Deciphering the Rhizosphere Microbiome for Disease-Suppressive Bacteria

Abstract

Disease-suppressive soils are exceptional ecosystems in which crop plants suffer less from specific soil-borne pathogens than expected owing to the activities of other soil microorganisms. For most disease-suppressive soils, the microbes and mechanisms involved in pathogen control are unknown. By coupling PhyloChip-based metagenomics of the rhizosphere microbiome with culture-dependent functional analyses, we identified key bacterial taxa and genes involved in suppression of a fungal root pathogen. More than 33,000 bacterial and archaeal species were detected, with Proteobacteria, Firmicutes, and Actinobacteria consistently associated with disease suppression. Members of the γ-Proteobacteria were shown to have disease-suppressive activity governed by nonribosomal peptide synthetases. Our data indicate that upon attack by a fungal root pathogen, plants can exploit microbial consortia from soil for protection against infections.

Dynamics of the bacterial community structure in the rhizosphere of a maize cultivar

“…Our results confirmed that these organisms predominate in the rhizosphere, presumably because labile organic substrates are more available than in bulk soil. In addition, Burkholderiaceae, Xanthomonadales and Actinobacteria harbor genera and species with anti-microbial activities (Mendes et al, 2011), which may enable them to operate as interference competitors in the rhizosphere.…”

“…The unique ecological niche shapes the structure of rhizosphere bacterial community through the interactions of plant species, the chemical nature of root exudates, soil properties, and many other factors (Savka and Farrand, 1997). While some detrimental microbes undermine plant health, mutualistic rhizosphere microbes provide plants with mineral nutrients, phytohormones, and protect the plant against phytopathogens (Mendes et al, 2011;Singh et al, 2004;Vercellino and Gómez, 2013). Thus, to understand the suite of bacterial interactions that may occur over the lifetime of a plant, it is important to know the rhizosphere bacterial community and its variation over plant growth stages.…”

Assembly of seed-associated microbial communities within and across successive plant generations

“…The plant microbiota can influence multiple plant traits such as biomass accumulation (Sugiyama et al 2013), metabolite production , drought tolerance (Lau and Lennon 2012;Rolli et al 2015), flowering time (Wagner et al 2014;PankeBuisse et al 2015;Dombrowski et al 2017) and disease resistance (Busby et al 2016;Ritpitakphong et al 2016;Mendes et al 2011;Santhanam et al 2015).…”

Synergistic and antagonistic effects of mixing monospecific soils on plant-soil feedbacks

“…First, the mixed inocula consisted of 50% of both monospecific soils, and as such only consisted of 50% of the density of soil microorganisms of both monospecific soils. Previous studies found that a reduction in volume of a soil inoculum reduces the effect of the inoculum on the plant (St-Denis et al 2017;Mendes et al 2011;Hol Fig. 2 Relationship between the difference among two monospecific inocula on plant biomass (a) and yellowness (b), and the difference between the observed and predicted effects when mixing these two inocula.…”