Metagenomics Profiling of Vigna Unguiculata (L.) Walp. Rhizosphere Microbiome Under Hydrocarbon Stress in a Microcosm

Hydrocarbon compounds are among the dominant soil contaminants and abiotic stressors affecting plant growth and soil communities. Recently, however, plant-microbe interaction has been exploited to alleviate the abiotic stress and remove the contaminants from soil, which offers a cheaper, safer, and eco-friendly alternative to currently available methods. In this study, microbial community profiling of the rhizosphere of Vigna unguiculata (L.) Walp. was conducted using a culture-independent approach with a view to unraveling plant-induced community changes. Soil samples were collected from rhizosphere and non-rhizosphere hydrocarbon-contaminated soils, from which 16S rDNA and 18S ITS were extracted, purified, and sequenced using Illumina Miseq sequencing. A total of 1191 and 1373 16S rDNA and 341 and 484 ITS operational taxonomic units (OTU) with a 97% similarity cutoff obtained from non-rhizosphere and rhizosphere soil were analyzed, respectively. Cowpea sustained richer and more diverse bacterial species, with 335 more variant species than the bulk soil, which had only 153 dissimilar species. Fewer but more diverse fungal species were detected in the non-rhizosphere, with only 94 OTUs out of 578 OTUs found in both the soils. Eight bacterial phyla, including Proteobacteria, Acidobacteriota, Actinobacteriota, Cyanobacteria, Patescibacteria, Chloroflexi, Firmicutes, and Bdellovibrionota, were predominant in both the soil samples. Cowpea rhizosphere was colonized by more Ascomycota in contrast to the non-rhizosphere, where Basidiomycota and other classified and unclassified fungal species were in abundance. Members of the genera Sphingomonas (~ 20%), species in Saccharimonadales, Curvularia, and Paraconiothyrium were the dominant species in the rhizosphere. In the non-rhizosphere, Acidobacteria (~ 20%), KCM−B−112 (in the Acidithiobacillaceae), Aspergillus, and Lepidosphaeria were the predominant. Beta diversity indices indicated significant differences in the community composition of the soils and a great divergence, especially between rhizosphere and non-rhizosphere bacterial species. Unnamed bacterial species, which account for 35% of the community, were more in the rhizosphere. The dissimilarity in the community membership and its structure is an indication of the special role played by the cowpea in shaping its rhizosphere. Therefore, a deeper understanding of the rhizosphere's ecological complexity will enhance bioremediation outcomes and also inform sustainable agricultural practices, especially in contaminated soil.