Endophytes and Epiphytes From the Grapevine Leaf Microbiome as Potential Biocontrol Agents Against Phytopathogens

Abstract

Plants harbor diverse microbial communities that colonize both below-ground and above-ground organs. Some bacterial members of these rhizosphere and phyllosphere microbial communities have been shown to contribute to plant defenses against pathogens. In this study, we characterize the pathogen-inhibiting potential of 78 bacterial isolates retrieved from endophytic and epiphytic communities living in the leaves of three grapevine cultivars. We selected two economically relevant pathogens, the fungus Botrytis cinerea causing gray mold and the oomycete Phytophthora infestans, which we used as a surrogate for Plasmopara viticola causing downy mildew. Our results showed that epiphytic isolates were phylogenetically more diverse than endophytic isolates, the latter mostly consisting of Bacillus and Staphylococcus strains, but that mycelial inhibition of both pathogens through bacterial diffusible metabolites was more widespread among endophytes than among epiphytes. Six closely related Bacillus strains induced strong inhibition (>60%) of Botrytis cinerea mycelial growth. Among these, five led to significant perturbation in spore germination, ranging from full inhibition to reduction in germination rate and germ tube length. Different types of spore developmental anomalies were observed for different strains, suggesting multiple active compounds with different modes of action on this pathogen. Compared with B. cinerea, the oomycete P. infestans was inhibited in its mycelial growth by a higher number and more diverse group of isolates, including many Bacillus but also Variovorax, Pantoea, Staphylococcus, Herbaspirillum, or Sphingomonas strains. Beyond mycelial growth, both zoospore and sporangia germination were strongly perturbed upon exposure to cells or cell-free filtrates of selected isolates. Moreover, three strains (all epiphytes) inhibited the pathogen’s growth via the emission of volatile compounds. The comparison of the volatile profiles of two of these active strains with those of two phylogenetically closely related, inactive strains led to the identification of molecules possibly involved in the observed volatile-mediated pathogen growth inhibition, including trimethylpyrazine, dihydrochalcone, and L-dihydroxanthurenic acid. This work demonstrates that grapevine leaves are a rich source of bacterial antagonists with strong inhibition potential against two pathogens of high economical relevance. It further suggests that combining diffusible metabolite-secreting endophytes with volatile-emitting epiphytes might be a promising multi-layer strategy for biological control of above-ground pathogens.

Seed Biopriming with Microbial Inoculant Triggers Local and Systemic Defense Responses against Rhizoctonia solani Causing Banded Leaf and Sheath Blight in Maize (Zea mays L.)

“…This could further augment the disease protection against BLSB. Bruisson et al [27] reported that "in general, plants are colonized by a variety of microorganisms, some of which (the epiphytes) stay on the surface of plant organs, while others can penetrate further inside the plants and are called endophytes" [27][28][29]. A recent study on the structure and function of the plant microbiome have focused on the host-mediated recruitment and shaping of their rhizosphere microbiome [42].…”

“…Now, the focus has been set on developing microbe-based strategies for the management of devastating pathogens along with resistant cultivars [1,2,[22][23][24][25]. Application of antagonistic endophytic microorganisms is another important aspect of crop protection [26][27][28][29]. The endophyte induces beneficial effects in the plants via a number of complex biochemical signaling processes [27][28][29].…”

“…Application of antagonistic endophytic microorganisms is another important aspect of crop protection [26][27][28][29]. The endophyte induces beneficial effects in the plants via a number of complex biochemical signaling processes [27][28][29]. In general, the mechanisms employed by endophytes include the production of plant growth regulators, such as auxins, cytokinins, abscisic acid, and gibberellins, as well as secretion of effector molecules and secondary metabolites through modulation of various pathways/cascades [30][31][32][33].…”

Iturin A Extracted From Bacillus subtilis WL-2 Affects Phytophthora infestans via Cell Structure Disruption, Oxidative Stress, and Energy Supply Dysfunction

“…In addition, P. infestans mycelium inhibited by Iturin A (different concentrations) at 20 • C for twelve days was collected with ice-cold sterile water and oscillated to obtain sporangia solution (1 × 10 7 CFU/mL) (Bruisson et al, 2019;Wang et al, 2020). Then, the inhibited sporangia were recovered to release zoospores at 4 • C for 3 h and maintained at 25 • C in the dark for 5 h to complete sporangium direct germination (Hunziker et al, 2015;Bruisson et al, 2019). Also, the sporangia solution (1 × 10 7 CFU/mL) from the mycelium incubated without Iturin A was treated similarly as the control.…”

The Rhizosphere Microbiome of Mikania micrantha Provides Insight Into Adaptation and Invasion

“…Many species belonging to Enterobacter and Pseudomonas ( Meena et al, 2017 ; Zheng et al, 2019 ) are well known plant-beneficial microbes, and Cupriavidus and Phenylobacterium species were reported to participate in the mineralization of soil organic P and degrade organic material ( De La Cruz-Barrón et al, 2017 ). In comparison, P. chinense rhizosphere was enriched with Variovorax , Bosea , and Acinetobacter , and some species of which could inhibit pathogens and supply N for plant growth ( Rilling et al, 2018 ; Bruisson et al, 2019 ), and P. scandens rhizosphere was enriched with Anaeromyxobacter , Frankia , Streptacidiphilus , and Amycolatopsis ( Figure 2 ), with nitrogen-fixing ( Chaia et al, 2010 ) and antimicrobial activity ( Buszewski et al, 2018 ). In summary, although many bacteria are shared among three plant species, each plant still recruits distinctive microbes in rhizosphere, possibly due to their different root exudates.…”