Table of Contents

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

Data were processed in SeaBird Seasave software, version 7.21a.  Raw hexadecimal data files were converted to base 10.  Temperature and conductivity data were low-pass filtered to match time constants.  The loopedit function was implemented to eliminate loops in the data due to ship roll, and the data were bin averaged to one-meter intervals.  Processed data were imported into Excel.

BCO-DMO Processing:

- served data via a toplevel file, adding columns for cruise_id, year, month, day, time_start, lat and lon, ISO_DateTime_UTC, and yrday_utc

version: 2015-09-11: same data as 2015-09-14 but no ISO_DateTime_UTC and yrday_utc

The use of DNA-based methods to measure microbial diversity has revealed a common pattern in which a small group of common species is accompanied by a very large group of rare ones. This pattern holds for bacteria, archaea, and microbial eukaryotes, including the ciliates that are the subject of this study. The project work will use denaturant gradient gel electrophoresis (DGGE) to quantify common species and Illumina pyrosequencing to quantify the rare ones. DGGE is rapid and inexpensive and will permit the study of ciliate biodiversity over a wide range of time and space scales. Illumina pyrosequencing, on the other hand, produces so many sequences from a given sample that even extremely rare forms can be quantified. Using these techniques in both experimental and observational approaches, the following objectives will be pursued:

Objective 1. Quantify the members of the ciliate "rare biosphere" over varied temporal scales to evaluate how change from rarity to commonness is related to ecosystem properties.

Objective 2. Determine the spatial and temporal scales over which the abundant ciliate assemblages in coastal waters are coherent.

Objective 3. Extend the breadth of taxonomic coverage to all microbial eukaryotes in some samples to evaluate how the presence of food and/or competitor organisms from other eukaryotic groups help to structures ciliate assemblages.

Objective 4. Elucidate the role of benthic-pelagic coupling in structuring planktonic assemblages by documenting the presence of metabolically active ciliates (i.e. by comparing DNA and RNA samples) from surface and deep plankton, fecal pellets and other large sinking marine aggregates, and sediments. 

Objective 5. Perform experiments on the role of grazing, temperature, ocean acidification, and phytoplankton composition in altering the relative abundances of common and rare species in natural ciliate assemblages.

This work will advance our understanding of global biodiversity by focusing on a single, ecologically important clade of microbial eukaryotes, the oligotrich and choreotrich ciliates. These micrograzers are responsible for a major portion of the consumption in planktonic food webs and they are, in turn, important food items for larval fish and invertebrates. They are thus centrally important for issues concerning food webs, productivity, and global environmental change. The new DNA-based techniques that have been developed in recent decades now allow unprecedented levels of information to be gathered on biodiversity. This information will provide important insights into ecosystem function and resilience in the face of change.

Note: This project is a renewal for the previous collaborative project, "Diversity and dynamics of planktonic ciliates - what can next-generation sequencing technologies tell us?", funded by awards OCE-1130033 and OCE-1129734.