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      Reclassification of the polyphyletic genus Prosthecomicrobium to form two novel genera, Vasilyevaea gen. nov. and Bauldia gen. nov. with four new combinations: Vasilyevaea enhydra comb. nov., Vasilyevaea mishustinii comb. nov., Bauldia consociata comb. nov. and Bauldia litoralis comb. nov.

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          Abstract

          Species of the genus Prosthecomicrobium are noted for their numerous cellular appendages or prosthecae that extend from the cells. This investigation confirms that the genus is polyphyletic based on an extensive analysis of the 16S rRNA gene sequences of several named species of the genus. The analyses indicate that some Prosthecomicrobium species are more closely related to non-prosthecate genera, including Devosia, Labrenzia, Blastochloris, Methylosinus, Mesorhizobium and Kaistia, than they are to other species of the genus Prosthecomicrobium. For this reason, two of the Prosthecomicrobium clades which are polyphyletic with the type species, Prosthecomicrobium pneumaticum, are renamed as new genera. The currently named species Prosthecomicrobium enhydrum, Prosthecomicrobium mishustinii, Prosthecomicrobium consociatum and Prosthecomicrobium litoralum are reclassified in two new genera, Vasilyevaea gen. nov. and Bauldia gen. nov. with four new combinations: Vasilyevaea enhydra comb. nov. (the type species) and Vasilyevaea mishustinii comb. nov., and Bauldia consociata comb. nov. and Bauldia litoralis comb. nov. (the type species). The type strain of Vasilyevaea enhydra is strain 9b T (=ATCC 23634 T =VKM B-1376 T). The type strain of the other species in this genus is Vasilyevaea mishustinii strain 17 T (=VKM B-2499 T =CCM 7569 T). The type strain of Bauldia litoralis is strain 524-16 T (= NCIB 2233 T =ATCC 35022 T). The type strain of the other species in this genus is Bauldia consociata strain 11 T (=VKM B-2498 T =CCM 7594 T).

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          Enrichment, isolation and some properties of methane-utilizing bacteria.

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            TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics

            Background Most analysis programs for inferring molecular phylogenies are difficult to use, in particular for researchers with little programming experience. Results TREEFINDER is an easy-to-use integrative platform-independent analysis environment for molecular phylogenetics. In this paper the main features of TREEFINDER (version of April 2004) are described. TREEFINDER is written in ANSI C and Java and implements powerful statistical approaches for inferring gene tree and related analyzes. In addition, it provides a user-friendly graphical interface and a phylogenetic programming language. Conclusions TREEFINDER is a versatile framework for analyzing phylogenetic data across different platforms that is suited both for exploratory as well as advanced studies.
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              The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy.

              The Ribosomal Database Project-II (RDP-II) pro-vides data, tools and services related to ribosomal RNA sequences to the research community. Through its website (http://rdp.cme.msu.edu), RDP-II offers aligned and annotated rRNA sequence data, analysis services, and phylogenetic inferences (trees) derived from these data. RDP-II release 8.1 contains 16 277 prokaryotic, 5201 eukaryotic, and 1503 mitochondrial small subunit rRNA sequences in aligned and annotated format. The current public beta release of 9.0 debuts a new regularly updated alignment of over 50 000 annotated (eu)bacterial sequences. New analysis services include a sequence search and selection tool (Hierarchy Browser) and a phylogenetic tree building and visualization tool (Phylip Interface). A new interactive tutorial guides users through the basics of rRNA sequence analysis. Other services include probe checking, phylogenetic placement of user sequences, screening of users' sequences for chimeric rRNA sequences, automated alignment, production of similarity matrices, and services to plan and analyze terminal restriction fragment polymorphism (T-RFLP) experiments. The RDP-II email address for questions or comments is rdpstaff@msu.edu.
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                Author and article information

                Journal
                Int J Syst Evol Microbiol
                ijs
                International Journal of Systematic and Evolutionary Microbiology
                Society for General Microbiology
                1466-5026
                1466-5034
                December 2010
                1 December 2011
                : 60
                : Pt 12
                : 2960-2966
                Affiliations
                [1 ]Department of Microbiology, University of Washington, Seattle, WA 98193, USA
                [2 ]School of Molecular and Microbial Sciences, University of Queensland, Brisbane, Australia
                Author notes
                Correspondence: James T. Staley: jtstaley@ 123456u.washington.edu
                Article
                2960
                10.1099/ijs.0.018234-0
                3052453
                20118292
                c3455dd8-931a-47cc-82b7-05920322f577
                Copyright © 2010, IUMS
                History
                Categories
                New Taxa

                Microbiology & Virology
                Microbiology & Virology

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