Occurrence, identification and characterization of diazotrophic bacteria from aerial roots of Rhynchostylis retusa (L.) Blume for plant growth-promoting activity

In this study, the diversity of diazotrophic bacteria of orchid Rhynchostylis retusa (L.) Blume and its potential application in plant growth promotion were evaluated. About 183 nitrogen-fixing bacteria were isolated to screen various plant growth-promoting traits viz. phosphate solubilization,IAA, siderophore, HCN, biofilm and ammonia production. Based on 16S rRNA gene sequencing analysis Achromobacter, Arthrobacter, Acinetobacter, Bacillus, Brevibacterium, Curtobacterium, Erwinia, Kosakonia, Lysinibacillus, Klebseilla, Microbacterium, Mixta, Pantoea, Pseudomonas and Stenotrophomonas isolates were selected and showed positive results for PGP traits. Overall, genus Pantoea, Brevibacterium, Achromobacter, Arthrobacter, Klebsiella, Mixta, Bacillus, and Pseudomonas had the most pronounced PGP characteristics and acetylene reduction among the screened isolates. BOX PCR fingerprinting analysis showed variation in polymorphic banding patterns among diazotrophic strains. PCR amplification of nifH gene and the presence of 37 kDa nitrogenase reductase enzyme band in western blot indicated presence of nitrogenase activity. Our study showed that orchid R. retusa diazotroph interaction helps orchid plant to fix nitrogen, essential nutrients, and control pathogen entry. To the best of our knowledge, this is the first report on characterization of diazotrophic bacterial community from aerial roots of R. retusa.

Endorhizosphere of indigenous succulent halophytes: a valuable resource of plant growth promoting bacteria

The adaptability of halophytes to increased soil salinity is related to complex rhizosphere interactions. In this study, an integrative approach, combining culture-independent and culture-dependent techniques was used to analyze the bacterial communities in the endorizosphere of indigenous succulent halophytes Salicornia europaea, Suaeda maritima, and Camphorosma annua from the natural salt marshes of Slano Kopovo (Serbia). The 16 S rDNA analyses gave, for the first time, an insight into the composition of the endophytic bacterial communities of S. maritima and C. annua. We have found that the composition of endophyte microbiomes in the same habitat is to some extent influenced by plant species. A cultivable portion of the halophyte microbiota was tested at different NaCl concentrations for the set of plant growth promoting (PGP) traits. Through the mining of indigenous halotolerant endophytes, we obtained a collection representing a core endophyte microbiome conferring desirable PGP traits. The majority (65%) of the selected strains belonged to the common halotolerant/halophilic genera Halomonas, Kushneria, and Halobacillus, with representatives exhibiting multiple PGP traits, and retaining beneficial traits in conditions of the increased salinity. The results suggest that the root endosphere of halophytes is a valuable source of PGP bacteria supporting plant growth and fitness in salt-affected soils.

Salinity alleviator bacteria in rice (Oryza sativa L.), their colonization efficacy, and synergism with melatonin

In this study, rhizospheric and endophytic bacteria were tested for the alleviation of salinity stress in rice. Endophytic isolates were taken from previous studies based on their salt stress-alleviating traits. The rhizospheric bacteria were isolated from rice and screened based on salt tolerance and plant growth-promoting traits. Molecular identification indicated the presence of class Gammaproteobacteria, Bacillota, and Actinomycetia. Two-two most potential isolates each from rhizospheric and endophytic bacteria were selected for in planta trials. Results showed that microbial inoculation significantly improved germination and seedling vigor under elevated salinity. The confocal scanning laser microscopy showed higher bacterial colonization in inoculated rice roots than in control. Based on this experiment, rhizospheric bacteria Brevibacterium frigoritolerans W19 and endophytic Bacillus safensis BTL5 were selected for pot trial along with a growth-inducing compound melatonin 20 ppm. Inoculation of these two bacteria improved the levels of chlorophyll, proline, phenylalanine ammonia-lyase, catalase, superoxide dismutase, polyphenol oxidase, root-shoot length, and dry weight under elevated salt concentration. The gene expression studies showed modulation of SOD1, CATa, NHX1, and PAL1 genes by the bacterial strains and melatonin application. The inoculation was found to have additive effects with 20 ppm melatonin. This enhancement in dry matter accumulation, compatible solute production, and oxidative stress regulation could help plants in mitigating the ill effects of high salinity. Exploring such a combination of microbes and inducer molecules could be potentially useful in developing stress-alleviating bioformulations.

Molecular identification and characterization of phytobeneficial osmotolerant endophytic bacteria inhabiting root nodules of the Saharan tree Vachellia tortilis subsp. raddiana

Nodular endophytes of drought-tolerant legumes are understudied. For this reason, we have isolated and studied non-symbiotic endophytic bacteria from nodules of Vachellia tortilis subsp. raddiana, a leguminous tree adapted to the harsh arid climate of Southern Morocco. Rep-PCR analysis followed by 16S rDNA sequencing revealed two main genera, Pseudomonas and Bacillus. Isolates responded variably to salt and water stresses, and mostly produced exopolysaccharides. Differences concerned also plant growth-promoting activities: phosphate, potassium, and zinc solubilization; biological nitrogen fixation; auxin, siderophore, ammonia, and HCN production; and ACC deaminase activity. Some strains exhibited antagonistic activities against phytopathogenic fungi (Fusarium oxysporum and Botrytis cinerea) and showed at least two enzymatic activities (cellulase, protease, chitinase). Four selected strains inoculated to vachellia plants under controlled conditions have shown significant positive impacts on plant growth parameters. These strains are promising bio-inoculants for vachellia plants to be used in reforestation programs in arid areas increasingly threatened by desertification.

Characterization of rhizobia isolated from leguminous plants and their impact on the growth of ICCV 2 variety of chickpea (Cicer arietinum L.)

Six rhizobia-like-bacterial strains in total, secluded from the root and stem nodules of various leguminous plants were characterized for growth promoting ability on ICCV 2 variety of chickpea. Bacterial strains showed production of IAA, NH₃, siderophore, HCN, ACC deaminase, hydrolytic enzyme production such as chitinase, amylase, protease, lipase, β-1, 3-glucanase and solubilization of nutrients such as phosphate, zinc and potassium. However the performance of PGP traits characterized in-vitro varied among the six bacterial strains. The sequences of 16S rRNA gene of bacterial strains IHSR, IHRG, IHAA, IHGN-3, IHCP-1 and IHCP-2 showed maximum identity with Rhizobium sp., Rhizobium tropici, Rhizobium multihospitium, Mesorhizobium sp., Burkholderia cepacia and Rhizobium pusense. In plate culture conditions the bacterial strains changed the colour of media (NFB) from green to blue and showed amplification of nifH gene by PCR, and also enhanced nodule formation in chickpea under greenhouse conditions, which explains their nitrogen fixing ability. Scanning electron microscopy studies of chickpea roots showed colonization by all the six bacterial strains in solo and by consortium (IHRG + IHGN-3). Under greenhouse conditions, chickpea plants inoculated with different strains showed improvement in plant height, number of branches, total chlorophyll, nodule number, nodule weight, shoot weight, root weight, root volume and root surface area at 30 and 45 days after sowing (DAS) over the uninoculated control plants. It was also observed at the crop maturity stage all the bacterial strains inoculated separately enhanced pod number, seed number and total NPK compared to uninoculated control plants. This study suggests that bacteria associated with root and stem nodules can be a promising resource to enhance nodulation, PGP and crop yields in chickpea.

Production of Plant Beneficial and Antioxidants Metabolites by Klebsiellavariicola under Salinity Stress

Bacteria that surround plant roots and exert beneficial effects on plant growth are known as plant growth-promoting rhizobacteria (PGPR). In addition to the plant growth-promotion, PGPR also imparts resistance against salinity and oxidative stress and needs to be studied. Such PGPR can function as dynamic bioinoculants under salinity conditions. The present study reports the isolation of phytase positive multifarious Klebsiella variicola SURYA6 isolated from wheat rhizosphere in Kolhapur, India. The isolate produced various plant growth-promoting (PGP), salinity ameliorating, and antioxidant traits. It produced organic acid, yielded a higher phosphorous solubilization index (9.3), maximum phytase activity (376.67 ± 2.77 U/mL), and copious amounts of siderophore (79.0%). The isolate also produced salt ameliorating traits such as indole acetic acid (78.45 ± 1.9 µg/mL), 1 aminocyclopropane-1-carboxylate deaminase (0.991 M/mg/h), and exopolysaccharides (32.2 ± 1.2 g/L). In addition to these, the isolate also produced higher activities of antioxidant enzymes like superoxide dismutase (13.86 IU/mg protein), catalase (0.053 IU/mg protein), and glutathione oxidase (22.12 µg/mg protein) at various salt levels. The isolate exhibited optimum growth and maximum secretion of these metabolites during the log-phase growth. It exhibited sensitivity to a wide range of antibiotics and did not produce hemolysis on blood agar, indicative of its non-pathogenic nature. The potential of K. variicola to produce copious amounts of various PGP, salt ameliorating, and antioxidant metabolites make it a potential bioinoculant for salinity stress management.

The Screening of Potassium- and Phosphate-Solubilizing Actinobacteria and the Assessment of Their Ability to Promote Wheat Growth Parameters

Soil fertility and plant nutrition require an adequate management of essential macronutrients such as potassium (K) and phosphorus (P), which are mandatory for plant development. Bioleaching of K and P bearing minerals improves their chemical weathering and increases the performance of the biofertilization strategies. In this study, in vitro and greenhouse experiments were carried out to investigate P and K solubilization traits of nine Actinobacteria (P13, P14, P15, P16, P17, P18, BC3, BC10, and BC11) under fertilization with rock phosphate (RP). K and P solubilization were evaluated on Alexandrov and NBRIP media containing mica and six RP samples, respectively. The actinobacterial strains were able to solubilize K in Alexandrov medium supplemented with RP. However, when soluble P was used instead of RP, only four strains of Actinobacteria (Streptomyces alboviridis P18–Streptomyces griseorubens BC3–Streptomyces griseorubens BC10 and Nocardiopsis alba BC11) solubilized K. The solubilization values of K ranged from 2.6 to 41.45 mg/L while those of P varied from 0.1 to 32 mg/L. Moreover, all strains were able to produce IAA, siderophore, HCN, and ammonia and significantly improved the germination rate and the vigor index of wheat. The pot experiments revealed that four strains (Streptomyces alboviridis P18, Streptomyces griseorubens BC3, Streptomyces griseorubens BC10, and Nocardiopsis alba BC11) significantly improved the growth parameters of wheat, namely root length (1.75–23.84%), root volume (41.57–71.46%), root dry weight (46.89–162.41%), shoot length (8.92–23.56%), and shoot dry weight (2.56–65.68%) compared to the uninoculated control. These findings showed that Streptomyces griseorubens BC10 and Nocardiopsis alba BC11 are promising candidates for the implementation of efficient biofertilization strategies to improve soil fertility and plant yield under rock P and rock K fertilization.

ACC deaminase and antioxidant enzymes producing halophilic Enterobacter sp. PR14 promotes the growth of rice and millets under salinity stress

Rhizobacteria are known to ameliorate salinity stress through a wide variety of mechanisms including the production of aminocyclopropane-1-carboxylate deaminase (ACCD). Application of ACCD positive halophilic rhizobacteria ameliorate soil salinity along with its plant growth promotion activity. An effect of the inoculation of ACCD and antioxidant positive and halophilic Enterobacter sp. PR14 was reported on the seed germination and growth of rice and millet seedlings grown in saline and alkaline soil was evaluated. The rhizobacterial strain grew well over a high level of NaCl (15-90 M); at a wide range of pH (5-9); and produced a wide variety of plant growth-promoting (PGP) traits viz. indole-acetic acid (13 µg mL-1), ACCD (5.20 M mg-1 h-1), phosphate solubilization (0.99 g mL-1) and antioxidant enzymes such as superoxide dismutase (5.143 IU mg-1 protein), catalase (0.43 IU mg-1 protein) and glutathione (19.077 µg mg-1 protein) during log phase (30 h) of its growth. The stress with alkaline pH (9) and high salinity (90 M) caused a further increase in the synthesis of PGP traits, ACCD, and antioxidant enzymes. The combined application of Enterobacter sp. PR14, ammonium sulfate (as a substitute of ACC), and NaCl (30 M) resulted in a further increase in the seed germination and vigor in rice and millets vis-à-vis control and other treatments. After 15 days of growth, 61.72% more seed germination in rice and millet and 63.15% increase in sorghum was recorded over the control, and after 30 days of growth, 99.67%, 30%, and 54%, root length 50%, 30% and 54% shoot length in rice, sorghum and millet were observed respectively. A significant increase of 38.13%, 30.75%, and 16.36% in dry weight of rice, sorghum, and millet shoots was recorded respectively. Enterobacter sp PR 14, showing multiple plant growth-promoting traits has a great potential to be used as an efficient bioinoculant for growth promotion of rice and millets under alkaline and saline conditions.

Antagonistic and plant-growth promoting novel Bacillus species from long-term organic farming soils from Sikkim, India

Three bacteria namely Bacillus luciferensis K2, Bacillus amyloliquefaciens K12 and Bacillus subtilis BioCWB possessing plant growth promotion and biocontrol potential against phytopathogens and rice leaf folder were identified from organic soils of Sikkim, India. The results revealed significant higher production of phytohormones IAA (97.1 μg mL^-1) and GA₃ (10.6 μg mL^-1) was found in K2, whereas BioCWB had higher phosphate solubilization (570.0 μg mL^-1) efficacy and also possessed nitrogen fixation ability (5.34 log copy number mL^-1 culture). All these bacteria had higher antagonistic activities against phytopathogens viz. Rhizoctonia solani, Fusarium proliferatum, Athelia rolfsii and Colletotrichum gloeosporioides and also had higher larvicidal activity against rice leaf folder Cnaphalocrocis medinalis (Guenne) under in vitro conditions. Molecular insights into the antagonistic mechanisms of Bacillus strains deciphered the presence of several antimicrobial peptides (ericin, subtilin, surfactin, iturin, bacilysin, subtilosin, fengycin and bacillomycin), volatiles (dimethyl disulphide, methyl-Furan, acetic acid, Z-1,3-pentadiene and 3-hexyn-2-ol) and soluble metabolites (9-octadecenamide, E-15-heptadecenal, E-3-eicosene and 5-octadecene). Furthermore, liquid microbial inoculum prepared using the bacterial strains (K2, K12 and BioCWB) were evaluated under glass house (rice) and field condition (capsicum), which significantly enhanced plant growth in rice and yield in capsicum compared to control. The present study revealed the combination of Bacillus spp. (K2, K12 and BioCWB) can be used as bio-inoculants for improving agricultural production in Sikkim. Moreover, for the first time, we demonstrated plant growth promoting (PGP) traits, antifungal and insecticidal properties of B. luciferensis.

Role of plant growth-promoting rhizobacterial consortium in improving the Vigna radiata growth and alleviation of aluminum and drought stresses

Aluminum (Al) is a major constraint for plant growth by inducing inhibition of root elongation in acid soils around the world. Besides, drought is another major abiotic stress that adversely affects growth and productivity of agricultural crops. The plant growth-promoting (PGP) rhizobacterial strains are useful choice to decrease these stressful effects and is now extensively in practice. However, the use of bacterial inoculation has not been attempted for the mitigation of Al stress in plants growing at high Al levels under drought stress. Therefore, in the present study, Al- and drought-tolerant bacterial strains were isolated from Lactuca sativa and Beta vulgaris rhizospheric soils. Among the bacterial isolates, two strains, CAM12 and CAH6, were selected based on their ability to tolerate high levels of Al (8 mM) and drought (15% PEG-6000, w/v) stresses. The bacterial strains CAM12 and CAH6 were identified as Bacillus megaterium and Pantoea agglomerans, respectively, by 16S rRNA gene sequence homology. Moreover, both strains showed multiple PGP traits even in the presence of abiotic stresses. In the pot experiments, inoculation of the strains CAM12 and CAH6 as individually or as included in a consortium improved the Vigna radiata growth under abiotic stress conditions and reduced Al uptake in plants. However, the most effective treatment was seen with bacterial consortium that allowed the plants to tolerate abiotic stress effectively and achieved better growth. These results indicate that bacterial consortium could be used as a bio-inoculant for enhancing V. radiata growth in soil with high Al levels subjected to drought conditions.

Petroleum degradation by endophytic Streptomyces spp. isolated from plants grown in contaminated soil of southern Algeria

Petroleum hydrocarbons are well known by their high toxicity and recalcitrant properties. Their increasing utilization around worldwide led to environmental contamination. Phytoremediation using plant-associated microbe is an interesting approach for petroleum degradation and actinobacteria have a great potential for that. For this purpose, our study aimed to isolate, characterize, and assess the ability of endophytic actinobacteria to degrade crude petroleum, as well as to produce plant growth promoting traits. Seventeen endophytic actinobacteria were isolated from roots of plants grown naturally in sandy contaminated soil. Among them, six isolates were selected on the basis of their tolerance to petroleum on solid minimal medium and characterized by 16S rDNA gene sequencing. All petroleum-tolerant isolates belonged to the Streptomyces genus. Determination by crude oil degradation by gas chromatorgraph-flame ionization detector revealed that five strains could use petroleum as sole carbon and energy source and the petroleum removal achieved up to 98% after 7 days of incubation. These isolates displayed an important role in the degradation of the n-alkanes (C₆-C₃₀), aromatic and polycyclic aromatic hydrocarbons. All strains showed a wide range of plant growth promoting features such as siderophores, phosphate solubilization, 1-aminocyclopropane-1-carboxylate deaminase, nitrogen fixation and indole-3-acetic acid production as well as biosurfactant production. This is the first study highlighting the petroleum degradation ability and plant growth promoting attributes of endophytic Streptomyces. The finding suggests that the endophytic actinobacteria isolated are promising candidates for improving phytoremediation efficiency of petroleum contaminated soil.

Characterization of multifarious plant growth promoting traits of rhizobacterial strain AR6 under Chromium (VI) stress

Plant growth promoting rhizobacteria (PGPR) can increase the host plant tolerance to cope up with heavy metal induced stress, which can be improve plant growth. Thus, the present study was designed to isolate Cr(VI) tolerant PGPR strain and evaluate its plant growth promoting (PGP) properties under Cr(VI) stress. Rhizobacterial strain AR6 was isolated from the rhizosphere of Phaseolus vulgaris L. and showed 99% homology with Cellulosimicrobium funkei (KM032184) in BLASTn analysis. Strain AR6 was specifically selected due to its high Cr(VI) tolerance (1200μg/ml) and substantial production of PGP substances. Strain AR6 produced 36.75μg/ml of indole acetic acid (IAA), 60.40μg/ml of ammonia and 14.23μg/ml of exopolysaccharide (EPS). Moreover, strain AR6 showed positive results for catalase, protease, amylase, lipase production and phosphate solubilization. A trend of Cr(VI) concentration dependent progressive decline for PGP traits of strain AR6 was observed excluding EPS which was regularly increased on increasing concentrations of Cr(VI). Among the four tested Cr(VI) concentrations, 250μg/ml showed the maximum toxicity to PGP activities of strain AR6. Inoculation of rhizobacterial strain AR6 significantly increased the root length of test crops in the presence of Cr(VI) and produced a considerable number of colonizes on the root of versatile dicot and monocot plants. Moreover, strain AR6 exhibited strong antagonistic activity against phytopathogen Aspergillus niger. Thus, the present study suggests that metal tolerant and PGP activities of the rhizobacterial strain AR6 could be exploited for environmental and agricultural issues.

Assessment of Culturable Tea Rhizobacteria Isolated from Tea Estates of Assam, India for Growth Promotion in Commercial Tea Cultivars

In the present study, 217 rhizobacterial isolates were obtained from six different tea estates of Assam, India and subjected to preliminary in vitro plant growth promotion (PGP) screening for indole acetic acid (IAA) production, phosphate solubilization, siderophore production and ammonia production. Fifty isolates showed all the PGP traits and five isolates did not exhibit any PGP traits. These 50 potential isolates were further analyzed for quantitative estimation of the PGP traits along with the aminocyclopropane-1-carboxylate (ACC) deaminase, protease and cellulose production. After several rounds of screening, four rhizobacteria were selected based on their maximum ability to produce in vitro PGP traits and their partial 16S rRNA gene sequence analysis revealed that they belong to Enterobacter lignolyticus strain TG1, Burkholderia sp. stain TT6, Bacillus pseudomycoides strain SN29 and Pseudomonas aeruginosa strain KH45. To evaluate the efficacy of these four rhizobacteria as plant growth promoters, three different commercially important tea clones TV1, TV19, and TV20 plants were inoculated with these rhizobacteria in greenhouse condition and compared to the uninoculated control plants. Though, all the rhizobacterial treatments showed an increase in plant growth compared to control but the multivariate PCA analysis confirmed more growth promotion by TG1 and SN29 strains than the other treatments in all three clones. To validate this result, the fold change analysis was performed and it revealed that the tea clone TV19 plants inoculated with the E. lignolyticus strain TG1 showed maximum root biomass production with an increase in 4.3-fold, shoot biomass with increase in 3.1-fold, root length by 2.2-fold and shoot length by 1.6-fold. Moreover, two way ANOVA analysis also revealed that rhizobacterial treatment in different tea clones showed the significant increase (P < 0.05) in growth promotion compared to the control. Thus, this study indicates that the potential of these indigenous plant growth promoting rhizobacteria isolates to use as microbial inoculation or biofertilizer for growth promotion of tea crops.

Indole-3-acetic acid (IAA) production trait, a useful screening to select endophytic and rhizosphere competent bacteria for rice growth promoting agents

Plants select plant growth promoting rhizobacteria (PGPR) that are competitively fit to occupy compatible niches without causing pathological stress on them. However, when screening bacteria for plant growth promoting (PGP) agents, it is better to select bacteria for achieving the most promising isolates having suitable colonization and PGP traits. In most researches, it has been seen that following incubation, bacterial flora are taken at random from petri dishes for further study. However, this type of selection may remove some superior bacteria in terms of PGP traits and high colonization ability. Therefore, it is essential to study all the isolated bacteria in an economic way and select the best bacteria in terms of PGP traits and high colonization rate. A simple screening method to detect endophytic and rhizosphere bacteria, isolated from the plants in rotation with rice, for rice PGP agents based on a root colonization bioassay and a PGP trait is characterized. •Selected bacterial isolates based on their IAA producing trait have the potential for more PGP and colonization of rice plant.•IAA may be the first PGP trait for screening bacteria isolated from plant rotated with rice for rice PGP agents.•The screening procedure appears to be very effective and less time consuming.