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

Comparative Metagenomic Analysis Reveals Rhizosphere Microbiome Assembly and Functional Adaptation Changes Caused by Clubroot Disease in Chinese Cabbage

Clubroot is a major disease and severe threat to Chinese cabbage, and it is caused by the pathogen Plasmodiophora brassicae Woron. This pathogen is an obligate biotrophic protist and can persist in soil in the form of resting spores for more than 18 years, which can easily be transmitted through a number of agents, resulting in significant economic losses to global Chinese cabbage production. Rhizosphere microbiomes play fundamental roles in the occurrence and development of plant diseases. The changes in the rhizosphere microorganisms could reveal the severity of plant diseases and provide the basis for their control. Here, we studied the rhizosphere microbiota after clubroot disease infections with different severities by employing metagenomic sequencing, with the aim of exploring the relationships between plant health, rhizosphere microbial communities, and soil environments; then, we identified potential biomarker microbes of clubroot disease. The results showed that clubroot disease severity significantly affected the microbial community composition and structure of the rhizosphere soil, and microbial functions were also dramatically influenced by it. Four different microbes that had great potential in the biocontrol of clubroot disease were identified from the obtained results; they were the genera Pseudomonas, Gemmatimonas, Sphingomonas, and Nocardioides. Soil pH, organic matter contents, total nitrogen, and cation exchange capacity were the major environmental factors modulating plant microbiome assembly. In addition, microbial environmental information processing was extremely strengthened when the plant was subjected to pathogen invasion, but weakened when the disease became serious. In particular, oxidative phosphorylation and glycerol-1-phosphatase might have critical functions in enhancing Chinese cabbage's resistance to clubroot disease. This work revealed the interactions and potential mechanisms among Chinese cabbage, soil environmental factors, clubroot disease, and microbial community structure and functions, which may provide a novel foundation for further studies using microbiological or metabolic methods to develop disease-resistant cultivation technologies.

Use of Pseudomonas protegens to Control Root Rot Disease Caused by Boeremia exigua var. exigua in Industrial Chicory (Cichorium intybus var. sativum Bisch.)

Boeremia exigua var. exigua is a recurrent pathogen causing root rot in industrial chicory. Currently, there is no chemical or varietal control for this disease, and thus, management strategies need to be developed. This study determined the biocontrol effect of strains of Pseudomonas protegens bacteria with antimicrobial compounds on the fungus B. exigua var. exigua under in vitro, in vivo, and field conditions. In addition, root colonization by these bacteria was estimated by the phlD-specific PCR-based dilution end point assay. Eighteen isolates of Pseudomonas spp were evaluated, and the strains that showed the greatest in vitro inhibition of fungal mycelial growth (mm), Ca10A and ChB7, were selected. Inoculation with the strain ChB7 showed less severity (necrotic area) under in vivo conditions (root trials) compared with the control inoculated with the pathogen (p ≤ 0.05). The molecular analysis revealed that the root colonization of plants grown in pots was equal to or greater than 70%. Similar levels were observed in the field trials conducted at the Selva Negra and Canteras experimental stations (2015-2016 season), with values ranging from 85.7 to 70.5% and from 75.0 to 79.5%, respectively. Regarding yield (ton ha-1), values were higher in the treatments inoculated with strains Ca10A and ChB7 (p ≤ 0.05) at both experimental sites, while a lower incidence and severity of root rot were observed at Selva Negra. These results suggest that the Chilean strains of P. protegens are a promising tool for the control of root diseases in industrial chicory.

Molecular and evolutionary basis of O-antigenic polysaccharide-driven phage sensitivity in environmental pseudomonads

IMPORTANCE

The application of plant-beneficial microorganisms to protect crop plants is a promising alternative to the usage of chemicals. However, biocontrol research often faces difficulties in implementing this approach due to the inconsistency of the bacterial inoculant to establish itself within the root microbiome. Beneficial bacterial inoculants can be decimated by the presence of their natural predators, notably bacteriophages (also called phages). Thus, it is important to gain knowledge regarding the mechanisms behind phage-bacteria interactions to overcome this challenge. Here, we evidence that the major long O-antigenic polysaccharide (O-PS, O-antigen) of the widely used model plant-beneficial bacterium Pseudomonas protegens CHA0 is the receptor of its natural predator, the phage ΦGP100. We examined the distribution of the gene cluster directing the synthesis of this O-PS and identified signatures of horizontal gene acquisitions. Altogether, our study highlights the importance of bacterial cell surface structure variation in the complex interplay between phages and their Pseudomonas hosts.

Incidence Rates of Root Rot in Sweetpotato Caused by Cultivation Soil and Soil Microorganisms During Storage Periods

Sweetpotatoes require a storage period for year-round use and improved sweetness by starch degradation. However, long-term storage can cause root rot, and a large amount of sweetpotatoes can be discarded. Root rot is typically caused by pathogenic soil-borne Fusarium spp., and the development of root rot induced by the characteristics of cultivating soil in stored sweetpotato has not yet been identified. In this study, the effect of Fusarium spp. and microbial community in the cultivated soil on the root rot of sweetpotatoes was to be elucidated. Wounded sweetpotato were treated in soil cultures inoculated with F. solani or F. oxysporum for 2 days, and showed symptoms of root rot after 2 months of storage. The three study fields (Naju, Yeongam A, and B) were subjected to the same curing and storage treatments after harvest, and the incidence of root rot was 1.7- to 1.8-fold different after 3 months of storage. Across the three fields, concentrations of Fusarium spp. and of microbial communities differed according to the cultivation soil and period. In particular, Naju, which had the lowest incidence of root rot, had the lowest concentration of Fusarium spp. before harvest, and the smallest change in diversity of the microbial community during the cultivation period. However, tuberous roots harvested from the fields showed no significant differences in antioxidant activity or lesion size with the treatment of 10⁶ conidia/ml F. solani. By solidifying the importance of cultivating soil and related microorganisms in the advancement of root rot of sweetpotato, our results may aid in preventing the decrease in the yield of cultivated sweetpotatoes through root rot control.

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.

Soil Microbiome Manipulation Gives New Insights in Plant Disease-Suppressive Soils from the Perspective of a Circular Economy: A Critical Review

This review pays attention to the newest insights on the soil microbiome in plant disease-suppressive soil (DSS) for sustainable plant health management from the perspective of a circular economy that provides beneficial microbiota by recycling agro-wastes into the soil. In order to increase suppression of soil-borne plant pathogens, the main goal of this paper is to critically discuss and compare the potential use of reshaped soil microbiomes by assembling different agricultural practices such as crop selection; land use and conservative agriculture; crop rotation, diversification, intercropping and cover cropping; compost and chitosan application; and soil pre-fumigation combined with organic amendments and bio-organic fertilizers. This review is seen mostly as a comprehensive understanding of the main findings regarding DSS, starting from the oldest concepts to the newest challenges, based on the assumption that sustainability for soil quality and plant health is increasingly viable and supported by microbiome-assisted strategies based on the next-generation sequencing (NGS) methods that characterize in depth the soil bacterial and fungal communities. This approach, together with the virtuous reuse of agro-wastes to produce in situ green composts and organic bio-fertilizers, is the best way to design new sustainable cropping systems in a circular economy system. The current knowledge on soil-borne pathogens and soil microbiota is summarized. How microbiota determine soil suppression and what NGS strategies are available to understand soil microbiomes in DSS are presented. Disturbance of soil microbiota based on combined agricultural practices is deeply considered. Sustainable soil microbiome management by recycling in situ agro-wastes is presented. Afterwards, how the resulting new insights can drive the progress in sustainable microbiome-based disease management is discussed.

Pseudomonas orientalis F9 Pyoverdine, Safracin, and Phenazine Mutants Remain Effective Antagonists against Erwinia amylovora in Apple Flowers

Pseudomonas orientalis F9 is an antagonist of the economically important phytopathogen Erwinia amylovora, the causal agent of fire blight in pomme fruit. On King’s B medium, P. orientalis F9 produces a pyoverdine siderophore and the antibiotic safracin. P. orientalis F9 transposon mutants lacking these factors fail to antagonize E. amylovora, depending on the in vitro assay. On isolated flowers and in soil microcosms, however, pyoverdine, safracin, and phenazine mutants control phytopathogens as clearly as their parental strains.

The recently characterized strain Pseudomonas orientalis F9, an isolate from apple flowers in a Swiss orchard, exhibits antagonistic traits against phytopathogens. At high colonization densities, it exhibits phytotoxicity against apple flowers. P. orientalis F9 harbors biosynthesis genes for the siderophore pyoverdine as well as for the antibiotics safracin and phenazine. To elucidate the role of the three compounds in biocontrol, we screened a large random knockout library of P. orientalis F9 strains for lack of pyoverdine production or in vitro antagonism. Transposon mutants that lacked the ability for fluorescence carried transposons in pyoverdine production genes. Mutants unable to antagonize Erwinia amylovora in an in vitro double-layer assay carried transposon insertions in the safracin gene cluster. As no phenazine transposon mutant could be identified using the chosen selection criteria, we constructed a site-directed deletion mutant. Pyoverdine-, safracin-, and phenazine mutants were tested for their abilities to counteract the fire blight pathogen Erwinia amylovoraex vivo on apple flowers or the soilborne pathogen Pythium ultimumin vivo in a soil microcosm. In contrast to some in vitro assays, ex vivo and in vivo assays did not reveal significant differences between parental and mutant strains in their antagonistic activities. This suggests that, ex vivo and in vivo, other factors, such as competition for resources or space, are more important than the tested antibiotics or pyoverdine for successful antagonism of P. orientalis F9 against phytopathogens in the performed assays.

IMPORTANCEPseudomonas orientalis F9 is an antagonist of the economically important phytopathogen Erwinia amylovora, the causal agent of fire blight in pomme fruit. On King’s B medium, P. orientalis F9 produces a pyoverdine siderophore and the antibiotic safracin. P. orientalis F9 transposon mutants lacking these factors fail to antagonize E. amylovora, depending on the in vitro assay. On isolated flowers and in soil microcosms, however, pyoverdine, safracin, and phenazine mutants control phytopathogens as clearly as their parental strains.

Conservation tillage and organic farming induce minor variations in Pseudomonas abundance, their antimicrobial function and soil disease resistance

Conservation tillage and organic farming are strategies used worldwide to preserve the stability and fertility of soils. While positive effects on soil structure have been extensively reported, the effects on specific root- and soil-associated microorganisms are less known. The aim of this study was to investigate how conservation tillage and organic farming influence the frequency and activity of plant-beneficial pseudomonads. Amplicon sequencing using the 16S rRNA gene revealed that Pseudomonas is among the most abundant bacterial taxa in the root microbiome of field-grown wheat, independent of agronomical practices. However, pseudomonads carrying genes required for the biosynthesis of specific antimicrobial compounds were enriched in samples from conventionally farmed plots without tillage. In contrast, disease resistance tests indicated that soil from conventional no tillage plots is less resistant to the soilborne pathogen Pythium ultimum compared to soil from organic reduced tillage plots, which exhibited the highest resistance of all compared cropping systems. Reporter strain-based gene expression assays did not reveal any differences in Pseudomonas antimicrobial gene expression between soils from different cropping systems. Our results suggest that plant-beneficial pseudomonads can be favoured by certain soil cropping systems, but soil resistance against plant diseases is likely determined by a multitude of biotic factors in addition to Pseudomonas.

Rhizosphere pseudomonads as probiotics improving plant health

Many root-colonizing microbes are multifaceted in traits that improve plant health. Although isolates designated as biological control agents directly reduce pathogen growth, many exert additional beneficial features that parallel changes induced in animal and other hosts by health-promoting microbes termed probiotics. Both animal and plant probiotics cause direct antagonism of pathogens and induce systemic immunity in the host to pathogens and other stresses. They also alter host development and improve host nutrition. The probiotic root-colonizing pseudomonads are generalists in terms of plant hosts, soil habitats and the array of stress responses that are ameliorated in the plant. This article illustrates how the probiotic pseudomonads, nurtured by the carbon (C) and nitrogen (N) sources released by the plant in root exudates, form protective biofilms on the root surface and produce the metabolites or enzymes to boost plant health. The findings reveal the multifunctional nature of many of the microbial metabolites in the plant-probiotic interplay. The beneficial effects of probiotics on plant function can contribute to sustainable yield and quality in agricultural production.

Antagonistic Potential of Fluorescent Pseudomonads Colonizing Wheat Heads Against Mycotoxin Producing Alternaria and Fusaria

Natural control of phytopathogenic microorganisms is assumed as a priority function of the commensal plant microbiota. In this study, the suitability of fluorescent pseudomonads in the phyllosphere of crop plants as natural control agents was evaluated. Under field conditions, ears of winter wheat were found to be colonized with high consistency and at a high density by pseudomonads at the late milk dough stage. Isolates of these bacteria were evaluated for their potential to protect the plants from phytopathogenic Alternaria and Fusarium fungi. More Pseudomonas isolates were antagonistically active against alternaria than against fusaria in the dual culture test. The alternaria responded species-specifically and more sensitively to bacterial antagonism than the strain-specific reacting fusaria. A total of 110 randomly selected Pseudomonas isolates were screened for genes involved in the biosynthesis of the antibiotics 2,4-diacetylphloroglucinol, phenazine-1-carboxylic acid, pyoluteorin, and pyrrolnitrin. The key gene for production of the phloroglucinol was found in none of these isolates. At least one of the genes, encoding the biosynthesis of the other antibiotics was detected in 81% of the isolates tested. However, the antagonistic effect found in the dual culture assay was not necessarily associated with the presence of these antibiotic genes. Wheat grains as natural substrate were inoculated with selected antagonistic Pseudomonas isolates and Alternaria and Fusarium strains, respectively. The fungal growth was only slightly delayed, but the mycotoxin production was significantly reduced in most of these approaches. In conclusion, the distribution of phytopathogenic fungi of the genera Alternaria and Fusarium in the field is unlikely to be inhibited by naturally occurring pseudomonads, also because the bacterial antagonists were not evenly distributed in the field. However, pseudomonads can reduce the production of Alternaria and Fusarium mycotoxins in wheat grains and thus have the potential to improve the crop quality.

Sub-lethal doses of widespread nanoparticles promote antifungal activity in Pseudomonas protegens CHA0

Nanoparticles are widely used as antimicrobial compounds. At sub-lethal concentrations, they may also stress microbes, potentially inducing antibiosis. Here we assess whether nanoparticles can serve as an enhancer of antibiosis in beneficial microbes. Several host-associated bacteria can suppress pathogens, providing therefore a first line of defense against diseases. In the present study, we assessed whether nanoparticles stimulate the antifungal activity of Pseudomonas protegens CHA0, a model plant-associated bacterium, against the ascomycete yeast Candida albicans. We synthesized and characterized four of the most common nanoparticles, namely Ag, SiO₂, TiO_2, and ZnO, with an average size of 25, 11, 25 and 35 nm, respectively. The dose-dependent effect of these nanoparticles on the growth of Pseudomonas protegens CHA0 was assessed. Ag, SiO₂, TiO_2, and ZnO nanoparticles inhibited the growth of Pseudomonas protegens by 100, 22, 15 and 15%, respectively at a concentration of 250 μg/mL. We then selected sub-lethal dose (500 ng/mL) and assessed whether the same nanoparticles stimulated the production of antifungal compounds inhibiting C. albicans. Incubating the bacteria in the presence of nanoparticles led to a four-fold increase in antifungal activity. We finally show that nanoparticles induce the expression of the prn operon, responsible for the production of antifungal compound pyrrolnitrin, within hours after nanoparticle exposure. This study shows that nanoparticle application may be a valuable tool to stimulate the antifungal activity of fluorescent pseudomonads, potentially assisting the development of future sustainable disease control strategies.

Pseudomonas orientalis F9: A Potent Antagonist against Phytopathogens with Phytotoxic Effect in the Apple Flower

In light of public concerns over the use of pesticides and antibiotics in plant protection and the subsequent selection for spread of resistant bacteria in the environment, it is inevitable to broaden our knowledge about viable alternatives, such as natural antagonists and their mode of action. The genus Pseudomonas is known for its metabolic versatility and genetic plasticity, encompassing pathogens as well as antagonists. We characterized strain Pseudomonas orientalis F9, an isolate from apple flowers in a Swiss orchard, and determined its antagonistic activity against several phytopathogenic bacteria, in particular Erwinia amylovora, the causal agent of fire blight. P. orientalis F9 displayed antagonistic activity against a broad suite of phytopathogenic bacteria in the in vitro tests. The promising results from this analysis led to an ex vivo assay with E. amylovora CFBP1430Rif and P. orientalis F9 infected detached apple flowers. F9 diminished the fire blight pathogen in the flowers but also revealed phytotoxic traits. The experimental results were discussed in light of the complete genome sequence of F9, which revealed the strain to carry phenazine genes. Phenazines are known to contribute to antagonistic activity of bacterial strains against soil pathogens. When tested in the cress assay with Pythium ultimum as pathogen, F9 showed results comparable to the known antagonist P. protegens CHA0.

Combined Field Inoculations of Pseudomonas Bacteria, Arbuscular Mycorrhizal Fungi, and Entomopathogenic Nematodes and their Effects on Wheat Performance

In agricultural ecosystems, pest insects, pathogens, and reduced soil fertility pose major challenges to crop productivity and are responsible for significant yield losses worldwide. Management of belowground pests and diseases remains particularly challenging due to the complex nature of the soil and the limited reach of conventional agrochemicals. Boosting the presence of beneficial rhizosphere organisms is a potentially sustainable alternative and may help to optimize crop health and productivity. Field application of single beneficial soil organisms has shown satisfactory results under optimal conditions. This might be further enhanced by combining multiple beneficial soil organisms, but this remains poorly investigated. Here, we inoculated wheat plots with combinations of three beneficial soil organisms that have different rhizosphere functions and studied their effects on crop performance. Plant beneficial Pseudomonas bacteria, arbuscular mycorrhizal fungi (AMF), and entomopathogenic nematodes (EPN), were inoculated individually or in combinations at seeding, and their effects on plant performance were evaluated throughout the season. We used traditional and molecular identification tools to monitor their persistence over the cropping season in augmented and control treatments, and to estimate the possible displacement of native populations. In three separate trials, beneficial soil organisms were successfully introduced into the native populations and readily survived the field conditions. Various Pseudomonas, mycorrhiza, and nematode treatments improved plant health and productivity, while their combinations provided no significant additive or synergistic benefits compared to when applied alone. EPN application temporarily displaced some of the native EPN, but had no significant long-term effect on the associated food web. The strongest positive effect on wheat survival was observed for Pseudomonas and AMF during a season with heavy natural infestation by the frit fly, Oscinella frit, a major pest of cereals. Hence, beneficial impacts differed between the beneficial soil organisms and were most evident for plants under biotic stress. Overall, our findings indicate that in wheat production under the test conditions the three beneficial soil organisms can establish nicely and are compatible, but their combined application provides no additional benefits. Further studies are required, also in other cropping systems, to fine-tune the functional interactions among beneficial soil organisms, crops, and the environment.

Screening and Characterization of Potentially Suppressive Soils against Gaeumannomyces graminis under Extensive Wheat Cropping by Chilean Indigenous Communities

Wheat production around the world is severely compromised by the occurrence of "take-all" disease, which is caused by the soil-borne pathogen Gaeumannomyces graminis var. tritici (Ggt). In this context, suppressive soils are those environments in which plants comparatively suffer less soil-borne pathogen diseases than expected, owing to native soil microorganism activities. In southern Chile, where 85% of the national cereal production takes place, several studies have suggested the existence of suppressive soils under extensive wheat cropping. Thus, this study aimed to screen Ggt-suppressive soil occurrence in 16 locations managed by indigenous "Mapuche" communities, using extensive wheat cropping for more than 10 years. Ggt growth inhibition in vitro screenings allowed the identification of nine putative suppressive soils. Six of these soils, including Andisols and Ultisols, were confirmed to be suppressive, since they reduced take-all disease in wheat plants growing under greenhouse conditions. Suppressiveness was lost upon soil sterilization, and recovered by adding 1% of the natural soil, hence confirming that suppressiveness was closely associated to the soil microbiome community composition. Our results demonstrate that long-term extensive wheat cropping, established by small Mapuche communities, can generate suppressive soils that can be used as effective microorganism sources for take-all disease biocontrol. Accordingly, suppressive soil identification and characterization are key steps for the development of environmentally-friendly and efficient biotechnological applications for soil-borne disease control.