Attempts to model the bloom dynamics of Pyrodinium, a tropical toxic dinoflagellate

For the first time, several models have been used to aid in the understanding of the bloom dynamics of Pyrodinium bahamense var. compressum, the major causal organism of toxic algal blooms in Manila Bay and several areas in the tropical world. The complex life cycle of Pyrodinium includes the formation of cysts that settle at the sediments, which can serve as the inoculum for the next bloom.The seasonal variation of temperature and salinity reflects the combined effects of convection and water column stability, which can control vertical movement of plankton and other parameters essential to its growth. The significance of wind forcing appears to be related to the potential to resuspend cysts. In the absence of wind, tidal currents in the inner part of the bay may be too weak to induce resuspension. The addition of wind results in a significant increase in bottom current velocity. Off Cavite at the southeast, bottom velocity is enhanced by orbital motion due to waves, one of the reasons why sediments off this area are dominated by sandy material. The strong vertical mixing of the water column at depths of less than 10 m may influence nutrient and consequently, plankton populations.The wave field during the southwest monsoon indicates that its contribution to the bottom velocity dominates in this area of the bay.Bloom simulations using combined bio-physical parameters show that direction of advection is almost always along wind direction. The dispersal distances increases if the Pyrodinium cells are found higher in the water column. For cells originating from southeastern (Cavite) sources, the direction of transport is slightly towards the north. In either case, the formation of cysts after a bloom is adjacent to the northern area (Pampanga) for blooms originating from the western side (Bataan) and along the eastern side (Parañaque–Manila) for blooms originating from the southeastern side (Cavite). Comparison with a few records of bloom occurrences in Manila Bay shows some consistent features. Reports of these blooms also showed that they occurred almost always during spring tides. There appears to be two main systems for bloom formation: one fed by cyst beds in the west (Bataan) which is advected along the west–northwest coast (Bataan–Bulacan) while the other one is fed by the southeast (Cavite) cyst beds that dominates in the east-southeast (Parañaque–Cavite) area.     

Isolation and characterization of a marine algicidal bacterium against the toxic dinoflagellate Alexandrium tamarense

Interactions between bacteria and harmful algal bloom (HAB) species have been acknowledged as an important factor regulating both the population dynamics and toxin production of these algae. A marine bacterium SP48 with algicidal activity to the toxic dinoflagellate, Alexandrium tamarense, was isolated from the Donghai Sea area, China. Genetic identification was achieved by polymerase chain reaction amplification and sequence analysis of 16S rDNA. Sequence analysis showed that the most probable affiliation of SP48 was to the γ-proteobacteria subclass and the genus Pseudoalteromonas. Bacterial isolate SP48 showed algicidal activity through an indirect attack. Additional organic nutrients but not algal-derived DOM was necessary for the synthesis of unidentified algicidal compounds but β-glucosidase was not responsible for the algicidal activity. The algicidal compounds produced by bacterium SP48 were heat tolerant, unstable in acidic condition and could be easily synthesized regardless of variation in temperature, salinity or initial pH for bacterial growth. This is the first report of a bacterium algicidal to the toxic dinoflagellate A. tamarense and the findings increase our knowledge of bacterial–algal interactions and the role of bacteria during the population dynamics of HABs.     

A practical approach to FRET-based PNA fluorescence in situ hybridization

Given the demand for improved methods for detecting and characterizing RNA variants in situ, we developed a quantitative method for detecting RNA alternative splicing variants that combines in situ hybridization of fluorescently labeled peptide nucleic acid (PNA) probes with confocal microscopy Förster resonance energy transfer (FRET). The use of PNA probes complementary to sequences flanking a given splice junction allows to specifically quantify, within the cell, the RNA isoform generating such splice junction as FRET efficiency measure. The FRET-based PNA fluorescence in situ hybridization (FP-FISH) method offers a conceptually new approach for characterizing at the subcellular level not only splice variant isoform structure, location, and dynamics but also potentially a wide variety of close range RNA–RNA interactions. In this paper, we explain the FP-FISH technique workflow for reliable and reproducible results.     

First record of the dynamics of domoic acid producing Pseudo-nitzschia spp. in Indonesian waters as a function of environmental variability

Within the past few decades, harmful algal blooms (HABs) have occurred frequently in Indonesian waters, resulting in environmental degradation, economic loss and human health problems. So far, HAB related studies mainly addressed ecological traits and species distribution, yet toxin measurements were virtually absent for Indonesian waters. The aim of the present study was to explore variability of the potentially toxic marine diatom genus Pseudo-nitzschia, as well as its neurotoxin domoic acid as a function of environmental conditions in Ambon Bay, eastern Indonesia. Weekly phytoplankton samples, oceanographic (CTD, nutrients) and meteorological (precipitation, wind) parameters were analyzed at 5 stations in the bay during the dry and wet seasons of 2018. Liquid chromatography – tandem mass spectrometry (LC–MS/MS) was used to detect particulate DA (pDA). Vegetative cells of Pseudo-nitzschia spp. and pDA were found in 98.6% and 51.4% of the samples, respectively. pDA levels were low, yet detected throughout the campaign, implying that Ambon Bay might potentially be subject to amnesic shellfish poisoning. The highest levels of both Pseudo-nitzschia spp. cell abundance and pDA were found in the wet season, showing a strong positive correlation between both parameters, compared to the dry season, (r = 0.87 and r = 0.66 (p < 0.01), respectively). Statistical analyses revealed that temperature and mixed layer depth positively correlated with Pseudo-nitzschia spp. and pDA during the dry season, while ammonium showed positive correlations in both seasons. This study represents the first successful investigation of the presence and variability of Pseudo-nitzschia spp. and its neurotoxin DA in Indonesian waters.     

The first report of the potentially harmful diatom Pseudo‐nitzschia caciantha from Australian coastal waters

The diatom Pseudo‐nitzschia is a significant component of coastal waters worldwide and a producer of the potent neurotoxin, domoic acid. Sixteen species belonging to this genus have been reported from Australian waters, but the potentially toxic species P. caciantha has not been previously known from this region. Two clonal strains of P. caciantha were isolated from Coogee Beach, south‐east Australia, and the morphological, molecular and toxicological evidence for this species delineation were examined using light and transmission electron microscopy, phylogenetic analysis based on sequences of the second internal transcribed spacer and domoic acid production as measured by liquid chromatography–mass spectrometry. The results unambiguously confirmed that these isolates are the potentially toxic species P. caciantha , being only the second report of this species in the Southern Hemisphere. The potential for further hidden Pseudo‐nitzschia diversity in these waters is considerable.     

3-Aminopyrrolidine-4-carboxylic acid as versatile handle for internal labeling of pyrrolidinyl PNA

Conformationally restricted pyrrolidinyl PNAs with an α/β-dipeptide backbone consisting of a nucleobase-modified proline and a cyclic five-membered amino acid spacer such as (1S,2S)-2-aminocyclopentanecarboxylic acid (ACPC) (acpcPNA) can form very stable hybrids with DNA with high Watson-Crick base pairing specificity. This work aims to explore the effect of incorporating 3-aminopyrrolidine-4-carboxylic acid (APC), which is isosteric to the ACPC spacer, into the acpcPNA. It is expected that the modification should not negatively affect the DNA binding properties, and that the additional nitrogen atom in the APC should provide a handle for internal modification. Orthogonally-protected (N(3)-Fmoc/N(1)-Boc and N(3)-Fmoc/N(1)-Tfa) APC monomers have been successfully synthesized and incorporated into the acpcPNA by Fmoc-solid-phase peptide synthesis. T(m), UV and CD spectroscopy confirmed that the (3R,4S)-APC could substitute the (1S,2S)-ACPC spacer in the acpcPNA with only slightly decreasing the stability of the hybrids formed between the modified acpc/apcPNA and DNA. In contrast, the (3S,4R) enantiomer of APC caused substantial destabilization of the hybrids. Furthermore, a successful on-solid-support internal labeling of the acpc/apcPNA via amide bond formation between pyrene-1-carboxylic acid or 4-(pyrene-1-yl) butyric acid and the pyrrolidine nitrogen atom of the APC spacer has been demonstrated. Fluorescence properties of the pyrene-labeled acpc/apcPNAs are sensitive to their hybridization states and can readily distinguish between complementary and single-mismatched DNA targets.     

Development and field application of rRNA-targeted probes for the detection of Cochlodinium polykrikoides Margalef in Korean coastal waters using whole cell and sandwich hybridization formats

The dinoflagellate, Cochlodinium polykrikoides Margalef, has been responsible for mass mortalities of both wild and farmed fish along the Korean coast on virtually an annual basis since 1982. Economic impacts to the fishing and aquaculture industries are extensive, with a loss of USD $95 million reported in 1995 alone. The use of taxon-specific molecular probes for harmful algal species is recognized as a promising approach for the early detection of bloom formation and as part of an effective mitigation strategy. We have developed and successfully applied large subunit ribosomal RNA (LSU rRNA)-targeted probes in both whole cell and sandwich hybridization assay (SHA) formats for the species-specific detection of C. polykrikoides in Korean coastal waters. Sequences of the D1–D3 variable regions used to design probes were identical between five Korean and one Hong Kong C. polykrikoides isolates, while sequences for several N. American Cochlodinium isolates differed to varying degrees from the former. The automated SHA detected C. polykrikoides at levels as low as 1–3 cells/L in the field, demonstrating its suitability for detecting the target species at pre-bloom concentrations. This method should thus prove valuable to existing monitoring programs aimed at providing aquaculture interests with an early warning of frequently devastating bloom events.     

Vertical migration of Karenia brevis in the northeastern Gulf of Mexico observed from glider measurements

The toxic marine dinoflagellate, Karenia brevis (the species responsible for most of red tides or harmful algal blooms in the Gulf of Mexico), is known to be able to swim vertically to adapt to the light and nutrient environments, nearly all such observations have been made through controlled experiments using cultures. Here, using continuous 3-dimensional measurements by an ocean glider across a K. brevis bloom in the northeastern Gulf of Mexico between 1 and 8 August 2014, we show the vertical migration behavior of K. brevis. Within the bloom where K. brevis concentration is between 100,000 and 1,000,000 cells L⁻¹, the stratified water shows a two-layer system with the depth of pycnocline ranging between 14–20 m and salinity and temperature in the surface layer being <34.8 and >28 °C, respectively. The bottom layer shows the salinity of >36 and temperature of <26 °C. The low salinity is apparently due to coastal runoff, as the top layer also shows high amount of colored dissolved organic matter (CDOM). Within the top layer, chlorophyll-a fluorescence shows clear diel changes in the vertical structure, an indication of K. brevis vertical migration at a mean speed of 0.5–1 m h⁻¹. The upward migration appears to start at sunrise at a depth of 8–10 m, while the downward migration appears to start at sunset (or when surface light approaches 0) at a depth of ∼2 m. These vertical migrations are believed to be a result of the need of K. brevis cells for light and nutrients in a stable, stratified, and CDOM-rich environment.     

Rapid identification of dinoflagellates using protein profiling with matrix-assisted laser desorption/ionization mass spectrometry

The occurrence of harmful algal blooms (HABs) or red tides is an important and expanding threat to human health, fishery resources, and the tourism industries. Toxic species post an additional treat of intoxication when consumed either in seafood or directly swallowed. Rapid and accurate identification of the HAB species is critical for minimizing or controlling the damage. We report the use of protein/peptide mass fingerprint profiles obtained with matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) for the identification of dinoflagellates, common causative agents of HABs. The method is simple, fast and reproducible. The peptide mass fingerprint spectral patterns are unique for different dinoflagellate species and are easily distinguishable by visual inspection. In addition to the whole mass spectra, several specific biomarkers were identified from the mass spectra of different species. These biomarker ions and the mass spectral patterns form an unambiguous basis for species discrimination.     

Comparison of the functional and numerical responses of resistant versus non-resistant populations of the copepod Acartia hudsonica fed the toxic dinoflagellate Alexandrium tamarense

The functional and numerical responses of grazers are key pieces of information in predicting and modeling predator–prey interactions. It has been demonstrated that exposure to toxic algae can lead to evolved resistance in grazer populations. However, the influence of resistance on the functional and numerical response of grazers has not been studied to date. Here, we compared the functional and numerical responses of populations of the copepod Acartia hudsonica that vary in their degree of resistance to the toxic dinoflagellate Alexandrium tamarense. In common environment experiments carried out after populations had been grown under identical conditions for several generations, female copepods were offered solutions containing different concentrations of either toxic A. tamarense or the non-toxic green flagellate Tetraselmis sp. ranging from 25 to 500 μgC L⁻¹, and ingestion and egg production rates were measured. Throughout most of the range of concentrations of the toxic diet, copepod populations that had been historically exposed to toxic blooms of Alexandrium exhibited significantly higher ingestion and egg production rates than populations that had little or no exposure to these blooms. In contrast, there were no significant differences between populations in ingestion or egg production for the non-toxic diet. Hence, the between population differences in functional and numerical response to A. tamarense were indeed related to resistance. We suggest that the effect of grazer toxin resistance should be incorporated in models of predator and toxic prey interactions. The potential effects of grazer toxin resistance in the development and control of Alexandrium blooms are illustrated here with a simple simulation exercise.     

A novel application of an adaptable modeling approach to the management of toxic microalgal bloom events in coastal areas

Harmful algal blooms have been increasing in frequency in recent years, and attention has shifted from describing to modeling and trying to predict these phenomena, since in many cases they pose a risk to human health and coastal activities. Predicting ecological phenomena is often time and resource consuming, since a large number of field collected data are required. We propose a novel approach that involves the use of modeled meteorological data as input features to predict the concentration of the toxic benthic dinoflagellate Ostreopsis cf. ovata in seawater. Ten meteorological features were used to train a Quantile Random Forests model, which was then validated using field collected concentration data over the course of a summer sampling season. The proposed model was able to accurately describe Ostreopsis abundance in the water column in response to meteorological variables. Furthermore, the predictive power of this model appears good, as indicated by the validation results, especially when the quantile for predictions is tuned to match management requirements. The Quantile Random Forests method was selected, as it allows for greater flexibility in the generated predictions, thus making this model suitable as a tool for coastal management. The application of this approach is novel, as no other models or tools that are adaptable to this degree are currently available. The model presented here was developed for a single species over a limited geographical extension, but its methodological basis appears flexible enough to be applied to the prediction of HABs in general and it could also be extended to the case of other ecological phenomena that are strongly dependent on meteorological drivers, that can be independently modeled and potentially globally available.     

Three-dimensional structure of a Karenia brevis bloom: Observations from gliders,satellites, and field measurements

Autonomous underwater gliders with customized sensors were deployed in October 2011 on the central West Florida Shelf to measure a Karenia brevis bloom, which was captured in satellite imagery since late September 2011. Combined with in situ taxonomy data, satellite measurements, and numerical circulation models, the glider measurements provided information on the three-dimensional structure of the bloom. Temperature, salinity, fluorescence of colored dissolved organic matter (CDOM) and chlorophyll-a, particulate backscattering coefficient, and K. brevis-specific chlorophyll-a concentrations were measured by the gliders over >250 km from the surface to about 30-m water depth on the shallow shelf. At the time of sampling the bloom was characterized by uniform vertical structures, with relatively high chlorophyll-a and CDOM fluorescence, low temperature, and high salinity. Satellite data extracted along the glider tracks demonstrated coherent spatial variations as observed by the gliders. Further, the synoptic satellite observations revealed the bloom evolution during the 7 months between late September 2011 and mid April 2012, and showed the maximum bloom size of ∼3000 km² around 23 November. The combined satellite and in situ data also confirmed that the ratio of satellite-derived fluorescence line height (FLH) to particulate backscattering coefficient at 547 nm (b_bp(547)) could be used as a better index than FLH alone to detect K. brevis blooms. Numerical circulation models further suggested that the bloom could have been initiated offshore and advected onshore via the bottom Ekman layer. The case study here demonstrates the unique value of an integrated coastal ocean observing system in studying harmful algal blooms (HABs).     

Thiolated pyrrolidinyl peptide nucleic acids for the detection of DNA hybridization using surface plasmon resonance

Thiolated pyrrolidinyl peptide nucleic acids (HS-PNAs) bearing d-prolyl-2-aminocyclopentanecarboxylic acid (ACPC) backbones with different lengths and types of thiol modifiers were synthesized and then characterized by MALDI–TOF mass spectrometry. These HS-PNAs were immobilized on gold-coated glass by self-assembled monolayer (SAM) formation via S atom linkage for the detection of DNA hybridization using surface plasmon resonance (SPR). The amount and the stability of the immobilized HS-PNAs, as well as the effects of spacer and blocking thiol on DNA hybridization efficiency, were determined. SPR results indicated that the hybridization efficiency was enhanced when the distance between the PNA portion and the thiol terminal was increased and/or when blocking thiol was used following the HS-PNA immobilization. The immobilized HS-PNA could discriminate between fully complementary DNA from one or two base mismatched DNA with a relatively high degree of mismatch discrimination (>45%) in PBS buffer at 25 °C. The lowest DNA concentration at which reliable discrimination between fully complementary and single mismatched DNA could still occur was at about 0.2 μM, which is equivalent to 10 pmol of DNA. This research demonstrates that using these novel thiolated PNAs in combination with the SPR technique offers a direct, rapid and non-label based method that could potentially be applied for the analysis of genomic or PCR-amplified DNA in the future.     

Alga-lytic activity of Pseudomonas fluorescens against the red tide causing marine alga Heterosigma akashiwo (Raphidophyceae)

A bacterial strain, HAK-13, exhibited strongest activity against Heterosigma akashiwo and was capable of controlling this bloom forming phytoplankton. Based on 16S rDNA sequences and biochemical and morphological characteristics, the strain HAK-13 was determined to be Pseudomonas fluorescens on the basis of 99.9% similarity with reference strains in the DNA databases. The growth of H. akashiwo was strongly suppressed by HAK-13 in all growth phases, with the strongest alga-lytic activity noted against harmful bloom-forming species in the exponential stage (6–22 days). Host range tests showed that HAK-13 also significantly inhibited the growth of Alexandrium tamarense and Cochlodinium polykrikoides but could not destroy Gymnodinium catenatum. P. fluorescens HAK-13 indirectly attacked H. akashiwo by alga-lytic substances that might be located at the compartment of cytoplasmic membrane of the bacterium at a level of 45.86 units/mg of specific activity. The results indicated that P. fluorescens HAK-13 caused cell lysis and death of H. akashiwo, A. tamarense, and C. polykrikoides dramatically and Prorocentrum dentatum slightly. Therefore, P. fluorescens HAK-13 has potential for use as a selective biocontrol of harmful algal blooms.     

Rapid detection of natural cells of Alexandrium tamarense and A. catenella (Dinophyceae) by fluorescence in situ hybridization

The marine toxic dinoflagellates Alexandrium tamarense (Lebor) Balech and A. catenella (Whedon and Kofoid) Taylor that cause paralytic shellfish poisoning (PSP) are identified on the basis of morphological features in routine monitoring. Rapid and simple identification is, however, often difficult because of the morphological similarity. Fluorescent in situ hybridization (FISH) using ribosomal RNA (rRNA)-targeted probes has been studied as a method of easily identifying and enumerating species responsible for harmful algal blooms (HABs). Its application to monitoring natural populations of HAB species, however, is limited. Here, we applied the FISH method to identify and enumerate cells of A. tamarense and A. catenella in natural plankton assemblages collected from Japanese coastal waters. A. tamarense-specific (Atm1) and A. catenella-specific (Act1) probes were established based on the D2 region of the large-subunit ribosomal RNA gene (28S rDNA). With these two probes, natural cells of A. tamarense or A. catenella in field samples could easily be identified when the following three conditions were met. First, cells should be concentrated by filtration, not centrifugation, in order to avoid the loss of cells. Second, autofluorescence should be minimized; acetone was an effective decolorization reagent. Third, samples should be stored at −20 or −80 °C for long-term preservation. The results indicate that FISH is a useful tool for the rapid identification of toxic Alexandrium spp. and can facilitate the analysis of numerous natural samples.     

Investigating the kinetics of DNA–DNA and PNA–DNA interactions using surface plasmon resonance-enhanced fluorescence spectroscopy

Plasmon surface polaritons, resonantly excited in the Kretschmann format, are used to enhance the fluorescence emission of chromophore-labeled oligonucleotides (15mers) binding to surface-attached (via biotin–streptavidin linkages) complement catcher probes. A detailed analysis of the association and dissociation kinetics as well as the affinity constants is given for a mismatch 1 hybrid, emphasizing, in particular, the experimental conditions that are required to allow for an artifact-free determination of rate constants. A first comparison between DNA- and peptide nucleic acid (PNA-) probes shows similar affinities, however, significant deviations from single-exponential kinetics predicted by a simple Langmuir model for the PNA case are found.     

Effects of Prorocentrum donghaiense and Alexandrium catenella on the material transfer in a simulated marine food chain

The biochemical composition of Prorocentrum donghaiense was analyzed and the effects of P. donghaiense and Alexandrium catenella on the transport of materials through a simulated marine food chain were investigated. The results showed that the content of phenylalanine, histidine and lysine in P. donghaiense was obviously lower than that in other dietary microalgae. Fed with P. donghaiense solely, the gross conversion efficiencies (GCEs) of A. salina increased gradually when the algal densities were lower than 4 × 104 cells/ml, and decreased gradually at higher densities. When fed with the mixture of P. donghaiense and the diatom Nitzschia. closterium, A. salina preferred grazing on P. donghaiense to grazing on N. closterium, and the GCEs of A. salina decreased with the increasing density of P. donghaiense. Exposed to A. catenella, A. salina lost weight and no Chlorophyll a was detected in the guts, which indicated that A. salina did not ingest the algal cells. When the re-suspended cells and cell-free medium of A. catenella were mixed with N. closterium or P. donghaiense, respectively, the grazing and GCEs of A. salina were all diminished. Consequently, the large-scale blooms of P. donghaiense and A. catenella in the East China Sea could adversely affect zooplankton owing to insufficient food or nutrition, and therefore impact the material transfer efficiency through the food chain.     

Molecular characterization and morphology of Cochlodinium strangulatum,the type species of Cochlodinium,and Margalefidinium gen. nov. for C. polykrikoides and allied species (Gymnodiniales,Dinophyceae)

Photosynthetic species of the dinoflagellate genus Cochlodinium such as C. polykrikoides, one of the most harmful bloom-forming dinoflagellates, have been extensively investigated. Little is known about the heterotrophic forms of Cochlodinium, such as its type species, Cochlodinium strangulatum. This is an uncommon, large (∼200 μm long), solitary, and phagotrophic species, with numerous refractile bodies, a central nucleus enclosed in a distinct perinuclear capsule, and a cell surface with fine longitudinal striae and a circular apical groove. The morphology of C. polykrikoides and allied species is different from the generic type. It is a bloom-forming species with single, two or four-celled chains, small cell size (25–40 μm long) with elongated chloroplasts arranged longitudinally and in parallel, anterior nucleus, eye-spot in the anterior dorsal side, and a cell surface smooth with U-shaped apical groove. Phylogenetic analysis based on LSU rDNA sequences revealed that C. strangulatum and C. polykrikoides/C. fulvescens formed two distally related, independent lineages. Based on morphological and phylogenetic analyses, the diagnosis of Cochlodinium is emended and C. miniatum is proposed as synonym of C. strangulatum. The new genus Margalefidinium gen. nov., and new combinations for C. catenatum, C. citron, C. flavum, C. fulvescens and C. polykrikoides are proposed.     

Evidence for Production of Sexual Resting Cysts by the Toxic Dinoflagellate Karenia mikimotoi in Clonal Cultures and Marine Sediments

The toxic dinoflagellate Karenia mikimotoi has been well-known for causing large-scale and dense harmful algal blooms (HABs) in coastal waters worldwide and serious economic loss in aquaculture and fisheries and other adverse effects on marine ecosystems. Whether K. mikimotoi forms resting cysts has been a puzzling issue regarding to the mechanisms of bloom initiation and geographic expansion of this species. We provide morphological and molecular confirmation of sexually produced thin-walled resting cysts by K. mikimotoi based on observations of laboratory cultures and their direct detection in marine sediments. Light and scanning electron microscopy evidences for sexual reproduction include attraction and pairing of gametes, gamete fusion, formation of planozygote and thin-walled cyst, and the documentation of the thin-walled cyst germination processes. Evidence for cysts in marine sediments was in three aspects: positive PCR detection of cysts using species-specific primers in the DNA extracted from whole sediments; fluorescence in situ hybridization detection of cysts using FISH probes; and single-cell PCR sequencing for cysts positively labeled with FISH probes. The existence of sexually produced, thin-walled resting cysts by K. mikimotoi provides a possible mechanism accounting for the initiation of annually recurring blooms at certain regions and global expansion of the species during the past decades.