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)

Website: https://www.bco-dmo.org/dataset/3507
Version: 2
Version Date: 2021-06-08

Project
» El Nino and the controls of marine virus diversity (El Nino and virus diversity)
» Evolutionary ecology of marine cyanophages (Cyanophage Evolutionary Ecology)
ContributorsAffiliationRole
Marston, MarciaRoger Williams University (RWU)Principal Investigator
Martiny, Jennifer B.H.University of California-Irvine (UC Irvine)Principal Investigator
Hughes, BradleyUniversity of California-Irvine (UC Irvine)Co-Principal Investigator
Copley, NancyWoods Hole Oceanographic Institution (WHOI BCO-DMO)BCO-DMO Data Manager


Coverage

Spatial Extent: N:41.6853 E:-71.2568 S:33.5735 W:-118.1078
Temporal Extent: 2007-11-15 - 2013-11-05

Dataset Description

Abundance (estimated number of infecting particles per ml seawater and standard error) of cyanophages infecting laboratory strains of Synechococcus at four southern California and three Rhode Island coastal locations. In California, four Synechococcus hosts were used at one site (Newport Beach), whereas only one host (WH7803) was used the other sites. In Rhode Island, Synechococcus 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).

Related Dataset:
Cyanomyovirus genome sequences


Acquisition Description

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 Synechococcus sp. WH7803 was estimated. For the CA samples, the abundance of cyanophages capable of infecting Synechococcus 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 Synechococcus 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.

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.

Seawater was collected from the shore surf zone.

Metadata taken prior to March 2009 are scattered and may be unreliable.

Salinity measured using a handheld refractometer and may be high.

 

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). 

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.

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. 

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.

Related files and references:

Clasen, J.L., C.A. Hanson, Y. Ibrahim, C. Weihe, M.F. Marston, & J.B.H. Martiny (2013) Diversity and temporal dynamics of Southern California coastal marine cyanophage isolates. Aquatic Microbial Ecology, 69:17-31.

Marston and Sallee (2003) Applied and Environmental Microbiology 69: 4639-4647.


Processing Description

BCO-DMO data manager processing notes
* Version 2 (2021-06-08) replaces version 1 (2014-06-17).   There was an unsupported character in the source file. Converted to utf-8 and made the following correction to the comment for readability.  Also added parameter info for column yrday_local which was missing in version 1.

Corrected comment "Overcast��_still; findlly sunny at 9am" to :
Pacific NP      33.598372       -117.901203     2010    17-Nov-10       0830    11      17      320.3458        40      16.6    8.3     16.1    0.16    1.68    0.22    0.28    1.97    cyano_wh7803    91.67   24.25   nd      nd      Overcast still; finally sunny at 9am


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Parameters

ParameterDescriptionUnits
sitelocation of samples collection: BI=Balboa Island; SB=Seal Beach; NP=Newport Pier; CC=Crystal Cove text
latlatitude; postive is North decimal degrees
lonlongitude; negative is West decimal degrees
strainbacterial strain of Synecoccus text
yearyear of sampling YYYY
date_locallocal date of sampling dd-mmm-yy
time_locallocal time of sampling HH:MM
salsalinity parts per thousand
temptemperature degrees Celsius
pH_swseawater pH pH scale
temp_airair temperature degrees Celsius
PO4phosphate micromoles/liter
SiO4silicate micromoles/liter
NO2nitrite micromoles/liter
NO3_NO2nitrate plus nitrite micromoles/liter
NH4ammonia micromoles/liter
commentsweather observations text
abundanceCyanophages infecting Syn strain number per milliliter
std_errstandard error of abundance values number
month_localmonth of sampling, local time
day_localsampling day of month in local time
basinocean basin where samples were collected unitless
lower95boundlower bound of the 95% confidence range unitless
upper95boundupper bound of the 95% confidence range unitless
yrday_localYearday (local). Decimal day of the year.


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Instruments

Dataset-specific Instrument Name
Refractometer
Generic Instrument Name
Refractometer
Dataset-specific Description
hand held, not highly accurate.
Generic 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.


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Deployments

lab_UCIrvine_Martiny

Website
Platform
Unknown Platform
Start Date
2007-11-15
End Date
2012-12-19
Description
Laboratory study: Abundance (estimated number of infecting particles per ml seawater and standard error) of cyanophages infecting laboratory strains of Synechococcus at three southern California locations. Four Synechococcus hosts were used at one site (Newport Beach), whereas only one host (WH7803) was used at two additional sites (Seal Beach and Crystal Cove). Date and time of sampling is recorded, along with various abiotic parameters including salinity, water temperature ("temp"), pH, air temperature, and nutrients (PO4, SiO4, NO2, NO3+NO2, NH4).

RWU_Marston_2014

Website
Platform
Marston_RI
Start Date
2009-06-30
End Date
2013-12-27


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Project Information

El Nino and the controls of marine virus diversity (El Nino and virus diversity)



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.

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.

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.


Evolutionary ecology of marine cyanophages (Cyanophage Evolutionary Ecology)


Coverage: Pacific and Atlantic coasts of North America


 ABSTRACT

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 Synechococcus as a model system. In this way they can compare the genotype and phenotype of each virus isolate.

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.

Relevant References:

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.

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.

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.

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.



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Funding

Funding SourceAward
NSF Division of Ocean Sciences (NSF OCE)
NSF Division of Ocean Sciences (NSF OCE)
NSF Division of Ocean Sciences (NSF OCE)

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