Evolutionary transitions between beneficial and phytopathogenic Rhodococcus challenge disease management.

Understanding how bacteria affect plant health is crucial for developing sustainable crop production systems. We coupled ecological sampling and genome sequencing to characterize the population genetic history of Rhodococcus and the distribution patterns of virulence plasmids in isolates from nurseries. Analysis of chromosome sequences shows that plants host multiple lineages of Rhodococcus, and suggested that these bacteria are transmitted due to independent introductions, reservoir populations, and point source outbreaks. We demonstrate that isolates lacking virulence genes promote beneficial plant growth, and that the acquisition of a virulence plasmid is sufficient to transition beneficial symbionts to phytopathogens. This evolutionary transition, along with the distribution patterns of plasmids, reveals the impact of horizontal gene transfer in rapidly generating new pathogenic lineages and provides an alternative explanation for pathogen transmission patterns. Results also uncovered a misdiagnosed epidemic that implicated beneficial Rhodococcus bacteria as pathogens of pistachio. The misdiagnosis perpetuated the unnecessary removal of trees and exacerbated economic losses.

Bacterial Canker of Sweet Cherry in Oregon-Infection of Horticultural and Natural Wounds, and Resistance of Cultivar and Rootstock Combinations.

This study was done to (i) compare seven types of natural or horticultural injuries and wounds for incidence, severity, and mortality of infection of sweet cherry (Prunus avium) by Pseudomonas syringae pv. syringae; (ii) determine the relative resistance to bacterial canker of 14 cultivar-rootstock combinations; (iii) determine if P. syringae pv. syringae is transmitted by contaminated pruning tools; and (iv) determine if summer and winter pruning cuts become resistant to infection. Infection occurred at all of the seven types of injury and wound sites on both cvs. Sunset Bing and Golden Heart. Infection of inoculated wounds made in spring and summer (heading cuts when trees were planted, scoring cuts, and summer pruning) resulted in the greatest canker incidence and severity. Inoculation of heading cuts resulted in the highest tree mortality (86%). 'Bing' and 'Sweetheart' were the most susceptible cultivars while 'Regina' and 'Rainier' appeared to be more resistant. Bing trees had the highest mortality of any cultivar with 70% dead at the end of the 3-year study. Canker severity of the three rootstocks varied considerably but mortality was greatest for trees on Gisela 6 (77%). Bacterial canker was not transmitted in summer or winter by cutting through active cankers, then immediately using the same pruning tool to make heading cuts on healthy trees. Heading cuts became resistant to infection after about 1 week in summer and 3 weeks in winter. Results are discussed as part of an integrated management program for bacterial canker of sweet cherry.

Description of Cryptosporiopsis kienholzii and species profiles of Neofabraea in major pome fruit growing districts in the Pacific Northwest USA.

The objectives of this study were i) to give a taxonomic description of a fungus phylogenetically related to Neofabraea and assign the name Cryptosporiopsis kienholzii to this fungus, ii) to expand previous Neofabraea species profiles from infected apple and pear fruit collected from major pome fruit production districts in Oregon and Washington, and iii) to determine the sensitivity of Neofabraea alba, Neofabraea malicorticis, Neofabraea perennans, and C. kienholzii to a range of fungicides. A name is given herein to the anamorph of the fungus previously called 'Neofabraea sp. nov.' in the literature, and the fungus is designated as C. kienholzii. The teleomorph of this fungus has never been observed in vivo or in vitro. N. alba, N. perennans, and C. kienholzii accounted for 61.3, 35.6, and 3.1 %, respectively, of 608 isolates obtained from pear fruit and 6.0, 81.3, and 12.7 % of 150 isolates from apple fruit. N. alba was the most common species in Oregon and N. perennans was most common in Washington. N. malicorticis was not found in any of the districts and may be limited to the wet climates west of the Cascade mountain range. C. kienholzii occurs in pome fruit orchards from southern Oregon to North Central Washington, and this is the first report of C. kienholzii in the state of Washington. The four most effective fungicides for control of bull's-eye rot caused by all species were thiabendazole, thiophanate-methyl, pyrimethanil, and pyraclostrobin+boscalid. Other fungicides gave acceptable control of some species of Neofabraea but not others. There was good agreement of the microbioassay with fungicide evaluations using wound-inoculated pear fruit for five of seven fungicides, but the microbioassay was not consistent enough for determination of the sensitivity of Neofabraea species to new fungicides.

Methodology for Determining Relationships Between Inoculum Concentration of Botrytis cinerea and Penicillium expansum and Stem End Decay of Pear Fruit.

The objective of this research was to determine quantitative relationships between incidence of stem end decay of pear fruit and inoculum concentration of Botrytis cinerea and Penicillium expansum using dry conidia applied to pear fruit in a settling tower. Five concentrations of conidia were applied to pear fruit, fruit were stored at -1°C for 8 months, and stem end decay was evaluated. In addition, conidia were washed from the surface of inoculated fruit, and DNA was extracted and quantified with real-time polymerase chain reaction (PCR). The linear regression relationships between percent stem end gray mold and B. cinerea conidia per liter of air or per square centimeter of fruit surface were significant (P = 0.01). At the highest inoculum dose introduced into the settling tower, conidia per liter of air, conidia per square centimeter, and percent stem end gray mold at 8 months after inoculation were 12, 31, and 39, respectively for 2000 and 6, 33, and 67, respectively for 2001. Similarly, the linear regression relationships between percent stem end blue mold and P. expansum conidia per liter of air or per square centimeter of fruit surface were significant (P = 0.01 and 0.05, respectively). At the highest inoculum dose introduced into the settling tower, conidia per square centimeter and percent stem end blue mold at 8 months after inoculation were 39 and 26, respectively for 2000 and 66 and 23, respectively for 2003. Real-time PCR provided a rapid, quantitative measure of B. cinerea and P. expansum DNA on pear fruit surfaces. Because of possible year-to-year shifts in susceptibility of fruit to decay, disease incidence:inoculum dose relationships may be of most value compared within years rather than across years. This would facilitate comparison of decay risk among orchards in order to determine which fruit is most suitable for long-term storage.

A five-gene phylogeny of Pezizomycotina.

Pezizomycotina is the largest subphylum of Ascomycota and includes the vast majority of filamentous, ascoma-producing species. Here we report the results from weighted parsimony, maximum likelihood and Bayesian phylogenetic analyses of five nuclear loci (SSU rDNA, LSU rDNA, RPB1, RPB2 and EF-lalpha) from 191 taxa. Nine of the 10 Pezizomycotina classes currently recognized were represented in the sampling. These data strongly supported the monophyly of Pezizomycotina, Arthoniomycetes, Eurotiomycetes, Orbiliomycetes and Sordariomycetes. Pezizomycetes and Dothideomycetes also were resolved as monophyletic but not strongly supported by the data. Lecanoromycetes was resolved as paraphyletic in parsimony analyses but monophyletic in maximum likelihood and Bayesian analyses. Leotiomycetes was polyphyletic due to exclusion of Geoglossaceae. The two most basal classes of Pezizomycotina were Orbiliomycetes and Pezizomycetes, both of which comprise species that produce apothecial ascomata. The seven remaining classes formed a monophyletic group that corresponds to Leotiomyceta. Within Leotiomyceta, the supraclass clades of Leotiomycetes s.s. plus Sordariomycetes and Arthoniomycetes plus Dothideomycetes were resolved with moderate support.

Inoculum Sources of Botrytis cinerea Important to Pear Orchards in Oregon.

Botrytis cinerea was capable of colonizing and persisting in tissue pieces of six common weed species found in pear orchards in Oregon from midsummer until pear harvest in early September. Sporulation occurred on blackberry mummies in orchard perimeters and ranged from 5,700 to 55,000 conidia per mummy at pear harvest. Conidia of B. cinerea also were observed on fresh blackberry fruit in 2 of 3 years. Sclerotia were present on only a few of the naturally infected pear fruit on the orchard floor through November; however, sclerotia production increased greatly between mid-November and mid-December. Over 90% of sclerotia from naturally infected, overwintered fruit germinated in the laboratory when collected 6 to 8 months after infection. Sclerotia formed on pear fruit inoculated with 28 different paired combinations of 22 isolates in the laboratory. Viability of sclerotia in inoculated pear fruit that overwintered on the orchard floor was 44 to 59% in March and April, and then declined steadily to about 25% at pear harvest. Germination of sclerotia was both sporogenic and myceliogenic. No apothecia were observed in the field or laboratory. An integrated approach to control is needed to deal with these multiple sources of potential inoculum.