Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.

/pdf/nuclear-ribosomal-internal-transcribed-spacer-its-region-as-9rhgb6gvih.pdf

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

Cryptococcosis is a global invasive mycosis associated with significant morbidity and mortality. These guidelines for its management have been built on the previous Infectious Diseases Society of America guidelines from 2000 and include new sections. There is a discussion of the management of cryptococcal meningoencephalitis in 3 risk groups: (1) human immunodeficiency virus (HIV)-infected individuals, (2) organ transplant recipients, and (3) non-HIV-infected and nontransplant hosts. There are specific recommendations for other unique risk populations, such as children, pregnant women, persons in resource-limited environments, and those with Cryptococcus gattii infection. Recommendations for management also include other sites of infection, including strategies for pulmonary cryptococcosis. Emphasis has been placed on potential complications in management of cryptococcal infection, including increased intracranial pressure, immune reconstitution inflammatory syndrome (IRIS), drug resistance, and cryptococcomas. Three key management principles have been articulated: (1) induction therapy for meningoencephalitis using fungicidal regimens, such as a polyene and flucytosine, followed by suppressive regimens using fluconazole; (2) importance of early recognition and treatment of increased intracranial pressure and/or IRIS; and (3) the use of lipid formulations of amphotericin B regimens in patients with renal impairment. Cryptococcosis remains a challenging management issue, with little new drug development or recent definitive studies. However, if the diagnosis is made early, if clinicians adhere to the basic principles of these guidelines, and if the underlying disease is controlled, then cryptococcosis can be managed successfully in the vast majority of patients.

/pdf/clinical-practice-guidelines-for-the-management-of-4n4mku8a14.pdf

Clinical practice guidelines for the management of cryptococcal disease: 2010 update by the infectious diseases society of america.

https://www.ruhr-uni-bochum.de/imperia/md/content/geobot/2007/hibbett_2007-a_higher-level-phylogenetic.pdf

A higher-level phylogenetic classification of the Fungi

Mangroves are woody plants that grow at the interface between land and sea in tropical and sub-tropical latitudes where they exist in conditions of high salinity, extreme tides, strong winds, high temperatures and muddy, anaerobic soils. There may be no other group of plants with such highly developed morphological and physiological adaptations to extreme conditions.

Because of their environment, mangroves are necessarily tolerant of high salt levels and have mechanisms to take up water despite strong osmotic potentials. Some also take up salts, but excrete them through specialized glands in the leaves. Others transfer salts into senescent leaves or store them in the bark or the wood. Still others simply become increasingly conservative in their water use as water salinity increases Morphological specializations include profuse lateral roots that anchor the trees in the loose sediments, exposed aerial roots for gas exchange and viviparous waterdispersed propagules.

Mangroves create unique ecological environments that host rich assemblages of species. The muddy or sandy sediments of the mangal are home to a variety of epibenthic, infaunal, and meiofaunal invertebrates Channels within the mangal support communities of phytoplankton, zooplankton and fish. The mangal may play a special role as nursery habitat for juveniles of fish whose adults occupy other habitats (e.g. coral reefs and seagrass beds).

Because they are surrounded by loose sediments, the submerged mangroves' roots, trunks and branches are islands of habitat that may attract rich epifaunal communities including bacteria, fungi, macroalgae and invertebrates. The aerial roots, trunks, leaves and branches host other groups of organisms. A number of crab species live among the roots, on the trunks or even forage in the canopy. Insects, reptiles, amphibians, birds and mammals thrive in the habitat and contribute to its unique character.

Living at the interface between land and sea, mangroves are well adapted to deal with natural stressors (e.g. temperature, salinity, anoxia, UV). However, because they live close to their tolerance limits, they may be particularly sensitive to disturbances like those created by human activities. Because of their proximity to population centers, mangals have historically been favored sites for sewage disposal. Industrial effluents have contributed to heavy metal contamination in the sediments. Oil from spills and from petroleum production has flowed into many mangals. These insults have had significant negative effects on the mangroves.

Habitat destruction through human encroachment has been the primary cause of mangrove loss. Diversion of freshwater for irrigation and land reclamation has destroyed extensive mangrove forests. In the past several decades, numerous tracts of mangrove have been converted for aquaculture, fundamentally altering the nature of the habitat. Measurements reveal alarming levels of mangrove destruction. Some estimates put global loss rates at one million ha y−1, with mangroves in some regions in danger of complete collapse. Heavy historical exploitation of mangroves has left many remaining habitats severely damaged.

These impacts are likely to continue, and worsen, as human populations expand further into the mangals. In regions where mangrove removal has produced significant environmental problems, efforts are underway to launch mangrove agroforestry and agriculture projects. Mangrove systems require intensive care to save threatened areas. So far, conservation and management efforts lag behind the destruction; there is still much to learn about proper management and sustainable harvesting of mangrove forests.

Mangroves have enormous ecological value. They protect and stabilize coastlines, enrich coastal waters, yield commercial forest products and support coastal fisheries. Mangrove forests are among the world's most productive ecosystems, producing organic carbon well in excess of the ecosystem requirements and contributing significantly to the global carbon cycle. Extracts from mangroves and mangrove-dependent species have proven activity against human, animal and plant pathogens. Mangroves may be further developed as sources of high-value commercial products and fishery resources and as sites for a burgeoning ecotourism industry. Their unique features also make them ideal sites for experimental studies of biodiversity and ecosystem function. Where degraded areas are being revegetated, continued monitoring and thorough assessment must be done to help understand the recovery process. This knowledge will help develop strategies to promote better rehabilitation of degraded mangrove habitats the world over and ensure that these unique ecosystems survive and flourish.

Biology of mangroves and mangrove Ecosystems

DNA barcoding and DNA taxonomy have recently been proposed as solutions to the crisis of taxonomy and received significant attention from scientific journals, grant agencies, natural history museums, and mainstream media. Here, we test two key claims of molecular taxonomy using 1333 mitochondrial COI sequences for 449 species of Diptera. We investigate whether sequences can be used for species identification ("DNA barcoding") and find a relatively low success rate (< 70%) based on tree-based and newly proposed species identification criteria. Misidentifications are due to wide overlap between intra- and interspecific genetic variability, which causes 6.5% of all query sequences to have allospecific or a mixture of allo- and conspecific (3.6%) best-matching barcodes. Even when two COI sequences are identical, there is a 6% chance that they belong to different species. We also find that 21% of all species lack unique barcodes when consensus sequences of all conspecific sequences are used. Lastly, we test whether DNA sequences yield an unambiguous species-level taxonomy when sequence profiles are assembled based on pairwise distance thresholds. We find many sequence triplets for which two of the three pairwise distances remain below the threshold, whereas the third exceeds it; i.e., it is impossible to consistently delimit species based on pairwise distances. Furthermore, for species profiles based on a 3% threshold, only 47% of all profiles are consistent with currently accepted species limits, 20% contain more than one species, and 33% only some sequences from one species; i.e., adopting such a DNA taxonomy would require the redescription of a large proportion of the known species, thus worsening the taxonomic impediment. We conclude with an outlook on the prospects of obtaining complete barcode databases and the future use of DNA sequences in a modern integrative taxonomy.

DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success.

The molecular systematics of 337 strains of basidiomycetous yeasts and yeast-like fungi, representing 230 species in 18 anamorphic and 24 teleomorphic genera, was determined by sequence analysis of the D1/D2 region of the large-subunit rDNA. The data were compared with published sequences of other basidiomycetous fungi. The results demonstrated that the yeast species and genera are phylogenetically distributed among the Microbotryum, Sporidiobolus, Agaricostilbum and Erythrobasidium clades of the Urediniomycetes; the Tremellales, Trichosporonales ord. nov., Filobasidiales and Cystofilobasidiales clades of the Hymenomycetes; and the Ustilaginales, Microstromatales and Malasseziales clades of the Ustilaginomycetes. Genera such as Bensingtonia, Cryptococcus, Rhodotorula and Sporobolomyces are polyphyletic, i.e. they occur in two or more clades. In contrast, other genera, e.g. Bullera, Cystofilobasidium, Fellomyces, Filobasidiella, Filobasidium, Kondoa, Kurtzmanomyces, Leucosporidium, Rhodosporidium, Sporidiobolus and Udeniomyces, are monophyletic. The majority of the species can be identified using D1/D2 analyses, although the internal transcribed spacer region is required to distinguish closely related species. The intergenic spacer region is recommended for additional differentiation of species and strains.

/pdf/biodiversity-and-systematics-of-basidiomycetous-yeasts-as-1q6tmxna17.pdf

Biodiversity and systematics of basidiomycetous yeasts as determined by large-subunit rDNA D1/D2 domain sequence analysis.

Yeasts are recovered from a wide range of aquatic, marine, atmospheric, and terrestrial habitats. Many yeasts occur widely, whereas some appear to be confined to specific habitats. Yeasts seldom occur in the absence of either molds or bacteria. Consequently, selective techniques are often used for recovery of yeasts, employing media that permit the yeasts to grow, while suppressing molds and bacteria. Under the morphological characterization of yeasts there are several factors that include: texture, color, surface, elevation, and margin. In texture, mucoid growth is frequently associated with encapsulation of cells from production of extracellular polysaccharides; membranous growth generally results from profuse formation of hyphae or pseudohyphae. In color, the presence of red, orange, or yellow nondiffusible carotenoid pigments is characteristic of certain genera, for instance, Phaffia, Rhodosporidium, and Sporidiobolus. In surface, the strains that are smooth when first isolated sometimes become rough when maintained on agar. This change is, in some cases, accompanied by a change in texture from butyrous to membranous. Restreaking generally results, once again, in formation of smooth and rough colonies. In elevation, the growth is flat, depressed in the center, raised and dome-like, or conical. And in margin, the edge of the streak or colony is entire, undulating, lobed, erose, or fringed with hyphae or pseudohyphae. © 2011 Elsevier B.V. All rights reserved.

https://www.researchgate.net/file.PostFileLoader.html?id=5475cb5dd4c11860048b45b5&assetKey=AS%3A273641080590336%401442252525533

Methods for isolation, phenotypic characterization and maintenance of yeasts

Basidiomycetous yeasts in the Urediniomycetes and Hymenomycetes were examined by sequence analysis in two ribosomal DNA regions: the D1/D2 variable domains at the 5' end of the large subunit rRNA gene (D1/D2) and the internal transcribed spacers (ITS) 1 and 2. Four major lineages were recognized in each class: Microbotryum, Sporidiobolus, Erythrobasidium and Agaricostilbum in the Urediniomycetes; Tremellales, Trichosporonales, Filobasidiales and Cystofilobasidiales in the Hymenomycetes. Bootstrap support for many of the clades within those lineages is weak; however, phylogenetic analysis provides a focal point for in-depth study of biological relationships. Combined sequence analysis of the D1/D2 and ITS regions is recommended for species identification, while species definition requires classical biological information such as life cycles and phenotypic characterization.

Systematics of basidiomycetous yeasts: a comparison of large subunit D1/D2 and internal transcribed spacer rDNA regions

Amplified fragment length polymorphism (AFLP) genotyping of isolates of the pathogenic fungus Cryptococcus neoformans suggested a considerable genetic divergence between the varieties C. neoformans var. neoformans and C. neoformans var. grubii on the one hand versus C. neoformans var. gattii on the other. This divergence is supported by additional phenotypic, biochemical, clinical and molecular differences. Therefore, the authors propose the existence of two species, C. neoformans (Sanfelice) Vuillemin and C. bacillisporus Kwon-Chung, which differ in geographical distribution, serotypes and ecological origin. Within each species three AFLP genotypes occur, which differ in geographical distribution and serotypes. Differences in ecological origin (AIDS patients, non-AIDS patients, animals or the environment) were found to be statistically not significant. In C. neoformans as well as in C. bacillisporus one of the genotypes represented a hybrid. The occurrence of hybridization has consequences for the reproductive biology of the species, as new genotypes with altered virulence or susceptibility to antifungal drugs may arise through the exchange of genetic material.

Jack W. Fell

Papers

Biodiversity and systematics of basidiomycetous yeasts as determined by large-subunit rDNA D1/D2 domain sequence analysis.

Methods for isolation, phenotypic characterization and maintenance of yeasts

Systematics of basidiomycetous yeasts: a comparison of large subunit D1/D2 and internal transcribed spacer rDNA regions

Hybrid genotypes in the pathogenic yeast Cryptococcus neoformans

(1557) Proposal to conserve the name Cryptococcus gattii against C. hondurianus and C. bacillisporus (Basidiomycota, Hymenomycetes, Tremellomycetidae)