Widén B, Lindroth A. 2003. A calibration system for soil carbon dioxide-efflux measurement chambers: description and application. Soil Science Society of America Journal, 67: 327-334.
These authors describe a system for the absolute calibration of CO2-flux from soils, for both open- and closed-chamber type systems. The basic design is a large box, topped with a layer of sand, into which CO2 is pumped at a known rate. The measurement chamber sits on top of the layer of sand, and the actual gas flux can be calculated and compared to that measured by the machine.
The system appears to be useful, and a significant improvement in the field. The authors caution that improvements need to be made to the system, cheifly in its size and consideration of the effects of water in the soil on gas flux variations.
Tuesday, March 17, 2009
Staal et al. 2001
Staal M, te Lintel-Hekkert S, Harren F, Stal L. 2001. Nitrogenase activity in cyanobacteria measured by the acetylene reduction assay: a comparison between batch incubation and on-line monitoring. Environmental Microbiology 3(5): 343-351.
These authors present two methods for measuring nitrogenase activity in cyanobacteria, both based on continuous on-line measurement of ethylene produced by the reduction of acetylene by nitrogenase. One method relies on a gas chromatograph to detect ethylene, the other on a not-yet-commercially available laser system. Nitrogenase normally reduces N2 to NH3, but will also reduce other triple bonds such as that between the carbon atoms in acetylene, hence this measurement assay was developed in the late 1960s. The nitrogenase enzyme is inhibited by oxygen, but is very energy-intensive when reducing N2, thus cyanobacteria may fix Nitrogen in a manner dependent upon but separated from photosynthesis in either (at night) time or space (specialized cells).
Previous ethylene-based methods were based on incubations of cells in air-tight containers, for incubation periods sufficient to saturate nitrogenase with acetylene and accumulate sufficient ethylene for detection. Changes in O2 and CO2 concentrations during these hours-long incubations introduce conflating variables; O2 is depleted and CO2 accumulates in the dark, vice-versa in the light. CO2 concentration affects pH, while O2 inhibits nitrogenase and indirectly relates to available energy. In addition, long incubations will fail to detect any event occuring on a frequency shorter than the incubation time, such that processes occurring on time scales of seconds to minutes will not be registered. Finally, saturation of nitrogenase with acetylene eventually leads to nitrogen starvation and the synthesis of more nitrogenase.
In contrast, on-line methods involve the continuous flow of gas over the sample. This can be used to measure gas flux only when the system reaches a steady state (however, see the discussion of steady-state and non-steady-state modes in gas sampling chambers in Davidson et al., 2002). For nitrogenase-ethylene, this steady state may be reached as quickly as 1 minute under ideal, high-surface-area conditions. In addition, while O2 and CO2 concentrations are controlled during on-line measurement, ethylene cannot accumulate, thus only very low concentrations will be present.
Nitrogenase activity was higher under light-saturation conditions than in the dark, but became inhibitory with longer incubation times. Changes in nitrogenase activity with time and light level probably relate to both energy limitation in the dark and oxygen inhibition in the light. Changes relating to growth, internal rythms, or energy depletion only occurred after very long incubations, such as 24 hours. I am not certain how long-term energy depletion is distinct from short term energy limitation in the dark.
This paper suggests it may be possible for us to measure nitrogenase activity with acetylene and ethylene using the Gasmet FTIR system and its chambers.
These authors present two methods for measuring nitrogenase activity in cyanobacteria, both based on continuous on-line measurement of ethylene produced by the reduction of acetylene by nitrogenase. One method relies on a gas chromatograph to detect ethylene, the other on a not-yet-commercially available laser system. Nitrogenase normally reduces N2 to NH3, but will also reduce other triple bonds such as that between the carbon atoms in acetylene, hence this measurement assay was developed in the late 1960s. The nitrogenase enzyme is inhibited by oxygen, but is very energy-intensive when reducing N2, thus cyanobacteria may fix Nitrogen in a manner dependent upon but separated from photosynthesis in either (at night) time or space (specialized cells).
Previous ethylene-based methods were based on incubations of cells in air-tight containers, for incubation periods sufficient to saturate nitrogenase with acetylene and accumulate sufficient ethylene for detection. Changes in O2 and CO2 concentrations during these hours-long incubations introduce conflating variables; O2 is depleted and CO2 accumulates in the dark, vice-versa in the light. CO2 concentration affects pH, while O2 inhibits nitrogenase and indirectly relates to available energy. In addition, long incubations will fail to detect any event occuring on a frequency shorter than the incubation time, such that processes occurring on time scales of seconds to minutes will not be registered. Finally, saturation of nitrogenase with acetylene eventually leads to nitrogen starvation and the synthesis of more nitrogenase.
In contrast, on-line methods involve the continuous flow of gas over the sample. This can be used to measure gas flux only when the system reaches a steady state (however, see the discussion of steady-state and non-steady-state modes in gas sampling chambers in Davidson et al., 2002). For nitrogenase-ethylene, this steady state may be reached as quickly as 1 minute under ideal, high-surface-area conditions. In addition, while O2 and CO2 concentrations are controlled during on-line measurement, ethylene cannot accumulate, thus only very low concentrations will be present.
Nitrogenase activity was higher under light-saturation conditions than in the dark, but became inhibitory with longer incubation times. Changes in nitrogenase activity with time and light level probably relate to both energy limitation in the dark and oxygen inhibition in the light. Changes relating to growth, internal rythms, or energy depletion only occurred after very long incubations, such as 24 hours. I am not certain how long-term energy depletion is distinct from short term energy limitation in the dark.
This paper suggests it may be possible for us to measure nitrogenase activity with acetylene and ethylene using the Gasmet FTIR system and its chambers.
Martin et al. 2004
Martin JG, Bolstad PV, Norman JM. 2004. A carbon dioxide flux generator for testing infrared gas analyzer-based soil respiration systems. Soil Science Society of America Journal 68: 514-518.
These authors constructed a system for calibrating soil CO2 flux using a closed-chamber Infrared Gas Analyzer (IRGA), in this case a Li-Cor 6400. Two detectors were used: one to monitor the CO2 concentration inside the reservoir, and one as the test machine placed on top of the artificial soil on top of the reservoir. The basic construction was quite simple, compared with the systems of Butnor and Johnsen (2004) and Widen and Lindroth (2003). Essentially, this system is just a cylinder topped by a level layer of uniform glass beads. CO2 is added to the reservoir beneath, apparently by the simple method of exhaling into the input valve, and diffuses through the reservoir (mixed by a small fan) and through the glass bead layer.
Much of the refinement of this system concerns the placement of mixing fans to 1) ensure the reservoir is well-mixed but not pressurized and 2) disrupt the boundary layer on top of the glass beads. Boundary layer effects are blamed for some of the measurement error reported here.
The test system underestimated low fluxes, and overestimated high fluxes. These authors suggest that wind-speed differences inside vs. outside the closed chamber, and associated boundary layer differences, are the main drivers of these measurement errors. They also strongly caution that variation in the set point inside the reservoir has a large effect on measured flux rates. Under field conditions, with soil composed of smaller particles, these errors are expected to be less important.
These authors constructed a system for calibrating soil CO2 flux using a closed-chamber Infrared Gas Analyzer (IRGA), in this case a Li-Cor 6400. Two detectors were used: one to monitor the CO2 concentration inside the reservoir, and one as the test machine placed on top of the artificial soil on top of the reservoir. The basic construction was quite simple, compared with the systems of Butnor and Johnsen (2004) and Widen and Lindroth (2003). Essentially, this system is just a cylinder topped by a level layer of uniform glass beads. CO2 is added to the reservoir beneath, apparently by the simple method of exhaling into the input valve, and diffuses through the reservoir (mixed by a small fan) and through the glass bead layer.
Much of the refinement of this system concerns the placement of mixing fans to 1) ensure the reservoir is well-mixed but not pressurized and 2) disrupt the boundary layer on top of the glass beads. Boundary layer effects are blamed for some of the measurement error reported here.
The test system underestimated low fluxes, and overestimated high fluxes. These authors suggest that wind-speed differences inside vs. outside the closed chamber, and associated boundary layer differences, are the main drivers of these measurement errors. They also strongly caution that variation in the set point inside the reservoir has a large effect on measured flux rates. Under field conditions, with soil composed of smaller particles, these errors are expected to be less important.
Marion et al. 1997
Marion GM, Henry GHR, Freckman DW, Johnstone J, Jones G, Jones MH, Levesque E, Molau U, Molgaard P, Parsons AN, Svoboda J, Virginia RA. 1997. Open-top designs for mainpulating field temperature in high-latitude ecosystems. Global Change Biology 3 (suppl. 1): 20-32.
These authors evaluated 4 different chamber designs under field conditions, examining many variables but focusing on temperature differences between the inside and outside of the chambers, and unintended ecological effects. The four designs were termed “ITEX corners”, “cone chambers”, “hexagon chambers”, and “plastic tent”. There were 6 field sites, 5 in the Arctic from Sweden to Canada, and 1 in Antarctica.
This paper represents one of the outcomes of a meeting that established the International Tundra Experiment (ITEX); at this meeting a list of requirements for long-term temperature manipulation devices was constructed, leading to these 4 designs and a requirement to measure ecological effects such as changes in snow accumulation or melting.
The results were fairly consistent across chamber designs. In general, open-top chambers cause fewer and less severe ecological side-effects than closed designs, but warm the surface of the soil by 1-2 degrees compared with up to 10 or 15 degrees for some closed designs. Side-effects of the open-top chambers included some shading and interception of PAR by the chamber materials, changes in moisture concentrations in the air immediately above the soil surface (though these may have been driven by changes in temperature), and the possibility of interference from animals, such as nutrient addition by birds perching on the chambers. However, CO2 concentrations were not affected by chambers.
One of these authors, GHR Henry, will be working with me this summer at Alexandra Fjord; this was also one of the study sites in this paper.
These authors evaluated 4 different chamber designs under field conditions, examining many variables but focusing on temperature differences between the inside and outside of the chambers, and unintended ecological effects. The four designs were termed “ITEX corners”, “cone chambers”, “hexagon chambers”, and “plastic tent”. There were 6 field sites, 5 in the Arctic from Sweden to Canada, and 1 in Antarctica.
This paper represents one of the outcomes of a meeting that established the International Tundra Experiment (ITEX); at this meeting a list of requirements for long-term temperature manipulation devices was constructed, leading to these 4 designs and a requirement to measure ecological effects such as changes in snow accumulation or melting.
The results were fairly consistent across chamber designs. In general, open-top chambers cause fewer and less severe ecological side-effects than closed designs, but warm the surface of the soil by 1-2 degrees compared with up to 10 or 15 degrees for some closed designs. Side-effects of the open-top chambers included some shading and interception of PAR by the chamber materials, changes in moisture concentrations in the air immediately above the soil surface (though these may have been driven by changes in temperature), and the possibility of interference from animals, such as nutrient addition by birds perching on the chambers. However, CO2 concentrations were not affected by chambers.
One of these authors, GHR Henry, will be working with me this summer at Alexandra Fjord; this was also one of the study sites in this paper.
Mastepanov et al. 2008
Mastepanov M, Sigsgaard C, Dlugokencky EJ, Houweling S, Strom L, Tamstorf MP, Christensen TR. 2008. Large tundra methane burst during onset of freezing. Nature 456: 628-631.
These authors describe a large emission of methane from a wet tundra site in the Greenland High Arctic, which occurred in late autumn and early winter as the ground froze. This burst of methane emission is of a similar magnitude to the total methane emission from this site during the growing season, and accounts for the previously observed “shoulder” of methane in autumn at high altitudes.
The site is Zackenberg Valley, in the north-east of Greenland at about 74ºN latitude. This site appears to be broadly similar to other High Arctic tundra meadows such as Truelove Lowlands (Devon Island) and Alexandra Fjord (Ellesmere Island) and large parts of northern Russia, with an active layer 20 to 100 cm thick. The growing season measurements here were similar to previous years, and similar to another study in Siberia.
These measurements were made using an automated methane-only laser-based system, that took readings of methane flux every hour, with a data-gathering time of 1 second. Late-season pulses of methane were not observed at lower-latitude sites, possibly because a deeper permafrost “floor” allows methane to diffuse down to deeper soil layers rather than being forced upwards. Spatial and temporal variablity of the freezing methane emissions were very high, suggesting the diffusion paths of methane squeezed out of the soil were dependent upon plant root systems and similar structures.
This paper is the reason my field season at Alexandra Fjord in 2009 may extend as late as August 25 (planned) or September 10 (worst-case scenario). The figures in this paper imply the difference between measured and modeled methane emissions became apparent approximately in late August.
These authors describe a large emission of methane from a wet tundra site in the Greenland High Arctic, which occurred in late autumn and early winter as the ground froze. This burst of methane emission is of a similar magnitude to the total methane emission from this site during the growing season, and accounts for the previously observed “shoulder” of methane in autumn at high altitudes.
The site is Zackenberg Valley, in the north-east of Greenland at about 74ºN latitude. This site appears to be broadly similar to other High Arctic tundra meadows such as Truelove Lowlands (Devon Island) and Alexandra Fjord (Ellesmere Island) and large parts of northern Russia, with an active layer 20 to 100 cm thick. The growing season measurements here were similar to previous years, and similar to another study in Siberia.
These measurements were made using an automated methane-only laser-based system, that took readings of methane flux every hour, with a data-gathering time of 1 second. Late-season pulses of methane were not observed at lower-latitude sites, possibly because a deeper permafrost “floor” allows methane to diffuse down to deeper soil layers rather than being forced upwards. Spatial and temporal variablity of the freezing methane emissions were very high, suggesting the diffusion paths of methane squeezed out of the soil were dependent upon plant root systems and similar structures.
This paper is the reason my field season at Alexandra Fjord in 2009 may extend as late as August 25 (planned) or September 10 (worst-case scenario). The figures in this paper imply the difference between measured and modeled methane emissions became apparent approximately in late August.
Kammann et al. 2005
Kammann C, Grünhage L, Grüters U, Janze S, Jäger H-J. 2005. Response of aboveground grassland biomass and soil moisture to moderate long-term CO2 enrichment. Basic and Applied Ecology 6: 351-365.
These authors present the results of the first 5 years of the GiFACE experiment in Germany (see Jäger et al. 2003). The major findings, as alluded to in the title, concern the response of aboveground biomass and soil moisture to moderate, year-round (but not 24-hour) CO2 enrichment in a temperate, mesic, semi-natural grassland ecosystem.
Compared to other similar studies, the GiFACE experiment found increased grass biomass under CO2 enrichment, no increase in forbs, and no changes in soil moisture. Other studies found less biomass increase, especially of grasses, generally increased forbs both by measures of diversity and by biomass, and generally increased soil moisture. Differences associated with GiFACE include the low CO2 step increase of 20% compared with much higher in other studies, such as doubling, the cutting frequency that is lower than most other studies, and the year-round CO2 enrichment compared with many studies enriching only during the active growing season. Additionally, the mix of species at Giessen may have been “right” for a strong biomass response, with an interaction from the low cutting frequency allowing these strongly responding grasses to increase above ground biomass to a large degree.
This paper suffers from an irritating flaw – a non-significant difference in annual biomass yield between enriched and control plots is described as “non-significantly higher”, an oxymoron. If it’s not significantly higher, it’s not higher.
These authors present the results of the first 5 years of the GiFACE experiment in Germany (see Jäger et al. 2003). The major findings, as alluded to in the title, concern the response of aboveground biomass and soil moisture to moderate, year-round (but not 24-hour) CO2 enrichment in a temperate, mesic, semi-natural grassland ecosystem.
Compared to other similar studies, the GiFACE experiment found increased grass biomass under CO2 enrichment, no increase in forbs, and no changes in soil moisture. Other studies found less biomass increase, especially of grasses, generally increased forbs both by measures of diversity and by biomass, and generally increased soil moisture. Differences associated with GiFACE include the low CO2 step increase of 20% compared with much higher in other studies, such as doubling, the cutting frequency that is lower than most other studies, and the year-round CO2 enrichment compared with many studies enriching only during the active growing season. Additionally, the mix of species at Giessen may have been “right” for a strong biomass response, with an interaction from the low cutting frequency allowing these strongly responding grasses to increase above ground biomass to a large degree.
This paper suffers from an irritating flaw – a non-significant difference in annual biomass yield between enriched and control plots is described as “non-significantly higher”, an oxymoron. If it’s not significantly higher, it’s not higher.
Jäger et al. 2003
Jäger HJ, Schmidt SW, Kammann C, Grünhage L, Müller C, Hanewald K. 2003. The University of Giessen free-air Carbon dioxide enrichment study: description of the experimental site and of a new enrichment system. Journal of Applied Botany – Angewandte Botanik 77: 117-127.
These authors describe the study site and technical details of the operation of a long-term experiment designed to study the impact of rising atmospheric Carbon dioxide concentrations, the GiFACE. In essence, this study system is unique and important, being the only such study currently ongoing in Europe, and is based on what appears to be the leading edge of relevant technology. At its heart, the system consists of a circular open-topped chamber into which CO2 is released under the control of a concentration monitor in the center. Release occurs at the upwind side of the ring, and consistently acheives the target enrichment of about 25% additional CO2 at 40cm above ground. Grassland canopy heights at this site and similar sites in Europe are almost never higher than 50cm.
Turbulence from the blowers disrupts microclimates in and near the rings during the ambient quiet at night, so the blowers are only run during daylight hours. Control plots without enrichment show the expected pattern of higher ambient CO2 concentrations at night, associated with nocturnal respiration and diurnal photosynthesis. These authors do not address the effects of this blower and enrichment schedule may have on a simulation of globally enriched atmospheric CO2.
This paper is the reference provided by Dr. Kammann to provide needed details for my application to the Canadian Food Inspection Agency to import soil samples from the GiFACE site to Canada.
These authors describe the study site and technical details of the operation of a long-term experiment designed to study the impact of rising atmospheric Carbon dioxide concentrations, the GiFACE. In essence, this study system is unique and important, being the only such study currently ongoing in Europe, and is based on what appears to be the leading edge of relevant technology. At its heart, the system consists of a circular open-topped chamber into which CO2 is released under the control of a concentration monitor in the center. Release occurs at the upwind side of the ring, and consistently acheives the target enrichment of about 25% additional CO2 at 40cm above ground. Grassland canopy heights at this site and similar sites in Europe are almost never higher than 50cm.
Turbulence from the blowers disrupts microclimates in and near the rings during the ambient quiet at night, so the blowers are only run during daylight hours. Control plots without enrichment show the expected pattern of higher ambient CO2 concentrations at night, associated with nocturnal respiration and diurnal photosynthesis. These authors do not address the effects of this blower and enrichment schedule may have on a simulation of globally enriched atmospheric CO2.
This paper is the reference provided by Dr. Kammann to provide needed details for my application to the Canadian Food Inspection Agency to import soil samples from the GiFACE site to Canada.
Holtan-Hartwig et al. 2002
Holtan-Hartwig L, Dörsch P, Bakken LR. 2002. Low temperature control of soil denitrifying communities: kinetics of N2O production and reduction. Soil Biology & Biochemistry 34: 1797-1806.
These authors measured the activation energies of N2O production and reduction in soils taken from agricultural settings in Finland, Sweden, and Germany. The underlying observation is that temperate soils show an unexpectedly large emission profile of N2O in late winter and early spring. Other authors have attributed this release to freeze-thaw effects, such as release of N2O trapped in frozen soils. Differences in activation energies could also explain these observations if these activation energies are asymmetrical at low temperatures, such that the activation energy of N2O reduction is much higher than that for N2O production.
N2O is both a greenhouse gas and an ozone-layer depleter. From soils, it is produced in the penultimate step in a series of reactions known collectively as the denitrification pathway: these reactions when run to completion convert nitrate (NO3-) to N2. N2 of course represents a net loss of nitrogen from an ecosystem, since it is no longer available to organisms. However, N2 is utterly harmless, while N2O has important physical effects on the atmosphere. The basic biochemistry and temperature response of this pathway is described in Firestone (1982).
Another underlying observation for this study is that the product ratio of N2O/N2 increases with decreasing temperature; in other words, proportionally more N2O is released from the system compared to N2. If N2O reduction (to N2) has a higher activation energy than N2O production (from NO), this would explain this observation. Another possibility is that the enzyme responsible for N2O reduction is strongly inhibited at some critical low temperature threshold.
The laboratory analyses carried out for this paper are strongly divergent from field conditions, involving anaerobic slurries with an excess of electron acceptors and the removal of NO3-. However, the differences observed between the different soils support other conclusions that N2O emissions from soils varies strongly with soil types and soil sources.
Previously reported activation energies for NO3- loss by denitrification range between about 41 and 89 kJ/mol; a similar range of activation energies was found here for both N2O production and reduction. This suggests that asymmetrical activation energies are not driving the observed changes in N2O flux by season. It seems temperatures close to 0ºC represent a particular challenge to the microbial communities of these soils, but the nature of this challenge remains unclear – this study did not examine community dynamics in any detail. Some details of the methods of preparing soils used here may be important in this regard.
Another possibility, not mutually exclusive with this threshold effect, is that strong decreases in metabolic rates at low temperatures (60-70% per 10ºC) combined with weak decreases in N2O diffusion rates (20-25% per 10ºC in water) allow N2O to escape the biological pathway as temperatures approach zero.
This paper was recommended to me by Dr. Steven Siciliano, as a guide to some of the calculations and comparisons we are doing with soils and greenhouse gases (including N2O) from Alexandra Fjord.
These authors measured the activation energies of N2O production and reduction in soils taken from agricultural settings in Finland, Sweden, and Germany. The underlying observation is that temperate soils show an unexpectedly large emission profile of N2O in late winter and early spring. Other authors have attributed this release to freeze-thaw effects, such as release of N2O trapped in frozen soils. Differences in activation energies could also explain these observations if these activation energies are asymmetrical at low temperatures, such that the activation energy of N2O reduction is much higher than that for N2O production.
N2O is both a greenhouse gas and an ozone-layer depleter. From soils, it is produced in the penultimate step in a series of reactions known collectively as the denitrification pathway: these reactions when run to completion convert nitrate (NO3-) to N2. N2 of course represents a net loss of nitrogen from an ecosystem, since it is no longer available to organisms. However, N2 is utterly harmless, while N2O has important physical effects on the atmosphere. The basic biochemistry and temperature response of this pathway is described in Firestone (1982).
Another underlying observation for this study is that the product ratio of N2O/N2 increases with decreasing temperature; in other words, proportionally more N2O is released from the system compared to N2. If N2O reduction (to N2) has a higher activation energy than N2O production (from NO), this would explain this observation. Another possibility is that the enzyme responsible for N2O reduction is strongly inhibited at some critical low temperature threshold.
The laboratory analyses carried out for this paper are strongly divergent from field conditions, involving anaerobic slurries with an excess of electron acceptors and the removal of NO3-. However, the differences observed between the different soils support other conclusions that N2O emissions from soils varies strongly with soil types and soil sources.
Previously reported activation energies for NO3- loss by denitrification range between about 41 and 89 kJ/mol; a similar range of activation energies was found here for both N2O production and reduction. This suggests that asymmetrical activation energies are not driving the observed changes in N2O flux by season. It seems temperatures close to 0ºC represent a particular challenge to the microbial communities of these soils, but the nature of this challenge remains unclear – this study did not examine community dynamics in any detail. Some details of the methods of preparing soils used here may be important in this regard.
Another possibility, not mutually exclusive with this threshold effect, is that strong decreases in metabolic rates at low temperatures (60-70% per 10ºC) combined with weak decreases in N2O diffusion rates (20-25% per 10ºC in water) allow N2O to escape the biological pathway as temperatures approach zero.
This paper was recommended to me by Dr. Steven Siciliano, as a guide to some of the calculations and comparisons we are doing with soils and greenhouse gases (including N2O) from Alexandra Fjord.
Davidson et al. 2002
Davidson EA, Savage K, Verchot LV, Navarro R. 2002. Minimizing artifacts and biases in chamber-based measurements of soil respiration. Agricultural and Forest Meteorology 113: 21-37.
These authors review published examples of measurements of CO2 flux from soils, especially forest soils, with an emphasis on identifying major sources of error in these measurements and possible strategies to minimize these errors. As suggested by the title, they divide these sources of error into artifacts (systematic errors caused by details of the construction or operation of measurement devices), biases (consistent patterns of over- or under-estimation of fluxes), and sampling uncertainties (including spatial and temporal heterogeneities in both actual and measured gas fluxes).
Photosynthesis is the primary driver of CO2 flux, with soil respiration a close second in terrestrial ecosystems. Soil respiration may account for 60-90% of the total respiration of a temperate forest, but can be difficult to measure. The two primary methods of measurement are eddy covariance, often using tower-based systems, and chambers that are typically placed on or embedded into the soil. Direct comparisons between these methods have found large variances, suggesting that one or both methods includes inherent artifacts and biases that need to be addressed.
Chambers can be operated in one of two modes: steady-state and non-steady-state. In the steady-state mode, the flux of gas from the soil is calculated based on the difference in CO2 concentration between the inflow and outflow openings into the chamber, after the conditions inside the chamber have reached dynamic equilibrium. In the non-steady-state mode, the rate of change of gas concentration inside the chamber is measured over some time interval. Both modes have inherent problems.
Achieving a steady-state is time consumming and uncertain. In addition, the details of the rate of flow of carrier gas through the chamber, as well as the soil type, moisture level, vegetation and litter, and other variables can have a large influence on the measurements of gas concentration. There are also significant difficulties associated with determining when a true equilibrium has been attained, and the relevance of that equilibrium to “natural” conditions immediately above undisturbed soil.
The non-steady-state is easier and quicker to achieve, but again there are difficulties and uncertainties surrounding a large number of other variables. Of principle importance is the concentration gradient of the gas of interest through the soil. Higher or lower pressures inside the chamber, either of total atmosphere or the partial pressure of the gas of interest, will alter the concentration gradient and thereby change the rate of gas diffusion (i.e. the flux).
These authors seem to prefer the non-steady-state mode, at least partly because it is very rapid to get measurements compared to the wait of up to days to ensure equilibrium under the steady-state mode. They include some helpful calculations, based mainly on linear regression, to smooth the process of measuring gas flux under non-steady-state conditions. Essentially, near-continuous monitoring of gas concentrations in the non-steady-state mode allows a fit to a regression, and the disturbance effects induced by placing and initiating the chamber can be ignored.
Despite these mathematical techniques, most chambers tend to underestimate true flux rates, usually by between a trivial amount and 15%. Taller chambers and deeper penetration of collars into soil tend to reduce these sources of error, though again many variables including wind conditions and soil parameters have strong influences.
Minimizing pressure effects is another important factor in reducing errors. Fans for mixing air inside the chamber are probably unnecessary except for the largest chamber designs, though vents are probably critical in nearly all cases. External air entering a chamber through the vents will cause some error, but this is likely to be trivial compared to the avoidance of a pressure differential between the inside and outside of the chamber, especially under windy conditions.
Other minor pieces of advice include always restricting the flow rate through the chamber with a valve, to even out the effects of battery charge on the pump, and careful recalibration of chambers after any change in configuration, especially of vents. The disturbance effects associated with the placement of collars or chambers are mostly attenuated within a day, such that it may be very beneficial to emplace collars well in advance of measuring gas flux with chambers.
Spatial and temporal variation can occur at scales both much larger and much smaller than the sampling footprint of a typical chamber. These authors provide statistical advice to determine the sampling design needed to achieve a given level of confidence that one is measuring something close to the actual mean flux; for a temperate forest system in New England, as few as 6 chambers monitored for a little as 5 minutes may be sufficient to achieve 90% confidence in being within 20% of the true mean.
Diel variation is an important part of the patterns of gas flux in soils. Night-time respiration by plants in the absence of photosynthesis can alter concentration gradients to a large degree, such that true long-term fluxes may only be estimated from 24-hour monitoring. How this may apply to Arctic systems experiencing 24-hour sunlight is beyond the scope of this review.
The extensive list of relevant literature in this paper may be very useful for more information and advice for the calibration, use, and analysis of our FTIR system.
These authors review published examples of measurements of CO2 flux from soils, especially forest soils, with an emphasis on identifying major sources of error in these measurements and possible strategies to minimize these errors. As suggested by the title, they divide these sources of error into artifacts (systematic errors caused by details of the construction or operation of measurement devices), biases (consistent patterns of over- or under-estimation of fluxes), and sampling uncertainties (including spatial and temporal heterogeneities in both actual and measured gas fluxes).
Photosynthesis is the primary driver of CO2 flux, with soil respiration a close second in terrestrial ecosystems. Soil respiration may account for 60-90% of the total respiration of a temperate forest, but can be difficult to measure. The two primary methods of measurement are eddy covariance, often using tower-based systems, and chambers that are typically placed on or embedded into the soil. Direct comparisons between these methods have found large variances, suggesting that one or both methods includes inherent artifacts and biases that need to be addressed.
Chambers can be operated in one of two modes: steady-state and non-steady-state. In the steady-state mode, the flux of gas from the soil is calculated based on the difference in CO2 concentration between the inflow and outflow openings into the chamber, after the conditions inside the chamber have reached dynamic equilibrium. In the non-steady-state mode, the rate of change of gas concentration inside the chamber is measured over some time interval. Both modes have inherent problems.
Achieving a steady-state is time consumming and uncertain. In addition, the details of the rate of flow of carrier gas through the chamber, as well as the soil type, moisture level, vegetation and litter, and other variables can have a large influence on the measurements of gas concentration. There are also significant difficulties associated with determining when a true equilibrium has been attained, and the relevance of that equilibrium to “natural” conditions immediately above undisturbed soil.
The non-steady-state is easier and quicker to achieve, but again there are difficulties and uncertainties surrounding a large number of other variables. Of principle importance is the concentration gradient of the gas of interest through the soil. Higher or lower pressures inside the chamber, either of total atmosphere or the partial pressure of the gas of interest, will alter the concentration gradient and thereby change the rate of gas diffusion (i.e. the flux).
These authors seem to prefer the non-steady-state mode, at least partly because it is very rapid to get measurements compared to the wait of up to days to ensure equilibrium under the steady-state mode. They include some helpful calculations, based mainly on linear regression, to smooth the process of measuring gas flux under non-steady-state conditions. Essentially, near-continuous monitoring of gas concentrations in the non-steady-state mode allows a fit to a regression, and the disturbance effects induced by placing and initiating the chamber can be ignored.
Despite these mathematical techniques, most chambers tend to underestimate true flux rates, usually by between a trivial amount and 15%. Taller chambers and deeper penetration of collars into soil tend to reduce these sources of error, though again many variables including wind conditions and soil parameters have strong influences.
Minimizing pressure effects is another important factor in reducing errors. Fans for mixing air inside the chamber are probably unnecessary except for the largest chamber designs, though vents are probably critical in nearly all cases. External air entering a chamber through the vents will cause some error, but this is likely to be trivial compared to the avoidance of a pressure differential between the inside and outside of the chamber, especially under windy conditions.
Other minor pieces of advice include always restricting the flow rate through the chamber with a valve, to even out the effects of battery charge on the pump, and careful recalibration of chambers after any change in configuration, especially of vents. The disturbance effects associated with the placement of collars or chambers are mostly attenuated within a day, such that it may be very beneficial to emplace collars well in advance of measuring gas flux with chambers.
Spatial and temporal variation can occur at scales both much larger and much smaller than the sampling footprint of a typical chamber. These authors provide statistical advice to determine the sampling design needed to achieve a given level of confidence that one is measuring something close to the actual mean flux; for a temperate forest system in New England, as few as 6 chambers monitored for a little as 5 minutes may be sufficient to achieve 90% confidence in being within 20% of the true mean.
Diel variation is an important part of the patterns of gas flux in soils. Night-time respiration by plants in the absence of photosynthesis can alter concentration gradients to a large degree, such that true long-term fluxes may only be estimated from 24-hour monitoring. How this may apply to Arctic systems experiencing 24-hour sunlight is beyond the scope of this review.
The extensive list of relevant literature in this paper may be very useful for more information and advice for the calibration, use, and analysis of our FTIR system.
Butnor and Johnsen 2004
Butnor JR, Johnsen KH. 2004. Calibrating soil respiration measures with a dynamic flux apparatus using artifical soil media of varying porosity. European Journal of Soil Science, 55: 639-647.
These authors describe a system for the absolute calibration of CO2-flux from soils for closed-chamber type measurement systems. The underlying principle of the large box they constructed is that there is no pressure difference between the footspace below the simulated soil and the atmosphere above. This means CO2 moves through the soil only by diffusion, and not by other processes.
The artificial soil was constructed from inorganic components of known and nearly-constant physical characteristics, and without water. This avoids the many confounding variables associated with real soils, such as microbial activity and changes in physical parameters with water content and water movement. However, there are still a large number of variables to account for in calculating and measuring CO2 flux through a porous material.
In general, the tested closed-chamber system, a Li-Cor 6400 Photosynthesis System, underestimated CO2 flux rates except when flux rates were very low. The authors speculate that this reversal of estimation situation was generated by the chamber’s airflow disturbing and capturing shallow pockets of soil air that would not otherwise be measured at very low flux rates.
Overall, this system appears to be an improvement over previous attempts to absolutely calibrate measures of soil CO2 flux. However, it is a large, expensive, and complicated system.
These authors describe a system for the absolute calibration of CO2-flux from soils for closed-chamber type measurement systems. The underlying principle of the large box they constructed is that there is no pressure difference between the footspace below the simulated soil and the atmosphere above. This means CO2 moves through the soil only by diffusion, and not by other processes.
The artificial soil was constructed from inorganic components of known and nearly-constant physical characteristics, and without water. This avoids the many confounding variables associated with real soils, such as microbial activity and changes in physical parameters with water content and water movement. However, there are still a large number of variables to account for in calculating and measuring CO2 flux through a porous material.
In general, the tested closed-chamber system, a Li-Cor 6400 Photosynthesis System, underestimated CO2 flux rates except when flux rates were very low. The authors speculate that this reversal of estimation situation was generated by the chamber’s airflow disturbing and capturing shallow pockets of soil air that would not otherwise be measured at very low flux rates.
Overall, this system appears to be an improvement over previous attempts to absolutely calibrate measures of soil CO2 flux. However, it is a large, expensive, and complicated system.
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