Decoding Wheat Endosphere–Rhizosphere Microbiomes in Rhizoctonia solani–Infested Soils Challenged by Streptomyces Biocontrol Agents

Abstract

The endosphere and the rhizosphere are pertinent milieus with microbial communities that perturb the agronomic traits of crop plants through beneficial or detrimental interactions. In this study, we challenged these communities by adding Streptomyces biocontrol strains to wheat seeds in soils with severe Rhizoctonia solani infestation. Wheat plants were grown in a glasshouse standardized system, and the bacterial and fungal microbiomes of 233 samples of wheat roots (endosphere) and rhizosphere soils were monitored for 20 weeks, from seed to mature plant stage. The results showed highly dynamic and diverse microbial communities that changed over time, with Sphingomonas bacteria and Aspergillus , Dipodascus , and Trichoderma fungi increasing over time. Application of biocontrol Streptomyces strains promoted plant growth and maturation of wheat heads and modulated the root microbiome, decreasing Paenibacillus and increasing other bacterial and fungal OTUs. The soils with the highest levels of R. solani had increased reads of Thanatephorus ( Rhizoctonia anamorph) and increased root disease levels and increased Balneimonas , Massilia , Pseudomonas , and unclassified Micrococcaceae . As we enter the era of biologically sustainable agriculture, it may be possible to reduce and limit the effects of serious fungal infestations by promoting a beneficial microbiome through the application of biocontrol agents during different periods of plant development.

Analogous wheat root rhizosphere microbial successions in field and greenhouse trials in the presence of biocontrol agents Paenibacillus peoriae SP9 and Streptomyces fulvissimus FU14

“…Two different soil types which were Pythium ‐infested were used and were challenged by adding biocontrol strains as seed coats in order to determine the plant and microbiota responses when exposed to such conditions. The effects observed in the wheat plants regarding root weight, plant length, and increased number of wheat heads in the presence of the FU14 strain were similar to previously published results for other biocontrol strains performed in our and other research laboratories (Cook et al , ; Franco et al , ; ; Orakçı et al , ; Yang et al , ; Cuppels et al , ; Araujo et al , ; ). In addition, it was possible not only to define a list of OTUs that characterized the core microbiota present in all stages of the crop growth but also a succession of OTUs and taxonomic groups found at particular stages.…”

“…Fungicides, such as metalaxyl, have been used as a treatment; however, they only provide partial control (Cook et al , ). Biological control employing certain strains, such as the strains P. peoriae SP9 and S. fulvissimus FU14 used in this study, can be advantageous against these diseases (Alabouvette et al , ; Barnett et al , ; Conn et al , ; El‐Tarabily et al , ; Mavrodi et al , ; Araujo et al , ; ; Schlatter et al , ) with generally low impact on microbial communities of the roots and rhizosphere soils during the 3‐month period. Streptomyces was one of the most abundant and genetically diverse taxa in this study, and it is frequently described as an excellent biocontrol agent for multiple plants such as wheat, barley, cucumber, and potato (Prévost et al , ; El‐Tarabily et al ., ; Araujo et al , ).…”

“…In the present study the physiological benefits of the biocontrol seed coating can be seen in terms of disease control, plant length, and early formation of wheat heads, as previously shown (Mavrodi et al , ; Araujo et al , ; ). Seed‐coated inoculants are present in abundance in wheat plants for the first 8 weeks and promote plant health in soils with early disease pressure and by priming the plant defence response (Conn and Franco, ) to prolong the effects of biocontrol strains.…”

“…From the perspective of microbiome management, it is important to understand which microbes are sensitive to cropping practices and whether they can be associated with other microbes to impact on plant heath, soil competition, and promote specific networking properties (Hirsch and Mauchline, ; Mendes et al , ; Massart et al , ; Schlaeppi and Bulgarelli, ; van der Heijden and Hartmann, ). Some bacterial endophytes have been shown to impact plant growth and provide protection to the plant (Araujo et al , ; ). Although the effects on plants tend to be small initially (Yang et al , ; Bokati et al , ; Araujo et al , ; Wemheuer et al , ), these valuable organisms can be used as a basis for developing safer ecological approaches to disease management, particularly against root rots that affect a range of cereals (Orakçı et al , ; Araujo et al , ).…”

“…Some bacterial endophytes have been shown to impact plant growth and provide protection to the plant (Araujo et al , ; ). Although the effects on plants tend to be small initially (Yang et al , ; Bokati et al , ; Araujo et al , ; Wemheuer et al , ), these valuable organisms can be used as a basis for developing safer ecological approaches to disease management, particularly against root rots that affect a range of cereals (Orakçı et al , ; Araujo et al , ). Some endophytes were shown to be able to reduce Pythium disease on wheat and other cereals, and their potential as biocontrol inoculants has been well documented (Mavrodi et al , ; Araujo et al , ).…”