Sphingomonas ginkgonis sp. nov., isolated from phyllosphere of Ginkgo biloba

Isolation and Characterization of Sphingomonas telluris, Sphingomonas caseinilyticus Isolated from Wet Land Soil

Two novel bacterial strains, designated as SM33^T and NSE70-1^T, were isolated from wet soil in South Korea. To get the taxonomic positions, the strains were characterized. The genomic information (both 16S rRNA gene and draft genome sequence analysis) show that both novel isolates (SM33^T and NSE70-1^T) belong to the genus Sphingomonas. SM33^T share the highest 16s rRNA gene similarity (98.2%) with Sphingomonas sediminicola Dae20^T. In addition, NSE70-1^T show 96.4% 16s rRNA gene similarity with Sphingomonas flava THG-MM5^T. The draft genome of strains SM33^T and NSE70-1^T consist of a circular chromosome of 3,033,485 and 2,778,408 base pairs with DNA G+C content of 63.9, and 62.5%, respectively. Strains SM33^T and NSE70-1^T possessed the ubiquinone Q-10 as the major quinone, and a fatty acid profile with C_16:0, C_18:1 2-OH_, C_16:1 ω7c/C_16:1 ω6c (summed feature 3) and C_18:1 ω7c/C_18:1 ω6c (summed feature 8) as major fatty acids. The major polar lipids of SM33^T and NSE70-1^T were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid and phosphatidylcholine, respectively. Moreover, genomic, physiological, and biochemical results allowed the phenotypic and genotypic differentiation of strains SM33^T and NSE70-1^T from their closest and other species of the genus Sphingomonas with validly published names. Therefore, the SM33^T and NSE70-1^T represent novel species of the genus Sphingomonas, for which the name Sphingomonas telluris sp. nov. (type strain SM33^T = KACC 22222^T = LMG 32193^T), and Sphingomonas caseinilyticus (type strain NSE70-1^T = KACC 22411^T = LMG 32495^T).

Sphingomonas caeni sp. nov., a phenolic acid-degrading bacterium isolated from activated sludge

A Gram-stain-negative, rod-shaped, polar flagellated or stalked and non-spore-forming bacterium, designated LB-2^T, was isolated from activated sludge. Growth was observed at 20-30 °C (optimum 28 °C), pH 6.0-8.0 (optimum pH 7.0) and salinity of 0-0.5% (w/v; optimum 0.5%). Phylogenetic analysis based on the 16S rRNA gene indicated that strain LB-2^T belongs to the genus Sphingomonas and showed the highest sequence similarity (96.7%) and less than 96.7% similarities to other type strains. The genome size of strain LB-2^T was 4.10 Mb, with 66.8 mol% G + C content. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strains LB-2^T and S. canadensis FWC47^T were 77.8% and 21%, respectively. The predominant cellular fatty acids were summed feature 8 (C_18:1ω7c and/or C_18 : 1ω6c) and C_16:0. The major polar lipids were aminolipid, glycolipid, sphingoglycolipid, phosphatidylcholine, phosphatidylglycerol, four unidentified lipids, glycophospholipid, phosphatidylethanolamine and diphosphatidylglycerol. The predominant respiratory quinone was Q-10 and the major polyamine was sym-homospermidine. On the basis of phenotypic, genotypic and phylogenetic evidences, strain LB-2^T represents a novel species in the genus Sphingomonas, for which the name Sphingomonas caeni sp. nov. is proposed. The type strain is LB-2^T (GDMCC 1.3630^T = NBRC 115,102^T).

Characterization of four novel bacterial species of the genus Sphingomonas, Sphingomonas anseongensis, Sphingomonas alba, Sphingomonas brevis and Sphingomonas hankyongi sp.nov., isolated from wet land

Four novel bacterial strains, designated as RG327^T, SE158^T, RB56-2^T and SE220^T, were isolated from wet soil in the Republic of Korea. To determine their taxonomic positions, the strains were fully characterized. On the basis of genomic information (16S rRNA gene and draft genome sequences), all four isolates represent members of the genus Sphingomonas. The draft genomes of RG327^T, SE158^T, RB56-2^T and SE220^T consisted of circular chromosomes of 2 226 119, 2 507 338, 2 593 639 and 2 548 888 base pairs with DNA G+C contents of 64.6, 63.6, 63.0 and 63.1 %, respectively. All the isolates contained ubiquinone Q-10 as the predominant quinone compound and a fatty acid profile with C_16 : 0, C_17 : 1ω6c, C_18 : 1 2-OH_, summed feature 3 (C_16 : 1ω7c/C_16 : 1ω6c) and summed feature 8 (C_18 : 1ω7c/C_18 : 1ω6c) as the major fatty acids, supporting the affiliation of strains RG327^T, SE158^T, RB56-2^T and SE220^T to the genus Sphingomonas. The major identified polar lipids in all four novel isolates were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid and phosphatidylcholine. Moreover, the physiological, biochemical results and low level of DNA-DNA relatedness and average nucleotide identity values allowed the phenotypic and genotypic differentiation of RG327^T, SE158^T, RB56-2^T and SE220^T from other species of the genus Sphingomonas with validly published names and indicated that they represented novel species of the genus Sphingomonas, for which the names Sphingomonas anseongensis sp. nov. (RG327^T = KACC 22409^T = LMG 32497^T), Sphingomonas alba sp. nov. (SE158^T = KACC 224408^T = LMG 324498^T), Sphingomonas brevis (RB56-2^T = KACC 22410^T = LMG 32496^T) and Sphingomonas hankyongi sp. nov., (SE220^T = KACC 22406^T = LMG 32499^T) are proposed.

Sphingomonas folii sp. nov., Sphingomonas citri sp. nov. and Sphingomonas citricola sp. nov., isolated from citrus phyllosphere

Three novel Gram-stain-negative, aerobic and rod-shaped bacterial strains, designated RHCKR7T, RRHST34T and RHCKR47T, were isolated from phyllosphere of healthy citrus collected in Renhua County, Guangdong Province, PR China. Phylogenetic analyses showed that they belonged to the genus Sphingomonas , among which both strains RHCKR7T and RRHST34T showed a close relationship with Sphingomonas yunnanensis YIM 003T with 16S rRNA gene similarity of 99.0 and 99.1%, respectively, and the similarity between the two novel strains was 99.2%, meanwhile strain RHCKR47T was most closely related to Sphingomonas palmae KACC 17591T (99.5%). Genome-derived average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between closely related novel strains RHCKR7T and RRHST34T were 90.43 and 40.80 %, respectively, and their most closely related type strain, S. yunnanensis YIM 003T, showed 90.43 % ANI and 40.7 % dDDH with RHCKR7T and 90.21 % and 42.9 % with RRHST34T, respectively, and the corresponding values between strain RHCKR47T and S. palmae KACC 17591T were 85.53 % and 29.30%, respectively. They all took C14 : 0 2-OH and summed feature 8 (C18 : 1  ω6c and/or C18 : 1  ω7c) as the major fatty acids, and ubiquinone 10 as the predominant respiratory quinone. The major polar lipids contained sphingoglycolipid, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and unidentified phospholipids. sym-Homospermidine was the major polyamine. Based on phenotypic, genotypic and chemotaxonomic analyses, the new isolates should be considered as representing three novel species of the genus Sphingomonas , for which the names Sphingomonas folli sp. nov., Sphingomonas citri sp. nov. and Sphingomonas citricola sp. nov. are proposed with RHCKR7T (=GDMCC 1.2663T=JCM 34794T), RRHST34T (=GDMCC 1.2665T=JCM 34796T) and RHCKR47T (=GDMCC 1.2664T=JCM 34795T) as the type strains, respectively.

Sphingomonas radiodurans sp. nov., a novel radiation-resistant bacterium isolated from the north slope of Mount Everest

A bacterial strain, designated S9-5T, was isolated from moraine samples collected from the north slope of Mount Everest at an altitude of 5 500 m above sea level. A polyphasic study confirmed the affiliation of the strain with the genus Sphingomonas . Strain S9-5T was an aerobic, Gram-stain-negative, non-spore-forming, non-motile and rod-shaped bacterium that could grow at 10–40 °C, pH 5–8 and with 0–9 % (w/v) NaCl. Q-10 was its predominant respiratory menaquinone. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid, an unidentified aminophospholipid and eight unidentified lipids comprised the polar lipids of strain S9-5T. Its major fatty acids were summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c) and C16 : 0. The G+C content was 65.75mol%. Phylogenetic analysis based on 16S rRNA sequences showed that strain S9-5T was phylogenetically closely related to Sphingomonas panaciterrae DCY91T (98.17 %), Sphingomonas olei K-1-16T (98.11 %) and Sphingomonas mucosissima DSM 17494T (97.39 %). The average nucleotide identity values among strain S9-5T and Sphingomonas panaciterrae DCY91T, Sphingomonas olei K-1-16T and Sphingomonas mucosissima DSM 17494T were 78.82, 78.87 and 78.29 %, respectively. Based on the morphological, physiological and chemotaxonomic data, strain S9-5T (=JCM 34750T=GDMCC 1.2714T) should represent a novel species of the genus Sphingomonas , for which we propose the name Sphingomonas radiodurans sp. nov.

Barks from avocado trees of different geographic locations have consistent microbial communities

Bark is a permanent surface for microbial colonization at the interface of trees and the surrounding air, but little is known about its microbial communities. We used shotgun metagenomic sequencing to analyze the bark microbiomes of avocado trees from two orchards, and compared one of them to rhizospheric soil. It was shown that the microbial communities of avocado bark have a well-defined taxonomic structure, with consistent patterns of abundance of bacteria, fungi, and archaea, even in trees from two different locations. Bark microbial communities were distinct from rhizospheric soil, although they showed overlap in some taxa. Thus, avocado bark is a well-defined environment, providing niches for specific taxonomic groups, many of which are also found in other aerial plant tissues. The present in-depth characterization of bark microbial communities can form a basis for their future manipulation for agronomical purposes.

Sphingomonas suaedae sp. nov., a chitin-degrading strain isolated from rhizosphere soil of Suaeda salsa

A Gram-stain-negative, aerobic, chitin-degrading, motile bacterial strain with a single polar flagellum, designated XS-10T, was isolated from saline soil sampled from the rhizosphere of Suaeda salsa, Tumd Right Banner, Inner Mongolia, PR China. Strain XS-10T grew at 10–40 °C (optimum, 35 °C), pH 5.0–9.0 (optimum, pH 8.0) and 0–12.5% NaCl (optimum 2.0 %). The phylogenetic analysis based on both the 16S rRNA gene and the phylogenomic tree revealed that strain XS-10T formed a clade with Sphingomonas turrisvirgatae MCT13T and Sphingomonas koreensis JSS-26T, sharing 98.4 and 97.5 % 16S rRNA gene similarities to S. koreensis JSS-26T and S. turrisvirgatae MCT13T, respectively. Spermidine and Q-10 were the major polyamine and the major respiratory quinone, respectively. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, two unidentified lipids and an unidentified aminophospholipid. The major fatty acids were summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c), C16 : 0 and C17 : 1  ω6c. The genome of strain XS-10T consisted of a 4 154 291 bp chromosome with a DNA G+C content of 65.5 mol%. The average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization values of strain XS-10T with S. turrisvirgatae MCT13T and S. koreensis JSS-26T were 77.8 and 78.6 %, 75.9 and 76.3 %, and 22.0 and 22.9 %, respectively. Based on the phylogenetic, phenotypic, and genotypic characteristics, strain XS-10T is considered to represent a novel species of the genus Sphingomonas , for which the name Sphingomonas suaedae sp. nov. is proposed. The type strain is XS-10T (=CGMCC 1.17078T=JCM 33850T).