Ningiella ruwaisensis gen. nov., sp. nov., a member of the family Alteromonadaceae isolated from marine water of the Arabian Gulf

Abstract

<jats:p>Strain B66<jats:sup>T</jats:sup> was isolated from a marine water sample collected at Al Ruwais, located on the northern tip of Qatar. Cells were Gram-stain-negative, strictly aerobic and short- rod-shaped with a polar flagellum. The isolate was able to grow at 15–45 °C (optimum, 30 °C), at pH 5–11 (optimum, pH 6.5–8) and with 0–6 % NaCl. 16S rRNA gene sequence analysis revealed that strain B66<jats:sup>T</jats:sup> was affiliated with the family <jats:italic> <jats:named-content content-type="family"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.2805" xlink:type="simple">Alteromonadaceae</jats:ext-link> </jats:named-content> </jats:italic>, sharing the highest sequence similarities to the genera <jats:italic> <jats:named-content content-type="genus"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.2806" xlink:type="simple">Alteromonas</jats:ext-link> </jats:named-content> </jats:italic> (93.7–95.4 %), <jats:italic> <jats:named-content content-type="genus"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.2829" xlink:type="simple">Aestuariibacter</jats:ext-link> </jats:named-content> </jats:italic> (94.0–95.1 %), <jats:italic> <jats:named-content content-type="genus"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.25644" xlink:type="simple">Agaribacter</jats:ext-link> </jats:named-content> </jats:italic> (93.3–93.7 %), <jats:italic> <jats:named-content content-type="genus"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.2844" xlink:type="simple">Glaciecola</jats:ext-link> </jats:named-content> </jats:italic> (92.0–93.7 %), <jats:italic>Marisendiminitalea</jats:italic> (93.2–93.3 %) and <jats:italic> <jats:named-content content-type="genus"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.29743" xlink:type="simple">Planctobacterium</jats:ext-link> </jats:named-content> </jats:italic> (92.9 %). In the phylogenetic trees, strain B66<jats:sup>T</jats:sup> demonstrated the novel organism formed a distinct lineage closely associated with <jats:italic> <jats:named-content content-type="genus"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.2829" xlink:type="simple">Aestuariibacter</jats:ext-link> </jats:named-content> </jats:italic> and <jats:italic> <jats:named-content content-type="genus"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.29743" xlink:type="simple">Planctobacterium</jats:ext-link> </jats:named-content> </jats:italic>. Major fatty acids were C<jats:sub>16 : 0</jats:sub>, summed feature 3 (C<jats:sub>16 : 1</jats:sub> <jats:italic> </jats:italic>ω<jats:italic>7c</jats:italic>/C<jats:sub>16 : 1</jats:sub> <jats:italic> </jats:italic>ω6<jats:italic>c</jats:italic>/iso-C<jats:sub>15 : 0</jats:sub> 2-OH and iso-C<jats:sub>15 : 0</jats:sub> 3-OH. The major respiratory quinone was ubiquinone-8 and the major polar lipids are phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content derived from the genome was 43.2 mol%. Based on the phenotypic, chemotaxonomic, phylogenetic and genomic data, strain B66<jats:sup>T</jats:sup> is considered to represent a novel species and genus for which the name <jats:italic>Ningiella ruwaisensis</jats:italic> gen. nov., sp. nov., is proposed. The type strain is B66<jats:sup>T</jats:sup> (=QCC B003/17<jats:sup>T</jats:sup>=LMG 30288 <jats:sup>T</jats:sup>=CCUG 70703<jats:sup>T</jats:sup>).</jats:p>

Out with the old and in with the new: time to rethink twentieth century chemotaxonomic practices in bacterial taxonomy

“…Such studies would renew appreciation of the utility of appropriately selected chemotaxonomic data, particularly at taxonomic ranks above the species. Moreover, collaboration between bioinformaticians and chemotaxonomists should allow the further development of biosynthetic/metabolic pathway analyses into ‘ in silico chemotaxonomy’ approaches [20, 23, 24]. Further development of spectral fingerprinting methods should also help overcome an intrinsic lack of ‘portability’ of data acquired from twentieth century chromatographic techniques and are likely to involve safer, ‘greener’ protocols than the often hazardous older methods.…”

Clostridium chrysemydis sp. nov., isolated from the faecal material of a painted turtle

“…Modern taxonomy is increasingly using in silico genome analysis with the dual goals of increasing the rate in the description of taxa and the accuracy and consistency of characteristics reported [34,35]. Phenotypic and chemotaxonomic traits derived from genome-based studies are now increasingly being used assign taxonomic affiliations of bacteria [36][37][38][39]. In this study, we used polar lipid analysis using the kegg database [40] to investigate glycerophospholipid metabolism (Fig.…”

Draft Genome Sequence of the Planctobacterium marinum Type Strain K7

“…The Alteromonadaceae are an ecologically diverse group, with members isolated from seafloor sediments ( 1 ), coastal ( 2 ), open, and hadal ( 3 , 4 ) marine waters, marine invertebrates, fish, and algae ( 5 ). Members of this family are also notable for harboring degradative genes and secondary metabolite synthetic gene clusters with desirable activities in their genomes ( 5 – 7 ).…”

“…The increasing availability of next-generation sequencing technologies has made whole-genome sequences essential for the representation of taxa of interest and have generated new standard measurements of genomic taxonomy ( 9 , 10 ). Because only phenotypic and 16S rRNA sequence data from P. marinum strain K7 were available for the analyses distinguishing two novel genera, Ningiella and Marisediminitalea ( 1 , 3 ), the availability of a draft whole-genome sequence of another type strain will further elucidate taxonomic differences between related strains in the Alteromonadaceae family.…”