Reclassification of 11 Members of the Family Rhodobacteraceae at Genus and Species Levels and Proposal of Pseudogemmobacter hezensis sp. nov

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, and their descriptions rely heavily on 16S rRNA gene analysis. Hundreds of genera have been reported within the two families and misclassifications have been a reoccurring problem, even when the taxonomies have been established based on genome-scale phylogenetic reconstructions. In this study, we conducted a comprehensive phylotaxonomic assessment of the families Paracoccaceae and Roseobacteraceae based on four ubiquitous gene sets, bac120 (120 genes in Bacteria), rhodo268 (268 genes in ‘ Rhodobacteraceae ’, defined in this study), rp1 (16 ribosomal protein genes in Prokaryote) and rp2 (23 ribosomal protein genes in Prokaryote), using two tree-inferring applications and two approaches (supermatrix and consensus). The results suggested that the four supermatrix trees based on bac120 and rhodo268 shared a high proportion of common nodes (>88.4 %) and the topology was reproducible among all the trees within most of the genera. The evolutionary distance (ED) analysis showed significant overlapping between the intergeneric and intrageneric comparisons, implying that the proposal of some genera seemed to be unnecessary. In addition, the bac120 gene set and the FastTree program were found to be the most cost-effective way to conduct phylogenomic analysis of the families Paracoccaceae and Roseobacteraceae . An ED threshold of 0.21–0.23 based on either bac120 or rhodo268 was proposed as one standard for later genus delimitation in these families. A comprehensive phylogenetic framework is presented in this study and the proposed genus definition will help to establish a more reasonable taxonomy in the families Paracoccaceae and Roseobacteraceae .

Cereibacter flavus sp. nov., a novel member of the family Rhodobacteraceae isolated from seawater of the South China Sea and reclassification of Rhodobacter alkalitolerans as Cereibacter alkalitolerans comb. nov

A Gram-stain-negative, aerobic, motile, ovoid-shaped and yellow-coloured strain, designated SYSU M79828T, was isolated from seawater collected from the South China Sea. Growth of this strain was observed at 4-37 °C (optimum, 28 °C), pH 6.0-8.0 (optimum, pH 7.0) and with 0-6% NaCl (optimum, 3.0 %, w/v). The respiratory quinone was found to be Q-10. Major fatty acid constituents were C18 : 1  ω7c/C18 : 1  ω6c, C18 : 1 ω7c11-methyl and C18 : 0 (>5 % of total). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, phosphoglycolipid, two unidentified phospholipid, one unidentified lipid and an unidentified glycolipid. The genomic DNA G+C content was 64.5 mol%. Phylogenetic analyses based on 16S rRNA gene sequences and core genes indicated that strain SYSU M79828T belonged to the genus Cereibacter and had the highest sequences similarity to 'Rhodobacter xinxiangensis' TJ48T (98.41 %). Based on 16S rRNA gene phylogeny, physiological and chemotaxonomic characterizations, we consider that strain SYSU M79828T represents a novel species of the genus Cereibacter, for which the name Cereibacter flavus sp. nov. is proposed. The type strain is SYSU M79828T (=GDMCC 1.3803T=KCTC 92893T). In addition, according to the results of phylogenetic analysis and similar taxonomic characteristics, we propose that Rhodobacter alkalitolerans should be reclassified as Cereibacter alkalitolerans comb. nov.

Phylogenomic reappraisal of the family Rhizobiaceae at the genus and species levels, including the description of Ectorhizobium quercum gen. nov., sp. nov

The family Rhizobiaceae contains 19 validly described genera including the rhizobia groups, many of which are important nitrogen-fixing bacteria. Early classification of Rhizobiaceae relied heavily on the poorly resolved 16S rRNA genes and resulted in several taxonomic conflicts. Although several recent studies illustrated the taxonomic status of many members in the family Rhizobiaceae, several para- and polyphyletic genera still needed to be elucidated. The rapidly increasing number of genomes in Rhizobiaceae has allowed for a revision of the taxonomic identities of members in Rhizobiaceae. In this study, we performed analyses of genome-based phylogeny and phylogenomic metrics to review the relationships of 155-type strains within the family Rhizobiaceae. The UBCG and concatenated protein phylogenetic trees, constructed based on 92 core genes and concatenated alignment of 170 single-copy orthologous proteins, demonstrated that the taxonomic inconsistencies should be assigned to eight novel genera, and 22 species should be recombined. All these reclassifications were also confirmed by pairwise cpAAI values, which separated genera within the family Rhizobiaceae with a demarcation threshold of ~86%. In addition, along with the phenotypic and chemotaxonomic analyses, a novel strain BDR2-2T belonging to a novel genus of the family Rhizobiaceae was also confirmed, for which the name Ectorhizobium quercum gen. nov., sp. nov. was proposed. The type strain is BDR2-2T (=CFCC 16492T = LMG 31717T).

Phocaeicola oris sp. nov., an anaerobic bacterium isolated from the saliva of a patient with oral squamous cell carcinoma

A Gram-stain-negative or -positive, strictly anaerobic, non-spore-forming and pleomorphic bacterium (designated 14-104^T) was isolated from the saliva sample of a patient with oral squamous cell carcinoma. It was an acid-tolerant neutralophilic mesophile, growing at between 20 and 40 °C (with optimum growth at 30 °C) and pH between pH 3.0 and 7.0 (with optimum growth at pH 6.0-7.0). It contained anteiso-C_15 : 0 and C_15 : 0 as the major fatty acids. The genome size of strain 14-104^T was 2.98 Mbp, and the G+C content was 39.6 mol%. It shared <87 % 16S rRNA sequence similarity, <71 % orthologous average nucleotide identity, <76 % average amino acid identity and <68 %% of conserved proteins with its closest relative, Phocaeicola abscessus CCUG 55929^T. Reconstruction of phylogenetic and phylogenomic trees revealed that strain 14-104^T and P. abscessus CCUG 55929^T were clustered as a distinct clade without any other terminal node. The phylogenetic and phylogenomic analyses along with physiological and chemotaxonomic data indicated that strain 14-104^T represents a novel species in the genus Phocaeicola, for which the name Phocaeicola oris sp. nov. is proposed. The type strain is 14-104^T (=BCRC 81305^T= NBRC 115041^T).

Description of Pseudogemmobacter faecipullorum sp. nov., isolated from poultry manure

A polyphasic taxonomic approach was used to characterize a novel bacterium, designated strain CC-YST710T, isolated from poultry manure sampled in Taiwan. Cells of strain CC-YST710T were aerobic, Gram-stain-negative, nonmotile, nonspore-forming rods, displaying positive reactions for catalase, and oxidase activities. Strain CC-YST710T was found to grow optimally at 30°C, pH 7.0, and in the presence of 2% (w/v) NaCl. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids, four unidentified aminolipids, one unidentified aminophospholipid, and five unidentified lipids. The major polyamine was spermidine. The dominating cellular fatty acids (> 5%) included C16:0, C18:0, and C18:1ω7c/C18:1ω6c. Based on 16S rRNA gene analysis, this isolate showed the closest phylogenetic relationship with 'Pseudogemmobacter humicola' (97.6%), followed by Pseudogemmobacter bohemicus (97.2%) and 'Pseudogemmobacter hezensis' (97.5%). The draft genome (4.3 Mb) had 62.9 mol% G + C content. CC-YST710T can be distinguished from other Pseudogemmobacter species due to the exclusive presence of key genes encoding p-hydroxybenzoate hydroxylase, protocatechuate 3, 4-dioxygenase (α and β chain), and homogentisate 1, 2-dioxygenase involved in the degradation of phenolic compounds such as p-hydroxybenzoic acid, protocatechuate, and homogentisate, respectively. Orthologous average nucleotide identity (OrthoANI) of the isolate with the type strains of the genera Pseudogemmobacter were 77.6%‒78.0% (n = 3), followed by Tabrizicola (72.3%‒73.7%, n = 5), and Gemmobacter(72.3%‒73.5%, n = 7). Based on its distinct phylogenetic, phenotypic, and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence, OrthoANI, digital DDH, and the phylogenomic placement, strain CC-YST710T is considered to represent a novel Pseudogemmobacter species, for which the name Pseudogemmobacter faecipullorum sp. nov. (type strain CC-YST710T = BCRC 81286T = JCM 34182T).

Genomic Analysis and Characterization of Pseudotabrizicola formosa sp. nov., a Novel Aerobic Anoxygenic Phototrophic Bacterium, Isolated from Sayram Lake Water

Aerobic anoxygenic photosynthetic bacteria (AAPB) are a kind of heterotrophic prokaryote that can use bacteriochlorophyll (BChl) for photosynthesis without oxygen production and they are widely distributed in aquatic environments, including oceans, lakes, and rivers. A novel aerobic anoxygenic photosynthetic bacterium strain XJSPT was isolated during a study of water microbial diversity in Sayram Lake, Xinjiang Province, China. Strain XJSPT was found to grow optimally at 33 °C, pH 7.5 with 1.0% (w/v) NaCl, and to produce bacteriochlorophyll a and carotenoids. Phylogenetic analysis based on 16S rRNA gene sequence and concatenated alignment sequences of 120 ubiquitous single-copy proteins both supported that strain XJSPT belonged to the genus Pseudotabrizicola. Both average nucleotide identity (ANI) and DNA-DNA hybridization (DDH) values were below the species delineation threshold. The primary polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unknown lipid, and one unidentified phospholipid. Based on the results of polyphasic analyses performed in this study, strain XJSPT represents a new member of the genus Pseudotabrizicola, for which the name Pseudotabrizicola formosa sp. nov. is proposed. The type strain is XJSPT (=KCTC 52636T = MCCC 1H00184T = SDUM 107003T). Comparative genomic analysis showed that four species of the genus Pseudotabrizicola shared 2570 core genes and possessed a complete anoxygenic photosystem II.