Identifying of Bacterial Communities Influenced by Isoflavonoids in the Soybean Rhizosphere Using a Metagenomics Analysis

Evidence points to the services provided by rhizodeposits to be the main reason for maintaining the highest microbial density in soils in close proximity to plant roots. Using RNAi gene silencing of isoflavone synthase (IFS) gene, Isoflavonoids have been identified as a vital component in soybean rhyzodeposits that help soybean plant roots retain advantageous interactions with surrounding microbiome. Our goal is to identify bacterial communities retaining vital ecological relationships with soybean's growth and productivity based on the analysis of microbial metagenomics data. The metagenomics data is the microbial whole genetic content recovered directly from the environments using the next-generation sequencing (NGS). Metagenomics data sequenced from soil samples was labelled as bulk soil (BULK), soil surrounding IFS-RNAi transformed soybean root (IFS-RNAi), vector-reformed-control soybean root (VC) and wild type soybean roots (WT), depending on different treatments applied. We analyzed microbial 16S rRNA metagenomics data using QIIME (Quantitative Insights into Microbial Ecology) pipeline to obtain an OTU (Operational Taxonomic Unit) table for each sample. OTU is an operational definition of a species or group of species inferred from sequence data. An OTU table records all OTUs that exist in a sample. Normalized OTU tables were subjected to feature selection and machine learning frameworks to extract out subset of OTUs that are sample specific. Next, we will use PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States), an open-source software, to investigate the biological functions of those sample specific OTUs. Our framework is capable of discovering biologically significant patterns from large microbial metagenomic data, which subsequently can be applied to variety of other big data in biology to answer various biological questions.