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Lamour J, Davidson KJ, Ely KS, Le Moguédec G, Anderson JA, Li Q, Calderón O, Koven CD, Wright SJ, Walker AP, Serbin SP, Rogers A. The effect of the vertical gradients of photosynthetic parameters on the CO 2 assimilation and transpiration of a Panamanian tropical forest. New Phytol 2023; 238:2345-2362. [PMID: 36960539 DOI: 10.1111/nph.18901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 03/14/2023] [Indexed: 05/19/2023]
Abstract
Terrestrial biosphere models (TBMs) include the representation of vertical gradients in leaf traits associated with modeling photosynthesis, respiration, and stomatal conductance. However, model assumptions associated with these gradients have not been tested in complex tropical forest canopies. We compared TBM representation of the vertical gradients of key leaf traits with measurements made in a tropical forest in Panama and then quantified the impact of the observed gradients on simulated canopy-scale CO2 and water fluxes. Comparison between observed and TBM trait gradients showed divergence that impacted canopy-scale simulations of water vapor and CO2 exchange. Notably, the ratio between the dark respiration rate and the maximum carboxylation rate was lower near the ground than at the top-of-canopy, leaf-level water-use efficiency was markedly higher at the top-of-canopy, and the decrease in maximum carboxylation rate from the top-of-canopy to the ground was less than TBM assumptions. The representation of the gradients of leaf traits in TBMs is typically derived from measurements made within-individual plants, or, for some traits, assumed constant due to a lack of experimental data. Our work shows that these assumptions are not representative of the trait gradients observed in species-rich, complex tropical forests.
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Affiliation(s)
- Julien Lamour
- Environmental & Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Kenneth J Davidson
- Environmental & Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, 11974, USA
| | - Kim S Ely
- Environmental & Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Gilles Le Moguédec
- AMAP, Université Montpellier, INRAE, Cirad CNRS, IRD, Montpellier, 34000, France
| | - Jeremiah A Anderson
- Environmental & Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Qianyu Li
- Environmental & Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Osvaldo Calderón
- Smithsonian Tropical Research Institute, Balboa, 0843-03092, Republic of Panama
| | - Charles D Koven
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - S Joseph Wright
- Smithsonian Tropical Research Institute, Balboa, 0843-03092, Republic of Panama
| | - Anthony P Walker
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Shawn P Serbin
- Environmental & Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Alistair Rogers
- Environmental & Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
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2
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Davidson KJ, Lamour J, Rogers A, Ely KS, Li Q, McDowell NG, Pivovaroff AL, Wolfe BT, Wright SJ, Zambrano A, Serbin SP. Short-term variation in leaf-level water use efficiency in a tropical forest. New Phytol 2023; 237:2069-2087. [PMID: 36527230 DOI: 10.1111/nph.18684] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
The representation of stomatal regulation of transpiration and CO2 assimilation is key to forecasting terrestrial ecosystem responses to global change. Given its importance in determining the relationship between forest productivity and climate, accurate and mechanistic model representation of the relationship between stomatal conductance (gs ) and assimilation is crucial. We assess possible physiological and mechanistic controls on the estimation of the g1 (stomatal slope, inversely proportional to water use efficiency) and g0 (stomatal intercept) parameters, using diurnal gas exchange surveys and leaf-level response curves of six tropical broadleaf evergreen tree species. g1 estimated from ex situ response curves averaged 50% less than g1 estimated from survey data. While g0 and g1 varied between leaves of different phenological stages, the trend was not consistent among species. We identified a diurnal trend associated with g1 and g0 that significantly improved model projections of diurnal trends in transpiration. The accuracy of modeled gs can be improved by accounting for variation in stomatal behavior across diurnal periods, and between measurement approaches, rather than focusing on phenological variation in stomatal behavior. Additional investigation into the primary mechanisms responsible for diurnal variation in g1 will be required to account for this phenomenon in land-surface models.
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Affiliation(s)
- Kenneth J Davidson
- Department of Environmental and Climate Sciences, Brookhaven National Laboratory, Building 490A, Upton, NY, 11973, USA
- Department of Ecology and Evolution, Stony Brook University, 650 Life Sciences Building, Stony Brook, NY, 11794, USA
| | - Julien Lamour
- Department of Environmental and Climate Sciences, Brookhaven National Laboratory, Building 490A, Upton, NY, 11973, USA
| | - Alistair Rogers
- Department of Environmental and Climate Sciences, Brookhaven National Laboratory, Building 490A, Upton, NY, 11973, USA
| | - Kim S Ely
- Department of Environmental and Climate Sciences, Brookhaven National Laboratory, Building 490A, Upton, NY, 11973, USA
| | - Qianyu Li
- Department of Environmental and Climate Sciences, Brookhaven National Laboratory, Building 490A, Upton, NY, 11973, USA
| | - Nate G McDowell
- Atmospheric Sciences and Global Change Division, Pacific Northwest National Laboratory, PO Box 999, Richland, WA, 99352, USA
- School of Biological Sciences, Washington State University, PO Box 644236, Pullman, WA, 99164-4236, USA
| | | | - Brett T Wolfe
- School of Renewable Natural Resources, Louisiana State University, Room 227, Renewable Natural Resources Bldg, Baton Rouge, LA, 70803, USA
- Smithsonian Tropical Research Institute, Apartado, 0843-03092, Balboa, Panama
| | - S Joseph Wright
- Smithsonian Tropical Research Institute, Apartado, 0843-03092, Balboa, Panama
| | - Alfonso Zambrano
- Smithsonian Tropical Research Institute, Apartado, 0843-03092, Balboa, Panama
| | - Shawn P Serbin
- Department of Environmental and Climate Sciences, Brookhaven National Laboratory, Building 490A, Upton, NY, 11973, USA
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3
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Wolfe BT, Detto M, Zhang YJ, Anderson-Teixeira KJ, Brodribb T, Collins AD, Crawford C, Dickman LT, Ely KS, Francisco J, Gurry PD, Hancock H, King CT, Majekobaje AR, Mallett CJ, McDowell NG, Mendheim Z, Michaletz ST, Myers DB, Price TJ, Rogers A, Sack L, Serbin SP, Siddiq Z, Willis D, Wu J, Zailaa J, Wright SJ. Leaves as bottlenecks: The contribution of tree leaves to hydraulic resistance within the soil-plant-atmosphere continuum. Plant Cell Environ 2023; 46:736-746. [PMID: 36564901 DOI: 10.1111/pce.14524] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/12/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Within vascular plants, the partitioning of hydraulic resistance along the soil-to-leaf continuum affects transpiration and its response to environmental conditions. In trees, the fractional contribution of leaf hydraulic resistance (Rleaf ) to total soil-to-leaf hydraulic resistance (Rtotal ), or fRleaf (=Rleaf /Rtotal ), is thought to be large, but this has not been tested comprehensively. We compiled a multibiome data set of fRleaf using new and previously published measurements of pressure differences within trees in situ. Across 80 samples, fRleaf averaged 0.51 (95% confidence interval [CI] = 0.46-0.57) and it declined with tree height. We also used the allometric relationship between field-based measurements of soil-to-leaf hydraulic conductance and laboratory-based measurements of leaf hydraulic conductance to compute the average fRleaf for 19 tree samples, which was 0.40 (95% CI = 0.29-0.56). The in situ technique produces a more accurate descriptor of fRleaf because it accounts for dynamic leaf hydraulic conductance. Both approaches demonstrate the outsized role of leaves in controlling tree hydrodynamics. A larger fRleaf may help stems from loss of hydraulic conductance. Thus, the decline in fRleaf with tree height would contribute to greater drought vulnerability in taller trees and potentially to their observed disproportionate drought mortality.
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Affiliation(s)
- Brett T Wolfe
- School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
- Smithsonian Tropical Research Institute, Balboa, Republic of Panama
| | - Matteo Detto
- Smithsonian Tropical Research Institute, Balboa, Republic of Panama
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - Yong-Jiang Zhang
- School of Biology and Ecology, University of Maine, Orono, Maine, USA
| | - Kristina J Anderson-Teixeira
- Smithsonian Tropical Research Institute, Balboa, Republic of Panama
- Conservation Ecology Center, Smithsonian's National Zoo & Conservation Biology Institute, Front Royal, Virginia, USA
| | - Tim Brodribb
- School of Natural Sciences, University of Tasmania, Hobart, Australia
| | - Adam D Collins
- Los Alamos National Laboratory, Earth and Environmental Sciences Division, Los Alamos, New Mexico, USA
| | - Chloe Crawford
- School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
| | - L Turin Dickman
- Los Alamos National Laboratory, Earth and Environmental Sciences Division, Los Alamos, New Mexico, USA
| | - Kim S Ely
- Brookhaven National Laboratory, Environmental and Climate Science Department, Upton, New York, USA
| | - Jessica Francisco
- School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
| | - Preston D Gurry
- School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
| | - Haigan Hancock
- School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
| | - Christopher T King
- School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
| | - Adelodun R Majekobaje
- School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
| | - Christian J Mallett
- School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
| | - Nate G McDowell
- Pacific Northwest National Lab, Atmospheric Sciences and Global Change Division, Richland, Washington, USA
- School of Biological Sciences, Washington State University, Pullman, Washington, USA
| | - Zachary Mendheim
- School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
| | - Sean T Michaletz
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Daniel B Myers
- School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
| | - Ty J Price
- School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
| | - Alistair Rogers
- Brookhaven National Laboratory, Environmental and Climate Science Department, Upton, New York, USA
| | - Lawren Sack
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA
| | - Shawn P Serbin
- Brookhaven National Laboratory, Environmental and Climate Science Department, Upton, New York, USA
| | - Zafar Siddiq
- Department of Botany, Government College University, Lahore, Pakistan
| | - David Willis
- School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, USA
| | - Jin Wu
- School of Biological Sciences, Research Area of Ecology and Biodiversity, The University of Hong Kong, Hong Kong, China
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Joseph Zailaa
- Conservation Ecology Center, Smithsonian's National Zoo & Conservation Biology Institute, Front Royal, Virginia, USA
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA
- School of the Environment, Yale University, New Haven, Connecticut, USA
| | - S Joseph Wright
- Smithsonian Tropical Research Institute, Balboa, Republic of Panama
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Crystal-Ornelas R, Varadharajan C, O’Ryan D, Beilsmith K, Bond-Lamberty B, Boye K, Burrus M, Cholia S, Christianson DS, Crow M, Damerow J, Ely KS, Goldman AE, Heinz SL, Hendrix VC, Kakalia Z, Mathes K, O’Brien F, Pennington SC, Robles E, Rogers A, Simmonds M, Velliquette T, Weisenhorn P, Welch JN, Whitenack K, Agarwal DA. Enabling FAIR data in Earth and environmental science with community-centric (meta)data reporting formats. Sci Data 2022; 9:700. [PMCID: PMC9663825 DOI: 10.1038/s41597-022-01606-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/01/2022] [Indexed: 11/16/2022] Open
Abstract
AbstractResearch can be more transparent and collaborative by using Findable, Accessible, Interoperable, and Reusable (FAIR) principles to publish Earth and environmental science data. Reporting formats—instructions, templates, and tools for consistently formatting data within a discipline—can help make data more accessible and reusable. However, the immense diversity of data types across Earth science disciplines makes development and adoption challenging. Here, we describe 11 community reporting formats for a diverse set of Earth science (meta)data including cross-domain metadata (dataset metadata, location metadata, sample metadata), file-formatting guidelines (file-level metadata, CSV files, terrestrial model data archiving), and domain-specific reporting formats for some biological, geochemical, and hydrological data (amplicon abundance tables, leaf-level gas exchange, soil respiration, water and sediment chemistry, sensor-based hydrologic measurements). More broadly, we provide guidelines that communities can use to create new (meta)data formats that integrate with their scientific workflows. Such reporting formats have the potential to accelerate scientific discovery and predictions by making it easier for data contributors to provide (meta)data that are more interoperable and reusable.
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5
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Lamour J, Davidson KJ, Ely KS, Le Moguédec G, Leakey ADB, Li Q, Serbin SP, Rogers A. An improved representation of the relationship between photosynthesis and stomatal conductance leads to more stable estimation of conductance parameters and improves the goodness-of-fit across diverse data sets. Glob Chang Biol 2022; 28:3537-3556. [PMID: 35090072 DOI: 10.1111/gcb.16103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 01/17/2022] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
Stomata play a central role in surface-atmosphere exchange by controlling the flux of water and CO2 between the leaf and the atmosphere. Representation of stomatal conductance (gsw ) is therefore an essential component of models that seek to simulate water and CO2 exchange in plants and ecosystems. For given environmental conditions at the leaf surface (CO2 concentration and vapor pressure deficit or relative humidity), models typically assume a linear relationship between gsw and photosynthetic CO2 assimilation (A). However, measurement of leaf-level gsw response curves to changes in A are rare, particularly in the tropics, resulting in only limited data to evaluate this key assumption. Here, we measured the response of gsw and A to irradiance in six tropical species at different leaf phenological stages. We showed that the relationship between gsw and A was not linear, challenging the key assumption upon which optimality theory is based-that the marginal cost of water gain is constant. Our data showed that increasing A resulted in a small increase in gsw at low irradiance, but a much larger increase at high irradiance. We reformulated the popular Unified Stomatal Optimization (USO) model to account for this phenomenon and to enable consistent estimation of the key conductance parameters g0 and g1 . Our modification of the USO model improved the goodness-of-fit and reduced bias, enabling robust estimation of conductance parameters at any irradiance. In addition, our modification revealed previously undetectable relationships between the stomatal slope parameter g1 and other leaf traits. We also observed nonlinear behavior between A and gsw in independent data sets that included data collected from attached and detached leaves, and from plants grown at elevated CO2 concentration. We propose that this empirical modification of the USO model can improve the measurement of gsw parameters and the estimation of plant and ecosystem-scale water and CO2 fluxes.
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Affiliation(s)
- Julien Lamour
- Environmental & Climate Sciences Department, Brookhaven National Laboratory, Upton, New York, USA
| | - Kenneth J Davidson
- Environmental & Climate Sciences Department, Brookhaven National Laboratory, Upton, New York, USA
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, USA
| | - Kim S Ely
- Environmental & Climate Sciences Department, Brookhaven National Laboratory, Upton, New York, USA
| | - Gilles Le Moguédec
- AMAP, Université Montpellier, INRAE, Cirad CNRS, IRD, Montpellier, France
| | - Andrew D B Leakey
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Qianyu Li
- Environmental & Climate Sciences Department, Brookhaven National Laboratory, Upton, New York, USA
| | - Shawn P Serbin
- Environmental & Climate Sciences Department, Brookhaven National Laboratory, Upton, New York, USA
| | - Alistair Rogers
- Environmental & Climate Sciences Department, Brookhaven National Laboratory, Upton, New York, USA
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6
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Lamour J, Davidson KJ, Ely KS, Li Q, Serbin SP, Rogers A. New calculations for photosynthesis measurement systems: what's the impact for physiologists and modelers? New Phytol 2022; 233:592-598. [PMID: 34605019 DOI: 10.1111/nph.17762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/13/2021] [Accepted: 09/19/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Julien Lamour
- Environmental & Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, 11973-5000, USA
| | - Kenneth J Davidson
- Environmental & Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, 11973-5000, USA
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, 11794-5245, USA
| | - Kim S Ely
- Environmental & Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, 11973-5000, USA
| | - Qianyu Li
- Environmental & Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, 11973-5000, USA
| | - Shawn P Serbin
- Environmental & Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, 11973-5000, USA
| | - Alistair Rogers
- Environmental & Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, 11973-5000, USA
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7
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Burnett AC, Serbin SP, Davidson KJ, Ely KS, Rogers A. Detection of the metabolic response to drought stress using hyperspectral reflectance. J Exp Bot 2021; 72:6474-6489. [PMID: 34235536 DOI: 10.1093/jxb/erab255] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 06/02/2021] [Indexed: 06/13/2023]
Abstract
Drought is the most important limitation on crop yield. Understanding and detecting drought stress in crops is vital for improving water use efficiency through effective breeding and management. Leaf reflectance spectroscopy offers a rapid, non-destructive alternative to traditional techniques for measuring plant traits involved in a drought response. We measured drought stress in six glasshouse-grown agronomic species using physiological, biochemical, and spectral data. In contrast to physiological traits, leaf metabolite concentrations revealed drought stress before it was visible to the naked eye. We used full-spectrum leaf reflectance data to predict metabolite concentrations using partial least-squares regression, with validation R2 values of 0.49-0.87. We show for the first time that spectroscopy may be used for the quantitative estimation of proline and abscisic acid, demonstrating the first use of hyperspectral data to detect a phytohormone. We used linear discriminant analysis and partial least squares discriminant analysis to differentiate between watered plants and those subjected to drought based on measured traits (accuracy: 71%) and raw spectral data (66%). Finally, we validated our glasshouse-developed models in an independent field trial. We demonstrate that spectroscopy can detect drought stress via underlying biochemical changes, before visual differences occur, representing a powerful advance for measuring limitations on yield.
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Affiliation(s)
- Angela C Burnett
- Environmental and Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Shawn P Serbin
- Environmental and Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Kenneth J Davidson
- Environmental and Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Kim S Ely
- Environmental and Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Alistair Rogers
- Environmental and Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, USA
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8
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Burnett AC, Anderson J, Davidson KJ, Ely KS, Lamour J, Li Q, Morrison BD, Yang D, Rogers A, Serbin SP. A best-practice guide to predicting plant traits from leaf-level hyperspectral data using partial least squares regression. J Exp Bot 2021; 72:6175-6189. [PMID: 34131723 DOI: 10.1093/jxb/erab295] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 06/14/2021] [Indexed: 06/12/2023]
Abstract
Partial least squares regression (PLSR) modelling is a statistical technique for correlating datasets, and involves the fitting of a linear regression between two matrices. One application of PLSR enables leaf traits to be estimated from hyperspectral optical reflectance data, facilitating rapid, high-throughput, non-destructive plant phenotyping. This technique is of interest and importance in a wide range of contexts including crop breeding and ecosystem monitoring. The lack of a consensus in the literature on how to perform PLSR means that interpreting model results can be challenging, applying existing models to novel datasets can be impossible, and unknown or undisclosed assumptions can lead to incorrect or spurious predictions. We address this lack of consensus by proposing best practices for using PLSR to predict plant traits from leaf-level hyperspectral data, including a discussion of when PLSR is applicable, and recommendations for data collection. We provide a tutorial to demonstrate how to develop a PLSR model, in the form of an R script accompanying this manuscript. This practical guide will assist all those interpreting and using PLSR models to predict leaf traits from spectral data, and advocates for a unified approach to using PLSR for predicting traits from spectra in the plant sciences.
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Affiliation(s)
- Angela C Burnett
- Terrestrial Ecosystem Science and Technology Group, Environmental and Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Jeremiah Anderson
- Terrestrial Ecosystem Science and Technology Group, Environmental and Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Kenneth J Davidson
- Terrestrial Ecosystem Science and Technology Group, Environmental and Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Kim S Ely
- Terrestrial Ecosystem Science and Technology Group, Environmental and Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Julien Lamour
- Terrestrial Ecosystem Science and Technology Group, Environmental and Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Qianyu Li
- Terrestrial Ecosystem Science and Technology Group, Environmental and Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Bailey D Morrison
- Terrestrial Ecosystem Science and Technology Group, Environmental and Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Dedi Yang
- Terrestrial Ecosystem Science and Technology Group, Environmental and Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Alistair Rogers
- Terrestrial Ecosystem Science and Technology Group, Environmental and Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Shawn P Serbin
- Terrestrial Ecosystem Science and Technology Group, Environmental and Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, USA
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9
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Wu J, Serbin SP, Ely KS, Wolfe BT, Dickman LT, Grossiord C, Michaletz ST, Collins AD, Detto M, McDowell NG, Wright SJ, Rogers A. The response of stomatal conductance to seasonal drought in tropical forests. Glob Chang Biol 2020; 26:823-839. [PMID: 31482618 DOI: 10.1111/gcb.14820] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 08/20/2019] [Indexed: 05/27/2023]
Abstract
Stomata regulate CO2 uptake for photosynthesis and water loss through transpiration. The approaches used to represent stomatal conductance (gs ) in models vary. In particular, current understanding of drivers of the variation in a key parameter in those models, the slope parameter (i.e. a measure of intrinsic plant water-use-efficiency), is still limited, particularly in the tropics. Here we collected diurnal measurements of leaf gas exchange and leaf water potential (Ψleaf ), and a suite of plant traits from the upper canopy of 15 tropical trees in two contrasting Panamanian forests throughout the dry season of the 2016 El Niño. The plant traits included wood density, leaf-mass-per-area (LMA), leaf carboxylation capacity (Vc,max ), leaf water content, the degree of isohydry, and predawn Ψleaf . We first investigated how the choice of four commonly used leaf-level gs models with and without the inclusion of Ψleaf as an additional predictor variable influence the ability to predict gs , and then explored the abiotic (i.e. month, site-month interaction) and biotic (i.e. tree-species-specific characteristics) drivers of slope parameter variation. Our results show that the inclusion of Ψleaf did not improve model performance and that the models that represent the response of gs to vapor pressure deficit performed better than corresponding models that respond to relative humidity. Within each gs model, we found large variation in the slope parameter, and this variation was attributable to the biotic driver, rather than abiotic drivers. We further investigated potential relationships between the slope parameter and the six available plant traits mentioned above, and found that only one trait, LMA, had a significant correlation with the slope parameter (R2 = 0.66, n = 15), highlighting a potential path towards improved model parameterization. This study advances understanding of gs dynamics over seasonal drought, and identifies a practical, trait-based approach to improve modeling of carbon and water exchange in tropical forests.
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Affiliation(s)
- Jin Wu
- Environmental & Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, USA
- School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong
| | - Shawn P Serbin
- Environmental & Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Kim S Ely
- Environmental & Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Brett T Wolfe
- Smithsonian Tropical Research Institute, Apartado, Panama
| | - L Turin Dickman
- Earth and Environmental Sciences Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Charlotte Grossiord
- Earth and Environmental Sciences Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Sean T Michaletz
- Earth and Environmental Sciences Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Adam D Collins
- Earth and Environmental Sciences Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Matteo Detto
- Smithsonian Tropical Research Institute, Apartado, Panama
- Ecology and Evolutionary Biology Department, Princeton University, Princeton, NJ, USA
| | - Nate G McDowell
- Earth and Environmental Sciences Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | | | - Alistair Rogers
- Environmental & Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, USA
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10
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Serbin SP, Wu J, Ely KS, Kruger EL, Townsend PA, Meng R, Wolfe BT, Chlus A, Wang Z, Rogers A. From the Arctic to the tropics: multibiome prediction of leaf mass per area using leaf reflectance. New Phytol 2019; 224:1557-1568. [PMID: 31418863 DOI: 10.1111/nph.16123] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 07/28/2019] [Indexed: 06/10/2023]
Abstract
Leaf mass per area (LMA) is a key plant trait, reflecting tradeoffs between leaf photosynthetic function, longevity, and structural investment. Capturing spatial and temporal variability in LMA has been a long-standing goal of ecological research and is an essential component for advancing Earth system models. Despite the substantial variation in LMA within and across Earth's biomes, an efficient, globally generalizable approach to predict LMA is still lacking. We explored the capacity to predict LMA from leaf spectra across much of the global LMA trait space, with values ranging from 17 to 393 g m-2 . Our dataset contained leaves from a wide range of biomes from the high Arctic to the tropics, included broad- and needleleaf species, and upper- and lower-canopy (i.e. sun and shade) growth environments. Here we demonstrate the capacity to rapidly estimate LMA using only spectral measurements across a wide range of species, leaf age and canopy position from diverse biomes. Our model captures LMA variability with high accuracy and low error (R2 = 0.89; root mean square error (RMSE) = 15.45 g m-2 ). Our finding highlights the fact that the leaf economics spectrum is mirrored by the leaf optical spectrum, paving the way for this technology to predict the diversity of LMA in ecosystems across global biomes.
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Affiliation(s)
- Shawn P Serbin
- Environmental and Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Jin Wu
- Environmental and Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Kim S Ely
- Environmental and Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Eric L Kruger
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Philip A Townsend
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Ran Meng
- Environmental and Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
- College of Natural Resources and Environment, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Brett T Wolfe
- Smithsonian Tropical Research Institute, Apartado, 0843-03092, Balboa, Panama
- School of Renewable Natural Resources, Louisiana State University, Baton Rouge, LA, USA
| | - Adam Chlus
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Zhihui Wang
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Alistair Rogers
- Environmental and Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, 11973, USA
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11
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Rogers A, Serbin SP, Ely KS, Wullschleger SD. Terrestrial biosphere models may overestimate Arctic CO 2 assimilation if they do not account for decreased quantum yield and convexity at low temperature. New Phytol 2019; 223:167-179. [PMID: 30767227 DOI: 10.1111/nph.15750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 02/10/2019] [Indexed: 06/09/2023]
Abstract
How terrestrial biosphere models (TBMs) represent leaf photosynthesis and its sensitivity to temperature are two critical components of understanding and predicting the response of the Arctic carbon cycle to global change. We measured the effect of temperature on the response of photosynthesis to irradiance in six Arctic plant species and determined the quantum yield of CO2 fixation ( ϕCO2 ) and the convexity factor (θ). We also determined leaf absorptance (α) from measured reflectance to calculate ϕCO2 on an absorbed light basis ( ϕCO2.a ) and enabled comparison with nine TBMs. The mean ϕCO2.a was 0.045 mol CO2 mol-1 absorbed quanta at 25°C and closely agreed with the mean TBM parameterisation (0.044), but as temperature decreased measured ϕCO2.a diverged from TBMs. At 5°C measured ϕCO2.a was markedly reduced (0.025) and 60% lower than TBM estimates. The θ also showed a significant reduction between 25°C and 5°C. At 5°C θ was 38% lower than the common model parameterisation of 0.7. These data show that TBMs are not accounting for observed reductions in ϕCO2.a and θ that can occur at low temperature. Ignoring these reductions in ϕCO2.a and θ could lead to a marked (45%) overestimation of CO2 assimilation at subsaturating irradiance and low temperature.
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Affiliation(s)
- Alistair Rogers
- Environmental and Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, 11973-5000, USA
| | - Shawn P Serbin
- Environmental and Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, 11973-5000, USA
| | - Kim S Ely
- Environmental and Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, 11973-5000, USA
| | - Stan D Wullschleger
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6301, USA
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12
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Dickman LT, McDowell NG, Grossiord C, Collins AD, Wolfe BT, Detto M, Wright SJ, Medina-Vega JA, Goodsman D, Rogers A, Serbin SP, Wu J, Ely KS, Michaletz ST, Xu C, Kueppers L, Chambers JQ. Homoeostatic maintenance of nonstructural carbohydrates during the 2015-2016 El Niño drought across a tropical forest precipitation gradient. Plant Cell Environ 2019; 42:1705-1714. [PMID: 30537216 DOI: 10.1111/pce.13501] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 11/26/2018] [Accepted: 12/02/2018] [Indexed: 06/09/2023]
Abstract
Nonstructural carbohydrates (NSCs) are essential for maintenance of plant metabolism and may be sensitive to short- and long-term climatic variation. NSC variation in moist tropical forests has rarely been studied, so regulation of NSCs in these systems is poorly understood. We measured foliar and branch NSC content in 23 tree species at three sites located across a large precipitation gradient in Panama during the 2015-2016 El Niño to examine how short- and long-term climatic variation impact carbohydrate dynamics. There was no significant difference in total NSCs as the drought progressed (leaf P = 0.32, branch P = 0.30) nor across the rainfall gradient (leaf P = 0.91, branch P = 0.96). Foliar soluble sugars decreased while starch increased over the duration of the dry period, suggesting greater partitioning of NSCs to storage than metabolism or transport as drought progressed. There was a large variation across species at all sites, but total foliar NSCs were positively correlated with leaf mass per area, whereas branch sugars were positively related to leaf temperature and negatively correlated with daily photosynthesis and wood density. The NSC homoeostasis across a wide range of conditions suggests that NSCs are an allocation priority in moist tropical forests.
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Affiliation(s)
- Lee Turin Dickman
- Earth & Environmental Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Nate G McDowell
- Earth Systems Analysis & Modeling, Pacific Northwest National Laboratory, Richland, Washington
| | - Charlotte Grossiord
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Forest Dynamics Research Unit, Birmensdorf, Switzerland
| | - Adam D Collins
- Earth & Environmental Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Brett T Wolfe
- Smithsonian Tropical Research Institute, Balboa, Panama
| | - Matteo Detto
- Ecology and Evolutionary Biology Department, Princeton University, Princeton, New Jersey
| | | | - José A Medina-Vega
- Smithsonian Tropical Research Institute, Balboa, Panama
- Forest Ecology and Forest Management Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Devin Goodsman
- Earth & Environmental Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Alistair Rogers
- Environmental & Climate Sciences Department, Brookhaven National Laboratory, New York, New York
| | - Shawn P Serbin
- Environmental & Climate Sciences Department, Brookhaven National Laboratory, New York, New York
| | - Jin Wu
- Environmental & Climate Sciences Department, Brookhaven National Laboratory, New York, New York
| | - Kim S Ely
- Environmental & Climate Sciences Department, Brookhaven National Laboratory, New York, New York
| | - Sean T Michaletz
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Chonggang Xu
- Earth & Environmental Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico
| | - Lara Kueppers
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Jeffrey Q Chambers
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, California
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13
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Ely KS, Burnett AC, Lieberman-Cribbin W, Serbin SP, Rogers A. Spectroscopy can predict key leaf traits associated with source-sink balance and carbon-nitrogen status. J Exp Bot 2019; 70:1789-1799. [PMID: 30799496 DOI: 10.1093/jxb/erz061] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 02/05/2019] [Indexed: 06/09/2023]
Abstract
Approaches that enable high-throughput, non-destructive measurement of plant traits are essential for programs seeking to improve crop yields through physiological breeding. However, many key traits still require measurement using slow, labor-intensive, and destructive approaches. We investigated the potential to retrieve key traits associated with leaf source-sink balance and carbon-nitrogen status from leaf optical properties. Structural and biochemical traits and leaf reflectance (500-2400 nm) of eight crop species were measured and used to develop predictive 'spectra-trait' models using partial least squares regression. Independent validation data demonstrated that the models achieved very high predictive power for C, N, C:N ratio, leaf mass per area, water content, and protein content (R2>0.85), good predictive capability for starch, sucrose, glucose, and free amino acids (R2=0.58-0.80), and some predictive capability for nitrate (R2=0.51) and fructose (R2=0.44). Our spectra-trait models were developed to cover the trait space associated with food or biofuel crop plants and can therefore be applied in a broad range of phenotyping studies.
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Affiliation(s)
- Kim S Ely
- Environmental & Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Angela C Burnett
- Environmental & Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Wil Lieberman-Cribbin
- Environmental & Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Shawn P Serbin
- Environmental & Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Alistair Rogers
- Environmental & Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, USA
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14
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Rogers A, Serbin SP, Ely KS, Sloan VL, Wullschleger SD. Terrestrial biosphere models underestimate photosynthetic capacity and CO 2 assimilation in the Arctic. New Phytol 2017; 216:1090-1103. [PMID: 28877330 DOI: 10.1111/nph.14740] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 07/08/2017] [Indexed: 05/13/2023]
Abstract
Terrestrial biosphere models (TBMs) are highly sensitive to model representation of photosynthesis, in particular the parameters maximum carboxylation rate and maximum electron transport rate at 25°C (Vc,max.25 and Jmax.25 , respectively). Many TBMs do not include representation of Arctic plants, and those that do rely on understanding and parameterization from temperate species. We measured photosynthetic CO2 response curves and leaf nitrogen (N) content in species representing the dominant vascular plant functional types found on the coastal tundra near Barrow, Alaska. The activation energies associated with the temperature response functions of Vc,max and Jmax were 17% lower than commonly used values. When scaled to 25°C, Vc,max.25 and Jmax.25 were two- to five-fold higher than the values used to parameterize current TBMs. This high photosynthetic capacity was attributable to a high leaf N content and the high fraction of N invested in Rubisco. Leaf-level modeling demonstrated that current parameterization of TBMs resulted in a two-fold underestimation of the capacity for leaf-level CO2 assimilation in Arctic vegetation. This study highlights the poor representation of Arctic photosynthesis in TBMs, and provides the critical data necessary to improve our ability to project the response of the Arctic to global environmental change.
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Affiliation(s)
- Alistair Rogers
- Environmental and Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, 11973-5000, USA
| | - Shawn P Serbin
- Environmental and Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, 11973-5000, USA
| | - Kim S Ely
- Environmental and Climate Sciences Department, Brookhaven National Laboratory, Upton, NY, 11973-5000, USA
| | - Victoria L Sloan
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6301, USA
| | - Stan D Wullschleger
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6301, USA
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