Antarcticimicrobium sediminis gen. nov., sp. nov., isolated from Antarctic intertidal sediment, transfer of Ruegeria lutea to Antarcticimicrobium gen. nov. as Antarcticimicrobium luteum comb. nov.

Abstract

The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequence and the genome sequence of strain S4J41 T are MK120109 and SMFP00000000, respectively. The GenBank/EMBL/DDBJ accession numbers for the genome sequences of Puniceibacterium confluentis KCTC 52765 T and 'Phaeobacter marinintestinus' CCTCC AB 2016288 T are VOJI00000000 and VOGO00000000, respectively. Seven supplementary tables and two supplementary figures available with the online version of this article.

Phylotaxonomic assessment based on four core gene sets and proposal of a genus definition among the families Paracoccaceae and Roseobacteraceae

“…The families Paracoccaceae and Roseobacteraceae comprise metabolically, phenotypically and genotypically diverse members that play critical roles in marine and other environments. Currently, hundreds of genera have been reported within these families, which makes it difficult to recognize their diversity and taxonomy comprehensively [11][12][13][14][15][16][17][18]. In this study, a phylotaxonomic assessment of the families Paracoccaceae and Roseobacteraceae was conducted based on four gene sets, bac120, rhodo268, rp1 and rp2, using different methods, and members within them were updated, respectively.…”

“…In terms of intraED analysis of the four gene sets, identical patterns of divergent levels were suggested among the 44 genera with two or more genomes taken in account. A total of 13 genera comprising six or more species, Thioclava (six species), Ruegeria (12), Yoonia (six), Sulfitobacter (13), Rhodovulum (seven), Shimia (six), Celeribacter (six), Tabrizicola (six), Litoreibacter (six), Pseudooceanicola (six), Gemmobacter (nine), Roseovarius (19) and Paracoccus (23), ranked 18th, 19th, 22nd, 24th, 25th, 26th, 30th, 32nd, 35th, 39th, 40th, 41st and 43rd in the list of the 44 genera from the most divergent to the least, respectively. In terms of the results for the bac120 gene set, the intraEDs in these genera were found to be 0.1013, 0.1127, 0.1297, 0.1326, 0.1334, 0.1341, 0.1559, 0.1563, 0.1648, 0.1811, 0.2011, 0.2243 and 0.2315, respectively.…”

“…The family 'Rhodobacteraceae' was named after the first described genus, Rhodobacter, which comprises metabolically, phenotypically and genotypically diverse members, and its description relied heavily on 16S rRNA gene analysis before 2020 [10,11]. As a consequence, hundreds of genera and species have been reported within this family for their essential ecological role in marine environments, and misclassifications have been a reoccurring problem, underscoring the instability of classifications based on the 16S rRNA gene [11][12][13][14][15][16][17][18][19]. In 2022, the family 'Rhodobacteraceae' was considered to be illegitimate because it contravenes Rule 51 of the International Code of Nomenclature of Prokaryotes (ICNP), and it was replaced by two families: Roseobacteraceae and Paracoccaceae [14,20,21].…”

“…According to the List of Prokaryotic names with Standing in Nomenclature (LPSN, accessed on 11 October 2023) [22], there were 205 genera validly published in the family ‘ Rhodobacteraceae ’, where 164 of them (80.0 %) included three or fewer members and 109 genera (53.2 %) had only one member. Furthermore, frequent reclassifications have been proposed within this family, even within the last 2 years [11–15, 17, 23–25], which has caused a great deal of confusion and inconvenience for scholars with a focus on these taxa. The primary cause of this problem stems from the fact that the evolutionary frameworks used to establish the taxonomy were drawn from different gene sets and strategies [11, 14, 17].…”