Bacterial community establishment in native and non-native soils and the effect of fungal colonization

Abstract

Bacterial communities are essential parts of living soils. However, we understand very little of how soil matrices govern the structure of the local microbiota. Here, we report on experiments that address such assembly rules for microbial communities in soil. Thus, indigenous soil bacterial communities were extracted from eight different soils (denoted V, B, G, WD, L, K, S and WG) and used to inoculate four selected presterilized sandy soils (V, B, G and WD) in microcosms. Then, these microcosms were subjected to colonization by the soil saprotrophic fungus Lyophyllum sp. strain Karsten, or were left uncolonized. Fifteen days following introduction, the microcosms were analyzed to enumerate culturable (dilution plating) and total bacteria (quantitative PCR) and bacterial community structures (PCR-DGGE), to assess the abundance and diversity of the bacterial communities. Moreover, fungal-selected culturable bacteria were identified. In all cases and irrespective of the presence of fungal mycelium, bacterial communities of around 1–5 x 10 8 CFU or 16S rRNA gene copies per g dry soil established. The data further clearly showed the influence of local soil conditions on the establishment of the inoculant bacteria in their native versus non-native soil. Thus, cluster analysis of the PCR-DGGE fingerprints revealed that two soils, i.e., V and B, were strong drivers of the established community structures from the eight source communities, whereas the two remaining soils (G and WD) revealed mixed effects. PCR-DGGE further revealed that the non-native bacterial communities obtained from sandy source soils were more similar to the established native communities than those from clayey soils. Overall, the bacterial communities showed decreased diversities and richness values in the fungal-colonized systems as compared to the non-fungal-affected ones (inoculation and migration sites). In the fungal-affected systems, the recipient soil matrix was of importance, in particular at the inoculation site of the V and B soil matrices and at the migration front of the G matrix. Analysis of the culturable bacterial community across different soils revealed that similar bacteria, even originating from different sources, were enriched by the colonizing fungus. Particular bacterial types, like Burkholderia and Pseudomonas spp., were found to be selected by the growing fungal hyphae. Further more, an enrichment of type three secretion systems (TTSS) was detected.