The fungal flora of soft fruits in relation to storage and spoilage

The fungal population of freshly harvested strawberries, raspberries and blackberries was studied throughout the fruiting seasons and the relative importance of fungi responsible for spoilage of stored fruit from different harvest dates was assessed. Botrytis cinerea, Cladosporium spp., Penicillium spp., Aureobasidium pullulans and Mucor spp. were consistently present on all three fruits while Colletotrichum gloeosporioides and Didymella applanata were prevalent on raspberries only and Epicoccum purpurascens and Alternaria spp. on blackberries only. Botrytis cinerea and Mucor mucedo were the predominant spoilage organisms of all three fruits, although the relative importance of the two fungi changed as the season progressed, especially for strawberries. Rhizopus stolonifer, Cladosporium spp., Penicillium spp. and Colletotrichum gloeosporioides were only of minor importance as spoilage organisms.     

Incidence, Aggressiveness and In Planta Interactions of Botrytis cinerea and other Filamentous Fungi Quiescent in Grape Berries and Dormant Buds in Central Washington State

Recovery of quiescent filamentous fungi from non‐symptomatic grape berries and dormant buds demonstrated dominance of Alternaria, Aureobasidium, Cladosporium, Ulocladium and other dematiaceous hyphomycetes. Up to 78% of berries contained fungi prior to harvest. Botrytis cinerea was recovered from 0.2 to 0.5% of surface‐disinfested berries just subsequent to fruit set, and 1.6–4.8% of surface‐disinfested, over‐wintered dormant buds. In laboratory inoculations of mature grape berries with strains of Alternaria, Aureobasidium, Cladosporium, Ulocladium and Botrytis, only the latter was aggressive in rotting berry fruits. Inoculations with B. cinerea alone and in combination with strains of Alternaria, Aureobasidium, Cladosporium and Ulocladium recovered from grape demonstrated that prior occupation of wound sites by the latter fungi resulted in reduced lesion size compared to inoculation with B. cinerea alone.     

The fungal flora of loganberries in relation to storage and spoilage

Botrytis cinerea, Cladosporium spp., Penicillium spp., Aureobasidium pullulans, Mucor mucedo, Phoma state of Didymella applanata, Cryptococcus laurentii var. laurentii, C. albidus var. albidus, Candida sake and Sporobolo-myces roseus were consistently present on freshly harvested loganberries. Botrytis cinerea was the main spoilage organism with Mucor mucedo of minor importance. The importance of benomyl-resistant strains of B. cinerea is discussed.     

Microbial population dynamics on Golden Delicious apples from bud to harvest and effect of fungicide applications

The microbial population dynamics on apples cv. Golden Delicious were analysed every 15 days between bud and harvest in a fully replicated experiment in northern Spain in 1994 and 1995. The total microbial populations varied with developmental stage, and with prevailing climatic conditions. The predominant mycroflora were the filamentous fungi Cladosporium and Alternaria spp. and white and pink yeasts. Other genera isolated included mainly species of Epicoccum, Fusarium and Acremonium. However, the most important post-harvest pathogens Penicillium expansum and Botrytis cinerea were seldom isolated from ripening apples. Maximum total filamentous fungal populations occurred after fruit set and during early ripening [2 × 10⁴cfu (colony-forming units) g^-1 approximately] while those of bacteria were maximum at bud stage (3.5 × 10⁵and 3.0 × 10⁴ cfu g^-1 in 1994 and 1995 respectively). White yeasts were more numerous than pink yeasts. Endophytic infection of apple buds by Alternaria spp., responsible for core rot, was found in almost all bud tissue. By contrast, Cladosporium spp. were initially isolated later from 12.5–50% of tissue samples during blooming and fruit set. The impact of a four-spray fungicide regime during apple development significantly decreased the total filamentous fungal populations in both years, and that of Cladosporium spp. in 1994. However, bacterial populations were often higher on apples from fungicide-treated plots. Fungicide sprays decreased populations of Cladosporium, Alternaria and white yeasts for a maximum of up to 15–30 days after application. Fungicide application had little effect on endophytic infection of apples by Alternaria spp. between bud and harvest.     

Effect of fungicides on survival of Rhizobium on seeds and the nodulation of bean (Phaseolus vulgaris L.)

The survival of Rhizobium leguminosarum biovar phaseoli on seeds of bean was tested, using the cultivar Carioca. The seeds were treated seven days before inoculation with Benlate, Vitavax, Banrot, Difolatan or Ridomil fungicides. The rhizobial strains used were: CIAT 899, CPAC 1135 and CIAT 652. Strain CIAT 899 showed greater survival on the seed with fungicide than the other strains. Two hours after the contact with fungicides strains CIAT 652 and CPAC 1135 had significantly lower numbers of rhizobia than the treatment without fungicide. The Benlate and Banrot fungicides had the greatest effect on survival of rhizobial strains. There was a drastic mortality of the two strains, CIAT 652 and CPAC 1135, on seeds treated with Benlate and Ridomil. Under field conditions, granular inoculation produced fewer nodules, but a similar total nodule weight as seed inoculation. Serological tests (ELISA) showed that seed treatment with Benlate in connection with seed inoculation reduced drastically the occurrence of inoculated strains in nodules, while the same fungicide treatment and inoculation applied in the seed furrow did not affect the survival of the inoculated strain.     

Investigating the inoculum dynamics of Cladosporium on the surface of raspberry fruits and in the air

Raspberry production is under threat from the emerging fungal pathogenic genus Cladosporium. We used amplicon-sequencing, coupled with qPCR, to investigate how fruit age, fruit location within a polytunnel, polytunnel location and sampling date affected the fruit epiphytic microbiome. Fruit age was the most important factor impacting the fungal microbiome, followed by sampling date and polytunnel location. In contrast, polytunnel location and fruit age were important factors impacting the bacterial microbiome composition, followed by the sampling date. The within-tunnel location had a small significant effect on the fungal microbiome and no effect on the bacterial microbiome. As fruit ripened, fungal diversity increased and the bacterial diversity decreased. Cladosporium was the most abundant fungus of the fruit epiphytic microbiome, accounting for nearly 44% of all fungal sequences. Rotorod air samplers were used to study how the concentration of airborne Cladosporium inoculum (quantified by qPCR) varied between location (inside and outside the polytunnel) and time (daytime vs. nighttime). Quantified Cladosporium DNA was significantly higher during the day than the night and inside the polytunnel than the outside. This study demonstrated the dynamic nature of epiphytic raspberry fruit microbiomes and airborne Cladosporium inoculum within polytunnels, which will impact disease risks on raspberry fruit.     

Contribution of Pathogens to Peach Fruit Rot in Northern Greece and their Sensitivity to Iprodione, Carbendazim, Thiophanate-methyl and Tebuconazole Fungicides

This study identified the main pathogens causing fruit rots of mature peaches in northern Greece, the major peach producing area of Greece. The brown rot pathogen Monilinia laxa was responsible for approximately 70% and 78% of rotted peaches in 2005 and 2006 respectively. Serious damage (up to 5%) was also caused with the fungus Phomopsis amygdali. Other pathogens isolated from rotted peaches at a low percentage were Alternaria alternata, Aspergillus niger, Aspergillus flavus, Botrytis cinerea, Sclerotinia sclerotiorum, Fusarium spp., Colletotrichum gloeosporioides, Rhizopus stolonifer and Gilbertella persicaria. Most fungal isolates originated from the rotted peaches were tested for their sensitivity to the fungicides iprodione, carbendazim, thiophanate methyl and tebuconazole at label recommended concentrations. All fungicides inhibited the growth of M. laxa, A. niger, A. flavus, S. sclerotiorum, P. amygdali and B. cinerea on poisoned agar. Apart from iprodione, all other fungicides inhibited the mycelium growth of the pathogen Fusarium sp. The mycelium growth of Fusarium sp. was significantly less with iprodione than control. Only iprodione and tebuconazole were effective against A. alternata and R. stolonifer. Tebuconazole inhibited the mycelium growth of R. stolonifer, while iprodione reduced significantly in comparison to control. The mycelium growth of the fungus C. gloeosporioides was inhibited by tebuconazole and reduced significantly by the fungicides thiophanate methyl, carbendazim and iprodione. Among all the fungi tested, only M. laxa and B. cinerea isolates were found resistant to benzimidazoles [the EC50 (50% effective concentration) value was 100–200 mg/l and 200–300 mg/l for the largest number of thiophanate methyl‐ and carbendazim‐resistant M. laxa isolates respectively, while the biggest number of B. cinerea thiophanate methyl‐ and carbendazim‐resistant isolates showed EC50 value 200–300 mg/l and 300–400 mg/l, respectively]. However, these strains were sensitive to tebuconazole and iprodione. Therefore, these fungicides can be used as an alternative method to control benzimidazole‐resistant Monilinia and Botrytis isolates.     

Storage diseases of carrots in East Anglia 1978 – 82, and the effects of some pre- and post-harvest factors

In a survey of nine carrot crops stored during four seasons 1978 – 82, the major causes of wastage were spreading soft rots caused by Botrytis cinerea and Rhizoctonia carotae; rots caused by Sclerotinia sclerotiorum, Mycocentrospora acerina and Stemphylium radicinum were only of secondary importance. Storage weight losses were lower and roots remained turgid for up to 40 wk in an ice-bank-cooled store at 0·5 °C, 97 – 98% r.h., whereas carrots in conventionally-cooled stores at 2 – 2.5 °C, 90 – 95% r.h. became flaccid after a few months. In some crops, losses due to fungal spoilage were also lower in the ice-bank store. In two seasons' losses, mostly due to B. cinerea, were similar in hand- and machine-harvested roots; pre-storage washing of carrots grown on mineral soils increased the incidence of Botrytis rots, and reduced rotting by R. carotae, but had no effect on spoilage of roots from peat soils. Post-harvest fungicide treatment with benomyl or iprodione (0·5 g/litre a.i.) effectively reduced rotting by B. cinerea and S. sclerotiorum, but not by R. carotae. The recoveries of sound carrots after 23 – 29 wk storage were consistently highest (mostly > 80%) from fungicide-dipped roots stored under ice-bank conditions, but recoveries from all treatments were lower and more erratic after 35 – 40 wk because of increased fungal spoilage. The practical applications of long-term ice-bank storage of UK-grown carrots are discussed.     

Occurrence of strains of Colletotrichum coffeanutn resistant to methyl benzimidazol-2-ylcarbamate (carbendazim) and chemically-similar compounds

Certain strains of Colletotrichum coffeanum (the causal fungus of coffee berry disease) which developed in coffee plots sprayed in 1973 and 1974 with carbendazim formulations Bavistin and Derosal and with Folicidin (cypendazol) were resistant to these fungicides and also to Benlate (benomyl). Strains resistant to cypendazol developed in plots sprayed with benomyl but these were not resistant to benomyl itself. There were also indications of strains resistant to carbendazim amongst the population of saprophytic species (C. acutatum and C. gloeosporoides) colonizing coffee bark. Resistant isolates of C. coffeanum in culture produced colour variants by sectoring more frequently than normal isolates. These sectors were equally pathogenic to coffee berries and their growth was slightly enhanced on media containing carbendazim.     

The involvement of fungi in the breakdown of sulphited strawberries

Between 8000 and 9000 tons of strawberries are used annually for jam manufacture in the UK, c. 65 % of which are stored in sulphite liquor (6 % SO₂+lime, c. pH 3.0). Sporadic cases of disintegration of sulphited strawberries have been observed increasingly in recent years. In laboratory experiments breakdown of whole berries in sulphite liquor was achieved by including berries partly rotted with Mucor mucedo, Rhizopus sexualis or R. stolonifer, 1.5-2.5 % infected material causing complete breakdown of all of the berries. The inclusion of up to 25 % berries infected with Botrytis cinerea caused no softening of the berries. The addition of culture filtrates to whole fruit in sulphite liquor confirmed observations with the above fungi but also showed that pectolytic enzymes from Aureobasidium pullulans and Trichosporon pullulans could cause breakdown. The incidence of spoilage fungi on commercially harvested fruit indicated that M. mucedo and R. sexualis were the main cause of breakdown, but that A. pullulans increased tenfold on fruit stored at 15 °C overnight before sulphiting. Results from commercially harvested fruit (cv. Cambridge Favourite) in 1975 and 1976 showed that: (I) fruit should be sulphited as soon as possible after harvest, since the storage of harvested fruit prior to sulphiting may give a poorer quality product; (2) there is little difference in breakdown of fruit from plants treated with the pre-harvest fungicides, Elvaron, Mildothane, or Daconil, and (3) fruit grown in different areas of the UK shows varying amounts of breakdown. This may be due to differences in the infection level of Phycomycetes and contamination by other pectolytic fungi or inherent differences in the susceptibility of the fruit to enzyme attack.     

The toolbox of Trichoderma spp. in the biocontrol of Botrytis cinerea disease

Botrytis cinerea is a necrotrophic fungal pathogen causing disease in many plant species, leading to economically important crop losses. So far, fungicides have been widely used to control this pathogen. However, in addition to their detrimental effects on the environment and potential risks for human health, increasing fungicide resistance has been observed in the B. cinerea population. Biological control, that is the application of microbial organisms to reduce disease, has gained importance as an alternative or complementary approach to fungicides. In this respect, the genus Trichoderma constitutes a promising pool of organisms with potential for B. cinerea control. In the first part of this article, we review the specific mechanisms involved in the direct interaction between the two fungi, including mycoparasitism, the production of antimicrobial compounds and enzymes (collectively called antagonism), and competition for nutrients and space. In addition, biocontrol has also been observed when Trichoderma is physically separated from the pathogen, thus implying an indirect systemic plant defence response. Therefore, in the second part, we describe the consecutive steps leading to induced systemic resistance (ISR), starting with the initial Trichoderma–plant interaction and followed by the activation of downstream signal transduction pathways and, ultimately, the defence response resulting in ISR (ISR‐prime phase). Finally, we discuss the ISR‐boost phase, representing the effect of ISR priming by Trichoderma spp. on plant responses after additional challenge with B. cinerea.     

Biofungicides as alternative to synthetic fungicide control of grey mould (Botrytis cinerea) – prospects and challenges

Botrytis cinerea is one of the most destructive pathogens of ve?getables and fruits both in the field and storage. There have been several research activities focused on developing biocontrol strategies for the pathogen due to its resistance to the commonly used synthetic fungicides. Additionally, concerns have been raised over residual effect of current synthetic fungicides used for its control. Most of these research activities have focused on Trichoderma spp., Ulocladium spp., Bacillus subtilis, plant extracts and their essential oils with some commercial products available on the market for the control of B. cinerea disease. This review summarises some of the current published information on the use of biocontrol agents and plant-based compounds for B. cinerea control. Some limitations and future prospects were also mentioned.     

The microflora of ripening barley grain and the effects of pre harvest fungicide application

Newly-emerged ears of barley soon became colonised by micro-organisms with numbers increasing to 5·8 × 10⁵ viable propagules/g dry weight by harvest. Bacteria were numerically predominant throughout. Yeasts and yeast-like fungi were also numerous during the early stages of grain development but were exceeded by propagules of filamentous fungi during ripening, with Cladosporium spp., Alternaria alternata, Epicoccum purpurascens and Verticillium lecanii most abundant. Numbers of most micro-organisms were greatest in a wet season but Alternaria was equally abundant in hot dry weather. Application of fungicides at or after anthesis modified the grain microflora. Captafol was most effective overall in decreasing numbers of fungi. However, benomyl decreased Cladosporium inoculum more than catpafol but was ineffective against Alternaria which became more numerous on benomyl-treated grain than on untreated. Yield increases of up to 4% were obtained by late fungicide treatment, least in a hot, dry year. Germination was also increased by some treatments by up to 5%.     

Grey mould of strawberry,a devastating disease caused by the ubiquitous necrotrophic fungal pathogen Botrytis cinerea

The fungal pathogen Botrytis cinerea causes grey mould, a commercially damaging disease of strawberry. This pathogen affects fruit in the field, storage, transport and market. The presence of grey mould is the most common reason for fruit rejection by growers, shippers and consumers, leading to significant economic losses. Here, we review the biology and epidemiology of the pathogen, mechanisms of infection and the genetics of host plant resistance. The development of grey mould is affected by environmental and genetic factors; however, little is known about how B. cinerea and strawberry interact at the molecular level. Despite intensive efforts, breeding strawberry for resistance to grey mould has not been successful, and the mechanisms underlying tolerance to B. cinerea are poorly understood and under-investigated. Current control strategies against grey mould include pre- and postharvest fungicides, yet they are generally ineffective and expensive. In this review, we examine available research on horticultural management, chemical and biological control of the pathogen in the field and postharvest storage, and discuss their relevance for integrative disease management. Additionally, we identify and propose approaches for increasing resistance to B. cinerea in strawberry by tapping into natural genetic variation and manipulating host factors via genetic engineering and genome editing.     

Biological control of strawberry crown rot,root rot and grey mould by the beneficial fungus Aureobasidium pullulans

Utilization of biocontrol agents is a sustainable approach to reduce plant diseases caused by fungal pathogens. In the present study, we tested the effect of the candidate biocontrol fungus Aureobasidium pullulans (De Bary) G. Armaud on strawberry under in vitro and in vivo conditions to control crown rot, root rot and grey mould caused by Phytophthora cactorum (Lebert and Cohn) and Botrytis cinerea Pers, respectively. A dual plate confrontation assay showed that mycelial growth of P. cactorum and B. cinerea was reduced by 33–48% when challenged by A. pullulans as compared with control treatments. Likewise, detached leaf and fruit assays showed that A. pullulans significantly reduced necrotic lesion size on leaves and disease severity on fruits caused by P. cactorum and B. cinerea. In addition, greenhouse experiments with whole plants revealed enhanced biocontrol efficacy against root rot and grey mould when treated with A. pullulans either in combination with the pathogen or pre-treated with A. pullulans followed by inoculation of the pathogens. Our results demonstrate that A. pullulans is an effective biocontrol agent to control strawberry diseases caused by fungal pathogens and can be an effective alternative to chemical-based fungicides.

     

Studies on the survival and infective ability of dicarboximide-resistant strains of Botrytis cinerea

Few dicarboximide-resistant strains of Botrytis cinerea produce macroconidia either on culture media or on natural substrates, although, the viability of such conidia was similar to those of sensitive strains. The ability of dicarboximide-resistant strains to infect strawberries was similar to that of sensitive strains and most of the resistant strains competed successfully with sensitive strains when inoculated in equal numbers onto detached strawberries and onto flowers of field-grown plants, especially after treatment with dicarboximide fungicides. All resistant strains tested survived for at least 9 months on inoculated strawberry leaf litter although their incidence was ‘diluted’ by wild type sensitive strains. Sporulation and dispersal of resistant strains from the litter was very limited resulting in a low incidence of fruit infection even after treatment with dicarboximides. Consequently, there was no significant increase of resistant strains in the plantation and control of infection was maintained with iprodione and dichlofluanid. Poor sporulation of dicarboximide-resistant strains of B. cinerea is considered to be the single most important factor in limiting their development in the field.     

Colonization ability as an indicator of enhanced biocontrol capacity—An example using two Bacillus amyloliquefaciens strains and Botrytis cinerea infection of tomatoes

An understanding of biocontrol activities is important when developing microorganism‐based alternatives to conventional fungicides. From our bacterial collection, we selected two strains (BBC023 and BBC047) for their outstanding antagonistic capacity against fungal phytopathogens and growth‐promoting abilities towards Arabidopsis thaliana. According to physiological and molecular characterizations, both strains were classified as Bacillus amyloliquefaciens and were tested against Botrytis cinerea in vitro and in a tomato. Both strains secrete lipopeptide‐like compounds that contribute to their in vitro antagonism. SEM‐images showed altered B. cinerea mycelial structures that were consistent with previous reports of the direct action of lipopeptides against fungal hyphae. The strains were applied to the roots (R), leaves (foliar ‐ F) or root/leaves (R/F) on tomato plants. All treatments significantly reduced the severity of B. cinerea infection (measured as a control index). However, only root applications (R and R/F) led to growth promotion in the tomato plants. We detected the production of indole acetic acid (IAA) and 2,3‐butanediol as growth promotion traits in the two strains. For both strains, the R/F treatment showed the highest control index, suggesting a synergic effect of direct antagonism against B. cinerea and resistance induction in the plant. In addition, in vitro antagonism of BBC023 and BBC047 against B. cinerea was similar; whereas in the F application, strain BBC047 significantly improved plant resistance and maintained a higher population density over time on tomato leaves, compared to BBC023. BBC047 was also able to produce a complex and robust biofilm in Msgg medium compared with that of BBC023. We linked the reduced biocontrol of BBC023 on leaves with its limited ability to generate robust biofilms and colonize the phylloplane. At last, we highlight the potential of the native Bacillus strains as promising alternatives for the development of bioproducts for sustainable agriculture.     

Biocontrol of aerial plant diseases in agriculture and horticulture: current approaches and future prospects

Until recently, the majority of research on the biological control of aerial plant diseases was focused on control of bacterial pathogens. Such research led to the commercialization of the biocontrol agent Pseudomonas fluorescens A506, as BlightBan A506™, for control of fire blight of pear. In contrast, chemical fungicides typically have provided adequate control of most foliar fungal pathogens. However, fungicide resistance problems, concerns regarding pesticide residues and revocation of registration of certain widely used fungicides have led to increased activity in the development of biocontrol agents of foliar fungal pathogens. Much of this activity has centered around the use of Trichoderma spp and Gliocladium spp to control Botrytis cinerea on grape and strawberry. The biocontrol agent Trichoderma harzianum T39 is commercially available in Israel, as Trichodex ™, for control of grey mold in grapes and may soon be registered for use in the US. Also targeted primarily against a foliar disease of grapes, in this case powdery mildew caused by Uncinula necator, is the biocontrol agent Ampelomyces quisqualis AQ10, marketed as AQ^{10  TM} biofungicide. Another promising development in the area of foliar disease control, though one which is not yet commercialized, is the use of rhizobacteria as seed treatments to induce systemic resistance in the host plant, a strategy which can protect the plant against a range of bacterial and fungal pathogens. Received 06 February 1997/ Accepted in revised form 05 June 1997     

Effect of fungicides on the mycelial growth of soft fruit spoilage fungi

The in vitro activity of a range of fungicides was tested on strains of Botrytis cinerea, Mucor mucedo, Rhizopus stolonifer, and R. sexualis. Di-chlofluanid and dichloran were more active than the other fungicides against all of the strains of B. cinerea, while dichloran, dichlorophen and the dithiocarbamate fungicides were the most active against the Rhizopus species. Only dichlorophen and thiram markedly inhibited the growth of M. mucedo.     

The most heat-resistant conidia observed to date are formed by distinct strains of Paecilomyces variotii

Fungi colonize habitats by means of spores. These cells are stress-resistant compared with growing fungal cells. Fungal conidia, asexual spores, formed by cosmopolitan fungal genera like Penicillium, Aspergillus and Peacilomyces are dispersed by air. They are present in places where food products are stored and as a result, they cause food spoilage. Here, we determined the heterogeneity of heat resistance of conidia between and within strains of Paecilomyces variotii, a spoiler of foods such as margarine, fruit juices, canned fruits and non-carbonized sodas. Out of 108 strains, 31 isolates showed a conidial survival >10% after a 10-min-heat treatment at 59°C. Three strains with different conidial heat resistance were selected for further phenotyping. Conidia of DTO 212-C5 and DTO 032-I3 showed 0.3% and 2.6% survival in the screening respectively, while survival of DTO 217-A2 conidia was >10%. The decimal reduction times of these strains at 60°C (D₆₀ value) were 3.7 ± 0.08, 5.5 ± 0.35 and 22.9 ± 2.00 min respectively. Further in-depth analysis revealed that the three strains showed differences in morphology, spore size distributions, compatible solute compositions and growth under salt stress. Conidia of DTO 217-A2 are the most heat-resistant reported so far. The ecological consequences of this heterogeneity of resistance, including food spoilage, are discussed.