Dataset: biogeochem_microbes

Name: Algae, bacteria, DOC, inorganic and organic nutrients collected from the Richard B Gump Research Station at Moorea LTER from 2010-2011 (MCR LTER and Coral DOM projects)
Published: 2013-12-21
Keywords: oceans

Cite This Dataset

DOI:10.1575/1912/bco-dmo.3670.2

Spatial Extent: N:-17.46267 E:-149.82165 S:-17.58794 W:-149.88848

Temporal Extent: 2010-09-09 - 2011-09-14

Project:

Moorea Coral Reef Long-Term Ecological Research site (MCR LTER)

The coupling between DOM, algae, and microbes on coral reef platforms (Coral DOM)

Program:

Emerging Topics in Biogeochemical Cycles (ETBC)

Long Term Ecological Research network (LTER)

Principal Investigator:

Craig A. Carlson (University of California-Santa Barbara, UCSB-MSI)

Contact:

Craig E. Nelson (University of Hawaiʻi at Mānoa, SOEST)

BCO-DMO Data Manager:

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2013-12-21

Restricted:

Validated:

Yes

Current State:

Final with updates expected

Algae, bacteria, DOC, inorganic and organic nutrients collected from the Richard B Gump Research Station at Moorea LTER from 2010-2011 (MCR LTER and Coral DOM projects)

Abstract:

This dataset contains experimental and survey biogeochemical and microbial data from samples collected at the Moorea Coral Reef LTER site (French Polynesia). Goals of the study were to investigate how benthic primary producers directly affect seawater chemistry (DO and DOC) and to examine impacts of released DOC on reef bacterioplankton growth and respiration. Rates of photosynthesis, respiration, and DOC relsease were assessed for several benthic reef organisms.

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2013-12-21	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.1575/1912/bco-dmo.3670.2	2019-02-22

Description

Methods & Sampling

2010 and 2011 Data Acquisition:
Sampling from small boats occurred along transects at the Moorea Coral Reef LTER sites during September 2010 and September 2011. Benthic producers were collected from water depths of 1.0 to 1.5 meters at back and fringe reef locations. Bacterioplankton abundance was determined using flow cytometry (Nelson et al. 2011). DOC was measured by a high-temperature TOC analyzer according to methods of Carlson et al. (2010). To assess DOC release by primary producers, each benthic species was incubated using the method of Herndl and Velimirov (Haas et al. 2011). To determine if DOC released by primary producers affects mirobial populations, ~48 hour dark dilution culture incubations were performed to measure changes in concentration of DO, DOC, and bacterioplankton over time (Haas et el. 2011).

For more details on methodology, quality assurance and control procedures, and precision and accuracy of methods used, see the following references (full citations are below):
Bacterioplankton flow cytometry methods: Nelson et al. 2011.

Experimental designs, dissolved oxygen, pH, temperature, and specimen surface area methods: Haas et al. 2011, Herndl & Velimirov B. 1986.

Dissolved organic carbon method: Carlson et al. 2010.

Chlorophyll method: Smith et al. 1981.

Dissolved inorganic nutrients, particulate organic nutrients, and isotope ratios methodological references, calibrations, precision, and accuracy are detailed at the UCSB MSI Analytical Lab Website.

Data Processing Description

BCO-DMO made the following modifications: changed parameter names to conform with BCO-DMO conventions; replaced blanks and 'NA' with 'nd' to indicate no data; calculated month_gmt, day_gmt, and time_gmt from the local dates and times provided (local to French Polynesia (Papeete, Tahiti; UTC/GMT -10 hours; Time Zone Code TAHT)); rounded the following to 4 decimal places (originally submitted in Excel file with 11 decimal places): POC, PON, d13C, d15N, algal_area_O2, algal_area_C; replaced '<' with 'lt_' (less than) and '>' with 'gt_' (greater than) in depth_bottom column; removed parameters defined as 'internal reference code'.

Data Files

File
biogeochem_microbes.csv (Comma Separated Values (.csv), 325.81 KB) MD5:6be44d685c82507499f3ad77071913ff Primary data file for dataset ID 3670

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-0927411

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
MCR10-1	Coral DOM 2010 Research Campaign	2010-09-05	Richard B Gump Research Station - Moorea LTER	Craig A. Carlson (Chief Scientist) Craig E. Nelson (Co-Chief Scientist) Craig E. Nelson (Contact)	data info
MCR11-1	Coral DOM 2011 Research Campaign	2011-09-07	Richard B Gump Research Station - Moorea LTER	Craig A. Carlson (Chief Scientist) Craig E. Nelson (Co-Chief Scientist) Craig E. Nelson (Contact)	data info

Instruments

Flow Cytometer

Supplied Description:

Instrument Type

Generic Name: Flow Cytometer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB37/

Generic Description:

Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells.
(from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm)

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
cruiseid	Name of the research campaign/cruise/deployment.	dimensionless	cruiseid
year	4-digit year. in YYYY format	unitless	year
campaign	Experiment or cruise event during which the sample was collected.	dimensionless	exp_id
sample	Unique identified code for each sample collected.	dimensionless	sample
month_gmt	2-digit month (GMT).	mm (01 to 12)	month_gmt
day_gmt	2-digit day of month (GMT).	dd (01 to 31)	day_gmt
time_gmt	Time (GMT). In HHMM format. 2400 hour clock.	HHMM	time_gmt
date_local	Date in local time.	mm/dd/yy	date_local
time_local	Time; local to French Polynesia (Papeete, Tahiti; UTC/GMT -10 hours; Time Zone Code TAHT).	HHMM	time_local
lat	Latitude in decimal degrees North (negative = south).	decimal degrees	lat
lon	Longitude in decimal degrees East (negative = west).	decimal degrees	lon
depth_bottom	Approximate bottom depth in meters.	meters	depth_bottom
depth	Sampling depth in meters.	meters	depth
bac_plank	Bacterioplankton abundance in 10^8 cells/Liter. Originally named 'BACT'. Methodological reference is Nelson et al. 2011, The ISME Journal.	10^8 cells per liter	abundance
phytopl_tot	Total Phytoplankton abundance in cells/mL by flow cytometry. (2011 data only.)	cells per milliliter	abundance
prochloro	Prochlorococcus abundance in cells/mL by flow cytometry. (2011 data only.)	cells per milliliter	coccus_p
synecho	Synechococcus abundance in cells/mL by flow cytometry. (2011 data only.)	cells per milliliter	coccus_s
DOC	Dissolved organic carbon concentration by HTCO in micromolar units. Glass fiber filtrate type GF/F (Whatman). Methodological reference is Carlson et al. 2010, DSRII.	micromolar (uM)	DOC
TDN	Total dissolved nitrogen by HTCO in micromolar units. Glass fiber filtrate type GF/F (Whatman). (2011 data only.)	micromolar (uM)	TDN
NO3	Nitrate concentration in micromolar units by flow injection autoanalyzer (Lachat QuikChem 8000; difference of nitrate+nitrite and nitrate). Glass fiber filtrate type GF/F (Whatman). (2010 data only.)	micromolar (uM)	NO3
NO2	Nitrite concentration in micromolar units by flow injection autoanalyzer (Lachat QuikChem 8000). Glass fiber filtrate type GF/F (Whatman).	micromolar (uM)	NO2
NO3_NO2	Nitrite+Nitrate concentration in micromolar units by flow injection autoanalyzer (Lachat QuikChem 8000). Glass fiber filtrate type GF/F (Whatman). (2011 data only.)	micromolar (uM)	NO3_NO2
PO4	Ortho-Phosphate concentration in micromolar units by flow injection autoanalyzer (Lachat QuikChem 8000). Glass fiber filtrate type GF/F (Whatman).	micromolar (uM)	PO4
silicate	Silicate concentration in micromolar units by flow injection autoanalyzer (Lachat QuikChem 8000). Glass fiber filtrate type GF/F (Whatman). (2011 data only.)	micromolar (uM)	Silicate
NH4	Ammonium ion concentration in micromolar units by flow injection autoanalyzer (Lachat QuikChem 8000). Glass fiber filtrate type GF/F (Whatman).	micromolar (uM)	NH4
chl_a_fluor	Chlorophyll-a concentration by acetone-extracted fluorometry (Turner AU-10). Reference is Smith et al. 1981, Ref. Rep. SIO. Collected on Glass fiber filter type GF/F (Whatman). (2010 data only.)	micrograms per liter (ug/L)	chl_a_fluor
POC	Particulate organic carbon measured by combustion analysis (CEC 440HA). Collected on Glass fiber filter type GF/F (Whatman). (2010 data only.)	micrograms per liter (ug/L)	POC
PON	Particulate organic nitrogen measured by combustion analysis (CEC 440HA). Collected on Glass fiber filter type GF/F (Whatman). (2010 data only.)	micrograms per liter (ug/L)	PON
delta_13C	Particulate carbon stable isotope ratios by combustion analysis and mass spectometry (Finnigan Delta Plus Advantage in Continuous Flow Mode). Collected on Glass fiber filter type GF/F (Whatman). (2010 data only.)	dimensionless	no_bcodmo_term
delta_15N	Particulate nitrogen stable isotope ratios by combustion analysis and mass spectometry (Finnigan Delta Plus Advantage in Continuous Flow Mode). Collected on Glass fiber filter type GF/F (Whatman). (2010 data only.)	dimensionless	no_bcodmo_term
temp_inc	Incubation temperature in degrees celsius/centigrade measured via Hach-Lange HQ40D handheld multimeter. Originally named 'DOpH Inc Temp'. (2010 data only.)	degrees C	temp_inc
time_inc_min	Incubation time in minutes. Originally named 'DOpH Incubation Time'. (2010 data only.)	minutes	time_inc
time_inc_hrs	Incubation time in hours. (2011 data only.)	hours	time_inc
algal_area_O2	Estimated algal/coral surface area from specimens used in oxygen/pH change measurements (methodology detailed in Haas et al. 2011 PLoS ONE). Originally named 'Surface area DOpH'. (2010 data only.)	square centimeters (cm^2)	no_bcodmo_term
weight_g	Coral/algal dry weight in grams; methodological reference is Haas et al. 2011 PLoS ONE. (2010 data only.)	grams	weight_g
algal_area_C	Estimated algal/coral surface area from specimens used in DOC release measurements (methodology detailed in Haas et al. 2011 PLoS ONE). Originally named 'Surface Area DOC'. (2010 data only.)	square centimeters (cm^2)	no_bcodmo_term
O2_umol_L	Dissolved oxygen in micromolar units (not salinity corrected) measured via Hach-Lange HQ40D handheld multimeter. Originally named 'DO'. (2010 data only.)	micromolar (uM)	O2_umol_L
pH	pH measured via Hach-Lange HQ40D handheld multimeter. (2010 data only.)	dimensionless	pH
ISO_DateTime_UTC	Date and time (UTC) formatted to ISO8601 standard. T indicates start of time string; Z indicates UTC.	yyyy-MM-dd'T'HH:mm:ss'Z'	ISO_DateTime_UTC