Here we describe a quantitative PCR-based approach to estimating the relative abundances of major taxonomic groups of bacteria and fungi in soil. Primers were thoroughly tested for specificity, and the method was applied to three distinct soils. The technique provides a rapid and robust index of microbial community structure.

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Assessment of soil microbial community structure by use of taxon-specific quantitative PCR assays.

Although Cryptococcus neoformans and cryptococcosis have existed for several millennia, a century has passed since the discovery of this encapsulated yeast and its devastating disease. With the advent of the AIDS pandemic, cryptococcal meningitis has emerged as a leading cause of infectious morbidity and mortality and a frequently life-threatening opportunistic mycosis among patients with AIDS. Both basic and clinical research have accelerated in the 1990s, and this review attempts to highlight some of these advances. The discussion covers recent findings, current concepts, controversies, and unresolved issues related to the ecology and genetics of C. neoformans; the surface structure of the yeast; and the mechanisms of host defense. Regarding cell-mediated immunity, CD4+ T cells are crucial for successful resistance, but CD8+ T cells may also participate significantly in the cytokine-mediated activation of anticryptococcal effector cells. In addition to cell-mediated immunity, monoclonal antibodies to the major capsular polysaccharide, the glucuronoxylomannan, offer some protection in murine models of cryptococcosis. Clinical concepts are presented that relate to the distinctive features of cryptococcosis in patients with AIDS and the diagnosis, treatment, and prevention of cryptococcosis in AIDS patients.

Cryptococcosis in the era of AIDS--100 years after the discovery of Cryptococcus neoformans.

The fungi comprise both members of the kingdom Fungi as we now recognize it (Ascomycota, Basidiomycota, Zygomycota, and Chytridiomycota) and fungal-like protists such as the Oomycota and the cellular and acellular slime molds (Myxomycota and Acrasiomycota). Treating this admittedly polyphyletic assemblage as a group is useful because these organisms often fill rather similar roles within ecosystems, and they have traditionally been studied almost exclusively by mycologists and plant pathologists. Throughout this review, Fungi will refer to the Kingdom, fungi to the organisms studied by mycologists. The fungi, as thus defined, are of great importance for the following reasons: (a) They are the primary decomposers in all terrestrial ecosystems; (b) they are important symbiotic associates of vascular plants both in mutualistic and parasitic relationships; (c) they constitute the overwhelming majority of plant pathogens and as such have a tremendous eco-

Fungal Molecular Systematics

http://www.ascofrance.fr/uploads/forum_file/1-s2.0-S0953756209804097-main-0001.pdf

Taxonomy and phylogeny of Gliocladium analysed from nuclear large subunit ribosomal DNA sequences

This revision of the classification of eukaryotes follows that of Adl et al., 2012 [J. Euk. Microbiol. 59(5)] and retains an emphasis on protists. Changes since have improved the resolution of many ...

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Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes

Detailed restriction analyses of many samples often require substantial amounts of time and effort for DNA extraction, restriction digests, Southern blotting, and hybridization. We describe a novel approach that uses the polymerase chain reaction (PCR) for rapid simplified restriction typing and mapping of DNA from many different isolates. DNA fragments up to 2 kilobase pairs in length were efficiently amplified from crude DNA samples of several pathogenic Cryptococcus species, including C. neoformans, C. albidus, C. laurentii, and C. uniguttulatus. Digestion and electrophoresis of the PCR products by using frequent-cutting restriction enzymes produced complex restriction phenotypes (fingerprints) that were often unique for each strain or species. We used the PCR to amplify and analyze restriction pattern variation within three major portions of the ribosomal DNA (rDNA) repeats from these fungi. Detailed mapping of many restriction sites within the rDNA locus was determined by fingerprint analysis of progressively larger PCR fragments sharing a common primer site at one end. As judged by PCR fingerprints, the rDNA of 19 C. neoformans isolates showed no variation for four restriction enzymes that we surveyed. Other Cryptococcus spp. showed varying levels of restriction pattern variation within their rDNAs and were shown to be genetically distinct from C. neoformans. The PCR primers used in this study have also been successfully applied for amplification of rDNAs from other pathogenic and nonpathogenic fungi, including Candida spp., and ought to have wide applicability for clinical detection and other studies.

M Hester

Papers

Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species.