Transcriptomic profiles reveal the genome-wide responses of the harmful dinoflagellate Cochlodinium polykrikoides when exposed to the algicide copper sulfate.

BACKGROUND: Harmful algal blooms (HABs) caused by the dinoflagellate Cochlodinium polykrikoides lead to severe environmental impacts in oceans worldwide followed by huge economic losses. Algicide agent copper sulfate (CuSO4) is regard as an economical and effective agent for HABs mitigation; its biochemical and physiological effects were revealed in C. polykrikoides. However, molecular mechanisms of CuSO4 effect on the C. polykrikoides, even other HAB species, have not been investigated. The present study investigated the transcriptional response of C. polykrikoides against CuSO4 treatments, with the aim of providing certain molecular mechanism of CuSO4 effect on the C. polykrikoides blooms. RESULTS: RNA-seq generated 173 million reads, which were further assembled to 191,212 contigs. 43.3 %, 33.9 %, and 15.6 % of contigs were annotated with NCBI NR, GO, and KEGG database, respectively. Transcriptomic analysis revealed 20.6 % differential expressed contigs, which grouped into 8 clusters according to K-means clustering analysis, responding to CuSO4; 848 contigs were up-regulated and 746 contigs were down-regulated more than 2-fold changes from 12 h to 48 h exposure. KEGG pathway analysis of eukaryotic homologous genes revealed the differentially expressed genes (DEGs) were involved in diverse pathway; amongst, the genes involved in the translation, spliceosome, and/or signal transduction genes were highly regulated. Most of photosystem related genes were down-regulated and most of mitochondria related genes were up-regulated. In addition, the genes involved in the copper ion binding or transporting and antioxidant systems were identified. Measurement of chlorophyll fluorescence showed that photosynthesis was significantly inhibited by CuSO4 exposure. CONCLUSIONS: This study reported the first transcriptome of the C. polykrikoides. The widely differential expressed photosystem genes suggested photosynthetic machinery were severely affected, and may further contribute to the cell death. Furthermore, gene translation and transcription processes may be disrupted, inhibiting cell growth and proliferation, and possibly accelerating cell death. However, antioxidant systems resistant to CuSO4 caused stress; mitochondrion may compensate for photosynthesis efficiency decreasing caused energy deficiency. In addition, various signal transduction pathways may be involved in the CuSO4 induced regulation network in the C. polykrikoides. These data provide the potential transcriptomic mechanism to explain the algicide CuSO4 effect on the harmful dinoflagellate C. polykrikoides.

Effects of Biocide Chlorine on Biochemical Responses of the Dinoflagellate Prorocentrum minimum.

Effects of the biocide sodium hypochlorite (NaOCl) on the dinoflagellate Prorocentrum minimum were assessed. Growth rate, pigment concentrations, and chlorophyll autofluorescence were monitored up to 72 hours after NaOCl exposure, and these parameters showed dose- and time-dependent decrease. The 72-hour EC50 was 0.983 mg/L. Additionally, enzymatic activities of lipid peroxidation and reduced glutathione were significantly altered with increasing NaOCl and exposure time. Thus, NaOCl at doses of 0.5 mg/L induces physiological and biochemical changes in P. minimum, suggesting that chlorine concentrations observed in power plant discharges and in drinking water systems are potentially detrimental to microalgae.

Molecular characterisation and expression analysis of a novel calreticulin (CRT) gene in the dinoflagellate Prorocentrum minimum.

Calreticulin is a multifunctional Ca(2+)-binding protein that has been well characterised in mammalian cells. Here, we characterised a novel calreticulin (CRT2) gene in the dinoflagellate Prorocentrum minimum, which codes for a calcium binding protein and examined its expression pattern following the addition of calcium and ethylene glycol-bis(2-aminoethylether)-N,N,N',N'-tetraacetic acid (EGTA). PmCRT2 is encoded in the nuclear genome of P. minimum without introns. The full length cDNA of PmCRT2 was found to be 1,493 base pairs (bp) in length, which ranges from the dinoflagellate spliced leader sequence to the poly (A) tail and contains a 1,173-bp open reading frame, a 70-bp 5'-untranslated region (UTR), and a 207-bp 3'-UTR. On the basis of in silico analyses that revealed the distinct domain architectures of PmCRT2, we classified this protein under the calreticulin family. PmCRT2 gene expression was up-regulated in the presence of excess calcium in a dose-dependent manner; however, PmCRT2 expression was down-regulated by the addition of EGTA. These results clearly indicate that PmCRT2 plays a vital role in calcium regulation and this may be involved in the stress response of P. minimum.

Effect of climate-ocean changes on the abundance of Pacific saury.

Effects of ocean climate changes on the population structure and abundance of Pacific saury (Cololabis sira) were investigated on the basis of climate indices, sea surface temperature (SST) anomalies, catch and body size information from the Tsushima Warm Current (TWC) region (Yellow Sea, East China Sea and East/Japan Sea) during the period 1950-2010. It is suggested that oceanic regime shifts in the early 1970s, late 1980s and late 1990s occurred in the TWC region in winter, but the regime shifts in the mid-1970s and in the late 1980s were not evident in the spring SST anomaly series. The abundance and body size of Pacific saury fluctuated in association with the winter oceanic changes in the TWC region. The catch rates and abundance of large size saury were far bellow average during their northward migrations in the TWC region in the years with abnormally cool winters (e.g., 1963, 1970, 1977, 1981-1989 and 2006) and above average in the years with warm winters. These patterns demonstrate decadal-scale variations together with large inter-annual fluctuations in the structure and abundance of Pacific saury in association with the climatic-oceanic changes. These results, along with an alternation of dominant pelagic fish species, indicate the status of the saury population in the TWC region is in good condition, similar to that in the Kuroshio-Oyashio Current (KOC) region during the warm regime after the late 1980s climate regime shift.

Genetic analysis of the purplish Washington clam (Saxidomus purpuratus Sowerby) of Korean coastal waters.

To investigate the genetic structure of the purplish Washington clam population, Saxidomus purpuratus Sowerby, in Korea. A portion of mitochondrial COI gene sequences (605 bp) for phylogenetic comparison was determined. Sequence analysis of 62 individuals collected from six regions revealed 13 haplotypes. Phylogenetic analysis using Phylogeny Inference Package (PHYLIP) subdivided the purplish Washington clam into two clades (termed clade A and B), weak supported groups (< 65 of bootstrap value). This haplotype subdivision was also in accordance with geographic separation; one each at Masan, Yeosu, Samcheonpo, Jubyeon and Geojedo, and the other at Sineju. Population genetic analysis subdivided these two population groups with a geographic distance (d = 0.431, p = 0.379). Furthermore, in the Sineju population, the maximum sequence divergence (2.67%) and minimum nucleotide diversity (0.0012426) were shown in which might be reflective of a relatively small population size and the geographical isolation of the population as compared with other populations. However, a very high migration rate (N(m) = 59.62-infinite) and a very low level of geographic distance (F(ST) = -0.076-0.055) were noted to exist among the South and East Sea populations, suggesting that individuals between populations should show a significantly active genetic mixing and migration regardless of geography. These findings allowed us to conclude that the purplish Washington clam populations occurring in the South and East Sea were formed with randomly dispersed individuals.

Grimontia marina sp. nov., a marine bacterium isolated from the Yellow Sea.

A novel species belonging to the genus Grimontia is described in this study. A Gram-negative, chemoheterotrophic, obligately aerobic, catalase- and oxidase-positive, motile by a single polar flagellum, and rod-shaped bacterium, designated IMCC5001(T), was isolated from surface seawater of the Yellow Sea. Strain IMCC5001(T) grew optimally at 30°C in the presence of 3.5% NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate was related most closely to Grimontia hollisae with a sequence similarity of 95.8%, and formed a robust phyletic lineage with Grimontia hollisae. Differential physiological characteristics between the new strain and Grimontia hollisae KCCM 41680(T) and chemotaxonomic characterization including determination of DNA G+C content, fatty acid methyl esters, quinone composition, and polar lipid profiles justified the assignment of strain IMCC5001(T) to the genus Grimontia as a novel species. In conclusion, strain IMCC5001(T) represents a new species, for which the name Grimontia marina sp. nov. is proposed, with the type strain IMCC5001(T) (=KCTC 22666(T) =NBRC 105794(T)).