Two new members of the genus Sphingobacterium: Sphingobacterium zhuxiongii sp. nov. and Sphingobacterium luzhongxinii sp. nov.

Four strains, designated dk4302T, dk4209, xlx-73T, and xlx-183, were isolated from Tibetan gazelle and red swamp crawfish collected from the Qinghai-Tibet Plateau and Jiangxi Province, PR China. The strains were Gram-stain-negative, aerobic, rod-shaped, non-motile, mucoid, and yellow-pigmented. Strains dk4302T and dk4209 grew at 10-40 °C and pH 6.0-9.0, while strains xlx-73T/xlx-183 grew at 15-40 °C and pH 6.0-10.0. Both strains exhibited growth in the presence of up to 3.5 % (w/v) NaCl. Phylogenetic and phylogenomic analyses based on the 16S rRNA gene sequences and 652 core genes, respectively, revealed that the four strains formed two distinct clusters in the genus Sphingobacterium. Strains dk4302T and dk4209 formed a distinct clade with Sphingobacterium hotanense XH4T and Sphingobacterium humi D1T. The most closely related strains to xlx-73T and xlx-183 were Sphingobacterium nematocida M-SX103T. The DNA G+C contents were 38.9 and 39.8 mol%. The digital DNA-DNA hybridization (dDDH) values between dk4302T and S. humi D1T and S. hotanense XH4T were 19.2 and 21.8 % (19.0 and 21.6 % for strain dk4209), respectively. The corresponding average nucleotide identity (ANI) values were 74.3 and 78.1 % (74.4 and 78.3 % for strain dk4209), respectively. The dDDH values between xlx-73T (xlx-183) and S. nematocida M-SX103T was 24.6 % (25.7 %). The corresponding ANI value was 85.7 % (85.5 % for strain xlx-183). The major fatty acid and respiratory quinone of dk4302T and xlx-73T were iso-C15:0 and MK7. The polar lipids identified in all of the novel strains were phosphatidylethanolamine, phosphoglycolipids, aminophospholipids, and phospholipids. A total of 61/190 (32.1 %) and 82/190 (43.2 %) carbon substrates were metabolized by strains dk4302T and xlx-73T in the Biolog MicroPlates, respectively. Based on the results from this polyphasic taxonomic study, two novel species in the genus Sphingobacteruim are proposed, namely Sphingobacteruim zhuxiongii sp. nov. (type strain dk4302T=CGMCC 1.16795T=JCM 33600T) and Sphingobacteruimluzhongxinii sp. nov. (type strain xlx-73T=GDMCC 1.1712T=JCM 33886T).

Sphingobacterium tenebrionis sp. nov., isolated from intestine of mealworm.

A bacterial strain designated PU5-4T was isolated from the mealworm (the larvae of Tenebrio molitor) intestines. It was identified to be Gram-stain-negative, strictly aerobic, rod-shaped, non-motile, and non-spore-forming. Strain PU5-4T was observed to grow at 10-40 °C, at pH 7.0-10.0, and in the presence of 0-3.0 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain PU5-4T should be assigned to the genus Sphingobacterium. The 16S rRNA gene sequence similarity analysis showed that strain PU5-4T was closely related to the type strains of Sphingobacterium lactis DSM 22361T (98.49 %), Sphingobacterium endophyticum NYYP31T (98.11 %), Sphingobacterium soli NCCP 698T (97.69 %) and Sphingobacterium olei HAL-9T (95.73 %). The predominant isoprenoid quinone is MK-7. The major fatty acids were identified as iso-C15 : 0, iso-C17 : 03-OH and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and summed feature 9 (iso-C17 : 0 ω9c). The polar lipids are phosphatidylethanolamine, one unidentified phospholipid, and six unidentified lipids. The genomic DNA G+C content of strain PU5-4T is 40.24 mol%. The average nucleotide identity of strain PU5-4T exhibited respective values of 73.88, 73.37, 73.36 and 70.84 % comparing to the type strains of S. lactis DSM 22361T, S. soli NCCP 698T, S. endophyticum NYYP31T and S. olei HAL-9T, which are below the cut-off level (95-96 %) for species delineation. Based on the above results, strain PU5-4T represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium temoinsis sp. nov. is proposed. The type strain is PU5-4T (=CGMCC 1.61908T=JCM 36663T).

Sphingobacterium oryzagri sp. nov., isolated from rice paddy soil.

An aerobic, Gram-stain-negative and short rod-shaped bacterial strain, designated M6-31T, was isolated from rice paddy soil sampled in Miryang, Republic of Korea. Growth was observed at 4-35 °C (optimum, 28 °C), pH 6.0-9.0 (optimum, pH 7.0-8.0) and in the presence of 0-4 % (w/v) NaCl (optimum, 0 % w/v). Phylogenetic analysis based on 16S rRNA gene sequences grouped strain M6-31T with Sphingobacterium bambusae IBFC2009T, Sphingobacterium griseoflavum SCU-B140T and Sphingobacterium solani MLS-26-JM13-11T in the same clade, with the 16S rRNA gene sequence similarities ranging from 95.8 to 96.6 %. A genome-based phylogenetic tree reconstructed by using all publicly available Sphingobacterium genomes placed strain M6-31T with S. bambusae KACC 22910T, 'Sphingobacterium deserti' ACCC 05744T, S. griseoflavum CGMCC 1.12966T and Sphingobacterium paludis CGMCC 1.12801T. Orthologous average nucleotide identity and digital DNA-DNA hybridization values between strain M6-31T and its closely related strains were lower than 74.6 and 22.0 %, respectively. The respiratory quinone was menaquinone-7, and the major polar lipid was phosphatidylethanolamine. The major fatty acids (>10 %) were C15 : 0 iso, C17 : 0 iso 3OH and summed feature 3. The phenotypic, chemotaxonomic and genotypic data obtained in this study showed that strain M6-31T represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium oryzagri sp. nov. (type strain M6-31T=KACC 22765T=JCM 35893T) is proposed.

Sphingobacterium faecale sp. nov., a 1-aminocyclopropane-1-carboxylate deaminase producing bacterium isolated from camel faeces.

An investigation of the diversity of 1-aminocyclopropane-1-carboxylate deaminase producing bacteria associated with camel faeces revealed the presence of a novel bacterial strain designated C459-1T. It was Gram-stain-negative, short-rod-shaped and non-motile. Strain C459-1T was observed to grow optimally at 35 °C, at pH 7.0 and in the presence of 0 % NaCl on Luria-Bertani agar medium. The cells were found to be positive for catalase and oxidase activities. The major fatty acids (>10 %) were identified as iso-C15 : 0, summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c) and iso-C17 : 0 3-OH. The predominant menaquinone was MK-7. The major polar lipids consisted of phosphatidylethanolamine, one sphingophospholipid, two unknown aminophospholipids, three unknown glycolipids and five unknown lipids. The genomic DNA G+C content was 40.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain C459-1T was affiliated with the genus Sphingobacterium and had the highest sequence similarity to Sphingobacterium tabacisoli h337T (97.0 %) and Sphingobacterium paucimobilis HER1398T (95.6 %). The average nucleotide identity and digital DNA-DNA hybridization values between strain C459-1T and S. tabacisoli h337T were 83.8 and 33.8 %, respectively. Phenotypic characteristics including enzyme activities and carbon source utilization differentiated strain C459-1T from other Sphingobacterium species. Based on its phenotypic, chemotaxonomic and phylogenetic properties, strain C459-1T represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium faecale sp. nov. is proposed, with strain is C459-1T (CGMCC 1.18716T=KCTC 82381T) as the type strain.

Sphingobacterium micropteri sp. nov. and Sphingobacterium litopenaei sp. nov., isolated from aquaculture water.

Two novel bacterial strains, designated as DN00404T and DN04309T, were isolated from aquaculture water and characterized by using a polyphasic taxonomic approach. Cells of strains DN00404T and DN04309T were Gram-stain-negative, aerobic, non-motile, oxidase-positive and catalase-positive. Cells of DN00404T were short rod-shaped and those of DN04309T were long rod-shaped. Strain DN00404T was found to grow at 15-37 °C (optimum, 25-30 °C), at pH 6.0-11.0 (optimum, pH 7.5) and in 0-2.0 % (w/v) NaCl (optimum, 1.0 %). Strain DN04309T was found to grow at 15-45 °C (optimum, 20-37 °C), at pH 5.5-11.0 (optimum, 7.5) and in 0-4.0 % (w/v) NaCl (optimum, 0.5 %). Phylogenetic analyses based on 16S rRNA gene and genome sequences revealed that the two strains belonged to the genus Sphingobacterium and were distinct from all known species of this genus. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the two strains and between each of the two strains and related type strains of this genus were well below the recognized thresholds of 95.0-96.0 % ANI and 70.0 % dDDH for species delineation. The genomic DNA G+C contents of strains DN00404T and DN04309T were 41.6 and 36.0 mol%, respectively. The respiratory quinone in both strains was identified as MK-7, and their major fatty acids were iso-C15 : 0 and summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c), which were similar to those of other species of this genus. The two major fatty acids C16 : 0 and iso-C17 : 0 3-OH were also found in strain DN00404T. Based on genotypic and phenotypic characteristics, two novel species of the genus Sphingobacterium are proposed: Sphingobacterium micropteri sp. nov. with DN00404T (=GDMCC 1.1865T=KACC 21924T) as the type strain and Sphingobacterium litopenaei sp. nov. with DN04309T (=GDMCC 1.1984T=KCTC 82348T) as the type strain.

Sphingobacterium hungaricum sp. nov. a novel species on the borderline of the genus Sphingobacterium.

A Gram-reaction-negative bacterial strain, designated Kb22T, was isolated from agricultural soil and characterized using a polyphasic approach to determine its taxonomic position. On the basis of 16S rRNA gene sequence analysis, the strain shows highest similarity (94.39 %) to Sphingobacterium nematocida M-SX103T. The highest average nucleotide identity value (71.83 %) was found with Sphingobacterium composti T5-12T, and the highest amino acid identity value (66.65 %) was found with Sphingobacterium olei HAL-9T. Cells are aerobic, non-motile rods. The isolate was found to be positive for catalase and oxidase tests. The assembled genome of strain Kb22T has a total length of 4,06 Mb, the DNA G+C content is 38.1 mol%. The only isoprenoid quinone is menaquinone 7 (MK-7). The major fatty acids are iso-C15:0 (28.4%), summed feature 3 (C16:1 ω7c and/or iso-C15:0 2-OH) (25.7 %) and iso-C17:0 3-OH (19.7 %). Based on phenotypic characteristics and phylogenetic results, it is concluded that strain Kb22T is a member of the genus Sphingobacterium and represents a novel species for which the name Sphingobacterium hungaricum sp. nov. is proposed. The type strain of the species is strain Kb22T (=LMG 31574T=NCAIM B.02638T).

Sphingobacterium prati sp. nov., isolated from agricultural soil and involved in lignocellulose deconstruction.

A bacterial strain, arapr2T, was isolated from agricultural soil sampled in Reims, France. Based on its 16S rRNA gene sequence, the strain was affiliated to the family Sphingobacteriaceae and more specifically to the genus Sphingobacterium. The strain had 98.31 % 16S rRNA gene sequence similarity to its closest relative Sphingobacterium canadense CR11T and 98.25 % to Sphingobacterium pakistanensis NCCP-246T. Genome relatedness indexes revealed that the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between arapr2T and its closest relative (S. canadense CR11T) were 92.97 % and 52.00 %, respectively; for S. pakistanensis NCCP-246T, the ANI and dDDH values were 82.46 and 27.6%, respectively. The genomic DNA of strain arapr2T was 6.02 Mbp long, had a DNA G+C content of 40.4 mol% and had 5504 protein-coding genes. The results obtained in this study suggests that strain arapr2T (CIP 111872T=LMG 31848T) represents a new species for which the name Sphingobacterium prati sp. nov. is proposed. Due to the fact that this strain has been isolated using wheat straw as carbon source, this novel bacterial strain represents a promising biotechnological tool for the fractionation of lignocellulosic biomass in the context of biorefinery development.

Sphingobacterium rhinopitheci sp. Nov., isolated from the faeces of Rhinopithecus bieti in China.

A novel bacterium, WQ 047T, was isolated from the faeces of Rhinopithecus bieti, a highly endangered primate endemic to China. The cells were aerobic, oval/rod-shaped, Gram-stain-negative, non-motile, catalase positive, and produced yellow pigmented colonies on Columbia Agar. The taxonomic position of WQ 047T was clarified by applying a polyphasic study based on 16S rRNA gene sequence phylogenetic analysis, extensive biological typing, and whole genome sequencing. Phylogenetic analysis indicated that stain WQ 047T belonged to the genus Sphingobacterium and its 16S rRNA gene sequence exhibited 96.47% pairwise similarity with that of the closest relatives Sphingobacterium nematocida M-SX103T. The calculated whole genome average nucleotide identity (ANI) value between strain WQ 047T and strain M-SX103 was 72.3%. The digital DNA-DNA hybridization value of strain WQ 047T and M-SX103T was 15.73%, which was obtained by calculating the genome-to-genome distance. The major fatty acids were C15:0 iso, C17:0 iso 3-OH, Summed Feature 3 (C16:1 ω7c/C16:1 ω6c) and Summed feature 9 (iso-C17:1ω9c and/or 10-methyl C16:0). The predominant polar lipids were PE, PL and APL. MK-7 was the predominant menaquinone. The G + C content of WQ 047T was 34.89 mol% according to genome analysis. All these characteristics were consistent with those of the genus of Sphingobacterium. Therefore, based on these results, we propose a novel species for which the name Sphingobacterium rhinopitheci sp. Nov. is proposed, with the type strain WQ 047T (= CCTCC AA 2020026T = KCTC82393T).

Sphingobacterium phlebotomi sp. nov., a new member of family Sphingobacteriaceae isolated from sand fly rearing substrate.

A Gram-stain-negative, rod-shaped, non-motile, non-spore-forming, aerobic bacterium, designated type strain SSI9T, was isolated from sand fly (Phlebotomus papatasi Scopoli; Diptera: Psychodidae) rearing substrate and subjected to polyphasic taxonomic analysis. Strain SSI9T contained phosphatidylethanolamine as a major polar lipid, MK-7 as the predominant quinone, and C16 : 1ω6c/C16 : 1ω7c, iso-C15 : 0, iso-C17 : 0 3-OH and C16 : 0 as the major cellular fatty acids. Phylogenetic analysis based on 16S rRNA gene sequences revealed that SSI9T represents a member of the genus Sphingobacterium, of the family Sphingobacteriaceae sharing 96.5-88.0 % sequence similarity with other species of the genus Sphingobacterium. The results of multilocus sequence analysis using the concatenated sequences of the housekeeping genes recA, rplC and groL indicated that SSI9T formed a separate branch in the genus Sphingobacterium. The genome of SSI9T is 5 197 142 bp with a DNA G+C content of 41.8 mol% and encodes 4395 predicted coding sequences, 49 tRNAs, and three complete rRNAs and two partial rRNAs. SSI9T could be distinguished from other species of the genus Sphingobacterium with validly published names by several phenotypic, chemotaxonomic and genomic characteristics. On the basis of the results of this polyphasic taxonomic analysis, the bacterial isolate represents a novel species within the genus Sphingobacterium, for which the name Sphingobacterium phlebotomi sp. nov. is proposed. The type strain is SSI9T (=ATCC TSD-210T=LMG 31664T=NRRL B-65603T).

Sphingobacterium lumbrici sp. nov., a novel bacterium isolated from wormcast of Eisenia foetida.

A novel Gram-stain-negative, rod-shaped, non-motile, yellowish bacterium, designated strain 1.3611T, was isolated from the wormcast of Eisenia foetida. The strain grew optimally at 30-37 ℃, at pH 7.0 and with 0-1.0 % (w/v) NaCl. Based on the results of 16S rRNA gene sequence and phylogenetic analyses, strain 1.3611T showed the highest degree of 16S rRNA gene sequence similarity to Sphingobacterium olei HAL-9T (97.0 %), followed by Sphingobacterium alkalisoli Y3L14T (95.8 %). The respiratory quinone of strain 1.3611T was menaquinone-7 (MK-7) and its major cellular fatty acids were iso-C15 : 0 (41.3 %), summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c, 22.1 %) and iso-C17 : 0 3-OH (16.2 %). The major polar lipids were sphingophospholipid, phosphatidylethanolamine, four unidentified glycolipids, two unidentified phospholipids and five unidentified polar lipids. The genomic DNA G+C content was 39.0 mol%. The digital DNA-DNA hybridization and average nucleotide identity values between the genomes of strain 1.3611T and S. olei HAL-9T were 37.9 and 88.9 %, respectively. According to the phenotypic and chemotaxonomic phylogenetic results, strain 1.3611T should represent a novel species of the genus Sphingobacterium, for which the name Sphingobacterium lumbrici sp. nov. is proposed, with strain 1.3611T (=KCTC 62980T=CCTCC AB 2018349T) as the type strain.

An alkali-tolerant phospholipase D from Sphingobacterium thalpophilum 2015: Gene cloning, overproduction and characterization.

The phospholipase pl-S.t gene of Sphingobacterium thalpophilum 2015 was cloned and the gene sequence was submitted to NCBI with Accession Number KX674735.1. The phylogenetic analysis showed that this PL-S.t was clustered to phospholipase D (PLD). As far as we know, the PL-S.t with a molecular mass of 22.5 kDa is the lowest of the currently purified bacterial PLDs, which belongs to a non-HKD PLD enzyme. This PL-S.t was resistant to a wide range of alkali pHs (7.5-9.0) after 1 h incubation, retaining more than 90% of its maximum activity. The PL-S.t activity can be enhanced by Ni2+, Co2+ and Mn2+. This PL-S.t has only one cysteine residue and fewer negatively-charged amino acids (AAs). The hydrogen bonds network was found around the cystein108, which may be beneficial to the stability and activity of PL-S.t in Ni2+ solution. This study has laid the foundation for further research on the molecular mechanism of the catalytic characteristics of low molecular weight alkalic PLD from S. thalpophilum 2015.

Sphingobacterium chungjuense sp. nov., isolated from a freshwater lake.

A Gram-stain-negative, rod-shaped, aerobic, non-flagellated, chemoheterotrophic bacterium, designated strain IMCC25678T, was isolated from an artificial freshwater reservoir, Chungju Lake, in the Republic of Korea. The 16S rRNA gene sequence analysis indicated that strain IMCC25678T belongs to the genus Sphingobacterium with ≤98.7 % sequence similarities to Sphingobacterium species. Whole genome sequencing of strain IMCC25678T revealed a 3.9 Mbp genome size with a DNA G+C content of 42.2 mol%. The IMCC25678T genome shared ≤89.7 % average nucleotide identity and ≤21.4 % digital DNA-DNA hybridization values with closely related species of the genus Sphingobacterium, indicating that the strain represents a novel species. Summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c), iso-C15 : 0 and iso-C17 : 0 3-OH were found to be the predominant cellular fatty acid constituents in the strain. The major respiratory quinone was MK-7. The major polar lipids were phosphatidylethanolamine, one unidentified phosphoglycolipid, one unidentified sphingolipid and three unidentified polar lipids. Based on the phylogenetic and phenotypic characteristics, strain IMCC25678T was considered to represent a novel species within the genus Sphingobacterium, for which the name Sphingobacterium chungjuense sp. nov. is proposed. The type strain is IMCC25678T (=KACC 19485T=NBRC 113130T).

Sphingomonas corticis sp. nov., and Sphingobacterium corticibacterium sp. nov., from bark canker.

Two Gram-stain-negative, aerobic, non-motile bacterial strains, 36D10-4-7T and 30C10-4-7T, were isolated from bark canker tissue of Populus × euramericana, respectively. 16S rRNA gene sequence analysis revealed that strain 36D10-4-7T shows 98.0 % sequence similarity to Sphingomonas adhaesiva DSM 7418T, and strain 30C10-4-7T shows highest sequence similarity to Sphingobacterium arenae H-12T (95.6 %). Average nucleotide identity analysis indicates that strain 36D10-4-7T is a novel member different from recognized species in the genus Sphingomonas. The main fatty acids and respiratory quinone detected in strain 36D10-4-7T are C18 : 1 ω7c and/or C18 : 1 ω6c and Q-10, respectively. The polar lipids are diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, aminolipid, phosphatidylethanolamine, sphingoglycolipid, two uncharacterized phospholipids and two uncharacterized lipids. For strain 30C10-4-7T, the major fatty acids and menaquinone are iso-C15 : 0, C16 : 1 ω7c and/or C16 : 1 ω6c and iso-C17 : 0 3-OH and MK-7, respectively. The polar lipid profile includes phosphatidylethanolamine, phospholipids, two aminophospholipids and six unidentified lipids. Based on phenotypic and genotypic characteristics, these two strains represent two novel species within the genera Sphingomonas and Sphingobacterium. The name Sphingomonas corticis sp. nov. (type strain 36D10-4-7T=CFCC 13112T=KCTC 52799T) and Sphingobacterium corticibacterium sp. nov. (type strain 30C10-4-7T=CFCC 13069T=KCTC 52797T) are proposed.

Sphingobacterium endophyticum sp. nov., a novel endophyte isolated from halophyte.

A bacterial strain designated NYYP31T was isolated from the leaves of an annual halophytes, Suaeda corniculata Bunge, collected from the southern edge of the Gurbantunggut desert, north-west China. Strain NYYP31T was Gram-staining negative, strictly aerobic, rod-shaped, non-motile, and non-spore-forming. Growth was observed at 4-42 °C, at pH 5.0-10.0, in the presence of up to 8% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences and coding sequences of 92 protein clusters showed that strain NYYP31T should be assigned to the genus Sphingobacterium. 16S rRNA gene sequence similarity analysis showed that strain NYYP31T was most closely related to the type strain of Sphingobacterium daejeonense (97.9%) and Sphingobacterium lactis (97.7%). The predominant isoprenoid quinone was MK-7. The major fatty acids were identified as iso-C15:0, iso-C17:0 3-OH and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c). The polar lipids were phosphatidylethanolamine, two unidentified phospholipids, three unidentified lipids, three unidentified amino phospholipids, and two unidentified glycolipids. The genomic DNA G + C content was 36.4 mol%. The average nucleotide identity (ANI) values for strain NYYP31T to the type strains of S. daejeonense and S. lactis were 77.9 and 74.1%, respectively, which were below the cut-off level (95-96%) for species delineation. Based on the above results, strain NYYP31T represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium endophyticum sp. nov. is proposed. The type strain is NYYP31T (= CGMCC 1.16979T = NBRC 114258T).

Sphingobacterium cavernae sp. nov., a novel bacterium isolated from soil sampled at Tiandong Cave.

A Gram-stain-negative, non-motile and rod-shaped bacterium, designated strain 5.0403-2T, was isolated from a cave soil sample collected from Tiandong Cave, Guizhou Province, south-west PR China. Cells showed positive oxidase and catalase reactions. The predominant isoprenoid quinone was MK-7. The major fatty acids were identified as iso-C15 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), iso-C17 : 0 3OH and summed feature 9 (iso-C17 : 1 ω9c or C16 : 0 10-methyl). The cellular polar lipids contained phosphatidylethanolamine, one unidentified phospholipid, three unidentified phosphoglycolipids and four unidentified lipids. The genomic DNA G+C content was 36.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 5.0403-2T should be assigned to the genus Sphingobacterium. Results of 16S rRNA gene sequence similarity analysis showed that strain 5.0403-2T was most similar to Sphingobacterium bovisgrunnientis KCTC 52685T (98.7 %), Sphingobacterium composti KCTC 12578T (98.0 %) and Sphingobacterium alimentarium DSM 22362T (97.3 %) and less than 95.0 % similar to other species of the genus Sphingobacterium. The average nucleotide identity values between strain 5.0403-2T and S. bovisgrunnientis KCTC 52685T, S. composti KCTC 12578T and S. alimentarium DSM 22362T were 94.2, 82.3 and 77.2 % respectively. The digitalDNA-DNA hybridization values between strain 5.0403-2T and S. bovisgrunnientis KCTC 52685T, S. composti KCTC 12578T and S. alimentarium DSM 22362T were 68.4, 25.6 and 20.7 %. These results indicated that the isolate represented a novel genomic species. The polyphasic taxonomic characteristics indicated that strain 5.0304-2T represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium cavernae sp. nov. (type strain 5.0403-2T=KCTC 62981T=CCTCC AB 2019257T) is proposed.

Sphingobacterium olei sp. nov., isolated from oil-contaminated soil.

A Gram-stain-negative, rod-shaped, non-motile and non-spore-forming bacterium, designated HAL-9T, was isolated from oil-contaminated soil in Daqing oilfield, Heilongjiang Province, PR China. Strain HAL-9T was able to degrade quizalofop-p-ethyl and diclofop-methyl. Growth was observed at 10-35 °C (optimum, 30 °C), pH 6.0-10.0 (optimum, pH 7.0) and salinity of 0 %-5.0 % (w/v; optimum 1.0 %). The results of phylogenetic analysis based on the 16S rRNA gene indicated that strain HAL-9T belongs to the genus Sphingobacterium and showed the highest sequence similarity (98.3 %) to Sphingobacterium alkalisoli Y3L14T, followed by Sphingobacterium mizutaii DSM 11724T (95.1 %) and Sphingobacterium lactis DSM 22361T (95.1 %). Menaquinone-7 (MK-7) was the only isoprenoid quinone. The predominant cellular fatty acids were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), iso-C15: 0 and iso-C17 : 0 3-OH. The major polar lipids were phosphatidylethanolamine, three phosphoglycolipids and three unidentified lipids. The draft genome of strain HAL-9T was 5.41 Mb. The G+C content of strain HAL-9T was 40.6 mol%. Furthermore, the average nucleotide identity and in silico DNA-DNA hybridization values between strain HAL-9T and S. alkalisoli Y3L14T were 86.2 % and 32.8 %, respectively, which were below the standard thresholds for species differentiation. On the basis of phenotypic, genotypic and phylogenetic evidence, strain HAL-9T represents a novel species in the genus Sphingobacterium, for which the name Sphingobacterium olei sp. nov. is proposed. The type strain is HAL-9T (=ACCC 61581T=CCTCC AB 2019176T=KCTC 72287T).

The applicability of gene sequencing and MALDI-TOF to identify less common gram-negative rods (Advenella, Castellaniella, Kaistia, Pusillimonas and Sphingobacterium) from environmental isolates.

Our aim was to identify less common non-fermenting gram-negative rods during the bioremediation process. Five genera were found: Advenella, Castellaniella, Kaistia, Pusillimonas and Sphingobacterium, for a total of 15 isolates. Therefore, we evaluated the applicability of four methods currently available for bacteria identification: (1) conventional biochemical methods, (2) the VITEK®-2 system, (3) MALDI-TOF mass spectrometry and (4) 16S rRNA gene sequencing. The biochemical methods and the VITEK®-2 system were reliable only for the Sphingobacterium isolate and solely at the genus level. Both MALDI-TOF mass spectrometry platforms (Bruker and VITEK® MS) did not achieve reliable identification results for any of these genera. 16S rRNA gene sequencing identified eight isolates to the species level but not to the subspecies level, when applicable. The remaining seven isolates were reliably identified through 16S rRNA gene sequencing to the genus level only. Our findings suggest that the detection and identification of less common genera (and species) that appeared at certain moments during the bioremediation process can be a challenge to microbiologists considering the most used techniques. In addition, more studies are required to confirm our results.

Sphingobacterium puteale sp. nov., isolated from a deep subsurface aquifer.

A bacterial strain M05W1-28T was isolated from a well that collected water for irrigation from a deep aquifer at a depth of 400 m. Cells were observed to be rod-shaped, non-motile, aerobic, stained Gram-negative. Optimal growth was obtained at pH 7.0 (range: 6.0-9.0), 28 °C (range: 15-37 °C) and 0 % NaCl (range: 0-1.5 %, w/v) in modified tryptic soy broth (mTSB) without added NaCl and R2A. The cells were found to be positive for catalase and oxidase activities. The major fatty acids (>10 %) were identified as summed feature 3 (C16 : 1 ω7c / C16 : 1 ω6c) and iso-C15 : 0. The major polar lipids were phosphatidylethanolamine, glycolipid, phosphoglycolipids, phospholipids, and unidentified lipids. The major respiratory quinone was menaquinone-7 (MK-7). The genomic G+C content of strain M05W1-28T was 40.7 %. Based on similarities of 16S rRNA gene sequences, strain M05W1-28T was affiliated with the genus Sphingobacterium, exhibiting the highest sequence similarities with S. multivorum LMG 8342T (97.5 %), S. ginsenosidimutans THG07T (97.1 %) and less than 97.0 % to other members of the genus. The average nucleotide identity (ANI) and digital DNA-DNA hybridisation values (dDDH) between M05W1-28T and S. multivorum LMG 8342T were 78.1 and 22.5 %, respectively. Phenotypic characteristics including enzyme activities and carbon source utilisation differentiated the strain from other Sphingobacterium species. The phenotypic, chemotaxonomic and phylogenetic properties suggested that strain M05W1-28T represented a novel species within the genus Sphingobacterium, for which the name Sphingobacterium puteale sp. nov. is proposed. The type strain is M05W1-28T (=CGMCC 1.13711T=KCTC 72027T).

Sphingobacterium corticibacter sp. nov., isolated from bark of Populus × euramericana.

One Gram-stain negative, aerobic, non-motile bacterial strain, 2c-3T, was isolated from symptomatic canker bark tissue of Populus × euramericana. It was studied by the genome sequence-derived average nucleotide identity (ANI), phylogenetic analysis based on 16S rRNA gene sequences and phenotypic characteristics. 16S rRNA gene data revealed that the novel isolate shares the greatest sequence similarity to Sphingobacterium populi 7Y-4T (97.0 %). The ANI values between the novel isolate and S. populi 7Y-4T was 81.19 %, lower than the proposed species boundary ANI cut-off (95-96 %). The major fatty acids are iso-C15 : 0, C16 : 1ω7c and iso-C17 : 0 3-OH. The polar lipids of the novel isolate included phosphatidylethanolamine, phospholipid, aminophospholipid and unknown lipids (L1-10). The menaquinone of the novel isolate was MK-7. The DNA G+C content was 41.96 mol %. Based on phenotypic and genotypic characteristics, the isolate represents a novel species within the genus Sphingobacterium, for which the name Sphingobacterium corticibacter is proposed. The type strain is 2c-3T (=CFCC 11898T=KCTC 52798T).

Sphingobacterium athyrii sp. nov., a cellulose- and xylan-degrading bacterium isolated from a decaying fern (Athyrium wallichianum Ching).

Assessment of the bacterial diversity associated with a decaying fern, Athyrium wallichianum Ching, revealed the presence of a novel bacterial strain named M46T. It was Gram-stain-negative, rod-shaped, non-motile and aerobic with cellulose and xylan degradation abilities. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain M46T was affiliated to the genus Sphingobacterium, exhibiting the highest sequence similarity of 97.9 % to Sphingobacterium ginsenosidimutans THG 07T, Sphingobacterium canadense CR11T and Sphingobacterium detergens6.2 ST. Multilocus sequence analysis (MLSA) based on concatenated sequences of the rpoB, cpn60 and 16S rRNA genes showed that strain M46T clustered together with S. canadense CR11T. The genome of strain M46T had a G+C content of 40.6 mol% and chromosome of 6 853 865 bp. Average nucleotide identity (ANI) between strain M46T and S. detergens 6.2 ST and S. siyangense SY1T was 85.1 and 78.1 %, respectively. DNA-DNA relatedness values among strain M46T and other closely related Sphingobacterium species were <70 %. ANI and DNA-DNA relatedness findings strongly supported M46T as a putative novel strain of Sphingobacterium. The predominant fatty acids of strain M46T were iso-C15 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and iso-C17 : 0 3-OH, and MK-7 was the dominant isoprenoid quinone. The polar lipid profile of strain M46T contained phosphatidylethanolamine as the dominant component, while minor amounts of phosphoglycolipid, one unidentified aminophospholipid, two unidentified phospholipids and four unidentified lipids were also detected. Based on 16S rRNA gene sequence similarities, MLSA results, genomic characteristics, and phenotypic and biochemotaxonomic analyses, strain M46T is considered to represent a novel species in the genus Sphingobacterium, for which the name Sphingobacterium athyrii sp. nov. is proposed. The type strain is M46T (=CGMCC 1.13466T=JCM 32543T).