## 3 Results
### Taxonomy Diversity and Community Structure  
In the R1 sample, bacteria accounted for 98.82% of the obtained sequences, followed by eukaryota, which accounted for 0.81%, and archaea was 0.29%. Of R2 sequences, 98.47% belonged to bacteria, 1.23% to eukaryota, and 0.2% to archaea. Sequences in bulk soil samples were assigned to bacteria at 98.61% and 98.53%, eukaryotes at 0.82% and 1.05%, and archaea at 0.48% and 0.34% in B1 and B2 samples, respectively, but there was no significant difference (\(p>0.05\)) across the two locations. The statistical value for the soil compartment (R1, B1 and R2, B2) is more than 0.05; hence, there was no significant difference. The small percentage of sequences unaccounted for in each sample were from viruses or unclassified. The most dominant phylum was the _Actinobacteria_, accounting for 44.19% and 45.37% for R1 and B1 respectively, while _Proteobacteria_ represented 37.99% and 34.43% of the total. _Acidobacteria_, _Bacteroides_, and _Planctomycetes_ had a relative abundance of 3.32%, 2.48%, and 2.42% for R1 and 2.76%, 3.19%, and 2.34% for B1, respectively (Figure 3). For sample R2, the most dominant phyla were _Actinobacteria_ 44.96%, _Proteobacteria_ 44.17%, _Bacteroides_ 1.58%, and _Firmicutes_ 1.39%, while B2 had _Proteobacteria_, _Actinobacteria_, _Acidobacteria_, and _Bacteroides_ as the dominant phyla with relative abundance of 41.05%, 38.95%, 4.67%, and 2.42%, respectively. There was no significant difference (\(p>0.05\)) in the phylum domain between the locations R1, B1 and R2, B2. In addition, there was no significant difference in the phylum domain of the rhizosphere and the bulk soil samples. At the genus level, there was no significant difference (\(p>0.05\)) between the rhizosphere and the bulk soil samples, nor between the locations. The dominant genera for  
Figure 3: Classification of the most abundant phyla observed using shotgun metagenomic sequences in the rhizosphere (R1 and R2) and bulk soil samples (B1 and B2) of two sunflower fields in South Africa, Palmieftontein (R1, B1) and Bloemhof (R2, B2). R1 are _Conexibacter_ 15%, _Streptomyces_ 8%, _Mycobacterium_ 7%, and _Geodermatophilus_ 5%, respectively, while for the R2 habitat, _Conexibacter_, _Nocardioides_, and _Streptomyces_ accounted for 17%, 8%, and 7% of the metagenomic sequence, respectively. _Conexibacter_ 15%, _Streptomyces_ 10%, _Arthobacter_ 5%, and _Nocardioides_ 5% dominated the B1 habitat, while B2 had _Conexibacter_ 12%, _Streptomyces_ 8%, and _Mycobacterium_ 7% as the dominant genera (Figure 4). Microbial Community Diversity Richness and Eveenness of Sunflower Rhizosphere R1, R2, and Bulk Soils B1, B2 Examined  
\(\alpha\) diversity indices (Shannon and evenness) at the genus level presented no significant difference (\(p>0.05\)) between the rhizosphere and bulk soil samples. R2 had the highest Shannon diversity, but no significant differences were detected (\(p>0.05\)) between the other microhabitats. In addition, there was no significant difference (\(p>0.05\)) between the microbial diversity of the two locations. The results showed that B2 had the least microbial community diversity (Table 2). To test for a significant difference between the \(\beta\) diversity of the rhizosphere soil samples and the bulk soil samples, ANOSIM showed that there was a significant difference between \(\beta\) diversity of the rhizosphere and bulk soil microbial community (\(p\)-value = 0.01; R = 0.58). The principal coordinates analysis (PCoA) was used to visualize the \(\beta\) diversity of samples based on the relative abundances of metagenomes obtained from the sunflower rhizosphere and bulk samples (Figure 5). Comparing the microbial communities showed that PCoA indicated no distinct clustering by the rhizosphere and bulk soils and the locations. For example, samples R2 (a-c) were distinct and far from samples B2 (a-c), which explains that microbial structures are unique to those of the rhizosphere R2.