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Zhang H, Plett JM, Catunda KLM, Churchill AC, Moore BD, Powell JR, Power SA, Yang J, Anderson IC. Rapid quantification of biological nitrogen fixation using optical spectroscopy. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:760-771. [PMID: 37891011 DOI: 10.1093/jxb/erad426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/27/2023] [Indexed: 10/29/2023]
Abstract
Biological nitrogen fixation (BNF) provides a globally important input of nitrogen (N); its quantification is critical but technically challenging. Leaf reflectance spectroscopy offers a more rapid approach than traditional techniques to measure plant N concentration ([N]) and isotopes (δ15N). Here we present a novel method for rapidly and inexpensively quantifying BNF using optical spectroscopy. We measured plant [N], δ15N, and the amount of N derived from atmospheric fixation (Ndfa) following the standard traditional methodology using isotope ratio mass spectrometry (IRMS) from tissues grown under controlled conditions and taken from field experiments. Using the same tissues, we predicted the same three parameters using optical spectroscopy. By comparing the optical spectroscopy-derived results with traditional measurements (i.e. IRMS), the amount of Ndfa predicted by optical spectroscopy was highly comparable to IRMS-based quantification, with R2 being 0.90 (slope=0.90) and 0.94 (slope=1.02) (root mean square error for predicting legume δ15N was 0.38 and 0.43) for legumes grown in glasshouse and field, respectively. This novel application of optical spectroscopy facilitates BNF studies because it is rapid, scalable, low cost, and complementary to existing technologies. Moreover, the proposed method successfully captures the dynamic response of BNF to climate changes such as warming and drought.
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Affiliation(s)
- Haiyang Zhang
- College of Life Sciences, Hebei University, Baoding, China
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - Jonathan M Plett
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - Karen L M Catunda
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - Amber C Churchill
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
- Department of Ecology, Evolution and Behavior, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Ave., St Paul, MN 55108, USA
| | - Ben D Moore
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - Jeff R Powell
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - Sally A Power
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - Jinyan Yang
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - Ian C Anderson
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
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2
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Soininen EM, Neby M. Small rodent population cycles and plants - after 70 years, where do we go? Biol Rev Camb Philos Soc 2024; 99:265-294. [PMID: 37827522 DOI: 10.1111/brv.13021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/14/2023]
Abstract
Small rodent population cycles characterise northern ecosystems, and the cause of these cycles has been a long-lasting central topic in ecology, with trophic interactions currently considered the most plausible cause. While some researchers have rejected plant-herbivore interactions as a cause of rodent cycles, others have continued to research their potential roles. Here, we present an overview of whether plants can cause rodent population cycles, dividing this idea into four different hypotheses with different pathways of plant impacts and related assumptions. Our systematic review of the existing literature identified 238 studies from 150 publications. This evidence base covered studies from the temperate biome to the tundra, but the studies were scattered across study systems and only a few specific topics were addressed in a replicated manner. Quantitative effects of rodents on vegetation was the best studied topic, and our evidence base suggests such that such effects may be most pronounced in winter. However, the regrowth of vegetation appears to take place too rapidly to maintain low rodent population densities over several years. The lack of studies prevented assessment of time lags in the qualitative responses of vegetation to rodent herbivory. We conclude that the literature is currently insufficient to discard with confidence any of the four potential hypotheses for plant-rodent cycles discussed herein. While new methods allow analyses of plant quality across more herbivore-relevant spatial scales than previously possible, we argue that the best way forward to rejecting any of the rodent-plant hypotheses is testing specific predictions of dietary variation. Indeed, all identified hypotheses make explicit assumptions on how rodent diet taxonomic composition and quality will change across the cycle. Passing this bottleneck could help pinpoint where, when, and how plant-herbivore interactions have - or do not have - plausible effects on rodent population dynamics.
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Affiliation(s)
- Eeva M Soininen
- Department of Arctic and Marine Biology, UiT-The Arctic University of Norway, Postboks 6050 Langnes, Tromsø, 9037, Norway
| | - Magne Neby
- Faculty of Applied Ecology, Agricultural Sciences and Biotechnology, Høyvangvegen 40, Ridabu, 2322, Norway
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3
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Brooker R, Brown LK, George TS, Pakeman RJ, Palmer S, Ramsay L, Schöb C, Schurch N, Wilkinson MJ. Active and adaptive plasticity in a changing climate. TRENDS IN PLANT SCIENCE 2022; 27:717-728. [PMID: 35282996 DOI: 10.1016/j.tplants.2022.02.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 01/24/2022] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Better understanding of the mechanistic basis of plant plasticity will enhance efforts to breed crops resilient to predicted climate change. However, complexity in plasticity's conceptualisation and measurement may hinder fruitful crossover of concepts between disciplines that would enable such advances. We argue active adaptive plasticity is particularly important in shaping the fitness of wild plants, representing the first line of a plant's defence to environmental change. Here, we define how this concept may be applied to crop breeding, suggest appropriate approaches to measure it in crops, and propose a refocussing on active adaptive plasticity to enhance crop resilience. We also discuss how the same concept may have wider utility, such as in ex situ plant conservation and reintroductions.
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Affiliation(s)
- Rob Brooker
- Department of Ecological Sciences, James Hutton Institute, Aberdeen, UK; Department of Ecological Sciences, James Hutton Institute, Dundee, UK.
| | - Lawrie K Brown
- Department of Ecological Sciences, James Hutton Institute, Dundee, UK
| | - Timothy S George
- Department of Ecological Sciences, James Hutton Institute, Dundee, UK
| | - Robin J Pakeman
- Department of Ecological Sciences, James Hutton Institute, Aberdeen, UK
| | - Sarah Palmer
- Institute of Biological, Environmental, and Rural Sciences (IBERS), Aberystwyth University, Plas Gogerddan, Aberystwyth, Ceredigion, UK
| | - Luke Ramsay
- Department of Ecological Sciences, James Hutton Institute, Dundee, UK
| | - Christian Schöb
- Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | | | - Mike J Wilkinson
- Institute of Biological, Environmental, and Rural Sciences (IBERS), Aberystwyth University, Plas Gogerddan, Aberystwyth, Ceredigion, UK
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Vasseur F, Cornet D, Beurier G, Messier J, Rouan L, Bresson J, Ecarnot M, Stahl M, Heumos S, Gérard M, Reijnen H, Tillard P, Lacombe B, Emanuel A, Floret J, Estarague A, Przybylska S, Sartori K, Gillespie LM, Baron E, Kazakou E, Vile D, Violle C. A Perspective on Plant Phenomics: Coupling Deep Learning and Near-Infrared Spectroscopy. FRONTIERS IN PLANT SCIENCE 2022; 13:836488. [PMID: 35668791 PMCID: PMC9163986 DOI: 10.3389/fpls.2022.836488] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 03/09/2022] [Indexed: 05/31/2023]
Abstract
The trait-based approach in plant ecology aims at understanding and classifying the diversity of ecological strategies by comparing plant morphology and physiology across organisms. The major drawback of the approach is that the time and financial cost of measuring the traits on many individuals and environments can be prohibitive. We show that combining near-infrared spectroscopy (NIRS) with deep learning resolves this limitation by quickly, non-destructively, and accurately measuring a suite of traits, including plant morphology, chemistry, and metabolism. Such an approach also allows to position plants within the well-known CSR triangle that depicts the diversity of plant ecological strategies. The processing of NIRS through deep learning identifies the effect of growth conditions on trait values, an issue that plagues traditional statistical approaches. Together, the coupling of NIRS and deep learning is a promising high-throughput approach to capture a range of ecological information on plant diversity and functioning and can accelerate the creation of extensive trait databases.
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Affiliation(s)
| | - Denis Cornet
- CIRAD, UMR AGAP Institut, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Grégory Beurier
- CIRAD, UMR AGAP Institut, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Julie Messier
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Lauriane Rouan
- CIRAD, UMR AGAP Institut, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Justine Bresson
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Martin Ecarnot
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Mark Stahl
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Simon Heumos
- Quantitative Biology Center (QBiC), University of Tübingen, Quantitative Biology Center (QBiC), University of Tübingen, Germany
- Biomedical Data Science, Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Marianne Gérard
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Hans Reijnen
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Pascal Tillard
- BPMP, Univ Montpellier, CNRS, INRAE, Montpellier, France
| | - Benoît Lacombe
- BPMP, Univ Montpellier, CNRS, INRAE, Montpellier, France
| | - Amélie Emanuel
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
- BPMP, Univ Montpellier, CNRS, INRAE, Montpellier, France
| | - Justine Floret
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
- LEPSE, Univ Montpellier, INRAE, Institut Agro, Montpellier, France
| | | | | | - Kevin Sartori
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | | | - Etienne Baron
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Elena Kazakou
- CEFE, Univ Montpellier, CNRS, EPHE, Institut Agro, IRD, Montpellier, France
| | - Denis Vile
- LEPSE, Univ Montpellier, INRAE, Institut Agro, Montpellier, France
| | - Cyrille Violle
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
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Liu W, Li Y, Tomasetto F, Yan W, Tan Z, Liu J, Jiang J. Non-destructive Measurements of Toona sinensis Chlorophyll and Nitrogen Content Under Drought Stress Using Near Infrared Spectroscopy. FRONTIERS IN PLANT SCIENCE 2022; 12:809828. [PMID: 35126433 PMCID: PMC8814108 DOI: 10.3389/fpls.2021.809828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
Drought is a climatic event that considerably impacts plant growth, reproduction and productivity. Toona sinensis is a tree species with high economic, edible and medicinal value, and has drought resistance. Thus, the objective of this study was to dynamically monitor the physiological indicators of T. sinensis in real time to ensure the selection of drought-resistant varieties of T. sinensis. In this study, we used near-infrared spectroscopy as a high-throughput method along with five preprocessing methods combined with four variable selection approaches to establish a cross-validated partial least squares regression model to establish the relationship between the near infrared reflectance spectroscopy (NIRS) spectrum and physiological characteristics (i.e., chlorophyll content and nitrogen content) of T. sinensis leaves. We also tested optimal model prediction for the dynamic changes in T. sinensis chlorophyll and nitrogen content under five separate watering regimes to mimic non-destructive and dynamic detection of plant leaf physiological changes. Among them, the accuracy of the chlorophyll content prediction model was as high as 72%, with root mean square error (RMSE) of 0.25, and the RPD index above 2.26. Ideal nitrogen content prediction model should have R 2 of 0.63, with RMSE of 0.87, and the RPD index of 1.12. The results showed that the PLSR model has a good prediction effect. Overall, under diverse drought stress treatments, the chlorophyll content of T. sinensis leaves showed a decreasing trend over time. Furthermore, the chlorophyll content was the most stable under the 75% field capacity treatment. However, the nitrogen content of the plant leaves was found to have a different and variable trend, with the greatest drop in content under the 10% field capacity treatment. This study showed that NIRS has great potential for analyzing chlorophyll nitrogen and other elements in plant leaf tissues in non-destructive dynamic monitoring.
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Affiliation(s)
- Wenjian Liu
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Yanjie Li
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | | | - Weiqi Yan
- Department of Computer Science, Auckland University of Technology, Auckland, New Zealand
| | - Zifeng Tan
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Jun Liu
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Jingmin Jiang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
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Petit Bon M, Böhner H, BrÅthen KA, Ravolainen VT, Jónsdóttir IS. Variable responses of carbon and nitrogen contents in vegetation and soil to herbivory and warming in high‐Arctic tundra. Ecosphere 2021. [DOI: 10.1002/ecs2.3746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Matteo Petit Bon
- Department of Arctic Biology University Centre in Svalbard (UNIS) PO Box 156 N‐9171 Longyearbyen Norway
- Department of Arctic and Marine Biology Faculty of Biosciences, Fisheries, and Economics Arctic University of Norway (UiT) N‐9037 Tromsø Norway
| | - Hanna Böhner
- Department of Arctic Biology University Centre in Svalbard (UNIS) PO Box 156 N‐9171 Longyearbyen Norway
- Department of Arctic and Marine Biology Faculty of Biosciences, Fisheries, and Economics Arctic University of Norway (UiT) N‐9037 Tromsø Norway
| | - Kari Anne BrÅthen
- Department of Arctic and Marine Biology Faculty of Biosciences, Fisheries, and Economics Arctic University of Norway (UiT) N‐9037 Tromsø Norway
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7
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Petit Bon M, Gunnarsdotter Inga K, Jónsdóttir IS, Utsi TA, Soininen EM, Bråthen KA. Interactions between winter and summer herbivory affect spatial and temporal plant nutrient dynamics in tundra grassland communities. OIKOS 2020. [DOI: 10.1111/oik.07074] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Matteo Petit Bon
- Dept of Arctic Biology, Univ. Centre in Svalbard (UNIS) PO Box 156 NO‐9171 Longyearbyen Norway
- Dept of Arctic and Marine Biology, Faculty of Biosciences, Fisheries, and Economics, Arctic Univ. of Norway (UiT) Tromsø Norway
| | - Katarina Gunnarsdotter Inga
- Dept of Arctic and Marine Biology, Faculty of Biosciences, Fisheries, and Economics, Arctic Univ. of Norway (UiT) Tromsø Norway
| | | | - Tove Aagnes Utsi
- Dept of Arctic and Marine Biology, Faculty of Biosciences, Fisheries, and Economics, Arctic Univ. of Norway (UiT) Tromsø Norway
| | - Eeva Marjatta Soininen
- Dept of Arctic and Marine Biology, Faculty of Biosciences, Fisheries, and Economics, Arctic Univ. of Norway (UiT) Tromsø Norway
| | - Kari Anne Bråthen
- Dept of Arctic and Marine Biology, Faculty of Biosciences, Fisheries, and Economics, Arctic Univ. of Norway (UiT) Tromsø Norway
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