Molecular Characterization of Indigenous Rhizobia from Kenyan Soils Nodulating with Common Beans

Abstract

Kenya is the seventh most prominent producer of common beans globally and the second leading producer in East Africa. However, the annual national productivity is low due to insufficient quantities of vital nutrients and nitrogen in the soils. Rhizobia are symbiotic bacteria that fix nitrogen through their interaction with leguminous plants. Nevertheless, inoculating beans with commercial rhizobia inoculants results in sparse nodulation and low nitrogen supply to the host plants because these strains are poorly adapted to the local soils. Several studies describe native rhizobia with much better symbiotic capabilities than commercial strains, but only a few have conducted field studies. This study aimed to test the competence of new rhizobia strains that we isolated from Western Kenya soils and for which the symbiotic efficiency was successfully determined in greenhouse experiments. Furthermore, we present and analyze the whole-genome sequence for a promising candidate for agricultural application, which has high nitrogen fixation features and promotes common bean yields in field studies. Plants inoculated with the rhizobial isolate S3 or with a consortium of local isolates (COMB), including S3, produced a significantly higher number of seeds and seed dry weight when compared to uninoculated control plants at two study sites. The performance of plants inoculated with commercial isolate CIAT899 was not significantly different from uninoculated plants (p > 0.05), indicating tight competition from native rhizobia for nodule occupancy. Pangenome analysis and the overall genome-related indices showed that S3 is a member of R. phaseoli. However, synteny analysis revealed significant differences in the gene order, orientation, and copy numbers between S3 and the reference R. phaseoli. Isolate S3 is phylogenomically similar to R. phaseoli. However, it has undergone significant genome rearrangements (global mutagenesis) to adapt to harsh conditions in Kenyan soils. Its high nitrogen fixation ability shows optimal adaptation to Kenyan soils, and the strain can potentially replace nitrogenous fertilizer application. We recommend that extensive fieldwork in other parts of the country over a period of five years be performed on S3 to check on how the yield changes with varying whether conditions.

Rhizosphere Microbe Affects Soil Available Nitrogen and Its Implication for the Ecological Adaptability and Rapid Growth of Dendrocalamus sinicus, the Strongest Bamboo in the World

“…In this study, the prediction results of bacterial functions showed dominant roles of nitrogen fixation, cellulolysis and ureolysis in the rhizosphere soil of D. sinicus, indicating a high capacity for carbohydrate conversion and biological nitrogen fixation [11]. Remarkably, the rhizosphere microbes of the straight type possessed higher nitrogen fixing capacity, which could lead to higher soil NH 4 + -N content compared to the introduced straight type (Tables 1 and S3) [48]. Furthermore, the FUNGuild analysis revealed a high proportion of saprotrophic fungi, which enhanced the availability of carbon and nitrogen [49,50].…”

“…Nitrogen (N) is one of the major elements essential for plant growth [6,48]. Soil N ammoniation and nitrification, as key processes in nitrogen cycling and plant nutrition absorption, are mainly mediated by soil microbes [4,5].…”

“…Soil N ammoniation and nitrification, as key processes in nitrogen cycling and plant nutrition absorption, are mainly mediated by soil microbes [4,5]. Currently, many studies found that microbial nitrogen fixation and mineralization were important ways of increasing the available nitrogen content in rhizosphere soil [10,35,48]. In the case of Bambusa vulgaris, supplementation of nitrogen fixing bacteria and vesicular-arbuscular mycorrhizae fungi could significantly increase growth [29].…”

“…Meanwhile, apart from a significantly higher Shannon index of bacterial community observed in August for the introduced straight type compared to the straight type, no statistically significant differences were found in other indices between the two types (Figure 2). The prediction results of soil bacterial functions showed that nitrogen fixation abundance was significantly lower in the introduced straight type compared to the straight type at each stage (Figure 4A, Table S3), which may be an important factor leading to the low soil NH 4 + -N content of the introduced straight type [48]. It was important to note that the rhizosphere soil of the introduced straight type exhibited a significantly higher abundance of the ureolysis function compared to the straight type in August (p < 0.05) (Figure 4A, Table S3).…”