High-efficient and sustainable biodegradation of microcystin-LR using Sphingopyxis sp. YF1 immobilized Fe3O4@chitosan.

The microcystin-LR (MC-LR) produced due to harmful cyanobacterial blooms have brought great harm to human and aquatic organisms, attracting a wide public health attention. To deal with MC-LR contamination, we synthesized a novel bio-functionalized composite for the high-efficient and sustainable biodegradation of microcystin-LR by covalent immobilizing Sphingopyxis sp. YF1 onto chitosan-grafted Fe3O4 magnetic particles (Fe3O4@CTS). The Fourier transform infrared spectroscopy (FTIR), Field emission scanning electron microscopy (SEM) and vibrating sample magnetometry (VSM) were utilized to characterize the structural properties of Fe3O4@CTS/Sphingopyxis sp. YF1. The immobilization conditions were optimized. And the MC-LR-degrading capabilities of Fe3O4@CTS/Sphingopyxis sp. YF1 were assessed under various conditions. The results showed that the optimal immobilization conditions containing 1.0 % (v/v) glutaraldehyde, immobilization for 4 h at 30 ℃. The Fe3O4@CTS/Sphingopyxis sp. YF1 showed an attractive degradation performance which possesed a wide torlerance to pH (6.0-9.0) and temperature (25-35 ℃). More interesting is that the Fe3O4@CTS/Sphingopyxis sp. YF1 exhibited significantly increased MC-LR-degrading capabilities after recycling and reusing which degradation rate reached 1.50 µg/mL/h in the sixth cycle, and it was easily recycled by using a magnet (Ms 21.5 emug-1). Two intermediates (tetrapeptide and Adda) and three degradation related genes (mlrA, mlrB and mlrC) were obtained in this study and the pathway for the degradation was proposed. These results revealed that Fe3O4@CTS/Sphingopyxis sp. YF1 can be potentially used for treatment of MC-LR contaminated environment.

Novosphingobium sp. PP1Y as a novel source of outer membrane vesicles.

Outer membrane vesicles (OMVs) are nanostructures of 20-200 nm diameter deriving from the surface of several Gram-negative bacteria. OMVs are emerging as shuttles involved in several mechanisms of communication and environmental adaptation. In this work, OMVs were isolated and characterized from Novosphingobium sp. PP1Y, a Gram-negative non-pathogenic microorganism lacking LPS on the outer membrane surface and whose genome was sequenced and annotated. Scanning electron microscopy performed on samples obtained from a culture in minimal medium highlighted the presence of PP1Y cells embedded in an extracellular matrix rich in vesicular structures. OMVs were collected from the exhausted growth medium during the mid-exponential phase, and purified by ultracentrifugation on a sucrose gradient. Atomic force microscopy, dynamic light scattering and nanoparticle tracking analysis showed that purified PP1Y OMVs had a spherical morphology with a diameter of ca. 150 nm and were homogenous in size and shape. Moreover, proteomic and fatty acid analysis of purified OMVs revealed a specific biochemical "fingerprint", suggesting interesting details concerning their biogenesis and physiological role. Moreover, these extracellular nanostructures do not appear to be cytotoxic on HaCaT cell line, thus paving the way to their future use as novel drug delivery systems.

Requirement of dark culture condition for enlargement of spheroplasts of the aerobic anoxygenic photosynthetic marine bacterium Erythrobacter litoralis.

In the present study, spheroplasts from the aerobic anoxygenic photosynthetic marine bacterium Erythrobacter litoralis were generated and cultivated. In the presence of penicillin, the spheroplasts grew and enlarged in marine broth without undergoing cell division. However, continuous light inhibited their enlargement, and they were therefore cultivated in the dark. Cellular DNA was quantified at various time points (0, 24, and 48 h) and temperatures (20°C, 25°C, and 30°C) using real-time quantitative PCR. The DNA content was highest at 30°C in the absence of penicillin, whereas there was no observable change with exposure to penicillin at all evaluated temperatures. During growth, larger spheroplasts were more frequently observed at 25°C in the presence of penicillin. These results demonstrate that the optimal culture conditions for the enlargement of spheroplasts in E. litoralis differ from those required for cell division.

A cytochrome P450 class I electron transfer system from Novosphingobium aromaticivorans.

Cytochrome P450 (CYP) enzymes of the CYP101 and CYP111 families from Novosphingobium aromaticivorans are heme monooxygenases that catalyze the hydroxylation of a range of terpenoid compounds. CYP101D1 and CYP101D2 oxidized camphor to 5-exo-hydroxycamphor. CYP101B1 and CYP101C1 oxidized beta-ionone to predominantly 3-R-hydroxy-beta-ionone and 4-hydroxy-beta-ionone, respectively. CYP111A2 oxidized linalool to 8-hydroxylinalool. Physiologically, these CYP enzymes could receive electrons from Arx, a [2Fe-2S] ferredoxin equivalent to putidaredoxin from the CYP101A1 system from Pseudomonas putida. A putative ferredoxin reductase (ArR) in the N. aromaticivorans genome, with high amino acid sequence homology to putidaredoxin reductase, has been over-produced in Escherichia coli and found to support substrate oxidation by these CYP enzymes via Arx with both high activity and coupling of product formation to NADH consumption. The ArR/Arx electron-transport chain has been co-expressed with the CYP enzymes in an E. coli host to provide in vivo whole-cell substrate oxidation systems that could produce up to 6.0 g L(-1) of 5-exo-hydroxycamphor at rates of up to 64 microM (gram of cell dry weight)(-1) min(-1). These efficient biocatalytic systems have potential uses in preparative scale whole-cell biotransformations.

Phylogenetic classification of heterotrophic bacteria associated with filamentous marine cyanobacteria in culture.

Fifty-one heterotrophic bacterial strains were isolated from the marine cyanobacterial cultures of heterocystous Nodularia harveyana strain Bo53 and non-heterocystous Oscillatoria brevis strain Bo10. Fluorescence in situ hybridisation and fingerprinting methods were used for a preliminary taxonomical classification of 44 of the 51 isolates. The strains obtained from Bo53 were mostly Alphaproteobacteria (10/24), followed by Bacteroidetes (7/24), and Gammaproteobacteria (3/24). The affiliation of the isolates originating from Bo10 was dominated by Alphaproteobacteria (8/20) and Bacteroidetes (7/20), followed by Gammaproteobacteria (3/20). The 16S rRNA genes of four selected isolates were sequenced. A red-coloured bacterium from Bo53 grouped with the alphaproteobacterial genus Porphyrobacter, while the other three strains, obtained from Bo10, belonged to the alphaproteobacterial genera Roseobacter (pink) and Rhodobacter (colourless), and to the genus Muricauda (yellow) of Bacteroidetes. The findings indicated that the aerobic anoxygenic phototroph Porphyrobacter and its relatives only occurred in Bo10 culture, whereas members of the Roseobacter clade and the Bacteroidetes bacterium Muricauda sp. seemed to be more ubiquitous.

Proposed oxidative metabolic pathway for polypropylene glycol in Sphingobium sp. strain PW-1.

Polypropylene glycol (PPG)-assimilating Sphingobium sp. strain PW-1 was grown on 0.5% PPG 700. PPG and its metabolites were analyzed by MALDI-TOF mass spectrometry. An oxidized form of a terminal alcohol group appeared with each molecular species as a metabolite. Cell-free extract showed PPG dehydrogenase activity. In this way, the oxidative metabolic pathway for PPG was confirmed.

Erythrobacter luteolus sp. nov., isolated from a tidal flat of the Yellow Sea in Korea.

A Gram-negative, non-spore-forming, yellow-pigmented, slightly halophilic bacterial strain, SW-109(T), was isolated from a tidal flat of the Yellow Sea in Korea, and subjected to a polyphasic taxonomic study. This isolate did not produce bacteriochlorophyll a and contained ubiquinone-10 as the predominant respiratory lipoquinone and C(18 : 1)omega7c as the major fatty acid. The DNA G + C content was 60.3 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain SW-109(T) is phylogenetically affiliated to the genus Erythrobacter of the family Sphingomonadaceae. Strain SW-109(T) exhibited levels of 16S rRNA gene sequence similarity to the type strains of Erythrobacter species of 94.0-96.3 %, making it possible to categorize strain SW-109(T) as a species that is separate from previously recognized Erythrobacter species. On the basis of its phenotypic properties and phylogenetic distinctiveness, SW-109(T) (= KCTC 12311(T) = JCM 12599(T)) was classified as the type strain of a novel Erythrobacter species, for which the name Erythrobacter luteolus sp. nov. is proposed.

Novosphingobium taihuense sp. nov., a novel aromatic-compound-degrading bacterium isolated from Taihu Lake, China.

A novel aromatic-compound-degrading bacterium, strain T3-B9(T), was isolated from sediment of Taihu Lake, Jiangsu Province, south-east China. This bacterial isolate assimilated several aromatic compounds such as phenol, aniline, nitrobenzene, 4-chloronitrobenzene and phenanthrene. The taxonomy of strain T3-B9(T) was studied by polyphasic methods. The organism showed a range of phenotypic and chemotaxonomic properties consistent with those of the genus Novosphingobium. The 16S rRNA gene sequence similarity of strain T3-B9(T) to members of the genus Novosphingobium ranged from 91.6 to 97.5 %, and this isolate clustered phylogenetically with members of genus Novosphingobium. The DNA-DNA relatedness values of strain T3-B9(T) to the most phylogenetically related species, Novosphingobium subterraneum DSM 12447(T), Novosphingobium aromaticivorans ATCC 700278(T) and Novosphingobium stygium ATCC 700280(T), were 31, 33 and 14 %, respectively. The combined genotypic and phenotypic data show that strain T3-B9(T) represents a novel species of the genus Novosphingobium, for which the name Novosphingobium taihuense sp. nov. is proposed. The type strain is T3-B9(T) (=AS 1.3432(T) = JCM 12465(T)).

Sphingopyxis baekryungensis sp. nov., an orange-pigmented bacterium isolated from sea water of the Yellow Sea in Korea.

A Gram-negative, motile, slightly halophilic bacterial strain, SW-150(T), was isolated from sea water of the Yellow Sea, Korea, and was characterized by a polyphasic taxonomic approach. Strain SW-150(T) grew optimally at 25-30 degrees C and in the presence of 2 % (w/v) NaCl. The isolate could be distinguished from other Sphingopyxis species in producing an orange pigment. It contained ubiquinone-10 as the predominant respiratory lipoquinone and C(18 : 1)omega7c and C(17 : 1)omega6c as the major fatty acids. No 3-hydroxy fatty acids were detected. Major polar lipids were sphingoglycolipid, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 63 mol%. Comparative 16S rRNA gene sequence analyses showed that strain SW-150(T) was phylogenetically affiliated to the genus Sphingopyxis of the family Sphingomonadaceae. Similarity values between the 16S rRNA gene sequences of strain SW-150(T) and the type strains of Sphingopyxis species ranged from 91.6 to 94.2 %, making it possible to categorize strain SW-150(T) as a species that is separate from previously described Sphingopyxis species. On the basis of phenotypic properties and phylogenetic distinctiveness, SW-150(T) (=KCTC 12231(T) = DSM 16222(T)) should be classified as the type strain of a novel Sphingopyxis species, for which the name Sphingopyxis baekryungensis sp. nov. is proposed.

Erythrobacter aquimaris sp. nov., isolated from sea water of a tidal flat of the Yellow Sea in Korea.

Three Gram-negative, non-motile, non-spore-forming, slightly halophilic rods (strains SW-110(T), SW-116 and SW-140) were isolated from sea water of a tidal flat of the Yellow Sea in Korea and subjected to a polyphasic taxonomic study. The three isolates did not produce bacteriochlorophyll a and were characterized chemotaxonomically by having ubiquinone-10 as the predominant respiratory lipoquinone and C(18 : 1)omega7c and C(17 : 1)omega6c as the major fatty acids. The DNA G+C content of the three isolates was between 62.2 and 62.9 mol%. Strains SW-110(T), SW-116 and SW-140 showed no difference in their 16S rRNA gene sequences, and their mean level of DNA-DNA relatedness was 94.8 %. Phylogenetic analyses based on 16S rRNA gene sequences showed that the three strains form a distinct phylogenetic lineage within the cluster comprising Erythrobacter species. Similarities between the 16S rRNA gene sequences of strains SW-110(T), SW-116 and SW-140 and the type strains of Erythrobacter species ranged from 98.4 % (with Erythrobacter longus) to 97.7 % (with Erythrobacter flavus). Levels of DNA-DNA relatedness between strains SW-110(T), SW-116 and SW-140 and the type strains of all recognized Erythrobacter species were in the range 5.3-12.7 %. On the basis of polyphasic taxonomic data, strains SW-110(T), SW-116 and SW-140 were classified as a novel Erythrobacter species, for which the name Erythrobacter aquimaris sp. nov. is proposed. The type strain is SW-110(T) (=KCCM 41818(T)=JCM 12189(T)).

Sphingomonas oligophenolica sp. nov., a halo- and organo-sensitive oligotrophic bacterium from paddy soil that degrades phenolic acids at low concentrations.

The taxonomic position of a halo- and organo-sensitive, oligotrophic soil bacterium, strain S213(T), was investigated. Cells were Gram-negative, non-motile, strictly aerobic, yellow-pigmented rods of short to medium length on diluted nutrient broth. When 0.1-0.4 % (w/v) NaCl was added to diluted media composed of peptone and meat extract, growth was inhibited with increasing NaCl concentration and the cells became long aberrant forms. When 6 mM CaCl(2) was added, the cells grew quite normally and aberrant cells were no longer found at 0.1-0.5 % (w/v) NaCl. Chemotaxonomically, strain S213(T) contains chemical markers that indicate its assignment to the Sphingomonadaceae: the presence of ubiquinone Q-10 as the predominant respiratory quinone, C(18 : 1) and C(16 : 0) as major fatty acids, C(14 : 0) 2-OH as the major 2-hydroxy fatty acid and sphingoglycolipids. 16S rRNA gene sequence analysis indicated that strain S213(T) belongs to the genus Sphingomonas, exhibiting high sequence similarity to the 16S rRNA gene sequences of Sphingomonas mali IFO 15500(T) (98.3 %), Sphingomonas pruni IFO 15498(T) (98.0 %), Sphingomonas asaccharolytica IFO 15499(T) (97.9 %) and Sphingomonas echinoides DSM 1805(T) (97.8 %). The results of DNA-DNA hybridization experiments and its phenotypic characteristics clearly distinguished the strain from its nearest neighbours and demonstrate that strain S213(T) represents a novel Sphingomonas species, for which the name Sphingomonas oligophenolica sp. nov. is proposed. The type strain is S213(T) (=JCM 12082(T)=CIP 107926(T)).

Porphyrobacter donghaensis sp. nov., isolated from sea water of the East Sea in Korea.

Two Gram-negative, motile, non-spore-forming, bacteriochlorophyll a-containing slightly halophilic strains, SW-132(T) and SW-158, were isolated from sea water of the East Sea in Korea, and subjected to a polyphasic taxonomic study. The two isolates were characterized chemotaxonomically as having Q-10 as the predominant respiratory lipoquinone and major amounts of unsaturated fatty acids C(18 : 1)omega7c and C(17 : 1)omega6c. The DNA G+C contents of the two strains were in the range 66.8-65.9 mol%. The 16S rRNA gene sequences of strains SW-132(T) and SW-158 were 99.9 % (1 nt difference) similar and their mean level of DNA-DNA relatedness was 86 %. The 16S rRNA gene sequence analysis showed that strains SW-132(T) and SW-158 are phylogenetically closely related to Porphyrobacter species and Erythromicrobium ramosum. Similarities between the 16S rRNA gene sequences of strains SW-132(T) and SW-158 and the type strains of Porphyrobacter species and E. ramosum ranged from 97.8 to 99.0 %. DNA-DNA relatedness data indicated that strains SW-132(T) and SW-158 are members of a genomic species that is separate from the four Porphyrobacter species. On the basis of phenotypic and phylogenetic data and genetic distinctiveness, strains SW-132(T) (=KCTC 12229(T)=DSM 16220(T)) and SW-158 (=KCTC 12230) are classified as a novel Porphyrobacter species, for which the name Porphyrobacter donghaensis sp. nov. is proposed.

Isolation and characterization of Erythrobacter sp. strains from the upper ocean.

Seven strains of marine aerobic anoxygenic phototrophs belonging to the genus Erythrobacter were isolated. The strains were characterized regarding their physiological and biochemical properties, 16S rDNA and pufM gene sequences, morphological features, substrate preference, as well as pigment and lipid composition. All strains had functional type-2 reaction centers containing bacteriochlorophyll, served by small, light-harvesting complex 1, and were photosynthetically competent. In addition, large pools of carotenoids were found, but only some of the accessory pigments transfer energy to the reaction centers. All of the isolates were facultative photoheterotrophs. They required an organic carbon substrate for growth; however, they are able to supplement a significant fraction of their metabolic requirements with photosynthetically derived energy.