Soil probiotic bacterial strains have differential effects on tree genotypes and resident microbiome diversity

Background/Question/Methods

Bacillus species are ubiquitous bacteria in soils, sometimes forming beneficial mutualisms that promote plant growth. Inoculating soils with probiotic solutions containing Bacillus strains is a current strategy used agriculturally to improve plant yields. An improved genetic understanding of these plant-microbe interactions will increase our ability to predict plant yields and design more productive crops. A critical first step is to ascertain how different Bacillus strains interact with tree genotypes. We conducted a greenhouse experiment to examine how five Bacillus strain introductions establish and affect four Populus genotypes. Bacillus strains were introduced to soils planted with either Populus deltoides (genotype 11347 or 16842), a F1 hybrid cross between P. deltoides and P. trichocarpa (7300 or 8360D), or a no-plant control. We introduced five strains of three Bacillus species: B. velezensis (GB03 or FZB42), B. subtilis (3610 or RO-NN-1), or B. amyloliquefaciens (DSM7). Plant growth parameters – photosynthetic rate, number of leaves, stem height, SPAD greenness index, and above and belowground biomass – were measured over the 5-week study to quantify the effect of microbial invaders on plants. After five weeks, we destructively harvested soils and plants. We characterized bacterial and fungal communities, via amplicon sequencing, in soil, rhizosphere, leaves, and roots.

Results/Conclusions

Plants and resident microbiomes responded variably to the five introduced Bacillus strains. Populus genotypes varied in percent healthy leaves, and the variation depended on which Bacillus strain they were inoculated with (P = 0.003). P. deltoides genotypes had fewer healthy leaves and faster growth rates when inoculated with B. velezensis compared to control. B. subtilis strains increased healthy leaves in F1 hybrid 7300 and stem growth rates when inoculated with B. subtilis strains (P < 0.001). Stomatal conductance, a component of photosynthetic activity, varied with a significant interaction between tree genotype and Bacillus strain (P = 0.006). Resident bacterial/archaeal rhizosphere microbiomes marginally increased in alpha diversity with increasing percent of healthy leaves (P = 0.07) but was unrelated to plant or bacterial strain identity. Beta diversity in the rhizosphere varied with plant genotype and strain combinations, photosynthetic efficiency, and plant growth rates. Soil diversity had increasingly different composition over the 5-week study. After 5 weeks, soils inoculated with B. velezensis strains had different compositions than those inoculated with B. subtilis strains. Bacillus inoculations in soil differentially benefited Populus genotypes and shifted the resident soil and rhizosphere microbiomes. Pairing plant genotypes with specific strains of probiotic bacteria could improve plant productivity.