Microbiome V3/V4 gene amplicon profiling in Casuarina root nodules using Illumina Miseq NGS sequencing

Abstract

Abstract Actinorhizal plant Casuarina sp. root nodules were gathered from a variety of environments, including hypersaline, saline, estuarine, and terrestrial soil. The bacteriome DNA was extracted from surface sterile root nodules using an adapted high salt method. Using specific primers, the acquired DNA was amplified for the V3-V4 regions' bacteriome marker gene.The amplified PCR genes were sequenced using the Illumina Hiseq 2500 platform's 16S rRNA gene amplicon sequencing system. In total, we obtained sequence lengths ranging from 430 to 470 bp with sequence numbers ranging from 0 to 150000. The root nodule bacteriome community profiles of Casuarina sp. were disclosed using the QIIME (1.9.1) pipeline, which revealed the abundance of operational taxonomic units (OTUs). We found 38 OTUs that were abundant in the bacterial community in the root nodules of Casuarina sp. from four different habitats. In all habitats, the abundance of bacteriome communities such as Frankiaceae, Pseudonocardiaceae, Pseudomonadaceae, and Mycobacteriaceae was obtained at the family level at OTUs. Similarly, at the genus level, at the OUTS abundance of the bacteriome community, Frankia, Pantoea, Pseudomonas, and Mycobacterium were discovered. In comparison to other habitats, Pantoea is only prominent in hypersaline and estuarine environments. Frankia, Pseudomonas, and Mycobacterium were found in all habitats; however, with the exception of Pantoea, Frankia is more prevalent in all habitats than the other bacterial communities. As a result, research on the bacteriome of actinorhizal Casuarina root nodules demonstrated the relative abundance of unique bacterial communities such as Pantoea, Mycobacterium, and Pseudomonas oryzihabitans in association with Frankia.