1b: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"] 1c:T571,The ADCP measures water currents with sound, using a principle of sound waves called the Doppler effect. A sound wave has a higher frequency, or pitch, when it moves to you than when it moves away. You hear the Doppler effect in action when a car speeds past with a characteristic building of sound that fades when the car passes. The ADCP works by transmitting "pings" of sound at a constant frequency into the water. (The pings are so highly pitched that humans and even dolphins can't hear them.) As the sound waves travel, they ricochet off particles suspended in the moving water, and reflect back to the instrument. Due to the Doppler effect, sound waves bounced back from a particle moving away from the profiler have a slightly lowered frequency when they return. Particles moving toward the instrument send back higher frequency waves. The difference in frequency between the waves the profiler sends out and the waves it receives is called the Doppler shift. The instrument uses this shift to calculate how fast the particle and the water around it are moving. Sound waves that hit particles far from the profiler take longer to come back than waves that strike close by. By measuring the time it takes for the waves to bounce back and the Doppler shift, the profiler can measure current speed at many different depths with each series of pings. (More from WHOI instruments listing).1d:T923,The microbial ecologist Tom Fenchel recently said, “The decoupling of molecular and classical (including experimental) approaches to environmental microbiology has not been fruitful and it represents one of the most important challenges for the field in the coming years.” (Fenchel 2005). Classical approaches center on the centuries-old tradition of describing individual species via meticulous observation and analysis to generate monographs, such as is done for plants and animals. Unfortunately, the rush to new molecular techniques has sometimes ignored this tradition, with claims about new lineages never seen before and reports of staggering diversity of microbial eukaryotes based on environmental DNA samples not backed up by even the most elementary microscopic observations. In the face of this disconnect between the traditional and the molecular, we propose a marriage of the two approaches in the study of marine ciliate diversity and gene flow. Our own data show that in some clades of planktonic ciliates (Strombidiidae) there is indeed a high level of molecular diversity underlying a relatively small number of morphospecies. In other clades (some choreotrichs), the opposite appears to be true, with morphological heterogeneity underlain by apparently clonal lines, based on molecular data. Currently, we do not understand what sustains diversity in some clades; nor do we know why other clades show low diversity. But this problem is amenable to both experimental and observational approaches. This proposal uses a two-pronged approach, combining molecular (clone libraries, DGGE,FISH) and traditional (light microscopy) techniques to address three broad questions: i. What are the most important physical and biological factors that affect distribution and diversity of planktonic marine ciliates? ii. What is the effective population size for marine ciliate populations, and how does this compare to census population sizes? iii. How well do traditional morphological descriptions of ciliate species fare when compared with molecular characterizations? Using a combination of molecular and microscopy methods, we will address these questions in coastal planktonic ciliates. Analyses of the resulting data will yield insights into the nature of ciliate species and patterns of gene flow within the North Atlantic.6:["$","$L1b",null,{"dataset":{"_id":"3653","description":"

Physical data from the LIS0507 cruise recorded by CTD and ADCP. Note that temperature, salinity, and oxygen concentration values are from CTD casts (averaged for depth of water) and not from the niskin bottles used to collect samples for DNA analysis. There is a lag in time and some drift of reaserch vessel between the two, since the niskin bottles were not on the CTD itself.

Related files and references:
\nDoherty, M, M Tamura, BA Costas, ME Ritchie, GB McManus, and LA Katz. 2010. Ciliate Diversity and Distribution Across an Environmental and Depth Gradient in Long Island Sound, USA. Environmental Microbiology 12:886-898. doi:10.1111/j.1462-2920.2009.02133.x (PDF)

\n","problem":"","acquisition":"

Physical data were collected during a 6-station sampling cruise in Long Island Sound on 01 June 2007. Samples were collected at an increasing distance from the shore, over increasing depths. Some lat, lon, and time values were estimated from the ship's log.

\n","processing":"

Physical data were processed with the SeaSoft program from SeaBird.

BCO-DMO made the following modifications to the dataset: format of parameter names was changed to conform to BCO-DMO conventions; blanks were replaced with 'nd;, lat and lon values were converted from degrees/decimal minutes to decimal degrees; missing time_gmt value for sample 264 was added; lon value of sample 267 was changed from 072 49.583 to 072 19.583 (presumed to be a typographical error).

\n","bcodmoProcessing":"","title":"Temperature, salinity, O2, velocity, and headings from R/V Challenger cruise LIS0507 in the Long Island Sound in 2007","nickname":"LIS0507_physical_data","dataUrl":"","currentState":"Final no updates expected","currentStateId":"7","validated":true,"restricted":false,"version":"14 May 2012","version_date":"2012-05-14T08:00:00.000Z","abstract":"","citation":"McManus, G., Katz, L. A. (2012) Temperature, salinity, O2, velocity, and headings from R/V Challenger cruise LIS0507 in the Long Island Sound in 2007. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 14 May 2012) Version Date 2012-05-14 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/3653 [access date]","citationParts":{"identifier":"http://lod.bco-dmo.org/id/dataset/3653","versionDate":"2012-05-14","versionId":"14 May 2012","year":"2012","title":"Temperature, salinity, O2, velocity, and headings from R/V Challenger cruise LIS0507 in the Long Island Sound in 2007","authors":"McManus, G., Katz, L. A.","publisher":"Biological and Chemical Oceanography Data Management Office (BCO-DMO)."},"doi":"","release_date":null,"field_dataset_location":"","temporal_extent":{"start":null,"end":null},"temporal":{"resolution":"","type":"","start":{"value":"","label":""},"end":{"value":"","label":""}},"spatial_extent":{"shape":"polygon","center":{"latitude":41.246200011468,"longitude":-72.330190020076},"wkt":" POLYGON((-72.33708 41.23428, -72.3233 41.23428, -72.3233 41.25812, -72.33708 41.25812, -72.33708 41.23428))","north":41.25812,"east":-72.3233,"south":41.23428,"west":-72.33708},"dataset_type":["Unknown"],"keywords":["oceans"],"data_files":[{"id":"899579","title":"LIS0507_physical.csv","url":"https://datadocs.bco-dmo.org/dataset/3653/file/8XXgy48cQ4Av2L/LIS0507_physical.csv","showTableUrl":"https://www.bco-dmo.org/dataset/3653/data/view/899579","description":"Primary data file for dataset ID 3653","filename":"LIS0507_physical.csv","bytesize":1710,"checksum":{"value":"643817c1714b36d2e660547f2aedb4c6","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}],"supplemental_files":[],"roles":[{"role":{"_id":"138","name":"Principal Investigator"},"performedBy":{"_id":"51375","name":"George McManus"},"performedAtOrganization":{"_id":"256","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":"145","name":"BCO-DMO Data Manager"},"performedBy":{"_id":"51498","name":"Shannon Rauch"},"performedAtOrganization":{"_id":"191","name":"Woods Hole Oceanographic Institution"}}],"deployments":[{"_id":"58821","name":"LIS0507","synonyms":[],"dates":{"start":"2007-06-01T00:00:00.000Z","end":"2007-06-01T00:00:00.000Z"},"platform":{"_id":"54220","name":"R/V Challenger"},"chiefScientists":[]}],"funding":[{"_id":"54975","name":"OCE-0648711","fundingSource":{"_id":"355","name":"NSF Division of Ocean Sciences"},"url":"https://www.nsf.gov/awardsearch/show-award?AWD_ID=0648711"}],"instruments":[{"_id":"5614","name":"Acoustic Doppler Current Profiler","description":"","type_id":"405","type_name":"Acoustic Doppler Current Profiler","type_desc":"$1c","type_acronym":"ADCP"},{"_id":"5613","name":"CTD Sea-Bird","description":"Temperature, salinity, and oxygen concentrations were recorded at each station using a SeaBird CTD.","type_id":"447","type_name":"CTD Sea-Bird","type_desc":"A Conductivity, Temperature, Depth (CTD) sensor package from SeaBird Electronics. This instrument designation is used when specific make and model are not known or when a more specific term is not available in the BCO-DMO vocabulary. Refer to the dataset-specific metadata for more information about the specific CTD used. More information from: http://www.seabird.com/","type_acronym":"CTD Sea-Bird"}],"parameters":[{"_id":"27544","name":"year","format":"","frictionlessType":"","description":"

Year the sample was taken, in YYYY format.

","units":{"_id":"","name":"dimensionless"},"type":{"_id":"1062","name":"year","description":"

year, reported as YYYY, e.g. 1995

"}},{"_id":"27545","name":"month_gmt","format":"","frictionlessType":"","description":"

Month in GMT format.

","units":{"_id":"","name":"dimensionless"},"type":{"_id":"894","name":"month_gmt","description":"

month of year, GMT time , i.e. 01-12

"}},{"_id":"27546","name":"day_gmt","format":"","frictionlessType":"","description":"

Day in GMT format.

","units":{"_id":"","name":"dimensionless"},"type":{"_id":"800","name":"day_gmt","description":"

day, GMT time e.g. 22.

"}},{"_id":"27547","name":"yrday_gmt","format":"","frictionlessType":"","description":"

Sequential day of the year on which the sample was taken.

","units":{"_id":"","name":"dimensionless"},"type":{"_id":"1065","name":"yrday_gmt","description":"

GMT day and decimal time, as 326.5 for the 326th day of the year, or November 22 at 1200 hours (noon). In the case of drifter data, year day may be continuous over a multi year period.

"}},{"_id":"27548","name":"station","format":"","frictionlessType":"","description":"

Numeric identifier of the sample station.

","units":{"_id":"","name":"dimensionless"},"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":"27549","name":"sample","format":"","frictionlessType":"","description":"

Unique identifier of the sample.

","units":{"_id":"","name":"dimensionless"},"type":{"_id":"960","name":"sample","description":"

unique sample identification or number; any combination of alpha numeric characters; precise definition is file dependent

"}},{"_id":"27550","name":"site_descrip","format":"","frictionlessType":"","description":"

Indicates if the sample site is located in ('in_plume') or out ('out_plume') of the plume.\t

","units":{"_id":"","name":"dimensionless"},"type":{"_id":"1740","name":"site_descrip","description":"

Description or characteristics of a sampling site

"}},{"_id":"27551","name":"time_local","format":"","frictionlessType":"","description":"

Local time at which the sample was taken.

","units":{"_id":"","name":"dimensionless"},"type":{"_id":"1007","name":"time_local","description":"

time of day, local time, using 2400 clock format

"}},{"_id":"27552","name":"time_gmt","format":"","frictionlessType":"","description":"

Time in GMT format (local time +4 hours).

","units":{"_id":"","name":"dimensionless"},"type":{"_id":"1005","name":"time_gmt","description":"

time of day, reported in GMT time, 24 hour clock

"}},{"_id":"27553","name":"lat","format":"","frictionlessType":"","description":"

Latitude. Positive values indicate North. Values have been converted from degrees and decimal-minutes to decimal degrees.

","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":"27554","name":"lon","format":"","frictionlessType":"","description":"

Longitude. Negative values indicate West. Values have been converted from degrees and decimal-minutes to decimal degrees.

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

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

"}},{"_id":"27555","name":"depth","format":"","frictionlessType":"","description":"

Sample depth in meters.

","units":{"_id":"","name":"meters"},"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":"27556","name":"temp","format":"","frictionlessType":"","description":"

Temperature of the water sample in degrees Celsius.

","units":{"_id":"","name":"degrees Celsius"},"type":{"_id":"733","name":"temperature","description":"

water temperature at measurement depth

"}},{"_id":"27557","name":"sal","format":"","frictionlessType":"","description":"

Salinity of the water sample.

","units":{"_id":"","name":"PSU"},"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":"27558","name":"O2_mg","format":"","frictionlessType":"","description":"

Oxygen level of water sample measured in mg/L.

","units":{"_id":"","name":"mg/L"},"type":{"_id":"1073","name":"no_bcodmo_term","description":"

An association with a community-wide standard parameter has not yet been made.

"}},{"_id":"27559","name":"u","format":"","frictionlessType":"","description":"

Eastward velocity measured by ADCP (in cm/s). Originally named 'East Velocity'.

","units":{"_id":"","name":"cm/s"},"type":{"_id":"1019","name":"u","description":"

eastward component of current velocity, Eastward flow is positive. Units vary, can be m/s, cm/s,...

"}},{"_id":"27560","name":"v","format":"","frictionlessType":"","description":"

Northward velocity measured by ADCP (in cm/s). Originally named 'NorthVelocity'.

","units":{"_id":"","name":"cm/s"},"type":{"_id":"1037","name":"v","description":"

northward component of current velocity, Northward flow is positive. Units vary, can be m/s, cm/s,...

"}},{"_id":"27561","name":"angle_from_N","format":"","frictionlessType":"","description":"

Angle from North, measured in degrees.

","units":{"_id":"","name":"degrees"},"type":{"_id":"793","name":"curr_dir_rel","description":"

relative current direction, in degrees

"}},{"_id":"27562","name":"magnitude","format":"","frictionlessType":"","description":"

Magnitude in cm/s.

","units":{"_id":"","name":"cm/s"},"type":{"_id":"1073","name":"no_bcodmo_term","description":"

An association with a community-wide standard parameter has not yet been made.

"}},{"_id":"27563","name":"compass_head","format":"","frictionlessType":"","description":"

Compass heading in degrees from true North.

","units":{"_id":"","name":"degrees"},"type":{"_id":"853","name":"heading","description":"

heading of ship or platform

"}},{"_id":"27578","name":"cruiseid","format":"","frictionlessType":"","description":"

Unique identifier of the cruise.

","units":{"_id":"","name":"dimensionless"},"type":{"_id":"789","name":"cruiseid","description":"

cruise identifier, e.g. en9402 R/V Endeavor cruise 9402

"}},{"_id":"30998","name":"ISO_DateTime_UTC","format":"","frictionlessType":"","description":"

Date and time formatted to ISO8601 standard. T indicates start of time string; Z indicates UTC.

","units":{"_id":"","name":"YYYY-MM-DDTHH:MM:SS.ssZ"},"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)

"}}],"related_publications":[],"related_datasets":[],"services":[{"grouping":"","items":[{"name":"View Data","description":"An in-browser view of the primary tabular data file","url":"https://www.bco-dmo.org/dataset/3653/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/3653/description","contentType":"text/html","actionType":"view"},{"name":"PDF","description":"A PDF of the HTML dataset metadata","url":"https://www.bco-dmo.org/dataset/3653/Dataset_description.pdf","contentType":"application/pdf","actionType":"download"},{"name":"ISO 19115-2 (NOAA Profile)","description":"","url":"https://www.bco-dmo.org/dataset/3653/iso","contentType":"application/xml","actionType":"download"}]}],"programs":[],"projects":[{"_id":"2213","name":"Testing hypotheses about diversity, gene flow, and effective population size in marine planktonic ciliates","acronym":"CiliateDivGenePop","description":"$1d"}],"archives":[],"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":109},"downloads":{"count":346}}},"fileId":"899579"}]