Characterisation of bacterial symbionts in selected drought-tolerant legumes for biofertilisers development for use in Namibia
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Date
2023
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Publisher
University of Namibia
Abstract
Namibia is a semi-arid country with approximately 1% of arable land. Crop cultivation
is profoundly challenged by nutrient-poor sandy soils combined with low water
retention. To meet the increasing food demand, farmers resort to applying synthetic
fertilisers and pesticides despite their environmental consequences. However, there is
increasing evidence that arid or semi-arid plant microbiomes offer an unexploited
reservoir that is pivotal to plant health, growth, and development. Plant growth promoting bacteria (PGPB) are of increased interest as they offer sustainable
alternatives to environmentally unfriendly and unsustainable chemical fertilisers. The
present study aimed to isolate, identify, and characterise plant-associated bacteria from
five drought-tolerant legumes grown in Namibia. Identification was done using 16S
rRNA sequencing and bioinformatics. Plant growth-promoting (PGP) abilities were
characterised based on exopolysaccharide production, antifungal activity, indole acetic
acid production, phosphate solubilization, siderophore production, and bacterial
nitrogen fixation. Using 16S Illumina metagenomic sequencing, this study
characterised the plant microbiomes of the nodules, roots, rhizosphere, and seeds.
Isolates identified from the roots and rhizosphere were from the Proteobacteria (72%),
Actinomycetota (15%), Bacteroidetes (5%) and Firmicutes (8%) phyla and included
known plant growth-promoting species such as Stenotrophomonas pavanii,
Streptomyces murinus, and Enterobacter cloacae. Nodule endophytes were mostly
from the phylum Firmicutes (88%). The identified genera include Bacillus, Priestia,
Paenibacillus, Gottfriedia, Neobacillus, Lysinibacillus, Fictibacillus, and
Brevibacillus. Characterisation found that rhizobacteria expressed more plant growth promoting traits compared to root endophytes. Siderophore production was observed
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in most root endophytes and rhizobacteria. The following isolates, CRhi10, CRhi15,
MBRhi17, HR5, RMBRhi4, RMBRhi1 and IPCRhi7 from the legume root
endospheres and rhizospheres showed the most potential as plant growth promoters.
A total of 34 nodule endophytes tested positive for at least one plant growth-promoting
trait. Isolates MB1, MB3.1, H14, M25-11, M8-16.1 and M8-16.2 showed the most
potential as plant-growth promoters. CRhi15 (S. maltophilia), HR5 (E. mori), H14 (P.
aryabhattai), M25-11 (L. boronitolerans), and M8-16.1 (Bacillus sp.) were selected
and assessed for their ability to induce drought tolerance on Vigna unguiculata seeds
in potted trials. The inoculants were also combined and assessed in a consortium.
Drought tolerance was observed to be highest with S. maltophilia (CRhi15), Bacillus
sp. (M8-16.1) and E. mori (HR5). The average root length under drought stress was
37.5 cm, 51.8 cm, and 33.7 cm respectively while the average shoot length was 63.1
cm, 80.6 cm, and 75.3 cm. Microbiome analysis of the root, rhizosphere and seed
microbiomes found important plant growth-promoting genera. These include Bacillus,
Mesorhizobium, Pseudomonas, and Bradyrhizobium. The nodule microbiome was
predominantly Bradyrhizobium. The relative abundance of the nitrogen-fixing
Bradyrhizobium genus was determined in four drought-tolerant legume species- Vigna
aconitifolia (mothbean), V. unguiculata (cowpea), Lablab purpureus (dolichos), and
Macrotyloma uniflorum (horsegram). Both culture-dependent and independent
methods revealed that these PGP bacteria can promote plant growth under drought,
nutrient and biotic stress conditions. Therefore, S. maltophilia (CRhi15), Bacillus sp.
(M8-16.1) and E. mori (HR5) may be further explored in field trials in efforts to
develop commercial biofertilisers
Description
A dissertation submitted in fulfilment of the requirements for the degree of doctor of philosophy in microbiology
Keywords
Commercial biofertilisers, Namibia, Crop cultivation, semi-arid plant, Bacterial symbionts, Drought tolerant legumes