Novosphingobium percolationis sp. nov. and Novosphingobium huizhouense sp. nov., isolated from landfill leachate of a domestic waste treatment plant.

Two strains designated as c1T and c7T, were isolated from the landfill leachate of a domestic waste treatment plant in Huizhou City, Guangdong Province, PR China. The cells of both strains were aerobic, rod-shaped, non-motile and formed yellow colonies on Reasoner's 2A agar plates. Strain c1T grew at 10-42 °C (optimum, 30 °C), pH 4.5-10.5 (optimum, pH 7.0) and 0-2.0 % (w/v) NaCl (optimum, 0-0.5 %). Strain c7T grew at 10-42 °C (optimum, 30 °C), pH 4.5-10.5 (optimum, pH 6.0) and 0-2.0 % (w/v) NaCl (optimum, 0-0.5 %). Phylogenetic analyses revealed that strains c1T and c7T belong to the genus Novosphingobium. The 16S rRNA gene sequence similarities of strains c1T and c7T to the type strains of Novosphingobium species were 94.5-98.2 % and 94.3-99.1 %, respectively. The calculated pairwise average nucleotide identity values among strains c1T, c7T and the reference strains were in the range of 75.2-85.9 % and the calculated pairwise average amino acid identity values among strains c1T, c7T and reference strains were in the range of 72.0-88.3 %. Their major respiratory quinone was Q-10, and the major cellular fatty acids were C18 : 1 ω7c, C18 : 0, C16 : 1 ω7c, C16 : 0 and C14 : 0 2OH. The major polar lipids of strains c1T and c7T were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, sphingoglycolipid, unidentified lipids and unidentified phospholipid. Based on phenotypic, chemotaxonomic, phylogenetic and genomic results from this study, strains c1T and c7T should represent two independent novel species of Novosphingobium, for which the names Novosphingobium percolationis sp. nov. (type strain c1T=GDMCC 1.2555T=KCTC 82826T) and Novosphingobium huizhouense sp. nov. (type strain c7T=GDMCC 1.2556T=KCTC 82827T) are proposed. The gene function annotation results of strains c1T and c7T suggest that they could play an important role in the degradation of organic pollutants.

Stakelama flava sp. nov., a novel endophytic bacterium isolated from a branch of Kandelia candel.

A Gram-stain-negative, aerobic, motile, non-spore-forming, short-rod-shaped strain that did not produce diffusible pigment, designated CBK3Z-3T, was isolated from a branch of Kandelia candel, collected from the Beilun Estuary National Nature Reserve in Guangxi Zhang Autonomous Region, PR China, and investigated by a polyphasic approach to determine its taxonomic position. Strain CBK3Z-3T grew at pH 5.0-10.0 (optimum, pH 8.0), 20-37 °C (optimum, 25-30 °C) and with 0-10 % (w/v) NaCl (optimum, 2-3 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CBK3Z-3T was closely related to species of genus Stakelama and had the highest 16S rRNA gene sequence similarity of 98.7 % to Stakelama pacifica CGMCC 1.7294T. The DNA G+C content value of strain CBK3Z-3T was 62.6 mol%. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid and the polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid, an unidentified aminolipid and an unidentified lipid. The major fatty acids were C18 : 1 ω7c and C16 : 0. The average nucleotide identity, estimated digital DNA-DNA hybridization and average amino acid identity values between strain CBK3Z-3T and the type strain of Stakelama pacifica CGMCC 1.7294T were 80.4, 23.1 and 81.5 %, respectively. Based on the phylogenetic, phenotypic and chemotaxonomic data, strain CBK3Z-3T should be designated as a novel species of the genus Stakelama, for which the name Stakelama flava sp.nov. is proposed. The type strain is CBK3Z-3T (=JCM 34534T=CGMCC 1.18972T).

Sphingosinicella flava sp. nov., indole acetic acid producing bacteria isolated from maize field soil.

A novel isolated yellow-pigmented bacterial designated strain UDD2T was isolated from a maize field soil sample collected in Ilsan, Republic of Korea. Cells of strain UDD2T were Gram-stain-negative, non-sporulating, long rod-shaped and exhibited flagellar motility. Cells could grow at 15-42 °C and pH 5.5-11.0. Strain UDD2T was sensitive to NaCl and barely tolerated up to 1 % NaCl (w/v). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain UDD2T formed a separate clade with the members of genus Sphingosinicella within the family Sphingomonadaceae. Strain UDD2T showed the highest 16S rRNA gene sequence similarity to Sphingosinicella vermicomposti KCTC 224446T (98.5 %) and Sphingosinicella humi KCTC 62519T (96.7 %), followed by members of the genus Sphingomonas (96.4-94.5 %) and Sphingobium (96.1-94.9 %), but they were located in other phylogenetic clusters. Average nucleotide identity and digital DNA-DNA hybridization values between strain UDD2T and S. vermicomposti KCTC 224446T and S. humi KCTC 62519T were 80.2/24.2 and 75.6/20.4 %, respectively. The total size of the genome was 2 421 697 bp and composed of one circular chromosome, with a G+C content of 63.7 mol%. Strain UDD2T produced indole acetic acid (IAA) in the presence of l-tryptophan. Bacterial IAA is a crucial phytohormone in plant growth and development. Gene clusters for indole-3-glycerol phosphate synthase and tryptophan synthase were found in the genome of strain UDD2T. To the best of our knowledge, no member of the genus Sphingosinicella has been reported to produce IAA to date. The major cellular fatty acids (>10 %) were found to be C16 : 0, C14 : 0 2OH and summed feature 3 (comprising C16  : 1 ω7c and/or iso-C15  :  0 2-OH). Strain UDD2T had ubiquinone Q-10 as the major respiratory quinone and homospermidine as the major polyamine. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid, phosphatidylglycerol, phosphatidylcholine, three unidentified phosphoglycolipids, one unidentified phospholipid, one unidentified aminoglycophospholipid, one unidentified glycolipid and one unidentified polar lipid. Based on the phylogenetic, phenotypic, chemotaxonomic and genotypic data, strain UDD2T represents a novel species of the genus Sphingosinicella, for which the name Sphingosinicella flava is proposed. The type strain is UDD2T (=KCTC 82357T=NBRC 114507T).

Parasphingopyxis marina sp. nov. isolated from coastal seawater.

A Gram-stain-negative, aerobic, yellow-pigmented and non-motile rod-shaped bacterium, designated as GrpM-11T, was isolated from coastal seawater collected from the East Sea, Republic of Korea. Strain GrpM-11T could grow at 10-40 °C (optimum, 35 °C), at pH 5.5-9.5 (optimum, pH 7.0) and in the presence of 0-8 % (w/v) NaCl (optimum, 3-4 %). Cells hydrolysed aesculin, gelatin and casein, but could not reduce nitrate to nitrite. The 16S rRNA gene sequence analysis showed that this strain formed a distinct phylogenic lineage with Parasphingopyxis algicola ATAX6-5T (96.2 % sequence identity) and Parasphingopyxis lamellibrachiae DSM 26725T (96.2 % identity) and belonged to the genus Parasphingopyxis. The predominant isoprenoid quinone was ubiquinone-10. The polar lipid profile of strain GrpM-11T consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, sphingoglycolipid and three unknown glycolipids. Cellular fatty acid analysis indicated that summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c; 42.8 %), C16 : 0 (19.0 %), C18 : 1 ω7c 11-methyl (13.3 %) and C18 : 1 ω7c (8.0 %) were the major fatty acids. The DNA G+C content of strain GrpM-11T was 63.7 mol%. Through whole genome sequence comparisons, the digital DNA-DNA hybridization and average nucleotide identity values between strain GrpM-11T and two species of the genus Parasphingopyxis were revealed to be in the ranges of 19.0-22.0 % and 76.3-79.7 %, respectively. Based on the results of polyphasic analysis, strain GrpM-11T represents a novel species of the genus Parasphingopyxis, for which the name Parasphingopyxis marina sp. nov. is proposed. The type strain is GrpM-11T (KCCM 43343T=JCM 34665T).

Aestuariisphingobium litorale Li et al. 2020 is a later heterotypic synonym of Chakrabartia godavariana Jani et al. 2019.

Chakrabartia godavariana PRB40T was compared with Aestuariisphingobium litorale SYSU M10002T to examine the taxonomic relationship between the two type strains. The 16S rRNA gene sequence of C. godavariana PRB40T had high similarity (99.8 %) to that of A. litorale SYSU M10002T. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that the two strains formed a tight cluster within the genus Chakrabartia. A draft genomic comparison between the two strains revealed an average nucleotide identity of 97.3 % and a digital DNA-DNA hybridization estimate of 79.5±2.9 %, strongly indicating that the two strains represented a single species. In addition, neither strain displayed any striking differences in metabolic, physiological or chemotaxonomic features. Therefore, we propose that Aestuariisphingobium litorale is a later heterotypic synonym of Chakrabartia godavariana.

Description of Novosphingopyxis iocasae sp. nov., isolated from deep sea sediment from the Mariana Trench, and emended description of the genus Novosphingopyxis.

In this study, we reported a Gram-stain-negative, orange-coloured, rod-shaped, motile and faculatively anaerobic bacterium named strain PB63T, which was isolated from the deep-sea sediment from the Mariana Trench. Growth of PB63T occurred at 10-35 °C (optimum, 28 °C), pH 5.0-8.0 (optimum, 5.0-6.0) and with 0-7 % (w/v) NaCl (optimum, 2-3 %). The results of phylogenetic analysis based on 16S rRNA gene sequences indicated that PB63T represented a member of the genus Novosphingopyxis and was closely related to Novosphingopyxis baekryungensis DSM 16222T (97.9 % sequence similarity). PB63T showed tolerance to a variety of heavy metals, including Co2+, Zn2+, Mn2+ and Cu2+. The complete genome of PB63T was obtained, and many genes involved in heavy metal resistance were found. The genomic DNA G+C content of PB63T was 62.8 mol%. The predominant respiratory quinone of PB63T was ubiquinone-10 (Q-10). The polar lipids of PB63T contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid, glycolipid, phosphatidylcholines and three unidentified lipids. The major fatty acids of PB63T included summed feature 8 (C18 : 1ω7c or/and C18 : 1ω6c), C14 : 0 2-OH, 11-methyl C18 : 1ω7c, C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C17 : 1ω6c. The results of phylogenetic, physiological, biochemical and morphological analyses indicated that strain PB63T represents a novel species of the genus Novosphingopyxis, and the name Novosphingopyxis iocasae sp. nov. is proposed with the type species PB63T (=CCTCC AB 2019195T=JCM 34178T).

Isolation of a novel strain, Sphingorhabdus sp. YGSMI21 and characterization of its enantioselective epoxide hydrolase activity.

Sphingorhabdus sp. YGSMI21, a novel microbial strain with an enantioselective epoxide hydrolase activity, was isolated from tidal samples contaminated by accidental oil spills subjected to enriched culture with polycyclic aromatic hydrocarbon. This strain was able to optically decompose (R)-styrene oxide (SO) and showed 100% optical purity. In addition, it showed a good enantioselectivity for the derivatives of (S)-SO, (S)-2-chlorostyrene oxide (CSO), (S)-3-CSO and (S)-4-CSO. For (S)-2-CSO, (S)-3-CSO and (S)-4-CSO, 99.9%ee was obtained with the yield of 26.2%, 24.8%, and 11.0%, respectively, when using 10 mg cells of Sphingorhabdus sp. YGSMI21 at pH 8.0 with 4 mM racemic substrates at pH 8.0 and 25°C. The values obtained in this study for (S)-2-CSO, particularly the yield of 26.2%, is noteworthy, considering that obtaining an enantiomerically pure form is difficult. Taken together, Sphingorhabdus sp. YGSMI21 can be regarded as a whole-cell biocatalyst in the production of various (S)-CSO with the chlorine group at a different position.

Parasphingorhabdus halotolerans sp. nov. isolated from marine sediment in Jeju Island.

A Gram-stain-negative, catalase- and oxidase-positive, rod-shaped bacterium, designated as JK6T was isolated from a coastal marine sediment in Jeju Island. Strain JK6T was characterized by polyphasic investigation including genome features. It grew at pH 5.0-9.0 (optimum 7.5), 18-30 °C (optimum 25 °C) and 1.0-7.0% (w/v) NaCl (optimum 2.0%). Strain JK6T utilized D-mannose, D-glucose, L-fucose, propionate and acetate as carbon and energy sources. The sole quinone was ubiquinone-10, and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, and sphingolipid. Strain JK6T was closely related to Parasphingorhabdus flavimaris SW-151T (98.2%), Parasphingorhabdus marina DSM 22363T (97.6%) and Parasphingorhabdus litoris FR1093T (97.6%) based on 16S rRNA gene sequence similarity. Genome length and GC content were 3.29 Mbp and 53.0%, respectively. Digital DNA-DNA relatedness, average nucleotide identity, and average amino acid identity between strain JK6T and P. flavimaris SW-151T were 16.6%, 73.9%, and 77.6%, respectively. These results showed that the strain can be recognized as a novel bacterium named Parasphingorhabdus halotolerans. The type strain of Parasphingorhabdus halotolerans sp. nov. is JK6T (= KCTC 72818T = VTCC 910111T).

Comparative genomic analysis of the genus Novosphingobium and the description of two novel species Novosphingobium aerophilum sp. nov. and Novosphingobium jiangmenense sp. nov.

Members of the genus Novosphingobium are well known for their metabolically versatile and great application potential in pollution elimination. The three novel bacterial strains, designated 4Y4T, 4Y9, and 1Y9AT, were isolated from aquaculture water and characterized by using a polyphasic taxonomic approach. The 16S rRNA gene sequences phylogenetic analysis revealed that the three strains belonged to the genus Novosphingobium. The phylogenomic analysis indicated that the three strains formed two independent and robust branches distinct from all reference strains. The analyses of dDDH values and ANIs between the three strains and their relatives further demonstrated that the three strains represented two different novel genospecies. Comparative genomic analysis of the three isolates and 32 type strains of the genus Novosphingobium showed that the most important central metabolic pathways of these strains appeared to be similar, while specific and specialized metabolic pathways were flexible and variable among these strains. Chemotaxonomic characterization exhibited that the predominant cellular fatty acids were summed feature 8, summed feature 3, and C14:0 2OH; the major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidyldimethylethanolamine, phosphatidylglycerol, and sphingoglycolipid; the major respiratory quinone and polyamine were Q-10 and spermidine. The DNA G + C contents were 67.6 and 64.7 %. Based on the genotypic and phenotypic characteristics, strains 4Y4T and 1Y9AT are concluded to represent two novel species of the genus Novosphingobium, for which the names Novosphingobium aerophilum sp. nov. (type strain 4Y4T = GDMCC 1.1828 T = KACC 21946 T) and Novosphingobium jiangmenense sp. nov. (type strain 1Y9AT = GDMCC 1.1936 T = KACC 22085 T) are proposed.

Assessment of Erythrobacter Species Diversity through Pan-Genome Analysis with Newly Isolated Erythrobacter sp. 3-20A1M.

Erythrobacter species are extensively studied marine bacteria that produce various carotenoids. Due to their photoheterotrophic ability, it has been suggested that they play a crucial role in marine ecosystems. It is essential to identify the genome sequence and the genes of the species to predict their role in the marine ecosystem. In this study, we report the complete genome sequence of the marine bacterium Erythrobacter sp. 3-20A1M. The genome size was 3.1 Mbp and its GC content was 64.8%. In total, 2998 genetic features were annotated, of which 2882 were annotated as functional coding genes. Using the genetic information of Erythrobacter sp. 3-20A1M, we performed pangenome analysis with other Erythrobacter species. This revealed highly conserved secondary metabolite biosynthesis-related COG functions across Erythrobacter species. Through subsequent secondary metabolite biosynthetic gene cluster prediction and KEGG analysis, the carotenoid biosynthetic pathway was proven conserved in all Erythrobacter species, except for the spheroidene and spirilloxanthin pathways, which are only found in photosynthetic Erythrobacter species. The presence of virulence genes, especially the plant-algae cell wall degrading genes, revealed that Erythrobacter sp. 3-20A1M is a potential marine plant-algae scavenger.

Novosphingobium olei sp. nov., with the ability to degrade diesel oil, isolated from oil-contaminated soil and proposal to reclassify Novosphingobium stygium as a later heterotypic synonym of Novosphingobium aromaticivorans.

Two yellow-pigmented, non-motile, Gram-stain-negative, and rod-shaped bacteria, designated TW-4T and TNP-2 were obtained from oil-contaminated soil. Both strains degrade diesel oil, hydrolyse aesculin, DNA, Tween 40 and Tween 60. A phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain TW-4T formed a lineage within the family Erythrobacteraceae and clustered as members of the genus Novosphingobium. The closest members of strain TW-4T were Novosphingobium subterraneum DSM 12447T (97.9 %, sequence similarity), Novosphingobium lubricantis KSS165-70T (97.8 %), Novosphingobium taihuense T3-B9T (97.8 %), Novosphingobium aromaticivorans DSM 12444T (97.7 %), Novosphingobium flavum UCT-28T (97.7 %), and Novosphingobium bradum STM-24T (97.6 %). The sequence similarity for other members was ≤97.6 %. The genome of strain TW-4T was 4 683 467 bp long with 44 scaffolds and 4280 protein-coding genes. The sole respiratory quinone was Q-10. The major cellular fatty acids were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0 and C14 : 0 2-OH. The major polar lipids were phosphatidylethanolamine (PE), phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), phosphatidylcholine (PC), phosphatidyl-n-methylethanolamine (PME) and sphingoglycolipid (SGL). The DNA G+C content of the type strain was 65.0 %. The average nucleotide identity (ANIu) and in silico DNA-DNA hybridization (dDDH) relatedness values between strain TW-4T and closest members were below the threshold value for species delineation. Based on polyphasic taxonomic analyses, strain TW-4T represents novel species in the genus Novosphingobium, for which the name Novosphingobium olei sp. nov. is proposed. The type strain is TW-4T (=KACC 21628T=NBRC 114364T) and strain TNP-2 (=KACC 21629=NBRC 114365) represents an additional strain. Based on new data obtained in this study, it is also proposed to reclassify Novosphingobium stygium as a later heterotypic synonym of Novosphingobium aromaticivorans.

Novosphingobium aquimarinum sp. nov., isolated from seawater.

A novel Gram-stain-negative, aerobic, and rod-shaped bacterial strain, M24A2MT, was isolated from seawater in the Republic of Korea. On the basis of the 16S rRNA gene phylogeny, strain M24A2MT was found to be closely related to Novosphingobium pentaromativorans US6-1T and Novosphingobium mathurense SM117T with pair-wise sequence similarities of 97.4 and 96.9 %, respectively. Phylogenetic analysis of 16S rRNA sequences indicated that M24A2MT formed a branch with Novosphingobium pentaromativorans US6-1T and represented a member of the genus Novosphingobium. The predominant cellular fatty acids were C14 : 0 2-OH, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The polar lipids of strain M24A2MT consisted mainly of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, one unidentified phospholipid, and two unidentified lipids. The respiratory quinone was ubiquinone Q-10. The genomic DNA G+C content was 63.9 %. Given the phenotypic characteristics along with the phylogenetic distinctness and chemotaxonomic features, strain M24A2MT is considered to represent a novel species within the genus Novosphingobium, for which the name Novosphingobium aquimarinum sp. nov. is proposed. The type strain of Novosphingobium aquimarinum sp. nov. is M24A2MT (=KCTC 72894T=JCM 33983T).

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

A marine alphaproteobacterium, designated as strain GH3-10T, was isolated from the rhizosphere mud of a halophyte (Suaeda japonica) collected at the seashore of Gangwha Island, Republic of Korea. The isolate was found to be Gram-stain-negative, strictly aerobic, catalase- and oxidase-positive, non-motile, short rods and produced orange-coloured colonies. The 16S rRNA gene- and whole genome-based phylogenetic analyses exhibited that strain GH3-10T belonged to the genus Aurantiacibacter and was most closely related to Aurantiacibacter atlanticus s21-N3T (98.7 % 16S rRNA gene sequence similarity) and Aurantiacibacter marinus KCTC 23554T (98.4 %). The major respiratory quinone was ubiquinone-10. The polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid and an unidentified lipid. The major fatty acids were C18 : 1 ω7c, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and C18 : 1 ω7c 10-methyl. The DNA G+C content was 61.3 mol% (by genome). Average nucleotide identity and DNA-DNA relatedness values between the isolate and its phylogenetically closest relatives, together with phenotypic distinctness warranted the taxonomic description of a new species. On the basis of data obtained by a polyphasic approach, strain GH3-10T (=KCTC 62379T=JCM 32444T) represents a novel species of the genus Aurantiacibacter, for which the name Aurantiacibacter rhizosphaerae sp. nov. is proposed. According to phylogenetic coherence based on 16S rRNA genes and core genomes, it is also proposed that Erythrobacter suaedae Lee et al. 2019. and Erythrobacter flavus Yoon et al. 2003 be transferred to Aurantiacibacter suaedae comb. nov. and Qipengyuania flava comb. nov., respectively.

Novosphingobium ovatum sp. nov., isolated from a freshwater mesocosm.

A bacterial strain, designated FSY-8T, was isolated from a freshwater mesocosm in Taiwan and characterized using the polyphasic taxonomy approach. Cells of strain FSY-8T were aerobic, Gram-stain-negative, rod-shaped, non-motile and formed yellow coloured colonies on Reasoner's 2A agar. Growth occurred at 20-40 °C (optimum, 30-37 °C) and pH 5-7 (optimum, pH 6) and in the presence of 0-0.5 % NaCl (optimum, 0 %, w/v). The major fatty acids (>10 %) of strain FSY-8T were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c). The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, sphingoglycolipid, diphosphatidylglycerol, an uncharacterized aminophospholipid, an uncharacterized glycolipid and an uncharacterized lipid. The major polyamine was spermidine. The major isoprenoid quinone was Q-10. The DNA G+C content was 64.8 mol %. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain FSY-8T formed a phylogenetic lineage in the genus Novosphingobium. Strain FSY-8T showed 71.6-77.2 % average nucleotide identity and 19.9-22.8 % digital DNA-DNA hybridization identity with the strains of other Novosphingobium species. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain FSY-8T should be classified in a novel species of the genus Novosphingobium, for which the name Novosphingobium ovatum sp. nov. is proposed. The type strain is FSY-8T (=BCRC 81051T=LMG 30053T=KCTC 52812T).

Isolation and characterization of a novel Sphingobium yanoikuyae strain variant that uses biohazardous saturated hydrocarbons and aromatic compounds as sole carbon sources.

Background: Green micro-alga, Chlamydomonas reinhardtii (a Chlorophyte), can be cultured in the laboratory heterotrophically or photo-heterotrophically in Tris- Phosphate- Acetate (TAP) medium, which contains acetate as the carbon source. Chlamydomonas can convert acetate in the TAP medium to glucose via the glyoxylate cycle, a pathway present in many microbes and higher plants. A novel bacterial strain, CC4533, was isolated from a contaminated TAP agar medium culture plate of a Chlamydomonas wild type strain. In this article, we present our research on the isolation, and biochemical and molecular characterizations of CC4533. Methods: We conducted several microbiological tests and spectrophotometric analyses to biochemically characterize CC4533. The 16S rRNA gene of CC4533 was partially sequenced for taxonomic identification. We monitored the growth of CC4533 on Tris-Phosphate (TP) agar medium (lacks a carbon source) containing different sugars, aromatic compounds and saturated hydrocarbons, to see if CC4533 can use these chemicals as the sole source of carbon. Results: CC4533 is a Gram-negative, non-enteric yellow pigmented, aerobic, mesophilic bacillus. It is alpha-hemolytic and oxidase-positive. CC4533 can ferment glucose, sucrose and lactose, is starch hydrolysis-negative, resistant to penicillin, polymyxin B and chloramphenicol. CC4533 is sensitive to neomycin. Preliminary spectrophotometric analyses indicate that CC4533 produces b-carotenes. NCBI-BLAST analyses of the partial 16S rRNA gene sequence of CC4533 show 99.55% DNA sequence identity to that of Sphingobium yanoikuyae strain PR86 and S. yanoikuyae strain NRB095. CC4533 can use cyclo-chloroalkanes, saturated hydrocarbons present in car motor oil, polyhydroxyalkanoate, and mono- and poly-cyclic aromatic compounds, as sole carbon sources for growth. Conclusions: Taxonomically, CC4533 is very closely related to the alpha-proteobacterium S. yanoikuyae, whose genome has been sequenced. Future research is needed to probe the potential of CC4533 for environmental bioremediation. Whole genome sequencing of CC4533 will confirm if it is a novel strain of S. yanoikuyae or a new Sphingobium species.

Sphingosinithalassobacter tenebrarum sp. nov., isolated from a deep-sea cold seep.

A Gram-stain-negative, facultatively anaerobic, yellow-pigmented, non-motile, rod-shaped bacterium, designated zrk23T, was isolated from a deep-sea cold seep. The strain was characterized by a polyphasic approach to clarify its taxonomic position. Phylogenetic analysis based on 16S rRNA gene sequences placed zrk23T within the genus Sphingosinithalassobacter and showed the highest similarity to Sphingosinithalassobacter portus FM6T (97.93 %). Growth occurs at temperatures from 16 to 45 °C (optimum, 30 °C), at pH values between pH 6.0 and 8.5 (optimum, pH 7.0) and in 0-5.0 % (w/v) NaCl (optimum, 1.5 %). The major fatty acids were C16 : 0, C14 : 0 2-OH and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The major isoprenoid quinone was ubiquinone-10. Predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol, one unidentified phosphoglycolipid, three unidentified glycolipids and three unidentified phospholipids. The G+C content of the genomic DNA was 64.69 %. The average nucleotide identity values between zrk23T and the most closely related available genome, of Sphingosinithalassobacter portus FM6T, was 82.21 %, indicating that zrk23T was clearly distinguished from S. portus. The analysis of genome sequence of zrk23T revealed that there were many genes associated with degradation of aromatic compounds existing in the genome of zrk23T. As a result of the combination of the results of phylogenetic analysis and phenotypic and chemotaxonomic data, zrk23T was considered to represent a novel species of the genus Sphingosinithalassobacter, for which the name Sphingosinithalassobacter tenebrarum sp. nov. is proposed. The type strain is zrk23T (=KCTC 72896T=MCCC 1K04416T).

Sandaracinobacter neustonicus sp. nov., isolated from the sea surface microlayer in the Southwestern Pacific Ocean, and emended description of the genus Sandaracinobacter.

A Gram-stain-negative, non-motile, facultatively anaerobic and rod-shaped bacterial strain, designated PAMC 28131T, was isolated from a sea surface microlayer sample in the open water of the Pacific Ocean. Phylogenetic analysis of the 16S rRNA gene sequence of strain PAMC 28131T revealed an affiliation to the genus Sandaracinobacter with the closest species Sandaracinobacter sibiricus RB16-17T (sequence similarity of 98.2 %). Strain PAMC 28131T was able to grow optimally with 0.5-1.0 % NaCl and at pH 6.5-7.0 and 30 °C. The polar lipids were phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids, an unidentified aminolipid, an unidentified glycolipid and an unidentified lipid. The major cellular fatty acids (>10 %) were C18 : 1 ω6c and/or C18 : 1 ω7c, (42.6 %), C17 : 1 ω6c (19.3 %) and C16 : 1 ω6c and/or C16 : 1 ω7c (15.8 %), and the respiratory quinone was Q-10. The genomic DNA G+C content was 65.3 mol%. The phylogenetic, phenotypic and chemotaxonomic data showed that strain PAMC 28131T could be clearly distinguished from S. sibiricus RB16-17T. Thus, strain PAMC 28131T should be classified as representing a novel species in the genus Sandaracinobacter, for which the name Sandaracinobacter neustonicus sp. nov. is proposed. The type strain is PAMC 28131T (=KCCM 43127T=JCM 30734T).

Description of Erythrobacter mangrovi sp. nov., an aerobic bacterium from rhizosphere soil of mangrove plant (Kandelia candel).

A novel Gram-stain negative, aerobic, non-motile, rod-shaped bacterium, designated as strain EB310T, was isolated from rhizosphere soil of mangrove plant Kandelia candel in Fugong village, Zhangzhou, China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain EB310T belonged to the genus Erythrobacter, clustering with Erythrobacter pelagi JCM 17468T, Erythrobacter lutimaris KCTC 42109T and Erythrobacter marisflavi KCTC 62896T, and showed the highest 16S rRNA gene sequence similarity of 97.5% to Erythrobacter pelagi JCM 17468T. The genomic average nucleotide identity and in silico DNA-DNA hybridization values between strain EB310T and the reference strains were 71.0-75.5% and 19.8-20.0%, respectively. Growth ranges of the isolate occurred at 10-45 °C (optimum 28-30 °C), pH 5.5-9.5 (optimum pH 7.5) and 0-9.0% NaCl concentrations (optimum 2.0%, w/v). The strain did not produce bacteriochlorophyll a and flexirubin, but produced carotenoids. The strain contained Q-10 as the predominant ubiquinone and summed feature 3 (C16:1 ω7c/C16:1 ω6c) and summed feature 8 (C18:1 ω6c/C18:1 ω7c) as the major fatty acids. The major polar lipids were sphingoglycolipid, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylcholine. Differential phenotypic characteristics, together with chemotaxonomic, phylogenetic and genomic distinctiveness, indicated that strain EB310T is distinguishable from other members of the genus Erythrobacter. On the basis of the data exhibited, strain EB310T is considered to represent a novel species of the genus Erythrobacter, for which the name Erythrobacter mangrovi sp. nov., is proposed. The type strain is EB310T (= KCTC 72109T = MCCC 1K03690T). The genomic DNA G + C content is 62.9 mol%.

Regulatory relationship between quality variation and environment of Cistanche deserticola in three ecotypes based on soil microbiome analysis.

The environment affects the composition and function of soil microbiome, which indirectly influences the quality of plants. In this study, 16S amplicon sequencing was used to reveal the differences in soil microbial community composition of Cistanche deserticola in three ecotypes (saline-alkali land, grassland and sandy land). Through the correlation analysis of microbial community abundance, phenylethanoid glycoside contents and ecological factors, the regulatory relationship between microbial community and the quality variation of C. deserticola was expounded. The metabolic function profile of soil microbiome was predicted using Tax4Fun. Data showed that the soil microbial communities of the three ecotypes were significantly different (AMOVA, P < 0.001), and the alpha diversity of grassland soil microbial community was the highest. Core microbiome analysis demonstrated that the soil microbial communities of C. deserticola were mostly have drought, salt tolerance, alkali resistance and stress resistance, such as Micrococcales and Bacillales. The biomarkers, namely, Oceanospirillales (saline-alkali land), Sphingomonadales (grassland) and Propionibacteriales (sandy land), which can distinguish three ecotype microbial communities, were excavated through LEfSe and random forest. Correlation analysis results demonstrated that 2'-acetylacteoside is positively correlated with Oceanospirillales in saline-alkali land soil. The metabolic function profiles displayed highly enriched metabolism (carbohydrate and amino acid metabolisms) and environmental information processing (membrane transport and signal transduction) pathways. Overall, the composition and function of soil microbiomes were found to be important factors to the quality variation of C. deserticola in different ecotypes. This work provided new insight into the regulatory relationship amongst the environment, soil microbial community and plant quality variation.

Sphingorhabdus lacus sp. nov. and Sphingorhabdus profundilacus sp. nov., isolated from freshwater environments.

Two Gram-stain-negative, aerobic, non-motile bacteria, designated IMCC1753T and IMCC26285T, were isolated from a shallow eutrophic pond and a deep oligotrophic lake, respectively. Results of 16S rRNA gene sequence analysis indicated that the two strains shared 99.8 % sequence similarity and were most closely related to Sphingorhabdus contaminans JC216T(98.7-98.8 %). The whole genome sequences of strains IMCC1753T and IMCC26285T were 3.5 and 2.9 Mbp in size with 56.6 and 55.5 mol% DNA G+C content, respectively. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the two strains were 82.2 and 25.8 %, respectively, indicating that they are separate species. The two strains showed ≤98.8 % 16S rRNA gene sequence similarities and ≤82.2 % ANI and ≤28.7 % dDDH values to closely related species of the genus Sphingorhabdus, indicating that the two strains each represent novel species. Major fatty acid constituents of strain IMCC1753T were C17 : 1 ω6c, C17 : 1 ω8c and summed features 3 (C16 : 1 ω6c and/or C16 : 1 ω7c) and 8 (C18 : 1 ω6c and/or C18 : 1 ω7c); those of strain IMCC26285T were summed features 3 and 8. The predominant isoprenoid quinone detected in both strains was ubiquinone-10 and the most abundant polyamine was spermidine. Both strains contained phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol and sphingoglycolipid as major polar lipids. On the basis of the phylogenetic and phenotypic characteristics, strains IMCC1753T and IMCC26285T were considered to represent two distinct novel species in the genus Sphingorhabdus, for which the names Sphingorhabdus lacus (IMCC1753T=KCTC 52480T=KACC 18985T=NBRC 112442T) and Sphingorhabdus profundilacus (IMCC26285T=KCTC 52479T=KACC 18986T=NBRC 112454T) are proposed, respectively.