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Background: Herbicides are integral to agricultural weed management but can adversely affect non-target organisms, soil health, and microbiome. We investigated the effects of herbicides on the total soil bacterial community composition using 16S rRNA gene amplicon community profiling. Further, we aimed to identify herbicide-tolerant bacteria with plant growth-promoting (PGP) capabilities as a mitigative strategy for these negative effects, thereby promoting sustainable agricultural practices. Results: A bacterial community analysis explored the effects of long-term S-metolachlor application on soil bacterial diversity, revealing that the herbicide's impact on microbial communities is less significant than the effects of temporal factors (summer vs. winter) or agricultural practices (continuous maize cultivation vs. maize-winter wheat rotation). Although S-metolachlor did not markedly alter the overall bacteriome structure in our environmental context, the application of enrichment techniques enabled the selection of genera such as Pseudomonas, Serratia, and Brucella, which were rare in metagenome analysis of soil samples. Strain isolation revealed a rich source of herbicide-tolerant PGP bacteria within the culturable microbiome fraction, termed the high herbicide concentration tolerant (HHCT) bacterial culture collection. Within the HHCT collection, we isolated 120 strains that demonstrated significant in vitro PGP and biocontrol potential, and soil quality improvement abilities. The most promising HHCT isolates were combined into three consortia, each exhibiting a comprehensive range of plant-beneficial traits. We evaluated the efficacy and persistence of these multi-strain consortia during 4-week in pot experiments on maize using both agronomic parameters and 16S rRNA gene community analysis assessing early-stage plant development, root colonization, and rhizosphere persistence. Notably, 7 out of 10 inoculated consortia partners successfully established themselves and persisted in the maize root microbiome without significantly altering host root biodiversity. Our results further evidenced that all three consortia positively impacted both seed germination and early-stage plant development, increasing shoot biomass by up to 47%. Conclusions: Herbicide-treated soil bacterial community analysis revealed that integrative agricultural practices can suppress the effects of continuous S-metolachlor application on soil microbial diversity and stabilize microbiome fluctuations. The HHCT bacterial collection holds promise as a source of beneficial bacteria that promote plant fitness while maintaining herbicide tolerance. [ABSTRACT FROM AUTHOR]

This study employs a cellular automata (CA) model to investigate the colonization process of Paraburkholderia phytofirmans (PsJN) in the rhizosphere, a complex ecological environment critical to plant–microbe interactions. The proposed CA model simulates bacterial population dynamics, comparing the behavior of the wild-type strain (PsJN WT) with a mutant strain (PsJN-BpI.1) that exhibits impaired quorum sensing (QS), affecting its motility and communication. The model uses a grid where each cell can either be empty or occupied by bacteria. The spread of bacterial colonies is influenced by the state of neighboring cells, with a circular neighborhood used to simulate colony formation. The transition function incorporates both bacterial motility and population control, two critical factors in rhizospheric colonization. Simulation results show that the wild-type strain demonstrates a higher concentration of colonies near the roots, while the mutant strain exhibits reduced growth in these regions. Comparing the simulations with real rhizosphere colonization images confirms the model’s accuracy and highlights the importance of carefully selecting parameters for reliable outcomes. This CA model successfully captures the colonization behavior of PsJN strains in the rhizosphere, providing valuable insights into bacterial ecology and plant–microbe interactions. [ABSTRACT FROM AUTHOR]

The ability of bacteria to colonize diverse environmental niches is often linked to their competence in biofilm formation. It depends on the individual characteristics of a strain, the nature of the colonized surface (abiotic or biotic), or the availability of certain nutrients. Pseudomonas donghuensis P482 efficiently colonizes the rhizosphere of various plant hosts, but a connection between plant tissue colonization and the biofilm formation ability of this strain has not yet been established. We demonstrate here that the potential of P482 to form biofilms on abiotic surfaces and the structural characteristics of the biofilm are influenced by the carbon source available to the bacterium, with glycerol promoting the process. Also, the type of substratum, polystyrene or glass, impacts the ability of P482 to attach to the surface. Moreover, P482 mutants in genes associated with motility or chemotaxis, the synthesis of polysaccharides, and encoding proteases or regulatory factors, which affect biofilm formation on glass, were fully capable of colonizing the root tissue of both tomato and maize hosts. Investigating the role of cellular factors in biofilm formation using these plant-associated bacteria shows that the ability of bacteria to form biofilm on abiotic surfaces does not necessarily mirror its ability to colonize plant tissues. Our research provides a broader perspective on the adaptation of these bacteria to various environments. [ABSTRACT FROM AUTHOR]

Sustainable food production, among other non-intensive production systems, involves the important interactions of myriads of plant growth-promoting microorganisms, plant, soil, soil fauna, and production of utilizable carbon in the rhizosphere capable of enhancing soil health, plant growth, and protection that lead to increased crop productivity. Plant growth-promoting rhizobacteria (PGPR) including symbiotic rhizobia and free-living rhizobacteria possess traits that help to enhance plant growth due to their many modes of action that start with the ability to colonize both the intracellular and extracellular rhizosphere niche in their search for a carbon source and reduction in the free use and quantity of agrochemicals. In the past few decades, the focus on developing biosafety agro-products has shifted from agrochemical-based applications to a more sustainable system without posing negative impacts on the soil microflora or fauna. The present review focuses on the application of PGPR inoculants on soils and seeds to improve biological nitrogen fixation, solubilization of phosphate, and secretion of phytohormones required for growth, especially application in a pressured environment. We discuss how PGPR enhances nutritional regulation and hormonal balance in plants, bacterial taxa enrichment, and improvement of carbon sources utilization beneficial for plant growth. We highlight the antagonistic and synergistic interactions with microorganisms within the rhizosphere and beyond in bulk soil which indirectly boosts plant growth rate and induces resistance against phytopathogens. While soil-borne pathogens continually oppose the functions of these microorganisms, PGPR has improved diverse strategies in the form of agro-compatibility, root colonization, nutrient, iron, and space competition, systemic resistance, antibiotics synthesis, lytic acid, hydrogen cyanide, and siderophore production for advanced food production. Finally, we highlighted the roles of PGPR in phytoremediation, techniques of applying microbial inoculants to enhance plant growth and commercialization of PGPR products and the challenges developing countries have to defeat.

Background and Aims: Intensifying chemotactic rhizocompetence is an effective approach to improving PGPR colonization in the plant rhizosphere and promoting plant growth. Whether increasing the efficient adaptational methylation modification of chemoreceptors enhances chemotactic rhizocompetence is unknown. Pseudomonas sp. UW4 is a typical PGPR, and 1-aminocyclopropane-1-carboxylic acid (ACC) is the strong chemoattractant that directs it to the rhizosphere. Methods: The chemoreceptor pentapeptide involved in UW4 chemotaxis were identified through molecular docking and methylation reactions in vitro. The pentapeptide was identified as PEKPR residing in the C-terminus of the chemoreceptor Mcp14 and shows no sequence conservation with that of other bacteria. Two chemoreceptor mutants were constructed: in one, the pentapeptide was additionally grafted to the ACC chemoreceptor McpACC (UW4-1); in the other, the pentapeptide was transferred to McpACC (UW4-2). Results: UW4-1 and UW4-2 showed unchanged chemotactic responses to arginine and succinic acid compared to UW4, whereas the chemotactic responses of UW4-1 to ACC were 36.0% and 17.2% higher than those of UW4 and UW4-2, respectively. Wheat rhizosphere colonization by UW4-1 in nonaxenic pot trials was 62.0% and 14.3% higher than rhizosphere colonization by UW4 and UW4-2, respectively, and the root and shoot dry weights of wheat inoculated with UW4-1 were 10.3% and 5.5% and 16.5% and 13.2% higher, respectively, than those of wheat inoculated with UW4 and UW4-2. Conclusion: Grafting the pentapeptide to the chemoreceptor corresponding to the strong rhizosphere chemoattractant for PGPR increases PGPR chemotactic response to the strong rhizosphere chemoattractant, increases plant rhizosphere colonization, and leads to higher plant growth promotion. [ABSTRACT FROM AUTHOR]

Among the key diseases affecting the asparagus crop (Asparagus officinalis L.), vascular wilting of asparagus caused by Fusarium oxysporum f. sp. asparagi stands out worldwide. This disease significantly shortens the longevity of the crop and limits economic production. Traditional control measures have been largely ineffective, and chemical control methods are difficult to apply, making biological control approaches, specifically the use of Trichoderma, an economical, effective, and risk-free alternative. This study aimed to identify the main factors that affect the efficacy of biopesticides studied as Biological Control Agents (BCAs) against Fusarium wilt in asparagus and to assess the efficacy of Trichoderma-based biopesticides under greenhouse and semi-field conditions. We evaluated the response of three Trichoderma spp. (T. atroviride, T. asperellum, and T. saturnisporum) to environmental variables, such as temperature and water activity, and their antagonistic capacity against Fusarium oxysporum f. sp. asparagi. All three Trichoderma species inhibited the growth of the pathogen in vitro. A decrease in water activity led to a greater reduction in the growth rate. The efficacy of the three biological control agents decreased with higher temperatures, resulting in minimal inhibition, particularly under conditions of restricted available water in the environment. The effect of the fungal inoculum density was also analyzed at two different temperatures. A direct correlation between the amount of inoculum and the score on the Disease Severity Index (DSI) was observed. A notable reduction in DSI was evident in treatments with high inoculum density (106 conidium/mL) for all three species of Trichoderma tested at both temperatures. In greenhouse and semi-field tests, we observed less disease control than expected, although T. asperellum and T. atroviride showed lower disease severity indices and increased the dry weight of seedlings and crowns, whereas T. saturnisporum resulted in the highest disease rate and lowest dry weight. This work highlights that the efficacy of Trichoderma as BCAs is influenced by various factors, including the quantity of soil inocula, and environmental conditions. The study findings have strong implications for selecting appropriate Trichoderma species for controlling specific pathogens under specific environmental conditions. [ABSTRACT FROM AUTHOR]

Among the key diseases affecting the asparagus crop (Asparagus officinalis L.), vascular wilting of asparagus caused by Fusarium oxysporum f. sp. asparagi stands out worldwide. This disease significantly shortens the longevity of the crop and limits economic production. Traditional control measures have been largely ineffective, and chemical control methods are difficult to apply, making biological control approaches, specifically the use of Trichoderma, an economical, effective, and risk-free alternative. This study aimed to identify the main factors that affect the efficacy of biopesticides studied as Biological Control Agents (BCAs) against Fusarium wilt in asparagus and to assess the efficacy of Trichoderma-based biopesticides under greenhouse and semi-field conditions. We evaluated the response of three Trichoderma spp. (T. atroviride, T. asperellum, and T. saturnisporum) to environmental variables, such as temperature and water activity, and their antagonistic capacity against Fusarium oxysporum f. sp. asparagi. All three Trichoderma species inhibited the growth of the pathogen in vitro. A decrease in water activity led to a greater reduction in the growth rate. The efficacy of the three biological control agents decreased with higher temperatures, resulting in minimal inhibition, particularly under conditions of restricted available water in the environment. The effect of the fungal inoculum density was also analyzed at two different temperatures. A direct correlation between the amount of inoculum and the score on the Disease Severity Index (DSI) was observed. A notable reduction in DSI was evident in treatments with high inoculum density (106 conidium/mL) for all three species of Trichoderma tested at both temperatures. In greenhouse and semi-field tests, we observed less disease control than expected, although T. asperellum and T. atroviride showed lower disease severity indices and increased the dry weight of seedlings and crowns, whereas T. saturnisporum resulted in the highest disease rate and lowest dry weight. This work highlights that the efficacy of Trichoderma as BCAs is influenced by various factors, including the quantity of soil inocula, and environmental conditions. The study findings have strong implications for selecting appropriate Trichoderma species for controlling specific pathogens under specific environmental conditions.

Bacilli are used as biocontrol agents (BCAs) against phytopathogens and most of them can produce poly-γ-glutamic acid (γ-PGA) as one of the major extracellular polymeric substances (EPSs). However, the role of γ-PGA in plant biocontrol is still unclear. In this study, Bacillus atrophaeus NX-12 (γ-PGA yield: 16.8g/l) was screened, which formed a strong biofilm and has been proved to be a promising BCA against Cucumber Fusarium wilt. Then, the γ-PGA synthesis gene cluster pgsBCA was knocked out by CRISPR-Cas9n. Interestingly, the antifungal ability of γ-PGA synthetase-deficient strain NX-12Δpgs (γ-PGA yield: 1.65g/l) was improved in vitro, while the biocontrol ability of NX-12Δpgs was greatly diminished in situ. Data proved that γ-PGA produced by NX-12 contributes to the biofilm formation and rhizosphere colonization, which effectively improved biocontrol capability. Taken together, these findings prove that the mechanism of γ-PGA promotes the colonization of NX-12 and thus assists in controlling plant diseases, which highlight the key role of γ-PGA produced by BCA in biocontrol. [ABSTRACT FROM AUTHOR]

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Rhizosphere colonization is a key requirement for the application of plant growth-promoting rhizobacteria (PGPR) as a biofertilizer. Signaling molecules are often exchanged between PGPR and plants, and genes in plants may respond to the action of PGPR. Here, the luciferase luxAB gene was electrotransformed into Pseudomonas sp. strain TK35, a PGPR with an affinity for tobacco, and the labelled TK35 (TK35-L) was used to monitor colonization dynamics in the tobacco rhizosphere and evaluate the effects of colonization on tobacco growth and root development. The transcript levels of the hydroxyproline-rich glycoprotein HRGPnt3 gene, a lateral root induction indicator, in tobacco roots were examined by qPCR. The results showed that TK35-L could survive for long periods in the tobacco rhizosphere and colonize new spaces in the tobacco rhizosphere following tobacco root extension, exhibiting significant increases in root development, seedling growth and potassium accumulation in tobacco plants. The upregulation of HRGPnt3 transcription in the inoculated tobacco suggested that TK35-L can promote tobacco root development by upregulating the transcript levels of the HRGPnt3 gene, which promotes tobacco seedling growth. These findings lay a foundation for future studies on the molecular mechanism underlying the plant growth-promoting activities of PGPR. Furthermore, this work provided an ideal potential strain for biofertilizer production.

Drought ranks among the most severe environmental stressors that adversely affect crop productivity. Use of stress-tolerant plant growth-promoting rhizobacteria (PGPR) is expected to ameliorate the drought stress in plants. Therefore, in this study, a novel strain, Pseudomonas azotoformans FAP5 with multifunctional traits was obtained from screening of 50 indigenous isolates. The criteria for selection of most promising strain were based on tolerance to water stress, production of PGP traits and biofilm-forming ability in vitro. Further, inoculation response of FAP5 on wheat growth parameters and physiological attributes under different drought conditions was executed under pot experiment. The drought-tolerant FAP5 strain revealed production of exopolysaccharides (EPS), indole 3 acetic acid (IAA), solubilized tricalcium phosphate and exhibited 1-aminpcyclopropane-1-carboxylate (ACC) deaminase (41.58 ± 2.10 μmol α-KB/mg Pr h) activity. ACC deaminase (acdS) and biofilm-associated (AdnA and FliC) genes were confirmed by PCR-based method. Production of PGP traits and biofilm development by FAP5 was exhibited even at water stress condition in vitro. The inoculated wheat plants with FAP5 strain were grown under drought stress showed significant (P < 0.05) improvement in growth attributes, photosynthetic pigment efficiency and other physiological attributes. Similarly, a significant (P < 0.05) antioxidative enzymatic activities in FAP5-inoculated plant were observed compared to uninoculated plants. Under drought stress condition, biofilm development by FAP5 was enhanced significantly and root colonization by inoculant strain was confirmed by viable count and scanning electron microscopy (SEM). The findings indicated that FAP5 strain is effective to drought stress alleviation in wheat plants through various biochemical mechanisms. [ABSTRACT FROM AUTHOR]

ABSTRACT It is widely recognized that plant-symbiotic fungi are supported by photosynthates; however, little is known about the molecular mechanisms underlying the utilization of plant-derived sugars by rhizospheric fungi. In the insect-pathogenic and plant-symbiotic fungus Metarhizium robertsii, we previously showed that the utilization of oligosaccharides by the transporter MRT (Metarhizium raffinose transporter) is important for rhizosphere competency. In this study, we identified a novel monosaccharide transporter (MST1) that is involved in the colonization of the rhizoplane and acts additively with MRT to colonize the rhizosphere. MST1 is not involved in infection of insects by M. robertsii. MST1 is an H+ symporter and is able to transport a broad spectrum of monosaccharides, including glucose, sorbose, mannose, rhamnose, and fructose. Deletion of the Mst1 gene impaired germination and mycelial growth in medium containing the sugars that it can transport. Homologs of MST1 were widely found in many fungi, including plant symbionts such as Trichoderma spp. and mycorrhizal fungi and plant pathogens such as Fusarium spp. This work significantly advances insights into the development of symbiotic relationships between plants and fungi. IMPORTANCE Over 90% of all vascular plant species develop an intimate symbiosis with fungi, which has an enormous impact on terrestrial ecosystems. It is widely recognized that plant-symbiotic fungi are supported by photosynthates, but little is known about the mechanisms for fungi to utilize plant-derived carbon sources. In the fungus Metarhizium robertsii, we identified a novel monosaccharide transporter (MST1) that is an H+ symporter and can transport a broad spectrum of monosaccharides, including glucose, sorbose, mannose, rhamnose, and fructose. MST1 is involved in the colonization of the rhizoplane and acts additively with the previously characterized oligosaccharide transporter MRT to colonize the rhizosphere. Homologs of MST1 were found in many fungi, including plant symbionts and plant pathogens, suggesting that the utilization of plant-derived sugars by MST1 homologs could also be important for other fungi to develop a symbiotic or parasitic relationship with their respective plant hosts.

• FO12 did not exert any evident pathogenic effects on eight herbaceous hosts. • FO12 promoted plant growth in cotton, cucumber, pepper, sunflower, and wheat. • FO12 colonized the root and stem tissues of all herbaceous hosts as an endophyte. • Confocal laser scanning microscopy imaging showed that FO12 root colorization progressed. The nonpathogenic strain Fusarium oxysporum FO12 has been characterized as an effective biological control agent against Verticillium dahliae in olive. Nevertheless, the endophytic role of FO12 in herbaceous hosts is still uncertain. Thus, the aim of this study was to demonstrate the nonpathogenic character of FO12 in eight V. dahliae -susceptible herbaceous hosts and to evaluate its ability to promote plant growth. To this end, plants of each host were grown in pots filled with sterile peat moss and inoculated by irrigation with a conidial suspension of FO12 (106 conidia ml−1) two times—at sowing and at the emergence of the first true leaves. Many plants irrigated with sterile distilled water were included as controls. Sampling was conducted at 7, 14, 21, and 28 days after the second inoculation. The fresh weight and length of the aerial parts, roots, and whole plants were determined at each sampling time. Fungal colonization was assessed via quantitative and qualitative methods, including microbiological isolation from roots and stems and confocal laser scanning microscopy (CLSM) imaging at each sampling time. FO12 exhibited the ability to endophytically colonize the roots and stems of the inoculated plants. However, the effect on growth and the degree of colonization varied depending on the host. FO12 did not exert any evident pathogenic effects or negative effects on plant growth or development. The growth of the eggplant, lettuce, and tomato plants in the FO12 treatment group was similar to that in the control group, whereas the relative area under the growth progress curve was significantly greater than that in the control group for plant length in cotton and cucumber; for root fresh weight in pepper, sunflower, and wheat; and for plant fresh weight in sunflower and wheat. These results highlight the need to continue researching the interaction between FO12 and V. dahliae in a wider range of plant species of agronomic interest. [Display omitted] [ABSTRACT FROM AUTHOR]

Azospirillum sp. is a plant growth-promoting rhizobacteria largely recognized for its potential to increase the yield of different important crops. In this work, we present a thorough genomic and phenotypic analysis of A. argentinense Az39T to provide new insights into the beneficial mechanisms of this microorganism. Phenotypic analyses revealed the following in vitro abilities: growth at 20–38 °C (optimum, 28 °C), pH 6.0–8.0 (optimum, pH 6.8), and in the presence of 1% (w/v) NaCl; production of variable amounts of PHB as intracellular granules; nitrogen fixation under microaerophilic conditions; IAA synthesis in the presence of L-tryptophan. Through biochemical (API 20NE) and carbon utilization profiling (Biolog) assays, we proved that A. argentinense Az39T is able to use 15 substrates and metabolize 19 different carbon substrates. Lipid composition indicated a predominance of medium and long-chain saturated fatty acids. A total of 6 replicons classified as one main chromosome, three chromids, and two plasmids, according to their tRNA and core essential genes contents, were identified. Az39T genome includes genes associated with multiple plant growth-promoting (PGP) traits such as nitrogen fixation and production of auxins, cytokinin, abscisic acid, ethylene, and polyamines. In addition, Az39T genome harbor genetic elements associated with physiological features that facilitate its survival in the soil and competence for rhizospheric colonization; this includes motility, secretion system, and quorum sensing genetic determinants. A metadata analysis of Az39T agronomic performance in the pampas region, Argentina, demonstrated significant grain yield increases in wheat and maize, proving its potential to provide better growth conditions for dryland cereals. In conclusion, our data provide a detailed insight into the metabolic profile of A. argentinense Az39T, the strain most widely used to formulate non-legume inoculants in Argentina, and allow a better understanding of the mechanisms behind its field performance. [ABSTRACT FROM AUTHOR]

Salinity is among the major environmental factors affecting the performance of both crop plants and soil bacterial inoculants beneficial to plant growth. Based on previous screening studies, a novel halotolerant biofilm-forming PGPR strain, namely Pantoea agglomerans -FAP10, was studied for its potential to protect wheat (Triticum aestivum ; var. 343) against salinity stress. The ability of this strain to produce biofilms on glass surfaces, 96 well microtiter plates, and seedling roots was characterized qualitatively and quantitatively using light and scanning electron microscopy (SEM). The FAP10 strain was tested for performance by inoculating wheat in a pot-soil system under varied salinity stresses (75, 125, 250, and 500 mM NaCl). The FAP10 strain exhibited discrete and multifarious plant growth-promoting traits as well as efficient rhizosphere and root colonization which could sustain wheat growth under salinity stress. The FAP10-induced modifications conferred enhanced plant salinity tolerance by regulating photosynthetic attributes (gs, Ci, E, iWUE, P N , PSII, and Rubisco enzyme activity), antioxidant system (SOD, CAT, GR, APX, GSH, MDA, and proline), and sulfur metabolism (sulfur and cysteine content, ATP-S, and SAT activity), and also sustained soil physicochemical characteristics and hydrolytic enzymes including urease, protease, DHA, ALP, ACP and β glucosidase. The findings of the current study can support future efforts to improve plant salinity tolerance by engineering rhizobacterial biofilms and exploiting the potential of native strains for agricultural applications in stressed environments. • Pantoea agglomerans FAP10 a novel biofilm forming and salt tolerant PGPR strain protects inoculated wheat plants against salinity stress • The impact of treatment of FAP10 on wheat plant showed restoration of physiological attributes to normal level from the salinity stress level. • Role of biofilm in effective rhizoplane and rhizosphere colonization by FAP10 strain further supported protection mechanisms against salinity stress and improved soil hydrolytic enzymes • Findings of this study strongly support future efforts in the management of plant salinity stress with the development of effective bioinoculant for agricultural use. [ABSTRACT FROM AUTHOR]

The persistence of pathogenic Agrobacterium strains as soil-associated saprophytes may cause an inconsistency in the efficacy of the biocontrol inoculants under field condition. The study of the interaction occurring in the rhizosphere between the beneficial and the pathogenic microbes is thus interesting for the development of effective biopesticides for the management of crown gall disease. However, very little is still known about the influence of these complex interactions on the biocontrol determinants of beneficial bacteria, especially Bacillus strains. This study aimed to evaluate the effect of the soil borne pathogen Agrobacterium tumefaciens C58 on root colonization and lipopeptide production by Bacillus velezensis strain 32a during interaction with tomato plants. Results show that the presence of A. tumefaciens C58 positively impacted the root colonization level of the Bacillus strain. However, negative impact on surfactin production was observed in Agrobacterium-treated seedling, compared with control. Further investigation suggests that these modulations are due to a modified tomato root exudate composition during the tripartite interaction. Thus, this work contributes to enhance the knowledge on the impact of interspecies interaction on the ecological fitness of Bacillus cells living in the rhizosphere. [ABSTRACT FROM AUTHOR]

Cerato-platanins (CPs) form a family of fungal small-secreted cysteine-rich proteins (SSCPs) and are of particular interest not only because of their surface activity but also their abundant secretion by fungi. We performed an evolutionary analysis for 283 CPs from 157 fungal genomes with the focus on the opportunistic plant-beneficial and mycoparasitic fungus Trichoderma. Our results revealed the long evolutionary history of CPs in Dikarya fungi that have undergone several events of lateral gene transfer and gene duplication. Three genes were maintained in the core genome of Trichoderma, while some species have up to four CP encoding genes. All Trichoderma CPs evolve under stabilizing natural selection pressure. The functional analysis of CPs in T. guizhouense and T. harzianum revealed that only EPL1 is active at all stages of the development but plays a minor role in interactions with other fungi and bacteria. The deletion of this gene results in increased colonization of tomato roots by Trichoderma spp. Similarly, the biochemical tests of the heterologously produced EPL1 by Pichia pastoris support the above claims. Based on the obtained results, we conclude that the function of CPs is probably linked to their surfactant properties and the ability to modify the hyphosphere of submerged mycelium and thus facilitate the nutritional versatility of fungi. The effector-like properties do not sufficiently describe the diversity and evolution of these proteins in fungi as they are also maintained, duplicated, or laterally transferred in the genomes of non-herbivore fungi. [ABSTRACT FROM AUTHOR]

Plant growth-promoting rhizobacteria (PGPR) are known for growth promotion and mitigating environmental stresses. Here, we examined the propitiousness of three indigenous salt-tolerant PGPR, i.e., Bacillus subtilis (NBRI 28B), B. subtilis (NBRI 33 N), and B. safensis (NBRI 12 M) for plant growth promotion and salt stress amelioration in Zea mays. Results of the in vitro plant growth-promoting attribute revealed NBRI 12 M demonstrated the highest values at 1 M salt (NaCl) concentration. Furthermore, the greenhouse experiment using three Bacillus strains confirmed plant growth-promoting and salt stress-ameliorating ability, through colonizing successfully and mitigating the adverse effects of ethylene by modulating 1-aminocyclopropane-1-carboxylic acid (ACC) accumulation, ACC-oxidase (ACO), and ACC-synthase (ACS) activities under salt stress. Bacillus sp. inoculation has also induced plant response for defense enzymes, chlorophyll, proline and soluble sugar under salt stress. Among three Bacillus strains, NBRI 12 M not only demonstrated higher values for plant growth-promoting (PGP) attributes but also the same was observed in the greenhouse experiment. Thus, the outcomes of this comparative study represent for the first time that salt-tolerant Bacillus strains exhibiting multiple PGP attributes under salt stress along with high rhizosphere competence can alleviate salt stress by reducing the stress ethylene level in the host plant. [ABSTRACT FROM AUTHOR]

Salinity ranks among the most severe environmental stressors that limit crop productivity. Use of microbial inoculants with desired traits is believed to be effective strategy to combat plant abiotic stress. Therefore, the objective was to isolate salt tolerant Bacillus spp. with multifunctional plant growth promoting traits including biofilm development and to evaluate its performance under salt stress conditions. We isolated and characterized a novel salt tolerant isolate of Bacillus sp. FAB10 with multifunctional traits by screening of 56 selected Bacillus isolates from rhizospheric soils. The isolate FAB10 was identified as B. pumilus based on 16S rRNA gene sequence analysis. The FAB10 isolate produced strong biofilm, enhanced amount of exopolysaccharides, IAA, ACC-deaminase activity and solubilized phosphate in vitro. The isolate FAB10 forms biofilm and expressed its associated traits at the different NaCl concentrations in vitro. Biofilm development on Wheat root surface was also demonstrated at 250 mM salt (NaCl) concentration. Successful root colonization by the FAB10 isolate was demonstrated via scanning electron microscopy and viable counts. Wheat plant var. 343 inoculated with Bacillus pumilus isolate FAB10 grown in the presence of different concentrations (0 to 250 mM) of NaCl under pot house conditions. At elevated concentration of NaCl adverse effect on wheat growth parameters and other biochemical attributes pertaining to photosynthesis, transpiration, and content of proline in plant tissue was recorded in uninoculated plants. However, inoculated plants showed a significant (p < 0.005) improvement in most of the above parameters. Similarly a significant (p < 0.005) reduction in antioxidant enzyme activities (catalase, superoxide dismutase, and glutathione reductase) and malonaldehyde content in wheat was observed in FAB10 inoculated plants than uninoculated plants in the presence of salt. The findings indicated that multifunctional traits of the FAB10 contribute to NaCl stress alleviation in wheat plants through multiple mode of action and it could be exploited under field condition. • Screening of rhizospheric Bacillus isolates resulted in selection of novel salt tolerant and biofilm forming strain of Bacillus pumilus FAB10 exhibiting multifunctional PGP traits. • The strain FAB10 colonized rhizosphere and formed biofilm on the root surface in the presence of NaCl upto 250 mM. • Modulation of plant physiological attributes and antioxidant enzymes level were observed by FAB10 inoculation under saline condition. • B. pumilus FAB10 could be effectively used for salt stress alleviation in wheat plant under pot house condition. [ABSTRACT FROM AUTHOR]

The rhizobacterium Pseudomonas pseudoalcaligenes AVO110, isolated by 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 molecular mechanisms linked to the interaction of this bacterium with R. necatrix. A total of 26 STM mutants out-competed by the parental strain in fungal exudate, but not in rich medium, were selected and named growth-attenuated mutants (GAM). Twenty-one genes were identified as 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 required for efficient colonization of the avocado rhizosphere. [ABSTRACT FROM AUTHOR]

The fungus Pochonia chlamydosporia is one of the most studied biological agents used to control plant-parasitic nematodes. This study found that the isolates Pc-3, Pc-10 and Pc-19 of this fungus promote the growth of tomato and lettuce seedlings. The isolate Pc-19 colonized the rhizoplane of tomato seedlings in only 15 days and produced a large quantity of chlamydospores. This isolate was able to use cellulose as a carbon source, in addition to glucose and sucrose. Scanning electron microscopy (SEM) revealed that hyphae of the P. chlamydosporia isolate Pc-10 penetrated the epidermal cells of the tomato roots. These three P. chlamydosporia isolates promote the growth of tomato and lettuce.

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.

High soil nitrate concentrations can lead to the secondary salinization of soils. Bacillus megaterium NCT-2 is a wild-type strain isolated from secondary salinized soil and is very effective in reducing nitrate. Laboratory and greenhouse experiments were carried out to investigate its nitrate reduction capabilities, colonization pattern, and plant growth promotion responses to nitrate content in the soil. B. megaterium NCT-2 was marked with a green fluorescent protein ( gfp ) gene and was left to successfully colonize maize roots and the rhizosphere. Inoculation with gfp -tagged NCT-2 significantly promoted nitrate removal from the soil and improved plant growth. Confocal microscopy results revealed that NCT-2 is an endophyte that can colonize the meristematic and elongation zones of the root tip, and the middle segment of the root. Soil nitrate concentration had no significant effect on NCT-2 distribution. The gfp -tagged NCT-2 populations in the roots and rhizosphere soil first increased, but then decreased, and at the end of the experiment, colonization levels in the rhizosphere soil stabilized at ∼5 × 10 4  CFU g −1 soil. However, the levels in the roots increased again to 1–3 × 10 4  CFU g −1 root in the different treatments. The NCT-2 population in the roots was significantly affected by nitrate content. A nitrate-nitrogen concentration of 72 mg kg −1 was the optimum concentration for NCT-2 colonization of maize roots. This study will improve the agricultural application of NCT-2 as a biofertilizer for nitrate removal and plant growth promotion. [ABSTRACT FROM AUTHOR]

Aims: The mechanisms by which rhizosphere bacteria increase the availability of mineral P precipitates for plant use are understudied. However, Paraburkholderia bryophila Ha185 is known to solubilize inorganic phosphate in vitro via a novel process. Therefore, this study aimed to demonstrate P solubilization by Ha185 in association with roots of perennial ryegrass (Lolium perenne L.).Methods: We developed a gnotobiotic plant assay to assess P solubilization by Ha185 on ryegrass roots under various nutrient conditions. A green fluorescent protein (GFP)-tagged derivative of Ha185 was used in conjunction with fluorescent microscopy and confocal microscopy to visualize colonization of ryegrass roots.Results: Ha185 solubilized mineral P (hydroxyapatite) in association with ryegrass roots and increased ryegrass growth by 20% under P-limited conditions. The GFP-tagged Ha185 strain colonized the rhizoplane and penetrated the primary root of ryegrass, possibly through “crack entry” at the point of lateral root emergence, but also by entering the epidermal cells via root hairs.Conclusions: Ha185 supported ryegrass growth under P-limited conditions, indicating this strain may improve availability of soil P for uptake by ryegrass. Tools developed in this study have broad application in the study of rhizobacteria-plant interactions. [ABSTRACT FROM AUTHOR]

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.

A wide variety of plant-associated soil bacteria (rhizobacteria) communicate with each other by quorum sensing (QS). Plants are able to detect and produce mimics and inhibitor molecules of the QS bacterial communicative process. Arachis hypogaea L. (peanut) establishes a nitrogen-fixing symbiosis with rhizobia belonging to the genus Bradyrhizobium. These bacteria use a QS mechanism dependent on the synthesis of N-acyl homoserine lactones (AHLs). Given the relevance that plant-rhizobacteria interactions have at the ecological level, this work addresses the involvement of peanut in taking part in the QS mechanism. By using biosensor bacterial strains capable of detecting AHLs, a series of standard and original bioassays were performed in order to determine both (i) the production of QS-like molecules in vegetal materials and (ii) the expression of the QS mechanism throughout plant-bacteria interaction. Mimic QS-like molecules (mQS) linked to AHLs with long acyl chains (lac-AHL), and inhibitor QS-like molecules (iQS) linked to AHLs with short acyl chains (sac-AHL) were detected in seed and root exudates. The results revealed that synthesis of specific signaling molecules by the plant (such as mQS and iQS) probably modulates the function and composition of the bacterial community established in its rhizosphere. Novel bioassays of QS detection during peanut- Bradyrhizobium interaction showed an intense production of QS signals in the contact zone between root and bacteria. It is demonstrated that root exudates stimulate the root colonization and synthesis of lac-AHL by Bradyrhizobium strains in the plant rhizosphere, which leads to the early stages of the development of beneficial plant-bacteria interactions. [ABSTRACT FROM AUTHOR]

Potato common scab (PCS) is an economically important disease caused by Streptomyces spp. which occurs in potato planting areas worldwide. In this paper, pot experiments were conducted in the greenhouse to evaluate the biocontrol effects of Brevibacillus laterosporus AMCC100017 on potato common scab, and to assess the impact of the biocontrol bacterium on soil bacterial communities at four plant growth stages of potato. Results revealed that B. laterosporus AMCC100017 colonized steadily in potato rhizosphere ranging from 5.47 to 6.87 Log 10 CFU g −1 soil detected by real-time PCR. It significantly (P < 0.05) reduced the pathogen population of Streptomyces bottropensis from 4.54 to 4.28 Log 10 CFU g −1 soil in the harvesting stage of potato, decreased the disease severity from 2.60 down to 0.77, and the biocontrol efficacy against common scab reached as great as 70.51%. Meanwhile, the relationship between B. laterosporus AMCC100017 and the functional microorganisms such as actinomycetes, Bacillus spp. and Pseudomonas spp. in the rhizosphere of potato, was discussed based on cultural method and the analyses of terminal restriction fragment length polymorphism (T-RFLP). The adding of B. laterosporus AMCC100017 had only slight transient impact on the native bacteria community in the flowering stage of potato. B. laterosporus AMCC100017 has the promising perspective developing into a biocontrol agent against potato common scab in the field. [ABSTRACT FROM AUTHOR]

The potential of 3 Pseudomonas aeriuginosa strains as biocontrol agents of rootinfecting fungi Macrophomina phaseolina, Fusarium solani and Rhizoctonia solani and the root-knot nematode Meloidogyne javanica was tested on chili and uridbean under greenhouse conditions. All the three strains significantly reduced nematode populations in soil, invasion, multiplication and gall formation due to M.javanica. Root infection by fungi was also effectively suppressed following P.aeruginosa application. Bacterial antagonists exhibited better biocontrol and growth promoting activity in 15-day-old plants than did those harvested at 30 or 45 days. Population of the bacterium in the rhizosphere declined rapidly after 15 days of nematode inoculation. Strain Pa-5 showed maximum nodulation in 15-day-old samplings while strain Pa-7 showed highest number of nodules in 30 and 45-day-old uridbean plants.

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. [ABSTRACT FROM AUTHOR]

We evaluated the persistence and proliferation of a ChineseMetarhizium anisopliaes.s. isolate (M202-1) at different distances from peanut roots during peanut development. The results showed that the duration, distance from root and depth resulted in significant effects and interactions on the survival of the fungus. The fungal population showed a rapid early decline, followed by a gradual stabilisation or a slight re-establishment. The rhizospheric population declined by 50% within 21 d, faster than other population away from the root. The decline reached the lowest level between days 60 and 90, with levels of 10.8–24.7% of the initial inoculum. In comparison, the rhizospheric population re-established earliest and increased to 52.9% of the initial on day 150. The 3–5-cm shallow layer was more suitable than the 13–15-cm layer for fungal persistence. WhenMetarhiziumwas applied outside the 11.5-cm radius around the root, it would diffuse inward in 30 d, causing a significant increase at the rhizosphere on day 90. In accordance with the sampling date corresponding to the root development stage, the results suggest that the rhizosphere of peanut middle–later development was conducive toMetarhiziumproliferation, promotingMetarhizium applicationfor pest control in the soil. [ABSTRACT FROM AUTHOR]

Plants can recruit beneficial microbes to help improve their fitness under abiotic or biotic stress. Our previous studies found that Panax notoginseng could enrich beneficial Burkholderia sp. B36 in the rhizosphere soil under autotoxic ginsenoside stress. Here, we clarified that ginsenoside stress activated the phenylpropanoid biosynthesis and α-linolenic acid metabolism pathways of roots to increase the secretion of cinnamic acid, 2-dodecenoic acid, and 12-oxo-phytodienoic acid. These metabolites could promote the growth of B36. Importantly, cinnamic acid could simultaneously promote the chemotaxis and growth of B36, enhance the colonization of B36 in the rhizosphere, and eventually increase the survival rate of P. notoginseng . Overall, the plants could promote the growth and colonization of beneficial bacteria through key metabolites in root exudates under autotoxin stress. This finding will facilitate the practical application of beneficial bacteria in agricultural production and lead to successful and reproducible biocontrol efficacy by the exogenous addition of key metabolites.

Efficiency of different concentrations of Trichoderma longibrachiatum T6 against Meloidogyne incognita and its rhizosphere colonization in cucumber were determined in greenhouse experiments. The results of rhizosphere colonization experiments showed that the number of colonies in cucumber soil and root increased significantly ten weeks after inoculation with the second stage juveniles of M. incognita and different concentrations of T. longibrachiatum T6, and there was significant difference in different concentrations of T. longibrachiatum T6, e.g., the maximum numbers of colonies in soil and root were 7.8×107 and 6.3×105 CFU·mL-1 respectively after treated with the spore suspension of 1.5×107 CFU·mL-1. Greenhouse experiments results showed that different concentrations of T. longibrachiatum T6 had significant control effect on different life stages of M. incognita, and the control effect increased with the concentration of T. longibrachiatum T6. T. longibrachiatum T6 significantly increased plant height, root length, above-ground and root fresh mass of cucumber inoculated by M. incognita. T. longibrachiatum T6 could colonize in cucumber rhizosphere, had control effect on M. incognita, and significantly improved the growth of cucumber. [ABSTRACT FROM AUTHOR]

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To study colonization of the tomato root system, we previously have described a gnotobiotic quartz sand system, in which seedlings inoculated with one or two bacterial strains were allowed to grow. Here we present a scanning electron microscope description of the colonization of the tomato root system by Pseudomonas fluorescens biocontrol strain WCS365, with emphasis on spatial-temporal colonization patterns, based on an improved scanning electron microscopy procedure. Upon inoculation of the germinated seed, proliferation on the seed coat was observed for 2 to 3 days. Within 1 to 3 days, micro-colonies developed, mainly at the root base. Most micro-colonies were localized in junctions between epidermal root cells, whereas others were found in indented parts of the epidermal surface. Downward to the root tip, only single bacterial cells were found. Colonization progressed down the root, initially as single cells. A semi-transparent film appeared to enclose the root surface and micro-colonies present on the root. After 7 days, micro-colonies had developed at positions where only single cells were observed previously and distribution of the bacteria along the root varied from ≈106 CFU per cm of root near the root base to ≈102 to 103 CFU per cm of root near the root tip. Similar colonization patterns were found for the P. fluorescens biocontrol strains CHA0 and F113, and P. putida strain WCS358, as well as for four species that have repeatedly been isolated from tomato roots from a commercial tomato field near Granada, Spain. In contrast, four Rhizobium strains and one Acinetobacter radioresistens strain showed poor colonization and micro-colonies were not observed. Based on the described data, we present a model for colonization of the deeper root parts after seed inoculation by P. fluorescens biocontrol strains, in which single cells occasionally establish on a deeper root section where they sometimes develop into micro-colonies. We hypothesize that micro-colonies are the sites where the intracellular N-acyl-L-homoserine lactone concentration is sufficiently high to cause maximal production of biocontrol factors such as antibiotics and exoenzymes and that micro-colonies explain the relatively high conjugation frequency observed between pseudomonads in the rhizosphere.

Studies on the use of Pochonia chlamydosporia isolates as biological control agents of root-knot nematodes (RKN, Meloidogyne spp.), showed that their efficacy relies on selected key factors such as fungal proliferation in soil, establishment in the rhizosphere, and ability to parasitize RKN eggs. A pot experiment was conducted to evaluate the performance of a Portuguese P. chlamydosporia isolate (Pc2) and of a non-native isolate (Pc10) against M. chitwoodi in a potato-maize-potato-potato crop rotation. The growth of P. chlamydosporia in soil and roots was monitored throughout the experiment by assessing the numbers of colony forming units (cfu). The prevalence in M. chitwoodi eggs and nematode reproduction was measured at the end of each crop. The cfu/g of soil varied over time and was particularly low for both isolates during the spring and summer 2009, when temperatures above 30ºC were registered. Native isolate Pc2 was more effective in establishing in soil than Pc10. Growth and survival of the fungus did not seem to depend on the presence of nematode or host plant species. Establishment of P. chlamydosporia in soil was slow and was only achieved after the full cropping sequence. The two P. chlamydosporia isolates revealed subtle differences in host preference, plant compatibility, or tolerance to abiotic conditions that may affect their efficacy as biocontrol agents in a long-lasting management programme. [ABSTRACT FROM AUTHOR]

Root exudates play important roles in root-soil microorganism interactions and can mediate tripartite interactions of beneficial microorganisms-plant-pathogen in the rhizosphere. However, the roles of organic acid components in this process have not been well studied. In this study the colonization of a plant growth-promoting rhizobacterium, Bacillus amyloliquefaciens SQR9, on cucumber root infected by Fusarium oxysporum f. sp. cucumerinum J. H. Owen ( FOC) was investigated. Chemotaxis and biofilm formation response of SQR9 to root exudates and their organic acid components were analysed. Infection of FOC on cucumber had a positive effect (3.30-fold increase) on the root colonization of SQR9 compared with controls. Root secretion of citric acid (2.3 ± 0.2 μM) and fumaric acid (5.7 ± 0.5 μM) was enhanced in FOC-infected cucumber plants. Bacillus amyloliquefaciens SQR9 exhibited enhanced chemotaxis to root exudates of FOC-infected cucumber seedlings. Further experiments demonstrated that citric acid acts as a chemoattractant and fumaric acid as a stimulator of biofilm formation in this process. These results suggest that root exudates mediate the interaction of cucumber root and rhizosphere strain B. amyloliquefaciens SQR9 and enhance its root colonization. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Abstract: This study is part of an effort to identify new biological control agents with broad spectrum activity against pathogenic soilborne fungi and pests. New strains of Pseudomonas spp. were isolated from agricultural soils, river silt, and rhizosphere soils from herbarium specimens. Provisional species assignments based on 16S ribosomal DNA typing were: Pseudomonas borealis, Pseudomonas chlororaphis, Pseudomonas fluorescens, Pseudomonas mandelii, Pseudomonas marginalis, Pseudomonas poae, Pseudomonas putida, Pseudomonas syringae and Pseudomonas vranovensis. We evaluated the strains for activity against root rot pathogens of wheat, with the view to discovery and deployment of new suppressive activities. Our objectives were to compare the strains relative to: (i) production of antifungal metabolites, (ii) suppression of Rhizoctonia and Pythium damage in greenhouse assays, (iii) plant growth promotion, and (iv) ability to colonize the wheat rhizosphere. Colonization assays showed that 11 strains rapidly established and maintained rhizosphere populations of ⩾log5CFUg−1 root. Strains 14B2R, 15G2R, 29G9R, 39A2R, 48G9R and Wood3R reduced disease symptoms of both Rhizoctonia solani AG-8 and Pythium ultimum, and the latter four also suppressed Rhizoctonia oryzae and Pythium irregulare. Four strains increased seedling shoot length and root weight but these growth promotion effects were correlated to disease suppression only for two strains. Finally, the strains differed in demonstrated and potential antifungal metabolite activities, indicating that no single factor could be correlated to disease suppression. We have identified several strains for genome sequencing and for long-term development of integrated management of soilborne diseases of wheat. [Copyright &y& Elsevier]

Background: As roots penetrate soil, specialized cells called 'border cells' separate from root caps and contribute a large proportion of exudates forming the rhizosphere. Their function has been unclear. Recent findings suggest that border cells act in a manner similar to that of white blood cells functioning in defense. Histone-linked extracellular DNA (exDNA) and proteins operate as 'neutrophil extracellular traps' to attract and immobilize animal pathogens. DNase treatment reverses trapping and impairs defense, and mutation of pathogen DNase results in loss of virulence. Scope: Histones are among a group of proteins secreted from living border cells. This observation led to the discovery that exDNA also functions in defense of root caps. Experiments revealed that exDNA is synthesized and exported into the surrounding mucilage which attracts, traps and immobilizes pathogens in a host-microbe specific manner. When this plant exDNA is degraded, the normal resistance of the root cap to infection is abolished. Conclusions: Research to define how exDNA may operate in plant immunity is needed. In the meantime, the specificity and stability of exDNA and its association with distinct microbial species may provide an important new tool to monitor when, where, and how soil microbial populations become established as rhizosphere communities. [ABSTRACT FROM AUTHOR]

Pseudomonas fluorescens 2P24 is an effective biological control agent of a number of soilborne plant diseases caused by pathogenic microorganisms. Among a range of secondary metabolites produced by strain 2P24, the antibiotic 2,4-diacetylphloroglucinol (2,4-DAPG) is the major determinant of its disease-suppressive capacity. In this study, we performed random mutagenesis using mini-Tn 5 in order to screen for the transcriptional regulators of the phlA gene, a biosynthase gene responsible for 2,4-DAPG production. The mutant PMphlA23 with significantly decreased phlA gene expression was identified from ∼10 000 insertion colonies. The protein sequence of the interrupted gene has 84% identity to Hfq, a key regulator important for stress resistance and virulence in Pseudomonas aeruginosa. Genetic inactivation of hfq resulted in decreased expression of phlA and reduced production of 2,4-DAPG. Furthermore, the hfq gene was also required for the expression of pcoI, a synthase gene for the LuxI-type quorum-sensing signaling molecule N-acyl-homoserine lactone. Additionally, the hfq mutation drastically reduced biofilm formation and impaired the colonization ability of strain 2P24 on wheat rhizospheres. Based on these results, we propose that Hfq functions as an important regulatory element in the complex network controlling environmental adaption in P. fluorescens 2P24. [ABSTRACT FROM AUTHOR]

Aims: To isolate the rhizosphere competence-defective transposon Tn 5 mutant of Pantoea agglomerans NBRISRM (SRM) and to identify the gene causing defect in its root colonization ability. Methods and Results: From over 5000 clones containing Tn 5, one mutant P. agglomerans NBRISRMT (SRMT) showing 6 log units less colonization when compared with SRM, after 30 days in sand-nonsterilized soil assay system was selected for further work to determine the effects of the mutation on rhizosphere competence. Southern hybridization analysis of restricted genomic DNA of SRMT demonstrated that the mutant had a single Tn 5 insert. SRM increased in titre to about 2 × 108 CFU g−1 root, compared with the indigenous bacterial population of heterotrophs of about 5 × 107 CFU g−1 root. In contrast, 30 days later, the titre value of SRMT was almost undetectable at 1 × 102 CFU g−1 root, demonstrating its inability to survive and colonize the rhizosphere. Sequencing of the flanking region of the Tn 5 mutant revealed that Tn 5 disrupted the purB gene. Conclusions: A defect in the colonization phenotype of the SRMT was attributed to the disruption in adenylosuccinate lyase (EC 4.3.2.2) which is encoded by the pur B gene and is required for rhizosphere colonization in P. agglomerans. Significantly less exopolysaccharide and biofilm was formed by SRMT when compared to SRM, because of the disruption of the purB gene. Significance and Impact of the Study: This work provides the first evidence for a functional role of purB gene in rhizosphere competence and root colonization by any rhizobacteria. [ABSTRACT FROM AUTHOR]

Summary: Unlike most bacteria, the nitrogen-fixing rice-associated Pseudomonas stutzeri A15 disposes of three different nitrate reductases that enable conversion of nitrate to nitrite through three physiologically distinct processes, called nitrate assimilation, nitrate respiration and nitrate dissimilation. To study the role of nitrate respiration in rhizosphere fitness, a Pseudomonas stutzeri narG mutant was constructed and characterized by assessing its growth characteristics and whole-cell nitrate reductase activity in different oxygen tensions. Unexpectedly, the Pseudomonas stutzeri A15 narG mutant appeared to be a better root colonizer, outcompeting the wild type strain in a wheat and rice hydroponic system. [Copyright &y& Elsevier]