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      A Taxonomic Revision of the Wallemia sebi Species Complex

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          Abstract

          Wallemia sebi is a xerophilic food- and air-borne fungus. The name has been used for strains that prevail in cold, temperate and tropical climates. In this study, multi-locus phylogenetic analyses, using the internal transcribed spacer (ITS) regions, DNA replication licensing factor ( MCM7), pre-rRNA processing protein ( TSR1), RNA polymerase II largest subunit ( RPB1), RNA polymerase II second largest subunit ( RPB2) and a new marker 3´-phosphoadenosine-5´-phosphatase ( HAL2), confirmed the previous hypothesis that W. sebi presents a complex of at least four species. Here, we confirm and apply the phylogenetic analyses based species hypotheses from a companion study to guide phenotypic assessment of W. sebi like strains from a wide range of substrates, climates and continents allowed the recognition of W. sebi sensu stricto and three new species described as W. mellicola, W. Canadensis, and W. tropicalis. The species differ in their conidial size, xerotolerance, halotolerance, chaotolerance, growth temperature regimes, extracellular enzyme activity profiles, and secondary metabolite patterns. A key to all currently accepted Wallemia species is provided that allow their identification on the basis of physiological, micromorphological and culture characters.

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          Phylogenetic species recognition and species concepts in fungi.

          The operational species concept, i.e., the one used to recognize species, is contrasted to the theoretical species concept. A phylogenetic approach to recognize fungal species based on concordance of multiple gene genealogies is compared to those based on morphology and reproductive behavior. Examples where Phylogenetic Species Recognition has been applied to fungi are reviewed and concerns regarding Phylogenetic Species Recognition are discussed.
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            Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits.

            Based on an overview of progress in molecular systematics of the true fungi (Fungi/Eumycota) since 1990, little overlap was found among single-locus data matrices, which explains why no large-scale multilocus phylogenetic analysis had been undertaken to reveal deep relationships among fungi. As part of the project "Assembling the Fungal Tree of Life" (AFTOL), results of four Bayesian analyses are reported with complementary bootstrap assessment of phylogenetic confidence based on (1) a combined two-locus data set (nucSSU and nucLSU rDNA) with 558 species representing all traditionally recognized fungal phyla (Ascomycota, Basidiomycota, Chytridiomycota, Zygomycota) and the Glomeromycota, (2) a combined three-locus data set (nucSSU, nucLSU, and mitSSU rDNA) with 236 species, (3) a combined three-locus data set (nucSSU, nucLSU rDNA, and RPB2) with 157 species, and (4) a combined four-locus data set (nucSSU, nucLSU, mitSSU rDNA, and RPB2) with 103 species. Because of the lack of complementarity among single-locus data sets, the last three analyses included only members of the Ascomycota and Basidiomycota. The four-locus analysis resolved multiple deep relationships within the Ascomycota and Basidiomycota that were not revealed previously or that received only weak support in previous studies. The impact of this newly discovered phylogenetic structure on supraordinal classifications is discussed. Based on these results and reanalysis of subcellular data, current knowledge of the evolution of septal features of fungal hyphae is synthesized, and a preliminary reassessment of ascomal evolution is presented. Based on previously unpublished data and sequences from GenBank, this study provides a phylogenetic synthesis for the Fungi and a framework for future phylogenetic studies on fungi.
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              Polyphasic taxonomy, a consensus approach to bacterial systematics.

              Over the last 25 years, a much broader range of taxonomic studies of bacteria has gradually replaced the former reliance upon morphological, physiological, and biochemical characterization. This polyphasic taxonomy takes into account all available phenotypic and genotypic data and integrates them in a consensus type of classification, framed in a general phylogeny derived from 16S rRNA sequence analysis. In some cases, the consensus classification is a compromise containing a minimum of contradictions. It is thought that the more parameters that will become available in the future, the more polyphasic classification will gain stability. In this review, the practice of polyphasic taxonomy is discussed for four groups of bacteria chosen for their relevance, complexity, or both: the genera Xanthomonas and Campylobacter, the lactic acid bacteria, and the family Comamonadaceae. An evaluation of our present insights, the conclusions derived from it, and the perspectives of polyphasic taxonomy are discussed, emphasizing the keystone role of the species. Taxonomists did not succeed in standardizing species delimitation by using percent DNA hybridization values. Together with the absence of another "gold standard" for species definition, this has an enormous repercussion on bacterial taxonomy. This problem is faced in polyphasic taxonomy, which does not depend on a theory, a hypothesis, or a set of rules, presenting a pragmatic approach to a consensus type of taxonomy, integrating all available data maximally. In the future, polyphasic taxonomy will have to cope with (i) enormous amounts of data, (ii) large numbers of strains, and (iii) data fusion (data aggregation), which will demand efficient and centralized data storage. In the future, taxonomic studies will require collaborative efforts by specialized laboratories even more than now is the case. Whether these future developments will guarantee a more stable consensus classification remains an open question.
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                Author and article information

                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                27 May 2015
                2015
                : 10
                : 5
                : e0125933
                Affiliations
                [1 ]Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
                [2 ]Department of Biology, Faculty of Science, University of Ottawa, Ottawa, Ontario, Canada
                [3 ]Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
                [4 ]Agricultural Institute of Slovenia, Ljubljana, Slovenia
                [5 ]Biodiversity (Mycology), Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
                [6 ]Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKeBiP), Ljubljana, Slovenia
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Conceived and designed the experiments: SJ HDTN JCF KAS NGC. Performed the experiments: SJ HDTN JCF. Analyzed the data: SJ HDTN JCF. Contributed reagents/materials/analysis tools: SJ HDTN JCF PZ KAS NGC. Wrote the paper: SJ HDTN JCF PZ HJS KAS NGC.

                Article
                PONE-D-14-50714
                10.1371/journal.pone.0125933
                4446336
                26017053
                2c9993c5-a605-4aac-93a3-44f38af7cc4c
                Copyright @ 2015

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

                History
                : 15 November 2014
                : 25 March 2015
                Page count
                Figures: 7, Tables: 3, Pages: 25
                Funding
                This work was funded by the Slovenian Research Agency ( https://www.arrs.gov.si/en/dobrodoslica.asp) through the Infrastructural Centre Mycosmo ( http://www.ex-genebank.com/) and the Young Researcher Grant to SJ, 1000-11-310102. This work was partly funded by Slovenian Ministry of Higher Education, Science and Technology ( http://www.arhiv.mvzt.gov.si/en/) and European Regional Development Fund through the Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKeBiP, http://cipkebip.org/, OP13.1.1.2.02.0005), and by grants to KAS and HDTN from the Alfred P. Sloan Foundation Program on the Microbiology of the Built Environment ( http://www.sloan.org/major-program-areas/). Parts of this work were realized within the frame of FP7 Project CropSustaIn (FP7-REGPOT-CT2012-316205). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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