Aurantiacibacter hainanensis sp. nov. and Qipengyuania zhejiangensis sp. nov., two novel Erythrobacteraceae species isolated from tidal flat sediments

Two Gram-stain-negative, rod-shaped, non-motile, aerobic and carotenoid-producing strains, belonging to the family Erythrobacteraceae, designated as H149T and Z2T, were isolated from tidal flat sediment samples collected in Hainan and Zhejiang, PR China, respectively. Growth of strain H149T occurred at 15-42 °C, 0-10.0 % (w/v) NaCl, and pH 6.0-8.5, with the optima at 35-37 °C, 3.0-3.5 % (w/v) NaCl and pH 7.0. Strain Z2T grew at 15-37 °C, 0-6.0 % (w/v) NaCl, and pH 6.0-9.5, with the optima at 25-30 °C, 0.5-1.0 % (w/v) NaCl and pH 6.0-6.5. Ubiquinone-10 was the sole ubiquinone in two strains. The predominant cellular fatty acids of strain H149T were C16 : 0, summed feature 3 and summed feature 8, while those of strain Z2T were C17 : 1  ω6c, summed feature 3 and summed feature 8. Strains H149T and Z2T shared diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and sphingoglycolipid as major polar lipids. The 16S rRNA gene sequence identity analysis indicated that strain H149T had the highest sequence identity of 98.4 % with Aurantiacibacter odishensis KCTC 23981T, and strain Z2T had that of 98.2 % with Qipengyuania pacifica NZ-96T. Phylogenetic trees based on 16S rRNA gene and core-genome sequences revealed that strains H149T and Z2T formed two independent clades in the genera Aurantiacibacter and Qipengyuania, respectively. Strain H149T had average nucleotide identity values of 74.0-81.3 % and in silico DNA-DNA hybridization values of 18.5-23.1 % with Aurantiacibacter type strains, while strain Z2T had values of 73.3-78.7 % and 14.5-33.3 % with Qipengyuania type strains. The genomic DNA G+C contents of strains H149T and Z2T were 64.3 and 61.8 %, respectively. Based on the genetic, genomic, phylogenetic, physiological and chemotaxonomic results, strains H149T (=KCTC 8397T=MCCC 1K08920T) and Z2T (=KCTC 8396T=MCCC 1K08946T) are concluded to represent two novel Erythrobacteraceae species for which the names Aurantiacibacter hainanensis sp. nov. and Qipengyuania zhejiangensis sp. nov. are proposed, respectively.

Aurantiacibacter sediminis sp. nov., a marine bacterium isolated from a tidal flat

A yellow-coloured bacterium, designated as strain JGD-13T, was isolated from a tidal flat in the Republic of Korea. Cells were Gram-stain-negative, aerobic, non-flagellated and rod-shaped. Growth was observed at 4–42 °C (optimum, 30 °C), at pH 6.0–12.0 (pH 7.0–8.0) and at 1–7 % (w/v) NaCl concentration (3 %). The 16S rRNA gene sequence analysis indicated that strain JGD-13T was closely related to Aurantiacibacter gangjinensis K7-2T with a sequence similarity of 98.2 %, followed by Aurantiacibacter aquimixticola JSSK-14T (98.1 %), Aurantiacibacter atlanticus s21-N3T (97.6 %), Aurantiacibacter zhengii V18T (97.6 %) and Aurantiacibacter luteus KA37T (97.5 %). The average nucleotide identity and digital DNA–DNA hybridization values with related strains were 70.3–76.2 % and 18.5–20.3 %. The genomic DNA G+C content was 60.2 mol%. Phylogenetic analysis using the maximum-likelihood method showed that strain JGD-13T formed a clade with A. aquimixticola JSSK-14T and A. gangjinensis K7-2T. The major fatty acids were summed feature 8 (39.7 %) and C17 : 1  ω6c (14.4 %). The predominant respiratory quinone was ubiquinone-10. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, one sphingoglycolipid and three unidentified lipids. On the basis of phylogenetic, phenotypic and chemotaxonomic characteristics, strain JGD-13T represents a novel species within the genus Aurantiacibacter , for which the name Aurantiacibacter sediminis JGD-13Tsp. nov. is proposed. The type strain is JGD-13T (=KCTC 72892T=KACC 21676T=JCM 33995T).

Qipengyuania pacifica sp. nov., a Novel Carotenoid-Producing Marine Bacterium of the Family Erythrobacteraceae, Isolated from Sponge (Demospongiae), and Antimicrobial Potential of Its Crude Extract

A marine Alphaproteobacterium designated as strain NZ-96T was isolated in February 2021, from a sponge species (Demospongiae) collected in muddy sediments with boulders and old chimneys in Otago/Canterbury Slope, Pacific Ocean, New Zealand. The isolate was found to be Gram-negative, rod-shaped, aerobic, motile, and produced yellow-colored colonies. The isolate was positive for alkaline phosphatase, leucine arylamidase, trypsin, catalase, and oxidase and negative for α-galactosidase and urease. It was resistant to many antibiotics including hygromycin, trimethoprim, spectinomycin, ampicillin, oxytetracycline, cephalosporin, bacitracin, and polymyxin. The 16S rRNA gene-based phylogenetic analyses exhibited that strain NZ-96T belonged to the genus Qipengyuania and showed 98.3–98.8% 16S rRNA gene sequence similarity to its closest relatives. The major respiratory quinone was ubiquinone-10 (Q-10). The polar lipid profile consisted of phosphatidylcholine, sphingoglycolipid, phosphatidylglycerol, one unknown polar lipid, and three unknown glycolipids. The major fatty acids were C18:1ω12t, C16:0, C16:1ω7c, C17:1ω6c, C16:02-OH, and C14:0 2-OH. Carotenoid were produced. The crude extract showed pronounced activity against Staphylococcus aureus Newman and Bacillus subtilis DSM 10. Pairwise ANI and dDDH values of strain NZ-96T and closely related phylogenetic hits were below the threshold values of 95% and 70%, respectively. Genes for trehalose biosynthesis, aspartate-semialdehyde dehydrogenase, flagellar biosynthesis, fatty acid biosynthesis, and antibiotics resistance were present, which aids in isolate survival in a sea or ocean environment. The DNA G+C content was 60.8% (by genome). Based on data obtained by the polyphasic approach, strain NZ-96T (= DSM 112811T = NCCB 100842T) represents a novel species of the genus Qipengyuania, for which the name Qipengyuania pacifica sp. nov. is proposed.

Alteriqipengyuania abyssalis sp. nov., a Novel Member of the Class Alphaproteobacteria Isolated from Sponge, and Emended Description of the Genus Alteriqipengyuania

A novel Gram-negative, aerobic, motile, lemon-yellow-colored, and non-spore-forming rod-shaped bacterium designated strain NZ-12BT was isolated in February 2021 from a sponge species (Crateromorpha) collected at the southern Kermadec Ridge, Pacific Ocean, New Zealand. Comparative 16S rRNA gene-based analyses indicated that strain NZ-12BT shared 98.58%, 96.44%, 96.23%, and 94.78% 16S rRNA sequence similarity to Alteriqipengyuania lutimaris S-5T, Qipengyuania pelagi UST081027-248T, Qipengyuania citreus RE35F/1T, and Alteriqipengyuania halimionae CPA5T, respectively. The major respiratory quinone was ubiquinone-10(Q-10). The polar lipid profile of NZ-12BT was composed of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidyl-N-methyl-ethanolamine, phosphatidylcholine, sphingoglycolipid, phosphatidylglycerol, one unknown polar lipid, three unknown phospholipids, and three unknown glycolipids. The major fatty acids of strain NZ-12BT were C18:1ω12t, C16:0, C17:1ω6c, and C14:02-OH. Carotenoids were present. Genome mining analysis revealed a biosynthetic gene cluster encoding for the terpene biosynthesis. Pairwise ANI and dDDH values of strain NZ-12BT and closely related phylogenetic neighbors were below the threshold values of 95% and 70%, respectively. The DNA G+C content was 65.4 mol% (by genome). Based on data obtained by a polyphasic approach, type strain NZ-12BT (=DSM 112810T = NCCB 100841T) represents a novel species of the genus Alteriqipengyuania, for which the name Alteriqipengyuania abyssalis sp. nov. is proposed.

Aurantiacibacter rhizosphaerae sp. nov., isolated from a rhizosphere mudflat of a halophyte and proposal to reclassify Erythrobacter suaedae Lee et al. 2019. and Erythrobacter flavus Yoon et al. 2003 as Aurantiacibacter suaedae comb. nov. and Qipengyuania flava comb. nov., respectively

A marine alphaproteobacterium, designated as strain GH3-10^T, was isolated from the rhizosphere mud of a halophyte (Suaeda japonica) collected at the seashore of Gangwha Island, Republic of Korea. The isolate was found to be Gram-stain-negative, strictly aerobic, catalase- and oxidase-positive, non-motile, short rods and produced orange-coloured colonies. The 16S rRNA gene- and whole genome-based phylogenetic analyses exhibited that strain GH3-10^T belonged to the genus Aurantiacibacter and was most closely related to Aurantiacibacter atlanticus s21-N3^T (98.7 % 16S rRNA gene sequence similarity) and Aurantiacibacter marinus KCTC 23554^T (98.4 %). The major respiratory quinone was ubiquinone-10. The polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid and an unidentified lipid. The major fatty acids were C_18 : 1  ω7c, summed feature 3 (C_16 : 1  ω7c and/or C_16 : 1  ω6c) and C_18 : 1  ω7c 10-methyl. The DNA G+C content was 61.3 mol% (by genome). Average nucleotide identity and DNA-DNA relatedness values between the isolate and its phylogenetically closest relatives, together with phenotypic distinctness warranted the taxonomic description of a new species. On the basis of data obtained by a polyphasic approach, strain GH3-10^T (=KCTC 62379^T=JCM 32444^T) represents a novel species of the genus Aurantiacibacter, for which the name Aurantiacibacter rhizosphaerae sp. nov. is proposed. According to phylogenetic coherence based on 16S rRNA genes and core genomes, it is also proposed that Erythrobacter suaedae Lee et al. 2019. and Erythrobacter flavus Yoon et al. 2003 be transferred to Aurantiacibacter suaedae comb. nov. and Qipengyuania flava comb. nov., respectively.

Genomic-based taxonomic classification of the family Erythrobacteraceae

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.

Erythrobacter insulae sp. nov., isolated from a tidal flat

A Gram-staining-negative, aerobic, non-motile and coccoid, ovoid or rod-shaped bacterial strain, designated as JBTF-M21T, was isolated from a tidal flat sediment on the Yellow Sea, Republic of Korea. The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences indicated that JBTF-M21T fell within the clade comprising the type strains of species of the genus Erythrobacter . JBTF-M21T exhibited 16S rRNA gene sequence similarities of 97.0–98.4 % to the type strains of Erythrobacter longus , Erythrobacter aquimaris , Erythrobacter nanhaisediminis , Erythrobacter vulgaris , Erythrobacter seohaensis , Erythrobacter litoralis and Erythrobacter citreus and 93.7–96.6 % to the type strains of the other species of the genus Erythrobacter . The ANI and dDDH values between JBTF-M21T and the type strains of E. longus , E. nanhaisediminis , E. seohaensis and E. litoralis were 70.83–72.93 % and 18.0–18.8 %, respectively. Mean DNA–DNA relatedness values between JBTF-M21T and the type strains of E. aquimaris , E. vulgaris and E. citreus were 12–24 %. The DNA G+C content of JBTF-M21T was 57.0 mol%. JBTF-M21T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c and C17 : 1ω6c as the major fatty acids. The major polar lipids ofJBTF-M21T were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and sphingoglycolipid. Distinguishing phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that JBTF-M21T is separated from species of the genus Erythrobacter with validly published names. On the basis of the data presented, strain JBTF-M21T is considered to represent a novel species of the genus Erythrobacter , for which the name Erythrobacter insulae sp. nov. is proposed. The type strain is JBTF-M21T (=KACC 19864T=NBRC 113584T).

Sulfur-Containing Carotenoids from A Marine Coral Symbiont Erythrobacter flavus Strain KJ5

Erythrobacter flavus strain KJ5 (formerly called Erythrobacter sp. strain KJ5) is a yellowish marine bacterium that was isolated from a hard coral Acropora nasuta in the Karimunjawa Islands, Indonesia. The complete genome sequence of the bacterium has been reported recently. In this study, we examined the carotenoid composition of this bacterium using high-performance liquid chromatography coupled with ESI-MS/MS. We found that the bacterium produced sulfur-containing carotenoids, i.e., caloxanthin sulfate and nostoxanthin sulfate, as the most abundant carotenoids. A new carotenoid zeaxanthin sulfate was detected based on its ESI-MS/MS spectrum. The unique presence of sulfated carotenoids found among the currently known species of the Erythrobacter genus were discussed.