Rhizosphere and soil microbiome in the management of plant pathogens and diseases

Abstract

Plant diseases are one of the most causes of loss in agriculture. The soil is a diverse ecosystem which harbor microorganisms that contribute to plant health, being its first line of defense. Alternative methods to intensive land use such as crop rotation, no-till and induction of suppressiveness to pathogens have been explored to increase soil quality and consequently plant productivity. Maize and soybean are the most cultivated grains in the world, while coconut is an important crop for tropical countries. Stimulation of soil microbiota, either by land uses or suppression induction are allies of a more sustainable agriculture model. In this context, in the first paper we studied the impact of maize and soybean rotation in soil microbial diversity and the inoculum of Fusarium spp. fumonisin producers (F. verticillioides and F. proliferatum), a maize pathogen, in the system. We conducted the experiments during seasons 2016/2017 to 2019/2020. Treatments were continuous soybean, continuous maize and rotation as land uses for the first three years and maize in total area in the fourth with the aim to evaluate the impact of land uses on maize soil diversity and pathogen incidence. Bulk soil samples were collected in the harvest of each season, while additional rhizosphere samples were collected in season 2019/2020 in two time points: blooming and harvest. In addition, maize stalks were left in the field during plant cycles to evaluate the influence of land uses on pathogen multiplication. Soil samples were sequenced targeting the 16SrRNA for Bacteria and Archaea and soils were submitted to qPCR targeting the gene fum1 of Fusarium verticillioides and F. proliferatum. The resulting sequences were clustered into operational taxonomic units (OTU) at a 97% of similarity threshold. We used cycle threshold as quantitative measure for Fusarium spp. fum1 inoculum. Our results showed three-year crop rotation did not increase soil diversity compared to continuous maize or soybean and precipitation was responsible for shaping communities in the first three seasons. Fusarium spp. fum1 decreased its concentration in soils under rotation systems although its occurrence decreased in maize stalks left in the field under continuous maize. In line, soils under continuous maize have decreased disease occurrence in maize plants cultivated in the last season. In the second paper, we evaluated the nature of soil suppressiveness to Ceratocystis paradoxa, a fungus that causes stem bleeding in coconut trees. We classified 54 soils into levels of suppressiveness. The five suppressive and conducive soils were contrasted to determine its nature. Soil physicochemical and biological analyses were analyzed in order to dissect the main factors involved in suppressiveness. Calcium carbonate and suppressive microbiota were tested and compared to the control of C. paradoxa by using baits colonization and number of perithecia. Total cultivable bacterial populations were the main biological property implicated in suppressiveness. Soil taxonomic profile showed Actinobacteria, Proteobacteria, Firmicutes and Chloroflexi as the more abundant phyla in contrasting soils although Actinobacteria showed highest abundance in suppressive samples. Suppressive microbiota reduced pathogen colonization in 93.8% compared to the control. Among physical and chemical properties, sand content, soil pH, calcium, magnesium, sum of bases, effective cation exchange capacity, base saturation, and aluminum were higher in suppressive soils while clay content and iron characterize non-suppressive. Calcium carbonate was effective in reduce pathogen colonization when compared to the other sources. The resulting pH from calcium and microbiota treatments ranged to neutral and significantly decrease pathogen recovery on banana baits. Our work contributes to the understanding of suppressive phenotype in Brazilian soils to Ceratocystis paradoxa and suggest soil microbiome, calcium carbonate and pH as the main drivers to this phenomenon.