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Background and aims - We examine the possibility of the independent evolution of the same features multiple times across the pennate diatom tree of life. Methods and key results - Features we have studied include symmetry, raphe number and amphoroid symmetry. Phylogenetic analysis, with both morphological and molecular data suggest in each of these cases that the features evolved from 5 to 6 times independently. We also look at the possibility of certain features having evolved once and diagnosing large genera of diatoms, suggestive of an adaptive radiation in genera such as Mastogloia, Diploneis and Stauroneis. Conclusion - Formal phylogenetic analyses and recognition of monophyletic groups allow for the recognition of homoplasious or homologous features. [ABSTRACT FROM AUTHOR]

Silicon transporters (SIT) are the proteins, which capture silicic acid in the aquatic environment and direct it across the plasmalemma to the cytoplasm of diatoms. Diatoms utilize silicic acid to build species-specific ornamented exoskeletons and make a significant contribution to the global silica cycle, estimated at 240 ±40 Tmol a year. Recently SaSIT genes of the freshwater araphid pennate diatom Synedra acus subsp. radians are found to be present in the genome as a cluster of two structural genes (SaSIT-TD and SaSIT-TRI) encoding several concatenated copies of a SIT protein each. These structural genes could potentially be transformed into “mature” SIT proteins by means of posttranslational proteolytic cleavage. In the present study, we discovered three similar structural SuSIT genes in the genome of a closely related freshwater diatom Synedra ulna subsp. danica. Structural gene SuSIT1 is identical to structural gene SuSIT2, and the two are connected by a non-coding nucleotide DNA sequence. All the putative “mature” SITs contain conserved amino acid motifs, which are believed to be important in silicon transport. The data obtained suggest that the predicted “mature” SIT proteins may be the minimal units necessary for the transport of silicon is S. ulna subsp. danica. The comparative analysis of all available multi-SITs has allowed us to detect two conservative motifs YQXDXVYL and DXDID, located between the “mature” proteins. Aspartic acid-rich DXDID motif can, in our opinion, serve as a proteolysis site during the multi-SIT cleavage. The narrow distribution of the distances between CMLD and DXDID motifs can serve as additional evidence to the conservation of their function. [ABSTRACT FROM AUTHOR]

The diatoms are one of the most important groups of organisms for biomonitoring studies. In Turkey, most previous applications of diatoms to water quality monitoring have focused on the pennate diatoms, with almost no attention given to the centric forms. The paper presents the centric diatoms in some river catchments in Central Anatolia (Konya closed catchment and Kızılırmak) and Western Anatolia (Marmara, Sakarya, Susurluk, Akarçay, Küçük Menderes, and Meriç-Ergene in the Marmara and Aegean regions). The survey of these catchments is based on samples collected between 2009 and 2013 from 33 different locations, including some springs from Türkmen Mountain and Domaniç forest, as well as small streams and big rivers of the Anatolian Peninsula. Altogether 30 taxa were found, of which 14 are new records for the freshwater diatom flora of Turkey. [ABSTRACT FROM AUTHOR]

A high-resolution diatom analysis of a varved sediment sequence from Lac Brûlé, southwestern Québec, was used to study temporal patterns of environmental change in the late Holocene. Key periods of interest in the record included theMedievalWarm Period (~800-1300 CE), the Little Ice Age (~1450-1850 CE), and post-European settlement (~1850-present). Subfossil diatom assemblages were compared to previously published pollen, cladocera, and sediment records from Lac Brûlé, revealing complex dynamics between terrestrial vegetation succession, nutrient fluxes, and trophic interactions. Generalized additive models showed a response to long-term climate variability in the diatom record, although it was not the most influential driver of community changes at Lac Brûlé. Catchment-mediated processes instead played the largest role in governing the structure of diatom assemblages in the lake. For example, nutrient loading following a local fire in the watershed at 1345 CE led to an abrupt and significant increase in Fragilaria spp. Human activity associated with deforestation and the Wallingford-Back Mine (1924-1972 CE) also had strong impacts on the landscape, which triggered further responses in the aquatic communities of Lac Brûlé. [ABSTRACT FROM AUTHOR]

Pre-ingestive selection has been identified as a feeding mechanism of oysters that may influence their uptake of particles and microalgal cells. Oysters can feed specifically on the pennate diatom Haslea ostrearia, which produces the blue pigment marennine that is responsible for the greening of oysters. Because the size of particles or cells plays a significant role in the selection process, and given that diatoms experience a decrease in size as a consequence of vegetative reproduction, H. ostrearia consumption and marennine uptake might be influenced by pre-ingestive selection. We examined the role of H. ostrearia cell size in the selective feeding of Crassostrea gigas. Individual flow-through chambers were used to deliver mixtures of H. ostrearia of varying cell length to oysters. Inflow, outflow and pseudofaecal samples were collected from chambers during oyster feeding. Video-endoscopy was used to sample material in the dorsal and ventral particle tracts. Diatom cells counts showed that pseudofaeces contained on average larger cells than the ambient medium. However, proportions of the different populations of H. ostrearia in pseudofaeces were identical to those in the ventral tracts, indicating that no selection was performed by the labial palps. Video-endoscopy, plus imaging by scanning electron microscopy, of gills and labial palps revealed that only those larger H. ostrearia that were orientated dorsoventrally could enter the principal filaments (pfs) and then access the dorsal acceptance tract. These results show that for particles like Haslea cells with only one axis exceeding the width of the pfs, the selection on the oyster gills is passive and based on cell size. [ABSTRACT FROM AUTHOR]

In the open Southern Ocean (SO), both modern and past size changes of the diatom Fragilariopsis kerguelensis appear to be strongly controlled by iron availability. Conversely, sea surface temperatures (SST) and sea ice seasonal dynamics take over in the seasonal sea-ice zone where iron is not limiting. No information exists on F. kerguelensis biometry from the subtropical SO, on the other extreme of the thermal and nutrient gradients. We present here new data on mean valve area of F. kerguelensis (FkergArea) from a sediment core covering the last ~42 cal kyrs from the southern Subtropical Front (SSTF) of the Indian sector of the SO, where iron and silica stocks are thought to have been consistently low over this period. Our results suggest that larger F. kerguelensis valves occurred during the Last Glacial period, and declined during the Holocene period. These findings indicate that more favourable SST, within the F. kerguelensis ecological range, during the Last Glacial period may have enabled F. kerguelensis to make better use of the low silica stocks prevailing in the subtropical zone leading to larger valves. Conversely, declining FkergArea during the deglacial and the Holocene periods may have been a result of higher SST which hampered the utilization of silica. [ABSTRACT FROM AUTHOR]

When grown under intermittent light (IL), the pennate diatom Phaeodactylum tricornutum forms ‘super’ non-photochemical fluorescence quenching (NPQ) in response to excess light. The current model of diatom NPQ mechanism involves two quenching sites, one of which detaches from photosystem II reaction centres (RCIIs) and aggregates into oligomeric complexes. Here we addressed how antenna reorganisation controls NPQ kinetics in P. tricornutum cells grown under continuous light (CL) and IL. Overall, IL acclimation induced: (i) reorganisation of chloroplasts, containing greater pigment pools without a strongly enhanced operation of the xanthophyll cycle, and (ii) ‘super NPQ’ causing a remarkable reduction of the chlorophyll excited state lifetime at Fm′. Regardless of different levels of NPQ formed in both culture conditions, its dark recovery was rapid and similar fractions of their antenna uncoupled (~ 50%). Although antenna detachment relieved excitation pressure, it provided a minor protective contribution equivalent to NPQ ~ 1, while the largest NPQ was 4.4 ± 0.2 (CL) and 13 ± 0.8 (IL). The PSII cross-section decrease took place only at relatively low NPQ values, beyond which the cross-section remained constant whilst NPQ continued to rise. This finding suggests that the energy trapping efficiency of diatom antenna quenchers cannot over-compete that of RCIIs, similarly to what has been observed on higher plants. We conclude that such ‘economic photoprotection’ operates to flexibly adjust the overall efficiency of diatom light harvesting. [ABSTRACT FROM AUTHOR]

The remarkable adaptability of diatoms living in a highly variable environment assures their prominence among marine primary producers. The present study integrates biochemical, biophysical and genomic data to bring new insights into the molecular mechanism of chromatic adaptation of pennate diatoms in model species Phaeodactylum tricornutum , a marine eukaryote alga possessing the capability to shift its absorption up to ~ 700 nm as a consequence of incident light enhanced in the red component. Presence of these low energy spectral forms of Chl a is manifested by room temperature fluorescence emission maximum at 710 nm (F710). Here we report a successful isolation of the supramolecular protein complex emitting F710 and identify a member of the Fucoxanthin Chlorophyll a / c binding Protein family, Lhcf15, as its key building block. This red-shifted antenna complex of P. tricornutum appears to be functionally connected to photosystem II. Phylogenetic analyses do not support relation of Lhcf15 of P . tricornutum to other known red-shifted antenna proteins thus indicating a case of convergent evolutionary adaptation towards survival in shaded environments. [ABSTRACT FROM AUTHOR]

Fistulifera sp. strain JPCC DA0580 is a newly sequenced pennate diatom that is capable of simultaneously growing and accumulating lipids. This is a unique trait, not found in other related microalgae so far. It is able to accumulate between 40 to 60% of its cell weight in lipids, making it a strong candidate for the production of biofuel. To investigate this characteristic, we used RNA-Seq data gathered at four different times while Fistulifera sp. strain JPCC DA0580 was grown in oil accumulating and non-oil accumulating conditions. We then adapted gene set enrichment analysis (GSEA) to investigate the relationship between the difference in gene expression of 7,822 genes and metabolic functions in our data. We utilized information in the KEGG pathway database to create the gene sets and changed GSEA to use re-sampling so that data from the different time points could be included in the analysis. Our GSEA method identified photosynthesis, lipid synthesis and amino acid synthesis related pathways as processes that play a significant role in oil production and growth in Fistulifera sp. strain JPCC DA0580. In addition to GSEA, we visualized the results by creating a network of compounds and reactions, and plotted the expression data on top of the network. This made existing graph algorithms available to us which we then used to calculate a path that metabolizes glucose into triacylglycerol (TAG) in the smallest number of steps. By visualizing the data this way, we observed a separate up-regulation of genes at different times instead of a concerted response. We also identified two metabolic paths that used less reactions than the one shown in KEGG and showed that the reactions were up-regulated during the experiment. The combination of analysis and visualization methods successfully analyzed time-course data, identified important metabolic pathways and provided new hypotheses for further research. [ABSTRACT FROM AUTHOR]

Could the abundant sulfate salts on Mars contain microfossils and/or viable microorganisms? Here we report a variety of microorganisms trapped both as solid inclusions and as potentially viable halophilic and acidophilic prokaryotes and eukaryotes within fluid inclusions in Mars-analog gypsum. We have documented pennate diatoms, green algae, and prokaryotes in gypsum precipitated from acid (pH 1.8-4.6) saline (5%-28% total dissolved solids) waters at Salars Gorbea and Ignorado in an active volcanic terrain in the high Andes (4000+ m) of northern Chile. These salars are strikingly similar in geology and geochemistry to Mars. We propose that this discovery should serve as a model for fossilization of possible life on Mars and may inform methodologies used in future missions to Mars. Furthermore, the potential long-term viability of microorganisms within fluid inclusions in gypsum suggests the possibility of a living, yet isolated and likely dormant, microbiological community on Mars today. [ABSTRACT FROM AUTHOR]

Diatoms represent an important class of aquatic phototrophs. They are not only one of the major contributors to global carbon fixation, but they also play a key role in the biogeochemical cycling of silica. Molecular identification methods based on conserved DNA sequences, such as internal transcribed spacer (ITS) have revolutionized our knowledge and understanding of conventional taxonomy. In this study, we aimed to compare the conventional identification methods with molecular identification methods. To do so, we isolated 4 diatom samples from the coast at Urla and characterized them using light microscopy (LM) and scanning electron microscopy (SEM) according to morphological features. Then we amplified ITS regions using a conventional polymerase chain reaction (PCR), sequenced the PCR products, and analyzed the sequences using bioinformatic tools. Bioinformatic analysis indicated that the isolated species had high sequence similarity to Pseudo-nitzschia delicatissima, Achnanthes taeniata, Amphora coffeaeformis, and Cylindrotheca closterium. We think that molecular identification methods enable rapid and more reliable identification of diatom species and are crucial for monitoring harmful algal blooms. [ABSTRACT FROM AUTHOR]

A novel ferritin was recently found in Pseudo-nitzschia multiseries (PmFTN), a marine pennate diatom that plays a major role in global primary production and carbon sequestration into the deep ocean. Crystals of recombinant PmFTN were soaked in iron and zinc solutions, and the structures were solved to 1.65- 2.2-Å resolution. Three distinct iron binding sites were identified as determined from anomalous dispersion data from aerobically grown ferrous soaked crystals. SitesAandBcomprise the conserved ferroxidase active site, and site C forms a pathway leading toward the central cavity where iron storage occurs. In contrast, crystal structures derived from anaerobically grown and ferrous soaked crystals revealed only one ferrous iron in the active site occupying site A. In the presence of dioxygen, zinc is observed bound to all three sites. Iron oxidation experiments using stopped-flow absorbance spectroscopy revealed an extremely rapid phase corresponding to Fe(II) oxidation at the ferroxidase site, which is saturated after adding 48 ferrous iron to apo-PmFTN (two ferrous iron per subunit), and a much slower phase due to iron core formation. These results suggest an ordered stepwise binding of ferrous iron and dioxygen to the ferroxidase site in preparation for catalysis and a partial mobilization of iron from the site following oxidation. [ABSTRACT FROM AUTHOR]

The pennate diatom Seminavis robusta, characterized by an archetypical diatom life cycle including a heterothallic mating system, is emerging as a model system for studying the molecular regulation of the diatom cell and life cycle. One of its main advantages compared with other diatom model systems is that sexual crosses can be made routinely, offering unprecedented possibilities for forward genetics. To date, nothing is known about the genetic basis of sex determination in diatoms. Here, we report on the construction of mating type-specific linkage maps for S. robusta, and use them to identify a single locus sex determination system in this diatom. We identified 13 mating type plus and 15 mating type minus linkage groups obtained from the analysis of 463 AFLP markers segregating in a full-sib family, covering 963.7 and 972.2 cM, respectively. Five linkage group pairs could be identified as putative homologues. The mating type phenotype mapped as a monogenic trait, disclosing the mating type plus as the heterogametic sex. This study provides the first evidence for a genetic sex determining mechanism in a diatom. [ABSTRACT FROM AUTHOR]

Abstract: Diatoms are major contributors to the photosynthetic productivity of marine phytoplankton. In these organisms, fucoxanthin-chlorophyll proteins (FCPs) serve as light-harvesting proteins. We have explored the FCP complexes in Phaeodactylum tricornutum under low light (LL) and high light (HL) conditions. Sub-fractionating the pool of major FCPs yielded different populations of trimeric complexes. Only Lhcf and Lhc-like proteins were found in the trimers. Under LL, the first polypeptide fraction contained six different Lhcfs and was mainly composed of Lhcf10. It was characterised by the highest amount of fucoxanthin (Fx). The second was dominated by Lhcf10, Lhcf5 and Lhcf2, and had a lower Fx/Chl c ratio. Little Fx/Chl c also characterised the most abundant FCP complexes, found in fraction 3, composed mainly of Lhcf5. These FCPs bound Fx molecules with the strongest bathochromic shift. The last two fractions contained FCP complexes that were built mainly of Lhcf4, harbouring more Fx molecules that absorbed at shorter wavelengths. Under HL, the same main polypeptides were retrieved in the different fractions and spectroscopic features were almost identical except for a higher diadinoxanthin content. The total amount of Lhcf5 was reduced under HL, whereas the amount of the last two fractions and thereby Lhcf4 was increased. Lhcf11 was identified in different LL fractions, but not detected in any HL fraction, while two new Lhc-like proteins were only found under HL. This is the first report on different trimeric FCP complexes in pennate diatoms, which differ in polypeptide composition and pigmentation, and are differentially expressed by light. [Copyright &y& Elsevier]

The pennate diatom Seminavis robusta, characterized by an archetypical diatom life cycle including a heterothallic mating system, is emerging as a model system for studying the molecular regulation of the diatom cell and life cycle. One of its main advantages compared with other diatom model systems is that sexual crosses can be made routinely, offering unprecedented possibilities for forward genetics. To date, nothing is known about the genetic basis of sex determination in diatoms. Here, we report on the construction of mating type-specific linkage maps for S. robusta, and use them to identify a single locus sex determination system in this diatom. We identified 13 mating type plus and 15 mating type minus linkage groups obtained from the analysis of 463 AFLP markers segregating in a full-sib family, covering 963.7 and 972.2 cM, respectively. Five linkage group pairs could be identified as putative homologues. The mating type phenotype mapped as a monogenic trait, disclosing the mating type plus as the heterogametic sex. This study provides the first evidence for a genetic sex determining mechanism in a diatom. [ABSTRACT FROM AUTHOR]

Diatoms are considered the most successful and widespread group of photosynthetic eukaryotes. Their contribution to primary production is remarkably significant to the earth's ecosystems. Diatoms are composed of two orders: Centrales and Pennales. Thus far, viruses infecting centric diatom species have been isolated and characterized; however, viruses infecting pennates have not been reported. Here, we describe the first isolations and preliminary characterizations of two distinct pennate diatom viruses, AglaRNAV (31 nm in diameter, accumulates in the host cytoplasm) and TnitDNAV (35 nm in diameter, accumulates in the host nuclei) infecting Asterionellopsis glacialis and Thalassionema nitzschioides, respectively. Their genomes contain a single-stranded RNA of approximately 9.5 kb, and a closed, circular single-stranded DNA of approximately 5.5 kb harboring a partially double-stranded region, respectively. Further analysis of these viruses may elucidate many aspects of diatom host-virus relationships. [ABSTRACT FROM AUTHOR]

The copepod Temora stylifera was fed with the pennate diatom Pseudo- nitzschia delicatissima for 15 days. This diatom does not produce polyunsaturated aldehydes (PUAs) but only synthesizes other oxylipins such as the hydroxyacid (5Z,8Z,11Z,13E,15S,17Z)-15-hydroxy-5,8,11,13,17-eicosapentaenoic acid (15S-HEPE). Effects of this monoalgal diet were compared to copepods fed with the PUA-producing diatom Skeletonema marinoi and the control dinoflagellate Prorocentrum minimum which does not produce any oxylipins. Both egg production and hatching success were negatively affected by the two diatoms compared to the control diet. Both diatoms also induced malformations in the offspring, with the number of malformed nauplii increasing dramatically with time. Malformed nauplii were apoptotic (TUNEL-positive) indicating imminent death. In terms of recruitment, only 4 healthy nauplii female day with S. marinoi and 9 healthy nauplii female day with P. delicatissima were produced during the 15-day experimental period. The results indicate that P. delicatissima induced negative effects comparable to those of S. marinoi even though it did not produce PUAs. This is the first study that tests the biological activity of oxylipins other than PUAs on copepod reproduction. [ABSTRACT FROM AUTHOR]

The pennate diatom Rhopalodia gibba harbours unusual cell inclusions termed spheroid bodies. These originated from unicellular cyanobacteria and are obligate intracellular endosymbionts with the ability to fix molecular nitrogen. As indicated by the fossil record, this endosymbiosis might be relatively young, thus making R. gibba an interesting model to study early stages of organelle development at the genetic as well as at the physiological level Here we describe a protocol for the cultivation of Rhopalodia gibba. [ABSTRACT FROM AUTHOR]

Background: Diatoms are largely responsible for production of biogenic silica in the global ocean. However, in surface seawater, Si(OH)4 can be a major limiting factor for diatom productivity. Analyzing at the global scale the genes networks involved in Si transport and metabolism is critical in order to elucidate Si biomineralization, and to understand diatoms contribution to biogeochemical cycles. Methodology/Principal Findings: Using whole genome expression analyses we evaluated the transcriptional response to Si availability for the model species Phaeodactylum tricornutum. Among the differentially regulated genes we found genes involved in glutamine-nitrogen pathways, encoding putative extracellular matrix components, or involved in iron regulation. Some of these compounds may be good candidates for intracellular intermediates involved in silicic acid storage and/or intracellular transport, which are very important processes that remain mysterious in diatoms. Expression analyses and localization studies gave the first picture of the spatial distribution of a silicic acid transporter in a diatom model species, and support the existence of transcriptional and post-transcriptional regulations. Conclusions/Significance: Our global analyses revealed that about one fourth of the differentially expressed genes are organized in clusters, underlying a possible evolution of P. tricornutum genome, and perhaps other pennate diatoms, toward a better optimization of its response to variable environmental stimuli. High fitness and adaptation of diatoms to various Si levels in marine environments might arise in part by global regulations from gene (expression level) to genomic (organization in clusters, dosage compensation by gene duplication), and by post-transcriptional regulation and spatial distribution of SIT proteins. [ABSTRACT FROM AUTHOR]

• In recent years, oxylipins (lipoxygenase-derived oxygenated fatty acid products) have been reported in several bloom-forming marine diatoms. Despite increasing attention on the ecophysiological role of these molecules in marine environments, their biosynthesis is largely unknown in these microalgae. • Biochemical methods, including tandem mass spectrometry, nuclear magnetic resonance and radioactive probes were used to identify structures, enzymatic activities and growth-dependent modulation of oxylipin biosynthesis in the pennate diatom Pseudo-nitzschia delicatissima. • Three major compounds, 15S-hydroxy-(5 Z,8 Z,11 Z,13 E,17 Z)-eicosapentaenoic acid (15S-HEPE), 15-oxo-5Z,9 E,11 E,13 E-pentadecatetraenoic acid and 13,14- threo-13 R-hydroxy-14 S,15 S- trans-epoxyeicosa-5 Z,8 Z,11 Z,17 Z-tetraenoic acid (13,14-HEpETE), were produced by three putative biochemical pathways triggered by eicosapentaenoic acid-dependent 15S lipoxygenase. Oxylipin production increases along the growth curve, with remarkable changes that precede the demise of the culture. At least one of the compounds, namely 15-oxoacid, is formed only in the stationary phase immediately before the collapse of the culture. • Synthesis and regulation of phyco-oxylipins seem to correspond to a signaling mechanism that governs adaptation of diatoms along the growth curve until bloom termination. Factors triggering the process are unknown but synthesis of 15-oxoacid, constrained within a time-window of a few days just before the collapse of the culture, implies the involvement of a physiological control not directly dependent on distress or death of diatom cells. [ABSTRACT FROM AUTHOR]

In Mexico there is little information about the symbiotic associations among diatoms on other marine microalgae and particularly, ciliates and marine planktonic crustaceans. For that reason, we report the first record of the epizoic symbiosis between the copepod Farranula gibbula and the diatom Pseudohimantidium pacificum as well as other microalgae associations with marine ciliates in Bahía de La Paz. Biological samples were collected using a 20-μm mesh plankton net in six sampling sites in Bahía de La Paz. Sixty-two male copepods of F. gibbula were found. From these, 27 specimens showed a bouquet composed of the diatom P. pacificum on its carapace. Average abundance values of P. pacificum for each sampling station ranged from 16 to 82 diatoms per copepod. Pennate diatoms were observed as epibionts on copepods belonging to the genus Acartia. In addition, other symbiotic relationships among ciliates, microalgae and cianobacteria were also encountered, outstanding the following ones: Chaetoceros coarctatum-Vorticella oceanica, Leptocylindrus mediterraneus-Solenicola setigera. The association between the diatom Fragilariopsis doliolus and the silicoflagellate Dictyocha pentagona with a Vorticella-like ciliate is reported for the first time. [ABSTRACT FROM AUTHOR]

Primary productivity in 30–40% of the world’s oceans is limited by availability of the micronutrient iron. Regions with chronically low iron concentrations are sporadically pulsed with new iron inputs by way of dust or lateral advection from continental margins. Addition of iron to surface waters in these areas induces massive phytoplankton blooms dominated primarily by pennate diatoms. Here we provide evidence that the bloom-forming pennate diatoms Pseudo-nitzschia and Fragilariopsis use the iron-concentrating protein, ferritin, to safely store iron. Ferritin has not been reported previously in any member of the Stramenopiles, a diverse eukaryotic lineage that includes unicellular algae, macroalgae and plant parasites. Phylogenetic analyses suggest that ferritin may have arisen in this small subset of diatoms through a lateral gene transfer. The crystal structure and functional assays of recombinant ferritin derived from Pseudo-nitzschia multiseries reveal a maxi-ferritin that exhibits ferroxidase activity and binds iron. The protein is predicted to be targeted to the chloroplast to control the distribution and storage of iron for proper functioning of the photosynthetic machinery. Abundance of Pseudo-nitzschia ferritin transcripts is regulated by iron nutritional status, and is closely tied to the loss and recovery of photosynthetic competence. Enhanced iron storage with ferritin allows the oceanic diatom Pseudo-nitzschia granii to undergo several more cell divisions in the absence of iron than the comparably sized, oceanic centric diatom Thalassiosira oceanica. Ferritin in pennate diatoms probably contributes to their success in chronically low-iron regions that receive intermittent iron inputs, and provides an explanation for the importance of these organisms in regulating oceanic CO2 over geological timescales. [ABSTRACT FROM AUTHOR]

Diatoms are photosynthetic secondary endosymbionts found throughout marine and freshwater environments, and are believed to be responsible for around one-fifth of the primary productivity on Earth. The genome sequence of the marine centric diatom Thalassiosira pseudonana was recently reported, revealing a wealth of information about diatom biology. Here we report the complete genome sequence of the pennate diatom Phaeodactylum tricornutum and compare it with that of T. pseudonana to clarify evolutionary origins, functional significance and ubiquity of these features throughout diatoms. In spite of the fact that the pennate and centric lineages have only been diverging for 90 million years, their genome structures are dramatically different and a substantial fraction of genes (∼40%) are not shared by these representatives of the two lineages. Analysis of molecular divergence compared with yeasts and metazoans reveals rapid rates of gene diversification in diatoms. Contributing factors include selective gene family expansions, differential losses and gains of genes and introns, and differential mobilization of transposable elements. Most significantly, we document the presence of hundreds of genes from bacteria. More than 300 of these gene transfers are found in both diatoms, attesting to their ancient origins, and many are likely to provide novel possibilities for metabolite management and for perception of environmental signals. These findings go a long way towards explaining the incredible diversity and success of the diatoms in contemporary oceans. [ABSTRACT FROM AUTHOR]

Diatom blooms in the middle reaches of the shallow, freshwater, Hunter River, Australia, are a frequent nuisance to river users. During a 4-year study, blooms of Cyclotella meneghiniana and Nitzschia spp. coincided with water temperatures above 23°C and flows below 400 Ml d−1 that lasted for more than 12 days. Redundancy analysis showed that water temperature was positively related, and antecedent flow was negatively related, to the abundance of both taxa. Addition experiments indicated that nutrients are seldom limiting to growth. It is suggested that a combination of faster growth rates at higher temperatures and longer retention times at low flows allows bloom populations to develop. Simulation modelling showed that flow regulation and water extraction have decreased flows in the river during summer, and consequently have probably increased the number of diatom blooms. Environmental flows have been provided to the river, but are not sufficient to prevent blooms. Discharges required for bloom suppression are described. [ABSTRACT FROM AUTHOR]

The association of Phaeocystis spp. with small pennate diatoms during three Phaeocystis-dominated spring blooms were investigated in the Eastern English Channel (2003 and 2004) and in coastal waters of Western Norway during a mesocosm experiment (2005). In each of these studies, colonization of the surface of large Phaeocystis spp. colonies by small needle-shaped diatoms ( Pseudo-nitzschia spp.) were observed. In the English Channel the diatom Pseudo-nitzschia delicatissima colonized the surface of large (>100 μm) Phaeocystis globosa colonies. The abundance of Pseudo-nitzschia delicatissima reached 130 cells per colony and formed up to 70% of the total carbon associated with Phaeocystis cells during late bloom stages. In Norwegian waters, the surface of large (>250 μm) Phaeocystis pouchetii colonies were colonized by Pseudo-nitzschia cf. granii var. curvata and to a lesser degree by other phytoplankton and protist species, although the abundance of these diatoms was never greater than 40 cells per colony. Based on these observations we suggest that diatoms utilize Phaeocystis colonies not only as habitat, but that they are able to utilize the colonial matrix as a growth substrate. Furthermore, these observations indicate that a considerable fraction of biomass (chlorophyll) associated with Phaeocystis colonies, especially large colonies concerned with intense and prolonged blooms, are due to co-occurring plankton species and not exclusively Phaeocystis cells. [ABSTRACT FROM AUTHOR]

Diatoms are one of the most important constituents of phytoplankton communities in aquatic environments, but in spite of this, only recently have large-scale diatom-sequencing projects been undertaken. With the genome of the centric species Thalassiosira pseudonana available since mid-2004, accumulating sequence information for a pennate model species appears a natural subsequent aim. We have generated over 12,000 expressed sequence tags (ESTs) from the pennate diatom Phaeodactylurn tricornutum, and upon assembly into a nonredundant set, 5,108 sequences were obtained. Significant similarity (E < 1E-04) to entries in the GenBank nonredundant protein database, the COG profile database, and the Pfam protein domains database were detected, respectively, in 45.0%, 21.5%, and 37.1% of the nonredundant collection of sequences. This information was employed to functionally annotate the P. tricornutum nonredundant set and to create an internet-accessible queryable diatom EST database. The nonredundant collection was then compared to the putative complete proteomes of the green alga Chlamydomonas reinhardtii, the red alga Cyanidioschyzon rnerolae, and the centric diatom T pseudonana. A number of intriguing differences were identified between the pennate and the centric diatoms concerning activities of relevance for general cell metabolism, e.g. genes involved in carbon-concentrating mechanisms, cytosolic acetyl-Coenzyme A production, and fructose-1,6-bisphosphate metabolism. Finally, codon usage and utilization of C and G relative to gene expression (as measured by EST redundance) were studied, and preferences for utilization of C and CpG doublets were noted among the P. tricornutum EST coding sequences. [ABSTRACT FROM AUTHOR]

We studied the silicic acid uptake kinetics of the pennate diatom Cylindrotheca fusiformis grown under a wide range of iron concentrations (from Fe-limiting to Fe-sufficient conditions) to assess the effect of iron availability on diatom cell size, silicon content, and silicic acid uptake kinetic parameters. As the iron stress increased, the growth rate slowed, cell size decreased, and silicification increased. A series of Si kinetic uptake experiments (from Si-limiting to Si-sufficient conditions) performed at different iron concentrations demonstrated the extent of the colimitation domain, where the specific Si uptake rate (VSi) varied as a function of both silicic acid and Fe availability. A decrease in maximal specific uptake rate of silicic acid (VSi-max) under iron limitation was observed along with a decrease in half-saturation constant for silicic acid uptake (KSi). Because VSi-max and KSi vary in the same direction, the specific affinity for silicic acid does not change under iron stress. The variation in cell size is an acclimation to low nutrient concentrations. Our study shows that Si uptake kinetics parameters, especially VSi-max, are strongly related to cell size, which is itself constrained by the degree of iron limitation. Thus, the surface to volume ratio should be related to silicic acid flows in size-based biogeochemical models of planktonic ecosystems. Another way to describe the observed variations of Si uptake over the full range of Si and Fe concentrations tested in the present study would be to implicitly take into account the variations in cell size through a scaling of the maximal specific uptake rate (Vmax) by the iron-limitation term in a multiplicative manner. [ABSTRACT FROM AUTHOR]

A new method for sediment toxicity testing using marine benthic pennate noncolonial diatom (Cylindrotheca closterium, formerly Nitzschia closterium) has been developed. This microalgae showed a good growth rate during the experimental period, even when low enriched media were used. Sediment spiked with heavy metals [cadmium (Cd), copper (Cu), and lead (Pb)] was employed to determine the EC50 values, using microalgal growth inhibition as the endpoint. The obtained results were as follows: Three heavy metals (Cd, Cu, and Pb), previously spiked on experimental sediment, were separately assayed in toxicity tests. The EC50 values for these heavy metals in microalgal growth inhibition tests resulted to be 79 mg kg−1 for Cd, 26 mg kg−1 for Cu, and 29 mg kg−1 for Pb (in experimental sediment). The influence of sediment granulometry on the growth of microalgal population was also studied, finding that the growth of the microalgal population on media containing sediment with a relation sand-size:silt size of 9:1 was not different from optimal growth (occurring in media containing 100% sand-sized sediment). The diatom C. closterium proved to be a suitable organism for sediment toxicity tests, due to its sensitivity and fast growth even in poorly enriched media. [Copyright &y& Elsevier]

The article offers information on the seasonal cycle of the plankton diatom, Melosira italica subarctica. It states that the perennation of fresh-water plankton algae which manifest a marked periodicity is to some degree an issue for speculation. It also mentions that in this research collections of plankton were made at weekly or shorter intervals in the north site of Esthwaite Water, east end of Blelham Tarn and in the central areas of the north and south basins of the Windermer from February or March 1945 to November 1952.

The article focuses on determination of a novel method to increase the transformation efficiency in bacterial cells. Nuclear transformation in pennate diatom Phaeodactylum tricornutum is described in which electro oration system is used to drive multi-sequence pulses. This helps in inducing foreign Danas into the cells. With pulse optimization diatom cells are transformed without affecting the silicon-based cell walls and high transformation efficacies is obtained.

A correction to the article "Transcriptional Orchestration of the Global Cellular Response of a Model Pennate Diatom to Diel Light Cycling under Iron Limitation," by Sarah R. Smith and colleagues is presented.

Presents a proposal to conserve the name Fragilariopsis, a genus of pinnate ribbon-forming diatoms initially believed to lack a raphe. Origin of the name; Credibility and appropriateness of the proposed new name; Basis for the contention; Implications of the new name on the botanical references of plant classification.