As we move into the era of sustainable food production we are developing microbial inputs that are applied to broad acre crop production at a scale which is disrupting traditional chemical usage in modern agriculture. These inputs are derived from, but also affect the microbiomes of the crop plants. The microbiomes within the endosphere and the rhizosphere of wheat seed and plants are dynamic systems which change with the age of crop, the soil, climate and the presence of phytopathogens in the soils.
In this study, we challenged these communities by adding Streptomyces and Paenibacillus biocontrol strains, separately, to wheat seeds growing with either severe Rhizoctonia solani disease or Pythium rootrot disease. Wheat plants were grown in the field and compared to plants grown in the same soil in a glasshouse. The bacterial and fungal microbiomes of wheat roots (endosphere) and rhizosphere soils were monitored for 20 weeks, from seed to mature plant stage. A total of 233 samples from a Rhizoctonia infested system and 254 samples from a Pythium infested system were analysed. The results showed highly dynamic and diverse microbial communities over the weeks, with crop age being the main differentiator followed by the presence of biocontrol agents. Bacteria played a stronger role in the early stages of wheat growth while fungi gained importance later on. The initial wheat microbiome was enriched was enriched by the rhizosphere soil microbiome with distinct fungi and bacteria admitted into the core microbiome at different time points.
Streptomyces biocontrol strains promoted plant growth and maturation and the root microbiome stressed such differences at OTU Level with specific disease-responsive OTUs revealed among fungi and bacteria and unclassified Micrococcaceae. Some differences in particular taxa were evident between field and glasshouse trials, but there was a consistency in microbial populations at each time point.
The application of biologically sustainable approaches in agriculture may limit the damaging effects of serious fungal diseases and preserve high levels of microbial biodiversity in soils.