Transcriptomics responses in marine diatom Thalassiosira pseudonana exposed to the polycyclic aromatic hydrocarbon benzo[a]pyrene

Thalassiosira pseudonana (Cyclotella nana) (Hustedt) Hasle et Heimdal (Bacillariophyceae): A genetically tractable model organism for studying diatom biology, including biological silica formation

In 2004, Thalassiosira pseudonana was the first eukaryotic marine alga to have its genome sequenced. Since then, this species has quickly emerged as a valuable model species for investigating the molecular underpinnings of essentially all aspects of diatom life, particularly bio-morphogenesis of the cell wall. An important prerequisite for the model status of T. pseudonana is the ongoing development of increasingly precise tools to study the function of gene networks and their encoded proteins in vivo. Here, we briefly review the current toolbox for genetic manipulation, highlight specific examples of its application in studying diatom metabolism, and provide a peek into the role of diatoms in the emerging field of silica biotechnology.

Transcriptome analysis of changes in M. aeruginosa growth and microcystin production under low concentrations of ethinyl estradiol

Ethinyl estradiol (EE2) is a synthetic environmental estrogen with considerable estrogenic activity. It has been found to consequently pose a significant threat to the aquatic ecosystem. Harmful algal blooms are a major aquatic ecological issue. However, the relationship between EE2 and cyanobacterial bloom is mainly unknown. In this study, the physiological and molecular responses of Microcystis aeruginosa to EE2 exposure were investigated. A low level of EE2 (0.02 μg/L) significantly enhanced the growth of algal cells (P < 0.05), whereas higher concentrations of EE2 (0.2-200 μg/L) inhibited it. EE2 at doses ranging from 0.02 to 200 μg/L promoted the production of microcystins (MCs), with genes mcyABD playing a key role in the regulation of MC synthesis. The alterations of chlorophyll-a, carotenoid, and phycocyanin contents caused by EE2 showed the same trend as cell growth. At the molecular level, 200 μg/L EE2 significantly down-regulated genes in photosynthetic pigment synthesis, light harvesting, electron transfer, NADPH, and ATP generation. High concentrations of EE2 caused oxidative damage to algal cells on the 4th d. After 12d exposure, although there was no significant change in superoxide dismutase (SOD) content and no damage observed in membrane lipids, genes related to SOD and glutathione were changed. In addition, due to the down-regulation of pckA, PK, gltA, nrtA, pstS, etc., carbon fixation, glycolysis, TCA cycle, nitrogen and phosphorus metabolism were hindered by EE2 (200 μg/L). Gene fabG in fatty acid biosynthesis was significantly up-regulated, promoting energy storage in cells. These findings provide important clues to elucidate the effects and mechanisms of cyanobacterial blooms triggered by EE2 and help to effectively prevent and control cyanobacterial blooms.

Effects of polycyclic aromatic hydrocarbons on marine and freshwater microalgae - A review

The first synthetic review of the PAHs effects on microalgae in experimental studies and aquatic ecosystems is provided. Phytoplankton and phytobenthos from marine and freshwaters show a wide range of sensitivities to PAHs, and can accumulate, transfer and degrade PAHs. Different toxicological endpoints including growth, chlorophyll a, in vivo fluorescence yield, membrane integrity, lipid content, anti-oxidant responses and gene expression are reported for both freshwater and marine microalgal species exposed to PAHs in culture and in natural assemblages. Photosynthesis, the key process carried out by microalgae appears to be the most impacted by PAH exposure. The effect of PAHs is both dose- and species-dependent and influenced by environmental factors such as UV radiation, temperature, and salinity. Under natural conditions, PAHs are typically present in mixtures and the toxic effects induced by single PAHs are not necessarily extrapolated to mixtures. Natural microalgal communities appear more sensitive to PAH contamination than microalgae in monospecific culture. To further refine the ecological risks linked to PAH exposure, species-sensitivity distributions (SSD) were analyzed based on published EC₅₀s (half-maximal effective concentrations during exposure). HC₅ (harmful concentration for 5% of the species assessed) was derived from SSD to provide a toxicity ranking for each of nine PAHs. The most water-soluble PAHs naphthalene (HC₅ = 650 µg/L), acenaphthene (HC₅ = 274 µg/L), and fluorene (HC₅ = 76.8 µg/L) are the least toxic to microalgae, whereas benzo[a]pyrene (HC₅ = 0.834 µg/L) appeared as the more toxic. No relationship between EC₅₀ and cell biovolume was established, which does not support assumptions that larger microalgal cells are less sensitive to PAHs, and calls for further experimental evidence. The global PAHs HC₅ for marine species was on average higher than for freshwater species (26.3 and 1.09 µg/L, respectively), suggesting a greater tolerance of marine phytoplankton towards PAHs. Nevertheless, an important number of experimental exposure concentrations and reported toxicity thresholds are above known PAHs solubility in water. The precise and accurate assessment of PAHs toxicity to microalgae will continue to benefit from more rigorously designed experimental studies, including control of exposure duration and biometric data on test microalgae.

Contrasting sensitivity among oligotrophic marine microbial communities to priority PAHs

Oligotrophic areas represent a large proportion of the oceans, wherein microbial food webs largely determine carbon flux dynamics and biogeochemical cycles. However, little is known regarding the sensitivity of microbial planktonic communities to pollutants in such areas. Organic pollutants such as polycyclic aromatic hydrocarbons (PAH/s) are toxic oil derivatives that occur as complex mixtures and reach marine environments through different sources. Therefore, our study analyzed the PAH tolerance of natural photosynthetic and heterotrophic bacteria and eukaryotes from the oligotrophic Red Sea, which is uniquely susceptible to high oil contamination. Natural communities sampled from the surface layer were exposed to a concentration gradient of a mixture of 16 priority PAHs at in situ conditions for 48 h. The populations of the dominant picocyanobacteria Synechococcus sp., picophytoeukaryotes, and low nucleic acid (LNA) bacteria decreased upon exposure to PAHs in a strong dose-dependent manner. Chlorophyll-a, which was measured as an indicator of the total autotrophic community response, also decreased substantially. High nucleic acid (HNA) bacteria, however, exhibited lower growth inhibition (<50%). The lethal concentration (LC₁₀) thresholds to the 16-PAH mixture demonstrated contrasting sensitivities among the microbial communities studied increasing from picoeukaryotes (5.98 ± 2.08 μg L^-1) < chlorophyll-a (19.51 ± 8.11 μg L^-1) < LNA bacteria (23.63 ± 10.64 μg L^-1) < Synechococcus sp. (26.77 ± 13.34 μg L^-1) < HNA bacteria (97.13 ± 17.28 μg L^-1). The sensitivity of Red Sea Synechococcus and picophytoeukaryotes to the 16-PAH mixture was between 2 and 6.5 times higher compared to single PAH compounds tested previously. However, some populations of HNA bacteria and Synechococcus sp., were highly tolerant, suggesting an adaptation to chronic pollution. Concerningly, the LC₁₀ toxicity thresholds approached the ambient PAH concentrations in the Red Sea, suggesting that environmental oil pollution actively shapes the microbial community structures in the region.

Lowering pO2 Interacts with Photoperiod to Alter Physiological Performance of the Coastal Diatom Thalassiosira pseudonana

Exacerbating deoxygenation is extensively affecting marine organisms, with no exception for phytoplankton. To probe these effects, we comparably explored the growth, cell compositions, photosynthesis, and transcriptome of a diatom Thalassiosira pseudonana under a matrix of pO₂ levels and Light:Dark cycles at an optimal growth light. The growth rate (μ) of T. pseudonana under a 8:16 L:D cycle was enhanced by 34% by low pO₂ but reduced by 22% by hypoxia. Under a 16:8 L:D cycle, however, the μ decreased with decreasing pO₂ level. The cellular Chl a content decreased with decreasing pO₂ under a 8:16 L:D cycle, whereas the protein content decreased under a 16:8 L:D cycle. The prolonged photoperiod reduced the Chl a but enhanced the protein contents. The lowered pO₂ reduced the maximal PSII photochemical quantum yield (F_V/F_M), photosynthetic oxygen evolution rate (Pn), and respiration rate (Rd) under the 8:16 or 16:8 L:D cycles. Cellular malondialdehyde (MDA) content and superoxide dismutase (SOD) activity were higher under low pO₂ than ambient pO₂ or hypoxia. Moreover, the prolonged photoperiod reduced the F_V/F_M and Pn among all three pO₂ levels but enhanced the Rd, MDA, and SOD activity. Transcriptome data showed that most of 26 differentially expressed genes (DEGs) that mainly relate to photosynthesis, respiration, and metabolism were down-regulated by hypoxia, with varying expression degrees between the 8:16 and 16:8 L:D cycles. In addition, our results demonstrated that the positive or negative effect of lowering pO₂ upon the growth of diatoms depends on the pO₂ level and is mediated by the photoperiod.

Influence of nutrient status on the response of the diatom Phaeodactylum tricornutum to oil and dispersant

Phytoplankton play a central role in our ecosystems, they are responsible for nearly 50 percent of the global primary productivity and major drivers of macro-elemental cycles in the ocean. Phytoplankton are constantly subjected to stressors, some natural such as nutrient limitation and some manmade such as oil spills. With increasing oil exploration activities in coastal zones in the Gulf of Mexico and elsewhere, an oil spill during nutrient-limited conditions for phytoplankton growth is highly likely. We performed a multifactorial study exposing the diatom Phaeodactylum tricornutum (UTEX 646) to oil and/or dispersants under nitrogen and silica limitation as well as co-limitation of both nutrients. Our study found that treatments with nitrogen limitation (-N and–N-Si) showed overall lower growth and chlorophyll a, lower photosynthetic antennae size, lower maximum photosynthetic efficiency, lower protein in exopolymeric substance (EPS), but higher connectivity between photosystems compared to non-nitrogen limited treatments (-Si and +N+Si) in almost all the conditions with oil and/or dispersants. However, certain combinations of nutrient limitation and oil and/or dispersant differed from this trend indicating strong interactive effects. When analyzed for significant interactive effects, the–N treatment impact on cellular growth in oil and oil plus dispersant conditions; and oil and oil plus dispersant conditions on cellular growth in–N-Si and–N treatments were found to be significant. Overall, we demonstrate that nitrogen limitation can affect the oil resistant trait of P. tricornutum, and oil with and without dispersants can have interactive effects with nutrient limitation on this diatom.

Contrasting transcriptomic responses of a microbial eukaryotic community to oil and dispersant

Dispersants can aid dispersion and biodegradation of oil in seawater, but the wider ecotoxicological effects of oil and dispersant to the base of marine food webs is unclear. Here we apply a metatranscriptomic approach to identify molecular responses of a natural marine microbial eukaryotic community to oil and chemically dispersed oil. Oil exposure stimulated the upregulation of ketogenesis in the eukaryotic community, which may alleviate carbon- and energy-limitation and reduce oxidative stress. In contrast, a chemically dispersed oil treatment stimulated eukaryotic genes and pathways consistent with nitrogen and oxygen depletion. These results suggest that the addition of dispersant may elevate bacterial biodegradation of crude oil, indirectly increasing competition for nitrogen between prokaryotic and eukaryotic communities as oxygen consumption induces bacterial anaerobic respiration and denitrification. Eukaryotic microbial communities may mitigate some of the negative effects of oil exposure such as reduced photosynthesis and elevated oxidative stress, through ketosis, but the addition of dispersant to the oil fundamentally alters the environmental and ecological conditions and therefore the biochemical response of the eukaryotic community.

Molecular mechanism of oil induced growth inhibition in diatoms using Thalassiosira pseudonana as the model species

The 2010 Deepwater Horizon oil-spill exposed the microbes of Gulf of Mexico to unprecedented amount of oil. Conclusive evidence of the underlying molecular mechanism(s) on the negative effects of oil exposure on certain phytoplankton species such as Thalassiosira pseudonana is still lacking, curtailing our understanding of how oil spills alter community composition. We performed experiments on model diatom T. pseudonana to understand the mechanisms underpinning observed reduced growth and photosynthesis rates during oil exposure. Results show severe impairment to processes upstream of photosynthesis, such as light absorption, with proteins associated with the light harvesting complex damaged while the pigments were unaffected. Proteins associated with photosynthetic electron transport were also damaged, severely affecting photosynthetic apparatus and depriving cells of energy and carbon for growth. Negative growth effects were alleviated when an organic carbon source was provided. Further investigation through proteomics combined with pathway enrichment analysis confirmed the above findings, while highlighting other negatively affected processes such as those associated with ferroxidase complex, high-affinity iron-permease complex, and multiple transmembrane transport. We also show that oxidative stress is not the primary route of negative effects, rather secondary. Overall, this study provides a mechanistic understanding of the cellular damage that occurs during oil exposure to T. pseudonana.

Identification of a Metacaspase Gene in the Bloom-Forming Dinoflagellate Prorocentrum minimum and its Putative Function Involved in Programmed Cell Death

Programmed cell death (PCD) in dinoflagellates has been introduced as a new concept that facilitates the demise of harmful algal blooms. Metacaspases (MCAs) play a role in PCD, but their function in dinoflagellates is unclear. Here, we cloned a novel MCA gene (PmMCA) from the harmful dinoflagellate Prorocentrum minimum and examined its molecular characteristics and gene expression during cell death. The gene was encoded in the nuclear genome with two introns. The putative protein contained 288 amino acids and three conserved MCA signature motifs. Phylogenetic analysis showed that PmMCA may have the same ancestor as other dinoflagellates. PmMCA expression and cell apoptosis were significantly induced under copper exposure, considerably affecting cell growth. These results suggest that PmMCA could be involved in PCD triggered by copper stress.

Marine phytoplankton responses to oil and dispersant exposures: Knowledge gained since the Deepwater Horizon oil spill

The Deepwater Horizon oil spill of 2010 brought the ecology and health of the Gulf of Mexico to the forefront of the public's and scientific community's attention. Not only did we need a better understanding of how this oil spill impacted the Gulf of Mexico ecosystem, but we also needed to apply this knowledge to help assess impacts from perturbations in the region and guide future response actions. Phytoplankton represent the base of the food web in oceanic systems. As such, alterations of the phytoplankton community propagate to upper trophic levels. This review brings together new insights into the influence of oil and dispersant on phytoplankton. We bring together laboratory, mesocosm and field experiments, including insights into novel observations of harmful algal bloom (HAB) forming species and zooplankton as well as bacteria-phytoplankton interactions. We finish by addressing knowledge gaps and highlighting key topics for research in novel areas.

Influence of fuel oil on Platymonas helgolandica: An acute toxicity evaluation to amino acids

It is highly likely that the toxicity of water accommodated fractions (WAF) will influence marine microalgae, and consequently lead to potential risk for the marine ecological environment. However, it was often neglected whether WAF can influence the transformation of relative compounds in organisms. The metabolism of amino acids (AAs) can be used to track physiological changes in microalgae because amino acids are the basis of proteins and enzymes. In this study, using marine Chlorophyta Platymonas helgolandica as the test organism, the effects of different concentrations of WAF on AA compositions and stable carbon isotope ratios (δ¹³C) of individual AAs of Platymonas helgolandica were investigated. The results showed that the WAF of #180 fuel oil had an obvious suppressing effect on the growth and chlorophyll a content of microalgae. The growth inhibitory rate at 96 h was 80.66% at a WAF concentration of 0.50 mg L^-1 compared with the control. Furthermore, seven among the 16 AAs, including alanine, cysteine, proline, aspartic acid, lysine, histidine and tyrosine, had relatively high abundance. Under the glycolysis pathway, the cysteine abundance was higher than control, meaning that the biosynthesized pathway of alanine through cysteine as a precursor could be damaged. Phosphoenolpyruvate (PEP) was an important synthesis precursor of alanine (leucine) and aromatic AA family (Phenylalanine and tyrosine), and played an important role in δ¹³C_AAs fractionation under the WAF stress. Under the TCA pathway, to protect cell metabolism activities under WAF stress, the δ¹³C value of threonine and proline abundance in microalgae with the increase in WAF stress. Therefore, δ¹³C_AAs fractionation can be used as a novel method for toxicity evaluation of WAF on future.

The molecular response mechanisms of a diatom Thalassiosira pseudonana to the toxicity of BDE-47 based on whole transcriptome analysis

Polybrominated diphenyl ethers (PBDEs) are ubiquitously distributed persistent organic pollutants (POPs) in marine environments. Phytoplankton are the entrance of PBDEs entering to biotic environments from abiotic environments, while the responding mechanisms of phytoplankton to PBDEs have not been full established. Therefore, we chose the model diatom Thalassiosira pseudonana in this study, by integrating whole transcriptome analysis with physiological-biochemical data, to reveal the molecular responding mechanisms of T. pseudonana to the toxicity of BDE-47. Our results indicated the changes of genes expressions correlated to the physiological-biochemical changes, and there were multiple molecular mechanisms of T. pseudonana responding to the toxicity of BDE-47: Gene expressions evidence explained the suppression of light reaction and proved the occurrence of cellular oxidative stress; In the meanwhile, up-regulations of genes in pathways involving carbon metabolisms happened, including the Calvin cycle, glycolysis, TCA cycle, fatty acid synthesis, and triacylglycerol synthesis; Lastly, DNA damage was found and three outcome including DNA repair, cell cycle arrest and programmed cell death (PCD) happened, which could finally inhibit the cell division and population growth of T. pseudonana. This study presented the most complete molecular responding mechanisms of phytoplankton cells to PBDEs, and provided valuable information of various PBDEs-sensitive genes with multiple functions for further research involving organic pollutants and phytoplankton.

qPCR-based assessment of microfaunal indicators of oil for monitoring benthos around oil and gas platforms

Today's benthic offshore biological monitoring of oil & gas (O&G) activities relies on macrofauna taxa enumeration. For the future, analysis of DNA isolated directly from sediments holds great potential for multi-trophic biodiversity surveys and the monitoring of a larger spectrum of benthic taxa, including micro-fauna. Here, we evaluate more specifically the potential of microfauna-specific gene quantification in relation to both petroleum-related discharge compounds and other seafloor environmental properties. We carried out this evaluation using sediment samples collected at drilling Region III on the Norwegian continental shelf where DNA metabarcoding of eukaryotic diversity was already performed. Generally, the quantification of microfauna indicator taxa related well to the gradient of contamination on the seafloor. Contrary to eukaryotic Euplotida, metabarcoding data and qPCR numbers for indicative prokaryotic taxa showed the same relationship to offshore contaminants (both showed positive relationship). We found absolute numbers of SSU rRNA gene copies of (1) Dinophyceae, Bacillariophyceae and Alcanivorax were correlated with the level of petroleum-related compounds but not with other environmental variables, (2) bacteria closely related to Shewanella were correlated with the concentration of Ba, PAH, as well to percent of gravel, (3) Desulfobacteriales correlated with petroleum-related contaminants, but as well with percent of gravel and grain size. Findings from our study suggest that biomonitoring surveys of O&G activities on benthos could benefit from quantification of specific micro-fauna indicators that is simpler and faster than the methods currently used for impact assessment of benthos.

A Genome-Scale Metabolic Model of Thalassiosira pseudonana CCMP 1335 for a Systems-Level Understanding of Its Metabolism and Biotechnological Potential

Thalassiosira pseudonana is a transformable and biotechnologically promising model diatom with an ability to synthesise nutraceuticals such as fucoxanthin and store a significant amount of polyglucans and lipids including omega-3 fatty acids. While it was the first diatom to be sequenced, a systems-level analysis of its metabolism has not been done yet. This work presents first comprehensive, compartmentalized, and functional genome-scale metabolic model of the marine diatom Thalassiosira pseudonana CCMP 1335, which we have termed iThaps987. The model includes 987 genes, 2477 reactions, and 2456 metabolites. Comparison with the model of another diatom Phaeodactylum tricornutum revealed presence of 183 unique enzymes (belonging primarily to amino acid, carbohydrate, and lipid metabolism) in iThaps987. Model simulations showed a typical C3-type photosynthetic carbon fixation and suggested a preference of violaxanthin-diadinoxanthin pathway over violaxanthin-neoxanthin pathway for the production of fucoxanthin. Linear electron flow was found be active and cyclic electron flow was inactive under normal phototrophic conditions (unlike green algae and plants), validating the model predictions with previous reports. Investigation of the model for the potential of Thalassiosira pseudonana CCMP 1335 to produce other industrially useful compounds suggest iso-butanol as a foreign compound that can be synthesized by a single-gene addition. This work provides novel insights about the metabolism and potential of the organism and will be helpful to further investigate its metabolism and devise metabolic engineering strategies for the production of various compounds.

Effect of water accommodated fractions of fuel oil on fixed carbon and nitrogen by microalgae: Implication by stable isotope analysis

Effect of water accommodated fractions (WAF) of #180 fuel oil on fixed carbon and nitrogen in microalgae was studied by stable isotopes. Platymonas helgolandica, Heterosigma akashiwo and Nitzschia closterium were exposed to five WAF concentrations for 96 h. The δ¹³C value of microalgae was significantly lower than that of the control group, indicated that carbon was limited in the WAF concentrations. The δ¹³C value of microalgae appeared peak valley at 48 h in control group, corresponding to the enhanced capacity in carbon fixation during microalgae photosynthesis. The physiological acclimation capacity of microalgae was revealed by the occurrence time when the δ13C value was in peak valley, and thus the physiological acclimation capacity of microalgae decreased in the order of Nitzschia closterium > Heterosigma akashiwo > Platymonas helgolandica. Principal component analysis (PCA) were applied to the δ13C value in order to verify the "hormesis" phenomenon in microalgae. The δ13C value could discriminate between stimulatory effects at low doses and inhibitory effects at high doses. In addition, the present study also investigated the effect of the nitrogen on microalgae growth. Because microalgae could still absorb the NO₃-N and release of NO₂-N and NH₄-N in present study, the nitrogen cycle in microalgae was in the equilibrium status. The δ¹⁵N value in microalgae exhibited no obvious change with the increasing of WAF concentrations at the same time. However, due to the enrichment of nitrogen, the δ¹⁵N value first increased gradually with the time and finally was stable. Overall, the fractionation of carbon and nitrogen stable isotopes illustrated that the effect of carbon on the growth of microalgae was more prominent than nitrogen. Stable isotopes was used to investigate the influence of WAF on fixed carbon and nitrogen in microalgae growth, providing a fundamental theoretical guidance for risk assessment of marine ecological environment.

Trait-dependent variability of the response of marine phytoplankton to oil and dispersant exposure

The Deepwater Horizon oil spill released millions of barrels of crude oil into the Gulf of Mexico, and saw widespread use of the chemical dispersant Corexit. We assessed the role of traits, such as cell size, cell wall, motility, and mixotrophy on the growth and photosynthetic response of 15 phytoplankton taxa to oil and Corexit. We collected growth and photosynthetic data on five algal cultures. These responses could be separated into resistant (Tetraselmis astigmatica, Ochromonas sp., Heterocapsa pygmaea) and sensitive (Micromonas pusilla, Prorocentrum minimum). We combined this data with 10 species previously studied and found that cell size is most important in determining the biomass response to oil, whereas motility/mixotrophy is more important in the dispersed oil. Our analysis accounted for a third of the variance observed, so further work is needed to identify other factors that contribute to oil resistance.

The toxic mechanisms of BDE-47 to the marine diatom Thalassiosira pseudonana-a study based on multiple physiological processes

Polybrominated diphenyl ethers (PBDEs), a series of highly persistent organic pollutants (POPs), are ubiquitous in marine ecosystems. As key primary producers, microalgae are of great importance on evaluating the environmental outcome of PBDEs pollution. In this study, the toxic mechanisms of BDE-47 on the marine diatom Thalassiosira pseudonana were evaluated by measuring multiple physiological processes. Three concentrations of BDE-47 (25, 15 and 5 μg L^-1) were used along with two controls (blank: no BDE-47 or DMSO; negative control: only DMSO). Experiments lasted 144 h (6 days), in which the actual BDE-47 concentrations, cell densities, nutrient (nitrate and phosphate) uptake, pigment compositions, photosynthetic physiology, cell morphology and cellular contents (organic carbon and nitrogen) were measured at 12-48 h intervals. The toxic mechanisms of BDE-47 on T. pseudonana cells were evaluated by measuring multiple physiological processes including photosynthesis, nutrient uptake, cellular material synthesis and cell cycle progressions. The cell divisions of T. pseudonana were severely inhibited by the stress of BDE-47, but the photosynthetic parameters were much less declined and recovered earlier than the cell divisions in the same BDE-47 treatments. The unsuppressed uptake rates of nutrients, increased cell volume and cellular contents indicated the cellular material synthesis proceeded normally. Finally, we found that the cell cycle was arrested in G2/M phase under the stress of BDE-47, we thus concluded that the inhibition of cell divisions by BDE-47 was not due to the lack of energy or cellular materials, where the cell cycle arrest happened; this might be the most important toxicological outcome.

Growth dynamics and domoic acid production of Pseudo-nitzschia sp. in response to oil and dispersant exposure

The diatom genus Pseudo-nitzschia is a common component of phytoplankton communities in the Gulf of Mexico and is potentially toxic as some species produce the potent neurotoxin domoic acid. The impact of oil and chemical dispersants on Pseudo-nitzschia spp. and domoic acid production have not yet been studied; preliminary findings from a mesocosm experiment suggest this genus may be particularly resilient. A toxicological study was conducted using a colony of Pseudo-nitzschia sp. isolated from a station off the coast of Louisiana in the Gulf of Mexico. The cultures were exposed to a water accommodated fraction (WAF) of oil and a diluted chemically enhanced WAF (DCEWAF) which was a mix of oil and dispersant (20:1). Exposure to WAF induced a lag phase but did not inhibit growth rates once in exponential growth. Cultures grown in DCEWAF did not experience a lag phase but had significantly lower growth rates than the Control and WAF cultures. The cellular quota of domoic acid was higher in cultures treated with DCEWAF and WAF relative to their control values, and half of the domoic acid had leaked out of the cells into the surrounding seawater in the DCEWAF cultures while all the domoic acid remained inside the cells in WAF-treated cultures. These results suggest that the presence of oil could lead to toxic blooms, but that the application of dispersant could decrease bioaccumulation of domoic acid through the food web.

ABC Transporters in Prorocentrum lima and Their Expression Under Different Environmental Conditions Including Okadaic Acid Production

Prorocentrum lima is a typical benthic toxic dinoflagellate, which can produce phycotoxins such as okadaic acid (OA). In this study, we identified three ABC transporter genes (ABCB1, ABCC1 and ABCG2) and characterized their expression patterns, as well as OA production under different environmental conditions in P. lima. We found that the three ABC transporters all showed high identity with related ABC proteins from other species, and contained classical features of ABC transport proteins. Among them, ABCG2 was a half size transporter. The three ABC transporter genes displayed various expression profiles under different conditions. The high concentration of Cu²⁺ could up-regulate ABCB1, ABCC1 and ABCG2 transcripts in P. lima, suggesting the potential defensive role of ABC transporters against metal ions in surrounding waters. Cu²⁺, in some concentration, could induce OA production; meanwhile, tributyltin inhibited OA accumulation. The grazer Artemia salina could induce OA production, and P. lima displayed some toxicity to the grazer, indicating the possibility of OA as an anti-grazing chemical. Collectively, our results revealed intriguing data about OA production and the expression patterns of three ABC transporter genes. However, we could not find any significant correlation between OA production and expression pattern of the three ABC transporters in P. lima. Our results might provide new molecular insights on the defensive responses of P. lima to the surrounding environment.

Diversity and evolution of cytochromes P450 in stramenopiles

MAIN CONCLUSION

Comparative genomic analysis of cytochromes P450 revealed high diversification and dynamic changes in stramenopiles, associated with transcriptional responsiveness to various environmental stimuli. Comparative genomic and molecular evolution approaches were used to characterize cytochromes P450 (P450) diversity in stramenopiles. Phylogenetic analysis pointed to a high diversity of P450 in stramenopiles and identified three major clans. The CYP51 and CYP97 clans were present in brown algae, diatoms and Nannochloropsis gaditana, whereas the CYP5014 clan mainly includes oomycetes. Gene gain and loss patterns revealed that six CYP families-CYP51, CYP97, CYP5160, CYP5021, CYP5022, and CYP5165-predated the split of brown algae and diatoms. After they diverged, diatoms gained more CYP families, especially in the cold-adapted species Fragilariopsis cylindrus, in which eight new CYP families were found. Selection analysis revealed that the expanded CYP51 family in the brown alga Cladosiphon okamuranus exhibited a more relaxed selection constraint compared with those of other brown algae and diatoms. Our RNA-seq data further evidenced that most of P450s in Saccharina japonica are highly expressed in large sporophytes, which could potentially promote the large kelp formation in this developmental stage. A survey of Ectocarpus siliculosus and diatom transcriptomes showed that many P450s are responsive to stress, nutrient limitation or light quality, suggesting pivotal roles in detoxification or metabolic processes under adverse environmental conditions. The information provided in this study will be helpful in designing functional experiments and interpreting P450 roles in this particular lineage.

Response of natural phytoplankton communities exposed to crude oil and chemical dispersants during a mesocosm experiment

During the 2010 Deepwater Horizon oil spill, the chemical dispersant Corexit was applied over vast areas of the Gulf of Mexico. Marine phytoplankton play a key role in aggregate formation through the production of extracellular polymeric materials (EPS), an important step in the biological carbon pump. This study examined the impacts of oil and dispersants on the composition and physiology of natural marine phytoplankton communities from the Gulf of Mexico during a 72-hour mesocosm experiment and consequences to carbon export. The communities were treated using the water accommodated fraction (WAF) of oil, which was produced by adding Macondo surrogate oil to natural seawater and mixed for 24 h in the dark. A chemically enhanced WAF (CEWAF) was made in a similar manner, but using a mixture of oil and the dispersant Corexit in a 20:1 ratio as well as a diluted CEWAF (DCEWAF). Phytoplankton communities exposed to WAF showed no significant changes in PSII quantum yield (F_v/F_m) or electron transfer rates (ETR_max) compared to Control communities. In contrast, both F_v/F_m and ETR_max declined rapidly in communities treated with either CEWAF or DCEWAF. Analysis of other photophysiological parameters showed that photosystem II (PSII) antenna size and PSII connectivity factor were not altered by exposure to DCEWAF, suggesting that processes downstream of PSII were affected. The eukaryote community composition in each experimental tank was characterized at the end of the 72 h exposure time using 18S rRNA sequencing. Diatoms dominated the communities in both the control and WAF treatments (52 and 56% relative abundance respectively), while in CEWAF and DCEWAF treatments were dominated by heterotrophic Euglenozoa (51 and 84% respectively). Diatoms made up the largest relative contribution to the autotrophic eukaryote community in all treatments. EPS concentration was four times higher in CEWAF tanks compared to other treatments. Changes in particle size distributions (a proxy for aggregates) over time indicated that a higher degree of particle aggregation occurred in both the CEWAF and DCEWAF treatments than the WAF or Controls. Our results demonstrate that chemically dispersed oil has more negative impacts on photophysiology, phytoplankton community structure and aggregation dynamics than oil alone, with potential implications for export processes that affect the distribution and turnover of carbon and oil in the water column.

Characterization of transcriptional responses mediated by benzo[a]pyrene stress in a new marine fish model of goby, Mugilogobius chulae

Benzo[a]pyrene (BaP) is one of the most studied targets among polycyclic aromatic hydrocarbons (PAHs). Because of the complexity of the toxicity mechanism in BaP, little is known about the molecular mechanism at the level of transcription of BaP in marine fishes. The primary objective of this study was to investigate the molecular basis of the effects of BaP on marine fish, using Mugilogobius chulae (Smith 1932) as the model. A closed colony of M. chulae was used for the BaP toxicity test. Two fish liver samples per replicate from each group were excised and blended into one sample by pooling an equal amount of liver tissue. Total RNA of all samples was extracted separately. Equal quantities of total RNA from the three replicates of the two groups were pooled for sequencing. The sequencing cDNA libraries were sequenced using Illumina HiSeq 2000 system. Differentially expressed genes were detected with the DEGSeq R package. In total, 52,364,032 and 53,771,748 clean nucleotide reads were obtained in the control and BaP-exposed libraries, respectively, with N50 lengths of 1277 and 1288 bp, respectively. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed a significant enrichment of genes related to detoxification, transportation, and lipid metabolism. We also identified, for the first time, an association between endoplasmic reticulum dysfunction and lipid metabolism resulting from BaP exposure. Using quantitative real-time PCR, some effective molecular biomarkers for monitoring of BaP-polluted seawater were identified. The results demonstrate that BaP enhanced the expression of genes involved in detoxification in M. chulae and inhibited that of genes related to lipid metabolism, possibly by suppressing the expression of numerous ER-related genes involved in fat digestion and absorption.

Morphological, physiological and molecular responses of Nitzschia palea under cadmium stress

The impact of cadmium on the diatom Nitzschia palea (Kützing) W. Smith 1856 was studied by examining the relation between valve deformities and response through biological processes and genetic expression. Cultures of N. palea were exposed to two Cd treatments (C₁ = 2.4 ± 0.6 and C₂ = 42.6 ± 4.2 µg Cd/L) along with a control (C₀ = 0 µg Cd/L) for 28 days. Cadmium bioaccumulation, diatoms growth, photosynthetic efficiencies, valve deformities and genetic expression were investigated during the course of the experiment. Cadmium exposure had significant effects on bioaccumulation, growth, valve deformities and genetic expression. Maximal effects for all studied endpoints were recorded after 7 days of exposure for the C₂ treatment, which corresponded to the sampling time and condition with maximum cadmium bioaccumulation. Abnormal raphe formations (deviation from its lateral position) were significantly more abundant in the C₂ treatment compared to the control. Molecular responses were related to cadmium level based on the number of genes impacted, intensity of the response and the frequency of observations. The expression of genes involved in the regulation of mitochondrial metabolism, photosynthesis, oxidative stress and silica metabolism was affected by cadmium exposure.

De novo transcriptome assembly of the new marine fish model of goby, Mugilogobius chulae

The yellowstripe goby (Mugilogobius chulae) is an ideal experimental marine fish model in the field of marine environmental toxicology. To clarify the mechanisms of molecular toxicity of benzo[a]pyrene (BaP) in standard laboratory fish, we carried out a genome-wide analysis of transcriptional profiles in M. chulae by RNA sequencing. A total of 47,979 unigenes were assembled de novo, with N50 lengths of 1658 bp. These results provide an important resource for future studies on the effects of BaP on marine animals.

Lipid metabolism and pro-oxidant/antioxidant balance of Halamphora oceanica from the Gulf of Mexico exposed to water accommodated fraction of Maya crude oil

Diatoms play key roles in primary production and carbon fixation at a global scale and in some cases these species live on marine ecosystems impacted by crude oil (CO) spills. Halamphora oceanica, a new diatom species from the Southwest of the Gulf of Mexico was isolated and cultured in the laboratory and was exposed to water accommodated fraction (WAF) of different Maya CO loads at 0.01, 0.1, 1 and 10g/L by 96h. A battery of biomarkers involved in oxidative stress (O₂•, H₂O₂, TBARS, ROOH, RC=O, SOD, CAT, GPx), biotransformation and conjugation (total CYP450 activity and GST) moreover fatty acid (FA) metabolism (FA levels, fatty-acid synthase and acyl-CoA oxidase) were measured. Obtained results suggest that increases of PAHs in the medium (below to EC₅₀) acts as external forces able to turn-on regulatory mechanisms on H. oceanica involved in both, on the PAHs uptake and changing its aerobic metabolism to anaerobic metabolism. However, the growth of this microalgae species evaluated as chlorophyll "a" and pheophytin levels increased as the WAF concentration indicating that PAHs and other hydrosoluble hydrocarbons were used as carbon and energy sources by unidentified enzymes not evaluated in the current study. Our hypothesis was also corroborated by IBRv2. In the current study, we suppose the change from aerobic to anaerobic metabolism as a strategy for Halamphora oceanica survival exposed to petroleum hydrocarbons.

Structural and functional diversity of caspase homologues in non-metazoan organisms

Caspases, the proteases involved in initiation and execution of metazoan programmed cell death, are only present in animals, while their structural homologues can be found in all domains of life, spanning from simple prokaryotes (orthocaspases) to yeast and plants (metacaspases). All members of this wide protease family contain the p20 domain, which harbours the catalytic dyad formed by the two amino acid residues, histidine and cysteine. Despite the high structural similarity of the p20 domain, metacaspases and orthocaspases were found to exhibit different substrate specificities than caspases. While the former cleave their substrates after basic amino acid residues, the latter accommodate substrates with negative charge. This observation is crucial for the re-evaluation of non-metazoan caspase homologues being involved in processes of programmed cell death. In this review, we analyse the structural diversity of enzymes containing the p20 domain, with focus on the orthocaspases, and summarise recent advances in research of orthocaspases and metacaspases of cyanobacteria, algae and higher plants. Although caspase homologues were initially proposed to be involved in execution of cell death, accumulating evidence supports the role of metacaspases and orthocaspases as important contributors to cell homeostasis during normal physiological conditions or cell differentiation and ageing.

The Combination of RNA and Protein Profiling Reveals the Response to Nitrogen Depletion in Thalassiosira pseudonana

Nitrogen (N) is essential for the growth of algae, and its concentration varies greatly in the ocean, which has been regarded as a limitation for phytoplankton growth. Despite its great importance, most of the existing studies on the mechanisms underlying the effects of N on diatoms have focused on physiology, biochemistry and a few target genes and have rarely involved whole genomic analyses. Therefore, in this study, we integrated physiological data with RNA and protein profiling data to reveal the response strategy of Thalassiosira pseudonana under N-depleted conditions. Physiological measurements indicated that the cell growth capacity and chlorophyll content of the cells decreased, as did the expression of photosynthesis- and chlorophyll biosynthesis-related genes or proteins. The RNA-Seq profile results showed that T. pseudonana responded to N deprivation through increases in glycolysis, the TCA cycle and N metabolism as well as down-regulation in the Calvin cycle, gluconeogenesis, pentose phosphate, oxidative phosphorylation and lipid synthesis. These results provide a basic understanding for further research addressing how N affects phytoplankton in terms of genomics.

Marine diatoms change their gene expression profile when exposed to microscale turbulence under nutrient replete conditions

Diatoms are a fundamental microalgal phylum that thrives in turbulent environments. Despite several experimental and numerical studies, if and how diatoms may profit from turbulence is still an open question. One of the leading arguments is that turbulence favours nutrient uptake. Morphological features, such as the absence of flagella, the presence of a rigid exoskeleton and the micrometre size would support the possible passive but beneficial role of turbulence on diatoms. We demonstrate that in fact diatoms actively respond to turbulence in non-limiting nutrient conditions. TURBOGEN, a prototypic instrument to generate natural levels of microscale turbulence, was used to expose diatoms to the mechanical stimulus. Differential expression analyses, coupled with microscopy inspections, enabled us to study the morphological and transcriptional response of Chaetoceros decipiens to turbulence. Our target species responds to turbulence by activating energy storage pathways like fatty acid biosynthesis and by modifying its cell chain spectrum. Two other ecologically important species were examined and the occurrence of a morphological response was confirmed. These results challenge the view of phytoplankton as unsophisticated passive organisms.

Accumulation of petroleum hydrocarbons in intracellular lipid bodies of the freshwater diatom Synedra acus subsp. radians

The accumulation of hydrophobic compounds by phytoplankton plays a crucial role in the biogeochemical cycle of persistent organic pollutants (POPs) in aquatic environments. We studied the accumulation of polycyclic aromatic hydrocarbons (PAHs) in the freshwater diatom Synedra acus subsp. radians during its cultivation with crude oil hydrocarbons, using epifluorescent and laser confocal microscopy as well as gas chromatography-mass spectrometry (GC/MS) analysis. Our results revealed that in the presence of crude oil or an extract of a crude oil/n-hexane solution (light oil), S. acus subsp. radians accumulated PAHs in its lipid bodies. During cultivation in the presence of a crude oil/n-hexane solution, the cells selectively accumulated C12-C18 alkanes, with a preference for C15 and C16 homologues. The length of n-alkane hydrocarbon chains accumulated in cells was similar to the acyl chains of fatty acids of the diatom. We therefore suggest that the insertion of n-alkanes into the membrane lipid bilayer promotes the transmembrane transport of PAH in diatoms. Our results confirm the hypothesis that diatoms play a role in the elimination of hydrophobic hydrocarbons from aquatic systems.

Genetic and physiological responses of three freshwater diatoms to realistic diuron exposures

This study examined the effects of diuron on strains of three major freshwater diatom species, Eolimna minima, Nitzschia palea and Planothidium lanceolatum. These species are frequently recorded in the Morcille River, where diuron runs off during phytosanitary treatments of the vineyards around. Here, there were three diatom exposure groups for each species: 0, 1 and 10 μg/L diuron during a 14-day laboratory assessment. Diuron water concentration, cell number, photosynthetic activity and gene expression were assessed at 6 h and 2, 7 and 14 days after contamination. Diuron exposure altered photosynthetic activity in that the optimal quantum yield of photosystem II (PSII) decreased between 40 and 50% and, for P. lanceolatum at 10 μg/L, there was complete inhibition. Genetic responses indicated diuron effects on both photosystem II and mitochondrial metabolism in all three species at both diuron exposure levels. Thus, analysis of the expression of psaA, d1, cox1, nad5 and 12s could be an early biomarker to detect pesticide pollution. Overall, this study revealed differences in diuron sensitivity among the three species: E. minima and N. palea appeared to be more tolerant than P. lanceolatum. These results suggest that the development of molecular tools, and more precisely of biomarkers, will aid in early assessment of contamination and water quality.

Different transcriptional responses of heat shock protein 20 in the marine diatom Ditylum brightwellii exposed to metals and endocrine-disrupting chemicals

Diatoms are sensitive indicators of water quality, and hence used for environmental hazard assessments; however, their toxicogenomic studies have been insufficiently attempted. In the present study, we determined the cDNA sequence of heat shock protein 20 (Hsp20) gene from the diatom Ditylum brightwellii, and examined the transcriptional responses of the gene after exposing it to environmental stressors such as thermal shock, metals, and endocrine-disrupting chemicals (EDCs). The open reading frame (ORF) of DbHsp20 was 531 bp long, encoding 177 amino acid residues (19.49 kDa) with a conserved C-terminal and α-crystallin domain. The genomic region of DbHsp20 did not contain introns. Phylogeny of eukaryotic Hsp20s showed D. brightwellii was closely related to other diatoms. With regard to the gene expressional profile, real-time PCR results showed that the gene was significantly upregulated (P < 0.001) under thermal stress, with the highest change of 3.2-fold. Metals' (copper and nickel) treatments showed that it was induced after a certain point of treated concentration. On the contrary, EDCs did not display noticeable change on the expression of DbHsp20. These results suggest that the diatom Hsp20 basically responds to thermal stress, but may differentially respond to toxic substances such as metals and organic compounds such as EDCs.

Pathway and time-resolved benzo[a]pyrene toxicity on Hepa1c1c7 cells at toxic and subtoxic exposure

Benzo[a]pyrene (B[a]P) is an environmental contaminant mainly studied for its toxic/carcinogenic effects. For a comprehensive and pathway orientated mechanistic understanding of the effects directly triggered by a toxic (5 μM) or a subtoxic (50 nM) concentration of B[a]P or indirectly by its metabolites, we conducted time series experiments for up to 24 h to study the effects in murine hepatocytes. These cells rapidly take up and actively metabolize B[a]P, which was followed by quantitative analysis of the concentration of intracellular B[a]P and seven representative degradation products. Exposure with 5 μM B[a]P led to a maximal intracellular concentration of 1604 pmol/5 × 10(4) cells, leveling at 55 pmol/5 × 10(4) cells by the end of the time course. Changes in the global proteome (>1000 protein profiles) and metabolome (163 metabolites) were assessed in combination with B[a]P degradation. Abundance profiles of 236 (both concentrations), 190 (only 5 μM), and 150 (only 50 nM) proteins were found to be regulated in response to B[a]P in a time-dependent manner. At the endogenous metabolite level amino acids, acylcarnitines and glycerophospholipids were particularly affected by B[a]P. The comprehensive chemical, proteome and metabolomic data enabled the identification of effects on the pathway level in a time-resolved manner. So in addition to known alterations, also protein synthesis, lipid metabolism, and membrane dysfunction were identified as B[a]P specific effects.

Structural and biological trait responses of diatom assemblages to organic chemicals in outdoor flow-through mesocosms

The sensitivity of diatom taxonomy and trait-based endpoints to chemicals has been poorly used so far in Environmental Risk Assessment. In this study, diatom assemblages in outdoor flow-through mesocosms were exposed to thiram (35 and 170 μg/L), and a hydrocarbon emulsion (HE; 0.01, 0.4, 2 and 20 mg/L). The effects of exposure were assessed for 12 weeks, including 9 weeks post-treatment, using taxonomic structure and diversity, bioindication indices, biological traits, functional diversity indices, indicator classes and ecological guilds. For both chemicals, diversity increased after the treatment period, and responses of ecological traits were roughly identical with an abundance increase of motile taxa tolerant to organic pollution and decrease of low profile taxa. Bioindication indices were not affected. Traits provided a complementary approach to biomass measurements and taxonomic descriptors, leading to a more comprehensive overview of ecological changes due to organic chemicals, including short- and long-term effects on biofilm structure and functioning.

Combined effects of pharmaceuticals, personal care products, biocides and organic contaminants on the growth of Skeletonema pseudocostatum

Organisms in the environment are exposed to a number of pollutants from different compound groups. In addition to the classic pollutants like the polychlorinated biphenyls, polyaromatic hydrocarbons (PAHs), alkylphenols, biocides, etc. other compound groups of concern are constantly emerging. Pharmaceuticals and personal care products (PPCPs) can be expected to co-occur with other organic contaminants like biocides, PAHs and alkylphenols in areas affected by wastewater, industrial effluents and intensive recreational activity. In this study, representatives from these four different compound groups were tested individually and in mixtures in a growth inhibition assay with the marine algae Skeletonema pseudocostatum (formerly Skeletonema costatum) to determine whether the combined effects could be predicted by models for additive effects; the concentration addition (CA) and independent action (IA) prediction model. The eleven tested compounds reduced the growth of S. pseudocostatum in the microplate test in a concentration-dependent manner. The order of toxicity of these chemicals were irgarol>fluoxetine>diuron>benzo(a)pyrene>thioguanine>triclosan>propranolol>benzophenone 3>cetrimonium bromide>4-tert-octylphenol>endosulfan. Several binary mixtures and a mixture of eight compounds from the four different compound groups were tested. All tested mixtures were additive as model deviation ratios, the deviation between experimental and predicted effect concentrations, were within a factor of 2 from one or both prediction models (e.g. CA and IA). Interestingly, a concentration dependent shift from IA to CA, potentially due to activation of similar toxicity pathways at higher concentrations, was observed for the mixture of eight compounds. The combined effects of the multi-compound mixture were clearly additive and it should therefore be expected that PPCPs, biocides, PAHs and alkylphenols will collectively contribute to the risk in areas contaminated by such complex mixtures.

Genomics in marine monitoring: new opportunities for assessing marine health status

This viewpoint paper explores the potential of genomics technology to provide accurate, rapid, and cost efficient observations of the marine environment. The use of such approaches in next generation marine monitoring programs will help achieve the goals of marine legislation implemented world-wide. Genomic methods can yield faster results from monitoring, easier and more reliable taxonomic identification, as well as quicker and better assessment of the environmental status of marine waters. A summary of genomic methods that are ready or show high potential for integration into existing monitoring programs is provided (e.g. qPCR, SNP based methods, DNA barcoding, microarrays, metagenetics, metagenomics, transcriptomics). These approaches are mapped to existing indicators and descriptors and a series of case studies is presented to assess the cost and added value of these molecular techniques in comparison with traditional monitoring systems. Finally, guidelines and recommendations are suggested for how such methods can enter marine monitoring programs in a standardized manner.

Transcriptome response to alkane biofuels in Saccharomyces cerevisiae: identification of efflux pumps involved in alkane tolerance

BACKGROUND

Hydrocarbon alkanes have been recently considered as important next-generation biofuels because microbial production of alkane biofuels was demonstrated. However, the toxicity of alkanes to microbial hosts can possibly be a bottleneck for high productivity of alkane biofuels. To tackle this toxicity issue, it is essential to understand molecular mechanisms of interactions between alkanes and microbial hosts, and to harness these mechanisms to develop microbial host strains with improved tolerance against alkanes. In this study, we aimed to improve the tolerance of Saccharomyces cerevisiae, a model eukaryotic host of industrial significance, to alkane biofuels by exploiting cellular mechanisms underlying alkane response.

RESULTS

To this end, we first confirmed that nonane (C9), decane (C10), and undecane (C11) were significantly toxic and accumulated in S. cerevisiae. Transcriptome analyses suggested that C9 and C10 induced a range of cellular mechanisms such as efflux pumps, membrane modification, radical detoxification, and energy supply. Since efflux pumps could possibly aid in alkane secretion, thereby reducing the cytotoxicity, we formed the hypothesis that those induced efflux pumps could contribute to alkane export and tolerance. In support of this hypothesis, we demonstrated the roles of the efflux pumps Snq2p and Pdr5p in reducing intracellular levels of C10 and C11, as well as enhancing tolerance levels against C10 and C11. This result provided the evidence that Snq2p and Pdr5p were associated with alkane export and tolerance in S. cerevisiae.

CONCLUSIONS

Here, we investigated the cellular mechanisms of S. cerevisiae response to alkane biofuels at a systems level through transcriptome analyses. Based on these mechanisms, we identified efflux pumps involved in alkane export and tolerance in S. cerevisiae. We believe that the results here provide valuable insights into designing microbial engineering strategies to improve cellular tolerance for highly efficient alkane biofuel production.

Different transcriptional responses of heat shock protein 70/90 in the marine diatom Ditylum brightwellii exposed to metal compounds and endocrine-disrupting chemicals

Environmental hazard assessments using diatoms have been well documented; however, their molecular toxicology has not been sufficiently studied. In this study, we characterized heat shock protein (HSP) 70/90 of the diatom Ditylum brightwellii (Db) and evaluated their transcriptional profiles in response to various environmental stresses (e.g., thermal shocks and metal and non-metal pollutants). Putative DbHSP70 (658aa, 71.7 kDa) and DbHSP90 (707aa, 80.2 kDa) proteins had conserved HSP family motifs but different C-terminus motifs, that is, "EEVD" in DbHSP70 and "MEEVD" in DbHSP90. Phylogenetic analyses of both proteins showed that D. brightwellii was well clustered with other diatoms. Real-time PCR analysis showed that thermal stress considerably upregulated DbHSP70 and DbHSP90. As for chemical pollutants, DbHSP70 greatly responded to CuSO4 and NiSO4 exposure, but not CuCl2 or NiCl2. However, DbHSP90 was significantly upregulated by all the metal compounds tested (CuSO4, NiSO4, CuCl2, and NiCl2). Strikingly, the expression of both genes was not induced by the organic pollutants tested, such as endocrine-disrupting chemicals. These data suggest that DbHSP70 and DbHSP90 are differentially involved in the defense response against various environmental stressors. Moreover, metal toxicity may be specifically affected by the conjugated anion in the metal compounds (e.g., SO4(2-) and Cl(-)).

Thiobencarb herbicide reduces growth, photosynthetic activity, and amount of Rieske iron-sulfur protein in the diatom Thalassiosira pseudonana

We investigated the effects of the herbicide thiobencarb on the growth, photosynthetic activity, and expression profile of photosynthesis-related proteins in the marine diatom Thalassiosira pseudonana. Growth rate was suppressed by 50% at a thiobencarb concentration of 1.26 mg/L. Growth and photosystem II activity (Fv /Fm ratio) were drastically decreased at 5 mg/L, at which the expression levels of 13 proteins increased significantly and those of 11 proteins decreased significantly. Among these proteins, the level of the Rieske iron-sulfur protein was decreased to less than half of the control level. This protein is an essential component of the cytochrome b6 f complex in the photosynthetic electron transport chain. Although the mechanism by which thiobencarb decreased the Rieske iron-sulfur protein level is not clear, these results suggest that growth was inhibited by interruption of the photosynthetic electron transport chain by thiobencarb.

The central carbon and energy metabolism of marine diatoms

Diatoms are heterokont algae derived from a secondary symbiotic event in which a eukaryotic host cell acquired an eukaryotic red alga as plastid. The multiple endosymbiosis and horizontal gene transfer processes provide diatoms unusual opportunities for gene mixing to establish distinctive biosynthetic pathways and metabolic control structures. Diatoms are also known to have significant impact on global ecosystems as one of the most dominant phytoplankton species in the contemporary ocean. As such their metabolism and growth regulating factors have been of particular interest for many years. The publication of the genomic sequences of two independent species of diatoms and the advent of an enhanced experimental toolbox for molecular biological investigations have afforded far greater opportunities than were previously apparent for these species and re-invigorated studies regarding the central carbon metabolism of diatoms. In this review we discuss distinctive features of the central carbon metabolism of diatoms and its response to forthcoming environmental changes and recent advances facilitating the possibility of industrial use of diatoms for oil production. Although the operation and importance of several key pathways of diatom metabolism have already been demonstrated and determined, we will also highlight other potentially important pathways wherein this has yet to be achieved.

Genome-wide diel growth state transitions in the diatom Thalassiosira pseudonana

Marine diatoms are important primary producers that thrive in diverse and dynamic environments. They do so, in theory, by sensing changing conditions and adapting their physiology accordingly. Using the model species Thalassiosira pseudonana, we conducted a detailed physiological and transcriptomic survey to measure the recurrent transcriptional changes that characterize typical diatom growth in batch culture. Roughly 40% of the transcriptome varied significantly and recurrently, reflecting large, reproducible cell-state transitions between four principal states: (i) "dawn," following 12 h of darkness; (ii) "dusk," following 12 h of light; (iii) exponential growth and nutrient repletion; and (iv) stationary phase and nutrient depletion. Increases in expression of thousands of genes at the end of the reoccurring dark periods (dawn), including those involved in photosynthesis (e.g., ribulose-1,5-bisphosphate carboxylase oxygenase genes rbcS and rbcL), imply large-scale anticipatory circadian mechanisms at the level of gene regulation. Repeated shifts in the transcript levels of hundreds of genes encoding sensory, signaling, and regulatory functions accompanied the four cell-state transitions, providing a preliminary map of the highly coordinated gene regulatory program under varying conditions. Several putative light sensing and signaling proteins were associated with recurrent diel transitions, suggesting that these genes may be involved in light-sensitive and circadian regulation of cell state. These results begin to explain, in comprehensive detail, how the diatom gene regulatory program operates under varying environmental conditions. Detailed knowledge of this dynamic molecular process will be invaluable for new hypothesis generation and the interpretation of genetic, environmental, and metatranscriptomic data from field studies.

Effects of silver nanoparticles in diatom Thalassiosira pseudonana and cyanobacterium Synechococcus sp

The aim of the present study was to investigate the effect of silver nanoparticles (AgNP) of different sizes toward two primary producer aquatic species. Thalassiosira pseudonana and Synechococcus sp. have been selected as representative models for the lower trophic organisms in marine and freshwater habitats, respectively. Time-dependent cellular growth was measured upon exposure to both AgNP and silver nitrate (AgNO(3)). In addition, AgNP behavior in freshwater and marine waters has been followed by CPS disc centrifuge, in the time frame of AgNP exposure studies, and the kinetic release of silver from AgNP of different sizes was measured by dialysis and inductively coupled plasma mass spectrometry (ICP-MS). The combination and interpretation of all these data suggest that a shared effect of AgNP and released silver was responsible for the toxicity in both organisms. Furthermore, the toxic effects induced by AgNP exposure in the present study seem to result from a mixture of parameters including aggregated state, size of the AgNP, stability of the preparation, and speciation of the released silver.