Genetic diversity and biocontrol potential of fluorescent pseudomonads producing phloroglucinols and hydrogen cyanide from Swiss soils naturally suppressive or conducive to Thielaviopsis basicola-mediated black root rot of tobacco

Unlocking the potential of ecofriendly guardians for biological control of plant diseases, crop protection and production in sustainable agriculture

Several beneficial microbial strains inhibit the growth of different phytopathogens and commercialized worldwide as biocontrol agents (BCAs) for plant disease management. These BCAs employ different strategies for growth inhibition of pathogens, which includes production of antibiotics, siderophores, lytic enzymes, bacteriocins, hydrogen cyanide, volatile organic compounds, biosurfactants and induction of systemic resistance. The efficacy of antagonistic strains could be further improved through genetic engineering for better disease suppression in sustainable farming practices. Some antagonistic microbial strains also possess plant-growth-promoting activities and their inoculation improved plant growth in addition to disease suppression. This review discusses the characterization of antagonistic microbes and their antimicrobial metabolites, and the application of these BCAs for disease control. The present review also provides a comprehensive summary of the genetic organization and regulation of the biosynthesis of different antimicrobial metabolites in antagonistic strains. Use of molecular engineering to improve production of metabolites in BCAs and their efficacy in disease control is also discussed. The application of these biopesticides will reduce use of conventional pesticides in disease control and help in achieving sustainable and eco-friendly agricultural systems.

Expanding the Pseudomonas diversity of the wheat rhizosphere: four novel species antagonizing fungal phytopathogens and with plant-beneficial properties

Plant-beneficial Pseudomonas bacteria hold the potential to be used as inoculants in agriculture to promote plant growth and health through various mechanisms. The discovery of new strains tailored to specific agricultural needs remains an open area of research. In this study, we report the isolation and characterization of four novel Pseudomonas species associated with the wheat rhizosphere. Comparative genomic analysis with all available Pseudomonas type strains revealed species-level differences, substantiated by both digital DNA-DNA hybridization and average nucleotide identity, underscoring their status as novel species. This was further validated by the phenotypic differences observed when compared to their closest relatives. Three of the novel species belong to the P. fluorescens species complex, with two representing a novel lineage in the Pseudomonas phylogeny. Functional genome annotation revealed the presence of specific features contributing to rhizosphere colonization, including flagella and components for biofilm formation. The novel species have the genetic potential to solubilize nutrients by acidifying the environment, releasing alkaline phosphatases and their metabolism of nitrogen species, indicating potential as biofertilizers. Additionally, the novel species possess traits that may facilitate direct promotion of plant growth through the modulation of the plant hormone balance, including the ACC deaminase enzyme and auxin metabolism. The presence of biosynthetic clusters for toxins such as hydrogen cyanide and non-ribosomal peptides suggests their ability to compete with other microorganisms, including plant pathogens. Direct inoculation of wheat roots significantly enhanced plant growth, with two strains doubling shoot biomass. Three of the strains effectively antagonized fungal phytopathogens (Thielaviopsis basicola, Fusarium oxysporum, and Botrytis cinerea), demonstrating their potential as biocontrol agents. Based on the observed genetic and phenotypic differences from closely related species, we propose the following names for the four novel species: Pseudomonas grandcourensis sp. nov., type strain DGS24T ( = DSM 117501T = CECT 31011T), Pseudomonas purpurea sp. nov., type strain DGS26T ( = DSM 117502T = CECT 31012T), Pseudomonas helvetica sp. nov., type strain DGS28T ( = DSM 117503T = CECT 31013T) and Pseudomonas aestiva sp. nov., type strain DGS32T ( = DSM 117504T = CECT 31014T).

Plant communication with rhizosphere microbes can be revealed by understanding microbial functional gene composition

Understanding rhizosphere microbial ecology is necessary to reveal the interplay between plants and associated microbial communities. The significance of rhizosphere-microbial interactions in plant growth promotion, mediated by several key processes such as auxin synthesis, enhanced nutrient uptake, stress alleviation, disease resistance, etc., is unquestionable and well reported in numerous literature. Moreover, rhizosphere research has witnessed tremendous progress due to the integration of the metagenomics approach and further shift in our viewpoint from taxonomic to functional diversity over the past decades. The microbial functional genes corresponding to the beneficial functions provide a solid foundation for the successful establishment of positive plant-microbe interactions. The microbial functional gene composition in the rhizosphere can be regulated by several factors, e.g., the nutritional requirements of plants, soil chemistry, soil nutrient status, pathogen attack, abiotic stresses, etc. Knowing the pattern of functional gene composition in the rhizosphere can shed light on the dynamics of rhizosphere microbial ecology and the strength of cooperation between plants and associated microbes. This knowledge is crucial to realizing how microbial functions respond to unprecedented challenges which are obvious in the Anthropocene. Unraveling how microbes-mediated beneficial functions will change under the influence of several challenges, requires knowledge of the pattern and composition of functional genes corresponding to beneficial functions such as biogeochemical functions (nutrient cycle), plant growth promotion, stress mitigation, etc. Here, we focus on the molecular traits of plant growth-promoting functions delivered by a set of microbial functional genes that can be useful to the emerging field of rhizosphere functional ecology.

Phytoremediation mechanism and role of plant growth promoting rhizobacteria in weed plants for eco-restoration of hazardous industrial waste polluted site: a review

Plants have numerous strategies for phytoremediation depending upon the characteristic of pollutants. Plant growth promoting rhizobacteria (PGPR) are essential to the process of phytoremediation and play a key part in it. The mechanism of PGPR for phytoremediation is mediated by two methods; under the direct method there is phytohormone production, nitrogen fixation, nutrient mineral solubilization, and siderophore production while the indirect method includes quorum quenching, antibiosis, production of lytic enzyme, biofilm formation, and hydrogen cyanide production. Due to their economic and environmental viability, most researchers have recently concentrated on the potential of weed plants for phytoremediation. Although weed plants are considered unwanted and noxious, they have a high growth rate and adaptability which opens a high scope for its role in phytoremediation of contaminated site. The interaction of plant with rhizobacteria starts from root exudates containing various organic acids and peptides which act as nutrients essential for colonization and siderophore production by the rhizospheric bacteria. The rhizobacteria, while colonizing, tend to promote plant growth and health either directly by providing phytohormones and minerals or indirectly by suppressing growth of possible phytopathogens. Recently, several weed plants have been reported for phytoextraction of heavy metals (Ni, Pb, Zn, Hg, Cd, Cu, As, Fe, and Cr) contaminants from various agro-based industries. These potential native weed plants have high prospect of eco-restoration of polluted site with complex organo-metallic waste for sustainable development.

Biodiversity and Functional Attributes of Rhizospheric Microbiomes: Potential Tools for Sustainable Agriculture

The quest for increasing agricultural yield due to increasing population pressure and demands for healthy food has inevitably led to the indiscriminate use of chemical fertilizers. On the contrary, the exposure of the crops to abiotic stress and biotic stress interferes with crop growth further hindering the productivity. Sustainable agricultural practices are of major importance to enhance production and feed the rising population. The use of plant growth promoting (PGP) rhizospheric microbes is emerging as an efficient approach to ameliorate global dependence on chemicals, improve stress tolerance of plants, boost up growth and ensure food security. Rhizosphere associated microbiomes promote the growth by enhancing the uptake of the nutrients, producing plant growth regulators, iron chelating complexes, shaping the root system under stress conditions and decreasing the levels of inhibitory ethylene concentrations and protecting plants from oxidative stress. Plant growth-promoting rhizospheric microbes belong to diverse range of genera including Acinetobacter, Achromobacter, Aspergillus, Bacillus, Burkholderia, Flavobacterium, Klebsiella, Micrococcus, Penicillium, Pseudomonas, Serratia and Trichoderma. Plant growth promoting microbes are an interesting aspect of research for scientific community and a number of formulations of beneficial microbes are also commercially available. Thus, recent progress in our understanding on rhizospheric microbiomes along with their major roles and mechanisms of action under natural and stressful conditions should facilitate their application as a reliable component in the management of sustainable agricultural system. This review highlights the diversity of plant growth promoting rhizospheric microbes, their mechanisms of plant growth promotion, their role under biotic and abiotic stress and status of biofertilizers. The article further focuses on the role of omics approaches in plant growth promoting rhizospheric microbes and draft genome of PGP microbes.

An Evaluation of Aluminum Tolerant Pseudomonas aeruginosa A7 for In Vivo Suppression of Fusarium Wilt of Chickpea Caused by Fusarium oxysporum f. sp. ciceris and Growth Promotion of Chickpea

Chickpea wilt, caused by Fusarium oxysporum f. sp. ciceris, is a disease that decreases chickpea productivity and quality and can reduce its yield by as much as 15%. A newly isolated, moss rhizoid-associated Pseudomonas aeruginosa strain A7, demonstrated strong inhibition of Fusarium oxysporum f. sp. ciceris growth. An in vitro antimicrobial assay revealed A7 to suppress the growth of several fungal and bacterial plant pathogens by secreting secondary metabolites and by producing volatile compounds. In an in vivo pot experiment with Fusarium wilt infection in chickpea, the antagonist A7 exhibited a disease reduction by 77 ± 1.5%, and significantly reduced the disease incidence and severity indexes. Furthermore, A7 promoted chickpea growth in terms of root and shoot length and dry biomass during pot assay. The strain exhibited several traits associated with plant growth promotion, extracellular enzymatic production, and stress tolerance. Under aluminum stress conditions, in vitro growth of chickpea plants by A7 resulted in a significant increase in root length and plant biomass production. Additionally, hallmark genes for antibiotics production were identified in A7. The methanol extract of strain A7 demonstrated antimicrobial activity, leading to the identification of various antimicrobial compounds based on retention time and molecular weight. These findings strongly suggest that the strain’s significant biocontrol potential and plant growth enhancement could be a potential environmentally friendly process in agricultural crop production.

Endophytic bacterial community of Stellera chamaejasme L. and its role in improving host plants' competitiveness in grasslands

Stellera chamaejasme has become a problematic weed in northern and south-western grasslands of China. To evaluate a possible role of endophytes in its strong competitive capacity, the endophytic bacterial community of S. chamaejasme was investigated by culture-dependent and independent methods, and the growth-promoting traits of some culturable isolates as well as the benefit of endophyte ST3CS3 (Brevundimonas sp.) on host plants growth were studied. The results showed that 823 OTUs were generated with a 97% similarity level in the culture-independent study. They were classified into 29 phyla, 61 classes, 147 orders, 237 families and 440 genera. Among them, Pseudomonas and Ralstonia were the most dominant genera in belowground parts (G) (64.25%) and aboveground parts (S) (26.54%) respectively. The diversity and species richness of endophytes in S were significantly higher than that of G (P < 0.001, t-test). Contrary to this, the number of culturable bacteria in S was a little lower than that of G (P > 0.05, t-test). Totally, 176 isolates belonging to 30 morphotypes were obtained in the culture-dependent study. Among them, Acinetobacter was the most dominant genus in G (51.30%), then followed by Pseudomonas (6.09%) and Brevundimonas (6.09%), while Lysinibacillus (21.31%) was the most dominant genus in S, followed by Pseudomonas (11.48%). Growth-promoting trait tests indicated that 93.65% of the tested isolates (63) exhibited nitrogen-fixing, IAA-synthesizing, phosphorus or potassium solubilizing capacity, in which 77.97% belonged to Proteobacteria, a phylum found to contain more active isolates. Pot experiments demonstrated that endophyte ST3CS3 can significantly improve host plants growth and increase its nitrogen and chlorophyll content (P < 0.01, t-test). Therefore, we suggest that strong competitiveness of S. chamaejasme may in part be due to possession of high ratios of plant growth-promoting proteobacterial endophytes such as Pseudomonas, Acinetobacter and Brevundimonas.

Phloroglucinol Derivatives in Plant-Beneficial Pseudomonas spp.: Biosynthesis, Regulation, and Functions

Plant-beneficial Pseudomonas spp. aggressively colonize the rhizosphere and produce numerous secondary metabolites, such as 2,4-diacetylphloroglucinol (DAPG). DAPG is a phloroglucinol derivative that contributes to disease suppression, thanks to its broad-spectrum antimicrobial activity. A famous example of this biocontrol activity has been previously described in the context of wheat monoculture where a decline in take-all disease (caused by the ascomycete Gaeumannomyces tritici) has been shown to be associated with rhizosphere colonization by DAPG-producing Pseudomonas spp. In this review, we discuss the biosynthesis and regulation of phloroglucinol derivatives in the genus Pseudomonas, as well as investigate the role played by DAPG-producing Pseudomonas spp. in natural soil suppressiveness. We also tackle the mode of action of phloroglucinol derivatives, which can act as antibiotics, signalling molecules and, in some cases, even as pathogenicity factors. Finally, we discuss the genetic and genomic diversity of DAPG-producing Pseudomonas spp. as well as its importance for improving the biocontrol of plant pathogens.

Rhizosphere Microbiome Cooperations: Strategies for Sustainable Crop Production

Interactions between microorganisms and host plants determine the growth and development as well as the health of the host plant. Various microbial groups inhabit the rhizosphere, each with its peculiar function. The survival of each microbial group depends to a large extent on its ability to colonize the plant root and outcompete the native organisms. The role of the rhizospheric microbiome in enhancing plant growth has not been fully maximized. An understanding of the complexities of microbial interactions and factors affecting their assembly in the community is necessary to benefit maximally from the cooperations of various microbial communities for sustainable crop production. In this review, we outline the various organisms associated with the plant rhizosphere with emphasis on their interactions and mechanisms used in plant growth promotion.

Disease-Suppressive Soils-Beyond Food Production: a Critical Review

In the pursuit of higher food production and economic growth and increasing population, we have often jeopardized natural resources such as soil, water, vegetation, and biodiversity at an alarming rate. In this process, wider adoption of intensive farming practices, namely changes in land use, imbalanced fertilizer application, minimum addition of organic residue/manure, and non-adoption of site-specific conservation measures, has led to declining in soil health and land degradation in an irreversible manner. In addition, increasing use of pesticides, coupled with soil and water pollution, has led the researchers to search for an environmental-friendly and cost-effective alternatives to controlling soil-borne diseases that are difficult to control, and which significantly limit agricultural productivity. Since the 1960s, disease-suppressive soils (DSS) have been identified and studied around the world. Soil disease suppression is the reduction in the incidence of soil-borne diseases even in the presence of a host plant and inoculum in the soil. The disease-suppressive capacity is mainly attributed to diverse microbial communities present in the soil that could act against soil-borne pathogens in multifaceted ways. The beneficial microorganisms employ some specific functions such as antibiosis, parasitism, competition for resources, and predation. However, there has been increasing evidence on the role of soil abiotic factors that largely influence the disease suppression. The intricate interactions of the soil, plant, and environmental components in a disease triangle make this process complex yet crucial to study to reduce disease incidence. Increasing resistance of the pathogen to presently available chemicals has led to the shift from culturable microbes to unexplored and unculturable microbes. Agricultural management practices such as tillage, fertilization, manures, irrigation, and amendment applications significantly alter the soil physicochemical environment and influence the growth and behaviour of antagonistic microbes. Plant factors such as age, type of crop, and root behaviour of the plant could stimulate or limit the diversity and structure of soil microorganisms in the rhizosphere. Further, identification and in-depth of disease-suppressive soils could lead to the discovery of more beneficial microorganisms with novel anti-microbial and plant promoting traits. To date, several microbial species have been isolated and proposed as key contributors in disease suppression, but the complexities as well as the mechanisms of the microbial and abiotic interactions remain elusive for most of the disease-suppressive soils. Thus, this review critically explores disease-suppressive attributes in soils, mechanisms involved, and biotic and abiotic factors affecting DSS and also briefly reviewing soil microbiome for anti-microbial drugs, in fact, a consequence of DSS phenomenon.

Exploring the efficacy of antagonistic rhizobacteria as native biocontrol agents against tomato plant diseases

As the environmental and health concerns alert the necessity to move towards a sustainable agriculture system, biological approach using indigenous plant growth-promoting rhizobacteria (PGPR) gains a strong impetus in the field of plant disease control. In this context, the present review article addresses the usage of rhizospheric antagonistic bacteria as a suitable alternative to control tomato fungal diseases namely Fusarium wilt and early blight disease. Biological control has been considered to be an eco-friendly, safe and effective method for disease management. The inherent traits of PGPR to antagonize a pathogen through various mechanisms has been investigated extensively to utilize them as potent biocontrol agents (BCA). Hence, the article provides a detailed account on different biocontrol mechanisms displayed by BCA. It is also suggested that the use of bacterial consortium ensures consistent performance by BCA in field conditions. Likewise, this review also deals with the opportunities and obstacles faced during commercialization of these antagonistic bacteria as biocontrol agents in the market.

Towards a Sustainable Agriculture: Strategies Involving Phytoprotectants against Salt Stress

Salinity is one of the main constraints for agriculture productivity worldwide. This important abiotic stress has worsened in the last 20 years due to the increase in water demands in arid and semi-arid areas. In this context, increasing tolerance of crop plants to salt stress is needed to guarantee future food supply to a growing population. This review compiles knowledge on the use of phytoprotectants of microbial origin (arbuscular mycorrhizal fungi and plant growth-promoting rhizobacteria), osmoprotectants, melatonin, phytohormones and antioxidant metabolism-related compounds as alleviators of salt stress in numerous plant species. Phytoprotectants are discussed in detail, including their nature, applicability, and role in the plant in terms of physiological and phenotype effects. As a result, increased crop yield and crop quality can be achieved, which in turn positively impact food security. Herein, efforts from academic and industrial sectors should focus on defining the treatment conditions and plant-phytoprotectant associations providing higher benefits.

HCN-producing Pseudomonas protegens CHA0 affects intraradical viability of Rhizophagus irregularis in Sorghum vulgare roots

Arbuscular mycorrhizal fungi (AMF) and plant growth-promoting rhizobacteria inhabit the plant rhizosphere. Both functional groups can influence plant community structures, and interactions between them can vary from being synergistic to antagonistic. HCN-producing Pseudomonas protegens CHA0 is a plant growth-promoting rhizobacterium. P. protegens CHA0 has been shown to weakly attach to AMF hyphae. Here, we analyze the effect of P. protegens CHA0 on the viability of intraradical AMF hyphae. Using pot experiments, we have grown mycorrhizal and nonmycorrhizal Sorghum vulgare var. M35 with P. protegens CHA0 or HCN^- mutant P. protegens CHA77, which did not produce HCN. Mycorrhizal and nonmycorrhizal Sorghum grown without CHA0 or CHA77 served as the control. While metabolically active AMF was not detected in mycorrhizal plants grown with HCN⁺ CHA0, the percentage of root colonization of metabolically active AMF in plants grown with HCN^- CHA77 was lower than in the control. Root phosphorus was highest in mycorrhizal plants grown with HCN⁺ CHA0, but root Fe was higher in plants grown with the bacterial strains. Our results indicate that HCN-producing P. protegens can affect the viability of intraradical AMF.

Metabolomics approaches for the discrimination of disease suppressive soils for Rhizoctonia solani AG8 in cereal crops using 1H NMR and LC-MS

The suppression of soilborne crop pathogens such as Rhizoctonia solani AG8 may offer a sustainable and enduring method for disease control, though soils with these properties are difficult to identify. In this study, we analysed the soil metabolic profiles of suppressive and non-suppressive soils over 2 years of cereal production. We collected bulk and rhizosphere soil at different cropping stages and subjected soil extracts to liquid chromatography-mass spectrometry (LC-MS) and proton nuclear magnetic resonance spectroscopy (¹H NMR) analyses. Community analyses of suppressive and non-suppressive soils using principal component analyses and predictive modelling of LC-MS and NMR datasets respectively, revealed distinct biochemical profiles for the two soil types with clustering based on suppressiveness and cropping stage. NMR spectra revealed the suppressive soils to be more abundant in sugar molecules than non-suppressive soils, which were more abundant in lipids and terpenes. LC-MS features that were significantly more abundant in the suppressive soil were identified and assessed as potential biomarkers for disease suppression. The structures of a potential class of LC-MS biomarkers were elucidated using accurate mass data and MS fragmentation spectrum information. The most abundant compound found in association with suppressive soils was confirmed to be a macrocarpal, which is an antimicrobial secondary metabolite. Our study has demonstrated the utility of environmental metabolomics for the study of disease suppressive soils, resulting in the discovery of a macrocarpal biomarker for R. solani AG8 suppressive soil which can be further studied functionally in association with suppression pot trials and microbial isolation studies.

Microbial Inoculants for Improving Crop Quality and Human Health in Africa

Current agricultural practices depend heavily on chemical inputs (such as fertilizers, pesticides, herbicides, etc.) which, all things being equal cause a deleterious effect on the nutritional value of farm product and health of farm workers and consumers. Excessive and indiscriminate use of these chemicals have resulted in food contamination, weed and disease resistance and negative environmental outcomes which together have a significant impact on human health. Application of these chemical inputs promotes the accumulation of toxic compounds in soils. Chemical compounds are absorbed by most crops from soil. Several synthetic fertilizers contain acid radicals, such as hydrochloride and sulfuric radicals, and hence increase the soil acidity and adversely affect soil and plant health. Highly recalcitrant compounds can also be absorbed by some plants. Continuous consumption of such crops can lead to systematic disorders in humans. Quite a number of pesticides and herbicides have carcinogenicity potential. The increasing awareness of health challenges as a result of consumption of poor quality crops has led to a quest for new and improved technologies of improving both the quantity and quality of crop without jeopardizing human health. A reliable alternative to the use of chemical inputs is microbial inoculants that can act as biofertilizers, bioherbicide, biopesticides, and biocontrol agents. Microorganisms are able to carry out the plant growth promotion, pest and disease and weed control. Microbial inoculants are beneficiary microorganisms applied to either the soil or the plant in order to improve productivity and crop health. Microbial inoculants are natural-based products being widely used to control pests and improve the quality of the soil and crop, and hence human health. Microbial inoculants involve a blend of microorganisms that work with the soil and the soil life to improve soil fertility and health and by extension improve human health. Microbial inoculants have the ability to minimize the negative impact of chemical input and consequently increase the quantity and quality of farm produce. Microbial inoculants are environmental-friendly and deliver plant nutrients to plants in a more sustainable manner. Microbial inoculants can help reduce chemical fertilizer application. Microbial inoculants could include bacteria, fungi and algae. This research summarizes the impact of agricultural chemical inputs on human health. The contribution of microbial inoculants in sustainable maintenance of human health will be expatiated. Advances in microbial inoculants and technology and strategies to explore this natural, user friendly biological resource for sustainable maintenance of plant health will be discussed.

Comparative Metatranscriptomics of Wheat Rhizosphere Microbiomes in Disease Suppressive and Non-suppressive Soils for Rhizoctonia solani AG8

The soilborne fungus Rhizoctonia solani anastomosis group (AG) 8 is a major pathogen of grain crops resulting in substantial production losses. In the absence of resistant cultivars of wheat or barley, a sustainable and enduring method for disease control may lie in the enhancement of biological disease suppression. Evidence of effective biological control of R. solani AG8 through disease suppression has been well documented at our study site in Avon, South Australia. A comparative metatranscriptomic approach was applied to assess the taxonomic and functional characteristics of the rhizosphere microbiome of wheat plants grown in adjacent fields which are suppressive and non-suppressive to the plant pathogen R. solani AG8. Analysis of 12 rhizosphere metatranscriptomes (six per field) was undertaken using two bioinformatic approaches involving unassembled and assembled reads. Differential expression analysis showed the dominant taxa in the rhizosphere based on mRNA annotation were Arthrobacter spp. and Pseudomonas spp. for non-suppressive samples and Stenotrophomonas spp. and Buttiauxella spp. for the suppressive samples. The assembled metatranscriptome analysis identified more differentially expressed genes than the unassembled analysis in the comparison of suppressive and non-suppressive samples. Suppressive samples showed greater expression of a polyketide cyclase, a terpenoid biosynthesis backbone gene (dxs) and many cold shock proteins (csp). Non-suppressive samples were characterised by greater expression of antibiotic genes such as non-heme chloroperoxidase (cpo) which is involved in pyrrolnitrin synthesis, and phenazine biosynthesis family protein F (phzF) and its transcriptional activator protein (phzR). A large number of genes involved in detoxifying reactive oxygen species (ROS) and superoxide radicals (sod, cat, ahp, bcp, gpx1, trx) were also expressed in the non-suppressive rhizosphere samples most likely in response to the infection of wheat roots by R. solani AG8. Together these results provide new insight into microbial gene expression in the rhizosphere of wheat in soils suppressive and non-suppressive to R. solani AG8. The approach taken and the genes involved in these functions provide direction for future studies to determine more precisely the molecular interplay of plant-microbe-pathogen interactions with the ultimate goal of the development of management options that promote beneficial rhizosphere microflora to reduce R. solani AG8 infection of crops.

Isolation and Molecular Characterization of a Model Antagonistic Pseudomonas aeruginosa Divulging In Vitro Plant Growth Promoting Characteristics

The use of microbial technologies in agriculture is currently expanding quite rapidly with the identification of new bacterial strains, which are more effective in promoting plant growth. In the present study 18 strains of Pseudomonas were isolated from soil sample of Balochistan coastline. Among isolated Pseudomonas strains four designated as SP19, SP22, PS24, and SP25 exhibited biocontrol activities against phytopathogenic fungi, that is, Rhizopus microsporus, Fusarium oxysporum, Aspergillus niger, Alternaria alternata, and Penicillium digitatum; PS24 identified as Pseudomonas aeruginosa by 16srRNA gene bank accession number EU081518 was selected on the basis of its antifungal activity to explore its potential as plant growth promotion. PS24 showed multiple plant growth promoting attributes such as phosphate solubilization activity, indole acetic acid (IAA), siderophore, and HCN production. In order to determine the basis for antifungal properties, antibiotics were extracted from King B broth of PS24 and analyzed by TLC. Pyrrolnitrin antibiotic was detected in the culture of strain PS24. PS24 exhibited antifungal activities found to be positive for hydrogen cyanide synthase Hcn BC gene. Sequencing of gene of Hcn BC gene of strain PS24 revealed 99% homology with the Pseudomonas aeruginosa strain PA01. The sequence of PS24 had been submitted in gene bank accession number KR605499. Ps. aeruginosa PS24 with its multifunctional biocontrol possessions can be used to bioprotect the crop plants from phytopathogens.

Mechanisms of action of plant growth promoting bacteria

The idea of eliminating the use of fertilizers which are sometimes environmentally unsafe is slowly becoming a reality because of the emergence of microorganisms that can serve the same purpose or even do better. Depletion of soil nutrients through leaching into the waterways and causing contamination are some of the negative effects of these chemical fertilizers that prompted the need for suitable alternatives. This brings us to the idea of using microbes that can be developed for use as biological fertilizers (biofertilizers). They are environmentally friendly as they are natural living organisms. They increase crop yield and production and, in addition, in developing countries, they are less expensive compared to chemical fertilizers. These biofertilizers are typically called plant growth-promoting bacteria (PGPB). In addition to PGPB, some fungi have also been demonstrated to promote plant growth. Apart from improving crop yields, some biofertilizers also control various plant pathogens. The objective of worldwide sustainable agriculture is much more likely to be achieved through the widespread use of biofertilizers rather than chemically synthesized fertilizers. However, to realize this objective it is essential that the many mechanisms employed by PGPB first be thoroughly understood thereby allowing workers to fully harness the potentials of these microbes. The present state of our knowledge regarding the fundamental mechanisms employed by PGPB is discussed herein.

Relationships between Root Pathogen Resistance, Abundance and Expression of Pseudomonas Antimicrobial Genes, and Soil Properties in Representative Swiss Agricultural Soils

Strains of Pseudomonas that produce antimicrobial metabolites and control soilborne plant diseases have often been isolated from soils defined as disease-suppressive, i.e., soils, in which specific plant pathogens are present, but plants show no or reduced disease symptoms. Moreover, it is assumed that pseudomonads producing antimicrobial compounds such as 2,4-diacetylphloroglucinol (DAPG) or phenazines (PHZ) contribute to the specific disease resistance of suppressive soils. However, pseudomonads producing antimicrobial metabolites are also present in soils that are conducive to disease. Currently, it is still unknown whether and to which extent the abundance of antimicrobials-producing pseudomonads is related to the general disease resistance of common agricultural soils. Moreover, virtually nothing is known about the conditions under which pseudomonads express antimicrobial genes in agricultural field soils. We present here results of the first side-by-side comparison of 10 representative Swiss agricultural soils with a cereal-oriented cropping history for (i) the resistance against two soilborne pathogens, (ii) the abundance of Pseudomonas bacteria harboring genes involved in the biosynthesis of the antimicrobials DAPG, PHZ, and pyrrolnitrin on roots of wheat, and (iii) the ability to support the expression of these genes on the roots. Our study revealed that the level of soil disease resistance strongly depends on the type of pathogen, e.g., soils that are highly resistant to Gaeumannomyces tritici often are highly susceptible to Pythium ultimum and vice versa. There was no significant correlation between the disease resistance of the soils, the abundance of Pseudomonas bacteria carrying DAPG, PHZ, and pyrrolnitrin biosynthetic genes, and the ability of the soils to support the expression of the antimicrobial genes. Correlation analyses indicated that certain soil factors such as silt, clay, and some macro- and micronutrients influence both the abundance and the expression of the antimicrobial genes. Taken together, the results of this study suggests that pseudomonads producing DAPG, PHZ, or pyrrolnitrin are present and abundant in Swiss agricultural soils and that the soils support the expression of the respective biosynthetic genes in these bacteria to various degrees. The precise role that these pseudomonads play in the general disease resistance of the investigated agricultural soils remains elusive.

Fluorescent Pseudomonas Strains with only Few Plant-Beneficial Properties Are Favored in the Maize Rhizosphere

Plant Growth-Promoting Rhizobacteria (PGPR) enhance plant health and growth using a variety of traits. Effective PGPR strains typically exhibit multiple plant-beneficial properties, but whether they are better adapted to the rhizosphere than PGPR strains with fewer plant-beneficial properties is unknown. Here, we tested the hypothesis that strains with higher numbers of plant-beneficial properties would be preferentially selected by plant roots. To this end, the co-occurrence of 18 properties involved in enhanced plant nutrition, plant hormone modulation, or pathogen inhibition was analyzed by molecular and biochemical methods in a collection of maize rhizosphere and bulk soil isolates of fluorescent Pseudomonas. Twelve plant-beneficial properties were found among the 698 isolates. Contrarily to expectation, maize preferentially selected pseudomonads with low numbers of plant-beneficial properties (up to five). This selection was not due to the predominance of strains with specific assortments of these properties, or with specific taxonomic status. Therefore, the occurrence of only few plant-beneficial properties appeared favorable for root colonization by pseudomonads.

Evolutionary patchwork of an insecticidal toxin shared between plant-associated pseudomonads and the insect pathogens Photorhabdus and Xenorhabdus

BACKGROUND

Root-colonizing fluorescent pseudomonads are known for their excellent abilities to protect plants against soil-borne fungal pathogens. Some of these bacteria produce an insecticidal toxin (Fit) suggesting that they may exploit insect hosts as a secondary niche. However, the ecological relevance of insect toxicity and the mechanisms driving the evolution of toxin production remain puzzling.

RESULTS

Screening a large collection of plant-associated pseudomonads for insecticidal activity and presence of the Fit toxin revealed that Fit is highly indicative of insecticidal activity and predicts that Pseudomonas protegens and P. chlororaphis are exclusive Fit producers. A comparative evolutionary analysis of Fit toxin-producing Pseudomonas including the insect-pathogenic bacteria Photorhabdus and Xenorhadus, which produce the Fit related Mcf toxin, showed that fit genes are part of a dynamic genomic region with substantial presence/absence polymorphism and local variation in GC base composition. The patchy distribution and phylogenetic incongruence of fit genes indicate that the Fit cluster evolved via horizontal transfer, followed by functional integration of vertically transmitted genes, generating a unique Pseudomonas-specific insect toxin cluster.

CONCLUSIONS

Our findings suggest that multiple independent evolutionary events led to formation of at least three versions of the Mcf/Fit toxin highlighting the dynamic nature of insect toxin evolution.

Community profiling of culturable fluorescent pseudomonads in the rhizosphere of green gram (Vigna radiata L.)

Study on microbial diversity in the unexplored rhizosphere is important to understand their community structure, biology and ecological interaction with the host plant. This research assessed the genetic and functional diversity of fluorescent pseudomonads [FP] in the green gram rhizophere. One hundred and twenty types of morphologically distinct fluorescent pseudomonads were isolated during vegetative as well as reproductive growth phase of green gram. Rep PCR, ARDRA and RISA revealed two distinct clusters in each case at 75, 61 and 70% similarity coefficient index respectively. 16S rRNA partial sequencing analysis of 85 distantly related fluorescent pseudomonads depicted Pseudomonas aeruginosa as the dominant group. Out of 120 isolates, 23 (19%) showed antagonistic activity towards phytopathogenic fungi. These bacterial isolates showed varied production of salicylic acid, HCN and chitinase, 2, 4-diacetylphloroglucinol (DAPG), phenazine-1-carboxylic acid (PCA) and pyoluteorin (PLT). Production efficiency of inherent level of plant growth promoting (PGP) traits among the 120 isolates demonstrated that 10 (8%) solubilised inorganic phosphates, 25 (20%) produced indoles and 5 (4%) retained ACC deaminase activity. Pseudomonas aeruginosa GGRJ21 showed the highest production of all antagonistic and plant growth promoting (PGP) traits. In a greenhouse experiment, GGRJ21 suppressed root rot disease of green gram by 28-93% (p = 0.05). Consistent up regulation of three important stress responsive genes, i.e., acdS, KatA and gbsA and elevated production efficiency of different PGP traits could promote GGRJ21 as a potent plant growth regulator.

Rhizosphere ecology and phytoprotection in soils naturally suppressive to Thielaviopsis black root rot of tobacco

Soil suppressiveness to disease is an intriguing emerging property in agroecosystems, with important implications because it enables significant protection of susceptible plants from soil-borne pathogens. Unlike many soils where disease suppressiveness requires crop monoculture to establish, certain soils are naturally suppressive to disease, and this type of specific disease suppressiveness is maintained despite crop rotation. Soils naturally suppressive to Thielaviopsis basicola-mediated black root rot of tobacco and other crops occur in Morens region (Switzerland) and have been studied for over 30 years. In Morens, vermiculite-rich suppressive soils formed on morainic deposits while illite-rich conducive soils developed on sandstone, but suppressiveness is of microbial origin. Antagonistic pseudomonads play a role in black root rot suppressiveness, including Pseudomonas protegens (formerly P. fluorescens) CHA0, a major model strain for research. However, other types of rhizobacterial taxa may differ in prevalence between suppressive and conducive soils, suggesting that the microbial basis of black root rot suppressiveness could be far more complex than solely a Pseudomonas property. This first review on black root rot suppressive soils covers early findings on these soils, the significance of recent results, and compares them with other types of suppressive soils in terms of rhizosphere ecology and plant protection mechanisms.

Effect of clay mineralogy on iron bioavailability and rhizosphere transcription of 2,4-diacetylphloroglucinol biosynthetic genes in biocontrol Pseudomonas protegens

Pseudomonas strains producing 2,4-diacetylphloroglucinol (DAPG) can protect plants from soilborne phytopathogens and are considered the primary reason for suppressiveness of morainic Swiss soils to Thielaviopsis basicola-mediated black root-rot disease of tobacco, even though they also occur nearby in conducive sandstone soils. The underlying molecular mechanisms accounting for this discrepancy are not understood. In this study, we assessed the hypothesis that the presence of iron-rich vermiculite clay (dominant in suppressive soils) instead of illite (dominant in neighboring conducive soils) translates into higher levels of iron bioavailability and transcription of Pseudomonas DAPG synthetic genes in the tobacco rhizosphere. Rhizosphere monitoring of reporter gene systems pvd-inaZ and phlA-gfp in Pseudomonas protegens indicated that the level of iron bioavailability and the number of cells expressing phl genes (DAPG synthesis), respectively, were higher in vermiculitic than in illitic artificial soils. This was in accordance with the effect of iron on phlA-gfp expression in vitro and, indeed, iron addition to the illitic soil increased the number of cells expressing phlA-gfp. Similar findings were made in the presence of the pathogen T. basicola. Altogether, results substantiate the hypothesis that iron-releasing minerals may confer disease suppressiveness by modulating iron bioavailability in the rhizosphere and expression of biocontrol-relevant genes in antagonistic P. protegens.

Does wheat genetically modified for disease resistance affect root-colonizing pseudomonads and arbuscular mycorrhizal fungi?

This study aimed to evaluate the impact of genetically modified (GM) wheat with introduced pm3b mildew resistance transgene, on two types of root-colonizing microorganisms, namely pseudomonads and arbuscular mycorrhizal fungi (AMF). Our investigations were carried out in field trials over three field seasons and at two locations. Serial dilution in selective King's B medium and microscopy were used to assess the abundance of cultivable pseudomonads and AMF, respectively. We developed a denaturing gradient gel electrophoresis (DGGE) method to characterize the diversity of the pqqC gene, which is involved in Pseudomonas phosphate solubilization. A major result was that in the first field season Pseudomonas abundances and diversity on roots of GM pm3b lines, but also on non-GM sister lines were different from those of the parental lines and conventional wheat cultivars. This indicates a strong effect of the procedures by which these plants were created, as GM and sister lines were generated via tissue cultures and propagated in the greenhouse. Moreover, Pseudomonas population sizes and DGGE profiles varied considerably between individual GM lines with different genomic locations of the pm3b transgene. At individual time points, differences in Pseudomonas and AMF accumulation between GM and control lines were detected, but they were not consistent and much less pronounced than differences detected between young and old plants, different conventional wheat cultivars or at different locations and field seasons. Thus, we conclude that impacts of GM wheat on plant-beneficial root-colonizing microorganisms are minor and not of ecological importance. The cultivation-independent pqqC-DGGE approach proved to be a useful tool for monitoring the dynamics of Pseudomonas populations in a wheat field and even sensitive enough for detecting population responses to altered plant physiology.

Pseudomonas viridiflava, a multi host plant pathogen with significant genetic variation at the molecular level

The pectinolytic species Pseudomonas viridiflava has a wide host range among plants, causing foliar and stem necrotic lesions and basal stem and root rots. However, little is known about the molecular evolution of this species. In this study we investigated the intraspecies genetic variation of P. viridiflava amongst local (Cretan), as well as international isolates of the pathogen. The genetic and phenotypic variability were investigated by molecular fingerprinting (rep-PCR) and partial sequencing of three housekeeping genes (gyrB, rpoD and rpoB), and by biochemical and pathogenicity profiling. The biochemical tests and pathogenicity profiling did not reveal any variability among the isolates studied. However, the molecular fingerprinting patterns and housekeeping gene sequences clearly differentiated them. In a broader phylogenetic comparison of housekeeping gene sequences deposited in GenBank, significant genetic variability at the molecular level was found between isolates of P. viridiflava originated from different host species as well as among isolates from the same host. Our results provide a basis for more comprehensive understanding of the biology, sources and shifts in genetic diversity and evolution of P. viridiflava populations and should support the development of molecular identification tools and epidemiological studies in diseases caused by this species.

Evolutionary history of synthesis pathway genes for phloroglucinol and cyanide antimicrobials in plant-associated fluorescent pseudomonads

Plant-beneficial fluorescent Pseudomonas spp. play important ecological roles. Here, their evolutionary history was investigated by a multilocus approach targeting genes involved in synthesis of secondary antimicrobial metabolites implicated in biocontrol of phytopathogens. Some of these genes were proposed to be ancestral, and this was investigated using a worldwide collection of 30 plant-colonizing fluorescent pseudomonads, based on phylogenetic analysis of 14 loci involved in production of 2,4-diacetylphloroglucinol (phlACBDE, phlF, intergenic locus phlA/phlF), hydrogen cyanide (hcnABC, anr) or global regulation of secondary metabolism (gacA, gacS, rsmZ). The 10 housekeeping loci rrs, dsbA, gyrB, rpoD, fdxA, recA, rpoB, rpsL, rpsG, and fusA served as controls. Each strain was readily distinguished from the others when considering allelic combinations for these 14 biocontrol-relevant loci. Topology comparisons based on Shimodaira-Hasegawa tests showed extensive incongruence when comparing single-locus phylogenetic trees with one another, but less when comparing (after sequence concatenation) trees inferred for genes involved in 2,4-diacetylphloroglucinol synthesis, hydrogen cyanide synthesis, or secondary metabolism global regulation with trees for housekeeping genes. The 14 loci displayed linkage disequilibrium, as housekeeping loci did, and all 12 protein-coding loci were subjected to purifying selection except for one positively-selected site in HcnA. Overall, the evolutionary history of Pseudomonas genes involved in synthesis of secondary antimicrobial metabolites important for biocontrol functions is in fact similar to that of housekeeping genes, and results suggest that they are ancestral in pseudomonads producing hydrogen cyanide and 2,4-diacetylphloroglucinol.

Pseudomonas protegens sp. nov., widespread plant-protecting bacteria producing the biocontrol compounds 2,4-diacetylphloroglucinol and pyoluteorin

Fluorescent Pseudomonas strains producing the antimicrobial secondary metabolite 2,4-diacetylphloroglucinol (Phl) play a prominent role in the biocontrol of plant diseases. A subset of Phl-producing fluorescent Pseudomonas strains, which can additionally synthesize the antimicrobial compound pyoluteorin (Plt), appears to cluster separately from other fluorescent Pseudomonas spp. based on 16S rRNA gene analysis and shares at most 98.4% 16S rRNA gene sequence identity with any other Pseudomonas species. In this study, a polyphasic approach based on molecular and phenotypic methods was used to clarify the taxonomy of representative Phl(+) Plt(+) strains isolated from tobacco, cotton or wheat on different continents. Phl(+) Plt(+) strains clustered separately from their nearest phylogenetic neighbors (i.e. species from the 'P. syringae', 'P. fluorescens' and 'P. chlororaphis' species complexes) based on rpoB, rpoD or gyrB phylogenies. DNA-DNA hybridization experiments clarified that Phl(+) Plt(+) strains formed a tight genomospecies that was distinct from P. syringae, P. fluorescens, or P. chlororaphis type strains. Within Phl(+) strains, the Phl(+) Plt(+) strains were differentiated from other biocontrol fluorescent Pseudomonas strains that produced Phl but not Plt, based on phenotypic and molecular data. Discriminative phenotypic characters were also identified by numerical taxonomic analysis and siderotyping. Altogether, this polyphasic approach supported the conclusion that Phl(+) Plt(+) fluorescent Pseudomonas strains belonged to a novel species for which the name Pseudomonas protegens is proposed, with CHA0(T) (=CFBP 6595(T), =DSM 19095(T)) as the type strain.

Genetic and functional diversity among the antagonistic potential fluorescent pseudomonads isolated from tea rhizosphere

Twenty-five fluorescent pseudomonads from rhizospheric soil of six tea gardens in four district of Upper Assam, India were isolated and screened for antagonistic activity against fungal pathogens such as Fusarium oxysporum f. sp. raphani (For), Fusarium oxysporum f. sp. ciceri (Foc), Fusarium semitectum (Fs), and Rhizoctonia solani (Rs); and bacterial pathogens-Staphylococcus aureus (Sa), Escherichia coli (Ec), and Klebsiella pneumoniae (Kp). Most of the isolates exhibited strong antagonistic activity against the fungal pathogens and gram-positive bacterium i.e. Staphylococcus aureus. Productions of siderophore, salicylic acid (SA), hydrogen cyanide (HCN), and cell wall-degrading enzyme (chitinase) were studied to observe the possible mechanisms of antagonistic activity of the isolates. Correlation between the antagonistic potentiality of some isolates and their levels of production of siderophore, salicylic acid, and hydrogen cyanide was observed. Out of the 25 isolates, antibiotic-coding genes, 2,4-diacetylphloroglucinol (DAPG) and pyoluteorin (PLT) were detected in the isolates, Pf12 and Pf373, respectively. Genetic diversity of these fluorescent pseudomonads were analyzed with reference to four strains of Pseudomonas fluorescens NICM 2099(T), P. aeruginosa MTCC 2582(T), P. aureofaciens NICM 2026(T), and P. syringae MTCC 673(T). 16S rDNA-RFLP analysis of these isolates using three tetra cutter restriction enzymes (HaeIII, AluI and MspI) revealed two distinct clusters. Cluster A comprised only two isolates Pf141 and 24-PfM3, and cluster B comprised 23 isolates along with four reference strains.

Interplay between wheat cultivars, biocontrol pseudomonads, and soil

There is a significant potential to improve the plant-beneficial effects of root-colonizing pseudomonads by breeding wheat genotypes with a greater capacity to sustain interactions with these bacteria. However, the interaction between pseudomonads and crop plants at the cultivar level, as well as the conditions which favor the accumulation of beneficial microorganisms in the wheat rhizosphere, is largely unknown. Therefore, we characterized the three Swiss winter wheat (Triticum aestivum) cultivars Arina, Zinal, and Cimetta for their ability to accumulate naturally occurring plant-beneficial pseudomonads in the rhizosphere. Cultivar performance was measured also by the ability to select for specific genotypes of 2,4-diacetylphloroglucinol (DAPG) producers in two different soils. Cultivar-specific differences were found; however, these were strongly influenced by the soil type. Denaturing gradient gel electrophoresis (DGGE) analysis of fragments of the DAPG biosynthetic gene phlD amplified from natural Pseudomonas rhizosphere populations revealed that phlD diversity substantially varied between the two soils and that there was a cultivar-specific accumulation of certain phlD genotypes in one soil but not in the other. Furthermore, the three cultivars were tested for their ability to benefit from Pseudomonas inoculants. Interestingly, Arina, which was best protected against Pythium ultimum infection by inoculation with Pseudomonas fluorescens biocontrol strain CHA0, was the cultivar which profited the least from the bacterial inoculant in terms of plant growth promotion in the absence of the pathogen. Knowledge gained of the interactions between wheat cultivars, beneficial pseudomonads, and soil types allows us to optimize cultivar-soil combinations for the promotion of growth through beneficial pseudomonads. Additionally, this information can be implemented by breeders into a new and unique breeding strategy for low-input and organic conditions.

Comparison of barley succession and take-all disease as environmental factors shaping the rhizobacterial community during take-all decline

The root disease take-all, caused by Gaeumannomyces graminis var. tritici, can be managed by monoculture-induced take-all decline (TAD). This natural biocontrol mechanism typically occurs after a take-all outbreak and is believed to arise from an enrichment of antagonistic populations in the rhizosphere. However, it is not known whether these changes are induced by the monoculture or by ecological rhizosphere conditions due to a disease outbreak and subsequent attenuation. This question was addressed by comparing the rhizosphere microflora of barley, either inoculated with the pathogen or noninoculated, in a microcosm experiment in five consecutive vegetation cycles. TAD occurred in soil inoculated with the pathogen but not in noninoculated soil. Bacterial community analysis using terminal restriction fragment length polymorphism of 16S rRNA showed pronounced population shifts in the successive vegetation cycles, but pathogen inoculation had little effect. To elucidate rhizobacterial dynamics during TAD development, a 16S rRNA-based taxonomic microarray was used. Actinobacteria were the prevailing indicators in the first vegetation cycle, whereas the third cycle-affected most severely by take-all-was characterized by Proteobacteria, Bacteroidetes, Chloroflexi, Planctomycetes, and Acidobacteria. Indicator taxa for the last cycle (TAD) belonged exclusively to Proteobacteria, including several genera with known biocontrol traits. Our results suggest that TAD involves monoculture-induced enrichment of plant-beneficial taxa.

Comparison of rhizobacterial community composition in soil suppressive or conducive to tobacco black root rot disease

Work on soils suppressive to Thielaviopsis basicola-mediated tobacco black root rot has focused on antagonistic pseudomonads to date. The role of non-Pseudomonas rhizosphere populations has been neglected, and whether they differ in black root rot-suppressive versus -conducive soils is unknown. To assess this possibility, tobacco was grown in a suppressive and a conducive soil of similar physicochemical properties, and rhizobacterial community composition was compared using a 16S rRNA taxonomic microarray. The microarray contains 1033 probes and targets 19 bacterial phyla. Among them, 398 probes were designed for Proteobacteria, Firmicutes, Actinomycetes, Cyanobacteria and Bacteroidetes genera/species known to include strains relevant for plant protection or plant growth promotion. Hierarchical clustering as well as principal component analysis of microarray data discriminated clearly between black root rot-suppressive and -conducive soils. In contrast, T. basicola inoculation had no impact on rhizobacterial community composition. In addition to fluorescent Pseudomonas, the taxa Azospirillum, Gluconacetobacter, Burkholderia, Comamonas and Sphingomonadaceae, which are known to comprise strains with plant-beneficial properties, were more prevalent in the suppressive soil. Mycobacterium, Bradyrhizobium, Rhodobacteraceae, Rhodospirillum and others were more prevalent in the conducive soil. For selected taxa, microarray results were largely corroborated by quantitative PCR and cloning/sequencing. In conclusion, this work identified novel bacterial taxa that could serve as indicators of disease suppressiveness in soil-quality assessments, and it extends the range of bacterial taxa hypothesized to participate in black root rot suppression.

Phenazine antibiotics produced by fluorescent pseudomonads contribute to natural soil suppressiveness to Fusarium wilt

Natural disease-suppressive soils provide an untapped resource for the discovery of novel beneficial microorganisms and traits. For most suppressive soils, however, the consortia of microorganisms and mechanisms involved in pathogen control are unknown. To date, soil suppressiveness to Fusarium wilt disease has been ascribed to carbon and iron competition between pathogenic Fusarium oxysporum and resident non-pathogenic F. oxysporum and fluorescent pseudomonads. In this study, the role of bacterial antibiosis in Fusarium wilt suppressiveness was assessed by comparing the densities, diversity and activity of fluorescent Pseudomonas species producing 2,4-diacetylphloroglucinol (DAPG) (phlD+) or phenazine (phzC+) antibiotics. The frequencies of phlD+ populations were similar in the suppressive and conducive soils but their genotypic diversity differed significantly. However, phlD genotypes from the two soils were equally effective in suppressing Fusarium wilt, either alone or in combination with non-pathogenic F. oxysporum strain Fo47. A mutant deficient in DAPG production provided a similar level of control as its parental strain, suggesting that this antibiotic does not play a major role. In contrast, phzC+ pseudomonads were only detected in the suppressive soil. Representative phzC+ isolates of five distinct genotypes did not suppress Fusarium wilt on their own, but acted synergistically in combination with strain Fo47. This increased level of disease suppression was ascribed to phenazine production as the phenazine-deficient mutant was not effective. These results suggest, for the first time, that redox-active phenazines produced by fluorescent pseudomonads contribute to the natural soil suppressiveness to Fusarium wilt disease and may act in synergy with carbon competition by resident non-pathogenic F. oxysporum.

Effect of long-term vineyard monoculture on rhizosphere populations of pseudomonads carrying the antimicrobial biosynthetic genes phlD and/or hcnAB

The impact of repeated culture of perennial plants (i.e. in long-term monoculture) on the ecology of plant-beneficial bacteria is unknown. Here, the influence of extremely long-term monocultures of grapevine (up to 1603 years) on rhizosphere populations of fluorescent pseudomonads carrying the biosynthetic genes phlD for 2,4-diacetylphloroglucinol and/or hcnAB for hydrogen cyanide was determined. Soils from long-term and adjacent short-term monoculture vineyards (or brushland) in four regions of Switzerland were baited with grapevine or tobacco plantlets, and rhizosphere pseudomonads were studied by most probable number (MPN)-PCR. Higher numbers and percentages of phlD(+) and of hcnAB(+) rhizosphere pseudomonads were detected on using soil from long-term vineyards. On focusing on phlD, restriction fragment length polymorphism profiling of the last phlD-positive MPN wells revealed seven phlD alleles (three exclusively on tobacco, thereof two new ones). Higher numbers of phlD alleles coincided with a lower prevalence of the allele displayed by the well-studied biocontrol strain Pseudomonas fluorescens F113. The prevalence of this allele was 35% for tobacco in long-term monoculture soils vs. >60% in the other three cases. We conclude that soils from long-term grapevine monocultures represent an untapped resource for isolating novel biocontrol Pseudomonas strains when tobacco is used as bait.

Influence of host plant genotype, presence of a pathogen, and coinoculation with Pseudomonas fluorescens strains on the rhizosphere expression of hydrogen cyanide- and 2,4-diacetylphloroglucinol biosynthetic genes in P. fluorescens biocontrol strain CHA0

The production of hydrogen cyanide (HCN) and 2,4-diacetylphloroglucinol (DAPG) is a major factor in the control of soil-borne diseases by Pseudomonas fluorescens CHA0. We investigated the impact of different biotic factors on the expression of HCN-in comparison to DAPG biosynthetic genes in the rhizosphere. To this end, the influence of plant cultivar, pathogen infection, and coinoculation with other biocontrol strains on the expression of hcnA-lacZ and phlA-lacZ fusion in strain CHA0 was monitored on the roots of bean. Interestingly, all the tested factors influenced the expression of the two biocontrol traits in a similar way. For both genes, we observed a several-fold higher expression in the rhizosphere of cv. Derakhshan compared with cvs. Goli and Naz, although bacterial rhizosphere colonization levels were similar on all cultivars tested. Root infection by Rhizoctonia solani stimulated total phlA and hcnA gene expression in the bean rhizosphere. Coinoculation of strain CHA0 with DAPG-producing P. fluorescens biocontrol strains Pf-68 and Pf-100 did neither result in a substantial alteration of hcnA nor of phlA expression in CHA0 on bean roots. To our best knowledge, this is the first study investigating the impact of biotic factors on HCN production by a bacterial biocontrol strain in the rhizosphere.

Evolutionary history of the phl gene cluster in the plant-associated bacterium Pseudomonas fluorescens

Pseudomonas fluorescens is of agricultural and economic importance as a biological control agent largely because of its plant association and production of secondary metabolites, in particular 2,4-diacetylphloroglucinol (2,4-DAPG). This polyketide, which is encoded by the eight-gene phl cluster, has antimicrobial effects on phytopathogens, promotes amino acid exudation from plant roots, and induces systemic resistance in plants. Despite its importance, 2,4-DAPG production is limited to a subset of P. fluorescens strains. Determination of the evolution of the phl cluster and understanding the selective pressures promoting its retention or loss in lineages of P. fluorescens will help in the development of P. fluorescens as a viable and effective inoculant for application in agriculture. In this study, genomic and sequence-based approaches were integrated to reconstruct the phylogeny of P. fluorescens and the phl cluster. It was determined that 2,4-DAPG production is an ancestral trait in the species P. fluorescens but that most lineages have lost this capacity through evolution. Furthermore, intragenomic recombination has relocated the phl cluster within the P. fluorescens genome at least three times, but the integrity of the cluster has always been maintained. The possible evolutionary and functional implications for retention of the phl cluster and 2,4-DAPG production in some lineages of P. fluorescens are discussed.

A new DGGE protocol targeting 2,4-diacetylphloroglucinol biosynthetic gene phlD from phylogenetically contrasted biocontrol pseudomonads for assessment of disease-suppressive soils

In the rhizosphere, biocontrol pseudomonads producing 2,4-diacetylphloroglucinol (Phl) can protect plants from soil-borne pathogens. DGGE of phlD has been proposed to monitor these bacteria, but two distinct protocols were needed for analysis of both the 'Pseudomonas fluorescens' species complex and the strains from rrs restriction group ARDRA-1. Here, a single DGGE protocol performed on 668-bp GC-clamp-containing phlD amplicons was effective with both types of pseudomonads, and 36 reference biocontrol strains from the 'P. fluorescens' complex or group ARDRA-1 gave a total of 11 distinct DGGE bands. phlD amplicons with at least two to seven nucleotidic differences could be discriminated, and the discrimination level was similar to that of phlD restriction analysis with four enzymes. Multiple phlD-DGGE bands were obtained when studying rhizosphere soil containing indigenous phlD+ pseudomonads, and phlD diversity was higher when DGGE was implemented after incubation of tobacco rhizosphere extracts in semi-selective medium (MPN approach) in comparison with approaches based on direct analysis of rhizosphere DNA extracts or assessment of phlD+colonies. phlD-DGGE profiles differed for a soil suppressive and a soil conducive to black root rot of tobacco, and each soil yielded new phlD sequences. In conclusion, this DGGE protocol was useful for monitoring indigenous rhizosphere consortia of phlD+ pseudomonads.

Multilocus sequence analysis of biocontrol fluorescent Pseudomonas spp. producing the antifungal compound 2,4-diacetylphloroglucinol

The genetic and evolutionary relationship among 2,4-diacetylphloroglucinol (Phl)-producing pseudomonads that protect plants from soil-borne pathogens were investigated by multilocus sequence typing. A total of 65 pseudomonads consisting of 58 Phl-positive biocontrol strains of worldwide origin and seven Phl-negative representatives of characterized Pseudomonas species were compared using 10 housekeeping genes (i.e. rrs, dsbA, gyrB, rpoD, fdxA, recA, rpoB, fusA, rpsL and rpsG). Multilocus sequence typing differentiated 51 strains among 58 Phl-positive pseudomonads and proved to be as discriminative as enterobacterial repetitive intergenic consensus polymerase chain reaction profiling. As phylogenetic trees inferred from each locus were rather incongruent with one another, we derived the topology from all concatenated loci, which led to the identification of six main groups of Phl-producing Pseudomonas spp. Taxonomically, these groups could correspond to at least six different species. Linkage disequilibrium analysis pointed to a rather clonal structure, even when the analysis was restricted to Phl-producing pseudomonads from a same geographic location or a same phylogenetic group. Intragenic recombination was evidenced for gyrB, rpoD and fdxA, but was shown to be a weaker force than mutation in the origin of intragenetic diversity. This is the first multilocus assessment of the phylogeny and population structure of an ecologically important bacterial group involved in plant disease suppression.

Genotypic and phenotypic diversity in populations of plant-probiotic Pseudomonas spp. colonizing roots

Several soil microorganisms colonizing roots are known to naturally promote the health of plants by controlling a range of plant pathogens, including bacteria, fungi, and nematodes. The use of theses antagonistic microorganisms, recently named plant-probiotics, to control plant-pathogenic fungi is receiving increasing attention, as they may represent a sustainable alternative to chemical pesticides. Many years of research on plant-probiotic microorganisms (PPM) have indicated that fluorescent pseudomonads producing antimicrobial compounds are largely involved in the suppression of the most widespread soilborne pathogens. Phenotype and genotype analysis of plant-probiotic fluorescent pseudomonads (PFP) have shown considerable genetic variation among these types of strains. Such variability plays an important role in the rhizosphere competence and the biocontrol ability of PFP strains. Understanding the mechanisms by which genotypic and phenotypic diversity occurs in natural populations of PFP could be exploited to choose those agricultural practices which best exploit the indigenous PFP populations, or to isolate new plant-probiotic strains for using them as inoculants. A number of different methods have been used to study diversity within PFP populations. Because different resolutions of the existing microbial diversity can be revealed depending on the approach used, this review first describes the most important methods used for the assessment of fluorescent Pseudomonas diversity. Then, we focus on recent data relating how differences in genotypic and phenotypic diversity within PFP communities can be attributed to geographic location, climate, soil type, soil management regime, and interactions with other soil microorganisms and host plants. It becomes evident that plant-related parameters exert the strongest influence on the genotypic and phenotypic variations in PFP populations.

In vitro suppression of fungi caused by combinations of apparently non-antagonistic soil bacteria

We hypothesized that apparently non-antagonistic soil bacteria may contribute to suppression of fungi during competitive interactions with other bacteria. Four soil bacteria (Brevundimonas sp., Luteibacter sp., Pedobacter sp. and Pseudomonas sp.) that exhibited little or no visible antifungal activity on different agar media were prescribed. Single and mixed strains of these species were tested for antagonism on a nutrient-poor agar medium against the plant pathogenic fungi Fusarium culmorum and Rhizoctonia solani and the saprotrophic fungus Trichoderma harzianum. Single bacterial strains caused little to moderate growth reduction of fungi (quantified as ergosterol), most probably due to nutrient withdrawal from the media. Growth reduction of fungi by the bacterial mixture was much stronger than that by the single strains. This appeared to be mostly due to competitive interactions between the Pseudomonas and Pedobacter strains. We argue that cohabitation of these strains triggered antibiotic production via interspecific interactions and that the growth reduction of fungi was a side-effect caused by the sensitivity of the fungi to bacterial secondary metabolites. Induction of gliding behavior in the Pedobacter strain by other strains was also observed. Our results indicate that apparently non-antagonistic soil bacteria may be important contributors to soil suppressiveness and fungistasis when in a community context.

Heterozygosis drives maize hybrids to select elite 2,4-diacethylphloroglucinol-producing Pseudomonas strains among resident soil populations

By comparing the distribution of two genomic markers among Pseudomonas strains recovered from the rhizosphere of two maize hybrids with those of strains recovered from the rhizosphere of their four respective parental lines, we showed that both hybrids supported more elite probiotic strains than the parents. Elite Pseudomonas strains showed genomic potential for both an appropriate in vitro 2,4-diacetylphloroglucinol (DAPG) productivity, and a superior root-colonization ability. The actual biocontrol and root-colonization abilities of these strains were confirmed by bioassays on five fungal strains and on axenic maize plants. Furthermore, results on the abundance and genetic diversity of resident DAPG+ Pseudomonas strains indicated that each hybrid was able to select its own specific DAPG+ population, whereas the four parental lines were not. The evidence that heterozygosis can drive maize plants to select elite probiotic rhizospheric DAPG+ Pseudomonas strains opens the way to a new strategy in the set up of plant breeding for low-input and organic agriculture.

Is the ability of biocontrol fluorescent pseudomonads to produce the antifungal metabolite 2,4-diacetylphloroglucinol really synonymous with higher plant protection?

The antifungal compound 2,4-diacetylphloroglucinol (Phl) contributes to biocontrol in pseudomonads, but whether or not Phl(+) biocontrol pseudomonads display higher plant-protecting activity than Phl(-) biocontrol pseudomonads remains to be demonstrated. This issue was addressed by assessing 230 biocontrol fluorescent pseudomonads selected from a collection of 3132 bacterial isolates obtained from 63 soils worldwide. One-third of the biocontrol pseudomonads were Phl(+) and almost all Phl(+) isolates also produced hydrogen cyanide (HCN). The only Phl(+) HCN(-) strain did harbor hcn genes, but with the deletion of a 134 bp hcnC fragment corresponding to an ADP-binding motif. Statistical analysis of biocontrol isolate distributions indicated that Phl production ability was associated with superior disease suppression activity in the Pythium-cucumber and Fusarium-tomato pathosystems, but this was also the case with HCN production ability. However, HCN significance was not as strong, as indicated both by the comparison of Phl(-) HCN(+) and Phl(-) HCN(-) strains and by correlation analyses. This is the first population-level demonstration of the higher plant-protecting activity of Phl(+) biocontrol pseudomonads in comparison with Phl(-) biocontrol pseudomonads.