Utilization of urea and expression profiles of related genes in the dinoflagellate Prorocentrum donghaiense

A step forward in sustainable pesticide production from Amphidinium carterae biomass via photobioreactor cultivation with urea as a nitrogen source

This study addresses the problem of replacing nitrate and ammonium with urea as a greener nitrogen source in the mass cultivation of the microalga Amphidinium carterae for the development of amphidinol-based phytosanitary products. To solve this problem, a nuclear magnetic resonance assisted investigation evaluated the effect of nitrogen sources on growth and metabolic profiles in photobioreactors. Urea-fed cultures exhibited growth kinetics comparable to nitrate-fed cultures (µmax = 0.30 day-1, Pbmax = 43 mgL-1day-1). Urea-fed cultures had protein, lipid, and carbohydrate contents of 39.5%, 14.5%, and 42.4%, respectively, while nitrate-fed cultures had 27.9 %, 17.5% and 48.1%, respectively. Metabolomics revealed nitrogen source-dependent metabotypes and a correlation between amphidinols and polyunsaturated fatty acids. The amphidinol-to-nitrogen yield coefficient in urea-fed cultures (135 mg/g) was approximately 2.5 times higher than in nitrate-fed cultures. The potent antiphytopathogenic activity exhibited by extracts from urea-fed cultures underscores the potential of urea as a sustainable nitrogen source in microalgae-based biorefineries.

New insights on the role of nitrogen in the resistance to environmental stress in an endosymbiotic dinoflagellate

Endosymbiotic dinoflagellates provide the nutritional basis for marine invertebrates, especially reef-building corals. These dinoflagellates are sensitive to environmental changes, and understanding the factors that can increase the resistance of the symbionts is crucial for the elucidation of the mechanisms involved with coral bleaching. Here, we demonstrate how the endosymbiotic dinoflagellate Durusdinium glynnii is affected by concentration (1760 vs 440 µM) and source (sodium nitrate vs urea) of nitrogen after light and thermal stress exposure. The effectiveness in the use of the two nitrogen forms was proven by the nitrogen isotopic signature. Overall, high nitrogen concentrations, regardless of source, increased D. glynnii growth, chlorophyll-a, and peridinin levels. During the pre-stress period, the use of urea accelerated the growth of D. glynnii compared to cells grown using sodium nitrate. During the luminous stress, high nitrate conditions increased cell growth, but no changes in pigments composition was observed. On the other hand, during thermal stress, a steep and steady decline in cell densities over time was observed, except for high urea condition, where there is cellular division and peridinin accumulation 72 h after the thermal shock. Our findings suggest peridinin has a protective role during the thermal stress, and the uptake of urea by D. glynnii can alleviate thermal stress responses, eventually mitigating coral bleaching events.

Effect of dissolved organic nutrients on the bloom of Prorocentrum donghaiense in the East China Sea coastal waters

Prorocentrum donghaiense blooms occur annually in the East China Sea coastal waters, degrading ecosystem functions and impeding economic development. Dissolved organic nitrogen and phosphorus (DON and DOP) are the main components in the marine nutrient pools and are closely related to harmful algal blooms. From April to June 2019, a survey was conducted along the East China Sea coast (Sansha and Lianjiang counties) to investigate the relationship between dissolved organic nutrients and P. donghaiense bloom. Our findings showed that dinoflagellates dominated the phytoplankton community, and dissolved organic nutrients were the major factors influencing community structure during the P. donghaiense bloom. Redundancy analysis indicated that P. donghaiense abundance was primarily affected by DON in the Sansha area while it was primarily affected by DON and DOP in the Lianjiang area. Correlation analysis also confirmed a strong positive correlation between dissolved organic nutrients and P. donghaiense abundance both in the Sansha and Lianjiang coastal areas (p < 0.001). Furthermore, a culture experiment was carried out during the bloom to further investigate the effect of dissolved organic nutrients on the phytoplankton community structure. After 10 days of culture, dinoflagellates' relative abundance decreased from 97.1% to 28.2% in the inorganic treatment, whereas dinoflagellates continued to dominate the phytoplankton community in the organic treatment (76.9%). As a result, we propose that dissolved organic nutrients are responsible for the P. donghaiense bloom outbreak and promote the phytoplankton community shift from diatoms to dinoflagellates.

3-Indoleacrylic acid from canola straw as a promising antialgal agent - Inhibition effect and mechanism on bloom-forming Prorocentrum donghaiense

Harmful algal blooms (HABs) have induced severe damage worldwide. A novel high-efficient antialgal natural chemical, 3-indoleacrylic acid (3-IDC) with a 5-day half-maximal inhibitory concentration (IC_{50, 5d}), was discovered from canola straw, and its algal inhibition mechanism was investigated. Adverse effects were observed on the growth of P. donghaiense with 3-IDC addition, following an increase in reactive oxygen species (ROS) production. 3-IDC also hindered the photosynthetic mechanism of P. donghaiense cells. Transcriptional results showed 3-IDC inhibiting the functions of all the nutrient assimilating genes, down-regulated ribulose-1,5-bisphosphate carboxylase/oxygenase II, and cytochrome f genes. The expression of heat shock protein (HSP) 70 and 90 and rhodopsin genes were also suppressed. The binding affinity of investigated receptors was observed. The conformational changes induced by the spatial microstructural alteration through 3-IDC may further contribute to the perturbation of those enzyme catalytic activities. The present results provide new insights on controlling HABs using 3-IDC.

An overview of Prorocentrum donghaiense blooms in China: Species identification, occurrences, ecological consequences, and factors regulating prevalence

Prorocentrum donghaiense Lu (also identified as Prorocentrum shikokuense Hada and Prorocentrum obtusidens Schiller) is a bloom-forming dinoflagellate species distributed worldwide. Blooms of P. donghaiense occur annually in adjacent waters of the East China Sea (ECS), especially in the waters near the Changjiang River Estuary. Blooms of this species have also been reported in nearby Japanese and Korean waters. There has been an apparent bloom-forming species succession pattern in the ECS since 2000, with diatom blooms in the early spring, shifting to long-lasting and large-scale dinoflagellate blooms dominated by P. donghaiense during the spring, and finally ended by diatom and/or Noctiluca scintillans blooms in summer. These bloom succession patterns were closely correlated with changes in environmental factors, such as temperature increase and anthropogenic eutrophication. Decreasing silicate by the construction of the Three Gorges Dam and increasing dissolved inorganic nitrogen flux were mainly influenced by high intensity human activities in the Changjiang River watershed, resulting in low Si/N ratio and high N/P ratios, possibly accelerating outbreak of P. donghaiense blooms. Phosphorous deficiency might be the most critical factor controlling the succession of microalgal blooms from diatoms to dinoflagellates. Prorocentrum donghaiense is a nontoxic species, but it can disrupt marine ecosystem by decreasing phytoplankton biodiversity and changing the structure of the food chain. Prorocentrum donghaiense blooms in the ECS have been intensively studied during the last two decades. Several possible mechanisms that contribute or trigger the annual blooms of this species have been proposed, but further research is required particularly on the aspect of nutrient budget, ecosystem impacts, as well as social-economic impact assessment.

Reduced forms of nitrogen control the spatial distribution of phytoplankton communities: The functional winner, dinoflagellates in an anthropogenically polluted estuary

The effects of reduced forms of nitrogen (NH₄⁺ and dissolved organic nitrogen (DON)) on the spatial distribution of diatoms and dinoflagellates in an estuarine-coastal water continuum were investigated from 2015 to 2019. The proportion of non-DIN in total nitrogen was utilized as an indicator of DON along with direct measurements of DON. While NO₃^- originated from Seomjin River, the abundant NH₄⁺ and DON occurred from Gwangyang Bay through Namhae. Diatoms were mostly confined to the upper estuarine system and dinoflagellates dominated in the regions with high levels of NH₄⁺ and DON. Generalized additive models also presented the different responses of diatoms and dinoflagellates to increases in NH₄⁺ and DON. Thus, our results highlight that diatoms dominate in NO₃^--replete water with full access to the source and dinoflagellates take over the ecologically open niche in an anthropogenically polluted estuary with full access to reduced forms of nitrogen.

Increased nitrate concentration differentially affects cell growth and expression of nitrate transporter and other nitrogen-related genes in the harmful dinoflagellate Prorocentrum minimum

The molecular mechanisms through which dinoflagellates adapt to nitrate fluctuations in aquatic environments remain poorly understood. Here, we sequenced the full-length cDNA of a nitrate transporter (NRT) gene from the harmful marine dinoflagellate Prorocentrum minimum Schiller. The cDNA length was 2431 bp. It encoded a 529-amino acid protein, which was phylogenetically clustered with proteins from other dinoflagellates. Nitrate supply promoted cell growth up to a certain concentration (∼1.76 mM) but inhibited it at higher concentrations. Interestingly, at the inhibitory concentrations, nitrite levels in the medium were considerably increased. Nitrate concentration affected the expression of PmNRT, nitrite transporter (PmNiRT), nitrate reductase (PmNR), and nitrite reductase (PmNiR). Specifically, PmNRT was upregulated after 24 h, with ∼6-fold change compared with the control level, in both nitrate-depleted and nitrate-repleted cultures. In addition, PmNR transcript levels increased to the maximum of 4-fold at 48 h but decreased thereafter. In contrast, PmNiR levels remained unchanged in both nitrate-repleted and nitrate-depleted cultures. Therefore, P. minimum likely copes with nitrate fluctuations in its environment by regulating a set of genes responsible for nitrate uptake.

Biochemical Mapping of Pyrodinium bahamense Unveils Molecular Underpinnings behind Organismal Processes

Proteins, lipids, and carbohydrates from the harmful algal bloom (HAB)-causing organism Pyrodinium bahamense were characterized to obtain insights into the biochemical processes in this environmentally relevant dinoflagellate. Shotgun proteomics using label-free quantitation followed by proteome mapping using the P. bahamense transcriptome and translated protein databases of Marinovum algicola, Alexandrium sp., Cylindrospermopsis raciborskii, and Symbiodinium kawagutii for annotation enabled the characterization of the proteins in P. bahamense. The highest number of annotated hits were obtained from M. algicola and highlighted the contribution of microorganisms associated with P. bahamense. Proteins involved in dimethylsulfoniopropionate (DMSP) degradation such as propionyl CoA synthethase and acryloyl-CoA reductase were identified, suggesting the DMSP cleavage pathway as the preferred route in this dinoflagellate. Most of the annotated proteins were involved in amino acid biosynthesis and carbohydrate degradation and metabolism, indicating the active roles of these molecules in the vegetative stage of P. bahamense. This characterization provides baseline information on the cellular machinery and the molecular basis of the ecophysiology of P. bahamense.

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.

Nitrogen availability improves the physiological resilience of coral endosymbiont Cladocopium goreaui to high temperature

The physiological response of symbiotic Symbiodiniaceae to high temperature is believed to result in coral bleaching. However, the potential effect of nitrogen availability on heat acclimatization of symbiotic Symbiodiniaceae is still unclear. In this study, physiological responses of Symbiodiniaceae Cladocopium goreaui to temperature and nitrogen nutrient stress conditions were investigated. Nitrogen deficiency caused significant declines in cell concentration and chlorophyll content per cell, but significant increases in nitric oxide synthase activity, caspase3 activation level, and cellular carbon content of C. goreaui at normal temperature. Algal cells under high temperature and nitrogen deficiency showed significant rises in Fv/Fm, catalase activity, and caspase3 activation level, but no significant changes in cell yield, cell size, chlorophyll content, superoxide dismutase, nitric oxide synthase activity, and cellular contents of nitrogen and carbon, in comparison with those under normal temperature and nitrogen deficiency. Growth, chlorophyll, and nitrogen contents of algal cells under the high temperature and nitrogen-replete conditions were significantly higher than those under high temperature or nitrogen deficiency alone, whereas nitric oxide synthase activity, superoxide dismutase activity, catalase activity, carbon content, and caspase3 activation level exhibited opposite trends of variation. Transcriptomic and network analyses revealed ion transport and metabolic processes mainly involved in regulating these physiological activities under different temperature and nitrogen nutrient. The totality of results shows that high temperature activates stress responses, induces antioxidant capacity of apoptosis, and limits the growth rate of C. goreaui. Adequate nitrogen nutrient can improve the resilience of this Symbiodiniaceae against heat stress through repressed apoptosis, promoted ion transport, and optimized metabolism.

Metaproteomics reveals the molecular mechanism underlying bloom maintenance of a marine dinoflagellate under low ambient CO2 and inorganic nutrients

Dinoflagellate blooming periods are paradoxically characterized by high biomass growth rate and low ambient dissolved CO₂ and inorganic nutrients, however, the underlying mechanisms linking cell growth and nutrient acquisition are poorly understood. Here, we compared metaproteomes of non-bloom, mid-blooming and late-blooming cells of a marine dinoflagellate Prorocentrum donghaiense. Cell division, metabolism of carbon, nitrogen, phosphorus, lipid, porphyrin and chlorophyll were more active in blooming cells than in non-bloom cells. Up-regulation of carbonic anhydrase, ribulose-1,5-bisphosphate carboxylase/oxygenase II, and C₄-cycle proteins enhanced CO₂ assimilation of P. donghaiense. Proteins participating in external organic nutrient acquisition and conversion, such as transporters for fatty acids, peptides and amino acids, external- and internal-phosphomonoester hydrolase, and diverse peptidases and amino acid transaminases, exhibited higher expression in blooming cells relative to non-bloom cells. Interestingly, dissolved organic nitrogen (DON) such as urea and aspartate significantly down-regulated expression and activity of carbon assimilation proteins except for RuBisCO form II, suggesting that DON provided sufficient carbon source which reduced the need to concentrate internal CO₂. This study demonstrates that coupling of efficient CO₂ assimilation with DON utilization are essential for bloom maintenance of P. donghaiense, and future efforts should be devoted to dissolved organic nutrients for prevention and management of dinoflagelllate blooms.

Transcriptome profiling reveals versatile dissolved organic nitrogen utilization, mixotrophy, and N conservation in the dinoflagellate Prorocentrum shikokuense under N deficiency

Harmful algal blooms formed by certain dinoflagellate species often occur when environmental nitrogen nutrients (N) are limited. However, the molecular mechanism by which dinoflagellates adapt to low N environments is poorly understood. In this study, we characterized the transcriptomic responses of Prorocentrum shikokuense to N deficiency, along with its physiological impact. Under N deficiency, P. shikokuense cultures exhibited growth inhibition, a reduction in cell size, and decreases in cellular chlorophyll a and nitrogen contents but an increase in carbon content. Accordingly, gene expression profiles indicated that carbon fixation and catabolism and fatty acid metabolism were enhanced. Transporter genes of nitrate/nitrite, ammonium, urea, and amino acids were significantly upregulated, indicating that P. shikokuense cells invest to enhance the uptake of available dissolved N. Notably, upregulated genes included those involved in endocytosis and phagosomes, evidence that P. shikokuense is a mixotrophic organism that activates phagotrophy to overcome N deficiency. Additionally, vacuolar amino acid transporters, the urea cycle, and urea hydrolysis genes were upregulated, indicating N recycling within the cells under N deficiency. Our study indicates that P. shikokuense copes with N deficiency by economizing nitrogen use and adopting multiple strategies to maximize N acquisition and reuse while maintaining carbon fixation. The remarkable low N adaptability may confer competitive advantages to P. shikokuense for forming harmful blooms in DIN-limited environments.

Dinoflagellates alter their carbon and nutrient metabolic strategies across environmental gradients in the central Pacific Ocean

Marine microeukaryotes play a fundamental role in biogeochemical cycling through the transfer of energy to higher trophic levels and vertical carbon transport. Despite their global importance, microeukaryote physiology, nutrient metabolism and contributions to carbon cycling across offshore ecosystems are poorly characterized. Here, we observed the prevalence of dinoflagellates along a 4,600-km meridional transect extending across the central Pacific Ocean, where oligotrophic gyres meet equatorial upwelling waters rich in macronutrients yet low in dissolved iron. A combined multi-omics and geochemical analysis provided a window into dinoflagellate metabolism across the transect, indicating a continuous taxonomic dinoflagellate community that shifted its functional transcriptome and proteome as it extended from the euphotic to the mesopelagic zone. In euphotic waters, multi-omics data suggested that a combination of trophic modes were utilized, while mesopelagic metabolism was marked by cytoskeletal investments and nutrient recycling. Rearrangement in nutrient metabolism was evident in response to variable nitrogen and iron regimes across the gradient, with no associated change in community assemblage. Total dinoflagellate proteins scaled with particulate carbon export, with both elevated in equatorial waters, suggesting a link between dinoflagellate abundance and total carbon flux. Dinoflagellates employ numerous metabolic strategies that enable broad occupation of central Pacific ecosystems and play a dual role in carbon transformation through both photosynthetic fixation in the euphotic zone and remineralization in the mesopelagic zone.

Symbiodiniaceae Dinoflagellates Express Urease in Three Subcellular Compartments and Upregulate its Expression Levels in situ in Three Organs of a Giant Clam (Tridacna squamosa) During Illumination

Giant clams harbor three genera of symbiotic dinoflagellates (Symbiodinium, Cladocopium, and Durusdinium) as extracellular symbionts (zooxanthellae). While symbiotic dinoflagellates can synthesize amino acids to benefit the host, they are nitrogen-deficient. Hence, the host must supply them with nitrogen including urea, which can be degraded to ammonia and carbon dioxide by urease (URE). Here, we report three complete coding cDNA sequences of URE, one for each genus of dinoflagellate, obtained from the colorful outer mantle of the giant clam, Tridacna squamosa. The outer mantle had higher transcript level of Tridacna squamosa zooxanthellae URE (TSZURE) than the whitish inner mantle, foot muscle, hepatopancreas, and ctenidium. TSZURE was immunolocalized strongly and atypically in the plastid, moderately in the cytoplasm, and weakly in the cell wall and plasma membrane of symbiotic dinoflagellates. In the outer mantle, illumination upregulated the protein abundance of TSZURE, which could enhance urea degradation in photosynthesizing dinoflagellates. The urea-nitrogen released could then augment synthesis of amino acids to be shared with the host for its general needs. Illumination also enhanced gene and protein expression levels of TSZURE/TSZURE in the inner mantle and foot muscle, which contain only small quantities of symbiotic dinoflagellate, have no iridocyte, and lack direct exposure to light. With low phototrophic potential, dinoflagellates in the inner mantle and foot muscle might need to absorb carbohydrates in order to assimilate the urea-nitrogen into amino acids. Amino acids donated by dinoflagellates to the inner mantle and the foot muscle could be used especially for synthesis of organic matrix needed for light-enhanced shell formation and muscle protein, respectively.

Dur3 and nrt2 genes in the bloom-forming dinoflagellate Prorocentrum minimum: Transcriptional responses to available nitrogen sources

The increasing inflow of nitrogen (N) substrates into marine nearshore ecosystems induces proliferation of harmful algal blooms (HABs) of dinoflagellates, such as potentially toxic invasive species Prorocentrum minimum. In this study, we estimated the influence of NO3-, NH4+ and urea on transcription levels and urea transporter dur3 and nitrate transporter nrt2 genes expression in these dinoflagellates. We identified dur3 and nrt2 genes sequences in unannotated transcriptomes of P. minimum and other dinoflagellates presented in MMETSP database. Phylogenetic analysis showed that these genes of dinoflagellates clustered to the distinct clade demonstrating evolutionary relationship with the other known dur3 and nrt2 genes of microalgae. The evaluation of expression levels of dur3 and nrt2 genes by RT-qPCR revealed their sensitivity to input of the studied N sources. Dur3 expression levels were downregulated after the supplementation of additional N sources and were 1.7-2.6-fold lower than in the nitrate-grown culture. Nrt2 expression levels decreased 1.9-fold in the presence of NH4+. We estimated total RNA and DNA synthesis rates by the analysis of incorporation of 3H-thymidine and 3H-uridine in batch and continuous cultures. Addition of N compounds did not affect the DNA synthesis rates. Transcription levels increased up to 12.5-fold after the N supplementation in urea-limited treatments. Investigation of various nitrogen sources as biomarkers of dinoflagellate proliferation due to their differentiated impact on expression of dur3 and nrt2 genes and transcription rates in P. minimum cells allowed concluding about high potential of the studied parameters for future modeling of HABs under global N pollution.

Utilization of various forms of nitrogen and expression regulation of transporters in the harmful alga Heterosigma akashiwo (Raphidophyceae)

Nitrogen (N) is an essential nutrient for phytoplankton growth. There is ample evidence that N enrichment promotes harmful algae blooms (HABs) but molecular mechanisms regulating N-nutrient uptake and metabolism are not so clear, especially for the raphidophyte Heterosigma akashiwo, which forms ichthyotoxic HABs in many coastal waters. In this study, the utilization of three different chemical forms of N (nitrate, ammonium, and urea) by H. akashiwo CCMA 369 was investigated in batch culture conditions. Results showed that H. akashiwo grew well on all three N compounds, and the highest cell yield occurred in the NH₄⁺ culture group. Reverse transcription quantitative PCR analysis revealed that the expression of high-affinity NO₃^- transporter (NIT), NH₄⁺ transporter (AMT) and high-affinity urea active transporter (DUR3), were significantly up-regulated under N-limitation compared to the N-replete control. The mRNA levels of AMT and DUR3 also displayed a clear diel rhythm, with high levels at midnight. In addition, NH₄⁺ addition (5 μM) did not depress the transcript abundance of any of the three N transporters. Compared with the co-occurring immobile diatom Skeletonema costatum, the high expression of AMT in dark period in H. akashiwo is consistent with its diel vertical migration behavior, which may promote N-nutrient acquisition from deeper layers and give advantages for H. akashiwo to form blooms.