Diatom Chloroplast Research Articles

Diatoms exhibit dynamic chloroplast calcium signals in response to high light and oxidative stress.

Diatoms are a group of silicified algae that play a major role in marine and freshwater ecosystems. Diatom chloroplasts were acquired by secondary endosymbiosis and exhibit important structural and functional differences from the primary plastids of land plants and green algae. Many functions of primary plastids, including photoacclimation and inorganic carbon acquisition, are regulated by calcium-dependent signalling processes. Calcium signalling has also been implicated in the photoprotective responses of diatoms; however, the nature of calcium elevations in diatom chloroplasts and their wider role in cell signalling remains unknown. Using genetically encoded calcium indicators, we find that the diatom Phaeodactylum tricornutum exhibits dynamic calcium elevations within the chloroplast stroma. Stromal calcium ([Ca2+]str) acts independently from the cytosol and is not elevated by stimuli that induce large cytosolic calcium ([Ca2+]cyt) elevations. In contrast, high light and exogenous hydrogen peroxide (H2O2) induce large, sustained [Ca2+]str elevations that are not replicated in the cytosol. Measurements using the fluorescent H2O2 sensor roGFP2-Oxidant Receptor Peroxidase 1 (Orp1) indicate that [Ca2+]str elevations induced by these stimuli correspond to the accumulation of H2O2 in the chloroplast. [Ca2+]str elevations were also induced by adding methyl viologen, which generates superoxide within the chloroplast, and by treatments that disrupt non-photochemical quenching (NPQ). The findings indicate that diatoms generate specific [Ca2+]str elevations in response to high light and oxidative stress that likely modulate the activity of calcium-sensitive components in photoprotection and other regulatory pathways.

Acquisition, Maintenance, and Ecological Roles of Kleptoplasts in Planoglabratella opercularis (Foraminifera, Rhizaria)

Kleptoplasty or acquisition of chloroplasts from ingested photosynthetic organisms, is thought to be a key factor in determining the trophic requirements and carbon mineralization of foraminifera, consequently influencing their ecology, evolution, and calcification. However, the acquisition, maintenance, and functions of “stolen” chloroplasts (kleptoplasts) in foraminiferal cells have not been well characterized. Using molecular phylogeny and experimental measurements of oxygen flux and intracellular (vacuole) pH, we characterized aspects of kleptoplast origin and function in Planoglabratella opercularis (d’Orbigny), a rocky-shore benthic foraminifera. We determined that the kleptoplasts in P. opercularis are derived from various species of epiphytic diatoms. The acquisition of epiphytic diatoms is congruent with the behaviour of P. opercularis, which crawls on the thalli of coralline algae and grazes on the microalgae on the algal surface. Kleptoplasts were located near the host foraminiferal cell periphery, just under the pore plug, mainly along the dorsal side, which is important for oxygenic photosynthesis. The lifespan of kleptoplasts varied according to food availability and to the intensity and duration of light irradiation. Planoglabratella opercularis was able to capture not only diatom chloroplasts but also those from Chlorella. Kleptoplastids of diatom origin decreased in autofluorescence and were digested within 11 days under light in the absence of food. This suggests that host foraminifera frequently capture new diatoms to sustain kleptoplasts. Kleptoplastid autofluorescence was prolonged in the dark or 24:24-h light:dark cycle, and when food was available. Host foraminifera metabolized food to maintain the activity of kleptoplasts and effectively utilized photosynthetic products from both organic and inorganic materials in response to the ambient environment. This suggests that P. opercularis behaves as a mixotroph. Simultaneously, kleptoplasts maintain a high intracellular pH environment, indicating that foraminifera capture kleptoplasts not only to gain their photosynthates but also to control the intracellular pH levels to construct a high magnesian calcite test.

Metabolic Innovations Underpinning the Origin and Diversification of the Diatom Chloroplast.

Of all the eukaryotic algal groups, diatoms make the most substantial contributions to photosynthesis in the contemporary ocean. Understanding the biological innovations that have occurred in the diatom chloroplast may provide us with explanations to the ecological success of this lineage and clues as to how best to exploit the biology of these organisms for biotechnology. In this paper, we use multi-species transcriptome datasets to compare chloroplast metabolism pathways in diatoms to other algal lineages. We identify possible diatom-specific innovations in chloroplast metabolism, including the completion of tocopherol synthesis via a chloroplast-targeted tocopherol cyclase, a complete chloroplast ornithine cycle, and chloroplast-targeted proteins involved in iron acquisition and CO2 concentration not shared between diatoms and their closest relatives in the stramenopiles. We additionally present a detailed investigation of the chloroplast metabolism of the oil-producing diatom Fistulifera solaris, which is of industrial interest for biofuel production. These include modified amino acid and pyruvate hub metabolism that might enhance acetyl-coA production for chloroplast lipid biosynthesis and the presence of a chloroplast-localised squalene synthesis pathway unknown in other diatoms. Our data provides valuable insights into the biological adaptations underpinning an ecologically critical lineage, and how chloroplast metabolism can change even at a species level in extant algae.

Extensive chloroplast genome rearrangement amongst three closely related Halamphora spp. (Bacillariophyceae), and evidence for rapid evolution as compared to land plants.

Diatoms are the most diverse lineage of algae, but the diversity of their chloroplast genomes, particularly within a genus, has not been well documented. Herein, we present three chloroplast genomes from the genus Halamphora (H. americana, H. calidilacuna, and H. coffeaeformis), the first pennate diatom genus to be represented by more than one species. Halamphora chloroplast genomes ranged in size from ~120 to 150 kb, representing a 24% size difference within the genus. Differences in genome size were due to changes in the length of the inverted repeat region, length of intergenic regions, and the variable presence of ORFs that appear to encode as-yet-undescribed proteins. All three species shared a set of 161 core features but differed in the presence of two genes, serC and tyrC of foreign and unknown origin, respectively. A comparison of these data to three previously published chloroplast genomes in the non-pennate genus Cyclotella (Thalassiosirales) revealed that Halamphora has undergone extensive chloroplast genome rearrangement compared to other genera, as well as containing variation within the genus. Finally, a comparison of Halamphora chloroplast genomes to those of land plants indicates diatom chloroplast genomes within this genus may be evolving at least ~4–7 times faster than those of land plants. Studies such as these provide deeper insights into diatom chloroplast evolution and important genetic resources for future analyses.

Complete chloroplast genome of the tiny marine diatom Nanofrustulum shiloi (Bacillariophyta) from the Adriatic Sea

We report the chloroplast genome sequence of Nanofrustulum shiloi, a tiny araphid pennate diatom collected from the Adriatic Sea. The 160,994-bp N. shiloi genome displays a quadripartite structure and its gene repertoire resembles those of other diatom chloroplast genomes. Besides the genes located in the inverted repeat, psbY is duplicated. A gene-poor region in the large single-copy region contains multiple ORFs sharing sequence similarities with plasmids and chloroplast ORFs found in other diatom species. The genome features a single intron, a group II intron in petB. Phylogenomic analysis identified N. shiloi at a basal position within the araphid 2 clade.

From phytoplankton to oil shale reservoirs: A 19-million-year record of the Late Cretaceous Tethyan upwelling regime in the Levant Basin

Abstract The complexity of sedimentary organic-matter formation, its source to burial, and influence on bottom-water communities are addressed in this study of the 19 million years-long Upper Cretaceous Tethyan upwelling regime in the Levant. A multi-proxy approach is amalgamated into a model through which the paleoceanographic complexity of an intense and long-lasting upwelling system is better understood. A shift in primary producer assemblages and reorganization of the bottom water bacterial consortium followed the Campanian-Maastrichtian boundary, enforcing conspicuous sedimentological and faunal changes. The siliceous and phosphatic-bearing sediments of the Campanian gave way to Maastrichtian uniform and regionally distributed organic-rich carbonates, accompanied by an increase in sedimentation rates from ∼1 to >6 cm/kyr. This has facilitated both the increase in organic-matter production and its excellent preservation, and through diagenetic pathways affected its elemental composition. These paleoceanographic modifications have also affected foraminiferal assemblages, from massive blooms of triserial (buliminid) benthic foraminifera during the Campanian which have sequestered diatom chloroplasts, to diverse trochospiral forms during the Maastrichtian using nitrate instead of oxygen for their respiratory pathways. We propose that shifts in the type of primary producers promote a change in the amount and type of preserved organic matter, in bottom water communities, on the lithological composition of the rock-mass, and ultimately on the hydrocarbon generation potential of the studied source rock. The continued rise of southern Tethyan sea level and global highstands during the Upper Maastrichtian, culminating into Arabian Plate-wide maximum flooding surfaces, cause the migration of upwelling activity away from the study area, terminating the high productivity sequence in the Levant.

Evidence for specific adaptations of fossil benthic foraminifera to anoxic–dysoxic environments

AbstractIt has generally been argued that the majority of fossil benthic foraminifera, the most common proxy for paleo bottom oceanic conditions, could not tolerate anoxia. Here we present evidence that fossil foraminifera were able to successfully colonize anoxic–dysoxic bottom waters, by using adaptations similar to those found in living species. Our study is based on a multi proxy micropaleontological and geochemical investigation of the Upper Cretaceous sediments from the Levant upwelling regime. A shift from buliminid to diverse trochospiral dominated assemblages was recorded in an interval with a distinct anoxic geochemical signature coinciding with a regional change in lithology. This change was triggered by an alteration in the type of primary producers from diatoms to calcareous nannoplankton, possibly causing modifications in benthic foraminiferal morphological and physiological adaptations to life in the absence of oxygen.Our data show that massive blooms of triserial (buliminid) benthic foraminifera with distinct apertural and test morphologies during the Campanian were enabled by their ability to sequester diatom chloroplasts and associate with bacteria, in a similar manner as their modern analogs. Diverse trochospiral forms existed during the Maastrichtian by using nitrate instead of oxygen for their respiratory pathways in a denitrifying environment. Species belonging to the Stilostomellidae and Nodosariidae families might have been affected by the change in food type arriving to the seafloor after the phytoplankton turnover at the Campanian/Maastrichtian boundary, in a similar manner as their mid Pleistocene descendants prior to their extinction. This study promotes the need for a re-evaluation of the current models used for interpreting paleoceanographic data and demonstrates that the identification of adaptations and mechanisms involved in promoting sustained life under anoxic to dysoxic conditions should become a standard in faunal paleoceanographic studies.

Dissecting signal and noise in diatom chloroplast protein encoding genes with phylogenetic information profiling

Previous analyses of single diatom chloroplast protein-encoded genes recovered results highly incongruent with both traditional phylogenies and phylogenies derived from the nuclear encoded small subunit (SSU) gene. Our analysis here of six individual chloroplast genes (atpB, psaA, psaB, psbA, psbC and rbcL) obtained similar anomalous results. However, phylogenetic noise in these genes did not appear to be correlated, and their concatenation appeared to effectively sum their collective signal. We empirically demonstrated the value of combining phylogenetic information profiling, partitioned Bremer support and entropy analysis in examining the utility of various partitions in phylogenetic analysis. Noise was low in the 1st and 2nd codon positions, but so was signal. Conversely, high noise levels in the 3rd codon position was accompanied by high signal. Perhaps counterintuitively, simple exclusion experiments demonstrated this was especially true at deeper nodes where the 3rd codon position contributed most to a result congruent with morphology and SSU (and the total evidence tree here). Correlated with our empirical findings, probability of correct signal (derived from information profiling) increased and the statistical significance of substitutional saturation decreased as data were aggregated. In this regard, the aggregated 3rd codon position performed as well or better than more slowly evolving sites. Simply put, direct methods of noise removal (elimination of fast-evolving sites) disproportionately removed signal. Information profiling and partitioned Bremer support suggest that addition of chloroplast data will rapidly improve our understanding of the diatom phylogeny, but conversely also illustrate that some parts of the diatom tree are likely to remain recalcitrant to addition of molecular data. The methods based on information profiling have been criticized for their numerous assumptions and parameter estimates and the fact that they are based on quartets of taxa. Our empirical results support theoretical arguments that the simplifying assumptions made in these methods are robust to “real-life” situations.

The chloroplast genome of the diatom Seminavis robusta: New features introduced through multiple mechanisms of horizontal gene transfer

The chloroplasts of heterokont algae such as diatoms are the result of a secondary endosymbiosis event, in which a red alga was engulfed by a non-photosynthetic eukaryote. The diatom chloroplast genomes sequenced to date show a high degree of similarity, but some examples of gene replacement or introduction of genes through horizontal gene transfer are known. The evolutionary origin of the gene transfers is unclear. We have sequenced and characterised the complete chloroplast genome and a putatively chloroplast-associated plasmid of the pennate diatom Seminavis robusta. The chloroplast genome contains two introns, a feature that has not previously been found in diatoms. The group II intron of atpB appears to be recently transferred from a Volvox-like green alga. The S. robusta chloroplast genome (150,905bp) is the largest diatom chloroplast genome characterised to date, mainly due to the presence of four large gene-poor regions. Open reading frames (ORFs) encoded by the gene-poor regions show similarity to putative proteins encoded by the chloroplast genomes of different heterokonts, as well as the plasmids pCf1 and pCf2 found in the diatom Cylindrotheca fusiformis. A tyrosine recombinase and a serine recombinase are encoded by the S. robusta chloroplast genome, indicating a possible mechanism for the introduction of novel genes. A plasmid with similarity to pCf2 was also identified. Phylogenetic analyses of three ORFs identified on pCf2 suggest that two of them are part of an operon-like gene cluster conserved in bacteria. Several genetic elements have moved through horizontal gene transfer between the chloroplast genomes of different heterokonts. Two recombinases are likely to promote such gene insertion events, and the plasmid identified may act as vectors in this process. The copy number of the plasmid was similar to that of the plastid genome indicating a plastid localization.

Fluorescent epibiotic microbial community on the carapace of a Bahamian ostracod

Ostracods collected from shallow coral reefs in the Bahamas were found to exhibit blue light-stimulated orange fluorescence at night. Fluorescent spectra revealed the presence of orange fluorescence with a maximum emission at ~595nm on the carapace of these ostracods, while scanning electron microscopy revealed a morphologically diverse microbial community covering the entire carapace of these ostracods. Pyrosequencing and cyanobacterial-specific 16S rRNA sequencing reveals that this epibiont community is highly diverse and highly variable between individual ostracods. Many species of Cyanobacteria in the orders Oscillatoriales and Chroococcales, as well as other Proteobacteria and diatom chloroplast sequences, were identified using the cyanobacterial-specific primers. While no fluorescent proteins or phycoerythrin were detected in these ostracods, it is possible that the observed orange fluorescence is the result of carotenoid fluorescence from Cyanobacteria. The microbial consortium forms an epibiotic biofilm on the carapace of these ostracods whose functions are unknown.

Complete Chloroplast Genome Sequence of Freshwater Araphid Pennate Diatom Alga Synedra acus from Lake Baikal

Complete chloroplast genome of diatom alga Synedra acus possesses canonical quadripartite structure with two inverted repeats containing ribosomal RNA gene loci that separate small and large single-copy regions. Chloroplast genome maps as a circular molecule of 116 251 bp. It encodes 27 tRNAs, three rRNAs, two small RNA genes, and 128 protein-coding genes. Comparison of the genic features across diatom chloroplast genomes reveals the absence of an overlap between atpD and atpF gene coding sequences that is present in other plastid genomes of diatom origin. This feature is a clear synapomorphy of S. acus plastid genome that is likely a result of either relaxed constraints or extensive selection forces acting upon atpF gene. We also characterized nuclear-encoded acyl-carrier protein gene with chloroplastic targeting in S. acus . The transfer of acpp gene into the nuclear host genome is hypothesized to have occurred independently in several lineages of diatoms.

High-throughput pyrosequencing of the chloroplast genome of a highly neutral-lipid-producing marine pennate diatom, Fistulifera sp. strain JPCC DA0580

The chloroplast genome of the highly neutral-lipid-producing marine pennate diatom Fistulifera sp. strain JPCC DA0580 was fully sequenced using high-throughput pyrosequencing. The general features and gene content were compared with three other complete diatom chloroplast genomes. The chloroplast genome is 134,918 bp with an inverted repeat of 13,330 bp and is slightly larger than the other diatom chloroplast genomes due to several low gene-density regions lacking similarity to the other diatom chloroplast genomes. Protein-coding genes were nearly identical to those from Phaeodactylum tricornutum. On the other hand, we found unique sequence variations in genes of photosystem II which differ from the consensus in other diatom chloroplasts. Furthermore, five functional unknown ORFs and a putative serine recombinase gene, serC2, are located in the low gene-density regions. SerC2 was also identified in the plasmids of another pennate diatom, Cylindrotheca fusiformis, and in the plastid genome of the diatom endosymbiont of Kryptoperidinium foliaceum. Exogenous plasmids might have been incorporated into the chloroplast genome of Fistulifera sp. by lateral gene transfer. Chloroplast genome sequencing analysis of this novel diatom provides many important insights into diatom evolution.

Recurring Seasonal Dynamics of Microbial Communities in Stream Habitats

Recurring seasonal patterns of microbial distribution and abundance in three third-order temperate streams within the southeast Pennsylvania Piedmont were observed over 4 years. Populations associated with streambed sediments and rocks (epilithon) were identified using terminal restriction length polymorphism (tRFLP) and sequencing of 16S rRNA genes selectively amplified with primers for the bacterial domain. Analyses of the relative magnitudes of tRFLP peak areas by using nonmetric multidimensional scaling resolved clear seasonal trends in epilithic and sediment populations. Oscillations between two dominant groups of epilithic genotypes, explaining 86% of the seasonal variation in the data set, were correlated with temperature and dissolved organic carbon. Sequences affiliated with epilithic phototrophs (cyanobacteria and diatom chloroplasts), a Rhodoferax sp., and a Bacillus species clustered in the summer, whereas sequences most closely related to "Betaproteobacteria" (putative Burkholderia sp.), and a putative cyanobacterium clustered in the fall/spring. The sediment genotypes also clustered into two groups, and these explained 85% of seasonal variation but correlated only with temperature. A summer tRFLP pattern was characterized by prevalence of "Betaproteobacteria," "Gammaproteobacteria," and a Bacillus sp., whereas the winter/spring pattern was characterized by phylotypes most closely related to "Firmicutes," "Gammaproteobacteria," and "Nitrospirae." A close association between these headwater streams and their watersheds was suggested by the recovery of sequences related to microbial populations provisionally attributed to not only freshwaters but also terrestrial habitats.

Intriguing microbial diversity associated with metal-rich particles from a freshwater reservoir

During the late summer to early fall, Horsetooth Reservoir in Fort Collins, CO, USA is fully stratified and exhibits seasonally high fluxes of iron, manganese, and metal-rich particles into the water column. Particles were collected from the mid-region of the hypolimnion and examined for metal content. Nucleic acids extracted from the particles were used to construct bacterial and archaeal 16S rDNA clone libraries. Surprisingly, 50% of cloned bacterial genes were closely related to a coherent cluster within Candidate Division OP10. To our knowledge, this is the first report of an environmental gene clone library that exhibits a dominance of OP10-related clones. Several other sequences, many with long branch lengths, clustered within eight separate bacterial divisions and the diatom chloroplasts. Most of these divisions are commonly found in freshwater environments. However, gene sequences from characterized metal-oxidizing or metal-reducing bacteria were not identified. The archaeal gene clone libraries contained diverse sequences, most with close homology to previously characterized gene clones of methanogens or uncultivated Crenarchaeota from soil and lacustrine environments. This study identified a unique environment where OP10 bacteria are potentially abundant. Furthermore, we demonstrated that the metal-rich particles from this reservoir support a diverse and interesting community of microorganisms.

Intriguing microbial diversity associated with metal-rich particles from a freshwater reservoir

During the late summer to early fall, Horsetooth Reservoir in Fort Collins, CO, USA is fully stratified and exhibits seasonally high fluxes of iron, manganese, and metal-rich particles into the water column. Particles were collected from the mid-region of the hypolimnion and examined for metal content. Nucleic acids extracted from the particles were used to construct bacterial and archaeal 16S rDNA clone libraries. Surprisingly, 50% of cloned bacterial genes were closely related to a coherent cluster within Candidate Division OP10. To our knowledge, this is the first report of an environmental gene clone library that exhibits a dominance of OP10-related clones. Several other sequences, many with long branch lengths, clustered within eight separate bacterial divisions and the diatom chloroplasts. Most of these divisions are commonly found in freshwater environments. However, gene sequences from characterized metal-oxidizing or metal-reducing bacteria were not identified. The archaeal gene clone libraries contained diverse sequences, most with close homology to previously characterized gene clones of methanogens or uncultivated Crenarchaeota from soil and lacustrine environments. This study identified a unique environment where OP10 bacteria are potentially abundant. Furthermore, we demonstrated that the metal-rich particles from this reservoir support a diverse and interesting community of microorganisms.

Stability and deformation of diatom chloroplasts during food uptake of the parasitic dinoflagellate, Paulsenella (Dinophyta)

Chloroplasts of the diatom, Streptotheca thamesis, are considerably deformed when they pass the feeding tube of the parasitic dinoflagellate, Paulsenella sp. Nevertheless, chloroplasts resume their normal shape and structure inside the food vacuole. Even the chloroplast ER is partially preserved. The feeding tube channel of Paulsenella chaetoceratis is narrow (about 0.2 μm in diameter) and may be very long (generally 100 μm). The feeding tube invades a seta of Chaetoceros decipiens through the apical or a lateral aperture and elongates until reaching the cell body of the host. The host chloroplasts are ruptured when they pass the feeding tube. However, large stacks of thylakoids remain intact. Stability of diatom chloroplasts and thylakoid stacks may be important in plankton research, e.g. using chlorophyll determinations as a measure for biomass production.

Abundance of nanoplankton-size chlorophyll-containing particles caused by diatom disruption in surface waters of the Southern Ocean (Antarctic Pensinsula region)

In samples taken during a cruise to the western Atlantic sector of the Southern Ocean (Antarctic Peninsula region), between 10 and 80% of chlorophyll a containing particles were smaller than 8 μm. At stations in the northern part of the survey area the percentage was highest; in the south (southern Bransfield Straits and northern Weddell Sea) most chlorophyll a was found in larger diatoms. Microscopic observations revealed that in many samples more than 50% of the nanoplankton-size chlorophyll-containing particles were free-floating chloroplasts; the relative abundance of 19′-hexanoyloxyfucoxanthin in acetone extracts of suspended matter indicates that the nanophytoplankton itself consisted mostly of Prymnesiophyceae (Haptophyceae). Experiments showed that diatom chloroplasts remain fluorescent for several days after cell disruption at the low temperature prevailing in the Southern Ocean. Evidence is presented that causes of algal cell disruption in the field include mechanical effects on cells during storms and during grazing by krill. Spatial variability in the proportion of chlorophyll a not associated with viable phytoplankton cells may impede the use of chlorophyll a as a measure of biomass and of primary productivity during large-scale surveys.

Isolation and characterization of cytoplasmic and chloroplastic ribosomes and their ribosomal RNAs from the diatom Cylindrotheca fusiformis.

The cytoplasmic and chloroplast ribosomes from the marine diatom Cylindrotheca fusiformis were isolated and characterized. The cytoplasmic ribosomes sedimented in sucrose at 84S and dissociated into subunits of 64S and 42S in the absence of Mg2+. It contained ribosomal RNAs with molecular weights of 1.31 X 10(6) and 0.70 X 10(6). The chloroplast ribosomes sedimented at 70S only in the presence of high Mg2+ concentrations (25-100 mM). No stable subunits were routinely observed and at very high levels of Mg2+ (greater than 100 mM) the 70S species was converted to a form sedimenting at 55S. At 4 degrees C ribosomal RNAs with molecular weights of 1.1 X 10(6) and 0.40 X 10(6) were detected on polyacrylamide gel electrophoresis. When the RNAs were resolved at room temperature the large molecular weight component disappeared while RNA with molecular weights of 0.65 X 10(6) and 0.53 X 10(6) were observed. Apparently the large chloroplast RNAs dissociated into two pieces of unequal molecular weight. These properties of the diatom's chloroplast ribosomes are very similar to those of the counterparts in unicellular green algae, which suggests that both types of algae have a common phylogenetic ancestor.