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At least 19 records

Leafweb: Leaf Gas Exchange and Pulse-Amplitude Modulated Fluorometry for C4 Species, June 2026 Release

This dataset contains leaf gas exchange and Pulse-Amplitude Modulated (PAM) fluorometry for 98 C4 species. The C4 photosynthetic pathway employs specialized CO2 concentration mechanisms and Kranz anatomy to enrich CO2 concentration around Rubisco, the enzyme that catalyzes carbon fixation in the Calvin-Benson cycle to suppress photorespiration and increase the use efficiencies of light, nitrogen, and water as compared to the C3 photosynthetic pathways. Large-scale C4 photosynthetic datasets are relatively scarce, which has affected C4 photosynthesis research. To improve C4 photosynthetic data availability, Leafweb organized an effort to systematically collect, compile, standardize, and organize measurements of leaf gas exchange and/or Pulse-Amplitude Modulated (PAM) fluorometry of C4 species. This derived a C4 photosynthetic dataset containing measurements made by independent researchers in multiple countries in various environments (field, garden, or greenhouse). It covers three biochemical subtypes – the nicotinamide adenine dinucleotide phosphate-malic enzyme (NADP-ME), nicotinamide adenine dinucleotide-malic enzyme (NAD-ME), and phosphoenolpyruvate carboxykinase (PEP-CK) subtypes. This dataset is useful for using Artificial Intelligence / Machine Learning and mechanistic models to study C4 photosynthesis and compare across different biochemical subtypes. This dataset contains 3 compressed (*.zip) folders containing 1,892 data files in comma-separate values (*.csv) format. Additional metadata are provided: one data dictionary and a file-level metadata file in comma-separate values (*.csv) format and a user guide in PDF (*.pdf) format.

Zhou, Haoran [Tianjin University, China]↗

Stomata in-sight: Integrating live confocal microscopy with leaf gas exchange and environmental control

Stomatal anatomy (aperture area, length, and width) influences leaf-level physiology traits including conductance to water vapor. Stomatal anatomy can be visualized in situ by microscopy, but the difficulty of regulating the atmospheric environment of a microscope stage means that the conditions under which imaging is done are rarely physiologically relevant. Alternatively, leaf gas exchange instruments that measure gas fluxes reflect stomatal anatomical characteristics in aggregate, but the relative strengths of anatomical traits to control water use (e.g. size vs density) cannot be firmly established. To reconcile the microscopic stomatal characteristics with leaf-level gas exchange, we describe a tool that combines laser scanning confocal microscopy, gas exchange instruments, and machine-learning image analysis to simultaneously observe anatomical characteristics of many (>40) stomata alongside leaf-level traits like photosynthesis, transpiration, and stomatal conductance. We demonstrate how the tool has the resolution capable of quantifying aperture sizes and variability in maize (Zea mays) leaves under 5 steady-state light/pCO 2 treatments while tightly controlling other environmental variables like relative humidity and temperature. A model used to calculate stomatal conductance from measured apertures and stomatal density accurately matched stomatal conductance measured by gas exchange. This technical advancement will provide insight on how stomatal anatomy and function trade off to influence stomatal conductance and leaf-level water use efficiency.

59 BASIC BIOLOGICAL SCIENCES↗

Leaf gas exchange raw data, 2015 - 2017, at Manaus, Brazil

This data package contains raw leaf gas exchange data from the NGEE Tropics K34 tower site on a plateau near Manaus, Brazil. Data was collected using sensor and leaf sample measurements. Leaves on a target tree were chosen by accessing a branch near the tower. In some cases, the branch was naturally positioned near the tower and in other cases, a small rope was used to pull the branch closer to the tower for better access to leaves. Mature leaves were targeted in nearly all cases. The gas exchange system was hauled with a climbing rope to the level of the branch on the tower and the sensor head/leaf enclosure was installed near the branch of interest using a magic arm. We measured leaf gas exchange from 5:00 AM to 5:00 PM, randomly cycling through the approximately 20 leaves in the targeted branch(es). Data were collected over two time periods, detailed within the files. The attached data files contain raw data, sensor manuals, and PDFs with detailed methods and procedures separated into multiple folders. Data is in Excel file format. See data references for data package containing related metadata. This dataset replaces the leaf gas exchange data of two retired packages, NGT0019 and NGT0040.

54 ENVIRONMENTAL SCIENCES↗

Leaf gas exchange, leaf water potential and spectral reflectance, BIONTE, Brazil, 2023

Leaf traits measured at the top of the canopy on 30 tree species in the BIONTE experimental forest, near Manaus, Brazil, at three time points during August to November, 2023. The aim of this study was to test the relationship between leaf water use efficiency and wood density. Leaf gas exchange was measured on top-of-canopy leaves accessed by an articulated boom lift. Response curves (A-Ci and A-Q), and dark adapted respiration were measured on cut branches. Survey gas exchange measurements were performed on attached leaves at various times during the day. Following gas exchange, leaves were harvested, and measured for leaf water potential and spectral reflectance. Data in this data package is presented in csv files, with metadata in csv and descriptive experimental protocols as pdf. Gas exchange data and metadata meets the requirements of the ESS-DIVE reporting format for leaf-level gas exchange data and metadata.

54 ENVIRONMENTAL SCIENCES↗

Leaf gas exchange, spectral reflectance and leaf composition, BIONTE, Brazil, 2022

Leaf traits measured at the top of the canopy on 10 species at the BIONTE experimental plot T1B4SB3, near Manaus, Brazil, in August and September, 2022. The aim of this study was to test the relationship between leaf water use efficiency and wood density. Ten tree species located in close proximity of each other (within 50 meters) were selected and classified by wood density (low or high). Sampling was carried out on top-of-canopy leaves accessed by an articulated boom lift. Survey gas exchange measurement were performed on attached leaves at various times during the day. Following gas exchange, the leaf was harvested, and measured for spectral reflectance, leaf water content, leaf mass per area and leaf carbon content and leaf nitrogen content. Additional leaves other than those used for gas exchange were also harvested from different branches on the same tree for spectral reflectance and leaf trait measurements. Data in this data package is presented in csv files, with metadata in csv and descriptive experimental protocols as pdf. Gas exchange data and metadata meets the requirements of the ESS-DIVE reporting format for leaf gas exchange data and metadata.

54 ENVIRONMENTAL SCIENCES↗

Leaf gas exchange data, Nov 2018 and May 2019, Daintree Rainforest, Australia

This data package contains leaf gas exchange data for 11 canopy tree species in the control and drought treatments at the Daintree Rainforest Observatory in Queensland, Australia (AU-DRO) with the purpose of testing for differences in gas exchange between treatments. Data were collected at the end of the dry season (November 2018) and end of the wet season (May 2019). Using a canopy crane, large branches (>1 m) were collected from the top of the canopy and immediately placed in a bucket of water, upon which the LI-6800 leaf chamber was clamped onto a recently mature leaf with minimal herbivory. Measurements were recorded every 3 seconds for 3 minutes total. The species included in the dataset are: Castanospermum australe, Cleistanthus myrianthus, Cryptocarya mackinnoniana, Dysoxylum papuanum, Elaeocarpus angustifolius (Elaeocarpus grandis), Endiandra microneura, Mallotus paniculatus, Myristica globosa, Rockinghamia angustifolia, Synima cordierorum, Syzygium spp. The two data files included are: 1. LICOR_Data_AU_DRO_2019_GasEx.csv (a compilation of individual LICOR output files, with correction of user input errors such as incorrect species spelling) 2. ESS_DIVE_Data_AU_DRO_2019_GasEx.csv (selected variables and converted units from LICOR_Data_AU_DRO_2019_GasEx.csv to follow the standard gas exchange reporting format from Ely et al. 2021 Ecological Informatics). The metadata files included are: (3) ESS_DIVE_Metadata_AU_DRO_2019_GasEx.xlsx (4) File_Submission_Metadata_AU_DRP_2019_GasEx.xlsx (5) E-Field_Log_AU_DRO_2019_GasEx.xlsx (6) Data_Column_Description_AU_DRO_2019_GasEx.xlsx.

54 ENVIRONMENTAL SCIENCES↗

ESS-DIVE reporting format for leaf-level gas exchange data and metadata

Here we present documentation of the ESS-DIVE reporting format for leaf-level gas exchange data and metadata. This reporting format provides guidance to data contributors on how to store data to maximize their discoverability, facilitate their efficient reuse, and add value to individual datasets. For data users, the reporting format will better allow data repositories to optimize data search and extraction, and more readily integrate similar data into harmonized synthesis products. The reporting format specifies data table variable naming and unit conventions, as well as metadata characterizing experimental conditions and protocols. For common data types that were the focus of this initial version of the reporting format, i.e., survey measurements, dark respiration, carbon dioxide and light response curves, and parameters derived from those measurements, we took a further step of defining required additional data that would maximize the potential reuse of those data types. To aid data contributors and the development of data ingest tools by data repositories we provided a translation table comparing the outputs of common gas exchange instruments. The reporting format presented here is intended to form a foundation for future development that will incorporate additional data types and variables as gas exchange systems and measurement approaches advance in the future. The reporting format documentation is maintained and updated on the ESS-DIVE Community Space GitHub. This data package is the first published version of this reporting format, and comprises a zip file of the complete content of https://github.com/ess-dive-community/essdive-leaf-gas-exchange v1.0. The zip contains the reporting format description, guidelines, variable tables and instructions in GitHub markdown language (*.md) and 2 metadata templates as spreadsheets with drop down options (*.xlsx files, also function in GoogleSheets).

54 ENVIRONMENTAL SCIENCES↗

Coupled Gas-Exchange Model for C4 Leaves Comparing Stomatal Conductance Models

Plant simulation models are abstractions of plant physiological processes that are useful for investigating the responses of plants to changes in the environment. Because photosynthesis and transpiration are fundamental processes that drive plant growth and water relations, a leaf gas-exchange model that couples their interdependent relationship through stomatal control is a prerequisite for explanatory plant simulation models. Here, we present a coupled gas-exchange model for C4 leaves incorporating two widely used stomatal conductance submodels: Ball–Berry and Medlyn models. The output variables of the model includes steady-state values of CO2 assimilation rate, transpiration rate, stomatal conductance, leaf temperature, internal CO2 concentrations, and other leaf gas-exchange attributes in response to light, temperature, CO2, humidity, leaf nitrogen, and leaf water status. We test the model behavior and sensitivity, and discuss its applications and limitations. The model was implemented in Julia programming language using a novel modeling framework. Our testing and analyses indicate that the model behavior is reasonably sensitive and reliable in a wide range of environmental conditions. The behavior of the two model variants differing in stomatal conductance submodels deviated substantially from each other in low humidity conditions. The model was capable of replicating the behavior of transgenic C4 leaves under moderate temperatures as found in the literature. The coupled model, however, underestimated stomatal conductance in very high temperatures. This is likely an inherent limitation of the coupling approaches using Ball–Berry type models in which photosynthesis and stomatal conductance are recursively linked as an input of the other.

59 BASIC BIOLOGICAL SCIENCES↗

Adaptations for gas exchange enabled the elongation of lepidopteran proboscises

The extensive biodiversification of butterflies and moths (Lepidoptera) is partly attributed to their unique mouthparts (proboscis [Pr]) that can span in length from less than 1 mm to over 280mm in Darwin's sphinx moths. Lepi-doptera, similar to other insects, are believed to inhale and exhale respiratory gases only through valve-like spi-racles on their thorax and abdomen, making gas exchange through the narrow tracheae (Tr) challenging for the elongated Pr. How Lepidoptera overcome distance effects for gas transport to the Pr is an open question that is important to understanding how the Pr elongated over evolutionary time. Here, we show with scanning electron microscopy and X-ray imaging that distance effects on gas exchange are overcome by previously unreported micropores on the Pr surface and by superhydrophobic Tr that prevent water loss and entry. We find that the density of micropores decreases monotonically along the Pr length with the maxima proportional to the Pr length and that micropore diameters produce a Knudsen number at the boundary between the slip and transition flow regimes. By numerical estimation, we further show that the respiratory gas exchange for the Pr predominantly occurs via diffusion through the micropores. In conclusion, these adaptations are key innovations vital to Pr elongation, which likely facilitated lepidopteran biodiversification and the radiation of angiosperms by coevolutionary processes.

59 BASIC BIOLOGICAL SCIENCES↗

High Temperature Acclimation of Leaf Gas Exchange, Photochemistry, and Metabolomic Profiles in Populus trichocarpa

High temperatures alter the thermal sensitivities of numerous physiological and biochemical processes that impact tree growth and productivity. Foliar and root applications of methanol have been implicated in plant acclimation to high temperature via the C 1 pathway. Here, we characterized temperature acclimation at 35°C of leaf gas exchange, chlorophyll fluorescence and extractable metabolites of potted Populus trichocarpa saplings and examined potential influences of mM concentrations of methanol added during soil watering over a two-month period. Relative to plants grown under the low growth temperature (LGT), high growth temperature (HGT) plants showed a suppression of leaf water use and carbon cycling including transpiration (E), net photosynthesis (P n ), an estimate of photorespiration (R p ), and dark respiration (R d ), attributed to reductions in stomatal conductance and direct negative effects on gas exchange and photosynthetic machinery. In contrast, HGT plants showed an upregulation of non-photochemical quenching (NPQ t ), the optimum temperature for ETR, and leaf isoprene emissions at 40°C. A large number of metabolites (867) were induced under HGT, many implicated in flavonoid biosynthesis highlighting a potentially protective role for these compounds. Methanol application did not significantly alter leaf gas exchange but slightly reduced the suppression of R d and R p by the high growth temperature while slightly impairing ETR, Fv’/Fm’, and q p . However, we were unable to determine if soil methanol was sufficiently taken up by the plant to have a direct effect on foliar processes. A small number of extracted leaf tissue metabolites (55 out of 10,015) showed significantly altered abundances under LGT and methanol treatments relative to water controls, and this increased in compound number (222) at the HGT. The results demonstrate the large physiological and biochemical impacts of high growth temperature on poplar seedlings and highlights the enhancement of the optimum temperature of ETR as a rapid thermal acclimation mechanism. Finally, although no large effect on leaf physiology was observed, the results are consistent with methanol both impairing photochemistry of the light reactions via formaldehyde toxicity, and stimulating photosynthesis and dark respiration through formate oxidation to CO 2 .

59 BASIC BIOLOGICAL SCIENCES↗

Leaf gas exchange and fitted parameters, two sites in Panama, 2022

Photosynthetic CO2 response curves (ACi curves), light response curves (AQ curves), dark adapted dark respiration, conductance curves, and survey measurements for leaves measured in the Parque Natural Metropolitano (PNM) and Gamboa, Panama, from January to April 2022 are presented. Measurements were made on leaves from 46 different tree, shrub and liana species, from sunlit canopy and understory locations. Leaf area index from 8 vertical profiles at PNM are also included. The aim of this measurement campaign was three-fold: (i) to improve our understanding of the vertical variation in leaf-level water use efficiency; (ii) to develop an understanding of the sensitivity of stomata to changes in environmental conditions, especially light, humidity, and temperature; (iii) to improve models which can predict leaf traits from leaf contact spectral measurements. All the gas exchange data and metadata are presented in .csv files and complete instrument output are included in .zip folders. Data and metadata meet the ESS-DIVE leaf-level gas exchange reporting format requirements. The protocol details are provided as pdf documents. In addition to gas exchange data reported here these samples were also used for measurement of leaf optical properties, carbon and nitrogen content, and leaf mass per unit leaf area (LMA). These data can be cross linked using the unique sample ID and are provided in separate data packages.

54 ENVIRONMENTAL SCIENCES↗

Leaf gas exchange and fitted parameters, San Lorenzo, Panama, 2020

This data package contains photosynthetic CO2 response curves (ACi curves), light response curves (AQ curves), dark adapted dark respiration, conductance curves, and survey measurements for leaves measured at the San Lorenzo forest canopy crane site, Panama (PA-SLZ) from January to March 2020. Leaves were sampled from both the top of the canopy and multiple heights within the canopy from 10 vertical profiles and included around 50 species. In addition, six core species were also measured, from the top of the canopy. Fitted maximum carboxylation rate (Vcmax), maximum electron transport rate (Jmax), and triose phosphate utilization rate (TPU) were derived from measured data as well as the convexity, light use efficiency, apparent quantum yield, and Rdark. The measurements can also be used to derive the conductance parameters g0 and g1 of stomatal model. All the gas exchange data and metadata are presented in .csv files and complete instrument output are included in .zip folders. Data and metadata meet the ESS-DIVE leaf-level gas exchange reporting format requirements. The protocol details are provided as pdf documents. In addition to gas exchange data described here these samples were also used for measurement of leaf optical properties, carbon and nitrogen content, and leaf mass per unit leaf area (LMA) these data can be cross linked using the unique sample ID and are provided in separate related data packages. Sample information including canopy elevation and leaf area index (LAI) can be found in the related “Leaf and canopy traits” data package.

54 ENVIRONMENTAL SCIENCES↗

Consistent responses of vegetation gas exchange to elevated atmospheric CO 2 emerge from heuristic and optimization models

Elevated atmospheric CO 2 concentration is expected to increase leaf CO 2 assimilation rates, thus promoting plant growth and increasing leaf area. It also decreases stomatal conductance, allowing water savings, which have been hypothesized to drive large-scale greening, in particular in arid and semiarid climates. However, the increase in leaf area could reduce the benefits of elevated CO 2 concentration through soil water depletion. The net effect of elevated CO 2 on leaf- and canopy-level gas exchange remains uncertain. To address this question, we compare the outcomes of a heuristic model based on the Partitioning of Equilibrium Transpiration and Assimilation (PETA) hypothesis and three model variants based on stomatal optimization theory. Predicted relative changes in leaf- and canopy-level gas exchange rates are used as a metric of plant responses to changes in atmospheric CO 2 concentration. Both model approaches predict reductions in leaf-level transpiration rate due to decreased stomatal conductance under elevated CO 2 , but negligible (PETA) or no (optimization) changes in canopy-level transpiration due to the compensatory effect of increased leaf area. Leaf- and canopy-level CO 2 assimilation is predicted to increase, with an amplification of the CO 2 fertilization effect at the canopy level due to the enhanced leaf area. The expected increase in vapour pressure deficit (VPD) under warmer conditions is generally predicted to decrease the sensitivity of gas exchange to atmospheric CO 2 concentration in both models. The consistent predictions by different models that canopy-level transpiration varies little under elevated CO 2 due to combined stomatal conductance reduction and leaf area increase highlight the coordination of physiological and morphological characteristics in vegetation to maximize resource use (here water) under altered climatic conditions.

54 ENVIRONMENTAL SCIENCES↗

Diurnal leaf gas exchange survey, Feb2016-May2016, PA-SLZ, PA-PNM: Panama

This data package contains the results of a diurnal leaf gas exchange survey measured on sunlit canopy trees within the NGEE Tropics sites Parque Natural Metropolitano (PA-PNM) and Bosque Protector San Lorenzo (PA-SLZ) in Panama. Measurements were taken on a monthly basis from February to May of 2016. This data was collected as part of the 2016 El Niño-Southern Oscillation (ENSO) campaign. Included in this data package are two Excel files with data (2016ENSO_Panama_DiurnalGasEx, 2016ENSO_Panama_AreaCorrections) and additional Excel files with associated metadata. Also included is a Word document (Metadata_description_2016_ENSO_Panama) with details such as data collection methods, equipment used, and site information. See related datasets for further sample details, leaf water potential, LMA, leaf spectra, other gas exchange and leaf chemistry. VERSION 2 update. The identification of a species from the PNM site has been corrected as follows: the identification of the tree initially identified as Pseudosamanea guachapele (ALBIED) has been revised to Albizia adinocephala (ALBIAD). The updated data package includes revised data, metadata and protocol documents updated to reflect this change.

54 ENVIRONMENTAL SCIENCES↗

CO2 response (ACi) gas exchange, calculated Vcmax & Jmax parameters, Feb2016-May2016, PA-SLZ, PA-PNM: Panama

This data package contains CO2 response (ACi) gas exchange and fitted Vcmax and Jmax parameters measured on sunlit canopy trees within the NGEE Tropics sites Parque Natural Metropolitano (PA-PNM) and Bosque Protector San Lorenzo (PA-SLZ) in Panama. Measurements were taken on a monthly basis from February to May of 2016. This data was collected as part of the 2016 El Niño-Southern Oscillation (ENSO) campaign. Included in this data package are two Excel files with data (2016ENSO_Panama_ACi, 2016ENSO_Panama_Fitted_Vcmax_Jmax) and three Excel files with associated metadata. Also included is a Word document (Metadata_description_2016_ENSO_Panama) with details such as data collection methods, equipment used, and site information and a pdf (NGEE_Tropics_ENSO_Aci_Protocol_V2). See related datasets for further sample details, leaf water potential, LMA, leaf spectra, diurnal gas exchange and leaf chemistry. VERSION 2 update. The identification of a species from the PNM site has been corrected as follows: the identification of the tree initially identified as Pseudosamanea guachapele (ALBIED) has been revised to Albizia adinocephala (ALBIAD). The updated data package includes revised data, metadata and protocol documents updated to reflect this change.

54 ENVIRONMENTAL SCIENCES↗

Raw leaf gas exchange data in the Amazon basin, 2014-2016

This data package contains raw leaf gas exchange data used to support the publication "Leaf isoprene and monoterpene emission distribution across hyperdominant tree genera in the Amazon basin," Phytochemistry, in-press. Data was collected from 162 individuals, distributed among 25 botanical families and 113 species, from four sites in the Amazon. The data was collected using a modified portable photosynthesis system for environmental control coupled to a thermal desorption tube for volatile isoprenoid collections. Collected TD tube samples were analysed in Manaus, Brazil, using thermal desorption-gas chromatography-mass spectrometry (TD-GC-MS). The dataset includes both photosynthesis and isoprene/monoterpene emission rates from leaves under standard environmental conditions as well as controlled light response curves. For detailed methods and raw data, refer to the publication and related material cited in Dataset References.

54 ENVIRONMENTAL SCIENCES↗

Seasonal trends in leaf-level photosynthetic capacity and water use efficiency in a North American Eastern deciduous forest and their impact on canopy-scale gas exchange

Vegetative transpiration (E) and photosynthetic carbon assimilation (A) are known to be seasonally dynamic, with changes in their ratio determining the marginal water use efficiency (WUE). Despite an understanding that stomata play a mechanistic role in regulating WUE, it is still unclear how stomatal and nonstomatal processes influence change in WUE over the course of the growing season. As a result, limited understanding of the primary physiological drivers of seasonal dynamics of canopy WUE remains one of the largest uncertainties in earth system model projections of carbon and water exchange in temperate deciduous forest ecosystems. Here, we investigated seasonal patterns in leaf-level physiological, hydraulic, and anatomical properties, including the seasonal progress of the stomatal slope parameter (g 1 ; inversely proportional to WUE) and the maximum carboxylation rate (V cmax ). V cmax and g 1 were seasonally variable; however, their patterns were not temporally synchronized. g 1 generally showed an increasing trend until late in the season, while V cmax peaked during the midsummer months. Seasonal progression of V cmax was primarily driven by changes in leaf structural, and anatomical characteristics, while seasonal changes in g 1 were most strongly related to changes in V cmax and leaf hydraulics. Using a seasonally variable V cmax and g 1 to parameterize a canopy-scale gas exchange model increased seasonally aggregated A and E by 3% and 16%, respectively.

54 ENVIRONMENTAL SCIENCES↗

Interactive effects of elevated CO 2 , warming, reduced rainfall, and nitrogen on leaf gas exchange in five perennial grassland species

Abstract Global changes can interact to affect photosynthesis and thus ecosystem carbon capture, yet few multi‐factor field studies exist to examine such interactions. Here, we evaluate leaf gas exchange responses of five perennial grassland species from four functional groups to individual and interactive global changes in an open‐air experiment in Minnesota, USA, including elevated CO 2 (eCO 2 ), warming, reduced rainfall and increased soil nitrogen supply. All four factors influenced leaf net photosynthesis and/or stomatal conductance, but almost all effects were context‐dependent, i.e. they differed among species, varied with levels of other treatments and/or depended on environmental conditions. Firstly, the response of photosynthesis to eCO 2 depended on species and nitrogen, became more positive as vapour pressure deficit increased and, for a C 4 grass and a legume, was more positive under reduced rainfall. Secondly, reduced rainfall increased photosynthesis in three functionally distinct species, potentially via acclimation to low soil moisture. Thirdly, warming had positive, neutral or negative effects on photosynthesis depending on species and rainfall. Overall, our results show that interactions among global changes and environmental conditions may complicate predictions based on simple theoretical expectations of main effects, and that the factors and interactions influencing photosynthesis vary among herbaceous species.

Pastore, Melissa A.↗