Isolation of a novel rhizobacteria having multiple plant growth promoting traits and antifungal activity against certain phytopathogens

Novel multifunctional plant growth-promoting bacteria isolated from the oil palm rhizosphere under long-term organic matter application

Most agricultural products are presently cultivated on marginal lands with poor soil properties and unfavorable environmental conditions (diseases and abiotic stresses), which can threaten plant growth and yield. Plant growth-promoting bacteria (PGPB) are beneficial bacteria that promote plant growth and biomass and act as biocontrols against diseases and stress. However, most isolated PGPBs have a single function and low survival rates owing to their limited growth behaviors. In this study, we isolated multifunctional PGPB from oil palm rhizosphere, quantitatively measured their activities, and evaluated their effectiveness in Brassica rapa (Komatsuna) cultivation. This is the first study to report the isolation of three multifunctional PGPB strains with ammonium production, phosphate-potassium-silicate solubilization, and indole-3-acetic acid (IAA) production from the oil palm rhizosphere, namely Kosakonia oryzendophytica AJLB38, Enterobacter quasimori AJTS77, and Lelliottia jeotgali AJTS83. Additionally, these strains showed antifungal activity against the oil palm pathogen Ganoderma boninense. These strains grow under high temperature, acidic and alkaline pH, and high salt concentration, which would result in their proliferation in various environmental conditions. The cultivation experiments revealed these strains improved the growth and biomass with half the dosage of chemical fertilizer application, which was not significantly different to the full dosage. Furthermore, the overall plant growth-promoting activities in quantitative assays and overall B. rapa growth in cultivation experiments were statistically correlated, which could contribute to the prediction of plant growth promotion without plant cultivation experiments. Thus, the selected PGPB could be valuable as a biofertilizer to improve soil health and quality and promote agricultural sustainability.

Rhizobacteria Isolated from Amazonian Soils Reduce the Effects of Water Stress on the Growth of Açaí (Euterpe oleracea Mart.) Palm Seedlings

Euterpe oleracea Mart., also known for its fruit açaí, is a palm native to the Amazon region. The state of Pará, Brazil, accounts for over 90% of açaí production. Demand for the fruit in national and international markets is increasing; however, climate change and diseases such as anthracnose, caused by the fungus Colletotrichum sp., lead to decreased production. To meet demand, measures such as expanding cultivation in upland areas are often adopted, requiring substantial economic investments, particularly in irrigation. Therefore, the aim of this study was to evaluate the potential of açaí rhizobacteria in promoting plant growth (PGPR). Rhizospheric soil samples from floodplain and upland açaí plantations were collected during rainy and dry seasons. Bacterial strains were isolated using the serial dilution method, and subsequent assays evaluated their ability to promote plant growth. Soil analyses indicated that the sampling period influenced the physicochemical properties of both areas, with increases observed during winter for most soil components like organic matter and C/N ratio. A total of 177 bacterial strains were isolated from rhizospheres of açaí trees cultivated in floodplain and upland areas across dry and rainy seasons. Among these strains, 24% produced IAA, 18% synthesized ACC deaminase, 11% mineralized organic phosphate, and 9% solubilized inorganic phosphate, among other characteristics. Interestingly, 88% inhibited the growth of phytopathogenic fungi of the genera Curvularia and Colletotrichum. Analysis under simulated water stress using Polyethylene Glycol 6000 revealed that 23% of the strains exhibited tolerance. Two strains were identified as Bacillus proteolyticus (PP218346) and Priestia aryabhattai (PP218347). Inoculation with these strains increased the speed and percentage of açaí seed germination. When inoculated in consortium, 85% of seeds germinated under severe stress, compared to only 10% in the control treatment. Therefore, these bacteria show potential for use as biofertilizers, enhancing the initial development of açaí plants and contributing to sustainable agricultural practices.

The Microbial Community Structure in the Rhizosphere of Theobroma cacao L. and Euterpe oleracea Mart. Is Influenced by Agriculture System in the Brazilian Amazon

This study tested the hypothesis that cocoa monoculture (MS) and cocoa-açai agroforestry systems (AFS) may influence the microbial community structure and populations of plant growth-promoting bacteria (PGPR). Accordingly, the aim was to analyze the microbial community structure and PGPR populations in different agroecosystems in the Brazilian Amazon. To achieve this, the rhizosphere microbial community of cocoa and açai plants in both Amazonian seasons (dry and rainy) was analyzed using culture-dependent (PGPR screening) and -independent methods [PCR-DGGE based on rrs, alp, nifH gene, and intergenic region (ITS) of fungi]. Concerning PGPR screening, out of 48 isolated bacterial strains, 25% were capable of siderophore production, 29% of mineralized organic phosphate, 8% of inorganic phosphate solubilization, and 4% of indole acetic acid production. Moreover, 17% of isolates could inhibit the growth of various phytopathogenic fungi. Statistical analyses of DGGE fingerprints (p < 0.05) showed that bacterial and fungal community structures in the rhizosphere were influenced by the seasons, supporting the results of the physicochemical analysis of the environment. Furthermore, as hypothesized, microbial communities differed statistically when comparing the MS and AFS. These findings provide important insights into the influence of climate and cultivation systems on soil microbial communities to guide the development of sustainable agricultural practices.

Biodegradation of carbofuran by Pseudomonas aeruginosa S07: biosurfactant production, plant growth promotion, and metal tolerance

Pesticides are an indispensable part of modern farming as it aids in controlling pests and hence increase crop yield. But, unmanaged use of pesticides is a growing concern for safety and conservation of the environment. In the present study, a novel biosurfactant-producing bacterium, Pseudomonas aeruginosa S07, was utilized to degrade carbofuran pesticide, and it was obtained at 150 mg/L concentration; 89.2% degradation was achieved on the 5th day of incubation in in vitro culture condition. GC-MS (gas chromatography and mass spectrometry) and LC-MS (liquid chromatography and mass spectrometry) analyses revealed the presence of several degradation intermediates such as hydroxycarbofurnan, ketocarbofuran, and hydroxybenzofuran, in the degradation process. The bacterium was found to exhibit tolerance towards several heavy metals: Cu, Co, Zn, Ni, and Cd, where maximum and least tolerance were obtained against Co and Ni, respectively. Additionally, the bacterium also possesses plant growth-promoting activity showing positive results in nitrogen fixation, phosphate solubilising, ammonia production, and potassium solubilizing assays. Thus, from the study, it can be assumed that the bacterium can be useful in the production of bioformulation for remediation and rejuvenation of pesticide-contaminated sites in the coming days.

Isolation and characterization of halotolerant plant growth promoting rhizobacteria from mangrove region of Sundarbans, India for enhanced crop productivity

Halotolerant plant growth promoting rhizobacteria (PGPR) are beneficial microorganisms utilized to mitigate the biotic and abiotic stresses in plants. The areas of Sundarban mangroves of West Bengal, India have been reported to be rich in halotolerant microflora, yet major area remains unexplored. The present study, therefore, aims to map down the region-specific native microbial community potent of salt tolerance, plant growth promoting (PGP) activity and antagonistic activity against fungal pathogens. Bacterial samples were isolated from the saline soil of the Sundarban mangroves. A total of 156 bacterial samples were isolated and 20 were screened for their salt tolerance potential. These isolates were characterised using morphological, biochemical, and molecular approaches. Based on 16s rRNA sequencing, they were classified into 4 different genera, including Arthrobacter sp. (01 isolate), Pseudomonas plecoglossicida (01 isolate), Kocuria rosea (01 isolate), and Bacillus (17 isolates). The halotolerant isolates which possessed plant growth promoting traits including phosphate, and zinc solubilization, indole acetic acid production, siderophore, and ammonia generation were selected. Further, the effect of two halotolerant isolates GN-5 and JR-12 which showed most prominent PGP activities was evaluated in pea plant under high salinity conditions. The isolates improved survival by promoting germination (36 to 43%) and root-shoot growth and weight of pea plant in comparison to non-inoculated control plants. In a subsequent dual culture confrontation experiment, both these halo-tolerant isolates showed antagonistic activities against the aggressive root rot disease-causing Macrophomina phaseolina (Tassi) Goid NAIMCC-F-02902. The identified isolates could be used as potential bioagents for saline soils, with potential antagonistic effect on root rot disease. However, further studies at the physiological and molecular level would help to delineate a detail mechanistic understanding of broad-spectrum defence against salinity and potential biotic pathogen.

The combination of multiple plant growth promotion and hydrolytic enzyme producing rhizobacteria and their effect on Jerusalem artichoke growth improvement

Rhizobacteria are well recognized for their beneficial multifunctions as key promoters of plant development, suppressing pathogens, and improving soil health. In this study, experiments focused on characterizing the plant growth promotion (PGP) and extracellular hydrolase production traits of rhizobacteria, and their impact on Jerusalem artichoke growth. A total of 50 isolates proved capable of either direct PGP or hydrolase-producing traits. Two promising strains (Enterobacter cloacae S81 and Pseudomonas azotoformans C2-114) showed potential on phosphate and potassium solubilization, IAA production, and 1-aminocyclopropane-1-carboxylic acid deaminase activity and hydrolase production. A hydrolase-producing strain (Bacillus subtilis S42) was able to generate cellulase, protease, amylase, β-glucosidase, and phosphatase. These three selected strains also gave positive results for indirect PGP traits such as siderophore, ammonia, oxalate oxidase, polyamine, exopolysaccharide, biofilm, motility, and tolerance to salinity and drought stress. Colonization was observed using a scanning electron microscope and rhizobacteria appeared at the root surface. Interestingly, inoculation with consortia strains (S42, S81, and C2-114) significantly increased all plant parameters, including height, biomass, root (length, surface, diameter, and volume), and tuber fresh weight. Therefore, we recommend that potential consortia of PGP and hydrolase-producing rhizobacteria be employed as a biofertilizer to improve soil and boost crop productivity.

New Bacillus subtilis Strains Isolated from Prosopis glandulosa Rhizosphere for Suppressing Fusarium Spp. and Enhancing Growth of Gossypium hirsutum L

Rhizobacteria from desert plants can alleviate biotic stress and suppress plant diseases, and consequently can enhance plant growth. Therefore, the current study was performed to isolate and identify Prosopis glandulosa-associating rhizobacteria based on their antagonistic activity against Fusarium species and plant growth-promoting properties. Three bacterial isolates were identified as Bacillus subtilis: LDA-1, LDA-2, and LDA-3. The molecular analysis suggests the biosynthesis of the bacteriocins subtilisin and subtilosin, as well as the lipopeptide iturin, by these strains. In addition, the antagonistic study by dual-culture assay showed a high efficacy of all B. subtilis strains against phytopathogenic fungi (Fusarium nygamai, F. equisseti, F. solani, F. solani ICADL1, and F. oxysporum ICADL2) with inhibition percentages ranging from 43.3 to 83.5% in comparison to the control. Moreover, atomic force microscopy (AFM) analysis showed significant differences in the cell wall topography of the F. solani ICADL1 among the treated mycelia and untreated control. As a result, these three B. subtilis strains were used as bioinoculants for cotton seedlings infected by F. solani ICADL1 in pot trials, and the results revealed that the bacterial inoculations as an individual or combined with F. solani ICADL1 significantly improved cotton root and stem length, lateral roots, indole acetic acid (IAA), and gibberellic acid (GA₃) contents, as well as increased antioxidants, flavonoids, and phenols in comparison to those obtained from healthy and infected control plants. In conclusion, the three bacterial strains of B. subtilis (i.e., LDA-1, LDA-2, and LDA-3) are considered promising tools as biocontrol agents for F. solani and cotton growth promoters, and consequently can be used as bio-ertilizer in sustainable agriculture systems.

Mustard seed–associated endophytes suppress Sclerotinia sclerotiorum causing Sclerotinia rot in mustard crop

Mustard-rapeseed cultivation is affected by Sclerotinia sclerotiorum resulting in loss of oil yield and degradation of crop quality. This study adopted an environment friendly biocontrol approach of screening mustard endophytes against the pathogen. Two bacterial isolates, Bacillus safensis (TS46 bac4) and Bacillus australimaris (SM2) showed potential biocontrol activity under both in vitro and in vivo conditions. Dual culture assay reported 90% inhibition of fungal growth. The bacterial cell free supernatant of isolate SM2 showed 52.89% inhibition and the other isolate TS46 bac4 showed 57.97% inhibition. The crude (10 mg/ml) and purified (10 mg/ml) metabolite extract of SM2 showed 100% and 97% inhibition respectively. Both crude (10 mg/ml) and purified (7.5 mg/ml) metabolite extract of TS46 bac4 exhibited 99% inhibition of the pathogen. Antifungal lipopeptides: surfactin, iturin and fengycin were identified in bacterial metabolite extract of the isolates. Both strains promoted healthy germination and prevented the formation of any disease symptoms in seedling. The selected Bacillus strains applied by spray method showed better results against fungal infection on mustard leaf and stem. Microscopic studies revealed degradation of fungal mycelial growth by both isolates. These findings support the employment of the bacterial strains as potential biocontrol agents to reduce the effects of S. sclerotiorum in mustard-rapeseed.

Organic Amendments for Mitigation of Salinity Stress in Plants: A Review

Natural and/or human-caused salinization of soils has become a growing problem in the world, and salinization endangers agro-ecosystems by causing salt stress in most cultivated plants, which has a direct effect on food quality and quantity. Several techniques, as well as numerous strategies, have been developed in recent years to help plants cope with the negative consequences of salt stress and mitigate the impacts of salt stress on agricultural plants. Some of them are not environmentally friendly. In this regard, it is crucial to develop long-term solutions that boost saline soil productivity while also protecting the ecosystem. Organic amendments, such as vermicompost (VC), vermiwash (VW), biochar (BC), bio-fertilizer (BF), and plant growth promoting rhizobacteria (PGPR) are gaining attention in research. The organic amendment reduces salt stress and improves crops growth, development and yield. The literature shows that organic amendment enhances salinity tolerance and improves the growth and yield of plants by modifying ionic homeostasis, photosynthetic apparatus, antioxidant machineries, and reducing oxidative damages. However, the positive regulatory role of organic amendments in plants and their stress mitigation mechanisms is not reviewed adequately. Therefore, the present review discusses the recent reports of organic amendments in plants under salt stress and how stress is mitigated by organic amendments. The current assessment also analyzes the limitations of applying organic amendments and their future potential.

Contrasting genome patterns of two pseudomonas strains isolated from the date palm rhizosphere to assess survival in a hot arid environment

The plant growth-promoting rhizobacteria (PGPRs) improve plant growth and fitness by multiple direct (nitrogen fixation and phosphate solubilization) and indirect (inducing systematic resistance against phytopathogens, soil nutrient stabilization, and maintenance) mechanisms. Nevertheless, the mechanisms by which PGPRs promote plant growth in hot and arid environments remain poorly recorded. In this study, a comparative genome analysis of two phosphate solubilizing bacteria, Pseudomonas atacamensis SM1 and Pseudomonas toyotomiensis SM2, isolated from the rhizosphere of date palm was performed. The abundance of genes conferring stress tolerance (chaperones, heat shock genes, and chemotaxis) and supporting plant growth (plant growth hormone, root colonization, nitrogen fixation, and phosphate solubilization) were compared among the two isolates. This study further evaluated their functions, metabolic pathways, and evolutionary relationship. Results show that both bacterial strains have gene clusters required for plant growth promotion (phosphate solubilization and root colonization), but it is more abundant in P. atacamensis SM1 than in P. toyotomiensis SM2. Genes involved in stress tolerance (mcp, rbs, wsp, and mot), heat shock, and chaperones (hslJ and hslR) were also more common in P. atacamensis SM1. These findings suggest that P. atacamensis SM1could have better adaptability to the hot and arid environment owing to a higher abundance of chaperone genes and heat shock proteins. It may promote plant growth owing to a higher load of root colonization and phosphate solubilization genes and warrants further in vitro study.

Individual and combined application of Cu-tolerant Bacillus spp. enhance the Cu phytoextraction efficiency of perennial ryegrass

Forage grasses have recently received a remarkable amount of attention as promising candidates for decontaminating metal-polluted soils, but this strategy is time-consuming and inefficient. The present study aimed to address the beneficial effects of screened plant growth-promoting rhizobacteria (PGPR) strains Bacillus sp. EhS5 and EhS7 on perennial ryegrass and tall fescue. Single or combined inoculation considerably increased the biomass yield and Cu content of inoculated ryegrass compared with uninoculated plants, thereby enhancing the extraction efficiency at different Cu contamination levels. Bioaugmentation did not show a positive impact on the improvement of fescue's phytoextraction efficiency. Principal component analysis (PCA) and Pearson correlation coefficient results identified root development and photosynthesis as the key variables influencing ryegrass biomass. Antioxidant activities and Cu bioavailability are the key variables influencing Cu accumulation. The inoculated ryegrass showed improved photosynthetic status as the photosystem II system efficiency parameters increased and energy dissipation in the form of heat (DI_o/RC) decreased with the help of PGPR. The root length, diameter, surface area, and forks of inoculated ryegrass increased remarkably. The levels of scavengers of reactive oxygen species were enhanced in these plants. Moreover, PGPR significantly increased soil Cu bioavailability by secreting siderophores and organic acid and by increasing soil organic carbon content. Dual inoculation showed better results than individual inoculation in improving ryegrass growth and Cu translocation under high Cu contamination level according to PCA. This study systematically explored the effects and mechanisms of the Bacillus-ryegrass combined remediation and provided a novel method for cleaning Cu-contaminated sites.