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Flow-regulated discharges of water from control structures into estuaries result in hydrologic and water chemistry conditions that impact spatial and temporal variability in the structure and biomass of phytoplankton communities, including the potential for harmful algal blooms (HABs). The relationships between regulated Caloosahatchee River (i.e., C-43 Canal) discharges and phytoplankton communities in the Caloosahatchee Estuary and adjacent nearshore regions on the southwest coast of Florida were investigated during two study periods, 2009–2010 and 2018–2019. During periods of low to moderate discharge rates, when mesohaline conditions predominated in the estuary, and water residence times were comparatively long, major blooms of the HAB dinoflagellate species Akashiwo sanguinea were observed in the estuary. Periods of high discharge were characterized by comparatively low phytoplankton biomass in the estuary and greater influence of a wide range of freshwater taxa in the upper reaches. By contrast, intense blooms of the toxic dinoflagellate Karenia brevis in the nearshore region outside of the estuary were observed during high discharge periods in 2018–2019. The latter events were significantly associated with elevated levels of nitrogen in the estuary compared to lower average concentrations in the 2009–2010 study period. The relationships observed in this study provide insights into the importance of managing regulated discharge regimes to minimize adverse impacts of HABs on the health of the estuary and related coastal environments.

Inorganic carbon acquisition is essential to algal growth, while the limitations of dissolved inorganic carbon (DIC) on phytoplankton are still less known in lakes. Sediment is an active hot spot for microbial metabolism, driving the migration and transformation of elements in shallow lakes, which may control the DIC availability to influence algal spatiotemporal dynamics. Hence, we investigated the spatiotemporal changes of phytoplankton, DIC and sediment respiration rates in a eutrophic shallow freshwater lake under non-bloom conditions. There was a widespread deficiency of DIC in the lake, except the estuary. Sediment respiration was positively associated with changes in DIC concentrations, indicating that carbon metabolic activity of sedimentary microorganisms was an important inorganic carbon source for water columns. The availability of DIC in water columns regulated by sediment microbial respiration influenced the algal biomass, composition and productivity. The synergistic effects of seasonal temperature changes and sediment microbial respiration influenced the vertical distribution and migration of phytoplankton. Our results emphasized that carbon metabolic intensity of sediment microorganisms might play a key role in dynamics of phytoplankton, further impacting the spatiotemporal pattern and formation of algal bloom in eutrophic shallow freshwater lakes.

Breaking‐wave induced bioluminescence is a critical component of the biogeochemical process in the ocean. Understanding bioluminescence is important for monitoring red tides caused by bioluminescent microorganisms. In this study, we present the first numerical effort to quantify bioluminescent light intensity based on high‐fidelity direct numerical simulations of breaking waves and a quantitative bioluminescent model. The dynamics of breaking waves are extensively validated through comparison with existing studies. We find that the time‐averaged and Lagrangian‐averaged shear stress saturates as surface tension effects decrease and wave steepness increases. The spatial distribution of light intensity correlates with the wave crest overturning and air bubbles generated in plunging breakers. Furthermore, we observe that the maximum light intensity asymptotically approaches the emission of single cells, suggesting the potential for cost‐effective prediction models in future studies. Plain Language Summary Marine microorganisms, such as dinoflagellates, flash when stimulated by mechanical forces caused by breaking waves. Understanding this phenomenon, also known as the ‘blue tears’ of ocean, is helpful for predicting ‘red tides’, a hazardous algal blooms caused by dinoflagellates. We use computer simulations to determine how much light is emitted when breaking waves stimulates bioluminescence. Our analysis show that there is an upper limit for the level of the mechanical force in breaking waves. We also find that the maximum bioluminescence light intensity is similar to that emitted by a single cell. Key Points A numerical framework is developed to quantify bioluminescence stimulated by ocean surface breaking waves The time‐averaged and Lagrangian‐averaged shear stress saturates as surface tension effects decrease and wave steepness increases Maximum bioluminescent light intensity asymptotically approaches single cell emission at the time of flashing

Nearly all annual blooms of the toxic dinoflagellate Karenia brevis ( K . brevis ) pose a serious threat to coastal Southwest Florida. These blooms discolor water, kill fish and marine mammals, contaminate shellfish, cause mild to severe respiratory irritation, and discourage tourism and recreational activities, leading to significant health and economic impacts in affected communities. Despite these issues, we still lack standard measures suitable for assessing bloom severity or for evaluating the efficacy of modeling efforts simulating bloom initiation and intensity. In this study, historical cell count observations along the southwest Florida shoreline from 1953 to 2019 were used to develop monthly and annual bloom severity indices (BSI). Similarly, respiratory irritation observations routinely reported in Sarasota and Manatee Counties from 2006 to 2019 were used to construct a respiratory irritation index (RI). Both BSI and RI consider spatial extent and temporal evolution of the bloom, and can be updated routinely and used as objective criteria to aid future socioeconomic and scientific studies of K . brevis . These indices can also be used to help managers and decision makers both evaluate the risks along the coast during events and design systems to better respond to and mitigate bloom impacts. Before 1995, sampling was done largely in response to reports of discolored water, fish kills, or respiratory irritation. During this timeframe, lack of sampling during the fall, when blooms typically occur, generally coincided with periods of more frequent-than-usual offshore winds. Consequently, some blooms may have been undetected or under-sampled. As a result, the BSIs before 1995 were likely underestimated and cannot be viewed as accurately as those after 1995. Anomalies in the frequency of onshore wind can also largely account for the discrepancies between BSI and RI during the period from 2006 to 2019. These findings highlighted the importance of onshore wind anomalies when predicting respiratory irritation impacts along beaches.

Dinoflagellates are a remarkable group of protists, not only for their association with harmful algal blooms and coral reefs but also for their numerous characteristics deviating from the rules of eukaryotic biology. Genome research on dinoflagellates has lagged due to their immense genome sizes in most species (~ 1-250 Gbp). Nevertheless, the last decade marked a fruitful era of dinoflagellate genomics, with 27 genomes sequenced and many insights attained. This review aims to synthesize information from these genomes, along with other omic data, to reflect on where we are now in understanding dinoflagellates and where we are heading in the future. The most notable insights from the decade-long genomics work include: (1) dinoflagellate genomes have been expanded in multiple times independently, probably by a combination of rampant retroposition, accumulation of repetitive DNA, and genome duplication; (2) Symbiodiniacean genomes are highly divergent, but share about 3,445 core unigenes concentrated in 219 KEGG pathways; (3) Most dinoflagellate genes are encoded unidirectionally and are not intron-poor; (4) The dinoflagellate nucleus has undergone extreme evolutionary changes, including complete or nearly complete loss of nucleosome and histone H1, and acquisition of dinoflagellate viral nuclear protein (DVNP); (5) Major basic nuclear protein (MBNP), histone-like protein (HLP), and bacterial HU-like protein (HCc) belong to the same protein family, and MBNP can be the unifying name; (6) Dinoflagellate gene expression is regulated by poorly understood mechanisms, but microRNA and other epigenetic mechanisms are likely important; (7) Over 50% of dinoflagellate genes are “dark” and their functions remain to be deciphered using functional genetics; (8) Initial insights into the genomic basis of parasitism and mutualism have emerged. The review then highlights functionally unique and interesting genes. Future research needs to obtain a finished genome, tackle large genomes, characterize the unknown genes, and develop a quantitative molecular ecological model for addressing ecological questions.

Background “Red tides” are harmful algal blooms caused by dinoflagellate microalgae that accumulate toxins lethal to other organisms, including humans via consumption of contaminated seafood. These algal blooms are driven by a combination of environmental factors including nutrient enrichment, particularly in warm waters, and are increasingly frequent. The molecular, regulatory, and evolutionary mechanisms that underlie the heat stress response in these harmful bloom-forming algal species remain little understood, due in part to the limited genomic resources from dinoflagellates, complicated by the large sizes of genomes, exhibiting features atypical of eukaryotes. Results We present the de novo assembled genome (~ 4.75 Gbp with 85,849 protein-coding genes), transcriptome, proteome, and metabolome from Prorocentrum cordatum , a globally abundant, bloom-forming dinoflagellate. Using axenic algal cultures, we study the molecular mechanisms that underpin the algal response to heat stress, which is relevant to current ocean warming trends. We present the first evidence of a complementary interplay between RNA editing and exon usage that regulates the expression and functional diversity of biomolecules, reflected by reduction in photosynthesis, central metabolism, and protein synthesis. These results reveal genomic signatures and post-transcriptional regulation for the first time in a pelagic dinoflagellate. Conclusions Our multi-omics analyses uncover the molecular response to heat stress in an important bloom-forming algal species, which is driven by complex gene structures in a large, high-G+C genome, combined with multi-level transcriptional regulation. The dynamics and interplay of molecular regulatory mechanisms may explain in part how dinoflagellates diversified to become some of the most ecologically successful organisms on Earth.

Since reservoirs perform many important functions, they are exposed to various types of unfavorable phenomena, e.g., eutrophication which leads to a rapid growth of algae (blooms) that degrade water quality. One of the solutions to combat phytoplankton blooms are effective microorganisms (EM). The study aims to evaluate the potential of EM in improving the water quality of the Turawa reservoir on the Mała Panew River in Poland. It is one of the first studies providing insights into the effectiveness of using EM in the bioremediation of water in a eutrophic reservoir. Samples for the study were collected in 2019–2021. The analysis showed that EM could be one of the most effective methods for cleaning water from unfavorable microorganisms (HBN22, HBN36, CBN, FCBN, FEN) — after the application of EM, a reduction in their concentration was observed (from 46.44 to 58.38% on average). The duration of their effect ranged from 17.6 to 34.1 days. The application of EM improved the trophic status of the Turawa reservoir, expressed by the Carlson index, by 7.78%. As shown in the literature review, the use of other methods of water purification (e.g., constructed wetlands, floating beds, or intermittent aeration) leads to an increase in the effectiveness and a prolongation of the duration of the EM action. The findings of the study might serve as a guide for the restoration of eutrophic reservoirs by supporting sustainable management of water resources. Nevertheless, further research should be conducted on the effectiveness of EM and their application in the remediation of eutrophic water reservoirs.

Interactions between bacterial microbiota and epibenthic species of the dinoflagellate Prorocentrum may define the onset and persistence of benthic harmful algal blooms (bHABs). Chemical ecological interactions within the dinoflagellate phycosphere potentially involve a complex variety of organic molecules, metabolites, and toxins, including undefined bioactive compounds. In this study, the bacterial diversity and core members of the dinoflagellate-associated microbiota were defined from 11 strains of three epibenthic Prorocentrum species, representing three geographically disjunct locations within Mexican coastal waters. Microbiota profiles in stable monoclonal Prorocentrum cultures were obtained by sequencing amplicons of the V3-V4 region of the 16S rRNA gene. Thirteen classes of bacteria were identified among dinoflagellate clones, where Alphaproteobacteria, Gammaproteobacteria, and Bacteroidia were consistently dominant. The bacterial community structure exhibited significantly different grouping by the location of origin of dinoflagellate clones. No significant diversity difference was found among free-living or unattached bacteria in the dinoflagellate culture medium (M) compared with those in closer association with the dinoflagellate host cells (H). Twelve taxa were defined as core members of the bacterial assemblage, representing the genera Algiphilus , Cohaesibacter , Labrenzia , Mameliella , Marinobacter , Marivita , Massilia , Muricauda , Roseitalea , and an unclassified member of the Rhodobacteraceae. The core members are inferred to significantly contribute to primary and secondary metabolic functions, but no direct correlation with dinoflagellate toxigenicity was apparent. Overall the bacterial profile and implied gene functionality indicated a suite of positive interactions, suggesting either mutualism or commensalism with the dinoflagellate. The further characterization and interpretation of specific gene functions and interactions between bacteria and dinoflagellates, such as epibenthic members of genus Prorocentrum , are key to understanding their role in toxigenesis and bHAB development.

The extensive Patagonian continental shelf in the Atlantic Ocean is renowned for its high productivity associated with nutrient-rich waters that fertilize massive phytoplankton blooms, especially along the shelf-break frontal system. Growing evidence reflects this ecosystem as a hotspot for harmful algal blooms (HABs). Whether these HABs reach coastal areas or are exported to the adjacent ocean basin by energetic edge currents remains unexplored. During two oceanographic cruises in spring 2021, a bloom of dinoflagellates of the Amphidomataceae family was sampled over the outer shelf with a 10 d interval, at stations 40 km apart. The bloom was first sampled on 16 November, with 32 ×106 cells L−1, and was still persistent on 25 November, with 14 ×106 cells L−1. The magnitude of this bloom is a global record for this group so far reported in the literature. The toxin azaspiracid-2 (AZA-2) was detected in both stages of the bloom, with values up to 2122 pg L−1. The most likely source of AZA-2 was Azadinium spinosum ribotype B. The bloom developed in vertically stable waters (60 m mixed layer depth) with elevated chlorophyll concentration. Water retention and the presence of fronts induced by horizontal stirring controlled the persistence and trajectory of the bloom in a localized area over the continental shelf, as evidenced by analysis of geostrophic surface currents, Lyapunov coefficients, and particle advection modelling. These findings underscore the importance of monitoring HABs in offshore environments and the need to understand biophysical interactions that govern bloom taxa assemblages and transport pathways.

We measured the concentrations of dissolved inorganic and organic nutrients, dissolved organic carbon (DOC), total hydrolyzable amino acids (THAA), fluorescent dissolved organic matter (FDOM), phytoplankton pigments, and δ 13 C-DOC during the summer of 2019 in the harmful dinoflagellate bloom regions of the southern coast of Korea. In the harmful dinoflagellate bloom region, the concentrations of inorganic nitrogen were depleted, inhibiting the growth of diatoms, while the concentrations of dissolved organic components (nutrients, DOC, FDOM, and amino acids) which fuel dinoflagellates were unusually high. Thus, we attempted to investigate the origins and characteristics of DOM which fuels the harmful dinoflagellate blooms. The δ 13 C-DOC values (− 22.2‰ to − 18.2‰) indicate that the elevated DOC concentrations result from in-situ biological production rather than terrestrial inputs. The enantiomeric (D/L) ratios of THAA indicate that dissolved organic nitrogen was more labile in the early stage of harmful dinoflagellate bloom and became more refractory in the final stage. Our results suggest that the marine production of bioavailable DOM plays an important role in initiating and sustaining harmful dinoflagellate blooms.