Maize microbial community modulates plant health in North West Province, South Africa

Abstract

Food sustainability is a serious agricultural issue that needs to be watched. The effective functioning of the rhizosphere microbiome significantly contributes to plant development, disease resistance, and agricultural sustainability. Hence, it is a significant predictor of plant health. Northern Corn Leaf Blight (NCLB) is the most prominent leaf disease of maize caused by the ascomycete Setosphaeria turcica and anamorph Exserohilum turcicum and is affecting maize production in South Africa. It is interesting to note that little is known about how this disease impacts the functional diversity and community structure of rhizosphere microbial communities associated with maize plants. Therefore, using a shotgun metagenomics method, we investigated the community structure and functional diversity of the microbiome living in the rhizosphere of NCLB diseased and healthy maize plants at selected farms in South Africa's North West Province. The study was carried out from NCLB diseased and healthy maize plant rhizosphere at the North West University Farm (Mafikeng) and a Farm in Lichtenburg. The rhizosphere soil samples tightly bound to maize roots were collected in replicates from different healthy and NCLB diseased maize plants from Lichtenberg and Mafikeng, North West Province, South Africa. The DNA was extracted and libraries were prepared and sequenced conducted with 300 cycles on an Illumina NovaSeq 6000 system. Each metagenome sequence was annotated against the M5NR database, and MG-RAST v4.0.3 server was used at default settings, to execute downstream analytical processing. Sequences were submitted to NCBI SRA with bioproject number PRJNA763110. With the aid of the SEED subsystem database, a total of 12 bacteria, 4 archaea, and 2 fungus phyla were discovered as being predominant across the fields. Proteobacteria, Dienococcus-Thermus, Gemmatimonadetes, Chlorobi, Cyanobacteria, Planctomycetes, Verrucomicrobia, Acidobacteria, Firmicutes, Chloroflexi, and Bacteroidetes were the most prevalent phyla of bacteria. Basidiomycota and Ascomycota were the two most prevalent fungal phyla, and Archaea was made up of Euryarchaeota, xiii Thaumarchaeota, Crenarchaeota, and Korachaeota. In the order LI > MA > LID > MAD, microbial abundance and diversity were higher in the rhizosphere of healthy maize (LI and MA) compared to the NCLB diseased (LID and MAD). We also found that the rhizosphere of the healthy maize plant was dominated by 24 functional categories, whereas the rhizosphere of the infected maize plant was dominated by 4 functional categories. Alpha diversity analysis revealed no difference between the healthy and diseased maize rhizospheres (p>0.05). The examination of beta diversity, however, revealed a substantial distinction. The significant abundance of functional groups found, particularly in LI, suggests that the presence of plant diseases changed how the soil microbiome works. The shotgun metagenomics study unveiled higher microbial abundance and diversity in the healthy rhizosphere. This positively influence the rhizosphere microbiome in modulating the microbial functions towards the management of NCLB and plant health.