Sphingomonas dokdonensis sp. nov., isolated from soil

Sphingomonas Immobilis sp. nov., and Sphingomonas natans sp. nov. bacteria isolated from soil

Two novel strains of bacteria, CA1-15T and BIUV-7T, were isolated from soil samples gathered in Cheonan-si, Republic of Korea, and Inje-gun, Republic of Korea, respectively. These bacteria are Gram-negative, aerobic, and non-motile. Phylogenetic evaluations, using the sequence of the 16S rRNA gene, showed that strains CA1-15T and BIUV-7T belong to a distinctive clade within the family Sphingomonadaceae (order Sphingomonadales, class Alphaproteobacteria). The strains exhibited the highest similarity in their genetic makeup with representatives of the genus Sphingomonas. Strain CA1-15T was closely related to Sphingomonas echinoides NRRL B-3126T (97.8% similarity in 16S rRNA gene sequence), Sphingomonas oligophenolica JCM 12,082T (97.8%), Sphingomonas glacialis C16yT (97.6%) and Sphingomonas psychrolutea MDB1-AT (97.3%). Strain BIUV-7T was closely related to Sphingomonas nostoxanthinifaciens AK-PDB1-5T (97.0%), Sphingomonas vulcanisoli SN6-13T (96.3%), Sphingomonas naphthae DKC-5-1T (96.2%), and Sphingomonas prati W18RDT (95.7%). The optimal growth conditions for strains CA1-15T and BIUV-7T were determined to be at pH 7.0 and a temperature of 25 °C. Analysis of the cellular fatty acids of strain CA1-15T and BIUV-7T revealed that summed feature 8 (C18:1ω7c/C18:1ω6c) (60.4%), summed feature 8 (C18:1ω7c/C18:1ω6c) (62.9%) were the major component, respectively. Additionally, both strains exhibited ubiquinone Q-10 as their major respiratory quinone, and diphosphatidylglycerol (DPG), glycosphingolipid (SGL), and phosphatidylethanolamine (PE) as the major polar lipid. The genome of strain CA1-15T measures 4,133,944 bp, comprising 4,026 coding sequences (CDSs) and 46 tRNA genes. Similarly, the genome of strain BIUV-7T is 4,563,252 bp, characterized by 4,226 CDSs and 44 tRNA genes. The average nucleotide identity (ANI) analysis and digital DNA-DNA hybridization (dDDH) values between strain CA1-15T and other Sphingomonas species range from 73.2 to 79.9% and 19.4-22.9%, respectively. Comparatively, ANI and dDDH values between strain BIUV-7T and other Sphingomonas species are in the range of 72.9-76.5% and 19.3-20.9%, respectively. Based on the biochemical, chemotaxonomic, and phylogenetic analyses, it is evident that strains CA1-15T and BIUV-7T represent two novel bacterial species within the genus Sphingomonas. Accordingly, the names Sphingomonas immobilis sp. nov. and Sphingomonas natans sp. nov. are proposed. also, CA1-15T(= KCTC 92960T = NBRC 116547T) is the type strain of Sphingomonas immobilis and BIUV-7T(= KCTC 92961T = NBRC 116546T) is the type strain of Sphingomonas natans.

Sphingomonas lycopersici sp. nov., isolated from tomato rhizosphere soil

Two aerobic, Gram-stain-negative, non-motile and non-spore-forming rods bacterial strains, designated MMSM20^T and MMSM24, were isolated from tomato rhizosphere soil and could produce indole-3-acetic acid and siderophore. Phylogenetic analyses based on 16S rRNA gene sequences and 92 core genes showed that strains MMSM20^T and MMSM24 belonged to the genus Sphingomonas and were most closely related to three validly published species Sphingomonas jeddahensis G39^T, Sphingomonas mucosissima DSM 17494^T and Sphingomonas dokdonensis DSM 21029^T. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strains MMSM20^T and MMSM24 were 97.6 and 81.0 %, respectively, demonstrating that they were conspecific. The ANI and dDDH values between the two strains and the three type strains above were below the threshold values for species delimitation. The genomic DNA G+C contents of strains MMSM20^T and MMSM24 were 66.6 and 66.4 mol%, respectively. The major fatty acids of the two strains were identified as C_14 : 0 2OH, summed feature 8 (C_18 : 1  ω7c and/or C_18 : 1  ω6c); the predominant quinone was ubiquinone 10; the polar lipids comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, sphingoglycolipid and unidentified lipids. Results of phenotypic and genotypic analyses supported that strains MMSM20^T and MMSM24 represent a novel species of the genus Sphingomonas, for which the name Sphingomonas lycopersici sp. nov. is proposed. The type strain is MMSM20^T (=GDMCC 1.3401^T=JCM 35647^T).

Valorization of Waste from Argan Seeds for Polyhydroxybutyrate Production Using Bacterial Strains Isolated from Argan Soils

The aim of this work was to study the valorization of argan seed pulp, a waste material obtained from argan oil extraction, for the biosynthesis of polyhydroxybutyrate (PHB). A new species that showed the metabolic capacity for the conversion of argan waste into the bio-based polymer was isolated from an argan crop located in Teroudant, a southwestern region of Morocco, where the arid soil is exploited for goat grazing. The PHB accumulation efficiency of this new species was compared to the previously identified species 1B belonging to the genus Sphingomonas, and results were reported as dry cell weight residual biomass and PHB final yield measured. Temperature, incubation time, pH, NaCl concentration, nitrogen sources, residue concentrations, and culture medium volumes were analyzed with the aim of obtaining a maximum accumulation of PHB. UV-visible spectrophotometry and FTIR analysis confirmed that PHB was present in the material extracted from the bacterial culture. The results of this wide investigation indicated that the new isolated species 2D1 had a higher efficiency in PHB production compared to the previously identified strain 1B, which was isolated from a contaminated argan soil in Teroudant. PHB final yield of the two bacterial species, i.e., the new isolated and 1B, cultivated under optimal culture conditions, in 500 mL MSM enriched with 3% argan waste, were 21.40% (5.91 ± 0.16 g/L) and 8.16% (1.92 ± 0.23 g/L), respectively. For the new isolated strain, the result of the UV-visible spectrum indicates the absorbance at 248 nm, while the FTIR spectrum showed peaks at 1726 cm^-1 and 1270 cm^-1: these characteristic peaks indicated the presence of PHB in the extract. The data from the species 1B UV-visible and FTIR spectra were previously reported and were used in this study for a correlation analysis. Furthermore, additional peaks, uncharacteristic of standard PHB, suggest the presence of impurities (e.g., cell debris, solvent residues, biomass residues) that persisted after extraction. Therefore, a further enhancement of the sample purification during extraction is recommended for more accuracy in the chemical characterization. If 470,000 tons of argan fruit waste can be produced annually, and 3% of waste is consumed in 500 mL culture by 2D1 to produce 5.91 g/L (21.40%) of the bio-based polymer PHB, it can be estimated that the amount of putative PHB that can be extracted annually from the total argan fruit waste is about 2300 tons.

A Novel Sphingomonas sp. Isolated from Argan Soil for the Polyhydroxybutyrate Production from Argan Seeds Waste

Polyhydroxybutyrate (PHB) is a biodegradable bio-based polymer synthesized by microorganisms under unfavorable conditions from agro-industrial residues as a source of carbon. These aspects make the bio-based polymer attractive for the mass production of biodegradable plastics, and a definitive replacement for petroleum-based plastics. The aim of this work was to characterize the putative PHB-producing bacterium 1B isolated from the argan soil, to identify the polymer produced, and quantify the PHB production using argan seeds waste. DNA extraction, PCR, and Sanger sequencing were conducted for the molecular identification of strain 1B; the residual biomass and the PHB quantification were measured and compared in the presence of simple sugars and pretreated argan seeds waste. The 1B growth and PHB synthesis were optimized by selecting physical and nutritional parameters: temperature, incubation time, pH, NaCl concentration, and nitrogen sources concentrations. A preliminary characterization of the bio-based polymer extracted was conducted by UV-Visible spectrophotometry and FTIR analysis. The strain 1B was identified as belonging to the genus Sphingomonas. The PHB final yield was higher in a growth culture enriched with argan waste (3.06%) than with simple sugars. The selected conditions for the bacterial optimal growth incremented the PHB final yield to 6.13%, while the increase in the argan residue concentration from 1 to 3% in a larger culture volume led to the PHB final yield of 8.16%. UV-Visible spectrophotometry of the extracted sample reported a remarkable peak at 248 nm, as well as FTIR spectra analysis, showed peaks at 1728 and 1282 wavenumber/cm. Both preliminary characterizations demonstrated that the extracted sample is the bio-based polymer polyhydroxybutyrate. The results reported in this work reveal how the costless available argan seeds can be used for polyhydroxybutyrate production using a novel Sphingomonas species.

Sphingosinithalassobacter portus gen. nov., sp. nov., a novel member of the family Sphingomonadaceae isolated from surface seawater

A Gram-stain-negative strain, designated FM6^T, was isolated from surface seawater sampled at the port in Xiamen, PR China. Strain FM6^T showed less than 96.3 % 16S rRNA gene sequence similarity to the type strains of species with validly published names. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain FM6^T belonged to the family Sphingomonadaceae and was closely related to species of the genera Sphingomonas (96.3 %) and Stakelama (96.0 %). Ubiquinone-10 was the predominant respiratory quinone. Cells were motile with a single polar flagellum. Growth occurred at temperatures from 20 to 45 °C (optimum, 30 °C), at pH values between pH 6.0 and 8.0 (optimum, pH 7.0) and in 0-4.0 % (w/v) NaCl (optimum, 1.0-1.5 %). Predominant polar lipids were sphingoglycolipid, phosphatidylcholine, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, five unidentified glycolipids and five unidentified polar lipids. The major fatty acids were summed feature 8 (containing C_18 : 1ω7c and/or C_18 : 1ω6c). The DNA G+C content of the type strain was 63.8 mol%. On the basis of the results of phylogenetic analysis, combined with phenotypic and chemotaxonomic data, strain FM6^T is considered to represent a novel species in a new genus in the family Sphingomonadaceae for which the name Sphingosinithalassobacter portus gen. nov., sp. nov. is proposed. The type strain of Sphingosinithalassobacter portus gen. nov., sp. nov. is FM6^T (=MCCC 1K03501^T=JCM 32714^T).

A strategy for securing unique microbial resources – focusing on Dokdo islands-derived microbial resources

This review focuses on the state of research on the microbial resources of Dokdo, Korea, as a strategy for securing national microbial resources. In the Korean peninsula, studies aimed at securing microbial resources are carried out across diverse natural environments, especially in the Dokdo islands. Until 2017, a total of 61 novel microbial genera, species, or newly recorded strains have been reported. Among these, 10 new taxa have had their whole genome sequenced and published, in order to find novel useful genes. Additionally, there have been multiple reports of bacteria with novel characteristics, including promoting plant growth or inducing systemic resistance in plants, calcite-forming ability, electrical activation, and production of novel enzymes. Furthermore, fundamental studies on microbial communities help to secure and define microbial resources in the Dokdo islands. This study will propose several tactics, based on ecological principles, for securing more microbial resources to cope with the current increase in international competition for biological resources.

Sphingomonas jeddahensis sp. nov., isolated from Saudi Arabian desert soil

A novel Sphingomonas strain was isolated from a sample of desert soil collected near Jeddah in Saudi Arabia. A polyphasic approach was performed to characterize this strain, initially designated as G39^T. Cells of strain G39^T are motile, Gram-negative, catalase- and oxidase-positive. The strain is able to grow aerobically at 20-35 °C, pH 6.5-8 and tolerates up to 4 % (w/v) NaCl. Based on 16S rRNA gene sequence similarity, the closest relative type strains of G39^T are Sphingomonas mucosissima DSM 17494^T (98.6 %), S. dokdonensis DSM 21029^T (98.4 %) and S. hankookensis DSM 23329^T (97.4 %). Furthermore, the average nucleotide identities between the draft genome sequence of strain G39^T and the genome sequences of all other available and related Sphingomonas species are significantly below the threshold of 94 %. The G+C content of the draft genome (3.12 Mbp) is 65.84 %. The prevalent (>5 %) cellular fatty acids of G39^T were C18 : 1ω7c, C16 : 1ω7c and/or C16 : 1ω6c, C14 : 0 2-OH and C16 : 0. The only detectable respiratory quinone was ubiquinone-10 and the polar lipids profile is composed of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid, as well as unidentified lipids, phospholipids and glycolipids. The results of the conducted polyphasic approach confirmed that this isolate represents a novel species of the genus Sphingomonas, for which the name Sphingomonas jeddahensis sp. nov. is proposed. The type strain of this species is G39^T (=DSM 103790^T=LMG 29955^T).

Draft Genome Sequences of Sphingomonas mucosissima DSM 17494 and Sphingomonas dokdonensis DSM 21029

Sphingomonas mucosissima and Sphingomonas dokdonensis are Gram-negative chemoheterotrophic strictly aerobic rods or cocci. The genomes (3.453 Mb and 3.587 Mb, respectively) contain 3,279 and 3,329 predicted protein-encoding genes, respectively. The genome of S. dokdonensis harbors a 90-kb plasmid.

Sphingomonas olei sp. nov., with the ability to degrade aliphatic hydrocarbons, isolated from oil-contaminated soil

A yellow-coloured, Gram-stain-negative, non-motile, rod-shaped bacterium, designated K-1-16T, that is capable of degrading aliphatic hydrocarbons was isolated from oil-contaminated soil at Biratnagar, Morang, Nepal. It was able to grow at 15-45 °C, at pH 5.5-9.5 and with 0-5 % (w/v) NaCl. This strain was taxonomically characterized by a polyphasic approach. Based on 16S rRNA gene sequence analysis, strain K-1-16T belongs to the genus Sphingomonas and is closely related to Sphingomonas mucosissima CP173-2T (98.6 % similarity), Sphingomonas dokdonensis DS-4T (97.9 %), Sphingomonas faeni MA-olkiT (97.9 %), Sphingomonas aurantiaca MA101bT (97.8 %) and Sphingomonas xinjiangensis 10-1-84T (96.6 %). The predominant respiratory quinone was ubiquinone Q-10 and the major polyamine was homospermidine. The polar lipid profile revealed the presence of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, phosphatidyldimethylethanolamine and sphingoglycolipid. The predominant fatty acids of strain K-1-16T were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C18 : 1ω7c 11-methyl and C14 : 0 2-OH. The genomic DNA G+C content was 64.8 mol%. Levels of DNA-DNA relatedness between strain K-1-16T and S. mucosissima DSM 17494T, S. dokdonensis KACC 17420T, S. faeni KCCM 41909T and S. aurantiaca KCCM 41908T were 49.7, 41.3, 43.7 and 36.7 %, respectively. The morphological, physiological, chemotaxonomic and phylogenetic analyses clearly distinguished this strain from its closest phylogenetic neighbours. Thus, strain K-1-16T represents a novel species of the genus Sphingomonas, for which the name Sphingomonas olei sp. nov. is proposed. The type strain is K-1-16T (=KEMB 9005-450T=KACC 19002T=JCM 31674T).

Phenol degradation and genotypic analysis of dioxygenase genes in bacteria isolated from sediments

The aerobic degradation of aromatic compounds by bacteria is performed by dioxygenases. To show some characteristic patterns of the dioxygenase genotype and its degradation specificities, twenty-nine gram-negative bacterial cultures were obtained from sediment contaminated with phenolic compounds in Wuhan, China. The isolates were phylogenetically diverse and belonged to 10 genera. All 29 gram-negative bacteria were able to utilize phenol, m-dihydroxybenzene and 2-hydroxybenzoic acid as the sole carbon sources, and members of the three primary genera Pseudomonas, Acinetobacter and Alcaligenes were able to grow in the presence of multiple monoaromatic compounds. PCR and DNA sequence analysis were used to detect dioxygenase genes coding for catechol 1,2-dioxygenase, catechol 2,3-dioxygenase and protocatechuate 3,4-dioxygenase. The results showed that there are 4 genotypes; most strains are either PNP (catechol 1,2-dioxygenase gene is positive, catechol 2,3-dioxygenase gene is negative, protocatechuate 3,4-dioxygenase gene is positive) or PNN (catechol 1,2-dioxygenase gene is positive, catechol 2,3-dioxygenase gene is negative, protocatechuate 3,4-dioxygenase gene is negative). The strains with two dioxygenase genes can usually grow on many more aromatic compounds than strains with one dioxygenase gene. Degradation experiments using a mixed culture representing four bacterial genotypes resulted in the rapid degradation of phenol. Determinations of substrate utilization and phenol degradation revealed their affiliations through dioxygenase genotype data.

Bidet toilet seats with warm-water tanks: residual chlorine, microbial community, and structural analyses

Despite the reported health-related advantages of the use of warm water in bidets, there are health-related disadvantages associated with the use of these toilet seats, and the bacterial research is sparse. We conducted a survey on the hygienic conditions of 127 warm-water bidet toilet seats in restrooms on a university campus. The spray water from the toilet seats had less residual chlorine than their tap water sources. However, the total viable microbial count was below the water-quality standard for tap water. In addition, the heat of the toilet seats' warm-water tanks caused heterotrophic bacteria in the source tap water to proliferate inside the nozzle pipes and the warm-water tanks. Escherichia coli was detected on the spray nozzles of about 5% of the toilet seats, indicating that the self-cleaning mechanism of the spray nozzles was largely functioning properly. However, Pseudomonas aeruginosa was detected on about 2% of the toilet seats. P. aeruginosa was found to remain for long durations in biofilms that formed inside warm-water tanks. Infection-prevention measures aimed at P. aeruginosa should receive full consideration when managing warm-water bidet toilet seats in hospitals in order to prevent opportunistic infections in intensive care units, hematology wards, and other hospital locations.

Taxonomic characterization and the bio-potential of bacteria isolated from glacier ice cores in the High Arctic

Glacier ice and firn cores have ecological and biotechnological importance. The present study is aimed at characterizing bacteria in crustal ice cores from Svalbard, the Arctic. Counts of viable isolates ranged from 10 to 7000 CFU/ml (mean 803 CFU/ml) while the total bacterial numbers ranged from 7.20 × 10(4) to 2.59 × 10(7)  cells ml(-1) (mean 3.12 × 10(6)  cells ml(-1) ). Based on 16S rDNA sequence data, the identified species belonged to seven species, namely Bacillus barbaricus, Pseudomonas orientalis, Pseudomonas oryzihabitans, Pseudomonas fluorescens, Pseudomonas syncyanea, Sphingomonas dokdonensis, and Sphingomonas phyllosphaerae, with a sequence similarity ranging between 93.5 and 99.9% with taxa present in the database. The isolates exhibited unique phenotypic properties, and three isolates (MLB-2, MLB-5, and MLB-9) are novel species, yet to be described. To the best of our knowledge, this is the first report on characterization of cultured bacterial communities from Svalbard ice cores. We conclude that high lipase, protease, cellulase, amylase, and urease activities expressed by most of the isolates provide a clue to the potential industrial applications of these organisms. These microbes, producing cold-adapted enzymes may provide an opportunity for biotechnological research.

Sphingomonas hengshuiensis sp. nov., isolated from lake wetland

A polyphasic taxonomic study was undertaken to establish the status of a novel bacterium, designated strain WHSC-8T, which was isolated from soil of Hengshui Lake Wetland Reserve in Hebei province, northern China. Colonies of this strain were yellow and cells were rod-shaped, polar-flagellated and obligately aerobic, exhibiting negative Gram reaction. The strain was able to grow at 0-1 % (w/v) NaCl, pH 5-10 and 20-35 °C, with optimal growth occurring at pH 7.0 and 28 °C without NaCl. Chemotaxonomic data revealed that strain WHSC-8T possesses ubiquinone Q-10 as the predominant respiratory quinone, C18 : 1ω7c, C16 : 0 and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) as the major fatty acids, and sym-homospermidine as the major polyamine. Sphingomonadaceae-specific sphingoglycolipid was detected in the polar lipid patterns. The G+C content of the genomic DNA was 68.7 mol%. All of the above characters corroborated the assignment of the novel strain to the genus Sphingomonas. Strain WHSC-8T shared less than 97.0 % 16S rRNA gene sequence similarity with the type strains of other species of the genus Sphingomonas, except for Sphingomonas asaccharolytica DSM 10564T (97.5 %). The low DNA-DNA relatedness value and distinct phenotypic and chemotaxonomic characteristics distinguished strain WHSC-8T from closely related species of the genus Sphingomonas. Therefore, strain WHSC-8T represents a novel species of the genus Sphingomonas, for which the name Sphingomonas hengshuiensis sp. nov. is proposed. The type strain is WHSC-8T ( = KCTC 42455T = CCTCC AB 2015265T).

Sphingomonas panaciterrae sp. nov., a plant growth-promoting bacterium isolated from soil of a ginseng field

Strain DCY91(T), a Gram-stain-negative, rod-shaped, aerobic, non-motile bacterium, was isolated from soil of ginseng field in Gyeonggi province, South Korea. Strain DCY91(T) shared the highest 16S rRNA gene sequence similarity with Sphingomonas mucosissima DSM 17494(T) (98.55%), Sphingomonas dokdonensis KACC 17420(T) (98.11%) and Sphingomonas xinjiangensis DSM 26736(T) (96.68%). The strain DCY91(T) was found to able to grow best in trypticase soy agar at 28 °C, at pH 7 and at 0.5 % NaCl. Ubiquinone 10 was identified as the isoprenoid quinone. The major polar lipids were identified as sphingoglycolipid, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine. The major fatty acids of strain DCY91(T) were identified as unsaturated C18:1 ω7c and saturated C16:0. The major polyamine content was sym-homospermidine. The DNA G + C content was determined to be 65.8 mol% (HPLC). After 6 days of incubation, strain DCY91(T) produced 9.64 ± 1.73 and 33.73 ± 4.66 µg/ml indole-3-acetic acid, using media without L-tryptophan and supplemented with L-tryptophan, respectively. Strain DCY91(T) was also weakly solubilized phosphate and produced siderophores. On the basis of the phenotypic characteristics, genotypic analysis and chemotaxonomic characteristics, strain DCY91(T) is considered to represent a novel species of the genus Sphingomonas, for which the name Sphingomonas panaciterrae sp. nov. is proposed. The type strain is DCY91(T) (=KCTC 42346(T) =JCM 30807(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).

Characterization and identification of a chlorine-resistant bacterium, Sphingomonas TS001, from a model drinking water distribution system

This study describes the identification and characterization of a new chlorine resistant bacterium, Sphingomonas TS001, isolated from a model drinking water distribution system. The isolate was identified by 16s rRNA gene analysis and morphological and physiological characteristics. Phylogenetic analysis indicates that TS001 belongs to the genus Sphingomonas. The model distribution system HPC results showed that, when the chlorine residual was greater than 0.7 mg L(-1), 100% of detected heterotrophic bacteria (HPC) was TS001. The bench-scale inactivation efficiency testing showed that this strain was very resistant to chlorine, and 4 mg L(-1) of chlorine with 240 min retention time provided only approximately 5% viability reduction of TS001. In contrast, a 3-log inactivation (99.9%) was obtained for UV fluencies of 40 mJ cm(-2). A high chlorine-resistant and UV sensitive bacterium, Sphingomonas TS001, was documented for the first time.

Novel zeaxanthin-producing bacteria isolated from a radioactive hot spring water

Zeaxanthin is a powerful antioxidant that is widely found in vegetables and fruits. Epidemiological evidences suggest that increasing the consumption of zeaxanthin in the diet is associated with a lower risk of age-related macular degeneration, helps prevent glaucoma and cataracts, and supports normal eye health. Zeaxanthin is a promising nutraceutical with many applications in the feed, food, and pharmaceutical industries. Currently, the commercial production of zeaxanthin is still dependant on synthetic routes with limitation for the biological one. Nevertheless, the biotechnological production of zeaxanthin is emerging due to its safety, potential large-scale production, and consumers' demand and preference for natural additives. Using a rapid screening method based on 16S rRNA gene and effective high-performance liquid chromatography (HPLC)-Diodearray-MS methods for carotenoids' analysis, we isolated effective zeaxanthin-producing bacteria (strain TDMA-5(T) and -16(T)) that belong to the family Sphingobacteriaceae and Sphingomonadaceae, respectively. In this chapter, we provide a detailed description of the HPLC-Diodearray-MS methods used for rapid analysis and identification of the carotenoids produced by both strains. In addition, the polyphasic taxonomic analysis of both novel strains and the description of a novel species and genus are described.

A novel radio-tolerant astaxanthin-producing bacterium reveals a new astaxanthin derivative: astaxanthin dirhamnoside

Astaxanthin is a red ketocarotenoid that exhibits extraordinary health-promoting activities such as antioxidant, anti-inflammatory, antitumor, and immune booster. The recent discovery of the beneficial roles of astaxanthin against many degenerative diseases such as cancers, heart diseases, and exercise-induced fatigue has raised its market demand as a nutraceutical and medicinal ingredient in aquaculture, food, and pharmaceutical industries. To satisfy the growing demand for this high-value nutraceuticals ingredient and consumer interest in natural products, many research efforts are being made to discover novel microbial producers with effective biotechnological production of astaxanthin. Using a rapid screening method based on 16S rRNA gene, and effective HPLC-Diodearray-MS methods for carotenoids analysis, we succeeded to isolate a unique astaxanthin-producing bacterium (strain TDMA-17(T)) that belongs to the family Sphingomonadaceae (Asker et al., Appl Microbiol Biotechnol 77: 383-392, 2007). In this chapter, we provide a detailed description of effective HPLC-Diodearray-MS methods for rapid analysis and identification of the carotenoids produced by strain TDMA-17(T). We also describe the methods of isolation and identification for a novel bacterial carotenoid (astaxanthin derivative), a major carotenoid that is produced by strain TDMA-17(T). Finally, we describe the polyphasic taxonomic analysis of strain TDMA-17(T) and the description of a novel species belonging to genus Sphingomonas.

Sphingomonas oryziterrae sp. nov. and Sphingomonas jinjuensis sp. nov. isolated from rhizosphere soil of rice (Oryza sativa L.)

Two Gram-reaction-negative, yellow–orange-pigmented, rod-shaped bacterial strains, designated YC6722T and YC6723T, were isolated from rhizosphere soil samples collected from rice fields in Jinju, Korea. Strains YC6722T and YC6723T grew optimally at 25–30 °C and at pH 7.0–8.5. Phylogenetic analyses of 16S rRNA gene sequences showed that strain YC6722T was most closely related to Sphingomonas jaspsi TDMA-16T (96.6 % sequence similarity) and strain YC6723T was related most closely to Sphingomonas aquatilis JSS7T (96.9 %). The two strains contained ubiquinone-10 (Q-10) as the major respiratory quinone system and sym-homospermidine as the major polyamine. The G+C contents of the genomic DNA of strains YC6722T and YC6723T were 63.3 and 61.0 mol%, respectively. The major fatty acid was C18 : 1ω7c. The polar lipids detected in the two strains were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, sphingoglycolipid, phosphatidyldimethylethanolamine and other unknown lipids. On the basis of their phylogenetic positions, and their biochemical and phenotypic characteristics, strains YC6722T and YC6723T represent two novel species of the genus Sphingomonas, for which the names Sphingomonas oryziterrae sp. nov. ( = KCTC 22476T  = DSM 21455T) and Sphingomonas jinjuensis sp. nov. (KCTC 22477T  = DSM 21457T) are proposed.

Sphingomonas xinjiangensis sp. nov., isolated from desert sand

A Gram-negative, aerobic, motile, Sphingomonas-like rod, strain 10-1-84(T), was isolated from a sand sample collected from the desert of Xinjiang, China. The isolate contained Q-10 as the predominant ubiquinone and C(18 : 1)ω7c, C(16 : 0), C(16 : 1)ω7c and C(14 : 0) 2-OH as the major fatty acids. The polyamine pattern contained predominantly sym-homospermidine. The main polar lipids were sphingoglycolipid, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidyldimethylethanolamine and an unknown polar lipid. The DNA G+C content was 63.3 mol%. 16S rRNA gene sequence similarity between strain 10-1-84(T) and the type strains of species of the genus Sphingomonas ranged from 91.11 to 96.54 %. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain 10-1-84(T) belonged to the genus Sphingomonas. On the basis of phylogenetic analysis and physiological and biochemical characterization, strain 10-1-84(T) represents a novel species of the genus Sphingomonas, for which the name Sphingomonas xinjiangensis sp. nov. is proposed. The type strain is 10-1-84(T) ( = CCTCC AB 208035(T)  = NRRL B-51332(T)).

Sphingomonas changbaiensis sp. nov., isolated from forest soil

Bacterial strain V2M44Twas isolated from forest soil from the Changbai Mountains, Heilongjiang Province, China. Cells of strain V2M44Twere Gram-negative, rod-shaped and 0.3–0.4 μm in diameter and 1.5–2.5 μm long. The cells were strictly aerobic and were motile by means of peritrichous flagella. Growth occurred at 20–33 °C (optimum, 29–31 °C), at pH 5–8 (optimum, pH 6.0–7.0) and in the presence of 0−0.1 % (w/v) NaCl (optimum, 0.05 %). Strain V2M44Tcontained C17 : 1ω6c(38.9 %) and summed feature 7 (comprising C18 : 1ω7c, C18 : 1ω9tand/or C18 : 1ω12t, 31.5 %) as the major cellular fatty acids and Q-10 as the major respiratory quinone. The major polar lipids were sphingoglycolipid, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol along with two unidentified phospholipids and four unidentified glycolipids. The major component in the polyamine pattern wassym-homospermidine. The DNA G+C content was 65.8 mol%. Analysis of 16S rRNA gene sequences indicated that strain V2M44Twas phylogenetically related to members of the genusSphingomonas, with sequence similarities ranging from 92.0–95.8 %. Based on these results, it is concluded that strain V2M44Trepresents a novel species of the genusSphingomonas, for which the nameSphingomonas changbaiensissp. nov. is proposed. The type strain is V2M44T(=CGMCC 1.7057T=NBRC 104936T).

Sphingomonas sanxanigenens sp. nov., isolated from soil

Strain NX02(T), a Gram-negative, non-spore-forming, rod-shaped bacterium, was isolated from soil, and its taxonomic position was investigated using a polyphasic approach. Chemotaxonomic analysis revealed that strain NX02(T) possessed Q-10 as the predominant ubiquinone, sym-homospermidine as the major polyamine and C(18 : 1)omega7c, C(16 : 0) and C(14 : 0) 2-OH as the major fatty acids. The main polar lipids were sphingoglycolipid, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine and an unidentified glycolipid. The DNA G+C content was 66.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain NX02(T) belongs to the alpha-4 subgroup of the Proteobacteria, exhibiting the highest sequence similarity with respect to Sphingomonas azotifigens NBRC 15497(T) (95.9 %), Sphingomonas pituitosa DSM 13101(T) (95.8 %) and Sphingomonas dokdonensis KCTC 12541(T) (95.8 %). On the basis of these results, strain NX02(T) represents a novel species of the genus Sphingomonas sensu stricto, for which the name Sphingomonas sanxanigenens sp. nov. is proposed. The type strain is NX02(T) (=DSM 19645(T) =CGMCC 1.6417(T)).

Novel methylotrophic bacteria isolated from the River Thames (London, UK)

Enrichment and elective culture for methylotrophs from sediment of the River Thames in central London yielded a diversity of pure cultures representing several genera of Gram-negative and Gram-positive bacteria, which were mainly of organisms not generally regarded as typically methylotrophic. Substrates leading to successful isolations included methanol, monomethylamine, dimethylamine, trimethylamine, methanesulfonate and dimethylsulfone. Several isolates were studied in detail and shown by their biochemical and morphological properties and 16S rRNA gene sequencing to be Sphingomonas melonis strain ET35, Mycobacterium fluoranthenivorans strain DSQ3, Rhodococcus erythropolis strain DSQ4, Brevibacterium casei strain MSQ5, Klebsiella oxytoca strains MMA/F and MMA/1, Pseudomonas mendocina strain TSQ4, and Flavobacterium sp. strains MSA/1 and MMA/2. The results show that facultative methylotrophy is present across a wide range of Bacteria, suggesting that turnover of diverse C(1)-compounds is of much greater microbiological and environmental significance than is generally thought. The origins of the genes encoding the enzymes of methylotrophy in diverse heterotrophs need further study, and could further our understanding of the phylogeny and antiquity of methylotrophic systems.

Sphingomonas mucosissima sp. nov. and Sphingomonas desiccabilis sp. nov., from biological soil crusts in the Colorado Plateau, USA

Two bacterial strains, CP173-2(T) and CP1D(T), were isolated from biological soil crusts (BSCs) collected in the Colorado Plateau, USA. Both strains were pigmented, Gram-negative, non-motile rods and produced abundant mucus. They contained C(16 : 0), C(18 : 1)omega7c and C(14 : 0) 2-OH as the predominant cellular fatty acids, ubiquinone-10 as the isoprenoid quinone and sphingoglycolipid. Based on the above characteristics, the isolates were assigned to the family Sphingomonadaceae; 16 rRNA gene signature nucleotides placed them within the genus Sphingomonas. Strains CP173-2(T) and CP1D(T) had a 16S rRNA gene sequence similarity of 96.7 % with each other and 91.6-98.9 % sequence similarity with other species in the genus, indicating that they represent two separate, and possibly novel, species. The closest species to strains CP173-2(T) and CP1D(T) were, respectively, Sphingomonas dokdonensis (98.9 % gene sequence similarity) and Sphingomonas panni (97.9 %). However, strain CP173-2(T) exhibited a DNA-DNA relatedness of only 32.5 % with the type strain of S. dokdonensis. Similarly, the DNA-DNA relatedness between strain CP1D(T) and the type strain of S. panni was only 18 %. Phenotypic characterization supported this low relatedness. On the basis of this evidence, we propose that the new strains represent two novel species, for which the names Sphingomonas mucosissima sp. nov. (with type strain CP173-2(T)=ATCC BAA-1239(T)=DSM 17494(T)) and Sphingomonas desiccabilis sp. nov. (with type strain CP1D(T)=ATCC BAA-1041(T)=DSM 16792(T)) are proposed.

Sphingomonas jaspsi sp. nov., a novel carotenoid-producing bacterium isolated from Misasa, Tottori, Japan

A yellow-pigmented, Gram-negative, motile, strictly aerobic, pleomorphic bacterium (strain TDMA-16T) was isolated from a freshwater sample collected at Misasa (Tottori, Japan). Strain TDMA-16T was slightly tolerant to gamma-ray irradiation and produced carotenoids, including zeaxanthin, nostoxanthin and an unknown carotenoid, effectively [1.7 mg (g dry cells)−1]. The DNA G+C content of strain TDMA-16T was 63.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences placed strain TDMA-16T in a distinct lineage in the family Sphingomonadaceae; sequence data showed that strain TDMA-16T was most closely related to Sphingomonas mali IFO 15500T (95.1 %), Sphingomonas aquatilis JSS7T (95.0 %), Sphingomonas pruni IFO 15498T (94.9 %), Sphingomonas melonis DSM 14444T (94.9 %) and Sphingomonas asaccharolytica IFO 15499T (94.5 %). The major fatty acids of strain TDMA-16T were C17 : 1 ω6c (34.5 %) and C18 : 1 ω7c (29.3 %). The presence of Q-10 as the main ubiquinone, the Sphingomonadaceae-specific sphingoglycolipid in the polar lipid profile and 2-hydroxy fatty acids, plus the absence of 3-hydroxy fatty acids, supported identification of this strain as a member of the genus Sphingomonas sensu stricto. Phylogenetic distinctiveness and unique phenotypic characteristics differentiated strain TDMA-16T from closely related Sphingomonas species. The results of polyphasic taxonomic analyses suggest that strain TDMA-16T represents a novel Sphingomonas species, for which the name Sphingomonas jaspsi sp. nov. is proposed. The type strain is strain TDMA-16T (=NBRC 102120T=DSM 18422T=CCUG 53607T).

Sphingomonas pseudosanguinis sp. nov., isolated from the water reservoir of an air humidifier

A yellow-pigmented bacterial isolate, strain G1-2T, obtained from the surface of an air humidifier, was characterized taxonomically. 16S rRNA gene sequence analysis, physiological characterization and estimation of the ubiquinone and polar lipid patterns and fatty acid composition revealed that strain G1-2T was similar to Sphingomonas yabuuchiae and Sphingomonas sanguinis, but also showed pronounced differences. On the basis of these results, a novel species of the genus Sphingomonas is described, for which the name Sphingomonas pseudosanguinis sp. nov. is proposed. The type strain is G1-2T (=CCUG 54232T=CIP 109431T).

Sphingomonas molluscorum sp. nov., a novel marine isolate with antimicrobial activity

An aerobic, Gram-negative, yellow-pigmented, non-motile bacterium, designated strain KMM 3882T, was isolated from a marine bivalve (Anadara broughtoni) collected from Peter the Great Bay, Sea of Japan, and was subjected to phenotypic and phylogenetic analyses. Strain KMM 3882T was found to exert a remarkable inhibitory activity against a number of Gram-positive micro-organisms. Phylogenetic analysis based on 16S rRNA gene sequences placed strain KMM 3882T within the genus Sphingomonas, as an independent lineage adjacent to Sphingomonas dokdonensis DS-4T and Sphingomonas panni DSM 15761T. Strain KMM 3882T showed the highest 16S rRNA gene sequence similarity to Sphingomonas dokdonensis DS-4T (97.3 %); similarities of 96.5–96.7 % were obtained with Sphingomonas pituitosa DSM 13101T, Sphingomonas azotifigens NBRC 15497T, Sphingomonas asaccharolytica NBRC 15499T, Sphingomonas trueperi DSM 7225T and Sphingomonas panni DSM 15761T. Chemotaxonomically, strain KMM 3882T contained sphingoglycolipid, C16 : 0 and C18 : 1 as predominant fatty acids and 2-OH C14 : 0 as a major 2-hydroxy fatty acid, confirming the affiliation of strain KMM 3882T with the genus Sphingomonas. On the basis of phylogenetic analysis, DNA–DNA hybridization and physiological and biochemical characterization, strain KMM 3882T should be classified as representing a novel species of the genus Sphingomonas, for which the name Sphingomonas molluscorum sp. nov. is proposed. The type strain is KMM 3882T (=An 18T=NRIC 0685T=JCM 14122T=CIP 109223T).