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      Aquimarina longa sp. nov., isolated from seawater, and emended description of Aquimarina muelleri

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          Abstract

          A novel Gram-stain-negative, rod-shaped, non-flagellated, strictly aerobic strain with gliding motility, designated SW024 T, was isolated from surface seawater of the South Pacific Gyre (26° 29′ S 137° 56′ W) during the Integrated Ocean Drilling Program Expedition 329. Phylogenetic analyses based on 16S rRNA gene sequences showed that the novel strain was related most closely to Aquimarina muelleri KMM 6020 T, Aquimarina macrocephali JAMB N27 T, Aquimarina addita JC2680 T, http://dx.doi.org/10.1601/nm.23278 Aquimarina mytili PSC33 T, Aquimarina intermedia KMM 6258 T, Aquimarina latercula ATCC 23177 T, Aquimarina spongiae A6 T, Aquimarina agarilytica ZC1 T and Aquimarina brevivitae SMK-19 T (96.1, 95.5, 95.0, 94.4, 94.3, 94.0, 93.4, 93.3 and 93.2 % similarities, respectively), demonstrating that the novel strain belonged to the genus Aquimarina . The DNA G+C content of strain SW024 T was 30.8 mol%. The major respiratory quinone of strain SW024 T was MK-6. The dominant fatty acids were iso-C 15 : 0, iso-C 17 : 0 3-OH, iso-C 15 : 1 G, C 16 : 0 10-methyl and/or iso-C 17 : 1ω 9c, and iso-C 15 : 0 3-OH. The polar lipids of strain SW024 T were phosphatidylethanolamine, three unknown aminolipids and five unknown polar lipids. On the basis of combined phenotypic and phylogenetic analyses, strain SW024 T represents a novel species of the genus Aquimarina , for which the name Aquimarina longa sp. nov. is proposed. The type strain is SW024 T ( = CGMCC 1.11007 T = JCM 17859 T). An emended description of A. muelleri is also proposed.

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          A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences.

          Some simple formulae were obtained which enable us to estimate evolutionary distances in terms of the number of nucleotide substitutions (and, also, the evolutionary rates when the divergence times are known). In comparing a pair of nucleotide sequences, we distinguish two types of differences; if homologous sites are occupied by different nucleotide bases but both are purines or both pyrimidines, the difference is called type I (or "transition" type), while, if one of the two is a purine and the other is a pyrimidine, the difference is called type II (or "transversion" type). Letting P and Q be respectively the fractions of nucleotide sites showing type I and type II differences between two sequences compared, then the evolutionary distance per site is K = -(1/2) ln [(1-2P-Q) square root of 1-2Q]. The evolutionary rate per year is then given by k = K/(2T), where T is the time since the divergence of the two sequences. If only the third codon positions are compared, the synonymous component of the evolutionary base substitutions per site is estimated by K'S = -(1/2) ln (1-2P-Q). Also, formulae for standard errors were obtained. Some examples were worked out using reported globin sequences to show that synonymous substitutions occur at much higher rates than amino acid-altering substitutions in evolution.
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            MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods.

            Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. Here, we announce the release of Molecular Evolutionary Genetics Analysis version 5 (MEGA5), which is a user-friendly software for mining online databases, building sequence alignments and phylogenetic trees, and using methods of evolutionary bioinformatics in basic biology, biomedicine, and evolution. The newest addition in MEGA5 is a collection of maximum likelihood (ML) analyses for inferring evolutionary trees, selecting best-fit substitution models (nucleotide or amino acid), inferring ancestral states and sequences (along with probabilities), and estimating evolutionary rates site-by-site. In computer simulation analyses, ML tree inference algorithms in MEGA5 compared favorably with other software packages in terms of computational efficiency and the accuracy of the estimates of phylogenetic trees, substitution parameters, and rate variation among sites. The MEGA user interface has now been enhanced to be activity driven to make it easier for the use of both beginners and experienced scientists. This version of MEGA is intended for the Windows platform, and it has been configured for effective use on Mac OS X and Linux desktops. It is available free of charge from http://www.megasoftware.net.
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              Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species.

              Despite recent advances in commercially optimized identification systems, bacterial identification remains a challenging task in many routine microbiological laboratories, especially in situations where taxonomically novel isolates are involved. The 16S rRNA gene has been used extensively for this task when coupled with a well-curated database, such as EzTaxon, containing sequences of type strains of prokaryotic species with validly published names. Although the EzTaxon database has been widely used for routine identification of prokaryotic isolates, sequences from uncultured prokaryotes have not been considered. Here, the next generation database, named EzTaxon-e, is formally introduced. This new database covers not only species within the formal nomenclatural system but also phylotypes that may represent species in nature. In addition to an identification function based on Basic Local Alignment Search Tool (blast) searches and pairwise global sequence alignments, a new objective method of assessing the degree of completeness in sequencing is proposed. All sequences that are held in the EzTaxon-e database have been subjected to phylogenetic analysis and this has resulted in a complete hierarchical classification system. It is concluded that the EzTaxon-e database provides a useful taxonomic backbone for the identification of cultured and uncultured prokaryotes and offers a valuable means of communication among microbiologists who routinely encounter taxonomically novel isolates. The database and its analytical functions can be found at http://eztaxon-e.ezbiocloud.net/.
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                Author and article information

                Journal
                International Journal of Systematic and Evolutionary Microbiology
                Microbiology Society
                1466-5026
                1466-5034
                April 01 2013
                April 01 2013
                : 63
                : Pt_4
                : 1235-1240
                Affiliations
                [1 ] College of Marine Life Sciences, Ocean University of China, Qingdao, PR China
                Article
                10.1099/ijs.0.041509-0
                22771683
                8b464668-2a4e-4d29-adea-d84a2e662eec
                © 2013
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