Respiration_chambers/raw_log_files and combined datasets of biomass and chamber data, and physical parameters

Brief description

General overview
The following datasets are described by this metadata record, and are available for download from the provided URL.

- Raw log files, physical parameters raw log files
- Raw excel files, respiration/PAM chamber raw excel spreadsheets
- Processed and cleaned excel files, respiration chamber biomass data
- Raw rapid light curve excel files (this is duplicated from Raw log files), combined dataset pH, temperature, oxygen, salinity, velocity for experiment
- Associated R script file for pump cycles of respirations chambers

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Physical parameters raw log files

Raw log files
1) DATE=
2) Time= UTC+11
3) PROG=Automated program to control sensors and collect data
4) BAT=Amount of battery remaining
5) STEP=check aquation manual
6) SPIES=check aquation manual
7) PAR=Photoactive radiation
8) Levels=check aquation manual
9) Pumps= program for pumps
10) WQM=check aquation manual

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Respiration/PAM chamber raw excel spreadsheets

Abbreviations in headers of datasets
Note: Two data sets are provided in different formats. Raw and cleaned (adj). These are the same data with the PAR column moved over to PAR.all for analysis. All headers are the same. The cleaned (adj) dataframe will work with the R syntax below, alternative add code to do cleaning in R.

Date: ISO 1986 - Check
Time:UTC+11 unless otherwise stated
DATETIME: UTC+11 unless otherwise stated
ID (of instrument in respiration chambers)
ID43=Pulse amplitude fluoresence measurement of control
ID44=Pulse amplitude fluoresence measurement of acidified chamber
ID=1 Dissolved oxygen
ID=2 Dissolved oxygen
ID3= PAR
ID4= PAR
PAR=Photo active radiation umols
F0=minimal florescence from PAM
Fm=Maximum fluorescence from PAM
Yield=(F0 – Fm)/Fm
rChl=an estimate of chlorophyll (Note this is uncalibrated and is an estimate only)
Temp=Temperature degrees C
PAR=Photo active radiation
PAR2= Photo active radiation2
DO=Dissolved oxygen
%Sat= Saturation of dissolved oxygen
Notes=This is the program of the underwater submersible logger with the following abreviations:
Notes-1) PAM=
Notes-2) PAM=Gain level set (see aquation manual for more detail)
Notes-3) Acclimatisation= Program of slowly introducing treatment water into chamber
Notes-4) Shutter start up 2 sensors+sample…= Shutter PAMs automatic set up procedure (see aquation manual)
Notes-5) Yield step 2=PAM yield measurement and calculation of control
Notes-6) Yield step 5= PAM yield measurement and calculation of acidified
Notes-7) Abatus respiration DO and PAR step 1= Program to measure dissolved oxygen and PAR (see aquation manual). Steps 1-4 are different stages of this program including pump cycles, DO and PAR measurements.

8) Rapid light curve data
Pre LC: A yield measurement prior to the following measurement
After 10.0 sec at 0.5% to 8%: Level of each of the 8 steps of the rapid light curve
Odessey PAR (only in some deployments): An extra measure of PAR (umols) using an Odessey data logger
Dataflow PAR: An extra measure of PAR (umols) using a Dataflow sensor.
PAM PAR: This is copied from the PAR or PAR2 column
PAR all: This is the complete PAR file and should be used
Deployment: Identifying which deployment the data came from

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Respiration chamber biomass data

The data is chlorophyll a biomass from cores from the respiration chambers. The headers are: Depth (mm) Treat (Acidified or control) Chl a (pigment and indicator of biomass) Core (5 cores were collected from each chamber, three were analysed for chl a), these are psudoreplicates/subsamples from the chambers and should not be treated as replicates.

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Associated R script file for pump cycles of respirations chambers

Associated respiration chamber data to determine the times when respiration chamber pumps delivered treatment water to chambers. Determined from Aquation log files (see associated files). Use the chamber cut times to determine net production rates. Note: Users need to avoid the times when the respiration chambers are delivering water as this will give incorrect results. The headers that get used in the attached/associated R file are start regression and end regression. The remaining headers are not used unless called for in the associated R script. The last columns of these datasets (intercept, ElapsedTimeMincoef) are determined from the linear regressions described below.

To determine the rate of change of net production, coefficients of the regression of oxygen consumption in discrete 180 minute data blocks were determined. R squared values for fitted regressions of these coefficients were consistently high (greater than 0.9). We make two assumptions with calculation of net production rates: the first is that heterotrophic community members do not change their metabolism under OA; and the second is that the heterotrophic communities are similar between treatments.

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Combined dataset pH, temperature, oxygen, salinity, velocity for experiment

This data is rapid light curve data generated from a Shutter PAM fluorimeter. There are eight steps in each rapid light curve. Note: The software component of the Shutter PAM fluorimeter for sensor 44 appeared to be damaged and would not cycle through the PAR cycles. Therefore the rapid light curves and recovery curves should only be used for the control chambers (sensor ID43).

The headers are
PAR: Photoactive radiation
relETR: F0/Fm x PAR
Notes: Stage/step of light curve
Treatment: Acidified or control


The associated light treatments in each stage. Each actinic light intensity is held for 10 seconds, then a saturating pulse is taken (see PAM methods).

After 10.0 sec at 0.5% = 1 umols PAR
After 10.0 sec at 0.7% = 1 umols PAR
After 10.0 sec at 1.1% = 0.96 umols PAR
After 10.0 sec at 1.6% = 4.32 umols PAR
After 10.0 sec at 2.4% = 4.32 umols PAR
After 10.0 sec at 3.6% = 8.31 umols PAR
After 10.0 sec at 5.3% =15.78 umols PAR
After 10.0 sec at 8.0% = 25.75 umols PAR

This dataset appears to be missing data, note D5 rows potentially not useable information

See the word document in the download file for more information.

Lineage

Progress Code: completed

Statement: The quality of the data is generally high with some data transfer and sensor failures which have been accounted for in final processed excel files. For example, some dataset didn't copy across well from the aquation data logger and some ID parameters were determined by deducting which ID belonged to which dissolved oxygen row label. Raw deployment files for the 2/2/15 had the PAR cable damage and adjacent PAR sensor should be used (with header labelled PAR.all).
The rapid light curve data for sensor 44 is corrupted and cannot be used. The rapid light curve data for sensor 43 is of high quality.