1
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LaManna JA, Hartig F, Myers JA, Freckleton RP, Detto M, Surendra A, Doolittle CJ, Bachelot B, Bagchi R, Comita LS, DeFilippis DM, Huanca-Nunez N, Hülsmann L, Jevon FV, Johnson DJ, Krishnadas M, Magee LJ, Mangan SA, Milici VR, Murengera ALB, Schnitzer SA, Smith DJB, Stein C, Sullivan MK, Torres E, Umaña MN, Delavaux CS. Consequences of Local Conspecific Density Effects for Plant Diversity and Community Dynamics. Ecol Lett 2024; 27:e14506. [PMID: 39354892 DOI: 10.1111/ele.14506] [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: 10/23/2023] [Revised: 08/05/2024] [Accepted: 08/11/2024] [Indexed: 10/03/2024]
Abstract
Conspecific density dependence (CDD) in plant populations is widespread, most likely caused by local-scale biotic interactions, and has potentially important implications for biodiversity, community composition, and ecosystem processes. However, progress in this important area of ecology has been hindered by differing viewpoints on CDD across subfields in ecology, lack of synthesis across CDD-related frameworks, and misunderstandings about how empirical measurements of local CDD fit within the context of broader ecological theories on community assembly and diversity maintenance. Here, we propose a conceptual synthesis of local-scale CDD and its causes, including species-specific antagonistic and mutualistic interactions. First, we compare and clarify different uses of CDD and related concepts across subfields within ecology. We suggest the use of local stabilizing/destabilizing CDD to refer to the scenario where local conspecific density effects are more negative/positive than heterospecific effects. Second, we discuss different mechanisms for local stabilizing and destabilizing CDD, how those mechanisms are interrelated, and how they cut across several fields of study within ecology. Third, we place local stabilizing/destabilizing CDD within the context of broader ecological theories and discuss implications and challenges related to scaling up the effects of local CDD on populations, communities, and metacommunities. The ultimate goal of this synthesis is to provide a conceptual roadmap for researchers studying local CDD and its implications for population and community dynamics.
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Affiliation(s)
- Joseph A LaManna
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, USA
| | - Florian Hartig
- Theoretical Ecology, University of Regensburg, Regensburg, Germany
| | - Jonathan A Myers
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Robert P Freckleton
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Matteo Detto
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - Akshay Surendra
- School of the Environment, Yale University, New Haven, Connecticut, USA
| | - Cole J Doolittle
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, USA
| | - Bénédicte Bachelot
- Department of Plant Biology, Ecology, and Evolution, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Robert Bagchi
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Liza S Comita
- School of the Environment, Yale University, New Haven, Connecticut, USA
| | - David M DeFilippis
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, USA
| | | | - Lisa Hülsmann
- Ecosystem Analysis and Simulation (EASI) Lab, University of Bayreuth, Bayreuth, Germany
- Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Fiona V Jevon
- School of the Environment, Yale University, New Haven, Connecticut, USA
| | - Daniel J Johnson
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, Florida, USA
| | - Meghna Krishnadas
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Lukas J Magee
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, Florida, USA
| | - Scott A Mangan
- Arkansas Biosciences Institute, Arkansas State University, Jonesboro, Arkansas, USA
| | - Valerie R Milici
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
| | | | - Stefan A Schnitzer
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, USA
| | - Daniel J B Smith
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
| | - Claudia Stein
- Department of Biology and Environmental Sciences, Auburn University at Montgomery, Montgomery, Alabama, USA
| | - Megan K Sullivan
- School of the Environment, Yale University, New Haven, Connecticut, USA
| | - Ethan Torres
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, USA
| | - María Natalia Umaña
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Camille S Delavaux
- Institute of Integrative Biology, ETH Zurich (Swiss Federal Institute of Technology), Zurich, Switzerland
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2
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Sun L, He Y, Cao M, Wang X, Zhou X, Yang J, Swenson NG. Tree phytochemical diversity and herbivory are higher in the tropics. Nat Ecol Evol 2024; 8:1426-1436. [PMID: 38937611 DOI: 10.1038/s41559-024-02444-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 05/20/2024] [Indexed: 06/29/2024]
Abstract
A long-standing but poorly tested hypothesis in plant ecology and evolution is that biotic interactions play a more important role in producing and maintaining species diversity in the tropics than in the temperate zone. A core prediction of this hypothesis is that tropical plants deploy a higher diversity of phytochemicals within and across communities because they experience more herbivore pressure than temperate plants. However, simultaneous comparisons of phytochemical diversity and herbivore pressure in plant communities from the tropical to the temperate zone are lacking. Here we provide clear support for this prediction by examining phytochemical diversity and herbivory in 60 tree communities ranging from species-rich tropical rainforests to species-poor subalpine forests. Using a community metabolomics approach, we show that phytochemical diversity is higher within and among tropical tree communities than within and among subtropical and subalpine communities, and that herbivore pressure and specialization are highest in the tropics. Furthermore, we show that the phytochemical similarity of trees has little phylogenetic signal, indicating rapid divergence between closely related species. In sum, we provide several lines of evidence from entire tree communities showing that biotic interactions probably play an increasingly important role in generating and maintaining tree diversity in the lower latitudes.
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Affiliation(s)
- Lu Sun
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
| | - Yunyun He
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
- University of Chinese Academy Sciences, Beijing, China
| | - Min Cao
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
| | - Xuezhao Wang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
- University of Chinese Academy Sciences, Beijing, China
| | - Xiang Zhou
- School of Ethnic Medicine, Key Lab of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission & Ministry of Education of China, Yunnan Minzu University, Kunming, China
| | - Jie Yang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China.
| | - Nathan G Swenson
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
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3
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Sierra AM, Meléndez O, Bethancourt R, Bethancourt A, Rodríguez-Castro L, López CA, Sedio BE, Saltonstall K, Villarreal A JC. Leaf Endophytes Relationship with Host Metabolome Expression in Tropical Gymnosperms. J Chem Ecol 2024:10.1007/s10886-024-01511-z. [PMID: 38809282 DOI: 10.1007/s10886-024-01511-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 05/07/2024] [Accepted: 05/17/2024] [Indexed: 05/30/2024]
Abstract
Plant-microbe interactions play a pivotal role in shaping host fitness, especially concerning chemical defense mechanisms. In cycads, establishing direct correlations between specific endophytic microbes and the synthesis of highly toxic defensive phytochemicals has been challenging. Our research delves into the intricate relationship between plant-microbe associations and the variation of secondary metabolite production in two closely related Zamia species that grow in distinct habitats; terrestrial and epiphytic. Employing an integrated approach, we combined microbial metabarcoding, which characterize the leaf endophytic bacterial and fungal communities, with untargeted metabolomics to test if the relative abundances of specific microbial taxa in these two Zamia species were associated with different metabolome profiles. The two species studied shared approximately 90% of the metabolites spanning diverse biosynthetic pathways: alkaloids, amino acids, carbohydrates, fatty acids, polyketides, shikimates, phenylpropanoids, and terpenoids. Co-occurrence networks revealed positive associations among metabolites from different pathways, underscoring the complexity of their interactions. Our integrated analysis demonstrated to some degree that the intraspecific variation in metabolome profiles of the two host species was associated with the abundance of bacterial orders Acidobacteriales and Frankiales, as well as the fungal endophytes belonging to the orders Chaetothyriales, Glomerellales, Heliotiales, Hypocreales, and Sordariales. We further associate individual metabolic similarity with four specific fungal endophyte members of the core microbiota, but no specific bacterial taxa associations were identified. This study represents a pioneering investigation to characterize leaf endophytes and their association with metabolomes in tropical gymnosperms, laying the groundwork for deeper inquiries into this complex domain.
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Affiliation(s)
- Adriel M Sierra
- Département de Biologie, Université Laval, Québec, (QC), G1V 0A6, Canada.
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, (QC), G1V 0A6, Canada.
| | - Omayra Meléndez
- Departamento de Microbiología y Parasitología, Facultad de Ciencias Naturales, Exactas y Tecnología, Universidad de Panamá, Panamá, Panamá
- Smithsonian Tropical Research Institute, Ancón, Panamá
| | - Rita Bethancourt
- Departamento de Microbiología y Parasitología, Facultad de Ciencias Naturales, Exactas y Tecnología, Universidad de Panamá, Panamá, Panamá
| | - Ariadna Bethancourt
- Departamento de Microbiología y Parasitología, Facultad de Ciencias Naturales, Exactas y Tecnología, Universidad de Panamá, Panamá, Panamá
| | - Lilisbeth Rodríguez-Castro
- Departamento de Microbiología, Facultad de Ciencias Naturales, Exactas y Tecnología, Universidad de Panamá, Panamá, Panamá
- Smithsonian Tropical Research Institute, Ancón, Panamá
| | - Christian A López
- Smithsonian Tropical Research Institute, Ancón, Panamá
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Brian E Sedio
- Smithsonian Tropical Research Institute, Ancón, Panamá
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | | | - Juan Carlos Villarreal A
- Département de Biologie, Université Laval, Québec, (QC), G1V 0A6, Canada.
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, (QC), G1V 0A6, Canada.
- Smithsonian Tropical Research Institute, Ancón, Panamá.
- Canada Research Chair in Genomics of Tropical Symbioses, Department of Biology, Université Laval, Québec, G1V 0A6, Canadá.
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4
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Volf M, Renoult SA, Panthee S, van Dam NM. Quantifying various aspects of chemical diversity in hybrid plants can help understanding ecological consequences of hybridization. AMERICAN JOURNAL OF BOTANY 2024; 111:e16283. [PMID: 38332482 DOI: 10.1002/ajb2.16283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 12/14/2023] [Accepted: 12/14/2023] [Indexed: 02/10/2024]
Affiliation(s)
- Martin Volf
- Biology Centre of the Czech Academy of Sciences, Branisovska 31, Ceske Budejovice, 37005, Czech Republic
- Faculty of Science, University of South Bohemia, Branisovska 31, Ceske Budejovice, 37005, Czech Republic
| | - Sofian A Renoult
- Biology Centre of the Czech Academy of Sciences, Branisovska 31, Ceske Budejovice, 37005, Czech Republic
- Faculty of Science, University of South Bohemia, Branisovska 31, Ceske Budejovice, 37005, Czech Republic
| | - Shristee Panthee
- Leibniz Institute for Vegetable and Ornamental Crops (IGZ) e.V., Theodor-Echtermeyer-Weg 1, Großbeeren, 14979, Germany
| | - Nicole M van Dam
- Leibniz Institute for Vegetable and Ornamental Crops (IGZ) e.V., Theodor-Echtermeyer-Weg 1, Großbeeren, 14979, Germany
- Institute of Biodiversity, Friedrich-Schiller-Universität Jena, Dornburgerstraße 159, Jena, 07745, Germany
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5
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Wang X, He Y, Sedio BE, Jin L, Ge X, Glomglieng S, Cao M, Yang J, Swenson NG, Yang J. Phytochemical diversity impacts herbivory in a tropical rainforest tree community. Ecol Lett 2023; 26:1898-1910. [PMID: 37776563 DOI: 10.1111/ele.14308] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 07/24/2023] [Accepted: 08/25/2023] [Indexed: 10/02/2023]
Abstract
Metabolomics provides an unprecedented window into diverse plant secondary metabolites that represent a potentially critical niche dimension in tropical forests underlying species coexistence. Here, we used untargeted metabolomics to evaluate chemical composition of 358 tree species and its relationship with phylogeny and variation in light environment, soil nutrients, and insect herbivore leaf damage in a tropical rainforest plot. We report no phylogenetic signal in most compound classes, indicating rapid diversification in tree metabolomes. We found that locally co-occurring species were more chemically dissimilar than random and that local chemical dispersion and metabolite diversity were associated with lower herbivory, especially that of specialist insect herbivores. Our results highlight the role of secondary metabolites in mediating plant-herbivore interactions and their potential to facilitate niche differentiation in a manner that contributes to species coexistence. Furthermore, our findings suggest that specialist herbivore pressure is an important mechanism promoting phytochemical diversity in tropical forests.
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Affiliation(s)
- Xuezhao Wang
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
- School of Ecology and Environment, Southwest Forestry University, Kunming, China
| | - Yunyun He
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Brian E Sedio
- Department of Integrative Biology, University of Texas at Austin, Texas, Austin, USA
- Smithsonian Tropical Research Institute, Ancón, Republic of Panama
| | - Lu Jin
- College of Life Sciences, South China Agricultural University, Guangzhou, China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Xuejun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Suphanee Glomglieng
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Min Cao
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
| | - Jianhong Yang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Nathan G Swenson
- Department of Biological Sciences, University of Notre Dame, Indiana, Notre Dame, USA
| | - Jie Yang
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
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6
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Salgado AL, Glassmire AE, Sedio BE, Diaz R, Stout MJ, Čuda J, Pyšek P, Meyerson LA, Cronin JT. Metabolomic Evenness Underlies Intraspecific Differences Among Lineages of a Wetland Grass. J Chem Ecol 2023; 49:437-450. [PMID: 37099216 DOI: 10.1007/s10886-023-01425-2] [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: 02/10/2023] [Revised: 03/20/2023] [Accepted: 04/05/2023] [Indexed: 04/27/2023]
Abstract
The metabolome represents an important functional trait likely important to plant invasion success, but we have a limited understanding of whether the entire metabolome or targeted groups of compounds confer an advantage to invasive as compared to native taxa. We conducted a lipidomic and metabolomic analysis of the cosmopolitan wetland grass Phragmites australis. We classified features into metabolic pathways, subclasses, and classes. Subsequently, we used Random Forests to identify informative features to differentiate five phylogeographic and ecologically distinct lineages: European native, North American invasive, North American native, Gulf, and Delta. We found that lineages had unique phytochemical fingerprints, although there was overlap between the North American invasive and North American native lineages. Furthermore, we found that divergence in phytochemical diversity was driven by compound evenness rather than metabolite richness. Interestingly, the North American invasive lineage had greater chemical evenness than the Delta and Gulf lineages but lower evenness than the North American native lineage. Our results suggest that metabolomic evenness may represent a critical functional trait within a plant species. Its role in invasion success, resistance to herbivory, and large-scale die-off events common to this and other plant species remain to be investigated.
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Affiliation(s)
- Ana L Salgado
- Department of Biological Sciences, Louisiana State University, Life Sciences Building, Baton Rouge, LA, 70803, USA.
| | - Andrea E Glassmire
- Department of Biological Sciences, Louisiana State University, Life Sciences Building, Baton Rouge, LA, 70803, USA
| | - Brian E Sedio
- Department of Integrative Biology, University of Texas, Austin, TX, 78712, USA
- Smithsonian Tropical Research Institute, Balboa, Ancón, Apartado, 0843-03092, Republic of Panama
| | - Rodrigo Diaz
- Department of Entomology, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Michael J Stout
- Department of Entomology, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Jan Čuda
- Department of Invasion Ecology, Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | - Petr Pyšek
- Department of Invasion Ecology, Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
- Department of Ecology, Faculty of Science, Charles University, Prague, CZ -128 44, Czech Republic
| | - Laura A Meyerson
- Department of Natural Resource Sciences, University of Rhode Island, Kingston, RI, 02881, USA
| | - James T Cronin
- Department of Biological Sciences, Louisiana State University, Life Sciences Building, Baton Rouge, LA, 70803, USA
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7
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Petrén H, Köllner TG, Junker RR. Quantifying chemodiversity considering biochemical and structural properties of compounds with the R package chemodiv. THE NEW PHYTOLOGIST 2023; 237:2478-2492. [PMID: 36527232 DOI: 10.1111/nph.18685] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
Plants produce large numbers of phytochemical compounds affecting plant physiology and interactions with their biotic and abiotic environment. Recently, chemodiversity has attracted considerable attention as an ecologically and evolutionary meaningful way to characterize the phenotype of a mixture of phytochemical compounds. Currently used measures of phytochemical diversity, and related measures of phytochemical dissimilarity, generally do not take structural or biosynthetic properties of compounds into account. Such properties can be indicative of the compounds' function and inform about their biosynthetic (in)dependence, and should therefore be included in calculations of these measures. We introduce the R package chemodiv, which retrieves biochemical and structural properties of compounds from databases and provides functions for calculating and visualizing chemical diversity and dissimilarity for phytochemicals and other types of compounds. Our package enables calculations of diversity that takes the richness, relative abundance and - most importantly - structural and/or biosynthetic dissimilarity of compounds into account. We illustrate the use of the package with examples on simulated and real datasets. By providing the R package chemodiv for quantifying multiple aspects of chemodiversity, we hope to facilitate investigations of how chemodiversity varies across levels of biological organization, and its importance for the ecology and evolution of plants and other organisms.
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Affiliation(s)
- Hampus Petrén
- Evolutionary Ecology of Plants, Department of Biology, Philipps-University Marburg, 35043, Marburg, Germany
| | - Tobias G Köllner
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, 07745, Jena, Germany
| | - Robert R Junker
- Evolutionary Ecology of Plants, Department of Biology, Philipps-University Marburg, 35043, Marburg, Germany
- Department of Environment and Biodiversity, University of Salzburg, 5020, Salzburg, Austria
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8
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Peters K, Blatt-Janmaat KL, Tkach N, van Dam NM, Neumann S. Untargeted Metabolomics for Integrative Taxonomy: Metabolomics, DNA Marker-Based Sequencing, and Phenotype Bioimaging. PLANTS (BASEL, SWITZERLAND) 2023; 12:881. [PMID: 36840229 PMCID: PMC9965764 DOI: 10.3390/plants12040881] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/07/2023] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
Integrative taxonomy is a fundamental part of biodiversity and combines traditional morphology with additional methods such as DNA sequencing or biochemistry. Here, we aim to establish untargeted metabolomics for use in chemotaxonomy. We used three thallose liverwort species Riccia glauca, R. sorocarpa, and R. warnstorfii (order Marchantiales, Ricciaceae) with Lunularia cruciata (order Marchantiales, Lunulariacea) as an outgroup. Liquid chromatography high-resolution mass-spectrometry (UPLC/ESI-QTOF-MS) with data-dependent acquisition (DDA-MS) were integrated with DNA marker-based sequencing of the trnL-trnF region and high-resolution bioimaging. Our untargeted chemotaxonomy methodology enables us to distinguish taxa based on chemophenetic markers at different levels of complexity: (1) molecules, (2) compound classes, (3) compound superclasses, and (4) molecular descriptors. For the investigated Riccia species, we identified 71 chemophenetic markers at the molecular level, a characteristic composition in 21 compound classes, and 21 molecular descriptors largely indicating electron state, presence of chemical motifs, and hydrogen bonds. Our untargeted approach revealed many chemophenetic markers at different complexity levels that can provide more mechanistic insight into phylogenetic delimitation of species within a clade than genetic-based methods coupled with traditional morphology-based information. However, analytical and bioinformatics analysis methods still need to be better integrated to link the chemophenetic information at multiple scales.
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Affiliation(s)
- Kristian Peters
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, 06108 Halle, Germany
- Bioinformatics and Scientific Data, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
| | - Kaitlyn L. Blatt-Janmaat
- Bioinformatics and Scientific Data, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
- Department of Chemistry, University of New Brunswick, Fredericton, NB E3B 5A3, Canada
| | - Natalia Tkach
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, 06108 Halle, Germany
| | - Nicole M. van Dam
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburgerstraße 159, 07743 Jena, Germany
- Plants Biotic Interactions, Leibniz Institute of Vegetable and Ornamental Crops (IGZ), Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
| | - Steffen Neumann
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, 06108 Halle, Germany
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9
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Gallon ME, Smilanich AM. Effects of Host Plants on Development and Immunity of a Generalist Insect Herbivore. J Chem Ecol 2023; 49:142-154. [PMID: 36763248 DOI: 10.1007/s10886-023-01410-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 02/11/2023]
Abstract
Secondary plant chemistry mediates a variety of communication signals among species, playing a fundamental role in the evolutionary diversification of communities and ecosystems. Herein, we explored diet-mediated host plant effects on development and immune response of a generalist insect herbivore. Vanessa cardui (Nymphalidae) caterpillars were reared on leaves of three host plants that vary in secondary metabolites, Plantago lanceolata (Plantaginaceae), Taraxacum officinale (Asteraceae) and Tithonia diversifolia (Asteraceae). Insect development was evaluated by larval and pupal viabilities, survivorship, and development rate. Immune response was measured as phenoloxidase (PO) activity. Additionally, chemical profiles of the host plants were obtained by liquid chromatograph-mass spectrometry (LC-MS) and the discriminant metabolites were determined using a metabolomic approach. Caterpillars reared on P. lanceolata exhibited the highest larval and pupal viabilities, as well as PO activity, and P. lanceolata leaves were chemically characterized by the presence of iridoid glycosides, phenylpropanoids and flavonoids. Taraxacum officinale leaves were characterized mainly by the presence of phenylpropanoids, flavones O-glycoside and germacranolide-type sesquiterpene lactones; caterpillars reared on this host plant fully developed to the adult stage, however they exhibited lower larval and pupal viabilities compared to individuals reared on P. lanceolata. Conversely, caterpillars reared on T. diversifolia leaves, which contain phenylpropanoids, flavones and diverse furanoheliangolide-type sesquiterpene lactones, were not able to complete larval development and exhibited the lowest PO activity. These findings suggested that V. cardui have adapted to tolerate potentially toxic metabolites occurring in P. lanceolata (iridoid glycosides), however caterpillars were not able to cope with potentially detrimental metabolites occurring in T. diversifolia (furanoheliangolides). Therefore, we suggest that furanoheliangolide-type sesquiterpene lactones were responsible for the poor development and immune response observed for caterpillars reared on T. diversifolia.
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Affiliation(s)
- Marilia Elias Gallon
- Department of Biology, University of Nevada, 1664 N. Virginia St., Reno, NV, 89557, USA. .,Núcleo de Pesquisa em Produtos Naturais e Sintéticos, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (USP), Av. do Café s/n°, Ribeirão Preto, SP, 14040-903, Brazil.
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10
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Feussner K, Abreu IN, Klein M, Feussner I. Metabolite fingerprinting: A powerful metabolomics approach for marker identification and functional gene annotation. Methods Enzymol 2023; 680:325-350. [PMID: 36710017 DOI: 10.1016/bs.mie.2022.08.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Non-targeted metabolome approaches aim to detect metabolite markers related to stress, disease, developmental or genetic perturbation. In the later context, it is also a powerful means for functional gene annotation. A prerequisite for non-targeted metabolome analyses are methods for comprehensive metabolite extraction. We present three extraction protocols for a highly efficient extraction of metabolites from plant material with a very broad metabolite coverage. The presented metabolite fingerprinting workflow is based on liquid chromatography high resolution accurate mass spectrometry (LC-HRAM-MS), which provides suitable separation of the complex sample matrix for the analysis of compounds of different polarity by positive and negative electrospray ionization and mass spectrometry. The resulting data sets are then analyzed with the software suite MarVis and the web-based interface MetaboAnalyst. MarVis offers a straightforward workflow for statistical analysis, data merging as well as visualization of multivariate data, while MetaboAnalyst is used in our hands as complementary software for statistics, correlation networks and figure generation. Finally, MarVis provides access to species-specific metabolite and pathway data bases like KEGG and BioCyc and to custom data bases tailored by the user to connect the identified markers or features with metabolites. In addition, identified marker candidates can be interactively visualized and inspected in metabolic pathway maps by KEGG pathways for a more detailed functional annotation and confirmed by mass spectrometry fragmentation experiments or coelution with authentic standards. Together this workflow is a valuable toolbox to identify novel metabolites, metabolic steps or regulatory principles and pathways.
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Affiliation(s)
- Kirstin Feussner
- University of Goettingen, Albrecht-von-Haller-Institute for Plant Sciences, Department of Plant Biochemistry, Goettingen, Germany; University of Goettingen, Goettingen Center for Molecular Biosciences (GZMB), Service Unit for Metabolomics and Lipidomics, Goettingen, Germany.
| | - Ilka N Abreu
- University of Goettingen, Albrecht-von-Haller-Institute for Plant Sciences, Department of Plant Biochemistry, Goettingen, Germany
| | - Moritz Klein
- University of Goettingen, Albrecht-von-Haller-Institute for Plant Sciences, Department of Plant Biochemistry, Goettingen, Germany
| | - Ivo Feussner
- University of Goettingen, Albrecht-von-Haller-Institute for Plant Sciences, Department of Plant Biochemistry, Goettingen, Germany; University of Goettingen, Goettingen Center for Molecular Biosciences (GZMB), Service Unit for Metabolomics and Lipidomics, Goettingen, Germany; University of Goettingen, Goettingen Center for Molecular Biosciences (GZMB), Department of Plant Biochemistry, Goettingen, Germany.
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11
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Morrison JA, Woldemariam M. Ecological and metabolomic responses of plants to deer exclosure in a suburban forest. Ecol Evol 2022; 12:e9475. [PMID: 36381402 PMCID: PMC9643135 DOI: 10.1002/ece3.9475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 09/28/2022] [Accepted: 10/05/2022] [Indexed: 11/11/2022] Open
Abstract
Trees and shrubs in suburban forests can be subject to chronic herbivory from abundant white-tailed deer, influencing survival, growth, secondary metabolites, and ecological success in the community. We investigated how deer affect the size, cover, and metabolomes of four species in the understory of a suburban forest in central New Jersey, USA: the woody shrubs Euonymus alatus and Lindera benzoin, the tree Nyssa sylvatica, and the semi-woody shrub Rosa multiflora. For each species, we compared plants in 38 16 m2 plots with or without deer exclosure, measuring proportion cover and mean height after 6.5 years of fencing. We scored each species in all plots for deer browsing over 8 years and assessed selection by deer among the species. We did untargeted metabolomics by sampling leaves from three plants of each species in an equal number of fenced and unfenced plots, conducting chloroform-methanol extractions followed by LC-MS/MS, and conducting statistical analysis on MetaboAnalyst. The proportion of a species browsed ranged from 0.24 to 0.35. Nyssa sylvatica appeared most selected by and susceptible to deer; in unfenced plots, both its cover and mean height were significantly lower. Only cover or height was lower for E. alatus and L. benzoin in unfenced plots, while R. multiflora height was greater. The metabolomic analysis identified 2333 metabolites, which clustered by species but not fencing treatment. However, targeted analysis of the top metabolites grouped by fencing for all samples and for each species alone and was especially clear in N. sylvatica, which also grouped by fencing using all metabolites. The most significant metabolites that were upregulated in fenced plants include some involved in defense-related metabolic pathways, e.g., monoterpenoid biosynthesis. In overbrowsed suburban forests, variation of deer impact on species' ecological success, potentially mediated by metabolome-wide chemical responses to deer, may contribute to changes in community structure.
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12
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Protective effect of the stressed supernatant from Lactococcus lactis subsp. lactis and its metabolic analysis. Arch Microbiol 2022; 204:428. [PMID: 35751720 DOI: 10.1007/s00203-022-03034-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 05/29/2022] [Accepted: 06/01/2022] [Indexed: 11/02/2022]
Abstract
There are numerous factors restricting wide application of lactic acid bacteria (LAB) in dairy industry, causing urgent demands for novel bioprotectants. Protective effects and metabolites of Lactococcus lactis subsp. lactis (L. lactis) from ultraviolet (UV)-induced supernatant were investigated and the protective mechanism was explored. The strain viability of the group treated with the supernatant of continuous UV irradiation (V1) and the group with intermittent UV irradiation (V2) was 8.45 and 14.13 times of the control group, respectively. Further exploration on the protective of L. lactis supernatant, under different dose of UV treatment, showed it was dose-dependent. The condition for the supernatant with best protective effect was vertical distance 50.00 cm, horizontal distance 25.00 cm, intermittent UV irradiation (30 s interval 30 s) for 4.5 min (V2), which was chose for untargeted metabolite analysis. And that in V1 was for comparative study. There were 181 up-regulated metabolites in V1 and 161 up-regulated metabolites in V2, respectively. Most of the up-regulated metabolites were related to secondary metabolite synthesis, environmental microbial metabolism, antibiotic synthesis and amino acid biosynthesis. Notably, production of dithiothreitol (DTT) in V2 was 65.2-fold higher than that in the control group. Trehalose in ABC transporter pathway was also up-regulated in the metabolites induced by UV. Results indicated that L. lactis could adapt to the UV stress by adjusting metabolic pathways and producing special metabolites to protect itself. This research offers the basis for robust strain development and contributes to initial study on potential bioprotectant.
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13
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Windley HR, Starrs D, Stalenberg E, Rothman JM, Ganzhorn JU, Foley WJ. Plant secondary metabolites and primate food choices: A meta-analysis and future directions. Am J Primatol 2022; 84:e23397. [PMID: 35700311 DOI: 10.1002/ajp.23397] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 05/06/2022] [Accepted: 05/11/2022] [Indexed: 11/07/2022]
Abstract
The role of plant secondary metabolites (PSMs) in shaping the feeding decisions, habitat suitability, and reproductive success of herbivorous mammals has been a major theme in ecology for decades. Although primatologists were among the first to test these ideas, studies of PSMs in the feeding ecology of non-human primates have lagged in recent years, leading to a recent call for primatologists to reconnect with phytochemists to advance our understanding of the primate nutrition. To further this case, we present a formal meta-analysis of diet choice in response to PSMs based on field studies on wild primates. Our analysis of 155 measurements of primate feeding response to PSMs is drawn from 53 studies across 43 primate species which focussed primarily on the effect of three classes of PSMs tannins, phenolics, and alkaloids. We found a small but significant effect of PSMs on the diet choice of wild primates, which was largely driven by the finding that colobine primates showed a moderate aversion to condensed tannins. Conversely, there was no evidence that PSMs had a significant deterrent effect on food choices of non-colobine primates when all were combined into a single group. Furthermore, within the colobine primates, no other PSMs influenced feeding choices and we found no evidence that foregut anatomy significantly affected food choice with respect to PSMs. We suggest that methodological improvements related to experimental approaches and the adoption of new techniques including metabolomics are needed to advance our understanding of primate diet choice.
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Affiliation(s)
- Hannah R Windley
- Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia.,Wildlife Ecology Laboratory, Department of Wildlife Biology, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
| | - Danswell Starrs
- Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Eleanor Stalenberg
- Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia.,Hawkesbury Institute of the Environment, Western Sydney University, Richmond, New South Wales, Australia
| | - Jessica M Rothman
- Department of Anthropology, Hunter College of the City University of New York, and New York Consortium in Evolutionary Primatology, New York, New York, USA
| | - Joerg U Ganzhorn
- Animal Ecology and Conservation, Universität Hamburg, Hamburg, Germany
| | - William J Foley
- Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia.,Animal Ecology and Conservation, Universität Hamburg, Hamburg, Germany
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14
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Rutz A, Sorokina M, Galgonek J, Mietchen D, Willighagen E, Gaudry A, Graham JG, Stephan R, Page R, Vondrášek J, Steinbeck C, Pauli GF, Wolfender JL, Bisson J, Allard PM. The LOTUS initiative for open knowledge management in natural products research. eLife 2022; 11:e70780. [PMID: 35616633 PMCID: PMC9135406 DOI: 10.7554/elife.70780] [Citation(s) in RCA: 82] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 03/22/2022] [Indexed: 12/17/2022] Open
Abstract
Contemporary bioinformatic and chemoinformatic capabilities hold promise to reshape knowledge management, analysis and interpretation of data in natural products research. Currently, reliance on a disparate set of non-standardized, insular, and specialized databases presents a series of challenges for data access, both within the discipline and for integration and interoperability between related fields. The fundamental elements of exchange are referenced structure-organism pairs that establish relationships between distinct molecular structures and the living organisms from which they were identified. Consolidating and sharing such information via an open platform has strong transformative potential for natural products research and beyond. This is the ultimate goal of the newly established LOTUS initiative, which has now completed the first steps toward the harmonization, curation, validation and open dissemination of 750,000+ referenced structure-organism pairs. LOTUS data is hosted on Wikidata and regularly mirrored on https://lotus.naturalproducts.net. Data sharing within the Wikidata framework broadens data access and interoperability, opening new possibilities for community curation and evolving publication models. Furthermore, embedding LOTUS data into the vast Wikidata knowledge graph will facilitate new biological and chemical insights. The LOTUS initiative represents an important advancement in the design and deployment of a comprehensive and collaborative natural products knowledge base.
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Affiliation(s)
- Adriano Rutz
- School of Pharmaceutical Sciences, University of GenevaGenevaSwitzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of GenevaGenevaSwitzerland
| | - Maria Sorokina
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University JenaJenaGermany
| | - Jakub Galgonek
- Institute of Organic Chemistry and Biochemistry of the CASPragueCzech Republic
| | - Daniel Mietchen
- Ronin InstituteMontclairUnited States
- Leibniz Institute of Freshwater Ecology and Inland FisheriesBerlinGermany
- School of Data Science, University of VirginiaCharlottesvilleUnited States
| | - Egon Willighagen
- Department of Bioinformatics-BiGCaT, Maastricht UniversityMaastrichtNetherlands
| | - Arnaud Gaudry
- School of Pharmaceutical Sciences, University of GenevaGenevaSwitzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of GenevaGenevaSwitzerland
| | - James G Graham
- Center for Natural Product Technologies and WHO Collaborating Centre for Traditional Medicine (WHO CC/TRM), Pharmacognosy Institute; College of Pharmacy, University of Illinois at ChicagoChicagoUnited States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at ChicagoChicagoUnited States
| | - Ralf Stephan
- Ontario Institute for Cancer Research (OICR), University Ave SuiteTorontoCanada
| | | | - Jiří Vondrášek
- Institute of Organic Chemistry and Biochemistry of the CASPragueCzech Republic
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University JenaJenaGermany
| | - Guido F Pauli
- Center for Natural Product Technologies and WHO Collaborating Centre for Traditional Medicine (WHO CC/TRM), Pharmacognosy Institute; College of Pharmacy, University of Illinois at ChicagoChicagoUnited States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at ChicagoChicagoUnited States
| | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences, University of GenevaGenevaSwitzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of GenevaGenevaSwitzerland
| | - Jonathan Bisson
- Center for Natural Product Technologies and WHO Collaborating Centre for Traditional Medicine (WHO CC/TRM), Pharmacognosy Institute; College of Pharmacy, University of Illinois at ChicagoChicagoUnited States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at ChicagoChicagoUnited States
| | - Pierre-Marie Allard
- School of Pharmaceutical Sciences, University of GenevaGenevaSwitzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of GenevaGenevaSwitzerland
- Department of Biology, University of FribourgFribourgSwitzerland
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15
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Reddy K, Stander MA, Stafford GI, Makunga NP. Mass Spectrometry Metabolomics and Feature-Based Molecular Networking Reveals Population-Specific Chemistry in Some Species of the Sceletium Genus. Front Nutr 2022; 9:819753. [PMID: 35425789 PMCID: PMC9001948 DOI: 10.3389/fnut.2022.819753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/02/2022] [Indexed: 11/21/2022] Open
Abstract
The Sceletium genus has been of medicinal importance in southern Africa for millennia and Sceletium tortuosum (Aizoaceae), one of eight species in the genus has gained pharmaceutical importance as an anxiolytic and anti-depressant due to the presence of mesembrine alkaloids. S. tortuosum is used for the manufacture of herbal teas, dietary supplements and other phytopharmaceutical products. This study aimed to provide a metabolomic characterization of S. tortuosum and its sister species as these are not easy to distinguish using morphology alone. Plant samples were thus collected from various locations in the succulent Karoo (South Africa) and analyzed through liquid chromatography-mass spectrometry (LC-MS), using MSE fragmentation as a putative tool for chemical identities. Metabolomics-based analyses in combination with molecular networking were able to distinguish between the four species of Sceletium based on the presence of 4-(3,4-dimethyoxyphenyl)-4-[2-acetylmethlamino)ethyl]cyclohexanone (m/z 334.2020; RT 6.60 min), mesembrine (m/z 290.1757; RT 5.10 min) and 4'-O-demethylmesembrenol (m/z 276.1597; RT 4.17 min). Metabolomic profiles varied according to the different localities and metabolites occurred at variable quantitative levels in Sceletium ecotypes. Molecular networking provided the added advantage of being able to observe mesembrine alkaloid isomers and coeluting metabolites (from the joubertiamine group) that were difficult to discern without this application. By combining high-throughput metabolomics together with global and feature based-molecular networking, a powerful metabolite profiling platform that is able to discern chemical patterns within and between populations was established. These techniques were able to reveal chemotaxonomic relationships and allowed for the discovery of chemical markers that may be used as part of monitoring protocols during the manufacture of phytopharmaceutical and dietary products based on Sceletium.
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Affiliation(s)
- Kaylan Reddy
- Department of Botany and Zoology, Faculty of Natural Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Marietjie A. Stander
- Department of Biochemistry, Faculty of Natural Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Gary I. Stafford
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Nokwanda P. Makunga
- Department of Botany and Zoology, Faculty of Natural Sciences, Stellenbosch University, Stellenbosch, South Africa
- *Correspondence: Nokwanda P. Makunga
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16
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Uckele KA, Jahner JP, Tepe EJ, Richards LA, Dyer LA, Ochsenrider KM, Philbin CS, Kato MJ, Yamaguchi LF, Forister ML, Smilanich AM, Dodson CD, Jeffrey CS, Parchman TL. Phytochemistry reflects different evolutionary history in traditional classes versus specialized structural motifs. Sci Rep 2021; 11:17247. [PMID: 34446754 PMCID: PMC8390663 DOI: 10.1038/s41598-021-96431-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 07/15/2021] [Indexed: 02/07/2023] Open
Abstract
Foundational hypotheses addressing plant-insect codiversification and plant defense theory typically assume a macroevolutionary pattern whereby closely related plants have similar chemical profiles. However, numerous studies have documented variation in the degree of phytochemical trait lability, raising the possibility that phytochemical evolution is more nuanced than initially assumed. We utilize proton nuclear magnetic resonance (1H NMR) data, chemical classification, and double digest restriction-site associated DNA sequencing (ddRADseq) to resolve evolutionary relationships and characterize the evolution of secondary chemistry in the Neotropical plant clade Radula (Piper; Piperaceae). Sequencing data substantially improved phylogenetic resolution relative to past studies, and spectroscopic characterization revealed the presence of 35 metabolite classes. Metabolite classes displayed phylogenetic signal, whereas the crude 1H NMR spectra featured little evidence of phylogenetic signal in multivariate tests of chemical resonances. Evolutionary correlations were detected in two pairs of compound classes (flavonoids with chalcones; p-alkenyl phenols with kavalactones), where the gain or loss of a class was dependent on the other's state. Overall, the evolution of secondary chemistry in Radula is characterized by strong phylogenetic signal of traditional compound classes and weak phylogenetic signal of specialized chemical motifs, consistent with both classic evolutionary hypotheses and recent examinations of phytochemical evolution in young lineages.
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Affiliation(s)
- Kathryn A Uckele
- Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV, 89557, USA
- Department of Biology, University of Nevada, Reno, NV, 89557, USA
- Hitchcock Center for Chemical Ecology, University of Nevada, Reno, NV, 89557, USA
| | - Joshua P Jahner
- Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV, 89557, USA.
- Department of Biology, University of Nevada, Reno, NV, 89557, USA.
| | - Eric J Tepe
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Lora A Richards
- Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV, 89557, USA
- Department of Biology, University of Nevada, Reno, NV, 89557, USA
- Hitchcock Center for Chemical Ecology, University of Nevada, Reno, NV, 89557, USA
| | - Lee A Dyer
- Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV, 89557, USA
- Department of Biology, University of Nevada, Reno, NV, 89557, USA
- Hitchcock Center for Chemical Ecology, University of Nevada, Reno, NV, 89557, USA
- Sección Invertebrados, Museo Ecuatoriano de Ciencias Naturales, Quito, Ecuador
| | | | - Casey S Philbin
- Hitchcock Center for Chemical Ecology, University of Nevada, Reno, NV, 89557, USA
| | - Massuo J Kato
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Lydia F Yamaguchi
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Matthew L Forister
- Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV, 89557, USA
- Department of Biology, University of Nevada, Reno, NV, 89557, USA
- Hitchcock Center for Chemical Ecology, University of Nevada, Reno, NV, 89557, USA
| | - Angela M Smilanich
- Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV, 89557, USA
- Department of Biology, University of Nevada, Reno, NV, 89557, USA
| | - Craig D Dodson
- Department of Chemistry, University of Nevada, Reno, NV, 89557, USA
| | - Christopher S Jeffrey
- Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV, 89557, USA
- Hitchcock Center for Chemical Ecology, University of Nevada, Reno, NV, 89557, USA
- Department of Chemistry, University of Nevada, Reno, NV, 89557, USA
| | - Thomas L Parchman
- Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV, 89557, USA
- Department of Biology, University of Nevada, Reno, NV, 89557, USA
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17
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Li P, Shen J, Li Y, Yao H, Yu M, He C, Xiao P. Metabolite Profiling Based on UPLC-Q-TOF-MS/MS and the Biological Evaluation of Medicinal Plants of Chinese Dichocarpum (Ranunculaceae). Chem Biodivers 2021; 18:e2100432. [PMID: 34351062 DOI: 10.1002/cbdv.202100432] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/05/2021] [Indexed: 12/16/2022]
Abstract
The genus Dichocarpum is endemic to East Asia, and many species have been used to treat various diseases. However, phytochemical researches of this genus have been limited to date. In the present study, a metabolomic approach based on UPLC-Q-TOF-MS/MS was used to explore the phytochemical profiles of 10 Chinese Dichocarpum species, and cannabinoid receptor (CB1/CB2) agonistic activities evaluation of these plants was performed. A total of 128 features were putatively annotated, belonging to alkaloids, flavonoids, triterpenes saponins, phenolic acids, and others. Semi-quantitative statistics demonstrated that alkaloids and flavonoids were widely distributed, with the former the most abundant, whereas triterpenes saponins were mainly distributed in D. fargesii and D. wuchuanense. The phylogenetic results obtained from DNA sequencing assigned the 10 species to three groups. Further results of in silico annotation revealed three chemical families and helped determine the characteristic features of the three groups. In addition, the plant extracts of nine species from this genus showed agonistic activity on CB2 receptors. This comprehensive analysis revealed the chemotype distribution and pharmacophylogenetic relationship, to provide clues for the prospective resource utilization of the medicinal plants from the genus Dichocarpum.
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Affiliation(s)
- Pei Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, P. R. China.,Key Laboratory of Bioactive Substances, Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Beijing, 100193, P. R. China
| | - Jie Shen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, P. R. China.,Key Laboratory of Bioactive Substances, Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Beijing, 100193, P. R. China
| | - Yue Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, P. R. China.,Key Laboratory of Bioactive Substances, Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Beijing, 100193, P. R. China
| | - Hui Yao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, P. R. China
| | - Meng Yu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, P. R. China
| | - Chunnian He
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, P. R. China.,Key Laboratory of Bioactive Substances, Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Beijing, 100193, P. R. China
| | - Peigen Xiao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, P. R. China.,Key Laboratory of Bioactive Substances, Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Beijing, 100193, P. R. China
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18
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Fontana S, Rasmann S, de Bello F, Pomati F, Moretti M. Reconciling trait based perspectives along a trait-integration continuum. Ecology 2021; 102:e03472. [PMID: 34260747 DOI: 10.1002/ecy.3472] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 04/09/2021] [Accepted: 05/18/2021] [Indexed: 11/08/2022]
Abstract
Trait based ecology has developed fast in the last decades, aiming to both explain mechanisms of community assembly, and predict patterns in nature, such as the effects of biodiversity shifts on key ecosystem processes. This body of work has stimulated the development of several conceptual frameworks and analytical methods, as well as the production of trait databases covering a growing number of taxa and organizational levels (from individuals to guilds). However, this breeding ground of novel concepts and tools currently lacks a general and coherent framework, under which functional traits can help ecologists organize their research aims, and serve as the common currency to unify several scientific disciplines. Specifically, we see a need to bridge the gaps between community ecology, ecosystem ecology, and evolutionary biology, in order to address the most pressing environmental issues of our time. To achieve this integration goal, we define a trait-integration continuum, which reconciles alternative trait definitions and approaches in ecology. This continuum outlines a coherent progression of biological scales, along which traits interact and hierarchically integrate from genetic information, to whole organism fitness-related traits, to trait syndromes and functional groups. Our conceptual scheme proposes that lower-level trait integration is closer to the inference of ecoevolutionary mechanisms determining population and community properties, whereas higher-level trait integration is most suited to the prediction of ecosystem processes. Within these two extremes, trait integration varies on a continuous scale, which relates directly to the inductive-deductive loop that should characterize the scientific method. With our proposed framework, we aim to facilitate scientists in contextualising their research based on the trait-integration levels that matter most to their specific goals. Explicitly acknowledging the existence of a trait-integration continuum is a promising way for framing the appropriate questions, thus obtaining reliable answers and results that are comparable across studies and disciplines.
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Affiliation(s)
- Simone Fontana
- Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, Zürcherstrasse 111, Birmensdorf, 8903, Switzerland.,Nature Conservation and Landscape Ecology, University of Freiburg, Tennenbacher Straße 4, Freiburg, 79106, Germany
| | - Sergio Rasmann
- Laboratory of Functional Ecology, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, Neuchâtel, 2000, Switzerland
| | - Francesco de Bello
- Department of Botany, Faculty of Sciences, University of South Bohemia, Na Zlate Stoce 1, České Budějovice, 370 05, Czech Republic.,Desertification Research Centre (CIDE-CSIC), Carretera Moncada-Náquera, Km 4,5, Moncada (Valencia), 46113, Spain
| | - Francesco Pomati
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, Dübendorf, 8600, Switzerland
| | - Marco Moretti
- Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, Zürcherstrasse 111, Birmensdorf, 8903, Switzerland
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19
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Li D, Gaquerel E. Next-Generation Mass Spectrometry Metabolomics Revives the Functional Analysis of Plant Metabolic Diversity. ANNUAL REVIEW OF PLANT BIOLOGY 2021; 72:867-891. [PMID: 33781077 DOI: 10.1146/annurev-arplant-071720-114836] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The remarkable diversity of specialized metabolites produced by plants has inspired several decades of research and nucleated a long list of theories to guide empirical ecological studies. However, analytical constraints and the lack of untargeted processing workflows have long precluded comprehensive metabolite profiling and, consequently, the collection of the critical currencies to test theory predictions for the ecological functions of plant metabolic diversity. Developments in mass spectrometry (MS) metabolomics have revolutionized the large-scale inventory and annotation of chemicals from biospecimens. Hence, the next generation of MS metabolomics propelled by new bioinformatics developments provides a long-awaited framework to revisit metabolism-centered ecological questions, much like the advances in next-generation sequencing of the last two decades impacted all research horizons in genomics. Here, we review advances in plant (computational) metabolomics to foster hypothesis formulation from complex metabolome data. Additionally, we reflect on how next-generation metabolomics could reinvigorate the testing of long-standing theories on plant metabolic diversity.
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Affiliation(s)
- Dapeng Li
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany;
| | - Emmanuel Gaquerel
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, 67084 Strasbourg, France;
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20
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Whitehead SR, Schneider GF, Dybzinski R, Nelson AS, Gelambi M, Jos E, Beckman NG. Fruits, frugivores, and the evolution of phytochemical diversity. OIKOS 2021. [DOI: 10.1111/oik.08332] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Susan R. Whitehead
- Dept of Biological Sciences, Virginia Polytechnic Inst. and State Univ. Blacksburg VI USA
| | | | - Ray Dybzinski
- School of Environmental Sustainability, Loyola Univ. Chicago IL USA
| | - Annika S. Nelson
- Dept of Biological Sciences, Virginia Polytechnic Inst. and State Univ. Blacksburg VI USA
| | - Mariana Gelambi
- Dept of Biological Sciences, Virginia Polytechnic Inst. and State Univ. Blacksburg VI USA
| | - Elsa Jos
- Dept of Biology and Ecology Center, Utah State Univ. Logan UT USA
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21
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Abstract
To cope with environmental challenges, plants produce a wide diversity of phytochemicals, which are also the source of numerous medicines. Despite decades of research in chemical ecology, we still lack an understanding of the organization of plant chemical diversity across species and ecosystems. To address this challenge, we hypothesized that molecular diversity is not only related to species diversity, but also constrained by trophic, climatic, and topographical factors. We screened the metabolome of 416 vascular plant species encompassing the entire alpine elevation range and four alpine bioclimatic regions in order to characterize their phytochemical diversity. We show that by coupling phylogenetic information, topographic, edaphic, and climatic variables, we predict phytochemical diversity, and its inherent composition, of plant communities throughout landscape. Spatial mapping of phytochemical diversity further revealed that plant assemblages found in low to midelevation habitats, with more alkaline soils, possessed greater phytochemical diversity, whereas alpine habitats possessed higher phytochemical endemism. Altogether, we present a general tool that can be used for predicting hotspots of phytochemical diversity in the landscape, independently of plant species taxonomic identity. Such an approach offers promising perspectives in both drug discovery programs and conservation efforts worldwide.
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22
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Padilla-González GF, Diazgranados M, Da Costa FB. Effect of the Andean Geography and Climate on the Specialized Metabolism of Its Vegetation: The Subtribe Espeletiinae (Asteraceae) as a Case Example. Metabolites 2021; 11:220. [PMID: 33916648 PMCID: PMC8065660 DOI: 10.3390/metabo11040220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/28/2021] [Accepted: 04/02/2021] [Indexed: 01/02/2023] Open
Abstract
The Andean mountains are 'center stage' to some of the most spectacular examples of plant diversifications, where geographic isolation and past climatic fluctuations have played a major role. However, the influence of Andean geography and climate as drivers of metabolic variation in Andean plants is poorly elucidated. Here, we studied the influence of those factors on the metabolome of the subtribe Espeletiinae (Asteraceae) using liquid chromatography coupled to high-resolution mass spectrometry data of over two hundred samples from multiple locations. Our results demonstrate that metabolic profiles can discriminate Espeletiinae taxa at different geographic scales, revealing inter- and intraspecific metabolic variations: at the country level, segregation between Colombian and Venezuelan taxa was observed; regionally, between páramo massifs; and locally, between páramo complexes. Metabolic differences in Espeletiinae were mainly explained by geographic isolation, although differences in taxonomic genera, temperature, and elevation, were also important. Furthermore, we found that different species inhabiting the same páramo complex showed stronger chemical similarities than the same species at different locations, corroborating that geographic isolation represents the main driver of metabolic change in Espeletiinae. The current study serves as a starting point to fill in the gaps in how Andean geography and climate have shaped the metabolism of its vegetation and reveal the potential of untargeted metabolomics to study the environmental physiology of plants.
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Affiliation(s)
- Guillermo F. Padilla-González
- AsterBioChem Research Team, Laboratory of Pharmacognosy, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto SP 14040-903, Brazil;
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Kew Road, London TW9 3AB, UK
| | - Mauricio Diazgranados
- Millennium Seed Bank, Royal Botanic Gardens, Kew, Ardingly, West Sussex, Haywards Heath RH17 6TN, UK;
| | - Fernando B. Da Costa
- AsterBioChem Research Team, Laboratory of Pharmacognosy, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto SP 14040-903, Brazil;
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23
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Tholl D, Hossain O, Weinhold A, Röse USR, Wei Q. Trends and applications in plant volatile sampling and analysis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:314-325. [PMID: 33506558 DOI: 10.1111/tpj.15176] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 01/09/2021] [Accepted: 01/14/2021] [Indexed: 05/12/2023]
Abstract
Volatile organic compounds (VOCs) released by plants serve as information and defense chemicals in mutualistic and antagonistic interactions and mitigate effects of abiotic stress. Passive and dynamic sampling techniques combined with gas chromatography-mass spectrometry analysis have become routine tools to measure emissions of VOCs and determine their various functions. More recently, knowledge of the roles of plant VOCs in the aboveground environment has led to the exploration of similar functions in the soil and rhizosphere. Moreover, VOC patterns have been recognized as sensitive and time-dependent markers of biotic and abiotic stress. This focused review addresses these developments by presenting recent progress in VOC sampling and analysis. We show advances in the use of small, inexpensive sampling devices and describe methods to monitor plant VOC emissions in the belowground environment. We further address latest trends in real-time measurements of volatilomes in plant phenotyping and most recent developments of small portable devices and VOC sensors for non-invasive VOC fingerprinting of plant disease. These technologies allow for innovative approaches to study plant VOC biology and application in agriculture.
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Affiliation(s)
- Dorothea Tholl
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Oindrila Hossain
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
- Emerging Plant Disease and Global Food Security Cluster, Norther Carolina State University, Raleigh, NC, 27695, USA
| | - Alexander Weinhold
- Molecular Interaction Ecology, Institute of Biodiversity, Friedrich Schiller University Jena, Jena, 07745, Germany
- Molecular Interaction Ecology, German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, 04103, Germany
| | - Ursula S R Röse
- School of Biological Sciences, University of New England, Biddeford, ME, 04005, USA
| | - Qingshan Wei
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, 27695, USA
- Emerging Plant Disease and Global Food Security Cluster, Norther Carolina State University, Raleigh, NC, 27695, USA
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24
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Metabolome-Wide, Phylogenetically Controlled Comparison Indicates Higher Phenolic Diversity in Tropical Tree Species. PLANTS 2021; 10:plants10030554. [PMID: 33809437 PMCID: PMC7998528 DOI: 10.3390/plants10030554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/13/2021] [Accepted: 03/14/2021] [Indexed: 11/17/2022]
Abstract
Tropical plants are expected to have a higher variety of defensive traits, such as a more diverse array of secondary metabolic compounds in response to greater pressures of antagonistic interactions, than their temperate counterparts. We test this hypothesis using advanced metabolomics linked to a novel stoichiometric compound classification to analyze the complete foliar metabolomes of four tropical and four temperate tree species, which were selected so that each subset contained the same amount of phylogenetic diversity and evenness. We then built Bayesian phylogenetic multilevel models to test for tropical–temperate differences in metabolite diversity for the entire metabolome and for four major families of secondary compounds. We found strong evidence supporting that the leaves of tropical tree species have a higher phenolic diversity. The functionally closer group of polyphenolics also showed moderate evidence of higher diversity in tropical species, but there were no differences either for the entire metabolome or for the other major families of compounds analyzed. This supports the interpretation that this tropical–temperate contrast must be related to the functional role of phenolics and polyphenolics.
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25
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Fine PVA, Salazar D, Martin RE, Metz MR, Misiewicz TM, Asner GP. Exploring the links between secondary metabolites and leaf spectral reflectance in a diverse genus of Amazonian trees. Ecosphere 2021. [DOI: 10.1002/ecs2.3362] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Paul V. A. Fine
- Department of Integrative Biology and Jepson and University Herbaria University of California, Berkeley 3040 Valley Life Sciences Building #3140 Berkeley California94720USA
| | - Diego Salazar
- Department of Biological Sciences, Institute of the Environment, and International Center for Tropical Botany Florida International University 11200 S.W. 8th Street Miami Florida33199USA
| | - Roberta E. Martin
- School of Geographical Sciences and Urban Planning Arizona State University P.O. Box 875302 Tempe Arizona85287USA
- Center for Global Discovery and Conservation Science Arizona State University Tempe Arizona85287USA
| | - Margaret R. Metz
- Department of Biology Lewis & Clark College 615 S Palatine Hill Rd Portland Oregon97219USA
| | - Tracy M. Misiewicz
- Department of Integrative Biology and Jepson and University Herbaria University of California, Berkeley 3040 Valley Life Sciences Building #3140 Berkeley California94720USA
| | - Gregory P. Asner
- School of Geographical Sciences and Urban Planning Arizona State University P.O. Box 875302 Tempe Arizona85287USA
- Center for Global Discovery and Conservation Science Arizona State University Tempe Arizona85287USA
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26
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Cavender-Bares J, Reich P, Townsend P, Banerjee A, Butler E, Desai A, Gevens A, Hobbie S, Isbell F, Laliberté E, Meireles JE, Menninger H, Pavlick R, Pinto-Ledezma J, Potter C, Schuman M, Springer N, Stefanski A, Trivedi P, Trowbridge A, Williams L, Willis C, Yang Y. BII-Implementation: The causes and consequences of plant biodiversity across scales in a rapidly changing world. RESEARCH IDEAS AND OUTCOMES 2021. [DOI: 10.3897/rio.7.e63850] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The proposed Biology Integration Institute will bring together two major research institutions in the Upper Midwest—the University of Minnesota (UMN) and University of Wisconsin-Madison (UW)—to investigate the causes and consequences of plant biodiversity across scales in a rapidly changing world—from genes and molecules within cells and tissues to communities, ecosystems, landscapes and the biosphere. The Institute focuses on plant biodiversity, defined broadly to encompass the heterogeneity within life that occurs from the smallest to the largest biological scales. A premise of the Institute is that life is envisioned as occurring at different scales nested within several contrasting conceptions of biological hierarchies, defined by the separate but related fields of physiology, evolutionary biology and ecology. The Institute will emphasize the use of ‘spectral biology’—detection of biological properties based on the interaction of light energy with matter—and process-oriented predictive models to investigate the processes by which biological components at one scale give rise to emergent properties at higher scales. Through an iterative process that harnesses cutting edge technologies to observe a suite of carefully designed empirical systems—including the National Ecological Observatory Network (NEON) and some of the world’s longest running and state-of-the-art global change experiments—the Institute will advance biological understanding and theory of the causes and consequences of changes in biodiversity and at the interface of plant physiology, ecology and evolution.
INTELLECTUAL MERIT
The Institute brings together a diverse, gender-balanced and highly productive team with significant leadership experience that spans biological disciplines and career stages and is poised to integrate biology in new ways. Together, the team will harness the potential of spectral biology, experiments, observations and synthetic modeling in a manner never before possible to transform understanding of how variation within and among biological scales drives plant and ecosystem responses to global change over diurnal, seasonal and millennial time scales. In doing so, it will use and advance state-of-the-art theory. The institute team posits that the designed projects will unearth transformative understanding and biological rules at each of the various scales that will enable an unprecedented capacity to discern the linkages between physiological, ecological and evolutionary processes in relation to the multi-dimensional nature of biodiversity in this time of massive planetary change. A strength of the proposed Institute is that it leverages prior federal investments in research and formalizes partnerships with foreign institutions heavily invested in related biodiversity research. Most of the planned projects leverage existing research initiatives, infrastructure, working groups, experiments, training programs, and public outreach infrastructure, all of which are already highly synergistic and collaborative, and will bring together members of the overall research and training team.
BROADER IMPACTS
A central goal of the proposed Institute is to train the next generation of diverse integrative biologists. Post-doctoral, graduate student and undergraduate trainees, recruited from non-traditional and underrepresented groups, including through formal engagement with Native American communities, will receive a range of mentoring and training opportunities. Annual summer training workshops will be offered at UMN and UW as well as training experiences with the Global Change and Biodiversity Research Priority Program (URPP-GCB) at the University of Zurich (UZH) and through the Canadian Airborne Biodiversity Observatory (CABO). The Institute will engage diverse K-12 audiences, the general public and Native American communities through Market Science modules, Minute Earth videos, a museum exhibit and public engagement and educational activities through the Bell Museum of Natural History, the Cedar Creek Ecosystem Science Reserve (CCESR) and the Wisconsin Tribal Conservation Association.
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Yin X, Fan H, Chen Y, Li LZ, Song W, Fan Y, Zhou W, Ma G, Alolga RN, Li W, Zhang B, Li P, Tran LSP, Lu X, Qi LW. Integrative omic and transgenic analyses reveal the positive effect of ultraviolet-B irradiation on salvianolic acid biosynthesis through upregulation of SmNAC1. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:781-799. [PMID: 32772407 DOI: 10.1111/tpj.14952] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 07/21/2020] [Accepted: 07/30/2020] [Indexed: 06/11/2023]
Abstract
Salvianolic acids (SalAs), a group of secondary metabolites in Salvia miltiorrhiza, are widely used for treating cerebrovascular diseases. Their biosynthesis is modulated by a variety of abiotic factors, including ultraviolet-B (UV-B) irradiation; however, the underlying mechanisms remain largely unknown. Here, an integrated metabolomic, proteomic, and transcriptomic approach coupled with transgenic analyses was employed to dissect the mechanisms underlying UV-B irradiation-induced SalA biosynthesis. Results of metabolomics showed that 28 metabolites, including 12 SalAs, were elevated in leaves of UV-B-treated S. miltiorrhiza. Meanwhile, the contents of several phytohormones, including jasmonic acid and salicylic acid, which positively modulate the biosynthesis of SalAs, also increased in UV-B-treated S. miltiorrhiza. Consistently, 20 core biosynthetic enzymes and numerous transcription factors that are involved in SalA biosynthesis were elevated in treated samples as indicated by a comprehensive proteomic analysis. Correlation and gene expression analyses demonstrated that the NAC1 gene, encoding a NAC transcriptional factor, was positively involved in UV-B-induced SalA biosynthesis. Accordingly, overexpression and RNA interference of NAC1 increased and decreased SalA contents, respectively, through regulation of key biosynthetic enzymes. Furthermore, ChIP-qPCR and Dual-LUC assays showed that NAC1 could directly bind to the CATGTG and CATGTC motifs present in the promoters of the SalA biosynthesis-related genes PAL3 and TAT3, respectively, and activate their expression. Our results collectively demonstrate that NAC1 plays a crucial role in UV-B irradiation-induced SalA biosynthesis. Taken together, our findings provide mechanistic insights into the UV-B-induced SalA biosynthesis in S. miltiorrhiza, and shed light on a great potential for the development of SalA-abundant varieties through genetic engineering.
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Affiliation(s)
- Xiaojian Yin
- State Key Laboratory of Natural Medicines, Department of Pharmacognosy, Institute of Pharmaceutical Science, China Pharmaceutical University, Nanjing, 210009, China
- Clinical Metabolomics Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Hui Fan
- State Key Laboratory of Natural Medicines, Department of Pharmacognosy, Institute of Pharmaceutical Science, China Pharmaceutical University, Nanjing, 210009, China
| | - Yan Chen
- Clinical Metabolomics Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Lan-Zhu Li
- Clinical Metabolomics Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Wei Song
- State Key Laboratory of Natural Medicines, Department of Pharmacognosy, Institute of Pharmaceutical Science, China Pharmaceutical University, Nanjing, 210009, China
| | - Yuanming Fan
- Clinical Metabolomics Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Wei Zhou
- Clinical Metabolomics Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Gaoxiang Ma
- Clinical Metabolomics Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Raphael N Alolga
- Clinical Metabolomics Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Weiqiang Li
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Department of Biology, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Baolong Zhang
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Science, Nanjing, 210014, China
| | - Ping Li
- Clinical Metabolomics Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Lam-Son P Tran
- Institute of Research and Development, Duy Tan University, 03 Quang Trung, Da Nang, Vietnam
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi, 230-0045, Japan
| | - Xu Lu
- Clinical Metabolomics Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Lian-Wen Qi
- Clinical Metabolomics Center, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
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28
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Glassmire AE, Zehr LN, Wetzel WC. Disentangling dimensions of phytochemical diversity: alpha and beta have contrasting effects on an insect herbivore. Ecology 2020; 101:e03158. [PMID: 32745232 DOI: 10.1002/ecy.3158] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 04/23/2020] [Accepted: 06/18/2020] [Indexed: 11/10/2022]
Abstract
Phytochemical diversity is comprised of two main dimensions-the average (alpha) within-plant neighbors or the difference (beta) in the composition of chemicals between plant neighbors. Research, however, has primarily examined the consequences of phytochemical diversity on herbivore performance through a single dimension, even though diversity is multidimensional. Furthermore, the ecological role of phytochemical diversity is not well understood because each of these dimensions exhibits unique biological effects on herbivore performance. Therefore, it has been difficult to tease apart the relative importance of alpha and beta chemical diversities on plant-herbivore interactions. We experimentally manipulated alpha and beta diversities along a chemical gradient to disentangle the relative effects of these dimensions on the performance of a mobile generalist herbivore, Trichoplusia ni (Hübner), using 16 genotypes from the Solanum pennellii introgression lines. First, we found contrasting effects of alpha and beta diversities on herbivore performance. Second, when comparing diversity across and within chemical classes, herbivore performance was reduced when plant neighbors had greater diversity within chemical classes that are biologically inhibiting at higher quantities (i.e., quantitative defenses such as phenolics and acyl sugars). However, herbivore performance was enhanced when plant neighbors had higher levels of chemical classes that are biologically toxic (i.e., qualitative defenses such as alkaloids). Finally, herbivores performed better on plant dicultures compared to monocultures, and performance was positively associated with plant dicultures only when there were high levels of average alpha diversity within plant neighbors. Our results suggest T. ni generalist caterpillars do better when plant neighbors are chemically different because differences provide options for them to choose or to switch between plants to balance chemical uptake. Overall, herbivores interact with a large diversity of plant chemicals at multiple scales, and our results indicate that not all chemical diversity is equal: specific dimensions of phytochemical diversity have unique effects on the dynamics of herbivore performance.
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Affiliation(s)
- Andrea E Glassmire
- Department of Entomology, Michigan State University, East Lansing, Michigan, 48824, USA.,Kellogg Biological Station, Hickory Corners, Michigan, 49060, USA
| | - Luke N Zehr
- Department of Entomology, Michigan State University, East Lansing, Michigan, 48824, USA
| | - William C Wetzel
- Department of Entomology, Michigan State University, East Lansing, Michigan, 48824, USA.,Kellogg Biological Station, Hickory Corners, Michigan, 49060, USA.,Ecology, Evolutionary Biology, & Behavior, Michigan State University, East Lansing, Michigan, 48824, USA.,AgBioResearch, Michigan State University, East Lansing, Michigan, 48824, USA
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29
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Sedio BE, Devaney JL, Pullen J, Parker GG, Wright SJ, Parker JD. Chemical novelty facilitates herbivore resistance and biological invasions in some introduced plant species. Ecol Evol 2020; 10:8770-8792. [PMID: 32884656 PMCID: PMC7452787 DOI: 10.1002/ece3.6575] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 06/11/2020] [Accepted: 06/22/2020] [Indexed: 11/30/2022] Open
Abstract
Ecological release from herbivory due to chemical novelty is commonly predicted to facilitate biological invasions by plants, but has not been tested on a community scale. We used metabolomics based on mass spectrometry molecular networks to assess the novelty of foliar secondary chemistry of 15 invasive plant species compared to 46 native species at a site in eastern North America. Locally, invasive species were more chemically distinctive than natives. Among the 15 invasive species, the more chemically distinct were less preferred by insect herbivores and less browsed by deer. Finally, an assessment of invasion frequency in 2,505 forest plots in the Atlantic coastal plain revealed that, regionally, invasive species that were less preferred by insect herbivores, less browsed by white-tailed deer, and chemically distinct relative to the native plant community occurred more frequently in survey plots. Our results suggest that chemically mediated release from herbivores contributes to many successful invasions.
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Affiliation(s)
- Brian E. Sedio
- Department of Integrative BiologyUniversity of Texas at AustinAustinTXUSA
- Smithsonian Tropical Research InstituteAncónRepublic of Panama
- Center for Biodiversity and Drug DiscoveryInstituto de Investigaciones Científicas y Servicios de Alta Tecnología‐AIPAncónRepublic of Panama
| | | | - Jamie Pullen
- Smithsonian Environmental Research CenterEdgewaterMDUSA
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30
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Bai Y, Jia Q, Su W, Yan Z, Situ W, He X, Peng W, Yao H. Integration of molecular networking and fingerprint analysis for studying constituents in Microctis Folium. PLoS One 2020; 15:e0235533. [PMID: 32634169 PMCID: PMC7340309 DOI: 10.1371/journal.pone.0235533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 06/16/2020] [Indexed: 12/25/2022] Open
Abstract
Microctis Folium is the dried leaves of a plant (Microcos paniculata L.) used to improve the digestive system, alleviate diarrhoea, and relieve fever, but information regarding its chemical composition has rarely been reported. The traditional research approach of determining chemical composition has included isolating, purifying, and identifying compounds with high-cost and time-consuming processes. In this study, molecular networking (MN) and fingerprint analysis were integrated as a comprehensive approach to study the chemical composition of Microctis Folium by an ultra fast liquid chromatography-photo diode array detector-triple-time of flight-tandem mass spectrometry (UFLC-DAD-Triple TOF-MS/MS). Large numbers of mass spectrometric data were processed to identify constituents, and the identified compounds and their unknown analogues were comprehensively depicted as visualized figures comprising distinct families by MN. A validated fingerprint methodology was established to quantitatively determine compounds in Microctis Folium. Ultimately, 165 constituents were identified in Microctis Folium for the first time and the identified compounds and approximately five hundred unknown analogues were applied to create visualized figures by MN, indicating compound groups and their chemical structure analogues in Microctis Folium. The validated fingerprint methodology was indicated to be specific, repeatable, precise, and stable and was used to determine 15 batches of samples during three seasons in three districts. Furthermore, seasonal or geographic environmental influences on the chemical profile were estimated by principal coordinate analysis. The results can be used to control the quality of Microctis Folium, observe seasonal or geographic environmental influences on the chemical profiles, and provide a reference for further exploitation of potential active unknown analogues in the future.
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Affiliation(s)
- Yang Bai
- Guangdong Engineering & Technology Research Center for Quality and Efficacy Reevaluation of Post-Market Traditional Chinese Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Qiang Jia
- Food Department, Guangzhou City Polytechnic, Guangzhou, China
| | - Weiwei Su
- Guangdong Engineering & Technology Research Center for Quality and Efficacy Reevaluation of Post-Market Traditional Chinese Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zenghao Yan
- Guangdong Engineering & Technology Research Center for Quality and Efficacy Reevaluation of Post-Market Traditional Chinese Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Wenhui Situ
- Guangdong Engineering & Technology Research Center for Quality and Efficacy Reevaluation of Post-Market Traditional Chinese Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xiang He
- Guangdong Engineering & Technology Research Center for Quality and Efficacy Reevaluation of Post-Market Traditional Chinese Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Wei Peng
- Guangdong Engineering & Technology Research Center for Quality and Efficacy Reevaluation of Post-Market Traditional Chinese Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Hongliang Yao
- Guangdong Engineering & Technology Research Center for Quality and Efficacy Reevaluation of Post-Market Traditional Chinese Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- * E-mail:
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31
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Li D, Halitschke R, Baldwin IT, Gaquerel E. Information theory tests critical predictions of plant defense theory for specialized metabolism. SCIENCE ADVANCES 2020; 6:eaaz0381. [PMID: 32577508 PMCID: PMC7286674 DOI: 10.1126/sciadv.aaz0381] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 04/14/2020] [Indexed: 05/15/2023]
Abstract
Different plant defense theories have provided important theoretical guidance in explaining patterns in plant specialized metabolism, but their critical predictions remain to be tested. Here, we systematically explored the metabolomes of Nicotiana attenuata, from single plants to populations, as well as of closely related species, using unbiased tandem mass spectrometry (MS/MS) analyses and processed the abundances of compound spectrum-based MS features within an information theory framework to test critical predictions of optimal defense (OD) and moving target (MT) theories. Information components of plant metabolomes were consistent with the OD theory but contradicted the main prediction of the MT theory for herbivory-induced dynamics of metabolome compositions. From micro- to macroevolutionary scales, jasmonate signaling was confirmed as the master determinant of OD, while ethylene signaling provided fine-tuning for herbivore-specific responses annotated via MS/MS molecular networks.
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Affiliation(s)
- Dapeng Li
- Max Planck Institute for Chemical Ecology, Department of Molecular Ecology, Jena, Germany
| | - Rayko Halitschke
- Max Planck Institute for Chemical Ecology, Department of Molecular Ecology, Jena, Germany
| | - Ian T. Baldwin
- Max Planck Institute for Chemical Ecology, Department of Molecular Ecology, Jena, Germany
- Corresponding author. (E.G.); (I.T.B)
| | - Emmanuel Gaquerel
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, Strasbourg, France
- Centre for Organismal Studies, University of Heidelberg, Heidelberg, Germany
- Corresponding author. (E.G.); (I.T.B)
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Wetzel WC, Whitehead SR. The many dimensions of phytochemical diversity: linking theory to practice. Ecol Lett 2019; 23:16-32. [PMID: 31724320 DOI: 10.1111/ele.13422] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 10/17/2019] [Indexed: 01/11/2023]
Abstract
Research on the ecological and evolutionary roles of phytochemicals has recently progressed from studying single compounds to examining chemical diversity itself. A key conceptual advance enabling this progression is the use of species diversity metrics for quantifying phytochemical diversity. In this perspective, we extend the theory developed for species diversity to further our understanding of what exactly phytochemical diversity is and how its many dimensions impact ecological and evolutionary processes. First, we discuss the major dimensions of phytochemical diversity - richness, evenness, functional diversity, and alpha, gamma and beta diversity. We describe their potential independent roles in biotic interactions and the practical challenges associated with their analysis. Second, we re-analyse the published and unpublished datasets to reveal that the phytochemical diversity experienced by an organism (or observed by a researcher) depends strongly on the scale of the interaction and the total amount of phytochemicals involved. We argue that we must account for these frames of reference to meaningfully understand diversity. Moving from a general notion of phytochemical diversity as a single measure to a precise definition of its multidimensional and multiscale nature yields overlooked testable predictions that will facilitate novel insights about the evolutionary ecology of plant biotic interactions.
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Affiliation(s)
- William C Wetzel
- Department of Entomology, Michigan State University, East Lansing, MI, 48824, USA.,Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI, 48824, USA
| | - Susan R Whitehead
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
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Sedio BE, Durant Archibold A, Rojas Echeverri JC, Debyser C, Boya P CA, Wright SJ. A comparison of inducible, ontogenetic, and interspecific sources of variation in the foliar metabolome in tropical trees. PeerJ 2019; 7:e7536. [PMID: 31579568 PMCID: PMC6756142 DOI: 10.7717/peerj.7536] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 07/23/2019] [Indexed: 11/20/2022] Open
Abstract
Plant interactions with other organisms are mediated by chemistry, yet chemistry varies among conspecific and within individual plants. The foliar metabolome—the suite of small-molecule metabolites found in the leaf—changes during leaf ontogeny and is influenced by the signaling molecule jasmonic acid. Species differences in secondary metabolites are thought to play an important ecological role by limiting the host ranges of herbivores and pathogens, and hence facilitating competitive coexistence among plant species in species-rich plant communities such as tropical forests. Yet it remains unclear how inducible and ontogenetic variation compare with interspecific variation, particularly in tropical trees. Here, we take advantage of novel methods to assemble mass spectra of all compounds in leaf extracts into molecular networks that quantify their chemical structural similarity in order to compare inducible and ontogenetic chemical variation to among-species variation in species-rich tropical tree genera. We ask (i) whether young and mature leaves differ chemically, (ii) whether jasmonic acid-inducible chemical variation differs between young and mature leaves, and (iii) whether interspecific exceeds intraspecific chemical variation for four species from four hyperdiverse tropical tree genera. We observed significant effects of the jasmonic acid treatment for three of eight combinations of species and ontogenetic stage evaluated. Three of the four species also exhibited large metabolomic differences with leaf ontogenetic stage. The profound effect of leaf ontogenetic stage on the foliar metabolome suggests a qualitative turnover in secondary chemistry with leaf ontogeny. We also quantified foliar metabolomes for 45 congeners of the four focal species. Chemical similarity was much greater within than between species for all four genera, even when within-species comparisons included leaves that differed in age and jasmonic acid treatment. Despite ontogenetic and inducible variation within species, chemical differences among congeneric species may be sufficient to partition niche space with respect to chemical defense.
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Affiliation(s)
- Brian E Sedio
- Smithsonian Tropical Research Institute, Balboa, Ancón, Republic of Panama.,Center for Biodiversity and Drug Discovery, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología-AIP, Ciudad del Saber, Republic of Panama.,Department of Integrative Biology, University of Texas at Austin, Austin, TX, United States of America
| | - Armando Durant Archibold
- Center for Biodiversity and Drug Discovery, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología-AIP, Ciudad del Saber, Republic of Panama
| | - Juan Camilo Rojas Echeverri
- Center for Biodiversity and Drug Discovery, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología-AIP, Ciudad del Saber, Republic of Panama
| | - Chloé Debyser
- Department of Biology, McGill University, Montréal, Québec, Canada
| | - Cristopher A Boya P
- Center for Biodiversity and Drug Discovery, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología-AIP, Ciudad del Saber, Republic of Panama.,Department of Biotechnology, Acharya Nagarjuna University, Guntur, India
| | - S Joseph Wright
- Smithsonian Tropical Research Institute, Balboa, Ancón, Republic of Panama
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Gallon ME, Silva-Junior EA, Amaral JG, Lopes NP, Gobbo-Neto L. Natural Products Diversity in Plant-Insect Interaction between Tithonia diversifolia (Asteraceae) and Chlosyne lacinia (Nymphalidae). Molecules 2019; 24:molecules24173118. [PMID: 31466223 PMCID: PMC6749194 DOI: 10.3390/molecules24173118] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/17/2019] [Accepted: 08/19/2019] [Indexed: 12/12/2022] Open
Abstract
The chemical ecology of plant-insect interactions has been driving our understanding of ecosystem evolution into a more comprehensive context. Chlosyne lacinia (Lepidoptera: Nymphalidae) is an olygophagous insect herbivore, which mainly uses host plants of Heliantheae tribe (Asteraceae). Herein, plant-insect interaction between Tithonia diversifolia (Heliantheae) and Chlosyne lacinia was investigated by means of untargeted LC-MS/MS based metabolomics and molecular networking, which aims to explore its inherent chemical diversity. C. lacinia larvae that were fed with T. diversifolia leaves developed until fifth instar and completed metamorphosis to the adult phase. Sesquiterpene lactones (STL), flavonoids, and lipid derivatives were putatively annotated in T. diversifolia (leaves and non-consumed abaxial surface) and C. lacinia (feces, larvae, pupae, butterflies, and eggs) samples. We found that several furanoheliangolide-type STL that were detected in T. diversifolia were ingested and excreted in their intact form by C. lacinia larvae. Hence, C. lacinia caterpillars may have, over the years, developed tolerance mechanisms for STL throughout effective barriers in their digestive canal. Flavonoid aglycones were mainly found in T. diversifolia samples, while their glycosides were mostly detected in C. lacinia feces, which indicated that the main mechanism for excreting the consumed flavonoids was through their glycosylation. Moreover, lysophospholipids were predominately found in C. lacinia samples, which suggested that they were essential metabolites during pupal and adult stages. These findings provide insights into the natural products diversity of this plant-insect interaction and contribute to uncovering its ecological roles.
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Affiliation(s)
- Marília Elias Gallon
- Núcleo de Pesquisa em Produtos Naturais e Sintéticos, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café s/n°, Ribeirão Preto, SP 14040-903, Brazil
| | - Eduardo Afonso Silva-Junior
- Núcleo de Pesquisa em Produtos Naturais e Sintéticos, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café s/n°, Ribeirão Preto, SP 14040-903, Brazil
- Centro Universitário do Vale do Araguaia, R. Moreira Cabral, Barra do Garças, MT 78600-000, Brazil
| | - Juliano Geraldo Amaral
- Instituto Multidisciplinar em Saúde-Campus Anísio Teixeira, Universidade Federal da Bahia, R. Hormindo Barros, 58, Qd 17, Lt 58, Vitória da Conquista, BA 45029-094, Brazil
| | - Norberto Peporine Lopes
- Núcleo de Pesquisa em Produtos Naturais e Sintéticos, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café s/n°, Ribeirão Preto, SP 14040-903, Brazil
| | - Leonardo Gobbo-Neto
- Núcleo de Pesquisa em Produtos Naturais e Sintéticos, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café s/n°, Ribeirão Preto, SP 14040-903, Brazil.
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Ernst M, Nothias LF, van der Hooft JJJ, Silva RR, Saslis-Lagoudakis CH, Grace OM, Martinez-Swatson K, Hassemer G, Funez LA, Simonsen HT, Medema MH, Staerk D, Nilsson N, Lovato P, Dorrestein PC, Rønsted N. Assessing Specialized Metabolite Diversity in the Cosmopolitan Plant Genus Euphorbia L. FRONTIERS IN PLANT SCIENCE 2019; 10:846. [PMID: 31333695 PMCID: PMC6615404 DOI: 10.3389/fpls.2019.00846] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 06/13/2019] [Indexed: 05/02/2023]
Abstract
Coevolutionary theory suggests that an arms race between plants and herbivores yields increased plant specialized metabolite diversity and the geographic mosaic theory of coevolution predicts that coevolutionary interactions vary across geographic scales. Consequently, plant specialized metabolite diversity is expected to be highest in coevolutionary hotspots, geographic regions, which exhibit strong reciprocal selection on the interacting species. Despite being well-established theoretical frameworks, technical limitations have precluded rigorous hypothesis testing. Here we aim at understanding how geographic separation over evolutionary time may have impacted chemical differentiation in the cosmopolitan plant genus Euphorbia. We use a combination of state-of-the-art computational mass spectral metabolomics tools together with cell-based high-throughput immunomodulatory testing. Our results show significant differences in specialized metabolite diversity across geographically separated phylogenetic clades. Chemical structural diversity of the highly toxic Euphorbia diterpenoids is significantly reduced in species native to the Americas, compared to Afro-Eurasia. The localization of these compounds to young stems and roots suggest a possible ecological relevance in herbivory defense. This is further supported by reduced immunomodulatory activity in the American subclade as well as herbivore distribution patterns. We conclude that computational mass spectrometric metabolomics coupled with relevant ecological data provide a strong tool for exploring plant specialized metabolite diversity in a chemo-evolutionary framework.
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Affiliation(s)
- Madeleine Ernst
- Natural History Museum of Denmark, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Louis-Félix Nothias
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Justin J. J. van der Hooft
- Bioinformatics Group, Department of Plant Sciences, Wageningen University & Research, Wageningen, Netherlands
| | - Ricardo R. Silva
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
| | | | - Olwen M. Grace
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Richmond, United Kingdom
| | - Karen Martinez-Swatson
- Natural History Museum of Denmark, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Gustavo Hassemer
- Natural History Museum of Denmark, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
- Department of Botany, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Luís A. Funez
- Department of Botany, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Henrik T. Simonsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Marnix H. Medema
- Bioinformatics Group, Department of Plant Sciences, Wageningen University & Research, Wageningen, Netherlands
| | - Dan Staerk
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Paola Lovato
- Front End Innovation, LEO Pharma A/S, Ballerup, Denmark
| | - Pieter C. Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, United States
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, United States
| | - Nina Rønsted
- Natural History Museum of Denmark, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
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Nothias-Esposito M, Nothias LF, Da Silva RR, Retailleau P, Zhang Z, Leyssen P, Roussi F, Touboul D, Paolini J, Dorrestein PC, Litaudon M. Investigation of Premyrsinane and Myrsinane Esters in Euphorbia cupanii and Euphobia pithyusa with MS2LDA and Combinatorial Molecular Network Annotation Propagation. JOURNAL OF NATURAL PRODUCTS 2019; 82:1459-1470. [PMID: 31181921 DOI: 10.1021/acs.jnatprod.8b00916] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The species Euphorbia pithyusa and Euphorbia cupanii are two closely related Mediterranean spurges for which their taxonomic relationships are still being debated. Herein, the diterpene ester content of E. cupanii was investigated using liquid chromatography coupled to tandem mass spectrometry. The use of molecular networking coupled to unsupervised substructure annotation ( MS2LDA) indicated the presence of new premyrsinane/myrsinane diterpene esters in the E. cupanii fractions. A structure-guided isolation procedure yielded 16 myrsinane (11a-h, 12, and 13) and premyrsinane esters (14a-c and 15a-c), along with four 4β-phorbol esters (16a-c and 17) that showed inhibitory activity against chikungunya virus replication. The structures of the 16 new compounds (11a-c, 11h, 12, 13, 14a-c, 15a-c, 16a-c, and 17) were characterized by NMR spectroscopy and X-ray crystallography. To further uncover the diterpene ester content of these two species, the concept of combinatorial network annotation propagation (C-NAP) was developed. By leveraging the fact that the diterpene esters of Euphorbia species are made up of limited building blocks, a combinatorial database of theoretical structures was created and used for C-NAP that made possible the annotation of 123 premyrsinane or myrsinane esters, from which 74% are not found in any compound database.
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Affiliation(s)
- Mélissa Nothias-Esposito
- Laboratory of Natural Products Chemistry, UMR CNRS SPE 6134 , University of Corsica , 20250 , Corte , France
- Institute of Natural Substances Chemistry, CNRS UPR 2301 , University of Paris-Saclay , 91198 , Gif-sur-Yvette , France
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California San Diego , La Jolla , California 92093 , United States
| | - Louis Felix Nothias
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California San Diego , La Jolla , California 92093 , United States
| | - Ricardo R Da Silva
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California San Diego , La Jolla , California 92093 , United States
| | - Pascal Retailleau
- Institute of Natural Substances Chemistry, CNRS UPR 2301 , University of Paris-Saclay , 91198 , Gif-sur-Yvette , France
| | - Zheng Zhang
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California San Diego , La Jolla , California 92093 , United States
| | - Pieter Leyssen
- Laboratory for Virology and Experimental Chemotherapy, Rega Institute for Medical Research , KU Leuven , 3000 Leuven , Belgium
| | - Fanny Roussi
- Institute of Natural Substances Chemistry, CNRS UPR 2301 , University of Paris-Saclay , 91198 , Gif-sur-Yvette , France
| | - David Touboul
- Institute of Natural Substances Chemistry, CNRS UPR 2301 , University of Paris-Saclay , 91198 , Gif-sur-Yvette , France
| | - Julien Paolini
- Laboratory of Natural Products Chemistry, UMR CNRS SPE 6134 , University of Corsica , 20250 , Corte , France
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences , University of California San Diego , La Jolla , California 92093 , United States
| | - Marc Litaudon
- Institute of Natural Substances Chemistry, CNRS UPR 2301 , University of Paris-Saclay , 91198 , Gif-sur-Yvette , France
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37
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Jiang CK, Ma JQ, Apostolides Z, Chen L. Metabolomics for a Millenniums-Old Crop: Tea Plant ( Camellia sinensis). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:6445-6457. [PMID: 31117495 DOI: 10.1021/acs.jafc.9b01356] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Tea cultivation and utilization dates back to antiquity. Today it is the most widely consumed beverage on earth due to its pleasant taste and several beneficial health properties attributed to specific metabolites. Metabolomics has a tremendous potential to correlate tea metabolites with taste and health properties in humans. Our review on the current application of metabolomics in the science of tea suggests that metabolomics is a promising frontier in the evaluation of tea quality, identification of functional genes responsible for key metabolites, investigation of their metabolic regulation, and pathway analysis in the tea plant. Furthermore, the challenges, possible solutions, and the prospects of metabolomics in tea science are reviewed.
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Affiliation(s)
- Chen-Kai Jiang
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs , Tea Research Institute of the Chinese Academy of Agricultural Sciences , Hangzhou 310008 , China
| | - Jian-Qiang Ma
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs , Tea Research Institute of the Chinese Academy of Agricultural Sciences , Hangzhou 310008 , China
| | - Zeno Apostolides
- Department of Biochemistry, Genetics and Microbiology , University of Pretoria , Pretoria 0002 , South Africa
| | - Liang Chen
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs , Tea Research Institute of the Chinese Academy of Agricultural Sciences , Hangzhou 310008 , China
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38
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Volf M, Salminen JP, Segar ST. Evolution of defences in large tropical plant genera: perspectives for exploring insect diversity in a tri-trophic context. CURRENT OPINION IN INSECT SCIENCE 2019; 32:91-97. [PMID: 31113638 DOI: 10.1016/j.cois.2018.12.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 09/22/2018] [Accepted: 12/17/2018] [Indexed: 06/09/2023]
Abstract
Divergence and escalation in defences promote chemical diversity in plants, and consequently the diversity of insect herbivores. This diversification cascades to insect parasitoids through direct effects on host herbivore susceptibility, changes in herbivore community composition, or disparity in plant volatiles. Large tropical plant genera represent an ideal model for studying these trends due to the high diversity of sympatric species and their insects. Novel measures of chemical structural similarity should be used to analyse evolutionary trends in both direct and indirect defences. Host chemical data need to be combined with detailed herbivore and parasitoid data. This will help to identify truly active compounds. Furthermore, resolved genomic phylogenies for plants and insects should be included to assign directionality in the processes.
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Affiliation(s)
- Martin Volf
- Molecular Interaction Ecology Group, German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
| | - Juha-Pekka Salminen
- Natural Chemistry Research Group, Department of Chemistry, University of Turku, Turku, Finland
| | - Simon T Segar
- Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic; Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic; Department of Crop and Environment Sciences, Harper Adams University, UK
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39
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Sedio BE. Recent advances in understanding the role of secondary metabolites in species-rich multitrophic networks. CURRENT OPINION IN INSECT SCIENCE 2019; 32:124-130. [PMID: 31113624 DOI: 10.1016/j.cois.2019.01.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 01/12/2019] [Accepted: 01/16/2019] [Indexed: 06/09/2023]
Abstract
Understanding coexistence in species-rich communities remains a primary challenge of ecology. Interactions mediated through multitrophic networks are thought to play an important role in sustaining species coexistence in the face of competition for resources. The identity of trophic partners and the intensity with which they interact are often mediated by diverse secondary metabolites. Recent innovations in organic-molecule bioinformatics and multivariate statistical analysis are rapidly advancing our understanding of metabolites and the multitrophic interactions they mediate. Here, I examine recent advances in the study of chemical ecology in species-rich multitrophic communities, with an emphasis on plant-herbivore networks, and explore the potential for chemically mediated interactions to shape community composition and sustain species diversity in ecological communities.
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Affiliation(s)
- Brian E Sedio
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancón, Panama; Center for Biodiversity and Drug Discovery, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología, Apartado 0843-01103, Ciudad del Saber, Ancón, Panama. https://twitter.com/@stri_panama
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40
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Smith SD, Angelovici R, Heyduk K, Maeda HA, Moghe GD, Pires JC, Widhalm JR, Wisecaver JH. The renaissance of comparative biochemistry. AMERICAN JOURNAL OF BOTANY 2019; 106:3-13. [PMID: 30629738 DOI: 10.1002/ajb2.1216] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 12/04/2018] [Indexed: 06/09/2023]
Affiliation(s)
- Stacey D Smith
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Ruthie Angelovici
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | - Karolina Heyduk
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, WI, USA
| | - Gaurav D Moghe
- Plant Biology Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, USA
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | - Joshua R Widhalm
- Department of Horticulture and Landscape Architecture and Center for Plant Biology, Purdue University, West Lafayette, IN, USA
| | - Jennifer H Wisecaver
- Department of Biochemistry and Center for Plant Biology, Purdue University, West Lafayette, IN, USA
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41
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Feussner K, Feussner I. Comprehensive LC-MS-Based Metabolite Fingerprinting Approach for Plant and Fungal-Derived Samples. Methods Mol Biol 2019; 1978:167-185. [PMID: 31119663 DOI: 10.1007/978-1-4939-9236-2_11] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Liquid chromatography-mass spectrometry (LC-MS)-based nontargeted metabolome approaches aim to detect chemotypes as markers for stress, disease, developmental, or genetic perturbation. Herein, we present a metabolite fingerprinting workflow, which is applicable for the analysis of tissues and fluids derived from plants and fungi. This is based on a broad metabolite coverage by a two-phase extraction and the separate analysis of polar, and nonpolar compounds by positive as well as negative electrospray ionization. For analysis of the resulting comprehensive data sets, the interactive and user-friendly data mining software MarVis-Suite is used. It supports statistical analysis, adduct correction, data merging, as well as visualization of multivariate data. Finally, MarVis shapes marker identification to the organism of interest. Therefore, it provides access to the species-specific databases KEGG and BioCyc and to custom databases tailored by the user.
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Affiliation(s)
- Kirstin Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, Goettingen, Germany.,Service Unit for Metabolomics and Lipidomics, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Goettingen, Germany
| | - Ivo Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, Goettingen, Germany. .,Service Unit for Metabolomics and Lipidomics, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Goettingen, Germany. .,Department of Plant Biochemistry, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Goettingen, Germany.
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42
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Sedio BE, Parker JD, McMahon SM, Wright SJ. Comparative foliar metabolomics of a tropical and a temperate forest community. Ecology 2018; 99:2647-2653. [DOI: 10.1002/ecy.2533] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 08/31/2018] [Accepted: 10/01/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Brian E. Sedio
- Smithsonian Tropical Research Institute Apartado 0843–03092 Balboa Ancón Republic of Panama
- Center for Biodiversity and Drug Discovery Instituto de Investigaciones Científicas y Servicios de Alta Tecnología Apartado 0843‐01103 Ciudad del Saber Ancón Republic of Panama
| | - John D. Parker
- Smithsonian Environmental Research Center 647 Contees Wharf Road Edgewater Mary Land 21037 USA
| | - Sean M. McMahon
- Smithsonian Environmental Research Center 647 Contees Wharf Road Edgewater Mary Land 21037 USA
| | - S. Joseph Wright
- Smithsonian Tropical Research Institute Apartado 0843–03092 Balboa Ancón Republic of Panama
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43
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Dyer LA. Multidimensional diversity associated with plants: a view from a plant-insect interaction ecologist. AMERICAN JOURNAL OF BOTANY 2018; 105:1439-1442. [PMID: 30151878 DOI: 10.1002/ajb2.1147] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 06/07/2018] [Indexed: 06/08/2023]
Affiliation(s)
- Lee A Dyer
- University of Nevada Reno, Reno, NV, USA
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Peters K, Worrich A, Weinhold A, Alka O, Balcke G, Birkemeyer C, Bruelheide H, Calf OW, Dietz S, Dührkop K, Gaquerel E, Heinig U, Kücklich M, Macel M, Müller C, Poeschl Y, Pohnert G, Ristok C, Rodríguez VM, Ruttkies C, Schuman M, Schweiger R, Shahaf N, Steinbeck C, Tortosa M, Treutler H, Ueberschaar N, Velasco P, Weiß BM, Widdig A, Neumann S, Dam NMV. Current Challenges in Plant Eco-Metabolomics. Int J Mol Sci 2018; 19:E1385. [PMID: 29734799 PMCID: PMC5983679 DOI: 10.3390/ijms19051385] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/24/2018] [Accepted: 04/25/2018] [Indexed: 12/22/2022] Open
Abstract
The relatively new research discipline of Eco-Metabolomics is the application of metabolomics techniques to ecology with the aim to characterise biochemical interactions of organisms across different spatial and temporal scales. Metabolomics is an untargeted biochemical approach to measure many thousands of metabolites in different species, including plants and animals. Changes in metabolite concentrations can provide mechanistic evidence for biochemical processes that are relevant at ecological scales. These include physiological, phenotypic and morphological responses of plants and communities to environmental changes and also interactions with other organisms. Traditionally, research in biochemistry and ecology comes from two different directions and is performed at distinct spatiotemporal scales. Biochemical studies most often focus on intrinsic processes in individuals at physiological and cellular scales. Generally, they take a bottom-up approach scaling up cellular processes from spatiotemporally fine to coarser scales. Ecological studies usually focus on extrinsic processes acting upon organisms at population and community scales and typically study top-down and bottom-up processes in combination. Eco-Metabolomics is a transdisciplinary research discipline that links biochemistry and ecology and connects the distinct spatiotemporal scales. In this review, we focus on approaches to study chemical and biochemical interactions of plants at various ecological levels, mainly plant⁻organismal interactions, and discuss related examples from other domains. We present recent developments and highlight advancements in Eco-Metabolomics over the last decade from various angles. We further address the five key challenges: (1) complex experimental designs and large variation of metabolite profiles; (2) feature extraction; (3) metabolite identification; (4) statistical analyses; and (5) bioinformatics software tools and workflows. The presented solutions to these challenges will advance connecting the distinct spatiotemporal scales and bridging biochemistry and ecology.
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Affiliation(s)
- Kristian Peters
- Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany.
| | - Anja Worrich
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger-Str. 159, 07743 Jena, Germany.
- UFZ-Helmholtz-Centre for Environmental Research, Department Environmental Microbiology, Permoserstraße 15, 04318 Leipzig, Germany.
| | - Alexander Weinhold
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger-Str. 159, 07743 Jena, Germany.
| | - Oliver Alka
- Applied Bioinformatics Group, Center for Bioinformatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany.
| | - Gerd Balcke
- Leibniz Institute of Plant Biochemistry, Cell and Metabolic Biology, Weinberg 3, 06120 Halle (Saale), Germany.
| | - Claudia Birkemeyer
- Institute of Analytical Chemistry, University of Leipzig, Linnéstr. 3, 04103 Leipzig, Germany.
| | - Helge Bruelheide
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, 06108 Halle (Saale), Germany.
| | - Onno W Calf
- Molecular Interaction Ecology, Institute for Water and Wetland Research (IWWR), Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
| | - Sophie Dietz
- Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany.
| | - Kai Dührkop
- Department of Bioinformatics, Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany.
| | - Emmanuel Gaquerel
- Centre for Organismal Studies, Heidelberg University, Im Neuenheimer Feld 360, 69120 Heidelberg, Germany.
| | - Uwe Heinig
- Weizmann Institute of Science, Faculty of Biochemistry, Department of Plant Sciences, 234 Herzl St., P.O. Box 26, Rehovot 7610001, Israel.
| | - Marlen Kücklich
- Institute of Biology, University of Leipzig, Talstraße 33, 04109 Leipzig, Germany.
| | - Mirka Macel
- Molecular Interaction Ecology, Institute for Water and Wetland Research (IWWR), Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
| | - Caroline Müller
- Chemical Ecology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany.
| | - Yvonne Poeschl
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
- Institute of Informatics, Martin Luther University Halle-Wittenberg, Von-Seckendorff-Platz 1, 06120 Halle (Saale), Germany.
| | - Georg Pohnert
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743 Jena, Germany.
| | - Christian Ristok
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
| | - Victor Manuel Rodríguez
- Group of Genetics, Breeding and Biochemistry of Brassica, Misión Biológica de Galicia (CSIC), Apartado 28, 36080 Pontevedra, Spain.
| | - Christoph Ruttkies
- Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany.
| | - Meredith Schuman
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany.
| | - Rabea Schweiger
- Chemical Ecology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany.
| | - Nir Shahaf
- Weizmann Institute of Science, Faculty of Biochemistry, Department of Plant Sciences, 234 Herzl St., P.O. Box 26, Rehovot 7610001, Israel.
| | - Christoph Steinbeck
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743 Jena, Germany.
| | - Maria Tortosa
- Group of Genetics, Breeding and Biochemistry of Brassica, Misión Biológica de Galicia (CSIC), Apartado 28, 36080 Pontevedra, Spain.
| | - Hendrik Treutler
- Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany.
| | - Nico Ueberschaar
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743 Jena, Germany.
| | - Pablo Velasco
- Group of Genetics, Breeding and Biochemistry of Brassica, Misión Biológica de Galicia (CSIC), Apartado 28, 36080 Pontevedra, Spain.
| | - Brigitte M Weiß
- Institute of Biology, University of Leipzig, Talstraße 33, 04109 Leipzig, Germany.
| | - Anja Widdig
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
- Institute of Biology, University of Leipzig, Talstraße 33, 04109 Leipzig, Germany.
- Research Group of Primate Kin Selection, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany.
| | - Steffen Neumann
- Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
| | - Nicole M van Dam
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger-Str. 159, 07743 Jena, Germany.
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Weber MG, Cacho NI, Phan MJQ, Disbrow C, Ramírez SR, Strauss SY. The evolution of floral signals in relation to range overlap in a clade of California Jewelflowers (Streptanthus s.l.). Evolution 2018; 72:798-807. [PMID: 29464694 DOI: 10.1111/evo.13456] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 02/05/2018] [Accepted: 02/06/2018] [Indexed: 01/18/2023]
Abstract
Because of their function as reproductive signals in plants, floral traits experience distinct selective pressures related to their role in speciation, reinforcement, and prolonged coexistence with close relatives. However, few studies have investigated whether population-level processes translate into detectable signatures at the macroevolutionary scale. Here, we ask whether patterns of floral trait evolution and range overlap across a clade of California Jewelflowers reflect processes hypothesized to shape floral signal differentiation at the population level. We found a pattern of divergence in floral scent composition across the clade such that close relatives had highly disparate floral scents given their age. Accounting for range overlap with close relatives explained additional variation in floral scent over time, with sympatric species pairs having diverged more than allopatric species pairs given their age. However, three other floral traits (flower size, scent complexity and flower color) did not fit these patterns, failing to deviate from a null Brownian motion model of evolution. Together, our results suggest that selection for divergence among close relatives in the composition of floral scents may play a key, sustained role in mediating speciation and coexistence dynamics across this group, and that signatures of these dynamics may persist at the macroevolutionary scale.
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Affiliation(s)
- Marjorie G Weber
- Center for Population Biology, University of California, Davis, California 95616.,Current Address: Department of Plant Biology and Ecology, Evolutionary Biology and Behavior Program, Michigan State University, East Lansing, Michigan 48823
| | - N Ivalú Cacho
- Instituto de Biología, Universidad Nacional Autónoma de México, CDMX 04510, México.,Department of Evolution and Ecology, University of California, Davis, California 95616
| | - Martin J Q Phan
- Department of Evolution and Ecology, University of California, Davis, California 95616
| | - Caprice Disbrow
- Department of Evolution and Ecology, University of California, Davis, California 95616
| | - Santiago R Ramírez
- Center for Population Biology, University of California, Davis, California 95616.,Department of Evolution and Ecology, University of California, Davis, California 95616
| | - Sharon Y Strauss
- Center for Population Biology, University of California, Davis, California 95616.,Department of Evolution and Ecology, University of California, Davis, California 95616
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Why Functional Traits Do Not Predict Tree Demographic Rates. Trends Ecol Evol 2018; 33:326-336. [PMID: 29605086 DOI: 10.1016/j.tree.2018.03.003] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 03/07/2018] [Accepted: 03/08/2018] [Indexed: 11/23/2022]
Abstract
Foundational to trait-based community ecology is the expectation that functional traits determine demographic outcomes. However, trait-demographic rate relationships are frequently weak, particularly in tree communities. The foundation of trait-based tree community ecology may, therefore, appear to be unstable. Here we argue that there are three core reasons why trait-demographic relationships are generally weak in tree communities. Specifically, important contextual information is frequently ignored, there is too much focus on species relative to individuals, and there are dimensions of tree function that are critical for determining tree demographic rates that are not captured by easily measured functional traits. Rather than being evidence that trait-based community ecology is fundamentally flawed, these issues elucidate a pathway towards a more robust research program.
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Sedio BE, Boya P. CA, Rojas Echeverri JC. A protocol for high-throughput, untargeted forest community metabolomics using mass spectrometry molecular networks. APPLICATIONS IN PLANT SCIENCES 2018; 6:e1033. [PMID: 29732263 PMCID: PMC5895185 DOI: 10.1002/aps3.1033] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 11/04/2017] [Indexed: 05/25/2023]
Abstract
PREMISE OF THE STUDY We describe a field collection, sample processing, and ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) instrumental and bioinformatics method developed for untargeted metabolomics of plant tissue and suitable for molecular networking applications. METHODS AND RESULTS A total of 613 leaf samples from 204 tree species was collected in the field and analyzed using UHPLC-MS/MS. Matching of molecular fragmentation spectra generated over 125,000 consensus spectra representing unique molecular structures, 26,410 of which were linked to at least one structurally similar compound. CONCLUSIONS Our workflow is able to generate molecular networks of hundreds of thousands of compounds representing broad classes of plant secondary chemistry and a wide range of molecular masses, from 100 to 2500 daltons, making possible large-scale comparative metabolomics, as well as studies of chemical community ecology and macroevolution in plants.
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Affiliation(s)
- Brian E. Sedio
- Smithsonian Tropical Research InstituteApartado 0843‐03092Balboa, AncónRepublic of Panama
- Center for Biodiversity and Drug DiscoveryInstituto de Investigaciones Científicas y Servicios de Alta TecnologíaApartado 0843‐01103Ciudad del SaberRepublic of Panama
| | - Cristopher A. Boya P.
- Center for Biodiversity and Drug DiscoveryInstituto de Investigaciones Científicas y Servicios de Alta TecnologíaApartado 0843‐01103Ciudad del SaberRepublic of Panama
- Department of BiotechnologyAcharya Nagarjuna UniversityNagarjuna Nagar, 522 510GunturIndia
| | - Juan Camilo Rojas Echeverri
- Center for Biodiversity and Drug DiscoveryInstituto de Investigaciones Científicas y Servicios de Alta TecnologíaApartado 0843‐01103Ciudad del SaberRepublic of Panama
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Coley PD, Endara MJ, Kursar TA. Consequences of interspecific variation in defenses and herbivore host choice for the ecology and evolution of Inga, a speciose rainforest tree. Oecologia 2018; 187:361-376. [PMID: 29428967 DOI: 10.1007/s00442-018-4080-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 11/26/2017] [Indexed: 01/08/2023]
Abstract
We summarize work on a speciose Neotropical tree genus, Inga (Fabaceae), examining how interspecific variation in anti-herbivore defenses may have evolved, how defenses shape host choice by herbivores and how they might regulate community composition and influence species radiations. Defenses of expanding leaves include secondary metabolites, extrafloral nectaries, rapid leaf expansion, trichomes, and synchrony and timing of leaf production. These six classes of defenses are orthogonal, supporting independent evolutionary trajectories. Moreover, only trichomes show a phylogenetic signature, suggesting evolutionary lability in nearly all defenses. The interspecific diversity in secondary metabolite profiles does not arise from the evolution of novel compounds, but from novel combinations of common compounds, presumably due to changes in gene regulation. Herbivore host choice is determined by plant defensive traits, not host phylogeny. Neighboring plants escape each other's pests if their defenses differ enough, thereby enforcing the high local diversity typical of tropical forests. Related herbivores feed on hosts with similar defenses, implying that there are phylogenetic constraints placed on the herbivore traits that are associated with host use. Divergence in defensive traits among Inga appears to be driven by herbivore pressure. However, the lack of congruence between herbivore and host phylogeny suggests that herbivores are tracking defenses, choosing hosts based on traits for which they already have adaptations. There is, therefore, an asymmetry in the host-herbivore evolutionary arms race.
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Affiliation(s)
- Phyllis D Coley
- Department of Biology, University of Utah, Salt Lake City, UT, 84112, USA. .,Smithsonian Tropical Research Institute, Panama City, Republic of Panama.
| | - María-José Endara
- Department of Biology, University of Utah, Salt Lake City, UT, 84112, USA.,Centro de Investigación de la Biodiversidad y Cambio Climático e Ingeniería en Biodiversidad y Recursos Genéticos, Facultad de Ciencias de Medio Ambiente, Universidad Tecnológica Indoamérica, EC170103, Quito, Ecuador
| | - Thomas A Kursar
- Department of Biology, University of Utah, Salt Lake City, UT, 84112, USA.,Smithsonian Tropical Research Institute, Panama City, Republic of Panama
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