Isolation and characterization of phosphate solubilizing bacterium Pseudomonas aeruginosa KUPSB12 with antibacterial potential from river Ganga, India

Rhizobium dioscoreae sp. nov., a plant growth-promoting bacterium isolated from yam (Dioscorea species)

This study investigated endophytic nitrogen-fixing bacteria isolated from two species of yam (water yam, Dioscorea alata L.; lesser yam, Dioscorea esculenta L.) grown in nutrient-poor alkaline soil conditions on Miyako Island, Okinawa, Japan. Two bacterial strains of the genus Rhizobium, S-93^T and S-62, were isolated. The phylogenetic tree, based on the almost-complete 16S rRNA gene sequences (1476 bp for each strain), placed them in a distinct clade, with Rhizobium miluonense CCBAU 41251^T, Rhizobium hainanense I66^T, Rhizobium multihospitium HAMBI 2975^T, Rhizobium freirei PRF 81^T and Rhizobium tropici CIAT 899^T being their closest species. Their bacterial fatty acid profile, with major components of C_19 : 0 cyclo ω8c and summed feature 8, as well as other phenotypic characteristics and DNA G+C content (59.65 mol%) indicated that the novel strains belong to the genus Rhizobium. Pairwise average nucleotide identity analyses separated the novel strains from their most closely related species with similarity values of 90.5, 88.9, 88.5, 84.5 and 84.4 % for R. multihospitium HAMBI 2975^T, R. tropici CIAT 899^T, R. hainanense CCBAU 57015^T, R. miluonense HAMBI 2971^T and R. freirei PRF 81^T, respectively; digital DNA–DNA hybridization values were in the range of 26–42 %. Considering the phenotypic characteristics as well as the genomic data, it is suggested that strains S-93^T and S-62 represent a new species, for which the name Rhizobium dioscoreae is proposed. The type strain is S-93^T (=NRIC 0988^T=NBRC 114257^T=DSM 110498^T).

Mitigation of drought stress in rice crop with plant growth-promoting abiotic stress-tolerant rice phyllosphere bacteria

In the search of effective drought-alleviating and growth-promoting phyllosphere bacteria, a total of 44 bacterial isolates were isolated from the leaf surface of drought-tolerant rice varieties, Mattaikar, Nootripattu, Anna R(4), and PMK3, and screened for their abiotic stress tolerance by subjecting their growth medium to temperature, salinity, and osmotic stress. Only eight isolates were found to grow and proliferate under different abiotic stress conditions. These isolates were identified using 16S ribosomal DNA gene sequence and submitted to the NCBI database. All the bacterial isolates were identified as Bacillus sp., except PB24, which was identified as Staphylococcus sp., and these isolates were further screened for plant growth-promoting (PGP) traits such as IAA production, GA production, ACC deaminase activity, and exopolysaccharide production under three different osmotic stress conditions adjusted using polyethylene glycol (PEG 6000). Additionally, mineral solubilization was measured under the normal condition. Bacillus endophyticus PB3, Bacillus altitudinis PB46, and Bacillus megaterium PB50 were found to have multifarious PGP traits. Consecutively, the performance of an individual strain to improve the plant growth was investigated under the osmotic stress (25% PEG 6000) and nonstress condition by inoculating them into rice seeds using hydroponics culture. Furthermore, the drought-alleviating potency of bacterial strains was assessed in the rice plants using pot experiment (-1.2 MPa) through bacterial foliar application during the reproductive stage. Finally, as a result of seed inoculation and foliar spray, the application of B. megaterium PB50 significantly improved the plant growth under osmotic stress, protected plants from physical drought through stomatal closure, and improved carotenoid, total soluble sugars, and total protein content. Metabolites of PB50 were profiled under both stress and nonstress conditions using gas chromatography-mass spectroscopy.

Phosphate Solubilizing Rhizobacteria Could Have a Stronger Influence on Wheat Root Traits and Aboveground Physiology Than Rhizosphere P Solubilization

Limited P availability in several agricultural areas is one of the key challenges facing current agriculture. Exploiting P-solubilizing bacteria (PSB) has been an emerging bio-solution for a higher rhizosphere P-availability, meanwhile the above- and below-ground interactions that PSB would trigger remain unclear over plant growing stages. We hypothesized that PSB effects on plant growth may be greater on root traits that positively links with aboveground physiology more than the commonly believed rhizosphere P bio-solubilization. In this study, five contrasting PSB (Pseudomonas spp.) isolates (low "PSB1", moderate "PSB2 and PSB4" and high "PSB3 and PSB5" P-solubilizing capacity "PSC") were used to investigate above- and below-ground responses in wheat fertilized with rock P (RP) under controlled conditions. Our findings show that all PSB isolates increased wheat root traits, particularly PSB5 which increased root biomass and PSB3 that had greater effect on root diameter in 7-, 15- and 42-day old plants. The length, surface and volume of roots significantly increased along with higher rhizosphere available P in 15- and 42-day old plants inoculated with PSB4 and PSB2. Shoot biomass significantly increased with both PSB2 and PSB5. Root and shoot physiology significantly improved with PSB1 (lowest PSC) and PSB4 (moderate PSC), notably shoot total P (78.38%) and root phosphatase activity (390%). Moreover, nutrients acquisition and chlorophyll content increased in inoculated plants and was stimulated (PSB2, PSB4) more than rhizosphere P-solubilization, which was also revealed by the significant above- and below-ground inter-correlations, mainly chlorophyll and both total (R = 0.75, p = 0.001**) and intracellular (R = 0.7, p = 0.000114*) P contents. These findings demonstrate the necessity to timely monitor the plant-rhizosphere continuum responses, which may be a relevant approach to accurately evaluate PSB through considering below- and above-ground relationships; thus enabling unbiased interpretations prior to field applications.

Beneficial Endophytic Bacterial Populations Associated With Medicinal Plant Thymus vulgaris Alleviate Salt Stress and Confer Resistance to Fusarium oxysporum

As a result of climate change, salinity has become a major abiotic stress that reduces plant growth and crop productivity worldwide. A variety of endophytic bacteria alleviate salt stress; however, their ecology and biotechnological potential has not been fully realized. To address this gap, a collection of 117 endophytic bacteria were isolated from wild populations of the herb Thymus vulgaris in Sheikh Zuweid and Rafah of North Sinai Province, Egypt, and identified based on their 16S rRNA gene sequences. The endophytes were highly diverse, including 17 genera and 30 species. The number of bacterial species obtained from root tissues was higher (n = 18) compared to stem (n = 14) and leaf (n = 11) tissue. The endophytic bacteria exhibited several plant growth-promoting activities in vitro, including auxin synthesis, diazotrophy, phosphate solubilization, siderophore production, and production of lytic enzymes (i.e., chitinase, cellulase, protease, and lipase). Three endophytes representing Bacillus species associated with T. vulgaris such as EGY05, EGY21, and EGY25 were selected based on their ex-situ activities for growth chamber assays to test for their ability to promote the growth of tomato (Solanum lycopersicum L.) under various NaCl concentrations (50-200 mM). All three strains significantly (P < 0.05) promoted the growth of tomato plants under salt stress, compared to uninoculated controls. In addition, inoculated tomato plants by all tested strains decreased (P < 0.05) the activity of antioxidant enzymes (superoxide dismutase, catalase, and peroxidase). Six strains, representing Bacillus and Enterobacter species EGY01, EGY05, EGY16, EGY21, EGY25, and EGY31 were selected based on in vitro antagonistic activity to F. oxysporum for pot experiments under salt stress. All tested strains reduced the disease severity index (DSI) of tomato plants at all tested salt concentrations. Gas-chromatography/mass-spectrometry analysis of cell-free extracts of B. subtilis (EGY16) showed at least ten compounds were known to have antimicrobial activity, with the major peaks being benzene, 1,3-dimethyl-, p-xylene, dibutyl phthalate, bis (2-ethylhexyl) phthalate, and tetracosane. This study demonstrates that diverse endophytes grow in wild thyme populations and that some are able to alleviate salinity stress and inhibit F. oxysporum pathogenesis, making them promising candidates for biofertilizers and biocontrol agents.

Identification and Characterization of the Phosphate-Solubilizing Bacterium Pantoea sp. S32 in Reclamation Soil in Shanxi, China

Phosphate solubilizing bacteria (PSB) can convert insoluble forms of phosphorus (P) to accessible forms. Five highly efficient PSB strains, H22, Y11, Y14, Y34, and S32, were screened and isolated from an alfalfa rhizosphere in heavy metal-contaminated reclamation area in Shanxi Province, China. Based on morphological observations, 16S rRNA sequencing, cellular fatty acid composition analysis, and the BIOLOG test, H22, Y11, and Y34 were identified as Pseudomonas sp., while Y14 and S32 were identified as Pantoea sp. Among them, S32 showed the highest P-solubilizing efficiency in culture medium containing Ca₃(PO₄)₂, lecithin, and powered phosphate rock. The culture medium conditions to obtain the highest P-solubilization efficiency were optimized as follows: the culture temperature was 30°C; the incubation time was 5 days; the initial pH was 7.0; and glucose served as the carbon source. Furthermore, the P-solubilization efficiency of S32 in media containing CaHPO₄, lecithin, phosphate rock (PR), FePO₄, or AlPO₄ was determined to be 18.38, 3.07, 0.16, 0.51, or 2.62%, respectively. In addition, the acid and alkali phosphatase activities of S32 were tested as 6.94 U/100 mL and 4.12 U/100 mL, respectively. The soil inoculation experiment indicated that inoculation with S32 resulted in an obvious improvement in the available P of both the experimental and reclaimed soil. The rice seedling growth experiment also suggested that the application of S32 significantly increased the plant height, biomass, root growth, and P uptake of rice in both experimental and reclaimed soil. Taken together, the isolated S32 strain showed high P-solubilization capacity for both Pi and Po, and its ameliorative effect on reclaimed soil recovery provides the theoretical basis for crop development in the reclaimed soil of mine field.

ACC Deaminase Producing Bacteria With Multifarious Plant Growth Promoting Traits Alleviates Salinity Stress in French Bean (Phaseolus vulgaris) Plants

Plant growth promoting rhizobacteria (PGPR) with 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity has the potential to promote plant growth and development under adverse environmental conditions. In the present study, rhizobacterial strains were isolated from Garlic (Allium sativum) rhizosphere and were screened in vitro ACC deaminase activity in DF salt minimal media supplemented with 3 mM ACC. Out of six isolates, two could degrade ACC into α-ketobutyrate, exhibiting ACC deaminase activity producing more than ∼1500 nmol of α-ketobutyrate mg protein^-1 h^-1, and assessed for other plant growth promoting (PGP) functions including indole acetic acid production (greater than ∼30 μg/ml), siderophore, Ammonia, Hydrogen cyanide production and inorganic Ca₃(PO₄)₂ (∼85 mg/L) and ZnSO₄ solubilization. Besides facilitating multifarious PGP activities, these two isolates augmented in vitro stress tolerance in response to 6% w/v NaCl salt stress and drought stress (-0.73 Mpa). The strains ACC02 and ACC06 were identified Aneurinibacillus aneurinilyticus and Paenibacillus sp., respectively on the basis of 16S rDNA gene sequence analysis and were evaluated for growth promoting potential in French bean seedlings under non-saline and salinity stress conditions through pot experiments. The seed bacterization by ACC02 and ACC06 revealed that treatment of plants with bacterial isolates in the form of consortia significantly declined (∼60%) stress stimulated ethylene levels and its associated growth inhibition by virtue of their ACC deaminase activity. The consortia treatment alleviated the negative effects of salinity stress and increased root length (110%), root fresh weight (∼45%), shoot length (60%), shoot fresh weight (255%), root biomass (220%), shoot biomass (425%), and total chlorophyll content (∼57%) of French bean seedlings subjected to salinity stress.

Glucose dehydrogenase gene containing phosphobacteria for biofortification of Phosphorus with growth promotion of rice

Phosphorus (P) is an essential plant nutrient, but often limited in soils for plant uptake. A major economic constraint in the rice production is excessive use of chemical fertilizers to meet the P requirement. Bioaugmentation of phosphate solubilizing rhizobacteria (PSB) can be used as promising alternative. In the present study 11 mineral PSB were isolated from Basmati rice growing areas of Pakistan. In broth medium, PSB solubilized tricalcium phosphate (27-354 μg mL^-1) with concomitant decrease in pH up to 3.6 due to the production of different organic acids, predominantly gluconic acid. Of these, 4 strains also have ability to mineralize phytate (245-412 μg mL^-1). Principle component analysis showed that the gluconic acid producing PSB strains (Acinetobacter sp. MR5 and Pseudomonas sp. MR7) have pronounced effect on grain yield (up to 55%), plant P (up to 67%) and soil available P (up to 67%), with 20% reduced fertilization. For simultaneous validation of gluconic acid production by MR5 and MR7 through PCR, new specific primers were designed to amplify gcd, pqqE, pqqC genes responsible for glucose dehydrogenase (gcd) mediated phosphate solubilization. These findings for the first time demonstrated Acinetobacter soli as potent P solubilizer for rice and expands our knowledge about genus specific pqq and gcd primers. These two gcd containing PSB Acinetobacter sp. MR5 (DSM 106631) and Pseudomonas sp. MR7 (DSM 106634) submitted to German culture collection (DSMZ), serve as global valuable pool to significantly increase the P uptake, growth and yield of Basmati rice with decreased dependence on chemical fertilizer in P deficit agricultural soils.

Synergistic plant-microbe interactions between endophytic bacterial communities and the medicinal plant Glycyrrhiza uralensis F

Little is known about the composition, diversity, and geographical distribution of bacterial communities associated with medicinal plants in arid lands. To address this, a collection of 116 endophytic bacteria were isolated from wild populations of the herb Glycyrrhiza uralensis Fisch (licorice) in Xinyuan, Gongliu, and Tekesi of Xinjiang Province, China, and identified based on their 16S rRNA gene sequences. The endophytes were highly diverse, including 20 genera and 35 species. The number of distinct bacterial genera obtained from root tissues was higher (n = 14) compared to stem (n = 9) and leaf (n = 6) tissue. Geographically, the diversity of culturable endophytic genera was higher at the Tekesi (n = 14) and Xinyuan (n = 12) sites than the Gongliu site (n = 4), reflecting the extremely low organic carbon content, high salinity, and low nutrient status of Gongliu soils. The endophytic bacteria exhibited a number of plant growth-promoting activities ex situ, including diazotrophy, phosphate and potassium solubilization, siderophore production, auxin synthesis, and production of hydrolytic enzymes. Twelve endophytes were selected based on their ex situ plant growth-promoting activities for growth chamber assays to test for their ability to promote growth of G. uralensis F. and Triticum aestivum (wheat) plants. Several strains belonging to the genera Bacillus (n = 6) and Achromobacter (n = 1) stimulated total biomass production in both G. uralensis and T. aestivum under low-nutrient conditions. This work is the first report on the isolation and characterization of endophytes associated with G. uralensis F. in arid lands. The results demonstrate the broad diversity of endophytes associated with wild licorice and suggest that some Bacillus strains may be promising candidates for biofertilizers to promote enhanced survival and growth of licorice and other valuable crops in arid environments.