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Effective rhizosphere colonization by plant growth promoting rhizobacteria (PGPR) is a prerequisite for its persistence performance under plant-root soil system. Therefore, to obtain effective strains, we have evaluated twelve strains of fluorescent Pseudomonas sp. from wheat rhizosphere exhibiting multifarious plant growth promoting (PGP) activities. These strains formed varying level of biofilm in vitro on abiotic surface. Two strains MW3 and MW4 with promising PGP activity but differing in biofilm forming ability. The biofilms were characterized by crystal violet assay, scanning electron and confocal laser scanning microscopy. The MW4 strain, a strong biofilm former is identified by16S rRNA gene sequence analysis. Strain MW4 showed strong biofilms compared to MW3. Similarly, wheat seeds treated with MW3 and MW4 revealed enhanced rhizospheric colonization by MW4 strain significantly (P ≤ 0.05) in higher number (logCFU g-1) up to 45 days after sowing compared to MW3. These findings suggested that strong biofilm forming ability of MW4 might have resulted in enhanced rhizosphere colonization. Therefore, biofilm forming ability of PGPR should be considered as an additional criterion in screening of fluorescent Pseudomonas sp.

Twelve Azotobacter isolates exhibited varying levels of biofilm formation in a microtiter plate assay. The most efficient biofilm-forming isolate, as identified by partial 16S rRNA gene sequencing analysis, was Azotobacter vinelandii (AZCH6). Two isolates (AZCH5 and AZCH6), showing similar plant growth-promoting traits but differing in in vitro biofilm forming capacity, were further investigated for biofilm characterization on glass coverslips and on roots of wheat seedlings using confocal laser scanning microscopy and scanning electron microscopy. Rhizosphere colonization by AZCH6 in terms of CFU g−1 of soil, was significantly higher (P≤0.05) as compared to AZCH5. The data revealed that AZCH6 and AZCH5 exhibits similar pattern between biofilm formation and rhizosphere colonization. Therefore, strong biofilm-forming ability of Azotobacter on plant roots should be considered an important criterion for selection of effective isolates for enhanced root colonization.

Microbial consortium of efficient strains for biological control helps in improving microbial efficacy, reliability, and consistency under diverse soil and environmental conditions. Different genera in consortial formulation occupy varied niches in the root zone, thereby restricting competition among them. In this review we have discussed critically the need of consortial application of bioagents, their role in rhizosphere colonization, and disease suppression. Potential of consortial application of bioagents against fungal, bacterial, and nematodes can be utilized to fullest extent by selecting most potential strains and not by arbitrary use of consortia. It was also discussed here that out of all the consortial formulation applied globally, very few show synergistic effect in consortia. A numerical analysis model to assess synergism is discussed in this chapter. Thus, it is essential to select strains of microbes very carefully to develop efficient consortia to suppress crop diseases.

1-aminocyclopropane-1-carboxylic acid (ACC) is a strong metabolism-dependent chemoattractant for the plant beneficial rhizobacterium Pseudomonas sp. UW4. It is unknown whether enhancing the metabolic rate of ACC can intensify the chemotaxis activity towards ACC and rhizocompetence. In this study, we selected four promoters to transcribe the UW4 ACC deaminase (AcdS) gene in the UW4 ΔAcdS mutant. PA is the UW4 AcdS gene promoter, PB20, PB10 and PB1 are synthetic promoters. The order of the AcdS gene expression level and AcdS activity of the four strains harboring the promoters were PB20 > PA > PB10 > PB1. Interestingly, the AcdS activity of the four strains and their parent strain UW4 was significantly positively correlated with their chemotactic activity towards ACC, rhizosphere colonization, roots elongation and dry weight promotion. The results released that enhancing the AcdS activity of PGPRenable them to achieve strong chemotactic responses to ACC, rhizocompetence and plant growth promotion.

Simple Summary Plant growth-promoting rhizobacteria (PGPR) are an eco-friendly alternative to the use of chemicals in agricultural production and crop protection. However, the efficacy of PGPR as bioinoculants can be diminished by a low capacity to colonize spaces in the rhizosphere. In this work, we review pioneering and recent developments on several important functions that rhizobacteria exhibit in order to compete, colonize, and establish themselves in the plant rhizosphere. Therefore, the use of highly competitive strains in open field trials should be a priority, in order to have consistent and better results in agricultural production activities. Abstract The application of plant growth-promoting rhizobacteria (PGPR) in the field has been hampered by a number of gaps in the knowledge of the mechanisms that improve plant growth, health, and production. These gaps include (i) the ability of PGPR to colonize the rhizosphere of plants and (ii) the ability of bacterial strains to thrive under different environmental conditions. In this review, different strategies of PGPR to colonize the rhizosphere of host plants are summarized and the advantages of having highly competitive strains are discussed. Some mechanisms exhibited by PGPR to colonize the rhizosphere include recognition of chemical signals and nutrients from root exudates, antioxidant activities, biofilm production, bacterial motility, as well as efficient evasion and suppression of the plant immune system. Moreover, many PGPR contain secretion systems and produce antimicrobial compounds, such as antibiotics, volatile organic compounds, and lytic enzymes that enable them to restrict the growth of potentially phytopathogenic microorganisms. Finally, the ability of PGPR to compete and successfully colonize the rhizosphere should be considered in the development and application of bioinoculants.

Verticillium wilt caused by a highly virulent, defoliating (D) pathotype of Verticillium dahliae is threatening olive production in Spain and other Mediterranean countries. This disease must be managed by an integrated strategy, in which biocontrol agents can play an important role. We have investigated the potential of Trichoderma asperellum strains for antagonism against V. dahliae and suppression of Verticillium wilt of olive caused by the D pathotype. First, we tested the antagonistic potential of T. asperellum strains Bt2, Bt3 and T25 against six V. dahliae isolates, four of the D and two of the nondefoliating (ND) pathotypes, in different in vitro assays. All T. asperellum strains overgrew the colonies of all V. dahliae isolates to a similar extent. However, extracellular compounds from strains Bt3 and T25 showed higher anti-V. dahliae activities than those of Bt2 in membrane assays. Also, growth of Bt2 was reduced by ND V. dahliae whereas that of Bt3 and T25 was not affected by V. dahliae-secreted compounds. In planta assays using strains Bt3 and T25, and ’Picual’ olive plants, showed that the two T. asperellum strains significantly reduced the severity of symptoms and the standardized area under the disease progress curve caused by highly virulent D V. dahliae, but not the final disease incidence. Strain T25 significantly increased growth of ‘Picual’ plants and displayed higher ability for colonizing the olive rhizosphere and establishing endophytic infection in olive roots than Bt3., This work was supported by projects from the “Consejería de Innovación, Ciencia y Empresa, Regional Government of Andalusia (P10-AGR 6082) and the Spanish Government MINECO (AGL2012-40041-C02), and co-financed with FEDER funds from the European Union. ICC was supported by a predoctoral fellowship of CICE, Regional Government of Andalusia (project P10-AGR 6082).

The field of agriculture requires new strategies to control the damage caused by phytopathogens and to effectively promote plant growth and production. Until recently, one of the best alternatives was the application of microorganisms exhibiting biocontrol and plant growth-promoting traits. Therefore, to select the best microorganisms, it is essential to analyse these beneficial activities based on reliable search methods and to ensure the greatest extent possible and their successful application in the field. In this chapter, we have summarized and compared different methods to detect direct and indirect activities that promote plant growth, with an emphasis on rhizobacteria. Moreover, we have compiled a detailed description of the methods that could be of interest for analysing bacterial isolates that exhibit potential plant growth-promoting activities.

Diseases associated with fungal root invasion cause a significant loss of fruit tree production worldwide. The bacterium Pseudomonas pseudoalcaligenes AVO110 controls avocado white root rot disease caused by Rosellinia necatrix by using mechanisms involving competition for nutrients and niches. Here, a functional genomics approach was conducted to identify the bacterial traits involved in the interaction with this fungal pathogen. Our results contribute to a better understanding of the multitrophic interactions established among bacterial biocontrol agents, the plant rhizosphere, and the mycelia of soilborne pathogens., The rhizobacterium Pseudomonas pseudoalcaligenes AVO110, isolated by the enrichment of competitive avocado root tip colonizers, controls avocado white root rot disease caused by Rosellinia necatrix. Here, we applied signature-tagged mutagenesis (STM) during the growth and survival of AVO110 in fungal exudate-containing medium with the goal of identifying the molecular mechanisms linked to the interaction of this bacterium with R. necatrix. A total of 26 STM mutants outcompeted by the parental strain in fungal exudate, but not in rich medium, were selected and named growth-attenuated mutants (GAMs). Twenty-one genes were identified as being required for this bacterial-fungal interaction, including membrane transporters, transcriptional regulators, and genes related to the metabolism of hydrocarbons, amino acids, fatty acids, and aromatic compounds. The bacterial traits identified here that are involved in the colonization of fungal hyphae include proteins involved in membrane maintenance (a dynamin-like protein and ColS) or cyclic-di-GMP signaling and chemotaxis. In addition, genes encoding a DNA helicase (recB) and a regulator of alginate production (algQ) were identified as being required for efficient colonization of the avocado rhizosphere. IMPORTANCE Diseases associated with fungal root invasion cause a significant loss of fruit tree production worldwide. The bacterium Pseudomonas pseudoalcaligenes AVO110 controls avocado white root rot disease caused by Rosellinia necatrix by using mechanisms involving competition for nutrients and niches. Here, a functional genomics approach was conducted to identify the bacterial traits involved in the interaction with this fungal pathogen. Our results contribute to a better understanding of the multitrophic interactions established among bacterial biocontrol agents, the plant rhizosphere, and the mycelia of soilborne pathogens.

Pseudomonas chlororaphis HT66, a plant growth-promoting rhizobacterium that produces phenazine-1-carboxamide with high yield, was compared with three genomic sequenced P. chlororaphis strains, GP72, 30–84 and O6. The genome sizes of four strains vary from 6.66 to 7.30 Mb. Comparisons of predicted coding sequences indicated 4833 conserved genes in 5869–6455 protein-encoding genes. Phylogenetic analysis showed that the four strains are closely related to each other. Its competitive colonization indicates that P. chlororaphis can adapt well to its environment. No virulence or virulence-related factor was found in P. chlororaphis. All of the four strains could synthesize antimicrobial metabolites including different phenazines and insecticidal protein FitD. Some genes related to the regulation of phenazine biosynthesis were detected among the four strains. It was shown that P. chlororaphis is a safe PGPR in agricultural application and could also be used to produce some phenazine antibiotics with high-yield., Highlights • The comparative genomic analysis showed that P. chlororaphis strains have 80% conserved genes. • Its competitive colonization indicates that P. chlororaphis can adapt well to its environment. • P. chlororaphis can synthesize different phenazine compounds and insecticidal proteins. • The plant growth-promoting activities and lack of virulence factor make P. chlororaphis suitable for applications.

Production of Pochonia spp. in laboratory conditions has facilitated studies on its biology, abundance, dispersion, rhizosphere colonization, host preference, and isolate virulence. Research in biological control of nematodes requires suitable, standardized methods. In this chapter we review the commonest, non-molecular, standard in vitro culture methods to isolate, screen, and select isolates, some of which may eventually be produced on a larger scale for application in combination with other management strategies for plant-parasitic nematodes.

Here we report the complete genome sequence of a plant growth-promoting rhizobacterium (PGPR), Paenibacillus polymyxa SQR-21, which consists of one circular chromosome of 5,828,438 bp with 5,024 coding sequences (CDS). The data presented highlight multiple sets of functional genes associated with its plant-beneficial characteristics.

Background Some Pseudomonas strains function as predominant plant growth-promoting rhizobacteria (PGPR). Within this group, Pseudomonas chlororaphis and Pseudomonas fluorescens are non-pathogenic biocontrol agents, and some Pseudomonas aeruginosa and Pseudomonas stutzeri strains are PGPR. P. chlororaphis GP72 is a plant growth-promoting rhizobacterium with a fully sequenced genome. We conducted a genomic analysis comparing GP72 with three other pseudomonad PGPR: P. fluorescens Pf-5, P. aeruginosa M18, and the nitrogen-fixing strain P. stutzeri A1501. Our aim was to identify the similarities and differences among these strains using a comparative genomic approach to clarify the mechanisms of plant growth-promoting activity. Results The genome sizes of GP72, Pf-5, M18, and A1501 ranged from 4.6 to 7.1 M, and the number of protein-coding genes varied among the four species. Clusters of Orthologous Groups (COGs) analysis assigned functions to predicted proteins. The COGs distributions were similar among the four species. However, the percentage of genes encoding transposases and their inactivated derivatives (COG L) was 1.33% of the total genes with COGs classifications in A1501, 0.21% in GP72, 0.02% in Pf-5, and 0.11% in M18. A phylogenetic analysis indicated that GP72 and Pf-5 were the most closely related strains, consistent with the genome alignment results. Comparisons of predicted coding sequences (CDSs) between GP72 and Pf-5 revealed 3544 conserved genes. There were fewer conserved genes when GP72 CDSs were compared with those of A1501 and M18. Comparisons among the four Pseudomonas species revealed 603 conserved genes in GP72, illustrating common plant growth-promoting traits shared among these PGPR. Conserved genes were related to catabolism, transport of plant-derived compounds, stress resistance, and rhizosphere colonization. Some strain-specific CDSs were related to different kinds of biocontrol activities or plant growth promotion. The GP72 genome contained the cus operon (related to heavy metal resistance) and a gene cluster involved in type IV pilus biosynthesis, which confers adhesion ability. Conclusions Comparative genomic analysis of four representative PGPR revealed some conserved regions, indicating common characteristics (metabolism of plant-derived compounds, heavy metal resistance, and rhizosphere colonization) among these pseudomonad PGPR. Genomic regions specific to each strain provide clues to its lifestyle, ecological adaptation, and physiological role in the rhizosphere.