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 : 1}ω 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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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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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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CLUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program CLUSTAL W. The new system is easy to use, providing an integrated system for performing multiple sequence and profile alignments and analysing the results. CLUSTAL X displays the sequence alignment in a window on the screen. A versatile sequence colouring scheme allows the user to highlight conserved features in the alignment. Pull-down menus provide all the options required for traditional multiple sequence and profile alignment. New features include: the ability to cut-and-paste sequences to change the order of the alignment, selection of a subset of the sequences to be realigned, and selection of a sub-range of the alignment to be realigned and inserted back into the original alignment. Alignment quality analysis can be performed and low-scoring segments or exceptional residues can be highlighted. Quality analysis and realignment of selected residue ranges provide the user with a powerful tool to improve and refine difficult alignments and to trap errors in input sequences. CLUSTAL X has been compiled on SUN Solaris, IRIX5.3 on Silicon Graphics, Digital UNIX on DECstations, Microsoft Windows (32 bit) for PCs, Linux ELF for x86 PCs, and Macintosh PowerMac.

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Author and article information

Journal

Title: International Journal of Systematic and Evolutionary Microbiology

Publisher: Microbiology Society

ISSN (Print): 1466-5026

ISSN (Electronic): 1466-5034

Publication date Created: April 01 2013

Publication date (Print): April 01 2013

Volume: 63

Issue: Pt_4

Pages: 1235-1240

Affiliations

[1 ] College of Marine Life Sciences, Ocean University of China, Qingdao, PR China

Article

DOI: 10.1099/ijs.0.041509-0

PubMed ID: 22771683

SO-VID: 8b464668-2a4e-4d29-adea-d84a2e662eec

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