Sphingobacterium nematocida sp. nov., a nematicidal endophytic bacterium isolated from tobacco

Ecotin: A versatile protease inhibitor of bacteria and eukaryotes

Serine protease inhibitors are a large family of proteins involved in important pathways and processes, such as inflammatory responses and blood clotting. Most are characterized by a precise mode of action, thereby targeting a narrow range of protease substrates. However, the serine-protease inhibitor ecotin is able to inhibit a broad range of serine proteases that display a wide range of specificities. This specificity is driven by special structural features which allow unique flexibility upon binding to targets. Although frequently observed in many human/animal-associated bacteria, ecotin homologs may also be found in plant-associated taxa and environmental species. The purpose of this review is to provide an update on the biological importance, role in host-microbe interactions, and evolutionary relationship between ecotin orthologs isolated from Eukaryotic and Prokaryotic species across the Tree of Life.

Sphingobacterium bovistauri sp. nov., Isolated from the Faeces of Bos Taurus

A novel bacterium designated WQ 366 ^T was isolated from the faeces of Bos taurus, foraging on the slopes of the Baima Snow Mountain in Yunnan, China. The isolate grew optimally at 30 ℃ and pH 7.0-8.0 without NaCl. The cells were Gram-stain-negative, aerobic, rod-shaped, non-gliding, catalase-positive, and produced yellow color colonies on Columbia Agar. A polyphasic study was applied to clarify its taxonomic position through 16S rRNA gene and genome sequence analysis, and other extensive biological typing. Phylogenetic analysis revealed that the isolate was affiliated to the genus Sphingobacterium and its 16S rRNA gene sequence was closely related to Sphingobacterium bovisgrunnientis YK2 ^T (97.3%), Sphingobacterium composti T5-12 ^T (96.4%), and Sphingobacterium cavernae 5.0403-2 ^T (96.4%). The calculated whole genome average nucleotide identity (ANI) and the digital DNA-DNA hybridization values between strain WQ 366 ^T and the three related strains were 78.3, 78.6, 73.9 and 21.2, 21.2, 21.0%, respectively. The predominant fatty acids (>10%) were iso-C_15:0, iso-C_17:0 3-OH, Summed Feature 3 (C_16:1 ω7c and/or C_16:1 ω6c), and Summed feature 9 (iso-C_17:1 ω9c and 10-methyl C_16:0). The main polar lipids were PE, GPL, GL, and PL. MK-7 was the major menaquinone. The genome size and the G + C content of WQ 366 ^T was 4.1 Mb and 34.6%, respectively. All these results indicated that strain WQ 366 ^T represents a novel species of the Sphingobacterium genus. Therefore, the name Sphingobacterium bovistauri sp. nov. is proposed, and the type strain is WQ 366 ^T (= CCTCC AA 2020029 ^T = KCTC 82395 ^T).

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

A Gram-reaction-negative bacterial strain, designated Kb22^T, 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-SX103^T. The highest average nucleotide identity value (71.83 %) was found with Sphingobacterium composti T5-12^T, and the highest amino acid identity value (66.65 %) was found with Sphingobacterium olei HAL-9^T. Cells are aerobic, non-motile rods. The isolate was found to be positive for catalase and oxidase tests. The assembled genome of strain Kb22^T 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-C_15:0 (28.4%), summed feature 3 (C_16:1 ω7c and/or iso-C_15:0 2-OH) (25.7 %) and iso-C_17:0 3-OH (19.7 %). Based on phenotypic characteristics and phylogenetic results, it is concluded that strain Kb22^T 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 Kb22^T (=LMG 31574^T=NCAIM B.02638^T).

Genome Annotation of Poly(lactic acid) Degrading Pseudomonas aeruginosa, Sphingobacterium sp. and Geobacillus sp

Pseudomonas aeruginosa and Sphingobacterium sp. are well known for their ability to decontaminate many environmental pollutants while Geobacillus sp. have been exploited for their thermostable enzymes. This study reports the annotation of genomes of P. aeruginosa S3, Sphingobacterium S2 and Geobacillus EC-3 that were isolated from compost, based on their ability to degrade poly(lactic acid), PLA. Draft genomes of the strains were assembled from Illumina reads, annotated and viewed with the aim of gaining insight into the genetic elements involved in degradation of PLA. The draft genome of Sphinogobacterium strain S2 (435 contigs) was estimated at 5,604,691 bp and the draft genome of P. aeruginosa strain S3 (303 contigs) was estimated at 6,631,638 bp. The draft genome of the thermophile Geobacillus strain EC-3 (111 contigs) was estimated at 3,397,712 bp. A total of 5385 (60% with annotation), 6437 (80% with annotation) and 3790 (74% with annotation) protein-coding genes were predicted for strains S2, S3 and EC-3, respectively. Catabolic genes for the biodegradation of xenobiotics, aromatic compounds and lactic acid as well as the genes attributable to the establishment and regulation of biofilm were identified in all three draft genomes. Our results reveal essential genetic elements that facilitate PLA metabolism at mesophilic and thermophilic temperatures in these three isolates.

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

A novel bacterium, WQ 047^T, 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 047^T 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 047^T 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-SX103^T. The calculated whole genome average nucleotide identity (ANI) value between strain WQ 047^T and strain M-SX103 was 72.3%. The digital DNA-DNA hybridization value of strain WQ 047^T and M-SX103^T was 15.73%, which was obtained by calculating the genome-to-genome distance. The major fatty acids were C_15:0 iso, C_17:0 iso 3-OH, Summed Feature 3 (C_16:1 ω7c/C_16:1 ω6c) and Summed feature 9 (iso-C_17:1ω9c and/or 10-methyl C_16:0). The predominant polar lipids were PE, PL and APL. MK-7 was the predominant menaquinone. The G + C content of WQ 047^T 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 047^T (= CCTCC AA 2020026^T = KCTC82393^T).

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).

Exemplifying endophytes of banana (Musa paradisiaca) for their potential role in growth stimulation and management of Fusarium oxysporum f. sp cubense causing panama wilt

In the present study, potentiality of endophytic microorganisms such as Rigidiporus vinctus AAU EF, Trichoderma reesei UH EF, and Sphingobacterium tabacisoli UH EB in the management of panama wilt and growth promotion of banana was assessed through artificial inoculation. During the study, a total of 220 bacterial and 110 fungal endophytes were isolated from root, pseudostem, and leaf samples of banana, and they were evaluated against Fusarium oxysporum f. sp cubense causing panama wilt. Out of total 330 bacterial and fungal endophytes, only five endophytes exhibited antagonism against Fusarium oxysporum f. sp cubense, out of which only three isolates, namely Trichoderma reesei UH EF, Rigidiporus vinctus AAU EF, and Sphingobacterium tabacisoli UH EB, produced indole acetic acid, siderophore, and hydrogen cyanide, except one bacterial strain Sphingobacterium tabacisoli UH EB which does not produce hydrogen cyanide. Furthermore, these three endophytes were identified through cultural and morphological characteristics as well as by the sequencing internal transcribed spacer (ITS) and 16S rRNA gene sequences analysis for bacteria, respectively. The response of host plant to endophyte inoculation was assessed by measuring the change in four growth parameters; plant height, pseudo stem girth (diameter), number of roots, and total number of leaves. The application of endophytes, irrespective of isolate and treatment type promoted the overall growth of the plant growth when compared with diseased plants with significant higher values recorded for all parameters assessed. The endophytes reported as growth promoters were found to have significant inhibition effect on Foc which can evidenced with lowest AUDPC values and epidemic rate at 99.09 units² and 0.02 unit/day, respectively.

Bacillus simplex treatment promotes soybean defence against soybean cyst nematodes: A metabolomics study using GC-MS

We aimed to profile the metabolism of soybean roots that were infected with soybean cyst nematodes and treated with Bacillus simplex to identify metabolic differences that may explain nematode resistance. Compared with control soybean roots, B. simplex-treated soybean roots contained lower levels of glucose, fructose, sucrose, and trehalose, which reduced the nematodes' food source. Furthermore, treatment with B. simplex led to higher levels of melibiose, gluconic acid, lactic acid, phytosphingosine, and noradrenaline in soybean roots, which promoted nematocidal activity. The levels of oxoproline, maltose, and galactose were lowered after B. simplex treatment, which improved disease resistance. Collectively, this study provides insight into the metabolic alterations induced by B. simplex treatment, which affects the interactions with soybean cyst nematodes.

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

A bacterial strain designated NYYP31^T 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 NYYP31^T 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 NYYP31^T should be assigned to the genus Sphingobacterium. 16S rRNA gene sequence similarity analysis showed that strain NYYP31^T 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-C_15:0, iso-C_17:0 3-OH and summed feature 3 (C_16:1 ω7c and/or C_16:1 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 NYYP31^T 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 NYYP31^T represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium endophyticum sp. nov. is proposed. The type strain is NYYP31^T (= CGMCC 1.16979^T = NBRC 114258^T).

Populations of the Parasitic Plant Phelipanche ramosa Influence Their Seed Microbiota

Seeds of the parasitic weed Phelipanche ramosa are well adapted to their hosts because they germinate and form haustorial structures to connect to roots in response to diverse host-derived molecular signals. P. ramosa presents different genetic groups that are preferentially adapted to certain hosts. Since there are indications that microbes play a role in the interaction especially in the early stages of the interaction, we studied the microbial diversity harbored by the parasitic seeds with respect to their host and genetic group. Twenty-six seed lots from seven cropping plots of three different hosts-oilseed rape, tobacco, and hemp-in the west of France were characterized for their bacterial and fungal communities using 16S rRNA gene and ITS (Internal transcribed spacer) sequences, respectively. First seeds were characterized genetically using twenty microsatellite markers and phenotyped for their sensibility to various germination stimulants including strigolactones and isothiocyanates. This led to the distinction of three P. ramosa groups that corresponded to their host of origin. The observed seed diversity was correlated to the host specialization and germination stimulant sensitivity within P. ramosa species. Microbial communities were both clustered by host and plot of origin. The seed core microbiota was composed of seventeen species that were also retrieved from soil and was in lower abundances for bacteria and similar abundances for fungi compared to seeds. The host-related core microbiota of parasitic seeds was limited and presumably well adapted to the interaction with its hosts. Two microbial candidates of Sphingobacterium species and Leptosphaeria maculans were especially identified in seeds from oilseed rape plots, suggesting their involvement in host recognition and specialization as well as seed fitness for P. ramosa by improving the production of isothiocyanates from glucosinolates in the rhizosphere of oilseed rape.

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

A bacterial strain M05W1-28^T 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 (C_16 : 1  ω7c / C_16 : 1  ω6c) and iso-C_15 : 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 M05W1-28^T was 40.7 %. Based on similarities of 16S rRNA gene sequences, strain M05W1-28^T was affiliated with the genus Sphingobacterium, exhibiting the highest sequence similarities with S. multivorum LMG 8342^T (97.5 %), S. ginsenosidimutans THG07^T (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 M05W1-28^T and S. multivorum LMG 8342^T 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 M05W1-28^T represented a novel species within the genus Sphingobacterium, for which the name Sphingobacterium puteale sp. nov. is proposed. The type strain is M05W1-28^T (=CGMCC 1.13711^T=KCTC 72027^T).

Sphingobacterium praediipecoris sp. nov. isolated from effluent of a dairy manure treatment plant

A novel Gram-reaction-negative, rod-shaped, non-motile bacterium, designated as strain G2-10^T was isolated from effluent of a dairy manure treatment plant. Growth occurred at 20-40 °C (optimum at 25-30 °C), pH 7.0-8.0 (optimum at pH 7.0). The range of NaCl concentration for growth was between 0% and 3% (w/v) (optimum 0-1%, w/v). Comparison of 16S rRNA gene sequence indicated that strain G2-10^T was moderately related to the type strains of Sphingobacterium nematocida M-SX103^T and Sphingobacterium suaedae T47^T with a pair-wise sequence similarity of 94.3% and 94.0%, respectively. The major fatty acid constituents of strain G2-10^T were identified as iso-C_15:0 (37.6%), summed feature 3 (consisting of C_16:1ω7c and/or C_16:1ω6c, 29.6%) and iso-C_17:0 3-OH (15.2%). Phosphatidylethanolamine was the major polar lipids of strain G2-10^T. Sphingophospholipids were present. The isoprenoid quinone was composed of only MK-7. The DNA G + C content of strain G2-10^T was found to be 42.5 mol%. The phenotypic, chemotaxonomic and phylogenetic properties suggest that strain G2-10^T represents a novel species within the genus Sphingobacterium, for which the name Sphingobacterium praediipecoris is proposed. The type strain is G2-10^T (= KCTC 52880^T = NBRC 112848^T).

Sphingobacterium haloxyli sp. nov., an endophytic bacterium isolated from Haloxylon ammodendron stems in Kumtag desert

A Gram-stain-negative, non-motile, aerobic, non-spore-forming, rod-shaped, bacterial strain, designated 5JN-11^T, was isolated from Haloxylonammodendron stems in Kumtag desert, Xinjiang province, China. Strain 5JN-11^T grew at salinities of 0-6 % (w/v; optimum 0-2 %), a pH of 7.0-9.0 (pH 7.0-8.0) and temperatures of 20-42 °C (28-30 °C). Based on 16S rRNA gene sequences, the strain was designated a member of the genus Sphingobacterium and the phylogenetic analysis showed that strain 5JN-11^T shared the highest similarity to Sphingobacterium gobiense H7^T, followed by Sphingobacterium chuzhouense DH-5^T and Sphingobacterium arenae H-12^T. The unfinished draft genome of strain 5JN-11^T was 4.69 Mb. The G+C content of strain 5JN-11^T was 42.8 mol%. The average nucleotide identity to S. gobiense H7^T was 90.5 %. The respiratory quinone was MK-7, and the major polar lipids were phosphatidylethanolamine and phosphoglycolipid. The predominant cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C15 : 0 and iso-C17 : 0 3-OH. On the basis of phenotypic, genotypic and phylogenetic evidence, strain 5JN-11^T represents a novel species in the genus Sphingobacterium, for which the name Sphingobacteriumhaloxyli sp. nov. is proposed. The type strain is 5JN-11^T (=ACCC 60072^T=KCTC 62457^T).

Sphingobacterium tabacisoli sp. nov., isolated from a tobacco field soil sample

A Gram-staining-negative, non-motile and rod-shaped bacterium, designated strain h337T, was isolated from an arable soil sample of a tobacco field in Kunming, south-west China. The cells showed oxidase-positive and catalase-positive reactions. Growth was observed at 10-35 °C, at pH 6.0-9.0 and in the presence of up to 3 % (w/v) NaCl, with optimal growth at 30 °C, pH 7.0 and with 1-2 % (w/v) NaCl. The predominant isoprenoid quinone was MK-7. The major fatty acids were identified as iso-C15 : 0, iso-C17 : 0 3-OH, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B). The cellular polar lipids contained phosphatidylethanolamine, sphingophospholipid, four unidentified phospholipids, five unidentified lipids and three unidentified aminophospholipids. The genomic DNA G+C content was 41.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain h337T should be assigned to the genus Sphingobacterium. 16S rRNA gene sequence similarity analysis showed that strain h337T was most closely related to 'Sphingobacteriumyamdrokense' 3-0-1 (98.8 %) and Sphingobacteriumyanglingense CCNWSP36-1T (98.5 %) and shared less than 97 % similarity with other species of the genus Sphingobacterium. DNA-DNA hybridization data indicated that the isolate represented a novel genomic species belonging to the genus Sphingobacterium. The characteristics determined in this polyphasic taxonomic study indicated that strain h337T represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium tabacisoli sp. nov. (type strain h337T=KCTC 52298T=CCTCC AB 2017155T) is proposed.

Sphingobacterium alkalisoli sp. nov., isolated from a saline-alkaline soil

A Gram-staining-negative, non-motile, non-spore-forming bacterium designated Y3L14T was isolated from the saline-alkaline soil of a farmland, Inner Mongolia, northern China. Strain Y3L14T could grow at 10-40 °C (optimally at 30 °C), pH 6.0-10.0 (optimally at pH 8.0), and in the presence of 0-6.0 % (w/v) NaCl (optimally with 0-2.0 %). Phylogenetic analysis based on the 16S rRNA gene and DNA gyrase subunit B (gyrB) gene sequences revealed that strain Y3L14T clustered with strains belonging to the genus Sphingobacterium, sharing the highest 16S rRNA gene sequence similarity with Sphingobacterium lactis WCC 4512T (94.99 %). Its major cellular fatty acids contained iso-C15 : 0, C16 : 0, iso-C17 : 0 3-OH and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c). Menaquinone-7 (MK-7) was the only isoprenoid quinone. Strain Y3L14T contained phosphatidylethanolamine, sphingophospholipid, two unknown phospholipids and three unknown lipids as the major polar lipids. The genomic DNA G+C content of strain Y3L14T was 36.0 mol%. Based on the phenotypic, phylogenetic and genotypic characteristics, strain Y3L14T represents a novel species within the genus Sphingobacterium, for which Sphingobacterium alkalisoli sp. nov. is proposed; the type strain is Y3L14T (=CGMCC 1.15782T=KCTC 52379T).

Sphingobacterium chuzhouense sp. nov., isolated from farmland soil

A novel Gram-staining-negative bacterium, designated DH-5T, was isolated from a farmland soil in Chuzhou, Anhui province, China. Cells of strain DH-5T were aerobic, non-motile, non-spore-forming and rod-shaped. The organism grew at 20-37 °C, pH 6.0-9.0 and with 0-5 % NaCl (w/v). The DNA G+C content was 42.8 mol%. The major fatty acids (>5 %) were iso-C15 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C17 : 0 3-OH and C16 : 0. The respiratory quinone was MK-7, and the major polar lipids were phosphatidylethanolamine and phosphoglycolipid. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain DH-5T was a member of the genus Sphingobacterium and shared the highest similarity with Sphingobacterium gobiense H7T (96.0 %), followed by Sphingobacterium arenae H-12T (94.5 %). Strain DH-5T exhibited low DNA-DNA relatedness with S. gobiense H7T (35.1±1.4 %) and S. arenae H-12T (21.4±1.0 %). On the basis of phenotypic, genotypic and phylogenetic evidence, DH-5T is considered to represent a novel species of the genus Sphingobacterium, for which the name Sphingobacterium chuzhouense sp. nov. is proposed. The type strain is DH-5T (=ACCC 19856T=KCTC 42746T).

Sphingobacterium jejuense sp. nov., with ginsenoside-converting activity, isolated from compost

A Gram-stain-negative, strictly aerobic, non-motile, light yellow, short-rod bacterium (designated GJ30-7T) isolated from compost, was characterized using a polyphasic approach, in order to clarify its taxonomic position. Strain GJ30-7T was observed to grow optimally at 30 °C and at pH 7.0 on R2A agar medium. Strain Gsoil GJ30-7T possessed β-glucosidase activity, which was responsible for its ability to transform ginsenosides Rb1 and Rc (the two main active components of ginseng) to ginsenoside F2. Phylogenetic analysis, based on 16S rRNA gene sequence similarities, indicated that GJ30-7T belongs to the genus Sphingobacterium of the family Sphingobacteriaceae and was most closely related to Sphingobacterium yanglingense JCM 30166T (92.6 %), Sphingobacterium psychroaquaticum KACC 18188T (92.6 %), and Sphingobacterium thermophilum KCTC 23708T (92.0 %). The DNA G+C content was 43 mol% and MK-7 was the major isoprenoid quinone. The main polar lipids were phosphatidylethanolamine, one unidentified phospolipid and one unknown polar lipid. In contrast to standard and reference strains, unidentified sphingolipid was also present. The predominant fatty acids of strain GJ30-7T were iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 1ω7c and/or C16 : 1ω6c (summed feature 3) and iso-C17 : 1ω9c and/or C16 : 0 10-methyl (summed feature 9), supporting the affiliation of strain GJ30-7T to the genus Sphingobacterium. However, strain GJ30-7T could be distinguished genotypically and phenotypically from species of the genus Sphingobacterium with validly published names. The novel isolate therefore represents a novel species, for which the name Sphingobacterium jejuense sp. nov. is proposed, with the type strain GJ30-7T (=KACC 18625T=JCM 30948T).

Sphingobacterium zeae sp. nov., an endophyte of maize

A yellow-pigmented strain (JM-1081^T) isolated from healthy stem tissue of Zea mays was taxonomically characterized. Cells of the strain were rod-shaped and Gram-stain-negative. Comparative 16S rRNA gene sequence analysis revealed closest relationship to the type strains of Sphingobacterium multivorum (98.1 % similarity), Sphingobacterium mucilaginosum (97.9 %) and Sphingobacterium siyangense (97.8 %). 16S rRNA gene sequence similarities to the type strains of all other Sphingobacterium species were below 97.8 %. Fatty acid analysis of whole-cell hydrolysates of the strain resulted in a pattern typical of the genus Sphingobacterium with iso-C15 : 0 2-OH and/or C16 : 1ω7c, iso-C15 : 0, iso-C17 : 0 3-OH and C16 : 0 and as major compounds. The polyamine pattern contained predominantly sym-homospermidine. The major quinone was menaquinone MK-7 and the only identified lipids in the polar lipid profile were phosphatidylethanolamine and phosphatidylserine. In addition, 15 unidentified lipids were detected in moderate to major amounts. Sphingolipid was detected. The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid. DNA-DNA hybridizations with two of the closely related type strains, those of S. multivorum and S. siyangense, as well as Sphingobacterium canadense resulted in values below 70 %. In addition to the genotypic differences, differential biochemical and chemotaxonomic properties confirmed that the isolate JM-1081^T represents a novel species, for which the name Sphingobacterium zeae sp. nov. is proposed. The type strain is JM-1081^T (=LMG 29191^T=CCM 8652^T).

Sphingobacterium suaedae sp. nov., isolated from the rhizosphere soil of Suaeda corniculata

A Gram-stain-negative, non-motile, non-spore-forming bacterium, designated T47T, was isolated from saline soil of the Suaeda corniculata rhizosphere, located on the bank of Wuliangsuhai Lake, Inner Mongolia, northern China. Strain T47T could grow at 10–40 °C (with 30 °C the optimal temperature), pH 6.0–8.0 (optimal pH 6.0) and in the presence of 0–6.0 % (w/v) NaCl [optimal 0–1.0 % (w/v)]. Phylogenetic analysis, based on 16S rRNA gene sequences, revealed that strain T47T formed a stable clade with Sphingobacterium composti 4M24T, Sphingobacterium bambusae IBFC2009T, Sphingobacterium paludis S37T and Sphingobacterium wenxiniae LQY-18T, with the 16S rRNA gene sequence similarities ranging from 91.9–95.4 %. Its major cellular fatty acids contained iso-C15 : 0 (39.9 %), summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c, 23.0 %), C16 : 0 (12.8 %) and iso-C17 : 0 3-OH (9.9 %). MK7 was the major menaquinone. The G+C content of the genomic DNA was 45.5 mol%. Based on the phenotypic, phylogenetic and genotypic characteristics, strain T47T represents a novel species within the genus Sphingobacterium, for which the name Sphingobacterium suaedae sp. nov. is proposed. The type strain is T47T ( = CGMCC 1.15277T = KCTC 42662T).

Sphingobacterium rhinocerotis sp. nov., isolated from the faeces of Rhinoceros unicornis

A novel Gram-negative, strictly aerobic, short rod-shaped, non-motile bacterium, designated YIM 101302(T), was isolated from the faeces of Rhinoceros unicornis dwelling in the Yunnan Wild Animal Park, Yunnan province, South-West China. The 16S rRNA gene sequence analysis revealed a clear affiliation of strain YIM 101302(T) to the genus Sphingobacterium. The newly isolated bacterium was found to be closely related to Sphingobacterium composti T5-12(T) (97.1% 16S rRNA sequence identity) and Sphingobacterium alimentarium WCC 4521(T) (95.6% 16S rRNA sequence identity) forming a distinct clade with these two species. Polar lipids of strain YIM 101302(T) were identified as phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylglycerol, phosphatidylinositol, an unidentified aminophospholipid, and three unidentified polar lipids; the predominant menaquinone as MK-7 and the major fatty as iso-C15:0. The genomic DNA G+C content was determined to be 38.9 mol%. The DNA-DNA hybridization values between strain YIM 101302(T) and S. composti T5-12(T), was 53.6 ± 5.8%. These results indicates that strain YIM 101302(T) represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium rhinocerotis sp. nov. is proposed. The type strain is YIM 101302(T) (=CCTCC AB 2013218(T) = KCTC 42533(T)).

Whole-genome optical mapping and finished genome sequence of Sphingobacterium deserti sp. nov., a new species isolated from the Western Desert of China

A novel Gram-negative bacterium, designated ZWT, was isolated from a soil sample of the Western Desert of China, and its phenotypic properties and phylogenetic position were investigated using a polyphasic approach. Growth occurred on TGY medium at 5-42°C with an optimum of 30°C, and at pH 7.0-11.0 with an optimum of pH 9.0. The predominant cellular fatty acids were summed feature 3 (C16:1ω7c/C16:1ω6c or C16:1ω6c/C16:1ω7c) (39.22%), iso-C15:0 (27.91%), iso-C17:0 3OH (15.21%), C16:0 (4.98%), iso-C15:0 3OH (3.03%), C16:0 3OH (5.39%) and C14:0 (1.74%). The major polar lipid of strain ZWT is phosphatidylethanolamine. The only menaquinone observed was MK-7. The GC content of the DNA of strain ZWT is 44.9 mol%. rDNA phylogeny, genome relatedness and chemotaxonomic characteristics all indicate that strain ZWT represents a novel species of the genus Sphingobacterium. We propose the name S. deserti sp. nov., with ZWT (= KCTC 32092T = ACCC 05744T) as the type strain. Whole genome optical mapping and next-generation sequencing was used to derive a finished genome sequence for strain ZWT, consisting of a circular chromosome of 4,615,818 bp in size. The genome of strain ZWT features 3,391 protein-encoding and 48 tRNA-encoding genes. Comparison of the predicted proteome of ZWT with those of other sphingobacteria identified 925 species-unique proteins that may contribute to the adaptation of ZWT to its native, extremely arid and inhospitable environment. As the first finished genome sequence for any Sphingobacterium, our work will serve as a useful reference for subsequent sequencing and mapping efforts for additional strains and species within this genus.

Sphingobacterium yanglingense sp. nov., isolated from the nodule surface of soybean

A Gram-staining-negative, non-motile, catalase- and oxidase-positive strain, designated CCNWSP36-1(T), was isolated from the nodule surface of soybean [Glycine max (L.) Merrill] cultivar Zhonghuang 13. The 16S rRNA gene sequence analysis clearly showed that the isolate represented a member of the genus Sphingobacterium. On the basis of pairwise comparisons of 16S rRNA gene sequences, strain CCNWSP36-1(T) showed 96.8% similarity to Sphingobacterium nematocida CCTCC AB 2010390(T) and less than 95.2% similarity to other members of the genus Sphingobacterium. Growth of strain CCNWSP36-1(T) occurred at 10-40 °C and at pH 5.0-9.0. The NaCl range (w/v) for growth was 0-4%. The predominant isoprenoid quinone was MK-7. The polar lipids were phosphatidylethanolamine and several unidentified polar lipids. Sphingolipid was present. The major fatty acids were iso-C(15:0) and summed feature 3 (comprising C(16:1)ω6c and/or C(16:1)ω7c). The G+C content of the genomic DNA was 41.1 mol%. As the physiological and biochemical characteristics of strain CCNWSP36-1(T) and the type strains of its closest phylogenetic neighbours showed clear differences, a novel species, Sphingobacterium yanglingense, is proposed. The type strain is CCNWSP36-1(T) ( =ACCC 19328(T) =JCM 30166(T)).

Sphingobacterium paludis sp. nov., isolated from wetland soil

A novel Gram-stain-negative bacteria, designated S37T, was isolated from soil of the Xixi wetland, Zhejiang province, China. Cells of strain S37T were aerobic, non-motile rods. Growth occurred at 10–37 °C (optimum, 25 °C), pH 5.0–9.7 (optimum, pH 7.5) and with 0–6 % (w/v) NaCl (optimum, 0.5 %). Based on 16S rRNA gene sequence analysis, strain S37T was found to be a member of the genus Sphingobacterium and shared highest similarity with Sphingobacterium composti 4M24T (95.78 %). The major fatty acids were summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C15 : 0 and iso-C17 : 0 3-OH, and the DNA G+C content was 43.8 mol%. The predominant respiratory quinone was MK-7. Based on its phenotypic and chemotaxonomic characteristics and phylogenetic data, strain S37T represents a novel species of the genus Sphingobacterium , for which the name Sphingobacterium paludis sp. nov. (type strain S37T = CGMCC 1.12801T = NBRC 110386T) is proposed.

Sphingobacterium gobiense sp. nov., isolated from soil of the Gobi Desert

A Gram-stain-negative, short rod-shaped, non-motile, non-spore-forming bacterial strain, designated H7(T), was isolated from the Gobi desert, Xinjiang Province of China. The temperature, NaCl and pH ranges for growth were 8-40 °C (optimum 30 °C), 0-5 % (w/v) NaCl and pH 6-10 (optimum pH 7), respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain H7(T) belonged to the genus Sphingobacterium and showed highest sequence similarity (91 %) to Sphingobacterium composti DSM 18850. The genomic DNA G+C content was 44.3 mol%. MK-7 was identified as the predominant respiratory quinone. Strain H7(T) contained C16 : 1ω7c and/or C16 : 1ω6c, iso-C15 : 0 and iso-C17 : 0 3-OH as major fatty acids. These data support the affiliation of strain H7(T) to the genus Sphingobacterium while phenotypic data indicated it is a representative strain of a novel species for which the name Sphingobacterium gobiense sp. nov. is proposed. The type strain is H7(T) ( = ACCC 05757(T) = KCTC 32293(T)).

Sphingobacterium arenae sp. nov., isolated from sandy soil

A novel, Gram-stain-negative, non-motile, non-spore-forming, short rod-shaped, aerobic bacterium designated H-12(T) was isolated from a mixed sandy soil sample collected from Xinjiang, China. Strain H-12(T) grew at 20-37 °C (optimum, 30 °C), pH 7.0-11.0 (optimum, pH 8.5) on TGY medium with 0-5 % NaCl (w/v). 16S rRNA gene sequence analysis indicated that strain H-12(T) shared sequence similarities with Sphingobacterium composti DSM 18850(T) (90.0 %). Strain H-12(T) showed a low level of DNA-DNA relatedness to Sphingobacterium composti DSM 18850(T) (45.5 %). The predominant isoprenoid quinone of strain H-12(T) was MK-7 and the major polar lipid was phosphatidylethanolamine. The predominant cellular fatty acids were C16:1ω7c and/or C16 : 1ω6c, iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 0, C16 : 0 3-OH and iso-C15 : 0 3-OH. DNA G+C content of strain H-12(T) was 44.15 mol%. On the basis of phenotypic, genetic and phylogenetic data, strain H-12(T) is proposed to be a representative of a novel species of the genus Sphingobacterium, for which the name Sphingobacterium arenae sp. nov. is suggested and the type strain is H-12(T) ( = ACCC 05758(T) = KCTC 32294(T)).

Sphingobacterium caeni sp. nov., isolated from activated sludge

The taxonomic status of a bacterium, strain DC-8T, isolated from activated sludge, was determined using a polyphasic taxonomic approach. The cells of strain DC-8T were Gram-negative, non-motile, non-spore-forming and rod-shaped. The isolate grew at temperature range of 10–40 °C (optimum 30–35 °C), pH range of 5.0–10.0 (optimum 6.5–8.0) and NaCl concentrations of 0–5 % (optimum 0–1 %). The predominant menaquinone of strain DC-8T was MK-7 and major fatty acids were summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c; 39.7 %), iso-C15 : 0 (33.7 %) and C16 : 0 (5.2 %). The DNA G+C content was 39.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparison revealed that strain DC-8T was a member of the genus Sphingobacterium . Strain DC-8T shared the highest similarity with Sphingobacterium siyangense SY1T (98.4 %), Sphingobacterium multivorum IAM 14316T (98.3 %), Sphingobacterium canadense CR11T (98.0 %) and Sphingobacterium detergens 6.2ST (97.9 %) and shared less than 97 % similarity with other members of the genus Sphingobacterium . DNA–DNA hybridization experiments showed that the DNA–DNA relatedness values between strain DC-8T and its closest phylogenetic neighbours were below 70 %. Based on the phylogenetic analysis, DNA–DNA hybridization, whole-cell fatty acid composition as well as biochemical characteristics, strain DC-8T was clearly distinguished from all recognized species of the genus Sphingobacterium and should be classified as a representative of a novel species of the genus Sphingobacterium , for which the name Sphingobacterium caeni sp. nov. is proposed. The type strain is DC-8T ( = CCTCC AB 2012020T = KACC 16850T).