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The location of microorganisms and substrates within soil pore networks plays a crucial role in organic carbon (C) processing, and its microbial utilization and turnover, and has direct consequences for C and nutrient cycling. An optimal approach to quantify responses to new C inputs from microorganisms residing in specific pores is the addition of new C to pores of target sizes in undisturbed soil cores. We used the matric potential approach to add 14C‐labelled glucose to small (< 40 μm, root free) or large (60–180 μm, potentially inhabited by roots) pores of undisturbed soil cores. Localization of glucose‐derived C via 14C imaging was related to pore size distributions and connectivity, characterized via X‐ray computed microtomography (μCT), and to β‐glucosidase activity, characterized via zymography. After 2‐week incubations, 1.3 times more glucose was mineralized (14CO2) when it was added to the large pores; however, more 14C remained in microbial biomass when glucose was added to the small pores. Consequently, although utilizing the same amounts of easily available C, the microorganisms localized in the large pores had faster turnover compared to microorganisms in small pores. Stronger associations between β‐glucosidase activity and glucose‐derived C were observed when glucose was added to the large pores. We conclude that (a) the matric potential approach allows placing, albeit not exactly, of soluble substrates into pores of target diameter range, and (b) microorganisms localized in large pores respond to new C inputs with faster turnover, greater growth and more intensive enzyme production compared to those inhabiting the small pores. [ABSTRACT FROM AUTHOR]

While renewable biofuels can reduce negative effects of fossil fuel energy consumption, the magnitude of their benefits depends on the magnitude of N2O emissions. High variability of N2O emissions overpowers efforts to curb uncertainties in estimating N2O fluxes from biofuel systems. In this study, we explored (a) N2O production via bacterial denitrification and (b) N2O emissions from soils under several contrasting bioenergy cropping systems, with specific focus on explaining N2O variations by accounting for soil pore characteristics. Intact soil samples were collected after 9 years of implementing five biofuel systems: continuous corn with and without winter cover crop, monoculture switchgrass, poplars, and early‐successional vegetation. After incubation, N2O emissions were measured and bacterial denitrification was determined based on the site‐preference method. Soil pore characteristics were quantified using X‐ray computed microtomography. Three bioenergy systems with low plant diversity, that is, corn and switchgrass systems, had low porosities, low organic carbon contents, and large volumes of poorly aerated soil. In these systems, greater volumes of poorly aerated soil were associated with greater bacterial denitrification, which in turn was associated with greater N2O emissions (R2 = 0.52, p < 0.05). However, the two systems with high plant diversity, that is, poplars and early‐successional vegetation, over the 9 years of implementation had developed higher porosities and organic carbon contents. In these systems, volumes of poorly aerated soil were positively associated with N2O emissions without a concomitant increase in bacterial denitrification. Our results suggest that changes in soil pore architecture generated by long‐term implementation of contrasting bioenergy systems may affect the pathways of N2O production, thus, change associations between N2O emissions and other soil properties. Plant diversity appears as one of the factors determining which microscale soil characteristics will influence the amounts of N2O emitted into the atmosphere and, thus, which can be used as effective empirical predictors. Long‐term implementation of bioenergy systems with contrasting plant diversity influences microscale pore architecture, which then affects predictors of N2O production and emission. [ABSTRACT FROM AUTHOR]

The development of environmentally and economically sound long term agricultural practices under changing climate conditions at the field scale requires implementation of predictive models that assess short and long term responses of agricultural systems to changing environmental conditions. Soil properties for such models are commonly taken from local or National Soil Surveys (SSURGO, STATSGO). This causes a mismatch between the modeling and data source scales. Different techniques can be implemented to upscale soil properties measured at plot scale for field-scale crop modeling, however little is known about the effect of scaling on the accuracy of crop models in predicting crop yields. The objective of this work was to examine: (i) the spatial variability of soybean yields across an agricultural field with different soils and inputs; (ii) how spatial variability in soil properties translates into the variability of measured and predicted yields; (iii) how scaling soil properties affects model accuracy in predicting soybean yields for different weather conditions. The study was conducted at LTER KBS in Michigan, USA. Soybean yield was measured at 2.2 ha and 4.9 ha fields at 2 × 5 m resolution in 2010. Soil properties were measured at the plot scale in 19 locations, selected to represent two soil types and two management practices on 3 topographical elements (i.e. summit, slope and depression). The DSSAT-CSM was calibrated and validated on soybean yield data measured at the plot scale in 2010 and 2013. The validated model was used to generate yields for 22 years with varying weather conditions in all selected locations. Then the model parameters were scaled up using different techniques, such as averaging plot-scale measured soil properties, averaging the model parameters estimated for each plot using measured soil properties, and using typical soil profile descriptions and the SSURGO soil database. The results of this study showed high variability in soybean yield for two soils and two management practices, which was associated with variability in soil texture and organic carbon content in the top 20-cm soil layer, but not with surface topography. Despite considerable differences in parameters, all upscaling techniques performed reasonably well for different weather conditions However, model performance appeared to be site specific in this study. [ABSTRACT FROM AUTHOR]

It has been generally recognized that micro-scale heterogeneity in soil environments can have a substantial effect on many soil physical, chemical, and biological processes driving physical protection of soil carbon (C). However, only recently the development of tools for micro-scale soil analyses, including X-ray computed micro-tomography (μCT), enabled quantitative analyses of these effects. X-ray μCT application to soil science is arguably one of the newest and fastest growing areas of soil science research; and its methodology is still being actively developed. The large amount of spatially explicit data that μ-CT scanning generates coupled with specially designed experiments can open new avenues for improved understanding of soil functioning and soil-plant interactions. Pores are both drivers and products of a variety of soil processes that ultimately determine physical protection of organic matter in soil by influencing its accessibility to microorganisms. The μCT tools are well suited for providing information on characteristics of soil physical micro-environments, a.k.a. soil pores. Here we review the experimental approaches currently employed by research groups around the world in exploring the role of pore characteristics in soil C processes, with specific focus on soil C decomposition and protection at 5–1000 μm spatial scale. We discuss pore/C/microbe relationships with emphasis 1) on direct and indirect effects of pore characteristics on soil microorganisms and subsequent microbial effects on decomposition of organic inputs; 2) on presence of feed-back effects of microorganisms on soil pore architecture; and 3) on importance of pore characteristics for decomposition of freshly added organic inputs/plant residues. The pore-oriented perspective will contribute to better structuring of the research efforts in deciphering the mechanisms of soil C protection/sequestration by soils. [ABSTRACT FROM AUTHOR]

Physical protection of soil carbon (C) is one of the important components of C storage. However, its exact mechanisms are still not sufficiently lucid. The goal of this study was to explore the influence of soil structure, that is, soil pore spatial arrangements, with and without presence of plant residue on (i) decomposition of added plant residue, (ii) CO2 emission from soil, and (iii) structure of soil bacterial communities. The study consisted of several soil incubation experiments with samples of contrasting pore characteristics with/without plant residue, accompanied by X-ray micro-tomographic analyses of soil pores and by microbial community analysis of amplified 16S–18S rRNA genes via pyrosequencing. We observed that in the samples with substantial presence of air-filled well-connected large (>30 µm) pores, 75–80% of the added plant residue was decomposed, cumulative CO2 emission constituted 1,200 µm C g-1 soil, and movement of C from decomposing plant residue into adjacent soil was insignificant. In the samples with greater abundance of water-filled small pores, 60% of the added plant residue was decomposed, cumulative CO2 emission constituted 2,000 µm C g-1 soil, and the movement of residue C into adjacent soil was substantial. In the absence of plant residue the influence of pore characteristics on CO2 emission, that is on decomposition of the native soil organic C, was negligible. The microbial communities on the plant residue in the samples with large pores had more microbial groups known to be cellulose decomposers, that is, Bacteroidetes, Proteobacteria, Actinobacteria, and Firmicutes, while a number of oligotrophic Acidobacteria groups were more abundant on the plant residue from the samples with small pores. This study provides the first experimental evidence that characteristics of soil pores and their air/water flow status determine the phylogenetic composition of the local microbial community and directions and magnitudes of soil C decomposition processes. [ABSTRACT FROM AUTHOR]

• Prairie vegetation forms medium pores (50–150 µm Ø) across various soil textures. • Prairie vegetation increases MBC with a positive influence in soil C gains. • Increases in C losses via CO 2 and DOC contributed to slower soil C gains. • Medium pores and soil C interact in a feedback loop across various soil textures. Perennial vegetation with high plant diversity, e.g., restored prairie, is known for stimulation of soil carbon (C) gains, due in part to enhanced formation of pore structure beneficial for long-term C storage. However, the prevalence of this phenomenon across soils of different types remains poorly understood. The aim of the study was to assess the associations between pore structure, soil C, and their differences in monoculture switchgrass and polyculture restored prairie vegetation across a wide range of soils dominating the Upper Midwest of the USA. Six experimental sites were sampled, representing three soil types with texture ranging from sandy to silt loams. The two vegetation systems studied at each site were (i) monoculture switchgrass (Panicum virgatum L.), and (ii) polyculture restored prairie, also containing switchgrass as one of its species. X-ray computed micro-tomography (µCT) was employed to analyze soil pore structure. Structural equation modeling and multiple path analyses were used to assess direct and indirect effects of soil texture and pore characteristics on microbial biomass C (MBC), particulate organic matter (POM), dissolved organic C (DOC), short-term respiration (CO 2), and, ultimately, soil organic C (SOC). Across studied sites, prairie increased fractions of medium (50–150 µm Ø) pores by 11–45 %, SOC by 3–69 %, and MBC by 18–59 % (except for one site). The greater were the prairie-induced increases in the medium pore volumes, the greater were the prairie-induced SOC gains. Greater C losses via CO 2 and DOC contributed to slower C accumulation in the prairie soil. We surmise that the interactive feedback loop relating medium pores and soil C acts across a wide range of soil textures and is an important mechanism through which perennial vegetation with high plant diversity, such as restored prairie, promotes rapid SOC gains. [ABSTRACT FROM AUTHOR]