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For microbes and their hosts, sensing of external cues is essential for their survival. For example, in the case of plant associated microbes, the light absorbing pigment composition of the plant as well as the ambient light conditions determine the well-being of the microbe. In addition to light sensing, some microbes can utilize xanthorhodopsin based proton pumps and bacterial photosynthetic complexes that work in parallel for energy production. They are called dual phototrophic systems. Light sensing requirements in these type of systems are obviously demanding. In nature, the photosensing machinery follows mainly the same composition in all organisms. However, the specific role of each photosensor in specific light conditions is elusive. In this study, we provide an overall picture of photosensors present in dual phototrophic systems. We compare the genomes of the photosensor proteins from dual phototrophs to those from similar microbes with "single" phototrophicity or microbes without phototrophicity. We find that the dual phototrophic bacteria obtain a larger variety of photosensors than their light inactive counterparts. Their rich domain composition and functional repertoire remains similar across all microbial photosensors. Our study calls further investigations of this particular group of bacteria. This includes protein specific biophysical characterization in vitro, microbiological studies, as well as clarification of the ecological meaning of their host microbial interactions., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

In an ongoing microbial tracking investigation of the International Space Station (ISS), several Sphingomonas strains were isolated. Based on the 16S rRNA gene sequence, phylogenetic analysis identified the ISS strains as Sphingomonas sanguinis ( n  = 2) and one strain isolated from the Kennedy Space Center cleanroom (used to assemble various Mars mission spacecraft components) as Sphingomonas paucimobilis. Metagenomic sequence analyses of different ISS locations identified 23 Sphingomonas species. An abundance of shotgun metagenomic reads were detected for S. sanguinis in the location from where the ISS strains were isolated. A complete metagenome-assembled genome was generated from the shotgun reads metagenome, and its comparison with the whole-genome sequences (WGS) of the ISS S. sanguinis isolates revealed that they were highly similar. In addition to the phylogeny, the WGS of these Sphingomonas strains were compared with the WGS of the type strains to elucidate genes that can potentially aid in plant growth promotion. Furthermore, the WGS comparison of these strains with the well-characterized Sphingomonas sp. LK11, an arid desert strain, identified several genes responsible for the production of phytohormones and for stress tolerance. Production of one of the phytohormones, indole-3-acetic acid, was further confirmed in the ISS strains using liquid chromatography-mass spectrometry. Pathways associated with phosphate uptake, metabolism, and solubilization in soil were conserved across all the S. sanguinis and S. paucimobilis strains tested. Furthermore, genes thought to promote plant resistance to abiotic stress, including heat/cold shock response, heavy metal resistance, and oxidative and osmotic stress resistance, appear to be present in these space-related S. sanguinis and S. paucimobilis strains. Characterizing these biotechnologically important microorganisms found on the ISS and harnessing their key features will aid in the development of self-sustainable long-term space missions in the future. IMPORTANCE Sphingomonas is ubiquitous in nature, including the anthropogenically contaminated extreme environments. Members of the Sphingomonas genus have been identified as potential candidates for space biomining beyond earth. This study describes the isolation and identification of Sphingomonas members from the ISS, which are capable of producing the phytohormone indole-3-acetic acid. Microbial production of phytohormones will help future in situ studies, grow plants beyond low earth orbit, and establish self-sustainable life support systems. Beyond phytohormone production, stable genomic elements of abiotic stress resistance, heavy metal resistance, and oxidative and osmotic stress resistance were identified, rendering the ISS Sphingomonas isolate a strong candidate for biotechnology-related applications.

Sphingomonas sp. Shah is a bacterium that was first isolated from mammalian cell cultures. According to ribotyping data it is very much homologous to the clinically important pathogen Sphingomonas paucimobilis, which has generated pseudo-outbreaks. Using a tissue culture system, Sphingomonas sp. Shah was discovered to induce apoptosis in human lung epithelial carcinoma. Apoptosis of infected cells was determined by numerous criteria including (1) visual alterations in cellular morphology, (2) initiation of nuclear marginalization and chromatin compaction condensation, (3) the attendance of a high percentage of cells with subG1 DNA content, and (4) caspase-3 activation. In the current study we demonstrate the induction of apoptosis in mammalian lung epithelial cells upon infection with Sphingomonas sp. Shah and provide insight into the molecular processes triggering apoptosis.

Alphaproteobacteria belonging to the group of the sphingomonads are frequently found in biofilms colonizing pure-water systems, where they cause technical and hygienic problems. In this study, physiological properties of sphingomonads for biofilm formation on plastic surfaces were analysed. Sphingomonas sp. strain S2M10 was isolated from a used water-filtration membrane and submitted to transposon mutagenesis for isolating mutants with altered biofilm formation. Mutants showing strongly decreased biofilm formation carried transposon insertions in genes for the biosynthesis of the polysaccharide sphingan and for flagellar motility. Flagella-mediated attachment was apparently important for biofilm formation on plastic materials of intermediate hydrophobicity, while a mutant with defect in spnB , encoding the first enzyme in sphingan biosynthesis, showed no biofilm formation on all tested materials. Sphingan-dependent biofilm formation was induced in the presence of specific carbon sources while it was not induced in complex medium with yeast extract and tryptone. The regulation of sphingan-based biofilm formation was investigated by interfering with the CckA/ChpT/CtrA phosphorelay, a central signal-transduction pathway in most Alphaproteobacteria. Construction and ectopic expression of a kinase-deficient histidine kinase CckA caused cell elongation and massive sphingan-dependent cell aggregation. In addition, it caused increased activity of the promotor of spnB . In conclusion, these results indicate that sphingan-based biofilm formation by sphingomonads might be triggered by specific carbon sources under prototrophic conditions resembling a milieu that often prevails in pure-water systems.

Plant growth-promoting rhizobacteria play vital roles not only in plant growth, but also in reducing biotic/abiotic stress. Sphingomonas panacis DCY99 T is isolated from soil and root of Panax ginseng with rusty root disease, characterized by raised reddish-brown root and this is seriously affects ginseng cultivation. To investigate the relationship between 159 sequenced Sphingomonas strains, pan-genome analysis was carried out, which suggested genomic diversity of the Sphingomonas genus. Comparative analysis of S. panacis DCY99 T with Sphingomonas sp. LK11 revealed plant growth-promoting potential of S. panacis DCY99 T through indole acetic acid production, phosphate solubilizing, and antifungal abilities. Detailed genomic analysis has shown that S. panacis DCY99 T contain various heavy metals resistance genes in its genome and the plasmid. Functional analysis with Sphingomonas paucimobilis EPA505 predicted that S. panacis DCY99 T possess genes for degradation of polyaromatic hydrocarbon and phenolic compounds in rusty-ginseng root. Interestingly, when primed ginseng with S . panacis DCY99 T during high concentration of iron exposure, iron stress of ginseng was suppressed. In order to detect S. panacis DCY99 T in soil, biomarker was designed using spt gene. This study brings new insights into the role of S . panacis DCY99 T as a microbial inoculant to protect ginseng plants against rusty root disease.

The species belonging to the Sphingomonas genus possess multifaceted functions ranging from remediation of environmental contaminations to producing highly beneficial phytohormones, such as sphingan and gellan gum. Recent studies have shown an intriguing role of Sphingomonas species in the degradation of organometallic compounds. However, the actual biotechnological potential of this genus requires further assessment. Some of the species from the genus have also been noted to improve plant-growth during stress conditions such as drought, salinity, and heavy metals in agricultural soil. This role has been attributed to their potential to produce plant growth hormones e.g. gibberellins and indole acetic acid. However, the current literature is scattered, and some of the important areas, such as taxonomy, phylogenetics, genome mapping, and cellular transport systems, are still being overlooked in terms of elucidation of the mechanisms behind stress-tolerance and bioremediation. In this review, we elucidated the prospective role and function of this genus for improved utilization during environmental biotechnology.

Background: Microbes isolated from hyperaccumulating plants have been reported to be effective in achieving higher phytoextraction efficiency. The plant growth-promoting bacteria (PGPB) SaMR12 from the cadmium (Cd)/zinc hyperaccumulator Sedum alfredii Hance could promote the growth of a non-host plant, oilseed rape, under Cd stress. However, the effect of SaMR12 on Brasscia juncea antioxidative response under Cd exposure was still unclear., Results: A hydroponic experiment was conducted to study the effects of Sphingomonas SaMR12 on its non-host plant Brassica juncea (L.) Czern. under four different Cd treatments. The results showed that SaMR12 could colonize and aggregate in the roots and then move to the shoots. SaMR12 inoculation promoted plant growth by up to 71% in aboveground biomass and 81% in root biomass over that of the non-inoculated plants. SaMR12-inoculated plants significantly enhanced root Cd accumulation in the 10 and 20 μM Cd treatments, with 1.72- and 0.86-fold increases, respectively, over that of the non-inoculated plants. SaMR12 inoculation not only decreased shoot hydrogen peroxide (H 2 O 2 ) content by up to 38% and malondialdehyde (MDA) content by up to 60% but also reduced proline content by 7-30% in shoots and 17-32% in roots compared to the levels in non-inoculated plants. Additionally, SaMR12 inoculation promoted the activities of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX) and facilitated the relative gene expression levels of dehydroascorbate reductase (DHAR) and glutathione reductase (GR) involved in the glutathione (GSH)-ascorbic acid (AsA) cycle., Conclusions: The results demonstrated that, under Cd stress, SaMR12 inoculation could activate the antioxidative response of B. juncea by decreasing the concentrations of H 2 O 2 , MDA and proline, increasing the activities of antioxidative enzymes, and regulating the GSH-AsA cycle. These results provide a theoretical foundation for the potential application of hyperaccumulator endophytic bacteria as remediating agents to improve heavy metal tolerance within non-host plant species, which could further improve phytoextraction efficiency.

The general stress response (GSR) represents an important trait to survive in the environment by leading to multiple stress resistance. In alphaproteobacteria, the GSR is under the transcriptional control of the alternative sigma factor EcfG. Here we performed transcriptome analyses to investigate the genes controlled by EcfG of Sphingomonas melonis Fr1 and the plasticity of this regulation under stress conditions. We found that EcfG regulates genes for proteins that are typically associated with stress responses. Moreover, EcfG controls regulatory proteins, which likely fine-tune the GSR. Among these, we identified a novel negative GSR feedback regulator, termed NepR2, on the basis of gene reporter assays, phenotypic analyses, and biochemical assays. Transcriptional profiling of signaling components upstream of EcfG under complex stress conditions showed an overall congruence with EcfG-regulated genes. Interestingly however, we found that the GSR is transcriptionally linked to the regulation of motility and biofilm formation via the single domain response regulator SdrG and GSR-activating histidine kinases. Altogether, our findings indicate that the GSR in S. melonis Fr1 underlies a complex regulation to optimize resource allocation and resilience in stressful and changing environments.

Among the plethora of unusual secondary metabolites isolated from Stachylidium bicolor are the tetrapeptidic endolides A and B. Both tetrapeptides contain 3-(3-furyl)-alanine residues, previously proposed to originate from bacterial metabolism. Inspired by this observation, we aimed to identify the presence of endosymbiotic bacteria in S. bicolor and to discover the true producer of the endolides. The endobacterium Burkholderia contaminans was initially detected by 16S rRNA gene amplicon sequencing from the fungal metagenome and was subsequently isolated. It was confirmed that the tetrapeptides were produced by the axenic B. contaminans only when in latency. Fungal colonies unable to produce conidia and the tetrapeptides were isolated and confirmed to be free of B. contaminans A second endosymbiont identified as related to Sphingomonas leidyi was also isolated. In situ imaging of the mycelium supported an endosymbiotic relationship between S. bicolor and the two endobacteria. Besides the technical novelty, our in situ analyses revealed that the two endobacteria are compartmentalized in defined fungal cells, prevailing mostly in latency when in symbiosis. Within the emerging field of intracellular bacterial symbioses, fungi are the least studied eukaryotic hosts. Our study further supports the Fungi as a valuable model for understanding endobacterial symbioses in eukaryotes. IMPORTANCE The discovery of two bacterial endosymbionts harbored in Stachylidium bicolor mycelium, Burkholderia contaminans and Sphingomonas leidyi , is described here. Production of tetrapeptides inside the mycelium is ensured by B. contaminans , and fungal sporulation is influenced by the endosymbionts. Here, we illustrate the bacterial endosymbiotic origin of secondary metabolites in an Ascomycota host., (Copyright © 2018 American Society for Microbiology.)

Sphingomonas paucimobilis, an oligotroph, is well recognized for its potential for biofilm formation. The present study explored the biofilm forming ability of a strain isolated from municipal drinking water on plumbing materials. The intensity of biofilm formation of this strain on different plumbing materials was examined by using 1 × 1 cm 2 pieces of six different pipe materials, i.e. polyvinyl chloride (PVC), polypropylene (PP), polyethylene (PE), aluminium (Al), copper (Cu) and rubber (R) and observing by staining with the chemical chromophore, Calcofluor. To understand whether biofilm formation occurs under flow through conditions, a laboratory-scale simulated distribution system, comprised of the above materials was fabricated. Biofilm samples were collected from the designed system at different biofilm ages (10, 40 and 90 hours old) and enumerated. The results indicated that the biofilm formation occurred on all plumbing materials with Cu and R as exceptions. The intensity of biofilm formation was found to be maximum on PVC followed by PP and PE. We also demonstrated the chemical chromophore (Calcofluor) successfully for rapid and easy visual detection of biofilms, validated by scanning electron microscope (SEM) analysis of the plumbing materials. Chlorination has little effect in preventing biofilm development.

Pesticide-polluted drinking water may be remediated by inoculating waterworks sand filters with specific degrading bacteria. However, degradation efficiency is often hampered by the poor adhesion behaviour of the introduced bacteria. The phenoxy acid herbicide 4-chloro-2-methyl-phenoxy-acetic acid (MCPA) is a widespread groundwater contaminant. The aim of this study was to investigate whether specific surface characteristics of MCPA-degrading bacteria could be linked to their degrading capabilities in sand filters. Four MCPA degraders with different taxonomic affiliations and original habitats (Sphingomonas sp. PM2, Sphingomonas sp. ERG5, Burkholderia sp. TFD34, Cupriavidus sp. TFD38) were characterised with regard to their motility, cell surface hydrophobicity, biofilm formation, adhesion behaviour and ability to mineralise MCPA. Strains PM2 and ERG5 were non-motile and hydrophobic, whilst strains TFD34 and TFD38 were motile and less hydrophobic. All the strains except ERG5 showed low biofilm formation on polystyrene, although it was significantly higher on glass. PM2 was the most efficient MCPA degrader as it displayed no lag phase and reached >50 % mineralisation at all concentrations (0.0016-25 mg L -1 ). PM2 adhered significantly better to sand than the other strains. No link was found between motility, biofilm formation and the ability to adhere to sand. PM2 completely removed MCPA for 14 days when inoculated in sand columns with a constant inlet of 1 mg L -1 MCPA. These results demonstrate that besides the ability to degrade the contaminant, surface hydrophobicity and adherence abilities are significant parameters controlling sustained degradation in flow-through sand columns and must be considered when selecting bacteria for bioaugmentation.

Hot water sanitization is a common means to maintain microbial control in process equipment for industries where microorganisms can degrade product or cause safety issues. This study compared the hot water inactivation kinetics of planktonic and biofilm-associated Sphingomonas parapaucimobilis at temperatures relevant to sanitization processes used in the pharmaceutical industry, viz. 65, 70, 75, and 80°C. Biofilms exhibited greater resistance to hot water than the planktonic cells. Both linear and nonlinear statistical models were developed to predict the log reduction as a function of temperature and time. Nonlinear Michaelis-Menten modeling provided the best fit for the inactivation data. Using the model, predictions were calculated to determine the times at which specific log reductions are achieved. While ≥80°C is the most commonly cited temperature for hot water sanitization, the predictive modeling suggests that temperatures ≥75°C are also effective at inactivating planktonic and biofilm bacteria in timeframes appropriate for the pharmaceutical industry.

Background: Ortho-phenylphenol (OPP) is a fungicide used in fruit packaging plants for the control of fungal infestations during storage. Its application leads to the production of large wastewater volumes which according to the European legislation should be treated on site. In spite of this, no efficient treatment systems are currently available, and the development of biological systems based on tailored-made pesticide-degrading inocula for the treatment of these wastewaters is an appealing solution., Results: Enrichment cultures from a soil collected from a wastewater disposal site resulted in the isolation of a pure Sphingomonas haloaromaticamans strain P3 able to degrade rapidly OPP and use it as an energy source. Its degrading capacity was dependent on the external supply of amino acids or on the presence of other bacteria that did not contribute to fungicide degradation. The isolated S. haloaromaticamans strain was able to metabolise up to 150 mg L(-1) of OPP within 7 days, in a wide range of pH (4.5-9) and temperatures (4-37 °C), and in the presence of other pesticides (thiabendazole and diphenylamine) co-used in the fruit packaging industry., Conclusion: Overall, the OPP-degrading bacterium isolated showed high potential for use in future biodepuration treatment systems and bioremediation strategies., (© 2015 Society of Chemical Industry.)

A Gram-negative, rod-shaped, non-motile, non-spore forming, aerobic, orange-pigmented bacterium, designated strain 6P(T), was isolated from a soil sample collected from the Hoh Xil basin, China. Strain 6P(T) grew optimally at 25 °C, pH 7.0-7.5 and NaCl concentration of 0-1 % (w/v). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 6P(T) belongs to the genus Sphingomonas, with high sequence similarity (97.1 %) to Sphingomonas fennica. The DNA-DNA hybridization homology with S. fennica DSM 13665(T) was 45.3 %. The DNA G+C content of the novel strain is 65.3 mol%. The isolate contained Q-10 as the only respiratory quinone. The major polar lipids are diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC) and sphingoglycolipid (SGL). C18:1 ω7c and C16:1 ω7c are the major fatty acids. On the basis of the polyphasic evidence presented, strain 6P(T) represents a novel species of the genus Sphingomonas, for which the name Sphingomonas arantia sp. nov. is proposed. The type strain is 6P(T) (=CGMCC 1.12702(T) = JCM 19855(T)).

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)).

The type strain DCY99(T) was isolated from soil collected from a ginseng field in Hwacheon, Republic of Korea. Strain DCY99(T) is Gram-negative, non-spore forming, motile, rod-shaped, and strictly aerobic. The bacteria grow optimally at 25-30 °C and pH 6.0-6.5. Phylogenetically, strain DCY99(T) is most closely related to Sphingomonas oligophenolica JCM 12082(T), followed by Sphingomonas asaccharolytica KCTC 2825(T), Sphingomonas mali KCTC 2826(T), Sphingomonas cynarae JCM17498(T), Sphingomonas pruni KCTC 2824(T), and Sphingomonas glacialis DSM 22294(T). The DNA-DNA relatedness between strain DCY99(T) and S. oligophenolica JCM 12082(T) was 15.6 ± 0.4 %, and the DNA G+C content of strain DCY99(T) was 64.4 mol%. An isoprenoid quinone was detected and identified as ubiquinone Q-10, and sym-homospermidine was identified as the major polyamine of DCY99(T). The major polar lipids were identified as sphingoglycolipid, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, and phosphatidylcholine. C14:02OH, C16:0, and summed feature 8 (C18:1 ω7c:/C18:1 ω6c) were identified as the major fatty acids present in DCY99(T). The results of physiological and biochemical tests allowed strain DCY99(T) to be differentiated phenotypically from other recognized species belonging to the genus Sphingomonas. Therefore, it is suggested that the newly isolated organism represents a novel species, for which the name Sphingomonas panacis sp. nov. is proposed with the type strain designated as DCY99(T) (=JCM 30806(T) =KCTC 42347(T)).

The CckA-ChpT-CtrA phosphorelay is central to the regulation of the cell cycle in Caulobacter crescentus. The three proteins are conserved in Alphaproteobacteria, but little is known about their roles in most members of this class. Here, we characterized the system in Sphingomonas melonis. We found that the transcription factor CtrA is the master regulator of flagella synthesis genes, the hierarchical transcriptional organization of which is herein described. CtrA also regulates genes involved in exopolysaccharide synthesis and cyclic-di-GMP signaling, and is important for biofilm formation. In addition, the ctrA mutant exhibits an aberrant morphology, suggesting a role for CtrA in cell division. An analysis of the regulation of CtrA indicates that the phosphorelay composed of CckA and ChpT is conserved and that the absence of the bifunctional kinase/phosphatase CckA apparently results in overactivation of CtrA through ChpT. Suppressors of this phenotype identified the hybrid histidine kinase CcsA. Phosphorelays initiated by CckA or CcsA were reconstituted in vitro, suggesting that in S. melonis, CtrA phosphorylation is controlled by a branched pathway upstream of ChpT. This study thus suggests that signals can directly converge at the level of ChpT phosphorylation through multiple hybrid kinases to coordinate a number of important physiological processes., (© 2015 John Wiley & Sons Ltd.)

A proteobacterial strain designated R1-3(T) was isolated from indoor air of a pharmaceutical environment. Cells were Gram-stain-negative, oxidase- and catalase-positive, aerobic, motile and rod-shaped. Strain R1-3(T) grew optimally at pH 7, 30 °C and in 0-2 % NaCl on R2A agar. The 16S rRNA gene sequence analysis indicated that strain R1-3(T) belongs to the genus Sphingomonas, and is closely related to Sphingomonas paucimobilis ATCC 29837(T) (98.4 % sequence similarity). However, the DNA-DNA relatedness between the two strains was 43 ± 5 % (reciprocal = 37 ± 3 %), which was well below the suggested level for species distinction. Sphingomonas yabuuchiae GTC868(T) (97.7 % 16S rRNA gene sequence similarity) and Sphingomonas pseudosanguinis G1-2(T) (97.6 %) were also found as distantly related taxa. Strain R1-3(T) was sensitive to most of the tested antibiotics except for erythromycin and streptomycin. The major fatty acid was a summed feature consisting of C18:1 ω7c and/or C18:1 ω6c, and minor proportions of C14:0 2-OH, C16:0 and a summed feature consisting of C16:1 ω7c and/or C16:1 ω6c were also present. The DNA G + C content was 67.2 ± 1.0 mol%. The major polyamines were sym-homospermidine and spermidine. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, and minor amounts of a sphingoglycolipid, a phospholipid, an aminoglycolipid and an unidentified lipid were also present. The phenotypic, phylogenetic and chemotaxonomic data not only supported the affiliation of strain R1-3(T) to the genus Sphingomonas, but also distinguished R1-3(T) from related species. On the basis of physiological, chemotaxonomic and phylogenetic evidences, strain R1-3(T) clearly merits recognition as a novel species of Sphingomonas, for which the name Sphingomonas aeria sp. nov. is proposed. The type strain is R1-3(T) (= KCTC 42061(T) = JCM 19859(T)).

In the present study, we investigate the possible contribution of Sphingomonas spp. glycosphingolipids (GSL) and its extracellular polymeric substances (EPS) to the initial colonization and development of biofilm bodies on reverse osmosis (RO) membranes. A combination of an RO cross-flow membrane lab unit, a quartz crystal microbalance with dissipation (QCM-D), and a rear stagnation point flow (RSPF) system with either model bacteria (Sphingomonas wittichii, Escherichia coli, and Pseudomonas aeruginosa) or vesicles made of the bacterial GSL or LPS was used. Results showed noticeable differences in the adhesion LPS versus GSL vesicles in the QCM-D, with the latter exhibiting 50% higher adhesion to polyamide coated crystals (mimicking an RO membrane surface). A similar trend was observed for EPS extracted from S. wittichii, when compared to the adhesion tendency of EPS extracted from P. aeruginosa. By applying the whole-cell approach in the RO lab unit, the cumulative impact of S. wittichii cells composing GSL and probably their EPS reduced the permeate flux during bacterial accumulation on the membrane surface. Experiments were conducted with the same amount of Sphingomonas spp. or Escherichia coli cells resulting in a two times greater flux decline in the presence of S. wittichii. The distinct effects of Sphingomonas spp. on RO membrane biofouling are likely a combination of GSL presence (known for enhancing adhesion when compared to non-GSL containing bacteria) and the EPS contributing to the overall strength of the biofilm matrix.

The endophytic bacterium, Sphingomonas SaMR12, isolated from Sedum alfredii Hance, appears to increase plant biomass and zinc-extraction from contaminated soil; however, the mechanism by which this occurs is not clear. Here, the ability of SaMR12 to promote zinc extraction and its effects on root morphology and exudation were examined in hydroponics. Zinc treatment increased shoot biomass by 30 to 45%, and by a further 10 to 19% when combined with SaMR12 inoculation. Zinc treatment also increased zinc accumulation modestly and this too was enhanced with SaMR12. Both biomass and zinc levels increased in a dose-dependent manner with significant effects seen at 50 µM zinc and apparent saturation at 500 µM. Zinc and the endophyte also increased levels of auxin but not at 50 µM and zinc increased levels of superoxide and hydrogen peroxide but mainly at 500 µM. As for root morphology, SaMR12 increased root branching, the number of root tips, and surface area. Zinc and SaMR12 also increased the exudation of oxalic acid. For most assays the effects of the endophyte and zinc were additive, with the notable exception of SaMR12 strongly reducing the production of reactive oxygen species at 500 µM zinc. Taken together, these results suggest that the promotion of growth and zinc uptake by exposure to zinc and to SaMR12 are independent of reactive oxygen and do not involve increases in auxin.

A novel bacterial strain designated 9PNM-6(T) was isolated from an abandoned lead-zinc ore mine site in Meizhou, Guangdong Province, China. The isolate was found to be Gram-negative, rod-shaped, orange-pigmented, strictly aerobic, oxidase- and catalase-positive. Growth occurred at 0-4 % NaCl (w/v, optimum, 0 %), at pH 6.0-8.0 (optimum, pH 7.0) and at 15-32 °C (optimum, 28-30 °C). Phylogenetic analysis based on 16S rRNA gene sequence similarities showed that strain 9PNM-6(T) belongs to the genus Sphingomonas, with the highest sequence similarities with Sphingomonas jejuensis NBRC 107775(T) (99.7 %), Sphingomonas koreensis KCTC 2882(T) (95.1 %) and Sphingomonas dokdonesis KCTC 12541(T) (95.1 %). The chemotaxonomic characteristics of strain 9PNM-6(T) were consistent with those of the genus Sphingomonas. The predominant respiratory quinone was identified as ubiquinone Q-10, the major polyamine as sym-homospermidine, and the major cellular fatty acids as C18:1 ω7c, C16:0, C16:1 ω7c and/or C16:1 ω6c and C14:0 2-OH. The major polar lipids are sphingoglycolipid, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatideylcholine, an unidentified phospholipid and four unidentified aminolipids. The genomic DNA G+C content of strain 9PNM-6(T) was determined to be 69.2 ± 0.6 mol%. Based on comparative analyses of morphological, physiological and chemotaxonomic data, and levels of DNA-DNA relatedness values, strain 9PNM-6(T) is considered to represent a novel species of the genus Sphingomonas, for which the name Sphingomonas gimensis sp. nov. (Type strain 9PNM-6(T) = GIMCC 1.655(T) = CGMCC 1.12671(T) = DSM 27569(T)) is proposed.

A Gram-staining negative bacterium, THG-DT81(T), which was isolated from soil of a ginseng field, was investigated using a polyphasic taxonomic approach. Cells were oxidase- and catalase-positive, aerobic, rod-shaped and motile with one polar flagellum. Strain THG-DT81(T) grew optimally at pH 7.0 and in the absence of NaCl on trypticase soy agar. Its optimum growth temperature was 25-28 °C. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain THG-DT81(T) belongs to the family Sphingomonadaceae and was related to Sphingomonas pituitosa EDIV(T) (98.0 % similarity), S. leidyi ATCC 15260(T) (97.8 %), S. trueperi LMG 2142(T) (97.1 %), S. azotifigens NBRC 15497(T) (97.1 %), S. koreensis JSS26 (T) (97.1 %) and S. dokdonensis DS-4(T) (97.0 %). Strain THG-DT81(T) contained Q-10 as the predominant ubiquinone and C18:1 ω7c and C16:0 as the major fatty acids. The G+C content of the genomic DNA was determined to be 66.8 mol %. The major component in the polyamine pattern was identified as sym-homospermidine. The major polar lipids detected in strain THG-DT81(T) were sphingoglycolipid, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and phosphatidylcholine. The DNA-DNA relatedness values of the strain THG-DT81(T) and its closest phylogenetically neighbors were below 21 %. The phenotypic characteristics and genotypic data demonstrated the affiliation of strain THG-DT81(T) to the genus Sphingomonas. On the basis of the polyphasic taxonomic data presented, strain THG-DT81(T) is described as a novel species of genus Sphingomonas, for which the name Sphingomonas kyeonggiense sp. nov. is proposed. The type strain is THG-DT81(T) (= KACC 17173(T) = JCM 18825(T)).

Background: Pyomyoma is a life-threatening complication of uterine leiomyoma. It may occur in post- menopausal women, during pregnancy and in the postpartum period. Fever may be the only manifestation during the early stages of the disease. We detail the first reported case of postpartum pyomyoma-related sepsis due to Sphingomonas paucimobilis, a Gram-negative bacillus that is gaining recognition as an important human pathogen., Case Presentation: A woman presented with an asymptomatic uterine fibroid and a two-week history of fever during the postpartum period. Suppurative uterine leiomyoma was diagnosed, and blood cultures grew Sphingomonas paucimobilis. The myoma was surgically removed from the uterus without hysterectomy. Intravenous antimicrobial therapy was given for fifteen days, and the patient was discharged from hospital in good condition., Conclusion: Pyomyoma should be considered in broad differential diagnosis of postpartum fever. This case highlights a unique disease manifestation of S. paucimobilis, an emerging opportunistic pathogen with increasing significance in the nosocomial setting.

The survival, physiology and gene expression profile of the phenanthrene-degrading Sphingomonas sp. LH128 was examined after an extended period of complete nutrient starvation and compared with a non-starved population that had been harvested in exponential phase. After 6 months of starvation in an isotonic solution, only 5 % of the initial population formed culturable cells. Microscopic observation of GFP fluorescent cells, however, suggested that a larger fraction of cells (up to 80 %) were still alive and apparently had entered a viable but non-culturable (VBNC) state. The strain displayed several cellular and genetic adaptive strategies to survive long-term starvation. Flow cytometry, microscopic observation and fatty acid methyl ester (FAME) analysis showed a reduction in cell size, a change in cell shape and an increase in the degree of membrane fatty acid saturation. Transcriptome analysis showed decreased expression of genes involved in ribosomal protein biosynthesis, chromosomal replication, cell division and aromatic catabolism, increased expression of genes involved in regulation of gene expression and efflux systems, genetic translocations, and degradation of rRNA and fatty acids. Those phenotypic and transcriptomic changes were not observed after 4 h of starvation. Despite the starvation situation, the polycyclic aromatic hydrocarbon (PAH) catabolic activity was immediate upon exposure to phenanthrene. We conclude that a large fraction of cells maintain viability after an extended period of starvation apparently due to tuning the expression of a wide variety of cellular processes. Due to these survival attributes, bacteria of the genus Sphingomonas, like strain LH128, could be considered as suitable targets for use in remediation of nutrient-poor PAH-contaminated environments.

This investigation is focused on the combined effect of bacterial physicochemical characteristics and motility on cell adhesion and deposition using a flow-through quartz crystal microbalance with dissipation (QCM-D). Three model flagellated strains with different degrees of motility were selected, including a highly motile Escherichia coli K12 MG1655, an environmental strain Sphingomonas wittichii RW1, and a nonmotile (with paralyzed flagella) Escherichia coli K12 MG1655 ΔmotA that is incapable of encoding the motor torque generator for flagellar movement. Of the three strains, S. wittichii RW1 is highly hydrophobic, while E. coli strains are equally hydrophilic. Consideration of the hydrophobicity provides an alternative explanation for the bacterial adhesion behavior. QCM-D results show that motility is a critical factor in determining bacterial adhesion, as long as the aquatic chemical conditions are conducive for motility and the substratum and bacterial surface are similarly hydrophobic or hydrophilic. Once their properties are not similar, the contribution of hydrophobic interactions becomes more pronounced. QCM-D results suggest that during adhesion of the hydrophobic bacterium, S. wittichii RW1, the initial step of adhesion and maturation of bacteria-substratum interaction on hydrophilic surface includes a dynamic change of the viscoelastic properties of the bond bacterium-surface becoming more viscously oriented.

Sedum alfredii Hance is a Zn and Cd co-hyperaccumulating plant species found in an old mining area in China. Four bacterial strains, Burkholderia sp. SaZR4, Burkholderia sp. SaMR10, Sphingomonas sp. SaMR12 and Variovorax sp. SaNR1, isolated from surface-sterilized S. alfredii plants were used to investigate their endophytic nature and root colonization patterns and effects on phytoextraction of Zn and Cd. Laser scanning confocal microscopy revealed that gfp-tagged SaZR4, SaMR12, and SaNR1 cells formed biofilms on roots and that SaZR4 and SaMR12 cells could invade root tissues. SaMR10 showed the lowest total population associated with S. alfredii and little effect on plant growth and phytoextraction. SaZR4 significantly promoted Zn-extraction but not Cd-extraction. SaMR12 and SaNR1 significantly promoted plant growth in substrates supplemented with Zn or Cd and phytoextraction of Zn and Cd. Together, this study have shown that the four native endophytic bacteria differently colonize the host plants and modulate metal uptake and growth of host plant, and that SaMR12 and SaNR1 strains are promising assistants of S. alfredii plants for phytoremediation of Zn/Cd-contaminated soil.

Members of the genus Sphingomonas are important catalysts for removal of polycyclic aromatic hydrocarbons (PAHs) in soil, but their activity can be affected by various stress factors. This study examines the physiological and genome-wide transcription response of the phenanthrene-degrading Sphingomonas sp. strain LH128 in biofilms to solute stress (invoked by 450 mM NaCl solution), either as an acute (4-h) or a chronic (3-day) exposure. The degree of membrane fatty acid saturation was increased as a response to chronic stress. Oxygen consumption in the biofilms and phenanthrene mineralization activities of biofilm cells were, however, not significantly affected after imposing either acute or chronic stress. This finding was in agreement with the transcriptomic data, since genes involved in PAH degradation were not differentially expressed in stressed conditions compared to nonstressed conditions. The transcriptomic data suggest that LH128 adapts to NaCl stress by (i) increasing the expression of genes coping with osmolytic and ionic stress such as biosynthesis of compatible solutes and regulation of ion homeostasis, (ii) increasing the expression of genes involved in general stress response, (iii) changing the expression of general and specific regulatory functions, and (iv) decreasing the expression of protein synthesis such as proteins involved in motility. Differences in gene expression between cells under acute and chronic stress suggest that LH128 goes through changes in genome-wide expression to fully adapt to NaCl stress, without significantly changing phenanthrene degrading activity.

Sphingomonas sp. strain Fr1 has recently been shown to protect Arabidopsis thaliana against the bacterial leaf pathogen Pseudomonas syringae DC3000. Here, we describe a forward genetic in planta screen to identify genes in Sphingomonas sp. Fr1 necessary for this effect. About 5,000 Sphingomonas sp. Fr1 mini-Tn5 mutants were assayed for a defect in plant protection against a luxCDABE-tagged P. syringae DC3000 derivative in a space-saving 24-well plate system. The bioluminescence of the pathogen was used as the indicator of pathogen proliferation and allowed for the identification of Sphingomonas sp. Fr1 mutants that had lost the ability to restrict pathogen growth before disease symptoms were visible. Potential candidates were validated using the same miniaturized experimental system. Of these mutants, 10 were confirmed as plant protection defective yet colonization competent. The mutants were subsequently evaluated in a previously described standard microbox system, and plants showed enhanced disease phenotypes after pathogen infection relative to those inoculated with the parental strain as a control. However, the disease severities were lower than those observed for control plants that were grown axenically prior to pathogen challenge, which suggests that several traits may contribute to plant protection. Transposon insertion sites of validated mutants with defects in plant protection were determined and mapped to 7 distinct genomic regions. In conclusion, the established screening protocol allowed us to identify mutations that affect plant protection, and it opens the possibility to uncover traits important for in planta microbe-microbe interactions.

An aerobic, Gram-negative-staining, motile, psychrophilic bacterium, designated strain S8-3(T), was isolated from alpine soil. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain S8-3(T) was related to the genus Sphingomonas and had highest 16S rRNA gene sequence similarity with Sphingomonas oligophenolica S213(T) (98.0%). 16S RNA gene sequence similarity between strain S8-3(T) and Sphingomonas paucimobilis ATCC 29837(T) (the type species of the genus Sphingomonas) was 93.0%. Strain S8-3(T) contained Q-10 as the ubiquinone and C(18:1)ω7c (65.0%) and C(14:0) 2-OH (13.4%) as the dominant fatty acids (>10%). The major polyamines were the triamine sym-homospermidine and spermidine. The polar lipid profile contained sphingoglycolipid, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylmonomethylethanolamine. The DNA G+C content was 64.1 mol%. Combined data from phenotypic, phylogenetic and DNA-DNA relatedness studies demonstrated that strain S8-3(T) is a representative of a novel species of the genus Sphingomonas, for which the name Sphingomonas alpina sp. nov. is proposed. The type strain is S8-3(T) (=DSM 22537(T)=LMG 26055(T)).

A novel bacterium (strain YIM 65583(T)) belonging to the genus Sphingomonas was isolated from surface-sterilized tissue of Artemisia annua L., which was collected from Yunnan province, south-west China. Its morphology, physiology and biochemical features were consistent with those of members of the genus Sphingomonas. Analysis of the 16S rRNA gene sequence of strain YIM 65583(T) further confirmed that it should be classified as a member of the genus Sphingomonas and was most closely related to Sphingomonas phyllosphaerae FA2(T) (99.7%) and Sphingomonas yunnanensis YIM 003(T) (98.3%). The isolate was Gram-negative and formed yellow-pigmented colonies on ISP 2 medium. It grew optimally at pH 6.0-8.0, at 20-37 °C and in the presence of 0-1% (w/v) NaCl. The major respiratory lipoquinone was ubiquinone-10; C(18:1)ω7c, anteiso-C(16:1), C(14:0)-2OH, C(17:1)ω6c, C(16:0) and C(15:0) were the major fatty acids. Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and sphingoglycolipid. The G+C content of the genomic DNA was 63.3 mol%. The DNA-DNA relatedness values of the isolate YIM 65583(T) with S. phyllosphaerae FA2(T) and S. yunnanensis YIM 003(T) were 43.1% and 37.9%, respectively. Based on these features, it is concluded that the strain represents a novel species of the genus Sphingomonas, for which the name Sphingomonas endophytica sp. nov. is proposed, with YIM 65583(T) (=CCTCC AA 209035(T)=JCM 17394(T)) as the type strain.

Sphingomonas sp. strain PAMC 26617 has been isolated from an Arctic lichen Umbilicaria sp. on the Svalbard Islands. Here we present the draft genome sequence of this strain, which represents a valuable resource for understanding the symbiotic mechanisms between endosymbiotic bacteria and lichens surviving in extreme environments.

Reprogramming gene expression is an essential component of adaptation to changing environmental conditions. In bacteria, a widespread mechanism involves alternative sigma factors that redirect transcription toward specific regulons. The activity of sigma factors is often regulated through sequestration by cognate anti-sigma factors; however, for most systems, it is not known how the activity of the anti-sigma factor is controlled to release the sigma factor. Recently, the general stress response sigma factor in Alphaproteobacteria, σ(EcfG), was identified. σ(EcfG) is inactivated by the anti-sigma factor NepR, which is itself regulated by the response regulator PhyR. This key regulator sequesters NepR upon phosphorylation of its PhyR receiver domain via its σ(EcfG) sigma factor-like output domain (PhyR(SL)). To understand the molecular basis of the PhyR-mediated partner-switching mechanism, we solved the structure of the PhyR(SL)-NepR complex using NMR. The complex reveals an unprecedented anti-sigma factor binding mode: upon PhyR(SL) binding, NepR forms two helices that extend over the surface of the PhyR(SL) subdomains. Homology modeling and comparative analysis of NepR, PhyR(SL), and σ(EcfG) mutants indicate that NepR contacts both proteins with the same determinants, showing sigma factor mimicry at the atomic level. A lower density of hydrophobic interactions, together with the absence of specific polar contacts in the σ(EcfG)-NepR complex model, is consistent with the higher affinity of NepR for PhyR compared with σ(EcfG). Finally, by reconstituting the partner switch in vitro, we demonstrate that the difference in affinity of NepR for its partners is sufficient for the switch to occur.

A Gram-reaction-negative, oxidase- and catalase-positive, non-gliding motile bacteriun, designated DCY58(T), was isolated from a ginseng field in Pocheon Province, South Korea. Colonies of strain DCY58(T) were circular, 0.5-1.5 mm in diameter, yellow, and convex on an R2A agar plate after 2 days. The 16S rRNA gene sequence analysis revealed that strain DCY58(T) belongs to the family of the Sphingomonadaceae and is most closely related to the species of genus Sphingomonas with similarity levels of 95.7-96.4%. Strain DCY58(T) contained Q-10 as the predominant ubiquinone. The major cellular fatty acids included Summed Feature 8 (containing C(18:1ω)6c and/or C(18:1ω)7c), C(14:0) 2-OH and C(16:0). The DNA G+C content was 65.1 mol%. Furthermore, strain DCY58(T) differed from other related Sphingomonas species by a number of phenotypic characteristics. On the basis of the evidence presented in this study, strain DCY58(T) is described as a novel species of genus Sphingomonas, for which the name Sphingomonas ginsengisoli sp. nov., is proposed. The type strain is DCY58(T) (=KCTC 23762(T) =JCM 18016(T)).

In this study, 20 samples from three different sources of animal feed were investigated and six bacterial isolates were identified. The susceptibility of four natural antimicrobials, namely, eugenol, cinnamaldehyde, thymol, and carvacrol, against six of these isolates was determined. Carvacrol and eugenol showed better inhibitory effects with larger zones of inhibition. The minimal inhibitory concentration for a range of antibiotics on the susceptibility of two isolates (namely, Sphingomonas paucimobilis and Klebsiella oxytoca) was investigated using the VITEK® 2 microbiological identification system. Both isolates showed a variety of resistance to 18 antibiotics. The minimal inhibitory concentration and fractional inhibitory concentration index of those two isolates for ampicillin and nitrofurantoin in combination with four phenolic compounds was determined. Synergistic interactions were found for most antimicrobial/antibiotic combinations; thymol and carvacrol were very effective (fractional inhibitory concentration ≤0.5) in combination with all antibiotics tested against S. paucimobilis and K. oxytoca, respectively. Ultra performance liquid chromatography techniques were used to investigate the physiological effects of the four natural antimicrobials against those two isolates. Two identical peaks were found to be systematically different between cinnamaldehyde-treated and -untreated cells. The identity of the peaks is unknown and further investigation is needed.

Two Gram-reaction-negative, yellow-orange-pigmented, rod-shaped bacterial strains, designated YC6722(T) and YC6723(T), were isolated from rhizosphere soil samples collected from rice fields in Jinju, Korea. Strains YC6722(T) and YC6723(T) grew optimally at 25-30 °C and at pH 7.0-8.5. Phylogenetic analyses of 16S rRNA gene sequences showed that strain YC6722(T) was most closely related to Sphingomonas jaspsi TDMA-16(T) (96.6 % sequence similarity) and strain YC6723(T) was related most closely to Sphingomonas aquatilis JSS7(T) (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 YC6722(T) and YC6723(T) were 63.3 and 61.0 mol%, respectively. The major fatty acid was C(18 : 1)ω7c. 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 YC6722(T) and YC6723(T) represent two novel species of the genus Sphingomonas, for which the names Sphingomonas oryziterrae sp. nov. ( = KCTC 22476(T)  = DSM 21455(T)) and Sphingomonas jinjuensis sp. nov. (KCTC 22477(T)  = DSM 21457(T)) are proposed.

Biofilms cause runnability problems in paper machines and are therefore controlled with biocides. Peracetic acid is usually effective in preventing bulky biofilms. This study investigated the microbiological status of a paper machine where low concentrations (≤ 15 ppm active ingredient) of peracetic acid had been used for several years. The paper machine contained a low amount of biofilms. Biofilm-forming bacteria from this environment were isolated and characterized by 16S rRNA gene sequencing, whole-cell fatty acid analysis, biochemical tests, and DNA fingerprinting. Seventy-five percent of the isolates were identified as members of the subclades Sphingomonas trueperi and S. aquatilis, and the others as species of the genera Burkholderia (B. cepacia complex), Methylobacterium, and Rhizobium. Although the isolation media were suitable for the common paper machine biofoulers Deinococcus, Meiothermus, and Pseudoxanthomonas, none of these were found, indicating that peracetic acid had prevented their growth. Spontaneous, irreversible loss of the ability to form biofilm was observed during subculturing of certain isolates of the subclade S. trueperi. The Sphingomonas isolates formed monoculture biofilms that tolerated peracetic acid at concentrations (10 ppm active ingredient) used for antifouling in paper machines. High pH and low conductivity of the process waters favored the peracetic acid tolerance of Sphingomonas sp. biofilms. This appears to be the first report on sphingomonads as biofilm formers in warm water using industries.

Diverse bacterial taxa live in association with plants without causing deleterious effects. Previous analyses of phyllosphere communities revealed the predominance of few bacterial genera on healthy dicotyl plants, provoking the question of whether these commensals play a particular role in plant protection. Here, we tested two of them, Methylobacterium and Sphingomonas, with respect to their ability to diminish disease symptom formation and the proliferation of the foliar plant pathogen Pseudomonas syringae pv. tomato DC3000 on Arabidopsis thaliana. Plants were grown under gnotobiotic conditions in the absence or presence of the potential antagonists and then challenged with the pathogen. No effect of Methylobacterium strains on disease development was observed. However, members of the genus Sphingomonas showed a striking plant-protective effect by suppressing disease symptoms and diminishing pathogen growth. A survey of different Sphingomonas strains revealed that most plant isolates protected A. thaliana plants from developing severe disease symptoms. This was not true for Sphingomonas strains isolated from air, dust, or water, even when they reached cell densities in the phyllosphere comparable to those of the plant isolates. This suggests that plant protection is common among plant-colonizing Sphingomonas spp. but is not a general trait conserved within the genus Sphingomonas. The carbon source profiling of representative isolates revealed differences between protecting and nonprotecting strains, suggesting that substrate competition plays a role in plant protection by Sphingomonas. However, other mechanisms cannot be excluded at this time. In conclusion, the ability to protect plants as shown here in a model system may be an unexplored, common trait of indigenous Sphingomonas spp. and may be of relevance under natural conditions.

A Gram-negative, non-motile, rod shaped, and orange-pigmented chemoheterotrophic bacterium, strain MS-31(T) was isolated from the marine sponge Hymeniacidon flavia, collected from near Jeju Island, Korea. The Strain MS-31(T) was subjected to a polyphasic taxonomic study. The phylogenetic analysis based on the 16S rRNA gene sequences revealed that the novel isolate could be affiliated within the genus Sphingomonas. The strain MS-31(T) showed 95.6% of 16S rRNA gene sequence similarity with the most closely related species Sphingomonas koreensis JSS26(T). The DNA G+C content of the strain MS-31(T) was 69.4 mol%. The major isoprenoid quinone was ubiqunone 10 and predominant cellular fatty acids were summed feature 7 (comprising C(18:1) ω7c, C(18:1) Ω9t and/or C(18:1) ωl2t, 39.7%), C(16:0) (16.3%), C(14:0) 2OH (15.9%) and summed feature 3 (comprising C(16:1) ω7c and/or C(15:0) iso 2OH, 11.7%). The polar lipids were sphingoglycolipid, phosphatidyletha-nolamine, phosphatidylglycerol, diphosphatidylglycerol and unidentified glycolipid. Based on the evidence from the polyphasic taxonomic study, the strain should be classified as a new species of the genus Sphingomonas. As a result, the name Sphingomonas jejuensis sp. nov. (type strain MS-31(T) =KCTC 23321(T) =NBRC 107775(T)) is proposed.

A non-motile, rod-shaped, yellow bacterium, designated C16y(T), was isolated from alpine glacier cryoconite. Cells behaved Gram-positively, were aerobic and psychrophilic (good growth at 1-25 °C). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain C16y(T) was related to the genus Sphingomonas and had highest 16S rRNA gene sequence similarity with Sphingomonas oligophenolica JCM 12082(T) (97.6  %) and Sphingomonas echinoides DSM 1805(T) (97.2  %). DNA-DNA hybridization demonstrated that strain C16y(T) could not be considered as a member of either Sphingomonas oligophenolica or Sphingomonas echinoides. Strain C16y(T) contained Q-10 as the predominant ubiquinone and C₁₈:₁ and C₁₆:₀ were the dominant fatty acids. The polar lipid profile contained phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid, five unidentified glycolipids, two unidentified aminophospholipids and two unidentified lipids. The major polyamines were the triamines sym-homospermidine and spermidine. The G+C content was 67.9 mol%. Combined data from phenotypic, phylogenetic and DNA-DNA relatedness studies demonstrated that strain C16y(T) is a representative of a novel species of the genus Sphingomonas, for which we propose the name Sphingomonas glacialis sp. nov. The type strain is C16y(T) (=DSM 22294(T) =CGMCC 1.8957(T) =CIP 110131(T) [corrected]).

The Gram-reaction-negative, strictly aerobic, non-motile, non-spore-forming, and rod-shaped bacterial strain designated Gsoil 1429(T) was isolated from the soil of ginseng cultivating field of Pocheon province in South Korea. This bacterium was characterized in order to determine its taxonomic position by using the polyphasic approach. Strain Gsoil 1429(T) grew well at 25-37°C and at pH 7.0 on R2A and nutrient agar without NaCl supplement. Strain Gsoil 1429(T) had -glucosidase activity, which was responsible for its ability to transform ginsenoside Rb1 (one of the dominant active components of ginseng) to F(2) via gypenoside XVII. On the basis of 16S rRNA gene sequence similarity, strain Gsoil 1429(T) was shown to belong to the family Sphingomonadaceae and to be related to Sphingomonas yunnanensis YIM 003(T) (98.2% sequence similarity), S. phyllosphaerae FA2(T) (97.5%), S. koreensis JSS26(T) (97.3%), and S. asaccharolytica IFO 15499(T) (97.1%). The G+C content of the genomic DNA was 65.6%. The major respiratory quinone was Q-10 and the major fatty acids were summed feature 8 (comprising C(18:1) 7c/ωt/12t), C(16:0) and C(14:0)2OH. DNA and chemotaxonomic data supported the affiliation of strain Gsoil 1429T to the genus Sphingomonas. The DNA-DNA relatedness values between strain Gsoil 1429(T) and its closest phylogenetically neighbours were below 28%. Strain Gsoil 1429(T) could be differentiated genotypically and phenotypically from the recognized species of the genus Sphingomonas. The isolate therefore represents a novel species, for which the name Sphingomonas ginsenosidimutans sp. nov. is proposed, with the type strain Gsoil 1429(T) (=KACC 14949(T) =JCM 17074(T) =LMG 25799(T)).

The aim of this study was to explore the physicochemical parameters that influence coaggregation between the freshwater bacteria Sphingomonas natatoria 2.1 and Micrococcus luteus 2.13. Using visual coaggregation assays, the effect of different buffers, solutions of differing ionic strength, pH, temperature, and viscosity on the degree of coaggregation was assessed. Coaggregation occurred maximally in distilled water but was inhibited when coaggregates were suspended in a commonly-used oral bacterial coaggregation buffer, saline solutions, and Tris-Cl buffers. Coaggregation was weakly expressed in standard laboratory buffers. The ionic strength of inorganic salt solutions required to inhibit coaggregation depended upon the inorganic salt being tested. Coaggregation occurred at a pH of 3-10, between 5 and 80°C and was inhibited in solutions with a viscosity of 22.5 centipoises at 20°C. Inhibition of coaggregation with NaCl impaired biofilm development. When developing buffers to test for coaggregation, the natural liquid environment should be considered. Coaggregation between S. natatoria 2.1 and M. luteus 2.13 is only affected by physicochemical conditions beyond those typically found in natural freshwater ecosystems. Such a robust ability to coaggregate may enhance the ability of S. natatoria 2.1 and M. luteus 2.13 to develop a niche in freshwater biofilms.

The presence of microcystin-LR -degrading bacteria in an active anthracite biofilter and in Lake Mead, Nevada was investigated. Four bacterial isolates from enrichment culture were identified using 16S rRNA analysis. Microcystin biodegradation tests were performed with both, the enrichment cultures and the respective isolates, using microcystin alone and acetate as carbon sources. A newly recognized microcystin-degrading bacterium, Morganella morganii, was isolated from the biofilter and from Lake Mead. The results of the biodegradation tests indicated that addition of a carbon source (acetate), significantly repressed the degradation of microcystin-LR. The findings of this study inform on the prevalence of microcystin-degrading bacteria in the environment indicating bioaugmentation may not be needed, if biofiltration is used to remove microcystin from waters. The results also imply that, in a biofilter, biodegradable naturally organic matter (NOM) and microcystin will compete and therefore lower toxin removals are likely in waters with higher NOM content. The feasibility of removing microcystin by biofiltration depends on the toxin concentration and the concentration of biodegradable carbon sources in the biofilter.

A Gram-negative, non-spore-forming, cream-coloured bacterial strain, UM2(T), was isolated from an open hexachlorocyclohexane (HCH) dump site at Ummari village in Lucknow, India. Data generated from a polyphasic approach including phenotypic, genotypic and chemotaxonomic analyses confirmed that strain UM2(T) belonged to the genus Sphingomonas. The highest similarity found to the 16S rRNA gene sequence of strain UM2(T) was 99.4 %, with Sphingomonas wittichii DSM 6014(T), whereas the DNA-DNA relatedness value between these strains was 31 %, indicating that they represent separate species. The DNA G+C content of UM2(T) was 66.9 mol%. The respiratory pigment ubiquinone Q-10 was present. The predominant fatty acids were summed feature 8 (C(18 : 1)omega6c and/or C(18 : 1)omega7c; 32.9 %), C(19 : 0) cyclo omega8c (15.5 %) and C(16 : 0) (12.1 %). The major polar lipids were phosphatidylcholine, phosphatidylglycerol and phosphatidyldimethylethanolamine. sym-Homospermidine was the major polyamine observed. On the basis of the data reported, it was concluded that UM2(T) represents a novel species of the genus Sphingomonas, for which the name Sphingomonas histidinilytica sp. nov. is proposed. The type strain is UM2(T) (=MTCC 9473(T) =CCM 7545(T)).

Bacterial strain V2M44(T) was isolated from forest soil from the Changbai Mountains, Heilongjiang Province, China. Cells of strain V2M44( T) were Gram-negative, rod-shaped and 0.3-0.4 mum in diameter and 1.5-2.5 mum long. The cells were strictly aerobic and were motile by means of peritrichous flagella. Growth occurred at 20-33 degrees C (optimum, 29-31 degrees 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 V2M44(T) contained C(17 : 1 )omega6c (38.9 %) and summed feature 7 (comprising C(18 : 1)omega7 c, C(18 : 1)omega9t and/or C(18 : 1)omega12t, 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 was sym-homospermidine. The DNA G+C content was 65.8 mol%. Analysis of 16S rRNA gene sequences indicated that strain V2M44(T) was phylogenetically related to members of the genus Sphingomonas, with sequence similarities ranging from 92.0-95.8 %. Based on these results, it is concluded that strain V2M44(T) represents a novel species of the genus Sphingomonas, for which the name Sphingomonas changbaiensis sp. nov. is proposed. The type strain is V2M44(T) (=CGMCC 1.7057(T)=NBRC 104936(T)).

A gram-negative, non-motile, non-spore-forming, small, orange, rod-shaped bacterium was isolated from soil in South Korea and characterized to determine its taxonomic position. Phylogenetic analysis based on 16S rRNA gene sequence examination revealed that strain PB323(T) belongs to the family Sphingomonadaceae. The highest degree of sequence similarity was found with Sphingomonas kaistensis PB56(T) (98.9%), followed by Sphingomonas astaxanthinifaciens TDMA-17(T) (98.3%). Chemotaxonomic characteristics (the G+C content of the genomic DNA 69.0 mol%, Q-10 quinone system, C(18:1) omega7c/omega9t/omega12t, C(16:1) omega7c/C(15:0) iso 2OH, C(17:1) omega6c, and C16:0 as the major fatty acids) corroborated assignment of strain PB323(T) to the genus Sphingomonas. Results of physiological and biochemical tests clearly demonstrate that strain PB323(T) represents a distinct species and support its affiliation with the genus Sphingomonas. Based on these data, PB323(T) (=KCTC 12341(T) =JCM 16603T =KEMB 9004-003(T)) should be classified as a type strain of a novel species, for which the name Sphingomonas humi sp. nov. is proposed.

The genes required for tetralin biodegradation by Sphingomonas macrogolitabida strain TFA are clustered in two divergent and closely linked operons. ThnR, a LysR-type regulator, activates transcription from each operon in response to tetralin. The regulatory thnR gene is co-transcribed with the catabolic genes thnC, thnA3 and thnA4, resulting in positive autoregulation. ThnR binds with different affinity to two primary binding sites, designated B and C, in the intervening region between the two operons and makes additional contact with secondary sites that extend towards the promoters. In addition, ThnR may interact with itself when bound to each site via the formation of a DNA loop, as evidenced by the distortion of the DNA between the primary binding sites and the elimination of the higher-order complexes following the introduction of a half-turn of the DNA helix between the primary binding sites. Transcription from each promoter is not fully independent since mutations in each binding site affected transcription from both promoters. Based on these results, we propose a model of transcription activation that involves the formation of a complex structure by interactions between ThnR molecules bound to distant binding sites and favours transcription from one promoter to the detriment of the other.

Coaggregation is hypothesized to enhance freshwater biofilm development. To investigate this hypothesis, the ability of the coaggregating bacterium Sphingomonas natatoria to form single- and dual-species biofilms was studied and compared to that of a naturally occurring spontaneous coaggregation-deficient variant. Attachment assays using metabolically inactive cells were performed using epifluorescence and confocal laser scanning microscopy. Under static and flowing conditions, coaggregating S. natatoria 2.1gfp cells adhered to glass surfaces to form diaphanous single-species biofilms. When glass surfaces were precoated with coaggregation partner Micrococcus luteus 2.13 cells, S. natatoria 2.1gfp cells formed densely packed dual-species biofilms. The addition of 80 mM galactosamine, which reverses coaggregation, mildly reduced adhesion to glass but inhibited the interaction and attachment to glass-surface-attached M. luteus 2.13 cells. As opposed to wild-type coaggregating cells, coaggregation-deficient S. natatoria 2.1COGgfp variant cells were retarded in colonizing glass and did not interact with glass-surface-attached M. luteus 2.13 cells. To determine if coaggregation enhances biofilm growth and expansion, viable coaggregating S. natatoria 2.1gfp cells or the coaggregation-deficient variant S. natatoria 2.1COGgfp cells were coinoculated in flow cells with viable M. luteus 2.13 cells and allowed to grow together for 96 h. Coaggregating S. natatoria 2.1gfp cells outcompeted M. luteus 2.13 cells, and 96-h biofilms were composed predominantly of S. natatoria 2.1gfp cells. Conversely, when coaggregation-deficient S. natatoria 2.1COGgfp cells were coinoculated with M. luteus 2.13 cells, the 96-h biofilm contained few coaggregation-deficient S. natatoria 2.1 cells. Thus, coaggregation promotes biofilm integration by facilitating attachment to partner species and likely contributes to the expansion of coaggregating S. natatoria 2.1 populations in dual-species biofilms through competitive interactions.

A novel bacterium (strain K4(T)) belonging to the genus Sphingomonas was isolated from tidal flat sediment in Korea. Its morphology, physiology, biochemical features and 16S rRNA gene sequence were characterized. Colonies of this strain are yellow in colour and the cells are rod-shaped, exhibiting negative Gram staining. The strain grows at 0-5 % (w/v) NaCl and 20-35 degrees C, with optimal growth occurring at 0 % (w/v) NaCl and 30 degrees C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain K4(T) is associated with the genus Sphingomonas. Within the phylogenetic tree, this novel strain shares a branching point with Sphingomonas asaccharolytica Y-345(T), with which it shares 97.3 % 16S rRNA gene sequence similarity. The polyamine pattern predominantly contains the Sphingomonas-specific triamine sym-homospermidine. Combined analysis of 16S rRNA gene sequences, DNA-DNA relatedness, physiological and biochemical test results identified genotypic and phenotypic differences between strain K4(T) and other Sphingomonas species. On the basis of these differentiating features, it is concluded that strain K4(T) (=KCTC 22050(T)=DSM 19475(T)) represents a novel species of the genus Sphingomonas, for which the name Sphingomonas aestuarii sp. nov. is proposed.

A Sphingomonas-like bacterium, strain KC7(T), was isolated from a marine crustacean specimen obtained from the Sea of Japan and subjected to a polyphasic study. Comparative 16S rRNA gene sequence analysis positioned the novel strain in the genus Sphingomonas as an independent lineage adjacent to a subclade containing Sphingomonas trueperi LMG 2142(T), Sphingomonas pituitosa EDIV(T) and Sphingomonas azotifigens NBRC 15497(T). Strain KC7(T) shared highest 16S rRNA gene sequence similarity (96.1 %) with S. trueperi LMG 2142(T), Sphingomonas dokdonensis DS-4(T) and S. azotifigens NBRC 15497(T); similarities to strains of other recognized Sphingomonas species were lower (96.0-93.9 %). The strain contained sphingoglycolipid and the predominant fatty acids were C(16 : 1), C(16 : 0) and C(18 : 1); 2-OH C(14 : 0) was the major 2-hydroxy fatty acid. Previously, these lipids have been found to be characteristic of members of the genus Sphingomonas sensu stricto. On the basis of phylogenetic analysis and physiological and biochemical characterization, strain KC7(T) represents a novel species of the genus Sphingomonas, for which the name Sphingomonas japonica sp. nov. is proposed. The type strain is KC7(T) (=KMM 3038(T) =NRIC 0738(T) =JCM 15438(T)).