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.

Thirteen strains referred to six asporogenous yeast species were isolated from soil, dung, and forest humus samples collected in Bhutan. The following species, including two new taxa of Cryptococcus, were recovered: Cryptococcus albidus,Cryptococcus bhutanensis sp. nov., Cryptococcus diffluens,Cryptococcus himalayensis sp. nov., Torulopsis Candida, and Rhodotorula glutinis.

Studies on Himalayan yeasts and molds. IV. Several asporogenous yeasts including two new taxa of Cryptococcus

Ten strains of Gram-stain-negative, rod-shaped, non-spore-forming bacteria were isolated from the burial mound soil collected before the dismantling and samples collected during the dismantling work on the Takamatsuzuka Tumulus in Asuka village, Nara Prefecture, Japan in 2007. On the basis of the 16S rRNA gene sequence analysis of the isolates, they were accommodated in the genus 
Gluconacetobacter
(class 
Alphaproteobacteria
) and can be separated into four groups within the cluster containing the genus 
Gluconacetobacter
. One of the groups demonstrated a phylogenetic position identical to that of 
Gluconacetobacter asukensis
, which was isolated from small holes on plaster walls of the stone chamber interior of Kitora Tumulus in Asuka village, Nara Prefecture, Japan. The remaining three groups consisted of novel lineages within the genus 
Gluconacetobacter
. A total of four isolates were selected from each group and carefully identified using a polyphasic approach. The isolates were characterized on the basis of their possessing Q-10 as the major ubiquinone system and C18 : 1ω7c (58.5–65.2 %) as the predominant fatty acid. A DNA–DNA hybridization test was used to determine that the three lineages represented novel species, for which the names Gluconacetobacter tumulisoli sp. nov., Gluconacetobacter takamatsuzukensis sp. nov. and Gluconacetobacter aggeris sp. nov. are proposed. The type strains are T611xx-1-4aT ( = JCM 19097T = NCIMB 14861T), T61213-20-1aT ( = JCM 19094T = NCIMB 14859T) and T6203-4-1aT ( = JCM 19092T = NCIMB 14860T), respectively.

Gluconacetobacter tumulisoli sp. nov., Gluconacetobacter takamatsuzukensis sp. nov. and Gluconacetobacter aggeris sp. nov., isolated from Takamatsuzuka Tumulus samples before and during the dismantling work in 2007

A hitherto undescribed ballistospore-forming yeast was isolated from Knightia excelsa infected by sooty molds collected in New Zealand It is characterized by ubiquinone-9 and the lack of xylose in the cells so that it is included in the genus Bensingtonia This yeast resembles B intermedia and B yamatoana but is easily distinguished from these two species by the assimilation of nitrate and lactose and the requirement of pyridoxine Bensingtonia ingoldii Nakase et Itoh sp nov is proposed for this yeast

Bensingtonia ingoldii sp. nov., a ballistospore-forming yeast isolated from Knightia excelsa collected in New Zealand.

Phenotypic, chemotaxonomic, and DNA-DNA hybridization studies of strains of Rhodopseudomonas rutila Akiba et al. 1983 and Rhodopseudomonas palustris (Molisch 1907) van Niel 1944 demonstrated synonymy between the two species. We propose that they be classified into a single species, retaining the name R. palustris.

Rhodopseudomonas rutila Is a Later Subjective Synonym of Rhodopseudomonas palustris

During a survey of yeast strains having high conversion effi ciency to ethanol from cellobiose, ‘Ogataea pini’ ATCC 28781 and ‘Pichia pini’ NBRC 1794 were found to be distinct from any known species and from each other by a BLAST homology search using the D1/D2 LSU rRNA gene sequences. The D1/D2 phylogeny showed that ‘O. pini’ ATCC 28781 and ‘P. pini’ NBRC 1794 belonged to the Ogataea cluster, whereas a comparison of the ITS 1 and 2 regions sequences showed that the ATCC and NBRC strains each formed a species distinct from O. ganodermae, O. pini, O. henricii, and P. zsoltii, based on the D1/D2 sequence divergence. The ATCC and NBRC strains formed two to four hat-shaped ascospores and two to four, or more ones per deliquescent ascus, respectively, were negative for DBB and urease reactions, assimilated methanol slowly and nitrate not at all, and had the major ubiquinone system Q-7. These characteristics coincided basically with the defi nition of Ogataea proposed by Yamada et al. in 1994, excluding the number of ascospores. On the other hand, the ATCC and NBRC strains differed not only from each other but from relatives in various phenotypic characteristics. These differences suggest that two new yeasts of Ogataea be described as novel. The new species and their type strains are as follows: O. neopini ATCC 28781 T ; and O. corticis NBRC 1794 T . In addition, the emendation of the genus Ogataea is made; besides, we propose the transfer of P. zsoltii, P. dorogensis, and P. trehaloabstinens, which were placed in the Ogataea cluster based on the D1/D2 sequence analysis, to the genus Ogataea as O. zsoltii comb. nov., O. dorogensis comb. nov., and O. trehaloabstinens comb. nov.

https://www.jstage.jst.go.jp/article/jgam/54/6/54_6_353/_pdf

Ogataea neopini sp. nov. and O. corticis sp. nov., with the emendation of the ascomycete yeast genus Ogataea, and transfer of Pichia zsoltii, P. dorogensis, and P. trehaloabstinens to it.

Junta Sugiyama

Papers

Studies on Himalayan yeasts and molds. IV. Several asporogenous yeasts including two new taxa of Cryptococcus

Gluconacetobacter tumulisoli sp. nov., Gluconacetobacter takamatsuzukensis sp. nov. and Gluconacetobacter aggeris sp. nov., isolated from Takamatsuzuka Tumulus samples before and during the dismantling work in 2007

Bensingtonia ingoldii sp. nov., a ballistospore-forming yeast isolated from Knightia excelsa collected in New Zealand.

Rhodopseudomonas rutila Is a Later Subjective Synonym of Rhodopseudomonas palustris

Ogataea neopini sp. nov. and O. corticis sp. nov., with the emendation of the ascomycete yeast genus Ogataea, and transfer of Pichia zsoltii, P. dorogensis, and P. trehaloabstinens to it.