Soils are among the extremely complicated materials with intricate internal pore geometries. Soil's hierarchical structures control various physical, chemical and biological processes at different scales. At soil aggregate scale, configuration of pore space plays an important role in determining carbon (C) sequestration, water and gas flow as well as bacteria survival and transport. Understanding the complex interaction between soil aggregate structure and these processes will greatly help us appreciate critical processes at larger scale. However, due to technical limitations on accessing aggregate interiors, it remained relatively poorly understood until recent advances of X-ray computed microtomography (μCT) imaging in soils. Overall, the dissertation aims to effectively utilize soil aggregate μCT imaging, to understand soil aggregate structure difference under contrasting land use and managements, and to investigate bacteria redistribution and transport pattern and its relation to aggregate pore characteristics.Synchrotron μCT provides a noninvasive approach to record three dimension (3D) information on soil aggregates with resolution of one to several microns. Image segmentation is the first step in μCT image analysis, however, lack of ground-truth images poses great challenge to soil image segmentation. Proposed simulation method successfully generated soil aggregate grey scale images from pore/solid binary images, thus provided ground-truth information. Indicator Kriging method was found preferable to other methods in this study when the image histogram is clearly bimodal. Region non-uniformity measure performs sufficiently well as a segmentation criterion. The second technical difficulty involves 3D soil aggregate boundary delineation. Image closing technique is a promising tool for boundary detection, yet it requires selecting optimal neighborhood parameter (r) so that aggregate exteriors can be properly defined - inclusion of all surface pores while keeping the surface sufficiently irregular. Examining the plots of the total aggregate volume, aggregate boundary fractal dimension against r could serve as useful criteria for selecting the optimal r value. After addressing these image processing issues, soil aggregates from long term contrasting soil types and land use practices were compared. Soil aggregate samples were from LTER site at Kellogg Biological Station, USA and CERN site at Shenyang, China. The studied soil managements are conventional tillage (CT), native succession vegetation (NS), and bare soil with no vegetation (BS). Significantly greater percent of pores > 15 μm in LTER-CT aggregates was observed as compared to those of LTER-NS. LTER-NS aggregates had more large pores (> 90 μm) than LTER-CT aggregates, while more medium sized pores (45-90 μm) were found in LTER-CT aggregates. Pores were larger in the aggregate interiors than in the exterior layers; while intermediate pores (45-90 μm) were more abundant in the aggregate exterior layers. This trend was present in all land use and management treatments of the study and was most pronounced in LTER-NS. These results implied that a general mechanism maybe responsible for aggregates formation, but long term land use could alter the magnitude and intensity of involved soil processes.The last part of the dissertation addressed E.coli redistribution and transport in soil aggregates. The studied soil aggregates were from LTER site with conventional tillage (CT), native succession vegetation (NS), and no-till (NT). E.coli redistribution within soil aggregates display a significant different spatial distribution pattern under air-dry and saturated flow condition. When E.coli was first applied to an air-dry aggregate, its resulting spatial distribution was highly heterogeneous in aggregates of all management practices. After saturation, equilibration, and water extraction the E.coli redistributed within the aggregate primarily in vertical direction and became more homogeneously spread. Only relatively small percent of E.coli has completely left the aggregates. Redistribution was most pronounced in CT aggregates, followed by NT, and was almost negligible in NS aggregates. E.coli spatial distribution was related to intra-aggregate pore characteristics; however, because of high variability of the intra-aggregate pores the relationships were weak.
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