LI-COR 6400-09 User manual

6400-09
Soil CO2Flux Chamber
Instruction Manual
Publication No. 9710-119
October, 1997
LI-COR, inc.
Environmental Division
4421 Superior Street
P.O. Box 4425
Lincoln, NE 68504 USA
Telephone: [phone]
FAX: [phone]
Toll-free 1-800-447-3576 (U.S. & Canada)
e-mail: [email protected]
URL: http://www.licor.com
© Copyright 1997, LI-COR, Lincoln, Nebraska USA

ii
NOTICE
The information contained 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. LI-COR shall not be liable for errors contained herein
or for incidental or consequential damages in connection with the furnishing,
performance, or use of this material.
This document contains proprietary information that is protected by copyright. All
rights are reserved. No part of this document may be photocopied, reproduced, or
translated to another language without prior written consent of LI-COR, Inc.
© Copyright 1997, LI-COR Inc.

iii
Table of Contents
Section 1. General Information
Considerations .......................................................................................... 1-1
Precautions ........................................................................................ 1-5
Reference........................................................................................... 1-5
Section 2. Attaching the Soil Chamber
General Description .................................................................................. 2-1
Attaching the Sensor Head to the 6400-09............................................... 2-3
Section 3. Software
Configuring OPEN for Soil Measurements .............................................. 3-1
Creating a Soil Chamber Configuration ............................................ 3-1
Implementing the Soil Chamber Configuration ................................ 3-1
The Soil Chamber Configuration.............................................................. 3-2
OPEN's Main Screen ......................................................................... 3-2
Calib Menu ........................................................................................ 3-2
New Measurements Function Keys................................................... 3-2
User Variables ................................................................................... 3-4
Autoprograms .................................................................................... 3-6
Section 4. Making Measurements
Measuring With Soil Collars .................................................................... 4-2
Measuring Without Soil Collars ............................................................... 4-2
Making Measurements.............................................................................. 4-2
Position the Air Supply Manifold...................................................... 4-2
Check Hose Connections................................................................... 4-3
Measurement Procedure .................................................................... 4-4

iv
Section 5. Maintenance
Spare Parts Kit .......................................................................................... 5-1
Soil Temperature Probe ............................................................................ 5-1
Making Soil Collars .................................................................................. 5-2
Zeroing the IRGAs.................................................................................... 5-3
Zeroing the IRGA While Attached to the Soil CO2Flux Chamber .. 5-3
Setting the IRGA Span ...................................................................... 5-4
Section 6. Equation Derivation
Appendix A. Specifications
Warranty

General Information 1-1
1General
Information
Considerations
Soil carbon dioxide is primarily produced by root respiration, decay of
organic matter, and activity of microbes. Rainwater can have direct effects
as well, by displacing gas in soil pore spaces (enhancing CO2flux at the
surface), and by interacting with limestone soils. Also, rainwater 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 pushing the chamber down over a sealed volume. Soil
water evaporation and heating of the air in the chamber head space also
induces pressure increases in an unvented chamber. The 6400-09 Soil CO2
Flux Chamber is vented so that pressures inside and outside the chamber are
in a dynamic equilibrium.
Soil CO2flux measured using a chamber system is dependent on the CO2
concentration in the measurement chamber. This is illustrated in Figure
1-1, which shows typical variations in measured soil CO2flux when the
chamber headspace CO2concentration was allowed to rise. Healy et. al.
(1996) used analytical and numerical models of gas diffusion to evaluate
chamber headspace concentration influence on estimates of soil CO2flux.
They found that chamber-induced perturbations of soil-gas concentration
gradients could result in substantial underestimate of soil CO2 flux (6 to
34% for a 30 minute measurement).
The LI-6400 Soil CO2Flux System has been designed to minimize
perturbation in the soil-gas concentration gradient. Before starting the
measurement, ambient CO2concentration at the soil surface is measured.
Once the chamber is installed, the CO2scrubber is used to draw the CO2in

Section 1
1-2 General Information
the closed system down below the ambient concentration. The scrubber is
turned off, and soil CO2flux causes the CO2concentration in the chamber
headspace to rise (Figure 1-2). Data are logged while the CO2
concentration rises through the ambient level. The software then computes
the flux appropriate for the ambient concentration. This measurement cycle
repeats for as many iterations as you select (Figure 1-3).
Chamber CO
2
Concentration (ppm)
0 400 800 1200 1600 2000 2400
Soil CO
2
Flux (µmol m
-2
s
-1
)
0
4
8
12
16
20
Figure 1-1. Soil CO
2
flux rates depend on the chamber CO
2
concentration.

Section 1
General Information 1-3
CHAMBER
SAMPLE
REF
INLET
IRGA
RS-232
AUXILIARY
Ol
Pressure Relief Fitting
Gas Analyzer Mixing Fan
LI-6400 Sensor Head
Analyzer Inlet Duct
Analyzer Outlet Duct
Pressure Relief Vent Tube
Manifold (CO2Scrub)
Manifold (Analyzer Outlet)
Plumbing Circuit for CO2Scrub Operation
escape
enter enter
Q
A
Z
1
!@
2#
3$
4
SDF
%
5^
6&
7
GHJK
*
8(
9)
0_
-+
=
L;
:"
'\
space
ctrl
WERTYU I OP {
[}
]
~
|
shift
XCVBNM,
<>
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/
shift
Figure 1-2. LI-6400 Soil CO
2
Flux System setup. The shaded plumbing circui
t

is for CO
2
scrub operations and is only used during the draw down portion of
a measurement cycle. During the actual measurement, mixing in the chamber
headspace is achieved with the gas analyzer mixing fan and the associated 
plumbing.

Section 1
1-4 General Information
Time
Chamber CO
2
measurement measurement
A
B
ambient
ambient
Pump off
Pump on
Chamber CO
2
Soil CO
2
Flux
Fluxes computed dring the
measurement phase of each cycle.
Final answer
Regression line
Figure 1-3. (A). Time series of a measurement cycle. Pumping reduced CO
2
air into the
chamber brings the CO
2
below ambient. After the pump turns off, CO
2
rises due to soil CO
2
efflux. During this phase, soil CO
2
flux is computed, and data for regressing flux as a function
of CO
2
is generated. (B). At the end of the measurement cycle, the final flux value is
computed by regressing flux vs CO
2
, and computing the flux that corresponds to the target
(ambient) concentration value.

Section 1
General Information 1-5
Precautions
●Keep the soil chamber shaded to avoid heating.
●If measurements are made on bare soil with no canopy, variation in the
measured flux can occur due to dynamic pressure fluctuations at the
pressure vent outlet caused by wind effects. The vent on the 6400-09 is
shielded to minimize direct wind effects, but you may wish to shield the
entire chamber from the wind.
●If a thin upper layer of soil becomes saturated from short intense rainfall,
a surface gas seal can form that causes CO2concentration to increase
below the saturated layer. A burst of CO2may be released when the
sharp edge of the chamber is inserted, causing excessively high flux
measurements when in actuality the undisturbed flux is very small. The
initial flux from the burst of CO2can be two or more times larger than
the actual flux that would be measured if the chamber were left installed
for several hours without disturbing it. Collars usually provide better
measurements under these conditions because of minimal disturbance;
great care must be taken not to disturb the collars when putting the
chamber onto them, however.
Reference
Healy, Richard W., R.G. Striegl, T.F. Russell, G.L. Hutchinson, and G.P.
Livingston, 1996. Numerical Evaluation of Static-Chamber Measurements
of Soil-Atmosphere Gas Exchange: Identification of Physical Processes.
Soil Sci. Soc. Am. J. 60:740-747.