Predictable communities of soil bacteria in relation to nutrient concentration and successional stage, in a laboratory culture experiment.

Abstract

The best hope of understanding the processes that govern soil bacterial communities is to represent them as simpler microcosms, which may give hints to the ecology of natural systems. We set up a microcosm culturing experiment with soil bacteria, at a range of nutrient concentrations, and compared these over time. DNA from each replicate was analyzed using HiSeq2000 Illumina sequencing of the 16S rRNA gene. We found that each nutrient treatment, and each time point during the experiment, produces characteristic bacterial communities that occur predictably between replicates. It is clear that within the context of this experiment, many soil bacteria have distinct niches from one another, in terms of both nutrient concentration, and successional time point since a resource first became available. This fine niche differentiation may in part help to explain the coexistence of a diversity of bacteria in soils. In this experiment, we show that the unimodal relationship between nutrient concentration/time and species diversity often reported in communities of larger organisms, is also evident in microbial communities.