RNA-Seq Analysis Reveals Genes Related to Photoreception, Nutrient Uptake, and Toxicity in a Noxious Red-Tide Raphidophyte Chattonella antiqua

Full-Length Transcriptome Analysis of the Ichthyotoxic Harmful Alga Heterosigma akashiwo (Raphidophyceae) Using Single-Molecule Real-Time Sequencing

The raphidophyte Heterosigma akashiwo is a harmful algal species. The bloom of this organism has been associated with the massive mortality of fish in many coastal waters. To investigate the molecular mechanism of H. akashiwo blooms, having a reliable reference transcriptome of this species is essential. Therefore, in this study, a full-length transcriptome of H. akashiwo was obtained by single-molecule real-time sequencing. In total, 45.44 Gb subread bases were generated, and 16,668 unigenes were obtained after the sequencing data processing. A total of 8666 (52.00%) unigenes were successfully annotated using seven public databases. Among them, mostly phosphorus and nitrogen metabolism genes were detected. Moreover, there were 300 putative transcription factors, 4392 putative long non-coding RNAs, and 7851 simple sequence repeats predicted. This study provides a valuable reference transcriptome for understanding how H. akashiwo blooms at a molecular level.

Full-length transcriptome analysis of the bloom-forming dinoflagellate Akashiwo sanguinea by single-molecule real-time sequencing

The dinoflagellate Akashiwo sanguinea is a harmful algal species and commonly observed in estuarine and coastal waters around the world. Harmful algal blooms (HABs) caused by this species lead to serious environmental impacts in the coastal waters of China since 1998 followed by huge economic losses. However, the full-length transcriptome information of A. sanguinea is still not fully explored, which hampers basic genetic and functional studies. Herein, single-molecule real-time (SMRT) sequencing technology was performed to characterize the full-length transcript in A. sanguinea. Totally, 83.03 Gb SMRT sequencing clean reads were generated, 983,960 circular consensus sequences (CCS) with average lengths of 3,061 bp were obtained, and 81.71% (804,016) of CCS were full-length non-chimeric reads (FLNC). Furthermore, 26,461 contigs were obtained after being corrected with Illumina library sequencing, with 20,037 (75.72%) successfully annotated in the five public databases. A total of 13,441 long non-coding RNA (lncRNA) transcripts, 3,137 alternative splicing (AS) events, 514 putative transcription factors (TFs) members from 23 TF families, and 4,397 simple sequence repeats (SSRs) were predicted, respectively. Our findings provided a sizable insights into gene sequence characteristics of A. sanguinea, which can be used as a reference sequence resource for A. sanguinea draft genome annotation, and will contribute to further molecular biology research on this harmful bloom algae.

Design Optimization of a Submersible Chemiluminescent Sensor (DISCO) for Improved Quantification of Reactive Oxygen Species (ROS) in Surface Waters

Reactive oxygen species (ROS) are key drivers of biogeochemical cycling while also exhibiting both positive and negative effects on marine ecosystem health. However, quantification of the ROS superoxide (O₂^-) within environmental systems is hindered by its short half-life. Recently, the development of the diver-operated submersible chemiluminescent sensor (DISCO), a submersible, handheld instrument, enabled in situ superoxide measurements in real time within shallow coral reef ecosystems. Here, we present a redesigned and improved instrument, DISCO II. Similar to the previous DISCO, DISCO II is a self-contained, submersible sensor, deployable to 30 m depth and capable of measuring reactive intermediate species in real time. DISCO II is smaller, lighter, lower cost, and more robust than its predecessor. Laboratory validation of DISCO II demonstrated an average limit of detection in natural seawater of 133.1 pM and a percent variance of 0.7%, with stable photo multiplier tube (PMT) counts, internal temperature, and flow rates. DISCO II can also be optimized for diverse environmental conditions by adjustment of the PMT supply voltage and integration time. Field tests showed no drift in the data with a percent variance of 3.0%. Wand tip adaptations allow for in situ calibrations and decay rates of superoxide using a chemical source of superoxide (SOTS-1). Overall, DISCO II is a versatile, user-friendly sensor that enables measurements in diverse environments, thereby improving our understanding of the cycling of reactive intermediates, such as ROS, across various marine ecosystems.

Transcriptomic response of the harmful algae Heterosigma akashiwo to polyphosphate utilization and phosphate stress

Phosphorus (P) is one of the major macronutrients necessary for phytoplankton growth. In some parts of the ocean, however, P is frequently scarce, hence, there is limited phytoplankton growth. To cope with P deficiency, phytoplankton evolved a variety of strategies, including, utilization of different P sources. Polyphosphate (polyP) is ubiquitously present and serves an essential function in aquatic environments, but it is unclear if and how this polymer is utilized by phytoplankton. Here, we examined the physiological and molecular responses of the widely present harmful algal bloom (HAB) species, Heterosigma akashiwo in polyP utilization, and in coping with P-deficiency. Our results revealed that two forms of inorganic polyP, namely, sodium tripolyphosphate and sodium hexametaphosphate, support H. akashiwo growth as efficiently as orthophosphate. However, few genes involved in polyP utilization have been identified. Under P-deficient conditions, genes associated with P transport, dissolved organic P utilization, sulfolipid synthesis, and energy production, were markedly elevated. In summary, our results indicate that polyP is bioavailable to H. akashiwo, and this HAB species have evolved a comprehensive strategy to cope with P deficiency.

Generation of Reactive Oxygen Species (ROS) by Harmful Algal Bloom (HAB)-Forming Phytoplankton and Their Potential Impact on Surrounding Living Organisms

Most marine phytoplankton with relatively high ROS generation rates are categorized as harmful algal bloom (HAB)-forming species, among which Chattonella genera is the highest ROS-producing phytoplankton. In this review, we examined marine microalgae with ROS-producing activities, with focus on Chattonella genera. Several studies suggest that Chattonella produces superoxide via the activities of an enzyme similar to NADPH oxidase located on glycocalyx, a cell surface structure, while hydrogen peroxide is generated inside the cell by different pathways. Additionally, hydroxyl radical has been detected in Chattonella cell suspension. By the physical stimulation, such as passing through between the gill lamellas of fish, the glycocalyx is easily discharged from the flagellate cells and attached on the gill surface, where ROS are continuously produced, which might cause gill tissue damage and fish death. Comparative studies using several strains of Chattonella showed that ROS production rate and ichthyotoxicity of Chattonella is well correlated. Furthermore, significant levels of ROS have been reported in other raphidophytes and dinoflagellates, such as Cochlodinium polykrikoides and Karenia mikimotoi. Chattonella is the most extensively studied phytoplankton in terms of ROS production and its biological functions. Therefore, this review examined the potential ecophysiological roles of extracellular ROS production by marine microalgae in aquatic environment.

Molecular phylogeny of fucoxanthin-chlorophyll a/c proteins from Chaetoceros gracilis and Lhcq/Lhcf diversity

Diatoms adapt to various aquatic light environments and play major roles in the global carbon cycle using their unique light-harvesting system, i.e. fucoxanthin chlorophyll a/c binding proteins (FCPs). Structural analyses of photosystem II (PSII)-FCPII and photosystem I (PSI)-FCPI complexes from the diatom Chaetoceros gracilis have revealed the localization and interactions of many FCPs; however, the entire set of FCPs has not been characterized. Here, we identify 46 FCPs in the newly assembled genome and transcriptome of C. gracilis. Phylogenetic analyses suggest that these FCPs can be classified into five subfamilies: Lhcr, Lhcf, Lhcx, Lhcz, and the novel Lhcq, in addition to a distinct type of Lhcr, CgLhcr9. The FCPs in Lhcr, including CgLhcr9 and some Lhcqs, have orthologous proteins in other diatoms, particularly those found in the PSI-FCPI structure. By contrast, the Lhcf subfamily, some of which were found in the PSII-FCPII complex, seems to be diversified in each diatom species, and the number of Lhcqs differs among species, indicating that their diversification may contribute to species-specific adaptations to light. Further phylogenetic analyses of FCPs/light-harvesting complex (LHC) proteins using genome data and assembled transcriptomes of other diatoms and microalgae in public databases suggest that our proposed classification of FCPs is common among various red-lineage algae derived from secondary endosymbiosis of red algae, including Haptophyta. These results provide insights into the loss and gain of FCP/LHC subfamilies during the evolutionary history of the red algal lineage.

The World of Algae Reveals a Broad Variety of Cryptochrome Properties and Functions

Algae are photosynthetic eukaryotic (micro-)organisms, lacking roots, leaves, and other organs that are typical for land plants. They live in freshwater, marine, or terrestrial habitats. Together with the cyanobacteria they contribute to about half of global carbon fixation. As primary producers, they are at the basis of many food webs and they are involved in biogeochemical processes. Algae are evolutionarily distinct and are derived either by primary (e.g., green and red algae) or secondary endosymbiosis (e.g., diatoms, dinoflagellates, and brown algae). Light is a key abiotic factor needed to maintain the fitness of algae as it delivers energy for photosynthesis, regulates algal cell- and life cycles, and entrains their biological clocks. However, excess light can also be harmful, especially in the ultraviolet range. Among the variety of receptors perceiving light information, the cryptochromes originally evolved as UV-A and blue-light receptors and have been found in all studied algal genomes so far. Yet, the classification, biophysical properties, wavelength range of absorbance, and biological functions of cryptochromes are remarkably diverse among algal species, especially when compared to cryptochromes from land plants or animals.

Recent Progress in the Study of Peroxiredoxin in the Harmful Algal Bloom Species Chattonella marina

Peroxiredoxin (Prx) is a relatively recently discovered antioxidant enzyme family that scavenges peroxides and is known to be present in organisms from biological taxa ranging from bacteria to multicellular eukaryotes, including photosynthetic organisms. Although there have been many studies of the Prx family in higher plants, green algae, and cyanobacteria, few studies have concerned raphidophytes and dinoflagellates, which are among the eukaryotic algae that cause harmful algal blooms (HABs). In our proteomic study using 2-D electrophoresis, we found a highly expressed 2-Cys peroxiredoxin (2-CysPrx) in the raphidophyte Chattonella marina var. antiqua, a species that induces mass mortality of aquacultured fish. The abundance of the C. marina 2-CysPrx enzyme was highest in the exponential growth phase, during which photosynthetic activity was high, and it then decreased by about a factor of two during the late stationary growth phase. This pattern suggested that 2-CysPrx is a key enzyme involved in the maintenance of high photosynthesis activity. In addition, the fact that the depression of photosynthesis by excessively high irradiance was more severe in the 2-CysPrx low-expression strain (wild type) than in the normal-expression strain (wild type) of C. marina suggested that 2-CysPrx played a critical role in protecting the cell from oxidative stress caused by exposure to excessively high irradiance. In the field of HAB research, estimates of growth potential have been desired to predict the population dynamics of HABs for mitigating damage to fisheries. Therefore, omics approaches have recently begun to be applied to elucidate the physiology of the growth of HAB species. In this review, we describe the progress we have made using a molecular physiological approach to identify the roles of 2-CysPrx and other antioxidant enzymes in mitigating environmental stress associated with strong light and high temperatures and resultant oxidative stress. We also describe results of a survey of expressed Prx genes and their growth-phase-dependent behavior in C. marina using RNA-seq analysis. Finally, we speculate about the function of these genes and the ecological significance of 2-CysPrx, such as its involvement in circadian rhythms and the toxicity of C. marina to fish.

Production of Extracellular Reactive Oxygen Species by Marine Biota

Reactive oxygen species (ROS) are produced ubiquitously across the tree of life. Far from being synonymous with toxicity and harm, biological ROS production is increasingly recognized for its essential functions in signaling, growth, biological interactions, and physiochemical defense systems in a diversity of organisms, spanning microbes to mammals. Part of this shift in thinking can be attributed to the wide phylogenetic distribution of specialized mechanisms for ROS production, such as NADPH oxidases, which decouple intracellular and extracellular ROS pools by directly catalyzing the reduction of oxygen in the surrounding aqueous environment. Furthermore, biological ROS production contributes substantially to natural fluxes of ROS in the ocean, thereby influencing the fate of carbon, metals, oxygen, and climate-relevant gases. Here, we review the taxonomic diversity, mechanisms, and roles of extracellular ROS production in marine bacteria, phytoplankton, seaweeds, and corals, highlighting the ecological and biogeochemical influences of this fundamental and remarkably widespread process.

Nutrient deficiency stimulates the production of superoxide in the noxious red-tide-forming raphidophyte Chattonella antiqua

The raphidophyte Chattonella antiqua is a single-celled alga that forms 'red tides' in coastal areas. C. antiqua produces superoxide anions (O₂^-), the excessive production of which has been associated with fish mortality. It is suggested that putative NADPH oxidase in the outer membrane oxidizes intracellular NADPH to produce O₂^- and secrete it externally. Earlier studies revealed that photosynthetic electron transport, a major producer of NADPH in photosynthetic organisms, is involved in the production of O₂^- in C. antiqua but the details of the O₂^- production mechanism have yet to be elucidated. Since nutrient deficiency adversely affects the formation of blooms of C. antiqua, in this study, we examined the effects of nutrient deficiency on O₂^- production in C. antiqua. When cells were grown under nitrogen (N)- or phosphorus (P)-deficient conditions, the production of O₂^- was stimulated. In particular, the extracellular levels of O₂^- under N- or P-deficient conditions were high during the dark period when photosynthetic activities in terms of actual quantum efficiency and photochemical quenching were low. The extracellular levels of O₂^- under the nutrient-deficient conditions were unaffected by the presence of 3-(3,4-dichlorophenyl)-1,1‑dimethylurea (DCMU), an inhibitor of photosynthetic electron transport, but decreased when the nutrients were present. Furthermore, the intracellular ratio of NADPH to NADP⁺ under N- or P-deficient conditions was higher than that under nutrient-replete conditions. These observations suggest that another metabolic pathway, independent of photosynthesis, provides NADPH for the production of O₂^- under nutrient deficiency.

Extracellular secretion of superoxide is regulated by photosynthetic electron transport in the noxious red-tide-forming raphidophyte Chattonella antiqua

The raphidophyte Chattonella antiqua is a noxious red-tide-forming alga that harms fish culture and the aquatic environment. Chattonella antiqua produces and secretes superoxide anions (O₂^-), and excessive secretion of O₂^- into the water has been associated with fish mortality. It is known that strong light stimulates the production of O₂^- in Chattonella spp. but the mechanism of the light-induced production of O₂^- remains to be clarified. In the present study, we examined the effects of light on extracellular levels of O₂^- and photosynthesis in C. antiqua. Extracellular levels of O₂^- rose during growth under high-intensity light, and the level of O₂^- was correlated with the photosynthetic parameter qP, which reflects the rate of transport of electrons downstream of photosystem II. The production of O₂^- was inhibited in the presence of 3-(3,4-dichlorophenyl)-1,1-dimethylurea, an inhibitor of photosynthetic electron transport, suggesting that reducing power derived from electron transport might be required for the production of O₂^-. By contrast, the production of O₂^- was enhanced in the presence of glycolaldehyde, an inhibitor of the Calvin-Benson cycle, suggesting that the accumulation of NADPH might stimulate the production of O₂^-. Thus, it is likely that the production of O₂^- is regulated by photosynthesis in C. antiqua.

A review of karenia mikimotoi: Bloom events, physiology, toxicity and toxic mechanism

Karenia mikimotoi is a worldwide bloom-forming dinoflagellate in the genus Karenia. Blooms of this alga have been observed since the 1930s and have caused mass mortalities of fish, shellfish, and other invertebrates in the coastal waters of many countries, including Japan, Norway, Ireland, and New Zealand. This species has frequently bloomed in China, causing great financial losses (more than 2 billion yuan, Fujian Province, 2012). K. mikimotoi can adapt to various light, temperature, salinity, and nutrient conditions, which together with its complex life history, strong motility, and density-dependent allelopathy, allows it to form blooms that are lethal to almost all marine organisms. However, its toxicity differs between subspecies and some target-species-specific toxicity has also been recorded. Significant gill disorder is observed in affected fish, to which the massive fish kills are attributed, rather than to the hypoxia that occurs in the fading stage of a bloom. However, although this species is haemolytic and cytotoxic, and generates reactive oxygen species, none of the isolated toxins or lipophilic extracts have toxic effects as extreme as those of the intact algal cells. The toxic effects of K. mikimotoi are strongly related to contact with intact cells. Several reasonable hypotheses of how and why this species blooms and causes mass mortalities have been proposed, but further research is required.