Metagenomic Insight into the Community Structure of Maize-Rhizosphere Bacteria as Predicted by Different Environmental Factors and Their Functioning within Plant Proximity

Abstract

The rhizosphere microbiota contributes immensely to nutrient sequestration, productivity and plant growth. Several studies have suggested that environmental factors and high nutrient composition of plant’s rhizosphere influence the structural diversity of proximal microorganisms. To verify this assertion, we compare the functional diversity of bacteria in maize rhizosphere and bulk soils using shotgun metagenomics and assess the influence of measured environmental variables on bacterial diversity. Our study showed that the bacterial community associated with each sampling site was distinct, with high community members shared among the samples. The bacterial community was dominated by Proteobacteria, Actinobacteria, Acidobacteria, Gemmatimonadetes, Bacteroidetes and Verrucomicrobia. In comparison, genera such as Gemmatimonas, Streptomyces, Conexibacter, Burkholderia, Bacillus, Gemmata, Mesorhizobium, Pseudomonas and Micromonospora were significantly (p ≤ 0.05) high in the rhizosphere soils compared to bulk soils. Diversity indices showed that the bacterial composition was significantly different across the sites. The forward selection of environmental factors predicted N-NO3 (p = 0.019) as the most influential factor controlling the variation in the bacterial community structure, while other factors such as pH (p = 1.00) and sulfate (p = 0.50) contributed insignificantly to the community structure of bacteria. Functional assessment of the sampling sites, considering important pathways viz. nitrogen metabolism, phosphorus metabolism, stress responses, and iron acquisition and metabolism could be represented as Ls > Rs > Rc > Lc. This revealed that functional hits are higher in the rhizosphere soil than their controls. Taken together, inference from this study shows that the sampling sites are hotspots for biotechnologically important microorganisms.

Soil bacterial communities of three types of plants from ecological restoration areas and plant-growth promotional benefits of Microbacterium invictum (strain X-18)

“…Gemmatimonas was found to be more abundant in the rhizospheric soil of healthy plants than in diseased soil (She et al, 2016), indicating its disease-suppressing properties. Besides, Gemmatimonas can solubilize insoluble elements, induce plant stress resistance or produce antifungal antibiotics (Mahanty et al, 2017;Shang and Liu, 2020;Akinola et al, 2021;Zhu et al, 2021). In the present study, Gemmatimonas was the dominant genus in the rhizospheric soil from three plant types, accounting for up to 3.36% of all OTUs from R. pseudoacacia.…”

Nitrogen use efficiency, rhizosphere bacterial community, and root metabolome reprogramming due to maize seed treatment with microbial biostimulants

“…), and some Acidobacteria and Chloroflexi spp. have been reported to provide positive functions at the rhizosphere level, particularly under stress conditions (Akinola et al, 2021; Khan et al, 2020; Lazcano et al, 2021; Yue et al, 2020). In particular, some Acidobacteria have been reported to possess the genetic capability to support nitrate, nitrite and nitric oxide reduction and to release serine endopeptidases, hence having the potential to improve nitrogen uptake (Kalam et al, 2020).…”

“…Noteworthy, Gemmatimonadetes and Gaiella spp. play a key role in plant abiotic stress (Khan et al, 2020; Yue et al, 2020), and both have been specifically linked to the level of N‐nitrate levels in maize (Akinola et al, 2021). Among the root metabolites showing the strongest correlation with rhizomicrobiota, flavonoids (sakuranetin and 2′,4,4′,6′‐tetrahydroxychalcone) and isoflavonoids (vestitone and 7,2,4,2′‐tetrahydroxy‐4′,5′‐methylenedioxyisoflav‐3‐ene) were the most represented, followed by the hydroxycinnamic phenolic cinnamoyl‐beta‐D‐glucoside, and the phenolic glycoside salicin.…”

2‐Aminoethylphosphonate utilization in Pseudomonas putida BIRD‐1 is controlled by multiple master regulators

“…Moreover, the abundance of 2AEP transporters and degradation pathways in bacterial meta‐omics datasets suggests 2AEP production is ubiquitous (Murphy et al ., 2021). We speculate that 2AEP acquisition provides a clear advantage during nutrient limiting growth conditions which are frequently observed in plant rhizospheres (Bell et al ., 2014; Cui et al ., 2018), by expanding the metabolic repertoire of BIRD‐1 to utilize substrates associated with the plant microbiome (Kuramae et al ., 2020; Akinola et al ., 2021). Indeed, 2AEP catabolism may present a key nutrient driving plant– Pseudomonas interactions and partially explain why this genus forms abundant components of rhizosphere, rhizoplane and root endophyte communities (Robinson et al ., 2016; Rathore et al ., 2017).…”