The rhizosphere microbiome plays a role in the resistance to soil-borne pathogens and nutrient uptake of strawberry cultivars under field conditions.

Microbial-root associations are important to help plants cope with abiotic and biotic stressors. Managing these interactions offers an opportunity for improving the efficiency and sustainability of agricultural production. By characterizing the bacterial and archaeal community (via 16S rRNA sequencing) associated with bulk and rhizosphere soil of sixteen strawberry cultivars in two controlled field studies, we explored the relationships between the soil microbiome and plant resistance to two soil-borne fungal pathogens (Verticillium dahliae and Macrophomina phaseolina). Overall, the plants had a distinctive and genotype-dependent rhizosphere microbiome with higher abundances of known beneficial bacteria such as Pseudomonads and Rhizobium. The rhizosphere microbiome played a significant role in the resistance to the two soil-borne pathogens as shown by the differences in microbiome between high and low resistance cultivars. Resistant cultivars were characterized by higher abundances of known biocontrol microorganisms including actinobacteria (Arthrobacter, Nocardioides and Gaiella) and unclassified acidobacteria (Gp6, Gp16 and Gp4), in both pathogen trials. Additionally, cultivars that were resistant to V. dahliae had higher rhizosphere abundances of Burkholderia and cultivars resistant to M. phaseolina had higher abundances of Pseudomonas. The mechanisms involved in these beneficial plant-microbial interactions and their plasticity in different environments should be studied further for the design of low-input disease management strategies.

Fungicide Sensitivity in Strawberry Powdery Mildew Caused by Podosphaera aphanis in California.

Field observations suggest that reduced fungicide sensitivity exists in field populations of Podosphaera aphanis, the causal agent of strawberry powdery mildew (SPM). SPM is one of the most common diseases in strawberry production and is controlled with foliar fungicide applications. This study characterizes the sensitivity of 19 P. aphanis isolates to the most common fungicides used against SPM in California. Isolates were collected from commercial fruit production fields in Oxnard, Ventura, Santa Maria, Salinas, and Watsonville and from a plant nursery in Balico, California. Healthy, unfurled strawberry leaves (cultivar Monterey) free of visual disease symptoms were removed from actively growing plants and treated with one of six commercially formulated fungicides at the minimum labeled rate and inoculated with conidia of P. aphanis. Inoculated leaves were incubated at 20°C under 16/8 h of day/night lighting and assessed for disease incidence after 14 days. Pathogen growth on the treated leaflets constituted a measure of insensitivity to the fungicide. The six fungicide treatments and their average disease incidence on treated leaves for the 19 isolates are penthiopyrad (51.4%), quinoxyfen (41.5%), myclobutanil (39.8%), trifloxystrobin (19.8%), cyflufenamid (19.3%), and fluopyram + trifloxystrobin (3.5%). The average disease incidence for the trifloxystrobin treatment was raised significantly by two isolates considered to be resistant to the product (disease incidence >66.6%). Two isolates collected from organic production systems were sensitive to all fungicides. We document compromised fungicide efficacy due to resistance to most of the fungicides currently used for control of SPM in California. This is the first report of resistance in P. aphanis to any fungicide in California and the first report of resistance in P. aphanis to penthiopyrad and quinoxyfen worldwide.

Strawberries at the Crossroads: Management of Soilborne Diseases in California Without Methyl Bromide.

Strawberry production has historically been affected by soilborne diseases such as Verticillium wilt. This disease was a major limiting factor in strawberry production in California in the 1950s and was the main reason that preplant soil fumigation with methyl bromide (MB) was developed in the late 1950s. MB fumigation was so successful that over 90% of the commercial strawberry fruit production in California utilized this technique. However, MB was subsequently linked to ozone depletion, and its use was phased out in 2005. The California strawberry industry was awarded exemption to the full phase-out until 2016, when all MB use in strawberry fruit production was prohibited. MB use continues in strawberry nurseries under an exemption to prevent spread of nematodes and diseases on planting stock. This review examines the impact of the MB phase-out on the California strawberry industry and evaluates the outlook for the industry in the absence of one of the most effective tools for managing soilborne diseases. New soilborne diseases have emerged, and historically important soilborne diseases have reemerged. Registration of new fumigants has been difficult and replacement of MB with a new and effective alternative is unlikely in the foreseeable future. Thus, crop losses due to soilborne diseases are likely to increase. Host plant resistance to soilborne diseases has become a top priority for strawberry breeding programs, and cultivars are increasingly selected for their resistance to soilborne diseases. The intelligent integration of a variety of management tactics is necessary to sustain strawberry production in California.

Within-Season Shift in Fungicide Resistance Profiles of Botrytis cinerea in California Strawberry Fields.

Sensitivity of Botrytis cinerea to seven fungicide chemical classes was determined for 888 isolates collected in 2016 from 47 California strawberry fields. Isolates were collected early season (minimum fungicide exposure) and late season (maximum fungicide exposure) from the same planting block in each field. Resistance was determined using a mycelial growth assay, and variable frequencies of resistance were observed to each fungicide at both sampling times (early season %, late season %): boscalid (12, 35), cyprodinil (12, 46), fenhexamid (53, 91), fludioxonil (1, 4), fluopyram (2, 7), iprodione (25, 8), isofetamid (0, 1), penthiopyrad (8, 25), pyraclostrobin (77, 98), and thiophanate-methyl (81, 96). Analysis of number of chemical class resistances (CCRs) revealed an increasing shift in CCR from the early to late season. Phenotypes of 40 isolates that were resistant or sensitive to different chemical classes were associated with presence or absence of mutations in target genes. Fungicide-resistance phenotypes determined in the mycelial growth assay closely matched (93.8%) the genotype observed. Previously described resistance-conferring mutations were found for each gene. A survey of fungicide use from 32 of the sampled fields revealed an average of 15 applications of gray mold-labeled fungicides per season at an average interval of 12 days. The most frequently applied fungicides (average number of applications during the 2016 season) were captan (7.3), pyraclostrobin (2.5), cyprodinil (2.3), fludioxonil (2.3), boscalid (1.8), and fenhexamid (1.4). Multifungicide resistance is widespread in California. Resistance management tactics that reduce selection pressure by limiting fungicide use, rotating among Fungicide Resistance Action Committee codes, and mixing/rotating site-specific fungicides with multisite fungicides need to be improved and implemented.

Natamycin, a New Biofungicide for Managing Crown Rot of Strawberry Caused by QoI-Resistant Colletotrichum acutatum.

Anthracnose crown rot of strawberry, caused by Colletotrichum acutatum, is an important disease affecting California nursery and fruit production. Preplant dip treatments of transplants with fludioxonil-cyprodinil or azoxystrobin are industry standards for managing the disease and have been used extensively. Following reports of reduced efficacy of azoxystrobin in the field, high levels of quinone outside inhibitor (QoI) resistance were detected in California isolates of the pathogen. Resistance was associated with the G143A mutation in the cytochrome b gene, similar to a previous report from Florida, and there were no detected fitness penalties in pathogenicity or virulence. Therefore, several alternative fungicides were investigated in laboratory and field studies. Subsequently, the new biofungicide natamycin was identified. Baseline sensitivities of 74 isolates of C. acutatum to natamycin were determined to be unimodal, with a range from 0.526 to 1.996 µg/ml (mean 0.973 µg/ml). Although this toxicity was considerably lower than that of azoxystrobin (using sensitive isolates), fludioxonil, or cyprodinil, dip treatments of transplants with natamycin (at 500 or 1000 mg/liter) were highly effective. Disease severity and plant mortality in field studies with inoculated transplants were reduced to similarly low levels as treatments containing fludioxonil, whereas azoxystrobin failed in inoculations with QoI-resistant isolates of C. acutatum. Fruit yield was also significantly increased by natamycin as compared with the inoculated control. Differences in disease susceptibility were observed among cultivars evaluated, with Monterey and Portola more susceptible than Fronteras. Natamycin has a unique mode of action that is different from other fungicides registered on strawberry and, based on this research, was registered in the United States as a preplant, biofungicide dip treatment of strawberry transplants for management of anthracnose crown rot.

Epidemiology and population biology of Pseudoperonospora cubensis: a model system for management of downy mildews.

The resurgence of cucurbit downy mildew has dramatically influenced production of cucurbits and disease management systems at multiple scales. Long-distance dispersal is a fundamental aspect of epidemic development that influences the timing and extent of outbreaks of cucurbit downy mildew. The dispersal potential of Pseudoperonospora cubensis appears to be limited primarily by sporangia production in source fields and availability of susceptible hosts and less by sporangia survival during transport. Uncertainty remains regarding the role of locally produced inoculum in disease outbreaks, but evidence suggests multiple sources of primary inoculum could be important. Understanding pathogen diversity and population differentiation is a critical aspect of disease management and an active research area. Underpinning advances in our understanding of pathogen biology and disease management has been the research capacity and coordination of stakeholders, scientists, and extension personnel. Concepts and approaches developed in this pathosystem can guide future efforts when responding to incursions of new or reemerging downy mildew pathogens.

Relationships of Preharvest Weather Conditions and Soil Factors to Susceptibility of Sweetpotato to Postharvest Decay Caused by Rhizopus stolonifer and Dickeya dadantii.

Postharvest soft rots of sweetpotato caused by Rhizopus stolonifer (Rhizopus soft rot) and Dickeya dadantii (bacterial root rot) occur sporadically and can result in significant losses. A 3-year field study related preharvest conditions, including soil texture, chemistry, and fertility; air temperature; soil temperature and moisture; and various cultural practices (153 total variables), to postharvest susceptibility to both diseases in 75 sweetpotato fields in North Carolina and 63 sweetpotato fields in Louisiana. Storage roots were sampled from each field, cured, stored, and inoculated with each pathogen after 100 to 120 days in storage. Disease susceptibility was measured as incidence of diseased storage roots 10 days following inoculation. There was wide variation from field to field in incidence of both diseases (0 to 100% for Rhizopus soft rot and 5 to 95% for bacterial root rot) in both states in each year. Correlations between disease incidence and each of the preharvest variables revealed numerous significant correlations but the variables that correlated with disease incidence were different between North Carolina and Louisiana. Models for both diseases were built by first using forward stepwise regression to identify variables of interest, followed by a mixed-model analysis to produce a final reduced model. For North Carolina fields, postharvest Rhizopus soft rot susceptibility was described by the percentage of the soil cation exchange capacity occupied by calcium, amount of plant-available soil phosphorus, percent soil humic matter, mean air temperature, mean volumetric soil moisture at 40 cm in depth, and mean soil temperature at 2 cm in depth. Postharvest bacterial soft rot susceptibility was described by soil pH and the number of days of high soil temperature late in the season. For Louisiana fields, Rhizopus soft rot susceptibility was described by a complex of variables, including late-season air and soil temperature and late-season days of extreme soil moisture. For bacterial root rot, days of low air temperature and days of high soil temperature late in the season as well as days of low soil moisture best described variation. Although the influence of preharvest variables on postharvest susceptibility was profound for each disease, the complexity of factors involved and differences between the data for the two states makes development of a predictive system extremely difficult.

Resurgence of Cucurbit Downy Mildew in the United States: A Watershed Event for Research and Extension.

In 2004, an outbreak of cucurbit downy mildew (CDM) caused by the oomycete Pseudoperonospora cubensis (Berk. & M. A. Curtis) Rostovzev resulted in an epidemic that stunned the cucumber (Cucumis sativus L.) industry in the eastern United States. The disease affects all major cucurbit crops, including cucumber, muskmelon, squashes, and watermelon. Although the 2004 epidemic began in North Carolina, the cucumber crop from Florida to the northern growing regions in the United States was devastated, resulting in complete crop loss in several areas. Many cucumber fields were abandoned prior to harvest. The rapid spread of the disease coupled with the failure of fungicide control programs surprised growers, crop consultants, and extension specialists. The epidemic raised several fundamental questions about the potential causes for the resurgence of the disease. Some of these questions revolved around whether the epidemic would recur in subsequent years and the possible roles that changes in the host, pathogen, and environment may have played in the epidemic.

Influence of preceding crop on wireworm (Coleoptera: Elateridae) abundance in the coastal plain of North Carolina.

Three studies were conducted to determine the effect of preceding crop on wireworm (Coleoptera: Elateridae) abundance in the coastal plain of North Carolina. In all three studies, samples of wireworm populations were taken from the soil by using oat, Avena sativa L., baits. Treatments were defined by the previous year's crop and were chosen to reflect common crop rotations in the region. Across all three studies, eight wireworm species were recovered from the baits: Conoderus amplicollis (Gyllenhal), Conoderus bellus (Say), Conoderus falli (Lane), Conoderus lividus (Degeer), Conoderus scissus (Schaeffer), Conoderus vespertinus (F.), Glyphonyx bimarginatus (Schaeffer), and Melanotus communis (Gyllenhal). The effect of corn, Zea mays L.; cotton, Gossypium hirsutum L.; fallow; soybean, Clycine max (L.) Merr.; sweet potato, Ipomoea batatas (L.) Lam.; and tobacco (Nicotiana spp.) was evaluated in a small-plot replicated study. M. communis was the most frequently collected species in the small-plot study and was found in significantly higher numbers following soybean and corn. The mean total number of wireworms per bait (all species) was highest following soybean. A second study conducted in late fall and early spring assessed the abundance of overwintering wireworm populations in commercial fields planted to corn, cotton, peanut (Arachis hypogaea L.), soybean, sweet potato, and tobacco in the most recent previous growing season. C. lividus was the most abundant species, and the mean total number of wireworms was highest following corn and soybean. A survey was conducted in commercial sweet potato in late spring and early summer in fields that had been planted to corn, cotton, cucurbit (Cucurbita pepo L.), peanut, soybean, sweet potato, or tobacco in the most recent previous growing season. C. vespertinus was the most abundant species, and the mean total number of wireworms per bait was highest following corn.

Permanent Genetic Resources added to Molecular Ecology Resources Database 1 May 2009-31 July 2009.

This article documents the addition of 512 microsatellite marker loci and nine pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Alcippe morrisonia morrisonia, Bashania fangiana, Bashania fargesii, Chaetodon vagabundus, Colletes floralis, Coluber constrictor flaviventris, Coptotermes gestroi, Crotophaga major, Cyprinella lutrensis, Danaus plexippus, Fagus grandifolia, Falco tinnunculus, Fletcherimyia fletcheri, Hydrilla verticillata, Laterallus jamaicensis coturniculus, Leavenworthia alabamica, Marmosops incanus, Miichthys miiuy, Nasua nasua, Noturus exilis, Odontesthes bonariensis, Quadrula fragosa, Pinctada maxima, Pseudaletia separata, Pseudoperonospora cubensis, Podocarpus elatus, Portunus trituberculatus, Rhagoletis cerasi, Rhinella schneideri, Sarracenia alata, Skeletonema marinoi, Sminthurus viridis, Syngnathus abaster, Uroteuthis (Photololigo) chinensis, Verticillium dahliae, Wasmannia auropunctata, and Zygochlamys patagonica. These loci were cross-tested on the following species: Chaetodon baronessa, Falco columbarius, Falco eleonorae, Falco naumanni, Falco peregrinus, Falco subbuteo, Didelphis aurita, Gracilinanus microtarsus, Marmosops paulensis, Monodelphis Americana, Odontesthes hatcheri, Podocarpus grayi, Podocarpus lawrencei, Podocarpus smithii, Portunus pelagicus, Syngnathus acus, Syngnathus typhle,Uroteuthis (Photololigo) edulis, Uroteuthis (Photololigo) duvauceli and Verticillium albo-atrum. This article also documents the addition of nine sequencing primer pairs and sixteen allele specific primers or probes for Oncorhynchus mykiss and Oncorhynchus tshawytscha; these primers and assays were cross-tested in both species.

Sensitivity of Watermelon Cultigens to Ambient Ozone in North Carolina.

Foliar ozone (O3) injury is common on watermelon grown in eastern North Carolina. During the 2000 and 2001 growing seasons, 93 cultivars and breeding lines (i.e., cultigens) were evaluated for foliar injury caused by ambient levels of O3. One tetraploid, 42 diploid, and 50 triploid cultigens were evaluated. Injury developed on all cultigens in both years, but severity of injury varied among cultigens and between years. Visible foliar injury (percent surface area necrotic or chlorotic) was rated 1 week after the first harvest in both years. Mean injury for all cultigens was 39% in 2000 (range = 16 to 66%) and 20% in 2001 (range = 2.5 to 60%). This corresponded to greater mean seasonal O3 levels (12-h [0900 to 2100 h EST] mean daily O3 concentration between early May and mid-June) in 2000 (58 ppb) than in 2001 (52 ppb). Triploid cultigens were less sensitive to injury than diploid cultigens. Mean injury for all triploids was 31% in 2000 and 16% in 2001, whereas injury for diploids was 47% in 2000 and 25% in 2001. Injury level was consistently negatively correlated with average number of days between transplanting and harvest. Correlations between injury level and yield, fruit size, fruit shape, and fruit sweetness were inconsistent between years and/or insignificant. O3 tolerance in watermelon cultivars should receive increased attention in watermelon breeding programs and in cultivar selection in areas of high O3 pollution.

Influence of Wound Type and Storage Duration on Susceptibility of Sweetpotatoes to Rhizopus Soft Rot.

Susceptibility of stored sweetpotato roots (cvs. Beauregard and Hernandez) to Rhizopus soft rot caused by Rhizopus stolonifer was tested at 4- to 6-week intervals over a storage period of 335 days in 1998-1999 (year 1) and 1999-2000 (year 2). In each experiment, roots were wounded by four methods (puncture, bruise, broken, and scrape), inoculated with freshly harvested spores from 4- to 10-day-old cultures, and compared with a nonwounded but inoculated control for their susceptibility to decay. Roots were totally resistant to infection after harvest for 60 days in year 1 and 30 days in year 2. The bruise wound type was most commonly associated with infection, with disease incidence peaking 100 and 175 days after harvest in years 1 and 2, respectively. Inoculation by the puncture method followed a similar pattern in Hernandez but was ineffective in Beauregard. Following the peak in disease incidence at 100 or 175 days, susceptibility of roots declined to levels comparable to that of freshly harvested roots. This period of heightened susceptibility was longer in Hernandez than in Beauregard. The effects of injury types broken and scrape were more variable and did not show the same trend in both years.

Physiochemical Characterization and Field Assessment of Lettuce Chlorosis Virus.

Lettuce chlorosis virus (LCV) was purified and partially characterized, and polyclonal antisera were produced and used to assess disease in the field. The antisera reliably detected LCV by indirect enzyme-linked immunosorbent assay (ELISA) in Nicotiana benthamiana. In Western blots, the LCV antisera distinguished between LCV and lettuce infectious yellows virus (LIYV)-infected plants. LCV particle lengths in partially purified preparations, as observed by transmission electron microscopy, were variable, with the majority between 750 and 950 nm long. A single, high molecular weight dsRNA and several lower molecular weight dsRNAs were isolated from LCV-infected N. benthamiana. A single RNA isolated from purified virion preparations was estimated to be 8,625 nucleotides long and was suspected to be the genomic RNA of LCV. LCV was present in experimental field plots in Holtville, California, during the lettuce growing seasons of 1995 to 1997. The percentage of symptomatic plants and yield of lettuce heads treated with insecticide, as well as dsRNA and ELISA reactions for the plots, are reported. A dsRNA consistent in size with LCV was isolated from four weed species in the Imperial Valley of California.