An Endophytic Strain of Bacillus amyloliquefaciens Suppresses Fusarium oxysporum Infection of Chinese Wolfberry by Altering Its Rhizosphere Bacterial Community

Root rot disease is a serious infection leading to production loss of Chinese wolfberry (Lycium barbarum). This study tested the potential for two bacterial biological control agents, Bacillus amyloliquefaciens HSB1 and FZB42, against five fungal pathogens that frequently cause root rot in Chinese wolfberry. Both HSB1 and FZB42 were found to inhibit fungal mycelial growth, in vitro and in planta, as well as to promote the growth of wolfberry seedlings. In fact, a biocontrol experiment showed efficiency of 100% with at least one treatment involving each biocontrol strain against Fusarium oxysporum. Metagenomic sequencing was used to assess bacterial community shifts in the wolfberry rhizosphere upon introduction of each biocontrol strain. Results showed that HSB1 and FZB42 differentially altered the abundances of different taxa present and positively influenced various functions of inherent wolfberry rhizosphere bacteria. This study highlights the application of biocontrol method in the suppression of fungal pathogens that cause root rot disease in wolfberry, which is useful for agricultural extension agents and commercial growers.

Structure and Function of Rhizosphere Soil and Root Endophytic Microbial Communities Associated With Root Rot of Panax notoginseng

Panax notoginseng (Burk.) F. H. Chen is a Chinese medicinal plant of the Araliaceae family used for the treatment of cardiovascular and cerebrovascular diseases in Asia. P. notoginseng is vulnerable to root rot disease, which reduces the yield of P. notoginseng. In this study, we analyzed the rhizosphere soil and root endophyte microbial communities of P. notoginseng from different geographical locations using high-throughput sequencing. Our results revealed that the P. notoginseng rhizosphere soil microbial community was more diverse than the root endophyte community. Rhodopseudomonas, Actinoplanes, Burkholderia, and Variovorax paradoxus can help P. notoginseng resist the invasion of root rot disease. Ilyonectria mors-panacis, Pseudomonas fluorescens, and Pseudopyrenochaeta lycopersici are pathogenic bacteria of P. notoginseng. The upregulation of amino acid transport and metabolism in the soil would help to resist pathogens and improve the resistance of P. notoginseng. The ABC transporter and gene modulating resistance genes can improve the disease resistance of P. notoginseng, and the increase in the number of GTs (glycosyltransferases) and GHs (glycoside hydrolases) families may be a molecular manifestation of P. notoginseng root rot. In addition, the complete genomes of two Flavobacteriaceae species and one Bacteroides species were obtained. This study demonstrated the microbial and functional diversity in the rhizosphere and root microbial community of P. notoginseng and provided useful information for a better understanding of the microbial community in P. notoginseng root rot. Our results provide insights into the molecular mechanism underlying P. notoginseng root rot and other plant rhizosphere microbial communities.

Autotoxin Rg 1 Induces Degradation of Root Cell Walls and Aggravates Root Rot by Modifying the Rhizospheric Microbiome

The accumulation of autotoxins and pathogens in soil has been reported as a primary driver of root rot disease and one of the key factors limiting sustainable development in agricultural production. However, less is known about the correlation of plants, their associated pathogens, and the microbiota mediated by autotoxins, as well as the contributions autotoxins make to the occurrence of root rot disease.

The influence of rhizosphere soil fungal diversity and complex community structure on wheat root rot disease

Wheat root rot disease due to soil-borne fungal pathogens leads to tremendous yield losses worth billions of dollars worldwide every year. It is very important to study the relationship between rhizosphere soil fungal diversity and wheat roots to understand the occurrence and development of wheat root rot disease. A significant difference in fungal diversity was observed in the rhizosphere soil of healthy and diseased wheat roots in the heading stage, but the trend was the opposite in the filling stage. The abundance of most genera with high richness decreased significantly from the heading to the filling stage in the diseased groups; the richness of approximately one-third of all genera remained unchanged, and only a few low-richness genera, such as Fusarium and Ceratobasidium, had a very significant increase from the heading to the filling stage. In the healthy groups, the abundance of most genera increased significantly from the heading to filling stage; the abundance of some genera did not change markedly, or the abundance of very few genera increased significantly. Physical and chemical soil indicators showed that low soil pH and density, increases in ammonium nitrogen, nitrate nitrogen and total nitrogen contributed to the occurrence of wheat root rot disease. Our results revealed that in the early stages of disease, highly diverse rhizosphere soil fungi and a complex community structure can easily cause wheat root rot disease. The existence of pathogenic fungi is a necessary condition for wheat root rot disease, but the richness of pathogenic fungi is not necessarily important. The increases in ammonium nitrogen, nitrate nitrogen and total nitrogen contributed to the occurrence of wheat root rot disease. Low soil pH and soil density are beneficial to the occurrence of wheat root rot disease.

Characterization of endophytic yeast and its suppressive effect on root rotting fungi of tomato under neem cake soil amendment

Background The exposure of crops to a variety of fungal and bacterial pathogens leads to huge economic losses. Different strategies are being adapted to control these diseases among which the application of chemicals fungicide is common. However, these chemicals are posing a serious threat to the environment. For biological management of root rot disease of tomato and better fruit quality, studies were conducted on the possible use of endophytic yeast as a biocontrol agent. Results Endophytic yeasts were isolated from healthy plants and identified. Identification of selected isolates was confirmed on the basis of 18S rDNA gene sequencing. They were evaluated for suppressive effect on root rotting fungi in vitro and also in vivo on tomato plants, used alone or under neem cake soil amendment. Seventy-six isolates of yeasts were evaluated against root rotting fungi Fusarium oxysporum, F. solani, Rhizoctonia solani and Macrophomina phaseolina using dual culture plate assay. Seventy-five isolates were found to suppress radial growth of F. oxysporum, F. solani and M. phaseolina by producing zones of inhibition or lysing the fungal hyphae. However, none of the isolates was found to inhibit R. solani in vitro. Most of the isolates also caused nematicidal activity at varying degree against Meloidogyne javanica. All test isolates produced indole acetic acid in vitro and solubilized phosphorus. In pots and field plot experiments, test isolates of yeasts were able to suppress root rotting fungi on tomato in natural soil and soil amended with neem cake with enhancement of growth of tomato plants. Yeasts were also found to ameliorate the plant resistance through enhancing polyphenolic contents, salicylic acid and antioxidant activity. Conclusions Endophytic yeasts were found effective against root rot disease of tomato and could be used as a potential biocontrol agent for the management of soil-borne diseases of tomatoes.

A simplified synthetic community rescues Astragalus mongholicus from root rot disease by activating plant-induced systemic resistance

Background Plant health and growth are negatively affected by pathogen invasion; however, plants can dynamically modulate their rhizosphere microbiome and adapt to such biotic stresses. Although plant-recruited protective microbes can be assembled into synthetic communities for application in the control of plant disease, rhizosphere microbial communities commonly contain some taxa at low abundance. The roles of low-abundance microbes in synthetic communities remain unclear; it is also unclear whether all the microbes enriched by plants can enhance host adaptation to the environment. Here, we assembled a synthetic community with a disease resistance function based on differential analysis of root-associated bacterial community composition. We further simplified the synthetic community and investigated the roles of low-abundance bacteria in the control of Astragalus mongholicus root rot disease by a simple synthetic community. Results Fusarium oxysporum infection reduced bacterial Shannon diversity and significantly affected the bacterial community composition in the rhizosphere and roots of Astragalus mongholicus. Under fungal pathogen challenge, Astragalus mongholicus recruited some beneficial bacteria such as Stenotrophomonas, Achromobacter, Pseudomonas, and Flavobacterium to the rhizosphere and roots. We constructed a disease-resistant bacterial community containing 10 high- and three low-abundance bacteria enriched in diseased roots. After the joint selection of plants and pathogens, the complex synthetic community was further simplified into a four-species community composed of three high-abundance bacteria (Stenotrophomonas sp., Rhizobium sp., Ochrobactrum sp.) and one low-abundance bacterium (Advenella sp.). Notably, a simple community containing these four strains and a thirteen-species community had similar effects on the control root rot disease. Furthermore, the simple community protected plants via a synergistic effect of highly abundant bacteria inhibiting fungal pathogen growth and less abundant bacteria activating plant-induced systemic resistance. Conclusions Our findings suggest that bacteria with low abundance play an important role in synthetic communities and that only a few bacterial taxa enriched in diseased roots are associated with disease resistance. Therefore, the construction and simplification of synthetic communities found in the present study could be a strategy employed by plants to adapt to environmental stress.