics in these models. In the present article, we summarise the main results obtained by these models according to six model outputs: growth and spatial organisation of microbial colonies, soil hydraulic conductivity, coexistence and trophic interactions of microorganisms, temporal dynamics of the amount of solid and dissolved organic matter in soil and, microbial production of CO2. For each of these outputs, we draw particular attention to the respective roles of soil architecture and microbial dynamics, and we report how microscale models allow for disentangling and quantifying them. We finally discuss limitations and future directions of microscale models in combination with the on-going development of high-performance imaging tools revealing the spatial heterogeneity of the actors of soil microbial activity. Highlights: We review the insights on soil functions derived from microscale models of soil microbial processes. Microscale models disentangle the complex interactions between soil architecture and microbial dynamics. Spatial accessibility of resources to microbes, growth and ecological interactions are key factors in soil functions. Translation of knowledge of interactions at the microscopic scale into larger scales is still in its infancy. © 2022 British Society of Soil Science. The research reported on in this article was supported by a grant from the French Agence Nationale de la Recherche to project Soil μ-3D (ANR-15-CE01-0006). Additionally, WO and XP received support from the National Environment Research Council (NE/P014208/1 and NE/S004920/1). XP is currently a María Zambrano Fellow at the Public University of Navarra (UPNA) and acknowledges funding from the European Union - NextGenerationEU through the Spanish program "Ayuda para la Recualificación del Sistema Universitario Español".

While rhizosphere priming effects are well-documented under laboratory and controlled-environment conditions, their significance in undisturbed systems under field conditions is less clear. This is in part because it is impracticable to measure rates of rhizodeposition in the field with high resolution over a substantial period. We propose that photosynthesis, closely linked to rhizodeposition, can be used as a proxy for plant root activity.We have used a field system containing 24 0.8-m diameter, 1-m deep lysimeters holding naturally-structured soil monoliths from two contrasting C3 soils sown with a C4 grass (Bouteloua dactyloides) to measure carbon (C) fluxes at a high temporal resolution, exploiting isotopic differences to allow partitioning of plant and soil fluxes. These fluxes are coupled to high-resolution measurements of soil temperature and moisture, alongside atmospheric temperature and solar radiation. This system has allowed measurement of both ecosystem resolution and net ecosystem exchange, and the partitioning of respiration between plant and soil sources using stable isotope methods. Using this system we have generated a dataset of measured and modelled respiration and photosynthesis fluxes over two years.Our dataset has revealed clear seasonal and diurnal patterns in plant and soil fluxes. We have assessed the relationship between diurnal patterns in soil respiration and potential drivers, and examined whether model estimates of soil respiration are improved by the inclusion of photosynthesis as an explanatory variable alongside soil moisture and temperature. We found a significant positive relationship between photosynthesis and soil respiration, and inclusion of photosynthesis improves models of soil respiration. This is best explained by rhizosphere priming enhancing soil C turnover.

There is a lack of field methods for measuring plant and soil processes controlling soil organic matter (SOM) turnover over diurnal, seasonal, and longer time-scales with which to develop datasets for modelling. We describe an automated field system for measuring plant and soil carbon fluxes over such time-scales using stable isotope methods, and we assess its performance. The system comprises 24 large (1-m deep, 0.8-m diameter) cylindrical lysimeters connected to gas-flux chambers and instruments. The lysimeters contain intact, naturally-structured C3 soil planted with a C4 grass. Fluxes of CO2 and their 13C isotope composition are measured 3-times daily in each lysimeter, and the isotope composition is used to partition the fluxes between plant and soil sources. We investigate the following potential sources of error in the measurement system and show they do not significantly affect the measured CO2 fluxes or isotope signatures: gas leaks; the rate of gas flow through sampling loops; instrument precision and drift; the concentration-dependence of isotope measurements; and the linearity of CO2 accumulation in the chambers and associated isotope fractionation resulting from different rates of 13CO2 and 12CO2 diffusion from the soil. For the loamy grassland soil and US prairie grass (Bouteloua dactyloides) tested, the precision of CO2 flux measurements was ± 0.04 % and that of the flux partitioning ± 0.40 %. We give examples of diurnal and seasonal patterns of plant and soil C fluxes and soil temperature and moisture. We discuss the limitations of the isotope methodology for partitioning fluxes as applied in our system. We conclude the system is suitable for measuring net ecosystem respiration fluxes and their plant and soil components with sufficient precision to resolve diurnal and seasonal patterns

Great potential exists to harness plant traits at the root-soil interface, mainly rhizodeposition and root hairs, to 'build' soils with better structure that can trap more carbon and resources, resist climate stresses, and promote a healthy microbiome. These traits appear to have been preserved in modern crop varieties, but scope exists to improve them further because they vary considerably between genotypes and respond to environmental conditions. From emerging evidence, rhizodeposition can act as a disperser, aggregator, and/or hydrogel in soil, and root hairs expand rhizosheath size. Future research should explore impacts of selecting these traits on plants and soils concurrently, expanding from model plants to commercial genotypes, and observing whether impacts currently limited to glasshouse studies occur in the field.

16 páginas.- 4 figuras.- referencias, In 1991, at the launch of a national symposium devoted to soil structure, the Australian Society of Soil Science invited Professor John Letey to deliver a keynote address, which was later published in the society’s journal. In his lecture, he shared the outcome of his reflexion about what the assessment of soil structure should amount to, in order to produce useful insight into the functioning of soils. His viewpoint was that the focus should be put on the openings present in the structure, rather than on the chunks of material resulting from its mechanical dismantlement. In the present article, we provide some historical background for Letey’s analysis, and try to explain why it took a number of years for the paradigm shift that he advocated to begin to occur. Over the last decade, his perspective that soil structure needs to be characterised via nondestructive methods appears to have gained significant momentum, which is likely to increase further in the near future, as we take advantage of recent technological advances. Other valuable lessons that one can derive from Letey’s pioneering article relate to the extreme value for everyone, even neophytes, to constantly ask questions about where research on given topics is heading, what its goals are, and whether the methods that are used at a certain time are optimal, Partial financial support obtained through a grant from the Agence Nationale de la Recherche (ANR, France) to project Soilμ3D, directed by Dr. Patricia Garnier.

International audience; Soil functions, including climate regulation and the cycling of water and nutrients, are of central importance for a number of environmental issues of great societal concern. To understand and manage these functions, it is crucial to be able to quantify the structure of soils, now increasingly referred to as their “architecture,” as it constraints the physical, chemical and biological processes in soils. This quantification was traditionally approached from two different angles, one focused on aggregates of the solid phase, and the other on the pore space. The recent development of sophisticated, non-disturbing imaging techniques has led to significant progress in the description of soil architecture, in terms of both the pore space and the spatial configuration of mineral and organic materials. We now have direct access to virtually all aspects of soil architecture. In the present article, we review how this affects the perception of soil architecture specifically when trying to describe the functions of soils. A key conclusion of our analysis is that soil architecture, in that context, imperatively needs to be explored in its natural state, with as little disturbance as possible. The same requirement applies to the key processes taking place in the hierarchical soil pore network, including those contributing to the emergence of a heterogeneous organo-mineral soil matrix by various mixing processes, such as bioturbation, diffusion, microbial metabolism and organo-mineral interactions. Artificially isolated aggregates are fundamentally inappropriate for deriving conclusions about the functioning of an intact soil. To fully account for soil functions, we argue that a holistic approach that centres on the pore space is mandatory while the dismantlement of soils into chunks may still be carried out to study the binding of soil solid components. In the future, significant progress is expected along this holistic direction, as new, advanced technologies become available.

Macroscopic models of soil organic matter (SOM) turnover have faced difficulties in reproducing SOM dynamics or in predicting the spatial distribution of carbon stocks. These models are based on a largely inadequate linear response of soil microorganisms to bulk concentrations of nutrients and it is clear that a new approach to SOM modelling is required. Introducing explicit microbial activity and organic matter (OM) reactivity in macroscopic models represents a challenge because of the fine spatial scales at which the processes occur. To get a better grasp on interactions that take place at the microscale, a new generation of SOM models have been developed at the spatial scale of the soil microenvironments where microorganisms evolve. These models are well adapted to challenge traditional hypotheses about the influence of soil architecture on soil microbial activity. Soil architecture provides the stage for a dynamic spatial accessibility of resources to microbes and the emergence of interactions between the actors in SOM decomposition. In this context, we review microscale models of microbial activity that have been designed for soils and soil analogues. To understand how these models account for spatial accessibility, we look in detail at how soil microenvironments are described in the different approaches and how microbial colonies are spatialized in these microenvironments. We present the advantages and disadvantages of the developed strategies and we discuss their limits.

Cover crop use is a well-established soil conservation technique and has been proven effective for erosion control and soil remediation in many arable systems. Whereas the obvious protection mechanism of cover crops occurs through the canopy, plant roots perform multiple functions. It is important to consider the soil functions delivered by different root systems in order to increase the uptake of cover crops for sustainable soil and water management. A classification of cover crop root systems up to 0.6 m deep based on functional traits will allow us to better study their potential role in soil bio-engineering; soil structural improvements for hydrological services and soil resource protection. A greenhouse experiment, using large 1 m3 containers filled with loam soil, loose top and compacted subsoil, in which 7 cover crop species (Oat, Rye, Buckwheat, Vetch, Radish, Mustard, Phacelia) were grown for 90 days. Root cores were taken at the end of the experiment, washed and imaged to determine root traits (total root length density, average root diameter, root specific length and root surface area) for both the top and subsoil layers. Root identity was determined from a distinctive combination of single root traits and related to 3 soil functional variables, representing soil structural improvement, runoff mitigation and erosion control. The results showed that total root length and root surface area correlate well with aggregate stability and soil macroporosity. Buckwheat, Mustard and Rye had significantly greater aggregate stability as well as 10, 8 and 7 % greater macroporosity respectively, at the interface with the compacted layer when compared to the control bare soil. Furthermore, average root diameter negatively correlated with soil macroporosity, indicating that cover crop with a fine root system are more beneficial for creating pore-space than those with thicker taproots. Selecting cover crop species with the right root traits is therefore crucial to improve soil health.

Purpose Simultaneously interacting rhizosphere processes determine emergent plant behaviour, including growth, transpiration, nutrient uptake, soil carbon storage and transformation by microorganisms. However, these processes occur on multiple scales, challenging modelling of rhizosphere and plant behaviour. Current advances in modelling and experimental methods open the path to unravel the importance and interconnectedness of those processes across scales. Methods We present a series of case studies of state-of-the art simulations addressing this multi-scale, multi-process problem from a modelling point of view, as well as from the point of view of integrating newly available rhizosphere data and images. Results Each case study includes a model that links scales and experimental data to explain and predict spatial and temporal distribution of rhizosphere components. We exemplify the state-of-the-art modelling tools in this field: image-based modelling, pore-scale modelling, continuum scale modelling, and functional-structural plant modelling. We show how to link the pore scale to the continuum scale by homogenisation or by deriving effective physical parameters like viscosity from nano-scale chemical properties. Furthermore, we demonstrate ways of modelling the links between rhizodeposition and plant nutrient uptake or soil microbial activity. Conclusion Modelling allows to integrate new experimental data across different rhizosphere processes and scales and to explore more variables than is possible with experiments. Described models are tools to test hypotheses and consequently improve our mechanistic understanding of how rhizosphere processes impact plant-scale behaviour. Linking multiple scales and processes including the dynamics of root growth is the logical next step for future research., Plant and Soil, 478, ISSN:0032-079X, ISSN:1573-5036

International audience; Over the last two decades, the fact that soils are significant sources of greenhouse gases (GHG), e.g., carbon dioxide (CO2), methane (CH4), nitrous oxide (N2O), and water vapor, has received considerable attention from the scientific community. Many laboratory and field experiments have been carried out to investigate the release of GHG by soils, and a wide range of computer modeling approaches have been explored to encapsulate what is known about the process, as well as to improve its prediction at various spatial and temporal scales.

Soil structure, lately referred to as the ''architecture'' is a key to explain and understand all soil functions. The development of sophisticated imaging techniques over the last decades has led to significant progress in the description of this architecture and in particular of the geometry of the hierarchically-branched pore space in which transport of water, gases, solutes and particles occurs and where myriads of organisms live. Moreover, there are sophisticated tools available today to also visualize the spatial structure of the solid phase including mineral grains and organic matter. Hence, we do have access to virtually all components of soil architecture.Unfortunately, it has so far proven very challenging to study the dynamics of soil architecture over time, which is of critical importance for soil as habitat and the turnover of organic matter. Several largely conflicting theories have been proposed to account for this dynamics, especially the formation of aggregates. We review these theories, and we propose a conceptual approach to reconcile them based on a consistent interpretation of experimental observations and by integrating known physical and biogeochemical processes. A key conclusion is that rather than concentrating on aggregate formation in the sense of how particles and organic matter reorganize to form aggregates as distinct functional units we should focus on biophysical processes that produce a porous, heterogeneous organo-mineral soil matrix that breaks into fragments of different size and stability when exposed to mechanical stress. The unified vision we propose for soil architecture and the mechanisms that determine its temporal evolution, should pave the way towards a better understanding of soil processes and functions.

International audience; The microscale physical characteristics of microbial habitats considerably affect the decomposition of organic matter in soils. One of the challenges is to identify microheterogeneities in soil that can explain the extent of carbon mineralization. The aim of this study was therefore to identify descriptors of mu m-scale soil heterogeneity that can explain CO2 fluxes obtained at the mm scale. A suite of methods and models that visualize soil heterogeneity at scales relevant to microorganisms has been developed over the last decade. Among the existing 3D models that simulate microbial activity in soils, Mosaic is able to simulate, within a short computation time, the microbial degradation of organic matter at the microhabitat scale in soil using real 3D images of soil porosity. Our approach was to generate scenarios of carbon mineralization for various microscale environmental conditions and determine how the descriptors of soil structure could explain CO2 evolution. First, we verified that the simulated diffusion of solutes in the soil samples obtained with Mosaic were the same as those obtained using the same parameter set from a robust 3D model based on a lattice Boltzmann approach. Then, we ran scenarios considering different soil pore architectures, water saturations and microorganism and organic matter placements. We found that the CO2 emissions simulated for the different scenarios could be explained by the distance between microorganisms and organic matter, the diffusion of the substrate and the concentration of the available substrate. For some of the scenarios, we proposed a descriptor of accessibility based on the geodesic distance between microorganisms and organic matter weighted by the amount of organic matter. This microscale descriptor is correlated to the simulated CO2 flux with a correlation coefficient of 0.69. Highlights Does the microscopic soil organisation explain the macroscopic mineralisation fluxes ? We present a new descriptor based on the geodesic distances between organic matter and microorganisms. We found a correlation between the descriptor of mu m-heterogeneity and the mineralization fluxes. Other scenarios should be carried out under wider environmental mu m-conditions to confirm our results.

Fusarium causes significant post-harvest quality losses and mycotoxin contamination in stored wheat but the colonisation dynamics of the grain and how this may be affected by the initial inoculum position in the grain mass is poorly understood. This study examined the 3D growth kinetics and mycotoxin production (deoxynivalenol and zearalenone) by F. graminearum during hyphal colonisation from different initial inoculum positions in wheat microcosms (top-centre, bottom-centre, and bottom-side) maintained at two water activities (aw, 0.95 and 0.97). Clear jars were used to visually follow the colonisation dynamics. Fungal respiration and associated dry matter loss (DML) and ergosterol were also quantified. Colonisation dynamics was shown to be affected by the inoculation position. At the end of the colonisation process, fungal respiration and DML were driven by the inoculation position, and the latter also by the prevailing aw. Fungal biomass (ergosterol) was mainly affected by the aw. The initial inoculum position did not affect the relative mycotoxin production. There was a positive correlation between respiration and ergosterol, and between mycotoxin production and colonisation indicators. We suggest that spatially explicit predictive models can be used to better understand the colonisation patterns and mycotoxin contamination of stored cereal commodities and to aid more effective post-harvest management.

For over a half a century, researchers have been aware of the fact that the physical and chemical characteristics of microenvironments in soils strongly influence the activity, growth and metabolism of microorganisms. However, many aspects of the effect of soil physical characteristics, such as the pore geometry, remain poorly understood. Therefore, the objective of the present research was to determine the influence of soil pore characteristics on the spread of bacteria, observed at the scale relevant to microbes. Pseudomonas fluorescens was introduced in columns filled with 1–2 mm soil aggregates, packed at different bulk densities. Soil microcosms were scanned at 10.87 μm voxel resolution using X‐ray computed tomography (CT) to characterize the geometry of pores. Thin sections were prepared to determine the spread and colonization of bacteria. The results showed that average bacterial cell density was 174 cells mm⁻² in soil with bulk density of 1.3 g cm⁻³ and 99 cells mm⁻² in soil with bulk density of 1.5 g cm⁻³. Soil porosity and solid‐pore interfaces influence the spread of bacteria and their colonization of the pore space at lower bulk density, resulting in relatively higher bacterial densities in larger pore spaces. The study also demonstrates that thin sectioning of resin‐impregnated soil samples can be combined with X‐ray CT to visualize bacterial colonization of a 3D pore volume. This research therefore represents a significant step towards understanding how environmental change and soil management impact bacterial diversity in soils. HIGHLIGHTS: We used a quantitative approach to study bacterial spread in soil at scales relevant to microbes. The rate of pseudomonas spread decreased with increased bulk density of soil. Soil porosity and soil‐pore interface influence Pseudomonas in lower bulk density soil. Soil structure with different pore characteristics effects spread and activity of bacteria in soil.

Currently, phosphorus (P) mine reserves are monopolised by several countries and its market price variations represents a challenge for modern agriculture systems. Consequently relying on alternative renewable sources of P such as sewage sludge (SS) is timely as its supply is expected to increase with population worldwide. However, this has to be carefully managed to ensure potential pollutant transport when applied to soils.However, alternative treatment options can reduce this risk and create greater value from SS as a P-fertiliser. By carbonizing the residues through Pyrolysis or Hydrothermal Carbonization (HTC), organic pollutants can be significantly decomposed, and its volume reduced, which ease enormously its management (R. Huang & Tang, 2015). Different characteristics will be obtained depending on the thermal process and the conditions to which the sample is subjected, differentiating the potential applications of the pyrochar/hydrochar obtained respectively. Nevertheless, the data gathered for yield crop responses from sewage sludge thermal derivatives is still very scarce and hence more information needs to be produced.The aim of this research is to evaluate interactions in phosphorus availability of spring wheat from SS and its thermally treated derivatives, when added on its own and in combination with raw SS as soil amendment. Two pyrochars were produced at the Polytechnic University of Madrid though pyrolysis at 400⁰C-1h and 300⁰C-1h using pre-oven dried (105⁰C-48h) sewage sludge from Spain. Two hydrochars were obtained through Hydrothermal Carbonization in another reactor at 180⁰C-4h and 240⁰C-4h using raw sludge adjusted to 15% d.m. All samples were analyzed for physical-chemical changes and applied to the soil in a glasshouse experiment.Results confirmed different degrees of carbonization through the selected treatments, gaining similar characteristics to sub-bituminous coals after pyrolysis and midpoint after HTC. A germination test indicated that the phytotoxicity of the raw material was reduced after all thermal treatments, with the best effect being through pyrolysis. However, P availability was reduced in all derivatives, 65.6% in Pyrochars and 41.5% HTC from the original SS. A 136 pots study with amended soils at different rates showed that despite P availability on initial conditions, after 3 months P became more available, being at least twice the amount found in the original soil, higher if the treatments were combined with additional wet SS (1:1). It also revealed a reduction of pHinitial=[7-8] to pHfinal=[6-7] after harvesting and a slight increment on the Electrical Conductivity [0.15-6.7]µS/cm (max value 16.6µS/cm) probably due the different mineralization of the derivatives amendments and the washing of the materials through the soil profiles.The data gathered with this research to date suggests that, the addition of the sewage sludge derivatives on their own indeed decreases the production of grain. However, with the combination of a commercialized sludge (SS2) at the highest rate, no negative effects have been reported after the first crop season. Derived pyrochar and hydrochar offer an alternative source of available phosphorus to mitigate the growing demand of mineral phosphorus reserves whilst providing at the same time a good base of organic matter for low fertile soils.

Our understanding of soil carbon (C) dynamics is limited; field measurements necessarily conflate fluxes from plant and soil sources and we therefore lack long-term field-scale data on soil C fluxes to use to test and improve soil C models. Furthermore, it is often unclear whether findings from lab-based studies, such as the presence of rhizosphere priming, apply to soil systems in the field. It is particularly important that we are able to understand the roles of soil temperature and moisture, and plant C inputs, as drivers of soil C dynamics in order to predict how changing climate and plant productivity may affect the net C balance of soils. We have developed a field laboratory with which to generate much-needed long-term C flux data under field conditions, giving near-continuous measurements of plant and soil C fluxes and their drivers.The laboratory contains 24 0.8-m diameter, 1-m deep, naturally-structured soil monoliths of two contrasting C3 soils (a clay-loam and a sandy soil) in lysimeters. These are sown with a C4 grass (Bouteloua dactyloides), providing a large difference in C isotope signature between C4 plant respiration and C3-origin soil organic matter (SOM) decomposition, which enables clear partitioning of the net C flux. This species is used as a pasture grass in the United States, and regular trimming through the growing season simulates low-intensity grazing. The soil monoliths are fitted with gas flux chambers and connected via an automated sampling loop to a cavity ring-down spectrometer, which measures the concentration and 12C:13C isotopic ratio of CO2 during flux chamber closure. Depth-resolved measurements of soil temperature and moisture in each monolith are made near-continuously, along with measurements of incoming solar radiation, rainfall, and air temperature a the field site. The gas flux chambers are fitted with removable reflective backout covers allowing flux measurements both incorporating, and in the absence of, photosynthesis.We have collected net ecosystem respiration data, measurements of photosynthesis, and recorded potential drivers of respiration over two growing seasons through 2018 and 2019. Through partitioning fluxes between plant respiration and SOM mineralisation we have revealed clear diurnal trends in both plant and soil C fluxes, along with overarching seasonal trends which modify both the magnitude of fluxes and their diurnal patterns. Rates of photosynthesis have been interpolated between measurement periods using machine learning to generate a predictive model, which has allowed us to investigate the effect of plant productivity on SOM mineralisation and assess whether rhizosphere priming can be detected in our system. Through regression analyses and linear mixed effects modelling we have evaluated the roles of soil temperature, soil moisture, and soil N content as drivers of variation in plant and soil respiration in our two contrasting soils. This has shown soil temperature to be the most important control on SOM mineralisation, with soil moisture content playing only a minor role. We have also used our empirical models to suggest how the carbon balance of pasture and grassland soils may respond to warming temperatures.

Plant growth promoting rhizobacteria can improve plant health by providing enhanced nutrition, disease suppression and abiotic stress resistance, and have potential to contribute to sustainable agriculture. We have developed a sphagnum peat-based compost platform for investigating plant-microbe interactions. The chemical, physical and biological status of the system can be manipulated to understand the relative importance of these factors for plant health, demonstrated using three case studies: 1. Nutrient depleted compost retained its structure, but plants grown in this medium were severely stunted in growth due to removal of essential soluble nutrients - particularly, nitrogen, phosphorus and potassium. Compost nutrient status was replenished with the addition of selected soluble nutrients, validated by plant biomass; 2. When comparing milled and unmilled compost, we found nutrient status to be more important than matrix structure for plant growth; 3. In compost deficient in soluble P, supplemented with an insoluble inorganic form of P (Ca3(PO4)2), application of a phosphate solubilising Pseudomonas strain to plant roots provides a significant growth boost when compared with a Pseudomonas strain incapable of solubilising Ca3(PO4)2. Our findings show that the compost system can be manipulated to impose biotic and abiotic stresses for testing how microbial inoculants influence plant growth.

Most past research on uranium (U) transport and reaction in the environment has been concerned with groundwater contamination and not with uptake by plants or soil biota, both of which operate over much smaller time and distance scales. We developed and tested a model of U diffusion and reaction in soil at scales appropriate for uptake by plant roots, based on a model we developed in an earlier paper. The model allows for the speciation of U with hydroxyl, carbonate and organic ligands in the soil solution, and the nature and kinetics of sorption reactions with the soil solid. The model predictions were compared with experimentally measured concentration–distance profiles of U in soil adjusted to different pHs and CO₂ pressures. Excellent agreement between observed and predicted profiles was obtained using model input parameters measured or otherwise estimated independently of the concentration–distance profiles, showing that the model was a correct description of the system and all important processes were allowed for. The importance of the kinetics of U adsorption and desorption for the timescale of diffusion through the soil is highlighted. The results are discussed in terms of the uptake of U by plant root systems, as modelled in the earlier paper. HIGHLIGHTS: We developed a model of U diffusion and reaction in soil on scales relevant to uptake by plant roots. We tested the model against measured diffusion profiles and obtained excellent agreement. The kinetics of U adsorption–desorption reactions are important. Reaction kinetics measured in shaken suspensions or flow‐through systems are likely to be misleading.

Editorial: Elucidating Microbial Processes in Soils and Sediments: Microscale Measurements and Modeling

In spite of the very significant role that fungi are called to play in agricultural production and climate change over the next two decades, very little is known at this point about the parameters that control the spread of fungal hyphae in the pore space of soils. Monitoring of this process in 3 dimensions is not technically feasible at the moment. The use of transparent micromodels simulating the internal geometry of real soils affords an opportunity to approach the problem in 2 dimensions, provided it is confirmed that fungi would actually want to propagate in such artificial systems. In this context, the key objectives of the research described in this article are to ascertain, first, that the fungus Rhizoctonia solani can indeed grow in a micromodel of a sandy loam soil, and, second, to identify and analyze in detail the pattern by which it spreads in the tortuous pores of the micromodel. Experimental observations show that hyphae penetrate easily inside the micromodel, where they bend frequently to adapt to the confinement to which they are subjected, and branch at irregular intervals, unlike in current computer models of the growth of hyphae, which tend to describe them as series of straight tubular segments. A portion of the time, hyphae in the micromodels also exhibit thigmotropism, i.e., tend to follow solid surfaces closely. Sub-apical branching, which in unconfined situations seems to be controlled by the fungus, appears to be closely connected with the bending of the hyphae, resulting from their interactions with surfaces. These different observations not only indicate different directions to follow to modify current mesoscopic models of fungal growth, so they can apply to soils, but they also suggest a wealth of further experiments using the same set-up, involving for example competing fungal hyphae, or the coexistence of fungi and bacteria in the same pore space.

To address a number of issues of great societal concern at the moment, like the sequestration of carbon, information is direly needed about interactions between soil architecture and microbial dynamics. Unfortunately, soils are extremely complex, heterogeneous systems comprising highly variable and dynamic micro-habitats that have significant impacts on the growth and activity of inhabiting microbiota. Data remain scarce on the influence of soil physical parameters characterizing the pore space on the distribution and diversity of bacteria. In this context, the objective of the research described in this article was to develop a method where X-ray microtomography, to characterize the soil architecture, is combined with fluorescence microscopy to visualize and quantify bacterial distributions in resin-impregnated soil sections. The influence of pore geometry (at a resolution of 13.4 μm) on the distribution of Pseudomonas fluorescens was analysed at macro- (5.2 mm × 5.2 mm), meso- (1 mm × 1 mm) and microscales (0.2 mm × 0.2 mm) based on an experimental setup simulating different soil architectures. The cell density of P. fluorescens was 5.59 x 107(SE 2.6 x 106) cells g−1 soil in 1–2 mm and 5.84 x 107(SE 2.4 x 106) cells g−1 in 2–4 mm size aggregates soil. Solid-pore interfaces influenced bacterial distribution at micro- and macroscale, whereas the effect of soil porosity on bacterial distribution varied according to three observation scales in different soil architectures. The influence of soil porosity on the distribution of bacteria in different soil architectures was observed mainly at the macroscale, relative to micro- and mesoscales. Experimental data suggest that the effect of pore geometry on the distribution of bacteria varied with the spatial scale, thus highlighting the need to consider an “appropriate spatial scale” to understand the factors that regulate the distribution of microbial communities in soils. The results obtained to date also indicate that the proposed method is a significant step towards a full mechanistic understanding of microbial dynamics in structured soils.

There is still no satisfactory understanding of the factors that enable soil microbial populations to be as highly biodiverse as they are. The present article explores in silico the hypothesis that the heterogeneous distribution of soil organic matter, in addition to the spatial connectivity of the soil moisture, might account for the observed microbial biodiversity in soils. A multi-species, individual-based, pore-scale model is developed and parameterized with data from 3 Arthrobacter sp. strains, known to be, respectively, competitive, versatile, and poorly competitive. In the simulations, bacteria of each strain are distributed in a 3D computed tomography (CT) image of a real soil and three water saturation levels (100, 50, and 25%) and spatial heterogeneity levels (high, intermediate, and low) in the distribution of the soil organic matter are considered. High and intermediate heterogeneity levels assume, respectively, an amount of particulate organic matter (POM) distributed in a single (high heterogeneity) or in four (intermediate heterogeneity) randomly placed fragments. POM is hydrolyzed at a constant rate following a first-order kinetic, and continuously delivers dissolved organic carbon (DOC) into the liquid phase, where it is then taken up by bacteria. The low heterogeneity level assumes that the food source is available from the start as DOC. Unlike the relative abundances of the 3 strains, the total bacterial biomass and respiration are similar under the high and intermediate resource heterogeneity schemes. The key result of the simulations is that spatial heterogeneity in the distribution of organic matter influences the maintenance of bacterial biodiversity. The least competing strain, which does not reach noticeable growth for the low and intermediate spatial heterogeneities of resource distribution, can grow appreciably and even become more abundant than the other strains in the absence of direct competition, if the placement of the resource is favorable. For geodesic distances exceeding 5 mm, microbial colonies cannot grow. These conclusions are conditioned by assumptions made in the model, yet they suggest that microscale factors need to be considered to better understand the root causes of the high biodiversity of soils.

How rainfall infiltration rate and soil hydrological characteristics develop over time under forests of different ages in temperate regions is poorly understood. In this study, infiltration rate and soil hydrological characteristics were investigated under forests of different ages and under grassland. Soil hydraulic characteristics were measured at different scales under a 250-year-old grazed grassland (GL), 6-year-old (6yr) and 48-year-old (48yr) Scots pine (Pinus sylvestris) plantations, remnant 300-year-old individual Scots pine (OT) and a 4000-year-old Caledonian Forest (AF). In situ field-saturated hydraulic conductivity (Kfs) was measured, and visible root:soil area was estimated from soil pits. Macroporosity, pore structure and macropore connectivity were estimated from X-ray tomography of soil cores, and from water-release characteristics. At all scales, the median values for Kfs, root fraction, macroporosity and connectivity values tended to AF > OT > 48yr > GL > 6yr, indicating that infiltration rates and water storage increased with forest age. The remnant Caledonian Forest had a huge range of Kfs (12 to >4922 mm h−1), with maximum Kfs values 7 to 15 times larger than those of 48-year-old Scots pine plantation, suggesting that undisturbed old forests, with high rainfall and minimal evapotranspiration in winter, may act as important areas for water storage and sinks for storm rainfall to infiltrate and transport to deeper soil layers via preferential flow. The importance of the development of soil hydrological characteristics under different aged forests is discussed.

The pore size distribution (PSD) of the void space is widely used to predict a range of processes in soils. Recent advances in X-ray computed tomography (CT) now afford novel ways to obtain exact data on pore geometry, which has stimulated the development of algorithms to estimate the pore size distribution from 3D data sets. To date there is however no clear consensus on how PSDs should be estimated, and in what form PSDs are best presented. In this article, we first review the theoretical principles shared by the various methods for PSD estimation. Then we select methods that are widely adopted in soil science and geoscience, and we use a robust statistical method to compare their application to synthetic image samples, for which analytical solutions of PSDs are available, and X-ray CT images of soil samples selected from different treatments to obtain wide ranging PSDs. Results indicate that, when applied to the synthetic images, all methods presenting PSDs as pore volume per class size (i.e., Avizo, CTAnalyser, BoneJ, Quantim4, and DTM), perform well. Among them, the methods based on Maximum Inscribed Balls (Bone J, CTAnalyser, Quantim4) also produce similar PSDs for the soil samples, whereas the Delaunay Triangulation Method (DTM) produces larger estimates of the pore volume occupied by small pores, and Avizo yields larger estimates of the pore volume occupied by large pores. By contrast, the methods that calculate PSDs as object population fraction per volume class (Avizo, 3DMA, DFS-FIJI) perform inconsistently on the synthetic images and do not appear well suited to handle the more complex geometries of soils. It is anticipated that the extensive evaluation of method performance carried out in this study, together with the recommendations reached, will be useful to the porous media community to make more informed choices relative to suitable PSD estimation methods, and will help improve current practice, which is often ad hoc and heuristic.

The morphology of roots and root systems influences the efficiency by which plants acquire nutrients and water, anchor themselves and provide stability to the surrounding soil. Plant genotype and the biotic and abiotic environment significantly influence root morphology, growth and ultimately crop yield. The challenge for researchers interested in phenotyping root systems is, therefore, not just to measure roots and link their phenotype to the plant genotype, but also to understand how the growth of roots is influenced by their environment. This review discusses progress in quantifying root system parameters (e.g. in terms of size, shape and dynamics) using imaging and image analysis technologies and also discusses their potential for providing a better understanding of root:soil interactions. Significant progress has been made in image acquisition techniques, however trade-offs exist between sample throughput, sample size, image resolution and information gained. All of these factors impact on downstream image analysis processes. While there have been significant advances in computation power, limitations still exist in statistical processes involved in image analysis. Utilizing and combining different imaging systems, integrating measurements and image analysis where possible, and amalgamating data will allow researchers to gain a better understanding of root:soil interactions.

Over the last decade, X-ray computed tomography (CT) has been used increasingly to characterise the microscale architecture of soils. As a result significant progress has been made in the acquisition and interpretation of X-ray CT data, as well as in the thresholding of 3D greyscale CT images in order to produce binary (black and white) ones. Nevertheless, sizeable uncertainties persist, in particular concerning optimal instrumental settings used to generate the greyscale images. In this context, the key aim of this study is to investigate in detail the effect of scanning resolution and reconstruction settings such as noise reduction and 32-bit to 8-bit mapping interval on the 3D X-ray CT imaging of soil structure and the impact on the performance of thresholding methods. To assess the quality of the X-ray CT greyscale images, measures of contrast, noise and sharpness are proposed and tested on a series of images of five different soil samples. At the same time, performance of four segmentation algorithms, i.e., three methods recently developed to deal specifically with soil samples and Otsu's method as a benchmark, was evaluated using functional measures of 3D binary images, including Minkowski functionals and surface pore connected fraction. Results of these analyses suggest that the acquisition and reconstruction parameters investigated significantly affect the quality of soil images, and the subsequent thresholding process. In particular, it was found that thresholding by any of the four methods is greatly affected by the quality of image sharpness, which for soil images appears to be mainly controlled by the scanning resolution. As a result, it is concluded that no matter what reconstruction resolution is required in a study, in order to allow an accurate identification of the pore space, the sample should always be scanned at the highest resolution permitted by the scanning instrument and the sample size. Results also suggest that the three segmentation methods recently developed for soil images thresholding are robust to different levels of noise as well as the choice of the 32-bit mapping interval, as long as lower and upper interval limits for mapping are chosen within suitable boundaries.

During the past 10 years, multidrug-resistant Gram-negative Enterobacteriaceae have become a substantial challenge to infection control. It has been suggested by clinicians that the effectiveness of antibiotics is in such rapid decline that, depending on the pathogen concerned, their future utility can be measured in decades or even years. Unless the rise in antibiotic resistance can be reversed, we can expect to see a substantial rise in incurable infection and fatality in both developed and developing regions. Antibiotic resistance develops through complex interactions, with resistance arising by de-novo mutation under clinical antibiotic selection or frequently by acquisition of mobile genes that have evolved over time in bacteria in the environment. The reservoir of resistance genes in the environment is due to a mix of naturally occurring resistance and those present in animal and human waste and the selective effects of pollutants, which can co-select for mobile genetic elements carrying multiple resistant genes. Less attention has been given to how anthropogenic activity might be causing evolution of antibiotic resistance in the environment. Although the economics of the pharmaceutical industry continue to restrict investment in novel biomedical responses, action must be taken to avoid the conjunction of factors that promote evolution and spread of antibiotic resistance.

The role of fungi in soil ecosystem sustainability is poorly understood, as is the extent to which it is affected by the microscale heterogeneity of soils with respect to structure, chemistry and biology. This is due to the complexity of soil ecosystems, presenting significant challenges to their study in situ. Many theoretical and simulation models have been developed to link nutrient levels to colony dynamics. Unfortunately, there is currently no model that can take both structural and nutritional microscale heterogeneity into account, and is parameterised for the soil environment. In this context, the objective of this article is to develop such a 3D spatially explicit model of fungal dynamics, and to calibrate it for a soil system using data from the literature. A sensitivity analysis is carried out to better understand the uncertainties in the input parameters and their effect on colony dynamics in terms of biomass yield and respiration rates. The results highlight simulation outcomes that are most suited to validation by experimentation. The results also indicate that predictions in biomass yield are sensitive to uncertainties in model parameters relative to the soil–fungal complex that at this point are insufficiently understood experimentally and still have to be estimated by model fitting. The latter parameters, which influence biomass yield and respiration, are associated with biomass recycling processes such as adsorption (,αni) desorption (βni, βi), insulation (ζni) and biomass yield efficiency (ɛ1), and translocation (Dv). The model now opens up great opportunities for hypothesis-driven research, combining theoretical models and novel types of experimentation, especially given the recently acquired ability to generate artificial, replicable soil-like microcosms on which to test model predictions.

Background and Aims: Biochar amendment to soil is a promising practice of enhancing productivity of agricultural systems. The positive effects on crop are often attributed to a promotion of beneficial soil microorganisms while suppressing pathogens e.g. This study aims to determine the influence of biochar feedstock on (i) spontaneous and fungi inoculated microbial colonisation of biochar particles and (ii) physical pore space characteristics of native and fungi colonised biochar particles which impact microbial habitat quality. Methods: Pyrolytic biochars from mixed woods and Miscanthus were investigated towards spontaneous colonisation by classical microbiological isolation, phylogenetic identification of bacterial and fungal strains, and microbial respiration analysis. Physical pore space characteristics of biochar particles were determined by X-ray μ-CT. Subsequent 3D image analysis included porosity, surface area, connectivities, and pore size distribution. Results: Microorganisms isolated from Wood biochar were more abundant and proliferated faster than those from the Miscanthus biochar. All isolated bacteria belonged to gram-positive bacteria and were feedstock specific. Respiration analysis revealed higher microbial activity for Wood biochar after water and substrate amendment while basal respiration was on the same low level for both biochars. Differences in porosity and physical surface area were detected only in interaction with biochar-specific colonisation. Miscanthus biochar was shown to have higher connectivity values in surface, volume and transmission than Wood biochars as well as larger pores as observed by pore size distribution. Differences in physical properties between colonised and non-colonised particles were larger in Miscanthus biochar than in Wood biochar. Conclusions: Vigorous colonisation was found on Wood biochar compared to Miscanthus biochar. This is contrasted by our findings from physical pore space analysis which suggests better habitat quality in Miscanthus biochar than in Wood biochar. We conclude that (i) the selected feedstocks display large differences in microbial habitat quality as well as physical pore space characteristics and (ii) physical description of biochars alone does not suffice for the reliable prediction of microbial habitat quality and recommend that physical and surface chemical data should be linked for this purpose. © 2016, Springer International Publishing Switzerland.