16S Metagenomics of Nitrifying Bacteria and Archaea Inhabiting Maize Rhizosphere and the Influencing Environmental Factors

The maize rhizosphere soil is unique with diverse microorganisms. Nitrifying bacteria and archaea are ubiquitous and can transform ammonia locked up in soil or manure into nitrate; a more soluble form of nitrogen. However, nitrifying bacteria and archaea inhabiting maize rhizosphere are yet to be identified. We elucidate the diversity and abundance of nitrifying bacteria and archaea associated with maize rhizosphere across different growth stages using 16S metagenomics sequencing. Also, the influence of environmental factors on the nitrifying communities was evaluated. The maize rhizosphere soil was collected from North-West University, Molelwane, South Africa. DNA was extracted using Nucleospin Soil DNA extraction kit and the V3-V4 hypervariable region was sequenced on Illumina Miseq platform. MG-RAST was used to analyze the raw sequences. The environmental factors were measured using standard procedure. The result revealed 9 genera of nitrifying bacteria; Nitrospira, Nitrosospira, Nitrobacter, Nitrosovibrio, Nitrosomonas, Nitrosococcus, Nitrococcus, unclassified (derived from Nitrosomonadales), unclassified (derived from Nitrosomonadaceae) and 1 archaeon Candidatus Nitrososphaera. The Nitrospirae phyla group which had the most nitrifying bacteria was more abundant at the tasselling stage (67.94%). Alpha diversity showed no significant difference. However, the Beta diversity showed significant difference (P=0.01, R=0.58) across the growth stages. The growth stages had no significant effect on the diversity of nitrifying bacteria and archaea, but the tasselling stage had the most abundant. A correlation was observed among some of the environmental factors. The research outcome can be put into consideration while carrying out a biotechnological process that involves nitrifying bacteria and archaea.

Metagenomic Analyses of Plant Growth-Promoting and Carbon-Cycling Genes in Maize Rhizosphere Soils with Distinct Land-Use and Management Histories

Many studies have shown that the maize rhizosphere comprises several plant growth-promoting microbes, but there is little or no study on the effects of land-use and management histories on microbial functional gene diversity in the maize rhizosphere soils in Africa. Analyzing microbial genes in the rhizosphere of plants, especially those associated with plant growth promotion and carbon cycling, is important for improving soil fertility and crop productivity. Here, we provide a comparative analysis of microbial genes present in the rhizosphere samples of two maize fields with different agricultural histories using shotgun metagenomics. Genes involved in the nutrient mobilization, including nifA, fixJ, norB, pstA, kefA and B, and ktrB were significantly more abundant (α = 0.05) in former grassland (F1) rhizosphere soils. Among the carbon-cycling genes, the abundance of 12 genes, including all those involved in the degradation of methane were more significant (α = 0.05) in the F1 soils, whereas only five genes were significantly more abundant in the F2 soils. α-diversity indices were different across the samples and significant differences were observed in the β diversity of plant growth-promoting and carbon-cycling genes between the fields (ANOSIM, p = 0.01 and R = 0.52). Nitrate-nitrogen (N-NO3) was the most influential physicochemical parameter (p = 0.05 and contribution = 31.3%) that affected the distribution of the functional genes across the samples. The results indicate that land-use and management histories impact the composition and diversity of plant growth-promoting and carbon-cycling genes in the plant rhizosphere. The study widens our understanding of the effects of anthropogenic activities on plant health and major biogeochemical processes in soils.

Stronger effect of maize rhizosphere than phosphorus fertilization on soil phosphatase activity and associated bacterial communities in acidic soil: distinct influences on phoC- and phoD-harboring bacteria

Aims The bacteria phoC and phoD genes encode acid and alkaline phosphatase (ACP and ALP), respectively, which mineralize organic phosphorus (P) to inorganic P. The relative importance of P fertilization and the plant rhizosphere on soil phosphatase activities and associated bacterial communities in acidic soils are poorly understood; whether phoC- and phoD-harboring bacterial communities display different responses remains undetermined. Methods Maize was grown in acidic soil supplemented with 0 (P0), 20 (P20), and 200 (P200) mg P2O5 kg− 1 for 42 days. Maize biomasses, plant nutrients, soil properties, phosphatase activities, and associated bacterial abundance and community composition were determined. Results Relative to bulk soils, rhizosphere showed increased ACP and ALP activities, phoC and phoD gene abundance, but these effects were reduced in strength with P200 treatment, except for phoC gene abundance. The rhizosphere effect increased α-diversity of phoC-harboring bacteria under P fertilization but reduced α-diversity of phoD-harboring bacteria under P0 and P20 treatments. The rhizosphere significantly influenced both phoC- and phoD-harboring bacterial community compositions, with stronger effect on phoD-harboring bacteria; while P fertilization affected phoD-harboring bacteria but not phoC-harboring bacteria. Immigrated and extinct species play important roles in reshaping phoC- and phoD-harboring bacterial communities, respectively, in response to the rhizosphere effect. Conclusions Compared with P fertilization, the maize rhizosphere more strongly influenced soil phosphatase activities and phoC- and phoD-harboring bacterial communities in acidic soils, with phoD-harboring bacteria responding more strongly to the rhizosphere effect and P fertilization. Notably, the strength of the rhizosphere effect heavily relied on P fertilization level.

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

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.