Genomic insights into plant growth promoting rhizobia capable of enhancing soybean germination under drought stress

Abstract

Background: The role of soil microorganisms in plant growth, nutrient utilization, drought tolerance as well as biocontrol activity cannot be over-emphasized, especially in this era when food crisis is a global challenge. This research was therefore designed to gain genomic insights into plant growth promoting (PGP) Rhizobium species capable of enhancing soybean (Glycine max L.) seeds germination under drought condition.

Results: Rhizobium sp. strain R1, Rhizobium tropici strain R2, Rhizobium cellulosilyticum strain R3, Rhizobium taibaishanense strain R4 and Ensifer meliloti strain R5 were found to possess the entire PGP traits tested. Specifically, these rhizobial strains were able to solubilize phosphate, produce exopolysaccharide (EPS), 1-aminocyclopropane-1-carboxylate (ACC), siderophore and indole-acetic-acid (IAA). These strains also survived and grew at a temperature of 45 °C and in an acidic condition with a pH 4. Consequently, all the Rhizobium strains enhanced the germination of soybean seeds (PAN 1532 R) under drought condition imposed by 4% poly-ethylene glycol (PEG); nevertheless, Rhizobium sp. strain R1 and R. cellulosilyticum strain R3 inoculations were able to improve seeds germination more than R2, R4 and R5 strains. Thus, genomic insights into Rhizobium sp. strain R1 and R. cellulosilyticum strain R3 revealed the presence of some genes with their respective proteins involved in symbiotic establishment, nitrogen fixation, drought tolerance and plant growth promotion. In particular, exoX, htrA, Nif, nodA, eptA, IAA and siderophore-producing genes were found in the two rhizobial strains.

Conclusions: Therefore, the availability of the whole genome sequences of R1 and R3 strains may further be exploited to comprehend the interaction of drought tolerant rhizobia with soybean and other legumes and the PGP ability of these rhizobial strains can also be harnessed for biotechnological application in the field especially in semiarid and arid regions of the globe.

Keywords: Drought stress; Nitrogen fixation; PGP; Soybean; Symbiotic establishment; Whole genome sequences.

Fig. 1

Geographical location of Bambara groundnut rhizospheric soil used for rhizobial species isolation. To the left, the upper sketch represents a map of South Africa showing North-West Province (red sketch) and below is a map of North-West Province accommodating a map of Mahikeng (the light-yellow region) which encompasses Ngaka Modiri Molema district (the green spot) the site of North-West University where Bambara groundnut rhizospheric soil was collected for bacterial isolation. To the right, is a sketch showing Bambara groundnut rhizospheric soil sample collection site

Fig. 2

The concentration of a ACC (produced under drought stress induced by − 0.30 MPa PEG), b EPS, c siderophore, d IAA and e diameter of clear (halo) zones produced by rhizobial species. R1 - Rhizobium sp. strain R1, R2 - Rhizobium tropici strain R, R3 - Rhizobium cellulosilyticum strain R3, R4 - Rhizobium taibaishanense strain R4 and R5 - Ensifer meliloti strain R5. ACC-1-aminocyclopropane-1-carboxylate, EPS – exopolysaccharide, IAA - Indole-acetic-acid, O.D – optical density. Data represent mean ± SE

Fig. 3

Bacterial growth response to different environmental temperatures on day a 4, b 8, c 12, s 16 and e 20. R1 - Rhizobium sp. strain R1, R2 - Rhizobium tropici strain R2, R3 - Rhizobium cellulosilyticum strain R3, R4 - Rhizobium taibaishanense strain R4 and R5 - Ensifer meliloti strain R5. Data represent mean ± SE

Fig. 4

Bacterial growth response to different environmental temperatures on day a 4, b 8, c 12, d 16 and e 20. R1 - Rhizobium sp. strain R1, R2 - Rhizobium tropici strain R2, R3 - Rhizobium cellulosilyticum strain R3, R4 - Rhizobium taibaishanense strain R4 and R5 - Ensifer meliloti strain R5. Data represent mean ± SE

Fig. 5

Rhizobial growth response to different environmental pH on day a 5, b 10, c 15 and d 20. R1 - Rhizobium sp. strain R1, R2 - Rhizobium tropici strain R2, R3 - Rhizobium cellulosilyticum strain R3, R4 - Rhizobium taibaishanense strain R4 and R5 - Ensifer meliloti strain R5. Data represent mean ± SE

Fig. 6

Rhizobial growth response to different environmental pH on day a 5, b 10, c 15 and d 20. R1 - Rhizobium sp. strain R1, R2 - Rhizobium tropici strain R2, R3 - Rhizobium cellulosilyticum strain R3, R4 - Rhizobium taibaishanense strain R4 and R5 - Ensifer meliloti strain R5. Data represent mean ± SE

Fig. 7

Percentage of soybean seeds inoculated with rhizobial species that germinated in Petri dishes. R1 - Rhizobium sp. strain R1, R3 - Rhizobium cellulosilyticum strain R3 and R5 - Ensifer meliloti strain R5. Data represent mean ± SE

Fig. 8

Feature context of a Signal transduction histidine-protein kinase BaeS b Exodeoxyribonuclease III c Extracellular serine protease d Microbial serine proteinase e Cysteine desulfurase SufS f Cysteine desulfurase IscS g putative MFS-type transporter YcaD and h Riboflavin transporter depicting gene names in the genome map of R1 strain. The blue bars represent the gene locations

Fig. 9

Feature context of a Catecholate siderophore Receptor Fiu b 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase c Isoaspartyl peptidase d Isoaspartyl peptidase e UDP-N-acetylmuramate--L-alanyl-gamma-D-glutamyl-meso-2,6-diaminoheptandioate ligase f Phosphoethanolamine transferase EptA depicting gene names in the genome map of R1 strain. The blue bars represent the gene locations

Fig. 10

Feature context of a Signal transduction histidine-protein kinase ArlS b Response regulator aspartate phosphatase J c Serine protease Do-like HtrA d Serine protease Do-like HtrA e Cysteine desulfurase IscS f Putative cysteine desulfurase NifS g Beta-N acetylglucosaminidase h Teichoic acid poly (ribitol-phosphate) polymerase depicting gene names in the genome map of R3 strain. The blue bars represent the gene locations

Fig. 11

Feature context of a putative siderophore transport system permease protein YfiZ b putative siderophore-binding lipoprotein YfiY c Inner membrane protein YiaA d tRNA dimethylallyltransferase e Heptaprenyl diphosphate synthase component 1 f Septation ring formation regulator EzrA depicting gene names in the genome map of R3. The blue bars represent the gene locations