To date, the majority of rhizobiome studies focused on model or crop plants grown in microcosms or monospecific culture. We aim to determine the influence of plant species, soil conditions, and root exudate composition on the assembly of rhizosphere bacterial communities in natural temperate grasslands under different edaphic and climatic conditions, and along a land use gradient. We hypothesize that the composition of root exudates has a discernible effect on the assembly of the active rhizosphere bacterial communities in temperate grasslands and that this effect is modulated by different physicochemical conditions in soils.
The specificity, patterns, and dynamics of bacterial colonization of soil minerals have rarely been assessed under natural conditions. We therefore buried a fresh mineral mixture, which was loaded with carbon substrates of varying recalcitrance, for up to two years in the natural setting of central European grassland soils with either high or low land use intensity. We hypothesize that the microbial communities establishing on the minerals would differ substantially from the surrounding soils and that both the type of carbon source and land use intensity affect bacterial colonization pattern. Furthermore, we postulate that individual bacteria follow different trajectories during mineral colonization with copiotrophic bacteria having an initial advantage.
Systematic studies to explore culturability of bacteria are rare. We use a multifactorial approach of different conditions of (i) sites in the Baltic Sea and Atlantic Ocean encompassing a salinity gradient, (ii) habitat type such as water column and sediment, (iii) incubation media composition, (iv) liquid or solid incubation medium, and (v) dilution gradients. As a factor of these variables, we will analyse culturability by enrichment cultures and the efficiency of subsequently obtaining pure isolates from initially successful enrichments. By analysing hundreds of isolates, we will determine the completeness of coverage of culturable isolates. Further, by comparison to the uncultured diversity (16S amplicon sequencing), we will address whether the cultured fraction is a dominant, rare or specific part of the natural microbial community. We additionally aim to disentangle cultivation variables, which increase phylogenetic novelty of isolates.