Dataset: SPOT environmental data

Name: Environmental measurements from ARISA samples, San Pedro Channel, 5 depths , 2014 (Bacterial, Archaeal, and Protistan Biodiversity project, Marine Viral Dynamics project)
Published: 2014-11-03
Keywords: 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)

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)

Student:

Jacob A. Cram (University of Southern California, USC)

Contact:

Jacob A. Cram (University of Southern California, USC)

BCO-DMO Data Manager:

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

Version:

2014-11-05

Version Date:

2014-11-03

Validated:

Yes

Current State:

Final with updates expected

Environmental measurements from ARISA samples, San Pedro Channel, 5 depths , 2014 (Bacterial, Archaeal, and Protistan Biodiversity project, Marine Viral Dynamics project)

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Description

All measurements were taken from August 2000 – January 2011 at five depths from the San Pedro Channel 5m, the Deep Chlorophyll Maximum (DCM or CMAX), 150m, 500m, 890m. Additional data will be added periodically.

Methods & Sampling

Water samples were collected on monthly trips to the SPOT station in the San Pedro Basin.

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
- split data into physical and biological datasets to reduce overall size of each dataset
- replaced NA with nd
- reformated data from m/d/yyyy to yyyy-mm-dd
- changed year from 1 or 2 digits to 4 digits
- added lat, lon, cruise_id, cruise_id2
- missing depth data added from CTD logs where available

Data Files

File
arisa_latlon_sort_vess_phys.csv (Comma Separated Values (.csv), 149.22 KB) MD5:03d42d4563c744671ff9d3bff87de850 Primary data file for dataset ID 537137

More Information about this dataset

Funding Sources

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

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.

Oxygen Sensor

Supplied Name: Dissolved Oxygen Sensor

Supplied Description:

Sea-bird, model 13

Instrument Type

Generic Name: Oxygen Sensor

Acronym: Dissolved Oxygen Sensor

Generic Description:

An electronic device that measures the proportion of oxygen (O2) in the gas or liquid being analyzed

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
year	year of sampling	YYYY	year
cruise_id2	cruise identification	unitless	cruise_id
cruise_id	secondary deployment identification: same for all lab work (lab_Fuhrman_2014)	unitless	cruise_id
lat	latitude; north is positive	decimal degrees	lat
lon	longitude; east is positive	decimal degrees	lon
month	month of sampling	MM	month
date_local	sampling date	YYYY-MM-DD	date
DayI	Day of the month (Imputed with 15 if day not recorded)	unitless	day
days_shift	Number of days since last sample	days	days
days_elapsed	Date - 08August2000	unitless	days
day_length	geosphere package in R; daylength(date; 33.55)	hours	length_day
day_length_change_per_month	geosphere package in R; daylength(date; 33.55)	hours	no_bcodmo_term
MEI	Multivariate ENSO Index	Standard Departure	no_bcodmo_term
PRCP	Precipitation	1/10 mm	precip_level
PrecipCat	Precipitation category	unitless	precip_type
AirTempMax	Maximum air temperature	1/10 degrees Celsius	temp_air
AirTempMin	Minimum air temperature	1/10 degrees Celsius	temp_air
Sverdrup_trans	Sverdrup transport	?	no_bcodmo_term
Upwelling	Bakun Upwelling Index	m^3/s/100mCoast	no_bcodmo_term
vert_vol_Eckman	Vertical velocity into the Eckman layer	?	no_bcodmo_term
WindGust	Maximum 2 minute Wind Gust Speed	1/10 m/s	wind_speed
DomWavePd	Dominant wave period	s	no_bcodmo_term
WaveHeight	Wave height	meters	wave_height
AvgWavePd	Average wave period	s	no_bcodmo_term
SSHD_Sat	Sea Surface Height Deviation - Aviso: 0.25 degrees; global; science quality; monthly average	meters	no_bcodmo_term
AvgWind	Average wind speed	1/10 m/s	wind_speed
Chl_A_Sat	Chlorophyll-a satellite monthly average	mg/m^3	chl_a
ChlA_Sat8	Chlorophyll-a satellite 8 day average	mg/m^3	chl_a
Prim_Prod	Primary productivity satellite monthly average	mg_C/m^2/day	production
Prim_Prod8	Primary productivity satellite 8 day average	mg_C/m^2/day	production
CDOM	Colored dissolved organic matter index	%	CDOM
depth	Actual depth	meters	depth
depth_n	sample depth; CMAX = depth of chlorophyl maximum	meters	depth_n
depth_mixlayr	Mixed layer depth	meters	depth_mixed_layer
Cmax_Depth	Chlorophyll maximum depth	meters	depth
temp	Temperature	degrees Celsius	temp
temp_CTD	CTD temperature	degrees Celsius	temp
sal	Salinity	psu	sal
sal_CTD	CTD salinity	PSU	sal_ctd
cond	CTD conductivity	S/m	cond
sigma_theta	Sigma theta	kg/m^3	sigma_theta
PAR	Photosynthetically active radiation	Einsteinm^-2day-1	PAR
NO2	Nitrite concentration	uM	NO2
NO3_NO2	Nitrate + Nitrite concentration	uM	NO3_NO2
PO4	Phosphate concentration	uM	PO4
Pstar_P_N	[Phosphate]- [Nitrate + Nitrite]/16	uM	no_bcodmo_term
POC	Particulate organic carbon	mg*m^-3	POC
SiO3	Silicate concentration	uM	Silicate
O2Wink	Winkler Oxygen	ml/L	O2
OxygenCS	Oxygen concentration	uM	O2
OxygenCTD	CTD Oxygen concentration	ml/l	O2
OxygenCurrent	CTD Oxygen current	uA	no_bcodmo_term
OxygenSaturation	CTD maximum Oxygen saturation potential	ml/l	O2sat
OxygenTemperature	CTD Oxygen temperature	degrees Celsius	temp
O2Combined	Winkler data measurment if available; if not - estimated from CTD measument and linear model comparing CTD to winkler measuments	ml/l	O2

Status message

Database

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Dataset: SPOT environmental data