Isolation and characterization of a bioactive compound from Sphingomonas sanguinis DM with cytotoxic and molecular docking analysis

Datura metel, a common plant in the Solanaceae family, is known for its valuable medicinal properties. The metabolites created by its rhizosphere bacterium, Sphingomonas sanguinis DM, have garnered interest for their potential biological effects. This study will discuss the steps involved in fermenting and processing a bacterial strain to extract potent secondary metabolites. The ethyl acetate extract of the propagated strain was subjected to fractionation and purification through various chromatographic techniques. The purified compound was characterized through multiple spectroscopic methods for structure elucidation, including UV, MS, 1D, and 2D-NMR. Its cytotoxic activity was assessed on malignant skin cells (A-431) using the MTT test compared with normal melanocytes (HFB 4). Furthermore, A-431 cells were double-stained with PI and annexin V-FITC and analyzed by flow cytometry to detect Apoptosis. Molecular investigations include PCR screening to detect genes related to the biosynthesis of bioactive metabolites, such as NRPS and lipopeptide ItuD genes. A prospective effective strategy to overcome tumor plasticity in melanoma is to target the Wnt signaling pathways. Molecular docking studies were conducted in the different proteins (Fz4-CRD, LRP6, GSK3β) of the Wnt signaling pathway and Protein Kinase B/Akt for the isolated compound to investigate the possible pathway to inhibit melanoma. Sphingomonas sanguinis DM produced bis (2-methylheptyl) benzene-1,4-dicarboxylate isolated for the first time from a natural source. It was cytotoxic against the A-431 human skin carcinoma cell line (IC50 = 191.61 µg/mL) but less effective against HFB 4 human normal melanocytes (IC50 = 416.23 µg/mL; selectivity index = 2.17). The A-431 cells showed a significant increase in early Apoptosis and a moderate rise in late Apoptosis. PCR amplification confirmed genes encoding A domain and Iturin A. Bacterial sequences are available in NCBI GenBank with accession codes OR597597 and OR597598. Consequently, Sphingomonas sanguinis DM synthesized a cytotoxic natural terephthalate diester derivative, along with the host specificity of the strain.

Warming and rainfall reduction alter soil microbial diversity and co-occurrence networks and enhance pathogenic fungi in dryland soils

In this 9-year manipulative field experiment, we examined the impacts of experimental warming (2 °C, W), rainfall reduction (30 % decrease in annual rainfall, RR), and their combination (W + RR) on soil microbial communities and native vegetation in a semi-arid shrubland in south-eastern Spain. Warming had strong negative effects on plant performance across five coexisting native shrub species, consistently reducing their aboveground biomass growth and long-term survival. The impacts of rainfall reduction on plant growth and survival were species-specific and more variable. Warming strongly altered the soil microbial community alpha-diversity and changed the co-occurrence network structure. The relative abundance of symbiotic arbuscular mycorrhizal fungi (AMF) increased under W and W + RR, which could help buffer the direct negative impacts of climate change on their host plants nutrition and enhance their resistance to heat and drought stress. Indicator microbial taxa analyses evidenced that the marked sequence abundance of many plant pathogenic fungi, such as Phaeoacremonium, Cyberlindnera, Acremonium, Occultifur, Neodevriesia and Stagonosporopsis, increased significantly in the W and W + RR treatments. Moreover, the relative abundance of fungal animal pathogens and mycoparasites in soil also increased significantly under climate warming. Our findings indicate that warmer and drier conditions sustained over several years can alter the soil microbial community structure, composition, and network topology. The projected warmer and drier climate favours pathogenic fungi, which could offset the benefits of increased AMF abundance under warming and further aggravate the severe detrimental impacts of increased abiotic stress on native vegetation performance and ecosystem services in drylands.

Phytochemical and biological assessment of secondary metabolites isolated from a rhizosphere strain, Sphingomonas sanguinis DM of Datura metel

BACKGROUND

The plant roots excrete a large number of organic compounds into the soil. The rhizosphere, a thin soil zone around the roots, is a hotspot for microbial activity, making it a crucial component of the soil ecosystem. Secondary metabolites produced by rhizospheric Sphingomonas sanguinis DM have sparked significant curiosity in investigating their possible biological impacts.

METHODS

A bacterial strain has been isolated from the rhizosphere of Datura metel. The bacterium's identification, fermentation, and working up have been outlined. The ethyl acetate fraction of the propagated culture media of Sphingomonas sanguinis DM was fractioned and purified using various chromatographic techniques. The characterization of the isolated compounds was accomplished through the utilization of various spectroscopic techniques, such as UV, MS, 1D, and 2D-NMR. Furthermore, the evaluation of their antimicrobial activity was conducted using the agar well diffusion method, while cytotoxicity was assessed using the MTT test.

RESULTS

The extract from Sphingomonas sanguinis DM provided two distinct compounds: n-dibutyl phthalic acid (1) and Bis (2-methyl heptyl) phthalate (2) within its ethyl acetate fraction. Furthermore, the 16S rRNA gene sequence of Sphingomonas sanguinis DM has been registered under the NCBI GenBank database with the accession number PP422198. The bacterial extract exhibited its effect against gram-positive bacteria, inhibiting Streptococcus mutans (12.6 ± 0.6 mm) and Staphylococcus aureus (10.6 ± 0.6 mm) compared to standard antibiotics. Conversely, compound 1 showed a considerable effect against phytopathogenic fungi such as Alternaria alternate (56.3 ± 10.6 mm) and Fusarium oxysporum (21.3 ± 1.5 mm) with a MIC value of 17.5 µg/mL. However, it was slightly active against Klebsiella pneumonia (11.0 ± 1.0 mm). Furthermore, compound 2 was the most active metabolite, having a significant antimicrobial efficacy against Rhizoctonia solani (63.6 ± 1.1 mm), Pseudomonas aeruginosa (16.7 ± 0.6 mm), and Alternaria alternate (20.3 ± 0.6 mm) with MIC value at 15 µg/mL. In addition, compound 2 exhibited the most potency against hepatocellular (HepG-2) and skin (A-431) carcinoma cell lines with IC50 values of 107.16 µg/mL and 111.36 µg/mL, respectively.

CONCLUSION

Sphingomonas sanguinis DM, a rhizosphere bacterium of Datura metel, was studied for its phytochemical and biological characteristics, resulting in the identification of two compounds with moderate antimicrobial and cytotoxic activities.

Sphingomonas sediminicola Dae20 Is a Highly Promising Beneficial Bacteria for Crop Biostimulation Due to Its Positive Effects on Plant Growth and Development

Current agricultural practices rely heavily on synthetic fertilizers, which not only consume a lot of energy but also disrupt the ecological balance. The overuse of synthetic fertilizers has led to soil degradation. In a more sustainable approach, alternative methods based on biological interactions, such as plant growth-promoting bacteria (PGPRs), are being explored. PGPRs, which include both symbiotic and free-living bacteria, form mutualistic relationships with plants by enhancing nutrient availability, producing growth regulators, and regulating stress responses. This study investigated the potential of Sphingomonas sediminicola Dae20, an α-Proteobacteria species commonly found in the rhizosphere, as a beneficial PGPR. We observed that S. sediminicola Dae20 stimulated the root system and growth of three different plant species in the Brassicaceae family, including Arabidopsis thaliana, mustard, and rapeseed. The bacterium produced auxin, nitric oxide, siderophores and showed ACC deaminase activity. In addition to activating an auxin response in the plant, S. sediminicola Dae20 exhibited the ability to modulate other plant hormones, such as abscisic acid, jasmonic acid and salicylic acid, which are critical for plant development and defense responses. This study highlights the multifunctional properties of S. sediminicola Dae20 as a promising PGPR and underscores the importance of identifying effective and versatile beneficial bacteria to improve plant nutrition and promote sustainable agricultural practices.

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).

Sphingomonas sediminicola Is an Endosymbiotic Bacterium Able to Induce the Formation of Root Nodules in Pea (Pisum sativum L.) and to Enhance Plant Biomass Production

The application of bacterial bio-inputs is a very attractive alternative to the use of mineral fertilisers. In ploughed soils including a crop rotation pea, we observed an enrichment of bacterial communities with Sphingomonas (S.) sediminicola. Inoculation experiments, cytological studies, and de novo sequencing were used to investigate the beneficial role of S. sediminicola in pea. S. sediminicola is able to colonise pea plants and establish a symbiotic association that promotes plant biomass production. Sequencing of the S. sediminicola genome revealed the existence of genes involved in secretion systems, Nod factor synthesis, and nitrogenase activity. Light and electron microscopic observations allowed us to refine the different steps involved in the establishment of the symbiotic association, including the formation of infection threads, the entry of the bacteria into the root cells, and the development of differentiated bacteroids in root nodules. These results, together with phylogenetic analysis, demonstrated that S. sediminicola is a non-rhizobia that has the potential to develop a beneficial symbiotic association with a legume. Such a symbiotic association could be a promising alternative for the development of more sustainable agricultural practices, especially under reduced N fertilisation conditions.

Sphingomonas cannabina sp. nov., isolated from Cannabis sativa L. 'Cheungsam'

A Gram-negative, aerobic, rod-shaped bacterium, designated DM2-R-LB4^T was isolated from Cannabis sativa L. 'Cheungsam' in Andong, Republic of Korea. The strain DM2-R-LB4^T grew at temperatures of 15-45 °C (optimum, 30-37 °C), pH of 5.5-9 (optimum, 8.0), and 0-2 % (w/v) NaCl concentration (optimum, 0%). Phylogenetic analyses based on the 16S rRNA gene sequences revealed that strain DM2-R-LB4^T is related to species of the genus Sphingomonas, and shared 97.8 and 97.5% similarity to Sphingomonas kyenggiensis KCTC 42244^T and Sphingomonas leidyi DSM 4733^T, respectively. The DNA G+C content was 67.9 mol% and genome analysis of the strain DM2-R-LB4^T revealed that the genome size was 4 386 171 bp and contained 4 009 predicted protein-coding genes. The average nucleotide identity (ANI) values between strain DM2-R-LB4^T and S. kyenggiensis KCTC 42244^T, and S. leidyi DSM 4733^T was 76.8 and 76.7 %, respectively, while the values of digital DNA-DNA hybridization (dDDH) were 20.7 and 20.6 %, respectively. C_14 : 0 2-OH, C_16 : 0, and summed feature 8 (C_18 : 1 ω6c and/or C_18 : 1 ω7c) were the major fatty acids (>10 %) in the strain DM2-R-LB4^T. The polar lipids comprised diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC), sphingoglycolipid (SGL), glycolipid (GL), phospholipid (PL), and two unidentified polar lipids (L1 and L2). Ubiquinone-10 (Q-10) was the only respiratory quinone. The polyamine pattern was found to contain homospermidine, putrescine, and spermidine. The results of phylogenetic anlayses, polyphasic studies, revealed that strain DM2-R-LB4^T represents a novel species of the genus Sphingomonas, for which the name Sphingomonas cannabina sp. nov., is proposed. The type strain is DM2-R-LB4^T (=KCTC 92075^T = GDMCC 1.3018^T).

Sphingomonas sabuli sp. nov., a carotenoid-producing bacterium isolated from beach sand

A Gram-stain-negative, aerobic and non-motile bacterium, strain sand1-3^T, was isolated from beach sand collected from Haeundae Beach located in Busan, Republic of Korea. Based on the results of 16S rRNA gene sequence and phylogenetic analyses, Sphingomonas daechungensis CH15-11^T (97.0 %), Sphingomonas edaphi DAC4^T (96.8 %), Sphingomonas xanthus AE3^T (96.5 %) and Sphingomonas oryziterrae YC6722^T (96.0 %) were selected for comparing phenotypic and chemotaxonomic characteristics. Cells of strain sand1-3^T grew at 7-50 °C (optimum, 30-35 °C), pH 5.0-8.0 (optimum, pH 7.0-8.0) and in the presence of 0-0.5 % (w/v) NaCl (optimum, 0 %). Major polar lipids included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, one unidentified glycolipid and one unidentified phosphoglycolipid. The major fatty acids were summed feature 8 (C_18 : 1 ω6c and/or C_18 : 1 ω7c) and C_18 : 1 2-OH. Moreover, the sole respiratory quinone and major polyamine were identified as ubiquinone-10 and homospermidine, respectively. The genomic DNA G+C content was 65.9 mol%. The digital DNA-DNA hybridization, average nucleotide identity and average amino acid identity values of strain sand1-3^T and its reference strains with publicly available genomes were 17.9-18.9 %, 72.0-75.3 % and 63.3-76.5 % respectively. Based on polyphasic evidence, we propose Sphingomonas sabuli sp. nov. as a novel species within the genus Sphingomonas. The type strain is sand1-3^T (=KCTC 82358^T=NBRC 114538^T).

Sphingomonas xanthus sp. nov., Isolated from Beach Soil

A light yellow-colored, Gram-stain-negative, aerobic, oxidase- and catalase-positive, flagellated bacterium with motility, designated as strain AE3^T was isolated from soil. Cells of strain AE3^T are rod-shaped, and the colonies are round and convex. Phylogenetic analysis based on 16S rRNA gene sequence revealed that strain AE3^T forms a lineage within the genus Sphingomonas of the family Sphingomonadaceae and is most closely related to Sphingomonas edaphi KCTC 62107 ^T (98.6%), Sphingomonas oryziterrae KCTC 22476 ^T (97.9%), and Sphingomonas jaspsi DSM 18422 ^T (97.4%). The growth of the strain AE3^T was observed under 18-42 °C (optimum, 37 °C), pH 6.0-9.0 (optimum, pH 6.5-7.0), and in the absence of NaCl. Strain AE3^T contains Q-10 as a predominant respiratory quinone, and the major fatty acids are C_17:1 ω6c, summed feature 8 (C_18:1 ω7c), and summed feature 3 (C_16:1 ω7c and/or C_16:1 ω6c). The major polar lipids are sphingoglycolipids, unidentified phospholipids, and phosphatidylethanolamine. The DNA G + C content of strain AE3^T is 63.6 mol%. The nearly complete genome of strain AE3^T consists of 2.2 Mbp, (2,168 total protein-coding genes, 45 tRNAs, 4 ncRNAs, and 3 rRNAs). Genomic taxonomy analysis demonstrates that the novel strain has < 75.9% average nucleotide identity value, and also shows < 24.9% in silico DNA-DNA hybridization value compared to related taxa, which clearly separates strain AE3^T from other species of the genus Sphingomonas with values below the thresholds for species delineation. Based on phenotypic, genotypic, and phylogenetic analyses, strain AE3^T represents a novel species of the genus Sphingomonas, for which the name Sphingomonas xanthus sp. nov. is proposed. The type strain of Sphingomonas xanthus is AE3^T (= KCTC 620106 ^T = JCM 32376 ^T).

Sphingomonas chungangi sp. nov., a bacterium isolated from garden soil sample

A novel bacterial strain, designated MAH-6^T, was isolated from a garden soil sample. Cells were Gram-stain-negative, aerobic, non-motile and rod-shaped. The colonies were light yellow, smooth, circular and 0.6-1.2 mm in diameter when grown on nutrient agar for 3 days. Strain MAH-6^T grew at 15-35 °C, at pH 5.0-7.0 and with 0-0.5 % NaCl. Cell growth occurred on nutrient agar and Reasoner's 2A (R2A) agar. The strain was positive for both catalase and oxidase tests. Cells were able to hydrolyse starch, aesculin, Tween 20 and Tween 80. According to 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Sphingomonas and was most closely related to Sphingomonas polyaromaticivorans B2-7^T (98.2 % sequence similarity), Sphingomonas oligoaromativorans SY-6^T (96.9 %) and Sphingomonas morindae NBD5^T (96.6 %). The novel strain MAH-6^T has a draft genome size of 4 370 740 bp (28 contigs), annotated with 4199 protein-coding genes, 46 tRNA and three rRNA genes. The genomic DNA G+C content of the strain was determined to be 66.2 mol% and the predominant isoprenoid quinone is Q-10. The major fatty acids were identified as summed feature 8 (comprising C_18 : 1  ω7c and/or C_18 : 1  ω6c), C_14 : 0 2OH and C_16 : 0. The main polar lipids were phosphatidylcholine, sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Based on the results of phenotypic, genotypic, chemotaxonomic and DNA-DNA hybridization studies, strain MAH-6^T represents a novel species, for which the name Sphingomonas chungangi sp. nov. is proposed, with MAH-6^T as the type strain (=KACC 19292^T=CGMCC1.13654^T).

Sphingomonas pokkalii sp. nov., a novel plant associated rhizobacterium isolated from a saline tolerant pokkali rice and its draft genome analysis

Three strains L3B27T, 3CNBAF, L1A4 isolated from a brackish cultivated pokkali rice rhizosphere were characterised using a polyphasic taxonomic approach. Phylogenetic analysis based on 16S rRNA and recA gene sequences revealed that these strains were highly similar among each other and formed a separate monophyletic cluster within the genus Sphingomonas with Sphingomonas pituitosa DSM 13101T, Sphingomonas azotifigens DSM 18530T and Sphingomonas trueperi DSM 7225T as their closest relatives sharing 97.9-98.3% 16S rRNA similarity and 91.3-94.0% recA similarity values, respectively. The average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridisation (dDDH) values between L3B27T (representative of the novel strains) and its phylogenetically closest Sphingomonas species were well below the established cut-off <94% (ANI/AAI) and <70% (dDDH) for species delineation. Further, the novel strains can be distinguished from its closest relatives based on several phenotypic traits. Thus, based on the polyphasic approach, we describe a novel Sphingomonas species for which the name Sphingomonas pokkalii sp. nov (type strain L3B27T=KCTC 42098T=MCC 3001T) is proposed. In addition, the novel strains were characterised for their plant associated properties and found to possess several phenotypic traits which probably explain its plant associated lifestyle. This was further confirmed by the presence of several plant associated gene features in the genome of L3B27T. Also, we could identify gene features which may likely involve in brackish water adaptation. Thus, this study provides first insights into the plant associated lifestyle, genome and taxonomy of a novel brackish adapted plant associated Sphingomonas.

Sphingomonas deserti sp. nov., isolated from Mu Us Sandy Land soil

A Gram-stain-negative, rod-shaped bacterium, designated as strain GL-C-18^T, was isolated from soil sample collected at Mu Us Sandy Land, China, and its taxonomic position was investigated using a polyphasic approach. Growth was observed in the presence of 0-1 % (w/v) NaCl (optimum, 0 %), pH 6.0-9.0 (optimum, pH 7.0-8.0) and 20-37 °C. On the basis of 16S rRNA gene sequence similarity, strain GL-C-18^T belonged to the family Sphingomonadaceae and was most closely related to Sphingosinicella vermicomposti YC7378^T (95.7 %), Sphingomonas oligophenolica S213^T (95.0 %) and Sphingobium boeckii 301^T (94.8 %). The draft genome of strain GL-C-18^T was 6.09 Mb, and the G+C content was 66.0 %. The average nucleotide identity value to Sphingosinicella vermicomposti YC7378^T was 83.7 %. The predominant respiratory quinone was Q-10. The major fatty acids were C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16:0 and C14 : 0 2OH. The main polar lipids were sphingoglycolipid, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. On the basis of chemotaxonomic, phylogenetic and phenotypic evidence, strain GL-C-18^T represents a novel species of the genus Sphingomonas, for which the name Sphingomonasdeserti sp. nov. is proposed. The type strain is GL-C-18^T (=ACCC 60076^T=KCTC 62411^T).

The Response of a 16S Ribosomal RNA Gene Fragment Amplified Community to Lead, Zinc, and Copper Pollution in a Shanghai Field Trial

Industrial and agricultural activities have caused extensive metal contamination of land throughout China and across the globe. The pervasive nature of metal pollution can be harmful to human health and can potentially cause substantial negative impact to the biosphere. To investigate the impact of anthropogenic metal pollution found in high concentrations in industrial, agricultural, and urban environments, 16S ribosomal RNA gene amplicon sequencing was used to track change in the amplified microbial community after metal contamination in a large-scale field experiment in Shanghai. A total of 1,566 operational taxonomic units (OTUs) identified from 448,108 sequences gathered from 20 plots treated as controls or with lead, zinc, copper, or all three metals. Constrained Analysis of Principal Coordinates ordination did not separate control and lead treatment but could separate control/lead, zinc, copper, and three metal treatment. DESeq2 was applied to identify 93 significantly differentially abundant OTUs varying in 211 pairwise instances between the treatments. Differentially abundant OTUs representing genera or species belonging to the phyla Chloroflexi, Cyanobacteria, Firmicutes, Latescibacteria, and Planctomycetes were almost universally reduced in abundance due to zinc, copper, or three metal treatment; with three metal treatment abolishing the detection of some OTUs, such as Leptolyngbya, Desmonostoc muscorum, and Microcoleus steenstrupii. The greatest increases due to metal treatment were observed in Bacteroidetes, Actinobacteria, Chlamydiae, Nitrospirae, and Proteobacteria (α, β, δ, and γ); the most (relative) abundant being uncharacterized species within the genera Methylobacillus, Solirubrobacter, and Ohtaekwangia. Three metal treatment alone resulted in identification of 22 OTUs (genera or species) which were not detected in control soil, notably including Yonghaparkia alkaliphila, Pedobacter steynii, Pseudolabrys taiwanensis, Methylophilus methylotrophus, Nitrosospira, and Lysobacter mobilis. The capacity to track alterations of an amplified microbial community at high taxonomic resolution using modern bioinformatic approaches, as well as identifying where that resolution is lost for technical or biological reasons, provides an insight into the complexity of the microbial world resisting anthropogenic pollution. While functional assessment of uncharacterized organisms within environmental samples is technically challenging, an important step is observing those organisms able to tolerate extreme stress and to recognize the extent to which important amplifiable community members still require characterization.

Sphingomonas morindae sp. nov., isolated from Noni (Morinda citrifolia L.) branch

Two yellow bacterial strains, designated NBD5(T) and NBD8, isolated from Noni (Morinda citrifolia L.) branch were investigated using a polyphasic taxonomic approach. Cells were Gram-stain-negative, aerobic, non-spore-forming, non-motile and short rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences suggested that the strains were members of a novel species of the genus Sphingomonas, the seven closest neighbours being Sphingomonas oligoaromativorans SY-6(T) (96.9% similarity), Sphingomonas polyaromaticivorans B2-7(T) (95.8%), Sphingomonas yantingensis 1007(T) (94.9%), Sphingomonas sanguinis IFO 13937(T) (94.7%), Sphingomonas ginsenosidimutans Gsoil 1429(T) (94.6%), Sphingomonas wittichii RW1(T) (94.6%) and Sphingomonas formosensis CC-Nfb-2(T) (94.5%). Strains NBD5T and NBD8 had sphingoglycolipid, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylcholine as the major polar lipids, ubiquinone 10 as the predominant respiratory quinone, and sym-homospermidine as the major polyamine. Strains NBD5(T) and NBD8 were clearly distinguished from reference type strains based on phylogenetic analysis, DNA-DNA hybridization, fatty acid composition data analysis, and comparison of a range of physiological and biochemical characteristics. It is evident from the genotypic and phenotypic data that strains NBD5(T) and NBD8 represent a novel species of the genus Sphingomonas, for which the name Sphingomonas morindae sp. nov. is proposed. The type strain is NBD5(T) ( = DSM 29151(T) = KCTC 42183(T) = CICC 10879(T)).

Sphingomonas zeae sp. nov., isolated from the stem of Zea mays

A yellow-pigmented bacterial isolate (strain JM-791T) obtained from the healthy internal stem tissue of 1-month-old corn (Zea mays, cultivar 'Sweet Belle') grown at the Plant Breeding Unit of the E.V. Smith Research Center in Tallassee (Elmore county), Alabama, USA, was taxonomically characterized. The study employing a polyphasic approach, including 16S RNA gene sequence analysis, physiological characterization, estimation of the ubiquinone and polar lipid patterns, and fatty acid composition, revealed that strain JM-791T shared 16S rRNA gene sequence similarities with type strains of Sphingomonas paucimobilis (98.3%), Sphingomonas pseudosanguinis (97.5%) and Sphingomonas yabuuchiae (97.4%), but also showed pronounced differences, both genotypically and phenotypically. On the basis of these results, a novel species of the genus Sphingomonas is described, for which we propose the name Sphingomonas zeae sp. nov. with the type strain JM-791T ( = LMG 28739T = CCM 8596T).

Sphingomonas daechungensis sp. nov., isolated from sediment of a eutrophic reservoir

Strain CH15-11T, isolated from a sediment sample taken from Daechung Reservoir, South Korea, during the late-blooming period of cyanobacteria, was found to be a Gram-stain-negative, non-motile, non-spore-forming, rod-shaped and aerobic bacterium. Strain CH15-11T grew optimally at pH 7 and 28–30 °C. According to a phylogenetic tree based on 16S rRNA gene sequences, strain CH15-11T belonged to the genus Sphingomonas and clustered with Sphingomonas sediminicola Dae 20T, with which it shared the highest 16S rRNA gene sequence similarity (97.6 %). Chemotaxonomic analysis showed that strain CH15-11T had characteristics typical of members of the genus Sphingomonas , such as the presence of sphingoglycolipid, ubiquinone Q-10 and sym-homospermidine. Plus, strain CH15-11T included summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0 as the major fatty acids. The genomic DNA G+C content was 65.6 mol%. Sequence data showed that strain CH15-11T was most closely related to Sphingomonas sediminicola Dae 20T (97.6 %), Sphingomonas ginsengisoli Gsoil 634T (97.2 %) and Sphingomonas jaspi TDMA-16T (97.0 %). However, the DNA–DNA relatedness values between strain CH15-11T and the most closely related type strains were within a range of 35–59 %. Thus, based on the phylogenetic, phenotypic and genetic data, strain CH15-11T was classified as a member of the genus Sphingomonas as a representative of a novel species, for which the name Sphingomonas daechungensis sp. nov. is proposed. The type strain is CH15-11T ( = KCTC 23718T = JCM 17887T).

Sphingomonas aerophila sp. nov. and Sphingomonas naasensis sp. nov., isolated from air and soil, respectively

Two strains, designated 5413J-26T and KIS18-15T, were isolated from the air and forest soil, respectively, in South Korea. Cells of the two strains were Gram-stain-negative, aerobic, polar-flagellated and rod-shaped. According to the phylogenetic tree, strains 5413J-26T and KIS18-15T fell into the cluster of Sphingomonas sensu stricto. Strain 5413J-26T showed the highest sequence similarities with Sphingomonas trueperi LMG 2142T (96.6 %), Sphingomonas molluscorum KMM 3882T (96.5 %), Sphingomonas azotifigens NBRC 15497T (96.3 %) and Sphingomonas pituitosa EDIVT (96.1 %), while strain KIS18-15T had the highest sequence similarity with Sphingomonas soli T5-04T (96.8 %), Sphingomonas pituitosa EDIVT (96.6 %), Sphingomonas leidyi ATCC 15260T (96.6 %), Sphingomonas asaccharolytica NBRC 15499T (96.6 %) and Sphingomonas koreensis JSS26T (96.6 %). The 16S rRNA gene sequence similarity between strains 5413J-26T and KIS18-15T was 95.4 %. Ubiquinone 10 was the predominant respiratory quinone and homospermidine was the major polyamine. The major polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and several unidentified phospholipids and lipids. The main cellular fatty acids (>10 % of the total fatty acids) of strain 5413J-26T were summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c), summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C14 : 0 2-OH, and those of strain KIS18-15T were summed feature 8 and C16 : 0. Based on the results of 16S rRNA gene sequence analysis, and physiological and biochemical characterization, two novel species with the suggested names Sphingomonas aerophila sp. nov. (type strain 5413J-26T = KACC 16533T = NBRC 108942T) and Sphingomonas naasensis sp. nov. (type strain KIS18-15T = KACC 16534T = NBRC 108943T) are proposed.

Sphingomonas kyungheensis sp. nov., a bacterium with ginsenoside-converting activity isolated from soil of a ginseng field

A bacterial strain THG-B283(T), which has β-glucosidase activity, was isolated from soil of a ginseng field. Cells were Gram-reaction-negative, oxidase- and catalase-positive, aerobic, motile with one polar flagellum and rod-shaped. The strain was subjected to a polyphasic taxonomic study. Strain THG-B283(T) grew optimally at around pH 7.0, at 25-28 °C and in the absence of NaCl on R2A agar. 16S rRNA gene sequence analysis revealed that strain THG-B283(T) belongs to the family Sphingomonadaceae and is closely related to Sphingomonas melonis DAPP-PG 224(T) (98.2 %), S. aquatilis JSS7(T) (98.1 %), S. insulae DS-28(T) (97.6 %), S. mali IFO 15500(T) (97.1 %) and S. pruni IFO 15498(T) (97.0 %). Strain THG-B283(T) contained Q-10 as the predominant ubiquinone. The major fatty acids included summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C18 : 1ω7c, C14 : 0 2-OH and C16 : 0. The DNA G+C content was 72.2 mol%. The major component in the polyamine pattern was sym-homospermidine. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidyldimethylethanolamine, phosphatidylcholine, sphingoglycolipid, diphosphatidylglycerol, an unidentified glycolipid, unidentified aminolipids, an unidentified phospholipid and unidentified lipids. Genomic and chemotaxonomic data supported the affiliation of strain THG-B283(T) to the genus Sphingomonas. DNA-DNA relatedness between strain THG-B283(T) and its closest phylogenetic neighbours was below 23 %. On the basis of phenotypic, phylogenetic and genetic data, strain THG-B283(T) represents a novel species of genus Sphingomonas, for which the name Sphingomonas kyungheensis sp. nov. is proposed. The type strain is THG-B283(T) ( = KACC 16224(T) = LMG 26582(T)).