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.

Summary1. Nitrification plays a key role in the functioning of many natural ecosystems. It is directly involved in plant nitrogen nutrition and soil N losses through leaching and denitrification. The control of this process by plants is poorly understood, although modifications of nitrification would allow plants to manipulate competition for N and induce changes in ecosystem N balance. In a wet tropical savanna ecosystem (Lamto, Côte d'Ivoire), the soil N cycle is characterized by distinct high-and low-nitrification sites. Previous publications showed that nitrification was positively or negatively correlated with root densities of the dominant grass covering these sites. These contrasting sites were chosen to investigate the extent to which vegetation controls longterm nitrification. 2. In situ experimental plots were created where grass individuals originating from high-or low-nitrifying soils were transplanted into both soils. Nitrifying enzyme activity (NEA) was measured up to 24 months after transplanting. Grasses from both sites significantly modified NEA up to rates similar to those at their respective control sites. 3. The level of individual plant control (inhibition and stimulation) was correlated with grass biomass. The potential mechanisms of this control is discussed, along with its consequences for ecosystem N cycling (such as N losses), as the denitrifying enzyme activity (DEA) is much higher in the high-nitrification site. Such results suggest that plant species can have important consequences for N cycling at the population level.

Although nitrogen (N) availability is a major determinant of ecosystem properties, little is known about the ecological importance of plants' preference for ammonium versus nitrate (b) for ecosystem functioning and the structure of communities. We modeled this preference for two contrasting ecosystems and showed that b significantly affects ecosystem properties such as biomass, productivity, and N losses. A particular intermediate value of b maximizes the primary productivity and minimizes mineral N losses. In addition, contrasting b values between two plant types allow their coexistence, and the ability of one type to control nitrification modifies the patterns of coexistence with the other. We also show that species replacement dynamics do not lead to the minimization of the total mineral N pool nor the maximization of plant productivity, and consequently do not respect Tilman's R* rule. Our results strongly suggest in the two contrasted ecosystems that b has important consequences for ecosystem functioning and plant community structure.