Wheat

Exploitation of the rhizosphere microbiome for a sustainable wheat production

Wheat is one of the world's most important crops, playing a crucial role in global food security. It provides a major source of carbohydrates, proteins, vitamins, and minerals, feeding billions of people worldwide. Wheat's adaptability to diverse climates and its high yield potential make it a staple food in many regions. However, wheat production often relies heavily on agrochemical inputs, which can harm the environment when used excessively. Understanding and optimizing the interactions between wheat plants and their rhizosphere microbiome is essential for sustainable agriculture.

The primary goal of our research is to enhance wheat productivity and sustainability by investigating the complex interactions between wheat plants and their rhizosphere microbiome, that is, the community of microorganisms living around the plant roots. Our objectives include:

• Characterizing the diversity and structure of bacterial, fungal, and cercozoan communities in wheat rhizospheres.
• Understanding how different wheat cultivars influence and are influenced by their microbial communities.
• Identifying microbial taxa and functions that contribute to disease resistance and overall plant health.
• Developing strategies to leverage beneficial plant-microbe interactions for sustainable crop production.

Microbiome Diversity and Network Complexity. We assessed the diversity of microbial communities in both landraces and modern wheat varieties. Dominant taxa include bacterial phyla Proteobacteria, Actinobacteria, and Acidobacteria; fungal phyla Ascomycota, Chytridiomycota, and Basidiomycota; and cercozoan classes Sarcomonadea, Thecofilosea, and Imbricatea. Our studies showed that microbial networks in wheat landraces have a more intricate topology compared to modern cultivars, suggesting that breeding selection may have reduced the plants' ability to recruit specific beneficial microbes. We have isolated and characterized genomes of beneficial bacteria from wheat rhizospheres, including Streptomyces virginiae, Paenibacillus ottowii, and Pseudomonas inefficax. These bacteria, isolated from different wheat landraces, show potential for enhancing plant health and growth.

Impact of Breeding on Microbial Communities. We found that changes in wheat cultivars, particularly the development of semi-dwarf varieties during the Green Revolution, influenced root traits and the assembly of rhizosphere bacterial communities. Tall cultivars had distinct microbial communities with higher abundance of Actinobacteria, Bacteroidetes, and Proteobacteria, whereas semi-dwarf cultivars had more Verrucomicrobia, Planctomycetes, and Acidobacteria. Network analysis revealed greater connectedness in microbial communities associated with tall cultivars compared to semi-dwarf ones.

Disease Suppressiveness. Our research on disease suppressiveness in wheat rhizospheres revealed that repeated exposure of susceptible wheat cultivars to the fungal pathogen Bipolaris sorokiniana led to significant reductions in disease severity over successive growth cycles. This effect was associated with changes in the taxonomic composition and functional traits of the rhizosphere microbiome. Key bacterial families like Chitinophagaceae, Anaerolineaceae, and Nitrosomonadaceae were linked to disease suppressiveness. Metagenome analysis identified biosynthetic gene clusters involved in producing compounds like terpenes and non-ribosomal peptides, which play roles in pathogen suppression.