Phosphorus physiological ecology and molecular mechanisms in marine phytoplankton

The effect of the aging processes of Ulva prolifera-derived dissolved organic nitrogen associated with green tide on the diatoms-dinoflagellates succession in the Southern Yellow Sea, China

Multitudinous dissolved organic nitrogen (DON) enters seawater from Ulva prolifera green tides impacting phytoplankton community structure in the Yellow Sea. Field investigations and cultural experiments on U. prolifera-derived DON aging revealed its regulatory effects. The green-tide outbreak area of the Southern Yellow Sea exhibits a seasonal cycle where dominance shifts from diatoms to dinoflagellates effected by young to aging U. prolifera-derived DON from summer to spring. Diatom abundance rose significantly following the summer green tide outbreak, fueled by young, protein-rich DON released by U. prolifera. After autumn and winter aging, U. prolifera-derived DON was dominant from protein-like to humic-like components, and dinoflagellates bloomed in the green tide outbreak area. An aging U. prolifera-derived DON adding culture experiment of Chaetoceros curvisetus and Prorocentrum minimum proved that old and young DON promoted dinoflagellate and diatom growth, respectively. Diatoms preferred 0 and 12 days-aged DON (DON0 and DON12) with tyrosine B and tryptophan T components, whereas dinoflagellate favored 80 days-aged DON (DON80) with humic acid E and UV fulvic acid A components. DON0 and DON12 can be absorbed by diatoms with higher uptake (kup) and growth (kG) constants than by dinoflagellates under low leucine aminopeptidase (LAP) conditions. Dinoflagellates absorb old DON with higher kup and kG values under higher LAP concentrations than diatoms. This was consistent with the loop of U. prolifera-derived DON turning over the seasonal succession of diatom dinoflagellates in the green-tide outbreak area. This study revealed mechanism of seasonal dinoflagellate-U. prolifera-diatom cycle, and provided new insights for impacts of U. prolifera green tides on phytoplankton regime shift, thus, acting as a basis for marine management strategies.

Transcriptomic response of marine dinoflagellate Prorocentrum cordatum to phosphorus deficiency

Phosphorus is crucial for marine phytoplankton viability as a key biogenic element. Under phosphorus deficiency, dinoflagellates exhibit changes in their feeding regime, alterations in transporters functioning, a reduction in cell proliferation rate and, in some cases, a transition to sexual reproduction. In this study, we performed RNA-sequencing analysis to assess the transcriptomic response of the dinoflagellate Prorocentrum cordatum to phosphorus deficiency in the cultivation medium. The aim of this work was to elucidate shifts in P. cordatum life cycle under these conditions focusing on the increase in the percentage of cells with a relative nuclear DNA content of 2C and the appearance of 4C cells, which may indicate a transition to the sexual process. We identified 196 differentially expressed genes - 169 up-regulated and 27 down-regulated-in cells grown for 14 days under phosphorus-depleted conditions. Analysis revealed up-regulation of pathways for phosphate uptake and assimilation, along with activation of RNA, protein, and lipid metabolic processes. Additionally, mechanisms regulating the cell cycle and inducing meiotic division were triggered. We identified up-regulated genes encoding proteins involved in meiotic recombination, including those promoting crossover. These findings indicate that phosphorus limitation can induce shift to sexual phase in P. cordatum life cycle.

Comparative secretome and proteome analysis unveils the response mechanism in the phosphorus utilization of Alexandrium pacificum

Phosphorus (P) acts as a crucial limiting nutrient for the growth of marine phytoplankton cells and the formation of algal blooms. The dinoflagellate Alexandrium pacificum is known for causing frequent and intense blooms in specific estuarine and coastal regions. In this study, we investigated the growth and physiological transformations under conditions characterized by P-deficiency, NaH2PO4, and ATP. For the first time, an integrated comparative analysis of the secretome and proteome was performed to investigate the global protein expression profile of A. pacificum, with 355 and 2308 differentially expressed proteins (DEPs), respectively. The results demonstrated that P-deficiency led to a reduction in growth and notable decreases in metabolic processes in A. pacificum. In P-deficient and ATP groups, the expression of secretory protein alkaline phosphatase A (PhoA) was increased, while intracellular acid phosphatase (ACP) displayed significant upregulation in P-deficient group, indicating that A. pacificum has evolved multiple organic P utilization strategies to adapt to low-P environments. A. pacificum can utilize the intracellular carbohydrate storage pools via glycolysis and the TCA cycle to replenish Calvin cycle intermediates. However, the growth of the ATP and NaH2PO4 groups showed no significant alteration. These results suggest that A. pacificum possesses distinct adaptive strategies towards P-deficiency in the environment and employs specific mechanisms for utilizing organic P, which may be a crucial factor in the formation of blooms in low inorganic P environments.

Synergistic Impacts of Phosphorus Deficiency Coupled with Thermal and High-Light Stress on Physiological Profiles of Cultivated Saccharina japonica

Global kelp farming is garnering growing attention for its contributions to fishery yields, environmental remediation, and carbon neutrality efforts. Kelp farming systems face escalating pressures from compounded climatic and environmental stressors. A severe outbreak disaster caused extensive kelp mortality and significant economic losses in Rongcheng, China, one of the world's largest kelp farming areas. This study investigated the growth and physiological responses of Saccharina japonica to combined stressors involving three levels of N:P ratios (10:1 as a control; 100:1 and 500:1 to represent phosphorus deficiency stress) and two temperature/light regimes (12 °C, 90 μmol photons m-2 s-1 as a control, and 17 °C, 340 μmol photons m-2 s-1 to represent thermal and high-light stress). The results demonstrated that phosphorus deficiency significantly inhibited the relative growth rate of kelp (24% decrease), and the strongest growth inhibition in kelp was observed at the N:P ratio of 500:1 combined with thermal and high-light stress. The algal tissue was whitened due to its progressive disintegration under escalating stress, coupled with damage to its chloroplasts and nucleus ultrastructures. Phosphorus-deficiency-induced declines in photochemistry (27-56% decrease) and chlorophyll content (63% decrease) were paradoxically and transiently reversed by thermal and high-light stress, but this "false recovery" accelerated subsequent metabolic collapse (a 60-75% decrease in the growth rate and a loss of thallus integrity). Alkaline phosphatase was preferentially activated to cope with phosphorus deficiency combined with photothermal stress, while acid phosphatase was subsequently induced to provide auxiliary support. S. japonica suppressed its metabolism but upregulated its nucleotides under phosphorus deficiency; however, the energy/amino acid/coenzyme pathways were activated and a broad spectrum of metabolites were upregulated under combined stressors, indicating that S. japonica employs a dual adaptive strategy where phosphorus scarcity triggers metabolic conservation. Thermal/light stress can override phosphorus limitations by activating specific compensatory pathways. The findings of this study provide a foundation for the sustainable development of kelp farming under climate and environmental changes.

Alkaline phosphatase-mediated hydrolysis of dissolved organic phosphorus enhances phosphorus cycling in the Yellow Sea

The utilization of dissolved organic phosphorus (DOP) driven by alkaline phosphatase hydrolysis contributes significantly to mitigating coastal nitrogen pollution through alleviating phosphorus (P) limitation. However, the lack of a parameterization for this process limits the quantitative assessment of its impact on marine nutrient pollution and cycling. Our study addresses this issue using data from a series of on-board microcosm experiments conducted in the Yellow Sea, where P limitation prevails. In addition to incorporating the conventional temperature-dependent DOP decomposition, we improve this process by accounting for the effects of dissolved inorganic phosphorus (DIP) and dissolved inorganic nitrogen (DIN) on DOP utilization, based on well-established relationships among these variables. The improved model well reproduces nutrient dynamics observed during the incubations. Simulation results further indicate that DOP utilization can contribute up to 80% of bioavailable P in DIP-deficient environments. Without this process, DIP concentrations would decrease by over 50% within 2-5 days, leading to a 20%-60% decrease in chlorophyll a concentration and an approximately 100% increase in P turnover time. Moreover, the DOP-to-DIP conversion efficiency (i.e., DOP utilization rate) exhibits substantial spatiotemporal variability in surface seawater, with rates as high as 0.1 day-1 in the central Yellow Sea during spring and summer, and notable interannual variations with changes up to 0.1 day-1 from 2003 to 2019. This study establishes a parameterization scheme modeling the dynamics of DOP utilization rate, providing valuable insights into the transformation and ecological effects of organic phosphorus in coastal waters influenced by anthropogenic nitrogen pollution.

The microbial phosphorus cycle in aquatic ecosystems

Phosphorus is an essential element for life, and phosphorus cycling is crucial to planetary habitability. In aquatic environments, microorganisms are a major component of phosphorus cycling and rapidly transform the diverse chemical forms of phosphorus through various uptake, assimilation and release pathways. Recent discoveries have revealed a more dynamic and complex aquatic microbial phosphorus cycle than previously understood. Some microorganisms have been shown to use and produce new phosphorus compounds, including those in reduced forms. New findings have also raised numerous unanswered questions that warrant further investigation. There is an expanding influence of human activity on aquatic ecosystems. Advancements in understanding the phosphorus biogeochemistry of evolving aquatic environments offer a unique opportunity to comprehend, anticipate and mitigate the effect of human activities. In this Review, I discuss the wealth of new aquatic phosphorus cycle research, spanning disciplines from omics and physiology to global biogeochemical modelling, with a focus on the current comprehension of how aquatic microorganisms sense, transport, assimilate, store, produce and release phosphorus. Of note, I delve into cellular phosphorus allocation, an underexplored topic with wide-ranging implications for energy and element flux in aquatic ecosystems.

Construction and evolution of artificial reef ecosystems: Response and regulation of marine microorganisms

Artificial reefs (ARs) are an important means of improving marine ecological environments and promoting the sustainable use of marine biological resources. After AR deployment, biological communities undergo dynamic changes as species succession and shifts in community structure. As the most sensitive frontier affected by the environment, the complex and dynamic changes of microbial communities play a crucial role in the health and stability of the ecosystem. This article reviews how AR construction affects the composition and function of marine microorganisms, their contributions to ecosystem stability, and the interaction mechanisms between microbial and macroecological systems. We focus on the responses and regulatory roles of microorganisms in AR ecosystems, including changes in microbial abundance, diversity, and distribution in the environment and on reef surfaces. Additionally, we examine their roles in nutrient cycling, the carbon sequestration, and their interactions with higher trophic organisms. We identify critical knowledge gaps and research deficiencies regarding microbial community risks that need to be addressed, which provide a framework for studying the complex relationships among marine environments, microbial communities and macrobiotic communities in the process of marine ranching construction.

Metaproteomics reveals metabolic activities potentially involved in bloom formation and succession during a mixed dinoflagellate bloom of Prorocentrum obtusidens and Karenia mikimotoi

Understanding metabolic activities involved in bloom formation during a single-species algal bloom has improved greatly. However, little is known about metabolic activities during a multi-species algal bloom. Here, we investigated protein expression profiles at different bloom stages of a mixed dinoflagellate bloom caused by Karenia mikimotoi and Prorocentrum obtusidens (syn. Prorocentrum donghaiense) using a metaproteomic approach. Our results indicated that both P. obtusidens and K. mikimotoi cells highly expressed proteins associated with essential cellular metabolisms such as cell growth and nutrient acquisition before their respective bloom occurrence. P. obtusidens preferentially enhanced uptake and utilization of ammonium, amino acid and organophosphorus-like phospholipid at the early bloom stage, and expressed highly abundant chloroplast peridinin-chlorophyll a-binding protein at the early and the P. obtusidens-dominated bloom stages, indicating their important roles in preferential occurrence and maintenance of P. obtusidens bloom. While absorption and utilization of nutrients, especially ammonium, urea, cyanate, phospholipid, and nucleotide, as well as endocytosis, in K. mikimotoi cells, were enhanced. Notably, both species increased photosynthesis, energy generation, cell proliferation, cell motility and cell defense before their respective blooms, which were beneficial to dealing with adverse external stresses, enabling them to be more competitive and advantageous in complex environments. Interestingly, diatom groups (Skeletonema, Pseudo-nitzschia, and Thalassiosira) decreased uptake and utilization of ambient nutrients and cell proliferation during the bloom period. This study demonstrates that niche differentiation and functional complementarity among phytoplankton species regulate bloom formation and succession during the mixed bloom.

Promoted growth with dynamic cellular stoichiometry driven by utilization of in-situ dissolved organic matter: Insights from bloom-forming dinoflagellate Prorocentrum donghaiense

Mixotrophic dinoflagellates frequently cause harmful algal blooms (HABs) in eutrophic waters that contain diverse dissolved organic matter (DOM), especially intensive mariculture areas. Compared to the extensive investigation of phagotrophy and single organic molecule uptake by causative species, we have limited knowledge about the capability of mixotrophic dinoflagellates to utilize in-situ DOM in mariculture waters and its contribution to HABs. Here we use filtered in-situ mariculture water as the sole medium to examine the physiological response of Prorocentrum donghaiense to the natural mariculture DOM. Our results showed an 87.2% increase in the cell growth rate, as well as photosynthesis (16.8%-29.2%) and cellular chlorophyll a (32.4%-70.7%) when cultured with DOM compared to those grown in the inorganic medium. Meanwhile, cellular stoichiometry varied greatly among the groups supplied with mariculture DOM of different seasons, and the ecological implications were then discussed. Additionally, parallel cultures revealed the phycosphere bacterioplankton community compete with the algae cell regarding the nutrient utilization. This study quantifies the efficient utilization of in-situ mariculture DOM by P. donghaiense and indicates its vital role in sustaining HAB events and great effects on the biogeochemical cycle.

Genetic diversity and distribution of Karenia in the eastern coastal seas of China and implications for the trends in Karenia blooms under global environmental changes

Species of Karenia G. Hansen & Moestrup gen. nov. frequently contribute to intense harmful algal blooms on a global scale, resulting in detrimental effects on fisheries, aquatic ecosystems, and human health. Over the past two decades, there has been noticeable increase in the reporting of Karenia blooms, with outbreaks attributed to newly recorded species, sometimes with multiple causative species. This trend highlights an insufficient understanding of species diversity and geographical distribution of Karenia and related key environment drivers under global environmental change. In this study, we employed a tailored barcode for genus Karenia combined with high-throughput sequencing to examine the species diversity and geographical dispersion of Karenia, as well as their relationships with environment factors in the eastern Chinese coastal seas (ECCS) in spring and autumn. Our findings revealed an unprecedented presence of both described and unrecorded Karenia species in the ECCS. K. mikimotoi was predominantly observed in the cold waters of the ECCS north of 35°N in autumn and the major waters of the ECCS in spring, while various Karenia species tend to co-inhabit in the warmer waters of autumn in the East China Sea. Sea temperatures were significantly correlated to the distribution patterns of Karenia species in the ECCS. In contrast, concentrations of inorganic nitrogen and phosphorus were not identified as major correlates to Karenia distribution. In light of the findings of this study and the understanding that Karenia species exhibit strong mixotrophic capabilities, it is suggested that ocean warming and increased coastal eutrophication, particularly the rise of dissolved and particulate organic substances, may contribute to the proliferation of Karenia blooms associated with undocumented species and/or multiple causative species.

Metabolic response to a heterologous poly-3-hydroxybutyrate (PHB) pathway in Phaeodactylum tricornutum

The marine diatom Phaeodactylum tricornutum is an emerging host for metabolic engineering, but little is known about how introduced pathways are integrated into the existing metabolic framework of the host or influence transgene expression. In this study, we expressed the heterologous poly-3-hydroxybutyrate (PHB) pathway using episomal expression, which draws on the precursor acetyl coenzyme-A (AcCoA). By experimentally perturbing cultivation conditions, we gained insight into the regulation of the endogenous metabolism in transgenic lines under various environmental scenarios, as well as on alterations in AcCoA flux within the host cell. Biosynthesis of PHB led to distinct shifts in the metabolome of the host, and further analysis revealed a condition-dependent relationship between endogenous and transgenic metabolic pathways. Under N limitation, which induced a significant increase in neutral lipid content, both metabolic and transcriptomic data suggest that AcCoA was preferably shunted into the endogenous pathway for lipid biosynthesis over the transgenic PHB pathway. In contrast, supply of organic carbon in the form of glycerol supported both fatty acid and PHB biosynthesis, suggesting cross-talk between cytosolic and plastidial AcCoA precursors. This is the first study to investigate the transcriptomic and metabolomic response of diatom cell lines expressing a heterologous multi-gene pathway under different environmental conditions, providing useful insights for future engineering attempts for pathways based on the precursor AcCoA. KEY POINTS: • PHB expression had minimal effects on transcription of adjacent pathways. • N limitation favoured native lipid rather than transgenic PHB synthesis. • Glycerol addition allowed simultaneous lipid and PHB accumulation.

Physiological and Transcriptional Responses to Phosphorus Deficiency and Glucose-6-Phosphate Supplementation in Neopyropia yezoensis

Neopyropia yezoensis, a marine red algae species, has significant economic and ecological value. However, phosphorus (P) deficiency has emerged as a growing concern in many cultivation regions, negatively impacting its growth. To adapt to P deficiency, algae have evolved various strategies, including using dissolved organic phosphorus (DOP) sources to sustain growth. Despite its prevalence as a form of DOP, the utilization mechanism of glucose-6-phosphate (G6P) by N. yezoensis remains unclear. In this study, the physiological and transcriptional responses of N. yezoensis to P deficiency and G6P supplementation were examined. The results demonstrated that prolonged P deficiency significantly inhibited the growth of N. yezoensis and had a negative impact on physiological indicators such as photosynthetic pigments and antioxidant enzyme activity. However, G6P treatment gradually alleviated these adverse effects over time. Both P deficiency and G6P treatment were associated with increased expression of genes involved in signal transduction and P starvation responses while concurrently downregulating genes related to photosynthesis and antioxidant defenses. In contrast, the suppression of gene expression was less significant under G6P treatment. This study elucidates the adaptive strategies of N. yezoensis in response to P deficiency and clarifies the regulatory pathways involved in G6P utilization, providing novel insights into its P nutrient acquisition and metabolic regulation.

Impacts of atmospheric particulate matter deposition on phytoplankton: A review

In many rapidly urbanizing and industrializing countries, atmospheric pollution causes severe environmental problems and compromises the health of humans and ecosystems. Atmospheric emissions, which encompass gases and particulate matter, can be transported back to the earth's surface through atmospheric deposition. Atmospheric deposition supplies chemical species that can serve as nutrients and/or toxins to aquatic ecosystems, resulting in wide-ranging responses of aquatic organisms. Among the aquatic organisms, phytoplankton is the basis of the aquatic food web and is a key player in global primary production. Atmospheric deposition alters nutrient availability and thus influences phytoplankton species abundance and composition. This review provides a comprehensive overview of the physiological responses of phytoplankton resulting from the atmospheric deposition of trace metals, nitrogen-containing compounds, phosphorus-containing compounds, and sulfur-containing compounds in particulate matter into aquatic ecosystems. Knowledge gaps and critical areas for future studies are also discussed.

Physiological and transcriptomic analyses to determine the responses of the harmful algae Akashiwo sanguinea to phosphorus utilization

Phosphorus (P) is an essential nutrient driving algal growth in aquatic ecosystems. Dissolved inorganic and organic P (DIP and DOP) are the main components in the marine P pools and are closely related to harmful algal blooms. The dinoflagellate Akashiwo sanguinea is a cosmopolitan species which frequently causes dense blooms in estuaries and coasts worldwide, while the availability of P to A. sanguinea still remain unclear. Herein, the physiological and transcriptomic responses of A. sanguinea grown under P-deficient, DIP-replete and DOP-replete conditions were compared. P-deficient adversely suppressed the growth and photosynthesis of A. sanguinea, while genes associated with P transport, DOP utilization, sulfolipid synthesis, and energy production, were markedly elevated. Three forms of DOP, namely, glucose-6-phosphate (G-6-P), adenosine 5-triphosphate (ATP), and β-Glycerol phosphate (SG-P), supported A. sanguinea growth as efficiently as DIP (NaH2PO4), and no significant difference was observed in biochemical compositions and photosynthesis of A. sanguinea between the DIP and DOP treatments. While the genes related to P transporter were markedly suppressed in DOP groups compared with the DIP group. Our results indicated that A. sanguinea is a good growth strategist under P-deficient/replete conditions, and this species had evolved a comprehensive strategy to cope with P deficiency, which might be a crucial factor driving bloom formation in a low inorganic P environment.

Prevalence and distribution of dissolved paralytic shellfish toxins in seawater in the Yellow Sea and the Bohai Sea, China

Paralytic shellfish toxins (PSTs) could be secreted by PSTs-producing microalgae or released by ruptured cells in seawater. In this study, the distribution of dissolved PSTs in the Yellow Sea and the Bohai Sea, China, was investigated by two cruises in April and July 2023. Seawater samples were collected from the surface, middle and bottom layers, and the profiles of PSTs were analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS), and the spatial distribution characteristics of dissolved PSTs and their correlation with environmental factors were explored. Results showed that C1/2, GTX1/4, GTX2/3 and dcGTX2/3, were detected in seawater samples in both spring and summer, with the detection rates 100 % and 97.6 %, respectively. The total PST (ΣPSTs) concentrations ranged in 12 ∼ 590 pmol L-1, 9.3 ∼ 546 pmol L-1, 12 ∼ 2,452 pmol L-1, and not detected (nd) ∼ 188 pmol L-1 in seawater samples collected from the surface, middle and bottom layers in spring, and the surface layer in summer, respectively. Concentrations of PSTs markedly varied in the vertical water column in different sea regions. Generally, concentrations of ΣPSTs in the bottom seawater were higher than those in the surface and middle layers in the Bohai Sea and the North Yellow Sea, but no significant difference in the different water layers in the South Yellow Sea. In addition, concentrations of ΣPSTs in surface waters were much lower in summer than those in spring. In both spring and summer, dissolved PSTs in surface seawater were mainly distributed in the South Yellow Sea. These results indicate that PSTs were prevalent in the Yellow Sea and the Bohai Sea, of which the potential hazard to marine organisms should be highly concerned.

Characterization of a Levanderina fissa Bloom in Aquaculture Ponds and Its Utilization of Dissolved Organic Phosphorus

Harmful algal blooms (HABs) pose significant threats to ecosystems and human health worldwide, with their frequency and intensity increasing substantially. The present study reports an algal bloom observed in an aquaculture pond near Haizhou Bay in July 2022. The causative species, identified through morphological observation and DNA barcoding analysis, was the dinoflagellate Levanderina fissa (Levander) Moestrup, Hakanen, Gert Hansen, Daugbjerg & M. Ellegaard, 2014, known for causing extensive HAB events in the coastal waters of China. A sharp decline in phytoplankton species diversity was observed during the transition from the pre-bloom to the bloom phase. Furthermore, the uptake of four types of dissolved organic phosphorus (DOP), including glucose-6-phosphate (G6P), adenosine-5-triphosphate (ATP), sodium tripolyphosphate (TPP), and glyphosate, by isolated L. fissa was investigated in the laboratory. The results showed that G6P, ATP, and TPP supported L. fissa growth as effectively as orthophosphate. Additionally, the elevated concentrations of dissolved inorganic phosphorus in the media of the three treatments indicated the involvement of extracellular hydrolysis. However, alkaline phosphatase was not responsible for the hydrolysis of these three forms of DOP. This study demonstrates that the ability of L. fissa to utilize DOP may confer a competitive advantage within phytoplankton communities, potentially leading to algal blooms in aquaculture ponds.

A decade of dinoflagellate genomics illuminating an enigmatic eukaryote cell

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.

Pseudomonas ZY-1 and Bacillus FY-1 protecting the rice seedlings from the harm of Pseudomonas aeruginosa via indirect seawead lysis

The local ecosystems, fishery and human health are all threatened by water blooms, so effectively controlling water blooms has become an urgent and challenging issue. Biological control of water blooms is given priority due to its low cost, high efficiency and environmental friendliness. In this study, Pseudomonas ZY-1 and Bacillus FY-1, two highly-effective algicidal bacteria strains which are able to indirectly lyse algae by separating and screening from the vigorous water body in the paddy alga of Northeast China were obtained. The two bacterial strains have stronger ability to lyse alga in the bacterial liquid concentration of 106 CFU/ml, and the alga-lysing rate on 7 d reached 84.03% and 83.11% respectively. The active substance secreted by ZY-1 is not sensitive to the changes of temperature and pH value, while as FY-1 cell-free filtrate is not stable in high temperature above 50 ℃ and pH of 5, it requires the sun light to have the algaecidal effect. The cell-free filtrates of strains ZY-1 and FY-1 had the best lysis effect on Microcystis aeruginosa cells, and the chlorophyll a content of algae decreased to 0.13 ± 0.02 mg/L and 0.14 ± 0.03 mg/L respectively and the Fv/Fm of Microcystis aeruginosa decreased by 97.22% after 7 days. The algaecidal process of ZY-1 and FY-1 may be that the cell-free filtrate inhibits the photosynthesis of Microcystis aeruginosa, and meanwhile it avoids the regeneration and repair of photosynthesis of algal cells by affecting the gene expression and damaging the repair system of algal cells, so the membrane lipid peroxidation is exacerbated and then the membrane of algal cells is broken, the algal cells can't do normal life activities, and finally the algal cell would be killed. The rice seedlings in the algal liquid treatment group are short and show root dysplasia, few roots and brown roots. After treated with cell-free filtrate of ZY-1 and FY-1, the oxidative damage of the rice is obviously reduced, and the harm from Microcystis aeruginosa is reduced, which has the repair effect to the roots of rice seedlings and its aboveground growth. The cell-free filtrate of FY-1 works better than ZY-1. The bacteria strains of ZY-1 and FY-1 have the indirect algaecide trait, which makes them the potential environmentally-friendly algaecidal bacteria and they show broad application in the agricultural production and the control of water blooms.

Mechanistic characterization of dissolved inorganic phosphorus in water during the red tide

The eutrophication of water, such as excessive nitrogen and phosphorus, are closely associated with the outbreak of red tide. However, the response of dissolved inorganic phosphorus (DIP) to red tide remained unclear in water. In this study, three species of diatoms capable of causing red tides were cultured in simulated seawater with different concentrations of DIP. The changes of biomass, chlorophyll a concentration and the carbon stable isotope composition of microalgae, the DIP concentration and pH of the culture medium were compared among the experimental groups. In addition, correlation verification was used to test the correlation between the change of DIP concentration and other indicators. The results showed that in the experimental period, the DIP concentration of each experimental group decreased significantly first, and the concentration dropped to less than 40% of the initial level. After that, the pH of the medium, the biomass, chlorophyll a concentration and carbon stable isotope composition of the microalgae showed varying degrees of increase, and then stabilized or decreased. These also marked the outbreak of red tide. Moreover, the correlation test showed that there was a correlation between them and the change of DIP concentration. Therefore, by exploring the relationship between the change of DIP concentration in water and the occurrence of red tide, this study provides a possible direction for the current prediction of red tide, and provides a basis for further investigation of the occurrence mechanism of red tide.

Microeukaryote metabolism across the western North Atlantic Ocean revealed through autonomous underwater profiling

Microeukaryotes are key contributors to marine carbon cycling. Their physiology, ecology, and interactions with the chemical environment are poorly understood in offshore ecosystems, and especially in the deep ocean. Using the Autonomous Underwater Vehicle Clio, microbial communities along a 1050 km transect in the western North Atlantic Ocean were surveyed at 10-200 m vertical depth increments to capture metabolic signatures spanning oligotrophic, continental margin, and productive coastal ecosystems. Microeukaryotes were examined using a paired metatranscriptomic and metaproteomic approach. Here we show a diverse surface assemblage consisting of stramenopiles, dinoflagellates and ciliates represented in both the transcript and protein fractions, with foraminifera, radiolaria, picozoa, and discoba proteins enriched at >200 m, and fungal proteins emerging in waters >3000 m. In the broad microeukaryote community, nitrogen stress biomarkers were found at coastal sites, with phosphorus stress biomarkers offshore. This multi-omics dataset broadens our understanding of how microeukaryotic taxa and their functional processes are structured along environmental gradients of temperature, light, and nutrients.

Dissolved organic phosphorus bond-class utilization by Synechococcus

Dissolved organic phosphorus (DOP) contains compounds with phosphoester, phosphoanhydride, and phosphorus-carbon bonds. While DOP holds significant nutritional value for marine microorganisms, the bioavailability of each bond-class to the widespread cyanobacterium Synechococcus remains largely unknown. This study evaluates bond-class specific DOP utilization by Synechococcus strains from open and coastal oceans. Both strains exhibited comparable growth rates when provided phosphate, a phosphoanhydride [3-polyphosphate and 45-polyphosphate], or a DOP compound with both phosphoanhydride and phosphoester bonds (adenosine 5'-triphosphate). Growth rates on phosphoesters [glucose-6-phosphate, adenosine 5'-monophosphate, bis(4-methylumbelliferyl) phosphate] were variable, and neither strain grew on selected phosphorus-carbon compounds. Both strains hydrolyzed 3-polyphosphate, then adenosine 5'-triphosphate, and lastly adenosine 5'-monophosphate, exhibiting preferential enzymatic hydrolysis of phosphoanhydride bonds. The strains' exoproteomes contained phosphorus hydrolases, which combined with enhanced cell-free hydrolysis of 3-polyphosphate and adenosine 5'-triphosphate under phosphate deficiency, suggests active mineralization of phosphoanhydride bonds by these exoproteins. Synechococcus alkaline phosphatases presented broad substrate specificities, including activity toward the phosphoanhydride 3-polyphosphate, with varying affinities between strains. Collectively, these findings underscore the potentially significant role of compounds with phosphoanhydride bonds in Synechococcus phosphorus nutrition and highlight varied growth and enzymatic responses to molecular diversity within DOP bond-classes, thereby expanding our understanding of microbially mediated DOP cycling in marine ecosystems.

Phosphorous Utilization in Microalgae: Physiological Aspects and Applied Implications

Phosphorus (P) is a fundamental element for life, playing an integral role in cellular metabolism including energy transfer, nucleic acid synthesis, and membrane structure. This nutrient is critical to the physiological ecology in all photosynthetic organisms including eukaryotic microalgae and cyanobacteria. The review, here presented, delves into the intricate mechanisms governing phosphorus acquisition from the environment, its utilization in plant metabolism, and regulation in these photosynthetic microorganisms. Furthermore, it comprehensively explores the strategies employed by microalgae to cope with phosphorus limitation, such as the activation of high-affinity phosphate transporters and the synthesis of phosphorus storage compounds. On the other hand, the ability to consume abundant phosphate makes microalgae exploitable organisms for environmental remediation processes. The knowledge synthesized in this review contributes to the broader understanding of microalgal physiology, offering insights into the ecological and biotechnological implications of phosphorus assimilation in these microorganisms.

Molecular mechanism of a coastal cyanobacterium Synechococcus sp. PCC 7002 adapting to changing phosphate concentrations

Phosphorus concentration on the surface of seawater varies greatly with different environments, especially in coastal. The molecular mechanism by which cyanobacteria adapt to fluctuating phosphorus bioavailability is still unclear. In this study, transcriptomes and gene knockouts were used to investigate the adaptive molecular mechanism of a model coastal cyanobacterium Synechococcus sp. PCC 7002 during periods of phosphorus starvation and phosphorus recovery (adding sufficient phosphorus after phosphorus starvation). The findings indicated that phosphorus deficiency affected the photosynthesis, ribosome synthesis, and bacterial motility pathways, which recommenced after phosphorus was resupplied. Even more, most of the metabolic pathways of cyanobacteria were enhanced after phosphorus recovery compared to the control which was kept in continuous phosphorus replete conditions. Based on transcriptome, 54 genes potentially related to phosphorus-deficiency adaptation were selected and knocked out individually or in combination. It was found that five mutants showed weak growth phenotype under phosphorus deficiency, indicating the importance of the genes (A0076, A0549-50, A1094, A1320, A1895) in the adaptation of phosphorus deficiency. Three mutants were found to grow better than the wild type under phosphorus deficiency, suggesting that the products of these genes (A0079, A0340, A2284-86) might influence the adaptation to phosphorus deficiency. Bioinformatics analysis revealed that cyanobacteria exposed to highly fluctuating phosphorus concentrations have more sophisticated phosphorus acquisition strategies. These results elucidated that Synechococcus sp. PCC 7002 have variable phosphorus response mechanisms to adapt to fluctuating phosphorus concentration, providing a novel perspective of how cyanobacteria may respond to the complex and dynamic environments.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-024-00244-y.

Removal mechanisms and metabolic responses of Chlorella pyrenoidosa to dissolved organic phosphorus

Microalgae-based biotechnology holds significant potential for addressing dual challenges of phosphorus removal and recovery from wastewater; however, the removal mechanism and metabolic adaptation of microalgae to dissolved organic phosphorus (DOP) are still unclear. This study investigated the removal mechanisms and metabolomic responses of the Chlorella pyrenoidosa to different DOP forms, including adenosine triphosphate (ATP), glucose-6-phosphate (G-6-P), and β-glycerophosphate (β-GP). The results showed C. pyrenoidosa could efficiently take up above 96% DOP through direct transport and post-hydrolysis pathways. The uptake of inorganic phosphorus (IP) followed pseudo first order kinetic model, while DOP followed pseudo second order kinetic model. Metabolite profiling revealed substantial alterations in central carbon metabolism depending on the DOP source. G-6-P upregulated glycolytic and TCA cycle intermediates, reflecting enhanced carbohydrates, amino acids and nucleotides biosynthesis. In contrast, ATP down-regulated carbohydrate and purine metabolism, inhibiting sustainable growth of microalgae. This study offers theoretical support for phosphorus-containing wastewater treatment using microalgae.

Getting Grip on Phosphorus: Potential of Microalgae as a Vehicle for Sustainable Usage of This Macronutrient

Phosphorus (P) is an important and irreplaceable macronutrient. It is central to energy and information storage and exchange in living cells. P is an element with a "broken geochemical cycle" since it lacks abundant volatile compounds capable of closing the P cycle. P fertilizers are critical for global food security, but the reserves of minable P are scarce and non-evenly distributed between countries of the world. Accordingly, the risks of global crisis due to limited access to P reserves are expected to be graver than those entailed by competition for fossil hydrocarbons. Paradoxically, despite the scarcity and value of P reserves, its usage is extremely inefficient: the current waste rate reaches 80% giving rise to a plethora of unwanted consequences such as eutrophication leading to harmful algal blooms. Microalgal biotechnology is a promising solution to tackle this challenge. The proposed review briefly presents the relevant aspects of microalgal P metabolism such as cell P reserve composition and turnover, and the regulation of P uptake kinetics for maximization of P uptake efficiency with a focus on novel knowledge. The multifaceted role of polyPhosphates, the largest cell depot for P, is discussed with emphasis on the P toxicity mediated by short-chain polyPhosphates. Opportunities and hurdles of P bioremoval via P uptake from waste streams with microalgal cultures, either suspended or immobilized, are discussed. Possible avenues of P-rich microalgal biomass such as biofertilizer production or extraction of valuable polyPhosphates and other bioproducts are considered. The review concludes with a comprehensive assessment of the current potential of microalgal biotechnology for ensuring the sustainable usage of phosphorus.

Deciphering the Impact of ZnO Nanoparticles and a Sunscreen Product Containing ZnO on Phosphorus Dynamics and Release in Chlorella pyrenoidosa in Aquatic Systems

Zinc oxide nanoparticles (ZnO NPs) expedite the conversion of organic phosphorus (OP) into PO4-P (Pi), facilitating phosphorus (P) absorption by algae. Our study explored the mechanisms of converting OP (2-aminoethylphosphonic acid (AEP) and β-glycerol phosphate (β-GP)) into Pi in Chlorella pyrenoidosa under P deficiency with sunscreen and ZnO NPs. Cell density followed the order of K2HPO4 > β-GP+ZnO > β-GP > AEP+ZnO > AEP > P-free. ZnO NPs promoted the conversion of β-GP, containing C-O-P bonds (0.028-0.041 mg/L), into Pi more efficiently than AEP, which possesses C-P bonds (0.022-0.037 mg/L). Transcriptomics revealed Pi transport/metabolism (phoB (3.99-12.01 fold), phoR (2.20-5.50 fold), ppa (4.49-10.40 fold), and ppk (2.50-5.40 fold)) and phospholipid metabolism (SQD1 (1.85-2.79 fold), SQD2 (2.60-6.53 fold), MGD (2.13-3.21 fold), and DGD (4.08-7.56 fold)) were up-regulated compared to K2HPO4. 31P nuclear magnetic resonance spectroscopy identified intracellular P as polyphosphate, orthophosphate, and pyrophosphate. Synchrotron radiation-based X-ray near-edge structure spectroscopy indicated that K2HPO4 and Zn3(PO4)2 in β-GP+ZnO were increased by 8.09% and 7.28% compared to AEP+ZnO, suggesting superior P storage in β-GP+ZnO. Overall, ZnO NPs improved photoinduced electron-hole pair separation and charge separation efficiency and amplified the ·OH and ·O2- levels, promoting OP photoconversion into Pi and algae growth.

Characterization of polyphosphate dynamics in the widespread freshwater diatom Achnanthidium minutissimum under varying phosphorus supplies

Polyphosphates (polyP) are ubiquitous biomolecules that play a multitude of physiological roles in many cells. We have studied the presence and role of polyP in a unicellular alga, the freshwater diatom Achnanthidium minutissimum. This diatom stores up to 2.0 pg·cell-1 of polyP, with chain lengths ranging from 130 to 500 inorganic phosphate units (Pi). We applied energy dispersive X-ray spectroscopy, Raman/fluorescence microscopy, and biochemical assays to localize and characterize the intracellular polyP granules that were present in large apical vacuoles. We investigated the fate of polyP in axenic A. minutissimum cells grown under phosphorus (P), replete (P(+)), or P deplete (P(-)) cultivation conditions and observed that in the absence of exogenous P, A. minutissimum rapidly utilizes their internal polyP reserves, maintaining their intrinsic growth rates for up to 8 days. PolyP-depleted A. minutissimum cells rapidly took up exogenous P a few hours after Pi resupply and generated polyP three times faster than cells that were not initially subjected to P limitation. Accordingly, we propose that A. minutissimum deploys a succession of acclimation strategies regarding polyP dynamics where the production or consumption of polyP plays a central role in the homeostasis of the diatom.

Nitrogen uptake rates and phytoplankton composition across contrasting North Atlantic Ocean coastal regimes north and south of Cape Hatteras

Understanding nitrogen (N) uptake rates respect to nutrient availability and the biogeography of phytoplankton communities is crucial for untangling the complexities of marine ecosystems and the physical, biological, and chemical forces shaping them. In the summer of 2016, we conducted measurements of bulk microbial uptake rates for six 15N-labeled substrates: nitrate, nitrite, ammonium, urea, cyanate, and dissolve free amino acids across distinct marine provinces, including the continental shelf of the Mid-and South Atlantic Bights (MAB and SAB), the Slope Sea, and the Gulf Stream, marking the first instance of simultaneously measuring six different N uptake rates in this dynamic region. Total measured N uptake rates were lowest in the Gulf Stream followed by the SAB. Notably, the MAB exhibited significantly higher N uptake rates compared to the SAB, likely due to the excess levels of pre-existing phosphorus present in the MAB. Together, urea and nitrate uptake contributed approximately 50% of the total N uptake across the study region. Although cyanate uptake rates were consistently low, they accounted for up to 11% of the total measured N uptake at some Gulf Stream stations. Phytoplankton groups were identified based on specific pigment markers, revealing a dominance of diatoms in the shelf community, while Synechococcus, Prochlorococcus, and pico-eukaryotes dominated in oligotrophic Gulf Stream waters. The reported uptake rates in this study were mostly in agreement with previous studies conducted in coastal waters of the North Atlantic Ocean. This study suggests there are distinct regional patterns of N uptake in this physically dynamic region, correlating with nutrient availability and phytoplankton community composition. These findings contribute valuable insights into the intricate interplay of biological and chemical factors shaping N dynamics in disparate marine ecosystems.

Full-length transcriptome analysis of a bloom-forming dinoflagellate Prorocentrum shikokuense (Dinophyceae)

Prorocentrum shikokuense (formerly P. donghaiense) is a pivotal dinoflagellate species associating with the HABs in the East China Sea. The complexity of its large nuclear genome hindered us from understanding its genomic characteristics. Full-length transcriptome sequencing offers a practical solution to decipher the physiological mechanisms of a species without the reference genome. In this study, we employed single-molecule real-time (SMRT) sequencing technology to sequence the full-length transcriptome of Prorocentrum shikokuense. We successfully generated 41.73 Gb of clean SMRT sequencing reads and isolated 105,249 non-redundant full-length non-chimeric reads. Our trial has led to the identification of 11,917 long non-coding RNA transcripts, 514 alternative splicing events, 437 putative transcription factor genes from 17 TF gene families, and 34,723 simple sequence repeats. Additionally, a total of 78,265 open reading frames were identified, of them 15,501 were the protein coding sequences. This dataset is valuable for annotating P. shikokuense genome, and will contribute significantly to the in-depth studies on the molecular mechanisms underlining the dinoflagellate bloom formation.

Nitrogen and phosphorus limitations promoted bacterial nitrate metabolism and propagation of antibiotic resistome in the phycosphere of Auxenochlorella pyrenoidosa

Despite that nitrogen (N) and phosphorus (P) play critical roles in the lifecycle of microalgae, how N and P further affect the distribution of bacteria and antibiotic resistance genes (ARGs) in the phycosphere is still poorly understood. In this study, the effects of N and P on the distribution of ARGs in the phycosphere of Auxenochlorella pyrenoidosa were investigated. Results showed that the growth and chlorophyll synthesis of microalgae were inhibited when N or P was limited, regardless of the N/P ratios, but the extracellular polymeric substances content and nitrate assimilation efficiency were enhanced in contrast. Metagenomic sequencing revealed that N or P limitation resulted in the recruitment of specific bacteria that highly contribute to the nitrate metabolism in the phycosphere. Besides, N or P limitation promoted the propagation of phycosphere ARGs, primarily through horizontal gene transfer mediated by mobile genetic elements. The enrichment of specific bacteria induced by changes in the algal physiology also contributed to the ARGs proliferation under nutrient limitation. Our results demonstrated that the reduction of algal cells caused by nutrient limitation could promote the propagation of ARGs, which provides new insights into the occurrence and spread of ARGs in the phycosphere.

Long-term response of interspecific competition among three typical bloom-forming species to changes in phosphorus and temperature

Phosphorus and temperature play an important role in the succession of diatom-dinoflagellate blooms. However, there is little long-term research on interspecific competition based on phosphorus source and temperature. Here, interspecific competition among Skeletonema costatum, Prorocentrum donghaiense and Karenia mikimotoi was studied using trialgal laboratory co-cultures under different phosphorus and temperature conditions. These results suggest that S. costatum and P. donghaiense alternated as competing dominant species during the experimental period, which coincides with the different phosphorus conditions. However, K. mikimotoi growth was significantly inhibited throughout the experiment. We suggest that this may be due to different algal requirements for phosphorus, optimal growth temperatures, and possible allelopathic effects. This study provides a comprehensive mechanism of interspecific competition between diatom-dinoflagellate in response to phosphorus and temperature and elucidates the seasonal succession of diatom-dinoflagellate from late spring to early summer in the Changjiang River Estuary and the adjacent East China Sea.

Oscillations of algal cell quota: Considering two-stage phosphate uptake kinetics

Elucidating the mechanism of effect of phosphate (PO43-) uptake on the growth of algal cells helps understand the frequent outbreaks of algal blooms caused by eutrophication. In this study, we develop a comprehensive mathematical model that incorporates two stages of PO43- uptake and accounts for transport time delay. The model parameter values are determined by fitting experimental data of Prorocentrum donghaiense and the model is validated using experimental data of Karenia mikimotoi. The numerical results demonstrate that the model successfully captures the general characteristics of algal growth and PO43- uptake under PO43- sufficient conditions. Significantly, the experimental and mathematical findings suggest that the time delay associated with the transfer of PO43- from the surface-adsorbed PO43- (Ps) pool to the intracellular PO43- (Pi) pool may serve as a physiologically plausible mechanism leading to oscillations of algal cell quota. These results have important implications for resource managers, enabling them to predict and deepen their understanding of harmful algal blooms.

Significance of phosphate adsorbed on the cellular surface as a storage pool and its regulation in marine microalgae

The increasing prevalence of phosphorus limitation in coastal waters has drawn attention to the bioavailability of cellular surface-adsorbed phosphorus (SP) as a reservoir of phosphorus in phytoplankton. This study examined the storage, utilization, and regulation of SP in the coastal waters of the East China Sea, as well as three cultivated algal bloom species (Skeletonema marinoi, Prorocentrum shikokuense, and Karenia mikimotoi) prevalent in the area. SP accounted for 14.3%-45.5% of particulate phosphorus in the field and laboratory species. After the depletion of external phosphate, the studied species can rapidly transport SP within 3-24 h. The storage of SP is regulated by both external phosphate conditions and the internal growth stage of cells, but it is not influenced by the various cellular surface structures of the studied species. This study highlights the significance of SP as a crucial phosphorus reservoir and the potential use of the SP level as an indicator of phosphorus deficiency in phytoplankton.

Phosphorus forms and zinc concentrations affect the physiological ecology and sinking rate of Thalassiosira weissflogii

The combined effects of phosphorus (P) forms and zinc (Zn) concentrations on diatom silicification remain unclear. In this study, we investigate the effects of different Zn concentrations on the growth, cellular silicon content and sinking rate of Thalassiosira weissflogii under different P forms. The results showed that under the dissolved inorganic phosphorus (DIP) treatments, the specific growth rate of T. weissflogii in Zn limitation culture was significantly lower than that in Zn-replete culture. However, T. weissflogii cellular silicon content and sinking rate increased. Moreover, the reduced specific growth rate (7 %, p < 0.05), enhanced ALP activity (63 %, p < 0.05), and sinking rate (20 %, p < 0.05) for Zn-deplete T. weissflogii implied that the bioavailability of dissolved organic phosphorus (DOP) was depressed under Zn deplete medium. This study demonstrates that the physiological ecology and sinking rate of the diatom T. weissflogii were affected by both individual and combined changes in P forms and Zn concentrations.

Relationship between chlorophyll-a, rainfall, and climate phenomena in tropical archipelagic estuarine waters

Similar to many estuaries worldwide with sources receiving nitrogen and phosphorus, i.e., nutrients, from point and diffuse sources, the waters in Jakarta Bay, Musi Estuary, and Rokan Estuary in Indonesia are facing negative impacts on water quality and ecosystems, i.e., eutrophication, because of rapid urbanization and human activities. The transport of nutrients through rivers and tributaries depends on rainfall and climate phenomena, ultimately dictating chlorophyll-a (Chl-a) concentrations and trophic levels in estuaries. The relationship between trophic level, Chl-a concentration, rainfall, and climate phenomena was explored in this study by examining monthly Chl-a concentrations from 2003 to 2021 in the three estuaries. Remote sensing Chl-a concentrations data from the NASA Aqua MODIS mission was subjected to Geographic Information System (GIS) and statistical analyses. The dynamic fluctuations of Chl-a concentrations in all estuaries showed eutrophic zones appearing at specific times, influenced by local rainfalls and their patterns. The first principal components of the Empirical Orthogonal Function (EOF) analysis of Chl-a concentration anomalies showed significant correlations with rainfall anomalies and the Indian Ocean Dipole (IOD) index. These relationships exhibited distinct patterns influenced by unique climate factors in each estuary. The study highlights the crucial role of wide-area continuous monitoring and early warning systems, facilitated by satellite remote sensing, in preserving the health of coastal ecosystems. The findings also offer valuable insights for designing future monitoring programs and targeted conservation efforts.

Glyphosate (Roundup) as phosphorus nutrient enhances carbon and nitrogen accumulation and up-regulates phosphorus metabolisms in the haptophyte Isochrysis galbana

Inorganic phosphate limitation for phytoplankton may be intensified with water stratification by global warming, and with the increasing nitrogen: phosphorus (N:P) ratio in coastal zones resulting from continuous anthropogenic N overloading. Under these circumstances, phytoplankton's ability to use dissolved organic phosphorus (DOP) will give species a competitive advantage. In our previous study, we have shown that the haptophyte Isochrysis galbana can use glyphosate (Roundup) as a P nutrient source to support growth, but the mechanism of how remains unexplored. Here, we show that three genes encoding PhnC (IgPhnCs), which exhibit up-regulated expression in glyphosate-grown cultures, are probably responsible for glyphosate uptake, while homologs of PhnK and PhnL (IgPhnK and IgPhnL) probably provide auxiliary support for the intracellular degradation of glyphosate. Meanwhile, we found the use efficiency of glyphosate was low compared with phosphate, probably because glyphosate uptake and hydrolysis cost energy and because glyphosate induces oxidative stress in I. galbana. Meanwhile, genes encoding 5-enolpyruvylshikimate 3-phosphate (EPSP) synthase, the target of the herbicide, were up-regulated in glyphosate cultures. Furthermore, our data showed the up-regulation of P metabolisms (transcription) in glyphosate-grown cultures, which further induced the up-regulation of nitrate/nitrite transport and biosynthesis of some amino acids. Meanwhile, glyphosate-grown cells accumulated more C and N, resulting in remarkably high C:N:P ratio, and this, along with the up-regulated P metabolisms, was under transcriptional and epigenetic regulation. This study sheds lights on the mechanism of glyphosate utilization as a source of P nutrient by I. galbana, and these findings have biogeochemical implications.

Effects and mechanisms of glyphosate as phosphorus nutrient on element stoichiometry and metabolism in the diatom Phaeodactylum tricornutum

The ability to utilize dissolved organic phosphorus (DOP) gives phytoplankton competitive advantages in P-limited environments. Our previous research indicates that the diatom Phaeodactylum tricornutum could grow on glyphosate, a DOP with carbon-phosphorus (C-P) bond and an herbicide, as sole P source. However, direct evidence and mechanism of glyphosate utilization are still lacking. In this study, using physiological and isotopic analysis, combined with transcriptomic profiling, we demonstrated the uptake of glyphosate by P. tricornutum and revealed the candidate responsible genes. Our data showed a low efficiency of glyphosate utilization by P. tricornutum, suggesting that glyphosate utilization costs energy and that the alga possessed an herbicide-resistant type of 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase. Compared to the P-limited cultures, the glyphosate-grown P. tricornutum cells up-regulated genes involved in DNA replication, cell growth, transcription, translation, carbon metabolism, and many genes encoding antioxidants. Additionally, cellular C and silicon (Si) increased remarkably while cellular nitrogen (N) declined in the glyphosate-grown P. tricornutum, leading to higher Si:C and Si:N ratios, which corresponded to the up-regulation of genes involved in the C metabolism and Si uptake and the down-regulation of those encoding N uptake. This has the potential to enhance C and Si export to the deep sea when P is limited but phosphonate is available. In sum, our study documented how P. tricornutum could utilize the herbicide glyphosate as P nutrient and how glyphosate utilization may affect the element content and stoichiometry in this diatom, which have important ecological implications in the future ocean.IMPORTANCEGlyphosate is the most widely used herbicide in the world and could be utilized as phosphorus (P) source by some bacteria. Our study first revealed that glyphosate could be transported into Phaeodactylum tricornutum cells for utilization and identified putative genes responsible for glyphosate uptake. This uncovers an alternative strategy of phytoplankton to cope with P deficiency considering phosphonate accounts for about 25% of the total dissolved organic phosphorus (DOP) in the ocean. Additionally, accumulation of carbon (C) and silicon (Si), as well as elevation of Si:C ratio in P. tricornutum cells when grown on glyphosate indicates glyphosate as the source of P nutrient has the potential to result in more C and Si export into the deep ocean. This, along with the differential ability to utilize glyphosate among different species, glyphosate supply in dissolved inorganic phosphorus (DIP)-depleted ecosystems may cause changes in phytoplankton community structure. These insights have implications in evaluating the effects of human activities (use of Roundup) and climate change (potentially reducing DIP supply in sunlit layer) on phytoplankton in the future ocean.

Unveiling the responses of Alexandrium pacificum to phosphorus utilization by physiological and transcriptomic analysis

Phosphorus (P) is an essential macronutrient impacting bloom formation of marine dinoflagellates. The dinoflagellate Alexandrium pacificum is a cosmopolitan species known to frequently cause dense blooms in estuarine and coastal waters worldwide, while the physiological and molecular responses of A. pacificum to P utilization are still not well understood. Herein, the growth, P utilization, toxin production and transcriptomes of A. pacificum grown under P-deficient, inorganic P-replete, and organic P-replete conditions were compared. The results indicated that P-deficient adversely affected the growth of A. pacificum and significantly down-regulated the expression of genes related to P transport and material metabolism, but enhanced the production of toxin. On the other hand, no significant differences were observed in growth and toxin production between the organic and inorganic P-replete treatments. However, genes involved in P transport, utilization and TCA cycle were significantly changed in the organic P-replete compared with the inorganic P-replete group, and the mechanisms underlying the use of various organic P compounds were different. These findings suggested that A. pacificum evolved diverse organic P utilization strategies to adapt to low P conditions, which might be a crucial factor driving bloom formation in a low inorganic P environment.

Chattonella marina blooms in a trophic gradient system: Interaction with environmental drivers

For coastal eutrophication, lots of studies focused on the influence from environmental factors, especially nitrogen and phosphorus, on algae blooms. The interaction between algae and environmental factors has been often ignored. Using Chattonella marina, a dominant species in marine algal blooms, we established a trophic gradient system that simulated C. marina blooms at three trophic levels: eutrophic, mesotrophic, and oligotrophic, and examined the life history patterns of C. marina and the interactions with environmental factors. Increased trophic levels influenced the growth potential of C. marina, while its unique cyst reproduction allowed it to thrive in nutrient-limited environments. Adequate nutrients caused changes in dissolved oxygen (DO) and pH led by C. marina, with the carbonate system playing a crucial role in regulating pH under nutrient-limited conditions. Limiting the growth of C. marina in areas with low nutrient by manipulating reactive silicate (SiO32-) availability may prove effective. Nitrate (NO3-) was the preferred nutrient for C. marina when its concentration exceeded that of ammonium (NH4+). Phosphorus played a crucial role in the growth and proliferation of C. marina, especially when other nutrients were scarce. The findings of this study may provide valuable insights into the effective management and prevention of algae blooms.

Membrane lipid remodeling and autophagy to cope with phosphorus deficiency in the dinoflagellate Prorocentrum shikokuense

Dinoflagellates, which are responsible for more than 80% of harmful algal blooms in coastal waters, are competitive in low-phosphate environments. However, the specific acclimated phosphorus strategies to adapt to phosphorus deficiency in dinoflagellates, particularly through intracellular phosphorus metabolism, remain largely unknown. Comprehensive physiological, biochemical, and transcriptomic analyses were conducted to investigate intracellular phosphorus modulation in a model dinoflagellate, Prorocentrum shikokuense, with a specific focus on membrane lipid remodeling and autophagy in response to phosphorus deficiency. Under phosphorus deficiency, P. shikokuense exhibited a preference to spare phospholipids with nonphospholipids. The major phospholipid classes of phosphatidylcholine and phosphatidylethanolamine decreased in content, whereas the betaine lipid class of diacylglyceryl carboxyhydroxymethylcholine increased in content. Furthermore, under phosphorus deficiency, P. shikokuense induced autophagy as a mechanism to conserve and recycle cellular phosphorus resources. The present study highlights the effective modulation of intracellular phosphorus in P. shikokuense through membrane phospholipid remodeling and autophagy and contributes to a comprehensive understanding of the acclimation strategies to low-phosphorus conditions in dinoflagellates.

Atmospheric deposition and river runoff stimulate the utilization of dissolved organic phosphorus in coastal seas

In coastal seas, the role of atmospheric deposition and river runoff in dissolved organic phosphorus (DOP) utilization is not well understood. Here, we address this knowledge gap by combining microcosm experiments with a global approach considering the relationship between the activity of alkaline phosphatases and changes in phytoplankton biomass in relation to the concentration of dissolved inorganic phosphorus (DIP). Our results suggest that the addition of aerosols and riverine water stimulate the biological utilization of DOP in coastal seas primarily by depleting DIP due to increasing nitrogen concentrations, which enhances phytoplankton growth. This "Anthropogenic Nitrogen Pump" was therefore identified to make DOP an important source of phosphorus for phytoplankton in coastal seas but only when the ratio of chlorophyll a to DIP [Log10 (Chl a / DIP)] is larger than 1.20. Our study therefore suggests that anthropogenic nitrogen input might contribute to the phosphorus cycle in coastal seas.

Pseudomonas taetrolens ULE-PH5 and Pseudomonas sp. ULE-PH6 Isolated from the Hop Rhizosphere Increase Phosphate Assimilation by the Plant

Most of the phosphorus incorporated into agricultural soils through the use of fertilizers precipitates in the form of insoluble salts that are incapable of being used by plants. This insoluble phosphorus present in large quantities in soil forms the well-known "phosphorus legacy". The solubilization of this "phosphorus legacy" has become a goal of great agronomic importance, and the use of phosphate-solubilizing bacteria would be a useful tool for this purpose. In this work, we have isolated and characterized phosphate-solubilizing bacteria from the rhizosphere of hop plants. Two particular strains, Pseudomonas taetrolens ULE-PH5 and Pseudomonas sp. ULE-PH6, were selected as plant growth-promoting rhizobacteria due to their high phosphate solubilization capability in both plate and liquid culture assays and other interesting traits, including auxin and siderophore production, phytate degradation, and acidic and alkaline phosphatase production. These strains were able to significantly increase phosphate uptake and accumulation of phosphorus in the aerial part (stems, petioles, and leaves) of hop plants, as determined by greenhouse trials. These strains are promising candidates to produce biofertilizers specifically to increase phosphate adsorption by hop plants.

Dissolved organic phosphorus promotes Cyclotella growth and adaptability in eutrophic tropical estuaries

Dissolved organic phosphorus (DOP) is an important nutrient for phytoplankton growth in oligotrophic oceans. However, little is known about the impact of DOP on phytoplankton growth in eutrophic waters. In the present study, we conducted field monitoring as well as in situ and laboratory experiments in the Pearl River estuary (PRE). Field observations showed an increase in the nitrogen-to-phosphorus ratio and DOP in recent years in the PRE. The phytoplankton community was dominated by nanophytoplankton Cyclotella in the upper and middle estuary, with high concentrations of DOP and light limitation during the ebb stage of the spring to neap tide in summer. The relative abundance of Cyclotella in natural waters was higher after enrichment with estuarine water with a background of 0.40-0.46 µM DOP, even when dissolved inorganic phosphorus was sufficient (0.55-0.76 µM). In addition, the relative abundance of Cyclotella in natural waters was higher after enrichment with phosphoesters. Laboratory culture results also confirmed that phosphoesters can enhance the growth rate of Cyclotella cryptica. Our study highlights that Cyclotella can become the dominant species in estuaries with increased levels of phosphoesters and low and fluctuating light adaptability and under the joint effect of dynamic processes such as upwelling and tides. Our results provide new insights into the role of Cyclotella in biogeochemical cycles affected by DOP utilization and potential applications in relieving the hypoxia of tropical eutrophic estuaries.IMPORTANCEThis study provides evidence that Cyclotella can become the dominant species in estuaries with increased levels of phosphoesters and low and fluctuating light adaptability and under the joint effect of dynamic processes such as upwelling and tides. Our study provides new insights into the role of Cyclotella in biogeochemical cycles affected by dissolved organic phosphorus utilization, especially affected by anthropogenic inputs and climate change. Potential applications include relieving the hypoxia of tropical eutrophic estuaries.

Aerobic methane production by phytoplankton as an important methane source of aquatic ecosystems: Reconsidering the global methane budget

Biological methane, a major source of global methane budget, is traditionally thought to be produced in anaerobic environments. However, the recent reports about methane supersaturation occurring in oxygenated water layer, termed as "methane paradox", have challenged this prevailing paradigm. Significantly, growing evidence has indicated that phytoplankton including prokaryotic cyanobacteria and eukaryotic algae are capable of generating methane under aerobic conditions. In this regard, a systematic review of aerobic methane production by phytoplankton is expected to arouse the public attention, contributing to the understanding of methane paradox. Here, we comprehensively summarize the widespread phenomena of methane supersaturation in oxic layers. The remarkable correlation relationships between methane concentration and several key indicators (depth, chlorophyll a level and organic sulfide concentration) indicate the significance of phytoplankton in in-situ methane accumulation. Subsequently, four mechanisms of aerobic methane production by phytoplankton are illustrated in detail, including photosynthesis-driven metabolism, reactive oxygen species (ROS)-driven demethylation of methyl donors, methanogenesis catalyzed by nitrogenase and demethylation of phosphonates catalyzed by CP lyase. The first two pathways occur in various phytoplankton, while the latter two have been specially discovered in cyanobacteria. Additionally, the effects of four crucial factors on aerobic methane production by phytoplankton are also discussed, including phytoplankton species, light, temperature and crucial nutrients. Finally, the measures to control global methane emissions from phytoplankton, the precise intracellular mechanisms of methane production and a more complete global methane budget model are definitely required in the future research on methane production by phytoplankton. This review would provide guidance for future studies of aerobic methane production by phytoplankton and emphasize the potential contribution of aquatic ecosystems to global methane budget.

Clustered Regularly Interspaced Short Palindromic Repeat/CRISPR-Associated Protein and Its Utility All at Sea: Status, Challenges, and Prospects

Initially discovered over 35 years ago in the bacterium Escherichia coli as a defense system against invasion of viral (or other exogenous) DNA into the genome, CRISPR/Cas has ushered in a new era of functional genetics and served as a versatile genetic tool in all branches of life science. CRISPR/Cas has revolutionized the methodology of gene knockout with simplicity and rapidity, but it is also powerful for gene knock-in and gene modification. In the field of marine biology and ecology, this tool has been instrumental in the functional characterization of 'dark' genes and the documentation of the functional differentiation of gene paralogs. Powerful as it is, challenges exist that have hindered the advances in functional genetics in some important lineages. This review examines the status of applications of CRISPR/Cas in marine research and assesses the prospect of quickly expanding the deployment of this powerful tool to address the myriad fundamental marine biology and biological oceanography questions.

The impact of extreme precipitation on physical and biogeochemical processes regarding with nutrient dynamics in a semi-closed bay

An extreme precipitation event in August 2012 changed the ecosystem of Jiaozhou Bay (JZB), China. Biochemical variables in the sea, river mouths, and rainwater were monitored simultaneously during the event. The impact of the following excessive riverine input and wet atmospheric deposition on nutrient dynamics were studied before. However, regulatory processes of nutrient dynamics were not quantified and analyzed. Therefore, a coupled physical-biological model (FVCOM-ERSEM) was used to study the physical and biochemical mechanisms of the variation of the dissolved inorganic nitrogen (DIN), phosphorus (DIP), and silicon (DISi), as well as chlorophyll-a (Chl-a). The results indicate that physical processes increase nutrients, while biological processes reduce them. The exchange with the Yellow Sea, as an important physical process, exports DIN to the Yellow Sea, but imports DIP and DISi to the JZB. Only 20 % of the excessive DIN due to extreme precipitation event was reduced by water exchange with the Yellow Sea. The rest (80 %) was reduced and changed into organic nitrogen through biological processes. This paper also examines the variation of the pelagic and benthic cycles of biochemical processes. In these cycles, phytoplankton take up and use nutrients in the bay, while zooplankton excretion in the pelagic cycle and benthic releases resupply them. Precipitation enriched the surface nutrients, which boosted primary production and organic matter transport to the bottom water.

Phosphate-related genomic islands as drivers of environmental adaptation in the streamlined marine alphaproteobacterial HIMB59

IMPORTANCE

These results shed light on the evolutionary strategies of microbes with streamlined genomes to adapt and survive in the oligotrophic conditions that dominate the surface waters of the global ocean. At the individual level, these microbes have been subjected to evolutionary constraints that have led to a more efficient use of nutrients, removing non-essential genes named as "streamlining theory." However, at the population level, they conserve a highly diverse gene pool in flexible genomic islands resulting in polyclonal populations on the same genomic background as an evolutionary response to environmental pressures. Localization of these islands at equivalent positions in the genome facilitates horizontal transfer between clonal lineages. This high level of environmental genomic heterogeneity could explain their cosmopolitan distribution. In the case of the order HIMB59 within the class Alphaproteobacteria, two factors exert evolutionary pressure and determine this intraspecific diversity: phages and the concentration of P in the environment.

Phosphorus nutrition strategies in a Symbiodiniacean species: Implications in coral-alga symbiosis facing increasing phosphorus deficiency in future warmer oceans

Coral reefs thrive in the oligotrophic ocean and rely on symbiotic algae to acquire nutrients. Global warming is projected to intensify surface ocean nutrient deficiency and anthropogenic discharge of wastes with high nitrogen (N): phosphorus (P) ratios can exacerbate P nutrient limitation. However, our understanding on how symbiotic algae cope with P deficiency is limited. Here, we investigated the responses of a coral symbiotic species of Symbiodiniaceae, Cladocopium goreaui, to P-limitation by examining its physiological performance and transcriptomic profile. Under P stress, C. goreaui exhibited decreases in algal growth, photosynthetic efficiency, and cellular P content but enhancement in carbon fixation, N assimilation, N:P ratio, and energy metabolism, with downregulated expression of carbohydrate exporter genes. Besides, C. goreaui showed flexible mechanisms of utilizing different dissolved organic phosphorus to relieve P deficiency. When provided glycerol phosphate, C. goreaui hydrolyzed it extracellularly to produce phosphate for uptake. When grown on phytate, in contrast, C. goreaui upregulated the endocytosis pathway while no dissolved inorganic phosphorus was released into the medium, suggesting that phytate was transported into the cell, potentially via the endocytosis pathway. This study sheds light on the survival strategies of C. goreaui and potential weakening of its role as an organic carbon supplier in P-limited environments, underscoring the importance of more systematic investigation on future projections of such effects.