Microbial diversity, community structure and functional characteristics of sunflower rhizospheric soil

PhD (Bibology), North-West University, Mahikeng Campus

Rhizosphere zones are ‘hubs’ for microbial diversity comprising of diverse microbiomes compared with the nearby bulk soils. Rhizospheric microorganisms play major roles in plant health, development and yield. The exploitation of the soil microbiome is a promising means to boost the production of economically viable and important agricultural crops, like sunflower (Helianthus annuus). The sustainable production of sunflower plants is important and one key way to achieve this feat is to have a better understanding of the connection between bacterial diversity, ecosystem functioning and their response to environmental variables. Likewise, the respiratory responses of these bacterial communities need to be studied to comprehend their roles in the ecosystem. The impact of agricultural practices in farmland ecosystems on the structure of soil bacterial communities and the effects on soil functioning was evaluated using 16S amplicon sequencing. Rhizospheric soil and corresponding bulk soil samples were collected from four farms namely Sheila/Ditsobottla, Itsoseng, Lichtenburg and Kraaipan/Krayburg. Employing the MicroResp™ method, community-level physiological profiles (CLPP) was used to explore the activities and functional diversity of the entire microbial communities in these sunflower soils. The taxonomic structures, distribution and diversity of the bacterial communities and significant relationships between the bacterial communities and soil properties were investigated. The effects of soil properties, agricultural practices and cropping system on bacterial community diversity of the soil samples from the farms were observed. Furthermore, effects of carbon substrate utilization on bacterial community diversity of sunflower rhizospheric soils obtained from Sheila (SHR) and Itsoseng (ITR), as well as Ditsobottla and Kraaipan were also investigated. The results obtained from sunflower rhizosphere soils grown in SHR and ITR showed that sodium (Na+) and clay content positively influenced Firmicutes, Deinococcus-Thermus, Cyanobacteria and Fibrobacteres, while soil resistivity (Res) and Magnesium (II) ion (Mg2+) positively influenced Actinobacteria, Bacteroidetes, Thaumarchaeota, Aquificae Planctomycetes and Chloroflexi. The CLPP analysis revealed that the microbial communities in SHR and ITR used the amino acids, including tryptophan and malic acid effectively. The metabolic rate of these carbon substrates may be due to the prevailing nature of some of the organisms, including Actinobacteria in the soils. Furthermore, the sunflower rhizospheric soils from Ditsobottla (R1) and Kraaipan (R2) were evaluated, it was observed that organic matter (OM) positively influenced Lactobacillales, Myxococcales, Rhizobiales, Bacillales, Burkholderiales, Enterobacteriales, Sphingomonadales, Flavobacteriales and Nitrosomonadales obtained from R1, while total N and pH positively influenced Cytophagales, Planctomycetales, Gemmatimonadales, Caulobacteriales and Nitrospirales from R2. The bacterial communities of the soil samples used the various carbon substrates (three amino acids, three carboxylic acids and six carbohydrates) as an energy source. Significant differences (P < 0.05) were only detected in tryptophan and methionine-amended soils. The effect of soil properties examined was observed to influence bacterial dispersal across the sites. Planctomycetes and Proteobacteria predominated the rhizosphere soils from Lichtenburg and Kraaipan sites. Significant differences (P < 0.05) in bacterial structure at phyla and family levels and predicted functional categories between soils across the sites were revealed. The effect of the analyzed soil parameters was observed to influence the bacterial spatial distribution across the sites. This study provides evidence of the dominant bacterial community structure in sunflower soils. The CLPP measurements of the rhizospheric soils were different from those of the bulk soil and the degree of the dissimilarities was based on the type of carbon substrates and the soil microbial composition. Further, various unclassified microbial groups were discovered across the study sites, 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 novel microbial species that can further be harnessed for biotechnological purpose and sustainable production of sunflower and other agricultural crops. Moreover, the predictive functional traits at growing stage are important for their future study and exploration as bioinoculants for enhanced crop production and management and for improved crop yields.

Doctoral