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Multiple Colletotrichum species have been found to be responsible for strawberry anthracnose, and prevalence of each species seems to vary by regions and/or host tissues. In this study, a total of 200 Colletotrichum isolates were obtained from different strawberry cultivars displaying anthracnose symptoms in the mid-Atlantic fields. Analysis of g3pdh, tub2, and/or internal transcribed spacer sequences revealed four Colletotrichum species, including C. nymphaeae, C. fioriniae, C. siamense, and C. lineola. C. nymphaeae was the predominant species, representing 90% of all isolates collected. This species was found from all strawberry organs/tissues examined, whereas C. siamense and C. fioriniae were limited to the crown and fruit, respectively. Further, all Colletotrichum isolates were screened for resistance to azoxystrobin in vitro, and all C. siamense isolates were additionally screened for resistance to thiophanate-methyl. The overall frequency of resistance to azoxystrobin and thiophanate-methyl was 48 and 67%, respectively. G143A in the cytochrome b gene was found in all C. nymphaeae and C. siamense isolates with high level of resistance, with EC50 >100 µg/ml, while F129L was found in two of the five C. nymphaeae isolates with moderate resistance, with EC50 values ranging from 2.6 to 7.8 µg/ml. All C. fioriniae isolates tested were found to be less sensitive to azoxystrobin, with EC50 values ranging from 9.7 to 14.4 µg/ml, despite no mutations detected in the cytochrome b gene. Moreover, E198A in tub2 was linked with C. siamense isolates resistant to thiophanate-methyl (EC50 >100 µg/ml). These results revealed that resistance in Colletotrichum spp. to primary fungicides is widespread in the mid-Atlantic strawberry fields.

From 2014 to 2019, 249 isolates of Botrytis spp. were collected from blackberry, black raspberry, grape, red raspberry, and strawberry showing gray mold symptoms. All isolates were phylogenetically characterized as Botrytis cinerea. A mycelial growth assay determined the following overall frequencies of resistance to fungicides: 92% to pyraclostrobin, 86% to cyprodinil, 71% to thiophanate-methyl, 48% to fenhexamid, 47% to iprodione, 26% to boscalid, 11% to fludioxonil, 8% to penthiopyrad, 7% to benzovindiflupyr, 4% to pydiflumetofen, and 4% to isofetamid. Isolates collected from blackberry, red raspberry, and strawberry had a higher median chemical class resistance value compared with isolates from black raspberry and grape. Resistance-conferring mutations were found in a selection of isolates characterized as resistant to thiophanate-methyl, iprodione, pyraclostrobin, fenhexamid, and boscalid, including E198A in β-tubulin; I365N/S, Q369P, and N373S in bos1; G143A in cytb; P238S, N369D, and F412I/S in erg27; and P225F and H272R/Y in sdhB, respectively. Also, multiple drug resistance (MDR) phenotypes MDR1 and MDR1h were identified by analyzing fludioxonil sensitivity and mrr1 sequences. MDR1 and MDR1h isolates had multiple amino acid variations and two insertions in mrr1 that resembled the group S genotype. A detached grape assay confirmed that the aforementioned mutations in isolates from different small fruit crops resulted in field-relevant resistance. An additional in vitro assay found that values for the effective concentration that inhibits mycelial growth by 50% of B. cinerea isolates to pydiflumetofen and inpyrfluxam averaged 0.4 and 1.0, 0.8 and 0.7, 149.8 and 23.2, 0.9 and 0.9, and 38.8 and 48.8 µg/ml for the wild-type, H272R, H272Y, N230I, and P225F genotypes, respectively. These results revealed widespread fungicide resistance in B. cinerea from Mid-Atlantic small fruit fields, highlighting the need for resistance management alternatives.

Anthracnose fruit rot (AFR) and Botrytis fruit rot (BFR) are primary diseases affecting strawberry (Fragaria × ananassa), which typically drive fungicide applications throughout the growing season. The Strawberry Advisory System (StAS), a disease forecasting tool, was originally developed in Florida to better time the fungicide sprays by monitoring AFR and BFR infection risk based on leaf wetness and temperature input in real-time. Thirteen field trials were conducted in Maryland and Virginia between 2017 and 2019 to evaluate the StAS performance in the Mid-Atlantic region. As a result, 55, 18, and 31% fewer sprays were recorded on average in the model-based StAS treatment compared with the grower standard treatment in 2017, 2018, and 2019, respectively. Marketable yield, as well as AFR and BFR incidence, were largely comparable between the two treatments. However, poor disease control occurred during the StAS treatment in four trials in 2017, presumably because of a missed fungicide spray during a high-risk infection event and attributable to heavy rainfall that led to impassable fields. The implementation of the StAS may be further challenged by the employment of floating row covers that are essential for growing strawberries in plasticulture systems in open fields in the Mid-Atlantic region. Preliminary results indicated that row covers can alter canopy-level microclimatic conditions, possibly increasing the risk for disease occurrence. Overall, the StAS can be a valuable tool for Mid-Atlantic growers to control AFR and BFR, but sprays may need to be promptly applied when consecutive or heavy rainfalls are predicted, especially for highly susceptible cultivars. Complications in disease forecasting and management arising from the use of row covers need to be further addressed in this region because of its highly diverse climate.

Few fungicides are effective against anthracnose, caused by Colletotrichum spp., and emerging resistance makes the search for chemical alternatives more relevant. Isolates of the Colletotrichum acutatum species complex were collected from South Carolina and Georgia peach orchards and phylogenetic analysis of the combined internal transcribed spacer region, glyceraldehyde-3-phosphate dehydrogenase, and β-tubulin gene sequences separated the isolates into C. nymphaeae and C. fioriniae. The sensitivity of these and three other previously reported Colletotrichum spp. from peach, including C. fructicola, C. siamense, and C. truncatum, to demethylation inhibitor (DMI) fungicides difenoconazole, propiconazole, tebuconazole, metconazole, flutriafol, and fenbuconazole was determined based upon mycelial growth inhibition. C. truncatum was resistant to tebuconazole, metconazole, flutriafol, and fenbuconazole and C. nymphaeae was resistant to flutriafol and fenbuconazole based on 50% effective concentration (EC50) values >100 μg/ml. C. fructicola and C. siamense were sensitive to all DMI fungicides (EC50 values of 0.2 to 13.1 μg/ml). C. fioriniae subgroup 2 isolates were less sensitive to DMI fungicides (EC50 values of 0.5 to 16.2 μg/ml) compared with C. fioriniae subgroup 1 (EC50 values of 0.03 to 2.1 μg/ml). Difenoconazole and propiconazole provided the best control efficacy in vitro to all five species, with EC50 values of 0.2 to 2.7 μg/ml. Tebuconazole and metconazole were effective against all Colletotrichum spp., except for C. truncatum. The strong in vitro activity of some DMI fungicides against Colletotrichum spp. may be exploited for improved anthracnose disease management of peach.

In 2009 and 2010, peaches (Prunus persica) with brown rot symptoms were collected from Zhejiang Plant Protection State Research Farm and a commercial orchard in Fujian Province in southeastern China. Affected fruit showed brown decay with zones of sporulation. Single-spore isolates from the diseased fruit were cultured on potato dextrose agar. After incubation at 25°C in the dark for 5 days, colonies were gray with concentric rings of sporulation. Mean mycelial growth of isolates MZ09-2a from Zhejiang Province and 0907-a from Fujian Province was 4.46 ± 0.58 and 7.05 ± 0.81 cm after 4 and 7 days of incubation, respectively. Lemon-shaped conidia were formed in branched, monilioid chains and mean size was 14.6 (9.6 to 21.6) × 10.3 (7.2 to 13.2) μm. Mean conidial germination was 97 ± 1% with one straight germ tube per conidium. These characteristics were consistent with descriptions of Monilinia fructicola (G. Wint.) Honey (3). Morphology-based species identification was confirmed by sequencing and analysis of ribosomal internal transcribed spacer (ITS) sequences. A 496-bp fragment including ITS 1 and 2 and the gene encoding the 5.8S small subunit of the ribosomal RNA from isolates MZ09-2a and 0907-a was amplified using the universal primer pair ITS1/ITS4 (4) and sequenced. Nucleotide sequences of both isolates were identical. Blast searches of the ITS sequences in GenBank showed the highest similarity (100%) with sequences of M. fructicola isolates from China (FJ515894), Italy (FJ411109), and Spain (EF207423). The isolates were also identified as M. fructicola using the Monilinia spp. PCR detection protocol based on sequence-characterized amplification region marker DNA sequences (2). Pathogenicity was confirmed by inoculating surface-sterilized, mature cv. Zhonghua 2 peaches with mycelial plugs of representative isolates. Fruit was stabbed at two points with a 5-mm-diameter sterile cork borer, mycelial plugs (5 mm in diameter) were removed from the periphery of a 4-day-old colony of each isolate and placed upside down into each wound; control fruit received water agar. Inoculated fruit developed typical brown rot symptoms with sporulating fungi while control fruit remained healthy after 3 days of incubation at 22°C in a moist chamber. Pathogens were reisolated from the inoculated fruit and confirmed to be M. fructicola on the basis of morphological characteristics. To our knowledge, this is the first report of M. fructicola in Zhejiang and Fujian provinces. Both provinces are located more than 1,000 km south of Beijing, Hebei, and Shandong provinces, where M. fructicola had been reported previously (1). References: (1) J. Y. Fan et al. Acta Phytophylacica Sin. (in Chinese) 34:289, 2007. (2) I. Gell et al. J. Appl. Microbiol. 103:2629, 2007. (3) G. C. M. van Leeuwen and H. A. van Kesteren. Can. J. Bot. 76:2041, 1998. (4) T. J. White et al. Page 315 in: PCR Protocols: A Guide to Methods and Applications. M. A. Innis et al., eds., Academic Press, San Diego, 1990.

Colletotrichum gloeosporioides, C. acutatum, and C. truncatum are causal agents of anthracnose disease of peach in South Carolina, but more recent investigations show that C. gloeosporioides is a species complex that has not yet been investigated among peach isolates. A total of 28 Colletotrichum spp. isolates associated with peach fruit anthracnose were collected in 2012 from Chesnee (10 isolates), McBee (10 isolates), Monetta (2 isolates), and Ridge Spring (6 isolates), South Carolina. Morphological characteristics indicated that all 28 isolates belonged to the C. gloeosporioides species complex. Phylogenetic analysis of the combined calmodulin (CAL), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and β-tubulin (TUB2) gene sequences identified two species, C. siamense and C. fructicola. Cultural characteristics such as colony growth rate, shape and size of conidia, and appressoria from representative isolates of the two species largely matched previous descriptions for C. siamense and C. fructicola. Koch’s postulates for C. siamense and C. fructicola were fulfilled, confirming pathogenicity of the two species on peach. A new, two-step multiplex PCR assay was developed to facilitate differentiation of the four known Colletotrichum spp. causing anthracnose of peach in South Carolina, including C. acutatum, C. truncatum, C. siamense, and C. fructicola. The first step distinguished C. acutatum from C. truncatum and the two members of the C. gloeosporioides species complex. The second assay distinguished C. siamense from C. fructicola isolates.

Polyoxin D is a Fungicide Resistance Action Committee (FRAC) code 19 fungicide that was recently registered for gray mold control of strawberry in the United States. In this study, we determined the sensitivity to polyoxin D zinc salt (hereafter, polyoxin D) of Botrytis cinerea isolates from 41 commercial strawberry farms in South Carolina, North Carolina, Maryland, Virginia, and Ohio and investigated the fitness of sensitive (S) and reduced sensitive (RS) isolates. Relative mycelial growth ranged between 0 and over 100% on malt extract agar amended with a discriminatory dose of polyoxin D at 5 μg/ml. Isolates that grew more than 70% at that dose were designated RS and were found in three of the five states. The 50% effective dose (EC50) values of three S and three RS isolates ranged from 0.59 to 2.27 and 4.6 to 5.8 μg/ml, respectively. The three RS isolates grew faster on detached tomato fruit treated with Ph-D WDG at recommended label dosage than S isolates (P < 0.008). In all, 25 randomly selected RS isolates exhibited reduced sporulation ability (P < 0.0001) and growth rate (P < 0.0001) but increased production of sclerotia (P < 0.0386) compared with 25 S isolates. Of 10 isolates tested per phenotype, the number of RS isolates producing sporulating lesions on apple, tomato, and strawberry was significantly lower compared with S isolates (P < 0.0001 for each fruit type). The results of this study indicate that resistance management is necessary for fungicides containing polyoxin D. To our knowledge, this is the first study demonstrating reduced sensitivity to FRAC 19 fungicides in B. cinerea isolates from the United States.

Gray mold is a devastating disease on strawberry, and may be caused by several species of Botrytis. The goal of this study was to better understand and characterize the species of Botrytis with reduced sensitivity to the fungicide Polyoxin D, particularly Botrytis fragariae. In total, 78 Botrytis isolates of unknown species that were sensitive (28 isolates; S), moderately sensitive (22 isolates; MS), or reduced sensitive (28 isolates; RS) to Polyoxin-D were collected from commercial strawberry fields of five states in the United States, identified to the species level, and characterized. The majority (75%) of S isolates were Botrytis cinerea and the majority (79%) of RS isolates were the recently described species B. fragariae, indicating an innate ability of B. fragariae to tolerate Polyoxin-D. B. fragariae produced fluffy, white mycelium and was less likely to sporulate on potato dextrose agar than B. cinerea. Isolates from a commercial field recovered from blossoms in early spring were all B. fragariae, those from leaves of the same plants in late spring were a mixture of B. fragariae and B. cinerea, and those from fruit in early summer were all B. cinerea, indicating that B. fragariae may preferentially colonize blossom tissue. A polymerase chain reaction-based assay was developed based on NEP2 sequence variability to distinguish B. fragariae from other Botrytis spp. that have been reported on strawberry, including B. cinerea, B. mali, B. caroliniana, and B. ricini. None of the isolates collected from Canada, California, or North Carolina nurseries were B. fragariae, indicating that the newly described species may not exist or not be widely distributed in planting stock.

Gray mold, caused by Botrytis spp., is among the most devastating diseases affecting strawberry worldwide. The great diversity present in the pathogen enhances its ability to survive and adapt in the field. In this study, we explored the genotypic and phenotypic diversity present in single strawberry flowers. In total, 192 isolates were collected from 19 flowers and four farms, and 9 to 12 isolates were collected from each flower. Forty-two haplotypes were found using microsatellite fragment analysis. Multiple haplotypes of two different Botrytis spp. (Botrytis cinerea and B. fragariae) were found in 12 flowers. In the remaining seven flowers, the single-spore isolates examined were of identical haplotypes. In three flowers, the two Botrytis spp. were found to coexist. Isolates were either sensitive (zero chemical class resistance) or resistant to one, two, three, four, or five chemical classes of fungicides. Resistance to multiple fungicides was commonly observed in both species but resistance to boscalid and penthiopyrad was only found in B. cinerea isolates. Resistance to cyprodinil was found in B. fragariae for the first time in the United States. Each haplotype was generally linked to a single resistance profile; however, a single resistance profile often was represented by multiple haplotypes. Isolates from the same flower of multiple haplotypes were largely identical in resistance profiles. This study is a first detailed investigation of genotypic diversity combined with phenotypic analysis of Botrytis spp. at the single-tissue level. It demonstrates that high genotypic and phenotypic diversity is present not only within fields but also in individual blossoms as well. This information is important for understanding the epidemiology of Botrytis and also has implications for fungicide resistance management, particularly related to resistance monitoring practices.

Succinate dehydrogenase inhibitor (SDHI) fungicides have been used to control gray mold of strawberry for more than a decade, and selection for resistance in the causal agent Botrytis cinerea has become a threat to producers. In total, 2,570 B. cinerea isolates were collected from strawberry fields in the eastern United States across three seasons and their sensitivity to the SDHI materials boscalid, fluopyram, fluxapyroxad, and penthiopyrad was assessed. Assays were based on visual assessment of presence or absence of mycelial growth on media amended with discriminatory fungicide doses to distinguish sensitive from resistant isolates, respectively. Overall frequencies of isolates resistant to boscalid, fluopyram, fluxapyroxad, and penthiopyrad increased over the 3 years to 30.0, 1.0, 5.5, and 7.4%, respectively. Four resistance patterns, designated A, B, C, or D, were found. Pattern A isolates were resistant to boscalid with the allele H272R at locus sdhB; pattern B isolates were resistant to boscalid and penthiopyrad with the allele H272R or H272Y at locus sdhB; pattern C isolates were resistant to boscalid, fluxapyroxad, and penthiopyrad with the allele H272Y at locus sdhB; and pattern D isolates were resistant to boscalid, fluopyram, fluxapyroxad, and penthiopyrad with alleles P225F or N230I at locus sdhB. Isolates with alleles H272Y, N230I, or P225F were sensitive to a new SDHI, benzovindiflupyr, with mean effective dose that inhibits 50% of mycelial growth values of less than 0.5 μg/ml for each genotype, suggesting that this fungicide may be useful for resistance management. Our data show an increase of B. cinerea isolates resistant to SDHI fungicides over three consecutive production seasons. Resistance management practices must be implemented for the sustained efficacy of SDHI fungicides against gray mold of strawberry.

Colletotrichum fioriniae Marcelino & Gouli ex R.G. Shivas & Y.P. Tan causes anthracnose and fruit rot in various hosts worldwide (Shivas and Tan 2009). In June 2019, 40% of red raspberry fruit (cv. Prelude) in a plot at the Wye Research and Education Center of the University of Maryland in Queenstown, MD, showed light to dark brown, rotten, and slightly sunken drupelets. Symptomatic berries (n = 17) were collected and incubated in plastic boxes at room temperature (22°C) to obtain 41 single-spore isolates. Colonies on potato dextrose agar (PDA) were gray to pale olivaceous, cottony, with aerial mycelium in compact tufts, and had a white rim and a pinkish-red to pale orange or yellow reverse and orange acervuli. Conidia were one-celled, hyaline, smooth-walled, with either both acute ends or one round and one pointed end, without setae. Conidial dimensions were recorded for two single-spore isolates and were in accordance with previous measurements (Damm et al. 2012): mean length ± SD × width ± SD = 12.9 ± 1.5 × 5.4 ± 0.9 μm on PDA (n = 60). DNA was extracted from mycelium of 11 single-spore isolates (Chi et al. 2009). Damm et al. (2012) showed that all subclades of the Colletotrichum acutatum complex can be identified by amplifying a 290-bp section of the glyceraldehyde-3-phosphate dehydrogenase (gapdh) gene (primers: Templeton et al. [1992]) and a 1,440-bp section of the β-tubulin-2 gene (tub2) (primers: T1 from O’Donnell and Cigelnik [1997], TubR1 from Hu et al. [2015]). Polymerase chain reaction products were sequenced from two directions. Three consensus sequences for each gene were deposited into GenBank: RB19-14.4S (MN520488, MN532086), RB19-13.3S (MN520489, MN532087), and RB19-26P (MN520490, MN532088). BLASTn search confirmed 100% identity with the Colletotrichum fioriniae sequences JQ949974 (491 bp, tub2) and JQ948653 (254 bp, gapdh) for RB19-14.4S and in total nine of the 11 isolates. For isolate RB19-26P the gapdh sequence (MN532088) was 100% identical with JQ948624 instead. Tub2 (MN520489) and gapdh (MN532087) sequences for isolate RB19-13.3S were 100 and 99.6% identical with C. fioriniae sequences JQ949944 and JQ948623, respectively. To confirm pathogenicity, healthy ripe red raspberries (cv. Jaclyn) were inoculated with a mixture of four single-spore isolates. Berries were surface sterilized by washing in 0.1% Tween 20 for 2 min, 70% ethanol for 30 s, 1% NaOCl for 1 min, and sterile water for 2 min. After air drying for 2 h, berries were either wounded with a sterile toothpick or not wounded and were inoculated with a 15-μl drop of spore suspension (5 × 10⁵ conidia/ml) or sterile water. Each treatment was replicated four times with eight berries per replicate. The experiment was conducted twice. After incubation for 3 days, both wounded and unwounded inoculated berries showed symptoms identical to those described above, and some lesions had orange acervuli. C. fioriniae was reisolated from inoculated berries but never from water-inoculated berries. Identity of the recovered isolates was confirmed morphologically and molecularly. Although C. fioriniae is an endophyte in various plant species worldwide (Freeman et al. 2001) and was previously isolated as an endophyte or from leaves of Rubus idaeus in New York (U.S.A.), Norway, and Mississippi (U.S.A.) (Marcelino et al. 2009; Sundelin et al. 2015; Zhang et al. 2016), it has not been described as a raspberry fruit pathogen causing anthracnose disease so far. To our knowledge this is the first report of C. fioriniae found on red raspberries in the Mid-Atlantic region of the United States.

Anthracnose fruit rot was observed in some late-season peach cultivars in South Carolina in the 2012 and 2013 production seasons as well as increased anthracnose leaf spot of blueberry in a commercial operation of the same state in 2012. Single-spore isolates of Colletotrichum siamense were either sensitive or resistant to both thiophanate-methyl and azoxystrobin with the concentration of the fungicide at which fungal development is inhibited by 50% of ≥100 μg/ml. Resistant isolates revealed the E198A mutation in β-tubulin and the G143A mutation in cytochrome b. Nucleotide sequence analysis of the complete CYTB gene from genomic DNA of C. siamense isolates revealed an intronless genotype (CsI) and a genotype revealing two introns (CsII) at amino acid positions 131 and 164. Resistance to thiophanate-methyl or azoxystrobin was not found in isolates of C. fructicola collected from peach fruit. The CYTB gene of isolates of this species was of the CfII genotype or revealed a unique CfIIa genotype. Phylogenetic analysis of C. siamense isolates from different locations and different crops showed that the resistant isolates were genetically closer to each other than to sensitive isolates, suggesting that field resistance to thiophanate-methyl and azoxystrobin fungicides is derived from a common ancestor.

Monilinia fructicola (G. Wint.) Honey is a causal agent of brown rot of stone fruits but may also affect pome fruits. M. fructicola is common in North America, Oceania, and South America as well as in Asia, but it is listed as a quarantine pathogen in Europe (3). Since its first discovery in Europe in 2001 (France), it has been reported in Spain, Slovenia, Italy, and Switzerland. Recently, the fungus was also detected in orchards of blackberries and plums in the State of Baden-Württemberg, Germany (4). In July 2010, apples (Malus domestica Borkh.) of the cultivar Jonagold were found in a residential backyard in Fronhausen an der Lahn located in the State of Hessen, Germany with symptoms resembling brown rot caused by Monilinia species. Affected apples were at or near maturity with brown decay that had spread throughout the fruits. On the surface of the decaying apples was tan to white zones of sporulation. Upon isolation, the mycelium grew at a linear rate of 9.2 mm per day at 22°C on potato dextrose agar forming branched, monilioid chains of grayish colonies with concentric rings and little sporulation. The lemon-shaped spores had an average size of 14 × 9 μm, a shape and size consistent with M. fructicola. The ribosomal ITS1-5.8S-ITS2 region was PCR-amplified from genomic DNA obtained from mycelium using primers ITS1 and ITS4. A BLAST search in GenBank revealed highest similarity (99%) to M. fructicola sequences from isolates collected in China, Italy, and Slovenia (GenBank Accession Nos. FJ515894.1, FJ411109.1, GU967379.1). The M. fructicola sequence from the apple isolate was submitted to GenBank (Accession No. JF325841). The pathogen was also identified to the species level and confirmed to be M. fructicola using two novel PCR techniques based on cytochrome b sequences (1,2). Pathogenicity was confirmed by inoculating three surface-sterilized, mature apples cv. Gala with a conidial suspension (105 spores/ml) of the apple isolate. Fruit were stab inoculated at three equidistant points to a depth of 10 mm using a sterile needle. A 30-μl droplet was placed on each wound; control fruit received sterile water without conidia. After 5 days of incubation at room temperature in air-tight plastic bags, the inoculated fruits developed typical brown rot symptoms with sporulating areas (as described above). The developing spores on inoculated fruit were confirmed to be M. fructicola. All control fruits remained healthy. To our knowledge, this is the first report of M. fructicola on apple in Germany and more indication of further geographical spread of the quarantine disease in Germany. References: (1) J.-M. Hily et al. Pest Manag. Sci. Online publication. doi 10.1002/ps.2074, 2011. (2) S. Miessner and G. Stammler. J. Plant Dis. Prot. 117:162, 2010. (3) OEPP/EPPO. EPPO A2 list of pests recommended for regulation as quarantine pests. Version 2009-09. Retrieved from http://www.eppo.org/QUARANTINE/listA2.htm , September 22, 2010. (4) OEPP/EPPO. Reporting Service. No. 1, January 2010. Retrieved from http://archives.eppo.org/EPPOReporting/2010/Rse-1001.pdf , September 22, 2010.