Targeted megagenomics

Research cruise on the R/V Seward Johnson from Bardados to Cape Verde and back, Summer 2006

There are still many uncultured marine protists – including within the pico-size fraction. An approach developed in the lab that has generated new discoveries on their evolution and ecology has been sequence partial genomes from cells taken directly from the environment. Because these pico algae have quite large genomes (especially as compared to bacteria), pursuing metagenomic information using “bulk samples” (i.e. collecting cells by filtration of many liters of seawater) has been challenging, and complex to tease apart bioinformatically. Starting in 2005 we combined flow sorting with multiple displacement amplification (developed in Roger Lasken’s lab) in order to specifically target and sequence picophytoeukaryote populations. Our interest has been in sequencing population metagenomes as opposed to single cells. Using this approach we published the first genome sequence (partial genome) for a haptophyte – in this case a pico-prymnesiophyte (Cuvelier et al. PNAS 2010), and a partial Bathycoccus genome (Monier et al. EM 2012, epubl Sept 2011) as well as the complete chloroplast genome of a wild pelagophyte (Worden et al. Current Biology 2012).

Some of these targeted metagenomes have now been used to analyze traditional Bulk Metagenomes from a well characterized transect from the Pacific coast to open ocean waters (Line 67) and other locations. High resolution contextual environmental data has been analyzed by a number of MBARI scientists — including Ken Johnson and Francisco Chavez. Melding Targeted Metagenomics with Bulk Metagenomics (using the Targeted Metagenomes as reference genomes for uncultureds) revealed the global distribution of a wild Pelagomonas, using a reference plastid genome sequenced directly from the environment (Worden et al. Current Biology 2012), as well as interesting HGT patterns between Ostreococcus andBathycoccus with marine prasinoviruses (Monier et al. EM 2012, epubl Sept 2011).

Science

Upper-ocean systems
Biological oceanography
Biological oceanography research
Publication—Global modes of sea surface temperature
Chemical sensors
Chemical data
Land/Ocean Biogeochemical Observatory in Elkhorn Slough
Listing of floats
SOCCOM float visualization
Periodic table of elements in the ocean
Profiling float
Marine microbes
Population dynamics of phytoplankton
Microbial predators
Microbe-algae interactions
Targeted metagenomics
In the news
Upcoming events and lab news
Past talks and presentations
Join the lab
Resources
Molecular ecology
Molecular systematics
SIMZ Project
Bone-eating worms
Gene flow and dispersal
Molecular-ecology expeditions
Interdisciplinary field experiments
Genomic sensors
Ocean observing system
Midwater research
Midwater ecology
Deep-sea squids and octopuses
Food web dynamics
Midwater time series
Respiration studies
Zooplankton biodiversity
Seafloor processes
Biology and ecology
Effects of humans
Ocean acidification, warming, deoxygenation
Lost shipping container study
Effects of upwelling
Faunal patterns
Past research
Technology development
High-CO2 / low-pH ocean
Benthic respirometer system
Climate change in extreme environments
Monitoring instrumentation suite
Sargasso Sea research
Antarctic research
Long-term time series
Geological changes
Arctic Shelf Edge
Continental Margins and Canyon Dynamics
Coordinated Canyon Experiment
Monterey Canyon: Stunning deep-sea topography revealed
Ocean chemistry of greenhouse gases
Emerging science of a high CO2/low pH ocean
Submarine volcanoes
Mid-ocean ridges
Magmatic processes
Volcanic processes
Explosive eruptions
Hydrothermal systems
Back arc spreading ridges
Seamounts
Near-ridge seamounts
Continental margin seamounts
Non-hot-spot linear chains
Eclectic seamounts topics
Margin processes
Hydrates and seeps
California borderland
Hot spot research
Hot-spot plumes
Magmatic processes
Volcanic processes
Explosive eruptions
Landslides
Volcanic hazards
Hydrothermal systems
Flexural arch
Coral reefs
ReefGrow software
Biogeography
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Submarine volcanism cruises
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Biology
Microscopic biology research
Open ocean biology research
Seafloor biology research
Chemistry
Automated chemical sensors
Methane in the seafloor
Geology
Volcanoes and seamounts
Hydrothermal vents
Methane in the seafloor
Submarine canyons
Earthquakes and landslides
Ocean acidification
Physical oceanography and climate change
Ocean circulation and algal blooms
Ocean cycles and climate change
Research publications