Microaggregates are hot spots of microbial activity at a scale that frequently poses a severe experimental challenge or defies a direct observation. Mathematical models that combine the mechanisms of spatially resolved organic matter transport with the processes of organic matter turnover can facilitate the understanding of soil microbial dynamics and the function of soils at these scales.

In this study, we investigate microbial population dynamics and the turnover of particulate organic matter (POM) in soil microaggregates. CT images of microaggregates obtained from samples of natural soils serve as basis for selecting the simulation domain. For different levels of water saturation, the fluid (liquid and gas) distribution within the pore space is calculated according to a morphological model. We consider bacteria and POM, which are heterogeneously distributed within the liquid phase. Dissolved organic carbon (DOC) is released by hydrolyzing POM, assuming a reaction following first-order kinetics. DOC spreads by diffusion and can subsequently be consumed by bacteria and turned into CO₂. The growth of bacteria is realized by a cellular automaton framework (CAM) and based on Michaelis–Menten kinetics due to the uptake of DOC.

Our simulations show that the heterogeneous distribution of substrate and bacteria results in an overall biodegradation kinetics and CO₂ output that strongly depends on the microaggregate scale (<250μm). Only very specific cases can be distinguished globally, e.g., when the substrates are isolated from bacteria due to a disconnected liquid phase. Locally, however, heterogeneities in substrate distribution impact the development of bacteria populations, e.g., a smaller geodesic distance of bacteria to the substrate promotes bacterial growth locally.

微团聚体是微生物活动的热点，其规模经常构成严重的实验挑战或无法直接观察。将空间分辨有机质传输机制与有机质周转过程相结合的数学模型可以促进对土壤微生物动力学和土壤在这些尺度上的功能的理解。

在这项研究中，我们调查了土壤微团聚体中微生物种群动态和颗粒有机物 (POM) 的周转。从天然土壤样本中获得的微团聚体 CT 图像可作为选择模拟域的基础。对于不同的含水饱和度，根据形态模型计算孔隙空间内的流体（液体和气体）分布。我们考虑细菌和 POM，它们在液相中不均匀分布。假定反应遵循一级动力学，通过水解 POM 释放溶解的有机碳 (DOC)。DOC 通过扩散传播，随后可被细菌消耗并转化为 CO ₂. 由于 DOC 的摄取，细菌的生长是通过细胞自动机框架 (CAM) 实现的，并基于 Michaelis-Menten 动力学。

我们的模拟表明，底物和细菌的异质分布导致整体生物降解动力学和 CO ₂输出强烈依赖于微团聚体尺度 (<250μm)。只有非常特殊的情况才能全局区分，例如，当底物由于液相不连贯而与细菌分离时。然而，在局部，底物分布的异质性影响细菌种群的发育，例如，细菌到底物的较小测地距离促进局部细菌生长。