Impact of cropping systems on the functional diversity of rhizosphere microbial communities associated with maize plant: a shotgun approach.

Understanding the functions carried out by rhizosphere microbiomes will further explore their importance in biotechnological improvement and agricultural sustainability. This study presents one of the foremost attempts to understand the functional diversity of the rhizosphere microbiome in mono-cropping and crop rotation farming sites using shotgun metagenomic techniques. We hypothesized that the functional diversity would vary in the cropping sites and more abundant in the rotational cropping site. Hence, we carried out complete DNA extraction from the bulk and rhizospheric soils associated with maize plant cultivated on the mono-cropping farm (LT and LTc) and the crop rotation farm (VD and VDc), respectively, and sequenced employing shotgun approach. Using the SEED subsystem, our result revealed that a total of 24 functional categories dominated the rotational cropping site, while four functional categories dominated the mono-cropping sites. Alpha diversity assessment showed that no significant difference (p > 0.05) was observed across the cropping sites, while beta diversity assessment revealed a significant difference. Going by the high abundance of functional groups observed in the samples from the crop rotational site, it is evident that cropping systems influenced the functions of soil microbiomes. Worthy of note is the high abundance of unknown functions associated with these maize rhizosphere microbiomes. This is an indication that there are still some under-investigated functional genes associated with the maize rhizosphere microbiome. It is, therefore, imperative that further studies explore these functional genes for their agricultural and biotechnological potentials.

Metagenomic profiling of rhizosphere microbial community structure and diversity associated with maize plant as affected by cropping systems.

Soil microbial diversity is believed to be vital in maintaining soil quality and health. Limited knowledge exists on the impact of cropping systems (mono-cropping and crop rotation) on the diversity of the whole soil microbiome. In this study, we investigated the effects of two cropping systems, namely crop rotation and mono-cropping, on the community structure and diversity of rhizosphere microbiome in the rhizosphere and bulk soil associated with maize plant using shotgun metagenomics. Whole DNA was extracted from bulk, and rhizosphere soils associated with maize plant from the mono-cropping (LT and LTc) and crop rotation (VD and VDc) sites, respectively, and sequenced employing shotgun metagenomics. The results obtained via the Subsystem database showed 23 bacteria, 2 fungi, and 3 archaea most abundant phyla. The major bacterial phyla are Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, Gemmatimonadetes, Acidobacteria, Cyanobacteria, Spirochaetes, Aquificae, Verrucomicrobia, Chloroflexi, Planctomycetes, and Chlorobi. The major fungi phyla observed were Ascomycota and Basidiomycota, while the dominant archaea phyla are Euryarchaeota, Thaumarchaeota, and Crenarchaeota. Our diversity assessment showed that the rhizosphere microbial community was more abundant in the samples from the rotational crop site following VD>VDc>LT>LTc. Alpha diversity showed that there was no significant difference (P>0.05) in the soil microbial communities (P>0.05), while better diversity indicated that a significant difference (P = 0.01) occurred. Taken together, crop rotational practice was found to positively influence the rhizosphere microbial community associated with the maize plant.