Development of a qPCR assay to detect and quantify ichthyotoxic flagellates along the Norwegian coast, and the first Norwegian record of Fibrocapsa japonica (Raphidophyceae)

A detection method for Prorocentrum minimum by an aptamer-gold nanoparticles based colorimetric assay

Here, to give early waring for harmful algal blooms caused by Prorocentrum minimum, we reported a simple and rapid colorimetric assay that is named aptamer-gold nanoparticles (GNPs) based colorimetric assay (AGBCA). The GNPs maintain a dispersed state and have a strong characteristic absorption peak at 520 nm. With the addition of NaCl, the stability of the solution will be destroyed and the dispersed GNPs will aggregate. Therefore, the characteristic absorption peak of the GNPs solution will change from 520 nm to 670 nm. Aptamers can be adsorbed on the surface of GNPs, effectively preventing the aggregation of GNPs. In the presence of P. minimum, aptamers will specifically bind to P. minimum, causing the dissociation of the aptamers from GNPs. Consequently, the GNPs will aggregate in the NaCl solution, corresponding to a new absorption peak at 670 nm. A linear relationship between the absorbance ratio variation (ΔA₆₇₀/A₅₂₀) and the P. minimum concentration was observed in the concentration range of 1 × 10² - 1 × 10⁷ cells mL^-1, with a low detection limit of 8 cells mL^-1. The developed AGBCA is characterized by simplicity, strong specificity, and high sensitivity and is thus promising for the quantitative detection of P. minimum in natural samples.

Monitoring harmful microalgal species and their appearance in Tokyo Bay, Japan, using metabarcoding

During the recent decade, high-throughput sequencing (HTS) techniques, in particular, DNA metabarcoding, have facilitated increased detection of biodiversity, including harmful algal bloom (HAB) species. In this study, the presence of HAB species and their appearance patterns were investigated by employing molecular and light microscopy-based monitoring in Tokyo Bay, Japan. The potential co-appearance patterns between the HAB species, as well as with other eukaryotes and prokaryotes were investigated using correlation and association rule-based time-series analysis. In total, 40 unique HAB species were detected, including 12 toxin-producing HAB species previously not reported from the area. More than half of the HAB species were present throughout the sampling season (summer to autumn) and no structuring or succession patterns associated with the environmental conditions could be detected. Statistically significant (p < 0.05, rS ranging from −0.88 to 0.90) associations were found amongst the HAB species and other eukaryotic and prokaryotic species, including genera containing growth-limiting bacteria. However, significant correlations between species differed amongst the years, indicating that variability in environmental conditions between the years may have a stronger influence on the microalgal community structure and interspecies interactions than the variability during the sampling season. The association rule-based time-series analysis allowed the detection of a previously reported negative relationship between Synechococcus sp. and Skeletonema sp. in nature. Overall, the results support the applicability of metabarcoding and HTS-based microalgae monitoring, as it facilitates more precise species identification compared to light microscopy, as well as provides input for investigating potential interactions amongst different species/groups through simultaneous detection of multiple species/genera.

Mapping the development of a Dinophysis bloom in a shellfish aquaculture area using a novel molecular qPCR assay

Diarrhetic shellfish toxins produced by certain species of the marine dinoflagellate Dinophysis can accumulate in shellfish in high concentrations, representing a significant food safety issue worldwide. This risk is routinely managed by monitoring programs in shellfish producing areas, however the methods used to detect these harmful marine microbes are not usually automated nor conducted onsite, and are often expensive and require specialized expertise. Here we designed a quantitative real-time polymerase chain reaction (qPCR) assay based on the ITS-5.8S ribosomal region of Dinophysis spp. and evaluated its specificity, efficiency, and sensitivity to detect species belonging to this genus. We designed and tested twenty sets of primers pairs using three species of Dinophysis - D. caudata, D. fortii and D. acuminata. We optimized a qPCR assay using the primer pair that sufficiently amplified each of the target species (Dacu_11F/Dacu_11R), and tested this assay for cross-reactivity with other dinoflagellates and diatoms in the laboratory (11 species) and in silico 8 species (15 strains) of Dinophysis, 3 species of Ornithocercus and 2 species of Phalacroma. The qPCR assay returned efficiencies of 92.4% for D. caudata, 91.3% for D fortii, and 91.5% for D. acuminata, while showing no cross-reactivity with other phytoplankton taxa. Finally, we applied this assay to a D. acuminata bloom which occurred in an oyster producing estuary in south eastern Australia, and compared cell numbers inferred by qPCR to those determined by microscopy counts (max abund. ∼6.3 × 10³ and 5.3 × 10³ cells L^-1 respectively). Novel molecular tools such as qPCR have the potential to be used on-farm, be automated, and provide an early warning for the management of harmful algal blooms.

q-PCR-based assay for the toxic dinoflagellate Karenia selliformis monitoring along the Tunisian coasts

Karenia selliformis is a marine dinoflagellate responsible for fish-kill events. Its presence has been reported along the Tunisian coasts (south-eastern Mediterranean Sea) since the 1990s. In the present study, a quantitative-PCR assay, based on the internal transcribed spacer (ITS) molecular marker, was developed to detect and quantify K. selliformis in environmental bivalve mollusk samples and in seawater samples. The assay was optimized, and its specificity was confirmed using cross-reactivity experiments against microalgal species commonly found on the Tunisian coasts and/or closely related to K. selliformis. Calibration curves were performed by tenfold dilutions of plasmid DNA harboring target sequence and genomic DNA, attaining a limit of detection of around 5 copies of target DNA per reaction, far below one K. selliformis cell per reaction. The field application of the developed assay showed a powerful detection capability. Thus, the designed assay could contribute to the deployment of in-field diagnostic tools for K. selliformis blooms monitoring.

Mechanism by Which MC Controls Harmful Algal Blooms Revealed by Cell Morphology of Aureococcus anophagefferens

On the basis of field experience, a bloom does not continue after treatment with modified clay (MC), even though the residual harmful algal bloom (HAB) biomass accounts for 20–30% of the initial cells. This interesting phenomenon indicates that, in addition to causing flocculation, MC can inhibit the growth of residual cells. Here, from a cell morphology perspective, Aureococcus anophagefferens was used as a model organism to explore this scientific issue and clarify the mechanism by which MC mitigates harmful algal blooms (HABs). The results showed that, at an ~70% removal efficiency, neutral clay (NC) could not effectively inhibit the growth of residual cells, although it caused various forms of damage to residual cells, such as cell deformation, cell breakage, decreased extracellular polysaccharides (EPS), increased cell membrane permeability, and increased cytoplasmic granularity, due to physical collisions. After modification, some physical and chemical properties of the clay particle surface were changed; for example, the surface electrical properties changed from negative to positive, lamellar spacing increased, hardness decreased, adhesion chains increased, adhesion improved, and the number of absorption sites increased, enhancing the occurrence of chemical and electrochemical effects and physical collisions with residual cells, leading to severe cell deformation and chemical cell breakage. Thus, MC effectively inhibited the growth of residual cells and controlled HABs.

A qPCR-based method for rapid quantification of six intestinal homeostasis-relevant bacterial genera in feces

Aim: Developing efficient methods for monitoring the complex microbial community to rapidly assess the health status. Materials & methods: The qPCR-based method was developed, verified and in situ applied in fecal samples. Results: Six primer pairs with high specificity were designed to perform qPCR assays under a unified reaction condition within 2.5 h. The limits of detection, amplification efficiency and feasibility of the qPCR-based method established here were verified. In situ application of 18 fecal samples showed that the amounts of Bacteroides, Streptococcus and Bifidobacterium in colorectal cancer patient feces were obviously lower than those of healthy volunteers. Conclusion: This qPCR-based method was a reliable tool for rapid quantification of the six intestinal homeostasis relevant bacterial genera in feces.

Using qPCR and high-resolution sensor data to model a multi-species Pseudo-nitzschia (Bacillariophyceae) bloom in southeastern Australia

Harmful algal blooms, including those caused by the toxic diatom Pseudo-nitzschia, can have significant impacts on human health, ecosystem functioning and ultimately food security. In the current study we characterized a bloom of species of Pseudo-nitzschia that occurred in a south-eastern Australian oyster-growing estuary in 2019. Using light microscopy, combined with molecular (ITS/5.8S and LSU D1-D3 rDNA regions) and toxicological evidence, we observed the bloom to consist of multiple species of Pseudo-nitzschia including P. cf. cuspidata, P. hasleana, P. fraudulenta and P. multiseries, with P. cf. cuspidata being the only species that produced domoic acid (3.1 pg DA per cell). As several species of Pseudo-nitzschia co-occurred, only one of which produced DA, we developed a rapid, sensitive and efficient quantitative real-time polymerase chain reaction (qPCR) assay to detect only species belonging to the P. pseudodelicatissima complex Clade I, to which P. cf. cuspidata belongs, and this indicated that P. cuspidata or closely related strains may have dominated the Pseudo-nitzschia community at this time. Finally, using high resolution water temperature and salinity sensor data, we modeled the relationship between light microscopy determined abundance of P. delicatissima group and environmental variables (temperature, salinity, rainfall) at two sites within the estuary. A total of eight General Linear Models (GLMs) explaining between 9 and 54% of the deviance suggested that the temperature (increasing) and/or salinity (decreasing) data were generally more predictive of high cell concentrations than the rainfall data at both sites, and that overall, cell concentrations were more predictive at the more oceanic site than the more upstream site, using this method. We conclude that the combination of rapid molecular methods such as qPCR and real-time sensor data modeling, can provide a more rapid and effective early warning of harmful algal blooms of species of Pseudo-nitzschia, resulting in more beneficial regulatory and management outcomes.

Molecular characterization of harmful algal blooms in the Bohai Sea using metabarcoding analysis

Although the occurrences of harmful algal blooms (HABs) have been intensifying, many HABs in coastal waters may have been neglected despite their damaging impact directly on ecology and indirectly on human and animal health. The current detection of HABs depends primarily on the water coloration, chlorophyll intensity, cell density, and mortality due to HAB toxicity. Such methods may not be adequately sensitive to detecting HABs that are relatively transient or small scale. The Bohai Sea is the largest inlet of the Yellow Sea located on the northeast coast of China and famous for shipping and marine aquacultures. HABs frequently occur in the Bohai Sea. In this study, we explored the composition, diversity, and distribution of HAB species using the metabarcoding approach. Through sequencing and the analyzing the 18S rDNA V4 region of 15 samples collected from spatially isolated sites in the Bohai Sea during an expedition in the summer of 2019, we identified 74 potential HAB species including 34 that had not been reported in the Bohai Sea in previous studies. This project provided a detailed analysis of phytoplankton composition, and molecular detection of HAB species in the Bohai Sea. In particular, these analyses revealed extremely high relative abundances of the ichthyotoxic phytoplankton species Vicicitus globosus (Dictyochophyceae) at multiple adjacent sampling sites in the Bohai Bay, which were close to the Yellow River Estuary during the expedition. The results revealed the occurrence of a potential HAB event that would be otherwise undetected using conventional methods, highlighting the sensitivity and power of metabarcoding analysis in detecting HABs and HAB species. This research suggested the value for routine and long-term monitoring of HAB species as an approach for monitoring HABs.

Development of an absolute quantification method for ribosomal RNA gene copy numbers per eukaryotic single cell by digital PCR

Recent increase of Harmful Algal Blooms (HAB) causes world-wide ecological, economical, and health issues, and more attention is paid to frequent coastal monitoring for the early detection of HAB species to prevent or reduce such impacts. Use of molecular tools in addition to traditional microscopy-based observation has become one of the promising methodologies for coastal monitoring. However, as ribosomal RNA (rRNA) genes are commonly targeted in molecular studies, variability in the rRNA gene copy number within and between species must be considered to provide quantitative information in quantitative PCR (qPCR), digital PCR (dPCR), and metabarcoding analyses. Currently, this information is only available for a limited number of species. The present study utilized a dPCR technology to quantify copy numbers of rRNA genes per single cell in 16 phytoplankton species, the majority of which are toxin-producers, using a newly developed universal primer set accompanied by a labeled probe with a fluorophore and a double-quencher. In silico PCR using the newly developed primers allowed the detection of taxa from 8 supergroups, demonstrating universality and broad coverage of the primer set. Chelex buffer was found to be suitable for DNA extraction to obtain DNA fragments with suitable size to avoid underestimation of the copy numbers. The study successfully demonstrated the first comparison of absolute quantification of 18S rRNA copy numbers per cell from 16 phytoplankton species by the dPCR technology.

Assessing the Use of Molecular Barcoding and qPCR for Investigating the Ecology of Prorocentrum minimum (Dinophyceae), a Harmful Algal Species

Prorocentrum minimum is a species of marine dinoflagellate that occurs worldwide and can be responsible for harmful algal blooms (HABs). Some studies have reported it to produce tetrodotoxin; however, results have been inconsistent. qPCR and molecular barcoding (amplicon sequencing) using high-throughput sequencing have been increasingly applied to quantify HAB species for ecological analyses and monitoring. Here, we isolated a strain of P. minimum from eastern Australian waters, where it commonly occurs, and developed and validated a qPCR assay for this species based on a region of ITS rRNA in relation to abundance estimates from the cultured strain as determined using light microscopy. We used this tool to quantify and examine ecological drivers of P. minimum in Botany Bay, an estuary in southeast Australia, for over ~14 months in 2016–2017. We compared abundance estimates using qPCR with those obtained using molecular barcoding based on an 18S rRNA amplicon. There was a significant correlation between the abundance estimates from amplicon sequencing and qPCR, but the estimates from light microscopy were not significantly correlated, likely due to the counting method applied. Using amplicon sequencing, ~600 unique actual sequence variants (ASVs) were found, much larger than the known phytoplankton diversity from this region. P. minimum abundance in Botany Bay was found to be significantly associated with lower salinities and higher dissolved CO₂ levels.

Easy detection of karlodinium veneficum using PCR-based dot chromatography strip

In this study, a novel detection method by PCR-based dot chromatography strip (PDCS) is proposed. To investigate the application of PDCS in the detection of harmful microalgae, the internal transcribed spacer sequence of Karlodinium veneficum, one of the most common bloom-forming species, was cloned and sequenced to design and screen specific primers with tag sequences and probes, including gold nanoparticle probe, test probe, and control probe. The PDCS was prepared manually, and PCR amplicons prepared from the genomic DNA of K. veneficum using tagged specific primers were analyzed by PDCS for visual detection of the target species. The resulting test strip showed red spots at the predicted test and control points visible to the naked eyes, showing the successful development of PDCS. This detection technique is independent of expensive experimental equipment (except a DNA thermal cycler for PCR) but requires an aliquot of PCR amplicons mixed with development buffer to apply to the sample pad of PDCS for approximately 10 min to visualize the analytical results. Cross-reactivity test with 21 microalgae, including K. veneficum, showed that the established PDCS technique has excellent specificity. The detection limit of PDCS was 9.13 × 10^-2 ng μL^-1 for genomic DNA and 5.3 × 10⁵ cells L ^- 1 for crude DNA extracts of the target alga. In summary, the PDCS with high sensitivity and specificity can be prepared by hand, which is less expensive than traditional strip, thus providing a promising alternative to the detection of K. veneficum in natural samples.

Distribution and abundance of azaspiracid-producing dinophyte species and their toxins in North Atlantic and North Sea waters in summer 2018

Representatives of the marine dinophyte family Amphidomataceae produce lipophilic phycotoxins called azaspiracids (AZA) which may cause azaspiracid shellfish poisoning (AZP) in humans after consumption of contaminated seafood. Three of the four known toxigenic species are observed frequently in the eastern North Atlantic. In 2018, a research survey was performed to strengthen knowledge on the distribution and abundance of toxigenic Amphidomataceae and their respective toxins in Irish coastal waters and in the North Sea. Species-specific quantification of the three toxigenic species (Azadinium spinosum, Azadinium poporum and Amphidoma languida) was based on recently developed qPCR assays, whose performance was successfully validated and tested with specificity tests and spike experiments. The multi-method approach of on-board live microscopy, qPCR assays and chemical AZA-analysis revealed the presence of Amphidomataceae in the North Atlantic including the three targeted toxigenic species and their respective AZA analogues (AZA-1, -2, -33, -38, -39). Azadinium spinosum was detected at the majority of Irish stations with a peak density of 8.3 x 10⁴ cells L^-1 and AZA (AZA-1, -2, -33) abundances up to 1,274 pg L^-1. Amphidoma languida was also present at most Irish stations but appeared in highest abundance in a bloom at a central North Sea station with a density of 1.2 x 10⁵ cells L^-1 and an AZA (AZA-38, -39) abundances of 618 pg L^-1. Azadinium poporum was detected sporadically at the Irish south coast and North Sea and was rather low in abundance during this study. The results confirmed the wide distribution and frequent occurrence of the target species in the North Atlantic area and revealed, for the first time, bloom abundances of toxigenic Amphidomataceae in this area. This emphasizes the importance of future studies and monitoring of amphidomatacean species and their respective AZA analogues in the North Atlantic.

An extraordinary Karenia mikimotoi "beer tide" in Kachemak Bay Alaska

In autumn of 2013 an immense dinoflagellate bloom developed in Kachemak Bay, AK, USA. Much of the Bay was discolored a dark amber color and raised public concerns as small scale fish kills were reported in a few locations. Light microscopy revealed a monospecific bloom of gymnodinoid dinoflagellates that were previously unknown from the Bay. Gene sequencing of SSU rDNA from cells collected from the bloom confirmed the causative species to be Karenia mikimotoi. This represents the first report of a K. mikimotoi bloom in Alaska. After the bloom organism was confirmed, a K. mikimotoi species-specific qPCR assay was developed and used to assess K. mikimotoi abundances in DNA extracted from phytoplankton samples from Kachemak Bay and Lower Cook Inlet (LCI) obtained over a six-year period. The K. mikimotoi abundances were compared with corresponding time series of environmental variables (water temperature, salinity, water column stability, nutrients, precipitation and wind speed) to assess the factors contributing to the development of the bloom. The results showed early bloom development occurred in August when snow melt reduced salinities and increased water column stability during a period of calm winds. Peak bloom concentrations occurred in late September (10⁷ cell eq. L^-1) even as water temperatures were decreasing. The bloom gradually declined over the winter but persisted until April of 2014. Karenia mikimotoi cells were not detected two years prior or three years following the bloom, suggesting cells were introduced to Kachemak Bay at a time when conditions allowed K. mikimotoi to thrive.

Establishment and application of hyperbranched rolling circle amplification coupled with lateral flow dipstick for the sensitive detection of Karenia mikimotoi

The dinoflagellate Karenia mikimotoi is a noxious and harmful algal bloom (HAB)-forming microalga. Establishing a rapid, accurate, and sensitive method of detecting this harmful alga is necessary to provide warnings of imminent HABs through field monitoring. Here, an isothermal amplification technique combined with a rapid analytical method for nucleic acid-based amplified products, i.e., hyperbranched rolling circle amplification (HRCA) coupled with lateral flow dipstick (LFD), hereafter denoted as HRCA-LFD, was established to detect K. mikimotoi. The HRCA-LFD assay relied on a padlock probe (PLP) targeting DNA template and an LFD probe targeting PLP. The sequenced internal transcribed spacer of K. mikimotoi through molecular cloning was used as the target of PLP. The optimized HRCA conditions was determined to be as follows: PLP concentration, 20 pM; ligation temperature, 65 °C; ligation time, 10 min; amplification temperature, 61 °C; and amplification time, 30 min. The developed HRCA-LFD assay was specific for K. mikimotoi, displaying no cross-reactivity with other common microalgae. Sensitivity-comparison tests indicated that HRCA-LFD assay was 100-fold more sensitive than PCR, with a detection limit of 0.1 cell mL^-1 when used to analyze spiked field samples. The analysis with field samples also indicated that HRCA-LFD assay was suitable for samples with a target cell density range of 1-1000 cells mL^-1. All of these results suggested that HRCA-LFD assay is an alternative method for the sensitive and reliable detection of K. mikimotoi from marine water samples.

Rapid and sensitive detection method for Karlodinium veneficum by recombinase polymerase amplification coupled with lateral flow dipstick

The dinoflagellate Karlodinium veneficum that is usually present at relatively low cell abundances is a globally-distributed harmful algal bloom-forming species, which negatively affects marine ecosystems, fisheries, and human health. Hence, an efficient detection platform for the rapid and sensitive identification of K. veneficum is highly demanded. In this study, a method referred to as recombinase polymerase amplification coupled with lateral flow dipstick (RPA-LFD) was developed for the rapid detection of K. veneficum. The primers for RPA and the detection probe for LFD were designed to specially target the internal transcribed spacer of K. veneficum by molecular cloning and multiple alignments of the related sequences. The developed RPA can gain an approximately 300 bp specific band from K. veneficum. Successful amplification for RPA could be achieved at a temperature range of 35 °C-45 °C. RPA for 30 min could produce enough products that could generate clearly visible electrophoresis bands and were adequate for subsequent LFD analysis. The RPA products can be visually detected by the naked eyes through an LFD after an automatic chromatography for 5 min at room temperature. The developed RPA-LFD was exclusively specific for K. veneficum and displayed no cross-reactivity with other algal species that are commonly distributed along the Chinese coast. In addition, the lowest detection limit of RPA-LFD was 10 ng μL^-1 of genomic DNA and 0.1 cell mL^-1, which was 100-fold sensitive than conventional PCR. In conclusion, the developed RPA-LFD assay in this study can be used as a rapid and sensitive method to monitor K. veneficum in the future.