Root exudate compounds change the bacterial community in bulk soil

Abstract

The soil bacteria are diverse in nature both physiologically and phylogenetically with spatial variations within the soil microenvironments. Plant roots secrete organic substances called root exudates which benefit bacteria able to incorporate these. Subsequently, as the root grows, it changes the organic carbon status of adjacent bulk soil, stimulating growth of some of the resident bacteria. This growth induces a shift in the soil bacterial community and causes modifications in its metabolic activities. This nutrient infusion could also activate resting structures such as endospores to grow. We asked how the bulk soil microbial community responds when encountering root exudates and hypothesized that bacteria able to grow rapidly would become predominant upon introduction of root exudates. We added synthetic root exudate cocktail (Dietz et al., 2020) to the bulk soil from a wheat field on day 0 and day 1. We determined the aerobic culturable count on R2A, and Bacillus cereus sensu lato on Mannitol Egg Yolk Polymyxin agar, and bacterial community composition by sequencing the V3–V4 regions of the 16S rRNA genes on days 0, 1, 2, 3, 4, 6, 8, 10, 12 and 14 of incubation. Alpha diversity (Shannon) decreased and recovered partially, indicating a shift in species evenness while the Chao1 index remained the same, indicating constant species richness. Beta diversity shifted substantially over time. Rare fast-growing genera like Paenarthrobacter and Pseudarthrobacter increased upon REC addition, while slow growing genera like Bradyrhizobium were constant over time. Some key genera like Stenotrophobacter responded only after ceasing of REC addition. Certain fast-growing genera like Bacillus did not increase in population density. Collectively, these results indicate that the bulk soil community shifted significantly when exposed to REC, and after termination of REC, continued to undergo shifts. This presents the root environment with diverse bacteria known to benefit growth, such as Paenarthrobacter and rhizobia.