Third-generation sequencing technology to define microbial diversity in wheat cultivated soils in Turkey

Official URL: https://risc01.sabanciuniv.edu/record=b2767156_(Table of contents)

Microbial consortia or communities are the hallmark of a healthy soil rhizosphere and contribute to the wellbeing of domestic plants and animals, and consequently to the food production and food safety sectors. As the world population is constantly expanding, it is today a burden to meet their needs in food crops and cultivation. However, these are threatened by several environmental challenges including the excessive use of chemical fertilizers and climate change, which can harm healthy microorganisms residing within the rhizosphere. Instead, microbial communities are a natural and suitable option that can meet these challenges. The metagenomics approach overcomes the limitations of bacterial clonal cultures by studying the genomes of multiple bacterial genera or species in a given environmental area simultaneously. To decode the microbial diversity in wheat cultivated soils from five different regions in Turkey, we particularly used MinION Mk1B as a unique third generation nanopore sequencing technology. The 16S rRNA gene sequencing data, processed using Epi2ME Labs, reveals Proteobacteria as the predominant bacterial phyla (96-98%), as well as Bacteroidetes, Planctomycetes, Firmicutes, Verrucomicrobia, Actinobacteria, Acidobacteria, and Chloroflexi. We were able to identify community bacterial genera, Ramlibacter and Massilia, based on their co-occurrence pattern of distribution across the soil samples. Also, Pseudoxanthomonas was claimed as a bacterial genus that exhibit selective distribution pattern in certain soil samples, with several downstream species that were found to be involved in soil detoxification and recycling in the literature.