Differential shifts in microbiome and pathogen populations associated with suppressive soil in long-term continuous corn field compared to rotation corn field

Abstract

Unraveling soil suppressiveness and the involvement of microbiome could provide the insight needed to advance development of cost-effective and eco-friendly alternatives for managing plant diseases. This could enhance global crops and subsequent food production without large-scale use of pesticides, which may cause pollution and negatively affect human health. The goal of this study was to evaluate changes in the microbiome and diversity of beneficial microbial communities in soils suppressive to soilborne pathogens under long-term continuous corn cultivation compared to rotation corn fields. Samples were collected three times during the year from four locations in Nebraska. Sequencing was conducted on the paired-end Illumina HiSeq platform with three primer sets, including 515F/806R, 1737F/2043R, and 1380F/1510R. Parameters evaluated for microbial activity showed a consistent pattern where they were significantly (p = 0.05) greater in continuous corn than rotation in one region of the state but no differences in another region. There were relatively higher operational taxonomic units (OTUs) for the potential biocontrol agents Bacillus, Paenibacillus, Massilia, Pseudomonas, and Sphingomonas in the long-term continuous corn field compared to the other three locations. This study identified certain microbial populations which appeared to drive community activities, the link between pathogens and beneficial organisms, the effect of soil nutrients, and the net feedback that played important roles in the development of soil suppressive properties. Additional research is needed to unravel the mechanisms and to fast-track the time required to attain soil suppressiveness.