Diatom Cultures Research Articles

Chemotaxis of Marinobacter adhaerens and Its Impact on Attachment to the Diatom Thalassiosira weissflogii

Alga-bacterium interactions are crucial for aggregate formation and carbon cycling in aquatic systems. To understand the initiation of these interactions, we investigated bacterial chemotaxis within a bilateral model system. Marinobacter adhaerens HP15 has been demonstrated to attach to the diatom Thalassiosira weissflogii and induce transparent exopolymeric particle and aggregate formation. M. adhaerens possesses one polar flagellum and is highly motile. Bacterial cells were attracted to diatom cells, as demonstrated by addition of diatom cell homogenate or diatom culture supernatant to soft agar, suggesting that chemotaxis might be important for the interaction of M. adhaerens with diatoms. Three distinct chemotaxis-associated gene clusters were identified in the genome sequence of M. adhaerens, with the clusters showing significant sequence similarities to those of Pseudomonas aeruginosa PAO1. Mutations in the genes cheA, cheB, chpA, and chpB, which encode histidine kinases and methylesterases and which are putatively involved in either flagellum-associated chemotaxis or pilus-mediated twitching motility, were generated and mutants with the mutations were phenotypically analyzed. ΔcheA and ΔcheB mutants were found to be swimming deficient, and all four mutants were impaired in biofilm formation on abiotic surfaces. Comparison of the HP15 wild type and its chemotaxis mutants in cocultures with the diatom revealed that the fraction of bacteria attaching to the diatom decreased significantly for mutants in comparison to that for the wild type. Our results highlight the importance of M. adhaerens chemotaxis in initiation of its interaction with the diatom. In-depth knowledge of these basic processes in interspecies interactions is pivotal to obtain a systematic understanding of organic matter flux and nutrient cycling in marine ecosystems.

Screening for competition effects and allelochemicals in benthic marine diatoms and cyanobacteria isolated from an intertidal flat (southern North Sea)

Scholz B. and Liebezeit G. 2012. Screening for competition effects and allelochemicals in benthic marine diatoms and cyanobacteria isolated from an intertidal flat (southern North Sea). Phycologia 51: 432–450. DOI: 10.2216/11-80.1Marine intertidal flats are colonized by diatom-dominated biofilms, whereas coccoid and filamentous cyanobacteria usually occur only at some stages during the growth season. Increasingly, cyanobacteria were most abundant during warmer seasons, outcompeting other taxa and we assumed direct competition between diatoms and cyanobacteria. Therefore, the most abundant species (25 diatoms and 10 cyanobacteria) were isolated from an intertidal flat in the Lower Saxonian Wadden Sea (southern North Sea) and the isolates were screened for allelochemical production (e.g. alkaloids, flavonoids) and allelopathic activities (e.g. algicidal, antimicrobial). Screenings were performed in single-species and mixed cultures of two, three and six species. Only polyunsaturated fatty acids, terpenes and sterols were found in single-species cultures, but aldehydes, flavonoids, alkaloids and phenols were detected in biomass extracts from mixed cultures. Chroococcus dimidiatus and Anabaena torulosa (Cyanophyceae) dominated other species in mixed cultures of cyanobacteria and diatoms; alkaloids were present in these mixed cultures. Cyanobacteria outgrew diatoms in cultures with two or three species, whereas the diatom Navicula phyllepta (Bacillariophyceae) outcompeted other diatoms and accumulated aldehydes. Six species (three diatoms and three cyanobacteria) were combined in the final test, which was conducted under different nitrogen regimes (800 µM and 250 µM). Navicula phyllepta outgrew the cyanobacteria and other diatoms under low-nitrogen conditions. Although on the basis of the current screening it was impossible to draw conclusions about the effective organisms in the mixed-species treatments, we highlighted both various bioactivities and potential bioactive chemicals in single-species and mixed cultures for a variety of benthic intertidal diatom and cyanobacterial strains.

Investigation of the algicidal exudate produced by Shewanella sp. IRI-160 and its effect on dinoflagellates

The bacterium, Shewanella sp. IRI-160, was previously shown to have negative effects on the growth of dinoflagellates, while having no negative effects on other classes of phytoplankton tested (Hare et al., 2005). In this study, we investigated the mode of algicidal activity for Shewanella sp. IRI-160 and found that the bacterium secretes a bioactive compound. The optimum temperature for production of the algicidal compound by this bacterium was at 30°C. Bacteria-free filtrate of medium containing the algicide (designated IRI-160AA) was stable at temperatures ranging from −80°C to 121°C, and could be stored at room temperature for at least three weeks with no loss in activity. Algicidal activity was eluted in the aqueous portion after C18 extraction, suggesting that the active compound is likely polar and water-soluble. The activity of IRI-160AA was examined on a broad range of dinoflagellates (Karlodinium veneficum, Karenia brevis, Gyrodinium instriatum, Cochlodinium polykrikoides, Heterocapsa triquetra, Prorocentrum minimum, Alexandrium tamarense and Oxyrrhis marina) and three species from other classes of algae as controls (Dunaliella tertiolecta, Rhodomonas sp. and Thalassiosira pseudonana). Algicidal activity was observed for each dinoflagellate and little to no negative effect was observed on chlorophyte and cryptophyte cultures, while a slight (non-significant) stimulatory effect was observed on the diatom culture exposed to the algicide. Finally, the effect of the algicide at different growth stages was investigated for K. veneficum and G. instriatum. IRI-160AA exhibited a significantly greater effect during logarithmic growth compared to stationary phase, suggesting a potential application of the algicide for prevention and control of harmful dinoflagellate blooms in the future.

Biosilica structures obtained from Nitzschia, Ditylum, Skeletonema, and Coscinodiscus diatom by a filtration-aided acid cleaning method

A filtration-aided acid cleaning method was used to collect biosilica structures from a diatom culture medium, natural seawater, or water bloom. Cell extraction, acid cleaning, and acid removal were all performed on a polytetrafluoroethylene (PTFE) filter cloth, significantly improving the treatment capacity and efficiency of the traditional acid wash method. Five typical diatoms were cultivated in the laboratory for acid cleaning. Different growth speeds were introduced, and different process parameters for acid cleaning were utilized. After the acid cleaning, biosilica structures were collected from the frustules of diatoms using different methods. Girdle bands and valves of Coscinodiscus sp. were separated by floating of the valves. Central spines of Ditylum brightwellii and valves of Skeletonema costatum were separately collected by settling or filtration. Rod-like frustules, such as those of Bacillaris paradoxa, are not suitable for large quantities of acid wash. The silica structures were observed and tested using an AFM-calibrated glass needle to determine their elasticity. Elasticity tests showed that ringent girdle bands are more flexible than complete ones (Coscinodiscus sp.) and that both long-chain clusters of Nitzschia palea and central spines of D. brightwellii have certain elasticities. The required pressure for deforming or breaking the biosilica structures of diatoms was also determined.

Photosynthetic and Biochemical Effects of Cold Storage on Marine Benthic Diatoms of the Mexican Pacific Coast

We determined the effects of 16 wk of storage at low temperature (4 C) in darkness on the viability, growth, photosynthetic parameters, and biochemical composition of four diatom cultures. Significant differences in cell density and proximal composition were observed for all diatoms throughout storage. Cell density increased with time of storage for all diatoms. Protein content increased for Navicula incerta, Nitzschia laevis, and Navicula sp., whereas lipid content increased during storage in only N. incerta. When the stored diatoms were used as inocula in fresh medium, they increased their viability, generating a lag phase for Nitzschia thermalis var. minor, N. incerta, and Navicula sp. cultures. There were noted species‐specific modifications in proximal composition, ash‐free dry weight, and photosynthetic parameters in response to storage. We conclude that N. thermalis, N. incerta, N. laevis, and Navicula sp. can be stored at 4 C for 16 wk and are viable in new cultures.

Immunomodulation in eastern oysters, Crassostrea virginica, exposed to a PAH-contaminated, microphytobenthic diatom

The trophic transfer of sediment-associated pollutants is a growing concern in shellfish harvesting areas. Previous studies have examined the role of phytoplankton in the transport of organic contaminants to bivalve species, but little information on microphytobenthic communities and their role as contaminant vectors exists. Polycyclic aromatic hydrocarbons (PAHs) are organic compounds formed during natural and industrial processes; they are termed “persistent organic pollutants” because they are only slowly degraded by natural processes. This study examined the transfer of PAH compounds (naphthalene, pyrene, and benzo(a)pyrene) by a microphytobenthic diatom to the eastern oyster, a commercially important shellfish species, to determine if dietary accumulation is a route of contaminant exposure capable of inducing physiological responses. PAH compounds were adsorbed to a diatom culture (Nitzschia brevirostris) in a range of concentrations (5, 125, 625, and 1000μgL−1), and eastern oysters were exposed experimentally to the contaminated diatom cultures to assess possible effects upon oyster hemocytes and selected immune-defense functions. A preliminary experiment was designed to identify individual effects of several PAH compounds (naphthalene, pyrene, and benzo(a)pyrene) on hemocyte viability and phagocytic activity. Results from this experiment revealed that the most-toxic compound, benzo(a)pyrene, at the highest concentration, stimulated an increase in agranular hemocyte counts. A follow-up study examined the effects of benzo(a)pyrene on hemocyte viability, adhesion, phagocytosis, and reactive oxygen species (ROS). These studies showed the ability of this benthic diatom to transport PAHs to the eastern oyster and to cause immunomodulation. Hemocyte responses to dietary PAH exposure included an increase in circulating hemocytes and increased production of reactive oxygen species by these cells.

Importance of bacterivory and preferential selection toward diatoms in larvae of Crepidula fornicata (L.) assessed by a dual stable isotope (13C, 15N) labeling approach

In Europe, the gastropod Crepidula fornicata is an invasive species characterized by a long reproductive period (from February to November). Thus, its larvae are exposed to variations in available food sources (in terms of quantity and quality). We aimed to investigate if bacteria could contribute to larval food both in presence or absence of phytoplankton, and to compare these results to seasonal variations of bacteria and phytoplankton abundances at a coastal site in the English Channel. First, ingestion of fluorescent beads of 0.5 to 2μm diameter, showed that larvae were able to ingest particles of typical bacterial size. Then we used a dual stable isotope labeling approach which consisted in labeling a bacterial pelagic community with 15N and a diatom (Chaetoceros gracilis) culture with 13C, and supplying larvae with 15N-labeled bacteria, 13C-labeled diatoms, and both labeled sources. This technique has, to our knowledge, never been applied to invertebrate larvae. After 24h of experiment, larvae were significantly enriched in all treatments: +21.5‰ (∆δ13C) when supplied with diatoms, +1364‰ (∆δ15N) when supplied with bacteria, and +24‰ (∆δ13C) and +135‰ (∆δ15N) when supplied with the two mixed sources. These results indicated that bacteria can contribute to the larval nutrition in C. fornicata, even in the presence of phytoplankton. Our results however suggested that larvae of C. fornicata preferentially used diatoms and showed that the supply of free bacteria did not alter the uptake of diatoms. Considering the seasonal variations of bacteria and phytoplankton abundances at the study site, these results suggested that bacteria may constitute a complementary resource for the larvae of C. fornicata when phytoplankton is abundant and may become a substitute resource when phytoplankton is less available. This approach offers promising perspectives to trace food sources and assess nitrogen and carbon fluxes between planktotrophic larvae and their preys.

CULTURE CONDITIONS INFLUENCE THE GROWTH DYNAMICS AND THE PRODUCTION OF COCCONEIS SCUTELLUM (BACILLARIOPHYTA)(1).

The optimal conditions for the growth of two conspecific benthic diatoms were defined through factorial experimentation. We investigated the roles of light spectrum, nutrient availability, and culture conditions on the laboratory production of Cocconeis scutellum scutellum Ehrenb. and C. scutellum parva Grunow. Diatoms were cultivated in petri dishes, and inverted optical microscopy was used to periodically record their abundance. Growth curves were constructed from these data for each culture condition. In addition, at the end of the experiment we performed weight measurements to determine the total production for each of the considered conditions. We found that cultivation in nonsealed (NS) petri dishes (permitting gas exchange) represented the most productive technique. Cell density and biomass varied among light spectra, although this effect was inconsistent. For example, the Sylvania Gro-Lux lamp (GL) produced the lowest cell density but highest biomass, suggesting that it may promote the production of larger cells. Surprisingly, of the culture media tested, f/2 (a media commonly used for the culture of diatoms) was the least productive. Diatom density and biomass were variably dependent on the combination of experimental culture conditions and strain used. These physical and chemical factors act mainly on given features of the diatom growth curve. These results permitted us to devise adequate culture protocols, to produce a biotechnologically important substance: a proapoptotic compound that specifically destroys the androgenic gland of a shrimp and could find novel applications in human medicine.

A procedure for establishing an axenic culture of the diatom Synedra acus subsp. radians (Kütz.) Skabibitsch. from Lake Baikal

Production of axenic cultures of diatoms is a highly relevant task, as these widespread organisms are objects of research in different fields of biology, from ecology to whole‐genome studies, and promising as producers of various organic molecules, including biologically active substances. However, culturing of diatoms isolated from natural communities is accompanied by the development of associated microorganisms. We propose a procedure for establishing an axenic culture of the freshwater diatom Synedra asus subsp. radians (Kütz.) Skabitsch. from Lake Baikal. Such a culture has been produced and maintained by subculturing in our laboratory. The procedure involves filtration (to remove free bacteria), detergent treatment (to remove microorganisms associated with diatom frustules), selection of effective antibiotics and their concentrations nontoxic for diatoms (by the disk diffusion method), cell treatment with the selected antibiotic (ciprofloxacin), repeated filtration, and monoclonal culturing of diatom cells. Axenity of the culture was verified microscopically (after DAPI staining) and by molecular biological methods.

Elstera litoralis gen. nov., sp. nov., isolated from stone biofilms of Lake Constance, Germany

An alphaproteobacterium, strain Dia-1(T), was isolated from algae-dominated biofilms on stones from the littoral zone of Lake Constance, Germany. This bacterium was isolated after initial enrichment in spent medium obtained after growth of a diatom culture. Numerous sugars and some organic acids and alcohols served as growth substrates. The bacterium grew slowly, was strictly aerobic but microaerophilic, and did not grow in cultures shaken under air. 16S rRNA gene sequence analysis indicated that strain Dia-1(T) was distantly related to representatives of the genera Azospirillum (90-91% sequence similarity), Skermanella (88-89%), Rhodocista (87-88%) and Dongia (88-89% sequence similarity). Based on this sequence comparison, on phenotypic characterization including substrate utilization patterns, and comparison of cellular fatty acids, quinones, polar lipids and polyamines, this isolate was found to be substantially different from the genera mentioned above. On the basis of these results, a novel genus and species is proposed for this strain. The name Elstera litoralis gen. nov., sp. nov. is suggested, with strain Dia-1(T) ( = DSM 19532(T) = LMG 24234(T)) as the type strain of the type species.

Stemming Epigenetics in Marine Stramenopiles

Epigenetics include DNA methylation, the modification of histone tails that affect chromatin states, and small RNAs that are involved in the setting and maintenance of chromatin modifications. Marine stramenopiles (MAS), which are a diverse assemblage of algae that acquired photosynthesis from secondary endosymbiosis, include single-celled organisms such as diatoms as well as multicellular forms such as brown algae. The recent publication of two diatom genomes that diverged ~90 million years ago (mya), as well as the one of a brown algae that diverged from diatoms ~250 Mya, provide a great system of related, yet diverged set of organisms to compare epigenetic marks and their relationships. For example, putative DNA methyltransferase homologues were found in diatoms while none could be identified in the brown algal genome. On the other hand, no canonical DICER-like protein was found in diatoms in contrast to what is observed in brown algae. A key interest relies in understanding the adaptive nature of epigenetics and its inheritability. In contrast to yeast that lack DNA methylation, homogeneous cultures of diatoms constitute an attractive system to study epigenetic changes in response to environmental conditions such as nutrient-rich to nutrient-poor transitions which is especially relevant because of their ecological importance. P. tricornutum is also of outstanding interest because it is observed as three different morphotypes and thus constitutes a simple and promising model for the study of the epigenetic phenomena that accompany cellular differentiation. In this review we focus on the insights obtained from MAS comparative genomics and epigenomic analyses.

Cold Storage of Six Marine Benthic Diatoms Native to the Mexico Pacific Coast

Cultures of six benthic diatoms were maintained in the dark to measure their viability and biochemical composition after 8 wk of storage at low temperature (4 C) in darkness by refrigeration. Cell density, growth rate, and viability for each benthic diatom changed significantly after storage. Significant differences were observed with regard to cell size (length and width) of Nitzschia laevis, Navicula sp., and Amphora tenerrima as a result of storage. In general, the proximal composition of the benthic diatom cultures changed after week 1 of storage and decreased after week 4 of storage for all the diatoms. These results demonstrate that under 1–4 wk of storage these diatoms maintain their viability and had changes in their proximal composition in species‐specific responses. Storage of preserved live microalgae cells is an alternative technique that can be used to reduce the need for continuous maintenance of live cultures and can provide live feed stock for aquaculture applications.

Winter studies on zooplankton in Arctic seas: the Storfjord (Svalbard) and adjacent ice-covered Barents Sea

Zooplankton was sampled in the Storfjord and ice-covered Barents Sea during March 2003. Environmental conditions represented a typical winter situation with low air temperatures, close pack ice, and extremely low chlorophyll concentrations. Polar water dominated the hydrographic regime in the upper layers. Zooplankton distribution reflected spatial variability of hydrography. The copepods Pseudocalanus spp., Oithona similis, Microsetella norvegica together with gastropod larvae were most numerous. Biomass averaged for the entire water column varied from 3.3 to 14.3 mg dry mass m−3, Calanus glacialis and Parasagitta elegans contributed most, followed by C. finmarchicus, Oithona similis, and Pseudocalanus spp. Various holoplankters showed reproductive activity, especially cyclopoid copepods and chaetognaths. A few C. glacialis females laid eggs in situ, but when fed diatom cultures rapidly increased their egg production. Meroplankton including larvae of nudibranchia, bivalvia, ophiuroida, polychaeta, and bryozoa were also present. Our data demonstrate that the pelagic community of the seasonally ice-covered Barents Sea was not in a “sleeping” state at the end of the winter, but in addition to dormant stages, a portion of mainly omnivorous and several carnivorous species was reproducing.

A comparison of Fe bioavailability and binding of a catecholate siderophore with virus-mediated lysates from the marine bacterium Vibrio alginolyticus PWH3a

We have examined the bioavailability of Fe complexed to a siderophore produced by the heterotrophic marine bacterium Vibrio alginolyticus isolate PWH3a and Fe from ligand-complexes present in virus-mediated lysates (using phage PWH3a-P1) of this same bacterium. Fe-binding functional groups, stability constants and the bioavailability of Fe associated with these two separate ligand pools were determined and contrasted to previous work. Under low-Fe growth conditions, axenic cultures of V. alginolyticus PWH3a were shown to produce catecholate siderophores, while neither catecholate nor hydroxamate-type Fe-binding moieties were detected in virus-generated cell lysates. Analysis of the overall binding strength using electrochemical techniques revealed that the siderophore-containing organic extract and the organics in the virus-mediated lysates had Fe-binding constants comparable to the weaker L 2-type ligands found throughout the water column in seawater. A further purification of the siderophore-containing extract revealed a ligand with a stability constant of logK′ FeL,Fe3+ = 22.3, typical for siderophores and L 1-type of ligands found in marine surface waters. In assimilation studies, the Fe in the lysate was found to be more bioavailable to our model heterotrophic bacterium, autotrophic cyanobacterium and eukaryotic diatom cultures than the catecholate siderophore produced by the Vibrio sp. This work demonstrates that the Fe-containing components of virus-mediated cell lysates are different than siderophores secreted by these same cells, and as such continues to build the argument supporting the importance of virus-mediated Fe regeneration in marine surface waters.

Biosynthesis of gold nanoparticles using diatoms—silica-gold and EPS-gold bionanocomposite formation

Novel synthesis of gold nanoparticles, EPS-gold, and silica-gold bionanocomposites by biologically driven processes employing two diatom strains (Navicula atomus, Diadesmis gallica) is described. Transmission electron microscopy (TEM) and electron diffraction analysis (SAED) revealed a presence of gold nanoparticles in the experimental solutions of the diatom culture mixed with tetrachloroaureate. Nature of the gold nanoparticles was confirmed by X-ray diffraction studies. Scanning electron microscopy (SEM) and TEM showed that the nanoparticles were associated with the diatom frustules and extracellular polysaccharides (EPS) excreted by the diatom cells. Due to its accessibility, simplicity, and effectiveness, this method of nanocomposites preparation has great importance for possible future applications.

Growth and release of extracellular organic compounds by benthic diatoms depend on interactions with bacteria

Phototrophic epilithic biofilms harbour a distinct assemblage of heterotrophic bacteria, cyanobacteria and photoautotrophic algae. Secretion of extracellular polymeric substances (EPS) by these organisms and the physicochemical properties of the EPS are important factors for the development of the biofilms. We have isolated representative diatom and bacteria strains from epilithic biofilms of Lake Constance. By pairwise co-cultivating these strains we found that diatom growth and EPS secretion by diatoms may depend on the presence of individual bacteria. Similar results were obtained after addition of spent bacterial medium to diatom cultures, suggesting that soluble substances from bacteria have an impact on diatom physiology. While searching for putative bacterial signal substances, we found that concentrations of various dissolved free amino acids (DFAA) within the diatom cultures changed drastically during co-cultivation with bacteria. Further, the secretion of extracellular carbohydrates and proteins can be influenced by bacteria or their extracellular substances. We have performed mass spectrometric peptide mapping to identify proteins which are secreted when co-cultivating the diatom Phaeodactylum tricornutum Bohlin and Escherichia coli. The identified proteins are possibly involved in signalling, extracellular carbohydrate modification and uptake, protein and amino acid modification, and cell/cell aggregation of diatom and bacteria strains. Our data indicate that diatom-bacteria biofilms might be regulated by a complex network of chemical factors involving EPS, amino acid monomers and other substances. Thus interactions with bacteria can be considered as one of the main factors driving biofilm formation by benthic diatoms.

Pilot study of the influence of thermoplastic starch based polymer packaging material on the growth of diatom population in sea water environment

Pilot study of the influence of thermoplastic starch based polymer packaging material on the growth of diatom population in sea water environment Novel polymeric packaging materials susceptible to environmentally friendly decomposition appeared on the global market. The paper is devoted to an investigation of the impact of degradable polymer packaging on marine life. The chosen polymer was a commercial packaging based on thermoplastic starch (TPS over 85%). The microorganism chosen was Phaeodactylum tricornutum diatom (identified in many aquatic reservoirs, with a tendency to flow with seawater plankton in places of great saline oscillation). The packaging material was incubated both in natural seawater and in the presence of diatom population. The chlorophyll a content was determined as the criterion of diatom growth in the presence of tested polymers. The polymer surface and the colour changes in the diatom culture were recorded photographically. The presence of polymeric samples significantly changed the kinetic of diatom growth in seawater during incubation affecting its biological balance. During the experiment in seawater, diatom adhered to polymer surfaces and the polymer stimulated their growth.

The stabilisation potential of individual and mixed assemblages of natural bacteria and microalgae.

It is recognized that microorganisms inhabiting natural sediments significantly mediate the erosive response of the bed (“ecosystem engineers”) through the secretion of naturally adhesive organic material (EPS: extracellular polymeric substances). However, little is known about the individual engineering capability of the main biofilm components (heterotrophic bacteria and autotrophic microalgae) in terms of their individual contribution to the EPS pool and their relative functional contribution to substratum stabilisation. This paper investigates the engineering effects on a non-cohesive test bed as the surface was colonised by natural benthic assemblages (prokaryotic, eukaryotic and mixed cultures) of bacteria and microalgae. MagPI (Magnetic Particle Induction) and CSM (Cohesive Strength Meter) respectively determined the adhesive capacity and the cohesive strength of the culture surface. Stabilisation was significantly higher for the bacterial assemblages (up to a factor of 2) than for axenic microalgal assemblages. The EPS concentration and the EPS composition (carbohydrates and proteins) were both important in determining stabilisation. The peak of engineering effect was significantly greater in the mixed assemblage as compared to the bacterial (x 1.2) and axenic diatom (x 1.7) cultures. The possibility of synergistic effects between the bacterial and algal cultures in terms of stability was examined and rejected although the concentration of EPS did show a synergistic elevation in mixed culture. The rapid development and overall stabilisation potential of the various assemblages was impressive (x 7.5 and ×9.5, for MagPI and CSM, respectively, as compared to controls). We confirmed the important role of heterotrophic bacteria in “biostabilisation” and highlighted the interactions between autotrophic and heterotrophic biofilm consortia. This information contributes to the conceptual understanding of the microbial sediment engineering that represents an important ecosystem function and service in aquatic habitats.

Gene biomarkers in diatom Thalassiosira pseudonana exposed to polycyclic aromatic hydrocarbons from contaminated marine surface sediments

Marine diatoms have a key role in the global carbon fixation and therefore in the ecosystem. We used Thalassiosira pseudonana as a model organism to assess the effects of exposure to environmental pollutants at the gene expression level. Diatoms were exposed to polycyclic aromatic hydrocarbons mixture (PAH) from surface sediments collected at a highly PAH contaminated area of the Mediterranean Sea (Genoa, Italy), due to intense industrial and harbor activities. The gene expression data for exposure to the sediment-derived PAH mixture was compared with gene expression data for in vitro exposure to specific polycyclic aromatic hydrocarbons. The data shows that genes involved in stress response, silica uptake, and metabolism were regulated both upon exposure to the sediment-derived PAH mixture and to the single component. Complementary monitoring of silica in the diatom cultures provide further evidence of a reduced cellular uptake of silica as an end-point for benzo[a]pyrene exposure that could be linked with the reduced gene and protein expression of the silicon transporter protein. However some genes showed differences in regulation indicating that mixtures of structurally related chemical compounds can elicit a slightly different gene expression response compared to that of a single component. The paper provides indications on the specific pathways affected by PAH exposure and shows that selected genes (silicon transporter, and silaffin 3) involved in silica uptake and metabolism could be suitable molecular biomarkers of exposure to PAHs.

PARAFAC modeling of three-way hyperspectral images: Endogenous fluorophores as health biomarkers in aquatic species

Demand for a renewable liquid-phase fuel has reinvigorated interest in the development of novel biofuels from algae. The effects of fluctuating nutrients, temperature, and predation which arise in algal aquaculture necessitate novel analytical methods to assess and optimize the health of these cultures. In this article we describe the use of trilinear modeling to these ends, using imaging data of endogenous fluorescence from the marine diatom, Thalassiosira pseudonana, collected on a hyperspectral fluorescence confocal microscope (HSF-CM). By combining the spatial and spectral data with the additional physical parameter introduced by the varying photobleach rates of endogenous fluorophores, we obtain a means for employing trilinear analysis in this system. In this case, analysis was implemented using the method of parallel factors analysis (PARAFAC) which alleviates the rotational ambiguities involved in multivariate analysis of 2-way data. By imposing a nutrient limitation in our diatom culture, and collecting single cell microscopy data at various time points during the nutritional stress, PARAFAC results reveal evolution of the spectral emission characteristics of six components and a background as a result of incremental photobleaching. Although the underlying mechanisms for these observations are not addressed, the differences observed between nutritively normal and nutritively stressed cells provide signatures for early detection of health deterioration in the algal culture. Finally, the combination of hyperspectral fluorescence microscopy with PARAFAC is generally applicable for the study of complex biological systems with endogenous fluorescence.