Field study reveals core plant microbiota and relative importance of their drivers

Abstract

Summary Harnessing plant microbiota can assist in sustainably increasing primary productivity to meet growing global demands for food and biofuel. However, development of rational microbiome‐based approaches for improving crop yield and productivity is currently hindered by a lack of understanding of the major biotic and abiotic factors shaping the crop microbiome under relevant field conditions. We examined bacterial and fungal communities associated with both aerial (leaves, stalks) and belowground (roots, soil) compartments of four commercial sugarcane varieties (Saccharum spp.) grown in several growing regions in Australia. We identified drivers of the sugarcane microbiome under field conditions and evaluated whether the plants shared a core microbiome. Sugarcane‐associated microbial assemblages were primarily determined by plant compartment, followed by growing region, crop age, variety and Yellow Canopy Syndrome (YCS). We detected a core set of microbiota and identified members of the core microbiome that were influenced by YCS incidence. Our study revealed key hub microorganisms in the core microbiome networks of sugarcane leaves, stalks, roots and rhizosphere soil despite location and time‐associated shifts in the community assemblages. Elucidating their functional roles and identification of the keystone core microbiota that sustain plant health could provide a technological breakthrough for a sustainable increase in crop productivity.

Assembly and seasonality of core phyllosphere microbiota on perennial biofuel crops

“…Here, among those that variables were significant, crop (switchgrass or miscanthus) had the lowest explanatory value ( Table 1 ). However, our work agrees with previous research that has shown a relationship between plant species/genotype and the leaf microbiota of perennial plants such as wild mustard 55 , sugar cane 37 , and tree species like birch, maple, and pine 56 . Time and measured abiotic factors had highest explanatory value ( Table 1 , Table S3 ).…”

“…Our data suggest a compensatory relationship between members within the Proteobacteria, where members of Gammaproteobacteria and Alphaproteobacteria replace one another over time ( Figure 5A ). Such community transitions have been observed on the phyllosphere of crops such as sugarcane 37 , common beans, soybeans, and canola 38 . A study of endophytic bacteria of prairie grasses, including switchgrass, showed the same trend in abundance of Gamma - and Alphaproteobacteria 52 suggesting that these phyllosphere taxa are facultative endophytes or are similarly affected by the plant development.…”

Influence of plant genotype and soil on the wheat rhizosphere microbiome: Evidences for a core microbiome across eight African and European soils

“…These results are consistent with large-scale microbiome studies that identified the core microbiome of different plants like Arabidopsis thaliana [16] or sugarcane [23] and a global soil microbiome study that highlighted that only 500 OTUs account for half of soil microbial communities worldwide [24].…”

Impact of plant genotype and plant habitat in shaping bacterial pathobiome: a comparative study in olive tree

“…Thus, the olive cultivar seems to influence the establishment of pathobiome communities in olive knots. Accordingly, previous studies have suggested that differences on microbial abundance and diversity between asymptomatic and symptomatic tissues were possibly related to the susceptibility of the plant host to a certain disease 16,[18][19][20][21] . We hypothesized that the detected greater differences in the bacterial composition of OK-susceptible cv.…”