Jeffrey K. Stone

Loss of foundation species: consequences for the structure and dynamics of forested ecosystems

In many forested ecosystems, the architecture and functional ecology of certain tree species define forest structure and their species-specific traits control ecosystem dynamics. Such foundation tree species are declining throughout the world due to introductions and outbreaks of pests and pathogens, selective removal of individual taxa, and over-harvesting. Through a series of case studies, we show that the loss of foundation tree species changes the local environment on which a variety of other species depend; how this disrupts fundamental ecosystem processes, including rates of decomposition, nutrient fluxes, carbon sequestration, and energy flow; and dramatically alters the dynamics of associated aquatic ecosystems. Forests in which dynamics are controlled by one or a few foundation species appear to be dominated by a small number of strong interactions and may be highly susceptible to alternating between stable states following even small perturbations. The ongoing decline of many foundation species provides a set of important, albeit unfortunate, opportunities to develop the research tools, models, and metrics needed to identify foundation species, anticipate the cascade of immediate, short- and long-term changes in ecosystem structure and function that will follow from their loss, and provide options for remedial conservation and management.

Simultaneous one-tube quantification of host and pathogen DNA with real-time polymerase chain reaction.

ABSTRACT Phaeocryptopus gaeumannii is a widespread foliar parasite of Douglas-fir. Although normally innocuous, the fungus also causes the defoliating disease Swiss needle cast in heavily infected needles. The extent of P. gaeumannii colonization in Douglas-fir foliage was estimated with real-time quantitative polymerase chain reaction (PCR) using TaqMan chemistry. In order to derive a normalized expression of colonization, both pathogen and host DNA were simultaneously amplified but individually detected by species-specific primers and TaqMan probes labeled with different fluorescent dyes. Detection of host DNA additionally provided an endogenous reference that served as both an internal positive control and adjusted for variation introduced by sample-to-sample differences in DNA extraction and PCR efficiencies. The genes employed for designing the TaqMan probes and primers were beta-tubulin for the pathogen and a LEAFY/FLORICAULA-like gene involved in floral development for the tree host. Both probe/primer sets exhibited high precision and reproducibility over a linear range of 4 orders of magnitude. This eliminated the need to analyze samples in multiple dilutions when comparing lightly with heavily infected needles. Quantification of the fungus within needles was successful as early as 1 month after initial infection. Real-time PCR is the only method currently available to quantify P. gaeumannii colonization early in the first year of the colonization process.

Microbial populations, fungal species diversity and plant pathogen levels in field plots of potato plants expressing theBacillus thuringiensis var.tenebrionis endotoxin

The environmental release of genetically engineered (transgenic) plants may be accompanied by ecological effects including changes in the plant-associated microflora. A field release of transgnic potato plants that produce the insecticidal endotoxin ofBacillus thuringiensis var.tenebrionis (Btt) was monitored for changes in total bacterial and fungal populations, fungal species diversity and abundance, and plant pathogen levels. The microflora on three phenological stages of leaves (green, yellow and brown) were compared over the growing season (sample days 0, 21, 42, 63 and 98) for transgenic potato plants, commercial Russet Burbank potato plants treated with systemic insecticide (Di-Syston) and commercial Russet Burbank potato plants treated with microbialBtt (M-Trak). In addition, plant and soil assays were performed to assess disease incidence ofFusarium spp.,Pythium spp.,Verticillium dahliae, potato leaf roll virus (PLRV) and potato virus Y (PVY). Few significant differences in phylloplane microflora among the plant types were observed and none of the differences were persisent. Total bacterial populations on brown leaves on sample day 21 and on green leaves on sample day 42 were significantly higher on the transgenic potato plants. Total fungal populations on gree leaves on sample day 63 were significantly different among the three plant types; lowest levels were on the commerical potato plants treated with systemic insecticide and highest levels were on the commercial potato plants treated with microbialBtt. Differences in fungal species assemblages and diversity were correlated with sampling dates, but relatively consistent among treatments.Alternaria alternata, a common saprophyte on leaves and in soil and leaf litter, was the most commonly isolated fungus species for all the plant treatments. Rhizosphere populations of the soilborne pathogensPythium spp.,Fusarium spp. andV. dahliae did not differ between the transgenic potato plants and the commercial potato plants treated with systemic insecticide. The incidence of tuber infection at the end of the growing season by the plant pathogenV. dahliae was highest for the transgenic potato plants but this difference was related to longer viability of the transgenic potato plants. This difference in longevity between the transgenic potato plants and the commercial + systemic insecticide potato plants also made comparison of the incidence of PVY and PLRV problematic. Our results indicate that under field conditions the microflora of transgenicBtt-producing potato plants differed minimally from that of chemically and microbially treated commerical potato plants.

Incidence and Impact of Swiss Needle Cast in Forest Plantations of Douglas-fir in Coastal Oregon

An epidemic of Swiss needle cast, caused by the ascomycete Phaeocryptopus gaeumannii, is causing defoliation and growth reductions in Douglas-fir forest plantations along the Oregon Coast. The area of symptomatic plantations has been monitored annually since 1996 by aerial survey; in spring 1999, 119,500 ha were affected. Pathogen and symptom development have also been monitored on nine permanent plots in stands of differing disease severity. Infection levels and symptom severity are greatest in low elevation plantations close to the coast. In areas of severe disease, trees retain only current year needles. Defoliation is proportional to the number of stomata occluded by pseudothecia of the fungus, with needles being shed when about 50% of stomata are occupied, regardless of needle age. Fungus sporulation and premature needle abscission are greatest on the upper branches of trees. Annual application of fungicides increases needle retention significantly. Tree height and diameter growth and total tree volume are reduced by disease, and tree volume is significantly correlated with needle retention on our plot trees. The epidemic continues to be most severe in Douglas-fir plantations established on sites where Sitka spruce and western hemlock or red alder predominated in earlier times.

The internal mycobiota of Juncus spp.: microscopic and cultural observations of infection patterns

Differences in species composition, infection frequencies and fungal colonization were compared in asymptomatic leaves and culms of one annual and three perennial Juncus species in western Oregon. Stagonospora innumerosa was the principal fungus species isolated from culms of the annual, J. bufonius , and two of the perennial, J. effusus and J. patens , host species; Phaeosphaeria juncicola and Drechslera sp. were isolated from leaves of J. bolanderi . Characteristic mechanisms of penetration and colonization corresponding to individual endophyte species were observed in host tissue. Infections limited to a single host epidermal cell were characteristic of S. innumerosa, Drechslera sp. and an unidentified endophyte of J. bufonius . Infections by P. junicola originate in the substomatal cavity followed by limited intercellular colonization of the mesophyll. Cladosporium cladosporioides and Alternaria alternata were isolated at low frequencies from J. effusus, J. patens and J. bolanderi . Infections by C. cladosporioides were restricted to the substomatal chambers, and this species did not colonize internal leaf tissue. Infections of A. alternata were also localized in the substomatal chamber, frequently with an intercellular colonization of the mesophyll tissue.

A climate-based model for predicting geographic variation in swiss needle cast severity in the Oregon coast range.

ABSTRACT Since the early 1990s, Swiss needle cast disease caused by Phaeocryptopus gaeumannii has been increasing in Douglas-fir plantations in the Oregon Coast Range. Considerable variation in disease severity across the affected area often has been noted. We investigated the influence of site microclimate on fungal colonization as a basis for this variation with a combination of seedling inoculation and field studies. Development of P. gaeumannii ascocarps on inoculated seedlings subjected to mist, irrigation, and shading treatments was followed for 10 months. Contrary to expectations, numbers of ascocarps on foliage were negatively correlated with shade and mist and positively correlated with temperature. Numbers of ascocarps on foliage, site temperature, and leaf wetness were monitored over 5 years at nine field sites in the Oregon Coast Range. Factors most highly correlated with ascocarp abundance were winter mean daily temperature and spring cumulative leaf wetness. Predictive models for disease severity on the basis of these correlations were tested against disease and climate data measured at field sites during 2003-2004. A temperature-based disease prediction model was developed in combination with geographical information systems (GIS)-linked climate databases to estimate disease levels across a portion of the Oregon Coast Range. This model can be used for hypothesis testing and as a decision support tool for forest managers.

Recommendations on generic names competing for use in Leotiomycetes (Ascomycota)

In advancing to one scientific name for fungi, this paper treats genera competing for use in the phylogenetically defined class Leotiomycetes except for genera of Erysiphales. Two groups traditionally included in the so-called “inoperculate discomycetes” have been excluded from this class and are also not included here, specifically Geoglossomycetes and Orbiliomycetes. A recommendation is made about the generic name to use in cases in which two or more generic names are synonyms or taxonomically congruent along with the rationale for the recommendation. In some cases the recommended generic name does not have priority or is based on an asexual type species, thus needs to be protected and ultimately approved according to Art. 57.2 of the International Code of Nomenclature for algae, fungi and plants (ICN). A table is presented listing all competing generic names and their type species noting the recommended generic name. New combinations are introduced for the oldest epithet in the recommended genus including Ascocalyx berenice, Ascoconidium purpurascens, Ascocoryne albida, A. trichophora, Blumeriella filipendulae, B. ceanothi, Botrytis arachidis, B. fritillariae-pallidoflori, Calloria urticae, Calycellina aspera, Dematioscypha delicata, Dermea abietinum, D. boycei, D. stellata, Diplocarpon alpestre, D. fragariae, Godroniopsis peckii, Grovesinia moricola, Heterosphaera sublineolata, Hyphodiscus brachyconium, H. brevicollaris, H. luxurians, Leptotrochila campanulae, Monilinia polystroma, Neofabraea actinidae, N. citricarpa, N. vagabunda, Oculimacula aestiva, O. anguioides, Pezicula brunnea, P. californiae, P. cornina, P. diversispora, P. ericae, P. melanogena, P. querciphila, P. radicicola, P. rhizophila, Phialocephala piceae, Pilidium lythri, Rhabdocline laricis, Streptotinia streptothrix, Symphyosirinia parasitica, S. rosea, Unguiculariopsis caespitosa, and Vibrissea laxa.

Eastern filbert blight of European hazelnut. It's becoming a manageable disease.

Hazelnut eastern filbert blight caused by Anisogramma anomala in Oregon, USA, is discussed. The subjects included are the infection biology, ascospores, disease management, host resistance and the prospects in the Oregon industry.

Predicting effects of climate change on Swiss needle cast disease severity in Pacific Northwest forests

Abstract Swiss needle cast of Douglas-fir (Pseudotsuga menziesii) is caused by the ascomycete Phaeocryptopus gaeumannii. Symptoms are foliage chlorosis and premature needle abscission due to occlusion of stomata by the ascocarps of the pathogen, resulting in impaired needle gas exchange. Growth losses of 20%-50% due to Swiss needle cast have been reported for approximately 150 000 ha of Douglas-fir plantations in western Oregon since 1996. In the western Coast Range of Oregon and in New Zealand, winter temperature is strongly correlated with pathogen abundance. Models for predicting disease severity based on winter temperature account for 77% and 78% of the variation in 1- and 2-year-old needles, respectively, for western Oregon sites and approximately 80% for New Zealand. A trend of temperatures increasing by 0.2–0.4 °C during the winter months and spring precipitation increasing by 0.7–1.5 cm/decade since 1970 suggests that regional climate trends are influencing the current distribution and severity of Swiss needle cast disease. Continuing winter temperature increases predicted for the Pacific Northwest of approximately 0.4 °C/decade through 2050 suggest that the severity and distribution of Swiss needle cast is likely to increase in the coming decades as a result of climate change, with significant consequences for Pacific Northwest forests.

Endophytic fungal DNA, the source of contamination in spruce needle DNA

DNA isolated and amplified from higher plants may originate from symbiotic microbes occupying plant tissues. A recent report on the phylogeny of Picea contained sequence data that upon later analysis proved to originate from filamentous ascomycetes. Isolates of endophytic fungi from Picea foliage collected from the same location as the original samples were examined to identify the source of the contaminating DNA. The ITS region of isolates was screened by Southern blotting using an oligonucleotide probe homologous to a unique portion of the reported ‘spruce’ sequences. This study identifies a DNA sequence originally attributed to Picea engelmannii (Engelmann spruce) as Hormonema dematioides, a ubiquitous foliar endophyte of conifers. Infections of plants by endophytic fungi are common and their presence is not revealed by external symptoms. Plant molecular researchers should be aware of the potential for this type of DNA contamination.