Phylogenetic relationships of Cochlodinium polykrikoides Margalef (Gymnodiniales,Dinophyceae) from the Mediterranean Sea and the implications of its global biogeography

Although the diversity of dinoflagellates has been intensively studied in several locations in the Mediterranean Sea since the 1950s, it is only during the last two decades that the morphotype of the toxic unarmoured dinoflagellate Cochlodinium polykrikoides Margalef has been detected, coinciding with its apparent worldwide expansion in marine coastal waters. In this study, vegetative cells of C. polykrikoides morphotype from the Catalan coast (NW Mediterranean Sea) were detected and isolated, and the DNA from collected cells was sequenced. While in the Mediterranean Sea, detections are scarce and C. polykrikoides is consistently present at low concentrations, we reported exceptional blooms of this species, in which the maximum abundance reached 2 × 10⁴ cells L⁻¹. Partial LSU rDNA region sequences showed that most C. polykrikoides populations from the Catalan coast formed a new differentiated ribotype, but others were included within the ‘Philippines’ ribotype, demonstrating their coexistence in the Mediterranean Sea. Thus, the current biogeographic nomenclature of the ribotypes is likely to be invalid with respect to the available information from populations comprising the ‘Philippines’ ribotype. The phylogeny suggests the existence of cryptic species that should be evaluated for species-level status. Accordingly, the ribotype determination must be carefully evaluated for all detections and bloom events, since accurate characterization of the morphology, ecophysiology and distribution of the ribotypes are not well resolved.     

Dynamics of bacterial community structure during blooms of Cochlodinium polykrikoides (Gymnodiniales,Dinophyceae) in Korean coastal waters

Recent studies of dinoflagellates have reported that blooms can be closely related to the characteristics of the associated bacteria, but studies of the correlation between the toxic dinoflagellate, Cochlodinium polykrikoides and their associated bacterial community composition has not been explored. To understand this correlation, changes in bacterial community structure through the evolution of a C. polykrikoides bloom in Korean coastal waters via clone library analysis were investigated. Although there were no apparent changes in physio-chemical factors during the onset of the C. polykrikoides bloom, the abundance of bacteria bourgeoned in parallel with C. polykrikoides densities. Alpha-, gamma-proteobacteria and Flavobacteria were found to be dominant phyletic groups during C. polykrikoides blooms. The proportion of gamma-proteobacteria was lower (11.8%) during peak of the bloom period compared to the post-bloom period (26.2%). In contrast, alpha-proteobacteria increased in dominance during blooms. Among the alpha-proteobacteria, members of Rhodobacterales abruptly increased from 38% of the alpha-proteobacteria before the bloom to 74% and 56% during the early bloom and peak bloom stages, respectively. Moreover, multiple sites concurrently hosting C. polykrikoides blooms also contained high portions of Rhodobacterales and principal component analysis (PCA) demonstrated that Rhodobacterales had a positive, significant correlation with C. polykrikoides abundances (p ≤ 0.01, Pearson correlation coefficients). Collectively, this study reveals the specific clades of bacteria that increase (Rhodobacterales) and decrease (gamma-proteobacteria) in abundance C. polykrikoides during blooms.     

Resolving the intra-specific succession within Cochlodinium polykrikoides populations in southern Korean coastal waters via use of quantitative PCR assays

While the toxic dinoflagellate Cochlodinium polykrikoides is known to form blooms that are maintained for extended periods, the genetic differentiation of these blooms are currently unknown. To assess this, we developed a real-time PCR assay to quantify C. polykrikoides at the intra-specific level, and applied this assay to field samples collected in Korean coastal waters from summer through fall. Assays were successfully developed to target the large-subunit ribosomal RNA region of the three major ribotypes of C. polykrikoides: Philippines, East Asian, and American/Malaysian. Significant linear relationships (r² ≥ 0.995) were established between C_t and the log of the copy number for each ribotype qPCR assay. Using these assays, C. polykrikoides blooms in Korean coastal waters were found to be comprised of Philippines and East Asian ribotypes but not the American/Malaysian ribotype. The Philippines ribotype was found to be highly abundant during summer bloom initiation and peak, whereas the East Asian ribotype became the dominant ribotype in the fall. As such, this newly developed qPCR assay can be used to quantify the cryptic ecological succession of sub-populations of C. polykrikoides during blooms that light microscopy and previously developed qPCR assays cannot resolve.     

Identification of the dinoflagellate community during Cochlodinium polykrikoides (Dinophyceae) blooms using amplified rDNA melting curve analysis and real-time PCR probes

The dinoflagellate community present during blooms of the fish killing dinoflagellate Cochlodinium polykrikoides was characterized by DNA melting curve analysis and direct sequencing of the SSU rDNA amplified from environmental sample extracts. PCR amplification of genomic DNA from Gaedo water samples using dinoflagellate-specific SSU rDNA primers yielded 280 clones, which were screened by closed tube PCR-melting curve analysis targeting a region of the SSU rDNA, enabling high throughput analysis. Twenty-eight clones producing distinct melting curve patterns were sequenced, and their phylogenetic information revealed that C. polykrikoides co-occurred with morphologically similar species including Gymnodinium impudicum and Gymnodinium catenatum. Temporal variations of C. polykrikoides and G. impudicum abundances in South Sea were also examined by species-specific real-time TaqMan-based PCR probes developed in this study. C. polykrikoides- and G. impudicum-specific real-time PCR probes were designed targeting the internal transcribed spacer 2 ribosomal DNA region. The probe specificity was confirmed by testing against related dinoflagellates and verified by sequencing PCR products from environmental samples. The real-time PCR assays showed that C. polykrikoides cell densities peaked in August at 16,928 cells mL^?1, while G. impudicum was present at low abundances (below 25 cells mL^?1). Our amplified rDNA melting curve protocol provides a facile method for the characterization of the dinoflagellate community, and the real-time PCR assay could be an alternative method for rapid and sensitive enumeration of harmful dinoflagellates in the marine environment.     

Control of ichthyotoxic Cochlodinium polykrikoides using the mixotrophic dinoflagellate Alexandrium pohangense: A potential effective sustainable method

Red tides dominated by Cochlodinium polykrikoides often lead to great economic losses and some methods of controlling these red tides have been developed. However, due to possible adverse effects and the short persistence of their control actions, safer and more effective sustainable methods should be developed. The non-toxic dinoflagellate Alexandrium pohangense is known to grow well mixotrophically feeding on C. polykrikoides, and populations are also maintained by photosynthesis. Thus, compared with other methods, the use of mass-cultured A. pohangense is safer and the effects can be maintained in the long term. To develop an effective method, the concentrations of A. pohangense cells and culture filtrate resulting in the death of C. polykrikoides cells were determined by adding the cells or filtrates to cultured and natural populations of C. polykrikoides. Cultures containing 800 A. pohangense cells ml⁻¹ eliminated almost all cultured C. polykrikoides cells at a concentration of 1000 cells ml⁻¹ within 24 h. Furthermore, the addition of A. pohangense cultures at a concentration of 800 cells ml⁻¹ to C. polykrikoides populations from a red-tide patch resulted in the death of most C. polykrikoides cells (99.8%) within 24 h. This addition of A. pohangense cells also lowered the abundances of total phototrophic dinoflagellates excluding C. polykrikoides, but did not lower the abundance of total diatoms. Filtrate from 800 cells ml⁻¹ A. pohangense cultures reduced the population of cultured C. polykrikoides by 80% within 48 h. This suggests that A. pohangense cells eliminate C. polykrikoides by feeding and releasing extracellular compounds. Over time, A. pohangense concentrations gradually increased when incubated with C. polykrikoides. Thus, an increase in the concentration of A. pohangense by feeding may lead to A. pohangense cells eliminating more C. polykrikoides cells in larger volumes. Based on the results of this study, a 1 m³ stock culture of A. pohangense at 4000 cells ml⁻¹ is calculated to remove all C. polykrikoides cells in ca. 200 m³ within 6 days. Furthermore, maintenance of A. pohangense populations through photosynthesis prepared A. pohangense to eliminate C. polykrikoides cells in future red-tide patches. Moreover, incubation of A. pohangense at 2000 cells ml⁻¹ with juvenile olive flounder Paralichthys olivaceus for 3 days did not result in the death of fish. Therefore, the method developed in this study is a safe and effective way of controlling C. polykrikoides populations and can be easily applied to aqua-tanks on land.     

Mapping the Distribution of Cysts from the Toxic Dinoflagellate Cochlodinium polykrikoides in Bloom-Prone Estuaries by a Novel Fluorescence In Situ Hybridization Assay

Cochlodinium polykrikoides is a cosmopolitan dinoflagellate that is notorious for causing fish-killing harmful algal blooms (HABs) across North America and Asia. While recent laboratory and ecosystem studies have definitively demonstrated that Cochlodinium forms resting cysts that may play a key role in the dynamics of its HABs, uncertainties regarding cyst morphology and detection have prohibited even a rudimentary understanding of the distribution of C. polykrikoides cysts in coastal ecosystems. Here, we report on the development of a fluorescence in situ hybridization (FISH) assay using oligonucleotide probes specific for the large subunit (LSU) ribosomal DNA (rDNA) of C. polykrikoides. The LSU rDNA-targeted FISH assay was used with epifluorescence microscopy and was iteratively refined to maximize the fluorescent reaction with C. polykrikoides and minimize cross-reactivity. The final LSU rDNA-targeted FISH assay was found to quantitatively recover cysts made by North American isolates of C. polykrikoides but not cysts formed by other common cyst-forming dinoflagellates. The method was then applied to identify and map C. polykrikoides cysts across bloom-prone estuaries. Annual cyst and vegetative cell surveys revealed that elevated densities of C. polykrikoides cysts (>100 cm⁻³) during the spring of a given year were spatially consistent with regions of dense blooms the prior summer. The identity of cysts in sediments was confirmed via independent amplification of C. polykrikoides rDNA. This study mapped C. polykrikoides cysts in a natural marine setting and indicates that the excystment of cysts formed by this harmful alga may play a key role in the development of HABs of this species.     

Differential effects of typhoons on ichthyotoxic Cochlodinium polykrikoides red tides in the South Sea of Korea during 2012–2014

The harmful dinoflagellate Cochlodinium polykrikoides is known to cause fish death by gill-clogging when its abundance exceeds approximately 1000 cells ml⁻¹. Thus, red tides of this dinoflagellate have caused considerable loss in the aquaculture industry worldwide. Typhoons carrying strong winds and heavy rains may alter the process of red tide events. To investigate the effects of typhoons on C. polykrikoides red tides, daily variations in the abundance of C. polykrikoides, and wind speeds in three study areas in the South Sea of Korea were analyzed during the periods of C. polykrikoides red tides and the passage of 14 typhoons during 2012–2014. The typhoons differentially affected Cochlodinium red tides during the study period, and the daily maximum wind speed generated by the typhoon was critical. Four typhoons with daily maximum wind speeds of >14 m s⁻¹ eliminated Cochlodinium red tides, while three typhoons with daily maximum wind speed of 5–14 m s⁻¹ only lowered the abundance. However, other typhoons with daily maximum wind speeds of <5 m s⁻¹ had no marked effect on the Cochlodinium abundance. Therefore, typhoons may sometimes eliminate C. polykrikoides red tide events, or reduce cell abundances to a level that is not harmful to caged fish cultivated in aquaculture industries. Thus, typhoons should be considered when compiling red tide dynamics and fish-kill models.     

Controls on the initiation and development of blooms of the dinoflagellate Cochlodinium polykrikoides Margalef in lower Chesapeake Bay and its tributaries

Massive blooms of the dinoflagellate Cochlodinium polykrikoides occur annually in the Chesapeake Bay and its tributaries. The initiation of blooms and their physical transport has been documented and the location of bloom initiation was identified during the 2007 and 2008 blooms. In the present study we combined daily sampling of nutrient concentrations and phytoplankton abundance at a fixed station to determine physical and chemical controls on bloom formation and enhanced underway water quality monitoring (DATAFLOW) during periods when blooms are known to occur. While C. polykrikoides did not reach bloom concentrations until late June during 2009, vegetative cells were present at low concentrations in the Elizabeth River (4 cells ml⁻¹) as early as May 27. Subsequent samples collected from the Lafayette River documented the increase in C. polykrikoides abundance in the upper branches of the Lafayette River from mid-June to early July, when discolored waters were first observed. The 2009 C. polykrikoides bloom began in the Lafayette River when water temperatures were consistently above 25 °C and during a period of calm winds, neap tides, high positive tidal residuals, low nutrient concentrations, and a low dissolved inorganic nitrogen (DIN) to dissolved inorganic phosphorous (DIP) ratio. The pulsing of nutrients associated with intense but highly localized storm activity during the summer months when water temperatures are above 25 °C may play a role in the initiation of C. polykrikoides blooms. The upper Lafayette River appears to be an important area for initiation of algal blooms that then spread to other connected waterways.     

Simplified DNA Extraction and Improved PCR Based Detection of Greening Bacterium in Citrus

Citrus greening disease caused by a fastidious bacterium is an important graft transmissible disease in commercial citrus in India and other parts of the world. Polymerase chain reaction (PCR) is a sensitive and convenient method for detection of greening bacterium. A non-phenol chloroform method of DNA extraction was evaluated for DNA quality and PCR based detection of greening bacterium. The method was comparable with a commercial DNA extraction kit (Qiagen) and better than a CTAB based DNA extraction method. To improve the reliability, three primer sets (primers A, B, and C yielding amplicons of 1160 bp, 703 bp and 451 bp, respectively) and two polymerase enzymes (Taq polymerase and Klen Taq polymerase) were evaluated. The primer set C provided better amplification when compared to primer sets A and B. Primer C in combination with Taq polymerase provided amplification band at a DNA template concentration of 100 pg but good amplification band was obtained at still lower DNA template concentration of 0.1 pg when Klen Taq polymerase was used. The standardized PCR protocol combining non-phenol chloroform method of DNA isolation, primer set C and Klen Taq polymerase enzyme was found very effective in detecting greening bacterium in citrus trees. The sequence of cloned amplicon from 16S ribosomal RNA gene had 89–100 % sequence identity with corresponding sequence of Candidatus Liberibacter asiaticus from China, Brazil, Japan and Pune isolate of India, C. Liberibacter americnus from Brazil and C. Liberibacter africanus from Africa.     

Algicidal effects of yellow clay and the thiazolidinedione derivative TD49 on the fish-killing dinoflagellate Cochlodinium polykrikoides in microcosm experiments

In order to evaluate the potential to control the fish-killing dinoflagellate Cochlodinium polykrikoides, we compared the algicidal effects of the thiazolidinedione derivative TD49 with those of yellow clay in 10-L microcosms. The responses of higher trophic level marine organisms and microbial loop communities to the algicide were also evaluated. In the yellow clay treatments, the concentration of C. polykrikoides was slightly reduced at day 1 of the experiment but remained higher than that of the control, suggesting that the reduction ratio of C. polykrikoides was <20 %. In the 0.8-μM TD49 treatment, the abundance of C. polykrikoides declined by 98 % 1 day following the addition of the algicide. The algicide did not affect nontarget algae including Chaetoceros spp., Skeletonema spp., Cylindrotheca spp., and other species. In all microcosms, bacterial abundance increased abruptly after day 1, then declined over the next 2 days as a result of predation by heterotrophic nanoflagellates and the small protozoan Uronema sp. Predation by the large protozoan species Euplotes sp. on Uronema sp. gradually increased with increasing incubation time in the TD49 treatment. Zooplankton were particularly affected by the environmental changes that occurred in the microcosms following collapse of the C. polykrikoides populations. Striped beak perch were not affected by the yellow clay treatments and concentrations of TD49?C. polykrikoides, whereas the algicide TD49 is effective in controlling the harmful alga. The results imply that the algicide has positive effects on natural microbial communities and is not toxic to nonharmful algae and higher trophic level marine organisms.     

Harmful algal bloom (HAB) in the East Sea identified by the Geostationary Ocean Color Imager (GOCI)

Harmful Cochlodinium polykrikoides blooms have frequently appeared and caused fatal harm to aquaculture in Korean coastal waters since 1995. We investigated the applicability of GOCI, the world's first Geostationary Ocean Color Imager, in monitoring the distribution and temporal movement of a harmful algal bloom (HAB) that was discovered in the East Sea near the Korean peninsula in August 2013. We identified the existence of C. polykrikoides at a maximum cell abundance of over 6000 cells/mL and a chlorophyll a concentration of over 400 mg/m³. In areas of C. polykrikoides blooms, GOCI remote sensing reflectance (R_rs) spectra demonstrated the typical radiometric features of a HAB, and from the diurnal variations using GOCI-derived chlorophyll concentration images, we were able to identify the vertical migration of the red tide species. We also found that the formation and propagation of the HAB had relations with cold water mass in the coastal region. GOCI can be effectively applied to the monitoring of short-term and long-term movements of red tides.     

Satellite detection of harmful algal bloom occurrences in Korean waters

Cochlodinium polykrikoides (p) is a planktonic dinoflagellate known to produce red tides responsible for massive fish kills and thereby serious economic loss in Korean coastal waters, particularly during summer and fall seasons. The present study involved analyzing chlorophyll-a (Chl-a) from SeaWiFS ocean color imagery collected over the period 1998–2002 to understand the spatial and temporal aspects of C. polykrikoides blooms that occurred in the enclosed and semi-enclosed bays of the Korean Southeast Sea. NOAA-AVHRR data were used to derive Sea Surface Temperature (SST) to elucidate physical factors affecting the spatial distribution and abundance of C. polykrikoides blooms. The time series of SeaWiFS-derived Chl-a gave an impression that recent red tide events with higher concentrations appeared to span more than 8 weeks during summer and fall seasons and were widespread in most of the Korean Southeast Sea coastal bays and neighboring oceanic waters. Coupled eutrophication and certain oceanic processes were thought to give rise to the formation of massive C. polykrikoides blooms with cell abundances ranging from 1000 to 30,000 cells ml⁻¹, causing heavy mortalities of aquaculture fish and other marine organisms in these areas. Our analysis indicated that Chl-a estimates from SeaWiFS ocean color imagery appeared to be useful in demarcating the locality, spatial extent and distribution of these blooms, but unique identification of C. polykrikoides from non-bloom and sediment dominated waters remains unsuccessful with this data alone. Thus, the classical spectral enhancement and classification techniques such as Forward Principal Component Analysis (FPCA) and Minimum Spectral Distance (MSD) to uniquely identify and better understand C. polykrikoides blooms characteristics from other optical water types were attempted on both low spatial resolution SeaWiFS ocean color imagery and high spatial resolution Landsat-7 ETM+ imagery. Application of these techniques could capture intricate and striking patterns of C. polykrikoides blooms from surrounding non-bloom and sediment dominated waters, providing improved capability of detecting, predicting and monitoring C. polykrikoides bloom in such optically complex waters. The result obtained from MSD classification showed that retrieval of C. polykrikoides bloom from the mixed phase of this bloom with turbid waters was not feasible with the SeaWiFS ocean color imagery, but feasible with Landsat-7 ETM+ imagery that provided more accurate and comparable spatial C. polykrikoides patterns consistent with in situ observations. The dense phase of the bloom estimated from these imageries occupied an area of more than 25 km² around the coastal bays and the mixed phase extended over several hundreds kilometers towards the Southeast Sea offshore due to exchange of water masses caused by coastal and oceanic processes. Sea surface temperature analyzed from AVHRR infrared data captured the northeastward flow of Tsushima Warm Current (TWC) waters that provided favorable environmental conditions for the rapid growth and subsequent southward initiation of C. polykrikoides blooms in hydrodynamically active regions in the Korean Southeast Sea offshore.     

Control of the harmful alga Cochlodinium polykrikoides by the naked ciliate Strombidinopsis jeokjo in mesocosm enclosures

Red tides dominated by the harmful dinoflagellate Cochlodinium polykrikoides have caused annual losses of USD $5–60 million to the Korean aquaculture industry annually since 1995 and a loss of USD $3 million during a 1999 net-pen fish mortality event in Canada. In order to evaluate the potential to control C. polykrikoides red tides dominated by using mass-cultured heterotrophic protistan grazers, we monitored the abundance of Strombidinopsis jeokjo (a naked ciliate) and C. polykrikoides after mass-cultured S. jeokjo was introduced into mesocosms (ca. 60 l) deployed in situ and containing natural red tide waters dominated by C. polykrikoides. Water temperature, salinity, and pH, as well as the abundance of co-occurring other protists and metazooplankton were measured concurrently. To compare the growth and ingestion rates of S. jeokjo feeding on cultured versus natural populations of C. polykrikoides, we also monitored the abundance of cultured C. polykrikoides and S. jeokjo in bottles during laboratory grazing experiments. S. jeokjo introduced into the mesocosms grew well, effectively reducing natural populations of C. polykrikoides from approximately 1000 cells ml⁻¹ to below 10 cells ml⁻¹ within 2 days. The growth and ingestion rates of cultured S. jeokjo on natural populations of C. polykrikoides in the mesocosms for the first 30 h (0.72 day⁻¹ and 51 ng C grazer⁻¹ day⁻¹) were 84% and 44%, respectively, of those measured in the laboratory during bottle incubations with similar initial prey concentrations. The calculated grazing impact of S. jeokjo on natural populations of C. polykrikoides suggests that large-scale cultures of this ciliate could be used for controlling red tides by C. polykrikoides in small areas.     

Development of real-time RT-PCR for detecting viable Cochlodinium polykrikoides (Dinophyceae) cysts in sediment

Morphological observations have confirmed that cysts are produced by dinoflagellates. However, finding a seed bed or unknown cysts in field samples by microscopy is extremely time consuming. Real-time PCR has been used to facilitate the detection of dinoflagellate cysts in sediment. However, DNA from dead vegetative cells remaining on the surface sediment may persist for a long period of time, which can cause false positive DNA detection. In this study, a non-quantitative RNA targeted probe using real-time RT-PCR was developed for detection of viable cysts in sediment. Large-subunit rRNA was used to develop a species-specific RNA targeted probe for the ichthyotoxic dinoflagellate Cochlodinium polykrikoides. The sediment samples were sieved and incubated at 30 °C for 3 h prior to RNA extraction to remove RNA from dead cells remaining in the sediment. Nested-PCR was conducted to maximize assay sensitivity. A field survey to determine the distribution of cysts at 155 sampling stations in the western and southern part of the Korean peninsula showed that C. polykrikoides cysts were detected at five sampling stations.     

Streamlining DNA Barcoding Protocols: Automated DNA Extraction and a New cox1 Primer in Arachnid Systematics

Background

DNA barcoding is a popular tool in taxonomic and phylogenetic studies, but for most animal lineages protocols for obtaining the barcoding sequences—mitochondrial cytochrome C oxidase subunit I (cox1 AKA CO1)—are not standardized. Our aim was to explore an optimal strategy for arachnids, focusing on the species-richest lineage, spiders by (1) improving an automated DNA extraction protocol, (2) testing the performance of commonly used primer combinations, and (3) developing a new cox1 primer suitable for more efficient alignment and phylogenetic analyses.

Methodology

We used exemplars of 15 species from all major spider clades, processed a range of spider tissues of varying size and quality, optimized genomic DNA extraction using the MagMAX Express magnetic particle processor—an automated high throughput DNA extraction system—and tested cox1 amplification protocols emphasizing the standard barcoding region using ten routinely employed primer pairs.

Results

The best results were obtained with the commonly used Folmer primers (LCO1490/HCO2198) that capture the standard barcode region, and with the C1-J-2183/C1-N-2776 primer pair that amplifies its extension. However, C1-J-2183 is designed too close to HCO2198 for well-interpreted, continuous sequence data, and in practice the resulting sequences from the two primer pairs rarely overlap. We therefore designed a new forward primer C1-J-2123 60 base pairs upstream of the C1-J-2183 binding site. The success rate of this new primer (93%) matched that of C1-J-2183.

Conclusions

The use of C1-J-2123 allows full, indel-free overlap of sequences obtained with the standard Folmer primers and with C1-J-2123 primer pair. Our preliminary tests suggest that in addition to spiders, C1-J-2123 will also perform in other arachnids and several other invertebrates. We provide optimal PCR protocols for these primer sets, and recommend using them for systematic efforts beyond DNA barcoding.     

Dynamics of Amoebophrya parasites during recurrent blooms of the ichthyotoxic dinoflagellate Cochlodinium polykrikoides in Korean coastal waters

During the bloom events of the harmful dinoflagellate Cochlodinium polykrikoides in August and October, 2012, infections by two different Amoebophrya species were observed in Korean coastal waters. To investigate the dynamics of the two parasites and their relative impact on the host populations, a quantitative real-time PCR (qPCR) method was applied to detect and quantify the parasites in the free-living and parasitic stages. Each specific primer set of the target species, Amoebophrya sp. 1 and sp. 2 was designed on the large subunit (LSU) and the first internal transcribed spacer (ITS1) of ribosomal RNA (rRNA) gene, respectively. Dynamics of the two Amoebophrya species via qPCR assay showed distinct patterns during the C. polykrikoides bloom events. Amoebophrya sp. 1 showed peaks during both bloom events in August and October with relatively low copies (10⁶ to 10⁷ copies L⁻¹), while Amoebophrya sp. 2 appeared only during the bloom event in October with very high copies (10⁹ to 10¹⁰ copies L⁻¹). Overall, the qPCR measurements for the dynamics of two Amoebophrya species in the parasitic stage (> 5 μm fractions) were consistent with parasite prevalence through microscopic observations. Amoebophrya sp. 1 infections were observed during both bloom events in August and October with relatively low parasite prevalence (0.1–1.5%), while Amoebophrya sp. 2 infections were detected only during the bloom event in October with high prevalence (up to 45%). Taken together, Amoebophrya sp. 1 may be a generalist and C. polykrikoides may not be its primary host, while Amoebophrya sp. 2 may be a specialist which can substantially impact host population dynamics.     

Integrated method for single-cell DNA extraction, PCR amplification, and sequencing of ribosomal DNA from harmful dinoflagellates Cochlodinium polykrikoides and Alexandrium catenella

A simplified technique was developed for DNA sequence-based diagnosis of harmful dinoflagellate species. This protocol integrates procedures for DNA extraction and polymerase chain reaction (PCR) amplification into a single tube. DNA sequencing reactions were performed directly, using unpurified PCR products as the DNA template for subsequent sequencing reactions. PCR reactions using DNA extracted from single cells of Cocodinium polykrikoides and Alexandrium catenella successfully amplified the target ribosomal DNA regions. DNA sequencing of the unpurified PCR products showed that DNA sequences corresponded to the expected locus of ribosomal DNA regions of both A. catenella and C. polykrikoides (each zero genetic distance and 100% sequence similarity). Using the protocol described in this article, there was little DNA loss during the purification step, and the technique was found to be rapid and inexpensive. This protocol clearly resolves the taxonomic ambiguities of closely related algal species (such as Alexandrium and Cochlodinium), and it constitutes a significant breakthrough for the molecular analysis of nonculturable dinoflagellate species.     

Grazers and vitamins shape chain formation in a bloom-forming dinoflagellate, Cochlodinium polykrikoides

Predators influence the phenotype of prey through both natural selection and induction. We investigated the effects of grazers and nutrients on chain formation in a dinoflagellate, Cochlodinium polykrikoides, which forms dense blooms and has deleterious effects on marine ecosystems around the world. Field populations of C. polykrikoides formed longer chains than laboratory cultures without grazers. In the field, chain length of C. polykrikoides was positively correlated with the abundance of the copepod Acartia tonsa. Chain length of C. polykrikoides increased when exposed to live females of A. tonsa or its fresh (<24 h post-isolation) exudates for 48 h. These results suggest that dissolved chemical cues released by A. tonsa induce chain formation in C. polykrikoides. Ingestion rate of A. tonsa on four-cell chains of C. polykrikoides was lower than on single cells, suggesting that chain formation may be an effective anti-grazing defense. Finally, nutrient amendment experiments demonstrated that vitamins (B₁, B₇, and B₁₂) increased the chain length of C. polykrikoides both singly and collectively, while trace metals and inorganic nutrients did not, showing that vitamins may also influence chain formation in this species.     

Comparison of DNA extraction methods for multiplex polymerase chain reaction

We compared six DNA extraction methods for obtaining DNA from whole blood and saliva for use in multiplex polymerase chain reaction (PCR) assays. The aim was to evaluate saliva sampling as an alternative to blood sampling to obtain DNA for molecular diagnostics, genetic genealogy, and research purposes. The DNA quantity, DNA purity (A_260/280), PCR inhibition ratio, and mitochondrial DNA/genomic DNA ratio were measured to compare the extraction methods. The different extraction methods resulted in variable DNA quantity and purity, but there were no significant differences in the efficiency of multiplex PCR and oligomicroarray signals after single-base extension on the arrayed primer extension 2 (APEX-2).     

Alteration of plankton communities and biogeochemical cycles by harmful Cochlodinium polykrikoides (Dinophyceae) blooms

Cochlodinium polykrikoides is a globally distributed, ichthyotoxic, bloom-forming dinoflagellate. Blooms of C. polykrikoides manifest themselves as large (many km²) and distinct patches with cell densities exceeding 10³ ml⁻¹ while water adjacent to these patches can have low cell densities (<100 cells ml⁻¹). While the effect of these blooms on fish and shellfish is well-known, their impacts on microbial communities and biogeochemical cycles are poorly understood. Here, we investigated plankton communities and the cycling of carbon, nitrogen, and B-vitamins within blooms of C. polykrikoides and compared them to areas in close proximity (<100 m) with low C. polykrikoides densities. Within blooms, C. polykrikoides represented more than 90% of microplankton (>20 μm) cells, and there were significantly more heterotrophic bacteria and picoeukaryotic phytoplankton but fewer Synechococcus. Terminal restriction fragment length polymorphism analysis of 16S and 18S rRNA genes revealed significant differences in community composition between bloom and non-bloom samples. Inside the bloom patches, concentrations of vitamin B₁₂ were significantly lower while concentrations of dissolved oxygen were significantly higher. Carbon fixation and nitrogen uptake rates were up to ten times higher within C. polykrikoides bloom patches. Ammonium was a more important source of nitrogen, relative to nitrate and urea, for microplankton within bloom patches compared to non-bloom communities. While uptake rates of vitamin B₁ were similar in bloom and non-bloom samples, vitamin B₁₂ was taken up at rates five-fold higher (>100 pmol⁻¹ L⁻¹ d⁻¹) in bloom samples, resulting in turn-over times of hours during blooms. This high vitamin demand likely led to the vitamin B₁₂ limitation of C. polykrikoides observed during nutrient amendment experiments conducted with bloom water. Collectively, this study revealed that C. polykrikoides blooms fundamentally change microbial communities and accelerate the cycling of carbon, some nutrients, and vitamin B₁₂.