Laboratory Flume Investigation into Hydrodynamic Properties of Select Stalk Forming Diatom Morphologies

Cell outline has been used as the principle metric for taxon recognition in diatoms, a single celled aquatic primary producer. This investigation examines the fluid dynamic implications of three stalk forming diatom outlines. This was accomplished by examining large scale shape differences between the gomphonemoid taxa Gomphoneis herculeana, and the Cymbelloid taxa Cymbella mexicana, as well as small morphological changes to the diatom Gomphonema acuminatum. Fluid dynamic investigations of microscopic diatoms were made possible through the production of scale models of selected diatoms using an atomic force microscope and 3-D rapid prototype printer, flows around these models were quantified through particle image velocimetry. In all cases the shape of the diatom cell influenced the fluid forces experienced. A comparison between the gomphonemoid and cymbelloid shapes demonstrated the potential for the gomphonemoid shape to exhibit a more streamlined body in unidirectional flow. The gomphonemoid shape, although less streamlined than the cymbelloid model in the dorsal leading edge orientation, has the potential advantage of minimal orientation effects due to its symmetry in the valve and girdle views. Outside of large differences in outline between taxa, small changes in ornamentation were also shown to have a measurable effect on the single taxa Gomphonema acuminatum. In this case the loss of the headpole apiculate end had a measurable effect on the wake properties downstream of the model. This investigation has made possible first hand observations into the unique fluid behavior in the understudied environment of the micro-benthos, as well as demonstrated fluid dynamic differences between common diatom morphologies

Historical and Current Perspectives on the Systematics of the ‘Enigmatic’ Diatom Genus Rhoicosphenia (Bacillariophyta), with Single and Multi-Molecular Marker and Morphological Analyses and Discussion on the Monophyly of ‘Monoraphid’ Diatoms

This study seeks to determine the phylogenetic position of the diatom genus Rhoicosphenia. Currently, four hypotheses based on the morphology of the siliceous valve and its various ultrastructural components, sexual reproduction, and chloroplasts have been proposed. Two previous morphological studies have tentatively placed Rhoicosphenia near members of the Achnanthidiaceae and Gomphonemataceae, and no molecular studies have been completed. The position of Rhoicosphenia as sister to &lsquo;monoraphid&rsquo; diatoms is problematic due to the apparent non-monophyly of that group, so hypotheses of &lsquo;monoraphid&rsquo; monophyly are also tested. Using an analysis of morphological and cytological features, as well as sequences from three genes, SSU, LSU, and rbcL, recovered from several freshwater Rhoicosphenia populations that have similar morphology to Rhoicosphenia abbreviata (Agardh) Lange-Bertalot, we have analyzed the phylogenetic position of Rhoicosphenia in the context of raphid diatoms. Further, we have used topology testing to determine the statistical likelihoods of these relationships. The hypothesis that Rhoicosphenia is a member of the Achnanthidiaceae cannot be rejected, while the hypothesis that it is a member of the Gomphonemataceae can be rejected. In our analyses, members of the Achnanthidiaceae are basal to Rhoicosphenia, and Rhoicosphenia is basal to the Cymbellales, or a basal member of the Cymbellales, which includes the Gomphonemataceae. Hypothesis testing rejects the monophyly of &lsquo;monoraphid&rsquo; diatoms.</p

New freshwater diatom genus, Edtheriotia gen. nov. of the Stephanodiscaceae (Bacillariophyta) from south‐central China

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/134437/1/pre12145.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/134437/2/pre12145_am.pd

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&ndash;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.</p

Developing an Evolutionary Roadmap to High Lipid Accumulating Diatoms: A Systematic Appraisal of Amphora Sensu Lato

Products derived from microalgal lipids have long been touted as an efficient and renewable alternative to the plant, animal and petroleum based products currently available. The great promise provided by algae as a biomass feedstock stems from their ubiquitous distribution, metabolic diversity, high productivity and ability to be grown on non-agricultural lands utilizing brackish and saltwater sources. Although promising, commercial production of algal products has not reached levels predicted by early investigators. Despite 40 years of algal biomass research, our basic understanding of the diversity and evolutionary history of these organisms remains in its infancy. If the great potential of algal derived products are to be realized, a biologically relevant approach to strain selection must be adopted. Presented here is a systematic investigation into the taxonomic, evolutionary and lipid accumulation diversity within the oleaginous diatom genus Amphora sensu lato. This is approached by first examining the taxonomic diversity of Amphora present within coastal and inland waters. From environmental collections made at these sites, a molecular phylogeny is produced to serve as the backbone for lipid accumulation experiments and comparisons. Based on the taxonomic and phylogenetic results, the Halamphora group within Amphora sensu lato was selected for a phylogenetically based appraisal of lipid production across cultured strains. This appraisal has demonstrated that ecological preference and cellular lipid accumulation within Halamphora exhibits a significant phylogenetic signal and therefore evolutionary relationships can be used as predictors of trait expression. The ecological and lipid data taken together with the taxonomic and phylogenetic data make for a predictive evolutionary based tool for the selection of high lipid accumulating lineages within Halamphora as well as laying the groundwork for future comparative research

Historical and Current Perspectives on the Systematics of the ‘Enigmatic’ Diatom Genus <i>Rhoicosphenia</i> (Bacillariophyta), with Single and Multi-Molecular Marker and Morphological Analyses and Discussion on the Monophyly of ‘Monoraphid’ Diatoms

<div><p>This study seeks to determine the phylogenetic position of the diatom genus <i>Rhoicosphenia</i>. Currently, four hypotheses based on the morphology of the siliceous valve and its various ultrastructural components, sexual reproduction, and chloroplasts have been proposed. Two previous morphological studies have tentatively placed <i>Rhoicosphenia</i> near members of the Achnanthidiaceae and Gomphonemataceae, and no molecular studies have been completed. The position of <i>Rhoicosphenia</i> as sister to ‘monoraphid’ diatoms is problematic due to the apparent non-monophyly of that group, so hypotheses of ‘monoraphid’ monophyly are also tested. Using an analysis of morphological and cytological features, as well as sequences from three genes, SSU, LSU, and <i>rbc</i>L, recovered from several freshwater <i>Rhoicosphenia</i> populations that have similar morphology to <i>Rhoicosphenia abbreviata</i> (Agardh) Lange-Bertalot, we have analyzed the phylogenetic position of <i>Rhoicosphenia</i> in the context of raphid diatoms. Further, we have used topology testing to determine the statistical likelihoods of these relationships. The hypothesis that <i>Rhoicosphenia</i> is a member of the Achnanthidiaceae cannot be rejected, while the hypothesis that it is a member of the Gomphonemataceae can be rejected. In our analyses, members of the Achnanthidiaceae are basal to <i>Rhoicosphenia</i>, and <i>Rhoicosphenia</i> is basal to the Cymbellales, or a basal member of the Cymbellales, which includes the Gomphonemataceae. Hypothesis testing rejects the monophyly of ‘monoraphid’ diatoms.</p></div

Sampling location information <i>Rhoicosphenia</i> populations sequenced including species, ID, State, County, Site Name, Latitude, Longitude, Type, and Collection number.

<p>Sampling location information <i>Rhoicosphenia</i> populations sequenced including species, ID, State, County, Site Name, Latitude, Longitude, Type, and Collection number.</p

Maximum likelihood phylogram from three-marker concatenated alignment.

<p>Node support values are for maximum likelihood bootstrap values (500 bootstraps)/Bayesian posterior probability (as a percentage). “*” = 100, “-” = node incongruent between the two analyses.</p

Summary of Hypothesis Testing Results.

<p>The first column states the molecular markers for the phylogeny being tested, while the first row represents the hypothesis being tested. The values in the table are the p-values from the Approximately Unbiased (AU) test [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0152797#pone.0152797.ref073" target="_blank">73</a>], and hypotheses that can be rejected based on the AU test are indicated with a “*”.</p