Michael Sieracki

Michael Sieracki
National Science Foundation | NSF · Division of Ocean Sciences (OCE)

PhD Biological Oceanography

About

139
Publications
32,480
Reads
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9,491
Citations
Citations since 2016
27 Research Items
4406 Citations
20162017201820192020202120220100200300400500600
20162017201820192020202120220100200300400500600
20162017201820192020202120220100200300400500600
20162017201820192020202120220100200300400500600
Additional affiliations
September 1991 - September 2013
Bigelow Laboratory for Ocean Sciences
Position
  • Senior Researcher

Publications

Publications (139)
Article
Full-text available
Significance The oceans are populated by an astronomical number of predominantly uncultured microbes, which altogether guarantee ecosystem function. Unicellular eukaryotic predators represent basal links in marine food webs and have so far been predominantly characterized as a functional group, despite having different ecologies and evolutionary hi...
Article
Full-text available
Heterotrophic lineages of stramenopiles exhibit enormous diversity in morphology, lifestyle, and habitat. Among them, the marine stramenopiles (MASTs) represent numerous independent lineages that are only known from environmental sequences retrieved from marine samples. The core energy metabolism characterizing these unicellular eukaryotes is poorl...
Preprint
Full-text available
Unicellular eukaryotic predators have a crucial role in the functioning of the ocean ecosystem by recycling nutrients and energy that are channeled to upper trophic levels. Traditionally, these evolutionary-diverse organisms have been combined into a single functional group (Heterotrophic flagellates), overlooking their organismal differences. Here...
Article
Full-text available
The predominant model of the role of viruses in the marine trophic web is that of the “viral shunt,” where viral infection funnels a substantial fraction of the microbial primary and secondary production back to the pool of dissolved organic matter. Here, we analyzed the composition of non-eukaryotic DNA associated with individual cells of small, p...
Article
The Stramenopiles are a large and diverse group of eukaryotes that possess various lifestyles required to thrive in a broad array of environments. The stramenopiles branch with the alveolates, rhizarians, and telonemids, forming the supergroup TSAR. Here, we present a new genus and species of aquatic nanoflagellated stramenopile: Mediocremonas medi...
Preprint
Full-text available
The Stramenopiles are a large and diverse group of eukaryotes that possess various lifestyles required to thrive in a broad array of environments. The stramenopiles branch with the alveolates, rhizarians, and telonemids, forming the supergroup TSAR. Here, we present a new genus and species of aquatic nanoflagellated stramenopile: Mediocremonas medi...
Article
Full-text available
Planktonic photosynthetic organisms of the class Mamiellophyceae include the smallest eukaryotes (less than 2 µm), are globally distributed and form the basis of coastal marine ecosystems. Eight complete fully annotated 13–22 Mb genomes from three genera, Ostreococcus , Bathycoccus and Micromonas , are available from previously isolated clonal cult...
Article
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Understanding the origins of animal multicellularity is a fundamental biological question. Recent genome data have unravelled the role that co-option of pre-existing genes played in the origin of animals. However, there were also some important genetic novelties at the onset of Metazoa. To have a clear understanding of the specific genetic innovati...
Article
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Marine planktonic protists are critical components of ocean ecosystems and are highly diverse. Molecular sequencing methods are being used to describe this diversity and reveal new associations and metabolisms that are important to how these ecosystems function. We describe here the use of the single cell genomics approach to sample and interrogate...
Article
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Predicting responses of plankton to variations in essential nutrients is hampered by limited in situ measurements, a poor understanding of community composition, and the lack of reference gene catalogs for key taxa. Iron is a key driver of plankton dynamics and, therefore, of global biogeochemical cycles and climate. To assess the impact of iron av...
Preprint
This protocol is part of Nucleic acids preparationsforViral to metazoan marine plankton nucleotide sequences from theTaraOceans expedition.
Preprint
This protocol describes the sequencing library preparation for theTaraOceans expedition and is part ofViral to metazoan marine plankton nucleotide sequences from theTaraOceans expedition. Figure 1: Overview of -omics analysis strategy applied on Tara Oceans samples.
Preprint
This protocol describes the 18S and 16S rRNA genes amplicon generation for eukaryotic and prokaryotic metabarcoding for theTaraOceans expedition and is part ofViral to metazoan marine plankton nucleotide sequences from theTaraOceans expedition. Figure 1: Overview of -omics analysis strategy applied on Tara Oceans samples.
Preprint
This protocol describes the handling of genomics samples for the Tara Oceans expedition and is part ofViral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition. Figure 1: Overview of -omics analysis strategy applied on Tara Oceans samples.
Preprint
The protocols in this collection are from the Alberti A., et al manuscript (Alberti A. 2017, Scientific Data). These protocols provide detailed procedures applied for genomic data generation, from nucleic acids extraction to sequence production, and we describe registries of genomics datasets available at the European Nucleotide Archive (ENA,www.eb...
Preprint
This protocol describes thenucleic acids preparations for theTaraOceans expedition and is part ofViral to metazoan marine plankton nucleotide sequences from theTaraOceans expedition. Figure 1: Overview of -omics analysis strategy applied on Tara Oceans samples.
Preprint
This protocol describes the sequencing and data quality control for theTaraOceans expedition and is part ofViral to metazoan marine plankton nucleotide sequences from theTaraOceans expedition. Figure 3:Overview of experimental pipeline from nucleic acids to sequences. (Red crosses highlight QC steps where experiments can be stopped.)
Article
Full-text available
A unique collection of oceanic samples was gathered by the Tara Oceans expeditions (2009–2013), targeting plankton organisms ranging from viruses to metazoans, and providing rich environmental context measurements. Thanks to recent advances in the field of genomics, extensive sequencing has been performed for a deep genomic analysis of this huge co...
Article
Full-text available
Marine Bacteroidetes constitute a very abundant bacterioplankton group in the oceans that plays a key role in recycling particulate organic matter and includes several photoheterotrophic members containing proteorhodopsin. Relatively few marine Bacteroidetes species have been described and, moreover, they correspond to cultured isolates, which in m...
Article
Full-text available
Pico-sized eukaryotes play key roles in the functioning of marine ecosystems, but we still have a limited knowledge on their ecology and evolution. The MAST-4 lineage is of particular interest, since it is widespread in surface oceans, presents ecotypic differentiation and has defied culturing efforts so far. Single cell genomics (SCG) are promisin...
Article
Full-text available
Bathycoccus is a cosmopolitan green micro-alga belonging to the Mamiellophyceae, a class of picophytoplankton that contains important contributors to oceanic primary production. A single species of Bathycoccus has been described while the existence of two ecotypes has been proposed based on metagenomic data. A genome is available for one strain cor...
Article
Full-text available
Marine plankton support global biological and geochemical processes. Surveys of their biodiversity have hitherto been geographically restricted and have not accounted for the full range of plankton size. We assessed eukaryotic diversity from 334 size-fractionated photic-zone plankton communities collected across tropical and temperate oceans during...
Article
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The ratio of two in situ optical measurements – chlorophyll fluorescence (Chl F) and optical particulate backscattering (b bp) – varied with changes in phytoplankton community composition during the North Atlantic Bloom Experiment in the Iceland Basin in 2008. Using ship-based measurements of Chl F , b bp , chlorophyll a (Chl), high-performance liq...
Article
Full-text available
Molecular surveys in planktonic marine systems have unveiled a large novel diversity of small protists. A large part of this diversity belongs to basal heterotrophic stramenopiles and is distributed in a set of polyphyletic ribogroups (described from rDNA sequences) collectively named as MAST (MArine STramenopiles). In the few groups investigated,...
Article
Full-text available
The ratio of two in situ optical measurements, chlorophyll fluorescence (Chl F) and optical particulate backscattering (bbp), varied with changes in phytoplankton community composition during the North Atlantic Bloom experiment in the Iceland Basin in 2008. Using ship-based measurements of Chl F, bp, chlorophyll a (Chl), HPLC pigments, phytoplankto...
Article
Full-text available
Understanding the origin and evolution of the eukaryotic cell and the full diversity of eukaryotes is relevant to many biological disciplines. However, our current understanding of eukaryotic genomes is extremely biased, leading to a skewed view of eukaryotic biology. We argue that a phylogeny-driven initiative to cover the full eukaryotic diversit...
Article
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Protists (unicellular eukaryotes) arguably account for most eukaryotic diversity and are central players of the biosphere. Known protist diversity and biology is largely based on cultured strains. Yet, environmental molecular surveys have unveiled entirely novel lineages that, as their prokaryotic counterparts, are essentially uncultured. Culture b...
Article
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The structure, robustness, and dynamics of ocean plankton ecosystems remain poorly understood due to sampling, analysis, and computational limitations. The Tara Oceans consortium organizes expeditions to help fill this gap at the global level.
Article
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With biology becoming quantitative, systems-level studies can now be performed at spatial scales ranging from molecules to ecosystems. Biological data generated consistently across scales can be integrated with physico-chemical contextual data for a truly holistic approach, with a profound impact on our understanding of life [1]–[5]. Marine ecosyst...
Article
Full-text available
Heterotrophic protists are a highly diverse and biogeochemically significant component of marine ecosystems, yet little is known about their species-specific prey preferences and symbiotic interactions in situ. Here we demonstrate how these previously unresolved questions can be addressed by sequencing the eukaryote and bacterial SSU rRNA genes fro...
Article
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Recent studies suggest that unidentified prokaryotes fix inorganic carbon at globally significant rates in the immense dark ocean. Using single-cell sorting and whole-genome amplification of prokaryotes from two subtropical gyres, we obtained genomic DNA from 738 cells representing most cosmopolitan lineages. Multiple cells of Deltaproteobacteria c...
Data
Representative biparametric flow cytometry plots showing a postinfection time series of E. huxleyi cells labeled with the lipid-specific fluorescence dye FM 1-43, (A) non-inoculated (virus-free) control culture, all cells are in a single cluster (red) with acquired high-orange fluorescence and (B) culture inoculated with EhV-86 viruses (virus-added...
Data
(A) Critical point (Cp) distribution for whole genome multiple displacement amplification on a microplate containing sorted E. huxleyi strain CCMP 1516 cells labeled with the lipid-specific FM 1-43 dye. Mean Cp is indicated for each group. (B) Example of kinetics curve in a single sorted cell well. (TIF)
Data
Representative biparametric flow cytometry plots showing a post-infection time series of E. huxleyi cells labeled with SYBR Green I fluorescence dye. (A) non-inoculated (virus-free) control culture and (B) culture inoculated with EhV-86 viruses (virus-added). Cells were discriminated on the basis of their red autofluorescence (610 nm) versus side s...
Data
List of PCR primers, and their sequences, used in this study. F and R denote forward and reverse primer respectively. (DOC)
Data
Representative biparametric flow cytometry plots showing a post-infection time series of E. huxleyi cells labeled with CM-H2DCFDA fluorescence dye. (A) non-inoculated (virus-free) control culture and (B) culture inoculated with EhV-86 viruses (virus-added). Cells were discriminated on the basis of their red autofluorescence (610 nm) or green dye fl...
Data
Representative biparametric flow cytometry plots showing a post-infection time series of E. huxleyi cells without addition of any fluorescence dye. (A) non-inoculated (virus-free) control culture and (B) culture inoculated with EhV-86 viruses (virus-added). Cells were discriminated on the basis of their red autofluorescence (610 nm) or green fluore...
Data
Suitability of the stained and sorted cells for MDA and PCR screening. (DOC)
Article
Full-text available
Discriminating infected from healthy cells is the first step to understanding the mechanisms and ecological implications of viral infection. We have developed a method for detecting, sorting, and performing molecular analysis of individual, infected cells of the important microalga Emiliania huxleyi, based on known physiological responses to viral...
Article
Full-text available
Recent discoveries suggest that photoheterotrophs (rhodopsin-containing bacteria (RBs) and aerobic anoxygenic phototrophs (AAPs)) and chemoautotrophs may be significant for marine and freshwater ecosystem productivity. However, their abundance and taxonomic identities remain largely unknown. We used a combination of single-cell and metagenomic DNA...
Data
Full-text available
Definition of physioregions in GoMA with a summary of area, volume, and mean depth for physioregions. (PDF)
Data
List of microalgae and cyanobacteria in GoMA. (XLS)
Article
Full-text available
In the Gulf of Maine area (GoMA), as elsewhere in the ocean, the organisms of greatest numerical abundance are microbes. Viruses in GoMA are largely cyanophages and bacteriophages, including podoviruses which lack tails. There is also evidence of Mimivirus and Chlorovirus in the metagenome. Bacteria in GoMA comprise the dominant SAR11 phylotype clu...
Article
Full-text available
Whole-genome shotgun sequence data from three individual cells isolated from seawater, followed by analysis of ribosomal DNA, indicated that the cells represented three divergent clades of picobiliphytes. In contrast with the recent description of this phylum, we found no evidence of plastid DNA nor of nuclear-encoded plastid-targeted proteins, whi...
Article
Full-text available
We review the current state of our capabilities for the systematic sustained observation of ocean ecosystems, concentrating primarily on planktonic ecosystems. First, we describe the structure of ocean ecosystems - from the nutrients that support primary production, up through the plankton, and then through the various predators, from juvenile finf...
Article
Full-text available
Recent applications of culture-independent, molecular methods have revealed unexpectedly high diversity in a variety of functional and phylogenetic groups of microorganisms in the ocean. However, none of the existing research tools are free from significant limitations, such as PCR and cloning biases, low phylogenetic resolution and others. Here, w...