Genomic-based taxonomic classification of the family Erythrobacteraceae

Abstract

The family Erythrobacteraceae , belonging to the order Sphingomonadales , class Alphaproteobacteria , is globally distributed in various environments. Currently, this family consist of seven genera: Altererythrobacter , Croceibacterium , Croceicoccus , Erythrobacter , Erythromicrobium , Porphyrobacter and Qipengyuania . As more species are identified, the taxonomic status of the family Erythrobacteraceae should be revised at the genomic level because of its polyphyletic nature evident from 16S rRNA gene sequence analysis. Phylogenomic reconstruction based on 288 single-copy orthologous clusters led to the identification of three separate clades. Pairwise comparisons of average nucleotide identity, average amino acid identity (AAI), percentage of conserved protein and evolutionary distance indicated that AAI and evolutionary distance had the highest correlation. Thresholds for genera boundaries were proposed as 70 % and 0.4 for AAI and evolutionary distance, respectively. Based on the phylo-genomic and genomic similarity analysis, the three clades were classified into 16 genera, including 11 novel ones, for which the names Alteraurantiacibacter, Altericroceibacterium, Alteriqipengyuania, Alteripontixanthobacter, Aurantiacibacter, Paraurantiacibacter, Parerythrobacter, Parapontixanthobacter, Pelagerythrobacter, Tsuneonella and Pontixanthobacter are proposed. We reclassified all species of Erythromicrobium and Porphyrobacter as species of Erythrobacter . This study is the first genomic-based study of the family Erythrobacteraceae , and will contribute to further insights into the evolution of this family.

Phylogenomic analyses of the Staphylococcaceae family suggest the reclassification of five species within the genus Staphylococcus as heterotypic synonyms, the promotion of five subspecies to novel species, the taxonomic reassignment of five Staphylococcus species to Mammaliicoccus gen. nov., and the formal assignment of Nosocomiicoccus to the family Staphylococcaceae

“…However, an AAI range of 60–80 % was observed in phylogenetically distinct but related genera [24] and phylogenies based on 16S rRNA gene sequences were complemented with core genome phylogenies to delineate higher taxonomic ranks [20]. More recently, OGRI metrics were successfully used to delineate genera within the families Erythrobacteracae , Lactobacillaceae , Leuconostocaceae and Rhodobacteraceae [29–31]. In the study conducted on the Erythrobacteraceae , cut-offs of 60–80 % AAI and 50 % percentage of conserved proteins (POCP) were used for genus-level delineations.…”

“…In the study conducted on the Erythrobacteraceae , cut-offs of 60–80 % AAI and 50 % percentage of conserved proteins (POCP) were used for genus-level delineations. In particular, they observed that AAI and evolutionary distance were strongly correlated [29]. In the analysis of the Lactobacillaceae and Leuconostocaceae families, the proposal of the novel genera was based on the following criteria: novel genera must represent monophyletic clades, possess rational AAI values both within and between genera, and exhibit some degree of phenotypic uniformity [30].…”

Tsuneonella suprasediminis sp. nov., isolated from the Pacific Ocean

“…The DNA G+C content of strain Ery12 T was 60.9 %, a value in the range reported for members of the genus Tsuneonella , i.e. 60.5–67.0 % [1].…”

“…The genus Tsuneonella belonging to the family Erythrobacteraceae , was proposed by Xu et al . [1]. At the time of writing, the genus Tsuneonella comprised of seven species with validly published names.…”

Distribution and abundance of aerobic anoxygenic phototrophic bacteria in the tropical coastal waters of Gunungkidul, Yogyakarta, Indonesia

“…However, not all of those species possess photosystem-II photosynthetic apparatus, hence not all of them belong to AAP bacteria. Species such as Roseobacter ponti , Roseobacter cerasinus (Muramatsu et al 2020), Erythrobacter aquimixticola (Park et al 2017), Erythrobacter arachoides (Xing et al 2017), Erythrobacter insulae (Park et al 2020) and Erythrobacter atlanticus (Zhuang et al 2015) are several species from both genera which do not possess phototrophic trait and hence are suggester for genera reclassification (Hördt et al 2020;Xu et al 2020) The ecological role of marine AAP bacteria was not really known until 2000, when it was discovered that photoheterotrophic ability might contribute to their survival in nutrient-poor marine environments, such as open ocean (Kolber et al 2000;Kirchman 2018). Marine AAP bacteria abundance was firstly reported in 2001 where it contributes to 10% of total bacterioplankton in Pacific Ocean, implying its significant contribution towards global carbon cycle (Kolber et al 2001;Ritchie and Johnson 2012).…”