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      The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks

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          Abstract

          SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive resource for up-to-date quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. SILVA provides a manually curated taxonomy for all three domains of life, based on representative phylogenetic trees for the small- and large-subunit rRNA genes. This article describes the improvements the SILVA taxonomy has undergone in the last 3 years. Specifically we are focusing on the curation process, the various resources used for curation and the comparison of the SILVA taxonomy with Greengenes and RDP-II taxonomies. Our comparisons not only revealed a reasonable overlap between the taxa names, but also points to significant differences in both names and numbers of taxa between the three resources.

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          Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.

          C Woese, O Kandler, M L Wheelis (1990)
          Molecular structures and sequences are generally more revealing of evolutionary relationships than are classical phenotypes (particularly so among microorganisms). Consequently, the basis for the definition of taxa has progressively shifted from the organismal to the cellular to the molecular level. Molecular comparisons show that life on this planet divides into three primary groupings, commonly known as the eubacteria, the archaebacteria, and the eukaryotes. The three are very dissimilar, the differences that separate them being of a more profound nature than the differences that separate typical kingdoms, such as animals and plants. Unfortunately, neither of the conventionally accepted views of the natural relationships among living systems--i.e., the five-kingdom taxonomy or the eukaryote-prokaryote dichotomy--reflects this primary tripartite division of the living world. To remedy this situation we propose that a formal system of organisms be established in which above the level of kingdom there exists a new taxon called a "domain." Life on this planet would then be seen as comprising three domains, the Bacteria, the Archaea, and the Eucarya, each containing two or more kingdoms. (The Eucarya, for example, contain Animalia, Plantae, Fungi, and a number of others yet to be defined). Although taxonomic structure within the Bacteria and Eucarya is not treated herein, Archaea is formally subdivided into the two kingdoms Euryarchaeota (encompassing the methanogens and their phenotypically diverse relatives) and Crenarchaeota (comprising the relatively tight clustering of extremely thermophilic archaebacteria, whose general phenotype appears to resemble most the ancestral phenotype of the Archaea.
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            A molecular view of microbial diversity and the biosphere.

            N Pace (1997)
            Over three decades of molecular-phylogenetic studies, researchers have compiled an increasingly robust map of evolutionary diversification showing that the main diversity of life is microbial, distributed among three primary relatedness groups or domains: Archaea, Bacteria, and Eucarya. The general properties of representatives of the three domains indicate that the earliest life was based on inorganic nutrition and that photosynthesis and use of organic compounds for carbon and energy metabolism came comparatively later. The application of molecular-phylogenetic methods to study natural microbial ecosystems without the traditional requirement for cultivation has resulted in the discovery of many unexpected evolutionary lineages; members of some of these lineages are only distantly related to known organisms but are sufficiently abundant that they are likely to have impact on the chemistry of the biosphere.
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              The new higher level classification of eukaryotes with emphasis on the taxonomy of protists.

              SINA M. ADL, ALASTAIR G. B. SIMPSON, MARK A. FARMER … (2005)
              This revision of the classification of unicellular eukaryotes updates that of Levine et al. (1980) for the protozoa and expands it to include other protists. Whereas the previous revision was primarily to incorporate the results of ultrastructural studies, this revision incorporates results from both ultrastructural research since 1980 and molecular phylogenetic studies. We propose a scheme that is based on nameless ranked systematics. The vocabulary of the taxonomy is updated, particularly to clarify the naming of groups that have been repositioned. We recognize six clusters of eukaryotes that may represent the basic groupings similar to traditional "kingdoms." The multicellular lineages emerged from within monophyletic protist lineages: animals and fungi from Opisthokonta, plants from Archaeplastida, and brown algae from Stramenopiles.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Nucleic Acids Res
                Journal ID (iso-abbrev): Nucleic Acids Res
                Journal ID (publisher-id): nar
                Journal ID (hwp): nar
                Title: Nucleic Acids Research
                Publisher: Oxford University Press
                ISSN (Print): 0305-1048
                ISSN (Electronic): 1362-4962
                Publication date (Print): January 2014
                Publication date (Electronic): 28 November 2013
                Publication date PMC-release: 28 November 2013
                Volume: 42
                Issue: D1 , Database issue
                Pages: D643-D648
                Affiliations
                1Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology, D-28359 Bremen, Germany, 2Department of Botany, University of British Columbia, Vancouver V6T 1Z4, Canada, 3Department of Zoology, University of British Columbia, Vancouver V6T 1Z4, Canada, 4Ribocon GmbH, D-28359 Bremen, Germany, 5School of Engineering and Science, Jacobs University Bremen gGmbH, D-28759 Bremen, Germany and 6Lehrstuhl für Mikrobiologie, Technische Universität München, D-853530 Freising, Germany
                Author notes
                *To whom correspondence should be addressed. Tel: +49 421 2028 970; Fax: +49 421 2028 580; Email: fog@ 123456mpi-bremen.de
                Correspondence may also be addressed to Pelin Yilmaz. Tel: +49 421 2028 980; Fax: +49 421 2028 580; Email: pyilmaz@ 123456mpi-bremen.de
                Article
                Publisher ID: gkt1209
                DOI: 10.1093/nar/gkt1209
                PMC ID: 3965112
                PubMed ID: 24293649
                SO-VID: 1cd3768d-6645-4670-aa2f-5d8d866aa6ff
                Copyright © © The Author(s) 2013. Published by Oxford University Press.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

                History
                Date received : 24 September 2013
                Date revision received : 4 November 2013
                Date accepted : 4 November 2013
                Page count
                Pages: 6
                Categories
                Subject: IV. Viruses, bacteria, protozoa and fungi
                Custom metadata
                cover-date 1 January 2014

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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