Thesis (Ph. D.)--University of Washington. / Bibliography: l. [243]-246.

Ramaria is a genus of epigeous fungi common to the coniferous forests of the Pacific Northwest of North America. The extensively branched basidiocarps and the positive chemical reaction of the context in ferric sulfate are distinguishing characteristics of the genus. The genus is estimated to contain between 200-300 species and is divided into four subgenera, i.) R. subgenus Ramaria, ii.) R. subgenus Laeticolora, iii.) R. subgenus Lentoramaria and iv.) R. subgenus Echinoramaria, according to macroscopic, microscopic and macrochemical characters. The systematics of Ramaria is problematic and confounded by intraspecific and possibly ontogenetic variation in several morphological traits. To test generic and intrageneric taxonomic classifications, two gene regions were sequenced and subjected to maximum parsimony analyses. The nuclear large subunit ribosomal DNA (nuc LSU rDNA) was used to test and refine generic, subgeneric and selected species concepts of Ramaria and the mitochondrial small subunit ribosomal DNA (mt SSU rDNA) was used as an independent locus to test the monophyly of Ramaria. Cladistic analyses of both loci indicated that Ramaria is paraphyletic due to several non-ramarioid taxa nested within the genus including Clavariadelphus, Gautieria, Gomphus and Kavinia. In the nuc LSU rDNA analyses, R. subgenus Ramaria species formed a monophyletic Glade and were indicated for the first time to be a sister group to Gautieria. Ramaria subgenus Ramaria and Gautieria were derived from R. subgenus Laeticolora, which formed a paraphyletic grade that included Gomphus. Ramaria subgenus Lentoramaria species also formed a paraphyletic grade in the nuc LSU rDNA analyses. The Phallales and Clavariadelphus were indicated as sister taxa to the R. stricta complex and Kavinia and R. abietina of R. subgenus Echinoramaria grouped with the basal species, R. pinicola, of R. subgenus Lentoramaria. In the mt SSU rDNA analyses, Gautieria and Gomphus again nested within Ramaria; however, the Phallales were indicated as a sister taxon to the Gomphales. A single evolutionary origin of the terrestrial habit was inferred for Ramaria with the terrestrial species, R. rainierensis, bridging the gap between the lignicolous R. subgenus Lentoramaria and the terrestrial R. subgenus Laeticolora. Species concepts tested included R. amyloidea and R. celerivirescens both of R. subgenus Laeticolora that differ primarily in the presence of clamp connections. The results supported these two taxa as distinct, sister species. These analyses were consistent with the ramarioid morphology as ancestral for the Gomphales with unique derivations of the club, false truffle and gomphoid morphologies. / Graduation date: 2000

Thesis (M.S.)--Oregon State University, 2009. / Printout. Includes bibliographical references (leaves 47-52). Also available on the World Wide Web.

Fungi are integral parts of terrestrial ecosystems. Sporocarps propagate by spreading their spores from fruiting bodies. Their fruiting bodies are looked for both by foragers and conservationists. Potential changes to spore production and the timing of fruit body production could be useful information for both foragers and conservationists. This report uses e-DNA from air filters gathered from Kiruna in northern Sweden to measure shifts in the spore-producing period of the fungal genera Boletus, Morchella, Coprinus, Cantharellus, Hydnellum, and Ramaria, both in terms of amount of spores released and timing of fruit body formation. The start week, peak week of sporulation, estimation of seasonal end, and cumulative sum of spores released for each genus were calculated and then correlated against each other. The relationship between these variables and the climatic variables of temperature and precipitation, both for the current year and previous year were also calculated.    The report found no significant trends in the timing of the start of sporulation, but spore production for both Morchella and Ramaria increased along the timeseries. The report found an overall positive response to increases in precipitation and temperature for the studied genera, with the exception of Boletus, indicating that climate change is unlikely to negatively impact these genera in northern Sweden.

Conselho Nacional de Desenvolvimento Científico e Tecnológico / The pathogenesis of the lesions of the Ramaria flavo-brunnescens poisoning in cattle was studied throughout a retrospective evaluation of selected tissues from nine spontaneous and four experimental cases of the disease. The pathogenesis of lesions observed in the tongue, esophagus, hoof, and tail was investigated analyzing microscopic lesions, histochemical and histochemical-ultrastuctural changes. Histochemical techniques utilized were Masson s Trichrome and Selective Oxidation of Keratin (SOK). The histochemicalultrastuctural study was acomplished throughout the Swift method under transmission electron microscopy. Hair shafts of the tip of the tail were analyzed under polarized light. Lesions of varying degrees of severity were observed. They were more severe in spontaneous than in experimental cases. In the tongue, most microscopic lesions showed keratinization defects, such as loss of the filiform papillae, thinning, irregular stratification, focal lamelar keratinization, and individual cell keratinization (dyskeratosis) in the dorsal epithelium. In the esophagus, there were thinness of superficial epithelium and multifocal ulcers. In the hoof, lesions were in the laminar stratum and characterized by different grades of fusion, shortness, multiple layers of non-keratinized cells in the laminar tip, irregular and discontinuous keratinization with nuclear persistency, individual cell keratinization with citoplasmic vacuolization of keratinocytes of the epidermal laminae. In the skin of the tip of the tail, changes could by separated in follicular wall lesions (affecting the outer [ORS] and the inner root sheets [IRS]) and changes of the hair shaft itself. The main changes observed in the follicular epithelium were disorganization, misalignment, and disceratosis of keratinocytes of the ORS. On tissue sections, main changes in the hair shafts showed irregular contour, tortuousness, and disintegration of shaft. Morphological changes similar to the ones observed on tissue sections and changes in polarizing patterns were seen on polarized light microscopy of hair shafts. Tissue sections stained by Masson s Trichrome technique (with picric acid) revealed defective hard keratinization of filliform papillae, of epidermal lamina of hoof, and of tail tip hair shafts. Sections stained by the SOK technique revealed strong loss of cistine contents, visualized as light staining of these same structures. On the histochemical-ultrastructural study of the hair cuticle, performed throughout the Swift technique under transmission electron microscopy, a low content of cistine was also observed. All changes observed in the keratinized structures studied, mostly in the hard keratin, showed defective keratinization. The morphologic study and the results obtained with SOK and Swift techniques showed that the defective keratinization results of low amounts of sulphur containing amino acids (cystine) in hard keratin structures. This is probably the main pathogenetic mechanism of the lesions observed in R. flavo brunnescens poisoning in cattle. / O estudo da patogênese da intoxicação pelo cogumelo Ramaria flavo-brunnescens em bovinos foi realizado através da avaliação retrospectiva de tecidos selecionados de nove casos espontâneos e quatro casos experimentais. Para a investigação da patogênese das lesões observadas na língua, esôfago, casco e cauda, foram avaliadas as alterações histopatológicas e aspectos histoquímicos e histoquímico-ultra-estruturais das lesões. As técnicas histoquímicas utilizadas foram o Tricrômico de Masson e a oxidação seletiva da ceratina (OSC). O estudo histoquímico-ultra-estrutural foi realizado através da técnica de Swift sob microscopia eletrônica de transmissão. Os pelos da vassoura da cauda foram examinados sob microscopia de luz polarizada. Nos tecidos examinados foram observados diferentes graus e estágios de lesões. Nos bovinos intoxicados espontaneamente as lesões foram mais acentuadas que nos casos experimentais. Na língua, a grande maioria das lesões histopatológicas observadas demonstrou defeitos na ceratinização como desaparecimento das papilas filiformes, adelgaçamento, estratificação irregular, ceratinização lamelar focal e ceratinização individual de células (disceratose) no epitélio de revestimento dorsal. No esôfago observaram-se adelgaçamento do epitélio superficial e úlceras multifocais. Nos cascos havia alterações no estrato laminar, caracterizadas por graus variáveis de fusão, encurtamento, múltiplas camadas de células não-ceratinizadas no topo, ceratinização irregular e descontínua com persistência de núcleos, ceratinização individual e vacuolização citoplasmática de ceratinócitos das lâminas epidérmicas. Na pele da região da vassoura da cauda, as alterações foram divididas em lesões da parede folicular (nas bainhas radicular externa e interna) e alterações nos pelos propriamente ditos. As principais alterações observadas no epitélio folicular foram desorganização, desalinhamento e disceratose de ceratinócitos da bainha radicular externa. Nas seções histológicas, as principais alterações nas hastes pilosas demonstraram contornos irregulares, tortuosidade e desintegração da haste. Alterações morfológicas semelhantes às descritas nas seções histológicas e alterações no padrão de birrefringência foram observadas através do exame polaroscópico dos pelos. Através da técnica do Tricrômico de Masson (com ácido pícrico) observou-se ceratinização dura defeituosa das papilas filiformes linguais, das lâminas epidérmicas do casco e dos pelos da cauda. A técnica da OSC revelou redução marcada do conteúdo de cistina, visualizado como fraca coloração rósea dessas mesmas estruturas. No estudo histoquímico-ultra-estrutural da cutícula pilosa, realizado através da técnica de Swift sob microscopia eletrônica de transmissão, observou-se também um baixo conteúdo de cistina. Todas as alterações observadas nas estruturas ceratinizadas estudadas, mas especialmente nas que sofrem ceratinização dura, revelaram defeitos na ceratinização. Aliando ao estudo morfológico os resultados obtidos através da técnica da OSC e da microscopia eletrônica/técnica de Swift pode-se associar os defeitos na ceratinização a uma redução na quantidade de aminoácidos sulfurados (cistina), principalmente nas estruturas que sofrem ceratinização dura, sendo este provavelmente o principal mecanismo patogenético na intoxicação por R. flavo brunnescens em bovinos.

Two oubreaks of poisoning by the mushroom Ramaria flavo-brunnescens are reported in cattle from two farms located in the municipalities of Santa Maria and São Gabriel, state of Rio Grande do Sul, Brazil during April-May 2005. Out of a total of 180 yearling calves that had access to a pasture with eucalyptus woods, 19 were affected and 10 died. The clinical courses were 8-15 days and clinical signs included depression, weight loss, dehydration, drooling, loosening and loss of the long hairs of the tip of the tail, smoothening of the dorsal surface of the tongue with occasional ulceration, loosening of the corneal encasement of horns, hard and ball-shaped feces covered with a film of mucous, hypopion, hyphema and corneal opacity. Two calves had leucocytosis due to mild regenerative left shift. Nine calves were necropsied. Necropsy findings confirmed the clinical observation and additionaly included fibrinonecrotic esophagitis, mainly in the distal third of the esophageal mucosa. Histopathological changes in the skin of the tail included orthokeratotic hyperkeratosis; hair folicles with irregular contours, and thickening of the tricolemmal keratin layer with occasional formation of keratin plugs, and degeneration and necrosis of the outer root sheath. At the laminar region of the hooves, there was hemorrhage, fibrin and neutrophilic infiltrate in the dermal laminae. hyperplasia of the top of epidermal laminae with irregular keratinization and retention of nuclei; several epidermal laminae were shortened and fused. In the mucosa of the tongue there was thinning of the covering epithelium, atrophy and loss of filiform papillae, multifocal areas of dyskeratosis, and spongiosis of the basal cell layer. In some parts the epithelium was lost and the surface consisted of granulation tissue and mixed inflammatory cell infiltrate. The esophageal mucosae of six calves had varying degree of epithelial necrosis and inflammation. The loss of the covering epithelium revealed an underneath area of granulation tissue with heavy inflammatory infiltrate composed predominantly of neutrophils and macrophages. In six calves there were focal symmetric bilateral areas of malacia observed at the level of obex in the medulla oblongata and affecting the white matter and parts of the dorsal nucleus of the vagus and of the hypoglossal nucleus. Ultrastructurally the keratinocytes of the dorsal epithelial surface of the tongue had decreased numbers of cytokeratin filament bundles. The epidemiology, clinical signs, pathology, and pathogenesis of poisoning by R. flavo-brunnescens in cattle are discussed. Additionally a case of R. flavo-brunnescens poisoning in a horse is described. / Dois surtos de intoxicação pelo cogumelo Ramaria flavo-brunnescens são relatados em bovinos de duas fazendas localizadas nos municípios de Santa Maria e São Gabriel, no Rio Grande do Sul, no período de abril-maio de 2005. De um total de 180 bovinos de sobreano que tiveram acesso a bosques de eucaliptos, 19 adoeceram e 10 morreram. A evolução clínica foi de 8-15 dias e os sinais clínicos incluíam depressão, perda de peso, desidratação, salivação excessiva, afrouxamento e perda dos pêlos longos da cauda, alisamento da superfície dorsal da língua com ocasional ulceração, afrouxamento do estojo córneo dos chifres, fezes em forma de cíbalos e recobertas por película de muco, hipópion, hifema e opacidade da córnea. Dois novilhos tinham leucocitose devido a leve desvio regenerativo à esquerda. Os achados de necropsia confirmaram as observações clínicas e adicionalmente incluíam esofagite fibrinonecrótica, principalmente no terço distal do esôfago. Alterações histopatológicas na pele da cauda incluíam hiperqueratose ortoqueratótica, folículos pilosos com contornos irregulares, espessamento da camada de queratina tricolemal e formação ocasional de tampões de queratina; degeneração e necrose da bainha radicular externa também era observada. Nos cascos havia hemorragia, fibrina e infiltrado neutrofílico nas lâminas dérmicas, hiperplasia do topo das lâminas epidérmicas com queratinização irregular e retenção dos núcleos; várias lâminas epidérmicas estavam encurtadas e fundidas. Na mucosa da língua o epitélio de revestimento estava adelgaçado, com atrofia e perda das papilas filiformes e havia áreas multifocais de disqueratose e espongiose das células da camada basal. Em algumas porções havia perda do epitélio e a superfície da língua era formada por tecido de granulação e infiltrado inflamatório misto. A mucosa esofágica de seis novilhos apresentava vários graus de necrose epitelial e inflamação. A perda do epitélio de revestimento revelava uma área subjacente de tecido de granulação com marcado infiltrado inflamatório predominantemente neutrofílico e macrofágico. Em seis novilhos, o bulbo, na altura do óbex, apresentava áreas focais bilaterais e simétricas de malacia que afetava a substância branca e partes do núcleo dorsal do vago e do núcleo hipoglosso. Ultra-estruturalmente, os queratinócitos do epitélio da superfície dorsal da língua apresentavam diminuição do número de feixes de filamentos de citoqueratina. São discutidos a epidemiologia, os sinais clínicos, a patologia e a patogênese da intoxicação por R. flavo-brunnescens em bovinos. Adicionalmente um caso de intoxicação por R. flavo-brunnescens é relatado em eqüino.

Mat-forming ectomycorrhizal (EcM) fungi represent a prevalent constituent of many temperate forest ecosystems and create dramatic changes in soil structure and chemistry. EcM mat soil have been shown to have increased microbial respiration rates and have been hypothesized to harbor unique assemblages of fungi and bacteria. The objectives of this dissertation were to characterize and examine the fungal and bacterial communities associated with EcM mats in old-growth forests of the H.J. Andrews Experimental Forest located in the Oregon Cascades. Additionally, this work assessed the application of traditional, emerging, and novel molecular sampling techniques for determining microbial communities of environmental samples. This research investigated the microbial communities associated with two common EcM mat genera found in old-growth Douglas fir stands in the Pacific Northwest; Piloderma (Atheliales, Basidiomycota) and Ramaria (Gomphales, Basidiomycota). Soil samples were collected from Piloderma and Ramaria mats and surrounding non- mat soil for molecular analysis of nucleic acids. First, a comparative study was conducted to determine the most appropriate rDNA molecular sampling technique for microbial community characterization. Two next-generation sequencing methods, Roche 454 pyrosequencing and Illumina-based environmental sequencing, the latter developed by the author, were compared to a more traditional sequencing approach, i.e., Sanger sequencing of clone libraries. These findings informed the subsequent sampling of the fungal ITS and bacterial 16S rDNA fragment with 454 pyrosequencing to determine the microbial communities within mat and non-mat soils. Second, this work utilized a pyrosequencing approach to explore fungal community structure in EcM mat and non-mat soils. This work concluded that differences in microbial communities do exist between Piloderma mat, Ramaria mat, and non-mat soils, but the differences are largely quantitative with relatively few distinct taxonomic shifts in microbial constituents. Piloderma, Ramaria and Russula, in addition to being the dominant taxa found on mycorrhizal root tips, were found to be the most abundant taxa in bulk soils within their respective mat types or non-mat sample. The background fungal communities within the EcM mats in this study exhibited considerable taxonomic overlap with the exception of Piloderma vs. non-mat comparisons; Russula species dominated nonmat soils but tended to be excluded or significantly underrepresented in Piloderma mats. Lastly, this study explored the bacterial communities associated with Piloderma and Ramaria mats using lower- coverage 454-Jr pyrosequencing. Bacterial communities exhibited significant structure as a function of mat-type, soil horizon and pH, but this finding should be interpreted with respect to the nonrandom distribution of Piloderma-mats in the O- horizon and the Ramaria-mats in the A-horizon, and the tendancy for EcM mats to be more acidic than surrounding soils. Nonetheless, the total microbial (bacterial and fungal) community was typically dominated by the mat-forming taxa, or Russula, in the case of non-mat soils. While the presence of Piloderma mats did enrich or restrict some bacterial groups, soil pH was also found to be a significant driver of bacterial richness and taxonomic diversity. Fungal and bacterial richness were also found to be positively related to one another, regardless of soil horizon or EcM mat type. This work, taken together, contributes to the understanding of hyperdiversity and heterogeneity of microbial communities of temperate forest soils and highlights the potential for fungal and bacterial communities to be influenced by the presence of EcM mats. / Graduation date: 2012