Subsurface structures and especially the interactions between pores, roots and other organic matter elements have a strong impact on ecosystem functioning. Yet despite recent progress in the application of X-ray Computed Microtomography (µCT) to soil structure in agricultural science, applications to the more complex and heterogeneous substrates found in natural soils, specifically wetland soils, remain sparse. We apply X-ray µCT to a complex heterogenous soil and develop a robust segmentation method to quantify the pores, live roots and necromass. This approach significantly improves the detection of the organic matter elements, and gives us unprecedented detail and resolution in the segmentation of pores, live roots and necromass at a high spatial resolution (62.5 µm in this study). We identify several situations where pores and organic matter interact in the soil, including the disconnected air spaces (aerenchyma) that run within the Spartina stem and roots, tubular-shaped pores left behind by decaying roots, and lateral roots deploying within structural fragilities in the sediment. The capacity of X-ray µCT to distinguish the connected live root system from the necromass opens possibilities for applications to determine key wetland soil functions such as soil cohesivity, soil nutrient exchanges and soil carbon dynamics.

地下结构，尤其是孔隙，根与其他有机质元素之间的相互作用，对生态系统的功能有很大的影响。尽管最近在农业科学中将X射线计算机断层摄影（µCT）应用于土壤结构方面取得了进展，但在自然土壤（尤其是湿地土壤）中发现的更复杂和非均质的基质上的应用仍然很少。我们将X射线µCT应用于复杂的异质土壤，并开发了一种鲁棒的分割方法来量化毛孔，活根和坏死瘤。这种方法显着改善了对有机物元素的检测，并以高空间分辨率（本研究中为62.5 µm）为我们提供了前所未有的细节和分辨率，可用于孔，活根和坏死的分割。Spartina茎和根，腐烂的根留下的管状孔以及在沉积物中结构脆弱的侧根。X射线µCT能够区分相连的活根系统和坏死生物，为确定关键的湿地土壤功能（如土壤粘性，土壤养分交换和土壤碳动态）提供了可能。