De novo assembly of Aureococcus anophagefferens transcriptomes reveals diverse responses to the low nutrient and low light conditions present during blooms

Nitrogen uptake by Scenedesmus quadricauda and its responses over environmental factors

Nitrogen is a vital nutrient for the growth of microalgae. Understanding the mechanism of nitrogen uptake by algae plays a crucial role in addressing and mitigating. Harmful algal blooms. This study compares the nitrogen uptake kinetics of Scenedesmus quadricauda on different nitrogen substrates: NO3-, NH4+, urea, and glycine. And the effects of four environmental factors on nitrogen uptake were also investigated. In the presence of four N substrates, Scenedesmus quadricauda took up four N substrates simultaneously. The order of uptake rates by Scenedesmus quadricauda was NH4+ > urea > NO3- > glycine. Scenedesmus quadricauda exhibited a strong preference for urea and NH4+. Moreover, the environmental factors of temperature, pH, and light intensity had significant effects on nitrogen uptake rates. Although changes in environmental factors affected nitrogen uptake rates, they did not alter the uptake preference for different nitrogen sources. Higher temperatures (35 °C), higher pH (9), optimal light intensity (7200 lx) and turbulence intensity (100 rpm) conditions were associated with the higher nitrogen uptake rates. The findings contribute to a better understanding of algal nitrogen metabolism and provide a basis for predicting and managing algal bloom occurrences in aquatic ecosystems.

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.

The consequences of viral infection on protists

Protists encompass a vast widely distributed group of organisms, surpassing the diversity observed in metazoans. Their diverse ecological niches and life forms are intriguing characteristics that render them valuable subjects for in-depth cell biology studies. Throughout history, viruses have played a pivotal role in elucidating complex cellular processes, particularly in the context of cellular responses to viral infections. In this comprehensive review, we provide an overview of the cellular alterations that are triggered in specific hosts following different viral infections and explore intricate biological interactions observed in experimental conditions using different host-pathogen groups.

Kratosvirus quantuckense: the history and novelty of an algal bloom disrupting virus and a model for giant virus research

Since the discovery of the first "giant virus," particular attention has been paid toward isolating and culturing these large DNA viruses through Acanthamoeba spp. bait systems. While this method has allowed for the discovery of plenty novel viruses in the Nucleocytoviricota, environmental -omics-based analyses have shown that there is a wealth of diversity among this phylum, particularly in marine datasets. The prevalence of these viruses in metatranscriptomes points toward their ecological importance in nutrient turnover in our oceans and as such, in depth study into non-amoebal Nucleocytoviricota should be considered a focal point in viral ecology. In this review, we report on Kratosvirus quantuckense (née Aureococcus anophagefferens Virus), an algae-infecting virus of the Imitervirales. Current systems for study in the Nucleocytoviricota differ significantly from this virus and its relatives, and a litany of trade-offs within physiology, coding potential, and ecology compared to these other viruses reveal the importance of K. quantuckense. Herein, we review the research that has been performed on this virus as well as its potential as a model system for algal-virus interactions.

Variation in intracellular polyphosphate and associated gene expression in response to different phosphorus conditions in the dinoflagellate Karenia mikimotoi

Polyphosphate (polyP) has long been recognized as a crucial intracellular reservoir for phosphorus in microorganisms. However, the dynamics of polyP and its regulatory mechanism in eukaryotic phytoplankton in response to variations in external phosphorus conditions remain poorly understood. A comprehensive investigation was conducted to examine the intracellular polyP-associated metabolic response of the dinoflagellate Karenia mikimotoi, a harmful algal bloom species, through integrated physiological, biochemical, and transcriptional analyses under varying external phosphorus conditions. Comparable growth curves and Fv/Fm between phosphorus-replete conditions and phosphorus-depleted conditions suggested that K. mikimotoi has a strong capability to mobilize the intracellular phosphorus pool for growth under phosphorus deficiency. Intracellular phosphate (IPi) and polyP contributed approximately 6-23 % and 1-3 %, respectively, to the overall particulate phosphorus (PP) content under different phosphorus conditions. The significant decrease in PP and increase in polyP:PP suggested that cellular phosphorus components other than polyP are preferred for utilization under phosphorus deficiency. Genes involved in polyP synthesis and hydrolysis were upregulated to maintain phosphorus homeostasis in K. mikimotoi. These findings provide novel insights into the specific cellular strategies for phosphorus storage and the transcriptional response in intracellular polyP metabolism in K. mikimotoi. Additionally, these results also indicate that polyP may not play a crucial role in cellular phosphorus storage in phytoplankton, at least in dinoflagellates.

Brown tides linked to the unique nutrient profile in coastal waters of Qinhuangdao, China

Brown tides caused by the pelagophyte Aureococcus anophagefferens have frequently occurred in the Bohai Sea since 2009 and have led to a dramatic collapse of the local scallop culture. To determine why brown tides occurred in the Bohai Sea rather than in other eutrophic coastal waters of China, phytoplankton communities and nutrients were evaluated and nutrient addition experiments were conducted in the Qinhuangdao coastal area. The concentration of dissolved organic nitrogen (DON) was nearly five times higher than that of dissolved inorganic nitrogen (DIN) during brown tides. High levels of phytoplankton biomass and nutrients were observed in the inshore waters, and the patterns of different nutrients were heterogeneous, which could be due to the uneven distribution of pelagophytes and non-brown tide phytoplankton populations (NBTP). The nutrient enrichment results indicated that the growth of the phytoplankton community was nitrogen-limited. Enrichment of DON, especially urea, could promote the growth of pelagophytes during the development stages of the brown tide. In brief, the results of this study imply that the unique nutrient profile (rich in DON but deficient in DIN) could support the outbreak of brown tides in the inshore waters of Qinhuangdao.

Identification, diversity and domain structure analysis of mucin and mucin-like genes in sea anemone Actinia tenebrosa

Background

Mucins are part of the glycoprotein family and the main proteinaceous component of mucus. The sea anemone species, Actinia tenebrosa (Phylum Cnidaria) produce large amounts of mucus, which have not been studied in detail. Furthermore, there has only been limited investigation of mucin genes in phylum Cnidaria. Therefore, the aim of current study was to identify and analyse the repertoire mucin genes present in A. tenebrosa and range of other sea anemone species to document their diversity in this group.

Methods

To achieve this aim, we undertook transcriptome sequencing, assembly, and annotation to identify mucin genes in A. tenebrosa.

Results

The results from this study demonstrated a diverse repertoire of mucin proteins, including mucin1-like, mucin4-like, and a range of mucin-like genes in the range of sea anemone species examined. The domain structure of the identified mucin genes was found to be consistent with the conserved domains found in the homologous proteins of vertebrate species. The discovery of a diverse range of mucin genes in sea anemone species provided a basic reference for future mucin studies in cnidarians and could lead to research into their application in the pharmacological, clinical, and cosmetic industries.

Aureococcus anophagefferens (Pelagophyceae) genomes improve evaluation of nutrient acquisition strategies involved in brown tide dynamics

The pelagophyte Aureococcus anophagefferens causes harmful brown tide blooms in marine embayments on three continents. Aureococcus anophagefferens was the first harmful algal bloom species to have its genome sequenced, an advance that evidenced genes important for adaptation to environmental conditions that prevail during brown tides. To expand the genomic tools available for this species, genomes for four strains were assembled, including three newly sequenced strains and one assembled from publicly available data. These genomes ranged from 57.11 to 73.62 Mb, encoding 13,191-17,404 potential proteins. All strains shared ~90% of their encoded proteins as determined by homology searches and shared most functional orthologs as determined by KEGG, although each strain also possessed coding sequences with unique functions. Like the original reference genome, the genomes assembled in this study possessed genes hypothesized to be important in bloom proliferation, including genes involved in organic compound metabolism and growth at low light. Cross-strain informatics and culture experiments suggest that the utilization of purines is a potentially important source of organic nitrogen for brown tides. Analyses of metatranscriptomes from a brown tide event demonstrated that use of a single genome yielded a lower read mapping percentage (~30% of library reads) as compared to a database generated from all available genomes (~43%), suggesting novel information about bloom ecology can be gained from expanding genomic space. This work demonstrates the continued need to sequence ecologically relevant algae to understand the genomic potential and their ecology in the environment.

TRAPID 2.0: a web application for taxonomic and functional analysis of de novo transcriptomes

Advances in high-throughput sequencing have resulted in a massive increase of RNA-Seq transcriptome data. However, the promise of rapid gene expression profiling in a specific tissue, condition, unicellular organism or microbial community comes with new computational challenges. Owing to the limited availability of well-resolved reference genomes, de novo assembled (meta)transcriptomes have emerged as popular tools for investigating the gene repertoire of previously uncharacterized organisms. Yet, despite their potential, these datasets often contain fragmented or contaminant sequences, and their analysis remains difficult. To alleviate some of these challenges, we developed TRAPID 2.0, a web application for the fast and efficient processing of assembled transcriptome data. The initial processing phase performs a global characterization of the input data, providing each transcript with several layers of annotation, comprising structural, functional, and taxonomic information. The exploratory phase enables downstream analyses from the web application. Available analyses include the assessment of gene space completeness, the functional analysis and comparison of transcript subsets, and the study of transcripts in an evolutionary context. A comparison with similar tools highlights TRAPID’s unique features. Finally, analyses performed within TRAPID 2.0 are complemented by interactive data visualizations, facilitating the extraction of new biological insights, as demonstrated with diatom community metatranscriptomes.

Transcriptomic and isotopic data reveal central role of ammonium in facilitating the growth of the mixotrophic dinoflagellate, Dinophysis acuminata

Dinophysis spp. are mixotrophs that are dependent on specific prey, but are also potentially reliant on dissolved nutrients. The extent to which Dinophysis relies on exogenous N and the specific biochemical pathways important for supporting its autotrophic and heterotrophic growth are unknown. Here, the nutritional ecology of Dinophysis was explored using two approaches: 1) ¹⁵N tracer experiments were conducted to quantify the concentration-dependent uptake rates and associated kinetics of various N compounds (nitrate, ammonium, urea) of Dinophysis cultures and 2) the transcriptomic responses of Dinophysis cultures grown with multiple combinations of prey and nutrients were assessed via dinoflagellate spliced leader-based transcriptome profiling. Of the N compounds examined, ammonium had the highest V_max and affinity coefficient, and lowest K_s for both pre-starved and pre-fed cultures, collectively demonstrating the preference of Dinophysis for this N source while little-to-no nitrate uptake was observed. During the transcriptome experiments, Dinophysis grown with nitrate and without prey had the largest number of genes with lower transcript abundances, did not increase abundance of transcripts associated with nitrate/nitrite uptake or reduction, and displayed no cellular growth, suggesting D. acuminata is not capable of growing on nitrate. When offered prey, the transcriptomic response of Dinophysis included the production of phagolysosomes, enzymes involved in protein and lipid catabolism, and N acquisition through amino acid degradation pathways. Compared with cultures only offered ammonium or prey, cultures offered both ammonium and prey had the largest number of genes with increased transcript abundances, the highest growth rate, and the unique activation of multiple pathways involved in cellular catabolism, further evidencing the ability of Dinophysis to grow optimally as a mixotroph. Collectively, this study evidences the key role ammonium plays in the mixotrophic growth of Dinophysis and reveals the precise biochemical pathways that facilitate its mixotrophic growth.

Mitochondrial Genome Evolution in Pelagophyte Algae

The Pelagophyceae are marine stramenopile algae that include Aureoumbra lagunensis and Aureococcus anophagefferens, two microbial species notorious for causing harmful algal blooms. Despite their ecological significance, relatively few genomic studies of pelagophytes have been carried out. To improve understanding of the biology and evolution of pelagophyte algae, we sequenced complete mitochondrial genomes for A. lagunensis (CCMP1510), Pelagomonas calceolata (CCMP1756), and five strains of Aureoc. anophagefferens (CCMP1707, CCMP1708, CCMP1850, CCMP1984, and CCMP3368) using Nanopore long-read sequencing. All pelagophyte mitochondrial genomes assembled into single, circular mapping contigs between 39,376 bp (P. calceolata) and 55,968 bp (A. lagunensis) in size. Mitochondrial genomes for the five Aureoc. anophagefferens strains varied slightly in length (42,401–42,621 bp) and were 99.4–100.0% identical. Gene content and order were highly conserved between the Aureoc. anophagefferens and P. calceolata genomes, with the only major difference being a unique region in Aureoc. anophagefferens containingDNA adenine and cytosine methyltransferase (dam/dcm) genes that appear to be the product of lateral gene transfer from a prokaryotic or viral donor. Although the A. lagunensis mitochondrial genome shares seven distinct syntenic blocks with the other pelagophyte genomes, it has a tandem repeat expansion comprising ∼40% of its length, and lacks identifiable rps19 and glycine tRNA genes. Laterally acquired self-splicing introns were also found in the 23S rRNA (rnl) gene of P. calceolata and the coxI gene of the five Aureoc. anophagefferens genomes. Overall, these data provide baseline knowledge about the genetic diversity of bloom-forming pelagophytes relative to nonbloom-forming species.

Internal Nitrogen Pools Shape the Infection of Aureococcus anophagefferens CCMP 1984 by a Giant Virus

The pelagophyte Aureococcus anophagefferens blooms annually in shallow bays around the world, where it is hypothesized to outcompete other phytoplankton in part by using alternative nitrogen sources. The high proportion of natural populations that are infected during the late stages of the bloom suggest viruses cause bloom collapse. We hypothesized that the Aureococcus anophagefferens Virus (AaV) infection cycle would be negatively influenced in cultures acclimated to decreasing external nitrogen conditions, but that the real-time external nitrogen concentration would not influence the infection cycle. Cultures acclimated in NO 3 - concentrations (0.0147 mM; N:P = 0.1225) that showed reduced end point cell abundances, forward scatter (a proxy for size) and red fluorescence (a proxy for chlorophyll a), also produced fewer viruses per cell at a slower rate. Decreasing the external concentration of nitrogen post infection did not alter burst size or time to lysis. These data suggest that the nitrogen used for new viral progeny is present within host cells at the time of infection. Flow cytometric data of an infection cycle showed a reduction in red fluorescence around twelve hours post infection, consistent with degradation of nitrogen-rich chloroplasts during the infection cycle. Using cell and virus quota estimates, we determined that A. anophagefferens cells had sufficient nitrogen and carbon for the lower ranges of burst sizes determined but did not contain enough phosphorous. Consistent with this observation, expression of nitrate and sugar transporters did not increase in the publicly available transcriptome data of the infection cycle, while several phosphorus transporters were. Our data demonstrate that dynamics of viruses infecting Aureococcus over the course of a bloom is dictated by the host cell state upon infection, which is set a priori by external nutrient supplies.

Influence of light on the infection of Aureococcus anophagefferens CCMP 1984 by a "giant virus"

The pelagophyte Aureococcus anophagefferens has caused recurrent brown tide blooms along the northeast coast of the United States since the mid-1980's, and more recently spread to other regions of the globe. These blooms, due to the high cell densities, are associated with severe light attenuation that destroys the sea grass beds which provide the basis for many fisheries. Data collected by transmission electron microscopy, PCR, and metatranscriptomic studies of the blooms, support the hypothesis that large dsDNA viruses play a role in bloom dynamics. While a large (~140 nm) icosahedral virus, with a 371 kbp genome, was first isolated more than a decade ago, the constraints imposed by environmental parameters on bloom infection dynamics by Aureococcus anophagefferens Virus, (AaV) remain unknown. To investigate the role light plays in infection by this virus, we acclimated A. anophagefferens to light intensities of 30 (low), 60 (medium) or 90 μmol photons m-2 s-1 (high) and infected cultures at these irradiance levels. Moreover, we completed light shift experiments where acclimated cultures were exposed to even lower light intensities (0, 5, and 15 μmol photons m-2 s-1) consistent with irradiance found during the peak of the bloom when cell concentrations are highest. The abundance of viruses produced per lytic event (burst size) was lower in the low irradiance acclimated cultures compared to the medium and high acclimated cultures. Transferring infected cultures to more-limiting light availabilities further decreased burst size and increased the length of time it took for cultures to lyse, regardless of acclimation irradiance level. A hypothetical mechanism for the reduced efficiency of the infection cycle in low light due to ribosome biogenesis was predicted from pre-existing transcriptomes. Overall, these studies provide a framework for understanding light effects on infection dynamics over the course of the summer months when A. anophagefferens blooms occur.

Progress and promise of omics for predicting the impacts of climate change on harmful algal blooms

Climate change is predicted to increase the severity and prevalence of harmful algal blooms (HABs). In the past twenty years, omics techniques such as genomics, transcriptomics, proteomics and metabolomics have transformed that data landscape of many fields including the study of HABs. Advances in technology have facilitated the creation of many publicly available omics datasets that are complementary and shed new light on the mechanisms of HAB formation and toxin production. Genomics have been used to reveal differences in toxicity and nutritional requirements, while transcriptomics and proteomics have been used to explore HAB species responses to environmental stressors, and metabolomics can reveal mechanisms of allelopathy and toxicity. In this review, we explore how omics data may be leveraged to improve predictions of how climate change will impact HAB dynamics. We also highlight important gaps in our knowledge of HAB prediction, which include swimming behaviors, microbial interactions and evolution that can be addressed by future studies with omics tools. Lastly, we discuss approaches to incorporate current omics datasets into predictive numerical models that may enhance HAB prediction in a changing world. With the ever-increasing omics databases, leveraging these data for understanding climate-driven HAB dynamics will be increasingly powerful.

Transcriptomic response to changing ambient phosphorus in the marine dinoflagellate Prorocentrum donghaiense

Dinoflagellates represent major contributors to the harmful algal blooms in the oceans. Phosphorus (P) is an essential macronutrient that limits the growth and proliferation of dinoflagellates. However, the specific molecular mechanisms involved in the P acclimation of dinoflagellates remain poorly understood. Here, the transcriptomes of a dinoflagellate Prorocentrum donghaiense grown under inorganic P-replete, P-deficient, and inorganic- and organic P-resupplied conditions were compared. Genes encoding low- and high-affinity P transporters were significantly down-regulated in the P-deficient cells, while organic P utilization genes were significantly up-regulated, indicating strong ability of P. donghaiense to utilize organic P. Up-regulation of membrane phospholipid catabolism and endocytosis provided intracellular and extracellular organic P for the P-deficient cells. Physiological responses of P. donghaiense to dissolved inorganic P (DIP) or dissolved organic P (DOP) resupply exhibited insignificant differences. However, the corresponding transcriptomic responses significantly differed. Although the expression of multiple genes was significantly altered after DIP resupplementation, few biological processes varied. In contrast, various metabolic processes associated with cell growth, such as translation, transport, nucleotide, carbohydrate and lipid metabolisms, were significantly altered in the DOP-resupplied cells. Our results indicated that P. donghaiense evolved diverse DOP utilization strategies to adapt to low P environments, and that DOPs might play critical roles in the P. donghaiense bloom formation.

Physiological response dynamics of the brown tide organism Aureococcus anophagefferens treated with modified clay

On the basis of experiences in mitigating harmful algal blooms (HABs) with modified clay (MC), a bloom does not continue after the dispersal of the MC, even though the density of the residual cells in the water remains as high as 20-30% of the initial cell density. This interesting phenomenon indicates that in addition to flocculation, MC has additional mechanisms of HAB control. Here, Aureococcus anophagefferens was selected as a model organism to study the physiological response dynamics of residual cells treated with MC, and RT-qPCR was used to measure the differential expression of 40 genes involved in anti-oxidation, photosynthesis, phospholipid synthesis, programmed cell death and cell proliferation at five time points. The results showed that every functional gene category exhibited a "V" shaped pattern with a turning point. It was reflected that there were two processes for MC inhibiting the growth of residual cells. One is the oxidative stress process (OSP) caused by ineffective collision with MC, whose effect weakened gradually; another is the programmed cell death process (PCDP) caused by the lysis of damaged residual cells, whose effect enhanced two days after MC treatment. In addition, the scanning electron micrographs verified that some of the residual cells were deformed or even lysed. Combined with the effects of OSP and PCDP in dynamics, the growth of residual cells was inhibited and was followed by gradual bloom disappearance. This study further elucidates the mechanism of MC controlling HABs at the molecular level and enable a more comprehensive understanding of HAB mitigation using MC.

Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes

BACKGROUND

De novo transcriptome assemblies are required prior to analyzing RNA sequencing data from a species without an existing reference genome or transcriptome. Despite the prevalence of transcriptomic studies, the effects of using different workflows, or "pipelines," on the resulting assemblies are poorly understood. Here, a pipeline was programmatically automated and used to assemble and annotate raw transcriptomic short-read data collected as part of the Marine Microbial Eukaryotic Transcriptome Sequencing Project. The resulting transcriptome assemblies were evaluated and compared against assemblies that were previously generated with a different pipeline developed by the National Center for Genome Research.

RESULTS

New transcriptome assemblies contained the majority of previous contigs as well as new content. On average, 7.8% of the annotated contigs in the new assemblies were novel gene names not found in the previous assemblies. Taxonomic trends were observed in the assembly metrics. Assemblies from the Dinoflagellata showed a higher number of contigs and unique k-mers than transcriptomes from other phyla, while assemblies from Ciliophora had a lower percentage of open reading frames compared to other phyla.

CONCLUSIONS

Given current bioinformatics approaches, there is no single "best" reference transcriptome for a particular set of raw data. As the optimum transcriptome is a moving target, improving (or not) with new tools and approaches, automated and programmable pipelines are invaluable for managing the computationally intensive tasks required for re-processing large sets of samples with revised pipelines and ensuring a common evaluation workflow is applied to all samples. Thus, re-assembling existing data with new tools using automated and programmable pipelines may yield more accurate identification of taxon-specific trends across samples in addition to novel and useful products for the community.

Transcriptional and Proteomic Choreography Under Phosphorus Deficiency and Re-supply in the N2 Fixing Cyanobacterium Trichodesmium erythraeum

The N₂ fixing cyanobacterium Trichodesmium is a critically important organism in oligotrophic marine ecosystems, supplying “new” nitrogen (N) to the otherwise N-poor tropical and subtropical regions where it occurs. Low concentrations of phosphorus (P) in these regions can constrain Trichodesmium distribution and N₂ fixation rates. Physiological characterization of a single species in a mixed community can be challenging, and ‘omic approaches are increasingly important tools for tracking nutritional physiology in a taxon-specific manner. As such, studies examining the dynamics of gene and protein markers of physiology (e.g., nutrient stress) are critical for the application and interpretation of such ‘omic data in situ. Here we leveraged combined transcriptomics, proteomics, and enzyme activity assays to track the physiological response of Trichodesmium erythraeum IMS101 to P deficiency and subsequent P re-supply over 72 h of sampling. P deficiency resulted in differential gene expression, protein abundance, and enzyme activity that highlighted a synchronous shift in P physiology with increases in the transcripts and corresponding proteins for hydrolyzing organic phosphorus, taking up phosphate with higher affinity, and modulating intracellular P demand. After P deficiency was alleviated, gene expression of these biomarkers was reduced to replete levels within 4 h of P amendment. A number of these gene biomarkers were adjacent to putative pho boxes and their expression patterns were similar to a sphR response regulator. Protein products of the P deficiency biomarkers were slow to decline, with 84% of the original P deficient protein set still significantly differentially expressed after 72 h. Alkaline phosphatase activity tracked with proteins for this enzyme. With the rapid turnover time of transcripts, they appear to be good biomarkers of a P stress phenotype, whereas proteins, with a slower turnover time, may better reflect cellular activities. These results highlight the importance of validating and pairing transcriptome and proteome data that can be applied to physiological studies of key species in situ.

Transcriptional Shifts Highlight the Role of Nutrients in Harmful Brown Tide Dynamics

Harmful algal blooms (HABs) threaten ecosystems and human health worldwide. Controlling nitrogen inputs to coastal waters is a common HAB management strategy, as nutrient concentrations often suggest coastal blooms are nitrogen-limited. However, defining best nutrient management practices is a long-standing challenge: in part, because of difficulties in directly tracking the nutritional physiology of harmful species in mixed communities. Using metatranscriptome sequencing and incubation experiments, we addressed this challenge by assaying the in situ physiological ecology of the ecosystem destructive alga, Aureococcus anophagefferens. Here we show that gene markers of phosphorus deficiency were expressed in situ, and modulated by the enrichment of phosphorus, which was consistent with the observed growth rate responses. These data demonstrate the importance of phosphorus in controlling brown-tide dynamics, suggesting that phosphorus, in addition to nitrogen, should be evaluated in the management and mitigation of these blooms. Given that nutrient concentrations alone were suggestive of a nitrogen-limited ecosystem, this study underscores the value of directly assaying harmful algae in situ for the development of management strategies.

Comparative expression profiling reveals widespread coordinated evolution of gene expression across eukaryotes

Comparative studies of gene expression across species have revealed many important insights, but have also been limited by the number of species represented. Here we develop an approach to identify orthologs between highly diverged transcriptome assemblies, and apply this to 657 RNA-seq gene expression profiles from 309 diverse unicellular eukaryotes. We analyzed the resulting data for coevolutionary patterns, and identify several hundred protein complexes and pathways whose expression levels have evolved in a coordinated fashion across the trillions of generations separating these species, including many gene sets with little or no within-species co-expression across environmental or genetic perturbations. We also detect examples of adaptive evolution, for example of tRNA ligase levels to match genome-wide codon usage. In sum, we find that comparative studies from extremely diverse organisms can reveal new insights into the evolution of gene expression, including coordinated evolution of some of the most conserved protein complexes in eukaryotes.

Gene pairs that are coexpressed across various environmental conditions in multiple species suggest functional similarity. Here the authors analyze patterns of gene expression co-evolution across diverse eukaryotes, and identify hundreds of protein complexes and pathways whose gene expression levels have co-evolved since their ancient divergence.

Comparative genome and transcriptome analysis of diatom, Skeletonema costatum, reveals evolution of genes for harmful algal bloom

Background

Diatoms play a great role in carbon fixation with about 20% of the whole fixation in the world. However, harmful algal bloom as known as red tide is a major problem in environment and fishery industry. Even though intensive studies have been conducted so far, the molecular mechanism behind harmful algal bloom was not fully understood. There are two major diatoms have been sequenced, but more diatoms should be examined at the whole genome level, and evolutionary genome studies were required to understand the landscape of molecular mechanism of the harmful algal bloom.

Results

Here we sequenced the genome of Skeletonema costatum, which is the dominant diatom in Japan causing a harmful algal bloom, and also performed RNA-sequencing analysis for conditions where harmful algal blooms often occur. As results, we found that both evolutionary genomic and comparative transcriptomic studies revealed genes for oxidative stress response and response to cytokinin is a key for the proliferation of the diatom.

Conclusions

Diatoms causing harmful algal blooms have gained multi-copy of genes related to oxidative stress response and response to cytokinin and obtained an ability to intensive gene expression at the blooms.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5144-5) contains supplementary material, which is available to authorized users.

Shifting metabolic priorities among key protistan taxa within and below the euphotic zone

A metatranscriptome study targeting the protistan community was conducted off the coast of Southern California, at the San Pedro Ocean Time-series station at the surface, 150 m (oxycline), and 890 m to link putative metabolic patterns to distinct protistan lineages. Comparison of relative transcript abundances revealed depth-related shifts in the nutritional modes of key taxonomic groups. Eukaryotic gene expression in the sunlit surface environment was dominated by phototrophs, such as diatoms and chlorophytes, and high abundances of transcripts associated with synthesis pathways (e.g., photosynthesis, carbon fixation, fatty acid synthesis). Sub-euphotic depths (150 and 890 m) exhibited strong contributions from dinoflagellates and ciliates, and were characterized by transcripts relating to digestion or intracellular nutrient recycling (e.g., breakdown of fatty acids and V-type ATPases). These transcriptional patterns underlie the distinct nutritional modes of ecologically important protistan lineages that drive marine food webs, and provide a framework to investigate trophic dynamics across diverse protistan communities.

Molecular Mechanism of Modified Clay Controlling the Brown Tide Organism Aureococcus anophagefferens Revealed by Transcriptome Analysis

The data and experiences in mitigating harmful algal blooms (HABs) by modified clay (MC) show that a bloom does not continue after the dispersal of the MC, even though the density of the residual cells in the water is still high, at 20-30% of the initial cell density. This interesting phenomenon indicates that in addition to flocculation, MC has an additional control mechanism. Here, transcriptome sequencing technology was used to study the molecular mechanism of MC in controlling HABs. In residual cells treated with MC, the photosynthetic light reaction was the most affected physiological process. Some genes related to the light harvesting complex, photosystem (PS) I and PS II, were significantly up-regulated ( p < 0.05), and several transcripts increased by as much as 6-fold. In contrast, genes associated with the dark reaction did not significantly change. In addition to genes associated with photosynthesis, numerous genes related to energy metabolism, stress adaptation, cytoskeletal functioning, and cell division also responded to MC treatment. These results indicated that following treatment with MC, the normal physiological processes of algal cells were disrupted, which inhibited cell proliferation and growth. Thus, these findings provide scientific proof that HABs are controlled by MC.

Coordinated gene expression between Trichodesmium and its microbiome over day-night cycles in the North Pacific Subtropical Gyre

Trichodesmium is a widespread, N₂ fixing marine cyanobacterium that drives inputs of newly fixed nitrogen and carbon into the oligotrophic ecosystems where it occurs. Colonies of Trichodesmium ubiquitously occur with heterotrophic bacteria that make up a diverse microbiome, and interactions within this Trichodesmium holobiont could influence the fate of fixed carbon and nitrogen. Metatranscriptome sequencing was performed on Trichodesmium colonies collected during high-frequency Lagrangian sampling in the North Pacific Subtropical Gyre (NPSG) to identify possible interactions between the Trichodesmium host and microbiome over day-night cycles. Here we show significantly coordinated patterns of gene expression between host and microbiome, many of which had significant day-night periodicity. The functions of the co-expressed genes suggested a suite of interactions within the holobiont linked to key resources including nitrogen, carbon, and iron. Evidence of microbiome reliance on Trichodesmium-derived vitamin B12 was also detected in co-expression patterns, highlighting a dependency that could shape holobiont community structure. Collectively, these patterns of expression suggest that biotic interactions could influence colony cycling of resources like nitrogen and vitamin B12, and decouple activities, like N₂ fixation, from typical abiotic drivers of Trichodesmium physiological ecology.

Comparative transcriptome analysis provides insights of anti-insect molecular mechanism of Cassia obtusifolia trypsin inhibitor against Pieris rapae

Pieris rapae, a serious Lepidoptera pest of cultivated crucifers, utilizes midgut enzymes to digest food and detoxify secondary metabolites from host plants. A recombinant trypsin inhibitor (COTI) from nonhost plant, Cassia obtusifolia, significantly decreased activities of trypsin-like proteases in the larval midgut on Pieris rapae and could suppress the growth of larvae. In order to know how COTI took effect, transcriptional profiles of P. rapae midgut in response to COTI was studied. A total of 51,544 unigenes were generated and 45.86% of which had homologs in public databases. Most of the regulated genes associated with digestion, detoxification, homeostasis, and resistance were downregulated after ingestion of COTI. Meanwhile, several unigenes in the integrin signaling pathway might be involved in response to COTI. Furthermore, using comparative transcriptome analysis, we detected differently expressing genes and identified a new reference gene, UPF3, by qRT-polymerase chain reaction (PCR). Therefore, it was suggested that not only proteolysis inhibition, but also suppression of expression of genes involved in metabolism, development, signaling, and defense might account for the anti-insect resistance of COTI.

Transcriptional response of the harmful raphidophyte Heterosigma akashiwo to nitrate and phosphate stress

The marine eukaryotic alga Heterosigma akashiwo (Raphidophyceae) is known for forming ichthyotoxic harmful algal blooms (HABs). In the past 50 years, H. akashiwo blooms have increased, occurring globally in highly eutrophic coastal and estuarine systems. These systems often incur dramatic physicochemical changes, including macronutrient (nitrogen and phosphorus) enrichment and depletion, on short timescales. Here, H. akashiwo cultures grown under nutrient replete, low N and low P growth conditions were examined for changes in biochemical and physiological characteristics in concert with transcriptome sequencing to provide a mechanistic perspective on the metabolic processes involved in responding to N and P stress. There was a marked difference in the overall transcriptional pattern between low N and low P transcriptomes. Both nutrient stresses led to significant changes in the abundance of thousands of contigs related to a wide diversity of metabolic pathways, with limited overlap between the transcriptomic responses to low N and low P. Enriched contigs under low N included many related to nitrogen metabolism, acquisition, and transport. In addition, metabolic modules like photosynthesis and carbohydrate metabolism changed significantly under low N, coincident with treatment-specific changes in photosynthetic efficiency and particulate carbohydrate content. P-specific contigs responsible for P transport and organic P use were more enriched in the low P treatment than in the replete control and low N treatment. These results provide new insight into the genetic mechanisms that distinguish how this HAB species responds to these two common nutrient stresses, and the results can inform future field studies, linking transcriptional patterns to the physiological ecology of H. akashiwo in situ.

Effects of silver nanoparticles on nitrification and associated nitrous oxide production in aquatic environments

Silver nanoparticles (AgNPs) are the most common materials in nanotechnology-based consumer products globally. Because of the wide application of AgNPs, their potential environmental impact is currently a highly topical focus of concern. Nitrification is one of the processes in the nitrogen cycle most susceptible to AgNPs but the specific effects of AgNPs on nitrification in aquatic environments are not well understood. We report the influence of AgNPs on nitrification and associated nitrous oxide (N₂O) production in estuarine sediments. AgNPs inhibited nitrification rates, which decreased exponentially with increasing AgNP concentrations. The response of nitrifier N₂O production to AgNPs exhibited low-dose stimulation (<534, 1476, and 2473 μg liter^-1 for 10-, 30-, and 100-nm AgNPs, respectively) and high-dose inhibition (hormesis effect). Compared with controls, N₂O production could be enhanced by >100% at low doses of AgNPs. This result was confirmed by metatranscriptome studies showing up-regulation of nitric oxide reductase (norQ) gene expression in the low-dose treatment. Isotopomer analysis revealed that hydroxylamine oxidation was the main N₂O production pathway, and its contribution to N₂O emission was enhanced when exposed to low-dose AgNPs. This study highlights the molecular underpinnings of the effects of AgNPs on nitrification activity and demonstrates that the release of AgNPs into the environment should be controlled because they interfere with nitrifying communities and stimulate N₂O emission.

Conserved Transcriptional Responses to Nutrient Stress in Bloom-Forming Algae

The concentration and composition of bioavailable nitrogen (N) and phosphorus (P) in the upper ocean shape eukaryotic phytoplankton communities and influence their physiological responses. Phytoplankton are known to exhibit similar physiological responses to limiting N and P conditions such as decreased growth rates, chlorosis, and increased assimilation of N and P. Are these responses similar at the molecular level across multiple species? To interrogate this question, five species from biogeochemically important, bloom-forming taxa (Bacillariophyta, Dinophyta, and Haptophyta) were grown under similar low N, low P, and replete nutrient conditions to identify transcriptional patterns and associated changes in biochemical pools related to N and P stress. Metabolic profiles, revealed through the transcriptomes of these taxa, clustered together based on species rather than nutrient stressor, suggesting that the global metabolic response to nutrient stresses was largely, but not exclusively, species-specific. Nutrient stress led to few transcriptional changes in the two dinoflagellates, consistent with other research. An orthologous group analysis examined functionally conserved (i.e., similarly changed) responses to nutrient stress and therefore focused on the diatom and haptophytes. Most conserved ortholog changes were specific to a single nutrient treatment, but a small number of orthologs were similarly changed under both N and P stress in 2 or more species. Many of these orthologs were related to photosynthesis and may represent generalized stress responses. A greater number of orthologs were conserved across more than one species under low P compared to low N. Screening the conserved orthologs for functions related to N and P metabolism revealed increased relative abundance of orthologs for nitrate, nitrite, ammonium, and amino acid transporters under N stress, and increased relative abundance of orthologs related to acquisition of inorganic and organic P substrates under P stress. Although the global transcriptional responses were dominated by species-specific changes, the analysis of conserved responses revealed functional similarities in resource acquisition pathways among different phytoplankton taxa. This overlap in nutrient stress responses observed among species may be useful for tracking the physiological ecology of phytoplankton field populations.

De novo assembly of the ringed seal (Pusa hispida) blubber transcriptome: A tool that enables identification of molecular health indicators associated with PCB exposure

The ringed seal, Pusa hispida, is a keystone species in the Arctic marine ecosystem, and is proving a useful marine mammal for linking polychlorinated biphenyl (PCB) exposure to toxic injury. We report here the first de novo assembled transcriptome for the ringed seal (342,863 transcripts, of which 53% were annotated), which we then applied to a population of ringed seals exposed to a local PCB source in Arctic Labrador, Canada. We found an indication of energy metabolism imbalance in local ringed seals (n=4), and identified five significant gene transcript targets: plasminogen receptor (Plg-R(KT)), solute carrier family 25 member 43 receptor (Slc25a43), ankyrin repeat domain-containing protein 26-like receptor (Ankrd26), HIS30 (not yet annotated) and HIS16 (not yet annotated) that may represent indicators of PCB exposure and effects in marine mammals. The abundance profiles of these five gene targets were validated in blubber samples collected from 43 ringed seals using a qPCR assay. The mRNA transcript levels for all five gene targets, (Plg-R(KT), r²=0.43), (Slc25a43, r²=0.51), (Ankrd26, r²=0.43), (HIS30, r²=0.39) and (HIS16, r²=0.31) correlated with increasing levels of blubber PCBs. Results from the present study contribute to our understanding of PCB associated effects in marine mammals, and provide new tools for future molecular and toxicology work in pinnipeds.

Growth on ATP Elicits a P-Stress Response in the Picoeukaryote Micromonas pusilla

The surface waters of oligotrophic oceans have chronically low phosphate (Pi) concentrations, which renders dissolved organic phosphorus (DOP) an important nutrient source. In the subtropical North Atlantic, cyanobacteria are often numerically dominant, but picoeukaryotes can dominate autotrophic biomass and productivity making them important contributors to the ocean carbon cycle. Despite their importance, little is known regarding the metabolic response of picoeukaryotes to changes in phosphorus (P) source and availability. To understand the molecular mechanisms that regulate P utilization in oligotrophic environments, we evaluated transcriptomes of the picoeukaryote Micromonas pusilla grown under Pi-replete and -deficient conditions, with an additional investigation of growth on DOP in replete conditions. Genes that function in sulfolipid substitution and Pi uptake increased in expression with Pi-deficiency, suggesting cells were reallocating cellular P and increasing P acquisition capabilities. Pi-deficient M. pusilla cells also increased alkaline phosphatase activity and reduced their cellular P content. Cells grown with DOP were able to maintain relatively high growth rates, however the transcriptomic response was more similar to the Pi-deficient response than that seen in cells grown under Pi-replete conditions. The results demonstrate that not all P sources are the same for growth; while M. pusilla, a model picoeukaryote, may grow well on DOP, the metabolic demand is greater than growth on Pi. These findings provide insight into the cellular strategies which may be used to support growth in a stratified future ocean predicted to favor picoeukaryotes.

De novo Transcriptome Assemblies of Rana (Lithobates) catesbeiana and Xenopus laevis Tadpole Livers for Comparative Genomics without Reference Genomes

In this work we studied the liver transcriptomes of two frog species, the American bullfrog (Rana (Lithobates) catesbeiana) and the African clawed frog (Xenopus laevis). We used high throughput RNA sequencing (RNA-seq) data to assemble and annotate these transcriptomes, and compared how their baseline expression profiles change when tadpoles of the two species are exposed to thyroid hormone. We generated more than 1.5 billion RNA-seq reads in total for the two species under two conditions as treatment/control pairs. We de novo assembled these reads using Trans-ABySS to reconstruct reference transcriptomes, obtaining over 350,000 and 130,000 putative transcripts for R. catesbeiana and X. laevis, respectively. Using available genomics resources for X. laevis, we annotated over 97% of our X. laevis transcriptome contigs, demonstrating the utility and efficacy of our methodology. Leveraging this validated analysis pipeline, we also annotated the assembled R. catesbeiana transcriptome. We used the expression profiles of the annotated genes of the two species to examine the similarities and differences between the tadpole liver transcriptomes. We also compared the gene ontology terms of expressed genes to measure how the animals react to a challenge by thyroid hormone. Our study reports three main conclusions. First, de novo assembly of RNA-seq data is a powerful method for annotating and establishing transcriptomes of non-model organisms. Second, the liver transcriptomes of the two frog species, R. catesbeiana and X. laevis, show many common features, and the distribution of their gene ontology profiles are statistically indistinguishable. Third, although they broadly respond the same way to the presence of thyroid hormone in their environment, their receptor/signal transduction pathways display marked differences.

Diversity of nitrogen assimilation pathways among microbial photosynthetic eukaryotes

In an effort to better understand the diversity of genes coding for nitrogen (N) uptake and assimilation pathways among microalgae, we analyzed the transcriptomes of five phylogenetically diverse single celled algae originally isolated from the same high arctic marine region. The five photosynthetic flagellates (a pelagophyte, dictyochophyte, chrysoph-yte, cryptophyte and haptophyte) were grown on standard media and media with only urea or nitrate as a nitrogen source; cells were harvested during late exponential growth. Based on homolog protein sequences, transcriptomes of each alga were interrogated to retrieve genes potentially associated with nitrogen uptake and utilization pathways. We further investigated the phylogeny of poorly characterized genes and gene families that were identified. While the phylogeny of the active urea transporter (DUR3) was taxonomically coherent, those for the urea transporter superfamily, putative nitrilases and amidases indicated complex evolutionary histories, and preliminary evidence for horizontal gene transfers. All five algae expressed genes for ammonium assimilation and all but the chrysophyte expressed genes involved in nitrate utilization and the urea cycle. Among the four algae with nitrate transporter transcripts, we detected lower expression levels in three of these (the dictyochophyte, pelagophyte, and cryptophyte) grown in the urea only medium compared with cultures from the nitrate only media. The diversity of N pathway genes in the five algae, and their ability to grow using urea as a nitrogen source, suggest that these flagellates are able to use a variety of organic nitrogen sources, which would be an advantage in an inorganic nitrogen - limited environment, such as the Arctic Ocean.

Metatranscriptome analyses indicate resource partitioning between diatoms in the field

Diverse communities of marine phytoplankton carry out half of global primary production. The vast diversity of the phytoplankton has long perplexed ecologists because these organisms coexist in an isotropic environment while competing for the same basic resources (e.g., inorganic nutrients). Differential niche partitioning of resources is one hypothesis to explain this "paradox of the plankton," but it is difficult to quantify and track variation in phytoplankton metabolism in situ. Here, we use quantitative metatranscriptome analyses to examine pathways of nitrogen (N) and phosphorus (P) metabolism in diatoms that cooccur regularly in an estuary on the east coast of the United States (Narragansett Bay). Expression of known N and P metabolic pathways varied between diatoms, indicating apparent differences in resource utilization capacity that may prevent direct competition. Nutrient amendment incubations skewed N/P ratios, elucidating nutrient-responsive patterns of expression and facilitating a quantitative comparison between diatoms. The resource-responsive (RR) gene sets deviated in composition from the metabolic profile of the organism, being enriched in genes associated with N and P metabolism. Expression of the RR gene set varied over time and differed significantly between diatoms, resulting in opposite transcriptional responses to the same environment. Apparent differences in metabolic capacity and the expression of that capacity in the environment suggest that diatom-specific resource partitioning was occurring in Narragansett Bay. This high-resolution approach highlights the molecular underpinnings of diatom resource utilization and how cooccurring diatoms adjust their cellular physiology to partition their niche space.