Rhizospheric, seed, and root endophytic-associated bacteria of drought-tolerant legumes grown in arid soils of Namibia

Abstract

Plant growth-promoting bacteria (PGPB) are of increased interest as they offer sustainable alternatives to the more common chemical fertilisers. Research, however, has increased into the use of PGPB as bioinoculants to improve yields. Legumes are known to interact with diazotroph PGPB which increase nutrient uptake, prevent pathogenic infections, and actively fix nitrogen. This study aimed to comprehensively describe PGPB associated with legumes grown in Namibia through analysis of the site-specific bacterial microbiomes. In the present study, we used the 16S rRNA sequencing approach to determine the structure of rhizosphere, root, and seed endosphere microbiomes of five drought-tolerant legume species: Macrotyloma uniflorum, Vigna radiata, Vigna aconitifolia, Vigna unguiculata and Lablab purpureus. Several important phyla were identified including Actinobacteriota, Bacteroidota, Firmicutes, Proteobacteria and Verrucomicrobiota. Overall, Proteobacteria was the most abundant phylum followed by Actinobacteria. The most important genera identified were Bacillus, Mesorhizobium, Pseudomonas, Bradyrhizobium and the Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium group. The relative abundance of these genera varied across sample types and legume species. This study identified important diazotrophs across all the legume species. Bacillus, an important PGPB, was found to be the most abundant genus among all the niches analysed and legume species, while Rhizobium spp. was particularly enriched in roots. This study ultimately provides previously undescribed information on legume-associated bacterial communities in Namibia.

Keywords: Bioinoculants; Endophytes; Microbiomes; Namibia; Plant growth-promoting bacteria; Rhizosphere.

Fig. 1

A) Potting strategy used for the 6 accessions. B) Bagani Research Station study field in Bagani in the Kavango East region in the north-eastern parts of Namibia. C) Falcon tubes in which surface sterilised seeds were germinated in sterile sawdust.

Fig. 2

Shannon index of the microbiome in the rhizosphere soil, seed, bulk soil, and roots of legume. The larger the Shannon index, the better the sample uniformity. In the case of the same species richness, the greater the uniformity of each species in the community, the greater the diversity of the community.

Fig. 3

Principal component analysis (PCA) based on unweighted unifrac distance calculated on rhizosphere, roots, seeds, and bulk soil samples. Statistical significance has been inferred using PERMANOVA (see Supplementary Fig. S1).

Fig. 4

Overall abundance of phyla identified.

Fig. 5

Phylum abundance according to sample type of the top 13 phyla.

Fig. 6

Genera abundance according to sample type of the top 50 genera.

Fig. 7

Heat map with the relative abundances of the bacterial genera in the five different legume crops and rhizosphere soil, and the endophytes of the roots and seeds.

Fig. 8

Relative abundance of Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium group.

Fig. 9

Venn diagram of shared and unique genera between all the microbiomes observed in this study.

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