Rhizosphere-Associated Microbiome Profile of Agricultural Reclaimed Lands in Egypt

Abstract

Plants especially in their natural habitat are considered part of a rich ecosystem that includes many various microorganisms in the soil. The current study aimed to identify the bacterial profile of agriculture-related soil samples using the metabarcoding technique to compare and explore relevant rhizosphere bacteria associated with plant cultivations in newly reclaimed land and habitual cultivated ones. The total environmental DNA was extracted from rhizosphere and noncultivated samples derived from three land types in Egypt. The bacterial 16S rDNA was amplified and sequenced by NGS technology to profile each sample. The microbial profile was characterized by statistical and literature-based methods. Among all samples, the most identified phyla were Actinobacteriota (28%), followed by Proteobacteriota (26%), Firmicutes (14%), Acidobacteriota and Chloroflexi (7%), Gemmatimonadota (5%), Bacteriodota and Crenarchaeota (3%), and Myxococcota (2%), in addition to 37 other phyla with <1% counts. A total of 74 OTUs were unique to the plant rhizosphere area and classified as Bacteriodota (5.1%:0.3%), Firmicutes (2.4%:0.1%), and Proteobacteria (3.5%:2%) phyla in agricultural and reclaimed lands, respectively. Moreover, the rhizosphere profile included a large portion of uncultured and unidentified bacterial species, which opened a window to further analysis. Our analysis provides a key knowledge about the rhizosphere microbiome and highlights its possible use to create microbial-based biofertilizers targeting plant performance in contrast to traditional fertilizers and their side effect on the agriculture sector.