Earthworm modifies microbial community and functional genes for lignocellulosic waste valorization: Isolating plant-growth-promoting bacteria via next generation sequencing

The primary motivation of this study is the lack of knowledge regarding the shift in microbial community and functional compositions in lignocellulosic waste-based composting and vermicomposting systems. To date, the next-generation sequencing approaches have scantily been made for the isolation of plant-growth-promoting microorganisms from vermicomposting systems. Therefore, two types of lignocellulosic waste (paddy straw and food waste) are mixed with and without cow dung in different ratios and vermicomposted with Eisenia fetida, while using a series of aerobic composting as a control. Significant decreases in pH, organic C (∼3 fold), and XRD-derived crystallinity are seen most evidently in the paddy straw-food waste (1:1) mixtures upon vermicomposting (compared to composting) along with a concurrent increment of nutrients (NPK) (∼2–3.5 fold). Significant augmentation (P < 0.01) in microbial activity (biomass and respiration) and growth (bacteria and fungus) is observed under vermicomposting. A considerable shift in taxonomic diversity, accompanied by differential functional diversity of the microbial communities, is detected between paddy straw-food waste (1:1) vermicompost and compost after 60 days of incubation. The overall gene volume is greater in the vermibed than in the compost, and genes of a few well-known microbial communities with good plant growth promoting traits (e.g., Beijerinckiaceae and Propionibacteriaceae) are exclusive to the vermicompost. Additionally, genes associated with beneficial microbial activities, such as amino acid transport, nuclear structure development, and lipid transport, are found to be more abundant in vermicompost than in compost. These data are helpful in identifying suitable feedstock for isolating scalable microbial species with beneficial traits. Subsequently, six multi-dimensional plant-growth-promoting endophytic bacterial species are isolated from both the vermibed and earthworm guts. Interestingly, close genetic resemblances are found for a few of these isolates with the metagenomically detected genes. In conclusion, this is the first study to identify the practical utility of next-generation sequencing-based metagenomic analyses for the meaningful isolation of economically viable microbial species from vermicomposting systems that might replace a sizeable portion of the chemical fertilizers used in agriculture.