Genome-Based Analysis Reveals the Taxonomy and Diversity of the Family Idiomarinaceae

Abstract

Idiomarinaceae is a family of Gram-stain negative, mesophilic euryhalophiles. To provide a robust framework for the evolutionary and taxonomic relationships of bacteria of this family, we compared herein the genomes of 36 type strains and 43 non-type strains using 16S rRNA gene sequences, core genome based 78 single-copy orthologous proteins, digital DNA-DNA hybridization and average nucleotide identity (ANI) estimation. The 79 bacteria of this family were consistently divided into taxon I, taxon II, and taxon III corresponding to the three genera Idiomarina, Pseudidiomarina, and Aliidiomarina, which contained 13 putative new genospecies in addition to 35 well-defined species represented by each type strain. Furthermore, genetic diversity of this family was evident at the genus- and species levels, and exceeded that which is defined currently by the named species. In view of multiple genotypic characteristics clearly distinct from the other two genera, we propose reinstating the genus Pseudidiomarina as a monophyletic taxon. Taken together, this is the first genome-based study of the taxonomy and diversity of bacteria within the family Idiomarinaceae, and will contribute to further insights into microbial evolution and adaptation to saline environments.

Pseudidiomarina piscicola sp. nov., isolated from cultured European seabass, Dicenthrarchus labrax

“…The draft genome of strain CECT 9734 T has an estimated size of 2.5 Mb, similar to the sizes found among Idiomarinaceae species, which are always below 3.1 Mb (Liu et al 2018 ). The G + C content of the genome is 49.5 mol%.…”

“…Finally, from a phenotypic point of view, the strain displays the main characteristics of genus Pseudidiomarina (as emended by Liu et al 2018). On the other hand, the strain displays several phenotypic traits that allow discrimination of CECT 9734 T from other species in the genus.…”

“…( 2009 ) based on the absence of distinguishing phenotypic characteristics, transferred the nine validly named species of the genus Pseudidiomarina to the genus Idiomarina. Recently, Liu et al ( 2018 ) performed a wide genome-based study of the family Idiomarinaceae , including the genus Aliidiomarina (Huang et al 2012 ), and proposed the genus Pseudidiomarina to be restored, establishing a taxonomic reclassification of many species in the family based on genomic analysis. As currently defined, Pseudidiomarina contains sixteen validly named species as stated in https://lpsn.dsmz.de/genus/pseudidiomarina (Parte 2018 ).…”

Genomic-based taxonomic classification of the family Erythrobacteraceae

“…Development of genome sequencing technologies has made bacterial genomic data more and more accessible, resulting in a revolution in bacterial taxonomy [52–54]. Phylogenomic reconstruction can provide a higher-resolution phylogeny than that based on 16S rRNA gene or several housekeeping genes [55–58]. In addition, genomic similarity calculations including average nucleotide identity (ANI), average amino acid identity (AAI) and percentage of conserved protein (POCP) provide numerical thresholds for delineation of each taxon [59–61].…”

Molecular identification of bacteria isolated from culture medium of the gold-lipped pearl oyster Pinctada maxima larvae

“…This genus is a member of the family Idiomarinaceae proposed by Innova et al(2000), to accommodate true marine bacterial species in the group of Alteromonas-like γ-Proteobacteria. The genus Idiomarina currently consists of about 27 species and are typically euryhalophiles thriving in wide salinity ranges of marine environment (Liu et al 2018). These include coastal and oceanic waters and sediments (Zhang et al 2012;Hameed et al 2016), saline-alkaline soil (Leon et al 2015), inland hypersaline wetlands (Zhong et al 2014), solar salt-making works (Lee et al 2015) and deep sea sediment (Du et al 2015).…”