Gimesia chilikensis sp. nov., a haloalkali-tolerant planctomycete isolated from Chilika lagoon and emended description of the genus Gimesia

Abstract

<jats:p>A Gram-stain-negative, aerobic, non-motile, salt- and alkali-tolerant, pear to oval shaped, rosette-forming, white coloured, bacterium, designated as strain JC646<jats:sup>T</jats:sup>, was isolated from a sediment sample collected from Chilika lagoon, India. Strain JC646<jats:sup>T</jats:sup> reproduced through budding, grew well at up to pH 9.0 and tolerated up to 7 % NaCl. Strain JC 646<jats:sup>T</jats:sup> utilized α-<jats:sc>d</jats:sc>-glucose, fumarate, lactose, sucrose, fructose, <jats:sc>d</jats:sc>-galactose, mannose, maltose and <jats:sc>d</jats:sc>-xylose as carbon sources. Peptone, <jats:sc>l</jats:sc>-isoleucine, <jats:sc>l</jats:sc>-serine, <jats:sc>l</jats:sc>-lysine, <jats:sc>l</jats:sc>-glutamic acid, <jats:sc>l</jats:sc>-aspartic acid, <jats:sc>dl</jats:sc>-threonine and <jats:sc>l</jats:sc>-glycine were used by the strain as nitrogen sources for growth. The respiratory quinone was MK6. Major fatty acids were C<jats:sub>16 : 1</jats:sub> ω7<jats:italic>c</jats:italic>/C<jats:sub>16 : 1</jats:sub> ω6<jats:italic>c</jats:italic> and C<jats:sub>16 : 0</jats:sub>. The polar lipids of strain JC646<jats:sup>T</jats:sup> comprised phosphatidyl-dimethylethanolamine, phosphatidylcholine, diphosphatidylglycerol, an unidentified amino lipid and two unidentified lipids. Strain JC646<jats:sup>T</jats:sup> had highest (97.3 %) 16S rRNA gene sequence identity to the only species of the genus <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.26438" xlink:type="simple">Gimesia</jats:ext-link> </jats:named-content> </jats:italic>, <jats:italic> <jats:named-content content-type="species"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.26439" xlink:type="simple">Gimesia maris</jats:ext-link> </jats:named-content> </jats:italic> DSM 8797<jats:sup>T</jats:sup>. The genome of strain JC646<jats:sup>T</jats:sup> was 7.64 Mbp with a DNA G+C content of 53.2 mol%. For the resolution of the phylogenetic congruence of the novel strain, the phylogeny was also reconstructed with the sequences of 92 housekeeping genes. Based on phylogenetic analyses, digital DNA–DNA hybridization (19.0 %), genome average nucleotide identity (74.5 %) and average amino acid identity/percentageof conserved proteins (77 %) results, chemotaxonomic characteristics, and differential physiological properties, strain JC646<jats:sup>T</jats:sup> is recognized as representing a new species of the genus <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.26438" xlink:type="simple">Gimesia</jats:ext-link> </jats:named-content> </jats:italic>, for which we propose the name <jats:italic>Gimesia chilikensis</jats:italic> sp. nov. The type strain is JC646<jats:sup>T</jats:sup> (=KCTC 72175<jats:sup>T</jats:sup>=NBRC 113881<jats:sup>T</jats:sup>).</jats:p>

Additions to the genus Gimesia: description of Gimesia alba sp. nov., Gimesia algae sp. nov., Gimesia aquarii sp. nov., Gimesia aquatilis sp. nov., Gimesia fumaroli sp. nov. and Gimesia panareensis sp. nov., isolated from aquatic habitats of the Northern Hemisphere

“…Notably, our analysis shows that the two described species G. chilikensis (Kumar et al 2020) and G. benthica (Wang et al 2020) do not seem to belong to different species by the here applied measures. We must assume that this inconsistency derives from the fact that G. benthica was described only a few weeks after G. chilikensis-and therefore each of these studies only compared the new strain to G. maris, rather than to each other.…”

“…While these features were also found in the recently described species Gimesia benthica (Wang et al 2020), they were however not identified in another recently described species of the genus, Gimesia chilikensis (Kumar et al 2020). While many Planctomycetes produce carotenoids as pigmenting compounds, probably for protection against UV radiation or oxidative stress (Kallscheuer et al 2019), the three previously described Gimesia species possess a white colony colour (Kumar et al 2020), indicating the inability to produce such pigments.…”

“…When reviewing 16S rRNA gene sequence-, as well as MLSA-based phylogeny, it was evident that all strains are close neighbours of G. maris 534-30 T (Bauld and Staley 1976;Scheuner et al 2014), the type strain of the type species of the genus Gimesia, and the recently described G. chilikensis JC646 T (Kumar et al 2020) and G. benthica E7 (Wang et al 2020) (Fig. 1).…”

“…16S rRNA gene sequence-based phylogeny was computed for the strains described here and the type strains of reference species. The analysis also included strains described in the last year (Boersma et al 2019;Dedysh et al 2020a;Kallscheuer et al 2020b;Kohn et al 2016Kohn et al , 2019Kohn et al , 2020Kumar et al 2020;Peeters et al 2020;Rivas-Marin et al 2020a, b;Vitorino et al 2020) and strains recently published, but not yet described (Wiegand et al 2020). The 16S rRNA gene sequences were aligned with SINA (Pruesse et al 2012).…”

Updates to the recently introduced family Lacipirellulaceae in the phylum Planctomycetes: isolation of strains belonging to the novel genera Aeoliella, Botrimarina, Pirellulimonas and Pseudobythopirellula and the novel species Bythopirellula polymerisocia and Posidoniimonas corsicana

“…Maximum likelihood 16S rRNA gene sequence-based phylogeny was computed for the eight novel strains, the type strains of all recently described planctomycetal species (as of June 2020) (Kallscheuer et al 2020b;Kumar et al 2020;Peeters et al 2020;Rivas-Marin et al 2020a, b;Schubert et al 2020) and all isolates recently published, but not yet described (Wiegand et al 2020). The 16S rRNA gene sequences were aligned with SINA (Pruesse et al 2012).…”