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Stejskal J, Čepl J, Neuwirthová E, Akinyemi OO, Chuchlík J, Provazník D, Keinänen M, Campbell P, Albrechtová J, Lstibůrek M, Lhotáková Z. Making the Genotypic Variation Visible: Hyperspectral Phenotyping in Scots Pine Seedlings. PLANT PHENOMICS (WASHINGTON, D.C.) 2023; 5:0111. [PMID: 38026471 PMCID: PMC10644830 DOI: 10.34133/plantphenomics.0111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 10/10/2023] [Indexed: 12/01/2023]
Abstract
Hyperspectral reflectance contains valuable information about leaf functional traits, which can indicate a plant's physiological status. Therefore, using hyperspectral reflectance for high-throughput phenotyping of foliar traits could be a powerful tool for tree breeders and nursery practitioners to distinguish and select seedlings with desired adaptation potential to local environments. We evaluated the use of 2 nondestructive methods (i.e., leaf and proximal/canopy) measuring hyperspectral reflectance in the 350- to 2,500-nm range for phenotyping on 1,788 individual Scots pine seedlings belonging to lowland and upland ecotypes of 3 different local populations from the Czech Republic. Leaf-level measurements were collected using a spectroradiometer and a contact probe with an internal light source to measure the biconical reflectance factor of a sample of needles placed on a black background in the contact probe field of view. The proximal canopy measurements were collected under natural solar light, using the same spectroradiometer with fiber optical cable to collect data on individual seedlings' hemispherical conical reflectance factor. The latter method was highly susceptible to changes in incoming radiation. Both spectral datasets showed statistically significant differences among Scots pine populations in the whole spectral range. Moreover, using random forest and support vector machine learning algorithms, the proximal data obtained from the top of the seedlings offered up to 83% accuracy in predicting 3 different Scots pine populations. We conclude that both approaches are viable for hyperspectral phenotyping to disentangle the phenotypic and the underlying genetic variation within Scots pine seedlings.
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Affiliation(s)
- Jan Stejskal
- Department of Genetics and Physiology of Forest Trees, Faculty of Forestry and Wood Sciences,
Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Jaroslav Čepl
- Department of Genetics and Physiology of Forest Trees, Faculty of Forestry and Wood Sciences,
Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Eva Neuwirthová
- Department of Genetics and Physiology of Forest Trees, Faculty of Forestry and Wood Sciences,
Czech University of Life Sciences Prague, Prague, Czech Republic
- Department of Experimental Plant Biology,
Charles University, Prague, Czech Republic
| | - Olusegun Olaitan Akinyemi
- Department of Genetics and Physiology of Forest Trees, Faculty of Forestry and Wood Sciences,
Czech University of Life Sciences Prague, Prague, Czech Republic
- Department of Environmental and Biological Sciences,
University of Eastern Finland, Joensuu, Finland
| | - Jiří Chuchlík
- Department of Genetics and Physiology of Forest Trees, Faculty of Forestry and Wood Sciences,
Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Daniel Provazník
- Department of Genetics and Physiology of Forest Trees, Faculty of Forestry and Wood Sciences,
Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Markku Keinänen
- Department of Environmental and Biological Sciences,
University of Eastern Finland, Joensuu, Finland
- Center for Photonic Sciences,
University of Eastern Finland, Joensuu, Finland
| | - Petya Campbell
- Department of Geography and Environmental Sciences,
University of Maryland Baltimore County, Baltimore, MD, USA
- Biospheric Sciences Laboratory,
NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | - Jana Albrechtová
- Department of Experimental Plant Biology,
Charles University, Prague, Czech Republic
| | - Milan Lstibůrek
- Department of Genetics and Physiology of Forest Trees, Faculty of Forestry and Wood Sciences,
Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Zuzana Lhotáková
- Department of Experimental Plant Biology,
Charles University, Prague, Czech Republic
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Kováč D, Novotný J, Šigut L, Ač A, Peñuelas J, Grace J, Urban O. Estimation of photosynthetic dynamics in forests from daily measured fluorescence and PRI data with adjustment for canopy shadow fraction. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 898:166386. [PMID: 37597564 DOI: 10.1016/j.scitotenv.2023.166386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/10/2023] [Accepted: 08/16/2023] [Indexed: 08/21/2023]
Abstract
We conducted year-long measurements of the photochemical reflectance index (PRI) and solar-induced fluorescence in the O2A oxygen band (SIFA) at a Norway spruce forest and a European beech forest to study relationships of these remote sensing variables to photosynthesis by trees in grown forest stands. Measured PRI and SIFA values were linked to changes in forest gross primary productivity (GPP) and light-use efficiency (LUE). Changes in the shadow fraction (αS) within tree crowns influenced PRI and fluorescence signals. In the spruce forest, the quantum yield of SIFA (FYSIFA) decreased around midday together with photosynthesis and GPP. Such decreases in FYSIFA were accompanied by an increase in the αS. In the beech forest, we detected an increase in FYSIFA together with a decrease in αS in the afternoon hours. The overall sensitivity of PRI to LUE was variable according to the season, presumably influenced by complex changes in photosynthetic pigments. PRI and FYSIFA showed weak correlations with canopy LUE; however, when considered together, the correlation was strengthened (R2 was 0.63 and 0.34 in spruce and beech forest, respectively). Our model predicting LUE dynamics includes a diurnal minimum of PRI and canopy αS to make allowances for seasonal changes in photosynthetic pigments and for diurnal variability of the shadow fraction in forests. The incorporation of these correcting factors allowed us to estimate LUE at R2 = 0.68 (spruce) and 0.53 (beech). The modeling equations appeared sensitive to the absorbed photosynthetically active radiation (APAR), but less sensitive to the GPP of these forests. Substituting pigments correction with introducing differential PRI (ΔPRI) into the model did not significantly improve the LUE estimation across the season. Our results show that the joint use of PRI and fluorescence improves LUE and GPP estimation accuracy in both daily and seasonal observations.
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Affiliation(s)
- Daniel Kováč
- Global Change Research Institute of the Czech Academy of Sciences, Bělidla 986/4a, 603 00 Brno, Czech Republic.
| | - Jan Novotný
- Global Change Research Institute of the Czech Academy of Sciences, Bělidla 986/4a, 603 00 Brno, Czech Republic
| | - Ladislav Šigut
- Global Change Research Institute of the Czech Academy of Sciences, Bělidla 986/4a, 603 00 Brno, Czech Republic
| | - Alexander Ač
- Global Change Research Institute of the Czech Academy of Sciences, Bělidla 986/4a, 603 00 Brno, Czech Republic
| | - Josep Peñuelas
- Global Change Research Institute of the Czech Academy of Sciences, Bělidla 986/4a, 603 00 Brno, Czech Republic; CSIC, Global Ecology Unit CREAF-CSIC-UAB, E-08193 Bellaterra, Catalonia, Spain; CREAF, E-08193 Cerdanyola del Vallès, Catalonia, Spain
| | - John Grace
- Global Change Research Institute of the Czech Academy of Sciences, Bělidla 986/4a, 603 00 Brno, Czech Republic; School of GeoSciences, University of Edinburgh, Crew Bldg, Kings Bldgs, Alexander Crum Brown Rd, Edinburgh EH9 3FF, UK
| | - Otmar Urban
- Global Change Research Institute of the Czech Academy of Sciences, Bělidla 986/4a, 603 00 Brno, Czech Republic
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Porcar-Castell A, Malenovský Z, Magney T, Van Wittenberghe S, Fernández-Marín B, Maignan F, Zhang Y, Maseyk K, Atherton J, Albert LP, Robson TM, Zhao F, Garcia-Plazaola JI, Ensminger I, Rajewicz PA, Grebe S, Tikkanen M, Kellner JR, Ihalainen JA, Rascher U, Logan B. Chlorophyll a fluorescence illuminates a path connecting plant molecular biology to Earth-system science. NATURE PLANTS 2021; 7:998-1009. [PMID: 34373605 DOI: 10.1038/s41477-021-00980-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 06/28/2021] [Indexed: 05/27/2023]
Abstract
For decades, the dynamic nature of chlorophyll a fluorescence (ChlaF) has provided insight into the biophysics and ecophysiology of the light reactions of photosynthesis from the subcellular to leaf scales. Recent advances in remote sensing methods enable detection of ChlaF induced by sunlight across a range of larger scales, from using instruments mounted on towers above plant canopies to Earth-orbiting satellites. This signal is referred to as solar-induced fluorescence (SIF) and its application promises to overcome spatial constraints on studies of photosynthesis, opening new research directions and opportunities in ecology, ecophysiology, biogeochemistry, agriculture and forestry. However, to unleash the full potential of SIF, intensive cross-disciplinary work is required to harmonize these new advances with the rich history of biophysical and ecophysiological studies of ChlaF, fostering the development of next-generation plant physiological and Earth-system models. Here, we introduce the scale-dependent link between SIF and photosynthesis, with an emphasis on seven remaining scientific challenges, and present a roadmap to facilitate future collaborative research towards new applications of SIF.
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Affiliation(s)
- Albert Porcar-Castell
- Optics of Photosynthesis Laboratory, Institute for Atmospheric and Earth System Research (INAR)/Forest Sciences, Viikki Plant Science Center (ViPS), University of Helsinki, Helsinki, Finland.
| | - Zbyněk Malenovský
- School of Geography, Planning, and Spatial Sciences, College of Sciences Engineering and Technology, University of Tasmania, Hobart, Tasmania, Australia
| | - Troy Magney
- Department of Plant Sciences, University of California, Davis, Davis, CA, USA
| | - Shari Van Wittenberghe
- Optics of Photosynthesis Laboratory, Institute for Atmospheric and Earth System Research (INAR)/Forest Sciences, Viikki Plant Science Center (ViPS), University of Helsinki, Helsinki, Finland
- Laboratory of Earth Observation, University of Valencia, Paterna, Spain
| | - Beatriz Fernández-Marín
- Department of Botany, Ecology and Plant Physiology, University of La Laguna (ULL), Tenerife, Spain
| | - Fabienne Maignan
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Yongguang Zhang
- International Institute for Earth System Sciences, Nanjing University, Nanjing, China
| | - Kadmiel Maseyk
- School of Environment, Earth and Ecosystem Sciences, The Open University, Milton Keynes, UK
| | - Jon Atherton
- Optics of Photosynthesis Laboratory, Institute for Atmospheric and Earth System Research (INAR)/Forest Sciences, Viikki Plant Science Center (ViPS), University of Helsinki, Helsinki, Finland
| | - Loren P Albert
- Institute at Brown for Environment and Society, Brown University, Providence, RI, USA
- Biology Department, West Virginia University, Morgantown, WV, USA
| | - Thomas Matthew Robson
- Organismal and Evolutionary Biology, Viikki Plant Science Centre (ViPS), Faculty of Biological and Environmental Science, University of Helsinki, Helsinki, Finland
| | - Feng Zhao
- School of Instrumentation Science and Opto-Electronics Engineering, Beihang University, Beijing, China
| | | | - Ingo Ensminger
- Department of Biology, Graduate Programs in Cell & Systems Biology and Ecology & Evolutionary Biology, University of Toronto, Mississauga, Ontario, Canada
| | - Paulina A Rajewicz
- Optics of Photosynthesis Laboratory, Institute for Atmospheric and Earth System Research (INAR)/Forest Sciences, Viikki Plant Science Center (ViPS), University of Helsinki, Helsinki, Finland
| | - Steffen Grebe
- Molecular Plant Biology, University of Turku, Turku, Finland
| | - Mikko Tikkanen
- Molecular Plant Biology, University of Turku, Turku, Finland
| | - James R Kellner
- Institute at Brown for Environment and Society, Brown University, Providence, RI, USA
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, USA
| | - Janne A Ihalainen
- Nanoscience Center, Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Uwe Rascher
- Institute of Bio- and Geosciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Barry Logan
- Biology Department, Bowdoin College, Brunswick, ME, USA
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Zhang C, Atherton J, Peñuelas J, Filella I, Kolari P, Aalto J, Ruhanen H, Bäck J, Porcar-Castell A. Do all chlorophyll fluorescence emission wavelengths capture the spring recovery of photosynthesis in boreal evergreen foliage? PLANT, CELL & ENVIRONMENT 2019; 42:3264-3279. [PMID: 31325364 DOI: 10.1111/pce.13620] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 07/02/2019] [Accepted: 07/15/2019] [Indexed: 06/10/2023]
Abstract
Chlorophyll a fluorescence (ChlF) is closely related to photosynthesis and can be measured remotely using multiple spectral features as solar-induced fluorescence (SIF). In boreal regions, SIF shows particular promise as an indicator of photosynthesis, in part because of the limited variation of seasonal light absorption in these ecosystems. Seasonal spectral changes in ChlF could yield new information on processes such as sustained nonphotochemical quenching (NPQS ) but also disrupt the relationship between SIF and photosynthesis. We followed ChlF and functional and biochemical properties of Pinus sylvestris needles during the photosynthetic spring recovery period to answer the following: (a) How ChlF spectra change over seasonal timescales? (b) How pigments, NPQS , and total photosynthetically active radiation (PAR) absorption drive changes of ChlF spectra? (c) Do all ChlF wavelengths track photosynthetic seasonality? We found seasonal ChlF variation in the red and far-red wavelengths, which was strongly correlated with NPQS , carotenoid content, and photosynthesis (enhanced in the red), but not with PAR absorption. Furthermore, a rapid decrease in red/far-red ChlF ratio occurred in response to a cold spell, potentially relating to the structural reorganization of the photosystems. We conclude that all current SIF retrieval features can track seasonal photosynthetic dynamics in boreal evergreens, but the full SIF spectra provides additional insight.
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Affiliation(s)
- Chao Zhang
- Optics of Photosynthesis Laboratory, Institute for Atmospheric and Earth System Research (INAR)/Forest Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, 00014, Finland
- CREAF, Center for Ecological Research and Forestry Applications, Bellaterra, 08193, Spain
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, Cerdanyola del Vallès, 08193, Spain
| | - Jon Atherton
- Optics of Photosynthesis Laboratory, Institute for Atmospheric and Earth System Research (INAR)/Forest Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, 00014, Finland
| | - Josep Peñuelas
- CREAF, Center for Ecological Research and Forestry Applications, Bellaterra, 08193, Spain
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, Cerdanyola del Vallès, 08193, Spain
| | - Iolanda Filella
- CREAF, Center for Ecological Research and Forestry Applications, Bellaterra, 08193, Spain
- CSIC, Global Ecology Unit CREAF-CSIC-UAB, Cerdanyola del Vallès, 08193, Spain
| | - Pasi Kolari
- Department of Physics, University of Helsinki, Helsinki, 00014, Finland
| | - Juho Aalto
- Department of Physics, University of Helsinki, Helsinki, 00014, Finland
- Station for Measuring Forest Ecosystem-Atmosphere Relations II (SMEAR II), Hyytiälä Forestry Field Station, University of Helsinki, Korkeakoski, 35500, Finland
| | - Hanna Ruhanen
- Natural Resources Institute Finland (Luke), Natural Resources and Bioproduction, Suonenjoki, 77600, Finland
| | - Jaana Bäck
- Department of Forest Sciences, University of Helsinki, Helsinki, 00014, Finland
| | - Albert Porcar-Castell
- Optics of Photosynthesis Laboratory, Institute for Atmospheric and Earth System Research (INAR)/Forest Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, 00014, Finland
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Lead-Induced Changes in Fluorescence and Spectral Characteristics of Pea Leaves. REMOTE SENSING 2019. [DOI: 10.3390/rs11161885] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Chlorophyll fluorescence parameters can provide useful indications of photosynthetic performance in vivo. Coupling appropriate fluorescence measurements with other noninvasive techniques, such as absorption spectroscopy or gas exchange, can provide insights into the limitations to photosynthesis under given conditions. Chlorophyll content is one of the dominant factors influencing the conditions of a vegetation growing season, and can be tested using both fluorescence and remote sensing methods. Hyperspectral remote sensing and recording the narrow range of the spectrum can be used to accurately analyze the parameters and properties of plants. The aim of this study was to analyze the influence of lead ions (Pb, 5 mM Pb(NO3)2) on the growth of pea plants using spectral properties. Hyperspectral remote sensing and chlorophyll fluorescence measurements were used to assess the physiological state of plants seedlings treated by lead ions during the experiment. The plants were growing in hydroponic cultures supplemented with Pb ions under various conditions (control, complete Knop + phosphorus (+P); complete Knop + phosphorus (+P) + Pb; Knop (-P) + Pb, distilled water + Pb) affecting lead uptake via the root system. Spectrometric measurements allowed us to calculate the remote sensing indices of vegetation, which were compared with chlorophyll and carotenoids content and fluorescence parameters. The lead contents in the leaves, roots, and stems were also analyzed. Spectral characteristics and vegetation properties were analyzed using statistical tests. We conclude that: (1) pea seedlings grown in complete Knop (with P) and in the presence of Pb ions were spectrally similar to the control plants because lead was not transported to the shoots of plants; (2) lead most influenced plants that were grown in water, according to the highest lead content in the leaves; and (3) the effects of lead on plant growth were confirmed by remote sensing indices, whereas fluorescence parameters identified physiological changes induced by Pb ions in the plants.
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Sun-Induced Chlorophyll Fluorescence II: Review of Passive Measurement Setups, Protocols, and Their Application at the Leaf to Canopy Level. REMOTE SENSING 2019. [DOI: 10.3390/rs11080927] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Imaging and non-imaging spectroscopy employed in the field and from aircraft is frequently used to assess biochemical, structural, and functional plant traits, as well as their dynamics in an environmental matrix. With the increasing availability of high-resolution spectroradiometers, it has become feasible to measure fine spectral features, such as those needed to estimate sun-induced chlorophyll fluorescence (F), which is a signal related to the photosynthetic process of plants. The measurement of F requires highly accurate and precise radiance measurements in combination with very sophisticated measurement protocols. Additionally, because F has a highly dynamic nature (compared with other vegetation information derived from spectral data) and low signal intensity, several environmental, physiological, and experimental aspects have to be considered during signal acquisition and are key for its reliable interpretation. The European Cooperation in Science and Technology (COST) Action ES1309 OPTIMISE has produced three articles addressing the main challenges in the field of F measurements. In this paper, which is the second of three, we review approaches that are available to measure F from the leaf to the canopy scale using ground-based and airborne platforms. We put specific emphasis on instrumental aspects, measurement setups, protocols, quality checks, and data processing strategies. Furthermore, we review existing techniques that account for atmospheric influences on F retrieval, address spatial scaling effects, and assess quality checks and the metadata and ancillary data required to reliably interpret retrieved F signals.
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