Dataset: SPOT virus environmental

Name: Environmental data for SPOT virus sampling in Southern California during 2014 (Bacterial, Archaeal, and Protistan Biodiversity project)
Published: 2015-01-29
Keywords: biota, oceans

Cite This Dataset

Spatial Extent: N:33.55 E:-118.4 S:33.55 W:-118.4

Project:

Marine viral dynamics and incorporation into microbial association networks (Marine Viral Dynamics)

MO: Assembly of Marine Microbial Communities (Mar. Microbial Communities)

Pattern and Process in Marine Bacterial, Archaeal, and Protistan Biodiversity, and Effects of Human Impacts (Bacterial, Archaeal, and Protistan Biodiversity)

Program:

Dimensions of Biodiversity (Dimensions of Biodiversity)

Principal Investigator:

Jed A. Fuhrman (University of Southern California, USC-WIES)

Contact:

Cheryl-Emiliane T. Chow (University of Southern California, USC-WIES)

BCO-DMO Data Manager:

Nancy Copley (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

2015-01-29

Version Date:

2015-01-29

Validated:

Yes

Current State:

Final no updates expected

Environmental data for SPOT virus sampling in Southern California during 2014 (Bacterial, Archaeal, and Protistan Biodiversity project)

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Description

These data pertain to the water samples for which the SPOT virus samples were collected. They include physical data plus nutrient concentrations, bacterial and viral abundances.

Methods & Sampling

Water samples were collected on monthly trips to the SPOT station in the San Pedro Basin beginning in 2000 and continuing through and past 2014.

Cruise logs are available at: http://dornsife.usc.edu/spot/document-access/

Data Processing Description

Detailed information on the methodology (pdf), including:
   Satellite measurements
   Assigning Taxonomic Identities to ARISA peaks
   Environmental parameter variability
   Seasonal variability of microbial community structure
   Mantel test approach
   Interannual variability of microbial community structure
   Alpha diversity:
       Variability between depths
       Relation to season
       Relation to community similarity between depths
       Relation to community change
       Environmental parameters and community structure: Mantel tests
   Temporal dynamics of microbial taxa over time
       Transformations
       Taxonomic Groups
       OTUs

Relevent References:

Beman JM, Steele JA, Fuhrman JA. (2011). Co-occurrence patterns for abundant marine archaeal and bacterial lineages in the deep chlorophyll maximum of coastal California. ISME J 5: 1077-1085.

* Cram JA, Chow C-ET, Sachdeva R, et al. (2014) Seasonal and interannual variability of the marine bacterioplankton community throughout the water column over ten years. The ISME Journal. doi: 10.1038/ismej.2014.153.

Frouin R, Franz BA, Werdell PJ (2003) The SeaWiFS PAR product. Algorithm updates for the fourth SeaWiFS data reprocessing 46-50.

Fuhrman J, Azam F (1982) Thymidine incorporation as a measure of heterotrophic bacterioplankton production in marine surface waters - evaluation and field results. marine biology 66:109-120.

Kirchman D, K’nees E, Hodson R (1985) Leucine incorporation and its potential as a measure of protein synthesis by bacteria in natural aquatic systems. Appl Environ Microbiol 49:599-607.

Morel A, Gentili B (2009) A simple band ratio technique to quantify the colored dissolved and detrital organic material from ocean color remotely sensed data. Remote Sensing of Environment 113:998-1011. doi: 10.1016/j.rse.2009.01.008

Noble RT, Fuhrman JA. (1998). Use of SYBR Green I for rapid epifluorescence counts of marine viruses and bacteria. Aquat. Microb. Ecol 14: 113-118.

Parsons TR (1984) A manual of chemical and biological methods for seawater analysis, 1st ed. Pergamon Press, Oxford [Oxfordshire]; New York

Patel A, Noble RT, Steele JA, Schwalbach MS, Hewson I, Fuhrman JA. (2007). Virus and prokaryote enumeration from planktonic aquatic environments by
epifluorescence microscopy with SYBR Green I. Nat Protoc 2: 269-276.

Stramski D, Reynolds RA, Babin M, et al. (2008) Relationships between the surface concentration of particulate organic carbon and optical properties in the eastern South Pacific and eastern Atlantic Oceans. Biogeosciences 5:171-201.

BCO-DMO Processing:

- added conventional header with dataset name, PI name, version date
- renamed parameters to BCO-DMO standard or more descriptive terms
- replaced na with nd
- reformated data from m/d/yyyy to yyyy-mm-dd
- reduced number of digits for most parameters

Data Files

File
SPOT_virus_environ.csv (Comma Separated Values (.csv), 7.27 KB) MD5:c56531a7805d82da409531b5f18dfbe2 Primary data file for dataset ID 550666

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1031743
NSF Division of Ocean Sciences	OCE-1136818
NSF Division of Molecular and Cellular Biosciences	MCB-0703159

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
lab_Fuhrman_2014	San Pedro Ocean Time-Series SPOT Microbial Observatory MO Wrigley Time Series Station WTSS	2014-10-17	USC	Jed A. Fuhrman (Principal Investigator)	data info

Instruments

CTD Sea-Bird

Supplied Description:

Instrument Type

Generic Name: CTD Sea-Bird

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/130/

Generic Description:

Conductivity, Temperature, Depth (CTD) sensor package from SeaBird Electronics, no specific unit identified. This instrument designation is used when specific make and model are not known. See also other SeaBird instruments listed under CTD. More information from Sea-Bird Electronics.

Fluorescence Microscope

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: Fluorescence Microscope

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB06/

Generic Description:

Instruments that generate enlarged images of samples using the phenomena of fluorescence and phosphorescence instead of, or in addition to, reflection and absorption of visible light. Includes conventional and inverted instruments.

Niskin bottle

Supplied Description:

Instrument Type

Generic Name: Niskin bottle

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/

Generic Description:

A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc.

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
cruise_id	cruise identification	unitless	cruise_id
platform	vessel name	unitless	platform
date	date of cruise	yyyy-mm-dd	date
time_start	cruise start time	HH:MM	time_start
time_end	cruise end time	HH:MM	time_end
lat	station latitude; north is positive	decimal degrees	lat
lon	station longitude; east is positive	decimal degrees	lon
day_len	length of day; geosphere package in R; daylength(date; 33.55)	hours	length_day
day_len_change_per_month	day length change per month: geosphere package in R; daylength(date; 33.55)	hours	no_bcodmo_term
SSHD_sat	Sea Surface Height Deviation - Aviso: 0.25 degrees; global; science quality; monthly average	meters	no_bcodmo_term
MEI	Multivariate ENSO Index	standard departure	no_bcodmo_term
temp	temperature	degrees Celsius	temp
sal	salinity	practical salinity units	sal
NO2	nitrite concentration	microMoles	NO2
NO2_NO3	nitrate concentration	microMoles	NO3
PO4	phosphate concentration	microMoles	PO4
pstar_P_N	[Phosphate]- [Nitrate + Nitrite]/16	microMoles	no_bcodmo_term
chl_a_sat	chlorophyll-a satellite monthly	mg/m^3	chl_a
chl_a	chlorophyll-a by Niskin measurements	mg/m^3	chl_a
prim_prod	primary productivity satellite monthly average	mg_C/m^2/day	PP
cmax_depth	depth of chlorophyll maximum	meters	depth
leu_uptake	bacterial Productivity (Leucine)	cells/ml/day	Leu
thy_uptake	bacterial Productivity (Thymidine)	cells/ml/day	bact_prod_thy
turnover_leu	[bacteria]/bacterial productivity (Leucine)	days	no_bcodmo_term
turnover_thy	[bacteria]/bacterial productivity (Thymedine)	days	no_bcodmo_term
bact_abun	bacterial abundance	cells/ml	bact_abund
viral_abund	viral abundance	VLP/ml	abundance
virus_bact_ratio	virus to bacteriaratio	unitless	no_bcodmo_term
ISO_DateTime_Local_start	local time formatted as ISO 8601:2004(E) standard	YYYY-MM-DDTHH:MM:SS.xx	ISO_DateTime_Local
yrday_local	Sequential day of the year with decimal.	decimal number	yrday_local

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Dataset: SPOT virus environmental