Abstract
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.
Highlights
The application of novel molecular techniques during the past two decades has uncovered a phenomenal bacterial diversity in soils
Compared to the vast amount of studies focusing on microbial diversity in soils, relatively little attention has been paid to spatial aspects of ecology in microbial systems at the scales at which cell-to-cell interactions occur there have been some attempts to characterize the spatial distribution of diversity and microbial processes at the scale of aggregates [20,21,22]
As we found that the Log Gaussian Cox Process (LGCP) model was adequate for modelling bacterial cell distributions in 2D, a similar modelling approach, based on LGCP, was used to estimate the number of neighbours a single bacterial cell had within a given distance in 3 dimensions
Summary
The application of novel molecular techniques (such as high throughput sequencing) during the past two decades has uncovered a phenomenal bacterial diversity in soils. Several studies have identified major environmental influences on soil bacterial diversity (such as soil pH [3], nitrogen [4], plant communities [5] or land use [6]) and soil bacterial biomass (soil organic carbon [7]), that vary between geographical regions and across biomes It is intriguing that experiments manipulating microbial diversity have found no or only weak links between diversity and many important microbial-driven processes, such as soil carbon mineralization [8,9,10], nitrite oxidation [8,9] or denitrification [8,9]. As microbial-driven ecosystem processes are sums of the activities of microbial cells, most of which are subject to cell-to-cell interactions, such interactions are likely to have significant effects on overall processes
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