http://lod.bco-dmo.org/id/dataset/3507
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2011-07-20
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Experimental data: El Nino virus abundance from Southern California and Rhode Island coast from 2007-2013 (El Nino and virus diversity project, Cyanophage Evolutionary Ecology project)
2021-06-08
publication
2021-06-08
revision
BCO-DMO Linked Data URI
2021-06-08
creation
http://lod.bco-dmo.org/id/dataset/3507
Marcia Marston
Roger Williams University
principalInvestigator
Jennifer B.H. Martiny
University of California-Irvine
principalInvestigator
Bradley Hughes
University of California-Irvine
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Martiny, J. B., Marston, M., Hughes, B. (2021) Experimental data: El Nino virus abundance from Southern California and Rhode Island coast from 2007-2013 (El Nino and virus diversity project, Cyanophage Evolutionary Ecology project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2) Version Date 2021-06-08 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/3507 [access date]
El Nino virus abundance Dataset Description: <p>Abundance (estimated number of infecting particles per ml seawater and standard error) of cyanophages infecting laboratory strains of <em>Synechococcus </em>at four southern California and three Rhode Island coastal locations. In California, four <em>Synechococcus </em>hosts were used at one site (Newport Beach), whereas only one host (WH7803) was used the other sites. In Rhode Island, <em>Synechococcus </em>WH7803 was used. Date and time of sampling is recorded, along with various abiotic parameters including salinity, water temperature, pH, air temperature, and nutrients (PO4, SiO4, NO2, NO3+NO2, NH4).</p>
<p><strong>Related Dataset:</strong><br />
<a href="https://www.bco-dmo.org/dataset/658729" target="_blank">Cyanomyovirus genome sequences</a></p> Methods and Sampling: <p>Viral abundance was estimated by Most Probable Number (MPN) assay as described in Marston and Sallee (2003) for the RI samples and Clasen et al (2013) for the CA samples. For the RI samples, the abundance of cyanophages capable of infecting&nbsp;<em>Synechococcus&nbsp;</em>sp. WH7803 was estimated. For the CA samples, the abundance of cyanophages capable of infecting&nbsp;<em>Synechococcus&nbsp;</em>sp. WH7803, WH8012, WH8018, WH 8101 was estimated. A subsample (60ml) of each replicate seawater sample was centrifuged to remove large particles and bacteria, and the supernatant was serially diluted with sterile natural seawater media (SN media (Waterbury et al. 1986)). A 100µl aliquot of this diluted seawater was added to 100µl of exponentially a growing&nbsp;<em>Synechococcus&nbsp;</em>strain in each well of 48-well microtiter plates (except control wells which received no seawater). After a 30 - 60 min incubation at room temperature, 500 ul of sterile SN media was added to each well. Plates were then incubated for two weeks at 25°C on a 14:10 hr day:night cycle at 19µE m-2 s-1 light intensity. After 14 days, the plates were visually monitored for lysis (wells with less visible pigmentation than control host-only wells), and the total number of lysed wells was recorded. Estimates of the concentration of infectious cyanophages were determined using MPN Calculator software.</p>
<p>Nutrient samples were filtered and sent to UC Santa Barbara's Marine Science Institute for analysis. Values are the mean of two samples. Nutrient detection limits: Phosphate 0.10; Silicate 1.00; Nitrite 0.10; Nitrite+Nitrate 0.20; Ammonia 0.10; all units are micromolar.</p>
<p>Seawater was collected from the shore surf zone.</p>
<p>Metadata taken prior to March 2009 are scattered and may be unreliable.</p>
<p>Salinity measured using a handheld refractometer and may be high.</p>
<p><br />
&nbsp;</p>
<p>Most Probable Numbers of cyanophage abundance are based on 3 dilutions and an MPN calculator (e.g., http://www.i2workout.com/mcuriale/mpn/index.html).&nbsp;</p>
<p>For the CA sites, the MPN estimate is the average estimate calculated separately for the three replicates (using 48 wells for each of three dilutions), and standard errors for the mean value are reported.</p>
<p>For the RI sites, the MPN estimate is calculated by combining the results of all three replicates (a total of 30 wells for each of three dilutions), and the 95% CIs (as estimated by the MPN calculator) are reported.&nbsp;</p>
<p>Detection limits for nutrients are indicated at top of the file. Nutrient values are average of two replicates, and may include values that are below detection limits.</p>
<p><strong>Related files and references:</strong></p>
<p>Clasen, J.L., C.A. Hanson, Y. Ibrahim, C. Weihe, M.F. Marston, &amp; J.B.H. Martiny (2013) Diversity and temporal dynamics of Southern California coastal marine cyanophage isolates. Aquatic Microbial Ecology, 69:17-31.</p>
<p>Marston and Sallee (2003) Applied and Environmental Microbiology 69: 4639-4647.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1005388 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1005388
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1031783 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1031783
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1029684 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1029684
completed
Marcia Marston
Roger Williams University
401-254-3673
Department of Biology 1 Old Ferry Road
Bristol
RI
02809
USA
mmarston@rwu.edu
pointOfContact
Jennifer B.H. Martiny
University of California-Irvine
949-824-0487
Dept. of Ecology and Evolutionary Biology 321 Steinhaus Hall
Irvine
CA
92697-2525
USA
jmartiny@uci.edu
pointOfContact
Bradley Hughes
University of California-Irvine
Dept. of Ecology and Evolutionary Biology 301 Steinhaus Hall
Irvine
CA
92697
bhughes@uci.edu
pointOfContact
asNeeded
Dataset Version: 2
Unknown
site
lat
lon
strain
year
date_local
time_local
sal
temp
pH_sw
temp_air
PO4
SiO4
NO2
NO3_NO2
NH4
comments
abundance
std_err
month_local
day_local
basin
lower95bound
upper95bound
yrday_local
Refractometer
theme
None, User defined
site
latitude
longitude
taxon
year
date_local
time_local
salinity
water temperature at measurement depth
pH seawater scale
air temperature
reactive phosphorus (PO4)
Silicate (reactive silica)
Nitrite
nitrate plus nitrite
Ammonium
comments
abundance
No BCO-DMO term
month_local
day_local
year day (Day of Year, or day of year and decimal time)
featureType
BCO-DMO Standard Parameters
Refractometer
instrument
BCO-DMO Standard Instruments
lab_UCIrvine_Martiny
RWU_Marston_2014
service
Deployment Activity
Southern California
Rhode Island coast
place
Locations
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
El Nino and the controls of marine virus diversity
http://jmartiny.bio.uci.edu/
El Nino and the controls of marine virus diversity
<p>In July 2009, the NOAA National Weather Service Climate Prediction Center announced the arrival of El Niño, an episode of abnormal warming of sea surface temperature (SST) in the equatorial Pacific that occurs every 3-8 years. This project will investigate the impact of El Niño on marine virus communities, using cyanophages that infect the cyanobacterium Synechoccocus as a model system. The upcoming El Niño presents an opportunity to advance research on the fundamental question of what drives temporal variability in cyanophage diversity.</p>
<p>The goals of this project are: (1) to disentangle various abiotic factors that influence cyanophage diversity and (2) to test the mechanisms behind temporal variability in cyanophage diversity, by comparing the evolutionary processes by which cyanophages adapt to temperature and host composition. To meet these objectives, ~150 cyanophage will be isolated monthly from three coastal sites in the Southern California Bight. The purified isolates will be characterized by sequencing their g20 gene. Phenotypic assays will be carried out on a selection of these isolates and isolates from the previous non-El Niño years.</p>
<p>The environmental variability that El Niño will provide is crucial to both parts of this project. It will help to disentangle the effect of covarying factors on in situ cyanophage composition. For instance, in Southern California, El Niño should provide higher-than-normal SST during months of relatively low UV intensity (fall and winter). It will also permit isolation of a broader genetic diversity of cyanophages from a wider array of environmental conditions, providing crucial statistical power to the laboratory experiments. The project will further our mechanistic understanding of the controls of marine virus diversity.</p>
El Nino and virus diversity
largerWorkCitation
project
Evolutionary ecology of marine cyanophages
http://jmartiny.bio.uci.edu/
Evolutionary ecology of marine cyanophages
<p> ABSTRACT</p>
<p>The evolutionary ecology of virus-host interactions are key to understanding viral-induced mortality rates in marine ecosystems, as the pattern and dynamics of virus-host interactions will ultimately determine the influence of viruses on nutrient cycling. Recent studies suggest that the diversity and composition of marine viruses appears to vary over time and space. The goal of this research is to move beyond simply documenting biogeographic patterns in marine viruses and to begin to ask why the genetic composition of marine viruses varies over time and space. Part of the challenge in doing this is that little is known about how the genetic diversity of a marine virus relates to its phenotype. To address this challenge, the PIs are taking an isolation approach, using lytic cyanophages that infect marine <em>Synechococcus</em> as a model system. In this way they can compare the genotype and phenotype of each virus isolate.</p>
<p>There are three specific goals to do this: (1) Identify genetic markers of cyanophage host range (the particular hosts that a phage can infect); (2) Conduct a time-series study of cyanophage isolates from the Pacific and Atlantic coasts of North America; and (3) Using isolates from the time series, characterize cyanophage phenotypes.</p>
<p><strong>Relevant References:</strong></p>
<p>Marston, M., S. Taylor, N. Sme, R. Parsons, T. Noyes, J.B.H. Martiny. "Marine cyanophages exhibit local and regional biogeography," Environmental Microbiology, v.15, 2013, p. 1452.</p>
<p>Clasen J.L.*, C.A. Hanson*, Y. Ibrahim, C. Weihe, M.F. Marston, and J.B.H. Martiny. "Diversity and temporal dynamics of southern California coastal marine cyanophage isolates," Aquatic Microbial Ecology, v.69, 2013, p. 17.</p>
<p>Marston, M.F., F.J. Pierciey, A. Shepard, G. Gearin, J. Qi, C. Yandava, S.C. Schuster, M.R. Henn, J.B.H. Martiny. "Rapid diversification of coevolving marine Synechococcus and a virus," Proceedings of the National Academy of Sciences, v.109, 2012, p. 4544.</p>
<p>Hanson, C.A., J.A. Fuhrman, M.C. Horner-Devine, J.B.H. Martiny. "Beyond biogeographic patterns: processes shaping the microbial landscape," Nature Reviews Microbiology, v.10, 2012, p. 497.</p>
Cyanophage Evolutionary Ecology
largerWorkCitation
project
eng; USA
biota
oceans
Southern California; Rhode Island coast
-118.1078
-71.2568
33.5735
41.6853
2007-11-15
2013-11-05
Pacific and Atlantic coasts of North America
0
BCO-DMO catalogue of parameters from Experimental data: El Nino virus abundance from Southern California and Rhode Island coast from 2007-2013 (El Nino and virus diversity project, Cyanophage Evolutionary Ecology project)
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/24854.rdf
Name: site
Units: text
Description: <p>location of samples collection: BI=Balboa Island; SB=Seal Beach; NP=Newport Pier; CC=Crystal Cove</p>
http://lod.bco-dmo.org/id/dataset-parameter/24855.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude; postive is North</p>
http://lod.bco-dmo.org/id/dataset-parameter/24856.rdf
Name: lon
Units: decimal degrees
Description: <p>longitude; negative is West</p>
http://lod.bco-dmo.org/id/dataset-parameter/24857.rdf
Name: strain
Units: text
Description: <p>bacterial strain of Synecoccus</p>
http://lod.bco-dmo.org/id/dataset-parameter/24858.rdf
Name: year
Units: YYYY
Description: <p>year of sampling</p>
http://lod.bco-dmo.org/id/dataset-parameter/24859.rdf
Name: date_local
Units: dd-mmm-yy
Description: <p>local date of sampling</p>
http://lod.bco-dmo.org/id/dataset-parameter/24861.rdf
Name: time_local
Units: HH:MM
Description: <p>local time of sampling</p>
http://lod.bco-dmo.org/id/dataset-parameter/24862.rdf
Name: sal
Units: parts per thousand
Description: <p>salinity</p>
http://lod.bco-dmo.org/id/dataset-parameter/24863.rdf
Name: temp
Units: degrees Celsius
Description: <p>temperature</p>
http://lod.bco-dmo.org/id/dataset-parameter/24864.rdf
Name: pH_sw
Units: pH scale
Description: <p>seawater pH</p>
http://lod.bco-dmo.org/id/dataset-parameter/24865.rdf
Name: temp_air
Units: degrees Celsius
Description: <p>air temperature</p>
http://lod.bco-dmo.org/id/dataset-parameter/24866.rdf
Name: PO4
Units: micromoles/liter
Description: <p>phosphate</p>
http://lod.bco-dmo.org/id/dataset-parameter/24867.rdf
Name: SiO4
Units: micromoles/liter
Description: <p>silicate</p>
http://lod.bco-dmo.org/id/dataset-parameter/24868.rdf
Name: NO2
Units: micromoles/liter
Description: <p>nitrite</p>
http://lod.bco-dmo.org/id/dataset-parameter/24869.rdf
Name: NO3_NO2
Units: micromoles/liter
Description: <p>nitrate plus nitrite</p>
http://lod.bco-dmo.org/id/dataset-parameter/24870.rdf
Name: NH4
Units: micromoles/liter
Description: <p>ammonia</p>
http://lod.bco-dmo.org/id/dataset-parameter/24871.rdf
Name: comments
Units: text
Description: <p>weather observations</p>
http://lod.bco-dmo.org/id/dataset-parameter/24872.rdf
Name: abundance
Units: number per milliliter
Description: <p>Cyanophages infecting Syn strain</p>
http://lod.bco-dmo.org/id/dataset-parameter/24873.rdf
Name: std_err
Units: number
Description: <p>standard error of abundance values</p>
http://lod.bco-dmo.org/id/dataset-parameter/34608.rdf
Name: month_local
Units: unknown
Description: <p>month of sampling, local time</p>
http://lod.bco-dmo.org/id/dataset-parameter/34609.rdf
Name: day_local
Units: unknown
Description: <p>sampling day of month in local time</p>
http://lod.bco-dmo.org/id/dataset-parameter/516982.rdf
Name: basin
Units: unitless
Description: <p>ocean basin where samples were collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/516983.rdf
Name: lower95bound
Units: unitless
Description: <p>lower bound of the 95% confidence range</p>
http://lod.bco-dmo.org/id/dataset-parameter/516984.rdf
Name: upper95bound
Units: unitless
Description: <p>upper bound of the 95% confidence range</p>
http://lod.bco-dmo.org/id/dataset-parameter/853209.rdf
Name: yrday_local
Units: dimensionless
Description: <p>Yearday (local). Decimal day of the year.</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
166229
https://datadocs.bco-dmo.org/file/wnnxNB0f0Vvkl8/virus_2014.csv
virus_2014.csv
Primary data file for dataset ID 3507
download
https://osprey.bco-dmo.org/dataset/3507/data/download
download
onLine
dataset
<p>Viral abundance was estimated by Most Probable Number (MPN) assay as described in Marston and Sallee (2003) for the RI samples and Clasen et al (2013) for the CA samples. For the RI samples, the abundance of cyanophages capable of infecting&nbsp;<em>Synechococcus&nbsp;</em>sp. WH7803 was estimated. For the CA samples, the abundance of cyanophages capable of infecting&nbsp;<em>Synechococcus&nbsp;</em>sp. WH7803, WH8012, WH8018, WH 8101 was estimated. A subsample (60ml) of each replicate seawater sample was centrifuged to remove large particles and bacteria, and the supernatant was serially diluted with sterile natural seawater media (SN media (Waterbury et al. 1986)). A 100µl aliquot of this diluted seawater was added to 100µl of exponentially a growing&nbsp;<em>Synechococcus&nbsp;</em>strain in each well of 48-well microtiter plates (except control wells which received no seawater). After a 30 - 60 min incubation at room temperature, 500 ul of sterile SN media was added to each well. Plates were then incubated for two weeks at 25°C on a 14:10 hr day:night cycle at 19µE m-2 s-1 light intensity. After 14 days, the plates were visually monitored for lysis (wells with less visible pigmentation than control host-only wells), and the total number of lysed wells was recorded. Estimates of the concentration of infectious cyanophages were determined using MPN Calculator software.</p>
<p>Nutrient samples were filtered and sent to UC Santa Barbara's Marine Science Institute for analysis. Values are the mean of two samples. Nutrient detection limits: Phosphate 0.10; Silicate 1.00; Nitrite 0.10; Nitrite+Nitrate 0.20; Ammonia 0.10; all units are micromolar.</p>
<p>Seawater was collected from the shore surf zone.</p>
<p>Metadata taken prior to March 2009 are scattered and may be unreliable.</p>
<p>Salinity measured using a handheld refractometer and may be high.</p>
<p><br />
&nbsp;</p>
<p>Most Probable Numbers of cyanophage abundance are based on 3 dilutions and an MPN calculator (e.g., http://www.i2workout.com/mcuriale/mpn/index.html).&nbsp;</p>
<p>For the CA sites, the MPN estimate is the average estimate calculated separately for the three replicates (using 48 wells for each of three dilutions), and standard errors for the mean value are reported.</p>
<p>For the RI sites, the MPN estimate is calculated by combining the results of all three replicates (a total of 30 wells for each of three dilutions), and the 95% CIs (as estimated by the MPN calculator) are reported.&nbsp;</p>
<p>Detection limits for nutrients are indicated at top of the file. Nutrient values are average of two replicates, and may include values that are below detection limits.</p>
<p><strong>Related files and references:</strong></p>
<p>Clasen, J.L., C.A. Hanson, Y. Ibrahim, C. Weihe, M.F. Marston, &amp; J.B.H. Martiny (2013) Diversity and temporal dynamics of Southern California coastal marine cyanophage isolates. Aquatic Microbial Ecology, 69:17-31.</p>
<p>Marston and Sallee (2003) Applied and Environmental Microbiology 69: 4639-4647.</p>
Specified by the Principal Investigator(s)
<p>BCO-DMO data manager processing notes<br />
* Version 2 (2021-06-08) replaces version 1 (2014-06-17).&nbsp; &nbsp;There was an unsupported character in the source file. Converted to utf-8 and made the following correction to the comment for readability.&nbsp; Also added parameter info for column yrday_local which was missing in version 1.</p>
<p><br />
Corrected comment "Overcast��_still; findlly sunny at 9am" to :<br />
Pacific NP&nbsp; &nbsp; &nbsp; 33.598372&nbsp; &nbsp; &nbsp; &nbsp;-117.901203&nbsp; &nbsp; &nbsp;2010&nbsp; &nbsp; 17-Nov-10&nbsp; &nbsp; &nbsp; &nbsp;0830&nbsp; &nbsp; 11&nbsp; &nbsp; &nbsp; 17&nbsp; &nbsp; &nbsp; 320.3458&nbsp; &nbsp; &nbsp; &nbsp; 40&nbsp; &nbsp; &nbsp; 16.6&nbsp; &nbsp; 8.3&nbsp; &nbsp; &nbsp;16.1&nbsp; &nbsp; 0.16&nbsp; &nbsp; 1.68&nbsp; &nbsp; 0.22&nbsp; &nbsp; 0.28&nbsp; &nbsp; 1.97&nbsp; &nbsp; cyano_wh7803&nbsp; &nbsp; 91.67&nbsp; &nbsp;24.25&nbsp; &nbsp;nd&nbsp; &nbsp; &nbsp; nd&nbsp; &nbsp; &nbsp; Overcast still; finally sunny at 9am</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Refractometer
Refractometer
PI Supplied Instrument Name: Refractometer PI Supplied Instrument Description:hand held, not highly accurate. Instrument Name: Refractometer Instrument Short Name:Refractometer Instrument 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.
Deployment: lab_UCIrvine_Martiny
lab_UCIrvine_Martiny
Unknown Platform
lab_UCIrvine_Martiny
Jennifer B.H. Martiny
University of California-Irvine
Deployment: RWU_Marston_2014
RWU_Marston_2014
Marston_RI
laboratory
RWU_Marston_2014
Marcia Marston
Roger Williams University
Unknown Platform