Plant-growth-promoting compounds produced by two agronomically important strains of Azospirillum brasilense, and implications for inoculant formulation

An Engineered Device for Indoleacetic Acid Production under Quorum Sensing Signals Enables Cupriavidus pinatubonensis JMP134 To Stimulate Plant Growth

The environmental effects of chemical fertilizers and pesticides have encouraged the quest for new strategies to increase crop productivity with minimal impacts on the natural medium. Plant growth promoting rhizobacteria (PGPR) can contribute to this endeavor by improving fitness through better nutrition acquisition and stress tolerance. Using the neutral (non PGPR) rhizobacterium Cupriavidus pinatubonensis JMP134 as the host, we engineered a regulatory forward loop that triggered the synthesis of the phytohormone indole-3-acetic acid (IAA) in a manner dependent on quorum sensing (QS) signals. Implementation of the device in JMP134 yielded synthesis of IAA in an autoregulated manner, improving the growth of the roots of inoculated Arabidopsis thaliana. These results not only demonstrated the value of the designed genetic module, but also validated C. pinatubonensis JMP134 as a suitable vehicle for agricultural applications, as it is amenable to genetic manipulations.

Genomic characterization of Nitrospirillum amazonense strain CBAmC, a nitrogen-fixing bacterium isolated from surface-sterilized sugarcane stems

Nitrospirillum amazonense is a nitrogen-fixing bacterium that shows potential to promote plant growth when inoculated into sugarcane and rice plants. This microorganism has been the subject of biochemical and genetic characterization to elucidate important functions related to host plant interaction and growth promotion, including the determination of draft genome sequences of two strains, Y2 and CBAmC, the second of which is the aim of the present study. CBAmC has been isolated from sugarcane (Saccharum spp.), and is currently used in a sugarcane consortium inoculant with four other nitrogen-fixing bacterial strains. The present paper describes a significant improvement in the genome sequence and assembly for the N. amazonense strain CBAmC, and determination for the first time of a complete genome sequence for this bacterial species, using PacBio technology. The analysis of the genomic data obtained allowed the discovery of genes coding for metabolic pathways and cellular structures that may be determinant for the success of the bacterial establishment and colonization into the host sugarcane plant, besides conferring important characteristics to the inoculant. These include genes for the use of sucrose and N-glycans, biosynthesis of autoinducer molecules, siderophore production and acquisition, auxin and polyamine biosynthesis, flagellum, σ-fimbriae, a variety of secretion systems, and a complete denitrification system. Concerning genes for nitrogenase and auxiliary proteins, it was possible to corroborate literature data that in N. amazonense these probably had originated from horizontal gene transfer, from bacteria of the Rhizobiales order. The complete genomic sequence of the CBAmC strain of N. amazonense revealed that the bacterium harbors four replicons, including three chromosomes and one chromid, a profile that coincides with that of other two strains, according to literature data, suggesting that as a replicon pattern for the species. Finally, results of phylogenomic analyses in this work support the recent reclassification of the species, separating it from the Azospirillum genus. More importantly, results of the present work shall guide subsequent studies on strain CBAmC as well as the development of a sugarcane inoculant.

Characterization of Indole-3-acetic Acid Biosynthesis and the Effects of This Phytohormone on the Proteome of the Plant-Associated Microbe Pantoea sp. YR343

Indole-3-acetic acid (IAA) plays a central role in plant growth and development, and many plant-associated microbes produce IAA using tryptophan as the precursor. Using genomic analyses, we predicted that Pantoea sp. YR343, a microbe isolated from Populus deltoides, synthesizes IAA using the indole-3-pyruvate (IPA) pathway. To better understand IAA biosynthesis and the effects of IAA exposure on cell physiology, we characterized proteomes of Pantoea sp. YR343 grown in the presence of tryptophan or IAA. Exposure to IAA resulted in upregulation of proteins predicted to function in carbohydrate and amino acid transport and exopolysaccharide (EPS) biosynthesis. Metabolite profiles of wild-type cells showed the production of IPA, IAA, and tryptophol, consistent with an active IPA pathway. Finally, we constructed an Δ ipdC mutant that showed the elimination of tryptophol, consistent with a loss of IpdC activity, but was still able to produce IAA (20% of wild-type levels). Although we failed to detect intermediates from other known IAA biosynthetic pathways, this result suggests the possibility of an alternate pathway or the production of IAA by a nonenzymatic route in Pantoea sp. YR343. The Δ ipdC mutant was able to efficiently colonize poplar, suggesting that an active IPA pathway is not required for plant association.

Plant growth promoting bacteria as an alternative strategy for salt tolerance in plants: A review

Approximately 5.2 billion hectare agriculture land are affected by erosion, salinity and soil degradation. Salinity stress has significantly affecting the fertile lands, and therefore possesses a huge impact on the agriculture and economy of a country. Salt stress has severe effects on the growth and development of plants as well as reducing its yield. Plants are inherently equipped with stress tolerance ability to responds the specific type of stress. Plants retained specific mechanisms for salt stress mitigation, such as hormonal stimulation, ion exchange, antioxidant enzymes and activation of signaling cascades on their metabolic and genetic frontiers that sooth the stressed condition. Additional to the plant inherent mechanisms, certain plant growth promoting bacteria (PGPB) also have specialized mechanism that play key role for salt stress tolerance and plant growth promotion. These bacteria triggers plants to produce different plant growth hormones like auxin, cytokinine and gibberellin as well as volatile organic compounds. These bacteria also produces growth regulators like siderophore, which fix nitrogen, solubilize organic and inorganic phosphate. Considering the importance of PGPB in compensation of salt tolerance in plants, the present study has reviewed the different aspect and mechanism of bacteria that play key role in promoting plants growth and yield. It can be concluded that PGPB can be used as a cost effective and economical tool for salinity tolerance and growth promotion in plants.

Phytohormones and induction of plant-stress tolerance and defense genes by seed and foliar inoculation with Azospirillum brasilense cells and metabolites promote maize growth

Azospirillum spp. are plant-growth-promoting bacteria used worldwide as inoculants for a variety of crops. Among the beneficial mechanisms associated with Azospirillum inoculation, emphasis has been given to the biological nitrogen fixation process and to the synthesis of phytohormones. In Brazil, the application of inoculants containing A. brasilense strains Ab-V5 and Ab-V6 to cereals is exponentially growing and in this study we investigated the effects of maize inoculation with these two strains applied on seeds or by leaf spray at the V2.5 stage growth—a strategy to relieve incompatibility with pesticides used for seed treatment. We also investigate the effects of spraying the metabolites of these two strains at V2.5. Maize growth was promoted by the inoculation of bacteria and their metabolites. When applied via foliar spray, although A. brasilense survival on leaves was confirmed by confocal microscopy and cell recovery, few cells were detected after 24 h, indicating that the effects of bacterial leaf spray might also be related to their metabolites. The major molecules detected in the supernatants of both strains were indole-3-acetic acid, indole-3-ethanol, indole-3-lactic acid and salicylic acid. RT-PCR of genes related to oxidative stress (APX1, APX2, CAT1, SOD2, SOD4) and plant defense (pathogenesis-related PR1, prp2 and prp4) was evaluated on maize leaves and roots. Differences were observed according to the gene, plant tissue, strain and method of application, but, in general, inoculation with Azospirillum resulted in up-regulation of oxidative stress genes in leaves and down-regulation in roots; contrarily, in general, PR genes were down-regulated in leaves and up-regulated in roots. Emphasis should be given to the application of metabolites, especially of Ab-V5 + Ab-V6 that in general resulted in the highest up-regulation of oxidative-stress and PR genes both in leaves and in roots. We hypothesize that the benefits of inoculation of Azospirillum on seeds or by leaf spray, as well as of leaf spraying of Azospirillum metabolites, are strongly correlated with the synthesis of phytohormones and by eliciting genes related to plant-stress tolerance and defense against pathogens.

Exploring the Potentials of Lysinibacillus sphaericus ZA9 for Plant Growth Promotion and Biocontrol Activities against Phytopathogenic Fungi

There is an ongoing hunt for biologically active compounds that can combat phytopathogenic fungi and improve plant growth without causing any hazards to the environment. Consequently the present study aims at deciphering the plant growth promotion and antifungal capability of Lysinibacillus sphaericus ZA9. The bacterium was previously isolated and identified in our laboratory from maize rhizosphere using 16S rRNA gene sequencing. The test bacterium L. sphaericus ZA9 was found to produce high quantity of IAA (697 μg/ mL); siderophores (195.79 μg/ mL), HCN and hydrolytic enzyme as compared to the reference strain Bacillus sphaericus Z2-7. The bacterium was also capable of solubilizing silicates (Si), phosphates (P), and potassium (K). The bacterium enhanced the seedling vigor and germination of seeds pretreated with it and promoted the shoot length of both cucumber and tomato seeds in greenhouse experiment. L. sphaericus ZA9 and its cell free culture supernatant showed varied antagonistic behavior against Alternaria alternata, Curvularia lunata, Aspergillus sp., Sclerotinia sp., Bipolaris spicifera, Trichophyton sp. Fermentation broth culture of L. sphaericus ZA9 was then used to isolate antifungal metabolites by silica column chromatography. Identification and determination of antifungal compounds was carried out by Thin-layer chromatography (TLC) followed by NMR spectroscopy. Two compounds were isolated and identified as 2-pentyl-4-quinolinecarboxylic acid (C₁₅H₁₇NO₂) which is a quinoline alkaloid and 1- methylcyclohexene which is a cycloalkene. Compound 1; 2-Penthyl-4-quinolinecarboxylic acid was found to be highly antagonistic against most of the fungi tested as compared to the bacterium itself. Its activity was comparable to that of fungicide Benlate, while compound 2; 1- methylcyclohexene did not show any antifungal activity.

In vitro PGPR properties and osmotic tolerance of different Azospirillum native strains and their effects on growth of maize under drought stress

Osmotic variations in the soil can affect bacterial growth diminishing the number of inoculated bacteria. In a scenario of water deficit having tolerant bacteria would be beneficial to achieve a better response of the plant to stress. Thus, selection of more resistant bacteria could be useful to design new inoculants to be used in arid zones. In this sense, a group of Azospirillum isolates deposited in INTA collection was characterized in order to select strains tolerant to osmotic stress. The results obtained demonstrated that Az19 strain has similar in vitro PGPR characteristics to Az39, the most used strain in Argentina for inoculants industries, with the advantage of a better tolerance to osmotic and salt stress. Inoculation of maize plants with this strain resulted in a better response against water deficit compared to Az39 strain, encouraging us to further study the behavior of this strain in greenhouse and field trials in view of developing new inoculants suitable for areas with water deficit.

Biofertilizers: a potential approach for sustainable agriculture development

The worldwide increase in human population raises a big threat to the food security of each people as the land for agriculture is limited and even getting reduced with time. Therefore, it is essential that agricultural productivity should be enhanced significantly within the next few decades to meet the large demand of food by emerging population. Not to mention, too much dependence on chemical fertilizers for more crop productions inevitably damages both environmental ecology and human health with great severity. Exploitation of microbes as biofertilizers is considered to some extent an alternative to chemical fertilizers in agricultural sector due to their extensive potentiality in enhancing crop production and food safety. It has been observed that some microorganisms including plant growth promoting bacteria, fungi, Cyanobacteria, etc. have showed biofertilizer-like activities in the agricultural sector. Extensive works on biofertilizers have revealed their capability of providing required nutrients to the crop in sufficient amounts that resulted in the enhancement of crop yield. The present review elucidates various mechanisms that have been exerted by biofertilizers in order to promote plant growth and also provides protection against different plant pathogens. The aim of this review is to discuss the important roles and applications of biofertilizers in different sectors including agriculture, bioremediation, and ecology.

Modulation of phytoremediation and plant growth by the treatment with PGPR, Ag nanoparticle and untreated municipal wastewater

The present attempt was made to determine the effects of untreated municipal wastewater (MW) on growth and physiology of maize and to evaluate the role of Ag nanoparticle and plant-growth-promoting rhizobacteria (PGPR) when interacting with MW used for irrigation. It was used for the isolation of PGPR. The isolates were identified and characterized based on the colony morphology, C/N source utilization pattern using miniaturized identification system (QTS 24), catalase (CAT) and oxidase tests, and 16S rRNA sequence analyses. The three PGPR isolates were Planomicrobium chinense (accession no. NR042259), Bacillus cereus (accession no. CP003187) and Pseudomonas fluorescens (accession no. GU198110). The isolates solubilized phosphate and exhibited antibacterial activities against pathogenic bacteria i.e., Staphylococcus aureus, Pseudomonas aeruginosa, Bacillus subtilis, Klebsiella pneumoniae and Escherichia coli and antifungal activities against Helminthosporium sativum and Fusarium solani. The untreated MW irrigation as well as Ag nanoparticle treatment resulted in significant accumulation of Ni in the rhizosphere soil. PGPR induced accumulation of Ni and Pb in the rhizosphere soil and maize shoot. Ag nanoparticle also caused Ni and Pb accumulation in maize shoot. Combined treatment with PGPR, Ag nanoparticle and MW resulted in decreased accumulation of Pb and Ni both in the rhizosphere soil and maize shoot. Combined treatment of Ag nanoparticle, MW and PGPR decreased Na accumulation and increased K accumulation. Ag nanoparticle increased Fe and Co accumulation but decreased Zn and Cu accumulation in MW treatment; in combined treatment, it reduced PGPR-induced accumulation of Co and Fe in the rhizosphere and Co accumulation in shoot. PGPR significantly increased root weight, shoot weight, root length, shoot length, leaf area, and proline, chlorophyll and carotenoid content of the maize plant. Ag nanoparticle also enhanced the leaf area, fresh weight, root length and antioxidant activities of maize. Treatment with Ag nanoparticle increased the gibberellic acid (GA) and abscisic acid (ABA) content of maize leaves but decreased the accumulation of GA in the presence of PGPR and MW.

Proteomic analyses of the interaction between the plant-growth promoting rhizobacterium Paenibacillus polymyxa E681 and Arabidopsis thaliana

Plant growth-promoting rhizobacteria (PGPR) facilitate the plant growth and enhance their induced systemic resistance (ISR) against a variety of environmental stresses. In this study, we carried out integrative analyses on the proteome, transcriptome, and metabolome to investigate Arabidopsis root and shoot responses to the well-known PGPR strain Paenibacillus polymyxa (P. polymyxa) E681. Shoot fresh and root dry weights were increased, whereas root length was decreased by treatment with P. polymyxa E681. 2DE approach in conjunction with MALDI-TOF/TOF analysis revealed a total of 41 (17 spots in root, 24 spots in shoot) that were differentially expressed in response to P. polymyxa E681. Biological process- and molecular function-based bioinformatics analysis resulted in their classification into seven different protein groups. Of these, 36 proteins including amino acid metabolism, antioxidant, defense and stress response, photosynthesis, and plant hormone-related proteins were up-regulated, whereas five proteins including three carbohydrate metabolism- and one amino acid metabolism-related, and one unknown protein were down-regulated, respectively. A good correlation was observed between protein and transcript abundances for the 12 differentially expressed proteins during interactions as determined by qPCR analysis. Metabolite analysis using LC-MS/MS revealed highly increased levels of tryptophan, indole-3-acetonitrile (IAN), indole-3-acetic acid (IAA), and camalexin in the treated plants. Arabidopsis plant inoculated P. polymyxa E681 also showed resistance to Botrytis cinerea infection. Taken together these results suggest that P. polymyxa E681 may promote plant growth by induced metabolism and activation of defense-related proteins against fungal pathogen.

Isolation and identification by 16S rRNA sequence analysis of plant growth-promoting azospirilla from the rhizosphere of wheat

The main objective of the present study was to isolate phytohormone-producing, phosphate-solubilizing strains of Azospirillum from wheat to be used as inoculants for plant growth promotion. Five Azospirillum strains were isolated from the rhizosphere of field-grown wheat (Triticum aestivum L.), and it was confirmed by BOX-polymerase chain reaction (PCR) that the isolates were different and not re-isolates of the same strain. Sequence analysis of the PCR-amplified 16S rRNA gene indicated that four isolates showed maximum similarity to Azospirillum brasilense and one isolate showed maximum similarity to Azospirillum zeae. This is the first report indicating the presence of an A. zeae like isolate in the wheat rhizosphere in Pakistan. The bacterial isolates were characterized for their plant growth-promoting traits, phosphate solubilization, and indole-3-acetic acid (IAA) production. None of the isolates showed phosphate solubilization activity in the commonly used Pikovskaya medium. However, all strains (except AzoK4) exhibited ability to solubilize tricalcium phosphate (TCP) in modified Pikovskaya medium in which sucrose was replaced by Na-malate, as well as in TCP-supplemented Luria-Bertani (LB) medium. Organic acids, such as acetic, citric, lactic, malic, and succinic acids, were detected in culture supernatants of the tested Azospirillum strains. All strains exhibited ability to produce IAA in the growth medium, except Azospirillum sp. AzoK1. Among the strains tested, the maximum IAA production (30.49±1.04mgL(-1)) and phosphate solubilization (105.50±4.93mgL(-1)) were shown by a pure culture of Azospirillum sp. AzoK2. In pot experiments, single-strain inocula of Azospirillum sp. AzoK1 and AzoK2 improved wheat plant growth.

A Carotenoid-Deficient Mutant in Pantoea sp. YR343, a Bacteria Isolated from the Rhizosphere of Populus deltoides, Is Defective in Root Colonization

The complex interactions between plants and their microbiome can have a profound effect on the health and productivity of the plant host. A better understanding of the microbial mechanisms that promote plant health and stress tolerance will enable strategies for improving the productivity of economically important plants. Pantoea sp. YR343 is a motile, rod-shaped bacterium isolated from the roots of Populus deltoides that possesses the ability to solubilize phosphate and produce the phytohormone indole-3-acetic acid (IAA). Pantoea sp. YR343 readily colonizes plant roots and does not appear to be pathogenic when applied to the leaves or roots of selected plant hosts. To better understand the molecular mechanisms involved in plant association and rhizosphere survival by Pantoea sp. YR343, we constructed a mutant in which the crtB gene encoding phytoene synthase was deleted. Phytoene synthase is responsible for converting geranylgeranyl pyrophosphate to phytoene, an important precursor to the production of carotenoids. As predicted, the ΔcrtB mutant is defective in carotenoid production, and shows increased sensitivity to oxidative stress. Moreover, we find that the ΔcrtB mutant is impaired in biofilm formation and production of IAA. Finally we demonstrate that the ΔcrtB mutant shows reduced colonization of plant roots. Taken together, these data suggest that carotenoids are important for plant association and/or rhizosphere survival in Pantoea sp. YR343.

Novel components of leaf bacterial communities of field-grown tomato plants and their potential for plant growth promotion and biocontrol of tomato diseases

This work aimed to characterize potentially endophytic culturable bacteria from leaves of cultivated tomato and analyze their potential for growth promotion and biocontrol of diseases caused by Botrytis cinerea and Pseudomonas syringae. Bacteria were obtained from inner tissues of surface-disinfected tomato leaves of field-grown plants. Analysis of 16S rRNA gene sequences identified bacterial isolates related to Exiguobacterium aurantiacum (isolates BT3 and MT8), Exiguobacterium spp. (isolate GT4), Staphylococcus xylosus (isolate BT5), Pantoea eucalypti (isolate NT6), Bacillus methylotrophicus (isolate MT3), Pseudomonas veronii (isolates BT4 and NT2), Pseudomonas rhodesiae (isolate BT2) and Pseudomonas cichorii (isolate NT3). After seed inoculation, BT2, BT4, MT3, MT8, NT2 and NT6 were re-isolated from leaf extracts. NT2, BT2, MT3 and NT6 inhibited growth of Botrytis cinerea and Pseudomonas syringae pv. tomato in vitro, produced antimicrobial compounds and reduced leaf damage caused by B. cinerea. Some of these isolates also promoted growth of tomato plants, produced siderophores, the auxin indole-3-acetic and solubilized inorganic phosphate. Thus, bacterial communities of leaves from field-grown tomato plants were found to harbor potentially endophytic culturable beneficial bacteria capable of antagonizing pathogenic microorganisms and promoting plant growth, which could be used as biological control agents and biofertilizers/biostimulators for promotion of tomato plant growth.

Establishing a Role for Bacterial Cellulose in Environmental Interactions: Lessons Learned from Diverse Biofilm-Producing Proteobacteria

Bacterial cellulose (BC) serves as a molecular glue to facilitate intra- and inter-domain interactions in nature. Biosynthesis of BC-containing biofilms occurs in a variety of Proteobacteria that inhabit diverse ecological niches. The enzymatic and regulatory systems responsible for the polymerization, exportation, and regulation of BC are equally as diverse. Though the magnitude and environmental consequences of BC production are species-specific, the common role of BC-containing biofilms is to establish close contact with a preferred host to facilitate efficient host-bacteria interactions. Universally, BC aids in attachment, adherence, and subsequent colonization of a substrate. Bi-directional interactions influence host physiology, bacterial physiology, and regulation of BC biosynthesis, primarily through modulation of intracellular bis-(3'→5')-cyclic diguanylate (c-di-GMP) levels. Depending on the circumstance, BC producers exhibit a pathogenic or symbiotic relationship with plant, animal, or fungal hosts. Rhizobiaceae species colonize plant roots, Pseudomonadaceae inhabit the phyllosphere, Acetobacteriaceae associate with sugar-loving insects and inhabit the carposphere, Enterobacteriaceae use fresh produce as vehicles to infect animal hosts, and Vibrionaceae, particularly Aliivibrio fischeri, colonize the light organ of squid. This review will highlight the diversity of the biosynthesis and regulation of BC in nature by discussing various examples of Proteobacteria that use BC-containing biofilms to facilitate host-bacteria interactions. Through discussion of current data we will establish new directions for the elucidation of BC biosynthesis, its regulation and its ecophysiological roles.

The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes

All plants are inhabited internally by diverse microbial communities comprising bacterial, archaeal, fungal, and protistic taxa. These microorganisms showing endophytic lifestyles play crucial roles in plant development, growth, fitness, and diversification. The increasing awareness of and information on endophytes provide insight into the complexity of the plant microbiome. The nature of plant-endophyte interactions ranges from mutualism to pathogenicity. This depends on a set of abiotic and biotic factors, including the genotypes of plants and microbes, environmental conditions, and the dynamic network of interactions within the plant biome. In this review, we address the concept of endophytism, considering the latest insights into evolution, plant ecosystem functioning, and multipartite interactions.

The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes

All plants are inhabited internally by diverse microbial communities comprising bacterial, archaeal, fungal, and protistic taxa. These microorganisms showing endophytic lifestyles play crucial roles in plant development, growth, fitness, and diversification. The increasing awareness of and information on endophytes provide insight into the complexity of the plant microbiome. The nature of plant-endophyte interactions ranges from mutualism to pathogenicity. This depends on a set of abiotic and biotic factors, including the genotypes of plants and microbes, environmental conditions, and the dynamic network of interactions within the plant biome. In this review, we address the concept of endophytism, considering the latest insights into evolution, plant ecosystem functioning, and multipartite interactions.

Cultivation-Based and Molecular Assessment of Bacterial Diversity in the Rhizosheath of Wheat under Different Crop Rotations

A field study was conducted to compare the formationand bacterial communities of rhizosheaths of wheat grown under wheat-cotton and wheat-rice rotation and to study the effects of bacterial inoculation on plant growth. Inoculation of Azospirillum sp. WS-1 and Bacillus sp. T-34 to wheat plants increased root length, root and shoot dry weight and dry weight of rhizosheathsoil when compared to non-inoculated control plants, and under both crop rotations. Comparing both crop rotations, root length, root and shoot dry weight and dry weight of soil attached with roots were higher under wheat-cotton rotation. Organic acids (citric acid, malic acid, acetic acid and oxalic acid) were detected in rhizosheaths from both rotations, with malic acid being most abundant with 24.8±2 and 21.3±1.5 μg g^-1 dry soil in wheat-cotton and wheat-rice rotation, respectively. Two sugars (sucrose, glucose) were detected in wheat rhizosheath under both rotations, with highest concentrations of sucrose (4.08±0.5 μg g^-1and 7.36±1.0 μg g^-1) and glucose (3.12±0.5 μg g^-1 and 3.01± μg g^-1) being detected in rhizosheaths of non-inoculated control plants under both rotations. Diversity of rhizosheath-associated bacteria was evaluated by cultivation, as well as by 454-pyrosequencing of PCR-tagged 16S rRNA gene amplicons. A total of 14 and 12 bacterial isolates predominantly belonging to the genera Arthrobacter, Azospirillum, Bacillus, Enterobacter and Pseudomonaswere obtained from the rhizosheath of wheat grown under wheat-cotton and wheat-rice rotation, respectively. Analysis of pyrosequencing data revealed Proteobacteria, Bacteriodetes and Verrucomicrobia as the most abundant phyla in wheat-rice rotation, whereas Actinobacteria, Firmicutes, Chloroflexi, Acidobacteria, Planctomycetes and Cyanobacteria were predominant in wheat-cotton rotation. From a total of 46,971 sequences, 10.9% showed ≥97% similarity with 16S rRNA genes of 32 genera previously shown to include isolates with plant growth promoting activity (nitrogen fixation, phosphate-solubilization, IAA production). Among these, the most predominant genera were Arthrobacter, Azoarcus, Azospirillum, Bacillus, Cyanobacterium, Paenibacillus, Pseudomonas and Rhizobium.

Isolation and characterization of multifunctional Streptomyces species with antimicrobial, nematicidal and phytohormone activities from marine environments in Egypt

Different strategies have been employed for selective isolation of Streptomycetes from 20 marine samples varied in their biological nature. The recovery of Streptomycetes isolates (112) was influenced preferentially by different strategies; sediment samples were the best source of potential candidate Streptomycetes. All isolates exhibited antimicrobial activities with variable spectrum; the most promising isolates (31) were phenotypically characterized and identified as Streptomyces sp.; these isolates exhibited variable capacity for secretion of numerous hydrolytic enzymes such as catalase, protease, amylase, lipase, lecithinase, asparaginase, chitinase and pectinase. All the strains resisted both penicillin and streptomycin, 29 were sensitive to neomycin; the majority of strains (25) showed multiple antibiotic resistance index greater than 0.2; 23, 22 and 13 degraded the shrimp shell, chicken feather and corn cob, respectively, producing bioactive substance(s) which indicates their diversity and their ecological role in the marine ecosystem. At least 28 strains exhibited nematicidal activity in vitro and in vivo against root-knot nematode and supported plant growth. In vitro, the assessed Streptomyces species exhibited the ability to produce gibberellic acid, indole acetic acid, abscisic acid, kinetin and benzyladenine. Except for indole acetic acid, this is the first report concerning the ability of marine Streptomyces to produce such phytohormones and the use of shrimp shell waste as a mono component medium for production of phytohormones. The study is efficacious in selecting effective biodiverse strains of marine Streptomyces that may work under diverse agro-ecological conditions as a useful element in plant nutrition and as biocontrol agents involved in integrated management programs.

Natural variation in the expression of ORGANIC CATION TRANSPORTER 1 affects root length responses to cadaverine in Arabidopsis

Polyamines, including cadaverine, are organic cations that affect numerous biological processes including transcription, translation, cell signalling, and ion channel activity. They often function in biotic and abiotic stress responses in plants. Because little is known about how plants respond to cadaverine, a quantitative natural variation approach was used to identify genetic factors that contribute to this response. Here it is shown that Arabidopsis thaliana accessions have varying root length responses to exogenous cadaverine: Cape Verde Islands (Cvi) was one of the most resistant accessions tested, whereas Landsberg erecta (Ler) was one of the most sensitive. Recombinant inbred lines, near isogenic lines, and a microarray were used to show that variation in ORGANIC CATION TRANSPORTER 1 (OCT1) is at least partially responsible for this difference. OCT1 expression was higher in Cvi than in Ler, and oct1 mutants were more sensitive to cadaverine than wild-type plants. In oct1 mutants transformed with an ectopic copy of OCT1 originating from either Cvi or Ler, the expression level of the transgene, not its accession, correlated with the cadaverine response. These results suggest that decreased OCT1 expression confers cadaverine sensitivity in some accessions.

Microorganisms associated to tomato seedlings growing in saline culture act as osmoprotectant

Less than 0.5% of total water in the world is available for human consumption and agriculture. The major part of the world’s water is saline and salinity in soils interferes in germination of seeds and the posterior development of the plant. In order to increase the osmotolerance of tomato, seedlings were associated with Azospirillum brasilense Cd, Azospirillum brasilense Cd transformed bacteria with a plasmid harboring a trehalose biosynthesis gene-fusion or Chlorella vulgaris. Two plant culture media: Hydroponic and Murashige and Skoog were tested. In the first set of studies seedlings were associated to single free cells meanwhile in a second set single and combined free cells were studied. A positive interaction between transformed Azospirillum and Chlorella vulagris and tomato plants was observed. Seedlings showed a salt concentration tolerance, as sodium chloride, up to 200 mM. According to our results, the association of plants with A. brasilense Cd-BIF and C. vulgaris is a viable approach to increase their salt tolerance and biomass, as consequence the possible use of sea water to irrigate horticultural plants.

Interaction with ectomycorrhizal fungi and endophytic Methylobacterium affects nutrient uptake and growth of pine seedlings in vitro

Tissues of Scots pine (Pinus sylvestris L.) contain several endophytic microorganisms of which Methylobacterium extorquens DSM13060 is a dominant species throughout the year. Similar to other endophytic bacteria, M. extorquens is able to colonize host plant tissues without causing any symptoms of disease. In addition to endophytic bacteria, plants associate simultaneously with a diverse set of microorganisms. Furthermore, plant-colonizing microorganisms interact with each other in a species- or strain-specific manner. Several studies on beneficial microorganisms interacting with plants have been carried out, but few deal with interactions between different symbiotic organisms and specifically, how these interactions affect the growth and development of the host plant. Our aim was to study how the pine endophyte M. extorquens DSM13060 affects pine seedlings and how the co-inoculation with ectomycorrhizal (ECM) fungi [Suillus variegatus (SV) or Pisolithus tinctorius (PT)] alters the response of Scots pine. We determined the growth, polyamine and nutrient contents of inoculated and non-inoculated Scots pine seedlings in vitro. Our results show that M. extorquens is able to improve the growth of seedlings at the same level as the ECM fungi SV and PT do. The effect of co-inoculation using different symbiotic organisms was seen in terms of changes in growth and nutrient uptake. Inoculation using M. extorquens together with ECM fungi improved the growth of the host plant even more than single ECM inoculation. Symbiotic organisms also had a strong effect on the potassium content of the seedling. The results indicate that interaction between endophyte and ECM fungus is species dependent, leading to increased or decreased nutrient content and growth of pine seedlings.

Growth-promoting Sphingomonas paucimobilis ZJSH1 associated with Dendrobium officinale through phytohormone production and nitrogen fixation

Growth-promoting Sphingomonas paucimobilis ZJSH1, associated with Dendrobium officinale, a traditional Chinese medicinal plant, was characterized. At 90 days post-inoculation, strain ZJSH1 significantly promoted the growth of D. officinale seedlings, with increases of stems by 8.6% and fresh weight by 7.5%. Interestingly, the polysaccharide content extracted from the inoculated seedlings was 0.6% higher than that of the control. Similar growth promotion was observed with the transplants inoculated with strain ZJSH1. The mechanism of growth promotion was attributed to a combination of phytohormones and nitrogen fixation. Strain ZJSH1 was found using the Kjeldahl method to have a nitrogen fixation activity of 1.15 mg l⁻¹, which was confirmed by sequencing of the nifH gene. Using high-performance liquid chromatography-mass spectrometry, strain ZJSH1 was found to produce various phytohormones, including salicylic acid (SA), indole-3-acetic acid (IAA), Zeatin and abscisic acid (ABA). The growth curve showed that strain ZJSH1 grew well in the seedlings, especially in the roots. Accordingly, much higher contents of SA, ABA, IAA and c-ZR were detected in the inoculated seedlings, which may play roles as both phytohormones and ‘Systemic Acquired Resistance’ drivers. Nitrogen fixation and secretion of plant growth regulators (SA, IAA, Zeatin and ABA) endow S. paucimobilis ZJSH1 with growth-promoting properties, which provides a potential for application in the commercial growth of D. officinale.

Complete Genome Sequence of the Model Rhizosphere Strain Azospirillum brasilense Az39, Successfully Applied in Agriculture

We present the complete genome sequence of Azospirillum brasilense Az39, isolated from wheat roots in the central region of Argentina and used as inoculant in extensive and intensive agriculture during the last four decades. The genome consists of 7.39 Mb, distributed in six replicons: one chromosome, three chromids, and two plasmids.

Phenotypic and molecular characterization of native Azospirillum strains from rice fields to improve crop productivity

Beneficial microorganisms have been considered as an important tool for crop improvement. Native isolates of Azospirillum spp. were obtained from the rhizospheres of different rice fields. Phenotypic, biochemical and molecular characterizations of these isolates led to the identification of six efficient strain of Azospirillum. PCR amplification of the nif genes (nifH, nifD and nifK) and protein profile of Azospirillum strains revealed inter-generic and inter-specific diversity among the strains. In vitro nitrogen fixation performance and the plant growth promotion activities, viz. siderophore, HCN, salicylic acid, IAA, GA, zeatin, ABA, NH3, phosphorus metabolism, ACC deaminase and iron tolerance were found to vary among the Azospirillum strains. The effect of Azospirillum formulations on growth of rice var. Khandagiri under field condition was evaluated, which revealed that the native formulation of Azospirillum of CRRI field (As6) was most effective to elevate endogenous nutrient content, and improved growth and better yield are the result. The 16S rRNA sequence revealed novelty of native Azospirillum lipoferum (As6) (JQ796078) in the NCBI database.

Biofertilizers function as key player in sustainable agriculture by improving soil fertility, plant tolerance and crop productivity

Current soil management strategies are mainly dependent on inorganic chemical-based fertilizers, which caused a serious threat to human health and environment. The exploitation of beneficial microbes as a biofertilizer has become paramount importance in agriculture sector for their potential role in food safety and sustainable crop production. The eco-friendly approaches inspire a wide range of application of plant growth promoting rhizobacteria (PGPRs), endo- and ectomycorrhizal fungi, cyanobacteria and many other useful microscopic organisms led to improved nutrient uptake, plant growth and plant tolerance to abiotic and biotic stress. The present review highlighted biofertilizers mediated crops functional traits such as plant growth and productivity, nutrient profile, plant defense and protection with special emphasis to its function to trigger various growth- and defense-related genes in signaling network of cellular pathways to cause cellular response and thereby crop improvement. The knowledge gained from the literature appraised herein will help us to understand the physiological bases of biofertlizers towards sustainable agriculture in reducing problems associated with the use of chemicals fertilizers.

Phenotypic and molecular characterisation of efficient nitrogen-fixing Azotobacter strains from rice fields for crop improvement

Biological nitrogen fixation (BNF) is highly effective in the field and potentially useful to reduce adverse effects chemical fertilisers. Here, Azotobacter species were selected via phenotypic, biochemical and molecular characterisations from different rice fields. Acetylene reduction assay of Azotobacter spp. showed that Azotobacter vinelandii (Az3) fixed higher amount of nitrogen (121.09 nmol C2H4 mg(-1) bacteria h(-1)). Likewise, its plant growth functions, viz. siderophore, hydrogen cyanide, salicylic acid, IAA, GA3, zeatin, NH3, phosphorus solubilisation, ACC deaminase and iron tolerance, were also higher. The profile of gDNA, plasmid DNA and cellular protein profile depicted inter-generic and inter-specific diversity among the isolates of A. vinelandii. The PCR-amplified genes nifH, nifD and nifK of 0.87, 1.4 and 1.5 kb , respectively, were ascertained by Southern blot hybridisation in isolates of A. vinelandii. The 16S rRNA sequence from A. vinelandii (Az3) was novel, and its accession number (JQ796077) was received from NCBI data base. Biofertiliser formulation of novel A. vinelandii isolates along with commercial one was evaluated in rice (Oriza sativa L. var. Khandagiri) fields. The present finding revealed that treatment T4 (Az3) (A. vinelandii) are highly efficient to improved growth and yield of rice crop.

Abscisic acid metabolizing rhizobacteria decrease ABA concentrations in planta and alter plant growth

Although endogenous phytohormones such as abscisic acid (ABA) regulate root growth, and many rhizobacteria can modulate root phytohormone status, hitherto there have been no reports of rhizobacteria mediating root ABA concentrations and growth by metabolising ABA. Using a selective ABA-supplemented medium, two bacterial strains were isolated from the rhizosphere of rice (Oryza sativa) seedlings grown in sod-podzolic soil and assigned to Rhodococcus sp. P1Y and Novosphingobium sp. P6W using partial 16S rRNA gene sequencing and phenotypic patterns by the GEN III MicroPlate test. Although strain P6W had more rapid growth in ABA-supplemented media than strain P1Y, both could utilize ABA as a sole carbon source in batch culture. When rice seeds were germinated on filter paper in association with bacteria, root ABA concentration was not affected, but shoot ABA concentration of inoculated plants decreased by 14% (strain P6W) and 22% (strain P1Y). When tomato (Solanum lycopersicum) genotypes differing in ABA biosynthesis (ABA deficient mutants flacca - flc, and notabilis - not and the wild-type cv. Ailsa Craig, WT) were grown in gnotobiotic cultures on nutrient solution agar, rhizobacterial inoculation decreased root and/or leaf ABA concentrations, depending on plant and bacteria genotypes. Strain P6W inhibited primary root elongation of all genotypes, but increased leaf biomass of WT plants. In WT plants treated with silver ions that inhibit ethylene perception, both ABA-metabolising strains significantly decreased root ABA concentration, and strain P6W decreased leaf ABA concentration. Since these changes in ABA status also occurred in plants that were not treated with silver, it suggests that ethylene was probably not involved in regulating bacteria-mediated changes in ABA concentration. Correlations between plant growth and ABA concentrations in planta suggest that ABA-metabolising rhizobacteria may stimulate growth via an ABA-dependent mechanism.

Genotypic characterization of Azotobacteria isolated from Argentinean soils and plant-growth-promoting traits of selected strains with prospects for biofertilizer production

The genetic diversity among 31 putative Azotobacter isolates obtained from agricultural and non-agricultural soils was assessed using rep-PCR genomic fingerprinting and identified to species level by ARDRA and partial 16S rRNA gene sequence analysis. High diversity was found among the isolates, identified as A. chroococcum, A. salinestris, and A. armeniacus. Selected isolates were characterized on the basis of phytohormone biosynthesis, nitrogenase activity, siderophore production, and phosphate solubilization. Indole-3 acetic-acid (IAA), gibberellin (GA3) and zeatin (Z) biosynthesis, nitrogenase activity, and siderophore production were found in all evaluated strains, with variation among them, but no phosphate solubilization was detected. Phytohormones excreted to the culture medium ranged in the following concentrations: 2.2-18.2 μ g IAA mL(-1), 0.3-0.7 μ g GA3 mL(-1), and 0.5-1.2 μ g Z mL(-1). Seed inoculations with further selected Azotobacter strains and treatments with their cell-free cultures increased the number of seminal roots and root hairs in wheat seedlings. This latter effect was mimicked by treatments with IAA-pure solutions, but it was not related to bacterial root colonization. Our survey constitutes a first approach to the knowledge of Azotobacter species inhabiting Argentinean soils in three contrasting geographical regions. Moreover, this phenotypic characterization constitutes an important contribution to the selection of Azotobacter strains for biofertilizer formulations.

Plant growth-promoting rhizobacteria and root system functioning

The rhizosphere supports the development and activity of a huge and diversified microbial community, including microorganisms capable to promote plant growth. Among the latter, plant growth-promoting rhizobacteria (PGPR) colonize roots of monocots and dicots, and enhance plant growth by direct and indirect mechanisms. Modification of root system architecture by PGPR implicates the production of phytohormones and other signals that lead, mostly, to enhanced lateral root branching and development of root hairs. PGPR also modify root functioning, improve plant nutrition and influence the physiology of the whole plant. Recent results provided first clues as to how PGPR signals could trigger these plant responses. Whether local and/or systemic, the plant molecular pathways involved remain often unknown. From an ecological point of view, it emerged that PGPR form coherent functional groups, whose rhizosphere ecology is influenced by a myriad of abiotic and biotic factors in natural and agricultural soils, and these factors can in turn modulate PGPR effects on roots. In this paper, we address novel knowledge and gaps on PGPR modes of action and signals, and highlight recent progress on the links between plant morphological and physiological effects induced by PGPR. We also show the importance of taking into account the size, diversity, and gene expression patterns of PGPR assemblages in the rhizosphere to better understand their impact on plant growth and functioning. Integrating mechanistic and ecological knowledge on PGPR populations in soil will be a prerequisite to develop novel management strategies for sustainable agriculture.

Alternative mechanism for the evaluation of indole-3-acetic acid (IAA) production by Azospirillum brasilense strains and its effects on the germination and growth of maize seedlings

We evaluated the production of indole-3-acetic acid (IAA) by Azospirillum brasilense strains in vitro (cell culture supernatants) and in vivo (stems and roots of maize seedlings) to clarify the role of this phytohormone as a signaling and effector molecule in the symbiotic interaction between maize and A. brasilense. The three strains all showed IAA production when cultured in NFb medium supplemented with 100 μg/ml L-tryptophan. The level of IAA production was 41.5 μg/ml for Yu62, 12.9 μg/ml for Az39, and 0.15 μg/ml for ipdC-. The release of IAA into culture medium by the bacteria appeared to be the main activator of the early growth promotion observed in the inoculated maize seedlings. The application of supernatants with different IAA contents caused significant differences in the seedling growth. This observation provides the basis for novel technological tools for effective quality control procedures on inoculants. The approach described can be incorporated into different inoculation methods, including line sowing, downspout, and foliar techniques, and increase the sustainability of symbiotic plant-bacteria systems.

Plant growth-promoting bacteria as a tool to improve salinity tolerance in sweet pepper

To characterise the effect of bacterial inoculants (Azospirillum brasilense and Pantoea dispersa) on the response of sweet pepper (Capsicum annuum L.) to saline stress, plants were exposed to 0, 40, 80 and 120mM NaCl in solution. The effect on plant growth; leaf gas exchange; NO3-, Cl-, K+ and Na+ accumulation; and chlorophyll fluorescence and content were investigated. Total plant DW was reduced significantly by salinity but when inoculants were applied, DW was increased. Inoculated plants showed higher DW accumulation in the roots. Salinity levels up to 80mM NaCl did not affect the net assimilation rate in inoculated plants but 40mM NaCl was enough to reduce this parameter in non-inoculated plants. The leaf area ratio was not modified substantially by inoculation. The leaf Cl- concentration of inoculated plants was reduced at the highest salinity, compared with control plants, and NO3- concentration increased markedly. A higher K+:Na+ ratio was found in inoculated plants. Leaf photosynthesis and stomatal conductance were impaired significantly at moderate, but not low, salinity, the effect of inoculation being enough to maintain higher stomatal conductance under higher stress. The photochemical efficiency of PSII and the relative chlorophyll content were not affected by the inoculants. Thus, the effects of the inoculants on the response to salinity were due mainly to stomatal regulation of photosynthesis rather than effects on biochemical limitations on photosynthesis. These results indicate the benefits of these bacterial inoculants in ameliorating the deleterious effect of NaCl in a salt-sensitive crop like sweet pepper.

Genetic and management approaches to boost UK wheat yields by ameliorating water deficits

Faced with the challenge of increasing global food production, there is the need to exploit all approaches to increasing crop yields. A major obstacle to boosting yields of wheat (an important staple in many parts of the world) is the availability and efficient use of water, since there is increasing stress on water resources used for agriculture globally, and also in parts of the UK. Improved soil and crop management and the development of new genotypes may increase wheat yields when water is limiting. Technical and scientific issues concerning management options such as irrigation and the use of growth-promoting rhizobacteria are explored, since these may allow the more efficient use of irrigation. Fundamental understanding of how crops sense and respond to multiple abiotic stresses can help improve the effective use of irrigation water. Experiments are needed to test the hypothesis that modifying wheat root system architecture (by increasing root proliferation deep in the soil profile) will allow greater soil water extraction thereby benefiting productivity and yield stability. Furthermore, better knowledge of plant and soil interactions and how below-ground and above-ground processes communicate within the plant can help identify traits and ultimately genes (or alleles) that will define genotypes that yield better under dry conditions. Developing new genotypes will take time and, therefore, these challenges need to be addressed now.

Response to saline stress and aquaporin expression in Azospirillum-inoculated barley seedlings

The ability of two strains of Azospirillum brasilense to mitigate NaCl stress in barley plants was evaluated. Barley seedlings were inoculated and subjected to 200 mM NaCl for 18 days. Several days after NaCl treatment, a significant decline in biomass as well as in height was observed in uninoculated plants. However, smaller reductions in biomass and height were detected in plants inoculated with strain Az39. All the stressed plants showed significantly higher Na(+) but lower K(+) contents in their shoots. The growth rate of uninoculated plants was adversely affected by saline treatment, which was associated with higher putrescine content and lower levels of HvPIP2;1 transcripts in the roots. Azospirillum inoculation triggered the transcription of this gene. Our results suggest that barley plants inoculated with A. brasilense may be better prepared to thrive under saline conditions. To our knowledge, this is the first report showing an effect of Azospirillum inoculation on the expression of PIP2;1, a gene involved in the synthesis of root water channels.