Exploring Biocontrol Agents From Microbial Keystone Taxa Associated to Suppressive Soil: A New Attempt for a Biocontrol Strategy

Abstract

Recent studies have observed differing microbiomes between disease-suppressive and disease-conducive soils. However, it remains unclear whether the microbial keystone taxa in suppressive soil are critical for the suppression of diseases. Bacterial wilt is a common soil-borne disease caused by Ralstonia solanacearum that affects tobacco plants. In this study, two contrasting tobacco fields with bacterial wilt disease incidences of 0% (disease suppressive) and 100% (disease conducive) were observed. Through amplicon sequencing, as expected, a high abundance of Ralstonia was found in the disease-conducive soil, while large amounts of potential beneficial bacteria were found in the disease-suppressive soil. In the fungal community, an abundance of the Fusarium genus, which contains species that cause Fusarium wilt, showed a positive correlation (p < 0.001) with the abundance of Ralstonia. Network analysis revealed that the healthy plants had more complex bacterial networks than the diseased plants. A total of 9 and 13 bacterial keystone taxa were identified from the disease-suppressive soil and healthy root, respectively. Accumulated abundance of these bacterial keystones showed a negative correlation (p < 0.001) with the abundance of Ralstonia. To complement network analysis, culturable strains were isolated, and three species belonging to Pseudomonas showed high 16S rRNA gene similarity (98.4–100%) with keystone taxa. These strains displayed strong inhibition on pathogens and reduced the incidence of bacterial wilt disease in greenhouse condition. This study highlighted the importance of keystone species in the protection of crops against pathogen infection and proposed an approach to obtain beneficial bacteria through identifying keystone species, avoiding large-scale bacterial isolation and cultivation.

Pseudomonas Inoculation Stimulates Endophytic Azospira Population and Induces Systemic Resistance to Bacterial Wilt

“…Three Pseudomonas strains, P. koreensis HCH2-3, P. rhodesiae MTD4-1, and P. lurida FGD5-2, were previously isolated from the rhizosphere of tobacco plants cultivated in Zunyi city, Guizhou Province, China (Zheng et al, 2021). The Pseudomonas strains were cultivated in Luria-Bertani (LB) medium at 28°C and stored in 20% (v/v) glycerol at −80°C.…”

“…All leaf samples were washed with cold distilled water, frozen with liquid nitrogen, and stored at −80°C. The sampling of the rhizosphere soil and roots was as follows: The rhizosphere soil (more than 1 g per sample) which was tightly bound to tobacco roots was obtained with a brush (Zheng et al, 2021), the root was collected by rinsing thoroughly with phosphate-buffered saline (PBS) solution and then soaked in alcohol (75%, v/v) for 1 min and sodium hypochlorite (5%, v/v) for 3 min, and the root was finally rinsed with sterile water for three times (Zheng et al, 2021). All rhizosphere soil, roots, and leaf samples were stored at −80°C prior to DNA or RNA extraction.…”

“…In our previous study, three Pseudomonas strains, i.e., Pseudomonas koreensis HCH2-3, Pseudomonas rhodesiae MTD4-1, and Pseudomonas lurida FGD5-2, were identified as keystone species of disease-suppressive soils (Zheng et al, 2021). However, the mechanisms of plant disease suppression by these keystone species are still unknown.…”

Engineering Multigenerational Host-Modulated Microbiota against Soilborne Pathogens in Response to Global Climate Change

“…With respect to suppressive soils, a total of 9 and 13 bacterial keystone taxa were identified from suppressive soils against Ralstonia solanacearum , and three species belonging to culturable strains of Pseudomonas showed high 16S rRNA gene similarity (98.4–100%) with keystone taxa [ 153 ]. However, another study showed that the keystone microbiome against Ralstonia solanacearum were comprised of the phyla Actinobacteria and Firmicutes and that these microbiota likely plan an important role in diminishing disease incidence [ 154 ].…”

Synergistically promoting plant health by harnessing synthetic microbial communities and prebiotics

“…The interactions of pathogens, hosts, and the environment determine the occurrence of plant diseases. The environment, especially soil characteristics, determines the source of microorganisms recruited by plant roots, which mainly affects disease outbreaks (Chiaramonte et al, 2021;Zheng et al, 2021). Diseases that spread through soil are called soil-borne plant diseases, and they adversely affect crop production worldwide, whereas some other types of organic matter might exert beneficial effects that reduce the presence of pathogens such as Fusarium, Phytophthora, Pythium, and Rhizoctonia (Jambhulkar et al, 2015).…”