Conversion of estriol to estrone: A bacterial strategy for the catabolism of estriol.

Natural estrogens, including estrone (E1), 17ß-estradiol (E2), and estriol (E3), are potentially carcinogenic pollutants commonly found in water and soil environments. Bacterial metabolic pathway of E2 has been studied; however, the catabolic products of E3 have not been discovered thus far. In this study, Novosphingobium sp. ES2-1 was used as the target strain to investigate its catabolic pathway of E3. The metabolites of E3 were identified by high performance liquid chromatography-high resolution mass spectrometry (HPLC-HRMS) combined with stable 13C3-labeling. Strain ES2-1 could almost completely degrade 20 mg∙L-1 of E3 within 72 h under the optimal conditions of 30°C and pH 7.0. When inoculated with strain ES2-1, E3 was initially converted to E1 and then to 4-hydroxyestrone (4-OH-E1), which was then cleaved to HIP (metabolite A6) via the 4, 5-seco pathway or cleaved to the B loop via the 9,10-seco pathway to produce metabolite with a long-chain ketone structure (metabolite B4). Although the ring-opening sequence of the above two metabolic pathways was different, the metabolism of E3 was achieved especially through continuous oxidation reactions. This study reveals that, E3 could be firstly converted to E1 and then to 4-OH-E1, and finally degraded into small molecule metabolites through two alternative pathways, thereby reducing E3 pollution in water and soil environments.

Novosphingobium beihaiensis sp. nov., a novel pesticide-tolerant bacterium isolated from mangrove sediments.

A novel Novosphingobium species, designated strain B2638T, was isolated from mangrove sediments which was collected from Beibu Gulf, Beihai, P. R. China. The isolate could grow in the presence of chlorpyrifos. Phylogenetic analysis based on 16S rRNA gene sequence revealed that the isolate belonged to the genus Novosphingobium, showing 99.9% sequence similarity with N. decloroationis 502str22T and less than 98% similarity with other type strain of species of this genus. Molecular typing by BOX-PCR divided strain B2638T and N. declorationis 502str22T into two clusters and indicated that they were not identical. Genomic comparison referenced by values of the DNA-DNA hybridization (dDDH) and the average nucleotide identity (ANI) between strain B2638T and its close phylogenetic neighbors were 20.0-29.5% and 75.3-85.3%, respectively, that were lower than proposed thresholds for bacterial species delineation. The major fatty acids (> 10%) were identified as C18:1 ω7c, C17:1 iso ω9c and C16:0. The main polar lipids contained diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid, phosphatidyl glycerol, unidentified lipid and unidentified aminolipid. Results from phenotypic, chemotaxonomic and genotypic analyses proposed that strain B2638T (= MCCC 1K07406T = KCTC 72968 T) is represented a novel species in the genus Novosphingobium, for which the names Novosphingobium beihaiensis sp. nov. is proposed.

Metagenomic insights into the mechanisms of triphenyl phosphate degradation by bioaugmentation with Sphingopyxis sp. GY.

Biodegradation of triphenyl phosphate (TPHP) by Sphingopyxis sp. GY was investigated, and results demonstrated that TPHP could be completely degraded in 36 h with intracellular enzymes playing a leading role. This study, for the first time, systematically explores the effects of the typical brominated flame retardants, organophosphorus flame retardants, and heavy metals on TPHP degradation. Our findings reveal that TCPs, BDE-47, HBCD, Cd and Cu exhibit inhibitory effects on TPHP degradation. The hydrolysis-, hydroxylated-, monoglucosylated-, methylated products and glutathione (GSH) conjugated derivative were identified and new degradation pathway of TPHP mediated by microorganism was proposed. Moreover, toxicity evaluation experiments indicate a significant reduction in toxicity following treatment with Sphingopyxis sp. GY. To evaluate its potential for environmental remediation, we conducted bioaugmentation experiments using Sphingopyxis sp. GY in a TPHP contaminated water-sediment system, which resulted in excellent remediation efficacy. Twelve intermediate products were detected in the water-sediment system, including the observation of the glutathione (GSH) conjugated derivative, monoglucosylated product, (OH)2-DPHP and CH3-O-DPHP for the first time in microorganism-mediated TPHP transformation. We further identify the active microbial members involved in TPHP degradation within the water-sediment system using metagenomic analysis. Notably, most of these members were found to possess genes related to TPHP degradation. These findings highlight the significant reduction of TPHP achieved through beneficial interactions and cooperation established between the introduced Sphingopyxis sp. GY and the indigenous microbial populations stimulated by the introduced bacteria. Thus, our study provides valuable insights into the mechanisms, co-existed pollutants, transformation pathways, and remediation potential associated with TPHP biodegradation, paving the way for future research and applications in environmental remediation strategies.

Fine-scale mapping of the microbiome on phylloplane and spermoplane of aromatic and non-aromatic rice genotypes.

Adaxial, abaxial phylloplane (leaf), and spermoplane (seed) are proximal yet contrasting habitats for a microbiota that needs to be adequately explored. Here, we proposed novel methods to decipher the adaxial/abaxial-phylloplane and spermoplane-microbiomes. Comparison of 22 meta barcoded-NGS datasets (size of total data set-1980.48 Mb) enabled us to fine-map the microbiome of the rice foliar niche, which encompasses the lower, middle, top leaf as well panicle. Here, the total- and the cultivable-microbiome profiling revealed 157 genera representing ten phyla and 87 genera from 4 bacterial phyla, respectively, with a predominance of Proteobacteria and Actinobacteria. Interestingly, more bacterial communities (124-genera) preferred the abaxial than the adaxial phylloplane (104-genera) and spermoplane (67-genera) for colonization. The microbiome profiles were nearly identical on the aromatic (125-genera) and non-aromatic rice (116-genera) with high representation of Pantoea, Methylobacterium, Curtobacterium, Sphingopyxis, and Microbacterium. The culturomics investigation confirmed the abundance of Pantoea, Chryseobacterium, Pseudomonas, Acinetobacter, Sphingobacterium, and Exiguobacterium. One hundred bacterial isolates characterized and identified by polyphasic-taxonomic tools revealed the dominance of Acinetobacter, Chryseobacterium, Enterobacter, Massilia, Pantoea, Pseudomonas, and Stenotrophomonas on adaxial/abaxial-phylloplane and spermoplane. The study culminated in identifying hitherto unexplored bacterial communities on the adaxial/abaxial phylloplane and spermoplane of rice that can be harnessed for microbiome-assisted rice cultivation in the future.

Highly efficient bioconversion of icariin to icaritin by whole-cell catalysis.

BACKGROUND: Icaritin is an aglycone of flavonoid glycosides from Herba Epimedii. It has good performance in the treatment of hepatocellular carcinoma in clinical trials. However, the natural icaritin content of Herba Epimedii is very low. At present, the icaritin is mainly prepared from flavonoid glycosides by α-L-rhamnosidases and ß-glucosidases in two-step catalysis process. However, one-pot icaritin production required reported enzymes to be immobilized or bifunctional enzymes to hydrolyze substrate with long reaction time, which caused complicated operations and high costs. To improve the production efficiency and reduce costs, we explored α-L-rhamnosidase SPRHA2 and ß-glucosidase PBGL to directly hydrolyze icariin to icaritin in one-pot, and developed the whole-cell catalytic method for efficient icaritin production. RESULTS: The SPRHA2 and PBGL were expressed in Escherichia coli, respectively. One-pot production of icaritin was achieved by co-catalysis of SPRHA2 and PBGL. Moreover, whole-cell catalysis was developed for icariin hydrolysis. The mixture of SPRHA2 cells and PBGL cells transformed 200 g/L icariin into 103.69 g/L icaritin (yield 95.23%) in 4 h in whole-cell catalysis under the optimized reaction conditions. In order to further increase the production efficiency and simplify operations, we also constructed recombinant E. coli strains that co-expressed SPRHA2 and PBGL. Crude icariin extracts were also efficiently hydrolyzed by the whole-cell catalytic system. CONCLUSIONS: Compared to previous reports on icaritin production, in this study, whole-cell catalysis showed higher production efficiency of icaritin. This study provides promising approach for industrial production of icaritin in the future.

Bioconversion of 4-hydroxyestradiol by extradiol ring-cleavage dioxygenases from Novosphingobium sp. PP1Y.

Livestock breeding activities and pharmaceutical wastes lead to considerable accumulation of steroid hormones and estrogens in wastewaters. Here estrogens act as pro-cancerogenic agents and endocrine disruptors interfering with the sexual development of aquatic animals and having toxic effects in humans. Environmental bacteria play a vital role in estrogens degradation. Their wide reservoir of enzymes, such as ring cleavage dioxygenases (RCDs), can degrade the steroid nucleus, catalyzing the meta-cleavage of A, B or D steroid rings. In this work, 4 extra-diol ring cleavage dioxygenases (ERCDs), PP28735, PP26077, PP00124 and PP00193, were isolated from the marine sphingomonad Novosphingobium sp. PP1Y and characterized. Enzymes kinetic parameters were determined on different synthetic catecholic substrates. Then, the bioconversion of catechol estrogens was evaluated. PP00124 showed to be an efficient catalyst for the degradation of 4-hydroxyestradiol (4-OHE2), a carcinogenic hydroxylated derivate of E2. 4-OHE2 complete cleavage was obtained using PP00124 both in soluble form and in whole recombinant E. coli cells. LC-MS/MS analyses confirmed the generation of a semialdehyde product, through A-ring meta cleavage. To the best of our knowledge, PP00124 is the first characterized enzyme able to directly degrade 4-OHE2 via meta cleavage. Moreover, the complete 4-OHE2 biodegradation using recombinant whole cells highlighted advantages for bioremediation purposes.

Hephaestia mangrovi sp. nov., a novel endophytic bacterium isolated from Aegiceras corniculatum.

A Gram-stain-negative, aerobic, motile, rod-shaped bacterium, designated CMS5P-6T, was isolated from a surface-sterilized bark of Aegiceras corniculatum collected from Guangxi Zhuang Autonomous Region, PR China, and investigated by a polyphasic approach to determine its taxonomic position. Strain CMS5P-6T was found to grow optimally with 0-1 % (w/v) NaCl, at 30 °C and pH 6.0-7.0. Substrate mycelia and aerial mycelia were not formed, and no diffusible pigments were observed on the media tested. Phylogenetic analysis showed that strain CMS5P-6T showed high 16S rRNA gene sequence similarity of 96.7 % to Hephaestia caeni DSM 25527T and Sphingomonas colocasiea CC-MHH0539T. The average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity values between strain CMS5P-6T and H. caeni DSM 25527T were 78.0, 21.7 and 70.8 %, respectively. The average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity values between strain CMS5P-6T and S. colocasiea JCM 31229T were 74.0, 19.9 and 61.4 %, respectively. Phylogenomic analyses based on genome sequences showed that strain CMS5P-6T and H. caeni DSM 25527T formed a distinct cluster within the family Sphingomonadaceae and far away from S. colocasiea JCM 31229T. The DNA G+C content of strain CMS5P-6T was determined to be 65.6 mol%. The cell-wall peptidoglycan was found to contain meso-diaminopimelic acid as the diagnostic diamino acid and ubiquinone Q-10 was identified as the respiratory lipoquinone. The polar lipids were found to comprise diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, sphingoglycolipid and two unidentified aminolipids, and the major fatty acids were identified as C18 : 1 ω7c, C19 : 0 cycloω8c and C16 : 0. On the basis of phylogenetic, genomic, chemotaxonomic and phenotypic data, strain CMS5P-6T can be concluded to represent a novel species of the genus Hephaestia, for which the name Hephaestia mangrovi sp. nov. is proposed. The type strain is CMS5P-6T (=JCM 33125T=CGMCC 1.13868T).

Winogradskyella luteola sp.nov., Erythrobacter ani sp. nov., and Erythrobacter crassostrea sp.nov., isolated from the hemolymph of the Pacific Oyster Crassostrea gigas.

Three new bacterial strains, WHY3T, WH131T, and WH158T, were isolated and described from the hemolymph of the Pacific oyster Crassostrea gigas utilizing polyphasic taxonomic techniques. The 16S rRNA gene sequence analysis revealed that strain WHY3T was a member of the genus Winogradskyella, whereas strains WHI31T and WH158T were members of the genus Erythrobacter. According to the polygenomic study the three strains formed individual lineages with strong bootstrap support. The comparison of dDDH-and ANI values, percentage of conserved proteins (POCP), and average amino acid identity (AAl) between the three strains and their relatives established that the three strains represented two separate genera. Menaquinone-6 was reported as the major respiratory quinone in strain WHY3T and Ubiquinone-10 for strains WH131T and WH158T, respectively. The major cellular fatty acids for strain WHY3T were C15:0, anteiso-C15:1 ω7c, iso-C15:0, C16:1ω7c. The major cellular fatty acids for strains WH131T and WH158T were C14:02-OH and t18:1ω12 for WH131T and C17:0, and C18:1ω7c for strain WH158T. Positive Sudan Black B staining Indicated the presence of polyhydroxyalkanoic acid granules for strains WH131T and WH158T but not for strain WHY3T. The DNA G + C contents of strains WHY3T, WH131T and WH158T were 34.4, 59.7 and 56.6%, respectively. Gene clusters predicted some important genes involved in the bioremediation process. Due to the accomplishment of polyphasic taxonomy, we propose three novel species Winogradskyella luteola sp.nov. (type strain WHY3T = DSM 111804T = NCCB 100833T), Erythrobacter ani sp.nov. (WH131T = DSM 112099T = NCCB 100824T) and Erythrobacter crassostrea sp.nov. (WH158T = DSM 112102T = NCCB 100877T).

Sphingopyxis yananensis sp. nov., a novel 2-nitropropane degrading bacterium isolated from a microbial fermentation bed substrate.

A rod-shaped, Gram-negative staining strain, FBM22T, was isolated from a microbial fermentation bed substrate from a pig farm. Its colonies appeared yellow and were 0.5-1.2 mm in diameter. Cells were 0.3-0.5 µm wide, 0.5-0.83 µm long. Optimal growth occurred at 30 °C and pH 7.0-8.0; NaCl was not required for growth. The strain performed denitrification and nitrate reduction functions. And it could produce catalase. FBM22-1T utilized the following organic substrates for growth: tyrosine, glutamic acid, D-glucose, and galactose. The novel isolate could degrade 2-nitropropane as carbon and nitrogen source. The dominant respiratory quinone was Q-10. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine and phosphatidylethanolamine. C18:1 ω7c, C16:1 ω7c and/ or C16:1 ω6c, and C14:0 2-OH were the major (≥ 8%) fatty acids. The G+C content was 56.8 mol%. FBM22T was found to be a member of the genus Sphingopyxis in the family Sphingomonadaceae of the class Alphaproteobacteria. It had the highest sequence similarity with the type strains Sphingopyxis terrae subsp. ummariensis UI2T (96.47%) and Sphingopyxis terrae subsp. terrae NBRC 15098T (96.40%). Furthermore, FBM22T had 18.7% and 18.4% relatedness (based on digital DNA-DNA hybridization) with its two relatives (S. terrae subsp. ummariensis UI2T and S. terrae subsp. terrae NBRC 15098T). The morphological, physiological, and genotypic differences identified in this study support the classification of FBM22T as a novel species within the genus Sphingopyxis, for which the name Sphingopyxis yananensis sp. nov. is proposed. The type strain is FBM22T (= KCTC 82290T = CCTC AB2020286T).

Stakelama flava sp. nov., a novel endophytic bacterium isolated from a branch of Kandelia candel.

A Gram-stain-negative, aerobic, motile, non-spore-forming, short-rod-shaped strain that did not produce diffusible pigment, designated CBK3Z-3T, was isolated from a branch of Kandelia candel, collected from the Beilun Estuary National Nature Reserve in Guangxi Zhang Autonomous Region, PR China, and investigated by a polyphasic approach to determine its taxonomic position. Strain CBK3Z-3T grew at pH 5.0-10.0 (optimum, pH 8.0), 20-37 °C (optimum, 25-30 °C) and with 0-10 % (w/v) NaCl (optimum, 2-3 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CBK3Z-3T was closely related to species of genus Stakelama and had the highest 16S rRNA gene sequence similarity of 98.7 % to Stakelama pacifica CGMCC 1.7294T. The DNA G+C content value of strain CBK3Z-3T was 62.6 mol%. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid and the polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid, an unidentified aminolipid and an unidentified lipid. The major fatty acids were C18 : 1 ω7c and C16 : 0. The average nucleotide identity, estimated digital DNA-DNA hybridization and average amino acid identity values between strain CBK3Z-3T and the type strain of Stakelama pacifica CGMCC 1.7294T were 80.4, 23.1 and 81.5 %, respectively. Based on the phylogenetic, phenotypic and chemotaxonomic data, strain CBK3Z-3T should be designated as a novel species of the genus Stakelama, for which the name Stakelama flava sp.nov. is proposed. The type strain is CBK3Z-3T (=JCM 34534T=CGMCC 1.18972T).

Erythrobacter rubeus sp. nov., a carotenoid-producing alphaproteobacterium isolated from coastal seawater.

A study based on a polyphasic taxonomic approach was carried out to identify and classify a novel marine alphaproteobacterium, designated as KMU-140T, isolated from coastal seawater collected at Jeju Island, Republic of Korea. Cells of strain KMU-140T were spherical, Gram-stain-negative, reddish-orange colored, strictly aerobic, catalase- and oxidase-positive, non-motile, and chemoorganoheterotrophic. The novel isolate was able to grow at NaCl concentrations of 0-5%, pH 6.0-9.5, and 10-45 °C. A phylogenetic analysis based on the 16S rRNA gene sequence showed that strain KMU-140T belongs to the family Erythrobacteraceae and was most closely related to Erythrobacter longus OCh101T (98.7%). Strain KMU-140T contained ubiquinone-10 (Q-10) as the only respiratory quinone and C18:1 ω7c, iso-C18:0, and C16:0 as the main (> 10%) cellular fatty acids. Strain KMU-140T produced carotenoid compounds that rendered the cell biomass a reddish-orange color. The assembled draft genome size of strain KMU-140T was 3.04 Mbp with G + C content of 60.6 mol%. The average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and average amino acid identity (AAI) values of KMU-140T and the species of the genus Erythrobacter were found to be 76.6-78.4%, 14.0-18.7%, and 69.6-77.8%, respectively. Phosphatidylethanolamine, phosphatidylglycerol, an unidentified phospholipid, and two unidentified lipids were identified as major polar lipids. On the basis of the polyphasic taxonomic features presented, the strain is considered to represent a novel species of the genus Erythrobacter for which the name Erythrobacter rubeus sp. nov. is proposed. The type strain of E. rubeus sp. nov. is KMU-140T (= KCCM 90479T = NBRC 115159T).

Bioaugmentation with zeolite-immobilized bacterial consortium OPK results in a bacterial community shift and enhances the bioremediation of crude oil-polluted marine sandy soil microcosms.

A pyrene-degrading consortium OPK containing Mycolicibacterium strains PO1 and PO2, Novosphingobium pentaromativorans PY1 and Bacillus subtilis FW1 effectively biodegraded medium- and long-chain alkanes as well as mixed hydrocarbons in crude oil. The detection of alkB and CYP153 genes in the genome of OPK members supports its phenotypic ability to effectively degrade a broad range of saturated hydrocarbons in crude oil. Zeolite-immobilized OPK was developed as a ready-to-use bioproduct and it exhibited 74% removal of 1000 mg L-1 crude oil within 96 h in sterilized seawater without nutrient supplementation and maintained high crude oil-removal activity under a broad range of pH values (5.0-9.0), temperatures (30-40 °C) and salinities (20-60‰). In addition, the immobilized OPK retained a high crude oil removal efficacy in semicontinuous experiments and showed reusability for at least 5 cycles. Remarkably, bioaugmentation with zeolite-immobilized OPK in sandy soil microcosms significantly increased crude oil (10,000 mg kg-1 soil) removal from 45% to 80.67% within 21 days compared to biostimulation and natural attenuation. Moreover, bioaugmentation with exogenous immobilized OPK stimulated an increase in the relative abundances of Alcanivorax genus, indigenous hydrocarbon-degrading bacteria, which in turn enhanced removal efficiency of crude oil contamination from sandy soil microcosms. The results indicate positive interactions between the bioaugmented immobilized consortium, harboring Mycolicibacterium as a key player, and indigenous Alcanivorax, which exhibited crucial functions for improving crude oil removal efficacy. The knowledge obtained forms an important basis for further synthesis and handling of a promising bio-based product for enhancing the in situ bioremediation of crude oil-polluted marine environments.

Erythrobacter aurantius sp. nov., isolated from intertidal seawater in Taizhou.

A Gram-stain-negative, aerobic, chemoheterotrophic and rod-shaped strain, designated as C5T, was isolated from intertidal surface seawater in Taizhou, Zhejiang Province, PR China and characterized using a polyphasic taxonomic approach. Strain C5T could produce carotenoids and bacteriochlorophyll a. Growth was observed at 20-45 °C, at pH 6.0-9.0 and with 0-8.0 % (w/v) NaCl. The 16S rRNA gene sequence identity analysis revealed that strain C5T was the most closely related to Qipengyuania nanhaisediminis CGMCC 1.7715T (98.8%) and Erythrobacter litoralis DSM 8509T (98.7%). The phylogenetic reconstruction based on core genes demonstrated that strain C5T was clustered into the members of the genus Erythrobacter. The average nucleotide identity and digital DNA-DNA hybridization values between strain C5T and Erythrobacter type strains were lower than 76 and 25 %, respectively. The predominant and minor respiratory quinones were identified as ubiquinone-10 and ubiquinone-9. The major fatty acids were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and iso-C18 : 0. Polar lipids included phosphatidylethanolamine, phosphatidylglycerol, a glycosphingolipid and an unidentified aminolipid. Based on the genetic, chemotaxonomic and phenotypic data, strain C5T is concluded to represent a novel species in the genus Erythrobacter, for which the name Erythrobacter aurantius sp. nov. is proposed. The type strain is C5T (=MCCC 1K05108T=KCTC 92307T).

Identification of the EdcR Estrogen-Dependent Repressor in Caenibius tardaugens NBRC 16725: Construction of a Cellular Estradiol Biosensor.

In this work, Caenibius tardaugens NBRC 16725 (strain ARI-1) (formerly Novosphingobium tardaugens) was isolated due to its capacity to mineralize estrogenic endocrine disruptors. Its genome encodes the edc genes cluster responsible for the degradation of 17ß-estradiol, consisting of two putative operons (OpA and OpB) encoding the enzymes of the upper degradation pathway. Inside the edc cluster, we identified the edcR gene encoding a TetR-like protein. Genetic studies carried out with C. tardaugens mutants demonstrated that EdcR represses the promoters that control the expression of the two operons. These genetic analyses have also shown that 17ß-estradiol and estrone, the second intermediate of the degradation pathway, are the true effectors of EdcR. This regulatory system has been heterologously expressed in Escherichia coli, foreseeing its use to detect estrogens in environmental samples. Genome comparisons have identified a similar regulatory system in the edc cluster of Altererythrobacter estronivorus MHB5, suggesting that this regulatory arrangement has been horizontally transferred to other bacteria.

Parasphingopyxis marina sp. nov. isolated from coastal seawater.

A Gram-stain-negative, aerobic, yellow-pigmented and non-motile rod-shaped bacterium, designated as GrpM-11T, was isolated from coastal seawater collected from the East Sea, Republic of Korea. Strain GrpM-11T could grow at 10-40 °C (optimum, 35 °C), at pH 5.5-9.5 (optimum, pH 7.0) and in the presence of 0-8 % (w/v) NaCl (optimum, 3-4 %). Cells hydrolysed aesculin, gelatin and casein, but could not reduce nitrate to nitrite. The 16S rRNA gene sequence analysis showed that this strain formed a distinct phylogenic lineage with Parasphingopyxis algicola ATAX6-5T (96.2 % sequence identity) and Parasphingopyxis lamellibrachiae DSM 26725T (96.2 % identity) and belonged to the genus Parasphingopyxis. The predominant isoprenoid quinone was ubiquinone-10. The polar lipid profile of strain GrpM-11T consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, sphingoglycolipid and three unknown glycolipids. Cellular fatty acid analysis indicated that summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c; 42.8 %), C16 : 0 (19.0 %), C18 : 1 ω7c 11-methyl (13.3 %) and C18 : 1 ω7c (8.0 %) were the major fatty acids. The DNA G+C content of strain GrpM-11T was 63.7 mol%. Through whole genome sequence comparisons, the digital DNA-DNA hybridization and average nucleotide identity values between strain GrpM-11T and two species of the genus Parasphingopyxis were revealed to be in the ranges of 19.0-22.0 % and 76.3-79.7 %, respectively. Based on the results of polyphasic analysis, strain GrpM-11T represents a novel species of the genus Parasphingopyxis, for which the name Parasphingopyxis marina sp. nov. is proposed. The type strain is GrpM-11T (KCCM 43343T=JCM 34665T).

Novosphingobium aureum sp. nov., a marine bacterium isolated from salt flat sediment.

A Gram-stain-negative, aerobic, pale yellow-coloured, rod-shaped marine bacterium designated strain YJ-S2-02T was isolated from salt flat sediment sampled in Yongyu-do, Republic of Korea. Strain YJ-S2-02T grew at pH 6.0-9.0 (optimum, pH 7.0), 10-40 °C (optimum, 30 °C) and with optimum 1 % (w/v) NaCl. The 16S rRNA gene sequence analysis indicated that strain YJ-S2-02T was closely related to Novosphingobium naphthalenivorans NBRC 102051T (97.8 %) followed by Novosphingobium mathurense SM117T (97.5 %), Novosphingobium indicum H25T (97.3 %), Novosphingobium pentaromativorans US6-1T (96.8 %), Novosphingobium fontis STM-14T (96.6 %), Novosphingobium endophyticum EGI60015T (96.5 %), Novosphingobium naphthae D39T (96.5 %) and Novosphingobium malaysiense MUSC 273T (95.9 %). The average nucleotide identity and estimated DNA-DNA hybridization values between YJ-S2-02T and related type strains were 77.0-77.9 % and 19.1-24.0 %. Strain YJ-S2-02T was characterized as having Q-10 as the predominant respiratory quinone and the principal fatty acids (>10 %) were summed feature 8 (C18 : 1 ω6c/ω7c, 20.7 %), C18 : 3 ω6c (16.3 %) and C17 : 1 ω6c (11.8 %). The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, sphingolipids and two unidentified lipids. The DNA G+C content of strain YJ-S2-02T was 65.6 mol%. On the basis of the polyphasic taxonomic evidence presented in this study, YJ-S2-02T should be classified as representing a novel species within the genus Novosphingobium, for which name Novosphingobium aureum is proposed, with the type strain YJ-S2-02T (=KACC 21677T =KCTC 72891T=JCM 33996T).

QM calculations predict the energetics and infrared spectra of transient glutamine isomers in LOV photoreceptors.

Photosensory receptors containing the flavin-binding light-oxygen-voltage (LOV) domain are modular proteins that fulfil a variety of biological functions ranging from gene expression to phototropism. The LOV photocycle is initiated by blue-light and involves a cascade of intermediate species, including an electronically excited triplet state, that leads to covalent bond formation between the flavin mononucleotide (FMN) chromophore and a nearby cysteine residue. Subsequent conformational changes in the polypeptide chain arise due to the remodelling of the hydrogen bond network in the cofactor binding pocket, whereby a conserved glutamine residue plays a key role in coupling FMN photochemistry with LOV photobiology. Although the dark-to-light transition of LOV photosensors has been previously addressed by spectroscopy and computational approaches, the mechanistic basis of the underlying reactions is still not well understood. Here we present a detailed computational study of three distinct LOV domains: EL222 from Erythrobacter litoralis, AsLOV2 from the second LOV domain of Avena sativa phototropin 1, and RsLOV from Rhodobacter sphaeroides LOV protein. Extended protein-chromophore models containing all known crucial residues involved in the initial steps (femtosecond-to-microsecond) of the photocycle were employed. Energies and rotational barriers were calculated for possible rotamers and tautomers of the critical glutamine side chain, which allowed us to postulate the most energetically favoured glutamine orientation for each LOV domain along the assumed reaction path. In turn, for each evolving species, infrared difference spectra were constructed and compared to experimental EL222 and AsLOV2 transient infrared spectra, the former from original work presented here and the latter from the literature. The good agreement between theory and experiment permitted the assignment of the majority of observed bands, notably the ∼1635 cm-1 transient of the adduct state to the carbonyl of the glutamine side chain after rotation. Moreover, both the energetic and spectroscopic approaches converge in suggesting a facile glutamine flip at the adduct intermediate for EL222 and more so for AsLOV2, while for RsLOV the glutamine keeps its initial configuration. Additionally, the computed infrared shifts of the glutamine and interacting residues could guide experimental research addressing early events of signal transduction in LOV proteins.

A crucial review on polycyclic aromatic Hydrocarbons - Environmental occurrence and strategies for microbial degradation.

Over the last century, contamination of polycyclic aromatic hydrocarbons (PAHs) has risen tremendously due to the intensified industrial activities like petrochemical, pharmaceutical, insecticides and fertilizers applications. PAHs are a group of organic pollutants with adverse effects on both humans and the environment. These PAHs are widely distributed in various ecosystems including air, soil, marine water and sediments. Degradation of PAHs generally occurs through processes like photolysis, adsorption, volatilization, chemical degradation and microbial degradation. Microbial degradation of PAHs is done by the utilization of diverse microorganisms like algae, bacteria, fungi which are readily compatible with biodegrading/bio transforming PAHs into H2O, CO2 under aerobic, or CH4 under anaerobic environment. The rate of PAHs degradation using microbes is mainly governed by various cultivation conditions like temperature, pH, nutrients availability, microbial population, chemical nature of PAHs, oxygen and degree of acclimation. Several microbial species including Selenastrum capricornutum, Ralstonia basilensis, Acinetobacter haemolyticus, Pseudomonas migulae, Sphingomonas yanoikuyae and Chlorella sorokiniana are known to degrade PAHs via biosorption and enzyme-mediated degradation. Numerous bacterial mediated PAHs degradation methods are studied globally. Among them, PAHs degradation by bacterial species like Pseudomonas fluorescence, Pseudomonas aeruginosa, Rhodococcus spp., Paenibacillus spp., Mycobacterium spp., and Haemophilus spp., by various degradation modes like biosurfactant, bioaugmentation, biostimulation and biofilms mediated are also investigated. In contrarily, PAHs degradation by fungal species such as Pleurotus ostreatus, Polyporus sulphureus, Fusarium oxysporum occurs using the activity of its ligninolytic enzymes such as lignin peroxidase, laccase, and manganese peroxidase. The present review highlighted on the PAHs degradation activity by the algal, fungal, bacterial species and also focused on their mode of degradation.

Parasphingorhabdus halotolerans sp. nov. isolated from marine sediment in Jeju Island.

A Gram-stain-negative, catalase- and oxidase-positive, rod-shaped bacterium, designated as JK6T was isolated from a coastal marine sediment in Jeju Island. Strain JK6T was characterized by polyphasic investigation including genome features. It grew at pH 5.0-9.0 (optimum 7.5), 18-30 °C (optimum 25 °C) and 1.0-7.0% (w/v) NaCl (optimum 2.0%). Strain JK6T utilized D-mannose, D-glucose, L-fucose, propionate and acetate as carbon and energy sources. The sole quinone was ubiquinone-10, and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, and sphingolipid. Strain JK6T was closely related to Parasphingorhabdus flavimaris SW-151T (98.2%), Parasphingorhabdus marina DSM 22363T (97.6%) and Parasphingorhabdus litoris FR1093T (97.6%) based on 16S rRNA gene sequence similarity. Genome length and GC content were 3.29 Mbp and 53.0%, respectively. Digital DNA-DNA relatedness, average nucleotide identity, and average amino acid identity between strain JK6T and P. flavimaris SW-151T were 16.6%, 73.9%, and 77.6%, respectively. These results showed that the strain can be recognized as a novel bacterium named Parasphingorhabdus halotolerans. The type strain of Parasphingorhabdus halotolerans sp. nov. is JK6T (= KCTC 72818T = VTCC 910111T).

Comparative genomic analysis of the genus Novosphingobium and the description of two novel species Novosphingobium aerophilum sp. nov. and Novosphingobium jiangmenense sp. nov.

Members of the genus Novosphingobium are well known for their metabolically versatile and great application potential in pollution elimination. The three novel bacterial strains, designated 4Y4T, 4Y9, and 1Y9AT, were isolated from aquaculture water and characterized by using a polyphasic taxonomic approach. The 16S rRNA gene sequences phylogenetic analysis revealed that the three strains belonged to the genus Novosphingobium. The phylogenomic analysis indicated that the three strains formed two independent and robust branches distinct from all reference strains. The analyses of dDDH values and ANIs between the three strains and their relatives further demonstrated that the three strains represented two different novel genospecies. Comparative genomic analysis of the three isolates and 32 type strains of the genus Novosphingobium showed that the most important central metabolic pathways of these strains appeared to be similar, while specific and specialized metabolic pathways were flexible and variable among these strains. Chemotaxonomic characterization exhibited that the predominant cellular fatty acids were summed feature 8, summed feature 3, and C14:0 2OH; the major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidyldimethylethanolamine, phosphatidylglycerol, and sphingoglycolipid; the major respiratory quinone and polyamine were Q-10 and spermidine. The DNA G + C contents were 67.6 and 64.7 %. Based on the genotypic and phenotypic characteristics, strains 4Y4T and 1Y9AT are concluded to represent two novel species of the genus Novosphingobium, for which the names Novosphingobium aerophilum sp. nov. (type strain 4Y4T = GDMCC 1.1828 T = KACC 21946 T) and Novosphingobium jiangmenense sp. nov. (type strain 1Y9AT = GDMCC 1.1936 T = KACC 22085 T) are proposed.