Microbial diversity in soilless rhizospheres using potato dextrose agar and root inoculants

Abstract

Microbiome diversities in soilless rhizospheres are becoming known as an important factor for urban agriculture and food security. Plant pathogens like Pythium are common in hydroponic systems, but symptoms can be prevented with an established rhizo-microbiome. This study explored the microbiome within a single greenhouse to compare the dominant microorganisms in different systems and crops. Petri dishes were sterilized by soaking in 16% sodium hypochlorite and then isopropyl alcohol (70%). Potato dextrose agar (PDA) was inoculated with six samples; vermicompost castings, liquid mycorrhizal Orca (Plant Revolution Inc.), surface sterilized roots from a rotting Kalanchoe sp. in soil, an aquaponic Fragaria x ananassa, hydroponic Ocimum basilicum, and Lactuca sativa. After 5 days of incubation, the plates showed a few types of colonies (1-6 organisms per dish), with many single organisms consuming the entire dish. The vermicompost castings had the greatest number of species compared to the other samples (p-value= 0.0426). Unknown microbes were stained with methylene blue dye and observed at 1000x magnification. Results showed that a rod-shaped, gram-positive bacteria was dominant in most dishes, and produced white to beige colonies with undulated edges and wrinkles around the center, suggesting its identification as Bacillus subtilis. Two distinct species grew on the agar from the Kalanchoe sp. root, and a zone of inhibition formed between them. Covering the majority of the agar was a white fuzz, presumed to be a pathogenic Pythium sp., except for a cm wide halo around a single bacterial colony, which appeared to be B. subtilis. This study indicates that B. subtilis can produce inhibitory effects on phytopathogens like Pythium. Further investigations should focus on isolating and identifying the strains of B. subtilis and Pythium from root samples and testing for inhibitory effects with petri dishes and live plants. Future trials can help determine if rhizo-microbiomes that contain organisms like B. subtilis prevent pathogens like Pythium from infecting roots.