Shifts in bacterial community structure associated with inputs of root exudate compounds to soil

Background/Question/Methods

Plant rhizodeposition of simple carbon substrates is a major driver of microbial activity and diversity in the rhizosphere.  However, it is not well understood if individual compounds found in root exudates influence microbial community structure regardless of soil type.  To determine if some microbial taxa may preferentially metabolize specific root exudates, we added three simple carbon substrates (glucose, glycine, and citric acid) to microcosms containing three distinct soils from a grassland, hardwood forest, and coniferous forest.  Microcosms were incubated at 27°C for 24 hours while monitoring CO₂ production.  Microbial community composition was assessed via 454-pyrosequencing of the 16s rRNA gene using bar-coded primers. 

Results/Conclusions

Although carbon additions significantly increased CO₂ production in all soils, there was no relationship between the magnitude of the increase in CO₂ production and the magnitude of the apparent shift in community composition.  While the glycine additions had little effect on overall community structures, the addition of glucose had a small significant effect in the coniferous forest soil. The addition of citric acid caused a large, significant shift in community structure relative to the control communities in all soils.  The community shifts in response to citric acid were driven by β-Proteobacteria, specifically Burkholderiales, in all three soils and by γ-Proteobacteria, specifically Pseudomonadaceae, in the coniferous forest soil.  These results suggest that some simple carbon substrates influence soil microbial community structure more so than others and that we can see the same taxonomic groups respond to a substrate across soil types at a coarse level of phylogenetic resolution.  These patterns were confirmed in a meta-analysis of previously published studies of rhizosphere and bulk soil bacterial communities.