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Summary Parasitic variability (PV) of Meloidogyne hapla populations exists in broad production landscapes. How PV relates to soil health as described by the soil food web (SFW) is unknown. In an experiment replicated three times, nine M. hapla populations from muck and mineral soils with degraded and disturbed SFW conditions from three regions were used to test a hypothesis that PV varies by SFW conditions. The populations were inoculated at 2000 and 4000 eggs in 300 cm3 soil per pot. While the populations’ reproductive potential varied by the SFW condition, soil group, region and/or their interactions, they clustered into high (Population 13), medium (Population 8), and low (all populations from muck and one from mineral soil) PV. Populations 8 and 13 are from degraded mineral soils and the low PV populations are from disturbed and degraded soils, indicating that the conditions where PV exists are variable within or across soil groups. Consequently, the hypothesis is not supported.

The advancements of agriculture practices and technologies in harnessing natural resources has been a major component of humanity's development to produce and maintain food safety. As the bed for agricultural crops, soils are a major natural resource, and soil structure plays a crucial role in agricultural productivity. Long term differences in land use and agronomic management result in differences in soil physical structure, which also translates into variations in pore networks. Decomposition of organic matter and, hence, soil carbon storage capacity are closely related to the pore domain, which is the main environment where chemical and biological processes leading to carbon protection or decomposition take place. In this study, we explored pore structure, carbon characteristics, and their relationships in contrasting ecological systems from a long-term (> 30 years) experiment located at Kellogg Biological Station (Michigan, USA). The studied systems are (i) an agricultural intensively managed system of corn-soybean-wheat rotation (CT), (ii) a native early successional community abandoned from agriculture in 1989 (ES), (iii) a mowed grassland that has never been tilled or in agriculture (NTG), and (iv) late-successional deciduous forest that has never been cleared for agriculture (DF). An x-ray tomography analysis of intact soil cores was used to investigate pore size distributions, connectivity, and morphology to assess soil pore structure. We also measured total soil carbon and nitrogen contents, mineral associated organic carbon (MAOM), and particulate organic carbon (POM), short- and long-term soil respiration, and microbial biomass carbon. Preliminary results showed that the volumes of the soil pores with 30-180 mm Ø, the size range considered as the optimal microbial habitat, followed the trend of DF>NTG »ES>CT. The nitrogen and carbon content of these systems are also in agreement with this trend. Interestingly, MAOM fraction, considered to be a more recalcitrant form of carbon, followed the same trend, while the ratio of MAOM to total organic carbon did not change notably among the systems.

O2 availability is one of the main factors influencing microbial processing of soil carbon and nitrogen and their cycling, and soil pore structure is what drives micro-scale patterns of O2 availability. The diffusivity of O2 is known to be a function of soil porosity and moisture content. However, the actual distribution of O2 in the soil is a product of dynamic interactions between physical (O2 diffusion) and microbial (O2 consumption) processes and is influenced by the soil pore structure. Measurements of gas diffusivity can be achieved via several laboratory techniques, while the determination of O2 consumption by microorganisms is challenging. The objectives of this study are, first, to propose a method for measurement of microbial O2 consumption under steady-state conditions in saturated soil and near saturated soil, and, second, to quantify the rate of O2 consumption in soil materials with contrasting pore structures but similar microbial compositions. The proposed method is based on Fick’s second law of diffusion, given as , where R(z) is an O2 consumption term, C is the concentration of O2, and Ds is the effective molecular diffusion coefficient of O2. The equation was solved for R(z) under steady-state conditions (near saturated soil) where the flux (J)=0. Two soil materials with contrasting pore structures, namely dominated by > 30 μm Ø pores (i.e., large-pore soil) and by < 10 μm Ø pores (i.e., small-pore soil), were prepared. The O2 profile was measured to the depth of 1 cm in the two materials under saturated and near-saturated conditions using O2 microsensor (Unisense, Aarhus, Denmark). As expected, the O2 diffusion was higher in large-pore soil as compared to the small-pore soil, however, the estimated rate of volumetric O2 consumption was also higher in the large-pore soil as compared to the small-pore soil. This finding supports the notion that large pores provide a better micro-environment for soil microorganisms stimulating their activity with subsequent increases in O2 consumption. Our ongoing work builds on these findings and explores the rate and spatial distribution patterns of O2 diffusion and microbial O2 consumption in soils with contrasting pore structures in the presence of plant residues.

Background. High plant diversity is known to increase carbon inputs to soils, impact soil microbial community composition and promote soil microbial activity. Large pores are likely to hold more roots residues, provide more efficient oxygen supply, and have more dissolved nutrients and carbon carried by water fluxes. Soil pore structure also impacts the activities of soil microbial communities. The aim of this study was to investigate the effects of 1) plant systems, representing a 9-year gradient of plant diversity (no plants, monoculture switchgrass (Panicum virgatum L.), and high diversity prairie), 2) soil pore size (small (4-10 µm Ø) and large (30-150 µm Ø)), and 3) incubation time (24 hr (short-term) and 30 days (long-term)) on the microbial communities involved in the utilization of a newly added carbon (glucose). This is the first work to explore the influence of soil micro-habitat, as presented by pores of different sizes ranges, on the microbial communities’ responses to new carbon inputs.Methods. The intact soil cores (5 cm Ø) from the three systems were supplied with either 50 μM C g-1 soil of 13C labeled glucose, unlabeled glucose, or no glucose. Glucose was added to small or large pores based on matrix potential approach. After 24 hr or 30 day incubations stable isotope probing (SIP) was used to identify the phylotypes actively responsible for glucose assimilation in the small and large pore micro-habitats. Both extracted DNA and the fractions separated by SIP were subject to 16S rRNA gene sequencing. PICRUST2 was used to predict the microbial functions of the sequencing data from KEGG orthologs.Results. The overall microbial communities were affected by multiple years of contrasting vegetation, but not by pore sizes or incubation times. Pseudomonas (Proteobacteria) played an important role in carbon uptake from glucose in all short-term incubations and in the long-term incubations within large pores. In the long-term incubations of both switchgrass and prairie systems’ soils, the community compositions of carbon consumers acting within the small and large pore micro-habitats differed and could be linked to disparate carbon assimilation strategies (r- vs. K-strategists) and to disparate carbon acquisition ecological strategies (plant polymer decomposers, microbial necromass decomposers, predators, and passive consumers). The predicted enriched functional genes indicated the dominance of glucokinase in the soil of the prairie, but not switchgrass system, suggesting a competitive advantage for consuming glucose.

Summary Despite considerable knowledge of distribution, biology and parasitic variability (PV) of Meloidogyne hapla in cropping systems, how its PV relates to soil health conditions remains unknown. This study investigated the relationship between the presence or absence of M. hapla with soil food web and the abundance of nematode community in muck (high organic matter) and mineral soils of 15 agricultural fields and adjacent natural vegetation across three vegetable production regions of Michigan, USA. Meloidogyne hapla was present in all regions and all muck soils, but only in some mineral soils. It was present in soils with degraded and disturbed soil food web conditions, but there was no pattern with nematode trophic group abundance. However, principal component analysis showed distinct relationships among M. hapla presence or absence, soils, nematode abundance parameters in agricultural and natural vegetation. The study lays down a foundation for more targeted investigations to understand any links between the PV of M. hapla and its soil environment.

Plant residues decomposing within the soil matrix are known to serve as hotspots of N2O production. However, the lack of technical tools for microscale in-situ N2O measurements limits understanding of hotspot functioning. Our aim was to assess performance of microsensor technology for evaluating the temporal patterns of N2O production in immediate vicinity to decomposing plant residues. We incorporated intact switchgrass leaves and roots into soil matrix and monitored O2 depletion and N2O production using electrochemical microsensors along with N2O emission from the soil. We also measured residue’s water absorption and b-glucosidase activity on the surface of the residue - the characteristics related to microenvironmental conditions and biological activity near the residue. N2O production in the vicinity of switchgrass residues began within 0–12 h after the wetting, reached peak at ~0.6 day and decreased by day 2. N2O was higher near leaf than near root residues due to greater leaf N contents and water absorption by the leaves. However, N2O production near the roots started sooner than near the leaves, in part due to high initial enzyme levels on root surfaces. Electrochemical microsensor is a useful tool for in-situ micro-scale N2O monitoring in immediate vicinity of soil incorporated plant residues. Monitoring provided valuable information on N2O production near leaves and roots, its temporal dynamic, and the factors affecting it. The N2O production from residues measured by microsensors was consistent with the N2O emission from the whole soil, demonstrating the validity of the microsensors for N2O hotspot studies.

Carbon inputs into soil take place primarily through rhizodeposition and root decay. Spatial inaccessibility of organic matter to organisms, i.e., physical protection, is a key factor for stabilizing such carbon in soils. Protection is governed by soil structure, i.e., the spatial arrangement of solids and voids, thus, differences in root distribution and in their rhizosphere physical properties influence carbon sequestration. This structure, in turn, is affected by roots, which explore the soil by rearranging existing soil particles and thus may compact the rhizosphere, especially, when the soil does not contain a well connected macropore system.Here we conducted a split root experiment to determine how plant roots grow into soil depending on the structure they encounter and how this affects the fate and distribution of SOM. Soil cores, with four different structures, either intact or destroyed by sieving, from monoculture switchgrass and prairie systems were incorporated into containers planted with Panicum virgatum L. (Switchgrass) and Rudbeckia hirta L. (Black-eyed Susan), plants with contrasting root characteristics.The cores were X-ray µCT scanned before and after plant growth, enabling explorations of the feedback interactions between roots and soil structure through analysis of pore size distributions, root distributions, and rhizosphere physical properties. To assess the fate of the plant-derived C, the plants were labelled by 14CO2; and presence of 14C in roots, rhizosphere, and rhizoplanes was examined. The cores were incubated for 30 days and 14CO2 and CO2 respiration was measured. Soil solution from pores of different sizes was collected by centrifugation and analyzed for 14C. This enabled to investigate the fate and distribution of carbon in correlation to the interactions of roots and structure derived from image analysis.Results suggest root soil contact as a universal driver that stimulates greater allocations of photo assimilated C (14C) to roots and to their immediate surroundings. When roots were growing into the dense soil matrix, greater 14C was detected within the roots, rhizosphere, and rhizoplane. In addition, more 14C was found as DOC. Although most of this carbon was released fast, in total more 14C also remained in the soil after the 30 day incubation. While the majority of roots from Black-Eyed-Susan grow into the dense soil matrix, Switchgrass roots, in contrast, preferentially grew into macropores (especially into switchgrass created biopores). When that happened, roots and rhizosphere had low quantities of freshly assimilated C (i.e., 14C), yet, surprisingly more 14C was found at greater distances from the roots in microsamples, which may be linked to mycorrhizae.The study is founded in part by the NSF DEB Program (Award # 1904267) and by the Great Lakes Bioenergy Research Center (Award # DE-SC0018409).

Greater plant diversity facilitates soil C gains, yet the exact mechanisms of this effect are still under intensive discussion. Whether a plant grows in monoculture or in an inter-cropped mixture can affect allocation of plant assimilates, belowground exudation, and microbial stimulation. The goal of this study was to examine the effects of inter-cropping on a previously overlooked aspect of plant-soil interactions, namely, on locations where plant assimilated C is allocated within the soil pore system and its subsequent fate in relation to soil pores. The soil for the study originated from a greenhouse experiment with switchgrass (Panicum virgatum L.) (var. Cave'n'Rock) (SW), big bluestem (Andropogon gerardii Vitman) (BB), and wild bergamot (Monarda fistulosa L.) (WB) grown in monocultures and in inter-cropped pairs and subjected to species specific C pulse labeling (Kravchenko et al., 2021). Intact soil cores (8 mm Ø) were collected from the experimental pots, subjected to a short-term (10 day) incubation, X-ray computed micro-tomography (μCT) scanning, and soil C micro-sampling "geo-referenced" to μCT images. Results indicated that in the plant systems with demonstrated interplant C transfer soil C was positively correlated with

Colloids are known to facilitate transport of a broad variety of chemicals and microorganisms in soils. Extracellular hydrolytic enzymes, produced by many soil microorganisms and plant roots, have high affinity to clay and silt particles constituting soil mineral colloids (SMC). Therefore, those enzymes can be released jointly with colloids from soil matrix during high water flow events and transported convectively attached to the colloids carried by the water flow. At the same time hydrolytic enzymes are often considered as free-mobile proteins with a self-propelled diffusion mechanism. Current literature lacks any information on enzyme transport in soils, and it is not clear whether enzymes are transported and, if so, whether they are transported in free- or colloid-associated form. Studying enzyme transport in soils is challenging due to infeasibility of their enumeration in soil solutions and suspensions, differences in activity of free and colloid-associated enzymes, the influence of colloid size and composition, pH and ionic strength in the colloidal suspensions on the enzyme activity. This study presents the first experimental evidence of enzyme transport in soils facilitated by SMC in sandy, loamy and two sandy-loam soils. Its results suggest from 50 to 80% of transported hydrolytic enzymes are associated with transport of coarse SMC. The remaining 20 to 50% of enzymes are likely transported by organic colloids and fine SMC (Ø < 1 mm). The ionic strength played a dual role in the joined enzyme and colloidal transport: (1) by affecting dispersion and release of SMC colloids from soil; and (2) modifying optimum pH of enzymatic activity in released colloidal suspensions. Our results provided insights into factors governing plant-soil-microbial interactions through the transport and activity of hydrolytic enzymes. Support for this research was provided by the NSF LTER Program (DEB 1027253) at the Kellogg Biological Station, by USDA NC1187 project, by the Great Lakes Bioenergy Research Center, U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under Award Number DE-SC0018409.

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.

Linking the distribution of enzyme activity to the size and properties of soil pores is a necessary prerequisite for mechanistic understanding of soil biochemical processes. In this study we used soil 2D zymography and X-ray computed tomography (μCT) to assess the relationship between enzymes and pores. The objectives of the study were (i) to assess spatial distribution patterns in the activity of six enzymes contributing to C, N and P cycles, namely, cellobiohydrolase, β-glucosidase, xylanase acid phosphatase, leucine aminopeptidase, and N-acetylglucosaminidase, in soils from five long-term land use and management practices, (ii) to study the correlation between enzyme activities and μCT information, i.e., pore characteristics and image grayscale values, and (iii) to explore the potential use of soil 2D zymography in predicting enzyme activities within 3D soil cores. 3D pore-size distributions were obtained from μCT images of 13 intact soil cores and then 8–15 2D zymography maps were taken from each core. Spatial distributions in the activities of all studied enzymes were auto-correlated; the spatial correlation ranges were equal to ∼7–8 mm. The relative activity of all enzymes was positively associated within 60–180 μm O pores. Combining 3D μCT information with 2D zymography maps visualized the overall patterns of enzyme activity distributions with respect to soil pores and particulate organic matter locations. Based on the findings we propose a conceptual scheme relating localization of microorganisms, enzymes and substrates to pores of different size ranges. Specifically, we suggest that pores in the tens of microns size range represent optimal microbial habitats, and as such are associated with greater microbial abundance, leading to high enzyme production and activity.

Increasing the potential of soil to store carbon (C) is an acknowledged and emphasized strategy for capturing atmospheric CO2. Well-recognized approaches for soil C accretion include reducing soil disturbance, increasing plant biomass inputs, and enhancing plant diversity. Yet experimental evidence often fails to support anticipated C gains, suggesting that our integrated understanding of soil C accretion remains insufficient. Here we use a unique combination of X-ray micro-tomography and micro-scale enzyme mapping to demonstrate for the first time that plant-stimulated soil pore formation appears to be a major, hitherto unrecognized, determinant of whether new C inputs are stored or lost to the atmosphere. Unlike monocultures, diverse plant communities favor the development of 30–150 µm pores. Such pores are the micro-environments associated with higher enzyme activities, and greater abundance of such pores translates into a greater spatial footprint that microorganisms make on the soil and consequently soil C storage capacity., The processes driving soil carbon accretion remain to be poorly understood. Here the authors combined X-ray micro-tomography and zymography to demonstrate that plant-stimulated soil pore formation is a major, hitherto unrecognized, determinant of whether new C inputs are stored or lost to the atmosphere.

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.

The object of research is the process of transportation of mined resources from offshore drilling platforms in the shelf of the seas to onshore reservoirs. One of the most problematic places is the need to choose the means of transport and the method of transporting the extracted hydrocarbons from offshore drilling platforms (ODP) to the onshore infrastructure. Using the method of equivalent values, the limiting values of the use of pipeline transport are established depending on the distance of offshore drilling platforms from the coast. During the study, an algorithm was developed to improve the organization of transportation of hydrocarbons produced in the seas to substantiate the mode of transportation depending on the distance between the ODP and the coast. As well as a reasonable criterion for choosing a vehicle was proved and a system of indicators for the formation of the criterion was considered. Methodical approach for the choice of transport consists of the following steps: indicators of capital, operating and reduced costs for each type of transport are formed; threshold value of the reduced costs for pipeline transport and for the delivery by shuttle tankers and with the help of marine barge-towing vehicles depending on the distance of the ODP from the coast is determined; criterion of the effectiveness of the choice of transportation mode is displayed; indicator of unit costs for marine and pipeline transport is calculated; threshold value of the use of one of several transportation modes is determined. A methodical approach is developed that ensures a reasonable approach to the choice of the transportation mode and type of transport when organizing the delivery of the extracted raw materials from the ODP to the onshore infrastructure, ensuring the lowest unit transportation costs. Compared with similar known methods that are used to select transport for land production and transportation, such methods have not been used in the offshore oil business.

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.

The use of non-invasive imaging techniques expands opportunities to characterize soil health and functioning, complementing the information from the traditional soil structure analyses. Soil pore architecture drives water and gas fluxes, chemical transport, activity and movement of soil biota; and imaging techniques are particularly suitable for quantifying it. Here we discuss the potential for X-ray computed micro-tomography (X-ray µCT) as a tool to characterize key parameters of soil pore architecture, such as measures of macroporosity, pore connectivity, pore shape, and solid-to-pore distance. We also provide a brief overview of the principles behind X-ray µCT, examples of the latest literature that implemented these pore measures for soil characterization, and recommendations for the methods that can be used to determine these characteristics using publicly available software ImagJ. We also assembled a list of resources where in-depth information and comprehensive reviews of the current literature can be found.

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.

Background The aim of the current study was the evaluation of initial biofilm adhesion and development on laser-microtextured implant collar surfaces and the examination of effectivity of different biofilm management methods. Methods Initial biofilm formation was investigated on hydrophobic machined and laser-microtextured (Laser-Lok) titanium surfaces and hydrophobic machined and laser-microtextured (Laser-Lok) titanium aluminium vanadium surfaces and compared to hydrophobic smooth pickled titanium surfaces, hydrophilic smooth and acid etched titanium surfaces, hydrophobic sandblasted large grid and acid etched titanium surfaces (titanium Promote) via erythrosine staining and subsequent histomorphometrical analysis and scanning electron microscopic investigations. After decontamination procedures, performed via tooth brushing and glycine powder blasting, clean implant surface was detected via histomorphometrical analysis. Results After 24 h mean initial plaque area was detected in the following descending order: smooth pickled titanium > titanium Promote > hydrophilic smooth and acid etched titanium > Laser-Lok titanium > Laser-Lok titanium aluminium vanadium. The same order was determined after 48 h of biofilm formation. After glycine powder blasting all samples depicted almost 100% clean implant surface. After tooth brushing, Laser-Lok titanium (67.19%) and Laser-Lok titanium aluminium vanadium (69.80%) showed significantly more clean implant surface than the other structured surfaces, hydrophilic smooth and acid etched titanium (50.34%) and titanium Promote (33.89%). Smooth pickled titanium showed almost complete clean implant surface (98.84%) after tooth brushing. Conclusions Both Laser-Lok surfaces showed less initial biofilm formation after 24 and 48 h than the other implant surfaces. In combination with the significant higher clean implant surfaces after domestic decontamination procedure via tooth brushing, both Laser-Lok surfaces could be a candidate for modified implant and abutment designs, especially in transmucosal areas.

Cover crops are known to increase macroporosity and pore connectivity, thus having a beneficial effect on soil hydraulic properties such as saturated hydraulic conductivity, However, cover crop species typically used encompass a variety of contrasting root architectures and their effects on small-scale pore properties are difficult to quantify.Here we explore the influence of five different cover crops (annual ryegrass, Austrian winter pea, dwarf essex rapeseed, oats, and oilseed radish) on soil structure with X-ray µCT. Undisturbed samples were taken from an experiment with these cover crops on Kellogg Biological Station (Michigan, USA) in October 2019. Two soil columns with a diameter of 5 cm were taken in 5 - 10 cm depth from each of three replicated plots per plant species and scanned with X-ray µCT at a resolution of 18 µm.These images will be used to characterize pore structure in terms of pore size distribution, pore connectivity. In addition, a new imaging protocol will be used, which combines existing ones with a random forest classifier to segment image features such as pores, biopores and roots simultaneously.First, the results reveal that different cover crops indeed result in different pore characteristics. The fibrous root system of oats leads to the highest volume of narrow macropores and increased their connectivity, while the tap root system of dwarf essex rapeseed mainly effected wide macropores. The highly diverse root system of Australian winter pea increased a wide range of pore sizes and thus resulted in the highest visible porosity.The current study is funded by a grant from USDA Organic Transition program

Plant roots and soil microorganisms produce hydrolytic extracellular enzymes to acquire nutrients via transformation of organic matter. Microorganisms inhabit hydraulically active pores, being attached to their surfaces or to organic and mineral colloids in soil solution. Therefore, diffusion of enzymes due to Brownian motion is constrained by their interactions with the surfaces of soil particles dispersed in the solution. It is generally unknown to which extent the extracellular enzymes are associated with solid and liquid soil phases and whether enzyme motility is affected by the movement of colloids occurring in soil solution. Therefore, the goal of our study was to quantify enzyme transport in soils with contrasting properties. Transport of ß-glucosidase, acid-phosphatase, xylosidase and cellobiohydrolase was studied in undisturbed non-sterile columns of soils with three contrasting textures: sandy, sandy loam and loam. The colloids, microorganisms, and enzymes inherent for each soil were applied via soil suspensions to the tops of the undisturbed columns. The suspensions were prepared by dispersing 1 g of each soil in 100 ml of de-ionized water, followed by 30 min sedimentation. Approximately 2.5 pore volumes of the applied suspensions were passed through the columns with continuous collection of the effluent from the bottom of the columns. The effluent was analyzed for colloid contents and enzyme activities before and after removal of soil particles of size 1-10 μm by centrifugation. From 7 to 49% of applied colloids recovered from the columns with higher colloid retention capacity in finer textured soils. The enzyme activity and colloid content were the highest in the first portions of the effluent and decreased as more suspension passed the columns, suggesting presence of enzymes and colloids in soil pores readily available for convective transport. Removal of soil particles of size 1-10 μm from the effluents by centrifugation reduced enzyme activity by factors 2-5, which was much larger than reduction in the enzyme solutions free of colloids centrifuged at the same settings (24- 30%). Our results indicated that most enzymes are present and transported through soil pores convectively while attached to soil colloids. Support for this research was provided by the USDA NIFA Program (Award # 2019-67019-29361), by the NSF LTER Program (DEB 1027253) at the Kellogg Biological Station, by USDA NC1187 project, by the Great Lakes Bioenergy Research Center, U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under Award Number DE-SC0018409.

Extracellular enzymes play an important role in soil biochemical processes as they are the key regulators of litter and soil organic matter degradation. However, understanding of the factors influencing their activity and fate in soil is still limited. In this study, we examined the relationship between soil pores and spatial patterns of extracellular enzyme activity in soils from two bioenergy cropping systems: monoculture switchgrass (Panicum virgatum L.) and restored prairie. Intact soil cores (5 cm Ø x 5 cm height) were collected at two contrasting topographical positions (depression and slope) within large topographically diverse fields where the switchgrass and prairie were grown since 2008. The cores were subjected to X-ray computed tomography scanning at 18 µm resolution. After the scanning, a switchgrass seedling was planted in these cores and allowed to grow for three months. Then the plants were terminated and the cores were rescanned. Pore characteristics were assessed using the image information, and b-glucosidase activity was characterized via 2D zymography. Preliminary results showed that soil of the prairie system had greater volumes of 60-180 mm Ø size pores compared to monoculture switchgrass system. However, enzyme activity was higher in the soil of monoculture switchgrass. Our preliminary results indicate that the soil pore size distribution and enzyme activity differ depending on the type of the bioenergy cropping system. Further analysis is conducted to determine microbial abundance, total C in soil and microbial biomass in these cropping systems to understand the effect of pores on microbial activity associated with C processes in soil.

Soil microorganisms preferably occupy intermediate-sized pores, which are the arena for most biochemical reactions due to high nutrient contents and beneficial air and water regimes in these pores. Extracellular enzymes produced by microorganisms for organic matter transformations are assumed to reside in the same pores. However, there is a lack of direct experimental evidence of enzymatic activity being associated with pores of particular sizes. In this study we measured activity of ß-glucosidase in soil pores Øβ-D-glucoside were applied to soil subsamples at vacuum corresponded to saturation of the three studied groups of pores and kept in soil for 30 min. Produced 4-methylumbelliferone (MUF) was then extracted from the soil. The results demonstrated that the enzyme activity increased in all groups of pores in the order G2

An understanding of the drivers of hotspot/hot moments of N2O production is required to better constrain the global N2O budget and to plan the mitigation strategies. Hot spots are areas with very high N2O emission rates relative to the surrounding area, while hot moments are short periods of time with very high emission rates. As the decomposition of fresh organic matter is transitory in nature, it may have a strong influence on hotspot and hot moment N2O production. Roots are well known to be hotspots for microbial activity but roots direct contribution to N2O production and emissions in soil remain poorly understood.In this study, we evaluated the role of root decomposition on N2O production and emissions, as a function of soil pore size and water content. We hypothesized that (i) the greatest N2O emissions will be observed from root decomposition in the soil dominated by large (>30 µm Ø) pores due to their high connectivity and (ii) enhanced N2O production by denitrification will be observed due to local anaerobic conditions, generated by O2 consumption by decomposers.To evaluate the role of root decomposition on N2O production we used soil microcosms cultivated with switchgrass (Panicum virgatum L. variety Cave-in-rock). From the same composite soil samples we created two soil materials with contrasting pore architectures, namely soil with prevalence of large pores (≥ 35 μm Ø) and small pores (≤ 10 μm Ø). After four months of growing in a greenhouse, plants were cut and soil microcosms with roots were incubated in the dark at room T for 21 days, at two contrasting soil moisture conditions: 40% and 70% water filled pore space (WFPS). Gas headspace samples were collected at different time points during incubation for N2O and CO2 concentration analysis and isotopic characterization of N2O (δ15Nbulk, site preference (SP), and δ18O).The daily emissions of N2O and CO2 from soil microcosms with grown roots showed the same trend during the incubation period and were significantly higher compared to soil microcosms without roots (control) (p < 0.05). Microcosm with large pores soil had significantly higher N2O flux rates compared to the microcosms with small pore soil for both soil moisture treatments (p < 0.001). The relationship between SP and δ18O (isotope mapping) indicated that heterotrophic bacterial denitrification strongly dominated N2O production between day 1 to 7 of the incubation (≥ 97%) and N2O reduction was higher during this period (40 – 60%) in soil microcosms with both pore size and moisture treatment. Later on, N2O reduction decreased (1 – 35%) while the share of nitrification/fungal sources increased for soil microcosms with large pores.Our results indicated that decomposing roots acted as hotspots enhancing N2O emissions and N2O hotspots occurring during root decomposition are strongly influenced by soil pore architecture. While differences in soil pore architecture did not cause differences in N2O production process at the initial phase of decomposition, it might influence the relative contribution of N2O microbial production pathways in later stage of decomposition.

High temporal and spatial variability of nitrous oxide (N2O) emission from soils has been a challenge for the systematic prediction of global climate change. It is attributed to multiple hotspots occurring simultaneously and affecting the N dynamics cumulatively on an ecosystem scale. Understanding the mechanisms and contributing factors of N2O emission in single hotspots is a prerequisite to overcoming this problem.We investigated the decomposing switchgrass roots as N2O hotspots, using isotope dual-labeling (15N and 13C) and zymography. Our main objectives were i) to quantify the contribution of decomposing roots to N2O emission along with the N contents in the soil (total, organic, and inorganic N) and microbial pools, and ii) to differentiate the extracellular enzyme activity in decomposing roots from the bulk soil, and test if the ‘spatially differentiated’ hotspot enzyme activity indeed related to ‘isotopically differentiated’ hotspot N2O emissions. We treated the soils of the same origin to have different moisture contents (40% and 70% water-filled pore space, WFPS) and pore size distributions (dominant pores of >30 Ø and < 10 mm Ø, referred to as coarse and fine soil), to evaluate how these variables change the contribution of decomposing roots to the N2O production.Our results showed that up to 0.4 % of the root driven N can be emitted as N2O gas, only within 21 days of the decomposition. Approximately 21 ~35% of root N was transformed to dissolved organic N, while less than 1 % of the root N remained as ammonium (NH4+) and nitrate (NO3-) during the incubation. Decreasing NH4+ and increasing NO3- suggested nitrification. Surprisingly, both inorganic and organic N content was greater in coarse soil, which likely led to intense hotspots of enzyme activity and N2O emission. However, there was no difference in microbial biomass between the soil materials. Higher chitinase activity and relatively large pores in coarse soils suggest that the fungal activity was higher in coarse soils compared to the fine soils. Root chitinase activity was positively correlated with the root driven N2O emission rate (p< 0.01, R2=0.22), supporting that the microbial hotspot formed near the root is the hotspots of N2O emission.Our study showed that the intensity of root driven N2O hotspots can highly depend on the soil physical characteristics, being mediated by decomposed substances, and enzyme activity. Tracking the fate of N during the plant root decomposition can provide a new perspective on the strategies to minimize N2O emissions in bioenergy systems.

Bioenergy crop cultivation is suggested as one of the promising options to increase soil organic carbon (SOC) stock, and thereby sequester atmospheric carbon dioxide. Yet, the increase in SOC varies greatly depending on the cropping system, with high plant diversity in particular appearing to be positive for carbon storage. This is recently linked to, among other things, the formation of a pore architecture favorable for microbial function and the storage of microbial degradation products. However, little is known about whether this observation holds true for a wide range of soil textures. Therefore, the objective of this research was to compare the abundance of pores with different sizes and SOC contents in soils with contrasting texture and plant diversity. Soil cores and surrounding soil samples were taken on seven long-term field experiments of monoculture switchgrass and restored prairie sites in Michigan, USA. In addition to texture and SOC analyses in disturbed soil samples, undisturbed cores with a diameter of 5 cm were scanned by micro-computer tomography (µCT) at a resolution of 18 µm. These will be used to analyze pore characteristics.such as pore size distribution.Results reveal, in highly sandy soil, high plant diversity was less effective to form narrow mid-size pores, and thus did not enhance SOC, while numerically higher SOC contents were observed in the restored prairie of less sandy soil, having higher abundance of mid-size pores compared to the monoculture. In conclusion, in the highly sandy soil, restored prairie with plant diversity was less effective to form pores in the mid-size range, and thus it couldn’t enhance the capability of C sequestration.

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.

Challenges with in situ visualization of nonparticulate organics in porous materials limit understanding and modeling processes of transport, decomposition, and storage of organic compounds. In par...

Soil zymography is a new technique developed to visualize two‐dimensional distributions of enzyme activities. The method consists of incubating a membrane saturated with an enzyme‐specific fluorogenic substrate on a surface of the soil sample, followed by recording the membrane image generated by a fluorescent product (e.g. MUF: methylumbelliferone) in ultraviolet light. Despite its relative ease of use, performing zymography involves multiple user‐made decisions that might affect the accuracy of enzyme activity estimates. Therefore, unification of the zymography methodology is required for correct estimations and comparisons of various studies. We evaluated the following methodological aspects of the implementation of zymography: (a) camera settings and image processing, (b) effects of evaporation and (c) calibration procedures. Camera settings (shutter speeds or exposure time) affected the intensity of background fluorescence and signal‐to‐noise ratios (SNR). However, because their combined effects varied depending on MUF concentrations, light and camera setting need to be optimized for the expected range of MUF concentrations prior to zymography. Evaporation of MUF solution from the membrane had no effect on fluorescence. Relations between MUF concentration and intensity of fluorescence during calibrations demonstrated a saturated pattern and were strongly affected by image noise outside the optimal range (e.g. 8–14 μm MUF pixel⁻¹). We developed a new calibration approach that is based on a piecewise linear regression. The new approach accounted for specific ranges of MUF concentration and uses nonuniformly saturated membranes, reflecting the real distribution of enzyme activities in soil. The new calibration algorithm eliminated biases of the standard calibration and resulted in greater accuracy in predicting MUF concentrations. HIGHLIGHTS: We developed a new approach to calibration for 2‐D soil zymography. The approach accounted for spatial nonuniformity of soil zymograms. Standard calibration resulted in systematic underestimation of enzyme activity. Soil zymography requires pixel‐based calibration with nonuniformly saturated membranes.

Soil membrane zymography enables 2D mapping of enzyme activities on the surface of soil samples. The method is based on diffusion of components of enzymatically-mediated reactions to/from membrane, and, thus, reflects the distribution of enzyme activities at the intact soil surface. Zymography has been already successfully implemented in numerous soil ecology applications. Here we identify two methodological aspects for further improvement and expansion of the method at micro and macro scales: first, accounting for the area of contact between the soil surface and the zymography membranes and, second, accounting for diffusion effects during the zymography procedure. We tested three methods, namely, laser-scanning, staining with a fluorescent product (e.g. MUF: 4-methylumbelliferone), and X-ray computed micro-tomography, for assessing the area of the soil surface in contact with the membranes. We quantified diffusion of MUF, enzymes and substrate between the substrate-saturated membrane and soil as well as diffusion processes during membrane zymography via HP2 software. Diffusion of the substrate from the membrane and of the MUF-product to the membrane was detected, while there were no clear evidence of enzyme diffusion to/in the membrane. According to the model simulations, the enzyme activities detected via 2D zymography probably represent only a small portion, about 20%, of the actual reactions within the soil volume that is in both direct contact and in hydrological contact with zymography membranes. This is a result of omnidirectional diffusion of reaction products. The membrane contact with the soil surface estimated by three methods ranged from 3.4 to 36.5% further signifying that only a fraction of enzymes activity is detectable in a course of 2D soil zymography.

Soil incorporation of aboveground plant residues contributes to enhancement of soil sustainability in agricultural systems with cover crops. However, incorporated plant fragments can affect N2O emissions by acting as micro-scale hotspots of N2O production. We hypothesize that water retention capacity of the incorporated plant material and soil pore-size distribution (PSD) are among the factors influencing the magnitude of N2O emissions from the soil subjected to aboveground plant residue additions. To test this hypothesis we compared CO2 and N2O emissions from two soil materials with contrasting PSD incubated with leaves from two legume species similar in their C and N contents, but differing in physical characteristics of their leaves, i.e., crimson and red clovers. In order to separate the effect of biochemical differences between the two species from the differences in the physical characteristics of their leaves we considered three leaf treatments: (i) intact leaves, (ii) ground leaf material aggregated to resemble the size of the intact leaves, and (iii) ground leaf material uniformly mixed with the soil. The latter two treatments minimized the physical differences between the leaves of the two species. Intact leaves of crimson clover retained more water than the red clover leaves. At the studied 50% of water filled pore space settings, both species retained more water when incubated in the soil material with prevalence of large (>30 μm) pores than in the soil material with prevalence of small ( 30 μm) pores.

The object of research is specialized vessels servicing production platforms (SPV) in the shelves of the seas. One of the most problematic places is the need to improve the efficiency of specialized service vessels for transporting personnel, building materials and supplies to oil platforms in the sea shelves during the operation of platforms for oil production.In the course of the study, in order to improve the SPV operation of the production platforms, the method of variants and the routing of the operation of vehicles were used to develop the methodology. This allowed to improve the work of the SPV in the maintenance of production platforms, due to the reduction in the cost of voyage.The best way to organize the SPV operation in the maintenance of mining platforms in the Black Sea shelf is received. Namely, possible routes of SPV operation were compiled during the pendulum and group-delivery mode of operation, and the best way of SPV operation for the best route was determined according to the chosen criterion. The economic effect of the SPV operation on the selected route and method, which amounted to about 44 000 dollars for the voyage. This result is due to the fact that the developed methodology for the selection of the best version of the SPV has a number of features, in particular, it consists of successive stages:select route schemes for the organization of the work of environmental protection;compiled options for routes of SPV operation for each scheme;selection criterion is assigned;calculated performance of the vessels;the optimal route and scheme are selected according to the adopted optimization criterion.The developed methodology provides the determination of the optimal route and a variant of the operation scheme of the SPV, which provides the lowest value of the cost of transportation of 1 ton-km of cargo. Compared with similar known methods that are used in road transport, similar methods have not been used in the offshore oil business., Объектом исследования являются специализированные судна снабжения добывающих платформ (ССП) в шельфах морей. Одним из самых проблемных мест является необходимость повышения эффективности работы специализированных судов снабжения платформ для доставки персонала, строительных материалов и снабжения на нефтяные платформы в шельфах морей во время эксплуатации платформ для добычи нефти.В ходе исследования для совершенствования работы ССП при разработке методологии использовались метод вариантов и маршрутизации работы транспортных средств. Это позволило усовершенствовать работу СПП при обслуживании добывающих платформ, благодаря снижению себестоимости выполнения рейсов.Получен наилучший способ организации работы ССП при обслуживании добывающих платформ в шельфе Чёрного моря (Украина). А именно, составлены возможные маршруты работы ССП при маятниковом и сборно-развозном способе работы, а также по выбранному критерию определен лучший способ работы ССП для наилучшего маршрута. Рассчитан экономический эффект от работы ССП по выбранному маршруту и способу, который составил около 44 тыс. дол. за рейс. Это связано с тем, что разработанная методология по выбору лучшего варианта работы ССП имеет ряд особенностей, в частности она состоит из последовательных этапов:выбираются схемы маршрутов по организации работы СПП;составляются варианты маршрутов работы ССП по каждой схеме;назначается критерий выбора схемы;рассчитываются показатели работы судов;выбирается оптимальный маршрут и схема по принятому критерию оптимизации.Разработанная методология обеспечивает определение оптимального маршрута и варианта схемы работы ССП, который обеспечивает наименьшее значение себестоимости перевозок 1 тонно-км грузов. По сравнению с аналогичными известными методами, которые применяются в автомобильном транспорте, в морском нефтедобывающем бизнесе подобные методы не применялись., Об’єктом дослідження є організація роботи спеціалізованих суден постачання видобувних платформ (СПП) в шельфах морів. Одним з найбільш проблемних місць є необхідність підвищення ефективності роботи спеціалізованих судів обслуговування для доставки персоналу, будівельних матеріалів і постачання на нафтові платформи в шельфах морів під час експлуатації платформ для видобутку нафти.В ході дослідження для вдосконалення роботи СПП при розробці методології використовувалися метод варіантів і маршрутизації роботи наземних транспортних засобів. Це дозволило удосконалити роботу СПП при обслуговуванні видобувних платформ, завдяки зниженню собівартості виконання рейсів.Отримано найкращий маршрут та спосіб організації роботи СПП при обслуговуванні видобувних платформ, на прикладі шельфу Чорного моря (Україна). А саме, складені можливі маршрути роботи СПП при маятниковому і збірно-розвізному способі роботи, а також за обраним критерієм визначено кращий спосіб роботи СПП для найкращого маршруту. Розраховано економічний ефект від роботи СПП за обраним маршрутом і способом, який склав близько 44 тис. дол. за рейс. Це пов'язано з тим, що розроблена методологія щодо вибору найкращого варіанту роботи СПП має ряд особливостей, зокрема вона складається з послідовних етапів:вибираються схеми маршрутів по організації роботи СПП;складаються варіанти маршрутів роботи СПП за кожною схемою;призначається критерій вибору схеми;розраховуються показники роботи судів;вибирається оптимальний маршрут і схема за прийнятим критерієм оптимізації.Розроблена методологія забезпечує визначення оптимального маршруту і варіанти схеми роботи СПП, який забезпечує найменше значення собівартості перевезень 1 тонно-км вантажів. У порівнянні з аналогічними відомими методами, які застосовуються в автомобільному транспорті, в морському нафтовидобувному бізнесі подібні методи не застосовувалися.

Oil incorporated plant residues are an important source of carbon inputs and its decomposition defines magnitudes of many soil processes. While soil properties, especially soil moisture levels, influence decomposition rates, the moisture level of plant residue itself can differ from that of the surrounding soil due to the so called “sponge effect”-water absorption by plant residue from the surrounding soil. Our study explored whether water absorption by plant residue varies depending on soil moisture and matric potential levels; and how soil characteristics and characteristics of the plant residue itself affect the magnitude of this effect. We examined water retention of two types of plant residue materials, namely, corn and soybean leaves, in soil materials with three contrasting particle size distributions (PSD); and analyzed water distribution patterns in the soil adjacent to the residue using X-ray computed micro-tomography. The results demonstrated that the sponge effect was especially pronounced when soil moisture levels ranged from 0.15 to 0.40 cm3 cm− 3 (~ 30–80% water filled pore space). The leaves were fully saturated with gravimetric water content levels exceeding 2.0 g g− 1 even when the soil moisture level was only 0.15 cm3 cm− 3. Subsequent increase in residue moisture level was achieved due to vertical swelling of residue and reached 3.0–4.0 g g− 1 at soil moisture levels > 0.30 cm3 cm− 3. The sponge effect was greater in the coarse textured soil materials with lower soil water retention than in the fine textured soil material with high water retention; it was greater in soybean than in corn, possibly due to greater porosity of soybean leaves. Our results indicate that plant residue fragments incorporated into soil likely create moisture microenvironments for microbial decomposers that differ from those of the surrounding soil; and which, in relatively dry soil, can be more beneficial for plant decomposition than what can be inferred from the information on moisture levels of the soil itself.

Greater plant diversity is known to facilitate soil C gains, yet the exact mechanisms of this effect are still under intensive discussion. Whether a plant grows in monoculture or in a multi-species mixture can affect allocation of plant assimilates, belowground exudation, and microbial stimulation. The goal of this study was to examine the effects of inter-cropping on a previously overlooked aspect of plant-soil interactions, namely, on locations where plant assimilated C is allocated within the soil pore system and its subsequent fate in relation to soil pore size distributions. The soil for the study originated from a greenhouse experiment with switchgrass (Panicum virgatum L.) (var. Cave'n'Rock) (SW), big bluestem (Andropogon gerardii Vitman) (BB), and wild bergamot (Monarda fistulosa L.) (WB) grown in monocultures and in inter-cropped pairs and subjected to species specific 13C pulse labeling (Kravchenko et al., 2021). Intact soil cores (8 mm O) were collected from the experimental pots, subjected to a short-term (10 day) incubation, X-ray computed micro-tomography (µCT) scanning, and soil 13C micro-sampling “geo-referenced” to µCT images. Results indicated that in the plant systems with demonstrated interplant C transfer soil 13C was positively correlated with