Responses of dinoflagellate cells to ultraviolet-C irradiation.

Dinoflagellates are important aquatic microbes and major harmful algal bloom (HAB) agents that form invasive species through ship ballast transfer. UV-C installations are recommended for ballast treatments and HAB controls, but there is a lack of knowledge in dinoflagellate responses to UV-C. We report here dose-dependent cell cycle delay and viability loss of dinoflagellate cells irradiated with UV-C, with significant proliferative reduction at 800 Jm-2 doses or higher, but immediate LD50 was in the range of 2400-3200 Jm-2 . At higher dosages, some dinoflagellate cells surprisingly survived after days of recovery incubation, and continued viability loss, with samples exhibiting DNA fragmentations per proliferative resumption. Sequential cell cycle postponements, suggesting DNA damages were repaired over one cell cycle, were revealed with flow cytometric analysis and transcriptomic analysis. Over a sustained level of other DNA damage repair pathways, transcript elevation was observed only for several components of base pair repair and mismatch repair. Cumulatively, our findings demonstrated special DNA damage responses in dinoflagellate cells, which we discussed in relation to their unique chromo-genomic characters, as well as indicating resilience of dinoflagellate cells to UV-C.

Phytochemical profiles of edible flowers of medicinal plants of Dendrobium officinale and Dendrobium devonianum.

The discovery of new edible flowers that are nontoxic, innocuous flowers having human health benefits, surveys of their phytochemicals and utilization are of great scientific and commercial interest. Dendrobium officinale and Dendrobium devonianum are precious Traditional Chinese Medicine. During the massive commercial cultivation, a lot of flowers were produced and certified as edible flowers, and the phytochemical profiles and bioactivities warrant evaluate. The present study aimed to investigate the phytochemicals and antioxidative activities in flowers of D. officinale (DOF) and D. devonianum (DDF). In total, 474 metabolites were identified using a widely targeted metabonomics method, 16 amino acids and 6 flavonoids were measured using high-performance liquid chromatography (HPLC), and 8 fatty acids were detected using gas chromatography-mass spectrometry (GC-MS). Both flowers contained various amino acids, including 7 essential amino acids, diverse flavonoids, especially quercetin, kaempferol and their derivatives, and high levels of methyl linoleate and methyl linolenate. The relative levels of quercetin, kaempferol and their glycosides were higher in DDF than in DOF, whereas the relative levels of several flavonoids C-glycosides were high in DOF. Ethanol extracts of both DOF and DDF showed antioxidative capacities including the scavenging of 1,1-diphenyl-2-picrylhydrazyl and hydroxyl radicals. Both edible flowers contained flavonoids, amino acids, and fatty acids and have antioxidative activities, which should be explored for use in functional foods and pharmaceuticals.

High Performance Liquid Chromatography and Metabolomics Analysis of Tannase Metabolism of Gallic Acid and Gallates in Tea Leaves.

Tannase (E.C. 3.1.1.20) is hypothesized to be involved in the metabolism of gallates and gallic acid (GA) in pu-erh tea fermentation. In this work, we measured tannase in Aspergillus niger fermented tea leaves and confirmed the production of fungal tannase during pu-erh tea fermentation. A decrease in catechin and theaflavin gallates and a significant increase in GA content and the relative peak areas of ethyl gallate, procyanidin A2, procyanidin B2, procyanidin B3, catechin-catechin-catechin, epiafzelechin, and epicatechin-epiafzelechin [variable importance in the projection (VIP) > 1.0, p < 0.05, and fold change (FC) > 1.5] were observed using high performance liquid chromatography (HPLC) and metabolomics analysis of tea leaves fermented or hydrolyzed by tannase. In vitro assays showed that hydrolysis by tannase or polymerization of catechins increased the antioxidant activity of tea leaves. In summary, we identified a metabolic pathway for gallates and their derivatives in tea leaves hydrolyzed by tannase as well as associated changes in gallate and GA concentrations caused by fungal tannase during pu-erh tea fermentation.

DNA Damage Response Pathways in Dinoflagellates.

Dinoflagellates are a general group of phytoplankton, ubiquitous in aquatic environments. Most dinoflagellates are non-obligate autotrophs, subjected to potential physical and chemical DNA-damaging agents, including UV irradiation, in the euphotic zone. Delay of cell cycles by irradiation, as part of DNA damage responses (DDRs), could potentially lead to growth inhibition, contributing to major errors in the estimation of primary productivity and interpretations of photo-inhibition. Their liquid crystalline chromosomes (LCCs) have large amount of abnormal bases, restricted placement of coding sequences at the chromosomes periphery, and tandem repeat-encoded genes. These chromosome characteristics, their large genome sizes, as well as the lack of architectural nucleosomes, likely contribute to possible differential responses to DNA damage agents. In this study, we sought potential dinoflagellate orthologues of eukaryotic DNA damage repair pathways, and the linking pathway with cell-cycle control in three dinoflagellate species. It appeared that major orthologues in photoreactivation, base excision repair, nucleotide excision repair, mismatch repair, double-strand break repair and homologous recombination repair are well represented in dinoflagellate genomes. Future studies should address possible differential DNA damage responses of dinoflagellates over other planktonic groups, especially in relation to possible shift of life-cycle transitions in responses to UV irradiation. This may have a potential role in the persistence of dinoflagellate red tides with the advent of climatic change.

Hyphomonas pacifica sp. nov., isolated from deep sea of the Pacific Ocean.

Three Gram-negative, aerobic, non-spore-forming, oval- to pear-shaped bacterial strains (T16B2(T), T24B3, and C76AD) were isolated from petroleum-degrading microbial communities through an enrichment of sediments and seawater samples from the Pacific Ocean. Phylogenetic analysis showed strains T16B2(T), T24B3, and C76AD to form a robust clade together with Hyphomonas atlanticus 22II1-22F38(T) and Hyphomonas beringensis 25B14_1(T) (16S rRNA identity ≥99.6 %). Genomic average nucleotide identity and DNA-DNA hybridization estimate values between strain T16B2(T) and nine type strains of the genus Hyphomonas are in the range of 82.9-88.2 and 18.3-33.6 %, respectively. The major cellular fatty acids in strains T16B2(T), T24B3, and C76AD are C16:0, C17:0, C18:1 ω7c-methyl, and summed feature 8 (C18:1 ω6c/ω7c). The DNA G+C content of strain T16B2(T) is 58.5 %. The predominant respiratory quinone of strain T16B2(T) is Q-11. Polar lipids comprise three unidentified glycolipids, one unidentified phospholipid, and two polar lipids. Combined phenotypic and genotypic data show strains T16B2(T), T24B3, and C76AD to represent a novel species of the genus Hyphomonas, for which the name Hyphomonas pacifica sp. nov. is proposed, with type strain T16B2(T) (=LMG 27911(T) = MCCC 1A04387(T)).

The status of the species Hyphomonas rosenbergii Weiner et al. 2000. Request for an Opinion.

On the basis of 16S rRNA gene sequence analysis and several key phenotypic features, it was ascertained that the culture cited as the type strain of the species Hyphomonas rosenbergii, ATCC 43869(T), does not conform to the description of the species, [Weiner, R. M., Melick, M., O'Neill, K. & Quintero, E. (2000). Int J Syst Evol Microbiol 50, 459-469]. The type strain does not exist in any other established culture collection or with the authors who described this species. Therefore, it cannot be included in any scientific study. It is proposed that the Judicial Commission place the name Hyphomonas rosenbergii on the list of rejected names if a suitable replacement type strain is not found or a neotype is not proposed within two years following the publication of this Request for an Opinion.

Draft Genome Sequence of the Algicidal Bacterium Mangrovimonas yunxiaonensis Strain LY01.

Mangrovimonas yunxiaonensis LY01, a novel bacterium isolated from mangrove sediment, showed high algicidal effects on harmful algal blooms of Alexandrium tamarense. Here, we present the first draft genome sequence of this strain to further understanding of the functional genes related to algicidal activity.

Hyphomonas beringensis sp. nov. and Hyphomonas chukchiensis sp. nov., isolated from surface seawater of the Bering Sea and Chukchi Sea.

Two Gram-negative, non-spore-forming, oval to pear shaped motile strains, designated 25B14_1(T) and BH-BN04-4(T), isolated from surface seawater from the Bering Sea and Chukchi Sea, respectively, were subjected to polyphasic taxonomic study. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that strains 25B14_1(T) and BH-BN04-4(T) clustered together with Hyphomonas atlanticus 22II1-22F38(T) and Hyphomonas oceanitis DSM 5155(T), respectively, within genus Hyphomonas. Based on whole genome sequence analysis, the calculated DDH and ANIm values between strain 25B14_1(T) and BH-BN04-4(T) are 18.8 and 83.19% respectively. The calculated DDH values of strain 25B14_1(T) and BH-BN04-4(T) with seven type strains ranged from 18.2 to 19.9% and from 18.4 to 40.4%, respectively. The ANIm values of strain 25B14_1(T) and BH-BN04-4(T) with seven type strains ranged from 83.00 to 84.67% and from 83.14 to 90.58%, respectively. Both isolates were found to contain Q-11 as the predominant respiratory quinone. The major fatty acids of strain 25B14_1(T) were identified as C(16:0), C(17:0), C(18:1)ω7c-methyl and Summed Feature 8 (C(18:1)ω6c/ω7c as defined by MIDI), while in the case of strain BH-BN04-4(T) they were identified as C(16:0), C(18:1)ω7c-methyl and Summed Feature 8 (C(18:1)ω6c/ω7c). The G+C contents of 25B14_1(T) and BH-BN04-4(T) were determined to be 58.4 and 61.0 mol%, respectively. The combined phenotypic and genotypic data show that the two isolates each represent novel species of the genus Hyphomonas, for which the names Hyphomonas beringensis sp. nov. and Hyphomonas chukchiensis sp. nov. are proposed, with the type strain 25B14_1(T) (=MCCC 1A07321(T) = LMG 27914(T)) and BH-BN04-4(T) (=MCCC 1A07481(T) = LMG 27915(T)), respectively.

Hyphomonas atlanticus sp. nov., isolated from the Atlantic Ocean and emended description of the genus Hyphomonas.

A taxonomic study was carried out on strains 22II1-22F38(T) and 22II-S13e, which were isolated from sea water and sediment from the Atlantic Ocean, respectively. The two strains were Gram-negative, oxidase and catalase positive, oval to pear shaped, and motile by a single polar flagellum. Phylogenetic analysis based on 16S rRNA gene sequences indicated that both strains belonged to the genus Hyphomonas, with highest sequence similarity (98.2%) to the type strains H. jannaschiana DSM 5153(T) and H. johnsonii ATCC 43964(T). The genomic ANIm values and DNA-DNA hybridization estimate values between strain 22II1-22F38(T) and seven type strains ranged from 82.84% to 84.10% and from 18.0% to 19.1%, respectively. Isolate 22II1-22F38(T) had a G+C content of 58.3% and used Q-11 as the predominant respiratory quinone. The combined phenotypic and genotypic data showed that both strains represented a novel species of the genus Hyphomonas, for which the name Hyphomonas atlanticus sp. nov. is proposed, with the type strain being 22II1-22F38(T) (=LMG 27916(T)=MCCC 1A09418(T)). In addition, we conclude that Hyphomonas hirschiana is a later synonym of Hyphomonas neptunium.

Multilocus sequence analysis for the assessment of phylogenetic diversity and biogeography in hyphomonas bacteria from diverse marine environments.

Hyphomonas, a genus of budding, prosthecate bacteria, are primarily found in the marine environment. Seven type strains, and 35 strains from our collections of Hyphomonas, isolated from the Pacific Ocean, Atlantic Ocean, Arctic Ocean, South China Sea and the Baltic Sea, were investigated in this study using multilocus sequence analysis (MLSA). The phylogenetic structure of these bacteria was evaluated using the 16S rRNA gene, and five housekeeping genes (leuA, clpA, pyrH, gatA and rpoD) as well as their concatenated sequences. Our results showed that each housekeeping gene and the concatenated gene sequence all yield a higher taxonomic resolution than the 16S rRNA gene. The 42 strains assorted into 12 groups. Each group represents an independent species, which was confirmed by virtual DNA-DNA hybridization (DDH) estimated from draft genome sequences. Hyphomonas MLSA interspecies and intraspecies boundaries ranged from 93.3% to 96.3%, similarity calculated using a combined DDH and MLSA approach. Furthermore, six novel species (groups I, II, III, IV, V and XII) of the genus Hyphomonas exist, based on sequence similarities of the MLSA and DDH values. Additionally, we propose that the leuA gene (93.0% sequence similarity across our dataset) alone could be used as a fast and practical means for identifying species within Hyphomonas. Finally, Hyphomonas' geographic distribution shows that strains from the same area tend to cluster together as discrete species. This study provides a framework for the discrimination and phylogenetic analysis of the genus Hyphomonas for the first time, and will contribute to a more thorough understanding of the biological and ecological roles of this genus.

Galbibacter marinus sp. nov., isolated from deep-sea sediment.

A taxonomic study was carried out on a novel bacterium, designated strain ck-I2-15(T), which was isolated from deep-sea sediment collected from the South-west Indian Ocean Ridge. Cells of strain ck-I2-15(T) were Gram-reaction-negative, rod-shaped, non-motile, moderately halophilic and capable of denitrification. Growth was observed with 0-9 % (w/v) NaCl and at temperatures of 10-37 °C. The novel strain was unable to degrade gelatin. The dominant cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 9 (iso-C17 : 1ω9c and/or 10-methyl C16 : 0). The major respiratory quinone was MK6 and the polar lipid profile comprised phosphatidylethanolamine, one unidentified phospholipid, two unidentified aminolipids, one unidentified glycolipid and four other unidentified lipids. The G+C content of the genomic DNA was 38 mol%. 16S rRNA gene sequence comparison indicated that strain ck-I2-15(T) was most closely related to Galbibacter mesophilus Mok-17(T) (92.9 % sequence similarity), followed by 'Joostella atrarenae' M1-2 (92.8 %), Joostella marina En5(T) (92.7 %) and Zhouia amylolytica HN-171(T) (91.6 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain ck-I2-15(T) formed a clade with the genus Galbibacter, within the family Flavobacteriaceae. Several phenotypic properties allowed strain ck-I2-15(T) to be distinguished from its closest phylogenetic relatives. On the basis of the phenotypic and phylogenetic data, strain ck-I2-15(T) represents a novel species of the genus Galbibacter, for which the name Galbibacter marinus is proposed. The type strain is ck-I2-15(T) ( = CCTCC AB 209062(T) = LMG 25228(T) = MCCC 1A03044(T)).

Genome sequence of Galbibacter marinum type strain ck-I2-15.

Galbibacter marinum strain ck-I2-15(T) was isolated from an arsenite-resistant consortium enriched from the deep sea sediment of a hydrothermal vent field on the Southwest Indian Ocean Ridge. Here, we present the draft genome of strain ck-I2-15(T), which contains 3,572,447 bp with a G+C content of 37.04% and contains 3,099 protein-coding genes and 38 tRNA genes.