New Insights into the Fungal Diversity of Cranberry Fruit Rot in Québec Farms Through a Large-Scale Molecular Analysis

A survey of cranberry fruit rots in commercial production beds in Oregon and Washington

Introduction

Fungal fruit rots are a perennial threat to the production of cranberries. Eleven genera of fungi have been reported to cause cranberry rot in the field and/or during cold storage. Oregon and Washington rank fourth and fifth in the production of cranberries in the USA, but much of the research on cranberry fruit rots has been conducted in Wisconsin, New Jersey, and Massachusetts.

Objective

The primary objective of this project was to describe the current composition of cranberry fruit rot complex in Oregon and Washington.

Methods

A survey of fungal fruit rot pathogens was conducted over four years in commercial cranberry farms located in the Pacific Ocean coastal zone in Oregon and Washington.

Results

Yield, rot incidence, and fungal pathogens isolated varied year-to-year. Pathogens isolated frequently from field-rotted cranberries included the cranberry fruit rot genera described in other cranberry production regions of the USA, such as Colletotrichum, Coleophoma, and Physalospora. Neofabraea actinidiae, a recently described cranberry fruit rot, was isolated consistently from field-rotted cranberries from beds with specific fungicide usage patterns. N. actinidiae also was one of the more common storage rot pathogens in this region, alongside other well-established storage rots like Coleophoma and black rots caused by Allantophomopsis cytisporea, A. lycopodina, and Strasseria geniculata.

Conclusions

These findings may have important implications for Washington cranberry production because a large proportion of the crop is dry-harvested, placed in cold storage, and then sold as fresh cranberries. Climatic differences among the cranberry production areas across the United States may affect the disease incidence and prevalence of different genera of cranberry fruit rot pathogens, as summer months in Oregon and Washington are often much cooler and dryer than in Wisconsin and east coast states and may account for differing presence of various cranberry fruit rot fungi.

Prevalence and spatial distribution of cranberry fruit rot pathogens in British Columbia, Canada and potential fungicides for fruit rot management

Twenty-eight cranberry farms in southwestern British Columbia were investigated for the prevalence and spatial distribution of fungal pathogens that contribute to fruit rot incidence. Farms were selected from six regions where most cranberry production is concentrated. Flowers, and green and ripe fruit (var. 'Stevens') samples, collected during two consecutive crop seasons, were analyzed for fruit rot pathogens. The most frequently isolated pathogens were identified as Allantophomopsis cytisporea, Botrytis cinerea, Coleophoma empetri, Colletotrichum fioriniae, Colletotrichum gloeosporioides, Fusicoccum putrefaciens, Glomerella sp., Phomopsis vaccinii, Phyllosticta elongata, Phyllosticta vaccinii and Physalospora vaccinii. The pathogens Allantophomopsis cytisporea, Phyllosticta spp., and Physalospora vaccinii were found at high incidence. These pathogens were present in all cranberry growing regions, although their mean percentage incidence varied from farm-to-farm and region-to-region. Amongst the pathogens from three phenological stages of cranberry crop examined, ripe fruit had the highest percentage incidence of fruit rot pathogens compared to that of flowers or green fruit; thus, indicating their presence at the early stages of crop development. The efficacy to inhibit the mycelial growth and spore germination of the fruit rot pathogens by twenty six fungicides, belonging to nine different modes of actions, were evaluated in vitro. The copper-based fungicides and captan of group M, flutriafol, triforine, difenoconazole, prothioconazole and propiconazole of group 3, benzovindiflupyr of group 7, and fosetyl-Al of group 33 demonstrated a high degree of efficacy in inhibiting the mycelial growth of all fruit rot pathogens. The fungicides chlorothalonil of group M, fenbuconazole of group 3, pyrimethanil and cyprodinil of group 9, and fludioxonil of group 12 also demonstrated activity against most fruit rot pathogens. The copper-based fungicides, chlorothalonil, captan, flutriafol, triforine, difenoconazole, prothioconazole, propiconazole, benzovindiflupyr, and fosetyl-Al effectively prevented the spore germination of most fruit rot pathogens. This demonstrated activity of the fungicides towards cranberry fruit rot pathogens should be assessed for efficacy in planta under field conditions. The current study identified the most critical fungal pathogens causing fruit rot of cranberry in British Columbia and potential fungicides that could be used in the management of fruit rot and to improve fruit quality and yield.

Fungi Present in the Clones and Cultivars of European Cranberry (Vaccinium oxycoccos) Grown in Lithuania

Fungi are associated with the European cranberry (Vaccinium oxycoccos L.) and play important roles in plant growth and disease control, especially in cranberry yields. This article presents the results of a study which was aimed to investigate the diversity of fungi found on different clones and cultivars of the European cranberry grown in Lithuania, causing twigs, leaf diseases and fruit rots. In this study seventeen clones and five cultivars of V. oxycoccos were selected for investigation. Fungi were isolated via the incubation of twigs, leaves and fruit on a PDA medium and identified according to their cultural and morphological characteristics. Microscopic fungi belonging to 14 genera were isolated from cranberry leaves and twigs, with Physalospora vaccinii, Fusarium spp., Mycosphaerella nigromaculans and Monilinia oxycocci being the most frequently isolated fungi. 'Vaiva' and 'Žuvinta' cultivars were the most susceptible to pathogenic fungi during the growing season. Among the clones, 95-A-07 was the most susceptible to Phys. vaccinii, 95-A-08 to M. nigromaculans, 99-Ž-05 to Fusarium spp. and 95-A-03 to M. oxycocci. Microscopic fungi belonging to 12 genera were isolated from cranberry berries. The most prevalent pathogenic fungi M. oxycocci were isolated from the berries of the cultivars 'Vaiva' and 'Žuvinta' and clones 95-A-03 and 96-K-05.

Nuclear Genome Sequence and Gene Expression of an Intracellular Fungal Endophyte Stimulating the Growth of Cranberry Plants

Ericaceae thrive in poor soil, which we postulate is facilitated by microbes living inside those plants. Here, we investigate the growth stimulation of the American cranberry (Vaccinium macrocarpon) by one of its fungal endosymbionts, EC4. We show that the symbiont resides inside the epidermal root cells of the host but extends into the rhizosphere via its hyphae. Morphological classification of this fungus is ambiguous, but phylogenetic inference based on 28S rRNA identifies EC4 as a Codinaeella species (Chaetosphaeriaceae, Sordariomycetes, Ascomycetes). We sequenced the genome and transcriptome of EC4, providing the first 'Omics' information of a Chaetosphaeriaceae fungus. The 55.3-Mbp nuclear genome contains 17,582 potential protein-coding genes, of which nearly 500 have the capacity to promote plant growth. For comparing gene sets involved in biofertilization, we annotated the published genome assembly of the plant-growth-promoting Trichoderma hamatum. The number of proteins involved in phosphate transport and solubilization is similar in the two fungi. In contrast, EC4 has ~50% more genes associated with ammonium, nitrate/nitrite transport, and phytohormone synthesis. The expression of 36 presumed plant-growth-promoting EC4 genes is stimulated when the fungus is in contact with the plant. Thus, Omics and in-plantae tests make EC4 a promising candidate for cranberry biofertilization on nutrient-poor soils.