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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. [PMCID: PMC9643135 DOI: 10.1002/ece3.9475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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
Affiliation(s)
- Janet A. Morrison
- Department of Biology The College of New Jersey Ewing New Jersey USA
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Sardans J, Gargallo‐Garriga A, Urban O, Klem K, Holub P, Janssens IA, Walker TWN, Pesqueda A, Peñuelas J. Ecometabolomics of plant–herbivore and plant–fungi interactions: a synthesis study. Ecosphere 2021. [DOI: 10.1002/ecs2.3736] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Jordi Sardans
- CSIC Global Ecology Unit CREAF‐CSIC‐UAB Bellaterra Catalonia 08193 Spain
- CREAF Cerdanyola del Valles Catalonia 08193 Spain
- Global Change Research Institute Czech Academy of Sciences Bělidla 986/4a Brno CZ‐60300 Czech Republic
| | - Albert Gargallo‐Garriga
- CSIC Global Ecology Unit CREAF‐CSIC‐UAB Bellaterra Catalonia 08193 Spain
- CREAF Cerdanyola del Valles Catalonia 08193 Spain
- Global Change Research Institute Czech Academy of Sciences Bělidla 986/4a Brno CZ‐60300 Czech Republic
| | - Otmar Urban
- Global Change Research Institute Czech Academy of Sciences Bělidla 986/4a Brno CZ‐60300 Czech Republic
| | - Karel Klem
- Global Change Research Institute Czech Academy of Sciences Bělidla 986/4a Brno CZ‐60300 Czech Republic
| | - Petr Holub
- Global Change Research Institute Czech Academy of Sciences Bělidla 986/4a Brno CZ‐60300 Czech Republic
| | - Ivan A. Janssens
- Department of Biology University of Antwerp Wilrijk 2610 Belgium
| | - Tom W. N. Walker
- Department of Environmental Systems Science Institute of Integrative Biology ETH Zürich Zurich 8092 Switzerland
| | - Argus Pesqueda
- CSIC Global Ecology Unit CREAF‐CSIC‐UAB Bellaterra Catalonia 08193 Spain
- CREAF Cerdanyola del Valles Catalonia 08193 Spain
| | - Josep Peñuelas
- CSIC Global Ecology Unit CREAF‐CSIC‐UAB Bellaterra Catalonia 08193 Spain
- CREAF Cerdanyola del Valles Catalonia 08193 Spain
- Global Change Research Institute Czech Academy of Sciences Bělidla 986/4a Brno CZ‐60300 Czech Republic
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Global Change and Forest Disturbances in the Mediterranean Basin: Breakthroughs, Knowledge Gaps, and Recommendations. FORESTS 2021. [DOI: 10.3390/f12050603] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Forest ecosystems in the Mediterranean Basin are mostly situated in the north of the Basin (mesic). In the most southern and dry areas, the forest can only exist where topography and/or altitude favor a sufficient availability of water to sustain forest biomass. We have conducted a thorough review of recent literature (2000–2021) that clearly indicates large direct and indirect impacts of increasing drought conditions on the forests of the Mediterranean Basin, their changes in surface and distribution areas, and the main impacts they have suffered. We have focused on the main trends that emerge from the current literature and have highlighted the main threatens and management solution for the maintenance of these forests. The results clearly indicate large direct and indirect impacts of increasing drought conditions on the forests of the Mediterranean Basin. These increasing drought conditions together with over-exploitation, pest expansion, fire and soil degradation, are synergistically driving to forest regression and dieback in several areas of this Mediterranean Basin. These environmental changes have triggered responses in tree morphology, physiology, growth, reproduction, and mortality. We identified at least seven causes of the changes in the last three decades that have led to the current situation and that can provide clues for projecting the future of these forests: (i) The direct effect of increased aridity due to more frequent and prolonged droughts, which has driven Mediterranean forest communities to the limit of their capacity to respond to drought and escape to wetter sites, (ii) the indirect effects of drought, mainly by the spread of pests and fires, (iii) the direct and indirect effects of anthropogenic activity associated with general environmental degradation, including soil degradation and the impacts of fire, species invasion and pollution, (iv) human pressure and intense management of water resources, (v) agricultural land abandonment in the northern Mediterranean Basin without adequate management of new forests, (vi) very high pressure on forested areas of northern Africa coupled with the demographic enhancement, the expansion of crops and higher livestock pressure, and the more intense and overexploitation of water resources uses on the remaining forested areas, and (vii) scarcity and inequality of human management and policies, depending on the national and/or regional governments and agencies, being unable to counteract the previous changes. We identified appropriate measures of management intervention, using the most adequate techniques and processes to counteract these impacts and thus to conserve the health, service capacity, and biodiversity of Mediterranean forests. Future policies should, moreover, promote research to improve our knowledge of the mechanisms of, and the effects on, nutrient and carbon plant-soil status concurrent with the impacts of aridity and leaching due to the effects of current changes. Finally, we acknowledge the difficulty to obtain an accurate quantification of the impacts of increasing aridity rise that warrants an urgent investment in more focused research to further develop future tools in order to counteract the negative effects of climate change on Mediterranean forests.
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Rodrigues AM, Miguel C, Chaves I, António C. Mass spectrometry-based forest tree metabolomics. MASS SPECTROMETRY REVIEWS 2021; 40:126-157. [PMID: 31498921 DOI: 10.1002/mas.21603] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 08/05/2019] [Indexed: 05/24/2023]
Abstract
Research in forest tree species has advanced slowly when compared with other agricultural crops and model organisms, mainly due to the long-life cycles, large genome sizes, and lack of genomic tools. Additionally, trees are complex matrices, and the presence of interferents (e.g., oleoresins and cellulose) challenges the analysis of tree tissues with mass spectrometry (MS)-based analytical platforms. In this review, advances in MS-based forest tree metabolomics are discussed. Given their economic and ecological significance, particular focus is given to Pinus, Quercus, and Eucalyptus forest tree species to better understand their metabolite responses to abiotic and biotic stresses in the current climate change scenario. Furthermore, MS-based metabolomics technologies produce large and complex datasets that require expertize to adequately manage, process, analyze, and store the data in dedicated repositories. To ensure that the full potential of forest tree metabolomics data are translated into new knowledge, these data should comply with the FAIR principles (i.e., Findable, Accessible, Interoperable, and Re-usable). It is essential that adequate standards are implemented to annotate metadata from forest tree metabolomics studies as is already required by many science and governmental agencies and some major scientific publishers. © 2019 John Wiley & Sons Ltd. Mass Spec Rev 40:126-157, 2021.
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Affiliation(s)
- Ana Margarida Rodrigues
- Plant Metabolomics Laboratory, GreenIT-Bioresources for Sustainability, Instituto de Tecnologia Química e Biológica António Xavie, Universidade Nova de Lisboa (ITQB NOVA) Avenida da República, Oeiras, 2780-157, Portugal
| | - Célia Miguel
- Forest Genomics & Molecular Genetics Lab, BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016, Lisboa, Portugal
- Instituto de Biologia Experimental e Tecnológica (iBET), 2780-157, Oeiras, Portugal
| | - Inês Chaves
- Forest Genomics & Molecular Genetics Lab, BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016, Lisboa, Portugal
- Instituto de Biologia Experimental e Tecnológica (iBET), 2780-157, Oeiras, Portugal
| | - Carla António
- Plant Metabolomics Laboratory, GreenIT-Bioresources for Sustainability, Instituto de Tecnologia Química e Biológica António Xavie, Universidade Nova de Lisboa (ITQB NOVA) Avenida da República, Oeiras, 2780-157, Portugal
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5
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Castaño C, Camarero JJ, Zas R, Sampedro L, Bonet JA, Alday JG, Oliva J. Insect defoliation is linked to a decrease in soil ectomycorrhizal biomass and shifts in needle endophytic communities. TREE PHYSIOLOGY 2020; 40:1712-1725. [PMID: 32785638 DOI: 10.1093/treephys/tpaa104] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 08/07/2020] [Indexed: 06/11/2023]
Abstract
Insect outbreaks of increasing frequency and severity in forests are predicted due to climate change. Insect herbivory is known to promote physiological changes in forest trees. However, little is known about whether these plant phenotypic adjustments have cascading effects on tree microbial symbionts such as fungi in roots and foliage. We studied the impact of defoliation by the pine processionary moth in two infested Pinus nigra forests through a multilevel sampling of defoliated and non-defoliated trees. We measured tree growth, nutritional status and carbon allocation to chemical defenses. Simultaneously, we analysed the putative impact of defoliation on the needle endophytes and on the soil fungal communities. Higher concentrations of chemical defenses were found in defoliated trees, likely as a response to defoliation; however, no differences in non-structural carbohydrate reserves were found. In parallel to the reductions in tree growth and changes in chemical defenses, we observed shifts in the composition of needle endophytic and soil fungal communities in defoliated trees. Defoliated trees consistently corresponded with a lower biomass of ectomycorrhizal fungi in both sites, and a higher alpha diversity and greater relative abundance of belowground saprotrophs and pathogens. However, ectomycorrhizal alpha diversity was similar between non-defoliated and defoliated trees. Specific needle endophytes in old needles were strongly associated with non-defoliated trees. The potential role of these endophytic fungi in pine resistance should be further investigated. Our study suggests that lower biomass of ectomycorrhizal fungi in defoliated trees might slow down tree recovery since fungal shifts might affect tree-mycorrhizal feedbacks and can potentially influence carbon and nitrogen cycling in forest soils.
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Affiliation(s)
- Carles Castaño
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden
| | - J Julio Camarero
- Instituto Pirenaico de Ecología (IPE-CSIC), 50192 Zaragoza, Spain
| | - Rafael Zas
- Misión Biológica de Galicia, Consejo Superior de Investigaciones Científicas (MBG-CSIC), Apdo 28, 36080 Pontevedra, Spain
| | - Luis Sampedro
- Misión Biológica de Galicia, Consejo Superior de Investigaciones Científicas (MBG-CSIC), Apdo 28, 36080 Pontevedra, Spain
| | - José Antonio Bonet
- Departament de Producció Vegetal i Ciència Forestal, Universitat de Lleida, Av. Rovira Roure, 191, E-25198 Lleida, Spain
- Joint Research Unit CTFC - AGROTECNIO, Av. Alcalde Rovira Roure 191, E25198 Lleida, Spain
| | - Josu G Alday
- Departament de Producció Vegetal i Ciència Forestal, Universitat de Lleida, Av. Rovira Roure, 191, E-25198 Lleida, Spain
- Joint Research Unit CTFC - AGROTECNIO, Av. Alcalde Rovira Roure 191, E25198 Lleida, Spain
| | - Jonàs Oliva
- Departament de Producció Vegetal i Ciència Forestal, Universitat de Lleida, Av. Rovira Roure, 191, E-25198 Lleida, Spain
- Joint Research Unit CTFC - AGROTECNIO, Av. Alcalde Rovira Roure 191, E25198 Lleida, Spain
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Montesinos-Navarro A, Pérez-Clemente RM, Sánchez-Martín R, Gómez-Cadenas A, Verdú M. Phylogenetic analysis of secondary metabolites in a plant community provides evidence for trade-offs between biotic and abiotic stress tolerance. Evol Ecol 2020. [DOI: 10.1007/s10682-020-10044-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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7
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Rodrigues AM, Ribeiro-Barros AI, António C. Experimental Design and Sample Preparation in Forest Tree Metabolomics. Metabolites 2019; 9:E285. [PMID: 31766588 PMCID: PMC6950530 DOI: 10.3390/metabo9120285] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/15/2019] [Accepted: 11/20/2019] [Indexed: 02/07/2023] Open
Abstract
Appropriate experimental design and sample preparation are key steps in metabolomics experiments, highly influencing the biological interpretation of the results. The sample preparation workflow for plant metabolomics studies includes several steps before metabolite extraction and analysis. These include the optimization of laboratory procedures, which should be optimized for different plants and tissues. This is particularly the case for trees, whose tissues are complex matrices to work with due to the presence of several interferents, such as oleoresins, cellulose. A good experimental design, tree tissue harvest conditions, and sample preparation are crucial to ensure consistency and reproducibility of the metadata among datasets. In this review, we discuss the main challenges when setting up a forest tree metabolomics experiment for mass spectrometry (MS)-based analysis covering all technical aspects from the biological question formulation and experimental design to sample processing and metabolite extraction and data acquisition. We also highlight the importance of forest tree metadata standardization in metabolomics studies.
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Affiliation(s)
- Ana M. Rodrigues
- Plant Metabolomics Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal; (A.M.R.); (A.I.R.-B.)
| | - Ana I. Ribeiro-Barros
- Plant Metabolomics Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal; (A.M.R.); (A.I.R.-B.)
- Plant Stress and Biodiversity Laboratory, Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia, Universidade de Lisboa (ISA/ULisboa), 1349-017 Lisboa, Portugal
| | - Carla António
- Plant Metabolomics Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), 2780-157 Oeiras, Portugal; (A.M.R.); (A.I.R.-B.)
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8
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Bai Q, He B, Cai Y, Lian H, Zhang Q. Transcriptomic and metabolomic analyses reveal several critical metabolic pathways and candidate genes involved in resin biosynthesis in Pinus massoniana. Mol Genet Genomics 2019; 295:327-341. [PMID: 31735985 DOI: 10.1007/s00438-019-01624-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 11/06/2019] [Indexed: 10/25/2022]
Abstract
Pine resin, which typically consists of terpenoids, is a natural product used in various industrial applications. Oleoresin can be obtained from the xylem tissue by wounding the stem bark. Pinus massoniana (masson pine) is an important resin-tapping tree species that originated in southern China. Masson pines with different genetic backgrounds typically have different resin-yielding capacities (RYCs). However, the mechanisms underlying high resin yield in masson pines are unclear. The aim of this study was to identify the possible genetic regulation pathways and functional genes that influence the resin yield. In this study, we conducted transcriptomic and metabolomic studies of masson pine secondary xylem with high, medium, and low RYCs. A total of 230,068 unigenes and 3894 metabolites were identified from the tissue of the secondary xylem. Several differentially expressed regulation factors, including WRKY, bHLH, and ERF, and functional genes such as PKc and LRR-RLKs, were identified among these masson pines. The Kyoto Encyclopedia of Genes and Genomes pathways were mainly focused on diterpenoid biosynthesis, plant hormone signal transduction, and ABC transporters. Furthermore, integration of the transcriptomic and metabolomic data indicated that the PKc- and LRR-RLK-related regulatory and metabolic pathways may play critical roles in the biosynthesis of terpenoids. These above results improve our understanding of the biosynthesis mechanism of oleoresin in P. massoniana and facilitate further research work into the functional analysis of these candidate genes.
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Affiliation(s)
- Qingsong Bai
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, 510520, China
| | - Boxiang He
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, 510520, China
| | - Yanling Cai
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, 510520, China
| | - Huiming Lian
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, 510520, China
| | - Qian Zhang
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, 510520, China.
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Rivas-Ubach A, Liu Y, Steiner AL, Sardans J, Tfaily MM, Kulkarni G, Kim YM, Bourrianne E, Paša-Tolić L, Peñuelas J, Guenther A. Atmo-ecometabolomics: a novel atmospheric particle chemical characterization methodology for ecological research. ENVIRONMENTAL MONITORING AND ASSESSMENT 2019; 191:78. [PMID: 30649631 DOI: 10.1007/s10661-019-7205-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 01/04/2019] [Indexed: 06/09/2023]
Abstract
Aerosol particles play important roles in processes controlling the composition of the atmosphere and function of ecosystems. A better understanding of the composition of aerosol particles is beginning to be recognized as critical for ecological research to further comprehend the link between aerosols and ecosystems. While chemical characterization of aerosols has been practiced in the atmospheric science community, detailed methodology tailored to the needs of ecological research does not exist yet. In this study, we describe an efficient methodology (atmo-ecometabolomics), in step-by-step details, from the sampling to the data analyses, to characterize the chemical composition of aerosol particles, namely atmo-metabolome. This method employs mass spectrometry platforms such as liquid and gas chromatography mass spectrometries (MS) and Fourier transform ion cyclotron resonance MS (FT-ICR-MS). For methodology evaluation, we analyzed aerosol particles collected during two different seasons (spring and summer) in a low-biological-activity ecosystem. Additionally, to further validate our methodology, we analyzed aerosol particles collected in a more biologically active ecosystem during the pollination peaks of three different representative tree species. Our statistical results showed that our sampling and extraction methods are suitable for characterizing the atmo-ecometabolomes in these two distinct ecosystems with any of the analytical platforms. Datasets obtained from each mass spectrometry instrument showed overall significant differences of the atmo-ecometabolomes between spring and summer as well as between the three pollination peak periods. Furthermore, we have identified several metabolites that can be attributed to pollen and other plant-related aerosol particles. We additionally provide a basic guide of the potential use ecometabolomic techniques on different mass spectrometry platforms to accurately analyze the atmo-ecometabolomes for ecological studies. Our method represents an advanced novel approach for future studies in the impact of aerosol particle chemical compositions on ecosystem structure and function and biogeochemistry.
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Affiliation(s)
- Albert Rivas-Ubach
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA.
| | - Yina Liu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
- Geochemical and Environmental Research Group, Texas A&M University, College Station, TX, 77845, USA
| | - Allison L Steiner
- Department of Climate and Space Sciences and Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jordi Sardans
- CREAF, Campus UAB, 08913, Cerdanyola del Vallès, Catalonia, Spain
- Global Ecology Unit CREAF-CSIC, Campus UAB, 08913, Cerdanyola del Vallès, Catalonia, Spain
| | - Malak M Tfaily
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Gourihar Kulkarni
- Atmospheric Sciences and Global Change Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Young-Mo Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Eric Bourrianne
- Faculté des Sicences et d'Ingénierie, Université de Toulouse III Paul Sabatier, 31400, Toulouse, France
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Josep Peñuelas
- CREAF, Campus UAB, 08913, Cerdanyola del Vallès, Catalonia, Spain
- Global Ecology Unit CREAF-CSIC, Campus UAB, 08913, Cerdanyola del Vallès, Catalonia, Spain
| | - Alex Guenther
- Department of Earth System Science, University of California, Irvine, Irvine, CA, 92697, USA
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Rivas-Ubach A, Peñuelas J, Hódar JA, Oravec M, Paša-Tolić L, Urban O, Sardans J. We Are What We Eat: A Stoichiometric and Ecometabolomic Study of Caterpillars Feeding on Two Pine Subspecies of Pinus sylvestris. Int J Mol Sci 2018; 20:E59. [PMID: 30586850 PMCID: PMC6337320 DOI: 10.3390/ijms20010059] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 12/17/2018] [Accepted: 12/20/2018] [Indexed: 11/28/2022] Open
Abstract
Many studies have addressed several plant-insect interaction topics at nutritional, molecular, physiological, and evolutionary levels. However, it is still unknown how flexible the metabolism and the nutritional content of specialist insect herbivores feeding on different closely related plants can be. We performed elemental, stoichiometric, and metabolomics analyses on leaves of two coexisting Pinus sylvestris subspecies and on their main insect herbivore; the caterpillar of the processionary moth (Thaumetopoea pityocampa). Caterpillars feeding on different pine subspecies had distinct overall metabolome structure, accounting for over 10% of the total variability. Although plants and insects have very divergent metabolomes, caterpillars showed certain resemblance to their plant-host metabolome. In addition, few plant-related secondary metabolites were found accumulated in caterpillar tissues which could potentially be used for self-defense. Caterpillars feeding on N and P richer needles had lower N and P tissue concentration and higher C:N and C:P ratios, suggesting that nutrient transfer is not necessarily linear through trophic levels and other plant-metabolic factors could be interfering. This exploratory study showed that little chemical differences between plant food sources can impact the overall metabolome of specialist insect herbivores. Significant nutritional shifts in herbivore tissues could lead to larger changes of the trophic web structure.
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Affiliation(s)
- Albert Rivas-Ubach
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA.
- CREAF, Center for Ecological and Forestry Applications, Cerdanyola del Vallès, 08913 Catalonia, Spain.
| | - Josep Peñuelas
- CREAF, Center for Ecological and Forestry Applications, Cerdanyola del Vallès, 08913 Catalonia, Spain.
- CSIC, Global Ecology Unit CREAF-CEAB-CSIC-UAB, Cerdanyola del Vallès, 08913 Catalonia, Spain.
| | - José Antonio Hódar
- Grupo de Ecología Terrestre, Departamento de Biología Animal y Ecología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain.
| | - Michal Oravec
- Global Change Research Institute, Czech Academy of Sciences, Bĕlidla 4a, CZ-603 00 Brno, Czech Republic.
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA.
| | - Otmar Urban
- Global Change Research Institute, Czech Academy of Sciences, Bĕlidla 4a, CZ-603 00 Brno, Czech Republic.
| | - Jordi Sardans
- CREAF, Center for Ecological and Forestry Applications, Cerdanyola del Vallès, 08913 Catalonia, Spain.
- CSIC, Global Ecology Unit CREAF-CEAB-CSIC-UAB, Cerdanyola del Vallès, 08913 Catalonia, Spain.
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11
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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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12
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Rivas-Ubach A, Liu Y, Bianchi TS, Tolić N, Jansson C, Paša-Tolić L. Moving beyond the van Krevelen Diagram: A New Stoichiometric Approach for Compound Classification in Organisms. Anal Chem 2018; 90:6152-6160. [PMID: 29671593 DOI: 10.1021/acs.analchem.8b00529] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
van Krevelen diagrams (O/C vs H/C ratios of elemental formulas) have been widely used in studies to obtain an estimation of the main compound categories present in environmental samples. However, the limits defining a specific compound category based solely on O/C and H/C ratios of elemental formulas have never been accurately listed or proposed to classify metabolites in biological samples. Furthermore, while O/C vs H/C ratios of elemental formulas can provide an overview of the compound categories, such classification is inefficient because of the large overlap among different compound categories along both axes. We propose a more accurate compound classification for biological samples analyzed by high-resolution mass spectrometry based on an assessment of the C/H/O/N/P stoichiometric ratios of over 130 000 elemental formulas of compounds classified in 6 main categories: lipids, peptides, amino sugars, carbohydrates, nucleotides, and phytochemical compounds (oxy-aromatic compounds). Our multidimensional stoichiometric compound classification (MSCC) constraints showed a highly accurate categorization of elemental formulas to the main compound categories in biological samples with over 98% of accuracy representing a substantial improvement over any classification based on the classic van Krevelen diagram. This method represents a signficant step forward in environmental research, especially ecological stoichiometry and eco-metabolomics studies, by providing a novel and robust tool to improve our understanding of the ecosystem structure and function through the chemical characterization of biological samples.
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Affiliation(s)
- Albert Rivas-Ubach
- Environmental Molecular Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Yina Liu
- Environmental Molecular Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States.,Geochemical and Environmental Research Group , Texas A&M University , College Station , Texas 77845 , United States
| | - Thomas S Bianchi
- Department of Geological Sciences , University of Florida , Gainesville , Florida 32611-2120 , United States
| | - Nikola Tolić
- Environmental Molecular Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Christer Jansson
- Environmental Molecular Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
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13
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Rivas-Ubach A, Sardans J, Hódar JA, Garcia-Porta J, Guenther A, Paša-Tolić L, Oravec M, Urban O, Peñuelas J. Close and distant: Contrasting the metabolism of two closely related subspecies of Scots pine under the effects of folivory and summer drought. Ecol Evol 2017; 7:8976-8988. [PMID: 29152192 PMCID: PMC5677489 DOI: 10.1002/ece3.3343] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 07/10/2017] [Accepted: 08/03/2017] [Indexed: 01/03/2023] Open
Abstract
Metabolomes, as chemical phenotypes of organisms, are likely not only shaped by the environment but also by common ancestry. If this is the case, we expect that closely related species of pines will tend to reach similar metabolomic solutions to the same environmental stressors. We examined the metabolomes of two sympatric subspecies of Pinus sylvestris in Sierra Nevada (southern Iberian Peninsula), in summer and winter and exposed to folivory by the pine processionary moth. The overall metabolomes differed between the subspecies but both tended to respond more similarly to folivory. The metabolomes of the subspecies were more dissimilar in summer than in winter, and iberica trees had higher concentrations of metabolites directly related to drought stress. Our results are consistent with the notion that certain plant metabolic responses associated with folivory have been phylogenetically conserved. The larger divergence between subspecies metabolomes in summer is likely due to the warmer and drier conditions that the northern iberica subspecies experience in Sierra Nevada. Our results provide crucial insights into how iberica populations would respond to the predicted conditions of climate change under an increased defoliation in the Mediterranean Basin.
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Affiliation(s)
- Albert Rivas-Ubach
- Environmental Molecular Sciences Division Pacific Northwest National Laboratory Richland WA USA.,CREAF Bellaterra, Barcelona Spain
| | - Jordi Sardans
- CREAF Bellaterra, Barcelona Spain.,CSIC Global Ecology Unit CREAF- CSIC-UAB Bellaterra, Barcelona Spain
| | - José Antonio Hódar
- Grupo de Ecología Terrestre Departamento de Biología Animal y Ecología Facultad de Ciencias Universidad de Granada Granada Spain
| | | | - Alex Guenther
- Department of Earth System Science University of California Irvine CA USA
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Division Pacific Northwest National Laboratory Richland WA USA
| | - Michal Oravec
- Global Change Research Institute Czech Academy of Sciences Bělidla 986/4a 603 00 Brno Czech Republic
| | - Otmar Urban
- Global Change Research Institute Czech Academy of Sciences Bělidla 986/4a 603 00 Brno Czech Republic
| | - Josep Peñuelas
- CREAF Bellaterra, Barcelona Spain.,CSIC Global Ecology Unit CREAF- CSIC-UAB Bellaterra, Barcelona Spain
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