Root rot disease incidence and severity on some legume species grown in Samsun and the fungi isolated from roots and soils

Abstract

Root rot disease is very common in the bean, soybean, faba bean and pea plants growing areas in Samsun province. Disease incidence and severity were detected the highest at 93.8% and 55.4% in the bean growing area, and the lowest at 64.0% and 24.3% in the faba bean growing area respectively. In this study, a total of 2714 fungal isolates were obtained from some legume plants and soil samples. The most common fungi isolated from root and soil samples were Fusarium spp., multinucleate Rhizoctonia (MNR), binucleate Rhizoctonia (BNR) and Pythium spp. respectively. Fusarium spp. were isolated at high rates from all the examined areas. MN Rhizoctonia and BN Rhizoctonia were isolated both from inner and coastal areas of the province, whereas Pythium spp. were isolated in costal areas, except for the Vezirköprü district which is situated in the inner area. When looking at the interactions among pathogens causing root rot, it was found the great majority of the samples (30.4%) isolated both Fusarium spp. and MNR-BNR group fungi, whereas Fusarium spp. and Pythium spp. were isolated together from 10.9% of the samples and MNR-BNR and Pythium spp. from only 1.5% of the samples.     

Integrated control of root rot and wilt disease of faba bean by soil amendment with suppressive compost in combination with seed coating with an antagonistic yeast

For this study, 21 isolates of fungi belonging to Rhizoctonia and Fusarium genera were isolated from the diseased faba bean plants, obtained from the different localities in Assiut governorate, showing root rot and wilt symptoms. The isolates proved to be pathogenic on Masr 1 faba bean cultivar under greenhouse conditions. F. oxysporum isolates caused wilt disease; however, the isolates of R. solani and other Fusarium species caused root rot. The virulence of isolates on the tested faba bean cultivar was different. The highly pathogenic isolates of these fungi were employed in this study. The effect of soil amendment with Planta Rich and Rich Composts (CMs) alone or in combination with seed coating by the antagonistic yeast Pichia guilliermondi before sowing on the severity of Rhizoctonia and Fusarium root rot and Fusarium wilt of faba bean was tested under greenhouse and field conditions. The tested isolates of yeast proved to be highly antagonistic to the pathogen in vitro. The test rates of CMs were equivalent to 2, 7, 10 and 14 ton/feddan in the greenhouse and 7 and 10 t/feddan in the field conditions. Uncomposted soil was used as a control. The results showed that the tested CMs have a suppressive effect on the severity of root rot and wilt diseases of faba bean under greenhouse and field conditions. The application of CMs (Planta Rich and Rich) alone at the rates equivalent to 2, 7, 10 and 14 t/feddan in greenhouse and 7 and 10 t/feddan in the field conditions to the soil infested with the tested pathogens reduced percentage of the tested diseases compared with uncomposted soil. Combined CMs treatments with yeast seed treatment increased the suppressive effect of CMs on the disease severity.     

Assessment of suitability and suppressiveness of on-farm green compost as a substitute of peat in the production of lavender plants

Suppression of root rot diseases of ornamental plants is a potential benefit of formulating soilless container media with compost. A green compost (green nursery compost, GNC), obtained by a circular-economy approach from residues of pruning of woody plants and grass clippings during the nursery activities was analysed for its suppressiveness of root rot diseases using lavender. To this end, a bioassay was develop by formulating potting mixes containing GNC with two rates of peat substitution (25% and 50%) and infested with the root rot pathogens Sclerotinia sclerotiorum, Rhizoctonia solani and Phytophthora nicotianae. Contrasting results were obtained by using both substrates with a significant reduction of root rot by S. sclerotiorum, no effect on the containment of that by P. nicotianae, and an increase of symptoms caused by R. solani. The specific suppressiveness observed may be attributed to the colonisation of compost by specific groups of antagonistic microorganisms. This hypothesis was investigated by the analysis of culturable fungal community, which resulted in the isolation of Trichoderma harzianum and T. atroviride as preponderant fungal species. Trichoderma representative isolates exerted in vitro antagonistic activities against the target pathogens with varying efficiencies indicating the employment of multiple complementary mechanisms, which may have contributed to the observed specific suppressiveness. Both substrates containing GNC resulted suitable for nursery cultivation of lavender, showing a growth performance similar to that obtained with peat-based substrate. Present results indicate that on-farm compost is a suitable component of mixed-peat substrates capable to support plant growth and provide specific disease suppression.     

The genus Pythium in Taiwan, China (1) — a synoptic review

The genus Pythium, with slightly over 280 described species, has been classified traditionally with other filamentous, coenocytic, sporangia-producing fungi as “Phycomyetes”. However, with recent advances in chemical, ultrastructural and molecular studies, Pythium spp. are now considered as “fungus-like organisms” or “pseudo-fungi” and are placed in the Kingdom Chromista or Kingdom Straminopila, distinct from the true fungi of the Kingdom Fungi or Kingdom Mycota. They are widely distributed throughout the world as soil saprophytes or plant pathogens. Because of the warm moist maritime climate, Taiwan, China, is especially rich in Pythium species. To date, 48 species of Pythium have been reported from Taiwan, China, with the dominant species being Py. vexans, Py. spinosum, Py. splendens, Py. aphanidermatum, Py. dissotocum and Py. acanthicum. There is no definite geographical distribution of Pythium spp. in Taiwan, China. Twenty nine species of Pythium have proven to be plant pathogens attacking a wide variety of woody and herbaceous plants primarily causing pre- and post-emergence seedling damping-off, root rot, stem rot and rotting of fruits, tubers and ginger rhizomes, resulting in serious economic losses. The most important plant pathogenic species include Py. aphanidermatum and Py. Myriotylum, which are most active during the hot and wet summer months; whereas Py. splendens, Py. spinosum, Py. ultimum and Py. irregulare cause the greatest damage in the cool winter. Most Pythium spp. are non-specific pathogens, infecting mainly juvenile or succulent tissues. This review attempts to assess the taxonomic position of the genus Pythium and provide details of the historical development of the study of Pythium as pathogens in Taiwan, China, causing diseases of sugarcane, trees, vegetables, fruits, specialty crops and flowering plants, as well as measures to control these diseases. Of special note is the introduction of the S-H mixture which, when used as soil amendment, effectively controls many soil-borne Pythium diseases during the early stages of plant growth. The diversity of Pythium species in Taiwan, China, is discussed in comparison with the situation in the mainland of China and suggestions are made to fully utilize Pythium spp. as agents for biological control, in industry and medicine.     

Replant problems in South Tyrol: role of fungal pathogens and microbial population in conventional and organic apple orchards

The South Tyrol, the main apple-growing area in Italy, is characterised by intensive soil cultivation. Previous investigations have revealed the existence of replant disorders although the main causes of these have not been evaluated. A survey was carried out in this area with two main aims: to evaluate the role of soil-borne pathogens in apple replant disease and to compare the impact of organic and conventional management on replant diseases caused by soil-borne pathogens. The experimental sites were chosen to obtain three pairs of contiguous conventional and organic apple orchards. There was a high level of organic matter in both the organic and the conventional apple orchards with no appreciable differences in humic fractions. The soil sickness test with apple seedlings revealed a significant reduction in growth for all soil samples as compared to the peat control. The growth score on soil samples from organic orchards was significantly higher than that obtained on conventional soil. Total fungal population in soil samples was positively correlated to the apple seedlings growth score and negatively correlated to the frequency of root colonisation. Most of the root-colonising pathogens belonged to the well-known root rot complex, Rhizoctonia solani and Pythium spp. being the most pathogenic on apple seedlings.     

Evaluation of endophytic actinobacteria as antagonists of Gaeumannomyces graminis var. tritici in wheat

Endophytic actinobacteria isolated from healthy cereal plants were assessed for their ability to control fungal root pathogens of cereal crops both in vitro and in planta. Thirty eight strains belonging to the genera Streptomyces, Microbispora, Micromonospora, and Nocardioidies were assayed for their ability to produce antifungal compounds in vitro against Gaeumannomyces graminis var. tritici (Ggt), the causal agent of take-all disease in wheat, Rhizoctonia solani and Pythium spp. Spores of these strains were applied as coatings to wheat seed, with five replicates (25 plants), and assayed for the control of take-all disease in planta in steamed soil. The biocontrol activity of the 17 most active actinobacterial strains was tested further in a field soil naturally infested with take-all and Rhizoctonia. Sixty-four percent of this group of microorganisms exhibited antifungal activity in vitro, which is not unexpected as actinobacteria are recognized as prolific producers of bioactive secondary metabolites. Seventeen of the actinobacteria displayed statistically significant activity in planta against Ggt in the steamed soil bioassay. The active endophytes included a number of Streptomyces, as well as Microbispora and Nocardioides spp. and were also able to control the development of disease symptoms in treated plants exposed to Ggt and Rhizoctonia in the field soil. The results of this study indicate that endophytic actinobacteria may provide an advantage as biological control agents for use in the field, where others have failed, due to their ability to colonize the internal tissues of the host plant.     

Microbiota in Wheat Roots,Rhizosphere and Soil in Crops Grown in Organic and Other Production Systems

Culturable microbial communities and diseases were compared in organic, integrated and conventional systems of winter wheat production and monoculture. Particular emphasis was placed on the density and diversity of cereal pathogens and their potential antagonists, and on the association of the active microbial populations with the health and productivity of wheat. In roots, rhizoplane and rhizosphere, fungi tended to be most abundant in the integrated system or monoculture, and bacteria in the organic system. The dominant fungal groups (with individual frequency >5%) included root pathogens (Fusarium, Gibberella, Haematonectria and Ilyonectria) and known pathogen antagonists (Acremonium strictum, Clonostachys, Chaetomium, Gliocladium and Trichoderma spp.). The 50 subdominant species (with individual frequency 1–5%) included the pathogens Alternaria, Cladosporium (leaf spot), Gaeumannomyces graminis (take‐all), Glomerella graminicola (anthracnose), Oculimacula yallundae (eyespot), Phoma spp. (leaf spots), and Pythium and Rhizoctonia (root rot). The 40 subrecedent species (with individual frequency <1%) included minor pathogens (Botrytis, Coniothyrium, Leptosphaeria). Antagonists in roots, rhizoplane and rhizosphere were most frequent in the organic system and least frequent in monoculture, suggesting that these systems had the most and least disease‐suppressive habitats, respectively. The other two systems were intermediate, with microbial communities suggesting that the conventional system produced a slightly more suppressive environment than the integrated system. The highest grain yield, in the integrated system, was associated with high abundance of fungi, including fungal pathogens, lowest abundance of Arthrobacter, Pseudomonas and Streptomyces in roots, rhizoplane and soil, and relatively high stem‐base and leaf disease severity. The lowest grain yields, in the organic system and monoculture, were associated with less abundant fungi and more abundant Pseudomonas. There is no clear indication that yields were affected by diseases.     

Greenhouse and field evaluations of potassium phosphonate: the control of Phytophthora foot rot of black pepper in Vietnam

Phytophthora foot rot of black pepper caused by Phytophthora capsici is a major disease of black pepper throughout production areas in Vietnam. The disease causes collar, foot and tap root rots and eventual death of the infected vine. Potassium phosphonate was evaluated for the control of this disease in greenhouse and field trials. In greenhouse trials three-month-old vines treated with phosphonate by soil drenching (10–20 g a.i./l) and then inoculated with P. capsici mycelium (2% v/v soil) had significantly less foot rot compared to vines grown in non-treated soil. In field trials mature vines were treated with phosphonate at 50–100 g a.i/pole soil drenching or 10 g a.i./l by root infusion. After 10 days root, stem and leaf specimens were removed for bioassay by inoculation with 5 ml of P. capsici zoospores suspension (10⁶–10⁸ spores/ml). Soil drenching with phosphonate inhibited the colonisation of pathogen on excised leaf, stem and root tissues, significantly more than phosphonate root infusion. Our study provides further evidence supporting the efficacy of potassium phosphonate in the management of black pepper foot rot caused by P. capsici. The excised leaf and stem bioassay used in this study is a rapid and useful technique for testing the efficacy of systemic fungicides in controlling this disease.     

Characteristics of a Pythium arrhenomanes with High Frequency in Barley Soils

Soils from two long-term crop rotation experiments were examined for incidence of root pathogens with a test tube method, where a great number (hundreds) of small portions (15–68g) of soil were biotested. There was a 4–5 times higher frequency of a root-infecting Pythium sp. In barley monoculture soil when compared to crop rotation soil, where winter turnip rape was the preceding crop. In pathogenicity tests the isolated pathogen caused severe root rot on barley, wheat and rye, but did not affect growth of oats, maize, peas and winter rape. In all essential morphological characters it resembles P. arrhenomanes and we classify it as belonging to this species.     

Effect of green manure on Pythium spp. population and microbial communities in intensive cropping systems

Saprophytic soil-borne pathogens can be either actively suppressed by organic amendments or enhanced, depending on soil health conditions. This can be deleterious in the event of selection of a soil-borne population by previous soil management and short crop rotation. Trials were performed in the open field and in pots, using naturally infected soil from intensive crop systems, i.e., soil from fields with 8 years of strawberry cultivation. The aim was to study short-term response of Pythium and soil microbial populations to green manure. The use of green manure in these naturally infested soils, 3–10 weeks after fresh tissue incorporation, caused Pythium populations to increase concurrent with an increase in soil microbial populations, and did not result in the suppression of the pathogen. A more elaborate trial was performed under controlled conditions, amending soil with fresh wheat plant material, air-dried wheat plant material and an organic fertilizer with a high level of humic substances. Although compared to the original soil, all amendments caused a similar increase in organic matter content and small differences in soil respiration, incorporation of fresh, not decomposed, plant material strongly increased Pythium, while the organic fertilizer did not affect the original level of the pathogen population. The increase in total number of fungi and bacteria did not have any suppressive effect on the Pythium population in naturally infested soil used for this study.     

Resident bacteria, nitric oxide emission and particle size modulate the effect of Brassica napus seed meal on disease incited by Rhizoctonia solani and Pythium spp

Amendment of orchard soil with low-glucosinolate Brassica napus (rape) seed meal (RSM) suppresses infection of apple roots by Rhizoctonia solani but increases incidence of Pythium spp. infection. Following incorporation of Brassica sp. seed meals, soils were monitored for changes in populations of selected saprophytic and plant pathogenic microorganisms. When conducted in pasteurized soil, which possessed high numbers of Bacillus spp. and lower than detectable numbers of Streptomyces spp., RSM amendment did not provide control of R. solani. Populations of streptomycetes in RSM-amended soil increased to stable levels >20-fold higher than in non-amended soil. Disease suppressiveness was restored to pasteurized RSM-amended soil by adding any of several Streptomyces strains. Maximal rates of nitrification in orchard soil, determined by nitric oxide emission, were observed within two weeks following RSM amendment and inhibition of nitrification via application of nitrapyrin abolished the capacity of RSM to suppress R. solani infection of apple roots when seedlings were planted one day after soil amendment. Apple seedling mortality and Pythium spp. root infection were highest for seedlings planted immediately following incorporation of B. napus cv. Athena RSM, particularly when meal was added in a flake rather than powder form. Lower infection frequencies were observed for seedlings planted four weeks after RSM incorporation, even for soil in which densities of culturable Pythium spp. had not declined. Our results demonstrate that suppression of Rhizoctonia root rot in response to RSM amendment requires the activity of the resident soil microbiota and that initial disease control is associated with the generation of nitric oxide through the process of nitrification.     

Interaction of soil microbes with mycorrhizal fungi in tomato

In this study, the interaction of soil microbes with mycorrhizal fungi (MF) was performed to understand the effect on tomato. A pot and a field experiment were employed to investigate the impact of soil microbes i.e. Fusarium oxysporum f. sp. lycopersici, Trichoderma harzianum, Aspergillus niger and Rhizobium leguminosarum, on AM fungi in pots and field studies. The soils without microbes which treated controls with or without mycorrhizal inoculation were also included. Plant growth and root colonisation were measured 36, 75 and 120?days post inoculation (dpi) in the both pot experiment and field study. Soil microbes’ effects on the growth behaviour of the tomato plant were determined via the shoot and root weight. R. leguminosarum and A. niger did not affect the colonisation ability much, but F. oxysporum f. sp. lycopersici and T. harzianum resulted in the inhibition of AM fungal colonisation in both pot and field studies. Our study provides evidence for the effects of soil microbes on the diversity of AM fungi and their effect on the tomato plants. The higher concentrations of phosphorus and of proteins in the root tissues, previously colonised with AM fungi, point out their effect as biofertilizers, according to the concept of sustainable agriculture.     

Soil suppressiveness to Rhizoctonia solani and microbial diversity

Rhizoctonia solani anastomosis group 2-2IIIB causes damping-off, black root rot and crown rot in sugar beet (Beta vulgaris). Based on experiences of growers and field experiments, soils can become suppressive to R. solani. The fungus may be present in the soil, but the plant does not show symptoms. Understanding the mechanisms causing soil suppressiveness to R. solani is essential for the development of environmentally friendly control strategies of rhizoctonia root rot in sugar beet. A bioassay that discriminates soils in their level of disease suppressiveness was developed. Results of bioassays were in accordance with field observations. Preliminary results indicate an active role of microbial communities. Our research is focused on the disentanglement of biological mechanisms causing soil suppressiveness to R. solani in sugar beet. Therefore, we are handling a multidisciplinary approach through experimental fields, bioassays, several in vitro techniques and molecular techniques (PCR-DGGE).     

Fungi associated with strawberry root rot in Illinois

A qualitative and quantitative study of the fungi associated with apparently healthy and root rot-diseased strawberry main roots was made during a 1-year period. Eighty-one genera were isolated from lesions and stele segments of diseased roots, and tips and segments 5–6 cm from the tip of apparently healthy roots. A diverse mycoflora was isolated from each segment of the root. However, each segment had a typical dominant mycoflora, indicating that a changing mycoflora is associated with the root as it passes from a healthy to a diseased condition.Pythium spp. andRhizoctonia Spp. accounted for 25.09 and 5.67 percent, respectively, of the isolates from Surecrop lesions, and 4.96 and 25.92 percent, respectively, of the isolates from Cyclone lesions.     

Mycoflora succession on strawberry roots developing root rot symptoms

Strawberry daughter plants of the Cyclone and Surecrop cultivars began rooting in two plantings in October. Main root tips became necrotic in the fall and winter, and the necrosis spread to the crowns, until all roots were severely rotted by June. Aspergillus and Penicillium were the dominant genera isolated from apparently healthy main root tips during October through February and apparently healthy main root segments 5 to 6 cm from the tip through April. During this time, Pythium, Fusarium, and Rhizoctonia were isolated in low frequencies from the same samples. Pythium was isolated most often from lesions and was isolated in high frequency from Surecrop lesions, December through April. Fusarium and Rhizoctonia were isolated in low to moderate frequencies from October through February, but increased to higher levels from April through October of the following year. During the year, low levels of Fusarium, Rhizoctonia, and Pythium were isolated from steles of diseased mother plants. This tissue yielded moderate levels of Chaetosphaeronema, Coniothyrium, Cephalosporium, and Penicillium.     

Interactions between indigenous arbuscular mycorrhizal fungi and <Emphasis Type="Italic">Aphanomyces euteiches</Emphasis> in field-grown pea

This is the first reported study of the interactions between indigenous arbuscular mycorrhizal fungi (AMF) and Aphanomyces euteiches in pea under field conditions. A. euteiches was applied to the soil by adding oospores produced in vitro. Attempts were made to create a non-mycorrhizal control by incorporating carbendazim (Derosal Fl) in the topsoil before sowing. However, all carbendazim-treated plants showed approximately 20% root colonisation with AMF. Pea plants not treated with carbendazim showed a wide variation in AMF colonisation of 35-70% at the full flowering stage. In these control plots, root length infected with oospores of A. euteiches and colonisation by AMF were negatively correlated. Application of carbendazim increased the percent root length infected with oospores by 50-70%, depending on inoculum density of A. euteiches. Despite the lower levels of AMF colonisation in these treated plots, a negative correlation with oospore-containing root length was still observed. No correlation was found between AMF colonisation and disease severity, disease incidence or pathogen enzymatic activity (glucose-6-phosphate dehydrogenase). Thus, AMF do not seem to influence the vegetative stage of pathogen development during which cortical root rotting takes place, but rather the reproductive stage when oospores are produced. The results of this study underline the importance of field experiments for validating the significance of mycorrhizal fungi for plant health.     

Effects of Fungal Root Pathogens on the Population Dynamics of Biocontrol Strains of Fluorescent Pseudomonads in the Wheat Rhizosphere

The influences of Gaeumannomyces graminis var. tritici (which causes take-all of wheat), Rhizoctonia solani AG-8 (which causes rhizoctonia root rot of wheat), Pythium irregulare, P. aristosporum, and P. ultimum var. sporangiiferum (which cause pythium root rot of wheat) on the population dynamics of Pseudomonas fluorescens 2-79 and Q72a-80 (bicontrol strains active against take-all and pythium root rot of wheat, respectively) in the wheat rhizosphere were examined. Root infection by either G. graminis var. tritici or R. solani resulted in populations of both bacterial strains that were equal to or significantly larger than their respective populations maintained on roots in the absence of these pathogens. In contrast, the population of strain 2-79 was significantly smaller on roots in the presence of any of the three Pythium species than on noninfected roots and was often below the limits of detection (50 CFU/cm of root) on Pythium-infected roots after 40 days of plant growth. In the presence of either P. aristosporum or P. ultimum var. sporangiiferum, the decline in the population of Q72a-80 was similar to that observed on noninfected roots; however, the population of this strain declined more rapidly on roots infected by P. irregulare than on noninfected roots. Application of metalaxyl (which is selectively inhibitory to Pythium spp.) to soil naturally infestated with Pythium spp. resulted in significantly larger rhizosphere populations of the introduced bacteria over time than on plants grown in the same soil without metalaxyl. It is apparent that root infections by fungal pathogens may either enhance or depress the population of fluorescent pseudomonads introduced for their control, with different strains of pseudomonads reacting differentially to different genera and species of the root pathogens.     

Mango stem end rot pathogens - Fruit infection by endophytic colonisation of the inflorescence and pedicel

The stem end rot pathogens of mango (Mangifera indica), (Dothiorella dominicana, Dothiorella mangiferae, Lasiodiplodia theobromae (Syn. Diplodia natalensis Phomopsis mangiferae, Cytosphaera mangiferae, Pestalotiopsis sp. and Dothiorella‘long’), as well as other fungi (including Alternaria alternata), were found to occur endophytically in the stem tissue of mango trees prior to inflorescence emergence. On samples from trees with a record of low stem end rot levels, colonisation did not extend into the most recently produced flush of stem tissue. At a site with a history of high stem end rot levels, sequential monitoring of inflorescence tissue between flowering and harvest by plating out small (c. 8 mm³) tissue pieces revealed, that at least some of the pathogens - Dothiorella spp., P. mangiferae, Pestalotiopsis sp. and C. mangiferae gradually colonised the inflorescence, reaching the pedicel tissue of young fruit - 8 wk after flowering. Subsequently, detection frequency of the pathogens in inflorescence tissue declined, possibly because of interference from copper residues (from field sprays) accumulating on tissue samples. The detection frequency of A. alternata also increased as Dothiorella spp. declined, however these changes could not be attributed to antagonistic interactions between the two fungi. Using larger tissue pieces (1–2 mm thick transverse sections, or a square of tissue 25 mm²× 3 mm thick) in isolations, endophytic colonisation by Dothiorella spp. and P. mangiferae was detected in stem, inflorescence and pedicel tissues of mature-fruit-specimens from two different sites, one unsprayed, and the other regularly sprayed with copper. The fungi were detected more frequently in the samples from unsprayed trees. Fruit from the sprayed orchard subsequently developed a high level of stem end rot caused by D. dominicana, while a lower level of stem end rot developed in unsprayed fruit, possibly because the latter fruit were also extensively diseased by anthracnose (Colletotrichum gloeosporioides Penz.). Endophytic colonisation of inflorescence and pedicel tissue was found to be a primary route of infection for fruit which develop stem end rot during ripening.     

Microbial and biochemical basis of a Fusarium wilt-suppressive soil

Crops lack genetic resistance to most necrotrophic pathogens. To compensate for this disadvantage, plants recruit antagonistic members of the soil microbiome to defend their roots against pathogens and other pests. The best examples of this microbially based defense of roots are observed in disease-suppressive soils in which suppressiveness is induced by continuously growing crops that are susceptible to a pathogen, but the molecular basis of most is poorly understood. Here we report the microbial characterization of a Korean soil with specific suppressiveness to Fusarium wilt of strawberry. In this soil, an attack on strawberry roots by Fusarium oxysporum results in a response by microbial defenders, of which members of the Actinobacteria appear to have a key role. We also identify Streptomyces genes responsible for the ribosomal synthesis of a novel heat-stable antifungal thiopeptide antibiotic inhibitory to F. oxysporum and the antibiotic''s mode of action against fungal cell wall biosynthesis. Both classical- and community-oriented approaches were required to dissect this suppressive soil from the field to the molecular level, and the results highlight the role of natural antibiotics as weapons in the microbial warfare in the rhizosphere that is integral to plant health, vigor and development.     

Genomic-assisted characterisation of Pseudomonas sp. strain Pf4, a potential biocontrol agent in hydroponics

In an attempt to select potential biocontrol agents against Pythium spp. and Rhizoctonia spp. root pathogens for use in soilless systems, 12 promising bacteria were selected for further investigations. Sequence analysis of the 16S rRNA gene revealed that three strains belonged to the genus Enterobacter, whereas nine strains belonged to the genus Pseudomonas. In in vitro assays, one strain of Pseudomonas sp., Pf4, closely related to Pseudomonas protegens (formerly Pseudomonas fluorescens), showed noteworthy antagonistic activity against two strains of Pythium aphanidermatum and two strains of Rhizoctonia solani AG 1-IB, with average inhibition of mycelial growth >80%. Strain Pf4 was used for in vivo treatments on lamb’s lettuce against R. solani root rot in small-scale hydroponics. Pf4-treated and untreated plants were daily monitored for symptom development and after two weeks of infection, a significant protective effect of Pf4 against root rot was recorded. The survival and population density of Pf4 on roots were also checked, demonstrating a density above the threshold value of 10⁵?CFU?g^?1 of root required for disease suppression. Known loci for the synthesis of antifungal metabolites, detected using PCR, and draft-genome sequencing of Pf4 demonstrated that Pseudomonas sp. Pf4 has the potential to produce an arsenal of secondary metabolites (plt, phl, ofa and fit-rzx gene clusters) very similar to that of the well-known biocontrol P. protegens strain Pf-5.