Determination and comparison of intraspecific variation in the bacterial strains resident in the rhizoplane and rhizosphere of Bambaranut (Vorandzeia subterranean L. thouars)
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The bacterial community found in the rhizosphere has been found to have more diversity compared to the rhizoplane due to the interaction of microbes and plants in the soil environment. The intraspecific variations of bacterial strains resident in the rhizosphere and rhizoplane of the bambaranut were identified, characterized and compared in the study. Soil and root samples were collected from the North-West University agricultural farm located in the Ngaka Modiri Molema district, North West Province, and from Vhembe district in Thohoyandou, Limpopo Province in South Africa. Bacteria were then isolated on fourteen cultivated sites. A total of twenty eight samples from both the rhizosphere and rhizoplane samples were studied. Isolates were biochemically and culturally characterized using conventional methods. Several bacterial plant growth-promoting (PGPR) traits were tested and revealed that 93% were positive for phosphate solubilzation, in both rhizosphere and rhizoplane isolates, 64% siderophore production for the rhizosphere and 57% for the rhizoplane, 64% indole acetic acid production for the rhizoplane and 79% of the rhizoplane, 64% chitinolytic activity for rhizosphere and rhizoplane, both the rhizosphere and rhizoplane isolates yielded 64% of ACCD activity. Moreover 64% of isolates tested positive for hydrogen cyanide production for both the rhizosphere and rhizoplane. Interestingly all isolates (100%) produced ammonia from both rhizosphere and rhizoplane isolates, which is a good indication that rhizobacteria can fix nitrogen, hence bambaranut is well known to make the soil around it fertile even for the other plants grown near it or intercropped with it. Polymerase chain reaction- restriction fragment length polymorphism (PCR-RFLP) revealed high bacterial diversity across the rhizosphere since it is directly influenced by root secretions (exudates) and competition in soil microorganisms is very high compared to the rhizoplane where soil particles and microbes attach. The bacterial taxa observed were consistent with findings from other studies that used culture-independent techniques to describe taxa abundances. Selected genomic DNA samples were subjected to Next Generation Sequencing (NGS); MS8, TS6 from the rhizosphere and MP7, TP5 from the rhizoplane were identified by the 16S rDNA as clusters of most abundant bacterial communities. All sequences clustered into groups (phyla or classes) according to the taxonomic classification. The NGS identified them as phyla belonging to Proteobacteria, Firmicutes, Actinobacteria, Cyanobacteria and Acidobacteria. A synthesis of available data suggests a two-step selection process by which the bacterial microbiota of roots is differentiated from the surrounding soil biome. Rhizodeposition appears to fuel an initial substrate-driven community shift in the rhizosphere, which converges with host genotype-dependent fine-tuning of microbiota profiles in the selection of root endophyte assemblages. Substrate-driven selection also underlies the establishment of phyllosphere communities but takes place solely at the immediate rhizoplane surface. Both the rhizoplane and rhizosphere contain bacteria that provide indirect pathogen protection, but the rhizosphere members appear to serve additional host functions through the acquisition of nutrients from soil for plant growth. Thus, the plant rhizosphere emerges as a fundamental trait that includes mutualism enabled through diverse biochemical mechanisms, as revealed by studies on plant growth-promoting and plant health-promoting bacteria. The rhizosphere and rhizoplane communities do not possess much of the variation though the degree of intimacy is most likely to be different. The study suggests that bacteria found in both rhizosphere and rhizoplane in agriculture might prove beneficial towards crop production and conservation. Moreover, they might prove beneficial in agriculture towards crop production and conservation in addition, the isolates are likely to be potential candidates for biofertilizers, biocontrol and biotechnological application of commercial value. This, along with other innovations could prove to be an environmentally friendly strategy to ensure sustainable agriculture. Population diversity and genomics combined with NGS will be the key for understanding how adaption and horizontal gene transfer come about, how it takes place and where it leads. Future efforts will be focused on studying these bacteria in defined communities in the soil with plants simulated based on next generation sequencing results to understand the impact of one species on the whole community, their metabolites production and impact on the plant itself.