Day Six: More research and compilation of blog

Today, I worked on doing a little more reading, and compiling the blog that you're reading right now!  I didn't complete any article summaries today, although I read 4 articles related to the topic that were cited in some of Chris Oishi's papers.  I also skimmed through his Ph.D dissertation, which was incredibly interesting by itself!  The blog compilation took a lot of time.  I also took the data from Thursday to today and put in Baseliner.  We don't have VPD or PAR measurements, so I didn't get any meaningful calibrations.  However, the sap flow measurements so far seem to indicate that there is a quantifiable amount of sap flowing, although it is not varying much between day and night, which indicates that to the tree, it is still winter!

I hope you enjoyed reading my blog!  I really enjoyed doing this project full-time during miniterm, and I really look forward to getting usable data when third trimester and spring starts!

Day Five: More Research

I'll cut right to the research that I did today.  I will attach the summaries.  I read a lot of articles today, but only deemed a few important enough to my project to necessitate a summary. Article reading is all I did today, other than monitoring the dogwood.  The phenology camera still has not come in.

A review of whole-plant water use studies in trees: Wullschleger Stan et al. 1998

The article described reviewed fifty two studies previously conducted on whole-plant water use, detailing the different techniques used in doing so.  The techniques vary from modern energy-balance and heat dissipation methods to older techniques such as weighing lysimeters, large-tree photometers, ventilated chambers, and radioisotopes.  The accuracy of water-use measurements between these techniques varies a great deal, and as such, the variation in trees studied ranged from 10 kg day^-1 to 1,180 kg day^-1, with the majority of measurements falling between 10-200 kg day^-1.  The merits and drawbacks of each category of technique was evaluated.  Weighing lysimeters are sensitive to small changes, but they are very expensive to maintain.  Large-tree photometers can often change the amount of water that the tree originally would have used.  Radioactive tracers like tritium are being phased out due to environmental and regulatory concerns.  Heat-pulse and heat-dissipation techniques are gaining widespread acceptance because of their relative inexpensiveness.  Drawbacks of the heat-pulse and heat-dissipation techniques include empirical calibration inaccuracies, and variation in flux through the depth of the sapwood, but many of these concerns are being addressed through new methods of applying the said techniques.  The article recommends the continued use of heat-pulse and heat-dissipation methods in the future to estimate whole-tree water use.

Physiological impacts: There are five main places the article elaborates on in terms of physiological impacts of measuring whole-tree water use.

Stomatal and boundary layer control of whole-tree water use:

Measuring whole-tree water use gives several benefits in evaluating the role of the stomata in controlling transpiration.  Having quantitative values allows scientists to make meaningful hypotheses about several factors.  In fact, Jarvis et al. (1986) elaborates by introducing a dimensionless decoupling coefficient (Ω) which measures the relative amount that the stomata affects the whole-tree transpiration rate.  The closer Ω is to zero, the more control the stomata has on the rate of transpiration of the whole tree.  Conversely, the closer Ω is to one, the less control the stomata has on the rate of transpiration.  For a tree with large leaves (Tectona grandis has a leaf size of 700 cm²), Ω approaches one and the stomata conductance is so high that it cannot influence the rate of transpiration in the tree.

Whole-tree estimates of hydraulic conductance:

Hydraulic conductance is the measure of water flow from the soil to the trunk via the roots of the tree.  With the advent of easily measurable whole-tree water use, hydraulic conductance is measurable simply by a conversion described by , where  is hydraulic conductance,  is an estimate of current transpiration, and  is the difference between maximum and current leaf water potential.  Estimating hydraulic conductance is important physiologically because it allows researchers to evaluate the benefits of certain designs of tree growth.  For example, scientists can assess the trade-offs between  and vulnerability to xylem cavitation – something that would be controlled through evolution.

Coordinated control of stomatal and hydraulic conductance:

Quantitative measurements of whole-tree water use can help scientists assess the correlation between stomatal and hydraulic conductance in trees.  There is substancial evidence that stomatal and hydralulic conductance are positively correlated – when  increases, stomatal conductance and leaf transpiration also sharply increase.  This shows that stomata respond quickly and sharply to changes in water transport efficiency.

Sapwood water storage:

In large trees such as oak, there is a considerable lag between changes in transpiration and changes in water flux at the base of the tree.  This lag shows that there is a significant storage of water inside the tree.  By measuring at both ends of the tree, it is possible to quantitatively determine the quantity of stored water inside the tree.  This measurement can help scientists measure the drought-resistance of certain trees. 

Granier’s Thermal Dissipation Probe (TDP) Method for Measuring Sap Flow in Trees: Theory and Practice: Ping Lu, Laurent Urban, Ping Zhao, et al.

This article thoroughly reviews the thermal dissipation method first described in Granier 1987.  This method is one of the most popular ones to determine whole-tree water use in modern day.  This is because of the Granier method’s simplicity, high degree of accuracy, and relatively low cost.  A comprehensive review of the technique will help refine future methods of measurement using the TDP method.  Several practical issues such as the determination of non-flow values, natural gradient, wounding effect, reversed sap flow, and flux scaling are discussed.

The original Granier method was published by Andre Granier in French.  Therefore, there have been many misunderstandings on the technique and misuse of the methods.  The purpose of the article is to clarify many of these misunderstandings and give a clear overview of the technique, including how to scale measurements from a point to cross section, and then to the tree level.

The theory behind the technique is as follows: the equilibrium of the system will be changed as the sap flux rate changes.  This changes the convection between the two sensors and changes the difference in voltage between the two.  Practically, the system consists of a pair of sensors embedded in the trunk of a tree.  One probe is heated while one is not.  The heated probe is embedded 10-15cm above the reference probe.  The reference (unheated) probe has two wires inside creating a thermocouple.  The two wires are made out of copper and constantan.  The heater probe has four wires consisting of a thermocouple and a heater.  The thermocouple is a copper-constantan pair, while the heater is a constantan-constantan pair.  The two thermocouples are joined together through the constantan wire, and linked to the data logger through the copper wires.  The two heater wires are routed to a 12v power supply where they will receive a constant 0.2 watts of power.  Now the circuit is complete, and by measuring the difference in voltage between the two probes, one can see the sap flux rate.  The conversion formula is .  The length and diameter of the probe is important in this empirical formula – any changes to the shape of the probe will most likely change the formula.  However, Granier calculated that a change in the tree should not change the formula that is applied.  Also, unlike the heat-pulse method, there is no real harm in varying the distance between the heater and reference probe, as long as the reference probe is not affected by the heat propagated by the heater probe.  An optimal distance, as shown in literature, is between 10-15 cm.

Determination of :

The parameter  is defined as the maximum difference in temperature between the two probes when the rate of sap flux is zero.  In the past, scientists assumed that the value of sap flux at night was zero, and simply calibrated the value of  each and every night.  We now know through different studies that the sap flux at night time is not zero.  This poses a problem – what is the true value of  every night?  The answer to this problem is not incredibly simple, but it is possible to estimate the true value of  at any given time.  Determining nights when the sap flux rates will be closest to zero can be done by looking at different variable such as Vapor Pressure Deficit (VPD) and Photosynthetically Active Radiation (PAR).  When a baseline is determined, scientists can then estimate the value of  through a linear regression.  Granier proposed in his 1987 paper to calculate the local maxima of  over a 10 day period, and then average the values to calculate a value – this has been used with some limited success.  Linear regression is the preferred method to calculate this.

Calculation of whole-tree sap flow from a point-value:

Scaling is a known issue with the Granier Thermal Dissipation Probe method.  Measurements by the probes can only determine the exact rate of flux at a specific location.  Scaling to the cross sectional level, the tree level, and the stand level relies on several calculations.  The current method to determine this is to find the centroid of the sap flux curve from the outer edge of the xylem to the sapwood, and then integrate this over the entire area of the cross section of the tree.  This can be further integrated to obtain the complete water use of the tree.  Additionally, one can take the curve of the sap flow for different depths all the way to the heartwood, and use calculus methods to rotate this curve around the center axis of the tree to get a rotated solid that will have the total calculated volume of water flow.

Day Four: Installation!

Today was a very big day!  The probes are installed and working!  I'm getting my first pieces of data - although they may not be very useful at this time in the year.  I did some reading in the morning, and Chris, Henry, Poy, and Dohyoung came around noon to begin installation.  Installation lasted for a good four hours!  We spliced some of the wire coming off the tree because of length issues, and we decided that the probes should be mounted 2.5m off the ground.  We installed two pairs of probes in each of the trees.  We had to use a pretty tall ladder to reach!  I personally installed several of the probes, gaining very valuable experience that I'll be sure to carry on with me!  We had a problem with the wire we bought - it was comprised of solid pieces of copper!  It was a little hard to twist the constantan and copper wires on the probes around a solid piece of copper!  We had to resort to a large amount of solder for each probe.  We eventually got everything together and into the tree.  Then, sensor six went offline.  No matter what we did, we could not get the sensor to come online!  We decided simply to leave the sensor alone for now and fix it if something else went wrong as well.  Everything else was plugged in and working, though.  Aluminum tins were fitted around the probes in order to provide some kind of environmental shielding.

Sensor five seems to be measuring a very high value - there's nothing we can do about that right now.  I also learned how to do the wiring for the datalogger and the power supply - it's a little complicated but it isn't anything impossible.  We got the datalogger to interface with my computer, although that was a challenge in itself.

Tomorrow I'll just be doing some more research and looking at the first day's data!

Day Three: Theory at Duke University

The main thing I did today was travel to Duke in order to meet with Chris, Henry, and Poy to talk about theory and learn how to analyze data once I begin to collect it.  We began by going over the Oishi articles that I read yesterday.  Fortunately, my analysis seemed to mesh pretty well with the way that Chris was describing it.  I understand most of the concepts, except maybe the empirical computations behind the Granier Temperature Dissipation Probes.  I had to think a little bit about the area of the rotated solid using a theorem that incorporated the centroid of the sap flux curve.  I eventually got it, though.  Once we finished talking about both of the articles, I chatted with the entire team for a while about how exactly the installl at NCSSM was going to be carried out.  The maintenance team had began to mount wire Wednesday morning, but I wasn't sure if they would be done by the end of the day.  We tentatively set tomorrow as the day where Chris, Henry, and Poy would come to help me install the probes into the trees.

After this discussion, we moved into using the software to collect data and convert it into sap flux values that accounted for non zero flux at night.  Three main pieces of software were used.  PC200W, SCWin, and BaseLiner.  PC200W is a program from Campbell Scientific that is purpose-built to interface with the CR1000 data logger that I have in the REX lab.  I learned how to plug it in to COM 3, use the interface between RS232 and USB, and how to connect to the data logger.  I learned how to extract the data from the logger and export it to a tab-delimited text file in order to view in other programs.  SCWin was the program used to actually program the datalogger to take fifteen second intervals, average them over 30 minutes, and plot the data in one space of memory.  The programming is not in any common programming language - it is in some kind of Campbell proprietary language.  However, the GUI based interface made it a little easier to set the datalogger the way I wanted it.  I created a program to import onto the logger, however, without a working logger in the REX lab, it may be a little difficult to implement this until tomorrow.  Finally, I learned how to use BaseLiner, which is an incredibly important program for converting change in voltage to a sap flux value while accounting for non-zero flux at night time.  The program takes raw data from the datalogger and allows you to manipulate the base line based on several variables such as Photosynthetically Active Radiation and Vapor Pressure Deficit.  Manually controlling this base line is actually a pretty difficult job - there are a bunch of different things to consider while doing it.  Chris Oishi walked me through the process pretty well, but I'm sure that I won't do a very good job at the very beginning.  I left duke and came back to NCSSM and practiced BaseLiner for the next few hours on some data that Chris gave me from the Duke site.

I got everything set up for the visit tomorrow to install the probes.  The wire is in the tree, so everything should go off without a hitch (hopefully).  I looked at the dogwood again, and everything seems to be OK!  We talked about mounting sap flux probes on the dogwood, and this may happen with either a car batter or the vernier data loggers.

Day Two: Independent Research

Today, I went over both of Chris Oishi's articles in depth, analyzing the detailed theory behind the Granier Thermal Dissipation Probe method to measure sap flux.  I then did some further searching and discovered another article relating to my research.  I coordinated with maintenance today in order to get the wiring mounted in the trees.  It was raining all day today, so the wiring has not gone up - however, some drilling has been done and everything is prepared.  I'm really excited to get everything into the tree and ready for data collection!  I'm a little worried about the wiring of the datalogger - it looks pretty complicated.  All the software is also designed for Windows XP or older, so it may be a little difficult to get everything to interface with each other in the beginning.  I'm still waiting on the phenology camera to arrive from Harvard and BU.  It may not arrive until earlier this week - there was some delay in getting everything packaged and sent.  Once it arrives, I'll have to coordinate with maintenance again in getting it installed on the roof of the art studio.  It'll measure visual physiological traits of the trees so that we can correlate and link it with the sap flux data that we'll hopefully begin recording tomorrow or the day after.  I have an appointment with Chris Oishi and his team (Henry, Poy) tomorrow.  I'm excited to be there!

Here are my article summaries for the two Oishi articles:

Estimating components of forest evapotranspiration: A footprint approach for scaling sap flux measurements: A. Christopher Oishi et al. 2008

This article described the methods used to resale sap flux methods in order to better match eddy covariance method measurements.  This is important because, only after understanding all the components of evapotranspiration can scientists begin to hypothesize and analyze fluctuations in specific components of the evapotranspiration.  Components included canopy interception, evaporation from soil, and transpiration from the canopy.  The equation for this is .  The sap flux sensors are the same thermal dissipation probes as described in Granier 1987.  Several trees of each species were outfitted with the probes and thens called first to the tree level, and then to the stand level.  The tree level is determined by the formula .   is the volume of the effective sapwood,  is the distance from the center of the tree to the centroid of the sap flux curve, and  is the integrated area beneath the fitted curve for a single tree.  This is further scaled o the stand level by comparing allometric relationships (size vs. sap flux) for the different trees.  This was the combined with LAI measurements to scale to the stand level.

There is a general decreasing trend in sap flux as we move from the outer edge of the xylem to the interior.This relationship is graphically displayed in Fig. 4 in the article.  The total amount of EVT that is actually transpiration is 54%.  This means that there is a significant amount of EVT that is related to either evaoporation from the soil or to the canopy interception.  Finally, the conversion from mV to sap flux can be quantified with the equation , where  is the maximum temperature differential where sap flux is zero.

The article reviewed focused a great deal on how to accurately apply Granier’s methods to the oak and pine trees found in the Duke Forest site. 

Interannual Invariability of Forest Evapotranspiration and Its Consequence to Water Flow Downstream: A. Christopher Oishi et al. 2010

This paper concerned itself with measuring the effect of drought conditions on transpiration and total evapotranspiration.  Data was taken from the same 2008 study that was described in Oishi et al. 2008.  This study revealed surprising results.  Transpiration rates, when integrated over a season or a year, actually did not significantly change over their non-drought counterparts.  That is to say, yearly transpiration remained around the same during years of drought and relative wetness.  The theory for these results is that the increased  in times of drought actually benefits transpiration compared to the low  in times of wetness.  So as a general trend, increasing Vapor Pressure Deficit results in an increased transpiration rate.

It appears that L. tulipifera showed the greatest sensitivity to drought conditions in this study, which concurs with earlier publications.  L. styraciflua showed low levels of sensitivity contrary to other studies.  Carya is one of the most drought resistant genera and reflected that in this study.  Finally, Quercus showed extreme sensitivity below a cutoff moisture level of 0.2m³m^-3.

Transpiration plays a significant role in the water budget, and this study shows that, at least for a short period of time, drought does not significantly affect transpiration.  The article notes that over a period of extended drought, however, transpiration rates would certainly fall.

I also reviewed another article:

Environmental controls on sap flow in a northern hardwood forest: Bovard, B. D. et al. 2005

The article describes how researchers empirically determined which of three factors affected sap flow in four different species of trees in Northern Michigan.  The three factors evaluated were photosynthetically active radiation (PAR), vapor pressure deficit (D), and soil water.  PAR is essentially a measure of the amount wavelength that a tree can use to photosynthesize, and has units .  The higher the value of PAR, the more light in these wavelengths is available to the tree. D describes the difference between the amount of water in the air and the maximum amount of moisture that the air can hold, and has units .  Soil water content is simply a measure of the saturation of soil, and is measured in percent.  The researchers monitored four species of trees within a certain radius of a measuring tower over two periods of drought, and looked for relationships between PAR, D, soil water, drought, and sap flux.  The researchers concluded that, day by day, soil water content only affected the sap flow rate if D was over a certain value (). 

The stand of trees was monitored for 61 days in 1999.  PAR was measured with a quantum sensor, air temperature with a shaded, ventilated thermocouple, water vapor partial pressure with an infrared gas analyzer, and precipitation with a tipping bucked rain gauge.  Wind speed and direction were measured, along with water vapor levels.  All data was taken in 30s means and put together. 

Researchers calculated aerodynamic conductance and then installed continuously heated thermocouples into the tree.  Continuously heated thermocouples are fundamentally different than heat-pulse thermocouples because the heat operates continuously and the reference thermocouple monitors differences in heat continuously.  The probes were inserted into the north side of the four species.  Measurements from the probe were extrapolated to the entire tree by finding the area of sapwood depth.  This was done by staining a tree core with 2% tetrazolium trimethyl-chloride, which stains the sapwood red. 

There was a significant difference in sap flow between species in the experiment.  There was an overall positive linear correlation between PAR and sap flow, along with D and sap flow.  However, there seemed to be little to no correlation between soil water concentration and sap flow in any species.  Soil water concentration seemed to only significantly affect sap flow when D was greater than 1.  The dominant controllers of sap flow at the individual level were the same as those at the ecosystem level.  The researchers determined that their calculations of sap flow for the entire stand were chronically undervalued.  They hypothesized that error in procedure could have resulted in a lower cross section area than was actually present. 

In conclusion, climate change that affects PAR, D, and soil water concentration will affect the ecosystem water use and the hydrologic cycle.  However, PAR and D are the two dominating factors.  As early successional species in the Northern Michigan stand are replaced with later succession species, the patterns of water use will also change.

Overall, I think that this was a successful day for research.  Not only did I read the three articles reviewed above, I looked over the phenology website and the Duke FACE site website.  These may all be places to look in once I begin getting data.  Tomorrow I'll be at Duke pretty much all day.

Day One: Beginning Research and Duke Visit

Today marked the official beginning of my project.  The first order of business was to find some articles that seemed promising to the topic I was researching.  I found an article reviewing the different methods employed currently to measure whole-tree water use.  They included a heat balance method, a sector balance method, a heat dissipation method, and a heat pulse method.  Although I thought that the heat pulse method seemed very promising, it turned out that the heat dissipation method made popular by Granier (1987) was the best tradeoff in terms of quality of measurement versus price of equipment and robustness.  My review of the article is as follows:

Measurement of sap flow in plant stems: Smith D. M. et al. 1996

Measuring sap flow is a method of determining the water uptake rate and the transpiration rate of a plant.  Sap flow can be measured several different ways, with different methods for plants of different sizes.  Transpiration is a measure of the amount of water lost by a plant or tree.  Determining transpiration is important because it can help us determine whether there is climate change in the area. 

Methods of measuring Sap Flow:

• Stem Heat Balance Method:
• This method of measuring sap flow can measure stems ranging in diameter from 4mm to 125mm.  A flexible heater with layers of shielding are wrapped around the plant, and two thermocouple pairs measure the temperature gradients  and . 
• Gauges should be installed in strategic locations on the tree trunk in order to have the most accurate measurements.  Loose bark and other obstructions should be removed around the gauges in order to not interfere with the device.
• Constant power is supplied to the heater in commercially available systems and the voltage is adjustable.
• Trunk Sector Heat Balance Method
• This method is used for tree trunks with diameters larger than 120mm.  Heat is applied internally to the a segment of the trunk rather than to the entire circumference of the trunk.  The equation  describes the measurement of sap flow using this method.
• P is electrical power dissipated as heat
• Qv is heat lost vertically
• Qr is heat lost radially
• Ql is heat lost laterally
• Qf is heat lost by convection in the moving sap stream
• Heat Pulse Method
• Sap flow rate is measured by determining the velocity of a short pulse of heat carried by the moving sap stream
• Only used on woody stems
• The heater and sensor probes are drilled into the sapwood.  Heat is pulsed into one sensor (the heat is released for one or two seconds) and the heat is carried by the moving sap and affects the downstream sensor.  The temperature of the sensors will be equal again at some time within 60 seconds.  The velocity of the heat pulse can therefore be described by:
• Correct orientation of the gauges in this method is also essential.  Accurate spacing is required so that the measurements are correct. 

Applications:

These methods can be extrapolated to an entire stand of trees by way of measuring how much influence on tree’s sap flow measurement has on the entire stand.  Transpiration in a Douglas-fir stand was evaluated using the heat pulse method combined with measuring the contribution of each tree to the stand. For example, the average percent of plot sapwood for a dominant crown was 19.9%, while a suppressed crown was 8.7%.  

I rewrote my summary going a little more in depth about each technique of measuring sap flux:

There are several ways to measure transpiration for small plants, however, measuring transpiration in larger trees is more difficult.  Main methods of measuring transpiration include stem heat balance, trunk sector heat balance, heat-pulse, and thermal dissipation:

The stem heat balance method involves wrapping a heater and cork around the entire stem/trunk of the plant being measured.  The cork serves to protect the heater from being influenced by external heat and radiation.  A thermocouple installed slightly above the heater serves as a reference point to measure change in temperature.  Change in temperature, , is calculated.  The total heat applied to the tree can be split into three parts: vertical heat loss by conduction in the stem, radial heat loss by conduction, and heat uptake by the moving sap stream.  The heat uptake by the moving sap stream is the only value we want, so the other two components are calculated and subtracted from the total heat applied to the tree to arrive at the total sap flow value.  This measuring technique is only useful on herbaceous or woody stems less than 120mm in diameter. 

The trunk sector heat balance method, in contrast, can be used on plants greater than 120mm in diameter.  It shares the main principles as the stem heat balance method; the main difference is that only a section of the circumference of the plant is measured.  Five electrodes are embedded in a portion of the circumference of the tree and an electrical current is applied.   is measured between the five electrodes, and the total heat equation is calculated again.  In this method, heat lost radially is split into two calculations.  The first is radial heat lost to heartwood; the second radial heat lost to adjacent sapwood.  Mass flow of sap is then calculated and scaled to the entire cross section of the plant at that point. 

The heat-pulse method is significantly different from the first two methods.  In the heat-pulse method, three probes are inserted into the full depth of the sapwood.  There is a singular heater probe and two reference sensor probes containing miniature thermistors.  Heat is applied to the heater probe for a set amount of time, and the time-to-reference probe is measured.  Velocity of the heat pulse is measured, and then converted into sap velocity.  Expanding this measurement to the entire cross section of the tree will result in sap flux at a point.

Finally, the thermal dissipation method is used to determine sap flux and transpiration in plants.  The thermal dissipation method is only applicable when the depth of sapwood in a tree exceeds 20mm; however, there is no maximum depth constraint for this method.  Two probes are inserted into the trunk of the tree – one heater and one reference probe.  The heater probe is inserted 10-15cm above the reference probe and is constantly heated.  Changing sap flux rates will change the temperature gradient between the two probes.  Measuring this number will allow one to conver

In the afternoon, Dr. Oishi and Henry came over to NCSSM to look at the installation site.  The wires were not installed yet, so we couldn't do much setup outside.  Instead, we installed important software on my computer.  The power supply was also not present - Dr. Oishi said that he would go get one for me.  We talked a lot about theory behind measuring sap flux, as well as some problems that may arise.  One of the oaks may be either dead or close to it, according to maintenance, and so some of the probes may not take data as well as we want them to.  Dr. Oishi gave me a list of articles to read for our next meeting on Wednesday.  I looked at the PlantCam next to the dogwood, and it seems to still be taking pictures just fine.