19:I[42426,["/_next/static/immutable/chunks/1xctgzqre-wsy.js","/_next/static/immutable/chunks/06_-wz6pdtp2b.js","/_next/static/immutable/chunks/30e52g49hg40p.js","/_next/static/immutable/chunks/02yq6tul2z-oh.js","/_next/static/immutable/chunks/10bx_ec2vj7n_.js","/_next/static/immutable/chunks/33bfn03fo8xnt.js","/_next/static/immutable/chunks/0tfjf78scu61b.js","/_next/static/immutable/chunks/31xnvej4n1bi9.js"],"default"] 1a:Teb1,NSF Award Abstract: Planktonic ciliates are key members of marine food webs where they serve diverse roles, including as food chain links between smaller microbes and larger plankton. Due to their small size and difficulties in identifying and cultivating them, we know less about ciliate diversity and distributions in the ocean than we do about larger organisms such as fish and invertebrates. Previous work from this team measured ciliate diversity in coastal waters and found that distinct genetic variants were separated in time and space in a way that could be related to factors such as ocean temperature, salinity, and depth gradients. Many questions remained unanswered, and it is important to understand the environmental factors that control the diversity and distribution of plankton such as ciliates to predict how these organisms may respond to a changing enviroment in the coming decades. This project focuses on: 1) how ciliate species are delineated using single-cell genomics and transcriptomics; 2) DNA-based studies of all ciliates and other planktonic members of the SAR clade (Stramenopila, Alveolata, Rhizaria), which will provide ecological context; 3) in situ gene expression by single-cell and meta- transcriptomics; and 4) laboratory studies of gene expression in cultivated ciliate species. This project involves training of postdoctoral scholars, graduate students, and undergraduates. The researchers are committed to creating diverse and inclusive research labs; recruitment of participants will be done through partnership with appropriate groups on our campuses. The project integrates with summer Research Experiences for Undergraduates (REU) activities at both Smith College and UCONN (including the UCONN/Mystic Aquarium joint REU), which are especially focused on underrepresented students. This project also enhances efforts to broaden understanding of biodiversity in partnership with the UCONN Noyce Scholars Program, which facilitates career-changing STEM professionals to become teachers in underserved secondary schools. This project will assess distributions of reproductively-isolated species, determined using a new method to characterize regions of the ciliate germline genome. Furthermore, it will use phylogenomic methods to identify clade-specific transcripts (e.g. those of spirotrich ciliates) within metatranscriptomes from the shelf environment and to expand knowledge of ciliate function with single-cell transcriptomics of field-collected cells. These approaches will be a substantial improvement over the culture-based methods that are potentially biased towards "weedy" species in the ocean. The combination of definitive species identification with assessment of function via single-cell and meta- transcriptomics promises to provide significant advances in marine plankton ecology. The research focuses on two broad questions: 1) does the observed high diversity in phylogenetically-informative genes reflect reproductive isolation and functional differentiation in planktonic ciliates? and 2) do different co-occurring species of planktonic ciliates show substantial functional differences that correspond to different niches in the ocean? The project assesses species boundaries (i.e. reproductive isolation) through analyses of patterns in the germline micronuclei of planktonic ciliate morphospecies; characterizes transitions of closely-related ciliates across ecological gradients in the ocean; and examines functional differences within and between species, and in communities, through analyses of transcriptomics. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.6:["$","$L19",null,{"dataset":{"_id":"879380","description":"","problem":"","acquisition":"

Seven stations on the shelf and slope south of Montauk, NY on 14-15 June 2022 were sampled. Basic hydrographic properties, including temperature, salinity, dissolved oxygen, and pH were measured and rosette samples were taken for chlorophyll, nutrients, and microplankton. Water was filtered for metagenomics and metatranscriptomics and picked individual microplankters for sequencing. Three to ten depths were sampled at each station. Our shallowest station was on the shelf at 38m and the deepest was at the slope edge at 2400m. Due to limitations of the CTD our deepest sampled depth was 1150m. At the two shallowest stations, we also deployed a Wetstar fluorometer for phytoplankton fluorescence.

\n","processing":"

The CTD data were processed with SeaBird's Seasoft program and converted to spreadsheet format.

\n","bcodmoProcessing":"","title":"CTD profiles collected with RV Connecticut on the Continental shelf and slope south of Montauk, NY on 14-15 June 2022.","nickname":"CTD profiles RV Connecticut June 2022","dataUrl":"","currentState":"Final","currentStateId":"7","validated":true,"restricted":false,"version":"1","version_date":"2022-09-16T04:00:00.000Z","abstract":"Seven stations on the shelf and slope south of Montauk, NY on 14-15 June 2022 were sampled. Basic hydrographic properties, including temperature, salinity, dissolved oxygen, and pH were measured and rosette samples were taken for chlorophyll, nutrients, and microplankton. Water was filtered for metagenomics and metatranscriptomics and picked individual microplankters for sequencing. Three to ten depths were sampled at each station. Our shallowest station was on the shelf at 38m and the deepest was at the slope edge at 2400m. Due to limitations of the CTD our deepest sampled depth was 1150m. At the two shallowest stations, we also deployed a Wetstar fluorometer for phytoplankton fluorescence. The CTD data were processed with SeaBird's Seasoft program and converted to spreadsheet format. ","citation":"McManus, G., Santoferrara, L., Katz, L. A. (2022) CTD profiles collected with RV Connecticut on the Continental shelf and slope south of Montauk, NY on 14-15 June 2022. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2022-09-16 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.879380.1 [access date]","citationParts":{"identifier":"doi:10.26008/1912/bco-dmo.879380.1","versionDate":"2022-09-16","versionId":"1","year":"2022","title":"CTD profiles collected with RV Connecticut on the Continental shelf and slope south of Montauk, NY on 14-15 June 2022.","authors":"McManus, G., Santoferrara, L., Katz, L. A.","publisher":"Biological and Chemical Oceanography Data Management Office (BCO-DMO)."},"doi":"10.26008/1912/bco-dmo.879380.1","release_date":null,"field_dataset_location":"","temporal_extent":{"start":"2022-06-14T04:00:00.000Z","end":"2022-06-15T04:00:00.000Z"},"temporal":{"resolution":"time:unitDay","type":"time:Interval","start":{"value":"1655179200","label":"2022-06-14"},"end":{"value":"1655265600","label":"2022-06-15"}},"spatial_extent":{"shape":"polygon","center":{"latitude":40.187200000009,"longitude":-71.536250000017},"wkt":"POLYGON ((-71.7138 39.3804, -71.3587 39.3804, -71.3587 40.994, -71.7138 40.994, -71.7138 39.3804))","north":40.994,"east":-71.3587,"south":39.3804,"west":-71.7138},"dataset_type":["Cruise Results"],"keywords":["oceans"],"data_files":[{"id":"903728","title":"ctd_all.csv","url":"https://datadocs.bco-dmo.org/dataset/879380/file/B11vAXViPE415A/ctd_all.csv","showTableUrl":"https://www.bco-dmo.org/dataset/879380/data/view/903728","description":"Primary data file for dataset ID 879380","filename":"ctd_all.csv","bytesize":40201605,"checksum":{"value":"173c3f3bd7c58dbd9b178181a0ca5e3f","Algorithm":{"_id":"190","name":"MD5"}},"mimetype":"text/csv","fileType":{"_id":"192","name":"Comma Separated Values (.csv)"},"isErddap":"","date":"","isPublicDuringEmbargo":false,"primaryDataFile":true,"showTable":true,"restricted":false},{"id":"879417","title":"CTD_files","url":"https://datadocs.bco-dmo.org/data/305/Ciliate_Omics/data/879380/CTD_files.zip","showTableUrl":"","description":"Original CTD Seabird files for RV Connecticut Cruise June 2022. Files are divided up per station number. ","filename":"CTD_files.zip","bytesize":3082456,"checksum":{"value":"5587a53921ab10da5f12fdad02145331","Algorithm":{"_id":"190","name":"MD5"}},"mimetype":"application/zip","fileType":{"_id":"196","name":"ZIP Archive (ZIP)"},"isErddap":"","date":"","isPublicDuringEmbargo":false,"primaryDataFile":false,"showTable":false,"restricted":false}],"supplemental_files":[],"roles":[{"role":{"_id":"138","name":"Principal Investigator"},"performedBy":{"_id":"51375","name":"George McManus"},"performedAtOrganization":{"_id":"85","name":"University of Connecticut"}},{"role":{"_id":"140","name":"Co-Principal Investigator"},"performedBy":{"_id":"51376","name":"Laura A. Katz"},"performedAtOrganization":{"_id":"255","name":"Smith College"}},{"role":{"_id":"140","name":"Co-Principal Investigator"},"performedBy":{"_id":"626644","name":"Luciana Santoferrara"},"performedAtOrganization":{"_id":"879412","name":"Hofstra University"}},{"role":{"_id":"133","name":"Contact"},"performedBy":{"_id":"51375","name":"George McManus"},"performedAtOrganization":{"_id":"85","name":"University of Connecticut"}},{"role":{"_id":"145","name":"BCO-DMO Data Manager"},"performedBy":{"_id":"748773","name":"Karen Soenen"},"performedAtOrganization":{"_id":"191","name":"Woods Hole Oceanographic Institution"}}],"deployments":[],"funding":[{"_id":"826125","name":"OCE-1924570","fundingSource":{"_id":"355","name":"NSF Division of Ocean Sciences"},"url":"https://www.nsf.gov/awardsearch/show-award?AWD_ID=1924570"},{"_id":"826130","name":"OCE-1924527","fundingSource":{"_id":"355","name":"NSF Division of Ocean Sciences"},"url":"https://www.nsf.gov/awardsearch/show-award?AWD_ID=1924527"}],"instruments":[{"_id":"880566","name":"","description":"","type_id":"488","type_name":"CTD Sea-Bird 9","type_desc":"The Sea-Bird SBE 9 is a type of CTD instrument package. The SBE 9 is the Underwater Unit and is most often combined with the SBE 11 Deck Unit (for real-time readout using conductive wire) when deployed from a research vessel. The combination of the SBE 9 and SBE 11 is called a SBE 911. The SBE 9 uses Sea-Bird's standard modular temperature and conductivity sensors (SBE 3 and SBE 4). The SBE 9 CTD can be configured with auxiliary sensors to measure other parameters including dissolved oxygen, pH, turbidity, fluorometer, altimeter, etc.). Note that in most cases, it is more accurate to specify SBE 911 than SBE 9 since it is likely a SBE 11 deck unit was used. more information from Sea-Bird Electronics","type_acronym":"CTD SBE 9"},{"_id":"879416","name":"Wetstar fluorometer","description":"Wetstar fluorometer for phytoplankton fluorescence","type_id":"474261","type_name":"WET Labs (Sea-Bird WETLabs) WETStar fluorometer","type_desc":"Submersible fluorometer designed for through-flow or pumped CTD applications manufactured by WetLabs and which can be configured for various types of fluorescence. The probe has a temperature range of 0-30 degrees C and a depth rating of 600 meters.","type_acronym":"WETStar"}],"parameters":[{"_id":"880567","name":"Station","format":"","frictionlessType":"integer","description":"

Station number

","units":{"_id":"","name":"unitless"},"type":{"_id":"987","name":"station","description":"

Station identifier; a unique number or alphanumeric string designating a general geographic location at which one or more sampling activities may occur.

"}},{"_id":"880568","name":"latitude","format":"","frictionlessType":"number","description":"

Station latitude, south is negative

","units":{"_id":"","name":"decimal degrees"},"type":{"_id":"730","name":"latitude","description":"

latitude, in decimal degrees, North is positive, negative denotes South; Reported in some datasets as degrees, minutes

"}},{"_id":"880569","name":"longitude","format":"","frictionlessType":"number","description":"

Station longitude, west is negative

","units":{"_id":"","name":"decimal degrees"},"type":{"_id":"731","name":"longitude","description":"

longitude, in decimal degrees, East is positive, negative denotes West; Reported in some datasets as degrees, minutes

"}},{"_id":"880570","name":"Date","format":"%Y-%m-%d","frictionlessType":"date","description":"

Date of CTD sampling

","units":{"_id":"","name":"unitless"},"type":{"_id":"1070","name":"date","description":"

date; generally reported in GMT as YYYYMMDD (year; month; day); also as MMDD (month; day); EqPac dates are local Hawaii time. ISO_Date format is YYYY-MM-DD (http://www.iso.org/iso/home/standards/iso8601.htm)

"}},{"_id":"880571","name":"Time","format":"%H:%M:%S","frictionlessType":"time","description":"

Start time of CTD sampling

","units":{"_id":"","name":"unitless"},"type":{"_id":"1075","name":"time","description":"

Time GMT defined as HHMM; time of day; generally reported in GMT as HHMM (hours and minutes) but may also be HH.H (decimal hours) or HHMMSS (hours; minutes and seconds); in EqPac time is reported as Hawaii local time

"}},{"_id":"880572","name":"density","format":"","frictionlessType":"string","description":"

Density

","units":{"_id":"","name":"kg/m^3"},"type":{"_id":"806","name":"density","description":"

density, in mass per unit volume

"}},{"_id":"880573","name":"depth","format":"","frictionlessType":"number","description":"

Depth

","units":{"_id":"","name":"meters (m)"},"type":{"_id":"808","name":"depth","description":"

Observation/sample depth below the sea surface. Units often reported as: meters, feet.

\nWhen used in a JGOFS/GLOBEC dataset the depth is a best estimate; usually but not always calculated from pressure; calculated either from CTD pressure using Fofonoff and Millard (1982; UNESCO Tech Paper #44) algorithm adjusted for 1980 equation of state for seawater (EOS80) or simply equivalent to nominal depth as recorded during sampling if CTD pressure was unavailable.

"}},{"_id":"880574","name":"Fluorescence","format":"","frictionlessType":"number","description":"

Fluorescence, arbitrary

","units":{"_id":"","name":"mg/m^3"},"type":{"_id":"835","name":"fluorescence","description":"

Fluorescence. Indirect measure of pigment concentration.

Units and collection method may vary. Units often reported in milligrams/meter^3 (mg/m3) or micromoles per liter (ug/L). Sometimes reported after being calibrated against extracted pigment concentrations.

In JGOFS/GLOBEC projects fluorescence is measured from CTD instrument sensor.

"}},{"_id":"880575","name":"oxygen","format":"","frictionlessType":"number","description":"

dissolved oxygen

","units":{"_id":"","name":"mg/L"},"type":{"_id":"910","name":"dissolved Oxygen","description":"

dissolved oxygen concentration

"}},{"_id":"880576","name":"pH","format":"","frictionlessType":"number","description":"

","units":{"_id":"","name":"unitless"},"type":{"_id":"1892","name":"pH","description":"

pH: The measure of the acidity or basicity of an aqueous solution

"}},{"_id":"880577","name":"salinity","format":"","frictionlessType":"number","description":"

Salinity

","units":{"_id":"","name":"unitless"},"type":{"_id":"955","name":"sal","description":"

Salinity: The amount (mass or quantity of matter) of salt per amount (volume or mass) of a body of water.

"}},{"_id":"880578","name":"scan","format":"","frictionlessType":"integer","description":"

sampling event number for station

","units":{"_id":"","name":"unitless"},"type":{"_id":"829","name":"event","description":"

Event or operation identifier; event or operation number; often derived from date/time (MMDDHHmm) of sampling and when combined with year (YYYY) is a unique sampling identifier/data processing key. Date/time is not necessarily in GMT.

"}},{"_id":"880579","name":"Temperature","format":"","frictionlessType":"number","description":"

Temperature

","units":{"_id":"","name":"Degrees Celsius (°C)"},"type":{"_id":"733","name":"temperature","description":"

water temperature at measurement depth

"}},{"_id":"880580","name":"flag","format":"","frictionlessType":"string","description":"

Quality flag

","units":{"_id":"","name":"untless"},"type":{"_id":"1730","name":"flag","description":"

Data flag. Multiple uses which are dataset dependent. Some uses: data quality, collection occurrence or success, depth indicator. See dataset documentation for specific details

"}},{"_id":"880581","name":"ISO_DateTime_Local","format":"%Y-%m-%dT%H:%M:%S","frictionlessType":"datetime","description":"

Sampling date and time (Eastern Daylight Time (GMT-4)) in ISO 8601 format yyyy-mm-ddTHH:MM:SS

","units":{"_id":"","name":"units"},"type":{"_id":"1908","name":"ISO_DateTime_UTC","description":"

Date/Time (UTC) ISO formatted
\nThis standard is based on ISO 8601:2004(E) and takes on any of the following forms:
\n2009-08-30T09:05:00[.xx] (local time)
\n2009-08-30T14:05:00[.xx]Z (UTC time)
\n2009-08-30T14:05:00[.xx]-05:00
\nThe dashes and the colons can be dropped.
\nThe T can also be dropped \"by mutual agreement\", but one needs the trailing Z if the time is UTC.

Sample ISO_datetime_utc:
\n2009-08-30T14:05:00[.xx]Z (UTC time)

Format: YYYY-mm-ddTHH:MM:SS[.xx]Z (UTC time)

"}},{"_id":"880582","name":"ISO_DateTime_UTC","format":"%Y-%m-%dT%H:%M:%SZ","frictionlessType":"datetime","description":"

Sampling date and time (UTC) in ISO 8601 format yyyy-mm-ddTHH:MM:SSZ

","units":{"_id":"","name":"units"},"type":{"_id":"1908","name":"ISO_DateTime_UTC","description":"

Sample ISO_datetime_utc:
\n2009-08-30T14:05:00[.xx]Z (UTC time)

Format: YYYY-mm-ddTHH:MM:SS[.xx]Z (UTC time)

"}}],"related_publications":[],"related_datasets":[{"_id":"988253","name":"Single-cell transcriptomics","url":"","relation_type":"IsRelatedTo","type_desc":"

The dataset is related to another dataset.

\n","relation_desc":"The Single-cell transcriptomics dataset (988253) and metabarcoding dataset (988266) are the omics data associated with the collections from the CTD dataset (879380). Both omics datasets used the same bottle samples collected with the CTD profiles.","citation":"Katz, L. A. (2025) Metabarcoding data from samples collected at shore-based tide pools and ocean samples in New England waters in 2019. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-11-04 http://lod.bco-dmo.org/id/dataset/988266"}],"services":[{"grouping":"","items":[{"name":"View Data","description":"An in-browser view of the primary tabular data file","url":"https://www.bco-dmo.org/dataset/879380/data/view","contentType":"text/html","actionType":"view"}]},{"grouping":"Metadata","items":[{"name":"HTML","description":"A simple HTML page of the dataset metadata","url":"https://www.bco-dmo.org/dataset/879380/description","contentType":"text/html","actionType":"view"},{"name":"PDF","description":"A PDF of the HTML dataset metadata","url":"https://www.bco-dmo.org/dataset/879380/Dataset_description.pdf","contentType":"application/pdf","actionType":"download"},{"name":"ISO 19115-2 (NOAA Profile)","description":"","url":"https://www.bco-dmo.org/dataset/879380/iso","contentType":"application/xml","actionType":"download"}]}],"programs":[],"projects":[{"_id":"826126","name":"Collaborative Research: Combining single-cell and community 'omics' to test hypotheses about diversity and function of planktonic ciliates","acronym":"Ciliate Omics","description":"$1a"}],"archives":[{"id_value":"10.26008/1912/bco-dmo.879380.1","url":"https://doi.org/10.26008/1912/bco-dmo.879380.1","date_assigned":"2022-09-16","version_date":"2022-09-16","archiver":"Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)","archiver_id":"272"}],"license":{"name":"Creative Commons Attribution 4.0","id":"CC-BY-4.0","uri":"https://creativecommons.org/licenses/by/4.0/","spdxUri":"https://spdx.org/licenses/CC-BY-4.0"},"metrics":{"views":{"count":229},"downloads":{"count":334}}}}]