+------------------------------------------------------------------+ | JORNADA LTER | | New Mexico State University | | Data Set Documentation Form | +------------------------------------------------------------------+ All Jornada Desert Site NSF/LTER data sets must be documented on the following form. This applies to any data set intended for permanent archiving. All raw data sets collected under the auspices of the Jornada NSF/LTER Program will be described by the following standardized form. Information that is not available at this time, must be included when available. See data manager for any questions regarding this form. -------------------------------------------------------------------- 1) Data set access (RESTRICTED or UNRESTRICTED): --------------------------------------------- UNRESTRICTED 2) Data set title: --------------- Drought recovery gas-exchange 3) Project title: -------------- Drought recovery of Larrea tridentata 4) Responsible investigator(s): ---------------------------- Vincent P. Gutschick, Biology, NMSU Connie J. Maxwell, Biology, NMSU / USDA - ARS 5) Date data collection commenced (mm/dd/yyyy): -------------------------------------------- 14 April 1996 6) Date data collection terminated (mm/dd/yyyy or ONGOING): -------------------------------------------------------- 14 August 2000 7) Expected duration of study: --------------------------- 4 years 4 months (study completed) 8) Frequency of measurement: ------------------------- Timed to rain events in growing season; intervals as short as 3 days post-rainfall, as long as two months in persistent drought 9) Researchers: (Personnel who will be obtaining data and who would need to be contacted directly if there is a problem in the raw data): ---------------------------------------------------------------- Vincent P. Gutschick, Biology, NMSU Connie J. Maxwell, Biology, NMSU / USDA - ARS 10) Methods of recording (field data sheets, instrumental, etc.): ---------------------------------------------------------------- Field data sheets with full details and key instrumental data; RAM within gas-exchange system for basic data 11) Site location (Describe in sufficient detail that the site can be relocated): ---------------------------------------------------------------- Residence at 4904 Calabazilla Rd., Las Cruces, with native vegetation substantially undisturbed and highly similar to Jornada Range vegetation, while available for rapid response studies 12) Data set description (State the hypothesis and / or objectives which collection of data set addresses): ---------------------------------------------------------------- Principal questions include: 1. How fast do key physiological functions (CO2 assimilation, stomatal conductance, leaf water status, leaf area, PS II function) recover upon soil rewetting after drought, and in what order? Details include: does stomatal conductance follow the Ball-Berry model, gs = m A hs/Cs + b, with A = CO2 assimilation rate, hs, Cs = relative humidity and CO2 mixing ratio at the leaf surface, and m, b= empirical constants (but almost universally near 10 and 0 for well- watered plants of diverse species and biomes) 2. Do the stomatal parameters vary systematically with leaf and soil water status? 3. Does recovery depend systematically upon neighbor biomass, net soil water input per area (dependent upon topography of water distribution), and plant size? 4. Conversely, how do the functions change on entry into drought? Initial analyses of these and allied data indicate: Leaf water potential has anomalous diurnal trend in drought, peaking in mid-morning. Also, psi(leaf) only recovers to about -2 MPa even with abundant soil water. Leaves lose apparent photosynthetic capacity (Vcmax) daily in drought; much of this is loss of PS II function as measured by chlorophll; fluorescence...but PS II function is restored nearly completely every day. Recovery may be closely tied to high dark-respiration rates seen even in intense drought. We hypothesize that continuous repair enables the shrubs to capitalize upon transient water supplies after erratic and small summer rainfalls. Stomatal conductance, gs, drops with drought and diurnally within drought episodes. However, leaf-internal CO2 concentration, Ci, is nearly unchanged and does not decrease to improver water-use efficiency. The signal for diurnal decreases in gs is not any simple measure of water status, particularly not bulk leaf water potential or soil water potential, unlike signals demonstrated in other plants to date. Mild recovery from drought (modest rainfall - ca. 10 mm total) induces recovery of photosynthetic capacity but no new leaf area in some individual plants, new leaf growth in others. In strong recoveries, both photosynthetic capacity and leaf area recover in all plants. 13) Attributes measured: ------------------------------------------------------------------- Variable name: blank Number of columns between fields CCCCCCCC See attribute description Format: C = character (C3: Three characters [XXX]) I = integer (I2: Integer with two places [##]) F = floating point (F4.2: Total places with decimal point = 4, with 2 decimal places. [#.##]) Variable code: * See attribute description listing See external listing of variable codes N/A = Not applicable VARIABLE MEASURED VARIABLE NAME FORMAT UNITS CODE ATTRIBUTE DESCRIPTION -------- -------- -------- -------- ------------------------- PAGE A2 NA A-Z A. This is the data page as stored AA-AZ in the memory of the LI-COR BA-BZ LI-6200 portable photosynthesis CA-CF system. It is irrelevant to computations but is used for quality control. DATE D8 NA NA B. mm/dd/yy (month/day/year) TIME A8 NA NA C. hh/mm/ss (hour:minute:second) Mountain Daylight-Saving Time is retained. SITE A6 NA JORN S D. "Jornada South," in reference to the site being a residential lot about 20 km S of the Jornada Range but of substantially the same vegetation, undisturbed. PLANT ID I2 NA 1-20 E. The 20 plants in the long-term study LEAF A1 NA A-D F. Two samples of leaf clusters, denoted A and B, are typically measured for gas exchange on each date. Sometimes a third sample, C, or even a fourth, D, is measured, particularly to check performance of plants measured early in the day (as samples A, B) against performance of the same plants late in the day (C or C, D). GENUS A4 NA LATR G. Larrea tridentata in this study QNTM micromol NA H. quantum flux density in the m-2 s-1 photosynthetically active region, in micromol m-2 s-1, as measured by the built-in quantum sensor TAIR gx Celcius NA I. air temperature in the leaf cuvette during gas exchange (as distinguished from air temperature before leaves were put in cuvette) TLEAF gx Celcius NA J. leaf temperature during gas exchange measurements PHOTO gx micromol NA K. Same as Agx above, the CO2 CO2 m-2 assimilation rate per leaf area s-1 during gas exchange, in micromol CO2 m-2 s-1. The proper leaf area has already been entered in computations within the LI-6200 system. COND gx mol m-2 NA L. stomatal conductance, gs, s-1 during gas exchange, in mol m-2 s-1, the units now in common use (when gas exchange is expressed as this "molar conductance" times the difference in mole fraction [of water vapor or CO2] between leaf and ambient air) CINT gx NA NA M. Same as Cigx = leaf-internal CO2 content, as mixing ratio (micromol mol-1), during gas exchange. Ci(Pa) gx Pascals NA N. Same as above, converted to partial pressure in Pascals CO2 gx micromol NA O. Defined earlier as Ca = mol-1 ambient CO2 mixing ratio (micromol mol-1) in bulk air of the leaf cuvette during gas exchange Ci/Ca gx NA NA P. The ratio of Ci/Ca (dimensionless) TRAN gx mmol m-2 NA Q. Transpiration rate per leaf s-1 area (mmol m-2 s-1): NOT USED in any calculations here, but used by LI-6200 in calculating gs. Bctot gx mol m-2 NA R. Total boundary-layer s-1 conductance estimated for leaves, from measured b-l conductance on filter paper of similar dimensions (see LI-6200 manual) and scaled as square root of linear dimension for leaves. Given in mol m-2 s-1. Corrected from one-sided to 2-sided or total conductance CCO2 gx mol m-2 NA S. Total (stomatal + s-1 boundary-layer) conductance for CO2, which is gtotCO2 noted earlier. Given in mol m-2 s-1 VPD gx mbar NA T. Vapor-pressure deficit (mbar, or 100 Pa), as the difference in water-vapor partial pressure from leaf interior to ambient air. Can be used for fits to other models of stomatal control than Ball-Berry EAIR gx mbar NA U. water-vapor partial pressure (mbar) in ambient air of leaf cuvette during gas exchange K gx NA NA V. The figure-of-merit, K, for accuracy of transpiration measurement, discussed earlier; dimensionless P Pascals NA W. Total pressure of air, in Pascals (Pa) T mean Celcius NA X. Mean air temperature during daylight hours of past 2 weeks, in oC, computed from near-site weather data (available at weather.nmsu.edu ,site "NMSU HORT FARM"). Used in estimating acclimation of dark respiration of leaves, Rd Agross gx micromol NA Y. Estimated gross photosynthesis m-2 s-1 = A(observed, measured) + Rd, in micromol m-2 s-1 Rd gx micromol NA Z. Dark respiration of leaves m-2 s-1 (micromol m-2 s-1), estimated as Rd(Tmean)*exp(0.07*(Tleaf-Tmean). This assumes that leaves acclimate to mean temperature, achieving Rd(Tmean) = 0.08*Agross. This relation has been independently verified for our shrubs in separate studies. Gamma gx Pascals NA AA. CO2 partial pressure (Pa) at compensation. Estimated as a function only of temperature from formulas of de Pury and Farquhar (1997): gamma = 3.69 + 0.188*(T-25) + 0.0036*(T-25)^2 Kc(Pa) gx Pascals NA AB. Michaelis constant (Pa) for binding of CO2 to Rubisco enzyme, estimated as a function of temperature from formulas of de Pury and Farquhar (1997): Kc = 40.4*exp(59400*(T-25)/[R*298.2 *(T+273.2)]), with R = universal gas constant, 8.314 J mol-1 K-1 Ko(Pa) gx Pascals NA AC. Michaelis constant (Pa) for binding of O2 to Rubisco, estimated similarly as Ko = 24800*exp(36000*(T-25)/[R*298.2 *(T+273.2)]) Kco (Pa) gx Pascals NA AD. Effective Michaelis constant (Pa) for binding of CO2 to Rubisco, Kco = Kc*(1 + O/Ko), with O = partial pressure of O2 in air = 0.21*Pair Vcmax@Tleaf gx micromol NA AE. Maximal carboxylation capacity of leaf per unit area (micromol m-2 s-1) at temperature of leaf during gas exchange, estimated as if assimilation is light-saturated: A = Vcmax*(Ci-gamma)/(Ci+Kco) --> Vcmax=A*(Gi+Kco)/(Ci-gamma) An estimate that is sometimes better is provided in column AH, described shortly. Vcmax@25 micromol NA AF. Vcmax (micromol m-2 s-1), m-2 s-1 scaled to a standard reference temperature of 25oC to enable comparisons among leaves measured in different conditions; this measure presumably reflects basic biochemical investment in Rubisco enzyme. Scaling is done with formula of de Pury and Farquhar (1997), Vcmax = Vcmax25*exp (64000*(T-25)/[R*298.2*(T+273.2)]) This assumes no thermal deactivation by high leaf temperature. Q00(provisional) mol CO2-1NA AG. Initial quantum yield of CO2 assimilation, at CO2 saturation (max. Q0), in mol CO2 [mol photons]-1. Taken from theory; compare Ehleringer and Bjorkman (1977) and recent discussions, as in de Pury and Farquhar (1997) theta (provisional) NA NA AH. Provisional estimate of convexity parameter in the transition of assimilation from light-limited to light-saturated conditions, as described earlier. Dimensionless. Using assumed universal value of 0.8 found in most plants Vcmax new@Tleaf gx micromol NA AI. Maximal carboxylation m-2 s-1 capacity (micromol m-2 s-1) obtained by inverting the full Johnson-Thornley form for A, theta*A^2 - A*(Asat + A(LL) ) + Asat*A(LL) = 0 with Asat expressed as in explanation for col. AD and A(LL) given by Eq. (2b) in item 18 of this documentation. While this equation nominally is superior to assuming light-saturated assimilation as in col. AE above, it is not always so; if assimilation is marginally light-saturated, the new equation here may represent an attempt to adjust A with Vcmax, to which it is numerically insensitive, so that large and erroneous adjustments in Vcmax are used. Vcmax25new micromol NA AJ. Vcmax with formula of col AI m-2 s-1 above, scaled to ref. T of 25oC by same method as in col. AF Esat(TL) gx Pascals NA AK. Saturated partial pressure of water vapor (Pa) at leaf temperature during gas exchange, estimated as that for pure water in the Smithsonian Institution tables, esat = 610.8*exp(17.269*T/(237.2+T)) BccorCO2 mol m-2 NA AL. Boundary-layer conductance of s-1 leaf (mol m-2 s-1), corrected to 2-sided value with the assumption that stomatal density is half as large on adaxial side as on abaxial side of leaf; see LI-6200 manual. HS gx NA NA AM. Relative humidity at leaf surface (dimensionless), beneath leaf boundary layer, estimated from Eq. (5) in item 18 above CS gx micromol NA AN. CO2 mixing ratio (micromol mol-1 mol-1) at the leaf surface, beneath the leaf boundary layer, estimated from Eq. (6) in item 18 above IBB gx mol m-2 NA AO. Ball-Berry index (mol m-2 s-1) s-1 computed for conditions during gas exchange as IBBgx = Ags hsgx / Csgx = (col. J)*(col. AL)/(col.AM) WIND calc. m s-1 NA AR (cols. AP, AQ blank). Average wind velocity at 2 m (m s-1), from near-site weather data at same time as measurement EAIR 0 mbar NA AS. Partial pressure of water vapor in ambient air (mbar), computed from near-site weather data (air T and relative humidity) CO2 0 micromol NA AT. CO2 in ambient air, as mixing mol-1 ratio (micromol mol-1), measured with LI-6200 cuvette with leaf absent Ca 0 Pascals NA AU. Same, converted to Pa as (mixing ratio)*(total air pressure)*10^-6 Tleaf 0 Celcius NA AV. Initial leaf temperature (oC), usually estimated by extrapolation of leaf T in cuvette at zero time; sometimes measured independently with thermal infrared instrument (gun or thermocouple) or contact thermocouple Gamma 0 Pascals NA AW. CO2 compensation partial pressure (Pa) at Tleaf0, computed analogously to col. AA above Kc (Pa) 0 Pascals NA AX. Michaelis constant (Pa) for CO2 binding to Rubisco, at Tleaf0; analogous to col. AB above Ko (Pa) 0 Pascals NA AY. Michaelis constant (Pa) for O2 binding; analogous to col. AC above Kco (Pa) 0 Pascals NA AZ. Effective Michaelis constant (Pa) for CO2 binding; analogous to col. AD above Vcmax@TL 0 micromol NA BA. Maximal carboxylation capacity m-2 s-1 at initial Tleaf (micromol m-2 s-1), estimated as if assimilation is light-saturated Rd @ 0 micromol NA BB. Dark respiration (micromol m-2 m-2 s-1 s-1) at initial Tleaf, estimated analogously to Rd@Tleafgx in col. Y, but using Tleaf0 Q00*IL 0 NA BC. CO2-saturated initial quantum yield at initial Tleaf0 and CO2(0), multiplied by irradiance on leaves; a term used in inverting the Johnson-Thornley form for assimilation, A, to estimate Ci at Tleaf0 Esat(TL) 0 Pascals NA BD. Saturated partial pressure of water vapor at Tleaf0 (Pa), from same formula as in col. AK above Leaf dimen micromol NA BE. Characteristic linear m-2 s-2 dimension, dleaf, of leaf (m), for computing leaf boudnary-layer resistance from windspeed using the formula gb = 0.264[mol m-2 s-1/2]*sqrt(u/dleaf) Bctot 0 Pascals NA BF. Total boundary-layer conductance for leaf in initial conditions; analogous to col. AL above Gt CO2 0 mol m-2 NA BG. Total conductance (stomatal + s-1 boundary-layer) for CO2 (mol m-2 s-1) in initial conditions, using Eq. (7) in item 18 above. B coeff NA BH. Coefficient of term linear in Ci in simpler approximation for assimilation at initial conditions. Consider A expressed as the transport equation, equated to A expressed with the carboxylation-kinetic equation FOR light-saturated conditions: gtotCO2*(Ca - Ci) = Vcmax*(Ci - gamma)/(Ci + Kco). Here, we use gtotCO2 computed with initial leaf conditions (free-air windspeed), Ca as Ca0 (free-air conditions; col. AU), and Vcmax, gamma, and Kco computed at initial Tleaf0 (cols.BA, AW, AZ) Multiply both sides by the denominator, Ci + Kco, to obtain a quadratic equation in Ci = Ci0 (to be estimated). Gather terms in Ci0^2 (coefficient is 1), Ci (coefficient is B coeff here), and the constant, Ci0^0 (coefficient is C coeff of next col, BI). C coeff NA BI. See paragraph above Note: solution for Ci0 in this "quadratic approximation" is deferred to col. BZ3, later C4 coeff NA BJ. Coefficient (C4) of Ci0^4 in more complete equation for assimilation at initial conditions, using the Johnson-Thornley form for A (see Eq. in col. AI). Proceeding analogously to the calculations in col. BH above but with theta*A^2, etc. from the Johnson-Thornley equation, we obtain a quartic equation in Ci = Ci0. Upon gathering terms, we have terms in Ci0^4 (the C4 coeff here), Ci0^3 (the C3 coeff), etc. C3 coeff NA BK. The coefficient of Ci0^3=constant, in the quartic equation for Ci0 described in col. BJ above. C2 coeff NA BL. The coefficient of Ci0^2=constant, in the quartic equation for Ci0 described in col. BJ above. C1 coeff NA BM. The coefficient of Ci0^1=constant, in the quartic equation for Ci0 described in col. BJ above. C0 coeff NA BN. The coefficient of Ci0^0=constant, in the quartic equation for Ci0 described in col. BJ above. quartic NA BO. The residual in C4*Ci0^4 + C3*Ci0^3 +C2*Ci0^2 +C1*Ci0 + C0 = 0 when we plug in a numerical estimate of Ci0. Used to test how accurate the solution is. Ssometimes a numerical estimate converges to a non-physical root, such as Ci0 >> Ca or Ci0 <0, and this residual is small; at other times, the numerical estimate has failed or has not been made, and the residual is large (>> 1). This column is an indicator of action needed. Ci (qrt) NA BP. Numerical solution for Ci0 in the quartic equation. Obtained from an external Fortran program, because Excel cannot automate the solution (Solve utility). Amax (qrt) micromol NA BQ. Light-saturated assimilation m-2 s-2 rate at Ci = Ci0 (micromol m-2 s-1) obtained by solving the quartic equation for Ci0 described above Q0*IL (qrt) micromol NA BR. Light-limited rate at same Ci = Ci0 (micromol m-2 s-1) A(gross qrt) NA BS. Acutal assimilation rate, Agross, estimated with the Johnson-Thornley equation, using Amax = Asat and Q0*IL = A(LL) above and convexity parameter theta = 0.8. This is before accounting for dark respiration. A(net qrt) micromol NA BT. Above, debited for dark respiration rate estimated as in col. BB; units are micromol m-2 s-1 HS 0 NA BU. Relative humidity at leaf surface in initial conditions, computed analogously to col. AM above but using initial leaf conditions; dimensionless CS 0, qrt micromol NA BV. CO2 mixing ratio (micromol mol-1 mol-1) at the leaf surface, computed with A0 = A(net qrt) of col. BT as Cs = Cs0 = Ca0 - A0*1.37/gb0 IBB(gross qrt) mol m-2 NA BW. Ball-Berry index (mol m-2 s-1) s-1 computed with initial gross A, hs, and Cs from cols. BS, BU, BV IBB(net qrt) mol m-2 NA BX. Ball-Berry index (mol m-2 s-1) s-1 computed with initial NET A, hs, and Cs from cols. BT, BU, BV Ci (qd) NA BY. Ci = Ci0 in initial free-air conditions, computed from quadratic equation for Ci described in col. BH A(gross qd) micromol NA BZ. Gross assimilation (micromol m-2 s-1 m-2 s-1) in initial conditions, computed with Ci0 of col. BY and light-saturated form of A, Eq. (1) of item 18 A(net qd) NA CA. Net assimilation, estimated as A(gross qd) above - Rd0 Cs (qd) micromol NA CB. CO2 mixing ratio (micromol mol-1 mol-1) estimated with net A0 from col. CA above IBB(gross qd) mol m-2 NA CC. Ball-Berry index (mol m-2 s-1) s-1 computed with initial GROSS A, hs, and Cs from cols. BZ, BU, BV IBB(net, qd) NA CD. Similar, but using NET A - cols. CA, BU, BV IBB (gx) NA CE. Replication of col. AO, used for ready comparison with these distant columns of alternative IBB forms Ci fortran NA CF. Solution of quartic equation for Ci = Ci0 (Pa) described in col. BJ. This is usually the final solution used in col. BP, which at first has an estimate from gas-exchange conditions, col. M, which estimate is exported to the Fortran program to serve as an initial estimate in a root-finding routine 14) Missing or questionable values (describe how these are represented in the data set): ---------------------------------------------------------------- 15) Methodology (Provide sufficient detail such that an unaware reader could repeat the described data collection procedures.) ---------------------------------------------------------------- Twenty shrubs of the species Larrea tridentata were chosen for their sampling of variation in size, topographic location (water redistribution), and neighbor density. Plant water status and photosynthetic attributes (gas exchange, and later, also chlorophyll fluorescence), plant leaf area, and soil water status were measured at intervals up to 2 months apart during gradual drydown of soil, but as frequently as 1 - 2 days apart as plants recovered from drought after modest to large rainfalls. On a day of measurement, the 20 plants were sampled in groups of 5 for gas exchange, leaf water potential, leaf relative water content, and chlorophyll fluorescence. On the same day, all the plants were also measured for soil water content at their bases (depth increments of 15 cm) and for leaf area index by image analysis of photographs. The methods for measurements other than gas exchange are presented in other files noted in item 20 below. Measurements required for study: A. Water status: i. Rainfall inputs (from weather stations and manual recording gauges read daily; data file "Drought recovery meteo data"). ii. Soil volumetric water content at 5 depths at each of 7 representative shrub bases, by time-domain reflectometry (data file "Drought recovery TDR") iii. Leaf water potential by pressure bomb at same time as leaf gas exchange is measured (file "Drought recovery P bomb"). iv. Leaf relative water content at same time (file "Drought recovery RWC"). This is defined as (water content per dry mass, leaves in situ) / (water content per dry mass, leaves rehydrated 2 h in dark). B. THIS DATA FILE: Leaf gas exchange with a portable photosynthesis system, A LI-COR LI-6200 in standard mode or highly modified by us to operate in continuous, open-flow mode ("open mode") in order to measure stomatal responses to varied humidities and other conditions. The open system also uses a PP Systems leaf cuvette with our own sensor electronics installed and our own Peltier heat pump to control leaf temperature. Most data are initially expressed per area of leaf. After leaf clusters were measured for gas exchange, they were removed from the leaf cuvette and trimmed to eliminate leaf area masked by cuvette gaskets. The remaining leaf area was manually stripped from the branches and measured with a leaf area meter (LI-COR LI-2000). The leaves were also oven-dried at 80oC for 2d and weighed to obtain dry mass. The basic data obtained during gas exchange are: i. Stomatal conductance, gs, via the standard computations performed in the LI-6200 system program, or by equivalent computations in the open mode via our own program (please see Web site mvar.nmsu.edu/biology/vince/licor.openmode for detailed description of the open system and its computations) ii. Leaf-internal CO2 concentration during gas exchange, Ci = Cigx (the gx suffix distinguishes this value from Ci at initial conditions, which is estimated by methods described shortly) iii. Leaf temperature during gas exchange, TLgx iv. CO2 assimilation rate, Agx v. Dark respiration, Rd. This is measured occasionally with a leaf chamber darkened by cloth or aluminum foil. We assume that Rd acclimates to mean leaf T over the past 2 weeks (ref.) and responds exponentially to short-term temperature changes as Rd = Rd(Tmean)*exp(-0.7*(T-Tmean)) (4) We report RD(Tmean), having obtained Tmean from weather records available at weather.nmsu.edu. vi. The microenvironment that existed just before the cuvette was placed on the leaf: windspeed u0 (and consequent boundary- layer conductance gb0), leaf temperature T0 (measured by thermal infrared or thermocouple or estimated by extrapolating Tleaf among two observations in the cuvette), CO2 and water-vapor partial pressures Ca0 and ea0. =================================================================== Data Quality Assurance A. Instrument calibration: this was done annually at the LI-COR facility. We also calibrated the CO2 and humidity responses less stringently with bottled CO2 and a humidity generator infrequently. B. Assuring representative physical and physiological conditions in leaves being sampled: we chose leaves that had been exposed to constant meteorological conditions and full sun for at least 10 min. Leaf clusters were selected visually as having the mean leaf density, color, and orientation of the whole shrub. We avoided sudden increases of CO2 from operator's breath by careful positioning of the operator and operator breath-holding during leaf emplacement in the cuvette. We continuously monitored CO2 partial pressure, Ca, and did not begin a gas-exchange measurement until Ca was within 10 ppm (umol mol-1 as a mixing ratio) of the long-term average at the site. Excessive changes in leaf temperature from emplacing the cuvette were avoided by shielding the cuvette in a cooled chamber inbetween measurements. The estimates of stomatal conductance and of Ci are most accurate if the humidity in the leaf cuvette changes little (so that leaf transpiration is computed mainly from reliable desiccant action, and as little as possible from changes in humidity that require less reliable estimation of desorption contributions). Following the LI-COR recommendations, we retained only those observations for which K = (transpiration contribution from desiccation)/(transpiration contribution from humidity change) had an absolute value equal to or greater than 5. C. Proper sensor operation: every several hours in the field, we perfomred the "K-test" recommended by LI-COR to correct the varying measurments of ea = water-vapor partial pressure for lags due to vapor adsorption to surfaces in the equipment. We avoided exposing the chamber temperature sensor to direct sunlight to avoid offsets from real air T caused by radiative loading. D. Checks for consistency: i. Among two separate, consecutive measurements ("observations") of gas exchange: we programmed the LI-6200 to take two consecutive observations of 10 s each. At times, a bolus or boli of high CO2 or high and then low CO2 were accidentally introduced into the cuvette. These boli cause erratic estimates of assimilation A. We rejected observations in which A and gs differed by more than about 10% of their values in the 2nd observation. ii. Consistency with physics and enzyme kinetics: positive assimilation requires Ci > gamma. Occasionally, gs is so small that calculations of Ci are not accurate and we violate the preceding condition. The data for such observations were rejected. 16) Key literature (Citations that describe sampling procedures, [reference of a published paper, thesis, etc.]): ---------------------------------------------------------------- de Pury DDG and GD Farquhar. 1997. Simple scaling of photosynthesis from leaves to canopies without the errors of big-leaf models. Plant Cell Environ. 20: 537-557. Farquhar GD, S von Caemmerer, and JA Berry. 1980. A biochemical model of photosynthetic CO2 assimilation in leaves of C3 species. Planta 149: 78-90. LI-COR, Inc. (1987). LI-6200 Technical Reference. LI-COR, Inc., Lincoln, NE. 17) Keywords (keywords that describe data set; maximum of 10): ---------------------------------------------------------------- leaf gas exchange, stomatal conductance, Ball-Berry model, photosynthetic capacity, leaf dark respiration 18) Treatment of data: (List any programs used in analysis of the data): [Note: Programs should be appended and stored with this form.] ---------------------------------------------------------------- A. Extraction of photosynthetic parameters: i. Photosynthetic capacity as maximal carboxylation capacity, Vcmax, by inverting the relation of assimilation rate A to leaf-internal CO2 concentration Ci and the kinetic parameters of carboxlation and electron transport. In a simple approximation, if A is light-saturated, we can express A = Asat = Vcmax [Ci - gamma]/[Ci + Kco], (1) where gamma is the compensation partial pressure and Kco is the effective Michaelis constant for CO2 binding, both being functions only of temperature and apparently independent of plant species; see GD Farquhar et al., Planta (1980). The gas-exchange system measures A and Ci; it also measures leaf temperature, from which gamma and Kco can be computed. Thus, we can invert the equation above to obtain Vcmax at leaf temperature. For comparisons among different conditions (times of day, etc.) for which Tleaf varies, we use standard equations of Rubisco temperature activation (DD de Pury and GD Farquhar, Plant Cell Environ. [1997]) to compute Vcmax referred to a reference temperature of 25oC, which we denote as Vcmax25. More generally, A is represented by a transition between light- saturated rate Asat above and the light-limited assimilation rate that depends on the initial quantum yield, Q0, and the irradiance on the leaf, IL: A(LL) = Q0*IL (2a) = Q00 *{ [Ci - gamma]/[Ci + 2*gamma] }*IL. (2b) Following Farquhar et al. (198), we write A under arbitrary conditions of irradiance, temperature, and Ci as theta*A^2 - A*[Asat+ A(LL)] + Asat*A(LL) = 0, (3) where theta is an empirical convexity, typically 0.8 in plants. This has an explicit solution as a quadratic. ii. Ball-Berry parameters of stomatal conductance, m and b, in the equation gs approx m A hs/ Cs + b We obtained m and b by regression on data from leaves at different conditions (humidity, irradiance, temperature, especially). That is, we compute the Ball-Berry index, IBBgx = A hs/Cs (The "gx" suffix refers to "gas-exchange" conditions). We use A, hs, and Cs in four forms: a. During gas-exchange conditions, with A = net assimilation b. Same, with A = gross assimilation, Anet + Rd c. With A = net assimilation computed for initial leaf conditions, by methods described shortly d. With A = gross assimilation computed for initial leaf conditions We compare the index under gas-exchange and initial conditions because gs presumably acclimated over long times but may not change rapidly when the leaf is put in the measurement cuvette. Stomata of some species do acclimate rapidly to the new conditions (sunflower, apparently; Gutschick, Simonneau, and Tardieu, in prep.), while others respond more slowly (woody species). We compare the index computed with both net and gross assimilation because the Ball- Berry formulation is empirical; the best fit is used, without appeal to a mechanistic basis. The methods of computing IBB are: a. During gas-exchange conditions, as if gs acclimated rapidly to the new environment in the leaf cuvette. We use the measured value of A. We compute hs from the measured water-vapor partial pressure in the cuvette, ea, the saturated partial pressure inside the leaf, ei, at leaf temperature, and the leaf boundary- layer conductance, gb (computed from calibrations and the leaf linear dimension, d, so that it scales as the square root of d). A formula one may readily derive from hs = es/ei and the relation es = partial pressure at the leaf surface = ei - E*Pair/gs = ea + E*Pair/gb, with E = transpiration rate and Pair = total air pressure, is hs = [ ea/ei + gs/gb]/[1 + gs/gb]. (5) We compute Cs from the ambient CO2 partial pressure in the cuvette, A, as Cs = Ca - 1.37*A*Pair/gb. (6) The factor 1.37 corrects for the lower diffusivity of CO2 relative to water vapor. b. In the microenvironment that existed just before the cuvette was placed on the leaf, with windspeed u0 (and consequent boundary- layer conductance gb0), leaf temperature T0 (measured by thermal infrared or thermocouple or estimated by extrapolating Tleaf among two observations in the cuvette), CO2 and water-vapor partial pressures Ca0 and ea0. We assume that gs remains unchanged and use the equations for Asat and A(LL) referered to T0 (gamma, Kco, Vcmax, Q00 are computed for T0). We do not know what Ci = Ci0 was, so we estimate it by using the Johnson-Thornley form for A (Eq. 3 above), replacing A by the transport-equation form, A = gtotCO2*(Ca - Ci), with gtotCO2 = 1/(1.6/gs + 1.37/gb). (7) This form, multiplied by the denominator factors (ci+2*gamma)(Ci+Kco), yields a quartic in Ci that may be solved numerically. (The solution can be done within a spreadsheet composed in Excel or other software, but each case must be run manually. It is more efficient to export the values of gamma0, Kco0, etc. to a Fortran program that we have written and then re-import the solutions for Ci0 derived by the Fortran program - especially with on the order of 1000 values to be solved. The Fortran program is available at our Web site noted earlier.) Having obtained the estimated Ci0, one can compute A0 from Eq. (3) and then hs0, Cs0 from Eqa. (5), (6). We can then compose the Ball-Berry index, IBB0 = A0 hs0 / Cs0. We wish to emphasize that only gs and microenvironmental conditions in this "free" or initial state should ever be used to estimate assimilation, transpiration, water-use efficiency, and other performance measures of plants. The values of Ci, WUE, etc. computed for gas-exchange conditions are NOT reliable, as they refer to a modified environment. The calculations, in direct mathematical form as well as in spreadsheet and Fortran programs, are given: (A) as formulas for an Excel spreadsheet; see accompanying file dr.equations.txt (B) on our Web site, mvar.nmsu.edu/biology/vince, in files licor.openmode and drought.recovery. 19) Associated computer accounts: ---------------------------------------------------------------- user=vince, host=wombat.nmsu.edu (operated by V. Gutschick in his own laboratory); also, user=cmaxwell on same host. 20) Files associated with this data set: ---------------------------------------------------------------- A) Metadata files FILE NAME DESCRIPTION OF FILES ------------ ----------------------------------------------- DR_LATR.prj Project documentation DRgasExc.dsd Data set documentation ------------ ----------------------------------------------- B) Data files FILE NAME DESCRIPTION OF FILES ------------ ----------------------------------------------- DRgasExc.dat Data file (CSV[comma separated values], ASCII) ------------ ----------------------------------------------- C) Data entry, verification, and analysis files FILE NAME DESCRIPTION OF FILES ------------ ----------------------------------------------- Dr_Equat.inf Drought recovery equations (ASCII) ------------ ----------------------------------------------- D) Other (Any other related files.) FILE NAME DESCRIPTION OF FILES ------------ ----------------------------------------------- ? Meteorological data at nearby site: "Drought recovery met data" ? Soil volumetric water content, by time-domain reflectometry: "Drought recovery TDR" ? Leaf water potential: "Drought recovery P bomb" ? Leaf relative water content: "Drought recovery RWC" ? Leaf PS II function by chlorophyll fluorescence: "Drought recovery Chl fluorescence" ------------ ----------------------------------------------- 21) Comments (Include any comments here that more fully describe this data set): ---------------------------------------------------------------- For more detailed discussions, please contact: Vincent P. Gutschick Dept. of Biology, 3AF New Mexico State University Las Cruces, NM 88003-0001, USA (505)646-5661; FAX -5665 email vince@nmsu.edu Data were acquired from April 1996 to August 2000 and were entered at a variety of dates. Basic gas-exchange data were downloaded from the LI-6200 gas-exchange system with the PC-6200 software (LI-COR, Inc.). Subsequent computations in an Excel spreadsheet were programmed at a variety of dates. A complete quality check was made in June, 2001 to assure consistent computations on all data lines and the accuracy of all equations. This certification was completed on 25 June 2001 by CJ Maxwell with the assistance of VP Gutschick. The data file is in tab-delimited ASCII format and thus does no incorporate the Excel formulas. Please note that formulas usually cannot be simply pasted back into an Excel spreadsheet unless one knows which columns use formulas and which do not. Thus, we are willing to provide the native Excel (MS Office 1997 version) spreadsheet to persons with legitimate access to the data who contact us; see item 21 below. The dataset herein, for leaf gas exchange, has many rows (one for each observation as a combination of date, plant and sample number, and one of 2 "observations" within a single 30-s gas-exchange measurement). 22) Data set documentation history log: ---------------------------------------------------------------- Data set title - Drought recovery gas-exchange Data set file name - DRgasExc.dsd ---------------------------------------------------------------- mm/dd/yyyy - Date of Comment Int - Initials of person making Comment VPG = Vince P. Gutschick JPA = John P. Anderson JL = Jim Lenz Changes/Updates - List any changes made to document mm/dd/yyyy Int Changes/Updates ---------- --- ----------------------------------------------- 08/18/2001 VPG Documentation completed 09/17/2001 JPA Formatting and validating documentation begun. 09/19/2001 JPA Attribute description information reformatted. 06/13/2002 JL Added Dataset ID and Project ID sections. 09/02/2003 JPA Changed to Unrestricted as per phone comm w/ VPG 23) Dataset ID: ----------- DSL2002070 24) Project ID: ----------- ------------------------------------------------------------------- END OF DATA SET FILE -------------------------------------------------------------------