A First Assessment of the Cranberry Fruit Rot Complex in Michigan

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.

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

Cranberry fruit rot (CFR) pathogens are widely reported in the literature, but performing large-scale analysis of their presence inside fruit has always been challenging. In this study, a new molecular diagnostic tool, capable of identifying simultaneously 12 potential fungal species causing CFR, was used to better define the impact of CFR across cranberry fields in Québec. For this purpose, 126 fields and 7,825 fruits were sampled in three cranberry farms distributed throughout the province and subjected to comparative analyses of fungal presence and abundance according to cultural practices, sampling times, and cranberry cultivars. All 12 pathogens were detected throughout the study, but as a first major finding, the analyses revealed that four species, Godronia cassandrae, Colletotrichum fructivorum, Allantophomopsis cytisporea, and Coleophoma empetri, were consistently predominant regardless of the parameters studied. Comparison of conventional and organic productions showed a significant reduction in fungal richness and relative abundance. Interestingly, Monilinia oxycocci was found almost exclusively in organic productions, indicating that fungicides had a strong and persistent effect on its population. Surprisingly, there were no significant differences in fungal relative abundance or species richness between fruit sampled at harvest or in storage, suggesting that there may not exist a clear distinction between field and storage rot, as was previously thought. Comparative analysis of fungal species found on eight different cranberry cultivars indicated that they were all infected by the same fungi but could not rule out differences in genetic resistance. This large-scale analysis allows us to draw an exhaustive picture of CFR in Québec and provides new information with respect to its management.

First report of Godronia cassandrae as a major cranberry fruit rot pathogen in Eastern Canada

The complex etiology of cranberry fruit rot (CFR) (Oudemans et al., 1998) has made it difficult to precisely identify the fungi involved in CFR and their relative importance in North America. To remedy this situation, a multiplex PCR approach targeting the 12 most commonly reported fungi in CFR was recently developed (Conti et al., 2019). However, in surveys conducted in Eastern Canada, the molecular tool revealed the presence of an unknown fungus in more than 30% of the collected samples. Analyses were thus undertaken to identify this species. From 117 rotten fruit collected at harvest in 2017, 34 samples of the unknown fungus, all morphologically similar, were isolated but not detected using the molecular tool. Their ITS ribosomal regions were sequenced using universal primers (Vilgalys and Hester, 1990; White et al., 1990) and searched against the GenBank database using the Blastn tool (Altschul et al., 1990). The top match was obtained with Godronia cassandrae (accession number: MH855281 (Vu et al., 2019), 98-100% of identity and an E-value of 0.0), even though some isolates had minor nucleotide differences, as presented in the tree. Sequences were deposited in GenBank as accession numbers MT599989 to MT600022. Since G. cassandrae had been reported, albeit rarely, on cranberry in Michigan (Olatinwo et al., 2003), it was supposed to amplify with the molecular tool developed from the strain DAOM C216021 (AAFC, Ottawa, ON) identified in 1993 on Vaccinium angustifolium as G. cassandrae. Analysis of the sequences used to build the specific primers from this strain confirmed the DAOM strain as being Neocucurbitaria juglandicola, which was never diagnosed in our cranberry samples. To confirm this revised diagnosis, a multi-sequence alignment (MSA) was performed on the ITS regions of the isolates from rotten cranberries and sequences available for the genus Godronia in the NCBI nucleotide database (NCBI txid269064). This MSA allowed us to find discriminant regions between Godronia spp. A pair of PCR primers specific to G. cassandrae found on cranberry fruit was then designed (the forward and reverse sequences are AAT CAG TGG CGG TGC CTG TC and TAC CGC TTC ACT CGC CGT TAC, respectively), generating 196 bp amplicons, with an annealing temperature of 65°C. The diagnosis of 7,835 fruit sampled at three time points (harvest, after three and after six weeks of storage) in 2018, from four cranberry farms located in Québec (CA) and Nova Scotia (CA), detected G. cassandrae in 2350 samples (30%). To assess the pathogenicity of four specimens from 2017, Koch's postulates were completed on two healthy fruit per isolate. The fruit were wounded with a sterilized pick and individually inoculated; two fruit were used as control. Based on our observations, the fungi isolated from cranberry fruit displayed a pale lemon yellow mycelium and black pycnidia. Conidia are hyaline, cylindrical and divided by a single septum. These morphological characters are similar to the ones described in the literature for G. cassandrae (Polashock et al., 2017). Rot symptoms appear as a discoloration from the firm, red and healthy cranberry fruit to a yellowish-orange softer fruit. Molecular characterization of the re-isolated fungus confirmed the presence of G. cassandrae. We report Godronia cassandrae for the first time as a major cause of CFR in Eastern Canada. Its prevalence in cranberry fields of Québec and Nova Scotia suggests that it supplants Physalospora as the main fungus involved in CFR in Eastern Canada.

The Role of Flowers in the Disease Cycle of Colletotrichum fioriniae and Other Cranberry Fruit Rot Fungi

Floral extracts (FEs) can influence the infectivity and epidemiology of fruit infecting Colletotrichum species. In this study, Colletotrichum fioriniae responded to cranberry FEs with an increased rate and magnitude of secondary conidiation and appressorium formation. Four other cranberry fruit rotting species also showed an increased rate of germination in the presence of FEs. However, increased appressorium formation was observed only in the latent pathogens Coleophoma cylindrospora, Colletotrichum fructivorum, and Colletotrichum fioriniae. Two other fruit rotting species, Phyllosticta vaccinii and Allantophomopsis lycopodina, did not form appressoria while secondary conidiation was only seen with the Colletotrichum spp. When conidia of Colletotrichum fioriniae were inoculated in the presence of FE, the incidence of disease was greater on cranberry fruit. Conidia of this species also formed appressoria at lower than expected temperatures in the presence of FE. Dissection of the flowers revealed that the corolla (with stamens and stigma) was the most stimulatory part of the inflorescence. These observations suggest an important and ephemeral role of flowers in the epidemiology of fruit rot. Stimulatory floral signals were readily detected using a conidial germination bioassay and rainwater samples collected from the plant canopy throughout the growing season confirmed that bioactivity was highest during the bloom period, and declined as the fruit developed. The data presented show that floral signals can alter the growth patterns of a larger than previously observed range of fungi and the mobility of floral signals within the canopy implicates these phenology-specific cues in modifying the disease cycles of numerous plant pathogens.

A Molecular Assay Allows the Simultaneous Detection of 12 Fungi Causing Fruit Rot in Cranberry

Cranberry fruit rot (CFR) is arguably one of the most limiting factors of cranberry (Vaccinium macrocarpon) production throughout its growing areas. The disease is caused by a group of closely related fungi that require identification using long and cumbersome steps of isolation and microscopic observations of structural features. The objective of this study was to develop a molecular assay to simultaneously detect and discriminate 12 of the most important fungal species reported to be pathogenic on cranberry fruit to facilitate the diagnosis of CFR. As the first approach, internal transcribed spacers and large subunit regions of all fungi were sequenced and confirmed with sequences available in the NCBI database. These data were used to develop primers able to differentiate seven of the 12 species. The five remaining species, including three in the Phacidiaceae family and two in the Glomerellaceae family, were differentiated on the basis of a more discriminant marker, the translation elongation factor 1-α. Two PCR reactions were optimized to clearly delineate the 12 species. The multiplex test was first validated using pure fungal cultures; it was subsequently validated using fruit collected in cranberry beds in eastern Canada. In the latter case, the test was rigorous enough to clearly discriminate the fungal pathogens from contaminants. Within the tested samples, Physalospora vaccinii and Coleophoma empetri were most commonly found. This molecular test offers scientists, diagnosticians, and growers a powerful tool that can rapidly and precisely identify fungi causing CFR so they can implement appropriate control methods.

Determining the Sources of Primary and Secondary Inoculum and Seasonal Inoculum Dynamics of Fungal Pathogens Causing Fruit Rot of Deciduous Holly

Fruit rot of deciduous holly, caused by species of the genera Alternaria, Colletotrichum, Diaporthe, and Epicoccum, is affecting plant production in Midwestern and Eastern U.S. nurseries. To determine the sources of inoculum, dormant twigs and mummified fruit were collected, and leaf spot development was monitored throughout the season from three Ohio nurseries over two consecutive years. Mummified fruit was the main source of primary inoculum for species of Alternaria and Epicoccum, whereas mummified fruit and bark were equally important for species of Colletotrichum and Diaporthe. Brown, irregular leaf spots developed in the summer, and disease incidence and severity increased along with leaf and fruit development. Coalesced leaf spots eventually resulted in early plant defoliation. When tested for their pathogenicity on fruit, leaf spot isolates were able to infect wounded mature fruit and induce rot symptoms, which indicated that leaf spots could serve as a source of secondary inoculum for fruit infections. In addition, spore traps were used to monitor seasonal inoculum abundance in the nurseries. Fruit rot pathogens were captured by the spore traps throughout the season, with peak dissemination occurring during flowering. In this study, we also attempted to understand the role of environmental factors on leaf spot development. Although leaf spot incidence and severity were negatively correlated to mean maximum, minimum and average temperature, a decrease in temperature also coincided with leaf senescence. The role of temperature on leaf spot development should be further studied to fully interpret these results.

Investigations on the Timing of Fruit Infection by Fungal Pathogens Causing Fruit Rot of Deciduous Holly

Fruit rot of deciduous holly is an emerging fungal disease that is affecting plant production across midwestern and eastern U.S. nurseries. To determine the growth stage(s) of host susceptibility to infection by the major pathogens associated with the disease, Alternaria alternata and Diaporthe ilicicola, and minor pathogens such as Colletotrichum fioriniae and Epicoccum nigrum, we conducted two sets of experiments over two consecutive seasons. In the first case we monitored the presence of the pathogens as well as disease progression in a commercial nursery under natural conditions by collecting plant tissues from the flower bud stage until fruit maturity. The target pathogens were consistently isolated from asymptomatic samples at all stages of fruit development and from symptomatic samples at fruit maturity across the 2 years of collection. A significant increase in fungal isolation frequency, primarily species of Alternaria and Colletotrichum, was observed right after flowering, but fruit rot symptoms only developed on mature fruit. In the second case we artificially inoculated containerized plants maintained outdoor at our research farm with individual or combined pathogens at different fruit developmental stages, and we assessed disease incidence on mature fruit to determine the time of host susceptibility to infection and, indirectly, whether pathogens in the fungal complex carry out latent infections. D. ilicicola could cause latent infection on deciduous holly fruit when inoculated at the full bloom and petal fall stages, and all inoculations made on wounded mature fruit resulted in fruit rot. These findings suggest that flowering represents a critical period to manage D. ilicicola infections and that mature fruit should be protected from any injury to avoid disease. In both experiments a negative correlation between disease incidence and temperature was found; however, the decrease in temperature also coincided with fruit ripening. The effects of temperature and changes in physiological properties of the fruit during maturation on disease development should be further investigated to fully interpret these findings.

Identification and Characterization of Fungal Pathogens Causing Fruit Rot of Deciduous Holly

Cut branches of deciduous holly (Ilex spp. L.) harboring colorful berries are traditionally used as ornaments in holiday decorations. Since 2012, a fruit rot of unspecified cause has resulted in significant yield reduction and economic losses across Midwestern and Eastern U.S. nurseries. In this study, symptomatic fruit samples collected from nine different locations over five years were analyzed, and several fungal species were isolated. A combination of morphological characterization, multilocus phylogenetic analyses, and pathogenicity assays revealed that Alternaria alternata and Diaporthe ilicicola sp. nov. were the primary pathogens associated with symptomatic fruit. Other fungi including A. arborescens, Colletotrichum fioriniae, C. nymphaeae, Epicoccum nigrum, and species in the D. eres species complex appeared to be minor pathogens in this disease complex. In detached fruit pathogenicity assays testing the role of wounding and inoculum concentration on disease development, disease incidence and severity increased when fruit was wounded and inoculated with a higher inoculum concentration. These findings indicate that management strategies that can protect fruit from injury or reduce inoculum may lower disease levels in the field. This research established the basis for further studies on this emerging disease and the design of research-based management strategies. To our knowledge, it also represents the first report of species of Alternaria, Colletotrichum, Diaporthe, and Epicoccum causing fruit rot of deciduous holly.

Pest risk assessment of Diaporthe vaccinii for the EU territory

As requested by the European Commission, the EFSA Panel on Plant Health (PLH) Panel assessed the risk of Diaporthe vaccinii in the EU, focusing on entry, establishment, spread and impacts on cultivated and wild Vaccinium species, the principal hosts being American and European cranberry and blueberry. Several outbreaks occurred in the EU since 1956, but most were eradicated except in Latvia. The Panel considered entry via fruits and plants for planting. The risk of establishment from discarded infected berries is much lower than from infected plants for planting, of which, potted plants and cuttings pose the greatest risk, while plug plants, derived from tissue culture and grown in pest free structures, pose a low risk. Nine per cent of the EU is highly suitable for establishment of the pathogen, mostly in the SE and NE. Following establishment, the pathogen could spread naturally over short range, and by human assistance over long range. Calculations with an integrated model for entry, establishment and spread, indicate that with current regulations, over a period of 5 years, a few hundred cultivated Vaccinium plants and several thousand Vaccinium plants in natural ecosystems would contract the disease. The associated loss of commercial production is small, less than one tonne of berries per year. On natural vegetation, the median impact after 5 years was estimated to be negligible affecting a negligible proportion of the natural Vaccinium population (2 × 10⁻⁸). However, the uncertainty of this estimate was high, due to uncertainty about the rate of spread; in a worst‐case scenario (99th percentile), almost 1% of plants in natural areas would become infected. Complete deregulation (scenario A1) was predicted to increase the impact substantially, especially in natural areas, while additional measures (scenario A2) would effectively eliminate the entry of infected plants for planting, further reducing the impacts below the current situation.

Synergisms between microbial pathogens in plant disease complexes: a growing trend

Plant diseases are often thought to be caused by one species or even by a specific strain. Microbes in nature, however, mostly occur as part of complex communities and this has been noted since the time of van Leeuwenhoek. Interestingly, most laboratory studies focus on single microbial strains grown in pure culture; we were therefore unaware of possible interspecies and/or inter-kingdom interactions of pathogenic microbes in the wild. In human and animal infections, it is now being recognized that many diseases are the result of multispecies synergistic interactions. This increases the complexity of the disease and has to be taken into consideration in the development of more effective control measures. On the other hand, there are only a few reports of synergistic pathogen-pathogen interactions in plant diseases and the mechanisms of interactions are currently unknown. Here we review some of these reports of synergism between different plant pathogens and their possible implications in crop health. Finally, we briefly highlight the recent technological advances in diagnostics as these are beginning to provide important insights into the microbial communities associated with complex plant diseases. These examples of synergistic interactions of plant pathogens that lead to disease complexes might prove to be more common than expected and understanding the underlying mechanisms might have important implications in plant disease epidemiology and management.

Polyphasic characterization of four new plant pathogenic Phyllosticta species from China, Japan, and the United States

The black rot disease of Vitis species and other host genera of Vitacease is caused by Phyllosticta ampelicida and allied taxa which is considered to be a species complex. In this paper, we introduce four new species of Phyllosticta, including two from the P. ampelicida complex, based on a polyphasic characterization including disease symptoms and host association, morphology, and molecular phylogeny. The phylogenetic analysis was conducted based on the ribosomal internal transcribed spacer (ITS) region and a combined multi-locus alignment of the ITS, actin (ACT), partial translation elongation factor 1-alpha (TEF-1), and glyceraldehydes 3-phosphate dehydrogenase (GPDH) gene regions. Our study confirms the phylogenetic distinctions of the four new species, as well as their phenotypic differences with known species in the genus.

Habitat and host indicate lineage identity in Colletotrichum gloeosporioides s.l. from wild and agricultural landscapes in North America

Understanding the factors that drive the evolution of pathogenic fungi is central to revealing the mechanisms of virulence and host preference, as well as developing effective disease control measures. Prerequisite to these pursuits is the accurate delimitation of species boundaries. Colletotrichum gloeosporioides s.l. is a species complex of plant pathogens and endophytic fungi for which reliable species recognition has only recently become possible through a multi-locus phylogenetic approach. By adopting an intensive regional sampling strategy encompassing multiple hosts within and beyond agricultural zones associated with cranberry (Vaccinium macrocarpon Aiton), we have integrated North America strains of Colletotrichum gloeosporioides s.l. from these habitats into a broader phylogenetic framework. We delimit species on the basis of genealogical concordance phylogenetic species recognition (GCPSR) and quantitatively assess the monophyly of delimited species at each of four nuclear loci and in the combined data set with the genealogical sorting index (gsi). Our analysis resolved two principal lineages within the species complex. Strains isolated from cranberry and sympatric host plants are distributed across both of these lineages and belong to seven distinct species or terminal clades. Strains isolated from V. macrocarpon in commercial cranberry beds belong to four species, three of which are described here as new. Another species, C. rhexiae Ellis & Everh., is epitypified. Intensive regional sampling has revealed a combination of factors, including the host species from which a strain has been isolated, the host organ of origin, and the habitat of the host species, as useful indicators of species identity in the sampled regions. We have identified three broadly distributed temperate species, C. fructivorum, C. rhexiae, and C. nupharicola, that could be useful for understanding the microevolutionary forces that may lead to species divergence in this important complex of endophytes and plant pathogens.

Incidence and Causes of Postharvest Fruit Rot in Stored Michigan Cranberries

The incidence of postharvest fruit rot and associated fungi was studied in stored cranberries in Michigan in 2000 and 2001. Ripe cranberries were harvested from eight commercial farms in southwest and northeast Michigan, including the Upper Peninsula. Eight cranberry cultivars were represented: Stevens, Searles, Le Munyon, Pilgrim, Ben Lear, Bergman, Beckwith, and WSU 61. Fruit rot incidence was assessed within 1 week after harvest. Remaining sound fruit was stored for 2 months at 5°C, and fungi were isolated from rotted fruit after 1 and 2 months of storage. Year and region, but not cultivar, significantly affected the overall rate of rot development in storage. Storage rot levels generally were lower in 2001 than in 2000, particularly in southern Michigan. A high incidence of field rot at harvest did not necessarily lead to a high incidence of storage rot. Storage rot tended to be more severe in the northern than in the southern growing region. Fungi most frequently associated with storage rot were Fusicoccum putrefaciens, Colletotrichum acutatum, Coleophoma empetri, Phomopsis vaccinii, and Phyllosticta elongata. F. putrefaciens was the predominant storage rot fungus in northern Michigan in both years and caused up to 80% fruit rot in storage. C. empetri and P. elongata also were isolated more frequently from beds in northern than southern Michigan in 2001. The cvs. Pilgrim and Stevens were more susceptible to storage rot caused by Colletotrichum acutatum, and Bergman and WSU 61 were more susceptible to storage rot caused by Phomopsis vaccinii than some of the other cultivars.