Spatial ecology of bacteria at the microscale in soil

PLoS One. 2014 Jan 28;9(1):e87217. doi: 10.1371/journal.pone.0087217. eCollection 2014.


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 (10(8) 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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Biodiversity
  • Microbial Interactions*
  • Models, Biological*
  • Nitrification
  • Soil Microbiology*

Grant support

This research was supported by the INSU EC2CO Microbiologie Environnementale and ANR Syscomm Programme MEPSOM. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.