Constrain model estimates of k > Make direct estimates of gas evasion
Determining Gas Exchange Rates Using N2/Ar
** If you are not acquainted with gas sampling you willlikely benefit from some basic training on how to collect and store gas samples - this protocol from NEON is very thorough**
Method follows Hall and Madinger (2018)
https://www.biogeosciences.net/15/3085/2018/
MATERIALS:
- Membrane Inlet Mass Spectrometer (MIMS)
- Tank of Ar (size 35-80)
- Ar regulator and adapter
- Tubing
- Micro Bubble Diffuser (Point Four™ Plastic Micro Bubble Diffuser (MBD); http://pentairaes.com/point-fourtm-plastic-micro-bubble-diffuser-mbd.html)
- 20 L solution of NaCl in a bucket or a carboy. Concentration and pump rate should be high enough to increase streamwater conductivity by 20-50 µS/cm. 1 g salt/L is about 2100 µS/cm.
- Peristaltic pump and tubing to inject conservative tracer (Cl – or something else). FMI pump would work fine too.
- Hand held conductivity meter with thermometer to estimate specific conductivity
- Field notebook and pencil
- Barometer
- 1-2 MIMS bongs (see appendix)
- 36 Exetainers with septa caps. These can be old and reused
- 50 m tape
- Cooler with ice
METHODS
Pre-field in the lab:
In the field:
Post-field in the lab:
***
APPENDIX
Sonde calibration in bubbling buckets
Bob Hall
Equipment:
Pentair DC8 air pump
12V battery, 18 Ah or larger
Pentair AS23S airstone with 3 m of 0.25-inch ID tubing
A bucket or tub large enough to submerse your sondes, probes, whatever. 40 L is often the needed size. 100L may not be too big
Extech SD700 barometer (don’t even think of using the one on your YSI or Hydrolab).
O2 and temp sensors. Be sure to calibrate O2 sensors with the temp sensor that you will use in the field! With sondes it is easy since the temp sensor is attached.
Fill tub with water. If lab, let sit overnight to equlibrate with lab temp. If field, put the tub in the stream or river so that temperature does not change much. Hook airstome to pump and run pump for 30 min. Add sondes, let sit until stable and calibrate to 100% saturation based on BP from your Extech barometer. Then record as if they were in the stream for 1 h. Very important! Upon retrieval, put sensors in bubbling tub for 45 min to check for drift. Then clean and recalibrate if necessary.
Bucket calibration
One problem with bubbling buckets is that they supersaturate water 1-3 % due to unequal gas transfer in and out of bubbles. Thus we need an absolute measure of DO from the buckets. The good news is that once you have a bubbling system, the supersaturation fraction should be constant, so only may need to be done every year or so for each lab. We will use MIMS to calibrate our bucket calibration. We will calibrate with Argon because it is unreactive and has the same diffusive properties of O2.
Equipment needed:
20+ 12 mL Exetainers
MIMS bong for sampling. See appendix.
Bubble tub as above. Turn on recording for sondes and record temperature using sonde thermometers at 1 min intervals. Record BP in mm Hg. Turn off bubbles. Insert mims bong into bucket without stopper. Move pvc tube through the water to trap a parcel of water. Stopper it and pull from water, stopper side down, allowing water to flow from vinyl tube. Fill an exetainer from the bottom, and overflow a lot. Pull tube out slowly to leave a rounded meniscus at the top of the tube. Cap immediately. Collect 2 more samples using the mims bong (do not fill 3 exetainers from one sample!). Record times for each of these samples so that they can be matched to the temperatures recorded by the sondes. Turn on bubbler, wait half hour. Repeat 3 samples. And again for at least 9 total samples. Ship these to a MIMS lab asap, preferably one that is the same or lower altitude than where the samples are collected. Let them know the bucket temps that you recorded with each sampling to nearest 0.01 °C and barometric pressure in mmHg.
In the MIMS lab, set the 2 water baths to a temperature so that [Ar] in the baths bracket closely (say 7% either direction, about 3 °C above and below target temp) [Ar] saturation in the bubbling bucket based on BP and temp in the bubbling bucket. As always, run the MIMS in the coldest bath. Then measure current of mass 40 of samples and the exetainers being sure to bracket the samples with the two standards every 4 samples. Convert to current to Ar in mg/L. The degree of oversaturation is Ar in the samples divided by predicted Ar based on temperature and BP in the bubbling bucket.
To estimate Ar saturation parameters, use the following code:
###water density of air saturated water. From Paterson and Morris 1994, Meterologia
watdens<-function(temp){
t<-temp
A <- 7.0132e-5
B <- 7.926295e-3
C <- -7.575477e-5
D<- 7.314701e-7
E <- -3.596363e-9
to<- 3.9818
dens<- (999.97358- (A*(t-to) + B*(t-to)^2 +C*(t-to)^3 + D*(t-to)^4+E*(t-to)^5) ) -4.873e-3 + 1.708e-4*t - 3.108e-6 * t^2
dens/1000
}
arsat<- function(temp, bp) {
ts<-log((298.15-temp) / (273.15 + temp))
a0<-2.79150
a1<-3.17609
a2<-4.13116
a3<-4.90379
u<-10^(8.10765-(1750.286/(235+temp)))
satar<-(exp(a0 + a1*ts + a2*ts^2 + a3*ts^3))*((bp-u)/(760-u))
watdens(temp)*satar*(39.948/1000)##converts umol/kg to mg/L
}
arsat(10,760)
MIMS bong: 1.5” ID * 15” PVC tube, 2’ of 1/8 ID vinyl tubing. Drill hole in PVC that is slightly smaller than the OD of your tubing.
** If you are not acquainted with gas sampling you willlikely benefit from some basic training on how to collect and store gas samples - this protocol from NEON is very thorough**
Method follows Hall and Madinger (2018)
https://www.biogeosciences.net/15/3085/2018/
MATERIALS:
- Membrane Inlet Mass Spectrometer (MIMS)
- Tank of Ar (size 35-80)
- Ar regulator and adapter
- Tubing
- Micro Bubble Diffuser (Point Four™ Plastic Micro Bubble Diffuser (MBD); http://pentairaes.com/point-fourtm-plastic-micro-bubble-diffuser-mbd.html)
- 20 L solution of NaCl in a bucket or a carboy. Concentration and pump rate should be high enough to increase streamwater conductivity by 20-50 µS/cm. 1 g salt/L is about 2100 µS/cm.
- Peristaltic pump and tubing to inject conservative tracer (Cl – or something else). FMI pump would work fine too.
- Hand held conductivity meter with thermometer to estimate specific conductivity
- Field notebook and pencil
- Barometer
- 1-2 MIMS bongs (see appendix)
- 36 Exetainers with septa caps. These can be old and reused
- 50 m tape
- Cooler with ice
METHODS
Pre-field in the lab:
- Prepare Cl solution in a carboy. How much salt to add is stream dependent. Remember that C1*F1 = C2*F2, where C1 is concentration in carboy, F1 is pump rate, F2 is stream discharge and C2 is concentration in the stream.
- …
In the field:
- Identify the stream reach of interest and visually estimate the mixing length. The stream reach should have the following characteristics: uniform in longitudinal slope, in hydraulic properties such as roughness, and cross sectional area with little or no inflow (Kilpatrick 1989). The length of stream to sample depends on K, so will require some trial and error. When in doubt go longer because if all the Ar disappears, you can confidently calculate it removal rate. If 10% disappears, you will have huge error on the removal rate. You want at least 50% of the Ar to disappear, so pick a reach long enough for that. For small mountain streams, 80 m is enough. Flat streams need about 400 m.
- Bring the supplies needed for bubbling the Ar and injecting the chloride solution to the injection site upstream of the reach of interest. The injection site should be far enough upstream of the first sampling location at the top of the reach to ensure complete mixing. Find a deep spot to inject the Ar into and make sure the airstone sits on the bottom. Do not pressurize the airstone until it is underwater!
- Record the date and time in a notebook so discharge can be determined for the sampling period from the level logger data
- Record the barometric pressure
- Establish 5-6 sampling sites downstream of the injection site. Roll out 50 m tape beginning at the injection site and heading downstream. Sites should be spaced out evenly.
- Prepare everything to begin the gas diffusion and tracer injection at the injection site
- Label TOC vials with 3 of each of the following: Pre-Inj. Site, Pre-S1, Pre-S2, and Pre-S3. Label each set of 3 with A, B, or C and the date. Repeat the same with another set except with “Post” before the site name. We have found that not knowing 'pre' is not that crucial, knowing post very much is. Based on temperature you can figure out was saturated N2:Ar should be. Collect at least 3 sample fr station for 5-6 stations.
- Place 6 vials at each of the 5-6 corresponding sampling locations for ease of access later
- Once everything is ready for the injection, take 3 replicate samples using the MIMS bong at each of the sampling locations into the “Pre” vials.
- Taking a sample using the MIMS bong: Put the MIMS bong into the stream without the stopper. Move the PVC tube through the water to trap a parcel of water. Stopper it and pull from the water, stopper side down, allowing water to flow from vinyl tube. Fill TOC vial from the bottom, and overflow a lot. Pull tube out slowly to leave a rounded meniscus at the top of the vial. Cap immediately. There should be no bubbles. Retake the sample if there are bubbles. If you find that the samples have bubbles in them before running, then the samples are worthless and the MIMS becomes an expensive random number generator. Bob Hall found this out the hard way. But do not fear, it is relatively easy to collect bubble free samples in an Exetainer.
- Record the temperature at each of the sampling locations and the time!
- Immediately after the “Pre” samples are taken, put them in the cooler with ice and begin the tracer injection and Ar diffuser. You should see a cloud of bubble coming from the Ar. It should look like a lot. Monitor pressure in the scond regulator throught the release to ensure that it stays the same. With Ar, more is better and Hall and Madinger provide explict advice on how much is enough and how much would be too much. You want to increase background Ar:N2 by at least 3%, 10% is better and we think that 20% would be better still. Given that Ar is ~1% of the partial pressure of gas in a stream, that would be ~1.2.% total, so not enough to displace a lot of N2.
- Record the time
- Using the handheld YSI, measure the specific conductivity across the stream width at each of the sampling stations
- Once the specific conductivity reaches a steady state and does not vary more than 5% across the stream width at any of the sampling locations, take another set of replicate samples into the “Post” TOC vials at each of the sites using the MIMS bong
- Record the temperature and time at each of the stations
- Once all of the samples are taken, put them in the cooler with ice
- Turn off the Ar diffuser and tracer peristaltic pump
- Before rolling up the measuring tape, measure the width and depth at 10-20 evenly-spaced transects spanning the study reach and record
- Mark the injection site for future reference by hammering a small piece of PVC into the bank or tying flagging to a branch or root before departing
Post-field in the lab:
- Bring the cooler with the filled Exetainers vials back to the lab
- If running the samples on the MIMS the same day, keep in the cooler
- If running the samples the next day, put in the cold room at 4°C
- Run the MIMS following the standard protocol (to be written) and run masses 28, 32, and 40
***
APPENDIX
Sonde calibration in bubbling buckets
Bob Hall
Equipment:
Pentair DC8 air pump
12V battery, 18 Ah or larger
Pentair AS23S airstone with 3 m of 0.25-inch ID tubing
A bucket or tub large enough to submerse your sondes, probes, whatever. 40 L is often the needed size. 100L may not be too big
Extech SD700 barometer (don’t even think of using the one on your YSI or Hydrolab).
O2 and temp sensors. Be sure to calibrate O2 sensors with the temp sensor that you will use in the field! With sondes it is easy since the temp sensor is attached.
Fill tub with water. If lab, let sit overnight to equlibrate with lab temp. If field, put the tub in the stream or river so that temperature does not change much. Hook airstome to pump and run pump for 30 min. Add sondes, let sit until stable and calibrate to 100% saturation based on BP from your Extech barometer. Then record as if they were in the stream for 1 h. Very important! Upon retrieval, put sensors in bubbling tub for 45 min to check for drift. Then clean and recalibrate if necessary.
Bucket calibration
One problem with bubbling buckets is that they supersaturate water 1-3 % due to unequal gas transfer in and out of bubbles. Thus we need an absolute measure of DO from the buckets. The good news is that once you have a bubbling system, the supersaturation fraction should be constant, so only may need to be done every year or so for each lab. We will use MIMS to calibrate our bucket calibration. We will calibrate with Argon because it is unreactive and has the same diffusive properties of O2.
Equipment needed:
20+ 12 mL Exetainers
MIMS bong for sampling. See appendix.
Bubble tub as above. Turn on recording for sondes and record temperature using sonde thermometers at 1 min intervals. Record BP in mm Hg. Turn off bubbles. Insert mims bong into bucket without stopper. Move pvc tube through the water to trap a parcel of water. Stopper it and pull from water, stopper side down, allowing water to flow from vinyl tube. Fill an exetainer from the bottom, and overflow a lot. Pull tube out slowly to leave a rounded meniscus at the top of the tube. Cap immediately. Collect 2 more samples using the mims bong (do not fill 3 exetainers from one sample!). Record times for each of these samples so that they can be matched to the temperatures recorded by the sondes. Turn on bubbler, wait half hour. Repeat 3 samples. And again for at least 9 total samples. Ship these to a MIMS lab asap, preferably one that is the same or lower altitude than where the samples are collected. Let them know the bucket temps that you recorded with each sampling to nearest 0.01 °C and barometric pressure in mmHg.
In the MIMS lab, set the 2 water baths to a temperature so that [Ar] in the baths bracket closely (say 7% either direction, about 3 °C above and below target temp) [Ar] saturation in the bubbling bucket based on BP and temp in the bubbling bucket. As always, run the MIMS in the coldest bath. Then measure current of mass 40 of samples and the exetainers being sure to bracket the samples with the two standards every 4 samples. Convert to current to Ar in mg/L. The degree of oversaturation is Ar in the samples divided by predicted Ar based on temperature and BP in the bubbling bucket.
To estimate Ar saturation parameters, use the following code:
###water density of air saturated water. From Paterson and Morris 1994, Meterologia
watdens<-function(temp){
t<-temp
A <- 7.0132e-5
B <- 7.926295e-3
C <- -7.575477e-5
D<- 7.314701e-7
E <- -3.596363e-9
to<- 3.9818
dens<- (999.97358- (A*(t-to) + B*(t-to)^2 +C*(t-to)^3 + D*(t-to)^4+E*(t-to)^5) ) -4.873e-3 + 1.708e-4*t - 3.108e-6 * t^2
dens/1000
}
arsat<- function(temp, bp) {
ts<-log((298.15-temp) / (273.15 + temp))
a0<-2.79150
a1<-3.17609
a2<-4.13116
a3<-4.90379
u<-10^(8.10765-(1750.286/(235+temp)))
satar<-(exp(a0 + a1*ts + a2*ts^2 + a3*ts^3))*((bp-u)/(760-u))
watdens(temp)*satar*(39.948/1000)##converts umol/kg to mg/L
}
arsat(10,760)
MIMS bong: 1.5” ID * 15” PVC tube, 2’ of 1/8 ID vinyl tubing. Drill hole in PVC that is slightly smaller than the OD of your tubing.
