Dataset: ARISA relative abundances

Name: ARISA relative abundances (bacterial community structure), San Pedro Channel, 5 depths, 2014 (Bacterial, Archaeal, and Protistan Biodiversity project, Marine Viral Dynamics project)
Published: 2014-11-03
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)

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 no updates expected

ARISA relative abundances (bacterial community structure), San Pedro Channel, 5 depths, 2014 (Bacterial, Archaeal, and Protistan Biodiversity project, Marine Viral Dynamics project)

Expand/Collapse All

Description

ARISA relative abundances (bacterial community structure) and environmental measurements. 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.

Related Dataset:
SPOT environmental data
ARISA Bin Taxonomy
SPOT cruises

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:

- split environmental and biological data into separate datasets to reduce overall size of each dataset
- added conventional header with dataset name, PI name, version date
- renamed parameters to BCO-DMO standard or more descriptive terms
- moved columns amoA through bcsim89 before the ARISA_# columns
- transformed ARISA_####.### columns to rows with new column 'arisa_frag' for the arisa name and 'rel_abund' for the values
- 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_bio.csv (Comma Separated Values (.csv), 48.04 MB) MD5:9f283db4482f7694c4a12983eb986c48 Primary data file for dataset ID 535915

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.

Fluorescence Microscope

Supplied Name: Epifluorescence Microscope

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.

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

Thermal Cycler

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
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
depth_mixlayr	Mixed layer depth	meters	depth_mixed_layer
Cmax_Depth	Chlorophyll maximum depth	meters	depth
depth	Actual depth	meters	depth
depth_n	sample depth; CMAX = depth of chlorophyl maximum	meters	depth_n
bact_abund	Bacterial abundance	cells/ml	abundance
viral_abund	Viral abundance	VLP/ml	abundance
virus_bact_ratio	Virus to bacteria ratio	unitless	no_bcodmo_term
amoA	Arch amoA gene from qPCR	copies/ng	no_bcodmo_term
Archaea_16S	Archaea 16S from qPCR	copies/ng	no_bcodmo_term
Group1_16S	Group 1 16S from qPCR	copies/ng	no_bcodmo_term
Leucine_uptake	[bacteria]/bacterial productivity (Leucine)	Days	no_bcodmo_term
TurnoverLeu	[bacteria]/bacterial productivity (Leucine)	Days	no_bcodmo_term
Thymedine_uptake	[bacteria]/bacterial productivity (Thymedine)	Days	no_bcodmo_term
TurnoverThy	[bacteria]/bacterial productivity (Thymedine)	Days	no_bcodmo_term
ShannonH	Shannon Biodiversity Index	unitless	no_bcodmo_term
InvSimpson	Inverse Simpson Index	unitless	no_bcodmo_term
Richness10000	Richness 0.01%	# operational taxonomic units	no_bcodmo_term
Richness1000	Richness 0.1%	# operational taxonomic units	no_bcodmo_term
Richness100	Richness 1%	# operational taxonomic units	no_bcodmo_term
PeilouJ	Pelou's Evenness Index	unitless	no_bcodmo_term
BrayCurtis_shift	Bray-Curtis Community Shift	unitless	no_bcodmo_term
BrayCurtissim_5m	Bray-Curtis similarity to 5m sample	unitless	no_bcodmo_term
BrayCurtissim_DCM	Bray-Curtis similarity to deep chlophyll maximum sample	unitless	no_bcodmo_term
BrayCurtissim_150m	Bray-Curtis similarity to 150m sample	unitless	no_bcodmo_term
BrayCurtissim_500m	Bray-Curtis similarity to 500m sample	unitless	no_bcodmo_term
BrayCurtissim_890m	Bray-Curtis similarity to 890m sample	unitless	no_bcodmo_term
arisa_frag	ARISA fragment identification	unitless	no_bcodmo_term
rel_abund	ARISA fragment relative abundance	proportion	relative_abund

Status message

Database

Contribute Data

Dataset: ARISA relative abundances