Bacteria may induce the secretion of mucin-like proteins by the diatom Phaeodactylum tricornutum

Proteomes reveal the lipid metabolic network in the complex plastid of Phaeodactylum tricornutum

Phaeodactylum tricornutum plastid is surrounded by four membranes, and its protein composition and function remain mysterious. In this study, the P. tricornutum plastid-enriched fraction was obtained and 2850 proteins were identified, including 92 plastid-encoded proteins, through label-free quantitative proteomic technology. Among them, 839 nuclear-encoded proteins were further determined to be plastidial proteins based on the BLAST alignments within Plant Proteome DataBase and subcellular localization prediction, in spite of the strong contamination by mitochondria-encoded proteins and putative plasma membrane proteins. According to our proteomic data, we reconstructed the metabolic pathways and highlighted the hybrid nature of this diatom plastid. Triacylglycerol (TAG) hydrolysis and glycolysis, as well as photosynthesis, glycan metabolism, and tocopherol and triterpene biosynthesis, occur in the plastid. In addition, the synthesis of long-chain acyl-CoAs, elongation, and desaturation of fatty acids (FAs), and synthesis of lipids including TAG are confined in the four-layered-membrane plastid based on the proteomic and GFP-fusion localization data. The whole process of generation of docosahexaenoic acid (22:6) from palmitic acid (16:0), via elongation and desaturation of FAs, occurs in the chloroplast endoplasmic reticulum membrane, the outermost membrane of the plastid. Desaturation that generates 16:4 from 16:0 occurs in the plastid stroma and outer envelope membrane. Quantitative analysis of glycerolipids between whole cells and isolated plastids shows similar composition, and the FA profile of TAG was not different. This study shows that the diatom plastid combines functions usually separated in photosynthetic eukaryotes, and differs from green alga and plant chloroplasts by undertaking the whole process of lipid biosynthesis.

Diatom-Bacteria Interactions in the Marine Environment: Complexity, Heterogeneity, and Potential for Biotechnological Applications

Diatom-bacteria interactions evolved during more than 200 million years of coexistence in the same environment. In this time frame, they established complex and heterogeneous cohorts and consortia, creating networks of multiple cell-to-cell mutualistic or antagonistic interactions for nutrient exchanges, communication, and defence. The most diffused type of interaction between diatoms and bacteria is based on a win-win relationship in which bacteria benefit from the organic matter and nutrients released by diatoms, while these last rely on bacteria for the supply of nutrients they are not able to produce, such as vitamins and nitrogen. Despite the importance of diatom-bacteria interactions in the evolutionary history of diatoms, especially in structuring the marine food web and controlling algal blooms, the molecular mechanisms underlying them remain poorly studied. This review aims to present a comprehensive report on diatom-bacteria interactions, illustrating the different interplays described until now and the chemical cues involved in the communication and exchange between the two groups of organisms. We also discuss the potential biotechnological applications of molecules and processes involved in those fascinating marine microbial networks and provide information on novel approaches to unveiling the molecular mechanisms underlying diatom-bacteria interactions.

On the role of cell surface associated, mucin-like glycoproteins in the pennate diatom Craspedostauros australis (Bacillariophyceae)

Diatoms are single-celled microalgae with silica-based cell walls (frustules) that are abundantly present in aquatic habitats, and form the basis of the food chain in many ecosystems. Many benthic diatoms have the remarkable ability to glide on all natural or man-made underwater surfaces using a carbohydrate- and protein-based adhesive to generate traction. Previously, three glycoproteins, termed FACs (Frustule Associated Components), have been identified from the common fouling diatom Craspedostauros australis and were implicated in surface adhesion through inhibition studies with a glycan-specific antibody. The polypeptide sequences of FACs remained unknown, and it was unresolved whether the FAC glycoproteins are indeed involved in adhesion, or whether this is achieved by different components sharing the same glycan epitope with FACs. Here we have determined the polypeptide sequences of FACs using peptide mapping by LC-MS/MS. Unexpectedly, FACs share the same polypeptide backbone (termed CaFAP1), which has a domain structure of alternating Cys-rich and Pro-Thr/Ser-rich regions reminiscent of the gel-forming mucins. By developing a genetic transformation system for C. australis, we were able to directly investigate the function of CaFAP1-based glycoproteins in vivo. GFP-tagging of CaFAP1 revealed that it constitutes a coat around all parts of the frustule and is not an integral component of the adhesive. CaFAP1-GFP producing transformants exhibited the same properties as wild type cells regarding surface adhesion and motility speed. Our results demonstrate that FAC glycoproteins are not involved in adhesion and motility, but might rather act as a lubricant to prevent fouling of the diatom surface.

Dinoflagellate Amphiesmal Dynamics: Cell Wall Deposition with Ecdysis and Cellular Growth

Dinoflagellates are a major aquatic protist group with amphiesma, multiple cortical membranous "cell wall" layers that contain large circum-cortical alveolar sacs (AVs). AVs undergo extensive remodeling during cell- and life-cycle transitions, including ecdysal cysts (ECs) and resting cysts that are important in some harmful algal bloom initiation-termination. AVs are large cortical vesicular compartments, within which are elaborate cellulosic thecal plates (CTPs), in thecate species, and the pellicular layer (PL). AV-CTPs provide cellular mechanical protection and are targets of vesicular transport that are replaced during EC-swarmer cell transition, or with increased deposition during the cellular growth cycle. AV-PL exhibits dynamical-replacement with vesicular trafficking that are orchestrated with amphiesmal chlortetracycline-labeled Ca²⁺ stores signaling, integrating cellular growth with different modes of cell division cycle/progression. We reviewed the dynamics of amphiesma during different cell division cycle modes and life cycle stages, and its multifaceted regulations, focusing on the regulatory and functional readouts, including the coral-zooxanthellae interactions.

Flavobacterial exudates disrupt cell cycle progression and metabolism of the diatom Thalassiosira pseudonana

Phytoplankton and bacteria form the base of marine ecosystems and their interactions drive global biogeochemical cycles. The effects of bacteria and bacteria-produced compounds on diatoms range from synergistic to pathogenic and can affect the physiology and transcriptional patterns of the interacting diatom. Here, we investigate physiological and transcriptional changes in the marine diatom Thalassiosira pseudonana induced by extracellular metabolites of a known antagonistic bacterium Croceibacter atlanticus. Mono-cultures of C. atlanticus released compounds that inhibited diatom cell division and elicited a distinctive morphology of enlarged cells with increased chloroplast content and enlarged nuclei, similar to what was previously observed when the diatom was co-cultured with live bacteria. The extracellular C. atlanticus metabolites induced transcriptional changes in diatom pathways that include recognition and signaling pathways, cell cycle regulation, carbohydrate and amino acid production, as well as cell wall stability. Phenotypic analysis showed a disruption in the diatom cell cycle progression and an increase in both intra- and extracellular carbohydrates in diatom cultures after bacterial exudate treatment. The transcriptional changes and corresponding phenotypes suggest that extracellular bacterial metabolites, produced independently of direct bacterial-diatom interaction, may modulate diatom metabolism in ways that support bacterial growth.

Genome evolution of a nonparasitic secondary heterotroph, the diatom Nitzschia putrida

Secondary loss of photosynthesis is observed across almost all plastid-bearing branches of the eukaryotic tree of life. However, genome-based insights into the transition from a phototroph into a secondary heterotroph have so far only been revealed for parasitic species. Free-living organisms can yield unique insights into the evolutionary consequence of the loss of photosynthesis, as the parasitic lifestyle requires specific adaptations to host environments. Here, we report on the diploid genome of the free-living diatom Nitzschia putrida (35 Mbp), a nonphotosynthetic osmotroph whose photosynthetic relatives contribute ca. 40% of net oceanic primary production. Comparative analyses with photosynthetic diatoms and heterotrophic algae with parasitic lifestyle revealed that a combination of gene loss, the accumulation of genes involved in organic carbon degradation, a unique secretome, and the rapid divergence of conserved gene families involved in cell wall and extracellular metabolism appear to have facilitated the lifestyle of a free-living secondary heterotroph.

Comparative Proteomic Analysis of the Diatom Phaeodactylum tricornutum Reveals New Insights Into Intra- and Extra-Cellular Protein Contents of Its Oval, Fusiform, and Triradiate Morphotypes

Phaeodactylum tricornutum is an atypical diatom since it can display three main morphotypes: fusiform, triradiate, and oval. Such pleomorphism is possible thanks to an original metabolism, which is tightly regulated in order to acclimate to environmental conditions. Currently, studies dedicated to the comparison of each morphotype issued from one specific strain are scarce and little information is available regarding the physiological significance of this morphogenesis. In this study, we performed a comparative proteomic analysis of the three morphotypes from P. tricornutum. Cultures highly enriched in one dominant morphotype (fusiform, triradiate, or oval) of P. tricornutum Pt3 strain were used. Pairwise comparisons highlighted biological processes, which are up- and down-regulated in the oval (e.g., purine and cellular amino acid metabolism) and triradiate morphotypes (e.g., oxido-reduction and glycolytic processes) compared to the fusiform one used as a reference. Intersection analysis allowed us to identify the specific features of the oval morphotype. Results from this study confirmed previous transcriptomic RNA sequencing observation showing that the oval cells present a distinct metabolism with specific protein enrichment compared to fusiform and triradiate cells. Finally, the analysis of the secretome of each morphotype was also performed.

Optimal Nitrate Supplementation in Phaeodactylum tricornutum Culture Medium Increases Biomass and Fucoxanthin Production

Phaeodactylum tricornutum is a model diatom with numerous potential applications in the industry, including the production of high-value carotenoid pigments such as fucoxanthin. This compound is a potent antioxidant currently extracted mainly from brown macroalgae. Fucoxanthin exhibits several biological properties with well-known beneficial effects in the treatment and prevention of lifestyle-related diseases. P. tricornutum offers a valuable alternative to macroalgae for fucoxanthin production as it has a specific productivity that is 10-fold higher as compared with macroalgae. However, production processes still need to be optimised to become a cost-effective alternative. In this work, we investigated the optimal supplementation of nitrate in a cultivation medium that is currently used for P. tricornutum and how this nitrate concentration affects cell growth and fucoxanthin production. It has previously been shown that the addition of sodium nitrate increases productivity, but optimal conditions were not accurately determined. In this report, we observed that the continuous increase in nitrate concentration did not lead to an increase in biomass and fucoxanthin content, but there was rather a window of optimal values of nitrate that led to maximum growth and pigment production. These results are discussed considering both the scale up for industrial production and the profitability of the process, as well as the implications in the cell’s metabolism and effects in fucoxanthin production.

Towards a Phaeodactylum tricornutum biorefinery in an outdoor UK environment

A series of commercial powdered media (Cell-Hi F2P, JWP and WP) and a hydroponics medium (FloraMicroBloom) were investigated for the cultivation of P. tricornutum, and compared with f/2 (a commonly employed laboratory cultivation medium; costlier to scale). Cell-Hi JWP showed good performance characteristics including cost-effectiveness. Outdoor cultivation of P. tricornutum in an airlift photobioreactor, using Cell-Hi JWP in the United Kingdom (UK) during September and October (average daily temperature ranging between 8 and 18 °C and natural sunlight) was comparable to cultivation indoors under controlled temperature and lighting. A strong positive correlation between fucoxanthin and chlorophyll a content, and a weak inverse correlation between eicosapentaenoic (EPA) content and temperature were observed. Commensal bacterial counts revealed a sinusoidal growth profile with a change in community dominance from Halomonas sp. to Marinobacter sp. This investigation reveals for the first time that a multi-product approach can be adopted with P. tricornutum in a UK outdoor environment using commercially viable powdered media.

Phytate as a phosphorus nutrient with impacts on iron stress-related gene expression for phytoplankton: insights from diatom Phaeodactylum tricornutum

Phytoplankton have evolved a capability to acquire phosphorus (P) from dissolved organic phosphorus (DOP) since the preferred form, dissolved inorganic phosphate (DIP, or Pi), is often limited in parts of the ocean. Phytic acid (PA) is abundantly synthesized in plants and rich in excreta of animals, potentially enriching the DOP pool in coastal oceans. However, whether and how PA may be used by phytoplankton are poorly understood. Here, we investigated PA utilization and underlying metabolic pathways in the diatom model Phaeodactylum tricornutum. The physiological results showed that P. tricornutum could utilize PA as a sole source of P nutrient to support growth. Meanwhile, the replacement of PA for DIP also caused changes in multiple cellular processes such as inositol phosphate metabolism, photosynthesis, and signal transduction. These results suggest that PA is bioavailable to P. tricornutum and can directly participate the metabolic pathways of PA-grown cells. However, our data showed that the utilization of PA was markedly less efficient than that of DIP, and PA-grown cells exhibited P and iron (Fe) nutrient stress signals. Implicated in these findings is the potential of complicated responses of phytoplankton to an ambient DOP species, which calls for more systematic investigation. IMPORTANCE PA is abundant in plants, and cannot be digested by non-ruminant animals. Hence, it is potentially a significant component of the DOP pool in the coastal waters. Despite the potential importance, there is little information about its bioavailability to phytoplankton as a source of P nutrient and if so what molecular mechanisms are involved. In this study, we found that part of PA could be utilized by the diatom P. tricornutum to support growth, and another portion of PA can act as a substrate directly participating in various metabolism pathways and cellular processes. However, our physiological and transcriptomic data show that PA-grown cells still exhibited signs of P stress and potential Fe stress. These results have significant implications in phytoplankton P nutrient ecology and provide a novel insight into multi-faceted impacts of DOP utilization on phytoplankton nutrition and metabolism.

Comparative Structural and Functional Analyses of the Fusiform, Oval, and Triradiate Morphotypes of Phaeodactylum tricornutum Pt3 Strain

The diatom Phaeodactylum tricornutum is a marine unicellular microalga that exists under three main morphotypes: oval, fusiform, and triradiate. Previous works have demonstrated that the oval morphotype of P. tricornutum Pt3 strain presents specific metabolic features. Here, we compared the cellular organization of the main morphotypes of the diatom P. tricornutum Pt3 strain through transmission electron and advanced light microscopies. The three morphotypes share similarities including spectral characteristics of the plastid, the location of the nucleus, the organization of mitochondria around the plastid as well as the existence of both a F-actin cortex, and an intracellular network of F-actin. In contrast, compared to fusiform and triradiate cells, oval cells spontaneously release proteins more rapidly. In addition, comparison of whole transcriptomes of oval versus fusiform or triradiate cells revealed numerous differential expression of positive and negative regulators belonging to the complex dynamic secretory machinery. This study highlights the specificities occurring within the oval morphotype underlying that the oval cells secrete proteins more rapidly.

Specific acclimations to phosphorus limitation in the marine diatom Phaeodactylum tricornutum

Phosphorus (P) is a crucial element and diatoms, unicellular phototrophic organisms, evolved efficient strategies to handle limiting phosphorus concentrations in the oceans. In the last decade, several groups investigated the model diatom Phaeodactylum tricornutum concerning phosphate homeostasis mechanisms. Here, we summarize the actual status of knowledge by linking the available data sets, thereby indicating experimental limits but also future research directions.

Evidence of Interdomain Ammonium Cross-Feeding From Methylamine- and Glycine Betaine-Degrading Rhodobacteraceae to Diatoms as a Widespread Interaction in the Marine Phycosphere

Dissolved organic nitrogen (DON) compounds such as methylamines (MAs) and glycine betaine (GBT) occur at detectable concentrations in marine habitats and are also produced and released by microalgae. For many marine bacteria, these DON compounds can serve as carbon, energy, and nitrogen sources, but microalgae usually cannot metabolize them. Interestingly though, it was previously shown that Donghicola sp. strain KarMa—a member of the marine Rhodobacteraceae—can cross-feed ammonium such that the ammonium it produces upon degrading monomethylamine (MMA) then serves as nitrogen source for the diatom Phaeodactylum tricornutum; thus, these organisms form a mutual metabolic interaction under photoautotrophic conditions. In the present study, we investigated whether this interaction plays a broader role in bacteria–diatom interactions in general. Results showed that cross-feeding between strain KarMa and P. tricornutum was also possible with di- and trimethylamine as well as with GBT. Further, cross-feeding of strain KarMa was also observed in cocultures with the diatoms Amphora coffeaeformis and Thalassiosira pseudonana with MMA as the sole nitrogen source. Regarding cross-feeding involving other Rhodobacteraceae strains, the in silico analysis of MA and GBT degradation pathways indicated that algae-associated Rhodobacteraceae-type strains likely interact with P. tricornutum in a similar manner as the strain KarMa does. For these types of strains (such as Celeribacter halophilus, Roseobacter denitrificans, Roseovarius indicus, Ruegeria pomeroyi, and Sulfitobacter noctilucicola), ammonium cross-feeding after methylamine degradation showed species-specific patterns, whereas bacterial GBT degradation always led to diatom growth. Overall, the degradation of DON compounds by the Rhodobacteraceae family and the subsequent cross-feeding of ammonium may represent a widespread, organism-specific, and regulated metabolic interaction for establishing and stabilizing associations with photoautotrophic diatoms in the oceans.

Mobilization and Cellular Distribution of Phosphate in the Diatom Phaeodactylum tricornutum

Unicellular organisms that live in marine environments must cope with considerable fluctuations in the availability of inorganic phosphate (P_i). Here, we investigated the extracellular P_i concentration-dependent expression, as well as the intracellular or extracellular localization, of phosphatases and phosphate transporters of the diatom Phaeodactylum tricornutum. We identified P_i-regulated plasma membrane-localized, ER-localized, and secreted phosphatases, in addition to plasma membrane-localized, vacuolar membrane-localized, and plastid-surrounding membrane-localized phosphate transporters that were also regulated in a P_i concentration-dependent manner. These studies not only add further knowledge to already existing transcriptomic data, but also highlight the capacity of the diatom to distribute P_i intracellularly and to mobilize P_i from extracellular and intracellular resources.

Phaeodactylum tricornutum: A Diatom Cell Factory

A switch from a petroleum-based to a biobased economy requires the capacity to produce both high-value low-volume and low-value high-volume products. Recent evidence supports the development of microalgae-based microbial cell factories with the objective of establishing environmentally sustainable manufacturing solutions. Diatoms display rich diversity and potential in this regard. We focus on Phaeodactylum tricornutum, a pennate diatom that is commonly found in marine ecosystems, and discuss recent trends in developing the diatom chassis for the production of a suite of natural and genetically engineered products. Both upstream and downstream developments are reviewed for the commercial development of P. tricornutum as a cell factory for a spectrum of marketable products.

Identification of proteins in the adhesive trails of the diatom Amphora coffeaeformis

Throughout all kingdoms of life, a large number of adhesive biomolecules have evolved to allow organisms to adhere to surfaces underwater. Proteins play an important role in the adhesion of numerous marine invertebrates (e.g. mussels, sea stars, sea urchins) whereas much less is known about the biological adhesives from marine plants, including the diatoms. Diatoms are unicellular microalgae that together with bacteria dominate marine biofilms in sunlit habitats. In this study we present the first proteomics analyses of the diatom adhesive material isolated from the tenacious fouling species Amphora coffeaeformis. We identified 21 proteins, of which 13 are diatom-specific. Ten of these proteins share a conserved C-terminal domain, termed GDPH domain, which is widespread yet not ubiquitously present in all diatom classes. Immunofluorescence localization of a GDPH domain bearing protein (Ac629) as well as two other proteins identified in this study (Ac1442, Ac9617) demonstrated that these are components of the adhesive trails that are secreted by cells that glide on surfaces. This article is part of the theme issue 'Transdisciplinary approaches to the study of adhesion and adhesives in biological systems'.

Phototrophic marine benthic microbiomes: the ecophysiology of these biological entities

Phototrophic biofilms are multispecies, self-sustaining and largely closed microbial ecosystems. They form macroscopic structures such as microbial mats and stromatolites. These sunlight-driven consortia consist of a number of functional groups of microorganisms that recycle the elements internally. Particularly, the sulfur cycle is discussed in more detail as this is fundamental to marine benthic microbial communities and because recently exciting new insights have been obtained. The cycling of elements demands a tight tuning of the various metabolic processes and require cooperation between the different groups of microorganisms. This is likely achieved through cell-to-cell communication and a biological clock. Biofilms may be considered as a macroscopic biological entity with its own physiology. We review the various components of some marine phototrophic biofilms and discuss their roles in the system. The importance of extracellular polymeric substances (EPS) as the matrix for biofilm metabolism and as substrate for biofilm microorganisms is discussed. We particularly assess the importance of extracellular DNA, horizontal gene transfer and viruses for the generation of genetic diversity and innovation, and for rendering resilience to external forcing to these biological entities.

Impact of Dinophysis acuminata Feeding Mesodinium rubrum on Nutrient Dynamics and Bacterial Composition in a Microcosm

The development of Dinophysis populations, producers of diarrhetic shellfish toxins, has been attributed to both abiotic (e.g., water column stratification) and biotic (prey availability) factors. An important process to consider is mixotrophy of the Dinophysis species, which is an intensive feeding of the Mesodinium species for nutrients and a benefit from kleptochloroplasts. During the feeding process, the nutritional status in the environment changes due to the preference of Mesodinium and/or Dinophysis for different nutrients, prey cell debris generated by sloppy feeding, and their degradation by micro-organisms changes. However, there is little knowledge about the role of the bacterial community during the co-occurrence of Mesodinium and Dinophysis and how they directly or indirectly interact with the mixotrophs. In this study, laboratory experiments were performed to characterize the environmental changes including those of the prey present, the bacterial communities, and the ambient dissolved nutrients during the co-occurrence of Mesodinium rubrum and Dinophysis acuminata. The results showed that, during the incubation of the ciliate prey Mesodinium with its predator Dinophysis, available dissolved nitrogen significantly shifted from nitrate to ammonium especially when the population of M. rubrum decayed. Growth phases of Dinophysis and Mesodinium greatly affected the structure and composition of the bacterial community. These changes could be mainly explained by both the changes of the nutrient status and the activity of Dinophysis cells. Dinophysis feeding activity also accelerated the decline of M. rubrum and contamination of cultures with okadaic acid, dinophysistoxin-1, and pectenotoxin-2, but their influence on the prokaryotic communities was limited to the rare taxa (<0.1%) fraction. This suggests that the interaction between D. acuminata and bacteria is species-specific and takes place intracellularly or in the phycosphere. Moreover, a majority of the dominant bacterial taxa in our cultures may also exhibit a metabolic flexibility and, thus, be unaffected taxonomically by changes within the Mesodinium-Dinophysis culture system.

Exploring the microbiome of the "star" freshwater diatom Asterionella formosa in a laboratory context

Most of our knowledge on the mechanisms underlying diatom-bacterial interactions has been acquired through studies involving isolation of culturable partners. Here, we established a laboratory model of intermediate complexity between complex natural communities and laboratory pure culture models. We investigated the whole community formed by the freshwater diatom Asterionella formosa and its associated bacteria in a laboratory context, including both culturable and unculturable bacteria. Combining cellular and molecular approaches, we showed that in laboratory cultures, A. formosa microbiome was dynamic and comprised of numerous bacterial species (mainly Proteobacteria and Bacteroidetes). Using metagenomics, we explored several metabolic potentials present within the bacterial community. Our analyses suggested that bacteria were heterotrophic although a third of them (Alpha- and Beta-proteobacteria) could also be phototrophic. About 60% of the bacteria, phylogenetically diverse, could metabolize glycolate. The capacity to synthesize molecules such as B vitamins appeared unevenly distributed among bacteria. Altogether, our results brought insights into the bacterial diversity found in diatom-bacterial communities and hinted at metabolic interdependencies within the community that could result in diatom-bacterial and bacterial-bacterial interactions. The present work allowed us to explore the functional architecture of the bacterial community associated with A. formosa in culture and is complementary to field studies.

A multi-step approach for testing non-toxic amphiphilic antifouling coatings against marine microfouling at different levels of biological complexity

Marine biofouling on artificial surfaces such as ship hulls or fish farming nets causes enormous economic damage. The time for the developmental process of antifouling coatings can be shortened by reliable laboratory assays. For designing such test systems, it is important that toxic effects can be excluded, that multiple parameters can be addressed simultaneously and that mechanistic aspects can be included. In this study, a multi-step approach for testing antifouling coatings was established employing photoautotrophic biofilm formation of marine microorganisms in micro- and mesoscoms. Degree and pattern of biofilm formation was determined by quantification of chlorophyll fluorescence. For the microcosms, co-cultures of diatoms and a heterotrophic bacterium were exposed to fouling-release coatings. For the mesocosms, a novel device was developed that permits parallel quantification of a multitude of coatings under defined conditions with varying degrees of shear stress. Additionally, the antifouling coatings were tested for leaching of potential compounds and finally tested in sea trials. This multistep-approach revealed that the individual steps led to consistent results regarding antifouling activity of the coatings. Furthermore, the novel mesocosm system can be employed for advanced antifouling analysis including metagenomic approaches for determination of microbial diversity attaching to different coatings under changing shear forces.

Intracellular metabolic pathway distribution in diatoms and tools for genome-enabled experimental diatom research

Diatoms are important primary producers in the oceans and can also dominate other aquatic habitats. One reason for the success of this phylogenetically relatively young group of unicellular organisms could be the impressive redundancy and diversity of metabolic isoenzymes in diatoms. This redundancy is a result of the evolutionary origin of diatom plastids by a eukaryote-eukaryote endosymbiosis, a process that implies temporary redundancy of functionally complete eukaryotic genomes. During the establishment of the plastids, this redundancy was partially reduced via gene losses, and was partially retained via gene transfer to the nucleus of the respective host cell. These gene transfers required re-assignment of intracellular targeting signals, a process that simultaneously altered the intracellular distribution of metabolic enzymes compared with the ancestral cells. Genome annotation, the correct assignment of the gene products and the prediction of putative function, strongly depends on the correct prediction of the intracellular targeting of a gene product. Here again diatoms are very peculiar, because the targeting systems for organelle import are partially different to those in land plants. In this review, we describe methods of predicting intracellular enzyme locations, highlight findings of metabolic peculiarities in diatoms and present genome-enabled approaches to study their metabolism.This article is part of the themed issue 'The peculiar carbon metabolism in diatoms'.