Use of Quantitative PCR Detection Methods to Study Biocontrol Agents and Phytopathogenic Fungi and Oomycetes in Environmental Samples

Quantitative polymerase chain reaction (qPCR) is a versatile technique for the accurate, sensitive, reliable and high‐throughput detection and quantification of target DNA in various environmental samples, and in recent years, it has greatly contributed to the advancement of knowledge in the plant pathology field. Indeed, this technique is ideal to evaluate inoculum threshold levels and to study the epidemiology, biology and ecology of phytopathogenic fungi and oomycetes, thus opening up new research opportunities to investigate host–pathogen interactions and to address tasks related to quarantine, eradication and biosecurity. Moreover, it can be a useful tool in breeding programs. The present review analyses the most relevant applications of qPCR for the detection and quantification of filamentous fungi and oomycetes within host tissues and in soil, air and water, along with brief paragraphs focusing on new application fields such as the detection and quantification of mycotoxigenic fungi and biocontrol agents. The high potentiality of qPCR for present and future applications is highlighted together with a critical analysis of major drawbacks that need to be corrected to definitively confirm it as a preferential routine quantitative detection method.     

Efficacy of natamycin for control of growth and ochratoxin A production by Aspergillus carbonarius strains under different environmental conditions

AIMS: To examine the efficacy of natamycin produced by Streptomyces natalensis against strains of Aspergillus carbonarius growth and ochratoxin A (OTA) production under different environmental factors on a grape juice-based medium. METHODS AND RESULTS: Detailed studies in the range 0-20 ng ml(-1) for control of growth and ochratoxin production by strains of A. carbonarius at 0.98, 0.96 and 0.94 water availabilities (a(w)) and 15-25 degrees C on a fresh red grape extract medium were examined. Inhibition of growth was depending on temperature and a(w) level. At 15 degrees C, 5-10 ng ml(-1) natamycin was effective in reducing growth almost completely. However, at 20-25 degrees C and all the three a(w) levels, growth was only slightly inhibited by 5-10 ng ml(-1) natamycin. There were strain differences with regard to inhibition of OTA production. At 15 degrees C and 0.98 a(w), 10 ng ml(-1) was required to inhibit production by >90%. However, at 0.96 and 0.94 a(w), almost complete inhibition occurred. At 20 degrees C, OTA production was only significantly inhibited by 10 ng ml(-1) natamycin at 0.94 a(w). At 0.96 and 0.98 a(w), some inhibition occurred with 5-10 ng ml(-1), but greater concentrations would be required for effective inhibition. At 25 degrees C, 5 ng ml(-1) was effective at all a(w) levels. However, at 15 degrees C and 25 degrees C and a wide range of a(w) levels, natamycin effectively controlled OTA production. CONCLUSIONS: Natamycin appears to be a very effective for controlling growth and OTA production by strains of A. carbonarius over a range of a(w) and temperature conditions on grape-based media. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first detailed study to demonstrate the impact of natamycin against A. carbonarius. This study suggests that use of natamycin at 50-100 ng ml(-1) can give complete inhibition of growth of A. carbonarius and OTA production over a range of environmental conditions. Natamycin could be an important component of a system to prevent OTA contamination of wine as well during the drying and production of vine fruits.     

Predictive assessment of ochratoxin A accumulation in grape juice based-medium by Aspergillus carbonarius using neural networks

Aims:  To study the ability of multi-layer perceptron artificial neural networks (MLP-ANN) and radial-basis function networks (RBFNs) to predict ochratoxin A (OTA) concentration over time in grape-based cultures of Aspergillus carbonarius under different conditions of temperature, water activity ( a _w) and sub-inhibitory doses of the fungicide carbendazim.
Methods and Results:  A strain of A. carbonarius was cultured in a red grape juice-based medium. The input variables to the network were temperature (20–28°C), a _w (0·94–0·98), carbendazim level (0–450 ng ml⁻¹) and time (3–15 days after the lag phase). The output of the ANNs was OTA level determined by liquid chromatography. Three algorithms were comparatively tested for MLP. The lowest error was obtained by MLP without validation. Performance decreased when hold-out validation was accomplished but the risk of over-fitting is also lower. The best MLP architecture was determined. RBFNs provided similar performances but a substantially higher number of hidden nodes were needed.
Conclusions:  ANNs are useful to predict OTA level in grape juice cultures of A. carbonarius over a range of a _w, temperature and carbendazim doses.
Significance and Impact of the Study:  This is a pioneering study on the application of ANNs to forecast OTA accumulation in food based substrates. These models can be similarly applied to other mycotoxins and fungal species.     

Fusarium kyushuense sp. nov. from Japan

Four trichothecene-producing strains originally isolated from diseased wheat and a vinyl plate in Kyushu and Shikoku, Japan are described and illustrated as a new species,Fusarium kyushuense. This species does not produce chalamydospores, which is the key morphological character which distinguishes it fromF. sporotrichioides with which it has been mistaken.Fusarium kyushuense is also differentiated from another morphologically similar species,F. arthrosporioides, by absence of sclerotia and by differences in conidiogenesis of obovate, conidia. InF. arthrosporioides conidia are partly holoblastic from the aerial conidiophores and mostly phialidic from the sporodochial conidiophores, while inF. kyushuense conidia are mostly holoblastic and only produced from aerial conidiophores.     

Application of beneficial rhizospheric microbes for the mitigation of seed-borne mycotoxigenic fungal infection and mycotoxins in maize

In the present investigation, seven rhizobacteria and nine Trichoderma spp. were evaluated to suppress seed-borne mycotoxigenic fungi (Aspergillus flavus and Fusarium verticillioides) and mycotoxin (aflatoxin and fumonisin) and to improve planting value of maize. Under in vitro conditions, these beneficial microorganisms suppressed the growth of A. flavus and F. verticillioides to various extents. Bacillus sp. (Bsp 3/aM), Pseudomonas putida (Has 1/c), Trichoderma asperellum (M5) and T. asperellum (T2) exhibited the greatest antagonistic effect on seed-borne mycotoxigenic fungi, and subsequently reduced mycotoxin concentrations in seeds. Under greenhouse conditions, these four biocontrol strains were also found to increase root length, shoot length, % germination, vigour index, fresh weight and dry weight of seedlings. Considering their overall performances, strains Bsp 3/aM, Has 1/c, M5 and T2 were selected for field studies as microbial talcum formulations. Among the tested microbial formulations, strain Bsp 3/aM significantly increased yield by 9.4% and 6.2% over the control in two maize cultivars Hema and Pearl, respectively. Increased plant growth and yield was also correlated with nutrient uptake in both the tested cultivars. All microbial formulation recorded significantly (p ≤ 0.05) reduced A. flavus infection and aflatoxin contamination in harvested seeds. But, none of the microbial formulations were found significant (p ≤ 0.05) in reducing F. verticilliodes incidence and fumonisin contamination. Our findings indicate that these microbial antagonists indirectly improve host health by suppressing seed-borne incidence of mycotoxigenic fungi and directly by facilitating nutrient uptake, thereby revealing their potential as both biofertilisers and biopesticides for maize production.