LI-COR LI-6800 User manual

Using the
LI-6800
Soil CO2Flux
Chamber

Using the LI-6800
Soil CO2Flux Chamber
LI-COR Biosciences
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Lincoln, Nebraska 68504
Phone: [phone]
Toll free: 800-447-3576 (U.S. and Canada)
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Germany
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United Kingdom
Phone: [phone]
[e-mail]
LI-COR Distributor Network:
www.licor.com/env/distributors

Notice
The information in this document is subject to change without notice.
LI-COR MAKES NO WARRANTY OF ANY KIND WITH REGARD TO THIS MATERIAL, INCLUDING BUT NOT
LIMITED TO THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
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ive owners.
The LI-6800 is protected by patents 8,610,072, 8,692,202, and 8,910,506. Additional patents pending in the U.S. and other
countries.
Printing History
© Copyright 2018, LI-COR, Inc. All rights reserved
Publication Number: 984-17218
Created on: Tuesday, January 28, 2020.
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Notes on Safety
This LI-COR product has been designed to be safe when operated in the manner described in this manual. The safety of
this product cannot be assured if the product is used in any other way than is specified in this manual. The product is
intended to be used by qualified personnel. Read this entire manual before using the product.
Equipment markings:
The product is marked with this symbol when it is necessary for you to refer to the manual or
accompanying documents in order to protect against injury or damage to the product.
The product is marked with this symbol when a hazardous voltage may be present.
The product is marked with this symbol if a Chassis Ground connection is required.
The product is marked with this symbol to indicate that a direct current (DC) power supply is
required.
WARNING Warnings must be followed carefully to avoid bodily injury.
CAUTION Cautions must be observed to avoid damage to your equipment.
Manual markings:
Warning Warnings must be followed carefully to avoid bodily injury.
Caution Cautions must be observed to avoid damage to your equipment.
Note Notes contain important information and useful tips on the operation of your equipment.
CE Marking:
This product is a CE-marked product. For conformity information, contact LI-COR Support at [e-mail].
Outside of the U.S., contact your local sales office or distributor.
California Proposition 65 Warning
WARNING: This product contains chemicals known to the State of California to cause cancer and birth defects or other
reproductive harm.
Federal Communications Commission Radio Interference Statement
WARNING: This equipment generates, uses, and can radiate radio frequency energy and if not installed in accordance
with the instruction manual, may cause interference to radio communications. It has been tested and found to comply
with the limits for a Class A computing device pursuant to Subpart J of Part 15 of FCC rules, which are designed to
provide a reasonable protection against such interference when operated in a commercial environment. Operation of this
equipment in a residential area is likely to cause interference in which case the user, at his own expense, will be required
to take whatever measures may be required to correct the interference.
Waste Electronic and Electrical Equipment (WEEE) Notice
This symbol indicates that the product is to be collected separately from unsorted municipal waste. The fol-
lowing applies to users in European countries: This product is designated for separate collection at an appro-
priate collection point. Do not dispose of as household waste. For more information, contact your local
distributor or the local authorities in charge of waste management.

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Contents
Section 1. Introduction to the LI-6800 soil chamber
What's what 1-2
Soil CO2 flux chamber 1-2
Head mounting bracket 1-2
Stevens HydraProbe 1-2
Custom chamber adapter block 1-2
Soil collars 1-3
Accessories kit 1-3
Useful software 1-4
Bluestem™ OS 1-4
SoilFluxPro™ Software 1-4
Introduction to soil gas flux measurements 1-4
The measurement cycle 1-6
Theory and equation summary 1-7
Section 2. Using the chamber
Installing the chamber on the LI-6800 head 2-1
Connecting soil sensors 2-4
Stevens HydraProbe II 2-4
Type E thermocouple 2-4
Installing soil collars 2-5
Tips for soil collars 2-5
Insertion depth 2-6
Measuring the chamber offset 2-7
Overview of the software 2-8
The Start Up tab 2-8
The Soil Flux tab 2-8
Section 3. Measurement tutorial
Preparations 3-1
Making measurements 3-1
Logging soil CO2 flux data in a standard file 3-3
Enabling prompt on log 3-4
Viewing results 3-5

Section 4. Soil variables and constants
The SoilConst group 4-1
The SoilConfig group 4-1
The SoilData group 4-2
The SoilComp2 group 4-3
Section 5. Troubleshooting and maintenance
Identifying an issue 5-1
Bellows pump runs intermittently after the chamber opens or closes 5-1
Chamber will not open or close, or it opens or closes very slowly 5-1
Noisy data 5-2
High initial CO2 concentrations 5-2
Low flow rate 5-2
Replacing the bellows pump air filter 5-3
Maintaining the gaskets 5-4
Foam gasket 5-5
Collar gasket 5-5
Neoprene gasket 5-5
Appendix A. Specifications
Appendix B. Warranty
vi

Section 1.
Introduction to the LI-6800 soil chamber
The LI-6800 Portable Photosynthesis System can be used to measure CO2efflux
from soils when outfitted with the soil CO2flux chamber. Here we describe the
components of the chamber and the theory of the measurements.
Figure 1-1. Components of the Soil CO2chamber.
1-1Using the LI-6800 Soil CO₂ Flux Chamber

Section 1. Introduction to the LI-6800 soil chamber
What's what
The soil CO2flux chamber includes the components listed below.
Soil CO2flux chamber
Part number:
6800-09
The chamber enables the LI-6800 to measure changes in CO2concentration inside
the chamber when it is closed over the soil. It has one connector for the Stevens
HydraProbe. It uses the SDI-12 communication protocol. An air inlet and outlet
connect to the custom chamber adapter block. The cable attaches directly to the LI-
6800 head connector labeled LS. There is also a dock where you can place the soil
probe when it is not in use.
Head mounting bracket
Part number:
9968-285
The chamber has a removable mounting bracket that is used to attach the LI-6800
head to the chamber. Be careful not to lose the bracket. It is a surprisingly expensive
custom-made part that must be purchased from LI-COR.
Stevens HydraProbe
Part number:
900-17114
The HydraProbe is equipped with a custom connector
for the soil gas flux chamber. The probe measures soil
moisture content, salinity, and temperature, which are
stored in the dataset. It uses the SDI-12 com-
munications protocol.
Custom chamber adapter block
Part number:
9968-182
The custom chamber adapter block is included with
the soil gas flux chamber. The accessories kit has Swa-
gelok fittings and plugs that are needed to plumb the
adapter block to the chamber.
1-2 Using the LI-6800 Soil CO₂ Flux Chamber

Soil collars
Part number:
6581-044
Three 20 cm soil collars are included with the chamber. Soil collars must be
installed at the measurement site at least 6 hours prior to measurements (24 or
more hours is better). Additional collars can be purchased from LI-COR or made in
a shop if you have access to suitable materials.
Accessories kit
Part number:
9968-290
The soil gas flux chamber accessories kit includes additional parts and replacement
parts.
Description Quantity Part Number
Disposable air filter 1 301-08119
O-ring; 6×1.5 mm 1 192-14314
O-ring; 15×1.5 mm 2 192-16274
Bev-a-line IV tubing; 2 meters total 1 222-01824
Swagelok 1/4" ferrule set 2 300-05375
Swagelok male connector 1 300-16268
Stainless steel male plug; 7/16 - 20 4 300-16271
Elbow connector; 5/16 - 24 × 1/4 1 300-16515
Chamber gasket kit 1 9981-198
Phillips panhead screw; 10-32 3/8" stainless steel 4 122-08312
Captive screw; 4-40 3/4" stainless steel 2 158-17847
Cap nut; 10-32 3/8" stainless steel 4 163-02618
Flat washer; #10, 0.438 by 0.063 4 167-00154
Gasket seal 3/8" W × 3/16"H × 12" L 1 224-07606
Soil collar foam gasket 1 6581-107
Soil collar gasket 1 6581-108
Manifold gasket 2 6581-206
Section 1. Introduction to the LI-6800 soil chamber
1-3Soil collars

Section 1. Introduction to the LI-6800 soil chamber
Useful software
You may need to acquire some software to make use of the soil chamber. Software
is available from www.licor.com/env/support. Select the LI-6800, and then select
Software. The following apps are available free of charge for LI-COR customers:
Bluestem™ OS
Bluestem Operating System runs on the LI-6800. Both the LI-6800 console and
head need to run software version 1.3 or newer in order to use the soil CO2flux
chamber.
SoilFluxPro™ Software
SoilFluxPro Software is a free PC- and Mac-compatible application for analyzing
soil efflux data sets. SoilFluxPro makes it easy to recompute data sets with altered
parameters, create graphs, and analyze results. Version 4.1 or newer is required to
read the .json data files created by the LI-6800.
Introduction to soil gas flux measurements
Carbon dioxide in soil is primarily produced by root respiration, decay of organic
matter, and activity of microbes. Rainwater can have direct effects as well, by dis-
placing gas in soil pore spaces, and by interacting with limestone soils. Also, rain-
water itself carries some dissolved CO2that can be released in the soil.
Thus, soil CO2flux is dependent on soil temperature, organic content, moisture
content and precipitation, and has a great deal of spatial variability. Soil CO2flux is
also extremely sensitive to pressure fluctuations. An unvented chamber will induce
significant pressure increases just by closing. Soil water evaporation and heating of
the air in the chamber head space also induce pressure increases in an unvented
chamber. The LI-6800 Soil CO2Flux Chamber is vented so that pressures inside
and outside the chamber are in a dynamic equilibrium.
The chamber is designed to mitigate factors that can induce variation in meas-
urements with the following features:
lA bellows-controlled closure mechanism, which ensures that placement of the
chamber has the same negligible effect with each measurement sample.
1-4 Using the LI-6800 Soil CO₂ Flux Chamber

lA patented chamber vent that maintains ambient pressure inside the chamber,
even in windy conditions.
lSoil collars, which, after installation, ensure consistency between samples.
In contrast with the LI-6800 leaf chambers, which are an open gas exchange sys-
tem, the soil CO2flux chamber is a closed system. Instead of sample and reference
gas analyzers, the LI-6800 uses the reference analyzer in this configuration. Instead
of using the console flow pump, the soil chamber has its own circulation pump.
When the chamber is closed, the chamber pump circulates air through the sample
analyzer exhaust to the chamber and then back to the sample analyzer.
Section 1. Introduction to the LI-6800 soil chamber
1-5Introduction to soil gas flux measurements

Section 1. Introduction to the LI-6800 soil chamber
The measurement cycle
When the chamber is placed on a soil collar it will remain open until the meas-
urement is started. When the measurement is started, the bellows pump closes the
chamber. Upon closing, the instrument begins logging data, and the dead band
starts (see Figure 1-2 below). The instrument continues to record data for the dur-
ation of the repetition, and then the chamber opens and pauses for the extra dur-
ation. The measurement repeats for the specified number of repetitions.
Repetition
Chamber
Closes
Chamber
Open
Chamber
Opens
Data
Rep Duration
Dead
Band
Time
CO2Concentration
(µmol/mol)
Extra
Figure 1-2. A typical measurement cycle.
1-6 Using the LI-6800 Soil CO₂ Flux Chamber

Theory and equation summary
Soil CO2flux (F) is computed with the following equation:
1-1
where Vis chamber volume (cm3), Pis atmospheric pressure (kPa), Wis the water
mole fraction in the chamber (mmol mol-1), Ris the gas constant (8.314 J K-1 mol
-1), Sis the exposed soil area (cm2), Tis chamber air temperature (°C), and C' is
dry CO2concentration (mol mol -1), given by:
1-2
Since the measurement occurs in a closed system, C' increases with time, reducing
the carbon dioxide gradient between the chamber and the soil beneath, which in
turn reduces the flux. Since CO2is diffusing from the soil into a closed volume, we
make the assumption that the relationship between C' and time is:
1-3
The rate of change (C') with time is then:
1-4
We want to compute the flux at the time (to) the chamber closed (and C'(to)=C'o),
so we need corresponding initial values of T,P,W. These are determined by fitting
a straight line to the first 10 seconds of data once the chamber closes, and com-
puting the intercept value. The initial rate of change comes from equation 1-4 eval-
uated at to.
1-5
Section 1. Introduction to the LI-6800 soil chamber
1-7Theory and equation summary

Section 1. Introduction to the LI-6800 soil chamber
Fo, the flux at t=to, is thus:
1-6
and flux (Ftarget) at any other target concentration (near C'o) can be computed by
solving equation 1-3 for tsuch that C' =C'target:
1-7
then using ttarget in equation 1-4 to compute the appropriate rate of change.
The constants Cxand ain equation 1-4 come from curve fitting equation 1-3,
which requires non-linear regression. During a measurement, and before the actual
curve t, we can estimate Foby noting the following: if we fit a line to plot-
ted against C', we can use its slope and intercept to get an estimate of aand C'x.
This relation comes from eliminating the exponential from equation 1-4 using
equation 1-3:
1-8
Thus, ais the negative of the slope of such a plot, and Cxis the intercept value
divided by a.
1-8 Using the LI-6800 Soil CO₂ Flux Chamber

Section 2.
Using the chamber
In this section we describe how to use the LI-6800 Soil CO2Flux Chamber. The
LI-6800 console must be running Bluestem OS version 1.3 or newer to use the soil
chamber. If you don't have the current software, go to www.licor.com/env/support
and download the latest software for the instrument. Update the instrument soft-
ware before connecting the chamber.
Installing the chamber on the LI-6800 head
The basic procedure involves attaching the LI-6800 head to the chamber, attaching
the air tubes to the head, connecting the data cable, and attaching the soil probe.
To take a measurement, you'll need to install soil collars at the measurement loc-
ations (at least 6 hours before measurements) and configure the software to take
the measurement. To attach the chamber:
1Attach the Head Mounting Bracket to the head.
2Attach the Custom Chamber Adapter.
2-1Using the LI-6800 Soil CO₂ Flux Chamber

Section 2. Using the chamber
3Install one brass Swagelok fitting and one steel 90° Swagelok fitting onto the Custom Chamber
Adapter.
Each plug and fitting must have an O-ring. The O-rings are preinstalled, but it is a
good idea to verify that they are in place prior to installing a cap or fitting.
Although not required, we recommend installing four steel cap plugs on the
unused fittings to prevent debris from entering the adapter.
4Install the air inlet and air outlet tubes on the adapter plate Swagelok fittings.
The Swagelok fittings have metal ferrules. Remove the metal ferrules and set them
aside for safekeeping. Retrieve two 30-cm pieces of tube and two plastic ferrule sets
(part number 300-05375) from the accessories kit. Install the Bev-a-line tube with
plastic ferrules in the Swagelok fittings. Tighten each tube snugly.
5Attach the head to the chamber.
The mounting bracket clips into place on the top of the soil chamber.
6Attach the tubes from the head to the chamber.
Each tube connects to a corresponding connector on the chamber.
7Attach the chamber cable to the LS connector on the head.
Remove the connector cover to access the connectors. Reinstall the cover after con-
necting the cable.
2-2 Using the LI-6800 Soil CO₂ Flux Chamber

8Attach the soil sensor or HydraProbe (optional).
The options are described in Connecting soil sensors on the next page.
9Attach the head cable between the LI-6800 head and console.
Note: We suggest that you do not connect the tube between the console and
head. When the console starts up, the console circulation pump may start run-
ning. If the tube is in place and the cap plugs are installed on the custom cham-
ber adapter plate, the console pump could pressurize the system and activate the
relief valve in the head.
Now you are ready to power on the LI-6800 system.
Figure 2-1. The assembled chamber will have two tubes from the LI-6800 head. The cable
connects to the LS terminal on the head.
Section 2. Using the chamber
2-3Section 2. Using the chamber

Section 2. Using the chamber
Connecting soil sensors
There are three options for soil moisture and temperature measurements: the
Stevens HydraProbe, a soil temperature thermocouple, or none. Soil moisture and
temperature are not essential for the flux calculation, but they can provide useful
ancillary data.
Stevens HydraProbe II
The Stevens HydraProbe offers the simplest connection and most informative data.
It measures soil moisture content, salinity, and temperature. The HydraProbe II
uses the SDI-12 communication protocol, and no configuration is necessary. Sim-
ply connect the cable and power on the LI-6800. The cable connector has a mark-
ing that faces up and a key that must be aligned before the connector can be
tightened.
Type E thermocouple
You'll connect the thermocouple adapter cable to either thermocouple jack on the
head (T1 or T2). The thermocouple adapter cable has a connector for an Omega™
Quick Disconnect Type E Chromega™-Constantan thermocouple. The adapter
cable (part number 9968-162) and a compatible thermocouple (part number 6000-
09TC) both can be purchased from LI-COR.
As a result of the cable junctions and length, the adapter cable may cause a tem-
perature measurement offset. The offset should be measured against a standard
(such as an ice bath) and entered into the software under Environment > Tem-
perature.
2-4 Using the LI-6800 Soil CO₂ Flux Chamber