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PubMed2004

Predator/prey interaction between Pfiesteria piscicida and Rhodomonas mediated by a marine alpha proteobacterium.

The dinoflagellate Pfiesteria piscicida coexists with bacteria in aquatic environments and as such, may interact with them at the physiological level. This study was designed to investigate the influence of bacteria, present in a clonal culture of Pfiesteria piscicida, on the predator/prey relationship of this dinoflagellate with the alga Rhodomonas. A series of replenishment experiments with bacteria isolated from P. piscicida clonal culture and the bacteria-free P. piscicida derived from the same culture were carried out. In the presence of bacteria, the number of P. piscicida increased significantly when incubated with alga Rhodomonas. This enhanced growth was almost entirely due to the increased consumption rate of Rhodomonas by P. piscicida since in bacteria-free (axenic) cultures Rhodomonas were consumed at significantly reduced rates relative to cultures with bacteria. Subsequent replenishment experiments with individual bacterial isolates showed that a single isolate was responsible for the increased predation rate of P. piscicida. The presence or absence of this specific bacterium determined the outcome of the interaction between P. piscicida and Rhodomonas. Partial sequence analysis of the 16S rDNA of this isolate indicated that it was a novel marine alpha proteobacterium with sequence similarities to a Roseobacter sp. and a bacterium recently isolated from a toxic dinoflagellate Alexandrium sp.

Alphaproteobacteria↗
PubMed2005

Partitioning of CO(2) incorporation among planktonic microbial guilds and estimation of in situ specific growth rates.

Partitioning of CO(2) incorporation into oxygenic phototrophic, anoxygenic phototrophic, and chemolithoautotrophic guilds was determined in a freshwater lake (Lake Cisó, Banyoles, Spain). CO(2) incorporation into the different types of microorganisms was studied at different depths, during diel cycles, and throughout the year. During winter holomixis, the whole lake became anoxic and both the anoxygenic and chemolithoautotrophic guilds were more active at the surface of the lake, whereas the activity of the oxygenic guild was negligible. During stratification, the latter guild was more active in the upper metalimnion, whereas the anoxygenic guild was more active in the lower metalimnion. Specific growth rates and doubling times were estimated for the most conspicuous phototrophic microorganisms. Doubling times for Cryptomonas phaseolus ranged between 0.5 and 192 days, whereas purple sulfur bacteria (Chromatiaceae-like) ranged between 1.5 and 238 days. These growth rates were similar to those calculated with a different approach in previous papers and indicate slow-growing populations with very large biomass. Overall, the annual total CO(2) incorporation in Lake Cisó was 220 g C m(-2). Most of the CO(2) incorporation, however, was due to the chemolithoautotrophic guild (61% during holomixis and 56% during stratification), followed by the anoxygenic phototrophic guild (35 and 19%, respectively) and the oxygenic phototrophs (4 and 25%, respectively), making dark carbon fixation the key process in the autotrophic metabolism of the lake.

Carbon Dioxide↗
PubMed2006

Sterol composition of freshwater algivorous ciliates does not resemble dietary composition.

Algivorous ciliates represent an important link in freshwater food webs, as they transfer energy and biochemical matter from their algal prey to mesozooplankton predators. However, it is still unknown how dietary composition influences the biochemical composition of ciliates. We analyzed the sterol composition of the algivorous ciliates Balanion planctonicum and Urotricha farcta and compared it to the sterol composition of their diet--the cryptomonad Cryptomonas phaseolus. The sterol composition of the ciliates did not resemble that of their algal diet. Ergosterol [(22E)-ergosta-5,7,22-trien-3beta-ol] was the sterol in highest concentration in C. phaseolus, whereas stigmasterol [(24S)-24-ethylcholesta-5,22E-dien-3beta-ol] was dominant in both B. planctonicum and U. farcta. Moreover, the occasionally higher sterol concentrations in the ciliates than in their algal diet suggest sterol accumulation by the ciliates. We conclude that dietary sterol composition influences the composition of the two algivorous ciliates studied, but species-specific differences in metabolism probably determine the ultimate sterol composition of the ciliates.

Animals↗
PubMed2005

Development of molecular probes for dinophysis (dinophyceae) plastid: a tool to predict blooming and explore plastid origin.

Dinophysis are species of dinoflagellates that cause diarrhetic shellfish poisoning. We have previously reported that they probably acquire plastids from cryptophytes in the environment, after which they bloom. Thus monitoring the intracellular plastid density in Dinophysis and the source cryptophytes occurring in the field should allow prediction of Dinophysis blooming. In this study the nucleotide sequences of the plastid-encoded small subunit ribosomal RNA gene and rbcL (encoding the large subunit of RuBisCO) from Dinophysis spp. were compared with those of cryptophytes, and genetic probes specific for the Dinophysis plastid were designed. Fluorescent in situ hybridization (FISH) showed that the probes bound specifically to Dinophysis plastids. Also, FISH on collected nanoplankton showed the presence of probe-hybridized eukaryotes, possibly cryptophytes with plastids identical to those of Dinophysis. These probes are useful not only as markers for plastid density and activity of Dinophysis, but also as tools for monitoring cryptophytes that may be sources of Dinophysis plastids.

Animals↗
PubMed2006

Diversity of secondary endosymbiont-derived actin-coding genes in cryptomonads and their evolutionary implications.

In the secondary endosymbiotic organisms of cryptomonads, the symbiont actin genes have been found together with the host one. To examine whether they are commonly conserved and where they are encoded, host and symbiont actin genes from Pyrenomonas helgolandii were isolated, and their specific and homologous regions were digoxigenin (DIG) labeled separately. Using these probes, Southern hybridization was performed on 13 species of cryptomonads. They were divided into three groups: (1) both host and symbiont actin gene signals were detected, (2) only the host actin gene signal was detected, and (3) host and unknown actin signals were detected. The phylogenetic analysis of these actin gene sequences indicated that the evolutionary rates of the symbiont actin genes were accelerated more than those of the hosts. The unknown actin signals were recognized as the highly diverged symbiont actin genes. One of the diverged symbiont actin sequences from Guillardia theta is presumed to be as a pseudogene or to its precursor. Southern hybridizations based on the samples divided by pulsed-field gel electrophoresis showed that all actin genes were encoded by the host nuclei. These results possibly represent the evolutionary fate of the symbiont actin gene in cryptomonads, which was firstly transferred from the symbiont nucleus or nucleomorph, to the host nucleus and became a pseudogene and then finally disappeared there.

Actins↗
PubMed2004

Diatom genomics: genetic acquisitions and mergers.

Diatom algae arose by two-step endosymbiosis. The complete genome of the diatom Thalassiosira pseudonana has now been sequenced, allowing us to reconstruct the remarkable intracellular gene transfers that occurred during this convoluted cellular evolution.

Cryptophyta↗
PubMed2005

Unique genetic compartmentalization of the SUF system in cryptophytes and characterization of a SufD mutant in Arabidopsis thaliana.

The mobilization of sulfur (SUF) system is one of three systems involved in iron-sulfur cluster biosynthesis and maintenance. In eukaryotes the SUF system is specific for the plastid and therefore of symbiotic origin. Analyses in cryptophytes showed a unique genetic compartmentalization of the SUF system, which evolved by at least two different gene transfer events. We analyzed one of the components, SufD, in the cryptophyte Guillardia theta and in Arabidopsis thaliana. We demonstrated that SufD fulfils house keeping functions during embryogenesis and in adult plants in A. thaliana.

Algal Proteins↗
PubMed2005

Biochemical composition of algivorous freshwater ciliates: you are not what you eat.

The focus of our study was to determine whether the biochemical composition of two algivorous ciliates, both fed the same alga, resembles that of their diet. By comparing both ciliated protozoa we intended to identify species-specific differences in the metabolic features of these ciliates. Carbon- and cell-specific concentrations of fatty acids and essential amino acids were investigated for the ciliates Balanion planctonicum and Urotricha farcta grown on the cryptomonad Cryptomonas phaseolus. Stepwise discriminant analyses (SDA) indicated differences in the biochemical composition between ciliates and their diet and between the two ciliated protozoa. Carbon-specific fatty acid concentrations were usually higher in the ciliates than in their diet, especially concentrations of monounsaturated and some polyunsaturated fatty acids. Except for tryptophan, valine, and lysine, amino acid concentrations were higher in the ciliates than in C. phaseolus. Furthermore, differences in the polyunsaturated fatty acids accounted for the largest discrepancies between the two ciliated protozoa. The higher concentrations in the ciliates compared to their diet suggest that these species are capable of efficiently ingesting, assimilating or possibly synthesizing some fatty acids and amino acids. We conclude that dietary fatty acid and amino acid composition influences the composition of the two ciliated protozoa to a minor extent, and that species-specific differences in fatty acid and amino acid metabolism may be more important determinants of the biochemical composition of the studied ciliates. Moreover, the metabolism of polyunsaturated fatty acids seems to differ more profoundly between the two ciliated protozoa than the metabolism of other fatty acid classes or amino acids.

Amino Acids, Essential↗
PubMed2004

Developing a structure-function model for the cryptophyte phycoerythrin 545 using ultrahigh resolution crystallography and ultrafast laser spectroscopy.

Cryptophyte algae differ from cyanobacteria and red algae in the architecture of their photosynthetic light harvesting systems, even though all three are evolutionarily related. Central to cryptophyte light harvesting is the soluble antenna protein phycoerythrin 545 (PE545). The ultrahigh resolution crystal structure of PE545, isolated from a unicellular cryptophyte Rhodomonas CS24, is reported at both 1.1A and 0.97A resolution, revealing details of the conformation and environments of the chromophores. Absorption, emission and polarized steady state spectroscopy (298K, 77K), as well as ultrafast (20fs time resolution) measurements of population dynamics are reported. Coupled with complementary quantum chemical calculations of electronic transitions of the bilins, these enable assignment of spectral absorption characteristics to each chromophore in the structure. Spectral differences between the tetrapyrrole pigments due to chemical differences between bilins, as well as their binding and interaction with the local protein environment are described. Based on these assignments, and considering customized optical properties such as strong coupling, a model for light harvesting by PE545 is developed which explains the fast, directional harvesting of excitation energy. The excitation energy is funnelled from four peripheral pigments (beta158,beta82) into a central chromophore dimer (beta50/beta61) in approximately 1ps. Those chromophores, in turn, transfer the excitation energy to the red absorbing molecules located at the periphery of the complex in approximately 4ps. A final resonance energy transfer step sensitizes just one of the alpha19 bilins on a time scale of 22ps. Furthermore, it is concluded that binding of PE545 to the thylakoid membrane is not essential for efficient energy transfer to the integral membrane chlorophyll a-containing complexes associated with PS-II.

Computer Simulation↗
PubMed2005

The use of (14)C tracer technique to assess the functional response of zooplankton community grazing to toxic impact.

The use of functional endpoints in risk assessment of pollutants for marine pelagic communities is scarce, especially for the function of zooplankton communities. This work presents a rapid, inexpensive and ecologically relevant technique to assess the effect of toxic compounds on the grazing rates of zooplankton communities. The combination of a (14)C-tracer labelling technique with a fast (< 3 h) and representative sub-sampling and handling makes it possible to measure changes in food uptake of freshly collected natural zooplankton communities in a short-term assay. The methodology is described and its validity is determined by a full account of the fate of isotope tracers (up to 15% taken up by zooplankton). Egg production of Acartia tonsa cultures exposed to DCOI yielded EC(50) values of 118+/-33 nM DCOI after three days, where EC(50) values from grazing of natural zooplankton communities was 136+/-29 nM DCOI, indicating that grazing was the more sensitive variable. Finally the method was tested in a mesocosm experiment designed to evaluate the toxicity of the antifouling compound zinc pyrithion (ZPT) with an EC(50) value of 17 nM ZPT (SD=3.3 nM, n=3). The method was found to be reproducible both at the community (CV=8-39%) and individual level (CV=23-53%), and could detect small changes in response to a toxicant in a natural pelagic system. The use of natural communities in combination with the fast and cost-effective procedure makes this technique a powerful tool in risk assessment, where lack of ecological relevance or reproducible results often results in unwanted high uncertainties.

Animals↗
PubMed2006

EFL GTPase in cryptomonads and the distribution of EFL and EF-1alpha in chromalveolates.

EFL (EF-like protein) is a member of the GTPase superfamily that includes several translation factors. Because it has only been found in a few eukaryotic lineages and its presence correlates with the absence of the related core translation factor EF-1alpha, its distribution is hypothesized to be the result of lateral gene transfer and replacement of EF-1alpha. In one supergroup of eukaryotes, the chromalveolates, two major lineages were found to contain EFL (dinoflagellates and haptophytes), while the others encode EF-1alpha (apicomplexans, ciliates, heterokonts and cryptomonads). For each of these groups, this distribution was deduced from whole genome sequence or expressed sequence tag (EST) data from several species, with the exception of cryptomonads from which only a single EF-1alpha PCR product from one species was known. By sequencing ESTs from two cryptomonads, Guillardia theta and Rhodomonas salina, and searching for all GTPase translation factors, we revealed that EFL is present in both species, but, contrary to expectations, we found EF-1alpha in neither. On balance, we suggest the previously reported EF-1alpha from Rhodomonas salina is likely an artefact of contamination. We also identified EFL in EST data from two members of the dinoflagellate lineage, Karlodinium micrum and Oxyrrhis marina, and from an ongoing genomic sequence project from a third, Perkinsus marinus. Karlodinium micrum is a symbiotic pairing of two lineages that would have both had EFL (a dinoflagellate and a haptophyte), but only the dinoflagellate gene remains. Oxyrrhis marina and Perkinsus marinus are early diverging sister-groups to dinoflagellates, and together show that EFL originated early in this lineage. Phylogenetic analysis confirmed that these genes are all EFL homologues, and showed that cryptomonad genes are not detectably related to EFL from other chromalveolates, which collectively form several distinct groups. The known distribution of EFL now includes a third group of chromalveolates, cryptomonads. Of the six major subgroups of chromalveolates, EFL is found in half and EF-1alpha in the other half, and none as yet unambiguously possess both genes. Phylogenetic analysis indicates EFL likely arose early within each subgroup where it is found, but suggests it may have originated multiple times within chromalveolates as a whole.

Animals↗
PubMed2006

Analysis of environmental 18S ribosomal RNA sequences reveals unknown diversity of the cosmopolitan phylum Telonemia.

Telonemia has recently been described as a new eukaryotic phylum with uncertain evolutionary origin. So far, only two Telonemia species, Telonema subtilis and Telonema antarcticum, have been described, but there are substantial variations in size and morphology among Telonema isolates and field observations, indicating a hidden diversity of Telonemia-like species and populations. In this study, we investigated the diversity and the global distribution of this group by analyzing 18S rDNA sequences from marine environmental clone libraries published in GenBank as well as several unpublished sequences from the Indian Ocean. Phylogenetic analyses of the identified sequences suggest that the Telonemia phylum includes several undescribed 18S rDNA phylotypes, probably corresponding to a number of different species and/or populations. The Telonemia phylotypes form two main groups, here referred to as Telonemia Groups 1 and 2. Some of the closely related sequences originate from separate oceans, indicating worldwide distributions of various Telonemia phylotypes, while other phylotypes seem to have limited geographical distribution. Further investigations of the evolutionary relationships within Telonemia should be conducted on isolated cultures of Telonema-like strains using multi-locus sequencing and morphological data.

Animals↗
PubMed2006

Correlating toxicities of organic compounds to select protozoa using the Abraham model.

The Abraham solvation parameter model is used to construct mathematical correlations for describing the nonspecific toxicity of organic compounds to three protozoas (Entosiphon sulcantum, Uronema parduczi and Chilomonas paramecium). The derived mathematical correlations describe the observed published toxicity data to within an overall average standard deviation of approximately 0.35 log units. The correlations can be used to estimate aquatic toxicities of organic chemicals to the three aquatic organisms studied, and to help in identifying compounds whose toxic mode of action might involve chemical specific reactivity, rather than nonpolar or polar narcosis. A principal component analysis of the correlation equations found in this work shows that no water-solvent system we have investigated is a good model for nonspecific aquatic toxicity towards the three protozoas. Furthermore, correlation equations for nonspecific aqueous toxicity towards various biological systems, that we have found in this work and in previous studies, cover such a wide range that no single water-solvent system could ever be a good model for all the biological systems.

Animals↗
PubMed2005

Advances in phylogeny reconstruction from gene order and content data.

Genomes can be viewed in terms of their gene content and the order in which the genes appear along each chromosome. Evolutionary events that affect the gene order or content are "rare genomic events" (rarer than events that affect the composition of the nucleotide sequences) and have been advocated by systematists for inferring deep evolutionary histories. This chapter surveys recent developments in the reconstruction of phylogenies from gene order and content, focusing on their performance under various stochastic models of evolution. Because such methods are quite restricted in the type of data they can analyze, we also present research aimed at handling the full range of whole-genome data.

Algorithms↗
PubMed2006

How energy funnels from the phycoerythrin antenna complex to photosystem I and photosystem II in cryptophyte Rhodomonas CS24 cells.

We report an investigation of energy migration dynamics in intact cells of the photosynthetic cryptophyte Rhodomonas CS24 using analyses of steady-state and time-resolved fluorescence anisotropy measurements. By fitting a specific model to the fluorescence data, we obtain three time scales (17, 58, and 113 ps) by which the energy is transferred from phycoerythrin 545 (PE545) to the membrane-associated chlorophylls (Chls). We propose that these time scales reflect both an angular distribution of PE545 around the photosystems and the relative orientations of the donor dihydrobiliverdin (DBV) bilin and the acceptor Chl. Contrary to investigations of the isolated antenna complex, it is demonstrated that energy transfer from PE545 does not occur from a single-emitting bilin, but rather both the peripheral dihydrobiliverdin (DBV) chromophores in PE545 appear to be viable donors of excitation energy to the membrane-bound proteins. The model shows an almost equal distribution of excitation energy from PE545 to both photosystem I (PSI) and photosystem II (PSII), whose trap times correspond well to those obtained from experiments on isolated photosystems.

Cryptophyta↗