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Background Microbial communities inhabiting the rhizosphere play pivotal roles in determining plant health and yield. Manipulation of the rhizosphere microbial community is a promising means to enhance the productivity of economically viable and important agricultural crops such as sunflower ( Helianthus annuus ). This study was designed to gain insights into the taxonomic and functional structures of sunflower rhizosphere and bulk soil microbiome at two different locations (Sheila and Itsoseng) in South Africa. Results Microbial DNA extracted from the sunflower rhizosphere and bulk soils was subjected to next-generation sequencing using 16S amplicon sequencing technique.  Firmicutes ,  Actnobacteria  and  Proteobacteria  predominated sunflower rhizosphere soils.  Firmicutes ,  Cyanobacteria ,  Deinococcus - Thermus  and  Fibrobacteres  were positively influenced by Na +  and clay content, while  Actinobacteria ,  Thaumarchaeota ,  Bacteroidetes ,  Planctomycetes ,  Aquificae  and  Chloroflexi  were positively influenced by soil resistivity (Res) and Mg 2+ . The community-level physiological profiling (CLPP) analysis showed that the microbial communities in SHR and ITR used the amino acids tryptophan and malic acid efficiently. The metabolisms of these carbon substrates may be due to the dominant nature of some of the organisms, such as  Actinobacteria  in the soils. Conclusion The CLPP measurements of soil from sunflower rhizosphere were different from those of the bulk soil and the degree of the variations were based on the type of carbon substrates and the soil microbial composition. This study has shown the presence of certain taxa of rhizobacteria in sunflower rhizosphere which were positively influenced by Na +  and Mg 2+ , and taxa obtained from SHR and ITR were able to effectively utilized tryptophan and malic acid. Many unclassified microbial groups were also discovered and it is therefore recommended that efforts should further be made to isolate, characterize and identify these unclassified microbial species, as it might be plausible to discover new microbial candidates that can further be harnessed for biotechnological purpose.

Comparative study of microbial structure and functional profile of sunflower rhizosphere grown in two fields