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.

Nine Zoogloea strains including the type strain of Z. ramigera (IAM 12136 = ATCC 19544 = N.C. Dondero 106) and newly isolated strains were investigated for isoprenoid quinone composition and whole-cell fatty acid profiles. Seven of the tested strains, having phenotypic properties typical of Zoogloea, were characterized by their production of both ubiquinone-8 and rhodoquinone-8 as major quinones, whereas the remaining two strains, Z. ramigera IAM 12669 (= K. Crabtree I-16-M) and IAM 12670 (= P.R. Dugan 115), formed ubiquinone-10 and ubiquinone-8, respectively, as the sole quinone. All rhodoquinone-producing strains contained palmitoleic acid and 3-hydroxy-decanoic acid as the major components of nonpolar and hydroxylated fatty acids, respectively. Marked differences were noted in the fatty acid composition between the strains with and without rhodoquinones. The chemotaxonomic data suggested that the rhodoquinone-lacking strains should be excluded from the genus Zoogloea. Since there have been no reliable taxonomic tools for Zoogloea, rhodoquinone analysis may provide a new criterion of great promise for identifying Zoogloea strains.

Isoprenoid quinones and fatty acids of Zoogloea

A description is provided for a new anamorph genus Sympodiomycopsis (Hyphomycetes), which is neither ballistosporogenous nor sterigmatosporogenous. The genus is typified by S. paphiopedili sp. nov. and accommodates one species which was isolated from nectar of Paphiopedilum primurinum in Japan. Phenotypically, the genus shows some similarity to Sympodiomyces because of the presence of a yeast morph with sympodial conidiogenous cell proliferation, but it is distinguished from that genus morphologically by a yeast morph with the enteroblastic-annellidic conidiogenesis and the conspicuous development of a hyphal morph with holoblastic-sympodial conidiogenous cells, and chemotaxonomically by the ubiquinone system Q-10 and 10% difference in the guanine plus cytosine (G+C) content of the nuclear DNA. Phylogenetically, the type of cell wall and septal pore ultrastructure, and the primary biochemical and chemotaxonomic characters of S. paphiopedili indicate a basidiomycetous affinity.

Sympodiomycopsis: a new yeast-like anamorph genus with basidiomycetous nature from orchid nectar.

Rhodotorula hasegawae IFO 1058 (holotype) with the major ubiquinone system, Q-10(H2), produces the teleomorph from a single cell withoutmating. Its apparent life cycle is presented here. It is concluded that this fungus is related to the filobasidiaceous yeasts in the Basidiomycotina since it lacks probasidia (teliospores) and phragmobasidia bearing sessile basidiospores that are not forcibly discharged. Therefore, R. hasegawae istransferred to a new teleomorph-genus Erythrobasidium placed in the family Filobasidiaceae, as Erythrobasidium hasegawae (Yamada et Komagata) Hamamoto, Sugiyama et Komagata, comb. nov.

Transfer of Rhodotorula hasegawae to a new basidiomycetous genus Erythrobasidium as Erythrobasidium hasegawae comb. nov.

In the genus Agrobacterium, terrestrial and plant pathogenic species and marine star-shaped-aggregate-forming species were reported (Conn, 1942; Jordan, 1984; Ophel and Kerr, 1990; Ruger and Hofle, 1992; Starr and Weiss, 1943). The phylogenetic positions of the terrestrial and plant pathogenic species have already been made clear, but those of the marine species have not been published yet. Since Stapp and Knosel (1954) grouped a marine species as Agrobacterium stellulatum based on their formation of star-shaped aggregation, many marine isolates resemble to A, stellulatum as a species of the genus Agrobacterium (Ahrens, 1968; Ahrens and Rheinheimer, 1967). However, intrageneric relationships between marine and terrestrial Agrobacterium species remain uncertain. Ruger and Hofle (1992) performed a phenotypic analysis on these Agrobacterium species in addition to their marine isolates, and they insisted that among these marine strains, five species could be recognized as a distinct taxon. They believe these five species form a group independently from the terrestrial Agrobacterium species, but there were no distinctive phenotypic characteristics to separate the marine species from the genus Agrobacterium. Therefore, they concluded that the genus Agrobacterium must be divided into two subdivisions, accommodating the terrestrial and plant pathogenic species in subdivision 1 and the marine star-shaped-aggregate-forming five species Agrobacterium atlanticum, Agrobacterium ferrugineum, Agrobacterium gelatinovorum, Agrobacterium meteori and A. stellulatum in subdivision 2, until further taxonomic data are available (Ruger and Hofle,1992). In this communication, we determined 165 ribosomal RNA gene sequences of these marine subdivision species, including the non-validated species "Agrobacterium agile" and "Agrobacterium kieliense ," and investigated their phylogenetic position to clarify the classification of marine Agrobacterium species. The bacterial strains used in this study were A. atlanticum IAM 14463T, A, ferrugineum IAM 12616T, A. gelatinovorum IAM 12617T, A. meteori IAM 14464T, A. stellulatum IAM 12614, A. stellulatum IAM 12621T , "A. agile" IAM 12615 and "A. kieliense" IAM 12618. All the strains were grown aerobically on the plate of Difco marine agar 2216 for 2 days at 25°C. Cells grown in the late exponential phase were harvested, washed with sterile water and stored at -20°C until use. The 165 rRNA gene was amplified by PCR using Takara 7 aq (Takara Shuzo, Kyoto, Japan), the three forward primers 8F (5'-AGAGTTTGATCCTGGCTCAG-3'), 520F (5'-CAGCAGCCGCGGTAATAC-3') and 926F (5'-AAACTCAAAGGAATTGACGG-3'), and three reverse primers 704R (5'-TCTACGCATTTCACC-3'), 1110R (5'GGGTTGCGCTCGTTG-3') and 1510R (5'-GGCTACCTTGTTACGA-3') [Escherichia coli numbering system], by the combination of 8F-704R, 520F1110R and 926F-1510R. Amplified fragments were cloned using an Invitrogen TA CloningTM Kit (Invitrogen, CA, U.S.A.). Extraction and purification of the plasmids were carried out using a QlAprep Spin Plasmid Kit (Qiagen, Hilden, Germany). The cloned plasmids were used for sequencing. Sequencing was carried out using an ABI PRISMTM Dye Primer Cycle Sequencing Ready Reaction Kit (Perkin-Elmer Co., CA, U.S.A.) and a model ABI 3735 automatic DNA sequencer (Perkin-Elmer Co.). Previously published 165 rRNA gene sequences, which were already aligned, * Address reprint requests to: Dr . Akira Yokota, ular and cellular Biosciences, The University Yayoi; Bunkyo-ku, Tokyo 113, Japan. Institute of Molec-

https://www.jstage.jst.go.jp/article/jgam1955/43/4/43_4_243/_pdf

Phylogenetic position of the marine subdivision of Agrobacterium species based on 16S rRNA sequence analysis.

The genetic relatedness of 60 strains in the basidiomycetous yeast genera Rhodosporidium and Rhodotorula was studied by the DNA-DNA hybridization using the nitrocellulose filter technique. Degrees of the intraspecific reassociation among the DNAs from the strains of Rhodosporidium infirmominiatum, Rhodosporidium diobovatum, Rhodosporidium sphaerocarpum, and Rhodosporidium dacryoidum ranged from 64 to 99%. The mating-type strains of Rhodosporidium toruloides were divided into four homology clusters. The degrees of DNA-DNA reassociation between the mating-type strains and the self-sporulating strains in Rhodosporidium toruloides were very low. (18%) indicating the absence of relatedness between them. The strains of Rhodotorula glutinis were divided into five homology clusters. Among these strains, some, including the type strain, showed close relatedness to Rhodosporidium diobovatum, some to Rhodosporidium toruloides (self-sporulating), and some to Rhodotorula rubra, and Rhodotorula pilimanae. The strains of Rhodotorula minuta were divided into four homology clusters. A close relationship was found between some strains of Rhodotorula minuta including the type strain and a strain of Rhodotorula pallida. There was a very close relationship between the Rhodotorula sinensis strain and the strains of Rhodosporidium infirmominiatum.

Junta Sugiyama

Papers

Isoprenoid quinones and fatty acids of Zoogloea

Sympodiomycopsis: a new yeast-like anamorph genus with basidiomycetous nature from orchid nectar.

Transfer of Rhodotorula hasegawae to a new basidiomycetous genus Erythrobasidium as Erythrobasidium hasegawae comb. nov.

Phylogenetic position of the marine subdivision of Agrobacterium species based on 16S rRNA sequence analysis.

Dna-dna reassociation studies of strains in the genera rhodosporidium and rhodotorula