Whole genome analysis of Enterobacter cloacae Rs-2 and screening of genes related to plant-growth promotion

Deciphering the genomic and physiological basis of pH dependent siderophore production in Enterobacter sp. DRP3 and mitigation of lead stress in rice seedlings

Anthropogenic activities like heavy metal pollution exert the most devastating effect on agriculture. Siderophores are small peptides capable to chelate iron and different heavy metals; thereby reduce metal toxicity. However, very little information is available about their physiology (siderophore types, effect of temperature, pH, toxic metals), and especially of their gene expression patterns. Here, we have carried out a detailed study on siderophore production dynamics along with their gene expression pattern in Enterobacter sp. DRP3. DRP3 was able to produce two different types of siderophores hydroxamate type (19.81 µg ml-1) during early stages and catecholate type (59.52 µg ml-1) later stages of its growth, especially at pH-6.8. DRP3 was able to produce similar concentrations of siderophores even under high lead concentrations. Further whole genome analysis has revealed the presence of enterobactin and aerobactin gene clusters. Quantitative real-time PCR observed a 5.02-fold and 1.90-fold overexpression of the enterobactin biosynthesis genes entC and entF, respectively, and a 3.12-fold upregulation of the aerobactin biosynthesis gene iucC in the absence of exogenously added Fe3+ by DRP3. Our study also highlighted that following root colonization DRP3 is excellent in mitigating Pb(II) stress in rice seedlings while promoting iron content and reducing lead content in plant tissue.

Developed BL-EF to acquire plant growth-promoting functions under salt stress by introducing the ACC deaminase gene

The application of plant growth-promoting rhizobacteria (PGPR) is a novel and effective strategy to ameliorate soil salinity and increase agricultural productivity. ACC deaminase (ACCD) in PGPR plays a key role in alleviating salt stress and promoting plant growth. This study aimed to investigate the potential of ACCD-producing strain BL-EF to mitigate salt stress in tomato plants. The ACCD gene was introduced into the non-PGPR Escherichia coli to successfully construct to construct BL-EF and produce catalytically active ACCD. The results showed that strain BL-EF significantly increased the height of tomato plants by 30.94% and 44.63%, under both normal and salt stress conditions, respectively. Strain BL-EF also modulated the photosynthetic pigmentation process in plants, promoting plant growth and increasing tomato tolerance to salt stress. The osmoregulatory system improved and the antioxidant enzyme activities increased to counteract reactive oxygen species-induced activities inoculated with BL-EF compared with those not inoculated with BL-EF. In addition, the inoculation with BL-EF strains increased soil enzyme activities and enhanced nutrients availability in the soil for plants uptake. In conclusion, the inoculation of ACC deaminase-producing strain BL-EF holds immense potential to alleviate salt stress in tomato plants, offering significant benefits to the agricultural sector.

Enterobacter-inoculation altered the C, N contents and regulated biomass allocation in Reaumuria soongorica to promote plant growth and improve salt stress tolerance

Soil salinization poses a significant ecological and environmental challenge both in China and across the globe. Plant growth-promoting rhizobacteria (PGPR) enhance plants' resilience against biotic and abiotic stresses, thereby playing a vital role in soil improvement and vegetation restoration efforts. PGPR assist plants in thriving under salt stress by modifying plant physiology, enhancing nutrient absorption, and synthesizing plant hormones. However, the mechanisms through which PGPR regulate the contents of carbon (C) and nitrogen (N), and biomass allocation of desert plant in response to salt stress is still unclear. This study explores the impact of PGPR on biomass allocation, C, and N contents of R. soongorica seedlings through a pot experiment. Strains P6, N20, and N21, identified as Enterobacter, were isolated from the rhizosphere of R. soongorica, and they exhibited various beneficial traits such as indole-3-acetic acid (IAA) production, phosphate solubilization, nitrogen fixation, and tolerance to up to 8% NaCl stress. We found that under NaCl stress, R. soongorica seedlings exhibit significant reductions in plant height, basal diameter, and root surface area (P<0.05). However, inoculation with strains P6, N20, and N21 reverses these trends. Compared to NaCl treatment alone, co-treatment with these strains significantly increases the biomass of roots, stems, and leaves, particularly root biomass, which increases by 99.88%, 85.55%, and 141.76%, respectively (P<0.05). Moreover, N contents decrease significantly in the roots, stems and leaves, C contents increase significantly in the roots and leaves compared to NaCl treatment (P<0.05). Specifically, N contents in roots decrease by 14.50%, 12.47%, and 8.60%, while C contents in leaves increase by 4.96%, 4.45%, and 4.94%, respectively (P<0.05). Additionally, stem and leaf biomasses exhibit a significant positive correlation with C contents and a significant negative correlation with N contents in these tissues. In conclusion, inoculation of Enterobacter strains enhanced the biomass of R. soongorica seedlings, regulated the biomass distribution, and modifies C and N contents to promote plant growth and improve salt stress tolerance. This study provides a novel adaptive strategy for the integrated use of PGPR and halophytes in saline-alkali soil improvement and vegetation restoration efforts.

Halotolerant Enterobacter asburiae A103 isolated from the halophyte Salix linearistipularis: Genomic analysis and growth-promoting effects on Medicago sativa under alkali stress

Soil salinization negatively affects plant growth and threatens food security. Halotolerant plant growth-promoting bacteria (PGPB) can alleviate salt stress in plants via diverse mechanisms. In the present study, we isolated salt-tolerant bacteria with phosphate-solubilizing abilities from the rhizosphere of Salix linearistipularis, a halophyte distributed in saline-alkali soils. Strain A103 showed high phosphate solubilization activity and was identified as Enterobacter asburiae based on genome analysis. In addition, it can produce indole-3-acetic acid (IAA), siderophores, and 1-aminocyclopropane-1-carboxylate (ACC) deaminase. Genome mining has also revealed the presence of several functional genes involved in the promotion of plant growth. Inoculation with A103 markedly improved alfalfa growth in the presence of 100 mM NaHCO3. Under alkali stress, the shoot and root dry weights after bacterial inoculation improved by 42.9 % and 21.9 %, respectively. Meanwhile, there was a 35.9-37.1 % increase in the shoot and root lengths after treatment with A103 compared to the NaHCO3-treated group. Soluble sugar content, peroxidase and catalase activities increased in A103-inoculated alfalfa under alkaline stress. A significant decrease in the malondialdehyde content was observed after treatment with strain A103. Metabolomic analysis indicated that strain A103 positively regulated alkali tolerance in alfalfa through the accumulation of metabolites, such as homocarnosine, panthenol, and sorbitol, which could reduce oxidative damage and act as osmolytes. These results suggest that halophytes are valuable resources for bioprospecting halotolerant beneficial bacteria and that the application of halotolerant growth-promoting bacteria is a natural and efficient strategy for developing sustainable agriculture.

Study the effect of Enterobacter cloacae on the gene expression, productivity, and quality traits of Curcuma longa L. Plant

Overuse of artificial chemical fertilizers could be detrimental to the environment. Utilizing beneficial microorganisms as biofertilizers is a sustainable technique that promotes soil health, crop yield, and ecosystem preservation. Curcuma longa L. is utilized as a medication since it has its antibacterial, anti-microbial, and anti-tumor characteristics, which reduce inflammation and hasten wound healing. The effect of E. cloacae strain MSR1, which is common in the roots of alfalfa grown in the Al-Ahsaa region, on C. longa plants is being investigated. C. longa rhizomes were planted under greenhouse conditions after being submerged in a solution of E. cloacae strain MSR1 (OD 500) or water treatment as a control for 12 hours. After 240 days of growing, ten randomly selected plants from each treatment were collected, and the vegetative growth and yield metrics were assessed. To investigate how E. cloacae influences C. longa production and chemical composition (photosynthetic pigment, nitrogen, phosphorus, potassium, and curcuminoid), measurements were conducted as well as genes diketide-CoA and curcumin synthases genes. Our research showed that C. longa's growth and yield were favorably impacted by E. cloacae. Significant increases in the related plants' chlorophyll a,b, carotenoid, nitrogen, phosphorus, and potassium levels were likewise a reflection of the enhanced effects shown in the growth and yield parameters. Treatment with E. cloacae raised the curcuminoid's three sub-components' compositions to varying degrees: bisdemethoxycurcumin, demethoxycurcumin, and curcumin. Comparing E. cloacae treated plants to the control, high expression levels of the genes diketide-CoA and curcumin synthase-1, -2, and 3 were also found. The treatment of E. cloacae is a good biostimulant candidate for boosting growth and yield as well as raising the medicinal qualities of C. longa, according to the overall results.

Genomic insight of phosphate solubilization and plant growth promotion of two taxonomically distinct winter crops by Enterobacter sp. DRP3

AIMS

Study of rhizospheric microbiome-mediated plant growth promotional attributes currently highlighted as a key tool for the development of suitable bio-inoculants for sustainable agriculture purposes. In this context, we have conducted a detailed study regarding the characterization of phosphate solubilizing potential by plant growth-promoting bacteria that have been isolated from the rhizosphere of a pteridophyte Dicranopteris sp., growing on the lateritic belt of West Bengal.

METHODS AND RESULTS

We have isolated three potent bacterial strains, namely DRP1, DRP2, and DRP3 from the rhizoids-region of Dicranopteris sp. Among the isolated strains, DRP3 is found to have the highest phosphate solubilizing potentiality and is able to produce 655.89 and 627.58 µg ml-1 soluble phosphate by solubilizing tricalcium phosphate (TCP) and Jordan rock phosphate, respectively. This strain is also able to solubilize Purulia rock phosphate moderately (133.51 µg ml-1). Whole-genome sequencing and further analysis of the studied strain revealed the presence of pyrroloquinoline quinone (PQQ)-dependent glucose dehydrogenase gdh gene along with several others that were well known for their role in phosphate solubilization. Further downstream, quantitative reverse transcriptase PCR-based expression study revealed 1.59-fold upregulation of PQQ-dependent gdh gene during the solubilization of TCP. Root colonization potential of the studied strain on two taxonomically distinct winter crops viz. Cicer arietinum and Triticum aestivum has been checked by using scanning electron microscopy. Other biochemical analyses for plant growth promotion traits including indole acetic acid production (132.02 µg ml-1), potassium solubilization (3 mg l-1), biofilm formation, and exopolymeric substances productions (1.88-2.03 µg ml-1) also has been performed.

CONCLUSION

This study highlighted the active involvement of PQQ-dependent gdh gene during phosphate solubilization from any Enterobacter group. Moreover, our study explored different roadmaps for sustainable farming methods and the preservation of food security without endangering soil health in the future.

Mitigation of Salt Stress in Rice by the Halotolerant Plant Growth-Promoting Bacterium Enterobacter asburiae D2

Salinity is a major abiotic stress that seriously affects crop growth worldwide. In this work, we aimed to isolate potential halotolerant plant growth-promoting rhizobacteria (PGPR) to mitigate the adverse impacts of salt stress in rice. An isolate, D2, with multiple plant growth-promoting (PGP) characteristics was identified as Enterobacter asburiae D2. Strain D2 could produce indole-3-acetic acid and siderophore. It also exhibited phosphate solubilization and 1-aminocyclopropane-1-carboxylic deaminase activity. Genome analysis further provided insights into the molecular mechanism of its PGP abilities. Strain D2 inoculation efficiently stimulated rice growth under both normal and saline conditions. Compared with the non-inoculated plants, a significant increase in plant height (18.1-34.7%), root length (25.9-57.1%), root dry weight (57.1-150%), and shoot dry weight (17.3-50.4%) was recorded in inoculated rice seedlings. Meanwhile, rice seedlings inoculated with strain D2 showed improvement in chlorophyll and proline content, while the oxidant damage was reduced in these plants in comparison with the control group. Moreover, the K+/Na+ ratio of the inoculated rice seedlings exposed to NaCl and Na2CO3 was higher than that of the uninoculated groups. These results imply that Enterobacter asburiae D2 is a potential PGPR that can be used for alleviation of salt stress in rice.

Complete genome sequence of Nguyenibacter sp. L1, a phosphate solubilizing bacterium isolated from Lespedeza bicolor rhizosphere

Phosphorus (P) deficiency is a predominant constraint on plant growth in acidified soils, largely due to the sequestration of P by toxic aluminum (Al) compounds. Indigenous phosphorus-solubilizing bacteria (PSBs) capable of mobilizing Al-P in these soils hold significant promise. A novel Al-P-solubilizing strain, Al-P Nguyenibacter sp. L1, was isolated from the rhizosphere soil of healthy Lespedeza bicolor plants indigenous to acidic terrains. However, our understanding of the genomic landscape of bacterial species within the genus Nguyenibacter remains in its infancy. To further explore its biotechnological potentialities, we sequenced the complete genome of this strain, employing an amalgamation of Oxford Nanopore ONT and Illumina sequencing platforms. The resultant genomic sequence of Nguyenibacter sp. L1 manifests as a singular, circular chromosome encompassing 4,294,433 nucleotides and displaying a GC content of 66.73%. The genome was found to host 3,820 protein-coding sequences, 12 rRNAs, and 55 tRNAs. Intriguingly, annotations derived from the eggNOG and KEGG databases indicate the presence of genes affiliated with phosphorus solubilization and nitrogen fixation, including iscU, glnA, and gltB/D associated with nitrogen fixation, and pqqBC associated with inorganic phosphate dissolution. Several bioactive secondary metabolite genes in the genome, including pqqCDE, phytoene synthase and squalene synthase predicted by antiSMASH. Moreover, we uncovered a complete metabolic pathway for ammonia, suggesting an ammonia-affinity property inherent to Nguyenibacter sp. L1. This study verifies the nitrogen-fixing and phosphate-dissolving abilities of Nguyenibacter sp. L1 at the molecular level through genetic screening and analysis. The insights gleaned from this study offer strategic guidance for future strain enhancement and establish a strong foundation for the potential incorporation of this bacterium into agricultural practices.