Development of a multiplex polymerase chain reaction assay for the parallel detection of harmful algal bloom-forming species distributed along the Chinese coast

Enhancing early warning: A DNA biosensor with polyaniline/graphene nanocomposite for label-free voltammetric detection of saxitoxin-producing harmful algae

Yearly reports of detrimental effects resulting from harmful algal blooms (HAB) are still received in Malaysia and other countries, particularly concerning fish mortality and seafood contamination, both of which bear consequences for the fisheries industry. The underlying reason is the absence of a dependable early warning system. Hence, this research aims to develop a single DNA biosensor that can detect a group of HAB species known for producing saxitoxin (SXT), which is commonly found in Malaysian waters. The screen-printed carbon electrode (SPCE)-based DNA biosensor was fabricated by covalent grafting of the 3' aminated DNA probe of the sxtA4 conserved domain in SXT-producing dinoflagellates on the reverse-phase polymerized polyaniline/graphene (PGN) nanocomposite electrode via carbodiimide linkage. The introduction of a carboxyphenyl layer to the PGN nanotransducing element was essential to augment the carboxylic groups on the graphene (RGO), facilitating attachment with the aminated DNA. The synergistic effect of the asynthesized nanocomposite of PANI and RGO, tremendously enhanced the electron transfer rate of the ferri/ferrocyanide redox probe at the SPCE transducer surface, allowing for the label-free bioanalytical assay of complementary DNA targets. The developed DNA biosensor featuring the capacity to detect a broad range of Alexandrium minutum (A. minutum) cell concentrations, ranging from 10 to 10,000,000 cells L-1. The quantification of A. minutum cells from pure algal culture by the electrochemical DNA biosensor has been well-validated with traditional microscopic techniques. Furthermore, Alexandrium tamiyavanichii, another toxigenic HAB species, exhibited a similar electrochemical characteristic signal to those observed with A. minutum, whilst the biosensor yielded appreciably distinctive results when subjected to a non-toxigenic microalgae species as a negative control, i.e. Isochrysis galbana. A compendium DNA biosensor design and electrochemical detection strategy at laboratory scale serves as a precursor to the potential development of portable device for on-site detection, thus expanding the utility and scope of biosensor technology.

Development of a Rapid Detection Method to Prorocentrum lima by Loop-Mediated Isothermal Amplification with Hydroxy Naphthol Blue

Prorocentrum lima, a widely distributed dinoflagellate known for its production of harmful biotoxins, poses a significant threat to humans, aquaculture, and marine ecosystems. As a result, the detection of this toxic alga in coastal waters has become an urgent research focus. In this study, a rapid, sensitive, and cost-effective detection method based on loop-mediated isothermal amplification (LAMP) was developed to identify P. lima. In this method, cell extracts of P. lima were diluted and used directly as templates for amplification, eliminating the need for nucleic acid purification and simplifying the detection process. Hydroxy naphthol blue (HNB) was incorporated into the reaction mix to facilitate result interpretation, enabling visual determination of the amplification outcome with the naked eye. The entire detection process, from DNA extraction to template amplification and product detection, could be completed within 80 min using a simple constant temperature-control device. This LAMP-based detection method demonstrated excellent reliability, specificity, and a low detection limit of 5.87 cells/mL for DNA crude extract. The assay offered an efficient alternative to PCR for rapid detection of P. lima. By streamlining the detection process and offering a visual readout, this technique holds promise for efficient and routine monitoring of harmful algal species, benefitting both research efforts and environmental management strategies.

Emerging Applications of Nanobiosensors in Pathogen Detection in Water and Food

Food and waterborne illnesses are still a major concern in health and food safety areas. Every year, almost 0.42 million and 2.2 million deaths related to food and waterborne illness are reported worldwide, respectively. In foodborne pathogens, bacteria such as Salmonella, Shiga-toxin producer Escherichia coli, Campylobacter, and Listeria monocytogenes are considered to be high-concern pathogens. High-concern waterborne pathogens are Vibrio cholerae, leptospirosis, Schistosoma mansoni, and Schistosima japonicum, among others. Despite the major efforts of food and water quality control to monitor the presence of these pathogens of concern in these kinds of sources, foodborne and waterborne illness occurrence is still high globally. For these reasons, the development of novel and faster pathogen-detection methods applicable to real-time surveillance strategies are required. Methods based on biosensor devices have emerged as novel tools for faster detection of food and water pathogens, in contrast to traditional methods that are usually time-consuming and are unsuitable for large-scale monitoring. Biosensor devices can be summarized as devices that use biochemical reactions with a biorecognition section (isolated enzymes, antibodies, tissues, genetic materials, or aptamers) to detect pathogens. In most cases, biosensors are based on the correlation of electrical, thermal, or optical signals in the presence of pathogen biomarkers. The application of nano and molecular technologies allows the identification of pathogens in a faster and high-sensibility manner, at extremely low-pathogen concentrations. In fact, the integration of gold, silver, iron, and magnetic nanoparticles (NP) in biosensors has demonstrated an improvement in their detection functionality. The present review summarizes the principal application of nanomaterials and biosensor-based devices for the detection of pathogens in food and water samples. Additionally, it highlights the improvement of biosensor devices through nanomaterials. Nanomaterials offer unique advantages for pathogen detection. The nanoscale and high specific surface area allows for more effective interaction with pathogenic agents, enhancing the sensitivity and selectivity of the biosensors. Finally, biosensors' capability to functionalize with specific molecules such as antibodies or nucleic acids facilitates the specific detection of the target pathogens.

Development of a rapid detection method for Karenia mikimotoi by using CRISPR-Cas12a

Harmful algal blooms (HABs), mainly formed by dinoflagellates, have detrimental effects on marine ecosystems and public health. Therefore, detecting HABs is crucial for early warning and prevention of HABs as well as the mitigation of their adverse effects. Although various methods, such as light microscopy, electron microscopy, real-time PCR, and microarrays, have already been established for the detection of HABs, they are still cumbersome to be exploited in the field. Therefore, rapid nucleic detection methods such as recombinase polymerase amplification (RPA) and loop-mediated isothermal amplification (LAMP)-lateral flow dipstick (LFD) have been developed for monitoring bloom-forming algae. However, the CRISPR/Cas-based detection of HABs has yet to be applied to this field. In this study, we developed a method for detecting Karenia mikimotoi (K. mikimotoi), a typical ichthyotoxic dinoflagellate responsible for global blooms. Our method utilized Cas12a from Lachnospiraceae bacterium ND2006 (LbCas12a) to target and cleave the internal transcribed spacer (ITS) of K. mikimotoi, guided by RNA. We leveraged the target-activated non-specific single-stranded deoxyribonuclease cleavage activity of LbCas12a to generate signals that can be detected using fluorescence-read machines or LFDs. By combining RPA and LbCas12a with reporters, we significantly enhanced the sensitivity, enabling the detection of ITS-harboring plasmids at concentrations as low as 9.8 aM and genomic DNA of K. mikimotoi at levels as low as 3.6 × 10-5 ng/μl. Moreover, we simplified the genomic DNA extraction method using cellulose filter paper (CFP) by directly eluting the DNA into RPA reactions, reducing the extraction time to < 30 s. The entire process, from genomic DNA extraction to result reporting, takes less than an hour, enabling the identification of nearly a single cell. In conclusion, our method provided an easy, specific, and sensitive approach for detecting K. mikimotoi, offering the potential for efficient monitoring and management of K. mikimotoi blooms.

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.

Establishment of a multiplex polymerase chain reaction detection assay for three common harmful microalgae in the East China Sea

It is urgent to develop techniques that can simultaneously detect multiple microalgae, due to the diversity of harmful algal blooms (HABs)-forming algal species. The target algae species in this study are Heterosigma akashiwo, Prorocentrum donghaiense and Karenia mikimotoi. These algae are the dominant species that cause HABs in the East China Sea, and the multiple detection technique focusing on these three algae is not common. Therefore, this study established a multiplex polymerase chain reaction(mPCR) to diagnose the three algae, which is simple and low cost. First, the corresponding specific primers were designed based on the D1-D2 region of the large subunit (LSU) ribosomal DNA sequence. Then, mPCR was established and the reaction conditions were optimized. And the specificity, sensitivity, and stability of mPCR were evaluated. The result of specificity test showed that the established mPCR had good specificity for the target microalgae and did not cross-react with eighteen non-target microalgae. The sensitivity of experiment was 3.3 × 10^-1 ng μL^-1, and the established mPCR was not affected by the interfering microalgae. Moreover, the practicability evaluation of mPCR by using the simulated natural water samples showed that the detection limit of target microalgae was 100 cells mL^-1, which could meet the demand for early warning of HABs. In summary, the established mPCR is characterized by strong specificity, good stability, and multiple analysis to detect H. akashiwo, P. donghaiense, and K. mikimotoi.

Easy detection of Prorocentrum donghaiense by polymerase chain reaction-nucleic acid chromatography strip

In recent years, Prorocentrum donghaiense, as a dominant species, has ranked first in terms of cumulative number and area of algal blooms in the East China Sea. In this study, the D1-D2 region of the large ribosomal subunit of P. donghaiense was used as the target gene, and specific primers DH-FP/DH-RP were designed according to the species-specific region of the target gene. An easy, sensitive and visual detection method refered to as polymerase chain reaction-nucleic acid chromatography strip (PCR-NACS) was established for P. donghaiense. The optimized parameters of the PCR amplification system are as follows: primer concentration, 0.15 μM; annealing temperature, 62 °C; and Mg²⁺ concentration, 1.5 mM. The specificity test showed that PCR-NACS was exlusively specific for the detection of the target algae. The sensitivity test show that the lowest detection limit (LDL) of PCR-NACS was 2.7 × 10^-2 ng·μL^-1 for genomic DNA and 3.58 × 10² copies·μL^-1 for plasmid DNA, respectively. The tests using both genomic DNA and plasmid DNA as templates showed that the sensitivity of PCR-NACS was 10 times higher than that of ordinary PCR. The stability test showed that the interfering algal species did not affect the detection of the target algae by PCR-NACS. In addition, the test with simulated natural samples containing target algae showed that the LDL of PCR-NACS could reach 1.27 × 10¹ cells·mL^-1. In summary, the PCR-NACS established in this study may provide a new method for easy identification of P. donghaiense in natural water samples.

A fast and accurate method for specific detection and quantification of the bloom-forming microalgae Karlodinium veneficum in the marine environment

Karlodinium veneficum is a toxic benthic globally distributed dinoflagellate which has direct impacts on human health and the environment. Early and accurate detection of this harmful algal bloom-forming species could be useful for potential risks monitoring and management. In the present work, a real-time PCR targeting the internal transcribed spacer ribosomal DNA region for the specific detection and absolute quantification of K. veneficum was designed. Then, the assay conditions were adjusted and validated. The developed qPCR was highly specific for the target species and displayed no cross-reactivity with closely related dinoflagellates and/or other microalgal species commonly distributed along the Tunisian coast. Its lowest detection limit was 5 rDNA copies per reaction, which is often considered satisfying. qPCR assay enumeration accuracy was evaluated using artificially inoculated environmental samples. The comparison of the cell abundance estimates obtained by qPCR assay with the theoretical estimates showed no statistically significant difference across a range of concentrations. We suggest that the qPCR approach developed in the present study may be a valuable tool to investigate the distribution and seasonal dynamics of K. veneficum in marine environments.

A Sensitive and Portable Double-Layer Microfluidic Biochip for Harmful Algae Detection

Harmful algal blooms (HABs) are common disastrous ecological anomalies in coastal waters. An effective algae monitoring approach is important for natural disaster warning and environmental governance. However, conducting rapid and sensitive detection of multiple algae is still challenging. Here, we designed an ultrasensitive, rapid and portable double-layer microfluidic biochip for the simultaneous quantitative detection of six species of algae. Specific DNA probes based on the 18S ribosomal DNA (18S rDNA) gene fragments of HABs were designed and labeled with the fluorescent molecule cyanine-3 (Cy3). The biochip had multiple graphene oxide (GO) nanosheets-based reaction units, in which GO nanosheets were applied to transfer target DNA to the fluorescence signal through a photoluminescence detection system. The entire detection process of multiple algae was completed within 45 min with the linear range of fluorescence recovery of 0.1 fM-100 nM, and the detection limit reached 108 aM. The proposed approach has a simple detection process and high detection performance and is feasible to conduct accurate detection with matched portable detection equipment. It will have promising applications in marine natural disaster monitoring and environmental care.

Advances in multiplex molecular detection technologies for harmful algae

As the eutrophication of natural water bodies becomes more and more serious, the frequency of outbreaks of harmful algal blooms (HABs) mainly formed by harmful algae also increases. HABs have become a global ecological problem that poses a serious threat to human health and food safety. Therefore, it is extremely important to establish methods that can rapidly detect harmful algal species for early warning of HABs. The traditional morphology-based identification method is inefficient and inaccurate. In recent years, the rapid development of molecular biology techniques has provided new ideas for the detection of harmful algae and has become a research hotspot. The current molecular detection methods for harmful algal species mainly include fluorescence in situ hybridization, sandwich hybridization, and quantitative PCR (qPCR), but all of these methods can only detect single harmful algal species at a time. The establishment of methods for the simultaneous detection of multiple harmful algal species has become a new trend in the development of molecular detection technology because various harmful algal species may coexist in the natural water environment. The established molecular techniques for multiple detections of harmful algae mainly include gene chip, multiplex PCR, multiplex qPCR, massively parallel sequencing, antibody chip, and multiple isothermal amplification. This review mainly focuses on the principles, advantages and disadvantages, application progress, and application prospects of these multiple detection technologies, aiming at providing effective references not only for the fisheries but also for economic activities, environment, and human health.

Harmful Microalgae Detection: Biosensors versus Some Conventional Methods

In the last decade, there has been a steady stream of information on the methods and techniques available for detecting harmful algae species. The conventional approaches to identify harmful algal bloom (HAB), such as microscopy and molecular biological methods are mainly laboratory-based and require long assay times, skilled manpower, and pre-enrichment of samples involving various pre-experimental preparations. As an alternative, biosensors with a simple and rapid detection strategy could be an improvement over conventional methods for the detection of toxic algae species. Moreover, recent biosensors that involve the use of nanomaterials to detect HAB are showing further enhanced detection limits with a broader linear range. The improvement is attributed to nanomaterials’ high surface area to volume ratio, excellent biological compatibility with biomolecules, and being capable of amplifying the electrochemical signal. Hence, this review presents the potential usage of biosensors over conventional methods to detect HABs. The methods reported for the detection of harmful algae species, ranging from conventional detection methods to current biosensor approaches will be discussed, along with their respective advantages and drawbacks to indicate the future prospects of biosensor technology for HAB event management.

A review of the current and emerging detection methods of marine harmful microalgae

In recent years, the scale and frequency of outbreaks of harmful algal blooms (HABs) have increased year by year due to the intensification of seawater eutrophication and global climate change. HABs have become a global marine ecological and environmental problem, which poses a serious threat to human health, marine ecological security, and economic development. The establishment of detection technology for harmful microalgae is fundamental to the early warning and prevention of HABs. To date, several detection methods have been developed for harmful microalgae, they however lack a unified classification standard. It is difficult to use a reasonable mix of all the developed methods to improve the accuracy of detection results. Here, all of the established detection methods for harmful microalgae were reviewed, including morphological structure-based detection methods, cytochrome-based detection techniques, immunoassays, and nucleic acid-based detection methods. The principles, advantages, and weaknesses of these methods were highlighted. Their application in the detection of harmful microalgae was summarized. Overall, different detection methods are suitable for different purposes. Further development of more accurate, cost-effective, efficient, and rapid detection technology is required in the future. This review is expected to provide a reference for research related to the monitoring of marine environment, early warning of HABs, and the molecular identification of harmful microalgae.

Rapid detection of Chattonella marina by PCR combined with dot lateral flow strip

In this study a novel technique referred to as PCR combined with dot lateral flow strip (PCDS) is proposed and its application to the detection of harmful microalgae was explored. For this purpose, using Chattonella marina as a test algal species, PCR targeting the D1-D2 region of large subunit ribosomal gene of this alga was performed with the tagged specific primers. The amplicons were then analyzed with the manually prepared dot lateral flow strip, and the strip could produce a test dot and a control dot that are naked-eye detectable, indicating the successful establishment of PCDS. The established PCDS assay does not require expensive instruments for the detection, and the results can be observed visually after adding 7.5 μL of PCR amplicons in combination with 92.5 μL of chromatography buffer to the sample pad of the strip for about 10 min. The PCR conditions were optimized to enhance the effectiveness of detection. The cross-reactivity test with 23 microalgae species, including Chattonella marina, showed good specificity of the PCDS. The detection limit of PCDS was 1.25 × 10^-2 ng µL^-1 for genomic DNA and 10¹ cells mL^-1 for crude cell extracts, which can meet the detection needs. In summary, the PCDS proposed in this study has low cost, clear, and intuitive detection results and good specificity and sensitivity, providing a novel detection method for C. marina.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10811-021-02667-x.

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.

Rapid and sensitive detection of Karlodinium veneficum by a novel double-nick rolling circle amplification

Harmful algal blooms caused by Karlodinium veneficum recently occurred with high incidence, posing a serious threat to the marine ecological environment, public health, and mariculture. It is therefore rather vital to establish a method for rapid detection of K. veneficum. In this study, the D1-D2 region of the large subunit rDNA (LSU rDNA D1-D2) of K. veneficum was cloned and sequenced to design the specific probes and primers. A novel method referred to as double-nick rolling circle amplification (dn-RCA) based on the designed probes and primers was initially established. The optimal reaction conditions for dn-RCA were as follows: probe concentration, 200 pM; ligation temperature, 57 °C; ligation time, 50 min; amplification temperature, 60 °C; and amplification time, 60 min. Furthermore, lateral flow dipstick (LFD) was employed instead of agarose gel electrophoresis to analyze dn-RCA products, which can simplify the detection procedure and reduce the operation time. The sensitivity of dn-RCA-LFD was tested with the genomic DNA, the recombinant plasmid containing the inserted LSU rDNA D1-D2, and the DNA crude extract of K. veneficum. The results showed that the sensitivity of dn-RCA-LFD was 10 times higher than that of conventional PCR; the detection limit of dn-RCA-LFD was 1.1 × 10^-4 ng μL^-1 for the genomic DNA, 360 copies μL^-1 for the recombinant plasmid, and 5.3 cells mL^-1 for DNA crude extract. The results of the cross-reactivity test with 22 control microalgal species showed that the dn-RCA-LFD had high specificity for K. veneficum. The stability of dn-RCA-LFD was tested by mixing the interfering genomic DNA with the target genomic DNA, which can be expected to simulate the natural samples containing different ratios of interfering cells to target cells. The results indicated that the performance of dn-RCA-LFD was immune to the DNA concentration of the interfering species. Finally, the practicability of dn-RCA-LFD was further confirmed by the test with field samples collected from the East China Sea. In conclusion, the established dn-RCA-LFD has advantages of high sensitivity, strong specificity, and stable performance, and is therefore promising for rapid detection of K. veneficum.

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.

Establishment of double probes rolling circle amplification combined with lateral flow dipstick for rapid detection of Chattonella marina

Chattonella marina is one of the main algae that could cause harmful algal blooms. It has killed a large number of cultured fish in coastal areas of many countries, causing serious economic losses. Therefore, it is necessary to establish a method that can specifically detect C. marina at pre-bloom abundance, so that timely measures can be taken before this alga causes harm. In this study, a long probe, a short probe and a pair of amplification primers were first designed by using the internal transcribed spacer (ITS) sequence of C. marina as the target gene and using the CD74 gene of a distant species Gallus gallus as the base sequence. The double probes rolling circle amplification (dpRCA) system was then established with the designed probes and amplification primers. A novel detection protocol referred to as dpRCA-LFD by combining the dpRCA products and lateral flow dipstick (LFD) was finally established, which can make the detection results visible to the naked eyes. The reaction conditions of dpRCA were optimized and the optimal conditions were as follows: cycle number of ligation reaction, 12; ligation temperature, 58 °C; amplification temperature, 60 °C; and amplification time, 60 min. The specificity test that was performed using the optimized dpRCA conditions indicated that dpRCA-LFD was exclusively specific for the target alga. The tests with the genomic DNA of C. marina and the recombinant plasmid containing the ITS sequence of C. marina showed that the sensitivity of dpRCA-LFD was 100 times higher than that of conventional PCR. The detection limit (DL) for the genomic DNA was 8.3 × 10^-3 ng µL^-1 (8.3 × 10^-3 ng per reaction), and the DL for the recombinant plasmid DNA was 7.8 copies µL^-1 (7.8 copies per reaction). The practicality of the developed dpRCA-LFD was further validated by test with the spiked samples containing C. marina and field samples. The simulative test showed that the dpRCA-LFD has a DL of 10 cells mL^-1. The dpRCA-LFD could successfully recognize the target cells from the field samples. In summary, the dpRCA-LFD established in this study has advantages of good specificity, high sensitivity, and easily visible detection results, and therefore is promising for the analysis of C. marina in field samples.