Name: the calibration and use of capacitance sensors to monitor stem water content in trees
Uploaded: 2017-12-27T15:00:00
Description: Watch this Scientific Journal Video about The Calibration and Use of Capacitance Sensors to Monitor Stem Water Content in Trees at JoVE.com

Funding for this study was provided by U.S. Department of Energy&#39;s Office of Science, Office of Biological and Environmental Research, Terrestrial Ecosystem Sciences Program Award No. DE-SC0007041, Ameriflux Management program under Flux Core Site Agreement No. 7096915 through Lawrence Berkeley National Laboratory, and the National Science Foundation Hydrological Science grant 1521238. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the funding agencies.

1. Select a Tree for Instrumentation
<ol>
	<li>Select trees for measurement. Ideally, select trees that are healthy with a generally round stem cross-section, and a diameter between 1-2 times the tine length, or a sapwood depth greater than the length of the sensor tines (~5 cm for the specific capacitance sensors demonstrated here). Measure the depth of the sapwood using tree cores, or for many species, calculate sapwood depth through allometric equations relating sapwood area to stem diameter 29</su...

Seasonal and diurnal patterns in stem water content observed via capacitance sensors align with trends in concurrent sap flux and environmental forcing measurements (Figure 3, Figure 4, Figure 5). Reservoirs of stem water storage are depleted diurnally when the pace of transpiration surpasses the rate of recharge through woody tissues, and seasonally when soil moisture limits root-water availability...

Water stored in plant material plays an integral role in plants&#39; ability to cope with short- and long-term water stress1,2. Plants store water in roots, stems, and leaves in both intracellular and extracellular (e.g., xylem vessels) spaces 2,3,4. This water has been shown to contribute between 10 and 50% of diurnally transpired water2,5,6,7,8. As such, plant hydraulic capacitance is a key component of the terrestrial water balance, can be used as an indicator of water stress, drought response, and recovery1, and is a critical factor necessary to correct for observed time lags between transpiration and sap flow9,10,11. Real-time monitoring of vegetation water content can also be used in agricultural applications to help constrain orchard and crop irrigation in order to increase watering efficiency12,13. However, measurements of continuous, in-situ stem-water content of woody species7,14,15,16,17,18,19 are rare relative to sap flux measurements20. Here, we outline a procedure for the calibration of capacitance sensors to monitor the volumetric water content within the stems of trees5,21.
Hydrodynamic behaviors and water-use regulation by vegetation are an integral component of the soil-plant-atmosphere continuum22,23 and are therefore important controls for the water and carbon fluxes between the biosphere and atmosphere24,25. The dynamics of stem water content are influenced by both biotic and abiotic factors. Depletion and recharge of stem-stored water are affected by short- and long-term trends in environmental conditions, in particular, vapor pressure deficit and soil water content1,26. The physical properties of the wood27 (e.g., density, vessel structure) and the emergent hydraulic strategy25 (e.g., iso- or anisohydric stomatal regulation) determine a plant&#39;s ability to store and use water19,26,28, and can vary widely by species29,30. Previous studies have demonstrated different roles of capacitance in tropical16,27,31,32,33 and temperate5,7,21 species, and in both angiosperms1,2,34 and gymnosperms6,11,17,19.
Improved knowledge of biomass water content will improve understanding of vegetation strategies for water acquisition and use1,2, along with species&#39; vulnerability to predicted changes in precipitation regimes35,36. Further understanding of plant water use strategies will help predict shifting demographic patterns under future climate scenarios37,38. Through model-data fusion techniques39, stem water content data obtained using this methodology can be used to inform and test scalable, plant-level hydrodynamics models40,41,42,43,44 in order to improve calculations of stomatal conductance and, thereby, simulations of both transpiration and photosynthetic carbon uptake. These advanced hydrodynamic models may provide a significant reduction in uncertainty and error when incorporated into larger land-surface and Earth systems models25,45,46,47,48.
Methods used to monitor or calculate stem water content include tree coring33,49, electronic dendrometers2,15,50, electrical resistance51, gamma radiation attenuation52, deuterium tracers19, networks of sap flux sensors32,33,53, stem psychrometers49, and amplitude11 and time4,12,13 domain reflectometry (TDR). Recent efforts have tested the viability of capacitance sensors that have traditionally been used to measure soil volumetric water content5,18,21,27. Frequency domain reflectometry (FRD)-style capacitance sensors are low cost and use relatively small amounts of energy for continuous measurements, making them an attractive tool for high temporal resolution measurements in field scenarios. The ease of automation of FDR over TDR-style sensors facilitates the collection of continuous sun-hourly data sets, and eliminates many of the challenges inherent in TDR measurements requiring substantial cable lengths13. The use of in-situ capacitance sensors eliminates the need for repetitive coring or branch harvesting, and may provide enhanced accuracy for hardwood species. Woody species that withdraw water principally from extracellular spaces, such as xylem vessels, or have high wood or bark moduli of elasticity, are generally not good candidates for popular dendrometer measurement techniques due to low elastic stem expansion2. Capacitance sensors estimate dielectric permittivity, which can be directly converted to volumetric water content. However, capacitance measurements are sensitive to the density of the media surrounding the sensor. Therefore, we advocate for species-specific calibrations that convert the output of the sensors to volumetric wood-water content5,21.
We present a protocol for a species-specific calibration to convert capacitance sensor output to volumetric water content of wood. Also provided are instructions for field installation of capacitance sensors in mature trees and a discussion of the method&#39;s strengths, weaknesses, and assumptions. These techniques are designed to monitor volumetric water content in the trunk, the largest tree water storage reservoir8, but can be easily expanded to the whole tree with installation of additional sensors along the branches. Measurements of dynamic plant water content will advance the fields of vegetation hydrodynamics, biometeorology, and land-surface modeling.

<table>
	<tbody>
		<tr>
			<td>Ruggedized Soil Moisture Sensor</td>
			<td>METER Group Inc.</td>
			<td>GS-3</td>
			<td>Capacitance sensors</td>
		</tr>
		<tr>
			<td>1/8&#34; drill bit</td>
			<td>Any</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>9/64&#34; drill bit</td>
			<td>Any</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>Drying oven</td>
			<td>Any</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>Chainsaw</td>
			<td>Any</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>Electric drill</td>
			<td>Any</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>Bucket for water bath</td>
			<td>Any</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>Alcohol swabs</td>
			<td>Any</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>Draw knife</td>
			<td>Any</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>Data logger</td>
			<td>Any</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>Silicon sealant</td>
			<td>Any</td>
			<td>N/A</td>
			<td></td>
		</tr>
	</tbody>
</table>

the calibration and use of capacitance sensors to monitor stem water content in trees

Water transport and storage through the soil-plant-atmosphere continuum is critical to the terrestrial water cycle, and has become a major research focus area. Biomass capacitance plays an integral role in the avoidance of hydraulic impairment to transpiration. However, high temporal resolution measurements of dynamic changes in the hydraulic capacitance of large trees are rare. Here, we present procedures for the calibration and use of capacitance sensors, typically used to monitor soil water content, to measure the volumetric water content in trees in the field. Frequency domain reflectometry-style observations are sensitive to the density of the media being studied. Therefore, it is necessary to perform species-specific calibrations to convert from the sensor-reported values of dielectric permittivity to volumetric water content. Calibration is performed on a harvested branch or stem cut into segments that are dried or re-hydrated to produce a full range of water contents used to generate a best-fit regression with sensor observations. Sensors are inserted into calibration segments or installed in trees after pre-drilling holes to a tolerance fit using a fabricated template to ensure proper drill alignment. Special care is taken to ensure that sensor tines make good contact with the surrounding media, while allowing them to be inserted without excessive force. Volumetric water content dynamics observed via the presented methodology align with sap flow measurements recorded using thermal dissipation techniques and environmental forcing data. Biomass water content data can be used to observe the onset of water stress, drought response and recovery, and has the potential to be applied to the calibration and evaluation of new plant-level hydrodynamics models, as well as to the partitioning of remotely sensed moisture products into above- and belowground components.

In this section, we present calibration data for five common eastern forest tree species, followed by a detailed analysis of field measurements of stem-water storage in three Acer rubrum individuals during the 2016 growing season. Calibration curves were generated for Acer rubrum, Betula papyrifera, Pinus strobus, Populus grandidentata, and Quercus rubra (Figure 1). Slopes of the curves differed by as much as 97.7% for P. grandi...

Watch this Scientific Journal Video about The Calibration and Use of Capacitance Sensors to Monitor Stem Water Content in Trees at JoVE.com

The Calibration and Use of Capacitance Sensors to Monitor Stem Water Content in Trees

The hydraulic capacitance of biomass is a key component of the vegetation water budget, which serves as a buffer against short and long-term drought stresses. Here, we present a protocol for the calibration and use of soil moisture capacitance sensors to monitor water content in the stems of large trees.

Water transport and storage through the soil-plant-atmosphere continuum is critical to the terrestrial water cycle, and has become a major research focus ...

The overall goal of this methodology is to continuously monitor the volumetric water content in the stems of mature living trees. This method can help answer key questions in the field of ecohydrology, such as how vegetation responds to moisture limitation, including when water stress begins and how quickly drought recovery occurs. The main advantage of this technique is that it allows for automated measurements of biomass water content and C2 at subhourly timesteps.The implications of this technique extend toward remote sensing because measurements of above-ground water content are necessary for the partitioning of remotely-sensed data products and to above-and below-ground components. Though this method can provide insight into drought response it can also be extended to other phenomena, such as monitoring fuel water content for forest fire ignition prediction. This is my undergraduate Rio Mursinna, who will help us with selecting a branch and harvesting branch segments.This is Kelly Malone, an undergraduate research assistant in my lab. After selecting a tree for instrumentation as described in the text protocol, proceed with collecting about four meters or more of wood from the trunk or a branch that is at least six centimeters in diameter. Larger diameters are better.Next remove any attached branches, leaves, lichen, or any other loose material. Then slice the sample into cylindrical sections that are about 15 centimeters long. Make at least 25 such sections.Then label each segment and record each segment's average diameter and length. Also record each segment's volume, assuming a cylindrical shape. Set aside a segment from the center and from the end for the baseline analysis.Then place one-third of the remaining segments in a water bath to rehydrate, and put the other two-thirds in a drying oven set to 60 degrees Celsius to dry. To begin, connect a capacitance sensor to a data-logging device and to a computer for real-time sensor readout visualization. Set it to collect data on 30-second intervals.Begin with analyzing the segments saved for the baseline analysis. Begin with drilling two new sets of holes for the sensor in each segment. Make the hole diameter slightly smaller than the tines.Place the hole sets about two centimeters apart vertically and 150 degrees apart radially. Next, weigh the segments to the nearest hundredth of a gram. Then seal the ends of the segments with plastic wrap so they do not dry out.Now clean the tines of the capacitance sensor with alcohol and insert them into one set of drilled holes such that the tines are completely buried in the wood. Next, wait a few minutes for readings to stabilize. Then collect 10 measurements over five minutes.Use the average value for future analyses. Now, gently remove the sensor and clean the tines with alcohol. When the output readings return to zero, take 10 measurements from the second set of holes.After taking measurements, remove the plastic and place the segments in the oven. During the first two days of drying, there is a lot of moisture loss, so take measurements twice a day. Later, take measurements just once per day.During each measurement session, only drill and analyze one or two segments. For the rehydrating segments, measure them once daily until each has been measured. Always dry them off before taking measurements.Once these segments have been fully rehydrated, transfer them to the oven to desiccate. To begin, select a location for the sensor installation on the tree of interest and record the stem diameter at that location. The standard pairing of sensor locations it to place one about a half meter above the ground into the trunk, and place the second just below the first major branching split.At the selected locations, use a draw blade to remove the bar to expose the cambium to create a flat surface where the sensor will be installed. The sensor must sit flush against the surface with no parts of the tines exposed, and the measurements must only come from the water content in the xylem, excluding the water content of the bark or phloem. Drilling appropriately-sized holes at the correct alignment and the correct depth is essential for the functionality of this method.If the sensor meets with too much resistance, carefully back the sensor out and widen the holes. Next drill the holes for the tines. In soft wood, use a drill bit slightly smaller than the diameter of the tines, whereas in hard wood, use a bit closer to the true size of the tines.Prior to installing a sensor, clean it with alcohol. When attempting to insert it, if there is too much resistance, use the drill to widen the holes slightly. Ultimately, all three tines should be fully inserted with the body of the sensor flush against the tree trunk.Use a silicone-based sealant to seal the sensor to the tree and prevent infestation. Then cover the sensor with reflective insulation to avoid external heating, and connect all of the sensors to a power source and to a compatible data logger. Using the laboratory-based technique with stem segments, calibrations were performed for five common Eastern forest tree species, representing a variety of wood densities and xylem structures.Calibration curves different by as much as 97.7%for populus grandidentata and acer rubrum, demonstrating to the need to perform species-specific calibration to obtain accurate VWC measurements. To evaluate the observed diurnal dynamics, the rate of change in total water content was compared to sap flux data, collected simultaneously in the same tree using Granier-style thermal dissipation sensors. Next, three acer rubrum trees were studied in the field.While total stem water storage is dependent on the volume of the trunk, all three individuals exhibited patterns of recharge and replenishment, consistent with seasonal trends and sap flux and available moisture in the top meter of soil. Stem-stored water, sap flux, and soil moisture were all at their lowest during the end-of-summer extended interstorm period. From this data, the drought recovery time for acer rubrum is estimated at 10 days.After watching this video, you should have a good understanding of how to calibrate, install, and operate a capacitance sensor to monitor water content in a living biomass. Following this procedure, additional sensors could be added along the branching structure to perform a whole-tree water balance. After its development, this technique paved the way for researchers in ecohydrology and land-surface modeling to evaluate model performance on the basis of ecosystem water storage and energy flux.

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Unraveling the Unseen Players in the Ocean - A Field Guide to Water Chemistry and Marine Microbiology

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Here, we present a comprehensive protocol to assess the organic and inorganic nutrient availability and the abundance and structure of microbial and viral communities in remote marine environments.

Here we introduce a series of thoroughly tested and well standardized research protocols adapted for use in remote marine environments. The sampling ...

Use of Chironomidae (Diptera) Surface-Floating Pupal Exuviae as a Rapid Bioassessment Protocol for Water Bodies

Rapid bioassessment protocols using benthic macroinvertebrate assemblages have been successfully used to assess human impacts on water quality. Unfortunately, traditional benthic larval sampling methods, such as the dip-net, can be time-consuming and expensive. An alternative protocol involves collection of Chironomidae surface-floating pupal exuviae (SFPE). Chironomidae is a species-rich family of flies (Diptera) whose immature stages typically occur in aquatic habitats. Adult chironomids emerge from the water, leaving their pupal skins, or exuviae, floating on the water&#8217;s surface. Exuviae often accumulate along banks or behind obstructions by action of the wind or water current, where they can be collected to assess chironomid diversity and richness. Chironomids can be used as important biological indicators, since some species are more tolerant to pollution than others. Therefore, the relative abundance and species composition of collected SFPE reflect changes in water quality. Here, methods associated with field collection, laboratory processing, slide mounting, and identification of chironomid SFPE are described in detail. Advantages of the SFPE method include minimal disturbance at a sampling area, efficient and economical sample collection and laboratory processing, ease of identification, applicability in nearly all aquatic environments, and a potentially more sensitive measure of ecosystem stress. Limitations include the inability to determine larval microhabitat use and inability to identify pupal exuviae to species if they have not been associated with adult males.

Use of Chironomidae Diptera Surface-Floating Pupal Exuviae as a Rapid Bioassessment Protocol for Water Bodies

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The Use of an Automated System GreenFeed to Monitor Enteric Methane and Carbon Dioxide Emissions from Ruminant Animals

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We describe a protocol for filtration of water samples with a filter cartridge and extraction of environmental DNA (eDNA) without having to cut open the housing to remove the filter. This protocol is developed for metabarcoding eDNA from fishes, but is also applicable to eDNA from other organisms.

Recent studies demonstrated the use of environmental DNA (eDNA) from fishes to be appropriate as a non-invasive monitoring tool. Most of these studies ...

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Repeated soil sampling has recently been shown to be an effective way to monitor forest soil change over years and decades. To support its use, a protocol is presented that synthesizes the latest information on soil resampling methods to aid in the design and implementation of successful soil monitoring programs.

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Here, we describe a protocol for the application of a novel, slow-release ClO2 product that reduces spoilage and extends the shelf life of fresh fruit. The slow-release ClO2 product was added to standard commercial grape tomato packaging and tested against Escherichia coli and Alternaria alternata.

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This paper describes a method for building an adaptable, low-cost and transportable incubator for microbial testing of drinking water. Our design is based on widely available materials and can operate under a range of field conditions, while still offering the advantages of higher-end laboratory-based models.

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Communities of nonvascular cryptogams, such as mosses or lichens, are an important part of the Earth's biodiversity, contributing to the regulation of the ...

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Here, we present a protocol to force flowering in mandarin trees under phytotron conditions. Water stress, high illuminance and a simulated spring photoperiod allowed viable flowers to be obtained in a short period of time. This methodology allows researchers to have several flowering periods in 1 year.

Phytotron has been widely used to assess the effect of numerous parameters on the development of many species. However, less information is available on ...