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Challenges with in situvisualization of nonparticulate organics in porous materials limit understanding and modeling processes of transport, decomposition, and storage of organic compounds. In particular, it impedes deciphering the mechanisms driving accumulation and protection of soil organic matter (SOM), processes crucial for sustaining soil fertility and mitigating effects of global climate change. A recently proposed method of staining soil organics by OsO4vapors with subsequent dual-energy X-ray computed microtomography scanning (μCT) offers new opportunities to visualize SOM within intact soil matrix. Our objective was to test the method’s performance in staining different organic materials located in media with contrasting pore characteristics: (1) roots of switchgrass (Panicum virgatumL.), either placed within fine and coarse sands or grown within soil microcores, (2) biochar fragments, and (3) soils with relatively low and high C contents. We found that the method was effective in staining organic materials of root origin and the organics associated with fine soil particles, but not the biochar. The estimated percent of total C that reacted with OsO4vapors ranged from 0.7% in plant roots to 3.2% in sand-free fraction of the high C soil and was only 0.2% in the studied biochar. Total soil C and Os concentrations were strongly linearly related, suggesting a potential for future method development. However, we would recommend caution when interpreting the results in cases when gas diffusion through the soil matrix is limited.

It is known that variability in the characteristics of soil physical microenvironments, e.g., locations and characteristics of soil pores, can have a major influence on microorganisms. This study compared the characteristics of intra‐aggregate pores and their relationships with bacterial community composition in 4‐ to 6‐mm soil macroaggregates from two contrasting agricultural systems, namely a corn (Zea maysL.)–soybean [Glycine max(L.) Merr.]–wheat (Triticum aestivumL.) rotation (i) with conventional chemical inputs and (ii) without chemical inputs but with legume cover crops. Characteristics of intra‐aggregate pores and particulate organic matter (POM) were obtained from three‐dimensional X‐ray computed microtomography aggregate images at 13‐μm resolution. Microbial community analyses were conducted using 16S rRNA pyrosequencing. We found that the aggregates from long‐term (>20 yr) organic management with cover crops differed from the aggregates from conventional management in terms of intra‐aggregate pore‐size distribution, intra‐aggregate pore variability, POM contents, as well as microbial community compositions. Relative abundances of Actinobacteria, Proteobacteria, and Firmicutes in the aggregates from cover‐crop‐based management were positively correlated with the presence of large (>110 μm) pores, while the presence of medium‐sized pores (32–84 μm) was significantly correlated with 30 to 40% of the top 100 bacterial operational taxonomic units identified during sequencing. The results suggested that the legacy of rhizosphere presence in terms of intra‐aggregate pore structure and microbial community composition can last in the studied soil for at least 4 to 9 mo. Our study demonstrated that working with bulk sieved soil samples can mask substantial differences present within distinct soil aggregate units.

Manganese (Mn) is known to be an active contributor to processing and cycling of soil organic carbon (C), yet the exact mechanisms behind its interactions with C are poorly understood. Plant diversity in terrestrial ecosystems drives feedback links between plant C inputs and soil pores, where the latter, in turn, impact the redox environment and Mn. This study examined associations between soil pores (>36 μm Ø) and Mn within intact soils from two grassland ecosystems, after their >6-year implementation in a replicated field experiment. We used μ-XRF imaging and XANES spectroscopy to explore spatial distribution patterns of Mn oxidation states, combined with X-ray computed microtomography and 2D zymography. A high plant diversity system (restored prairie) increased soil C and modified spatial distribution patterns of soil pores as compared to a single species system (monoculture switchgrass). In switchgrass, the abundance of oxidized and reduced Mn oxidation states varied with distance from pores consistently with anticipated O2diffusion, while in the soil from restored prairie, the spatial patterns suggested that biological activity played a greater role in influencing Mn distributions. Based on the findings, we propose a hypothesis that Mn transformations promote C gains in soils of high plant diversity grasslands.

Soil water flow models are based on simplified assumptions about the mechanisms, processes, and parameters of water retention and flow. That causes errors in soil water flow model predictions. Data assimilation (DA) with the ensemble Kalman filter (EnKF) corrects modeling results based on measured state variables, information on uncertainty in measurement results and uncertainty in modeling results. The objectives of this work were (i) to evaluate pedotransfer functions (PTFs) as a source of data to generate an ensemble of Richards′ equation‐based models for the EnKF application to the assimilation of soil water content data and (ii) to research how effective assimilation of soil moisture sensor data can be in correcting simulated soil water content profiles in field soil. Data from a field experiment were used in which 60 two‐rod time domain reflectometry (TDR) probes were installed in a loamy soil at five depths to monitor the soil water content. The ensemble of models was developed with six PTFs for water retention and four PTFs for the saturated hydraulic conductivity (Ksat). Measurements at all five depths and at one or two depths were assimilated. Accounting for the temporal stability of water contents substantially decreased the estimated noise in data. Applicability of the Richards′ equation was confirmed by the satisfactory calibration results. In absence of calibration and data assimilation, simulations developed a strong bias caused by the overestimation of Ksatfrom PTFs. Assimilating measurements from a single depth of 15 cm or of 35 cm provided substantial improvements at all other observation depths. An increase in data assimilation frequency improved model performance between the assimilation times. Overall, bringing together developments in pedotransfer functions, temporal stability of soil water patterns, and soil water content sensors can create a new source of data to improve modeling results in soil hydrology and related fields.

The effects of large macropores, cracks, and other large heterogeneities within the capacitance sensor sensitivity volume are of concern in application of these sensors. The objective of this work was to evaluate the sensitivity of the Enviroscan sensors to the presence of macropores. The artificial macropores were manufactured from polystyrene tubes and placed in contact with the access tube and at distances of 1.5 cm and 2.5 cm in air, water, and wetted sand. Measurements were obtained during sequential filling with water eight macropores at the same distance from the access tube. The dependencies of the raw frequencies on the number of filled macropores were linear with r2> 0.98. The macropore sensitivity, defined as the decrease in frequency per one filled macropore, deceased exponentially with the distance from the access tube. For a given distance from the access tube, the macropore sensitivity depended linearly on the scaled frequency. The effect of the water-filled macropores on the bulk soil water content estimate decreased with the increase in soil water content. The estimated errors of measurement were approximately 0.002 cm3cm−3(0.001 cm3cm−3) per 1% of soil volume near the access tube occupied by the macropore for the water content of bulk soil of 0.10 cm3cm−3(0.30 cm3cm−3) and were about three times smaller at the 1.5 cm distance from the access tube. Overall, macropores near the access tube had only moderate effect on the soil water content measurements with capacitance sensors when they occupied less than 13% of soil volume near the access tube.

Manure-borne microorganisms and organic particles can move in soils in large interconnected pores or in long macropores. These pathways in structured soils are located between soil aggregates or peds. Therefore, interaction with soil aggregates may substantially affect the ability of macropores to serve as bacterial conduits.