Green waste compost impacts microbial functions related to carbohydrate use and active dispersal in plant pathogen-infested soil

Authors: Leblanc, Nicholas; Harrigian, Fiona

Submitted to: Microbial Ecology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/13/2024
Publication Date: 2/17/2024
Citation: LeBlanc, N.R., Harrigian, F.C. 2024. Green waste compost impacts microbial functions related to carbohydrate use and active dispersal in plant pathogen-infested soil. Microbial Ecology. 87. Article 44. https://doi.org/10.1007/s00248-024-02361-8.
DOI: https://doi.org/10.1007/s00248-024-02361-8

Interpretive Summary: Compost is commonly added to soil to increase nutrients for plants in organic production systems and improve soil carbon sequestration across agricultural landscapes. Use of compost can also reduce the activity of common plant pathogenic fungi in soil and suppress diseases they cause on plants. This compost-based pathogen and disease suppression is poorly understood, but microorganisms in soil are thought to play an important role. In this research, we tested how compost influences the plant pathogenic fungus Fusarium oxysporum and other microorganisms in soil that might interact with and suppress this pathogen. Experiments were conducted by collecting samples from soil that received no compost, a low rate of compost, or high rate of compost. The effects of compost on the pathogen F. oxysporum and other microorganisms was measured using molecular tools and analyzing soil DNA sequence data. Compared to untreated soil, addition of compost reduced the amount of the plant pathogenic fungus F. oxysporum in soil. Compost also increased different types of bacteria in soil that may actively suppress this pathogen. This study suggests adding compost to soil will reduce soilborne diseases and provides new information on which microorganisms may be responsible for pathogen suppression.

Technical Abstract: The effects of compost on chemical and physical characteristics of soil are well-studied, but impacts on soil microbiomes are poorly understood. This research tested effects of compost on bacterial communities in soil microbiomes infested with the plant pathogen Fusarium oxysporum. Compost was added to pathogen-infested soil and maintained in mesocosms in a greenhouse experiment and replicated growth chamber experiments. Bacteria and F. oxysporum biomass were quantified using quantitative PCR. Taxonomic and functional characteristics of bacterial communities were measured using shotgun metagenome sequencing. Compost significantly increased bacterial biomass at 8-weeks after amendment in one experiment. In all experiments, compost significantly reduced biomass of F. oxysporum and altered the taxonomic composition of soil bacterial communities. Sixteen bacterial genera were significantly increased from compost in every experiment, potentially playing a role in pathogen suppression. In all experiments there was a consistent negative effect of compost on functional traits related to carbohydrate use and the type 2 secretion system and a positive effect on traits linked to motility and chemotaxis. Results from this work demonstrate compost can reduce the abundance of soilborne plant pathogens and raise questions about the role of microbial dispersal in plant pathogen suppression.