Bryant et al. 2022 Dataset:
	Title: Data from: Boosts in leaf-level photosynthetic capacity aid Pinus ponderosa recovery from wildfire 
	Dataset DOI: 10.7923/cn15-jw37 

Data, code and/or products within this dataset support the following manuscript:
	Manuscript Title: Boosts in leaf-level photosynthetic capacity aid Pinus ponderosa recovery from wildfire 
	Journal: Environmental Research Letters
	Manuscript DOI: NA, In Review

Description/Abstract:
	Forests mitigate climate change by sequestering massive amounts of carbon, but recent increases in wildfire activity are threatening carbon storage. Currently, our understanding of wildfire impacts on forest resilience and the mechanisms controlling post-fire recovery remains unresolved due to a lack of empirical data on mature trees in natural settings. Here, we quantify the physiological mechanisms controlling carbon uptake immediately following wildfire in mature individuals of ponderosa pine (Pinus ponderosa), a wide-spread and canopy-dominant tree species in fire-prone forests. While photosynthetic capacity was lower in burned than unburned trees due to an overall depletion of resources, we show that within the burned trees, photosynthetic capacity increases with the severity of damage. Our data reveal that boosts in the efficiency of carbon uptake at the leaf-level may compensate for whole-tree damage, including the loss of leaf area and roots. We further show that heightened photosynthetic capacity in remaining needles on burned trees may be linked with reduced water stress and leaf nitrogen content, providing pivotal information about post-fire physiological processes. Our results have implications for Earth system modeling efforts because measurements of species-level physiological parameters are used in models to predict ecosystem and landscape-level carbon trajectories. Finally, current land management practices do not account for physiological resilience and recovery of severely burned trees. Our results suggest premature harvest may remove individuals that may otherwise survive, irrevocably altering forest carbon balance.

	**Data Use**:
	*License*: Creative Commons Attribution ([CC-BY 4.0](https://creativecommons.org/licenses/by/4.0/))
    *Recommended Citation*: Bryant, K., Kwon, H., Kolden, C., Stenzel, J., Mathias, J., Lynch, L., & Hudiburg, T. (2022). Data from: Boosts in leaf-level photosynthetic capacity aid Pinus ponderosa recovery from wildfire (Version 2.0) [Data set]. University of Idaho. https://doi.org/10.7923/CN15-JW37

Resource URL: https://data.nkn.uidaho.edu/dataset/data-boosts-leaf-level-photosynthetic-capacity-aid-pinus-ponderosa-recovery-wildfire	

Creator(s):	
	1. Kelsey Bryant
		Unique identifier: https://orcid.org/0000-0003-3443-0466
		Affiliation(s): University of Idaho, Department of Forest, Rangeland, and Fire Sciences
	2. Hyojung Kwon
		Unique identifier: https://orcid.org/0000-0002-1713-3104
		Affiliation(s): Oregon State University, Department of Forest Ecosystems and Society
	3. Crystal Kolden
		Unique identifier: https://orcid.org/0000-0001-7093-4552
		Affiliation(s): University of California, Merced, Department of Management of Complex Systems
	4. Jeffrey Stenzel
		Unique identifier: https://orcid.org/0000-0001-8881-0566
		Affiliation(s): University of California, Merced, Department of Management of Complex Systems
	5. Justin Mathias
		Unique identifier: https://orcid.org/0000-0001-5470-4167 
		Affiliation(s): University of Idaho, Department of Forest, Rangeland, and Fire Sciences
	6. Laurel Lynch
		Unique identifier: https://orcid.org/0000-0002-8825-9417
		Affiliation(s): University of Idaho, Department of Soil and Water Systems
	7. Tara W. Hudiburg
		Unique identifier: https://orcid.org/0000-0003-4422-1510
		Affiliation(s): University of Idaho, Department of Forest, Rangeland, and Fire Sciences
	
Other Contributor(s): NA 

Publisher: 
	University of Idaho

Publication Year:
	2022

Language(s):
	American English

Subject(s):
	1. Natural sciences
		1.5 Earth and related Environmental sciences
		1.6 Biological sciences

Keywords/Tags:
	wildfire response, conifer physiology, photosynthesis, water potential, root density

Resource Type General: 
	Dataset
		
Dates: NA

Date available for the public: 2022-09-15
	
Sizes: 803 KB (total)
	Leaf_water_potential_data_2021.csv - 3 KB
	Needle_nitrogen_data_2021.csv - 2 KB
	Photosynthesis_data_Amax_2020_2021.csv - 8 KB
	R_code_all_models.R - 7 KB
	readme.txt - 24 KB
	Root density and tree damage data_2021.csv - 14 KB
	Soil respiration data_2020_2021.csv - 642 bytes
	Soil_water_content_2020_2021.csv - 736 KB
	Vcmax data_2021.csv - 1 KB
	 
Format(s):
	.csv (7)
	.R (1)
	.txt (1)
 
Version: 2.0 
	
Funding References: 
	US National Science Foundation 
		Division of Environmental Biology
			Award: DEB-2052571
			URL: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2052571
			Title: RAPID: Collaborative Research: In-situ forest ecosystem response to wildfire
 
Spatial/Geographical Coverage Location: 
	Study Area Description: Cascade Range in central Oregon USA
		Point Location: -121.967, 44.06667 
			Details: The study site is a mature ponderosa pine forest located east of the Cascade Range in central Oregon (44°4’N, 121°55W) and is a long-term AmeriFlux site. The overstory is dominated by ponderosa pine (Pinus ponderosa), with a mean tree age of 60 – 80 years. Prior to the fire, incense cedar (Calocedrus decurrens) was intermittently dispersed in the sub-canopy, but not prevalent. Understory shrubs consisted mainly of bitterbrush (Purshia tridentata) and greenleaf manzanita (Arctostaphylos patula) preceding the fire, and were completely consumed with no re-sprout. Average tree height was approximately 20 m and average diameter at breast height (DBH) was around 40 cm (height and DBH recorded in 2020 during initial measurements post-fire). Total basal area was ca. 33 m2 ha-1 post-fire. 
			Climate: The climate is semiarid with warm, dry summers and cool, wet winters that provide the majority of the annual precipitation (300 – 600 mm). Prolonged summer drought is typical for these forests, but substantial water availability from winter snow melt is enough to sustain the trees through dry summers. The site sits on a flat plain at 1255 m elevation atop sandy loam and well-drained soils and is located just east of the north-south oriented Green Ridge. 
	 
Temporal Coverage: 
	Start Data: 2020-09-01
	End Date: 2021-08-20
 
Granularity of the Data: Monthly/seasonal, tree/site-level 
 
Contact Info: 
	Contact Name: Kelsey Bryant
	Contact Email: kelseybryant@uidaho.edu
 
Related Content: 
	Peer Reviewed Manuscript-Environmental Research Letters (In Review):   
	Lab Website: https://iteamlab.weebly.com/ 	

Data Files:
	Leaf_water_potential_data_2021.csv: Data file containing leaf water potential (in megapascals) values, which represent tree water stress, in trees that were burned compared to trees that were unburned. Data were collected in June and August 2021, less than one-year after the fire and during the first growing season. Burned trees are further described by a continuous variable quantifying the degree of tree damage inflicted by the fire.
		Header Key:
			Month: Categorical assignment based on the month the sample/observation was collected
				Values:
					June: Categorical assignment for all measurements collected in June 2021
					August: Categorical assignment for all measurements collected in August 2021
			Tree.ID: Categorical assignment based on the individual tree identification; random numeric value assigned during initial tree surveys
			Burn.status: Categorical assignment based on whether the tree was burned or not
				Values:
					Burned: Categorical assignment for all trees that were burned, regardless of degree of damage 
					Unburned: Categorical assignment for trees that were not burned at all, and thus, have no tree damage
			Branch.replicate: Integer-based assignment for branch replicates within a single tree
			leaf.replicate: Integer-based assignment for leaf replicates within a single branch
			water.potential: Continuous variable; only negative values. Describes the leaf water potential measured on each needle with a Scholander pressure chamber, and represents the degree of water stress in the tree
			sample.height_m: Continuous variable for height at which branch samples were extracted from the tree; measured in meters with a Laser RangeFinder
			Tree.damage: Continuous variable describing the degree of fire damage on the tree; correlates to the amount of green needles remaining. Calculated as the ratio of the heighest red needle to the total height of the tree. All heights measured in meters with a Laser RangeFinder
	Photosynthesis_data_Amax_2020_2021.csv: Data file containing measurements of maximum photosynthetic rate (Amax; measured in micromoles of CO2 per meter squared per second) in trees that were burned compared to trees that were unburned. Data were collected monthly immediately after the fire, and during the following growing season. Burned trees are further described by a continuous variable quantifying the degree of tree damage inflicted by the fire.
		Header Key:
			Date: Date sample/observation was collected in ISO8601 format (yyyy-mm-dd)
			Month: Categorical assignment based on the month sample/observation was collected 
				Values:
					September: Categorical assignment for all measurements collected in September 2020
					October: Categorical assignment for all measurements collected in October 2020
					November: Categorical assignment for all measurements collected in November 2020
					June: Categorical assignment for all measurements collected in June 2021
					August: Categorical assignment for all measurements collected in August 2021
			Tree.ID: Categorical assignment based on the individual tree identification; random numeric value assigned during initial tree surveys
			Needle.Replicate: Integer-based assignment for replicates within a single needle
			Tree.damage: Continuous variable describing the degree of fire damage on the tree; correlates to the amount of green needles remaining. Calculated as the ratio of the highest red needle to the total height of the tree. All heights measured in meters with a Laser RangeFinder
			Photo: Continuous variable describing the maximum photosynthetic rate on an individual leaf using a Li-Cor 6400 Infrared Gas Analyzer (portable photosynthesis system); Values are point measurements obtained by exposing the needle to ideal environmental conditions (1500 PAR, ambient CO2 [~400ppm], 20 Celsius) inside of a closed chamber and allowing the sample to acclimate for two minutes before logging a measurement.
			Burn.status: Categorical assignment based on whether the tree was burned or not
				Values:
					Burned: Categorical assignment for all trees that were burned, regardless of degree of damage
					Unburned: Categorical assignment for trees that were not burned at all, and thus, have no tree damage
	Root_density_and_tree_damage_data_2021.csv: Data file containing maximum photosynthesis (Amax) values (represents tree water stress) in trees that were burned; burned trees are further described by a continuous variable (BurnIndex) quantifying the degree of tree damage inflicted by the fire.
		Header Key:
			Species: Categorical assignment for individuals of trees within a single species
				Values:
					Pipo: Categorical assignment for individuals of trees within the species Pinus ponderosa; the abbreviation is the first two letters of both the genus and species names
			Tree.ID: Categorical assignment based on the individual tree identification; random numeric value assigned during initial tree surveys
			Dripline: Categorical assignment describing location where the sample was taken relative to the canopy/crown area of the associated tree
				Values:
					In: Categorical assignment for samples extracted inside of the relative area of the tree crown
					Out: Categorical assignment for samples extracted outside of the relative area of the tree crown
			BurnSide: Categorical assignment for location where the sample was taken relative to the degree of fire damage of the associated tree
				Values:
					HighBurn: Categorical assignment for samples taken on the side of the tree that was most severely damaged by fire
					LowBurn: Categorical assignment for samples taken on the side of the tree that was least damaged by fire
					Control: Categorical assignment for samples taken on unburned trees that were not damaged at all by fire
			Direction_degrees: Integer-based assignment describing the direction (relative to the associated tree) where each sample was taken
			RootSize_mm: Categorical assignment describing size of roots (millimeters) included in each sample
				Values:
					<2: Categorical assignment referring to roots that are less than two millimeters in diameter
					2-5: Categorical assignment referring to roots that are between two and five millimeters in diameter
					>5: Categorical assignment referring to roots that are more than five millimeters in diameter
			DryRootWeight_g: Continuous variable quantifying the total mass (grams) of dried root sample within each category, in each sample
			CoreDepth_cm: Continuous variable quantifying the depth at which the sample cores were taken
			RootDensity_mgRoot_cm3Soil: Continuous variable quantifying the density (milligrams) of root sample relative to the total volume of the sample
			dbh_cm: Continuous variable describing the diameter (in centimeters) of each tree; refers to diameter at breast height and was measured with DBH tape at ~4.36 meters on each tree
			BurnIndex: Continuous variable describing the degree of fire damage on the tree; synonymous with 'Tree damage' and is calculated as the ratio of the highest red needle to the total height of the tree. All heights measured in meters with a Laser RangeFinder
			ht_m: Continuous variable describing the total height (in meters) of each tree; measured with a Laser RangeFinder
			bole.char.ht_m: Continuous variable describing the total height (in meters) of the visible fire damage (referred to as char) on the stem (referred to as bole) of each tree; measured with a Laser RangeFinder
	Soil_respiration_data_HK_2020_2021.xlsx: Data including summary soil respiration values (measured in micromoles of CO2 per meter squared per second) immediately after and following the fire. Measurements were collected with a Li-Cor 6400 Infrared Gas Analyzer using a specialized soil respiration chamber.
		Header Key:
			Year: Integer-based assignment based on the year in which samples/observations were collected
				Values:
					2020: Categorical assignment for all measurements collected during 2020, immediately after fire
					2021: Categorical assignment for all measurements collected during 2021, during first growing season after fire
			Month: Categorical assignment based on the month sample/observation was collected 
				Values:
					Sept: Categorical assignment for all measurements collected in September 2020
					Oct: Categorical assignment for all measurements collected in October 2020
					Nov: Categorical assignment for all measurements collected in November 2020
					June: Categorical assignment for all measurements collected in June 2021
					August: Categorical assignment for all measurements collected in August 2021
			Soil.burn.severity: Categorical assignment based on level of damage of soil inflicted by fire; determined using the Field Guide for Mapping Post-Fire Soil Burn Severity (Parsons et al. 2010, USDA)
				Values:
					Low: Categorical assignment for areas of soil with low soil damage; Surface organic layers are not completely consumed and are still recognizable. Structural aggregate stability is not changed from its unburned condition, and roots are generally unchanged because the heat pulse below the soil surface was not great enough to consume or char any underlying organics. The ground surface, including any exposed mineral soil, may appear brown or black (lightly charred), and the canopy and understory vegetation will likely appear “green.”
					Moderate: Categorical assignment for areas of soil with moderate soil damage; Up to 80 percent of the pre-fire ground cover (litter and ground fuels) may be consumed but generally not all of it. Fine roots (~0.1 inch or 0.25 cm diameter) may be scorched but are rarely completely consumed over much of the area. The color of the ash on the surface is generally blackened with possible gray patches. There may be potential for recruitment of effective ground cover from scorched needles or leaves remaining in the canopy that will soon fall to the ground. The prevailing color of the site is often “brown” due to canopy needle and other vegetation scorch. Soil structure is generally unchanged.
					High: Categorical assignment for areas of soil with high soil damage; All or nearly all of the pre-fire ground cover and surface organic matter (litter, duff, and fine roots) is generally consumed, and charring may be visible on larger roots. The prevailing color of the site is often “black” due to extensive charring. Bare soil or ash is exposed and susceptible to erosion, and aggregate structure may be less stable. White or gray ash (up to several centimeters in depth) indicates that considerable ground cover or fuels were consumed. Sometimes very large tree roots (> 3 inches or 8 cm diameter) are entirely burned extending from a charred stump hole. Soil is often gray, orange, or reddish at the ground surface where large fuels were concentrated and consumed.
			Mean.soil.respiration: Continous variable quantifying mean soil respiration (micromols of CO2 per meter squared per second) for each category of soil damage, for each month
			Std. error: Continuous variable for the standard error associated with the mean measurement of soil respiration
			seven.year.mean: Continuous variable quantifying mean soil respiration for previous seven years (2012-2019) for each month
			seven.year.std.error: Continuous variable for standard error associated with the seven-year mean values for each month	
	Soil_water_content_2020_2021.csv: Data file containing soil water content values (measured as volumetric water content) for each area of soil damage
		Header Key:
			Measurement.Time: Time that the sample/observation was measured in ISO8601 format yyyy-mm-dd HH:MM:SS with hour in 24-hour format and recorded in the USA Pacific Time Zone.
			DOY: Integer-based assignment representing the numeric day of the current calendar year.
			VWC: Continuous variable quantifying the volumetric water content (%/%) for each area of soil damage
			soil.burn.sev: Categorical assignment based on level of damage of soil inflicted by fire; determined using the Field Guide for Mapping Post-Fire Soil Burn Severity (Parsons et al. 2010, USDA)
				Values:
					Low: Categorical assignment for areas of soil with low soil damage; Surface organic layers are not completely consumed and are still recognizable. Structural aggregate stability is not changed from its unburned condition, and roots are generally unchanged because the heat pulse below the soil surface was not great enough to consume or char any underlying organics. The ground surface, including any exposed mineral soil, may appear brown or black (lightly charred), and the canopy and understory vegetation will likely appear “green.”
					Moderate: Categorical assignment for areas of soil with moderate soil damage; Up to 80 percent of the pre-fire ground cover (litter and ground fuels) may be consumed but generally not all of it. Fine roots (~0.1 inch or 0.25 cm diameter) may be scorched but are rarely completely consumed over much of the area. The color of the ash on the surface is generally blackened with possible gray patches. There may be potential for recruitment of effective ground cover from scorched needles or leaves remaining in the canopy that will soon fall to the ground. The prevailing color of the site is often “brown” due to canopy needle and other vegetation scorch. Soil structure is generally unchanged.
					High: Categorical assignment for areas of soil with high soil damage; All or nearly all of the pre-fire ground cover and surface organic matter (litter, duff, and fine roots) is generally consumed, and charring may be visible on larger roots. The prevailing color of the site is often “black” due to extensive charring. Bare soil or ash is exposed and susceptible to erosion, and aggregate structure may be less stable. White or gray ash (up to several centimeters in depth) indicates that considerable ground cover or fuels were consumed. Sometimes very large tree roots (> 3 inches or 8 cm diameter) are entirely burned extending from a charred stump hole. Soil is often gray, orange, or reddish at the ground surface where large fuels were concentrated and consumed.
	Vcmax_data_2021.csv: Data containing measurements of the maximum rate of carboxylation (VCmax) for burned trees with varying degrees of fire damage
		Header Key:
			Month: Categorical assignment based on the month the sample/observation was collected
				Values:
					June: Categorical assignment for all measurements collected in June 2021
					August: Categorical assignment for all measurements collected in August 2021
			Burn.status: Categorical assignment based on whether the tree was burned or not
				Values:
					Burned: Categorical assignment for all trees that were burned, regardless of degree of damage
					Unburned: Categorical assignment for trees that were not burned at all, and thus, have no tree damage
			Tree.ID: Categorical assignment based on the individual tree identification; random numeric value assigned during initial tree surveys
			Tree.damage: Continuous variable describing the degree of fire damage on the tree; correlates to the amount of green needles remaining. Calculated as the ratio of the heighest red needle to the total height of the tree. All heights measured in meters with a Laser RangeFinder
			Vcmax: Continuous variable quantifying the maximum rate of carboxylation (VCmax; measured in micromoles of CO2 per meter squared per second). Referred to as photosynthetic capacity and is calculated from A/Ci curves using the Li-Cor 6400 Infrared gas analyzer (portable photosynthesis system)
			Vcmax_SE: Continuous variable for the standard error associated with the Vcmax values for each tree
			Water.potential: Continuous variable; only negative values. Describes the leaf water potential measured on each needle with a Scholander pressure chamber, and represents the degree of water stress in the tree. 
			water.pot_SE: Continuous variable for the standard error associated with the water potential measurements in this data set
	Needle_nitrogen_data_2021.csv:
		Header Key:
			Month: Categorical assignment based on the month the sample/observation was collected
				Values:
					June: Categorical assignment for all measurements collected in June 2021
					August: Categorical assignment for all measurements collected in August 2021
			Tree.ID: Categorical assignment based on the individual tree identification; random numeric value assigned during initial tree surveys
			Tree.damage: Continuous variable describing the degree of fire damage on the tree; correlates to the amount of green needles remaining. Calculated as the ratio of the heighest red needle to the total height of the tree. All heights measured in meters with a Laser RangeFinder
			Burn.status: Categorical assignment based on whether the tree was burned or not
				Values:
					Burned: Categorical assignment for all trees that were burned, regardless of degree of damage
					Unburned: Categorical assignment for trees that were not burned at all, and thus, have no tree damage
			d15N: delta 15 Nitrogen, refers to the isotopic composition and represents the ratio of stable nitrogen isotopes in per mil notation
			percentN: percent nitrogen; represents percent of total needle tissue that is made up of nitrogen
Code Files:
	R_code_all_models.R: Script file that contains R code to run all models and analyses