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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A Field Book on Measuring Ecosystem Gas Exchange and Areal Emission Rates. , (2013).</li><li>Pan, Y., 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=A+Large+and+Persistent+Carbon+Sink+in+the+World&#8217;s+Forests.">A Large and Persistent Carbon Sink in the World&#8217;s Forests.</a> Science. 333, 988-993 (2011).</li><li>Wofsy, S. C., 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=Net+exchange+of+CO2+in+a+midlatitude+forest.">Net exchange of CO2 in a midlatitude forest.</a> Science. 260 (5112), 1314-1317 (1993).</li><li>Luyssaert, S., 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=CO2+balance+of+boreal,+temperate,+and+tropical+forests+derived+from+a+global+database.">CO2 balance of boreal, temperate, and tropical forests derived from a global database.</a> Global Change Biology. 13, 2509-2537 (2007).</li><li>Knohl, A., 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=Carbon+dioxide+exchange+of+a+Russian+boreal+forest+after+disturbance+by+wind+throw.">Carbon dioxide exchange of a Russian boreal forest after disturbance by wind throw.</a> Global Change Biology. 8, 231-246 (2002).</li><li>Lindauer, M., 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=Net+ecosystem+exchange+over+a+non-cleared+wind-throw-disturbed+upland+spruce+forest-Measurements+and+simulations.">Net ecosystem exchange over a non-cleared wind-throw-disturbed upland spruce forest-Measurements and simulations.</a> Agricultural and Forest Meteorology. 197, 219-234 (2014).</li><li>Schulze, E. 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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. S., Chen, B., Nesic, Z. <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+of+the+carbon+balance+of+three+different-aged+Douglas-fir+stands+in+the+Pacific+Northwest.">Interannual variability of the carbon balance of three different-aged Douglas-fir stands in the Pacific Northwest.</a> Journal of Geophysical Research. 114, 1-18 (2009).</li><li>Reichstein, M., 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=On+the+separation+of+net+ecosystem+exchange+into+assimilation+and+ecosystem+respiration:+Review+and+improved+algorithm.">On the separation of net ecosystem exchange into assimilation and ecosystem respiration: Review and improved algorithm.</a> Global Change Biology. 11, 1424-1439 (2005).</li><li>Falge, E., 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=Gap+filling+strategies+for+defensible+annual+sums+of+net+ecosystem+exchange.">Gap filling strategies for defensible annual sums of net ecosystem exchange.</a> Agricultural and Forest Meteorology. 107, 43-69 (2001).</li><li>Ooba, M., Hirano, T., Mogami, J. I., Hirata, R., Fujinuma, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comparisons+of+gap-filling+methods+for+carbon+flux+dataset:+A+combination+of+a+genetic+algorithm+and+an+artificial+neural+network.">Comparisons of gap-filling methods for carbon flux dataset: A combination of a genetic algorithm and an artificial neural network.</a> Ecological Modelling. 198, 473-486 (2006).</li><li>Papale, D., Valentini, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+new+assessment+of+European+forests+carbon+exchanges+by+eddy+fluxes+and+artificial+neural+network+spatialization.">A new assessment of European forests carbon exchanges by eddy fluxes and artificial neural network spatialization.</a> Global Change Biology. 9, 525-535 (2003).</li><li>Baldocchi, D. D., Vogel, C. 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 ...

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