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Genome Diversity and Evolution in the Budding Yeasts (Saccharomycotina)
| YEASTBOOK GENOME ORGANIZATION AND INTEGRITY Genome Diversity and Evolution in the Budding Yeasts (Saccharomycotina) Bernard A. Dujon*,†,1 and Edward J. Louis‡,§ *Department Genomes and Genetics, Institut Pasteur, Centre National de la Recherche Scientifique UMR3525, 75724-CEDEX15 Paris, France, †University Pierre and Marie Curie UFR927, 75005 Paris, France, ‡Centre for Genetic Architecture of Complex Traits, and xDepartment of Genetics, University of Leicester, LE1 7RH, United Kingdom ORCID ID: 0000-0003-1157-3608 (E.J.L.) ABSTRACT Considerable progress in our understanding of yeast genomes and their evolution has been made over the last decade with the sequencing, analysis, and comparisons of numerous species, strains, or isolates of diverse origins. The role played by yeasts in natural environments as well as in artificial manufactures, combined with the importance of some species as model experimental systems sustained this effort. At the same time, their enormous evolutionary diversity (there are yeast species in every subphylum of Dikarya) sparked curiosity but necessitated further efforts to obtain appropriate reference genomes. Today, yeast genomes have been very informative about basic mechanisms of evolution, speciation, hybridization, domestication, as well as about the molecular machineries underlying them. They are also irreplaceable to investigate in detail the complex relationship between genotypes and phenotypes with both theoretical and practical implications. This review examines these questions at two distinct levels offered by the broad evolutionary range of yeasts: inside the best-studied Saccharomyces species complex, and across the entire and diversified subphylum of Saccharomycotina. While obviously revealing evolutionary histories at different scales, data converge to a remarkably coherent picture in which one can estimate the relative importance of intrinsic genome dynamics, including gene birth and loss, vs. -
Desulfuribacillus Alkaliarsenatis Gen. Nov. Sp. Nov., a Deep-Lineage
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by PubMed Central Extremophiles (2012) 16:597–605 DOI 10.1007/s00792-012-0459-7 ORIGINAL PAPER Desulfuribacillus alkaliarsenatis gen. nov. sp. nov., a deep-lineage, obligately anaerobic, dissimilatory sulfur and arsenate-reducing, haloalkaliphilic representative of the order Bacillales from soda lakes D. Y. Sorokin • T. P. Tourova • M. V. Sukhacheva • G. Muyzer Received: 10 February 2012 / Accepted: 3 May 2012 / Published online: 24 May 2012 Ó The Author(s) 2012. This article is published with open access at Springerlink.com Abstract An anaerobic enrichment culture inoculated possible within a pH range from 9 to 10.5 (optimum at pH with a sample of sediments from soda lakes of the Kulunda 10) and a salt concentration at pH 10 from 0.2 to 2 M total Steppe with elemental sulfur as electron acceptor and for- Na? (optimum at 0.6 M). According to the phylogenetic mate as electron donor at pH 10 and moderate salinity analysis, strain AHT28 represents a deep independent inoculated with sediments from soda lakes in Kulunda lineage within the order Bacillales with a maximum of Steppe (Altai, Russia) resulted in the domination of a 90 % 16S rRNA gene similarity to its closest cultured Gram-positive, spore-forming bacterium strain AHT28. representatives. On the basis of its distinct phenotype and The isolate is an obligate anaerobe capable of respiratory phylogeny, the novel haloalkaliphilic anaerobe is suggested growth using elemental sulfur, thiosulfate (incomplete as a new genus and species, Desulfuribacillus alkaliar- T T reduction) and arsenate as electron acceptor with H2, for- senatis (type strain AHT28 = DSM24608 = UNIQEM mate, pyruvate and lactate as electron donor. -
Identification and Phylogeny of Ascomycetous Yeasts from Analysis
Antonie van Leeuwenhoek 73: 331–371, 1998. 331 © 1998 Kluwer Academic Publishers. Printed in the Netherlands. Identification and phylogeny of ascomycetous yeasts from analysis of nuclear large subunit (26S) ribosomal DNA partial sequences Cletus P. Kurtzman∗ & Christie J. Robnett Microbial Properties Research, National Center for Agricultural Utilization Research, Agricultural Research Ser- vice, U.S. Department of Agriculture, Peoria, Illinois 61604, USA (∗ author for correspondence) E-mail: [email protected] Received 19 June 1998; accepted 19 June 1998 Key words: Ascomycetous yeasts, phylogeny, ribosomal DNA, systematics Abstract Approximately 500 species of ascomycetous yeasts, including members of Candida and other anamorphic genera, were analyzed for extent of divergence in the variable D1/D2 domain of large subunit (26S) ribosomal DNA. Divergence in this domain is generally sufficient to resolve individual species, resulting in the prediction that 55 currently recognized taxa are synonyms of earlier described species. Phylogenetic relationships among the ascomycetous yeasts were analyzed from D1/D2 sequence divergence. For comparison, the phylogeny of selected members of the Saccharomyces clade was determined from 18S rDNA sequences. Species relationships were highly concordant between the D1/D2 and 18S trees when branches were statistically well supported. Introduction lesser ranges of nDNA relatedness than those found among heterothallic species. Disadvantages of nDNA reassociation studies in- Procedures commonly used for yeast identification clude the need for pairwise comparisons of all isolates rely on the appearance of cellular morphology and dis- under study and that resolution is limited to the ge- tinctive reactions on a standardized set of fermentation netic distance of sister species, i.e., closely related and assimilation tests. -
Identifying and Characterizing Novel Bacilli Capable of Degrading Recalcitrant Polymers
University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Doctoral Dissertations Graduate School 12-2019 Breaking the Chain: Identifying and Characterizing Novel Bacilli Capable of Degrading Recalcitrant Polymers Kyle Bonifer University of Tennessee, [email protected] Follow this and additional works at: https://trace.tennessee.edu/utk_graddiss Recommended Citation Bonifer, Kyle, "Breaking the Chain: Identifying and Characterizing Novel Bacilli Capable of Degrading Recalcitrant Polymers. " PhD diss., University of Tennessee, 2019. https://trace.tennessee.edu/utk_graddiss/5738 This Dissertation is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a dissertation written by Kyle Bonifer entitled "Breaking the Chain: Identifying and Characterizing Novel Bacilli Capable of Degrading Recalcitrant Polymers." I have examined the final electronic copy of this dissertation for form and content and recommend that it be accepted in partial fulfillment of the equirr ements for the degree of Doctor of Philosophy, with a major in Microbiology. Todd Reynolds, Major Professor We have read this dissertation and recommend its acceptance: Elizabeth Fozo, Gladys Alexandre, Jennifer Debruyn Accepted for the Council: Dixie L. Thompson Vice Provost and Dean of the Graduate School (Original signatures are on file with official studentecor r ds.) Breaking the Chain: Identifying and Characterizing Novel Bacilli Capable of Degrading Recalcitrant Polymers A Dissertation Presented for the Doctor of Philosophy Degree The University of Tennessee, Knoxville Kyle Sabastian Bonifer December 2019 Copyright © 2019 by Kyle S. -
Fungi Associated with Ips Acuminatus (Coleoptera: Curculionidae) in Ukraine with a Special Emphasis on Pathogenicity of Ophiostomatoid Species
EUROPEAN JOURNAL OF ENTOMOLOGYENTOMOLOGY ISSN (online): 1802-8829 Eur. J. Entomol. 114: 77–85, 2017 http://www.eje.cz doi: 10.14411/eje.2017.011 ORIGINAL ARTICLE Fungi associated with Ips acuminatus (Coleoptera: Curculionidae) in Ukraine with a special emphasis on pathogenicity of ophiostomatoid species KATERYNA DAVYDENKO 1, 2, RIMVYDAS VASAITIS 2 and AUDRIUS MENKIS 2 1 Ukrainian Research Institute of Forestry & Forest Melioration, Pushkinska st. 86, 61024 Kharkiv, Ukraine; e-mail: [email protected] 2 Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, P.O. Box 7026, SE-75007, Uppsala, Sweden; e-mails: [email protected], [email protected] Key words. Coleoptera, Curculionidae, pine engraver beetle, Scots pine, Ips acuminatus, pathogens, Ophiostoma, Diplodia pinea, insect-fungus interaction Abstract. Conifer bark beetles are well known to be associated with fungal complexes, which consist of pathogenic ophiostoma- toid fungi as well as obligate saprotroph species. However, there is little information on fungi associated with Ips acuminatus in central and eastern Europe. The aim of the study was to investigate the composition of the fungal communities associated with the pine engraver beetle, I. acuminatus, in the forest-steppe zone in Ukraine and to evaluate the pathogenicity of six associated ophiostomatoid species by inoculating three-year-old Scots pine seedlings with these fungi. In total, 384 adult beetles were col- lected from under the bark of declining and dead Scots pine trees at two different sites. Fungal culturing from 192 beetles resulted in 447 cultures and direct sequencing of ITS rRNA from 192 beetles in 496 high-quality sequences. -
Biodiversity and Activity of Gut Fungal Communities Across the Life History of Trypophloeus Klimeschi (Coleoptera: Curculionidae: Scolytinae)
International Journal of Molecular Sciences Article Biodiversity and Activity of Gut Fungal Communities across the Life History of Trypophloeus klimeschi (Coleoptera: Curculionidae: Scolytinae) Guanqun Gao 1, Jing Gao 1, Chunfeng Hao 2, Lulu Dai 1 and Hui Chen 1,3,* ID 1 College of Forestry, Northwest A&F University, Yangling 712100, China; [email protected] (G.G.); [email protected] (J.G.); [email protected] (L.D.) 2 Tianjin Forestry Pest Control and Quarantine Station, Tianjin 300000, China; [email protected] 3 State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China * Correspondence: [email protected]; Tel.: +86-29-8708-2083 Received: 7 May 2018; Accepted: 5 July 2018; Published: 10 July 2018 Abstract: We comprehensively investigated the biodiversity of fungal communities in different developmental stages of Trypophloeus klimeschi and the difference between sexes and two generations by high throughput sequencing. The predominant species found in the intestinal fungal communities mainly belong to the phyla Ascomycota and Basidiomycota. Fungal community structure varies with life stage. The genera Nakazawaea, Trichothecium, Aspergillus, Didymella, Villophora, and Auricularia are most prevalent in the larvae samples. Adults harbored high proportions of Graphium. The fungal community structures found in different sexes are similar. Fusarium is the most abundant genus and conserved in all development stages. Gut fungal communities showed notable variation in relative abundance during the overwintering stage. Fusarium and Nectriaceae were significantly increased in overwintering mature larvae. The data indicates that Fusarium might play important roles in the survival of T. -
Nakazawaea Todaengensis F.A., Sp. Nov., a Yeast Isolated from a Peat
TAXONOMIC DESCRIPTION Polburee et al., Int J Syst Evol Microbiol 2017;67:2377–2382 DOI 10.1099/ijsem.0.001961 List of Publications for 2017 Khanok RAAAKHAOKCHAI Nakazawaea todaengensis f.a., sp. nov., a yeast isolated from a 1. Phitsuwan, P., Permsriburasuk, C., Baramee, S., Teeravivattanakit, T., and peat swamp forest in Thailand Ratanakhanokchai, K. (2017). Structural analysis of alkaline pretreated rice straw for 1,5 1 2 3 1,4, ethanol production. International Journal of Polymer Science 17: Article ID Pirapan Polburee, Noppon Lertwattanasakul, Pitayakon Limtong, Marizeth Groenewald and Savitree Limtong * 4876969, 9 pages. https://doi.org/10.1155/2017/4876969. Abstract 2. Teeravivattanakit, T., Baramee, B., Phitsuwan, P., Sornyotha, S., Waeonukul, R., T Pason, P., Tachaapaikoon, C., Poomputsa, K., Kosugi, A., Sakka, K., and Strain DMKU-PS11(1) was isolated from peat in a swamp forest in Thailand. DNA sequence analysis showed that it belonged to a novel species that was most closely related to Nakazawaea laoshanensis. However, it differed from the type strain of Ratanakhanokchai, K. (2017). Chemical pretreatment-independent saccharifications N. laoshanensis (NRRL Y-63634T) by 2.3 % nucleotide substitutions in the D1/D2 region of the large subunit (LSU) rRNA gene, of xylan and cellulose of rice straw by bacterial weak lignin-binding xylanolytic and 1.0 % nucleotide substitutions in the small subunit (SSU) rRNA gene and 8.0 % nucleotide substitutions in the internal cellulolytic enzymes. Applied and Environmental Microbiology 83: no.22, transcribed spacer (ITS) region. The phylogenetic analyses based on the combined sequences of the SSU and the D1/D2 region e01522-17. -
D-Fructose Assimilation and Fermentation by Yeasts
microorganisms Article D-Fructose Assimilation and Fermentation by Yeasts Belonging to Saccharomycetes: Rediscovery of Universal Phenotypes and Elucidation of Fructophilic Behaviors in Ambrosiozyma platypodis and Cyberlindnera americana Rikiya Endoh *, Maiko Horiyama and Moriya Ohkuma Microbe Division/Japan Collection of Microorganisms, RIKEN BioResource Research Center (RIKEN BRC-JCM), 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan; [email protected] (M.H.); [email protected] (M.O.) * Correspondence: [email protected] Abstract: The purpose of this study was to investigate the ability of ascomycetous yeasts to as- similate/ferment D-fructose. This ability of the vast majority of yeasts has long been neglected since the standardization of the methodology around 1950, wherein fructose was excluded from the standard set of physiological properties for characterizing yeast species, despite the ubiquitous presence of fructose in the natural environment. In this study, we examined 388 strains of yeast, mainly belonging to the Saccharomycetes (Saccharomycotina, Ascomycota), to determine whether they can assimilate/ferment D-fructose. Conventional methods, using liquid medium containing Citation: Endoh, R.; Horiyama, M.; yeast nitrogen base +0.5% (w/v) of D-fructose solution for assimilation and yeast extract-peptone Ohkuma, M. D-Fructose Assimilation +2% (w/v) fructose solution with an inverted Durham tube for fermentation, were used. All strains and Fermentation by Yeasts examined (n = 388, 100%) assimilated D-fructose, whereas 302 (77.8%) of them fermented D-fructose. Belonging to Saccharomycetes: D D Rediscovery of Universal Phenotypes In addition, almost all strains capable of fermenting -glucose could also ferment -fructose. These and Elucidation of Fructophilic results strongly suggest that the ability to assimilate/ferment D-fructose is a universal phenotype Behaviors in Ambrosiozyma platypodis among yeasts in the Saccharomycetes. -
DNA Barcoding Analysis of More Than 1000 Marine Yeast Isolates Reveals Previously Unrecorded Species
bioRxiv preprint doi: https://doi.org/10.1101/2020.08.29.273490; this version posted August 29, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. DNA barcoding analysis of more than 1000 marine yeast isolates reveals previously unrecorded species Chinnamani PrasannaKumar*1,2, Shanmugam Velmurugan2,3, Kumaran Subramanian4, S. R. Pugazhvendan5, D. Senthil Nagaraj3, K. Feroz Khan2,6, Balamurugan Sadiappan1,2, Seerangan Manokaran7, Kaveripakam Raman Hemalatha8 1Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Panaji, Goa-403004, India 2Centre of Advance studies in Marine Biology, Annamalai University, Parangipettai, Tamil Nadu- 608502, India 3Madawalabu University, Bale, Robe, Ethiopia 4Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Tamil Nadu-600119, India. 5Department of Zoology, Arignar Anna Government Arts College, Cheyyar, Tamil Nadu- 604407, India 6Research Department of Microbiology, Sadakathullah Appa College, Rahmath Nagar, Tirunelveli Tamil Nadu -627 011 7Center for Environment & Water, King Fahd University of Petroleum and Minerals, Dhahran-31261, Saudi Arabia 8Department of Microbiology, Annamalai university, Annamalai Nagar, Chidambaram, Tamil Nadu- 608 002, India Corresponding author email: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.08.29.273490; this version posted August 29, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. -
Reorganising the Order Bacillales Through Phylogenomics
Systematic and Applied Microbiology 42 (2019) 178–189 Contents lists available at ScienceDirect Systematic and Applied Microbiology jou rnal homepage: http://www.elsevier.com/locate/syapm Reorganising the order Bacillales through phylogenomics a,∗ b c Pieter De Maayer , Habibu Aliyu , Don A. Cowan a School of Molecular & Cell Biology, Faculty of Science, University of the Witwatersrand, South Africa b Technical Biology, Institute of Process Engineering in Life Sciences, Karlsruhe Institute of Technology, Germany c Centre for Microbial Ecology and Genomics, University of Pretoria, South Africa a r t i c l e i n f o a b s t r a c t Article history: Bacterial classification at higher taxonomic ranks such as the order and family levels is currently reliant Received 7 August 2018 on phylogenetic analysis of 16S rRNA and the presence of shared phenotypic characteristics. However, Received in revised form these may not be reflective of the true genotypic and phenotypic relationships of taxa. This is evident in 21 September 2018 the order Bacillales, members of which are defined as aerobic, spore-forming and rod-shaped bacteria. Accepted 18 October 2018 However, some taxa are anaerobic, asporogenic and coccoid. 16S rRNA gene phylogeny is also unable to elucidate the taxonomic positions of several families incertae sedis within this order. Whole genome- Keywords: based phylogenetic approaches may provide a more accurate means to resolve higher taxonomic levels. A Bacillales Lactobacillales suite of phylogenomic approaches were applied to re-evaluate the taxonomy of 80 representative taxa of Bacillaceae eight families (and six family incertae sedis taxa) within the order Bacillales. -
Actinobacteria Bacteroidetes Chloroflexi Firmicutes
Table 2b. Genera of Actinobacteria, Bacterioidetes Cloroflexi and Firmicutes members of anisakids microbiota. Colors represent the clusters in which they are in Figure 5. Asterisks denote the most contributive in the ordination of Factorial Space Actinobacteria Bacteroidetes Chloroflexi Firmicutes Rubrobacteria Actinobacteria Coriobacteria Bacteroidia Flavobacteria Sphingobacteria Anaerolineae Caldilineae Chloroflexia Bacilli Mollicutes Erysipelotrichia Clostridia Rubrobacterales Acidimicrobiales Actinomycetales Bifidobacteriales Coriobacteriales Bacteroidales Flavobacteriales Sphingobacteriales Anaerolineales Caldilineales Chloroflexales Bacillales Lactobacillales Mycoplasmatales Erysipelotrichales Clostridiales Thermoanaerobacterales Rubrobacteriaceae Rubrobacter Acidimicrobiaceae (5) unclassified Actinomyces* Actinomycetaceae (2) Mobiluncus Brevibacteriaceae (2) Brevibacterium* Cellulomonadaceae unclassified Corynebacteriaceae Corynebacterium* Dermabacteraceae Brachybacterium* Dermatophilaceae unclassified Dietziaceae Dietzia Blastococcus Geodermatophilaceae Geodermatophilus Glycomycetaceae Glycomyces Intrasporangiaceae Ornithinicoccus Kineosporiaceae Kineococcus Microbacteriaceae unclassified Micrococcus* Rothia * Micrococcaceae Kocuria Arthrobacter Micromonosporaceae Actinoplanes Mycobacteriaceae Mycobacterium* Rhodococcus Nocardiaceae Gordonia Nocardia Nocardioides* Nocardioidaceae Aeromicrobium Kribbella Propionibacterium* Propionibacteriaceae Friedmanniella Pseudonocardia Pseudonocardiaceae Amycolatopsis Sporichthyaceae hgcI_clade -
Kroppenstedtia Eburnea Gen. Nov., Sp. Nov., A
International Journal of Systematic and Evolutionary Microbiology (2011), 61, 2304–2310 DOI 10.1099/ijs.0.026179-0 Kroppenstedtia eburnea gen. nov., sp. nov., a thermoactinomycete isolated by environmental screening, and emended description of the family Thermoactinomycetaceae Matsuo et al. 2006 emend. Yassin et al. 2009 Mathias von Jan,1 Nicole Riegger,2 Gabriele Po¨tter,1 Peter Schumann,1 Susanne Verbarg,1 Cathrin Spro¨er,1 Manfred Rohde,3 Bettina Lauer,2 David P. Labeda4 and Hans-Peter Klenk1 Correspondence 1DSMZ – German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany Hans-Peter Klenk 2Microbiology, Vetter Pharma-Fertigung GmbH & Co. KG, 88212 Ravensburg, Germany [email protected] 3HZI – Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany 4National Center for Agricultural Utilization Research, USDA-ARS, Peoria, IL 61604, USA A Gram-positive, spore-forming, aerobic, filamentous bacterium, strain JFMB-ATET, was isolated in 2008 during environmental screening of a plastic surface in grade C in a contract manufacturing organization in southern Germany. The isolate grew at temperatures of 25–50 6C and at pH 5.0–8.5, forming ivory-coloured colonies with sparse white aerial mycelia. Chemotaxonomic and molecular characteristics of the isolate matched those described for members of the family Thermoactinomycetaceae, except that the cell-wall peptidoglycan contained LL-diaminopimelic acid, while all previously described members of this family display this diagnostic diamino acid in meso-conformation. The DNA G+C content of the novel strain was 54.6 mol%, the main polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol, and the major menaquinone was MK-7. The major fatty acids had saturated C14–C16 branched chains.