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

Denitrification is a distinct means of energy conservation, making use of N oxides as terminal electron acceptors for cellular bioenergetics under anaerobic, microaerophilic, and occasionally aerobic conditions. The process is an essential branch of the global N cycle, reversing dinitrogen fixation, and is associated with chemolithotrophic, phototrophic, diazotrophic, or organotrophic metabolism but generally not with obligately anaerobic life. Discovered more than a century ago and believed to be exclusively a bacterial trait, denitrification has now been found in halophilic and hyperthermophilic archaea and in the mitochondria of fungi, raising evolutionarily intriguing vistas. Important advances in the biochemical characterization of denitrification and the underlying genetics have been achieved with Pseudomonas stutzeri, Pseudomonas aeruginosa, Paracoccus denitrificans, Ralstonia eutropha, and Rhodobacter sphaeroides. Pseudomonads represent one of the largest assemblies of the denitrifying bacteria within a single genus, favoring their use as model organisms. Around 50 genes are required within a single bacterium to encode the core structures of the denitrification apparatus. Much of the denitrification process of gram-negative bacteria has been found confined to the periplasm, whereas the topology and enzymology of the gram-positive bacteria are less well established. The activation and enzymatic transformation of N oxides is based on the redox chemistry of Fe, Cu, and Mo. Biochemical breakthroughs have included the X-ray structures of the two types of respiratory nitrite reductases and the isolation of the novel enzymes nitric oxide reductase and nitrous oxide reductase, as well as their structural characterization by indirect spectroscopic means. This revealed unexpected relationships among denitrification enzymes and respiratory oxygen reductases. Denitrification is intimately related to fundamental cellular processes that include primary and secondary transport, protein translocation, cytochrome c biogenesis, anaerobic gene regulation, metalloprotein assembly, and the biosynthesis of the cofactors molybdopterin and heme D1. An important class of regulators for the anaerobic expression of the denitrification apparatus are transcription factors of the greater FNR family. Nitrate and nitric oxide, in addition to being respiratory substrates, have been identified as signaling molecules for the induction of distinct N oxide-metabolizing enzymes.

/pdf/cell-biology-and-molecular-basis-of-denitrification-red4l5iffz.pdf

Cell biology and molecular basis of denitrification.

In an effort to establish a suitable alternative to the widely used 18S rRNA system for molecular systematics of fungi, we examined the nuclear gene RPB2, encoding the second largest subunit of RNA polymerase II. Because RPB2 is a single-copy gene of large size with a modest rate of evolutionary change, it provides good phylogenetic resolution of Ascomycota. While the RPB2 and 18S rDNA phylogenies were highly congruent, the RPB2 phylogeny did result in much higher bootstrap support for all the deeper branches within the orders and for several branches between orders of the Ascomycota. There are several strongly supported phylogenetic conclusions. The Ascomycota is composed of three major lineages: Archiascomycetes, Saccharomycetales, and Euascomycetes. Within the Euascomycetes, plectomycetes, and pyrenomycetes are monophyletic groups, and the Pleosporales and Dothideales are distinct sister groups within the Loculoascomycetes. We confirm the placement of Neolecta within the Archiascomycetes, suggesting that fruiting body formation and forcible discharge of ascospores were characters gained early in the evolution of the Ascomycota. These findings show that a slowly evolving protein-coding gene such as RPB2 is useful for diagnosing phylogenetic relationships among fungi.

/pdf/phylogenetic-relationships-among-ascomycetes-evidence-from-40ck3fbkz2.pdf

Phylogenetic relationships among ascomycetes: evidence from an RNA polymerse II subunit.

The skin is the human body's largest organ, colonized by a diverse milieu of microorganisms, most of which are harmless or even beneficial to their host. Colonization is driven by the ecology of the skin surface, which is highly variable depending on topographical location, endogenous host factors and exogenous environmental factors. The cutaneous innate and adaptive immune responses can modulate the skin microbiota, but the microbiota also functions in educating the immune system. The development of molecular methods to identify microorganisms has led to an emerging view of the resident skin bacteria as highly diverse and variable. An enhanced understanding of the skin microbiome is necessary to gain insight into microbial involvement in human skin disorders and to enable novel promicrobial and antimicrobial therapeutic approaches for their treatment.

The skin microbiome

Summary 1 Summary All plants in natural ecosystems appear to be symbiotic with fungal endophytes. This highly diverse group of fungi can have profound impacts on plant communities through increasing fitness by conferring abiotic and biotic stress tolerance, increasing biomass and decreasing water consumption, or decreasing fitness by altering resource allocation. Despite more than 100 yr of research resulting in thousands of journal articles, the ecological significance of these fungi remains poorly characterized. Historically, two endophytic groups (clavicipitaceous (C) and nonclavicipitaceous (NC)) have been discriminated based on phylogeny and life history traits. Here, we show that NC-endophytes represent three distinct functional groups based on host colonization and transmission, in planta biodiversity and fitness benefits conferred to hosts. Using this framework, we contrast the life histories, interactions with hosts and potential roles in plant ecophysiology of C- and NC-endophytes, and highlight several key questions for future work in endophyte biology.

https://courses.washington.edu/cfr523/documents/2009TansleyReview.pdf

Fungal endophytes: diversity and functional roles.

"Black particles", the major colonizers on the ceiling stone of the stone chamber interior of the Kitora Tumulus, Japan, are the bulbilliferous basidiomycete fungus Burgoa anomala

The massively parallel DNA sequencer is a powerful tool for the genome sequencing project. The sequencing is performed at random. So, even if we do not know the genome size or chromosome number of the target organism for sequencing, we can start to sequence the genome. On the other hand, a lot of sequence fragments are needed in order to assemble the fragments and obtain the complete genome sequence. Recently fungal genome sequences using massively parallel DNA sequencers have been published (DiGuistini et al., 2009; Martinez et al., 2009; Nowrousian et al., 2010). The aim of this article is to describe the draft genome sequence of the enigmatic fungus Mixia somundae and discuss the phylogeny. The phylum Basidiomycota consists of three subphyla Agaricomycotina, Pucciniomycotina, and Ustilaginomycotina (Hibbett et al., 2007). The subphylum Pucciniomycotina consists of eight classes (Hibbett et al., 2007). However, the phylogenetic relationships among the eight classes remain uncertain. The class Mixiomycetes is one of the eight classes. The class Mixiomycetes consists of a single order, Mixiales, and a single family, Mixiaceae (Bauer et al., 2006). The family Mixiaceae consists of a single genus, Mixia. The genus Mixia consists of a single species, Mixia osmundae, parasitic on Osmunda japonica (Japanese royal fern). Thus, at present, the class Mixiomycetes consists of only Mixia osmundae. We believe that this fungus is a key (essential) fungus to elucidate the phylogenetic relationships among the eight classes of Puccinomycotina. Nishida (1911) described Taphrina osmundae, based on two specimens collected in Japan. Mix (1947) added three specimens from Japan and also emended the description of Taphrina osmundae. Kramer (1958) proposed Mixia, a new genus typifi ed by Mixia osmundae (basionym: Taphrina osmundae Nishida) and tentatively placed the genus in the Protomycetaceae. Subsequently Kramer (1987) accommodated this genus in the new family Mixiaceae (Protomycetales). Recently the name Taphrina osmundae has been lectotypifi ed by Sugiyama and Katumoto (2008). On the other hand, based on evidence from the 18S rDNA sequence, morphological, and ultrastructural characters, Nishida et al. (1995) showed that Mixia osmundae is not a member of the Ascomycota, but a member of the Basidiomycota. Mixia osmundae has a unique phylogenetic position inferred from ribosomal RNA sequence comparison and a unique sporangium in the J. Gen. Appl. Microbiol., 57, 63‒67 (2011)

Draft genome sequencing of the enigmatic basidiomycete Mixia osmundae.

The Kitora tumulus, which is thought to have been built around the late seventh to early eighth century, has beautiful mural paintings which were executed directly on a very thin layer of plaster in the stone chamber. When the paintings were found, the plaster was partly detached from the stone wall and the murals were therefore considered to be likely to fall off the wall with a casual touch or stimulation. Therefore, it was decided to detach the mural paintings and to store them flat and under controlled environmental conditions. This was initiated immediately after the excavation of the tumulus in 2004. However, fungal growth and biofilm development were observed within the stone chamber during the relocation work. In 2005, small holes containing black substances were observed on certain areas of the ceiling plaster, and following investigation an acetic acid bacterium, Gluconacetobacter sp., was isolated from the black substances. The bacterium was also isolated from the ceiling, floor, and ea...

Investigation of acetic acid bacteria isolated from the Kitora tumulus in Japan and their involvement in the deterioration of the plaster of the mural paintings

Septal pore ultrastructure of Leucosporidium lari-marini, a basidiomycetous yeast, and its taxonomic implications

Two new Cladophialophora species, C. tumbae sp. nov. and C. tumulicola sp. nov., and chaetothyrialean fungi from biodeteriorated samples in the Takamatsuzuka and Kitora Tumuli

Junta Sugiyama

Papers

"Black particles", the major colonizers on the ceiling stone of the stone chamber interior of the Kitora Tumulus, Japan, are the bulbilliferous basidiomycete fungus Burgoa anomala

Draft genome sequencing of the enigmatic basidiomycete Mixia osmundae.

Investigation of acetic acid bacteria isolated from the Kitora tumulus in Japan and their involvement in the deterioration of the plaster of the mural paintings

Septal pore ultrastructure of Leucosporidium lari-marini, a basidiomycetous yeast, and its taxonomic implications

Two new Cladophialophora species, C. tumbae sp. nov. and C. tumulicola sp. nov., and chaetothyrialean fungi from biodeteriorated samples in the Takamatsuzuka and Kitora Tumuli