Desertivirga arenae gen. nov., sp. nov. and Desertivirga brevis sp. nov., isolated from desert soil, and reclassification of Pedobacter xinjiangensis as Desertivirga xinjiangensis comb. nov. and Pedobacter mongoliensis as Paradesertivirga mongoliensis gen.nov., comb. nov

Two novel bacterial strains, designated as SYSU D00823T and SYSU D00873T, were isolated from sandy soil of the Gurbantunggut Desert in Xinjiang, north-west China. SYSU D00823T and SYSU D00873T shared 99.0 % 16S rRNA gene sequence identity, and were both most closely related to Pedobacter xinjiangensis 12157T with 96.1 % and 96.0 % similarities, respectively. Phylogenetic and phylogenomic analyses revealed that the two isolates and P. xinjiangensis 12157T formed a separate distinct cluster in a stable subclade with the nearby species Pedobacter mongoliensis 1-32T, as well as the genera Pararcticibacter and Arcticibacter. Furthermore, P. mongoliensis 1-32T formed a separate deep-branching lineage and did not form a cluster with members of the genus Pedobacter. The average nucleotide identity and digital DNA-DNA hybridization values between SYSU D00823T and SYSU D00873T and related species were well below the thresholds for species delineation (<81.0 % and <24.0 %, respectively). The genomes of SYSU D00823T and SYSU D00873T were 6.19 and 6.43 Mbp in size with 40.4 % and 40.5 % DNA G+C contents, respectively. The predominant fatty acids (>10 %) of SYSU D00823T and SYSU D00873T were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c). Menaquinone-7 was the only respiratory quinone. The major polar lipids were phosphatidylethanolamine, glycosphingolipid, aminoglycolipid/glycolipid, aminophospholipid and three or four unidentified polar lipids. These data indicated that strains SYSU D00823T and SYSU D00873T should be assigned to two novel species of a new genus within the family Sphingobacteriaceae, for which the names Desertivirga arenae gen. nov., sp. nov. and Desertivirga brevis sp. nov. are proposed. The type strains are SYSU D00823T (=CGMCC 1.18630T=MCCC 1K04973T=KCTC 82278T) and SYSU D00873T (=CGMCC 1.18629T=MCCC 1K04974T=KCTC 82281T), respectively. Accordingly, the reclassification of P. xinjiangensis as Desertivirga xinjiangensis comb. nov., and P. mongoliensis as Paradesertivirga mongoliensis gen. nov., comb. nov. are also proposed.

Aurantibacillus circumpalustris gen. nov., sp. nov., the first characterized representative of the Bacteroidota candidate family env.OPS 17 and proposal of Aurantibacillaceae fam. nov

16S rRNA sequence types associated with the candidate family env.OPS 17 have been reported from various environments, but no representatives have been characterized and validly named. Bacteria of env.OPS 17 are affiliated with the order Sphingobacteriales and were first detected more than two decades ago in the vicinity of a thermal spring in Yellowstone National Park. Strain Swamp196T, isolated from the soil surrounding a swamp in Northern Germany, is the first characterized representative of candidate family env.OPS 17. Cells of strain Swamp196T are rod-shaped, non-motile, non-spore-forming, non-capsulated and stain Gram-negative. Colonies are small and orange-coloured. The strain is mesophilic and grows under aerobic or microaerophilic conditions. It grows chemo-organotrophically over a narrow range of pH and exclusively on proteinaceous substrates. The major cellular fatty acids are iso-C15 : 0, iso-C15 : 1  ω10c, C18 : 1  ω9c and C16 : 1  ω7c and the major polar lipids are two unidentified aminophospholipids, one unidentified aminolipid and one unidentified lipid. The predominant respiratory quinone is MK-7. The DNA G+C content of genomic DNA is 35.5 mol%. Strain Swamp196T is related to Pedobacter cryophilus AR-3-17T, Arcticibacter pallidicorallinus Hh36T and Pedobacter daechungensis Dae 13T with 16S rRNA gene sequence similarity of 84.1, 83.8 and 83.5 %, respectively. Based on our phenotypic, genomic and phylogenetic analysis, we propose the novel species Aurantibacillus circumpalustris sp. nov (type strain Swamp196T=DSM 105849T=CECT 30420T) of the novel genus Aurantibacillus gen. nov. and the novel family Aurantibacillaceae fam. nov.

Pararcticibacter amylolyticus gen. nov., sp. nov., Isolated from a Rotten Hemp Rope, and Reclassification of Pedobacter tournemirensis as Pararcticibacter tournemirensis comb. nov

A Gram-stain-negative, rod-shaped, non-motile, facultatively anaerobic bacterium, designated FJ4-8^T, was isolated from a rotten hemp rope in Chongqing City, PR China. Phylogenetic analysis of 16S rRNA gene sequences indicated that the isolate was closely related to members of the family Sphingobacteriaceae, with the highest similarity to Pedobacter tournemirensis TF5-37.2-LB10^T (95.3%) and low similarities to all other species of the genus Pedobacter (90.4-93.9%). Phylogenetic analyses demonstrated that strain FJ4-8^T formed a stable subclade with Pedobacter tournemirensis TF5-37.2-LB10^T. The clade with these two strains branched adjacent to a clade containing three species of the genus Arcticibacter. MK-7 was detected as the only respiratory quinone. The major fatty acids composed iso-C_15:0, iso-C_17:0 3-OH and summed feature three. Phosphatidylethanolamine, three aminophospholipids and one unidentified lipid were found as the major polar lipids. The major polyamine was identified as sym-homospermidine. The DNA-DNA hybridization value between strain FJ4-8^T and Pedobacter tournemirensis TF5-37.2-LB10^T was 42.0 ± 2.5%. Based on its phylogenetic, chemotaxonomic and phenotypic characteristics, the novel strain and TF5-37.2-LB10^T were found to be different from members of genera Pedobacter and Arcticibacter. FJ4-8^T and TF5-37.2-LB10^T represented different species. Therefore, FJ4-8^T should be classified as a novel species of a novel genus in the family Sphingobacteriaceae, for which the name Pararcticibacter amylolyticus gen. nov., sp. nov. is proposed. The type strain is FJ4-8^T (= KCTC 62640^T = CCTCC AB 2018052^T). The draft genome sequence is 6290, 449 bp in length, the genomic DNA G+C content was 44.4 mol%. Pedobacter tournemirensis TF5-37.2-LB10^T should be transferred to the novel genus as Pararcticibacter tournemirensis comb. nov. (The type strain is TF5-37.2-LB10^T (= DSM 23085^T = CIP 110085^T = MOLA 820^T).

Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes

Although considerable progress has been made in recent years regarding the classification of bacteria assigned to the phylum Bacteroidetes, there remains a need to further clarify taxonomic relationships within a diverse assemblage that includes organisms of clinical, piscicultural, and ecological importance. Bacteroidetes classification has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees and a limited number of phenotypic features. Here, draft genome sequences of a greatly enlarged collection of genomes of more than 1,000 Bacteroidetes and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa proposed long ago such as Bacteroides, Cytophaga, and Flavobacterium but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which can be considered valuable taxonomic markers. We detected many incongruities when comparing the results of the present study with existing classifications, which appear to be caused by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. The few significant incongruities found between 16S rRNA gene and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences and the impediment in using ordinary bootstrapping in phylogenomic studies, particularly when combined with too narrow gene selections. While a significant degree of phylogenetic conservation was detected in all phenotypic characters investigated, the overall fit to the tree varied considerably, which is one of the probable causes of misclassifications in the past, much like the use of plesiomorphic character states as diagnostic features.

Pedobacter helvus sp. nov., isolated from farmland soil

A strictly aerobic, Gram-stain-negative, rod-shaped, yellow, non-spore-forming bacterial strain, designated P-25^T, was isolated from soil collected in Yantai, Shandong Province, PR China. The temperature, pH and NaCl concentration ranges for the growth of strain P-25^T were 10-37 °C (optimum, 28-30 °C), pH 6.0-9.0 (optimum, pH 7.5-8.0) and 0-4 % (w/v) (optimum, 1 % w/v), respectively. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain P-25^T was most closely related to Pedobacter xixiisoli S27^T (98.1 % 16S rRNA gene sequence similarity), followed by Pedobacter chitinilyticus CM134L-2^T (97.2 %) and Pedobacter ureilyticus THG-T11^T (97.1 %). The genomic DNA G+C content of strain P-25^T based on its draft genome sequence was 38.1 %. MK-7 was the major respiratory quinone, and iso-C_15 : 0, C_16 : 1ω7c and/or C_16 : 1ω6c (summed feature 3) and iso-C_17 : 0 3-OH were the major fatty acids. The major polar lipids were phosphatidylethanolamine, one unidentified aminophospholipid, one unidentified phospholipid, two unidentified lipids, five unidentified aminolipids and two unidentified glycolipids. Average nucleotide identity values for the draft genomes between strain P-25^T and strains S27^T, CM134L-2^T and THG-T11^T were 81.8, 77.6 and 81.2 %, respectively, and the digital DNA-DNA hybridization (dDDH) values were 30.0, 19.2 and 27.6 %, respectively. Based on their phylogenetic and phenotypic characteristics, chemotaxonomic data, and dDDH results, strain P-25^T is considered to represent a novel species of the genus Pedobacter, for which the name Pedobacter helvus sp. nov. is proposed; the type strain is strain P-25^T (KCTC 62821^T=CCTCC AB 2018185^T).

Pedobacter rivuli sp. nov., isolated from a freshwater stream

A Gram-staining-negative, rod-shaped, red strain, HME8457T, was isolated from a freshwater stream located in the Republic of Korea. A phylogenetic tree based on 16S rRNA gene sequences showed that strain HME8457T formed a lineage within the genus Pedobacter . Strain HME8457T was most closely related to species of the genus Pedobacter : Pedobacter daechungensis Dae 13T (96.4 % sequence similarity), Pedobacter lentus DS-40T (95.3 %), Pedobacter terricola DS-45T (94.9 %), Pedobacter glucosidilyticus 1-2T (94.2 %) and ‘Pedobacter soyangensis’ HME6451 (93.6 %). The major fatty acids were iso-C15 : 0 (28.8 %), summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c; 21.7 %), iso-C17 : 0 3-OH (7.7 %) and anteiso-C15 : 0 (6.2 %). The only respiratory quinone was MK-7. Polar lipid analysis revealed the presence of phosphatidylethanolamine, one unidentified aminolipid and two unidentified polar lipids. Sphingolipid was present. The DNA G+C content was 33.3 mol%. On the basis of the evidence presented in this study, strain HME8457T represents a novel species of the genus Pedobacter , for which the name Pedobacter rivuli sp. nov. is proposed; the type strain is HME8457T ( = KACC 17312T = CECT 8291T).

Pedobacter pituitosus sp. nov., isolated from a waterfall

A taxonomic study was carried out on a novel bacterial strain, designated MIC2002T, which was isolated from Wibong falls in Korea. Cells were Gram-stain-negative, aerobic, non-motile and rods, 0.3–0.5 µm wide and 4.0–5.0 µm long. The optimum temperature and pH range for growth were 25 °C and pH 6.5–7.0, respectively. Catalase and oxidase activities were positive. Flexirubin pigments were not produced. Comparison of the 16S rRNA gene sequences indicated that the isolate belonged to the genus Pedobacter , with Pedobacter daechungensis as its closest relative, with a similarity of 94.4 %. It contained iso-C15 : 0, anteiso-C15 : 0, C16 : 0, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and iso-C17 : 0 3-OH as the major fatty acids and menaquinone MK-7 as isoprenoid quinone. The polar lipid profile of strain MIC2002T revealed the presence of phosphatidylethanolamine and an unknown lipid. The DNA G+C content of the strain was 34.7 mol%. On the basis of the evidences presented, it was concluded that strain MIC2002T represents a novel species of the genus Pedobacter within the family Sphingobacteriaceae , for which the name Pedobacter pituitosus sp. nov. is proposed. The type strain is MIC2002T ( = KACC 17064T = JCM 18729T).

Pedobacter xixiisoli sp. nov., isolated from bank soil

A Gram-stain-negative, rod-shaped, yellow, non-motile, aerobic bacterium (strain S27T) was isolated from bank soil of the Xixi wetland in Zhejiang province, PR China. Phylogenetic analysis, based on its 16S rRNA gene sequence, revealed that strain S27T could represent a novel species of the genus Pedobacter showing highest similarity to Pedobacter koreensis WPCB189T (95.45 %), followed by ‘Pedobacter zeaxanthinifaciens’ TDMA-5 (95.22 %). The temperature, pH and NaCl concentration ranges for growth were 6–37 °C (optimum 28 °C), pH 5.0–9.0 (optimum pH 7.5) and 0–3 % (w/v) [optimum 0.5 % (w/v)], respectively. The DNA G+C content was 36.1 mol%, MK-7 was the only respiratory quinone, and iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) were the major fatty acids. These data all support the affiliation of strain S27T to the genus Pedobacter . The polar lipids of strain S27T comprised phosphatidylethanolamine, one unidentified aminophospholipid, four unidentified aminolipids and three unidentified lipids. However, strain S27T could be distinguished from other members of the genus Pedobacter due to its physiological and biochemical characteristics. Therefore, strain S27T represents a novel species of the genus Pedobacter , for which the name Pedobacter xixiisoli sp. nov. is proposed; the type strain is S27T ( = CGMCC 1.12803T = NBRC 110388T).

Draft genome sequence of Pedobacter agri PB92T, which belongs to the family Sphingobacteriaceae

Strain PB92(T) of Pedobacter agri, which belongs to the family Sphingobacteriaceae, was isolated from soil in the Republic of Korea. The draft genome of strain PB92(T) contains 5,141,552 bp, with a G+C content of 38.0%. This is the third genome sequencing project of the type strains among the Pedobacter species.