A5029637743- Microbial Community Ecology and Physiology
- Protist diversity and phylogeny
- Marine and coastal ecosystems
- Marine Biology and Ecology Research
- Genomics and Phylogenetic Studies
- Environmental DNA in Biodiversity Studies
- Bacteriophages and microbial interactions
- Methane Hydrates and Related Phenomena
- Aquatic Ecosystems and Phytoplankton Dynamics
- Coral and Marine Ecosystems Studies
- Water Quality Monitoring Technologies
- Coastal and Marine Management
- Cell Image Analysis Techniques
- Fish Ecology and Management Studies
- Identification and Quantification in Food
- Oceanographic and Atmospheric Processes
- Genetics, Bioinformatics, and Biomedical Research
- Diatoms and Algae Research
- Marine Bivalve and Aquaculture Studies
- Marine and fisheries research
- Environmental Monitoring and Data Management
- Geology and Paleoclimatology Research
- Atmospheric and Environmental Gas Dynamics
- Marine and Offshore Engineering Studies
- Algal biology and biofuel production
Association Clinique et Thérapeutique Infantile du Val de Marne
2024
University of Maryland Center for Environmental Science
2024
U.S. National Science Foundation
2007-2021
Bigelow Laboratory for Ocean Sciences
2009-2020
Division of Ocean Sciences
2020
University of California, Davis
2008
University of Rhode Island
1986-2005
Scripps Institution of Oceanography
2005
Monterey Bay Aquarium Research Institute
2005
Woods Hole Oceanographic Institution
1998
Microbes are dominant drivers of biogeochemical processes, yet drawing a global picture functional diversity, microbial community structure, and their ecological determinants remains grand challenge. We analyzed 7.2 terabases metagenomic data from 243 Tara Oceans samples 68 locations in epipelagic mesopelagic waters across the globe to generate an ocean reference gene catalog with >40 million nonredundant, mostly novel sequences viruses, prokaryotes, picoeukaryotes. Using 139...
Marine plankton support global biological and geochemical processes. Surveys of their biodiversity have hitherto been geographically restricted not accounted for the full range size. We assessed eukaryotic diversity from 334 size-fractionated photic-zone communities collected across tropical temperate oceans during circumglobal Tara Oceans expedition. analyzed 18S ribosomal DNA sequences intermediate plankton-size spectrum smallest unicellular eukaryotes (protists, >0.8 micrometers) to small...
Unialgal cultures were used to investigate relationships between cell volume and the carbon nitrogen content of nondiatomaceous marine nanophytoplankton. Cell dimensions determined by image‐analyzed epifluorescence microscopy particulate C N high‐temperature dry combustion. Volumes calculated direct integration with published algorithms (biovolume), but could be estimated equally well from linear as prolate spheres. Preservation 0.5% glutaraldehyde reduced volumes 29% on average....
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 from two subtropical gyres, we obtained genomic DNA 738 cells representing most cosmopolitan lineages. Multiple Deltaproteobacteria cluster SAR324, Gammaproteobacteria clusters ARCTIC96BD-19 Agg47, some Oceanospirillales lower mesopelagic contained ribulose-1,5-bisphosphate carboxylase-oxygenase sulfur...
The structure, robustness, and dynamics of ocean plankton ecosystems remain poorly understood due to sampling, analysis, computational limitations. Tara Oceans consortium organizes expeditions help fill this gap at the global level.
MEPS Marine Ecology Progress Series Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout JournalEditorsTheme Sections 168:285-296 (1998) - doi:10.3354/meps168285 An imaging-in-flow system for automated analysis of marine microplankton Christian K. Sieracki*, Michael E. Sieracki, Charles S. Yentsch Bigelow Laboratory Ocean Sciences, PO Box 475 McKown Point, West Boothbay Harbor, Maine 04575, USA *E-mail: csieracki@bigelow.org...
Abstract The Tara Oceans expedition (2009–2013) sampled contrasting ecosystems of the world oceans, collecting environmental data and plankton, from viruses to metazoans, for later analysis using modern sequencing state-of-the-art imaging technologies. It surveyed 210 in 20 biogeographic provinces, over 35,000 samples seawater plankton. interpretation such an extensive collection their ecological context requires means explore, assess access raw validated sets. To address this challenge,...
While our knowledge about the roles of microbes and viruses in ocean has increased tremendously due to recent advances genomics metagenomics, research on marine microbial eukaryotes zooplankton benefited much less from these new technologies because their larger genomes, enormous diversity, largely unexplored physiologies. Here, we use a metatranscriptomics approach capture expressed genes open Tara Oceans stations across four organismal size fractions. The individual sequence reads cluster...
The difficulty associated with the cultivation of most microorganisms and complexity natural microbial assemblages, such as marine plankton or human microbiome, hinder genome reconstruction representative taxa using metagenomic approaches. Here we used an alternative, single cell sequencing approach to obtain high-quality assemblies two uncultured, numerically significant microorganisms. We employed fluorescence-activated sorting multiple displacement amplification hundreds micrograms...
Marine protist cells from the wild environment contain DNA several viruses and bacteria, but apparently lack plastids.
Abstract 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 recent advances in field genomics, extensive sequencing has been performed for a deep genomic analysis this huge samples. strategy based on different approaches, such as metabarcoding, metagenomics, single-cell genomics metatranscriptomics, chosen size-fractionated...
Marine planktonic eukaryotes play critical roles in global biogeochemical cycles and climate. However, their poor representation culture collections limits our understanding of the evolutionary history genomic underpinnings ecosystems. Here, we used 280 billion
The identification of predominant microbial taxa with specific metabolic capabilities remains one the biggest challenges in environmental microbiology, because limits current metagenomic and cell culturing methods. We report results from direct analysis multiple genes individual marine bacteria cells, demonstrating potential for high-throughput assignment yet-uncultured taxa. protocol uses high-speed fluorescence-activated sorting, whole-genome displacement amplification (MDA), subsequent...
The term plankton is used to include phytoplankton and zooplankton.While most of the current study on image classification has focused mesozooplankton, challenges involved are common microzooplankton phytoplankton.
ABSTRACT Two new fluorochromes, PicoGreen® and SYTOX Green™ stain (Molecular Probes, Inc.), are useful with flow cytometry for quantitative detection of cellular DNA in a variety marina phytoplankton. The basic instrument configuration modern low‐power cytometers (15 mW, 488 nm excitation) is sensitive enough to detect the signal nearly all 121 strains (from 12 taxonomic classes)examined. major advantages these dyes over others 1)suitability direct use seawater, 2)green fluorescence emission...
Epifluorescence microscopy is now being widely used to characterize planktonic procaryote populations. The tedium and subjectivity of visual enumeration sizing have been largely alleviated by our use an image analysis system consisting a modified Artek 810 analyzer Olympus BHT-F epifluorescence microscope. This digitizes the video autofluorescing or fluorochrome-stained cells in microscope field. digitized can then be stored, edited, analyzed for total count individual cell size shape...
ABSTRACT While several studies have suggested that bacterium-phytoplankton interactions the potential to dramatically influence harmful algal bloom dynamics, little is known about how bacteria and phytoplankton communities interact at species composition level. The objective of current study was determine whether there are specific associations between diverse co-occur with them. We determined phylogenetic diversity bacterial assemblages associated 10 Alexandrium strains representatives...
•There is an important bias in eukaryotic knowledge, affecting cultures and genomes.•Eukaryotic genomics are biased towards multicellular organisms their parasites.•A phylogeny-driven initiative needed to overcome the genomic bias.•We propose sequence neglected increase culturing efforts.•Single-cell should be embraced as a tool explore diversity. Understanding origin evolution of cell full diversity eukaryotes relevant many biological disciplines. However, our current understanding genomes...
Abstract Single-celled eukaryotes (protists) are critical players in global biogeochemical cycling of nutrients and energy the oceans. While their roles as primary producers grazers well appreciated, other aspects life histories remain obscure due to challenges culturing sequencing natural diversity. Here, we exploit single-cell genomics metagenomics data from circumglobal Tara Oceans expedition analyze genome content apparent oceanic distribution seven prevalent lineages uncultured...
Abstract. The ratio of two in situ optical measurements – chlorophyll fluorescence (Chl F) and particulate backscattering (bbp) varied with changes phytoplankton community composition during the North Atlantic Bloom Experiment Iceland Basin 2008. Using ship-based Chl F, bbp, a (Chl), high-performance liquid chromatography (HPLC) pigments, carbon biomass, we found that oscillations plankton composition; hence refer to F/bbp as an "optical index". index by more than factor 2, low values...