Dataset: Bugula neritina Genotype Distribution

Name: Bugula neritina host genotype and symbiotic status of colonies along the East Coast, USA, ranging from latitudes 38.61283 to 29.753272
Published: 2018-08-23
Keywords: biota, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.719479.2

Spatial Extent: N:38.61283 E:-75.072524 S:29.753272 W:-81.421

Temporal Extent: 2015-03-16 - 2016-06-15

Project:

Biogeography of a marine defensive microbial symbiont: relative importance of host defense vs. abiotic factors (BiogeogDefensiveSymb)

Principal Investigator:

Nicole Lopanik (Georgia Institute of Technology, GA Tech)

Co-Principal Investigator:

Grace Lim-Fong (Randolph-Macon College)

BCO-DMO Data Manager:

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2018-08-23

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Bugula neritina host genotype and symbiotic status of colonies along the East Coast, USA, ranging from latitudes 38.61283 to 29.753272

Abstract:

Bugula neritina host genotype and symbiotic status of colonies along the East Coast, USA, ranging from latitudes 38.61283 to 29.753272.

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2018-08-23	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.719479.2	2020-11-25

Description

Bugula neritina host genotype and symbiotic status of colonies along the East Coast.

Methods & Sampling

Bugula neritina colonies were collected by hand using a haphazardly placed 15x15 cm grid on submerged area of floating dock, and placed into a tube of RNAlater. Colonies were collected along the Western Atlantic coast, ranging from latitudes 38.61283 to 29.753272. Surface waters, on sides of floating docks.Host genotype, either Type S or Type N, was determined by PCR amplification of the host cytochrome oxidase I gene followed by restriction analysis as in Linneman et al. 2014. The presence of the symbiont, either + for present or – for absent, was determined by PCR assays with two portions of the functional bryostatin biosynthetic gene documented in Sudek et al. 2007.

Temperature was measured with a digital thermometer, and salinity with a refractometer at the time of collection.

Data Processing Description

We have analyzed the proportions at differing latitudes and performed regression analysis with various factors (latitude, longitude, temperature, salinity) using SPSS Statistics 24.

BCO-DMO Processing:
- applied date, location name, location code, lat, lon, temp, and sal to each relevant row (was only included the first row for each sample set);
- created location_descrip column for more detailed location place name;
- modified parameter names;
- moved "Total" to the "Grid" column;
- removed commas and apostrophes from place names; replaced spaces with underscores;
- replaced blanks and "N/A" with "nd" (no data).

Data Files

File
B_neritina_genotype_dist.csv (Comma Separated Values (.csv), 22.10 KB) MD5:eabc8067e7e2b41cec56890604ef35b4 Primary data file for dataset ID 719479

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1608709

Deployments

None available yet

Instruments

digital thermometer

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: digital thermometer

Generic Description:

An instrument that measures temperature digitally.

Refractometer

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: Refractometer

Generic Description:

A refractometer is a laboratory or field device for the measurement of an index of refraction (refractometry). The index of refraction is calculated from Snell's law and can be calculated from the composition of the material using the Gladstone-Dale relation.

In optics the refractive index (or index of refraction) n of a substance (optical medium) is a dimensionless number that describes how light, or any other radiation, propagates through that medium.

Thermal Cycler

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: Thermal Cycler

Generic Description:

A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.

(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
date_collected	Date of collection, formatted as mm/dd/yyyy	unitless	date
location	Location samples collected	unitless	site
location_descrip	Specific area within location where samples were collected	unitless	site
location_code	Location code	unitless	Site_ID
Latitude	Latitude of location	decimal degrees	lat
Longitude	Longitude of location	decimal degrees	lon
temp	Water temperature	degrees Celsius	temp
salinity	Water salinity	parts per thousand	sal
grid_num	Sampling effort replicate	unitless	replicate
num_B_neritina	Total number of B. neritina colonies in grid	unitless	count
num_Type_S_symb	Number of Type S symbiotic colonies	unitless	count
num_Type_S_asymb	Number of Type S aposymbiotic colonies	unitless	count
num_Type_N_symb	Number of Type N symbiotic colonies	unitless	count
num_Type_N_asymb	Number of Type N aposymbiotic colonies	unitless	count
prop_Type_S_symb	Proportion of Type S symbiotic colonies	unitless	no_bcodmo_term
prop_Type_S_asymb	Proportion of Type S aposymbiotic colonies	unitless	no_bcodmo_term
prop_Type_N_symb	Proportion of Type N symbiotic colonies	unitless	no_bcodmo_term
prop_Type_N_asymb	Proportion of Type N aposymbiotic colonies	unitless	no_bcodmo_term

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Database

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Dataset: Bugula neritina Genotype Distribution