Proteomic Analysis of Rhizoplane Microbiomes as Treatments for Hydroponic Phytopathogens

Plant pathogens such as the oomycetes Phytophthora and Pythium spp. commonly cause root rot in hydroponic systems and represent major threats to food security. The current study aims to examine how plant-growth-promoting microbes prevent root rot in hydroponic systems by examining the rhizosphere proteome. Microbiomes are typically studied using genomics for taxonomic identification, but proteomics has potential to provide more insight, such as understanding the mechanisms of infection, measuring the effectiveness of biocontrol treatments and for diagnostics. Amaranthus tricolor seeds were planted on burlap in a series of hydroponic systems and treated with rhizobacteria and mycorrhizae, then infected with an unknown oomycete isolate cultured in a vegetable-based broth. Root rot spread rapidly in the trials, and the treatment failed to prevent symptoms. Roots were harvested and sonicated in water then filtered through cheesecloth to collect the rhizosphere microbes. Proteins were extracted using phenol and sodium dodecyl sulfate. Protein extracts were then analyzed using MALDI-TOF mass spectrometry. Data yielded over 22,874 proteins across 12 samples, showing that the sonication and extraction methods worked well. Among the proteins identified using BLAST analysis were specific to Phytophthora, Pythium, and Fusarium. Given that there were multiple proteins specific to Phytophthora, there is a strong possibility that the unknown isolate utilized in the study is Phytophthora. However, the isolated pathogen could include more than one genus. More analysis is needed to determine if proteomics can be used for agricultural biocontrol analyses.