Spatial Ecology of Bacteria at the Microscale in Soil

Despite an exceptional number of bacterial cells and species in soils, bacterial diversity seems to have little effect on soil processes, such as respiration or nitrification, that can be affected by interactions between bacterial cells. The aim of this study is to understand how bacterial cells are distributed in soil to better understand the scaling between cell-to-cell interactions and what can be measured in a few milligrams, or more, of soil. Based on the analysis of 744 images of observed bacterial distributions in soil thin sections taken at different depths, we found that the inter-cell distance was, on average 12.46 µm and that these inter-cell distances were shorter near the soil surface (10.38 µm) than at depth (>18 µm), due to changes in cell densities. These images were also used to develop a spatial statistical model, based on Log Gaussian Cox Processes, to analyse the 2D distribution of cells and construct realistic 3D bacterial distributions. Our analyses suggest that despite the very high number of cells and species in soil, bacteria only interact with a few other individuals. For example, at bacterial densities commonly found in bulk soil (108 cells g−1 soil), the number of neighbours a single bacterium has within an interaction distance of ca. 20 µm is relatively limited (120 cells on average). Making conservative assumptions about the distribution of species, we show that such neighbourhoods contain less than 100 species. This value did not change appreciably as a function of the overall diversity in soil, suggesting that the diversity of soil bacterial communities may be species-saturated. All in all, this work provides precise data on bacterial distributions, a novel way to model them at the micrometer scale as well as some new insights on the degree of interactions between individual bacterial cells in soils.

尽管土壤中细菌细胞数量与物种多样性均极为可观，但细菌多样性似乎对受细菌细胞间相互作用影响的土壤过程（如呼吸作用、硝化作用等）影响甚微。本研究旨在阐明细菌细胞在土壤中的分布模式，以更好地理解细胞间相互作用与数毫克乃至更多土壤样品中可观测到的过程之间的尺度关联。本研究基于对744张不同深度土壤薄切片中细菌分布观测图像的分析，发现细菌细胞间的平均间距为12.46 μm；受细胞密度变化影响，土壤表层附近的细胞间距（10.38 μm）显著小于深层土壤（>18 μm）。此外，我们利用这些图像构建了基于对数高斯Cox过程（Log Gaussian Cox Processes）的空间统计模型，用于分析细菌细胞的二维分布并重建具有生态学真实性的三维细菌分布格局。研究结果显示，尽管土壤中细菌细胞与物种数量极多，但单个细菌仅能与少量其他个体发生相互作用。例如，在原状土壤中常见的细菌密度（10^8 细胞·g^-1 土壤）下，单个细菌在约20 μm的相互作用距离内的邻体数量相对有限（平均约120个）。在保守假设物种分布格局的前提下，我们发现此类邻体群落包含的物种数不足100种；且该数值并未随土壤整体多样性水平发生显著变化，这暗示土壤细菌群落的多样性可能处于物种饱和状态。综上，本研究提供了关于土壤细菌分布的精准实测数据，提出了一种全新的微米级细菌分布建模方法，并为土壤中单个细菌细胞间的相互作用程度提供了新的认知视角。