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1.
FEMS Microbiol Ecol ; 100(3)2024 Feb 14.
Article in English | MEDLINE | ID: mdl-38308512

ABSTRACT

Mixotrophic plankton can comprise a substantial portion of the plankton community compared to phytoplankton and zooplankton. However, there is a gap in the understanding of conditions that influence mixotroph prevalence and activity in situ because current methods often over- or underestimate mixotroph abundance. A labeled prey-tracer method was utilized to identify active mixotrophs present at two locations in a temperate estuary over a year. The tracer method was combined with light microscopy data to estimate active mixotroph abundance and proportion. This study estimated that actively grazing mixotrophic taxa were more abundant in the spring and autumn compared to summer. Dinoflagellates typically dominated the mixotrophic taxa except during autumn at the low salinity location when cryptophytes dominated. Further analysis suggested that active mixotroph abundances might not be only regulated by environmental conditions favorable to mixotrophy but, instead, environmental conditions favorable to different mixotrophs utilization of phagotrophy. By focusing on mixotrophic taxa that were identified to be actively grazing at time of sampling, this study provided a more nuanced estimation of mixotroph abundance, increasing the understanding of how mixotrophic abundance and proportion in situ are influenced by the planktonic community composition and environmental factors.


Subject(s)
Dinoflagellida , Plankton , Animals , Phytoplankton , Zooplankton , Cryptophyta
2.
J Plankton Res ; 45(4): 576-596, 2023.
Article in English | MEDLINE | ID: mdl-37483910

ABSTRACT

Phago-mixotrophy, the combination of photoautotrophy and phagotrophy in mixoplankton, organisms that can combine both trophic strategies, have gained increasing attention over the past decade. It is now recognized that a substantial number of protistan plankton species engage in phago-mixotrophy to obtain nutrients for growth and reproduction under a range of environmental conditions. Unfortunately, our current understanding of mixoplankton in aquatic systems significantly lags behind our understanding of zooplankton and phytoplankton, limiting our ability to fully comprehend the role of mixoplankton (and phago-mixotrophy) in the plankton food web and biogeochemical cycling. Here, we put forward five research directions that we believe will lead to major advancement in the field: (i) evolution: understanding mixotrophy in the context of the evolutionary transition from phagotrophy to photoautotrophy; (ii) traits and trade-offs: identifying the key traits and trade-offs constraining mixotrophic metabolisms; (iii) biogeography: large-scale patterns of mixoplankton distribution; (iv) biogeochemistry and trophic transfer: understanding mixoplankton as conduits of nutrients and energy; and (v) in situ methods: improving the identification of in situ mixoplankton and their phago-mixotrophic activity.

3.
Proc Natl Acad Sci U S A ; 120(28): e2303356120, 2023 07 11.
Article in English | MEDLINE | ID: mdl-37399413

ABSTRACT

Diatoms are a group of phytoplankton that contribute disproportionately to global primary production. Traditional paradigms that suggest diatoms are consumed primarily by larger zooplankton are challenged by sporadic parasitic "epidemics" within diatom populations. However, our understanding of diatom parasitism is limited by difficulties in quantifying these interactions. Here, we observe the dynamics of Cryothecomonas aestivalis (a protist) infection of an important diatom on the Northeast U.S. Shelf (NES), Guinardia delicatula, with a combination of automated imaging-in-flow cytometry and a convolutional neural network image classifier. Application of the classifier to >1 billion images from a nearshore time series and >20 survey cruises across the broader NES reveals the spatiotemporal gradients and temperature dependence of G. delicatula abundance and infection dynamics. Suppression of parasitoid infection at temperatures <4 °C drives annual cycles in both G. delicatula infection and abundance, with an annual maximum in infection observed in the fall-winter preceding an annual maximum in host abundance in the winter-spring. This annual cycle likely varies spatially across the NES in response to variable annual cycles in water temperature. We show that infection remains suppressed for ~2 mo following cold periods, possibly due to temperature-induced local extinctions of the C. aestivalis strain(s) that infect G. delicatula. These findings have implications for predicting impacts of a warming NES surface ocean on G. delicatula abundance and infection dynamics and demonstrate the potential of automated plankton imaging and classification to quantify phytoplankton parasitism in nature across unprecedented spatiotemporal scales.


Subject(s)
Diatoms , Animals , Diatoms/physiology , Temperature , Phytoplankton , Eukaryota , Zooplankton
4.
Front Microbiol ; 13: 844856, 2022.
Article in English | MEDLINE | ID: mdl-35651490

ABSTRACT

During a cruise from October to November 2019, along the West Antarctic Peninsula, between 64.32 and 68.37°S, we assessed the diversity and composition of the active microbial eukaryotic community within three size fractions: micro- (> 20 µm), nano- (20-5 µm), and pico-size fractions (5-0.2 µm). The communities and the environmental parameters displayed latitudinal gradients, and we observed a strong similarity in the microbial eukaryotic communities as well as the environmental parameters between the sub-surface and the deep chlorophyll maximum (DCM) depths. Chlorophyll concentrations were low, and the mixed layer was shallow for most of the 17 stations sampled. The richness of the microplankton was higher in Marguerite Bay (our southernmost stations), compared to more northern stations, while the diversity for the nano- and pico-plankton was relatively stable across latitude. The microplankton communities were dominated by autotrophs, mostly diatoms, while mixotrophs (phototrophs-consuming bacteria and kleptoplastidic ciliates, mostly alveolates, and cryptophytes) were the most abundant and active members of the nano- and picoplankton communities. While phototrophy was the dominant trophic mode, heterotrophy (mixotrophy, phagotrophy, and parasitism) tended to increase southward. The samples from Marguerite Bay showed a distinct community with a high diversity of nanoplankton predators, including spirotrich ciliates, and dinoflagellates, while cryptophytes were observed elsewhere. Some lineages were significantly related-either positively or negatively-to ice coverage (e.g., positive for Pelagophyceae, negative for Spirotrichea) and temperature (e.g., positive for Cryptophyceae, negative for Spirotrichea). This suggests that climate changes will have a strong impact on the microbial eukaryotic community.

5.
J Eukaryot Microbiol ; 69(4): e12920, 2022 07.
Article in English | MEDLINE | ID: mdl-35491969

ABSTRACT

The Gonyaulacales includes some of the most intensely investigated genera of harmful dinoflagellates. The knowledge of the evolutionary relationships is necessary, but incomplete because genera such as Schuettiella have not been studied by contemporary methods. The morphology and molecular phylogeny of type species of the genus Schuettiella, S. mitra, have been investigated from Brazil. The first scanning electron micrographs reveal a distinctive thecal ornamentation with sunken stripes and rows with exclamation mark-shaped pores in the postcingular plates. The Kofoidean plate formula Po, 2', 1a, 6″ is re-interpreted as Po, 3', 1a, 5″, after considering the narrow mid-ventral plate as homologous to the first apical plate, although it does not reach the apex. In the rRNA gene phylogenies, the sequences of S. mitra clustered as an independent lineage closely related to the globular and planktonic Protoceratiaceae (Ceratocorys, Pentaplacodinium, Protoceratium) and the laterally compressed benthic genus Carinadinium (formerly Thecadinium). Schuettiella and Carinadinium are considered members of the Protoceratiaceae. The possession of a single anterior intercalary plate is an apomorphic trait of this family. This reinforces the value of the number of intercalary plates as a diagnostic character for the classification of the gonyaulacalean families despite the differences in the general appearance.


Subject(s)
Dinoflagellida , Brazil , Dinoflagellida/genetics , Humans , Phylogeny
6.
Environ Microbiol ; 24(4): 1818-1834, 2022 04.
Article in English | MEDLINE | ID: mdl-35315564

ABSTRACT

Protists are integral to marine food webs and biogeochemical cycles; however, there is a paucity of data describing specific ecological niches for some of the most abundant taxa in marker gene libraries. Syndiniales are one such group, often representing the majority of sequence reads recovered from picoplankton samples across the global ocean. However, the prevalence and impacts of syndinian parasitism in marine environments remain unclear. We began to address these critical knowledge gaps by generating a high-resolution time series (March-October 2018) in a productive coastal pond. Seasonal shifts in protist populations, including parasitic Syndiniales, were documented during periods of higher primary productivity and increased summer temperature-driven stratification. Elevated concentrations of infected hosts and free-living parasite spores occurred at nearly monthly intervals in July, August, and September. We suggest intensifying stratification during this period correlated with the increased prevalence of dinoflagellates that were parasitized by Group II Syndiniales. Infections in some protist populations were comparable to previously reported large single-taxon dinoflagellate blooms. Infection dynamics in Salt Pond demonstrated the propagation of syndinian parasites through mixed protist assemblages and highlighted patterns of host/parasite interactions that better reflect many other marine environments where single taxon blooms are uncommon.


Subject(s)
Dinoflagellida , Parasitic Diseases , Dinoflagellida/genetics , Ecosystem , Host-Parasite Interactions , Humans , Ponds
7.
J Phycol ; 57(2): 694-697, 2021 04.
Article in English | MEDLINE | ID: mdl-33492676

ABSTRACT

Gymnodinium gracile, described from the coasts of Denmark in 1881, is one of the first described unarmored dinoflagellates. Individuals that morphologically fit with the original description were isolated from the English Channel (North-East Atlantic). The SSU rRNA gene sequences were identical to the sequences identified as Balechina pachydermata and Gymnodinium amphora from the Mediterranean Sea and Brazil. We propose the transfer of Gymnodinium gracile into the genus Balechina as B. gracilis comb. nov. These sequences constitute an independent lineage, clustering with numerous environmental sequences from polar to tropical waters. The widespread distribution, the high plasticity in size, shape and coloration and the difficulties in discerning the fine longitudinal striae have contributed to the description of numerous synonyms: Amphidinium vasculum, Balechina pachydermata (=Gymnodinium pachydermatum), Gymnodinium achromaticum, G. abbreviatum, G. amphora, G. dogielii, G. lohmannii (=G. roseum sensu Lohmann 1908), G. situla, and Gyrodinium cuneatum (=G. gracile sensu Pouchet 1885).


Subject(s)
Dinoflagellida , Brazil , DNA, Ribosomal/genetics , Dinoflagellida/genetics , Mediterranean Sea , Phylogeny , Sequence Analysis, DNA
8.
Eur J Protistol ; 71: 125636, 2019 Oct.
Article in English | MEDLINE | ID: mdl-31585232

ABSTRACT

The parasitic dinoflagellate Syltodinium listii was investigated from the open waters of the English Channel, southern North Sea and the NW Mediterranean Sea. Syltodinium listii has been unreported since its original description in the North Sea. Cells of S. listii were able to infect copepod eggs of different species, and even nauplii, and after each infection formed up to 32 cells embedded in a mucous envelope. Infection of the same host by more than one dinoflagellate was frequent; although overall, the progeny were reduced in number. Molecular phylogeny based on the small subunit ribosomal RNA (SSU rRNA) gene revealed that S. listii clusters with a group of environmental sequences from the cold North Atlantic region as a sister group of Gymnodinium aureolum. The large subunit ribosomal RNA (LSU rRNA) gene sequences of S. listii from the English Channel and cf. Gyrodinium undulans from the Mediterranean Sea were identical. Thus, we propose Syltodinium undulans comb. nov. for Gyrodinium undulans. The first internal transcribed spacer (ITS) and complete SSU rRNA gene sequences of Dissodinium pseudolunula are provided. The parasitic species of Chytriodinium, Dissodinium and Syltodinium cluster together within the family Chytriodiniaceae, including the free-living species Gymnodinium aureolum, G. corollarium and G. plasticum.


Subject(s)
Dinoflagellida/classification , Phylogeny , DNA, Protozoan/genetics , Dinoflagellida/genetics , Mediterranean Sea , RNA, Ribosomal, 18S/genetics , Species Specificity
9.
Proc Natl Acad Sci U S A ; 116(36): 17934-17942, 2019 09 03.
Article in English | MEDLINE | ID: mdl-31427512

ABSTRACT

Plastid endosymbiosis has been a major force in the evolution of eukaryotic cellular complexity, but how endosymbionts are integrated is still poorly understood at a mechanistic level. Dinoflagellates, an ecologically important protist lineage, represent a unique model to study this process because dinoflagellate plastids have repeatedly been reduced, lost, and replaced by new plastids, leading to a spectrum of ages and integration levels. Here we describe deep-transcriptomic analyses of the Antarctic Ross Sea dinoflagellate (RSD), which harbors long-term but temporary kleptoplasts stolen from haptophyte prey, and is closely related to dinoflagellates with fully integrated plastids derived from different haptophytes. In some members of this lineage, called the Kareniaceae, their tertiary haptophyte plastids have crossed a tipping point to stable integration, but RSD has not, and may therefore reveal the order of events leading up to endosymbiotic integration. We show that RSD has retained its ancestral secondary plastid and has partitioned functions between this plastid and the kleptoplast. It has also obtained genes for kleptoplast-targeted proteins via horizontal gene transfer (HGT) that are not derived from the kleptoplast lineage. Importantly, many of these HGTs are also found in the related species with fully integrated plastids, which provides direct evidence that genetic integration preceded organelle fixation. Finally, we find that expression of kleptoplast-targeted genes is unaffected by environmental parameters, unlike prey-encoded homologs, suggesting that kleptoplast-targeted HGTs have adapted to posttranscriptional regulation mechanisms of the host.


Subject(s)
Dinoflagellida/physiology , Gene Transfer, Horizontal , Mutagenesis, Insertional , Plastids/genetics , Symbiosis , Electron Transport , Gene Expression Profiling , Gene Expression Regulation, Plant , Models, Biological
10.
Biochim Biophys Acta Bioenerg ; 1860(1): 102-110, 2019 01.
Article in English | MEDLINE | ID: mdl-30414926

ABSTRACT

Light state transitions (STs) is a reversible physiological process that oxygenic photosynthetic organisms use in order to minimize imbalances in the electronic excitation delivery to the reaction centers of Photosystems I and II, and thus to optimize photosynthesis. STs have been studied extensively in plants, green algae, red algae and cyanobacteria, but sparsely in algae with secondary red algal plastids, such as diatoms and haptophytes, despite their immense ecological significance. In the present work, we examine whether the haptophyte alga Phaeocystis antarctica, and dinoflagellate cells that host kleptoplasts derived from P. antarctica, both endemic in the Ross Sea, Antarctica, are capable of light adaptive STs. In these organisms, Chl a fluorescence can be excited either by direct light absorption, or indirectly by electronic excitation (EE) transfer from ultraviolet light absorbing mycosporine-like amino acids (MAAs) to Chl a (Stamatakis et al., Biochim. Biophys. Acta 1858 [2017] 189-195). Here we show that, on adaptation to PS II-selective light, dark-adapted P. antarctica cells shift from light state 1 (ST1; more EE ending up in PS II) to light state 2 (ST2; more EE ending up in PS I), as revealed by the spectral distribution of directly-excited Chl a fluorescence and by changes in the macro-organization of pigment-protein complexes evidenced by circular dichroism (CD) spectroscopy. In contrast, no STs are clearly detected in the case of the kleptoplast-hosting dinoflagellate cells, and in the case of indirectly excited Chls a, via MAAs, in P. antarctica cells.


Subject(s)
Dinoflagellida/radiation effects , Energy Transfer , Haptophyta/radiation effects , Photosystem I Protein Complex/physiology , Photosystem II Protein Complex/physiology , Chlorophyll A/metabolism , Chloroplasts/radiation effects , Electron Transport , Fluorescence , Light , Plastids
11.
Dis Aquat Organ ; 131(1): 29-37, 2018 10 16.
Article in English | MEDLINE | ID: mdl-30324912

ABSTRACT

The morphology and molecular phylogeny of the parasitic dinoflagellates Ichthyodinium chabelardi and Amyloodinium ocellatum was investigated off Brazil (South Atlantic Ocean). This is the first record of Ichthyodinium and the first molecular data of both parasites from the southern hemisphere. I. chabelardi infected the yolk of eggs of wild populations of Argentine anchovy Engraulis anchoita (Engraulidae) and Brazilian sardinella Sardinella brasiliensis (Clupeidae) in different seasons. The small subunit (SSU) rRNA and internal transcribed spacer (ITS) gene sequences were identical and confirmed Ichthyodinium as a host generalist. The new sequences clustered with the type species I. chabelardi from the North Atlantic and environmental sequences from the Pacific Ocean. A second species from the western Pacific remains undescribed. A. ocellatum was isolated from the gills of a cultured cobia Rachycentron canadum after causing mortality. The SSU rRNA gene sequence of the Brazilian isolate was almost identical to those from the northern hemisphere. This suggests a single species with a widespread distribution, although it is uncertain whether the species has a natural pantropical distribution or is the result of artificial distribution due to human-induced fish transport.


Subject(s)
Dinoflagellida/physiology , Fish Diseases/parasitology , Fishes/parasitology , Parasitic Diseases, Animal/parasitology , Animals , Aquatic Organisms , Atlantic Ocean/epidemiology , Dinoflagellida/genetics , Fish Diseases/epidemiology , Parasitic Diseases, Animal/epidemiology , Phylogeny , RNA, Ribosomal/genetics
12.
Biochim Biophys Acta Bioenerg ; 1858(2): 189-195, 2017 Feb.
Article in English | MEDLINE | ID: mdl-27940021

ABSTRACT

The haptophyte Phaeocystis antarctica and the novel Ross Sea dinoflagellate that hosts kleptoplasts derived from P. antarctica (RSD; R.J. Gast et al., 2006, J. Phycol. 42 233-242) were compared for photosynthetic light harvesting and for oxygen evolution activity. Both chloroplasts and kleptoplasts emit chlorophyll a (Chl a) fluorescence peaking at 683nm (F683) at 277K and at 689 (F689) at 77K. Second derivative analysis of the F689 band at 77K revealed two individual contributions centered at 683nm (Fi-683) and at 689 (Fi-689). Using the p-nitrothiophenol (p-NTP) treatment of Kobayashi et al. (Biochim. Biophys. Acta 423 (1976) 80-90) to differentiate between Photosystem (PS) II and I fluorescence emissions, we could identify PS II as the origin of Fi-683 and PS I as the origin of Fi-689. Both emissions could be excited not only by Chl a-selective light (436nm) but also by mycosporine-like amino acids (MAAs)-selective light (345nm). This suggests that a fraction of MAAs must be proximal to Chls a and, therefore, located within the plastids. On the basis of second derivative fluorescence spectra at 77K, of p-NTP resolved fluorescence spectra, as well as of PSII-driven oxygen evolution activities, PS II appears substantially less active (~1/5) in dinoflagellate kleptoplasts than in P. antarctica chloroplasts. We suggest that a diminished role of PS II, a known source of reactive oxygen species, and a diminished dependence on nucleus-encoded light-harvesting proteins, due to supplementary light-harvesting by MAAs, may account for the extraordinary longevity of RSD kleptoplasts.


Subject(s)
Chloroplasts/metabolism , Dinoflagellida/metabolism , Haptophyta/metabolism , Light-Harvesting Protein Complexes/metabolism , Longevity/physiology , Oxygen/metabolism , Photosystem II Protein Complex/metabolism , Amino Acids/metabolism , Antarctic Regions , Chlorophyll/analogs & derivatives , Chlorophyll/metabolism , Chlorophyll A , Fluorescence , Light , Photosynthesis/physiology , Plastids/metabolism
13.
J Eukaryot Microbiol ; 62(5): 688-93, 2015.
Article in English | MEDLINE | ID: mdl-25851049

ABSTRACT

Sequencing hypervariable regions from the 18S rRNA gene is commonly employed to characterize protistan biodiversity, yet there are concerns that short reads do not provide the same taxonomic resolution as full-length sequences. A total of 7,432 full-length sequences were used to perform an in silico analysis of how sequences of various lengths and target regions impact downstream ecological interpretations. Sequences that were longer than 400 nucleotides and included the V4 hypervariable region generated results similar to those derived from full-length 18S rRNA gene sequences. Present high-throughput sequencing capabilities are approaching protistan diversity estimation comparable to whole gene sequences.


Subject(s)
Eukaryota/genetics , Genetic Variation , High-Throughput Nucleotide Sequencing , Genes, rRNA , Molecular Sequence Data , Phylogeny , RNA, Ribosomal, 18S/genetics , Sequence Analysis, DNA
14.
Environ Microbiol ; 17(5): 1510-9, 2015 May.
Article in English | MEDLINE | ID: mdl-25041758

ABSTRACT

Here we investigated whether there is evidence of local adaptation in strains of an ancestrally marine dinoflagellate to the lacustrine environment they now inhabit (optimal genotypes) and/or if they have evolved phenotypic plasticity (a range of phenotypes). Eleven strains of Polarella glacialis were isolated and cultured from three different environments: the polar seas, a hyposaline and a hypersaline Antarctic lake. Local adaptation was tested by comparing growth rates of lacustrine and marine strains at their own and reciprocal site conditions. To determine phenotypic plasticity, we measured the reaction norm for salinity. We found evidence of both, limited local adaptation and higher phenotypic plasticity in lacustrine strains when compared with marine ancestors. At extreme high salinities, local lake strains outperformed other strains, and at extreme low salinities, strains from the hyposaline lake outperformed all other strains. The data suggest that lake populations may have evolved higher phenotypic plasticity in the lake habitats compared with the sea, presumably due to the high temporal variability in salinity in the lacustrine systems. Moreover, the interval of salinity tolerance differed between strains from the hyposaline and hypersaline lakes, indicating local adaptation promoted by different salinity.


Subject(s)
Acclimatization/physiology , Dinoflagellida/physiology , Lakes/parasitology , Salt Tolerance/physiology , Antarctic Regions , Base Sequence , DNA, Ribosomal Spacer/genetics , Dinoflagellida/classification , Dinoflagellida/isolation & purification , Ecosystem , Environment , Genotype , Oceans and Seas , Salinity , Sequence Analysis, DNA
15.
Environ Sci Technol ; 49(1): 451-8, 2015 Jan 06.
Article in English | MEDLINE | ID: mdl-25479559

ABSTRACT

Culturable enterococci and a suite of environmental variables were collected during a predominantly dry summer at a beach impacted by nonpoint source pollution. These data were used to evaluate sands as a source of enterococci to nearshore waters, and to assess the relationship between environmental factors and dry-weather enterococci abundance. Best-fit multiple linear regressions used environmental variables to explain more than half of the observed variation in enterococci in water and dry sands. Notably, during dry weather the abundance of enterococci in dry sands at the mean high-tide line was significantly positively related to sand moisture content (ranging from <1-4%), and the daily mean ENT in water could be predicted by a linear regression with turbidity alone. Temperature was also positively correlated with ENT abundance in this study, which may indicate an important role of seasonal warming in temperate regions. Inundation by spring tides was the primary rewetting mechanism that sustained culturable enterococci populations in high-tide sands. Tidal forcing modulated the abundance of enterococci in the water, as both turbidity and enterococci were elevated during ebb and flood tides. The probability of samples violating the single-sample maximum was significantly greater when collected during periods with increased tidal range: spring ebb and flood tides. Tidal forcing also affected groundwater mixing zones, mobilizing enterococci from sand to water. These data show that routine monitoring programs using discrete enterococci measurements may be biased by tides and other environmental factors, providing a flawed basis for beach closure decisions.


Subject(s)
Bathing Beaches , Enterococcus , Environmental Microbiology , Water Quality , Animals , Dogs , Groundwater , Humans , Seasons , Silicon Dioxide , Weather
16.
Microb Ecol ; 70(1): 21-9, 2015 Jul.
Article in English | MEDLINE | ID: mdl-25482369

ABSTRACT

Antarctic phototrophs are challenged by extreme temperatures, ice cover, nutrient limitation, and prolonged periods of darkness. Yet this environment may also provide niche opportunities for phytoplankton utilizing alternative nutritional modes. Mixotrophy, the combination of photosynthesis and particle ingestion, has been proposed as a mechanism for some phytoplankton to contend with the adverse conditions of the Antarctic. We conducted feeding experiments using fluorescent bacteria-sized tracers to compare the effects of light and nutrients on bacterivory rates in three Antarctic marine photosynthetic nanoflagellates representing two evolutionary lineages: Cryptophyceae (Geminigera cryophila) and Prasinophyceae (Pyramimonas tychotreta and Mantoniella antarctica). Only G. cryophila had previously been identified as mixotrophic. We also measured photoautotrophic abilities over a range of light intensities (P vs. I) and used dark survival experiments to assess cell population dynamics in the absence of light. Feeding behavior in these three nanoflagellates was affected by either light, nutrient levels, or a combination of both factors in a species-specific manner that was not conserved by evolutionary lineage. The different responses to environmental factors by these mixotrophs supported the idea of tradeoffs in the use of phagotrophy and phototrophy for growth.


Subject(s)
Adaptation, Biological/physiology , Chlorophyta/physiology , Cryptophyta/physiology , Food/statistics & numerical data , Light , Phototrophic Processes/physiology , Phytoplankton/physiology , Analysis of Variance , Antarctic Regions , Fluorescence , Population Dynamics
17.
Appl Environ Microbiol ; 80(14): 4363-73, 2014 Jul.
Article in English | MEDLINE | ID: mdl-24814788

ABSTRACT

Next-generation DNA sequencing (NGS) approaches are rapidly surpassing Sanger sequencing for characterizing the diversity of natural microbial communities. Despite this rapid transition, few comparisons exist between Sanger sequences and the generally much shorter reads of NGS. Operational taxonomic units (OTUs) derived from full-length (Sanger sequencing) and pyrotag (454 sequencing of the V9 hypervariable region) sequences of 18S rRNA genes from 10 global samples were analyzed in order to compare the resulting protistan community structures and species richness. Pyrotag OTUs called at 98% sequence similarity yielded numbers of OTUs that were similar overall to those for full-length sequences when the latter were called at 97% similarity. Singleton OTUs strongly influenced estimates of species richness but not the higher-level taxonomic composition of the community. The pyrotag and full-length sequence data sets had slightly different taxonomic compositions of rhizarians, stramenopiles, cryptophytes, and haptophytes, but the two data sets had similarly high compositions of alveolates. Pyrotag-based OTUs were often derived from sequences that mapped to multiple full-length OTUs at 100% similarity. Thus, pyrotags sequenced from a single hypervariable region might not be appropriate for establishing protistan species-level OTUs. However, nonmetric multidimensional scaling plots constructed with the two data sets yielded similar clusters, indicating that beta diversity analysis results were similar for the Sanger and NGS sequences. Short pyrotag sequences can provide holistic assessments of protistan communities, although care must be taken in interpreting the results. The longer reads (>500 bp) that are now becoming available through NGS should provide powerful tools for assessing the diversity of microbial eukaryotic assemblages.


Subject(s)
Biodiversity , Eukaryota/classification , RNA, Ribosomal, 18S/genetics , Sequence Analysis, DNA/methods , Chromosome Mapping , Eukaryota/genetics , High-Throughput Nucleotide Sequencing/methods , Seawater/microbiology , Water Microbiology
18.
FEMS Microbiol Ecol ; 89(2): 388-401, 2014 Aug.
Article in English | MEDLINE | ID: mdl-24689998

ABSTRACT

Protists are traditionally described as either phototrophic or heterotrophic, but studies have indicated that mixotrophic species, organisms that combine both strategies, can have significant impacts on prey populations in marine microbial food webs. While estimates of active mixotroph abundances in environmental samples are determined microscopically by fluorescent particle ingestion, species identification is difficult. We developed SYBR-based qPCR strategies for three Antarctic algal species that we identified as mixotrophic. This method and traditional ingestion experiments were applied to determine the total mixotroph abundance in Antarctic water samples, to ascertain the abundance of known mixotrophic species, and to identify environmental variables that impact the distribution and abundance of these species. Despite differences in sampling locations and years, mixotroph distribution was strongly influenced by season. Environmental variables that best explained variation in the individual mixotroph species abundances included temperature, oxygen, date, fluorescence, conductivity, and latitude. Phosphate was identified as an additional explanatory variable when nutrients were included in the analysis. Utilizing culture-based grazing rates and qPCR abundances, the estimated summed impact on bacterial populations by the three mixotrophs was usually < 2% of the overall mixotrophic grazing, but in one sample, Pyramimonas was estimated to contribute up to 80% of mixotrophic grazing.


Subject(s)
Chlorophyta/genetics , Cryptophyta/genetics , Antarctic Regions , Autotrophic Processes , Biomass , Chlorophyta/metabolism , Cryptophyta/isolation & purification , Cryptophyta/metabolism , Heterotrophic Processes , Microscopy, Electron, Transmission , Microscopy, Fluorescence , Molecular Sequence Data , Molecular Typing , Oceans and Seas , Photosynthesis , Phylogeny , RNA, Ribosomal, 18S/genetics , Seasons , Sequence Analysis, DNA
19.
PLoS One ; 9(3): e90815, 2014.
Article in English | MEDLINE | ID: mdl-24599478

ABSTRACT

Recreational water quality, as measured by culturable fecal indicator bacteria (FIB), may be influenced by persistent populations of these bacteria in local sands or wrack, in addition to varied fecal inputs from human and/or animal sources. In this study, pyrosequencing was used to generate short sequence tags of the 16S hypervariable region ribosomal DNA from shallow water samples and from sand samples collected at the high tide line and at the intertidal water line at sites with and without FIB exceedance events. These data were used to examine the sand and water bacterial communities to assess the similarity between samples, and to determine the impact of water quality exceedance events on the community composition. Sequences belonging to a group of bacteria previously identified as alternative fecal indicators were also analyzed in relationship to water quality violation events. We found that sand and water samples hosted distinctly different overall bacterial communities, and there was greater similarity in the community composition between coastal water samples from two distant sites. The dissimilarity between high tide and intertidal sand bacterial communities, although more similar to each other than to water, corresponded to greater tidal range between the samples. Within the group of alternative fecal indicators greater similarity was observed within sand and water from the same site, likely reflecting the anthropogenic contribution at each beach. This study supports the growing evidence that community-based molecular tools can be leveraged to identify the sources and potential impact of fecal pollution in the environment, and furthermore suggests that a more diverse bacterial community in beach sand and water may reflect a less contaminated site and better water quality.


Subject(s)
Bacteria/growth & development , Bathing Beaches/standards , Soil Microbiology , Water Microbiology , Water Quality , Animals , Base Sequence , Biodiversity , California , Environmental Monitoring , Feces/microbiology , Humans , Massachusetts , Phylogeny
20.
J Phycol ; 50(6): 1081-8, 2014 Dec.
Article in English | MEDLINE | ID: mdl-26988789

ABSTRACT

The peridinin-containing plastid found in most photosynthetic dinoflagellates is thought to have been replaced in a few lineages by plastids of chlorophyte, diatom, or haptophyte origin. Other distinct lineages of phagotrophic dinoflagellates retain functional plastids obtained from algal prey for different durations and with varying source species specificity. 18S rRNA gene sequence analyses have placed a novel gymnodinoid dinoflagellate isolated from the Ross Sea (RSD) in the Kareniaceae, a family of dinoflagellates with permanent plastids of haptophyte origin. In contrast to other species in this family, the RSD contains kleptoplastids sequestered from its prey, Phaeocystis antarctica. Culture experiments were employed to determine whether the RSD fed selectively on P. antarctica when offered in combination with another polar haptophyte or cryptophyte species, and whether the RSD, isolated from its prey and starved, would take up plastids from P. antarctica or from other polar haptophyte or cryptophyte species. Evidence was obtained for selective feeding on P. antarctica, plastid uptake from P. antarctica, and increased RSD growth in the presence of P. antarctica. The presence of a peduncle-like structure in the RSD suggests that kleptoplasts are obtained by myzocytosis. RSD cells incubated without P. antarctica were capable of survival for at least 29.5 months. This remarkable longevity of the RSD's kleptoplasts and its species specificity for prey and plastid source is consistent with its prolonged co-evolution with P. antarctica. It may also reflect the presence of a plastid protein import mechanism and genes transferred to the dinokaryon from a lost permanent haptophyte plastid.

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