uid=HFR,o=lter,dc=ecoinformatics,dc=org all public read doi:10.6073/pasta/f1f40c560f0afaf084423c33fa7d44fa Christopher Williams https://orcid.org/0000-0002-5047-0639 Sophie Dillen Researcher Myroslava Khomik https://orcid.org/0000-0002-0377-8833 Researcher Richard MacLean Researcher Melanie Vanderhoof Researcher 2023 English

Clearcutting a forest ecosystem can result in a drastic reduction of the stand’s productivity. Despite the severity of this disturbance type, past studies have found that the productivity of young regenerating stands can quickly rebound, approaching that of mature undisturbed stands within a few years. One of the obvious reasons is increased leaf area with each year of recovery. However, a less obvious reason may be the variability in species composition and distribution during the natural regeneration process. The purpose of this study was to investigate to what extent the increase in GEP, observed during the first four years of recovery, in a naturally regenerating clearcut stand was due to 1) an overall expansion of leaf area, and 2) an increase in the canopy’s photosynthetic capacity stemming from either species compositional shifts or drift in physiological traits within species. We found that the multi-year rise in GEP following harvest was clearly attributed to the expansion of leaf area rather than a change in vegetation composition. Sizeable changes in relative abundance of species were masked by remarkably similar leaf physiological attributes for a range of vegetation types present in this early successional environment. Comparison of upscaled leaf-chamber to eddy-covariance-based light-response curves revealed broad consistency in both maximum photosynthetic capacity and quantum yield efficiency. The approaches presented here illustrate how chamber- and ecosystem-scale measurements of gas exchange can be blended with species-level leaf area data to draw conclusive inferences about changes in ecosystem processes over time in a highly dynamic environment.

aboveground production carbon dioxide gas flux leaves photosynthesis photosynthetically active radiation plant physiology transpiration LTER controlled vocabulary primary production disturbance LTER core area Harvard Forest HFR LTER USA HFR default

This dataset is released to the public under Creative Commons CC0 1.0 (No Rights Reserved). Please keep the dataset creators informed of any plans to use the dataset. Consultation with the original investigators is strongly encouraged. Publications and data products that make use of the dataset should include proper acknowledgement.

Creative Commons Zero v1.0 Universal https://spdx.org/licenses/CC0-1.0.html CC0-1.0 https://harvardforest.fas.harvard.edu/exist/apps/datasets/showData.html?id=hf224 Prospect Hill Tract (Harvard Forest). Coordinates based on WGS84 datum. -72.174 -72.174 +42.546 +42.546 403 403 meter 2010 2012 genus Acer species rubrum red maple genus Aralia species nudicaulis wild sarsaparilla genus Betula species papyrifera paper birch genus Carex species spp. sedge genus Dennstaedtia species punctilobula hayscented fern genus Dryopteris species spp. woodfern genus Maianthemum species canadense Canadian may-lily genus Oryzopsis species asperifolia rough-leaved rice grass genus Polygonum species sp. knotweed genus Prunus species pensylvanica pin cherry species serotina black cherry genus Quercus species rubra red oak genus Rubus species allegheniensis Allegheny blackberry genus Sambucus species pubens elderberry complete Information Manager Harvard Forest

324 North Main Street Petersham MA 01366 USA

(978) 724-3302 hf-im@lists.fas.harvard.edu Harvard Forest

324 North Main Street Petersham MA 01366 USA

(978) 724-3302 (978) 724-3595 https://harvardforest.fas.harvard.edu

1. Select mid-canopy, well lit (normally in sun) leaf. Make sure it’s healthy looking. Make note of it in your notebook and also write a remark in the file on LI-6400. 2. Adjust tri-pod, to leaf level and angle. 3. Set Reference CO2 to 380 ppm (note your CO2 should be on full scrub and desiccant on BYPASS) – this will be temporary, shortly we will switch to sample control. 4. Set leaf temperature to ambient Tair (measure ambient Tair with open chamber first). 5. Set light to 1800 umol/s. 6. Clamp onto the selected leaf and monitor H2OS_mml value, make note of it in your note book. Then set flow control for constant water mole fraction targeting the value you noted. 7. Set Sample CO2 to 380 ppm. 8. When CO2 and H2O are stabilized, match IRGAs. 9. wait about 10-15 minutes for Ci to stabilize (that is when stomata will be fully adjusted). 10. Log (you’ll be prompted for stomatal ratio, leaf area, species, replicate). Note the date of measurement, file name, your name (person collecting the data, species name, leaf replicate #, and the measured values: light level, stable Ci, and logged photosynthesis and conductivity values in your field notebook – a table is good. 11. Next, change the light to 1200 and repeat steps 9 and 10. 12. Repeat step 11, going through the following light levels: 1000, 800, 600, 400, 200, 50, 0 (light off and branch shaded). 13. Remove the leaf from the chamber. 14. Carefully detach it and place in envelope. Mark the envelope with: CLARKU/Williams, the date of measurement (mmm.dd.yyyy), file name, species, replicate, and “LIGHT CURVE”. If area below 6cm2, will need to scan. 15. Put envelopes in ziplock bags into COOLER, till end of day. Take out of cooler and ziplock bags and dry in Oven for 24 hours at 70oC (158 oF). Make sure to dry as soon as possible, don’t want leaf to rot. 16. Prep dried leaves for CN analysis.

1. Select mid-canopy, well lit (normally in sun) leaf. Make sure it’s healthy looking. Make note of it in your notebook and also write a remark in the file on LI-6400. 2. Adjust tri-pod, to leaf level and angle. 3. Set Reference CO2 to 380 ppm (note your CO2 should be on full scrub and desiccant at mid range). 4. Set leaf temperature to ambient Tair (measure ambient Tair with open chamber first). 5. Set light to 1800 µmol/s. 6. Clamp onto the selected leaf and monitor H2OS_mml value, make note of it in your note book. Then set flow control for constant water mole fraction targeting the value you noted (but flow should be at about 400 µmol/s). 7. When CO2 and H2O are stabilized, match IRGAs. You will need to match IRGAs after every time you change CO2 concentration. 8. Wait for Ci to stabilize (that is when stomata will be fully adjusted). Make sure not to wait too long at low CO2 concentrations, so not to deactivate RUBISCO. 9. Log (you’ll be prompted for stomatal ratio, leaf area, species, replicate). Note the date of measurement, file name, your name (person collecting the data, species name, leaf replicate #, and logged PAR, photosynthesis and conductivity values in your field notebook – a table is good. 10. Move onto the next leaf. 11. Repeat step 10, going through the following CO2 levels (in this order): 100, 50, 380, 380 (yes that’s a duplicate), 500, 800, 1000. 12. Remove the leaf from the chamber. 13. Carefully detach it and place in envelope. Mark the envelope with: CLARKU/Williams, the date of measurement (mmm.dd.yyyy), file name, species, replicate, and “LIGHT CURVE”. If area below 6cm2, will need to scan. 14. Put envelopes in ziplock bags into COOLER, till end of day. Take out of cooler and ziplock bags and dry in Oven for 24 hours at 70oC (158 oF). Make sure to dry as soon as possible, don’t want leaf to rot. 15. Prep dried leaves for CN analysis.

1. Select mid-canopy, well lit (normally in sun) leaf. Make sure it’s healthy looking. Make note of it in your notebook and also write a remark in the file on LI-6400. 2. Mark the branch with flagging tape, and note the leaf location (you will be measuring the same leaf throughout the summer, so you do this step only once). 3. Adjust tri-pod, to leaf level and angle. 4. Set Sample CO2 to 380 ppm (note your CO2 should be on full scrub and desiccant on full BYPASS). 5. Set leaf temperature to ambient Tair (measure ambient Tair with open chamber first). 6. Set light to follow the outside PAR sensor. 7. Set flow to high (~ 500 umol/s). 8. When CO2 and H2O are stabilized, match IRGAs. (match once on 1st leaf and then every 30 minutes, or so, esp. if temperature changes). 9. wait for photosynthesis and conductivity to stabilize. 10. Log (you’ll be prompted for stomatal ratio, leaf area, species, replicate). Note the date of measurement, file name, your name (person collecting the data, species name, leaf replicate #, and the measured values CO2 concentration, stable Ci, and logged photosynthesis and conductivity values in your field notebook – a table is good.). 11. Gently release the leaf from the chamber and move onto the next species. 12. Repeat steps 1 to 3 and 9 to 11 (going through all 5-10 species, with 3 replicates per species). Make sure to match every 30 minutes to an hour and to check ambient Tair (over the course of a day it will likely change). Note: if area is smaller than 6cm2, you will need to detach that leaf and measure it’s area with the scanner at the end of the season.

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(978) 724-3302 (978) 724-3595 https://harvardforest.fas.harvard.edu https://ror.org/059cpzx98 pointOfContact The Harvard Forest Long-Term Ecological Research (LTER) program examines ecological dynamics in the New England region resulting from natural disturbances, environmental change, and human impacts. National Science Foundation LTER grants: DEB-8811764, DEB-9411975, DEB-0080592, DEB-0620443, DEB-1237491, DEB-1832210. hf224-01-leaf-gas.csv leaf gas exchange hf224-01-leaf-gas.csv 273217 47a0e024cc72ea0ed61cafcccda5704b 1 \r\n column , https://harvardforest.fas.harvard.edu/data/p22/hf224/hf224-01-leaf-gas.csv datetime date and time of measurement YYYY-MM-DDThh:mm:ss 1 second NA missing value year year sampled YYYY 1 year NA missing value month month sampled month sampled NA missing value day day of month day of month NA missing value doy corresponding day of the year nominalDay 1 natural NA missing value date date sampled YYYY-MM-DD 1 day NA missing value am whether or not sampling was done in the morning 0 not sampled in the morning 1 sampled in the morning NA missing value pm whether or not sampling was done in the afternoon 0 sampling was not done in the afternoon 1 sampling was done in the afternoon NA missing value obs observation number observation number NA missing value time time of measurement hh:mm:ss 1 second NA missing value leaf leaf number - measured on the same plant leaf number - measured on the same plant NA missing value plant plant number plant number NA missing value species species name rual Rubus allegheniensis depu Dennstaedtia punctilobula prpe Prunus pensylvanica acru Acer rubrum quru Quercus rubra sapu Sambucus pubens posp1 Polygonum sp. prse Prunus serotina drsp Dryopteris spp. casp Carex spp. oras Oryzopsis asperifolia bepa Betula papyrifera maca Maianthemum canadense grass grass arnu Aralia nudicaulis NA missing value photo net assimilation in micromols CO2 per meter squared per second micromolePerMeterSquaredPerSecond 0.01 real NA missing value cond conductance to H2O in millimols of H2O per meter squared per second millimolePerMeterSquaredPerSecond 0.001 real NA missing value ci intercellular CO2 concentration (calculated) in micromols CO2 per mol dimensionless 1 real NA missing value trans transpiration rate in millimol H2O per meter squared per second millimolePerMeterSquaredPerSecond 0.01 real NA missing value area total area of leaf enclosed within the chamber squareCentimeters 0.1 real NA missing value stm.ratio stomatal ratio used in calculations dimensionless 0.1 real NA missing value tair temperature in sample cell celsius 0.01 real NA missing value tleaf temperature of leaf thermocouple celsius 0.01 real NA missing value co2.r reference cell CO2 concentration in micromol CO2 per mol (ppm) dimensionless 0.01 real NA missing value co2.s sample cell CO2 concentration in micromol CO2 per mol (ppm) dimensionless 0.01 real NA missing value h2o.r reference cell H2O concentration in millimol H2O per mol (ppm) dimensionless 0.001 real NA missing value h2o.s sample cell H2O concentration in millimol H2O per mol (ppm) dimensionless 0.001 real NA missing value rh.r relative humidity in the reference cell (%) dimensionless 0.01 real NA missing value rh.s relative humidity in the sample cell (%) dimensionless 0.01 real NA missing value par.in quantum sensor inside the chamber micromolePerMeterSquaredPerSecond 1 real NA missing value par.out external quantum sensor micromolePerMeterSquaredPerSecond 1 real NA missing value press atmospheric pressure kilopascal 0.01 real NA missing value sp.code code for species sampled bb Rubus allegheniensis hf Dennstaedtia punctilobula pc Prunus pensylvanica rm Acer rubrum ro Quercus rubra eb Sambucus pubens kw Polygonum sp. bc Prunus serotina rr Oryzopsis asperifolia wf Dryopteris spp. grass Carex spp. pb Betula papyrifera canadian Maianthemum canadense ws Aralia nudicaulis NA missing value notes notes notes NA missing value 1638 hf224-02-light-response.csv light response curves hf224-02-light-response.csv 400822 37543d2ce1c8c771e70d3456996b0297 1 \r\n column , https://harvardforest.fas.harvard.edu/data/p22/hf224/hf224-02-light-response.csv data.id data id data id NA missing value datetime date and time of measurement YYYY-MM-DDThh:mm 1 second NA missing value date date sampled YYYY-MM-DD 1 day NA missing value year year sampled YYYY 1 year NA missing value month month sampled month sampled NA missing value day day of month day of month NA missing value doy corresponding day of the year nominalDay 1 natural NA missing value common.name common species name common species name NA missing value scientific.name scientific species name scientific species name NA missing value short.code two letter code for species name two letter code for species name NA missing value species.code two letter code for species name two letter code for species name NA missing value curve.no curve number curve number NA missing value time time hh:mm 1 min NA missing value leaf leaf replicate leaf replicate NA missing value anet net assimilation in micromols CO2 per meter squared per second micromolePerMeterSquaredPerSecond 0.1 real NA missing value cond conductance to H2O in millimols of H2O per meter squared per second millimolePerMeterSquaredPerSecond 0.001 real NA missing value ci intercellular CO2 concentration (calculated) in micromols CO2 per mol dimensionless 1 real NA missing value trans transpiration rate in millimol H2O per meter squared per second millimolePerMeterSquaredPerSecond 0.1 real NA missing value vpdl vapour pressure deficit based on leaf temperature (kPa) kilopascal 0.1 real NA missing value ctleaf computed leaf temperature. Same as Tleaf unless doing energy balance celsius 0.1 real NA missing value area total area of leaf enclosed within the chamber in centimeters squared squareCentimeters 0.1 real NA missing value stm.ratio stomatal Ratio used in calculations dimensionless 0.1 real NA missing value tair temperature in sample cell celsius 0.1 real NA missing value tleaf temperature of leaf thermocouple celsius 0.1 real NA missing value tblk temperature of cooler block celsius 0.1 real NA missing value co2.r reference cell CO2 concentration in micromol CO2 per mol (ppm) dimensionless 1 real NA missing value co2.s sample cell CO2 concentration in micromol CO2 per mol (ppm) dimensionless 1 real NA missing value h2o.r reference cell H2O concentration in millimol H2O per mol (ppm) dimensionless 0.1 real NA missing value h2o.s sample cell H2O concentration in millimol H2O per mol (ppm) dimensionless 0.1 real NA missing value rh.r relative humidity in the reference cell (%) dimensionless 1 real NA missing value rh.s relative humidity in the sample cell (%) dimensionless 1 real NA missing value flow flow rate to the sample cell in micromols per second micromolePerSecond 1 real NA missing value par.in quantum sensor inside the chamber micromolePerMeterSquaredPerSecond 1 real NA missing value par.out external quantum sensor micromolePerMeterSquaredPerSecond 1 real NA missing value press atmospheric pressure kilopascal 0.1 real NA missing value stability stability status dimensionless 0.1 real NA missing value status LI6400 stability diagnostics LI6400 stability diagnotics NA missing value period.sd period when measured, according to Sophie Dyllan period when measured, according to Sophie Dyllan NA missing value species.sd species code used by Sophie Dyllan species code used by Sophie Dyllan NA missing value tree.sd tree number used by Sophie Dyllan tree number used by Sophie Dyllan NA missing value n.id code used to match up leaf nitrogen analysis with gas flux measurements code used to match up leaf nitrogen analysis with gas flux measurements NA missing value leaf.n leaf nitrogen in milligrams of N per gram of dry leaf milligramPerGram 0.1 real NA missing value 1927 hf224-03-co2-response.csv CO2 response curves hf224-03-co2-response.csv 477425 477aeba6eb7b224beb8b508342217ee9 1 \r\n column , https://harvardforest.fas.harvard.edu/data/p22/hf224/hf224-03-co2-response.csv data.id data id data id NA missing value datetime date and time of measurement YYYY-MM-DDThh:mm 1 second NA missing value date date sampled YYYY-MM-DD 1 day NA missing value year year sampled YYYY 1 year NA missing value month month sampled month sampled NA missing value day day of month day of month NA missing value doy corresponding day of the year nominalDay 1 natural NA missing value common.name common species name common species name NA missing value scientific.name scientific species name scientific species name NA missing value short.code shortened code for scientific name shortened code for scientific name NA missing value species.code two letter code for species name two letter code for species name NA missing value curve.no curve number curve number NA missing value time time hh:mm 1 minute NA missing value leaf leaf replicate leaf replicate NA missing value photo net assimilation in micromols CO2 per meter squared per second micromolePerMeterSquaredPerSecond 0.1 real NA missing value cond conductance to H2O in millimols of H2O per meter squared per second millimolePerMeterSquaredPerSecond 0.001 real NA missing value ci intercellular CO2 concentraion (calculated) in micromols CO2 per mol dimensionless 1 real NA missing value trans transpiration rate in millimol H2O per meter squared per second millimolePerMeterSquaredPerSecond 0.1 real NA missing value vpdl vapour pressure deficit based on leaf temperature kilopascal 0.01 real NA missing value ctleaf computed leaf temperature. Same as Tleaf unless doing energy balance celsius 0.1 real NA missing value area total area of leaf enclosed within the chamber in centimeters squared squareCentimeters 1 real NA missing value stm.ratio stomatal ratio used in calculations dimensionless 0.1 real NA missing value tair temperature in sample cell celsius 0.1 real NA missing value tleaf temperature of leaf thermocouple celsius 0.1 real NA missing value tblk temperature of leaf thermocouple celsius 0.1 real NA missing value co2.r reference cell CO2 concentration in micromol CO2 per mol (ppm) dimensionless 1 real NA missing value co2.s sample cell CO2 concentration in micromol CO2 per mol (ppm) dimensionless 1 real NA missing value h2o.r reference cell H2O concentration in millimol H2O per mol (ppm) dimensionless 0.1 real NA missing value h2o.s sample cell H2O concentration in millimol H2O per mol (ppm) dimensionless 0.1 real NA missing value rh.r relative humidity in the reference cell (%) dimensionless 1 real NA missing value rh.s relative humidity in the sample cell (%) dimensionless 1 real NA missing value flow flow rate to the sample cell in micromols per second micromolePerSecond 1 real NA missing value par.in quantum sensor inside the chamber micromolePerMeterSquaredPerSecond 1 real NA missing value par.out external quantum sensor micromolePerMeterSquaredPerSecond 1 real NA missing value press atmospheric pressure kilopascal 0.1 real NA missing value stability stability status dimensionless 0.1 real NA missing value status LI6400 stability diagnostics LI6400 stability diagnostics NA missing value period.sd period when measured, according to Sophie Dyllan period when measured, according to Sophie Dyllan NA missing value species.sd species code used by Sophie Dyllan species code used by Sophie Dyllan NA missing value tree.sd tree number used by Sophie Dyllan tree number used by Sophie Dyllan NA missing value n.id code used to match up leaf nitrogen analysis with gas flux measurements code used to match up leaf nitrogen analysis with gas flux measurements NA missing values leaf.n leaf nitrogen in milligrams of N per gram of dry leaf milligramPerGram 0.1 real NA missing value 2288 informatics atmosphere community short-term measurement modeling https://wordpress.clarku.edu/cwilliams/ https://harvardforest.fas.harvard.edu/exist/apps/datasets/showData.html?id=hf223 https://harvardforest.fas.harvard.edu/exist/apps/datasets/showData.html?id=hf222 millimolePerMeterSquaredPerSecond SI unit of amount of substance flux milligramPerGram