Table of Contents

• Dataset Description
  • Methods & Sampling
  • Data Processing Description
• Data Files
• Parameters
• Instruments
• Deployments
• Project Information
• Funding

Accessions for 18S rDNA , chloroplast and metagenomics data

Biliphyte sequences from this study have been deposited in GenBank under Accession No. EU368003-EU368039

Cuvelier ML, Ortiz A, Kim E, Moehlig H, Richardson DE, Heidelberg JF, Archibald JM, Worden AZ (2008).
Widespread distribution of a unique marine protistan lineage. Environmental Microbiology. Vol. 10:1621-1634.

Prymnesiophyte sequences from this study have been deposited in GenBank under Accession Nos.
HM581528-HM581638 and HM565909-HM565914. Other scaffolds with predicted genes from this Whole
Genome Shotgun/454 project have been deposited at DNA Data Bank of Japan/European Molecular Biology
Laboratory/GenBank under the accession no. AEAR00000000. The version described in this paper is
the first version, AEAR01000000.

Cuvelier ML, Allen* AE, Monier* A, McCrow JP, Messie M, Tringe SG, Woyke T, Welsh RM, Ishoey T,
Lee JH, Binder BJ, DuPont CL, Latasa M, Guigand C, Buck KR, Hilton J, Thiagarajan M, Caler E,
Read B, Lasken RS, Chavez FP & AZ Worden (2010). Targeted metagenomics and ecology of globally
important uncultured eukaryotic phytoplankton. Proceedings of the National Academy of Sciences USA.

Alveolate sequences from this study have been deposited in GenBank under:
EU818567-EU818691, EU836584-EU836597, EU818578-EU818566, EU817966-EU818077,
EU836613-EU836615; EU817882-EU817965; EU836616-EU816617

Guillou L, Viprey M, Chambouvet A, Welsh RM, Kirkham AR, Massana R, Scanlan DJ and AZ Worden (2008).
Widespread occurrence and genetic diversity of marine parasitoids belonging to Syndiniales (Alveolata).
Environmental Microbiology. DOI: 10.1111/j.1462-2920.2008.01731.x

Samples were typically taken at the surface and deep chlorophyll maximum using a niskin rosette, all contextual data available (typically temperature and salinity) was deposited with the GenBank Submission for each sequence.

Field sites and sample collection
Five cruises were conducted, two transects from coastal New England to the BATS site (R/V Endeavor cruise EN351 and R/V Oceanus cruise OC413) and three transects across the Florida Straits (R/V Walton Smith cruises WS0503, WS0518, WS0528) with characteristics as in Table 1. Samples were collected in surface and DCM waters using a Sea-Bird Niskin Rosette equipped with standard CTD and PAR detectors (see also below). For DNA extraction samples, 1 l of seawater was gravity filtered through 2 um pore size filters (GE Osmonics, Minnetonka, MN, USA) and then onto a 0.45 um pore size (2001) or 0.2 um pore size (2005) Supor filter (Pall Gelman, Ann Arbor, MI, USA) using vacuum. For FISH samples whole seawater (no size fractionation) was preserved with 1% paraformaldahyde (final concentration) for at least 1 h in the dark at 4°C. For each replicate, volumes of 180 ml or more of seawater were gently filtered onto a 25 mm, 0.2 um Anodisc filter (Whatman, Maidstone, England). The filters were then subjected to an ethanol dehydration series at 50%, 80%, 100% (diluted in sterile, 18.2 ° H2O) for 3 min each and stored at -80°C. Flow cytometry samples were preserved with 0.25% (final concentration) fresh electron microscopy grade glutaraldehyde (Tousimis, Rockville, MD, USA), flash frozen in liquid nitrogen and moved to -80°C for long-term storage.

PCR, cloning and Sanger sequencing for all 18S rDNA
sequences; metagenomic data was produced by multiple
displacement amplification of flow cytometrically sorted
cells with subsequent Sanger and 454-FLX sequencing. See
Cuvelier et al. 2008 and Cuvelier et al. 2010 for greater
detail if desired.

The growth rates and fate of primary producers in the oceans are key factors
regulating carbon flux in the biosphere. While resource limitation is known to
play a major regulatory role, the specific factors controlling growth and mortality
of picophytoplankton (<2 microm diameter) are poorly understood. In particular,
due to the small size and low sinking quotient of these dominant primary producers,
determinants of their fate and transport in the water column are critical to the
development of predictive models of carbon flux and its likely perturbation due to
climate change. Picophytoplankton is composed of cyanobacteria, (Prochlorococcus
and Synechococcus) and small eukaryotes. While the picocyanobacteria have received
much attention, little is known about the distribution and dynamics of picophytoeukaryotes,
particularly in oceanic settings. The few comparative measurements made to date indicate
that the productivity of picophytoeukaryotes can rival that of picocyanobacteria. Hence,
knowledge regarding the role of picophytoeukaryotes in open ocean environments is urgently
needed. However, this knowledge is only valuable when put in the context of the total
picophytoplankton community and, therefore, quantification of picocyanobacteria must also
be included.

The overall goal is to develop a method for determining underlying physiological controls
of picophytoeukaryotes. A targeted approach will be used, combining flow sorting, cDNA
libraries and Expressed Sequence Tags (EST), allowing real-time expressional responses to
be identified. This knowledge will highlight key physiological constraints and information
on molecular underpinnings of picoeukaryotic population dynamics as well as aiding future
efforts to isolate open-ocean picoeukaryotes. This is an important additional benefit from
the work since environmental clone library data has demonstrated that such picoeukaryotes
are poorly represented in culture collections. Long-term, the environmental genomic approach
developed will also provide a high throughput mechanism for profiling expressional responses
(mRNA) in the field. In the proposed work, expressional responses will be evaluated in two
ocean basins, the equatorial Atlantic and the South Pacific.

PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH
Cuvelier et al. "Widespread distribution of a unique marine protistan lineage.," Environmental Microbiology, 2008.

Note:
All contextual data available (typically temperature and salinity) was deposited with the GenBank Submission for each sequence.