Phylogenomic analyses and comparative genomics of Pseudomonas syringae associated with almond (Prunus dulcis) in California

We sequenced and comprehensively analysed the genomic architecture of 98 fluorescent pseudomonads isolated from different symptomatic and asymptomatic tissues of almond and a few other Prunus spp. Phylogenomic analyses, genome mining, field pathogenicity tests, and in vitro ice nucleation and antibiotic sensitivity tests were integrated to improve knowledge of the biology and management of bacterial blast and bacterial canker of almond. We identified Pseudomonas syringae pv. syringae, P. cerasi, and P. viridiflava as almond canker pathogens. P. syringae pv. syringae caused both canker and foliar (blast) symptoms. In contrast, P. cerasi and P. viridiflava only caused cankers, and P. viridiflava appeared to be a weak pathogen of almond. Isolates belonging to P. syringae pv. syringae were the most frequently isolated among the pathogenic species/pathovars, composing 75% of all pathogenic isolates. P. cerasi and P. viridiflava isolates composed 8.3 and 16.7% of the pathogenic isolates, respectively. Laboratory leaf infiltration bioassays produced results distinct from experiments in the field with both P. cerasi and P. syringae pv. syringae, causing significant necrosis and browning of detached leaves, whereas P. viridiflava conferred moderate effects. Genome mining revealed the absence of key epiphytic fitness-related genes in P. cerasi and P. viridiflava genomic sequences, which could explain the contrasting field and laboratory bioassay results. P. syringae pv. syringae and P. cerasi isolates harboured the ice nucleation protein, which correlated with the ice nucleation phenotype. Results of sensitivity tests to copper and kasugamycin showed a strong linkage to putative resistance genes. Isolates harbouring the ctpV gene showed resistance to copper up to 600 μg/ml. In contrast, isolates without the ctpV gene could not grow on nutrient agar amended with 200 μg/ml copper, suggesting ctpV can be used to phenotype copper resistance. All isolates were sensitive to kasugamycin at the label-recommended rate of 100μg/ml.

Effects of Temperature on Spore Germination and Mycelial Growth of Calosphaeria pulchella, Cytospora sorbicola, and Eutypa lata Isolates Associated with Sweet Cherry Canker Diseases

Although fungal canker diseases constitute a limiting factor to orchard productivity and longevity, little is known about the effects of temperature on spore germination and mycelial growth of the fungal causal agents. Accordingly, the germination of spores and colony growth of Calosphaeria pulchella, Cytospora sorbicola, and Eutypa lata were evaluated after incubation on 2% water agar and 4% potato dextrose agar, respectively, at 5, 10, 15, 20, 25, 30, 35, and 40°C. Temperature optima for spore germination and mycelial growth were derived from nonlinear models fitted to germination rates and colony diameter data. The optimal temperatures for spore germination of Cal. pulchella were 28.5°C for ascospores and 29.2°C for conidia. The optimal temperatures for Cyt. sorbicola conidia and E. lata ascospore germination were 25.8 and 23.1°C, respectively. The germination of ascospores and conidia of Cal. pulchella at temperatures below 15°C required an incubation time of at least 72 h. Ascospores of E. lata and conidia of Cyt. sorbicola germinated at 10°C after 36 h. The optimal temperature for colony growth of Cal. pulchella was 24.6°C, whereas it was 21.7°C for both Cyt. sorbicola and E. lata. Our study indicates that temperature requirements for basic biological functions are higher for Cal. pulchella than for Cyt. sorbicola and E. lata. The overall higher temperatures of California relative to other cherry-producing regions in the United States or worldwide could explain the prevalence of Calosphaeria canker in the state. Conversely, Cyt. sorbicola and E. lata appear better adapted to cooler temperatures.

Seasonal Susceptibility of Sweet Cherry Pruning Wounds to Calosphaeria pulchella, Cytospora sorbicola, and Eutypa lata

Fungal canker pathogens commonly infect trees at pruning wounds leading to branch dieback and loss of productivity in sweet cherry orchards. However, the seasonal susceptibility of sweet cherry pruning wounds to Calosphaeria pulchella, Cytospora sorbicola, and Eutypa lata is not well understood. This study compared the susceptibility of sweet cherry pruning wounds made during the dormant season (January) and the postharvest season (late May to June) to infection by main canker pathogens in California. Field trials were conducted in three cherry orchards and trees were pruned at the different periods over 2 years. Fresh pruning wounds were inoculated with spores of each pathogen, and pathogen recovery was assessed through microbiological isolations at 3 to 4 months after inoculations. Pruning wounds made in late May and June resulted in significantly higher infection by Cal. pulchella compared to pruning wounds made in January. Pruning wounds made during both seasons were generally equally susceptible to Cyt. sorbicola and E. lata infections. However, there was one orchard where dormant pruning wounds were more susceptible to infection by E. lata and there was one particularly cold winter where Cyt. sorbicola did not infect pruning wounds. Overall, our findings suggest that Cal. pulchella infections of cherry pruning wounds are more likely to occur during periods of warm temperatures such as late spring and early summer. However, infections by Cyt. sorbicola and E. lata can occur year-round if inoculum is present and if winter temperatures are not abnormally low for California. Finally, our results suggest that the emergence of Cal. pulchella as a major canker pathogen of sweet cherry in California may be the result of a shift from dormant to after-harvest pruning of sweet cherry trees.

Field Evaluation of Fungicides for the Management of Neofabraea Leaf Lesion of Olive in California

Field experiments were conducted during the fall-winter seasons of 2017 to 2018 and 2018 to 2019 to evaluate the efficacy of various fungicides to control Neofabraea leaf lesion of olive. Field trials were conducted in the highly susceptible cultivar Arbosana in a commercial, super-high-density orchard in San Joaquin County, California. Up to eight fungicidal products were applied using an air blast backpack sprayer, and their efficacy was compared with different application strategies. Results showed that most products were effective in reducing infection by the pathogens and limiting disease severity. Overall, best disease control was achieved by thiophanate-methyl, cyprodinil, difenoconazole + cyprodinil, and chlorothalonil, providing up to 75% reduction in disease severity. Copper hydroxide did not control the disease. In 2018 to 2019, the fungicides difenoconazole + cyprodinil and ziram were evaluated in additional field trials using different application strategies (single, dual, and combined applications) suitable for pathogen resistance management. Results showed that both products provided significant reduction in disease severity (∼50%), although no differences in efficacy were found between the two products nor between the different application strategies. Both products performed equally using one or two applications at 2-week intervals following harvest.

Whole genome sequencing and analysis of multiple isolates of Ceratocystis destructans, the causal agent of Ceratocystis canker of almond in California

Ceratocystis canker caused by Ceratocystis destructans is a severe disease of almond, reducing the longevity and productivity of infected trees. Once the disease has established in an individual tree, there is no cure, and management efforts are often limited to removing the infected area of cankers. In this study, we present the genome assemblies of five C. destructans isolates isolated from symptomatic almond trees. The genomes were assembled into a genome size of 27.2 ± 0.9 Mbp with an average of 6924 ± 135 protein-coding genes and an average GC content of 48.8 ± 0.02%. We concentrated our efforts on identifying putative virulence factors of canker pathogens. Analysis of the secreted carbohydrate-active enzymes showed that the genomes harbored 83.4 ± 1.8 secreted CAZymes. The secreted CAZymes covered all the known categories of CAZymes. AntiSMASH revealed that the genomes had at least 7 biosynthetic gene clusters, with one of the non-ribosomal peptide synthases encoding dimethylcoprogen, a conserved virulence determinant of plant pathogenic ascomycetes. From the predicted proteome, we also annotated cytochrome P450 monooxygenases, and transporters, these are well-established virulence determinants of canker pathogens. Moreover, we managed to identify 57.4 ± 2.1 putative effector proteins. Gene Ontology (GO) annotation was applied to compare gene content with two closely related species C. fimbriata, and C. albifundus. This study provides the first genome assemblies for C. destructans, expanding genomic resources for an important almond canker pathogen. The acquired knowledge provides a foundation for further advanced studies, such as molecular interactions with the host, which is critical for breeding for resistance.

Evaluation of Biological Control Agents for the Protection of Almond Pruning Wounds Against Infection by Fungal Canker Pathogens

Fungal canker pathogens of almond initiate infection in trees primarily through pruning wounds. Biological control agents (BCAs) have the potential to provide long-term protection of pruning wounds by colonizing the wound surfaces and underlying tissues. Laboratory and field tests were performed to assess the efficacy of various commercial and experimental BCAs as wound protectants against almond canker pathogens. Four Trichoderma-based BCAs were evaluated using detached almond stems in the laboratory against the canker pathogens Cytospora plurivora, Eutypa lata, Neofusicoccum parvum, and Neoscytalidium dimidiatum. Results indicated that Trichoderma atroviride SC1 and T. paratroviride RTFT014 significantly reduced infections by all four pathogens. The abilities of these four BCAs to protect almond pruning wounds against E. lata and N. parvum were further evaluated in field trials using two almond cultivars and during two consecutive years. Both T. atroviride SC1 and T. paratroviride RTFT014 protected almond pruning wounds against E. lata and N. parvum as efficiently as thiophanate-methyl, the recommended fungicide for treatment of almond pruning wounds. Comparisons of different application timings of BCA in relation to pathogen inoculation revealed a significant improvement in wound protection when inoculations were conducted 7 days versus 24 h post-BCA application for N. parvum, but not for E. lata. T. atroviride SC1 and T. paratroviride RTFT014 are promising candidates for the preventive protection of almond pruning wounds and for inclusion in integrated pest management programs and organic almond production systems.

Development of PCR-Based Assays for Rapid and Reliable Detection and Identification of Canker-Causing Pathogens from Symptomatic Almond Trees

Trunk and scaffold canker diseases (TSCDs) of almond cause significant yield and tree losses and reduce the lifespan of orchards. In California, several pathogens cause TSCDs, including Botryosphaeriaceae, Ceratocystis destructans, Eutypa lata, Collophorina hispanica, Pallidophorina paarla, Cytospora, Diaporthe, and Phytophthora spp. Field diagnosis of TSCDs is challenging because symptom delineation among the diseases is not clear. Accurate diagnosis of the causal species requires detailed examination of symptoms and subsequent isolation on medium and identification using morphological criteria and subsequent confirmation using molecular tools. The process is time-consuming and difficult, particularly as morphological characteristics are variable and overlap among species. To facilitate diagnosis of TSCD, we developed PCR assays using 23 species-specific primers designed by exploiting sequence differences in the translation elongation factor, β-tubulin, or internal transcribed spacer gene. Using genomic DNA from pure cultures of each fungal and oomycete species, each primer pair successfully amplified a single DNA fragment from the target pathogen but not from selected nontarget pathogens or common endophytes. Although 10-fold serial dilution of fungal DNA extracted from either pure cultures or infected wood samples detected as little as 0.1 pg of DNA sample, consistent detection required 10 ng of pathogen DNA from mycelial samples or from wood chips or drill shavings from artificially or naturally infected almond wood samples with visible symptoms. The new PCR assay represents an improved tool for diagnostic laboratories and will be critical to implement effective disease surveillance and control measures.

Comparative Profiling of Wood Canker Pathogens from Spore Traps and Symptomatic Plant Samples Within California Almond and Walnut Orchards

Fungi causing wood canker diseases are major factors limiting productivity and longevity of almond and walnut orchards. The goal of this study was to compare pathogen profiles from spore traps with those of plant samples collected from symptomatic almond and walnut trees and assess if profiles could be influenced by orchard type and age, rainfall amount and frequency, and/or neighboring trees. Three almond orchards and one walnut orchard with different characteristics were selected for this study. Fungal inoculum was captured weekly from nine trees per orchard using a passive spore-trapping device, during a 30-week period in the rainy season (October to April) and for two consecutive years. Fungal taxa identified from spore traps were compared with a collection of fungal isolates obtained from 61 symptomatic wood samples collected from the orchards. Using a culture-dependent approach coupled with molecular identification, we identified 18 known pathogenic species from 10 fungal genera (Ceratocystis destructans, Collophorina hispanica, Cytospora eucalypti, Diaporthe ampelina, Diaporthe chamaeropis/rhusicola, Diaporthe eres, Diaporthe novem, Diplodia corticola, Diplodia mutila, Diplodia seriata, Dothiorella iberica, Dothiorella sarmentorum, Dothiorella viticola, Eutypa lata, Neofusicoccum mediterraneum, Neofusicoccum parvum, Neoscytalidium dimidiatum, and Pleurostoma richardsiae), plus two unidentified Cytospora and Diaporthe species. However, only four species were identified with both methods (Diplodia mutila, Diplodia seriata, Dothiorella Iberica, and E. lata), albeit not consistently across orchards. Our results demonstrate a clear disparity between the two diagnostic methods and caution against using passive spore traps to predict disease risks. In particular, the spore trap approach failed to capture: insect-vectored pathogens such as Ceratocystis destructans that were often recovered from almond trunk and scaffold; Diaporthe chamaeropis/rhusicola commonly isolated from wood samples likely because Diaporthe species have a spatially restricted dispersal mechanism, as spores are exuded in a cirrus; and pathogenic species with low incidence in wood samples such as P. richardsiae and Collophorina hispanica. We propose that orchard inoculum is composed of both endemic taxa that are characterized by frequent and repeated trapping events from the same trees and isolated from plant samples, as well as immigrant taxa characterized by rare trapping events. We hypothesize that host type, orchard age, precipitation, and alternative hosts at the periphery of orchards are factors that could affect pathogen profile. We discuss the limitations and benefits of our methodology and experimental design to develop guidelines and prediction tools for fungal wood canker diseases in California orchards.

Floral Microbes Suppress Growth of Monilinia laxa with Minimal Effects on Honey Bee Feeding

Management of Monilinia laxa, the causal agent of brown rot blossom blight in almond (Prunus dulcis), relies heavily on the use of chemical fungicides during bloom. However, chemical fungicides can have nontarget effects on beneficial arthropods, including pollinators, and select for resistance in the pathogen of concern. Almond yield is heavily reliant on successful pollination by healthy honey bees (Apis mellifera); thus, identifying sustainable, effective, and pollinator-friendly control methods for blossom blight during bloom is desirable. Flower-inhabiting microbes could provide a natural, sustainable form of biocontrol for M. laxa, while potentially minimizing costly nontarget effects on almond pollinators and the services they provide. As pollinators are sensitive to floral microbes and their associated taste and scent cues, assessing effects of prospective biocontrol species on pollinator attraction is also necessary. Here, our objective was to isolate and identify potential biocontrol microbes from an array of agricultural and natural flowering hosts and test their efficacy in suppressing M. laxa growth in culture. Out of an initial 287 bacterial and fungal isolates identified, 56 were screened using a dual culture plate assay. Most strains reduced M. laxa growth in vitro. Ten particularly effective candidate microbes were further screened for their effect on honey bee feeding. Of the 10, nine were found to both strongly suppress M. laxa growth in culture and not reduce honey bee feeding. These promising results suggest a number of strong candidates for augmentative microbial biocontrol of brown rot blossom blight in almond with potentially minimal effects on honey bee pollination.

Identification and Characterization of Phytophthora Species Associated with Crown and Root Rot of Pistachio Trees in California

Pistachio is one of the most widely cultivated nut crops in California, with approximately 115,000 ha of bearing pistachio trees. In recent years, several orchards were identified, with declining trees leading to substantial tree losses. Symptoms included trees with poor vigor, yellowing and wilting of leaves, crown rot, and profuse gumming on the lower portion of trunks. Thirty-seven Phytophthora-like isolates were obtained from crown rot tissues in the rootstock of grafted pistachio trees and characterized by means of multilocus phylogeny comprising internal transcribed spacer rDNA, beta-tubulin, and mt cox1 sequence data. The analysis provided strong support for the delineation and identification of three Phytophthora species associated with declining pistachio trees, including P. niederhauserii, P. mediterranea, and Phytophthora taxon walnut. Pathogenicity studies in potted University of California Berkeley I (UCBI) rootstocks (clonal and seeded) confirmed that all three Phytophthora species can cause crown and root rot of pistachio, thus fulfilling Koch's postulates. The widespread occurrence of Phytophthora crown rot in recently planted pistachio orchards and the susceptibility of UCBI rootstocks suggest this disease constitute an emerging new threat to the pistachio industry of California. To the best of our knowledge, this study is the first to report P. niederhauserii, P. mediterranea, and Phytophthora taxon walnut as causal agents of crown and root rots of pistachio.

Pleurostoma Decline of Olive Trees Caused by Pleurostoma richardsiae in California

A single fungal pathogen was consistently isolated from symptomatic wood of olive trees (Olea europaea) displaying branch and trunk cankers in superhigh-density orchards in the Sacramento and San Joaquin Valleys of California. Morphological characters of the pathogen included two distinct types of conidia (thick-walled, dark brown, and globose and thin-walled, hyaline, and oblong to ellipsoid) and three types of phialides, indicating a pleurostoma-like fungus. Phylogenetic results of four nuclear loci including the internal transcribed spacer (ITS) region (ITS1-5.8S-ITS2) and partial sequences of the actin, beta-tubulin, and translation elongation factor 1-α genes confirmed the isolates as Pleurostoma richardsiae. Pathogenicity trials conducted in the field involving 2- to 3-year-old branches of three widely planted oil olive cultivars (Arbequina, Arbosana, and Koroneiki) satisfied Koch's postulates and confirmed the pathogenic nature of this species to cause the decline of olive trees in California. All three cultivars were equally susceptible to Pl. richardsiae, indicating no detectable resistance to the pathogen. Additional isolations from symptomatic hosts including almond, peach, pistachio, and plum, also confirmed this species, suggesting that Pl. richardsiae is widespread in agricultural systems and should be considered an emerging pathogen of fruit and nut crops in California.

Fungal Pathogens Associated With Canker Diseases of Almond in California

Almond canker diseases are destructive and can reduce the yield as well as the lifespan of almond orchards. These diseases may affect the trunk and branches of both young and mature trees and can result in tree death soon after orchard establishment in severe cases. Between 2015 and 2018, 70 almond orchards were visited throughout the Central Valley of California upon requests from farm advisors for canker disease diagnosis. Two major canker diseases were identified, including Botryosphaeriaceae cankers and Ceratocystis canker. In addition, five less prevalent canker diseases were identified, including Cytospora, Eutypa, Diaporthe, Collophorina, and Pallidophorina canker. Seventy-four fungal isolates were selected for multilocus phylogenetic analyses of internal transcribed spacer region ITS1-5.8S-ITS2 and part of the translation elongation factor 1-α, β-tubulin, and glyceraldehyde 3-phosphate dehydrogenase gene sequences; 27 species were identified, including 12 Botryosphaeriaceae species, Ceratocystis destructans, five Cytospora species, Collophorina hispanica, four Diaporthe species, two Diatrype species, Eutypa lata, and Pallidophorina paarla. The most frequently isolated species were Ceratocystis destructans, Neoscytalidium dimidiatum, and Cytospora californica. Pathogenicity experiments on almond cultivar Nonpareil revealed that Neofusicoccum parvum, Neofusicoccum arbuti, and Neofusicoccum mediterraneum were the most virulent. Botryosphaeriaceae cankers were predominantly found in young orchards and symptoms were most prevalent on the trunks of trees. Ceratocystis canker was most commonly found in mature orchards and associated with symptoms found on trunks or large scaffold branches. This study provides a thorough examination of the diversity and pathogenicity of fungal pathogens associated with branch and trunk cankers of almond in California.

Olive Twig and Branch Dieback in California Caused by Cytospora oleicola and the Newly Described Species Cytospora olivarum sp. nov

Field surveys conducted throughout California olive-growing regions in 2008 and 2009 resulted in a collection of 101 Cytospora-like isolates from olive twig and branch dieback symptoms. Cytospora isolates were isolated from multiple cvs. in different olive orchards in Fresno, Madera, Merced, Napa, Riverside, Santa Barbara, Sonoma, Tulare, and Ventura counties. Taxonomic studies of macro- and microscopic structures along with multigene phylogenetic analyses of the internal transcribed spacer region, including the 5.8S rDNA (ITS1-5.8S-ITS2), and fragments of the translation elongation factor 1-α, beta-tubulin, and actin genes identified two species, Cytospora oleicola and C. olivarum sp. nov. Pathogenicity studies conducted in mature olive trees cvs. Manzanillo and Sevillano showed both species to be pathogenic and able to cause vascular necrosis and cankers in olive branches. This study adds to the current knowledge on the etiology of olive twig and branch dieback and provides new important information for the development of effective control strategies against canker diseases affecting olive in California.

Macrophomina Crown and Root Rot of Pistachio in California

In this study, declining pistachio rootstocks were detected in newly planted commercial pistachio orchards in Kern County, California. Symptoms were characterized by wilted foliage combined with crown rot in the rootstock. From diseased trees, 42 isolates were obtained, and all had similar cultural and morphological characteristics of Macrophomina phaseolina. Analyses of nucleotide sequences of three gene fragments, the internal transcribed spacer region (ITS1-5.8S-ITS2), partial sequences of β-tubulin, and translation elongation factor 1-α (TEF1) confirmed this identification, and 20 representative isolates are presented in the phylogenetic study. Testing of Koch's postulates showed that M. phaseolina, when inoculated to stems and roots of the pistachio rootstocks using mycelial plugs or a microsclerotial suspension, is indeed pathogenic to this host. The widely used clonal University of California Berkeley I (UCBI) rootstock appeared highly susceptible to M. phaseolina, suggesting that this pathogen is an emerging threat to the production of pistachio in California. This study confirmed the association of M. phaseolina with the decline of pistachio trees and represents the first description of this fungus as a crown rot-causing agent of pistachio in California.

Identification and Characterization of Neofabraea kienholzii and Phlyctema vagabunda Causing Leaf and Shoot Lesions of Olive in California

California produces over 95% of the olives grown in the United States. In 2017, California's total bearing acreage for olives was 14,570 hectares producing 192,000 tons of olives valued at $186.6 million. During the early spring of 2016, unusual leaf and shoot lesions were detected in olive trees from superhigh-density orchards in the Northern San Joaquin and Sacramento valleys of California. Affected trees displayed numerous leaf and shoot lesions developing at wounds created by mechanical harvesters. The 'Arbosana' cultivar was highly affected by the disease, whereas the disease was sporadic in 'Arbequina' and not found in 'Koroneiki' cultivar. Two fungal species, Neofabraea kienholzii and Phlyctema vagabunda, were found to be consistently associated with the disease, and Koch's postulates were completed. Species identity was confirmed by morphology and molecular data of the partial large subunit rDNA, the internal transcribed spacer region, and partial beta-tubulin region. The disease signs and symptoms are described and illustrated.

Identification and Pathogenicity of Fungal Species Associated with Canker Diseases of Pistachio in California

A survey was conducted during 2015 and 2016 in pistachio orchards throughout the San Joaquin Valley of California to investigate the occurrence of canker diseases and identify the pathogens involved. Cankers and dieback symptoms were observed mainly in orchards aged >15 years. Symptoms of canker diseases included brown to dark brown discoloration of vascular tissues, wood necrosis, and branch dieback. In total, 58 fungal isolates were obtained from cankers and identified based on multilocus phylogenetic analyses (internal transcribed spacer, glyceraldehyde 3-phosphate dehydrogenase, β-tubulin, calmodulin, actin 1, and translation elongation factor 1α) representing 11 fungal species: Colletotrichum karstii, Cytospora californica, Cytospora joaquinensis, Cytospora parapistaciae, Cytospora pistaciae, Diaporthe ambigua, Didymella glomerata, Diplodia mutila, Neofusicoccum mediterraneum, Phaeoacremonium canadense, and Schizophyllum commune. Pathogenicity tests conducted in the main pistachio cultivars Kerman, Golden Hills, and Lost Hills using the mycelium-plug method indicated that all fungal species were pathogenic to Pistacia vera. All species tested caused cankers in pistachio branches, although virulence among species varied from high to moderate. Overall, N. mediterraneum and Cytospora spp. were the most widespread and virulent species associated with canker diseases of pistachio in California.

Characterization of Fusarium and Neocosmospora Species Associated With Crown Rot and Stem Canker of Pistachio Rootstocks in California

California produces 99.1% of pistachios grown in the United States, and diseases affecting pistachio rootstocks represent a constant challenge to the industry. Field surveys of fungi associated with pistachio rootstocks with symptoms of crown rot and stem canker in three central California counties followed by phylogenetic analyses of translation elongation factor 1-α and second largest subunit of RNA polymerase II gene fragments identified three Fusarium species (Fusarium equiseti, Fusarium oxysporum, and Fusarium proliferatum) and two Neocosmospora species (Neocosmospora falciformis and Neocosmospora solani). F. oxysporum and N. falciformis were the fungal species most frequently recovered from symptomatic pistachio trees. Inoculations of detached twigs of cultivar Kerman pistachio Pioneer Gold I and clonal University of California, Berkeley I (UCBI) rootstocks showed that all five species could colonize pistachio wood and cause vascular discolorations. Pathogenicity tests in potted pistachio trees completed Koch's postulates and confirmed that F. oxysporum, F. proliferatum, N. falciformis, and N. solani were capable of producing rot and discoloration in stems of clonal UCBI rootstocks, the most widely planted pistachio rootstock in California. To our knowledge, this study is the first to present insights into the biodiversity and biology of Fusarium and Neocosmospora species associated with pistachio trees in California.

Identification, Pathogenicity, and Spore Trapping of Colletotrichum karstii Associated with Twig and Shoot Dieback in California

Colletotrichum Corda, 1831 species are well-documented pathogens of citrus that are associated with leaf and fruit anthracnose diseases. However, their role in twig and shoot dieback diseases of citrus has recently become more prominent. Recent surveys of orchards in the Central Valley of California have revealed C. gloeosporioides and a previously undocumented species, C. karstii, to be associated with twig and shoot dieback. Pathogenicity tests using clementine (cv. 4B) indicated that both C. karstii and C. gloeosporioides are capable of producing lesions following inoculation of citrus stems. Pathogenicity tests also revealed C. karstii to be the most aggressive fungal species producing the longest lesions after 15 months. The majority of spores trapped during this study were trapped during or closely following a precipitation event with the majority of spores being trapped from January through May. These findings confirm C. karstii as a new pathogen of citrus in California.

Taxonomic revision and multi-locus phylogeny of the North American clade of Ceratocystis

The North American clade (NAC) of Ceratocystis includes pathogenic species that infect a wide range of woody hosts. Previous phylogenetic analyses have suggested that this clade includes cryptic species and a paraphyletic C. variospora. In this study, we used morphological data and phylogenetic analyses to characterize NAC taxa, including Ceratocystis isolates causing a serious disease of almond trees in California. Phylogenetic analyses based on six gene regions supported two new species of Ceratocystis. Ceratocystis destructans is introduced as the species causing severe damage to almond trees in California, and it has also been isolated from wounds on Populus and Quercus in Iowa. It is morphologically similar to C. tiliae, a pathogen on Tilia and the most recently characterized species in the NAC. Ceratocystis betulina collected from Betula platyphylla in Japan is also newly described and is the sister taxon to C. variospora. Our six-locus phylogenetic analyses and morphological characterization resolved several cryptic species in the NAC.

Neoscytalidium dimidiatum Causing Canker, Shoot Blight and Fruit Rot of Almond in California

Almond trees with trunk and branch cankers were observed in several orchards across almond-producing counties in California. Symptoms of cankers included bark lesions, discoloration of xylem tissues, longitudinal wood necrosis, and extensive gumming. Spur and shoot blight associated with rotted fruit were detected in two orchards in Kern County. The fungus Neoscytalidium dimidiatum was consistently recovered from the various cankers, infected fruit, and blighted shoots and its identity was confirmed based on phylogenetic and morphological studies. Phylogenetic analyses of the internal transcribed spacer, translation elongation factor 1-α, and β-tubulin genes comparing 47 strains from California with reference specimens within the family Botryosphaeriaceae and coupled with detailed morphological observations validated the identity of the pathogenic fungus. Pathogenicity tests conducted in the field using 1- to 2-year-old branches inoculated with mycelium plugs or conidial suspensions and attached fruit inoculated with conidial suspensions fulfilled Koch's postulates. N. dimidiatum appeared highly virulent in almond-producing cankers of up to 22 cm in length within 4 weeks using mycelium plug inoculations as well as severe fruit rot combined with spur blight on the fruit-bearing spurs. This study reports, for the first time, the fungus N. dimidiatum as a pathogen of almond in California causing canker, shoot blight, and fruit rot. Disease symptoms are described and illustrated.

Discovery of Viruses and Virus-Like Pathogens in Pistachio using High-Throughput Sequencing

Pistachio (Pistacia vera L.) trees from the National Clonal Germplasm Repository (NCGR) and orchards in California were surveyed for viruses and virus-like agents by high-throughput sequencing (HTS). Analyses of sequence information from 60 trees identified a novel virus, provisionally named "Pistachio ampelovirus A" (PAVA), in the NCGR that showed low amino acid sequence identity (approximately 42%) compared with members of the genus Ampelovirus (family Closteroviridae). A putative viroid, provisionally named "Citrus bark cracking viroid-pistachio" (CBCVd-pis), was also found in the NCGR and showed approximately 87% similarity to Citrus bark cracking viroid (CBCVd, genus Cocadviroid, family Pospiviroidae). Both PAVA and CBCVd-pis were graft transmissible to healthy UCB-1 hybrid rootstock seedlings (P. atlantica × P. integerrima). A field survey of 123 trees from commercial orchards found no incidence of PAVA but five (4%) samples were infected with CBCVd-pis. Of 675 NCGR trees, 16 (2.3%) were positive for PAVA and 172 (25.4%) were positive for CBCVd-pis by reverse-transcription polymerase chain reaction. Additionally, several contigs across multiple samples exhibited significant sequence similarity to a number of other plant virus species in different families. These findings require further study and confirmation. This study establishes the occurrence of viral and viroid populations infecting pistachio trees.

Molecular phylogeny of Cytospora species associated with canker diseases of fruit and nut crops in California, with the descriptions of ten new species and one new combination

Cytospora species are destructive canker and dieback pathogens of woody hosts in natural and agroecosystems around the world. In this genus, molecular identification has been limited due to the paucity of multi-locus sequence typing studies and the lack of sequence data from type specimens in public repositories, stalling robust phylogenetic reconstructions. In most cases a morphological species concept could not be applied due to the plasticity of characters and significant overlap of morphological features such as spore dimensions and fruiting body characters. In this study, we employed a molecular phylogenetic framework with the inclusion of four nuclear loci (ITS, translation elongation factor 1-alpha, actin, and beta-tubulin) to unveil the biodiversity and taxonomy of this understudied important genus of plant pathogens. Phylogenetic inferences based on 150 Californian isolates revealed 15 Cytospora species associated with branch and twig cankers and dieback of almond, apricot, cherry, cottonwood, olive, peach, pistachio, plum, pomegranate, and walnut trees in California. Of the 15 species recovered in this study, 10 are newly described and typified, in addition to one new combination. The pathogenic status of the newly described Cytospora species requires further investigation as most species were associated with severe dieback and decline of diverse and economically important fruit and nut crops in California.

Botryosphaeriaceae species associated with dieback and canker disease of bay laurel in northern California with the description of Dothiorella californica sp. nov

Members of the Botryosphaeriaceae are cosmopolitan fungi that may exist as seemingly innocuous endophytes or as destructive pathogens of numerous woody hosts, including fruit and nut crops, urban ornamental trees and shrubs, and forest trees. Surveys of bay laurel in northern California have revealed symptoms of dieback and branch canker of unknown aetiology. The goals of this study were to identify and clarify the species of Botryosphaeriaceae associated with these symptoms and to confirm their pathogenicity. To understand the role of members of the Botryosphaeriaceae in the dieback and canker disease of bay laurel, 23 isolates were isolated from symptomatic wood. Phylogenetic analyses of ITS, translation elongation factor 1-α, and beta-tubulin revealed three species: Botryosphaeria dothidea, Neofusicoccum nonquaesitum, and the newly described and typified species Dothiorella californica sp. nov. When select isolates were inoculated to 2- to 3-year-old branches of Umbellularia californica in a natural forest, both B. dothidea and N. nonquaesitum were pathogenic with N. nonquaesitum producing the largest lesions at 12- and 18-months post inoculation, respectively, while Do. californica did not cause wood lesions significantly greater than the mock-inoculated controls. This study represents the first attempt to identify and test the pathogenicity of Botryosphaeriaceae species associated with dieback and canker disease of bay laurel in a northern California forest.

Cryptosphaeria Dieback of Fremont Cottonwood Caused by Cryptosphaeria pullmanensis and C. multicontinentalis in California

Fremont cottonwood is a large and tall tree native to riparian areas in the southwestern United States. It grows along streams, rivers, and wetlands and serves many ecological and socioeconomic functions. In recent years, we observed a severe decline of Fremont cottonwood trees in California. Trees showed branches dying back, with dark-brown internal discoloration and decay of the wood of twigs, branches, or trunks. Eventually, the cambium and the bark were killed, causing a canker. The fungus Cryptosphaeria pullmanensis was isolated consistently from the necrotic wood of branches and twigs. On rare occasion, C. multicontinentalis was also isolated from symptomatic wood. Therefore, we investigated the pathogenicity in Fremont cottonwood of C. pullmanensis and C. multicontinentalis. Koch's postulates were completed in saplings and both species appeared highly virulent, producing internal necrosis and staining of the wood. This study is the first to report Cryptosphaeria dieback of Populus fremontii caused by C. pullmanensis and C. multicontinentalis. Symptoms and signs of this new disease are described and illustrated.

The genus Cryptosphaeria in the western United States: taxonomy, multilocus phylogeny and a new species, C. multicontinentalis

This study investigates the diversity and taxonomy of Cryptosphaeria species occurring in the western United States on the basis of morphological characters and multilocus phylogenetic analyses of the ribosomal internal transcribed spacer region, parts of a β-tubulin gene, the DNA-dependent RNA polymerase II second-largest subunit gene and the nuclear ribosomal large subunit gene. Cryptosphaeria multicontinentalis sp. nov is described from the Sierra Nevada and central coast of California on Populus tremuloides, P. balsamifera subsp. trichocarpa and P. fremontii. Cryptosphaeria pullmanensis is reported from a wide geographic area in the western United States on the main host, P. fremontii. The pathogen C. lignyota is reported for the first time from the Sierra Nevada of California on P. tremuloides. The phylogenetic analyses showed that C. multicontinentalis is a sister species to C. lignyota. Both species were closely related to C. subcutanea and more distantly related to C. pullmanensis. Characteristics of both teleomorph and anamorph of the newly introduced species C. multicontinentalis are described and illustrated.

Pathogenicity of Diatrypaceous Fungi on Grapevines in Australia

In addition to Eutypa lata, which causes Eutypa dieback, numerous other fungi in the Diatrypaceae family have been isolated from diseased grapevines (Vitis vinifera) and other woody hosts. Pathogenicity trials comprising 70 strains of diatrypaceous fungi representing nine species in six genera were conducted to determine whether these fungi, collected in Australia, were pathogenic to grapevines. When inoculated into wounded trunks of 'Cabernet Sauvignon', eight species, including E. lata, E. leptoplaca, Cryptovalsa ampelina, C. rabenhorstii, Eutypella citricola, E. microtheca, Diatrypella vulgaris, and a Diatrype sp. produced necrotic lesions significantly longer than on controls. In addition, all nine species (including a Cryptosphaeria sp.) were reisolated from the margins of developing lesions and at varying distances above and below the point of inoculation. Diatrypaceous fungi were frequently isolated from asymptomatic or otherwise healthy tissue several centimeters ahead of the disease margin. Methods to control diseases associated with diatrypaceous fungi must take into account their propensity to colonize woody tissues ahead of or in the absence of visible symptoms. Current recommendations for the management of Eutypa dieback using remedial surgery and pruning wound protection appear sufficient for the control of the other diatrypaceous fungi included in this study.

Calosphaeria Canker of Sweet Cherry Caused by Calosphaeria pulchella in California and South Australia

California is the second largest sweet cherry producer in the United States with annual revenues up to $200 million. The South Australian cherry industry generates about 10% of Australia's overall production with approximately 1,500 metric tons of cherries produced yearly. In California, perennial canker diseases and subsequent branch dieback are responsible for extensive damage throughout sweet cherry orchards, reducing annual yields and tree longevity. Surveys of cherry orchards and isolation work were conducted in California to identify the main canker-causing agents. Calosphaeria pulchella was the main fungus isolated from cankers, followed by Eutypa lata and Leucostoma persoonii, respectively. Preliminary surveys in cherry orchards in South Australia documented C. pulchella and L. persoonii in cankers. The pathogenicity of C. pulchella in sweet cherry was confirmed following field inoculations of 2- to 3-year-old branches. C. pulchella was able to infect healthy wood and produce cankers with as much virulence as E. lata or L. persoonii. Spore trapping studies were conducted in two sweet cherry orchards in California to investigate the seasonal abundance of C. pulchella spores. Experiments showed that rain and sprinkler irrigation were important factors for aerial dissemination. Finally, this study illustrates the symptoms and signs of the new disease Calosphaeria canker.

Host range, biological variation, and phylogenetic diversity of Eutypa lata in California

The objectives of this study were to investigate the host range of Eutypa lata in the major grape-growing regions in California and to analyze the phenotypic variation and phylogenetic diversity of E. lata isolates. Perithecia of E. lata were found on grapevines, in apricot, almond, cherry, apple, and pear tree orchards, and on ornamentals (oleander) and native plant species (California buckeye, big leaf maple, and willow). Multigene phylogenies of ribosomal DNA internal transcribed spacer, β-tubulin, and RPB2 genes confirmed the identity of E. lata recovered from the various host plants but also revealed sequence differences among isolates. The intraspecific phylogenetic diversity of E. lata did not correspond to geography or source of isolation, and intraspecific groups were not consistent across the different DNA phylogenies. Significant phenotypic variation also was detected among E. lata isolates, including ascospore and conidium length as well as level of aggressiveness on grapevines. Pathogenicity studies proved that all isolates were infectious to grapevine, suggesting that the native vegetation surrounding vineyards can serve as inoculum sources that may constitute an important element in the epidemiology of Eutypa dieback in grapevines.

First Report of Twig and Branch Dieback of English Walnut (Juglans regia) Caused by Neofusicoccum mediterraneum in California

California produces 99% of the U.S. English walnut crop with more than 30 cultivars on ~89,000 ha. Production for 2008 was ~436,000 tons with a value of $527 million. In early summer of 2009 and 2010, branch and twig dieback of English walnut (Juglans regia L.) was detected in orchards in Yolo County and submitted to our diagnostic laboratory. Disease symptoms included death of twig tips, branch dieback, wood lesions, and canker formation. Pycnidia were embedded within the bark of dead twigs. Conidia from pycnidia were hyaline, fusoid-ellipsoidal, widest usually in the middle, and 21 to 24 (-27) × 5 to 7 μm (n = 30). Isolations from cankers yielded the fungus Neofusicoccum mediterraneum Crous, M.J. Wingf. & A.J.L. Phillips (1). Fungal colonies of N. mediterraneum grew light olive green to gray on potato dextrose agar, becoming dark olive green with age. Identification of fungal isolates was confirmed by sequence comparison of Californian isolates with ex-type (CBS 121558) sequences in GenBank (3) using the internal transcribed spacer region of the rDNA, a portion of the β-tubulin gene, and part of the translation elongation factor. Sequences of Californian isolates (GenBank HM443604-HM443609) were identical to the ex-type sequences for all three genes. Previous studies in California reported the occurrence and pathogenicity of N. mediterraneum into grapevine (Vitis vinifera L.) (3) and almond trees (Prunis dulcis L.) (2). Inderbitzin et al (2) investigated the host range of N. mediterraneum in California and reported the occurrence of pycnidia on English walnut trees. However, this study did not investigate the pathogenicity of N. mediterraneum on this host. In the current study, the pathogenicity of N. mediterraneum in J. regia cvs. Hartley and Chandler was investigated in an orchard at UC Davis using two fungal isolates. Pathogenicity tests were performed by inoculating eight 2- to 4-year-old branches of mature J. regia trees. Inoculations were made in June 2009 with a 5-mm cork borer to remove bark and placing an 8-day-old 5-mm-diameter agar plug bearing fresh mycelium of the fungal isolates directly into the fresh wound, mycelium side down. An additional eight branches of each cultivar were inoculated with noncolonized agar plugs to serve as controls. Inoculated wounds were covered with petroleum jelly and wrapped with Parafilm to retain moisture. Branches were harvested after 10 months of incubation and checked for canker development. The extent of vascular discoloration was measured in each branch and isolations were made from the edge of discolored tissue to confirm Koch's postulates. Statistical analyses were performed with analysis of variance and Dunnett's t-test to assess significant differences in the extent of vascular discoloration between inoculations with N. mediterraneum and the control. Necrosis length for the two isolates averaged 131.5 mm in Hartley branches and 110 mm in the Chandler branches. Average necrosis lengths in the control branches were 18.5 mm and 16.7 mm, respectively, significantly lower (P < 0.05) than the average necrosis length found in branches inoculated with N. mediterraneum. Fungal recovery was 75% in both varieties. To our knowledge, this study is the first report of N. mediterraneum as a pathogen of J. regia trees in California. References: (1) P. W. Crous et al. Fungal Planet 19, 2007. (2) P. Inderbitzin et al. Mycologia. Online publication. doi:10.3852/10-006, 2010. (3) J. R. Úrbez-Torres et al. Plant Dis. 94:785, 2010.

First Report of Calosphaeria pulchella Associated with Branch Dieback of Sweet Cherry Trees in California

California is the second largest sweet cherry producer in the United States with approximately 10,800 ha and an average annual crop value of approximately $150 million. Perennial canker diseases constitute major threats to the cherry industry productivity by reducing tree health, longevity, and yields. During the course of summer 2006, we observed severe limb and branch dieback of sweet cherry (Prunus avium L.) in San Joaquin, San Benito, Contra Costa, and Stanislaus counties of California. Isolation from diseased branches repeatedly yielded the fungus Calosphaeria pulchella (Pers.: Fr.) J. Schröt. (1,2). Cankers and vascular necroses had developed in tree limbs and branches, generally initiating from the heart wood and later spreading into the sapwood. External symptoms of disease may be unapparent throughout the early stages of infection, particularly in large diameter shoots. Older infections often appeared as wilted leaves. Branches and trunks affected with cankers from which C. pulchella was isolated also generally bore perithecia of C. pulchella beneath the periderm. Perithecia were nonstromatic and arranged in dense, circinate groups, with elongated necks converging radially and fissuring the periderm. Asci were unitunicate, clavate, and 45 to 55 × 5 to 5.5 μm. Ascospores were allantoid to suballantoid, hyaline, and 5 to 6 × 1 μm. Colonies on potato dextrose agar (PDA) were dark pink to red in their center with a white margin. Conidia were hyaline, allantoid to oblong-ellipsoidal, and (3-) 4 to 6 (-9) × 1.5 to 2 (-2.5) μm. Identification of C. pulchella isolates also was confirmed by sequence comparison in GenBank database using the internal transcribed spacer region (ITS1-5.8S-ITS2) of the rDNA. Sequences of California isolates shared 100% similarity with C. pulchella reference isolate CBS 115999 (EU367451) (2). ITS sequences of the California isolates used in this study were deposited into GenBank (Nos. HM237297 to HM237300). Pathogenicity of four isolates recovered from the margin of active cankers was determined by branch inoculations. In December 2006, 2- to 4-year-old twigs of P. avium cv. Bing were inoculated with a 5-mm cork borer to remove bark and by placing an agar plug from the growing margin of 8-day-old colonies directly into the fresh wound, mycelium side down. Ten branches per isolate were inoculated. Ten control shoots were inoculated with noncolonized agar plugs. Inoculations were covered with vaseline and wrapped with Parafilm to retain moisture. Branches were harvested in July 2007 and taken to the laboratory to be examined for canker development, and the extent of vascular discoloration in each branch was assessed. Isolations from the edge of discolored tissue were conducted to fulfill Koch's postulates. After 8 months, C. pulchella was reisolated from 100% of the inoculated branches. Length of vascular discoloration averaged 62.5 mm in branches inoculated with the four C. pulchella isolates and 16.5 mm in the control twigs. No fungi were reisolated from the slightly discolored tissue of the controls. To our knowledge, this study constitutes the first report of C. pulchella as a pathogen of sweet cherry trees in California. References: (1) M. E. Barr. Mycologia 77:549, 1985. (2) U. Damm et al. Persoonia 20:39, 2008.

Pathogenicity of Diatrypaceae Species in Grapevines in California

Diatrypaceous fungi have been isolated from cankered wood of grapevines (Vitis vinifera) in California. However, the pathogenicity of these fungi and their potential to cause diseases in grapevine was unknown. A series of pathogenicity tests were conducted to determine if these fungi were grapevine pathogens. In all experiments, species of the family Diatrypaceae were re-isolated from the margins of developing lesions, although frequency of re-isolation and average length of vascular discolorations varied among isolates. Cryptovalsa ampelina, Diatrype stigma, and Eutypa leptoplaca were capable of colonizing dormant canes and causing vascular necrosis. Cryptosphaeria pullmanensis, C. ampelina, D. stigma, Diatrype whitmanensis, and E. leptoplaca infected and caused lesions in green shoots of the new vegetative growth. Diatrype oregonensis and Diatrypella verrucaeformis isolates did not produce lesions that were significantly different from those produced in the control shoots and canes. This suggests that D. oregonensis and D. verrucaeformis fungi may be saprophytic rather than pathogenic to grapevine.

Identification and characterization of Eutypa leptoplaca, a new pathogen of grapevine in Northern California

Although Eutypa lata is the main agent of Eutypa dieback of grapevine, another species of Eutypa has been isolated from diseased grapevines in Northern California. Stromata of this recently discovered Eutypa were also collected from Acer macrophyllum, A. negundo, and Fraxinus latifolia in the vicinity of vineyards, and appeared commonly on Umbellularia californica in some mixed-evergreen forests of Napa and Sonoma counties. This second species of Eutypa was distinguished from E. lata because of the sulcate ostiole of the perithecium and smaller ascospores. A morphological comparison with type specimens revealed identical features between the Californian isolates and E. leptoplaca sensu Rappaz (1987). This identification was confirmed through phylogenetic analyses of Eutypa spp. based on the complete sequence of the internal transcribed spacer (ITS) of the rDNA and partial sequence of the beta-tubulin gene. These analyses also separated collections of E. maura, E. sparsa, E. lejoplaca, E. tetragona, E. leptoplaca and E. lata, confirming the previously proposed species concepts. The pathogenicity of E. leptoplaca on grapevine was established using isolates collected from Vitis vinifera, U. californica, and A. macrophyllum. The importance of E. leptoplaca in relation to Eutypa dieback and its role as a necrotrophic pathogen are discussed.