Name: measurements of co2 fluxes at non-ideal eddy covariance sites
Uploaded: 2019-06-24T14:00:00
Description: Watch this Scientific Journal Video about Measurements of CO2 Fluxes at Non-Ideal Eddy Covariance Sites at JoVE.com

This research was supported by funding from General Directorate of the State Forests, Warsaw, Poland (project LAS, No OR-2717/27/11). We would like to express our gratitude to the entire research group from the Department of Meteorology, Poznan University of Life Sciences, Poland, involved in this protocol implementation and their help during creating its visual version.

1. Site location and instrumentation setup
<ol>
	<li>Choose a measuring site location in relatively homogeneous and flat terrain to meet basic requirements of the EC method. Avoid places with complicated landforms (depressions, slopes) or located near aerodynamic obstacles (e.g., surviving tree stands), which can distort the air flow.
	<ol>
		<li>Check species composition and plant cover. Choose a place with the most similar characteristics: age and height of the main vegetation type.</li>
		<li>If possible, conduct so...

<ol>
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P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+three-dimensional+backward+Lagrangian+footprint+model+for+a+wide+range+of+boundary-layer+stratifications.">A three-dimensional backward Lagrangian footprint model for a wide range of boundary-layer stratifications.</a> Boundary Layer Meteorology. 103, 205-226 (2002).</li><li>Foken, T., Wichura, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tools+for+quality+assessment+of+surface-based+flux+measurements.">Tools for quality assessment of surface-based flux measurements.</a> Agricultural and Forest Meteorology. 78, 83-105 (1996).</li><li>Mauder, M., Foken, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Impact+of+post-field+data+processing+on+eddy+covariance+flux+estimates+and+energy+balance+closure.">Impact of post-field data processing on eddy covariance flux estimates and energy balance closure.</a> Meteorologische Zeitschrift. 15, 597-609 (2006).</li><li>Gu, L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Objective+threshold+determination+for+nighttime+eddy+flux+filtering.">Objective threshold determination for nighttime eddy flux filtering.</a> Agricultural and Forest Meteorology. 128 (3-4), 179-197 (2005).</li><li>Papale, D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Towards+a+standardized+processing+of+Net+Ecosystem+Exchange+measured+with+eddy+covariance+technique:+algorithms+and+uncertainty+estimation.">Towards a standardized processing of Net Ecosystem Exchange measured with eddy covariance technique: algorithms and uncertainty estimation.</a> Biogeosciences. 3 (4), 571-583 (2006).</li><li>Barr, A. G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Interannual+variability+in+the+leaf+area+index+of+a+boreal+aspen-hazelnut+forest+in+relation+to+net+ecosystem+production.">Interannual variability in the leaf area index of a boreal aspen-hazelnut forest in relation to net ecosystem production.</a> Agricultural and Forest Meteorology. 126, 237-255 (2004).</li><li>Krishnan, P., Black, T. A., Jassal, R. 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A., Hall, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Seasonal+variation+of+carbon+dioxide+exchange+rates+above+and+below+a+boreal+jack+pine+forest.">Seasonal variation of carbon dioxide exchange rates above and below a boreal jack pine forest.</a> Agricultural and Forest Meteorology. 83, 147-170 (1997).</li><li>Lloyd, J., Taylor, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=On+the+Temperature+Dependence+of+Soil+Respiration.">On the Temperature Dependence of Soil Respiration.</a> Functional Ecology. 8, 315-323 (1994).</li><li>Lasslop, G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Separation+of+net+ecosystem+exchange+into+assimilation+and+respiration+using+a+light+response+curve+approach:+critical+issues+and+global+evaluation.">Separation of net ecosystem exchange into assimilation and respiration using a light response curve approach: critical issues and global evaluation.</a> Global Change Biology. 16, 187-208 (2010).</li><li>Kljun, N., Calanca, P., Rotach, M. 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This protocol presents the eddy covariance (EC) method to be used at non-ideal sites (here a reforested windthrow site): site location and measuring infrastructure setup, net CO2 fluxes computation and post-processing, as well as some issues regarding gap filling and fluxes partitioning procedures.
Even though the EC technique is commonly used at many measuring sites around the world, most of them are non-disturbed ecosystems, where the design and the following data processing can b...

Nowadays, the most commonly used technique in the atmosphere-land ecosystem carbon dioxide (CO2) exchange studies is the eddy covariance (EC) technique1. The EC method has been used for decades, and comprehensive descriptions of issues concerning all the methodological, technical and practical aspects have already been published2,3,4. Compared with other techniques used for similar purposes, the EC method allows for obtaining the spatially and temporally averaged net CO2 fluxes from automatic, point measurements that consider the contribution of all elements in complicated ecosystems, instead of laborious, manual measurements (e.g., chamber techniques) or the requirement of taking many samples1.
Among land ecosystems, forests play the most significant role in C cycling and many scientific activities have focused on investigating their CO2 cycle, carbon storage in woody biomass and their mutual relationships with changing climatic conditions by both direct measurement or modeling5. Many EC sites, including one of the longest flux records6, were set up above different types of forests7. Usually, the site location was carefully chosen before the measurements started, with the goal of the most homogenous and largest area possible. Although, in disturbed forest sites, such as windthrows, the number of EC measuring stations are still insufficient8,9,10. One reason is logistical difficulties in measuring site setup and, most of all, a small number of suddenly appearing locations. In order to obtain the most informative results at windthrow areas, it is crucial to start as soon as possible after such an incidental event, which may cause additional problems. In contrast to untouched forest sites, the EC measurements at windthrow sites are more challenging and can deviate from already established procedures3. Since some extreme wind phenomena create spatially limited areas, there is a need for a thoughtful measuring station location and careful data processing in order to derive as much reliable flux values as possible. Similar difficulties in EC method application have occurred (e.g., Finish studies performed above a long but narrow lake) where measured CO2 fluxes required rigorous data filtering11,12 in order to assure their spatial representativeness.
Hence, the presented protocol is an example of the use of the EC method at non-typical locations, designed not only for windthrow areas, but for all other types of short vegetation with the limited area (e.g., croplands situated between taller vegetation types). The biggest advantage of the proposed methodology is a general description of complicated procedures, requiring advanced knowledge, from the site location choice and instrumentation set up to the final outcome: a complete dataset of high-quality CO2 fluxes. The technical novelty of the measuring protocol is the use of a unique base construction for the EC system placement (e.g., tripod with a defined height that is a &#8220;mini- tower&#8221; with an adjustable, electrically operated mast, allowing changing the final height of sensors according to individual needs).

<table>
	<tbody>
		<tr>
			<td>Adjustable mast with metal rails and electric engine (24 V)</td>
			<td>maszty.net</td>
			<td>-</td>
			<td>Alternative basic construction. To be designed and made by professionals</td>
		</tr>
		<tr>
			<td>EddyPro</td>
			<td>LI-COR, Inc.</td>
			<td>ver. 6.2.0.</td>
			<td>Free commercial software for fluxes calculation. Available on a website: https://www.licor.com/env/products/eddy_covariance/software.html, on request</td>
		</tr>
		<tr>
			<td>Enclosed-path infrared gas analyzer</td>
			<td>LI-COR, Inc.</td>
			<td>LI-7200</td>
			<td>One of two instruments of the eddy covariance system (EC) used for CO2 fluxes measurements. Other types of fast analyzers (&#62;10Hz sampling frequency) can be used</td>
		</tr>
		<tr>
			<td>REddyProc</td>
			<td>-</td>
			<td>-</td>
			<td>Free software for EC fluxes gap filling and partitioning. Available on Max Planck Institute for Biogeochmistry: https://www.bgc-jena.mpg.de/bgi/index.php/Services/REddyProcWeb. Both online tool and R package are provided.</td>
		</tr>
		<tr>
			<td>Short aluminum tower base with concrete foundation</td>
			<td>maszty.net</td>
			<td>-</td>
			<td>Alternative basic construction (pioneering solution). To be designed and made by professionals</td>
		</tr>
		<tr>
			<td>Sonic anemometer</td>
			<td>Gill Instruments</td>
			<td>Gill Windmaster</td>
			<td>One of two instruments of the eddy covariance system (EC) used for wind speed measurements. Other types of three-dimensional sonic anemometers can be used</td>
		</tr>
		<tr>
			<td>Stainless-steel tripod</td>
			<td>Campbel Scientific, Inc.</td>
			<td>CM110 10 ft</td>
			<td>The basic construction for eddy covariance (EC) system. Can be constructed by yourself- materials to be found in a hardware store</td>
		</tr>
		<tr>
			<td>Sunshine sensor</td>
			<td>Delta-T Devices Ltd.</td>
			<td>BF5</td>
			<td>One of the exemplary instruments for photosynthetic photon flux density measurements (PPFD). To be bought from several commercial companies. Remember to place it above the canopy, far from reflective surfaces.</td>
		</tr>
		<tr>
			<td>Thermistors</td>
			<td>Campbel Scientific, Inc.</td>
			<td>T107</td>
			<td>One of the exemplary instruments for soil temperature measurements. To be bought from several commercial companies. It is advisable to have a profile of soil temperature</td>
		</tr>
		<tr>
			<td>Thermohygrometer</td>
			<td>Vaisala Oyj</td>
			<td>HMP155</td>
			<td>One of the exemplary instruments for air temperature and humidity measurements. To be bought from several commercial companies. Remember to place it inside radiation shield at similar height as the EC system.</td>
		</tr>
	</tbody>
</table>

measurements of co2 fluxes at non-ideal eddy covariance sites

This protocol is an example of utilizing the eddy covariance (EC) technique to investigate spatially and temporally averaged net CO2 fluxes (net ecosystem production, NEP), in non-typical ecosystems, on a currently reforested windthrow area in Poland. After a tornado event, a relatively narrow &#8220;corridor&#8221; was created within surviving forest stands, which complicates such kind of experiments. The application of other measuring techniques, such as the chamber method, is even more difficult under these circumstances, because especially at the beginning, fallen trees and in general great heterogeneity of the site provide a challenging platform to perform flux measurements and then to properly upscale obtained results. In comparison with standard EC measurements carried out in untouched forests, the case of windthrow areas requires special consideration when it comes to the site location and data analysis in order to ensure their representativeness. Therefore, here we present a protocol of real-time, continuous CO2 flux measurements at a dynamically changing, non-ideal EC site, which includes (1) site location and instrumentation setup, (2) flux computation, (3) rigorous data filtering and quality control, and (4) gap filling and net fluxes partitioning into CO2 respiration and absorption. The main advantage of the described methodology is that it provides a detailed description of the experimental setup and measurement performance from scratch, which can be applied to other spatially limited ecosystems. It can also be viewed as a list of recommendations on how to deal with unconventional site operation, providing a description for non-specialists. Obtained quality-checked, gap filled, half-hour values of net CO2, as well as absorption and respiration fluxes, can be finally aggregated into daily, monthly, seasonal or annual totals.

One of the crucial steps in flux filtering and quality control at non-ideal EC sites is the assessment of the measured fluxes&#8217; spatial representativeness. The simplest way to perform such analysis, given the fact that calculations were done using commercial, widely applied software, is to include measurements from desired area only, on the basis of wind direction and footprint estimations (see section 3.7). Thus, the wind rose plot, with a chosen wind direction and maximal acceptabl...

Watch this Scientific Journal Video about Measurements of CO2 Fluxes at Non-Ideal Eddy Covariance Sites at JoVE.com

Measurements of CO2 Fluxes at Non-Ideal Eddy Covariance Sites

The presented protocol uses the eddy covariance method at non-typical locations, applicable to all types of short-canopy ecosystems with limited area, on a currently reforested windthrow site in Poland. Details of measuring site setup rules, flux calculations and quality control, and final result analysis, are described.

Measurements of CO2 Fluxes at Non-Ideal Eddy Covariance Sites

This protocol is an example of utilizing the eddy covariance (EC) technique to investigate spatially and temporally averaged net CO2 fluxes (net ecosystem ...

The protocol is a step-by-step description of the eddy covariance site setup and measurements performance from the scratch, which can be successfully applied in spatially limited ecosystems. We believe the protocol make it easier to realize that, however, strict requirements need to be met. The covariance technique can be satisfactorily applied also in not non-ideal locations.Once it is presented in a visual form, the protocol can be used as a first and relatively easy choice for non-specialists forced or willing to use the eddy covariance technique. To begin, on a height map, choose a measuring site location in relatively homogeneous and flat terrain to meet the basic requirements of the EC method. Select a location with no obstacles and ensure that the area to be investigated extends in each direction at least 100 times the height of the sensor to be placed.At the site, use an anemometer to investigate prevailing wind directions for one year or analyze data from the nearest meteorological station. Decide which EC system to use. Open the path infrared gas analyzer with lower power consumption or a closed path analyzer with a short intake tube if there are no limitations to power supply or if in harsh environments.At the site, place a tripod with a vertical pole to mount the EC system on top. Position the infrared gas analyzer and the 3D sonic anemometer close to each other. Place the sonic anemometer at a perfectly vertical position.Tilt the gas analyzer slightly to allow rainwater to run off easily. Elevate the instruments to a height twice the canopy height from the soil surface and at least one and a half to two meters above the top of the canopy. Avoid mounting any unnecessary elements close to the EC system, which can distort the airflow.For further computation and flux analysis, measure some auxiliary variables at the same time, including at least air and soil temperature, relative humidity of the air, photosynthetic photon flux density, incoming solar radiation, and precipitation. To compute carbon dioxide flux, use commercially available free software EddyPro that includes correction applications for EC flux computation. First, create a new project and then in the project info tab specify the raw data file format and choose a metadata file.Go to the flux info tab, choose the dataset and output directories, specify the raw file name format, and check the list of items for flux computation. Then, go to the processing options tab and choose raw data processing settings. Choose the rotation method for correction of the anemometer's measurements, which allows accounting for any misalignment of the sonic anemometer with respect to the local wind streamline.Tick the first planar fit approach for non-deal heterogeneous locations. Choose the 012 type of flagging policy. Select the preferred footprint method for the area of the influence on measured fluxes.Leave all other settings unchanged. Click run in advanced mode to start flux computations at the end. Create a spreadsheet that contains the results from the flux calculation software and auxiliary measurements.Use filtering tools in the spreadsheet to filter out carbon dioxide fluxes measured during unfavorable weather conditions and instrument malfunctions. For an enclosed path analyzer, check the average signal strength value. Then, mark and discard all fluxes measured with ASS lower than the 60%threshold suggested in the instrument's manual.Discard the fluxes measured during any rain events with P greater than or equal to 0.1 millimeters. To account for inappropriate conditions for eddy covariance method application, discard the flux data with poor quality having carbon dioxide flagged values greater than one in the common results file. Use the nighttime period indicator, daytime equaling zero, given in the output file to filter out the carbon dioxide flux values measured at night.Plot the nighttime carbon dioxide fluxes against the corresponding friction velocity values and find the U-star value at which these fluxes stopped increasing. Mark the obtained value as the friction velocity threshold to be used as a measure of insufficient turbulence conditions. Discard from the dataset all carbon dioxide fluxes having a U-star value less than the threshold, indicating insufficient turbulence.Now, plot the wind rose on the map of investigated area for flux spatial representativeness constraints. According to the estimation of the cross-wind integrated footprints, choose 70%as the probability for spatially limited sites to be used for further analysis. Next, orient a map and a wind rose the same way and using north direction as an indicator, check if any direction at the area of interest has obstacles, for example, other kinds of ecosystems, and mark them as not representative.Choose the wind direction sectors and the footprint values that are most representative of the measuring site, check the dimension, and specify the maximum length. Filter out flux values that do not meet both requirements. To perform gap filling for carbon dioxide data, choose the method for quality checked carbon dioxide flux gap filling and partitioning into absorption and respiration from three basic groups:process-based approach, statistical methods, and the use of neural networks.The weakest point of the protocol is the gap filling and flux partitioning description since suggested methods were individually developed by other specialists and only implemented here as proposed techniques. An example of the process-based approach is from the FLUXNET Canada Research Network. To fill the gaps, not only in the carbon dioxide but also other EasyFlux values, such as sensible and latent heat, as well as in the important meteorological elements, use the REddyProc online tool, which is also available as an R software package.Next, in, for example, R software, calculate daily, monthly, and annual totals of all gap-filled carbon dioxide fluxes, including net ecosystem production, gross ecosystem production, and ecosystem respiration. The wind rose plot on the background of the TLEN 1 site area shows the blue-shaded polygons for the chosen wind direction and the red-shaded polygons within them as sectors of a circle with a radius of 200 meters, representing maximal acceptable extent of flux footprints. This figure shows the results of a filtering procedure on the example of one year of net ecosystem production fluxes measurements from the TLEN 1 wind throw site.The smallest number of data points was discarded due to unfavorable weather conditions and instrument malfunctions. While the last part of the quality assurance protocol, considering flux spatial representativeness constraints, yielded a final data coverage of only 1/3 of all raw net ecosystem production fluxes measured by EC.The relationship between net ecosystem production fluxes, gap filled for the process-based method, and a statistical approach shows a simple linear regression, suggesting that in general, both techniques are comparable and thus can be used for net ecosystem production fluxes gap filling. By using the two methods, daily ecosystem respiration flux totals were also obtained from the partitioning procedure.It has to be remembered that one of the crucial steps in data filtering and quality control at non-ideal sites is the assessment of measured fluxes'spatial representativeness.

Research

JoVE Journal

Environment

Multimodal Optical Microscopy Methods Reveal Polyp Tissue Morphology and Structure in Caribbean Reef Building Corals

An integrated suite of imaging techniques has been applied to determine the three-dimensional (3D) morphology and cellular structure of polyp tissues ...

Measuring Fluxes of Mineral Nutrients and Toxicants in Plants with Radioactive Tracers

Unidirectional influx and efflux of nutrients and toxicants, and their resultant net fluxes, are central to the nutrition and toxicology of plants. ...

Physical, Chemical and Biological Characterization of Six Biochars Produced for the Remediation of Contaminated Sites

The physical and chemical properties of biochar vary based on feedstock sources and production conditions, making it possible to engineer biochars with ...

A CO2 Concentration Gradient Facility for Testing CO2 Enrichment and Soil Effects on Grassland Ecosystem Function

A CO2 Concentration Gradient Facility for Testing CO2 Enrichment and Soil Effects on Grassland Ecosystem Function

Continuing increases in atmospheric carbon dioxide concentrations (CA) mandate techniques for examining impacts on terrestrial ecosystems. Most ...

Measuring Carbon-based Contaminant Mineralization Using Combined CO2 Flux and Radiocarbon Analyses

Measuring Carbon-based Contaminant Mineralization Using Combined CO2 Flux and Radiocarbon Analyses

A method is described which uses the absence of radiocarbon in industrial chemicals and fuels made from petroleum feedstocks which frequently contaminate ...

Calibrated Passive Sampling - Multi-plot Field Measurements of NH3 Emissions with a Combination of Dynamic Tube Method and Passive Samplers

Calibrated Passive Sampling - Multi-plot Field Measurements of NH3 Emissions with a Combination of Dynamic Tube Method and Passive Samplers

Agricultural ammonia (NH3) emissions (90% of total EU emissions) are responsible for about 45% airborne eutrophication, 31% soil acidification and 12% ...

Measurement of the Rheology of Crude Oil in Equilibrium with CO2 at Reservoir Conditions

Measurement of the Rheology of Crude Oil in Equilibrium with CO2 at Reservoir Conditions

A rheometer system to measure the rheology of crude oil in equilibrium with carbon dioxide (CO2) at high temperatures and pressures is described. The ...

Adherence of Bacteria to Plant Surfaces Measured in the Laboratory

This manuscript describes a method to measure bacterial binding to axenic plant surfaces in the light microscope and through the use of viable cell ...

Assessment of Methane and Nitrous Oxide Fluxes from Paddy Field by Means of Static Closed Chambers Maintaining Plants Within Headspace

This protocol describes the measurement of greenhouse gas (GHG) emissions from paddy soils using the static closed chamber technique. This method is based ...

High-throughput, Microscale Protocol for the Analysis of Processing Parameters and Nutritional Qualities in Maize (Zea mays L.)

High-throughput, Microscale Protocol for the Analysis of Processing Parameters and Nutritional Qualities in Maize Zea mays L.

Maize is an important grain crop in the United States and worldwide. However, maize grain must be processed prior to human consumption. Furthermore, whole ...