From the sxtA4 Gene to Saxitoxin Production: What Controls the Variability Among Alexandrium minutum and Alexandrium pacificum Strains?

An On-Farm Workflow for Predictive Management of Paralytic Shellfish Toxin-Producing Harmful Algal Blooms for the Aquaculture Industry

Paralytic shellfish toxins (PSTs) produced by marine dinoflagellates significantly impact shellfish industries worldwide. Early detection on-farm and with minimal training would allow additional time for management decisions to minimize economic losses. Here, we describe and test a standardized workflow based on the detection of sxtA4, an initial gene in the biosynthesis of PSTs. The workflow is simple and inexpensive and does not require a specialized laboratory. It consists of (1) water collection and filtration using a custom gravity sampler, (2) buffer selection for sample preservation and cell lysis for DNA, and (3) an assay based on a region of sxtA, DinoDtec lyophilized quantitative polymerase chain reaction (qPCR) assay. Water samples spiked with Alexandrium catenella showed a cell recovery of >90% when compared to light microscopy counts. The performance of the lysis method (90.3% efficient), Longmire's buffer, and the DinoDtec qPCR assay (tested across a range of Alexandrium species (90.7-106.9% efficiency; r2 > 0.99)) was found to be specific, sensitive, and efficient. We tested the application of this workflow weekly from May 2016 to 30th October 2017 to compare the relationship between sxtA4 copies L-1 in seawater and PSTs in mussel tissue (Mytilus galloprovincialis) on-farm and spatially (across multiple sites), effectively demonstrating an ∼2 week early warning of two A. catenella HABs (r = 0.95). Our tool provides an early, accurate, and efficient method for the identification of PST risk in shellfish aquaculture.

Development of saxitoxin biosynthesis gene sxtB-targeted qPCR assay for the quantification of toxic dinoflagellates Alexandrium catenella (group I) and A. pacificum (group IV) occurring in the Korean coast

Toxic dinoflagellate Alexandrium can produce saxitoxins (STXs) and cause paralytic shellfish poisoning (PSP), and thus they are monitored for environmental safety management. Microscopic discrimination of dinoflagellates is difficult to distinguish between toxic and non-toxic species due to their similar morphology. Meanwhile, an alternative quantitative PCR (qPCR) assay is sensitive, rapid, and cost-effective for harmful species monitoring. Herein, we developed a novel qPCR assay to detect the STXs biosynthesis gene sxtB of Alexandrium catenella and A. pacificum, the leading cause of PSP outbreaks in Asian coasts and worldwide. The newly designed sxtB TaqMan probes target the species without any positive signal in other relative dinoflagellates. Deming regression analysis revealed that the sxtB copy number of A. catenella and A. pacificum was 3.6 and 4.1 copies per cell, respectively. During the blooming periods (April 13th-14th, 2020), only A. catenella cells were detected through the qPCR assay, ranging from 5.0 × 10 to 2.5 × 104 eq cells L-1. In addition, sxtB qPCR quantified more accurately compared to large subunit (LSU) rRNA targeting qPCR assay that overestimate cell density. Besides, the sensitivity of sxtB was higher compared to the microscope when the species were rarely present (5.0 × 102 cells L-1). These suggest that the sxtB qPCR assay can be applied to toxic Alexandrium monitoring in the Korean coast, even in the early stage of bloomings.

Effects of nitrate on the saxitoxins biosynthesis revealed by sxt genes in the toxic dinoflagellate Alexandrium pacificum (group IV)

The dinoflagellate Alexandrium pacificum (group IV) is of particular interest because of its involvement in harmful algal blooms and production of saxitoxin (STX), which causes paralytic shellfish poisoning. The toxicity from STX and its analogues (STXs) is suspected to be affected by nitrogen (N) availability. However, the toxicity-associated behavior and STX-biosynthesis gene responses of the toxic A. pacificum under N fluctuations have not been sufficiently investigated. In the present study, we identified the sxtI gene involved in sxt biosynthesis pathway and evaluated the effects of nitrate (NO3-) on STXs production and the expression of four sxt core genes (sxtA4, sxtG, sxtB, and sxtI). Quantification of total STXs levels in the cultures under different NO3- regimes showed that NO3- concentration influenced STXs production. In addition, the proportion and concentration of STXs varied depending on the NO3- concentration. Core sxt transcript abundance was also influenced by available NO3- in a time-dependent manner. Expressional levels and patterns of sxtI were correlated with those of sxtA and sxtB. The relationship between the toxins and sxt responses in A. pacificum under various NO3- regimes suggests the direct involvement of N in the STXs biosynthesis pathway. Understanding this link would provide a tool to understand the toxin dynamics of dinoflagellates following N shifts in marine environments.

Genomic copy number variability at the genus, species and population levels impacts in situ ecological analyses of dinoflagellates and harmful algal blooms

The application of meta-barcoding, qPCR, and metagenomics to aquatic eukaryotic microbial communities requires knowledge of genomic copy number variability (CNV). CNV may be particularly relevant to functional genes, impacting dosage and expression, yet little is known of the scale and role of CNV in microbial eukaryotes. Here, we quantify CNV of rRNA and a gene involved in Paralytic Shellfish Toxin (PST) synthesis (sxtA4), in 51 strains of 4 Alexandrium (Dinophyceae) species. Genomes varied up to threefold within species and ~7-fold amongst species, with the largest (A. pacificum, 130 ± 1.3 pg cell-1 /~127 Gbp) in the largest size category of any eukaryote. Genomic copy numbers (GCN) of rRNA varied by 6 orders of magnitude amongst Alexandrium (102- 108 copies cell-1) and were significantly related to genome size. Within the population CNV of rRNA was 2 orders of magnitude (105 - 107 cell-1) in 15 isolates from one population, demonstrating that quantitative data based on rRNA genes needs considerable caution in interpretation, even if validated against locally isolated strains. Despite up to 30 years in laboratory culture, rRNA CNV and genome size variability were not correlated with time in culture. Cell volume was only weakly associated with rRNA GCN (20-22% variance explained across dinoflagellates, 4% in Gonyaulacales). GCN of sxtA4 varied from 0-102 copies cell-1, was significantly related to PSTs (ng cell-1), displaying a gene dosage effect modulating PST production. Our data indicate that in dinoflagellates, a major marine eukaryotic group, low-copy functional genes are more reliable and informative targets for quantification of ecological processes than unstable rRNA genes.

Marine natural products

Covering: January to December 2021This review covers the literature published in 2021 for marine natural products (MNPs), with 736 citations (724 for the period January to December 2021) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1425 in 416 papers for 2021), together with the relevant biological activities, source organisms and country of origin. Pertinent reviews, biosynthetic studies, first syntheses, and syntheses that led to the revision of structures or stereochemistries, have been included. An analysis of the number of authors, their affiliations, domestic and international collection locations, focus of MNP studies, citation metrics and journal choices is discussed.

Strong population genomic structure of the toxic dinoflagellate Alexandrium minutum inferred from meta-transcriptome samples

Despite theoretical expectations, marine microeukaryote population are often highly structured and the mechanisms behind such patterns remain to be elucidated. These organisms display huge census population sizes, yet genotyping usually requires clonal strains originating from single cells, hindering proper population sampling. Estimating allelic frequency directly from population wide samples, without any isolation step, offers an interesting alternative. Here, we validate the use of meta-transcriptome environmental samples to determine the population genetic structure of the dinoflagellate Alexandrium minutum. Strain and meta-transcriptome based results both indicated a strong genetic structure for A. minutum in Western Europe, to the level expected between cryptic species. The presence of numerous private alleles, and even fixed polymorphism, would indicate ancient divergence and absence of gene flow between populations. Single nucleotide polymorphisms (SNPs) displaying strong allele frequency differences were distributed throughout the genome, which might indicate pervasive selection from standing genetic variation (soft selective sweeps). However, a few genomic regions displayed extremely low diversity that could result from the fixation of adaptive de novo mutations (hard selective sweeps) within the populations.

Genetic association of toxin production in the dinoflagellate Alexandrium minutum

Dinoflagellates of the genus Alexandrium are responsible for harmful algal blooms and produce paralytic shellfish toxins (PSTs). Their very large and complex genomes make it challenging to identify the genes responsible for toxin synthesis. A family-based genomic association study was developed to determine the inheritance of toxin production in Alexandrium minutum and identify genomic regions linked to this production. We show that the ability to produce toxins is inheritable in a Mendelian way, while the heritability of the toxin profile is more complex. We developed the first dinoflagellate genetic linkage map. Using this map, several major results were obtained: 1. A genomic region related to the ability to produce toxins was identified. 2. This region does not contain any polymorphic sxt genes, known to be involved in toxin production in cyanobacteria. 3. The sxt genes, known to be present in a single cluster in cyanobacteria, are scattered on different linkage groups in A. minutum. 4. The expression of two sxt genes not assigned to any linkage group, sxtI and sxtG, may be regulated by the genomic region related to the ability to produce toxins. Our results provide new insights into the organization of toxicity-related genes in A. minutum, suggesting a dissociated genetic mechanism for the production of the different analogues and the ability to produce toxins. However, most of the newly identified genes remain unannotated. This study therefore proposes new candidate genes to be further explored to understand how dinoflagellates synthesize their toxins.

Apparent biogeographical trends in Alexandrium blooms for northern Europe: identifying links to climate change and effective adaptive actions

The marine dinoflagellate Alexandrium Halim represents perhaps the most significant and intensively studied genus with respect to species diversity, life history strategies, toxigenicity, biogeographical distribution, and global magnitude and consequences harmful algal blooms (HABs). The socioeconomic impacts, environmental and human health risks, and mitigation strategies for toxigenic Alexandrium blooms have also been explored in recent years. Human adaptive actions based on future scenarios of bloom dynamics and shifts in biogeographical distribution under climate-change parameters remain under development and not yet implemented on a regional scale. In the CoCliME (Co-development of climate services for adaptation to changing marine ecosystems) project these issues were addressed with respect to past, current and anticipated future status of key HAB genera and expected benefits of enhanced monitoring. Data on the distribution and frequency of Alexandrium blooms related to paralytic shellfish toxin (PST) events from key CoCliME Case Study areas, comprising the North Sea and adjacent Kattegat-Skagerrak, Norwegian Sea, and Baltic Sea, and eastern North Atlantic marginal seas, were evaluated in a contemporary and historical context over the past several decades. The first evidence of possible biogeographical expansion of Alexandrium taxa into eastern Arctic gateways was provided from DNA barcoding signatures. Various key climate change indicators, such as salinity, temperature, and water-column stratification, relevant to Alexandrium bloom initiation and development were identified. The possible influence of changing variables on bloom dynamics, magnitude, frequency and spatial and temporal distribution were interpreted in the context of regional ocean climate models. These climate change impact indicators may play key roles in selecting for the occurrence and diversity of Alexandrium species within the broader microeukaryote communities. For example, shifts to higher temperature and lower salinity regimes predicted for the southern North Sea indicate the potential for increased Alexandrium blooms, currently absent from this area. Ecological and socioeconomic impacts of Alexandrium blooms and effects on fisheries and aquaculture resources and coastal ecosystem function are evaluated, and, where feasible, effective adaptation strategies are proposed herein as emerging climate services.

Cyanotoxin-encoding genes as powerful predictors of cyanotoxin production during harmful cyanobacterial blooms in an inland freshwater lake: Evaluating a novel early-warning system

Freshwater harmful cyanobacterial blooms (HCBs) potentially produce excessive cyanotoxins, mainly microcystins (MCs), significantly threatening aquatic ecosystems and public health. Accurately predicting HCBs is thus essential to developing effective HCB mitigation and prevention strategies. We previously developed a novel early-warning system that uses cyanotoxin-encoding genes to predict cyanotoxin production in Harsha Lake, Ohio, USA, in 2015. In this study, we evaluated the efficacy of the early-warning system in forecasting the 2016 HCB in the same lake. We also examined potential HCB drivers and cyanobacterial community composition. Our results revealed that the cyanobacterial community was stable at the phylum level but changed dynamically at the genus level over time. Microcystis and Planktothrix were the major MC-producing genera that thrived in June and July and produced high concentrations of MCs (peak level 10.22 μg·L^-1). The abundances of the MC-encoding gene cluster mcy and its transcript levels significantly correlated with total MC concentrations (before the MC concentrations peaked) and accurately predicted MC production as revealed by logistic equations. When the Microcystis-specific gene mcyG reached approximately 1.5 × 10³ copies·mL^-1 or when its transcript level reached approximately 2.4 copies·mL^-1, total MC level exceeded 0.3 μg L^-1 (a health advisory limit) approximately one week later (weekly sampling scheme). This study suggested that cyanotoxin-encoding genes are promising predictors of MC production in inland freshwater lakes, such as Harsha Lake. The evaluated early-warning system can be a useful tool to assist lake managers in predicting, mitigating, and/or preventing HCBs.

Metal stresses modify soluble proteomes and toxin profiles in two Mediterranean strains of the distributed dinoflagellate Alexandrium pacificum

HABs involving Alexandrium pacificum have been reported in metal-contaminated ecosystems, suggesting that this distributed species adapts to and/or can tolerate the effects of metals. Modifications in soluble proteomes and PST contents were characterized in two Mediterranean A. pacificum strains exposed to mono- or polymetallic stresses (zinc, lead, copper, cadmium). These strains were isolated from two anthropized locations: Santa Giusta Lagoon (Italy, SG C10-3) and the Tarragona seaport (Spain, TAR C5-4F). In both strains, metals primarily downregulated key photosynthesis proteins. Metals also upregulated other proteins involved in photosynthesis (PCP in both strains), the oxidative stress response (HSP 60, proteasome and SOD in SG C10-3; HSP 70 in TAR C5-4F), energy metabolism (AdK in TAR C5-4F), neoglucogenesis/glycolysis (GAPDH and PEP synthase in SG C10-3) and protein modification (PP in TAR C5-4F). These proteins, possibly involved in adaptive proteomic responses, may explain the development of these A. pacificum strains in metal-contaminated ecosystems. The two strains showed different proteomic responses to metals, with SG C10-3 upregulating more proteins, particularly PCP. Among the PSTs, regardless of the metal and the strain studied, C2 and GTX4 predominated, followed by GTX5. Under the polymetallic cocktail, (i) total PSTs, C2 and GTX4 reached the highest levels in SG C10-3 only, and (ii) total PSTs, C2, GTX5 and neoSTX were higher in SG C10-3 than in TAR C5-4F, whereas in SG C10-3 under copper stress, total PSTs, GTX5, GTX1 and C1 were higher than in the controls, revealing variability in PST biosynthesis between the two strains. Total PSTs, C2, GTX4 and GTX1 showed significant positive correlations with PCP, indicating that PST production may be positively related to photosynthesis. Our results showed that the A. pacificum strains adapt their proteomic and physiological responses to metals, which may contribute to their ecological success in highly anthropized areas.

Temperature influences the content and biosynthesis gene expression of saxitoxins (STXs) in the toxigenic dinoflagellate Alexandrium pacificum

Temperature may affect the production of saxitoxin (STX) and its derivatives (STXs); however, this is still controversial. Further, STX-biosynthesis gene regulation and the relation of its toxicity with temperature are not clearly understood. In the present study, we evaluated the effects of different temperatures (12 °C, 16 °C, and 20 °C) on the growth, toxin profiles, and expression of two core STX-biosynthesis genes, sxtA and sxtG, in the toxic dinoflagellate Alexandrium pacificum Alex05, isolated from Korean coasts. We found that temperature significantly affected cell growth, with maximum growth recorded at 16 °C, followed by 20 °C and 12 °C. HPLC analysis revealed mostly 12 of STXs from the tested cultures. Interestingly, the contents of STXs increased in the cells cultured at 16 °C and exposed to cold stress, compared to the 20 °C culture and heat stress; however, toxin components were much more diverse under heat stress. These toxin profiles generally matched with the sxtA and sxtG expression levels. Incubation at lower temperatures (12 °C and 16 °C) and exposure to cold stress increased sxtA and sxtG expressions in the cells, whereas heat stress showed little change or downregulated the transcription of both genes. Principal component analysis (PCA) showed low correlation between STXs eq and expressional levels of sxtA and sxtG in heat-stressed cells. These results suggest that temperature might be a crucial factor affecting the level and biosynthesis of STXs in marine toxic dinoflagellates.

Unknown Extracellular and Bioactive Metabolites of the Genus Alexandrium: A Review of Overlooked Toxins

Various species of Alexandrium can produce a number of bioactive compounds, e.g., paralytic shellfish toxins (PSTs), spirolides, gymnodimines, goniodomins, and also uncharacterised bioactive extracellular compounds (BECs). The latter metabolites are released into the environment and affect a large range of organisms (from protists to fishes and mammalian cell lines). These compounds mediate allelochemical interactions, have anti-grazing and anti-parasitic activities, and have a potentially strong structuring role for the dynamic of Alexandrium blooms. In many studies evaluating the effects of Alexandrium on marine organisms, only the classical toxins were reported and the involvement of BECs was not considered. A lack of information on the presence/absence of BECs in experimental strains is likely the cause of contrasting results in the literature that render impossible a distinction between PSTs and BECs effects. We review the knowledge on Alexandrium BEC, (i.e., producing species, target cells, physiological effects, detection methods and molecular candidates). Overall, we highlight the need to identify the nature of Alexandrium BECs and urge further research on the chemical interactions according to their ecological importance in the planktonic chemical warfare and due to their potential collateral damage to a wide range of organisms.

Isolation from a fish kill and transcriptomic characterization of Gyrodinium jinhaense off Long Island Sound

First found in Korean coastal water, the dinoflagellate Gyrodinium jinhaense is a recently established species with unclear global distribution and unexplored genomic characteristics. From a laboratory fish mortality event off Long Island Sound, USA, we isolated a dinoflagellate, and by microscopic and molecular (18S rRNA gene; >99% identical) analyses found that it resembles G. jinhaense, hence named G. jinhaense strain AP17. Towards developing a genetic database for this dinoflagellate, a transcriptome of this species was sequenced using RNA-seq, producing 6 Gbp of data that was assembled into over 70,000 unigenes. The assembled transcriptome GC content was approximately 56% and the total Benchmarking Universal Single-Copy Orthologs for Eukaryota and Alveolata databases were approximately 50% and 57%, respectfully. Genes involved in grazing, energy generation, genome architecture, and protein synthesis, processing, and degradation were highly represented in the transcriptome. Moreover, fragments of polyketide synthase and saxitoxin genes were found but saxitoxins were not detected in high performance liquid chromatography measurements. With the first reported transcriptome for the Gyrodinium genus, this study will serve as a baseline for future Gyrodinium genomics and toxicological studies.

Insights into Alexandrium minutum Nutrient Acquisition, Metabolism and Saxitoxin Biosynthesis through Comprehensive Transcriptome Survey

Simple Summary

Alexandrium minutum is one of the causing organisms for the occurrence of harmful algae bloom (HABs) in marine ecosystems. This species produces saxitoxin, one of the deadliest neurotoxins which can cause human mortality. However, molecular information such as genes and proteins catalog on this species is still lacking. Therefore, this study has successfully characterized several new molecular mechanisms regarding A. minutum environmental adaptation and saxitoxin biosynthesis. Ultimately, this study provides a valuable resource for facilitating future dinoflagellates’ molecular response to environmental changes.

Abstract

The toxin-producing dinoflagellate Alexandrium minutum is responsible for the outbreaks of harmful algae bloom (HABs). It is a widely distributed species and is responsible for producing paralytic shellfish poisoning toxins. However, the information associated with the environmental adaptation pathway and toxin biosynthesis in this species is still lacking. Therefore, this study focuses on the functional characterization of A. minutum unigenes obtained from transcriptome sequencing using the Illumina Hiseq 4000 sequencing platform. A total of 58,802 (47.05%) unigenes were successfully annotated using public databases such as NCBI-Nr, UniprotKB, EggNOG, KEGG, InterPRO and Gene Ontology (GO). This study has successfully identified key features that enable A. minutum to adapt to the marine environment, including several carbon metabolic pathways, assimilation of various sources of nitrogen and phosphorus. A. minutum was found to encode homologues for several proteins involved in saxitoxin biosynthesis, including the first three proteins in the pathway of saxitoxin biosynthesis, namely sxtA, sxtG and sxtB. The comprehensive transcriptome analysis presented in this study represents a valuable resource for understanding the dinoflagellates molecular metabolic model regarding nutrient acquisition and biosynthesis of saxitoxin.

Recent developments in quantitative PCR for monitoring harmful marine microalgae

Marine microalgae produce a variety of specialised metabolites that have toxic effects on humans, farmed fish, and marine wildlife. Alarmingly, many of these compounds bioaccumulate in the tissues of shellfish and higher trophic organisms, including species consumed by humans. Molecular methods are emerging as a potential alternative and complement to the conventional microscopic diagnosis of toxic or otherwise harmful microalgal species. Quantitative PCR (qPCR) in particular, has gained popularity over the past decade as a sensitive, rapid, and cost-effective method for monitoring harmful microalgae. Assays targeting taxonomic marker genes provide the opportunity to identify and quantify (or semi-quantify) microalgal species and importantly to pre-empt bloom events. Moreover, the discovery of paralytic shellfish toxin biosynthesis genes in dinoflagellates has enabled researchers to directly monitor toxigenic species in coastal waters and fisheries. This review summarises the recent developments in qPCR detection methods for harmful microalgae, with emphasis on emerging toxin gene monitoring technologies.

Relationship between paralytic shellfish toxin content and sxtA gene copy number in different growth phases of Gymnodinium catenatum (Dinophyceae)

Paralytic shellfish toxin (PST) content in the dinoflagellate Gymnodinium catenatum changes with culture age, with a higher toxin concentration in the logarithmic phase that decreases when the culture ages. The gene copy number (GCN) of domains sxtA1 and sxtA4 was higher in the lag and stationary phase, and lag phase, respectively. No relationship was found between the GCN of the domains sxtA4 and sxtA1 with the PST content in G. catenatum.

Low Temperature and Cold Stress Significantly Increase Saxitoxins (STXs) and Expression of STX Biosynthesis Genes sxtA4 and sxtG in the Dinoflagellate Alexandrium catenella

Toxic dinoflagellate Alexandrium spp. produce saxitoxins (STXs), whose biosynthesis pathway is affected by temperature. However, the link between the regulation of the relevant genes and STXs' accumulation and temperature is insufficiently understood. In the present study, we evaluated the effects of temperature on cellular STXs and the expression of two core STX biosynthesis genes (sxtA4 and sxtG) in the toxic dinoflagellate Alexandrium catenella Alex03 isolated from Korean waters. We analyzed the growth rate, toxin profiles, and gene responses in cells exposed to different temperatures, including long-term adaptation (12, 16, and 20 °C) and cold and heat stresses. Temperature significantly affected the growth of A. catenella, with optimal growth (0.49 division/day) at 16 °C and the largest cell size (30.5 µm) at 12 °C. High concentration of STXs eq were detected in cells cultured at 16 °C (86.3 fmol/cell) and exposed to cold stress at 20→12 °C (96.6 fmol/cell) compared to those at 20 °C and exposed to heat stress. Quantitative real-time PCR (qRT-PCR) revealed significant gene expression changes of sxtA4 in cells cultured at 16 °C (1.8-fold) and cold shock at 20→16 °C (9.9-fold). In addition, sxtG was significantly induced in cells exposed to cold shocks (20→16 °C; 19.5-fold) and heat stress (12→20 °C; 25.6-fold). Principal component analysis (PCA) revealed that low temperature (12 and 16 °C) and cold stress were positively related with STXs' production and gene expression levels. These results suggest that temperature may affect the toxicity and regulation of STX biosynthesis genes in dinoflagellates.