1
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Pavlin J, Nagel TA, Svitok M, Di Filippo A, Mikac S, Keren S, Dikku A, Toromani E, Panayotov M, Zlatanov T, Haruta O, Dorog S, Chaskovskyy O, Bače R, Begović K, Buechling A, Dušátko M, Frankovič M, Janda P, Kameniar O, Kozák D, Marchand W, Mikoláš M, Rodrigo R, Svoboda M. Pathways and drivers of canopy accession across primary temperate forests of Europe. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167593. [PMID: 37802334 DOI: 10.1016/j.scitotenv.2023.167593] [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: 06/09/2023] [Revised: 10/01/2023] [Accepted: 10/03/2023] [Indexed: 10/08/2023]
Abstract
Canopy accession strategies reveal much about tree life histories and forest stand dynamics. However, the protracted nature of ascending to the canopy makes direct observation challenging. We use a reconstructive approach based on an extensive tree ring database to study the variability of canopy accession patterns of dominant tree species (Abies alba, Acer pseudoplatanus, Fagus sylvatica, Picea abies) in temperate mountain forests of Europe and elucidate how disturbance histories, climate, and topography affect canopy accession. All four species exhibited high variability of radial growth histories leading to canopy accession and indicated varying levels of shade tolerance. Individuals of all four species survived at least 100 years of initial suppression. Fir and particularly beech, however, survived longer periods of initial suppression, exhibited more release events, and reached the canopy later on average, with a larger share of trees accessing the canopy after initially suppressed growth. These results indicate the superior shade tolerance of beech and fir compared to spruce and maple. The two less shade-tolerant species conversely relied on faster growth rates, revealing their competitive advantage in non-suppressed conditions. Additionally, spruce from higher-elevation spruce-dominated forests survived shorter periods of initial shading and exhibited fewer releases, with a larger share of trees reaching the canopy after open canopy recruitment (i.e. in absence of suppression) and no subsequent releases compared to spruce growing in lower-elevation mixed forests. Finally, disturbance factors were identified as the primary driver of canopy accession, whereby disturbances accelerate canopy accession and consequently regulate competitive interactions. Intensifying disturbance regimes could thus promote shifts in species composition, particularly in favour of faster-growing, more light-demanding species.
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Affiliation(s)
- Jakob Pavlin
- Department of Forest Ecology, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcka 129, 165 21 Prague, Czech Republic.
| | - Thomas A Nagel
- Department of Forest Ecology, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcka 129, 165 21 Prague, Czech Republic; Department of Forestry and Renewable Forest Resources, Biotechnical Faculty, University of Ljubljana, Večna pot 83, 1000 Ljubljana, Slovenia
| | - Marek Svitok
- Department of Forest Ecology, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcka 129, 165 21 Prague, Czech Republic; Department of Biology and General Ecology, Faculty of Ecology and Environmental Sciences, Technical University in Zvolen, Masaryka 24, 96053 Zvolen, Slovakia
| | - Alfredo Di Filippo
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, Via SC de Lellis, 01100 Viterbo, Italy
| | - Stjepan Mikac
- Department of Forest Ecology and Silviculture, Faculty of Forestry, University of Zagreb, Svetošimunska cesta 25, 10000 Zagreb, Croatia
| | - Srdjan Keren
- Faculty of Forestry, University of Agriculture in Krakow, Al. 29 Listopada 46, 31-425 Kraków, Poland
| | | | - Elvin Toromani
- Faculty of Forestry Sciences, Agricultural University of Tirana, 1029 Koder-Kamez, Albania
| | - Momchil Panayotov
- Department of Dendrology, University of Forestry Sofia, Kliment Ohridski 10 Blvd., 1797 Sofia, Bulgaria
| | - Tzvetan Zlatanov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Gagarin Street 2, 1113 Sofia, Bulgaria
| | - Ovidiu Haruta
- Forestry and Forest Engineering Department, University of Oradea, Oradea, Romania
| | - Sorin Dorog
- Forestry and Forest Engineering Department, University of Oradea, Oradea, Romania
| | - Oleh Chaskovskyy
- Institute of Forest Management, Ukrainian National Forestry University, Vul. Henerala Chuprynky 103, 79031 Lviv, Ukraine
| | - Radek Bače
- Department of Forest Ecology, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcka 129, 165 21 Prague, Czech Republic
| | - Krešimir Begović
- Department of Forest Ecology, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcka 129, 165 21 Prague, Czech Republic
| | - Arne Buechling
- Department of Forest Ecology, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcka 129, 165 21 Prague, Czech Republic
| | - Martin Dušátko
- Department of Forest Ecology, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcka 129, 165 21 Prague, Czech Republic
| | - Michal Frankovič
- Department of Forest Ecology, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcka 129, 165 21 Prague, Czech Republic
| | - Pavel Janda
- Department of Forest Ecology, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcka 129, 165 21 Prague, Czech Republic
| | - Ondrej Kameniar
- Department of Forest Ecology, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcka 129, 165 21 Prague, Czech Republic
| | - Daniel Kozák
- Department of Forest Ecology, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcka 129, 165 21 Prague, Czech Republic
| | - William Marchand
- Department of Forest Ecology, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcka 129, 165 21 Prague, Czech Republic
| | - Martin Mikoláš
- Department of Forest Ecology, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcka 129, 165 21 Prague, Czech Republic
| | - Ruffy Rodrigo
- Department of Forest Ecology, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcka 129, 165 21 Prague, Czech Republic
| | - Miroslav Svoboda
- Department of Forest Ecology, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcka 129, 165 21 Prague, Czech Republic
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2
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Girard-Tercieux C, Maréchaux I, Clark AT, Clark JS, Courbaud B, Fortunel C, Guillemot J, Künstler G, le Maire G, Pélissier R, Rüger N, Vieilledent G. Rethinking the nature of intraspecific variability and its consequences on species coexistence. Ecol Evol 2023; 13:e9860. [PMID: 36911314 PMCID: PMC9992775 DOI: 10.1002/ece3.9860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 01/20/2023] [Accepted: 02/09/2023] [Indexed: 03/14/2023] Open
Abstract
Intraspecific variability (IV) has been proposed to explain species coexistence in diverse communities. Assuming, sometimes implicitly, that conspecific individuals can perform differently in the same environment and that IV increases niche overlap, previous studies have found contrasting results regarding the effect of IV on species coexistence. We aim at showing that the large IV observed in data does not mean that conspecific individuals are necessarily different in their response to the environment and that the role of high-dimensional environmental variation in determining IV has largely remained unexplored in forest plant communities. We first used a simulation experiment where an individual attribute is derived from a high-dimensional model, representing "perfect knowledge" of individual response to the environment, to illustrate how large observed IV can result from "imperfect knowledge" of the environment. Second, using growth data from clonal Eucalyptus plantations in Brazil, we estimated a major contribution of the environment in determining individual growth. Third, using tree growth data from long-term tropical forest inventories in French Guiana, Panama and India, we showed that tree growth in tropical forests is structured spatially and that despite a large observed IV at the population level, conspecific individuals perform more similarly locally than compared with heterospecific individuals. As the number of environmental dimensions that are well quantified at fine scale is generally lower than the actual number of dimensions influencing individual attributes, a great part of observed IV might be represented as random variation across individuals when in fact it is environmentally driven. This mis-representation has important consequences for inference about community dynamics. We emphasize that observed IV does not necessarily impact species coexistence per se but can reveal species response to high-dimensional environment, which is consistent with niche theory and the observation of the many differences between species in nature.
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Affiliation(s)
| | | | - Adam T Clark
- Institute of Biology Karl-Franzens University of Graz Graz Austria
| | - James S Clark
- Nicholas School of the Environment Duke University Durham North Carolina USA.,Univ. Grenoble Alpes, INRAE, LESSEM St-Martin-d'Hères France
| | - Benoît Courbaud
- Univ. Grenoble Alpes, INRAE, LESSEM St-Martin-d'Hères France
| | - Claire Fortunel
- AMAP, Univ. Montpellier, CIRAD, CNRS, INRAE, IRD Montpellier France
| | - Joannès Guillemot
- Eco&Sols, Univ. Montpellier, CIRAD, INRAE, IRD, Institut Agro Montpellier France
| | | | - Guerric le Maire
- Eco&Sols, Univ. Montpellier, CIRAD, INRAE, IRD, Institut Agro Montpellier France
| | - Raphaël Pélissier
- AMAP, Univ. Montpellier, CIRAD, CNRS, INRAE, IRD Montpellier France.,Department of Ecology French Institute of Pondicherry Puducherry India
| | - Nadja Rüger
- Department of Economics University of Leipzig Leipzig Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig Leipzig Germany.,Smithsonian Tropical Research Institute Balboa Panama
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3
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Li TX, Shen-Tu XL, Xu L, Zhang WJ, Duan JP, Song YB, Dong M. Intraspecific and sex-dependent variation of leaf traits along altitude gradient in the endangered dioecious tree Taxus fuana Nan Li & R.R. Mill. FRONTIERS IN PLANT SCIENCE 2022; 13:996750. [PMID: 36325570 PMCID: PMC9618961 DOI: 10.3389/fpls.2022.996750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
Plant intraspecific trait variation (ITV) including sex-dependent differences are matters of many ecological consequences, from individual to ecosystem, especially in endangered and rare species. Taxus fuana is an endangered dioecious species with small and isolated populations endemic to the Himalayas region. Little is known about its trait variation between sexes, and among populations. In this study, 18 leaf traits from 179 reproductive trees (males and females) along the altitude (2600-3200m a.s.l.) of the T. fuana populations distributed in Gyirong County, Tibet, China, were measured. ITV and sources of variation in leaf traits were assessed. The relationship between leaf traits of males and females and altitude was analyzed separately. Variations in leaf traits of T. fuana ranged from 3.1% to 24.2%, with the smallest in leaf carbon content and the largest in leaf thickness to area ratio. On average 78.13% of the variation in leaf traits was from within populations and 21.87% among populations. The trends in leaf width, leaf nitrogen to phosphorus ratio, leaf carbon to nitrogen ratio, leaf carbon isotope ratio, and leaf nitrogen isotope ratio in relation to altitude were the same for males and females. Leaf length to width ratio varied significantly with altitude only in males, while leaf phosphorus content, leaf nitrogen content, and leaf carbon to phosphorus ratio varied significantly with altitude only in females. The correlation coefficients of most leaf traits of females with altitude were larger than that of males. In the relationship between leaf traits, there was a high similarity among males and females, but the altitude accounted for more explanation in females than in males. Our results suggested that the variation in leaf traits of T. fuana was small and did not dominate the interspecific competition in the local communities. Adaptation to the altitude gradient of T. fuana might be through altering nutrient storage processes and water use efficiency. Adaptation of male and female T. fuana to environmental changes showed differences, where the males were more tolerant and the females responded greatly to altitude. The differences in adaptation strategies between male and female T. fuana may be detrimental to the maintenance of their populations.
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Affiliation(s)
| | | | | | | | | | | | - Ming Dong
- *Correspondence: Yao-Bin Song, ; Ming Dong,
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4
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Wang F, Mi X, Chen L, Xu W, Durka W, Swenson NG, Johnson DJ, Worthy SJ, Xue J, Zhu Y, Schmid B, Liang Y, Ma K. Differential impacts of adult trees on offspring and non-offspring recruits in a subtropical forest. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1905-1913. [PMID: 36098896 DOI: 10.1007/s11427-021-2148-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
An important mechanism promoting species coexistence is conspecific negative density dependence (CNDD), which inhibits conspecific neighbors by accumulating host-specific enemies near adult trees. Natural enemies may be genotype-specific and regulate offspring dynamics more strongly than non-offspring, which is often neglected due to the difficulty in ascertaining genetic relatedness. Here, we investigated whether offspring and non-offspring of a dominant species, Castanopsis eyrei, suffered from different strength of CNDD based on parentage assignment in a subtropical forest. We found decreased recruitment efficiency (proxy of survival probability) of offspring compared with non-offspring near adult trees during the seedling-sapling transition, suggesting genotype-dependent interactions drive tree demographic dynamics. Furthermore, the genetic similarity between individuals of same cohort decreased in late life history stages, indicating genetic-relatedness-dependent tree mortality throughout ontogeny. Our results demonstrate that within-species genetic relatedness significantly affects the strength of CNDD, implying genotype-specific natural enemies may contribute to population dynamics in natural forests.
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Affiliation(s)
- Fang Wang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiangcheng Mi
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Lei Chen
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Wubing Xu
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103, Leipzig, Germany
| | - Walter Durka
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103, Leipzig, Germany
- Department Community Ecology, Centre for Environmental Research-UFZ, Theodor-Lieser-Str. 4, Halle, 06120, Germany
| | - Nathan G Swenson
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, 46556, USA
- University of Notre Dame Environmental Research Center, Land O'Lakes, Wisconsin, 54540, USA
| | - Daniel J Johnson
- School of Forest, Fisheries, and Geomatics Sciences, University of Florida, Gainesville, Florida, 32611, USA
| | - Samantha J Worthy
- Department of Biology, University of Maryland, College Park, Maryland, 20742, USA
| | - Jianhua Xue
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yan Zhu
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Bernhard Schmid
- Department of Geography, Remote Sensing Laboratories, University of Zürich, Zürich, CH-8006, Switzerland
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, 100085, China
| | - Yu Liang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Keping Ma
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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5
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Intraspecific competitive interactions rapidly evolve via spontaneous mutations. Evol Ecol 2022. [DOI: 10.1007/s10682-022-10205-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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6
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Holdridge EM, Vasseur DA. Intraspecific variation promotes coexistence under competition for essential resources. THEOR ECOL-NETH 2022. [DOI: 10.1007/s12080-022-00539-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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7
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Li QM, Cai CN, Xu WM, Cao M, Sha LQ, Lin LX, He TH. Adaptive genetic diversity of dominant species contributes to species co-existence and community assembly. PLANT DIVERSITY 2022; 44:271-278. [PMID: 35769594 PMCID: PMC9209874 DOI: 10.1016/j.pld.2021.11.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 10/28/2021] [Accepted: 11/05/2021] [Indexed: 06/15/2023]
Abstract
The synthesis of evolutionary biology and community ecology aims to understand how genetic variation within one species can shape community properties and how the ecological properties of a community can drive the evolution of a species. A rarely explored aspect is whether the interaction of genetic variation and community properties depends on the species' ecological role. Here we investigated the interactions among environmental factors, species diversity, and the within-species genetic diversity of species with different ecological roles. Using high-throughput DNA sequencing, we genotyped a canopy-dominant tree species, Parashorea chinensis, and an understory-abundant species, Pittosporopsis kerrii, from fifteen plots in Xishuangbanna tropical seasonal rainforest and estimated their adaptive, neutral and total genetic diversity; we also surveyed species diversity and assayed key soil nutrients. Structural equation modelling revealed that soil nitrogen availability created an opposing effect in species diversity and adaptive genetic diversity of the canopy-dominant Pa. chinensis. The increased adaptive genetic diversity of Pa. chinensis led to greater species diversity by promoting co-existence. Increased species diversity reduced the adaptive genetic diversity of the dominant understory species, Pi. kerrii, which was promoted by the adaptive genetic diversity of the canopy-dominant Pa. chinensis. However, such relationships were absent when neutral genetic diversity or total genetic diversity were used in the model. Our results demonstrated the important ecological interaction between adaptive genetic diversity and species diversity, but the pattern of the interaction depends on the identity of the species. Our results highlight the significant ecological role of dominant species in competitive interactions and regulation of community structure.
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Affiliation(s)
- Qiao-Ming Li
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China
- Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China
| | - Chao-Nan Cai
- School of Advanced Study, Taizhou University, Taizhou, 318000, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, 318000, Zhejiang, China
| | - Wu-Mei Xu
- School of Energy and Environment Science, Yunnan Normal University, Kunming, 650500, Yunnan, China
| | - Min Cao
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China
| | - Li-Qing Sha
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China
| | - Lu-Xiang Lin
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China
| | - Tian-Hua He
- School of Molecular and Life Sciences, Curtin University, PO Box U1987, Perth, WA, 6845, Australia
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8
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Gefei Z, Zhao W, Xiaofen W. The importance of facilitation on community assembly disappears under severe drought stress. Funct Ecol 2022. [DOI: 10.1111/1365-2435.14043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zhang Gefei
- Linze Inland River Basin Research Station Northwest Institute of Eco‐Environment and Resources Chinese Academy of Sciences CN‐730000 Lanzhou China
| | - Wenzhi Zhao
- Linze Inland River Basin Research Station Northwest Institute of Eco‐Environment and Resources Chinese Academy of Sciences CN‐730000 Lanzhou China
| | - Wang Xiaofen
- Prata cultural College Gansu Agricultural University CN‐730000 Lanzhou China
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9
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Bin Y, Li Y, Russo SE, Cao H, Ni Y, Ye W, Lian J. Leaf trait expression varies with tree size and ecological strategy in a subtropical forest. Funct Ecol 2022. [DOI: 10.1111/1365-2435.14003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Yue Bin
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems Guangdong Provincial Key Laboratory of Applied Botany South China Botanical Garden, Chinese Academy of Sciences Guangzhou 510650 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) Guangzhou 511458 China
| | - Yanpeng Li
- Forest Ecology Research Center Research Institute of Tropical Forestry Chinese Academy of Forestry Guangzhou 510520 USA
| | - Sabrina E. Russo
- School of Biological Sciences University of Nebraska Lincoln NE USA 68588‐0118
- Center for Plant Science Innovation University of Nebraska Lincoln NE USA 68588‐0660
| | - Honglin Cao
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems Guangdong Provincial Key Laboratory of Applied Botany South China Botanical Garden, Chinese Academy of Sciences Guangzhou 510650 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) Guangzhou 511458 China
| | - Yunlong Ni
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems Guangdong Provincial Key Laboratory of Applied Botany South China Botanical Garden, Chinese Academy of Sciences Guangzhou 510650 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) Guangzhou 511458 China
| | - Wanhui Ye
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems Guangdong Provincial Key Laboratory of Applied Botany South China Botanical Garden, Chinese Academy of Sciences Guangzhou 510650 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) Guangzhou 511458 China
| | - Juyu Lian
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems Guangdong Provincial Key Laboratory of Applied Botany South China Botanical Garden, Chinese Academy of Sciences Guangzhou 510650 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) Guangzhou 511458 China
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10
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Pélissier R, Violle C, Morel JB. Plant immunity: Good fences make good neighbors? CURRENT OPINION IN PLANT BIOLOGY 2021; 62:102045. [PMID: 33965754 DOI: 10.1016/j.pbi.2021.102045] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 03/24/2021] [Accepted: 03/28/2021] [Indexed: 06/12/2023]
Abstract
Plant immunity is modulated by several abiotic factors, and microbiome has emerged as a major biotic driver of plant resistance. Recently, a few studies showed that plants also modify resistance to pests and pathogens in their neighborhood. Several types of neighborhood could be identified depending on the biological processes at play: intraspecific and interspecific competition, kin and stranger recognition, plant-soil feedbacks, and danger signaling. This review highlights that molecules exchanged aboveground and belowground between plants can modulate plant immunity, either constitutively or after damage or attack. An intriguing relationship between allelopathy and immunity has been evidenced and should merit further investigation. Interestingly, most reported cases of modulation of immunity by the neighbors are positive, opening new perspectives for the understanding of natural plant communities as well as for the design of more diverse cultivated systems.
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Affiliation(s)
- Rémi Pélissier
- PHIM Plant Health Institute, CEFE, Univ Montpellier, Institut Agro, INRAE, CIRAD, TA A-54/K Campus International de Baillarguet, 34398, Montpellier Cedex 5, France
| | - Cyrille Violle
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry, Campus du CNRS, 1919, Route de Mende, 34293 Montpellier Cedex 5, France
| | - Jean-Benoit Morel
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, TA A-54 / K Campus International de Baillarguet, 34398, Montpellier Cedex 5, France.
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11
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Zaiats A, Germino MJ, Serpe MD, Richardson BA, Caughlin TT. Intraspecific variation mediates density dependence in a genetically diverse plant species. Ecology 2021; 102:e03502. [PMID: 34314039 DOI: 10.1002/ecy.3502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 05/06/2021] [Indexed: 11/06/2022]
Abstract
Interactions between neighboring plants are critical for biodiversity maintenance in plant populations and communities. Intraspecific trait variation and genome duplication are common in plant species and can drive eco-evolutionary dynamics through genotype-mediated plant-plant interactions. However, few studies have examined how species-wide intraspecific variation may alter interactions between neighboring plants. We investigate how subspecies and ploidy variation in a genetically diverse species, big sagebrush (Artemisia tridentata), can alter the demographic outcomes of plant interactions. Using a replicated, long-term common garden experiment that represents range-wide diversity of A. tridentata, we ask how intraspecific variation, environment, and stand age mediate neighbor effects on plant growth and survival. Spatially explicit models revealed that ploidy variation and subspecies identity can mediate plant-plant interactions but that the effect size varied in time and across experimental sites. We found that demographic impacts of neighbor effects were strongest during early stages of stand development and in sites with greater growth rates. Within subspecies, tetraploid populations showed greater tolerance to neighbor crowding compared to their diploid variants. Our findings provide evidence that intraspecific variation related to genome size and subspecies identity impacts spatial demography in a genetically diverse plant species. Accounting for intraspecific variation in studies of conspecific density dependence will improve our understanding of how local populations will respond to novel genotypes and biotic interaction regimes. As introduction of novel genotypes into local populations becomes more common, quantifying demographic processes in genetically diverse populations will help predict long-term consequences of plant-plant interactions.
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Affiliation(s)
- Andrii Zaiats
- Department of Biological Sciences, Boise State University, Boise, Idaho, 83725, USA
| | - Matthew J Germino
- U.S. Geological Survey, Forest and Rangeland Ecosystem Science Center, Boise, Idaho, 83706, USA
| | - Marcelo D Serpe
- Department of Biological Sciences, Boise State University, Boise, Idaho, 83725, USA
| | - Bryce A Richardson
- USDA Forest Service, Rocky Mountain Research Station, Moscow, Idaho, 83843, USA
| | - T Trevor Caughlin
- Department of Biological Sciences, Boise State University, Boise, Idaho, 83725, USA
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12
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Govaert L, Altermatt F, De Meester L, Leibold MA, McPeek MA, Pantel JH, Urban MC. Integrating fundamental processes to understand eco‐evolutionary community dynamics and patterns. Funct Ecol 2021. [DOI: 10.1111/1365-2435.13880] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Lynn Govaert
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland
- Department of Aquatic Ecology Eawag: Swiss Federal Institute of Aquatic Science and Technology Dübendorf Switzerland
- URPP Global Change and BiodiversityUniversity of Zurich Zurich Switzerland
- Leibniz Institut für Gewässerökologie und Binnenfischerei (IGB) Berlin Germany
| | - Florian Altermatt
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland
- Department of Aquatic Ecology Eawag: Swiss Federal Institute of Aquatic Science and Technology Dübendorf Switzerland
- URPP Global Change and BiodiversityUniversity of Zurich Zurich Switzerland
| | - Luc De Meester
- Leibniz Institut für Gewässerökologie und Binnenfischerei (IGB) Berlin Germany
- Laboratory of Aquatic Ecology, Evolution and Conservation KU Leuven Leuven Belgium
- Institute of Biology Freie Universität Berlin Berlin Germany
| | | | - Mark A. McPeek
- Department of Biological Sciences Dartmouth College Hanover NH USA
| | - Jelena H. Pantel
- Department of Computer Science, Mathematics, and Environmental Science The American University of Paris Paris France
| | - Mark C. Urban
- Center of Biological Risk and Department of Ecology and Evolutionary Biology University of Connecticut Storrs CT USA
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13
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Yu AO, Goldman EA, Brooks JT, Golomb BL, Yim IS, Gotcheva V, Angelov A, Kim EB, Marco ML. Strain diversity of plant-associated Lactiplantibacillus plantarum. Microb Biotechnol 2021; 14:1990-2008. [PMID: 34171185 PMCID: PMC8449665 DOI: 10.1111/1751-7915.13871] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 06/04/2021] [Accepted: 06/06/2021] [Indexed: 01/05/2023] Open
Abstract
Lactiplantibacillus plantarum (formerly Lactobacillus plantarum) is a lactic acid bacteria species found on plants that is essential for many plant food fermentations. In this study, we investigated the intraspecific phenotypic and genetic diversity of 13 L. plantarum strains isolated from different plant foods, including fermented olives and tomatoes, cactus fruit, teff injera, wheat boza and wheat sourdough starter. We found that strains from the same or similar plant food types frequently exhibited similar carbohydrate metabolism and stress tolerance responses. The isolates from acidic, brine‐containing ferments (olives and tomatoes) were more resistant to MRS adjusted to pH 3.5 or containing 4% w/v NaCl, than those recovered from grain fermentations. Strains from fermented olives grew robustly on raffinose as the sole carbon source and were better able to grow in the presence of ethanol (8% v/v or sequential exposure of 8% (v/v) and then 12% (v/v) ethanol) than most isolates from other plant types and the reference strain NCIMB8826R. Cell free culture supernatants from the olive‐associated strains were also more effective at inhibiting growth of an olive spoilage strain of Saccharomyces cerevisiae. Multi‐locus sequence typing and comparative genomics indicated that isolates from the same source tended to be genetically related. However, despite these similarities, other traits were highly variable between strains from the same plant source, including the capacity for biofilm formation and survival at pH 2 or 50°C. Genomic comparisons were unable to resolve strain differences, with the exception of the most phenotypically impaired and robust isolates, highlighting the importance of utilizing phenotypic studies to investigate differences between strains of L. plantarum. The findings show that L. plantarum is adapted for growth on specific plants or plant food types, but that intraspecific variation may be important for ecological fitness and strain coexistence within individual habitats.
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Affiliation(s)
- Annabelle O Yu
- Department of Food Science and Technology, University of California, Davis, Davis, CA, USA
| | - Elissa A Goldman
- Department of Food Science and Technology, University of California, Davis, Davis, CA, USA
| | - Jason T Brooks
- Department of Food Science and Technology, University of California, Davis, Davis, CA, USA
| | - Benjamin L Golomb
- Department of Food Science and Technology, University of California, Davis, Davis, CA, USA
| | - Irene S Yim
- Department of Food Science and Technology, University of California, Davis, Davis, CA, USA
| | - Velitchka Gotcheva
- Department of Biotechnology, University of Food Technologies, Plovdiv, Bulgaria
| | - Angel Angelov
- Department of Biotechnology, University of Food Technologies, Plovdiv, Bulgaria
| | - Eun Bae Kim
- Department of Applied Animal Science, Kangwon National University, Chuncheon, Gangwon-Do, South Korea
| | - Maria L Marco
- Department of Food Science and Technology, University of California, Davis, Davis, CA, USA
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14
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Roubeau Dumont E, Larue C, Michel HC, Gryta H, Liné C, Baqué D, Maria Gross E, Elger A. Genotypes of the aquatic plant Myriophyllum spicatum with different growth strategies show contrasting sensitivities to copper contamination. CHEMOSPHERE 2020; 245:125552. [PMID: 31846788 DOI: 10.1016/j.chemosphere.2019.125552] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 11/16/2019] [Accepted: 12/04/2019] [Indexed: 06/10/2023]
Abstract
Genotypic variability has been considered for years as a key attribute in species adaptation to new environments. It has been extensively studied in a context of chemical resistance, but remains poorly studied in response to chemical exposure in a context of global change. As aquatic ecosystems are particularly affected by environmental changes, we aimed to study how genotypic variability could inflect the sensitivity of aquatic plants to chemicals. Seven genotypes of Myriophyllum spicatum were exposed to three copper concentrations at 0, 0.15 and 0.5 mg/L. The sensitivity of the different genotypes was assessed through several endpoints such as relative growth rate (RGR) and morphological traits, as well as physiological markers, such as plant biomacromolecular composition. Our results showed that genotypes exhibited significant differences in their life-history traits in absence of chemical contamination. Some trait syndromes were observed, and three growth strategies were identified: (1) biomass production and main shoot elongation, (2) dry matter storage with denser whorls to promote resource conservation and (3) lateral shoot production. An up to eightfold difference in sensitivity for growth-related endpoints was observed among genotypes. Differences in sensitivity were partly attributed to morphological life-history traits. Our results confirm that genotypic variability can significantly affect M. spicatum sensitivity to Cu, and may influence the outcomes of laboratory testing based on the study of one single genotype. We recommend including genotypic variation as an assessment factor in ecological risk assessment and to study this source of variability more in depth as a possible driver of ecosystem resilience.
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Affiliation(s)
| | - Camille Larue
- EcoLab, Université de Toulouse, CNRS, Toulouse, France
| | - Hiram Castillo Michel
- Beamline ID21, ESRF-The European Synchrotron, CS40220, 38043, Grenoble Cedex 9, France
| | - Hervé Gryta
- Laboratoire Evolution & Diversité Biologique (EDB UMR 5174), Université de Toulouse, CNRS, IRD, UPS, 118 route de Narbonne, Bat 4R1, 31062, Toulouse, France
| | - Clarisse Liné
- EcoLab, Université de Toulouse, CNRS, Toulouse, France; CIRIMAT, UMR CNRS 5085/LCMI, Université Paul-Sabatier, F 31062, Toulouse Cedex 4, France
| | - David Baqué
- EcoLab, Université de Toulouse, CNRS, Toulouse, France
| | | | - Arnaud Elger
- EcoLab, Université de Toulouse, CNRS, Toulouse, France
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15
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Orellana JI, Valdivia CE. Putative local adaptations modulate the interactions of the carnivorous plant Drosera uniflora
Willd (1809) (Droseraceae) with cushion and shrub nurse plants. AUSTRAL ECOL 2019. [DOI: 10.1111/aec.12762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- José I. Orellana
- Laboratorio de Vida Silvestre; Departamento de Ciencias Biológicas y Biodiversidad; Universidad de Los Lagos; Avenida Fuchslocher 1305 Osorno Chile
- Programa de Doctorado en Ciencias, mención Conservación y Manejo de Recursos Naturales; Universidad de Los Lagos; Puerto Montt Chile
| | - Carlos E. Valdivia
- Laboratorio de Vida Silvestre; Departamento de Ciencias Biológicas y Biodiversidad; Universidad de Los Lagos; Avenida Fuchslocher 1305 Osorno Chile
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16
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Roubeau Dumont E, Larue C, Lorber S, Gryta H, Billoir E, Gross EM, Elger A. Does intraspecific variability matter in ecological risk assessment? Investigation of genotypic variations in three macrophyte species exposed to copper. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2019; 211:29-37. [PMID: 30913512 DOI: 10.1016/j.aquatox.2019.03.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 03/09/2019] [Accepted: 03/15/2019] [Indexed: 06/09/2023]
Abstract
To limit anthropogenic impact on ecosystems, regulations have been implemented along with global awareness that human activities are harmful to the environment. Ecological risk assessment (ERA) is the main procedure which allows to assess potential impacts of stressors on the environment as a result of human activities. ERA is typically implemented through different steps of laboratory testing. The approaches taken for ERA evolve along with scientific knowledge, to improve predictions on ecological risks for ecosystems. We here address the importance of intraspecific variability as a potential source of error in the laboratory evaluation of pollutants. To answer this question, three aquatic macrophyte species with different life-history traits but with their leaves directly in contact with the water were chosen; Lemna minor and Myriophyllum spicatum, two OECD model species, and Ceratophyllum demersum. For each species, three or four genotypes were exposed to 7-8 copper concentrations (up to 1.9 mg/L, 2 mg/L or 36 mg/L for C. demersum, L. minor and M. spicatum, respectively). To assess species sensitivity, growth-related endpoints such as Relative Growth Rate (RGR), based either on biomass production or on length/frond production, and chlorophyll fluorescence Fv/Fm, were measured. For each endpoint, the effective concentration 50% (EC50) was calculated. Almost all endpoints were affected by Cu exposure, except Fv/Fm of M. spicatum, and resulted in significant differences among genotypes for Cu sensitivity. Genotypes of L. minor exhibited up to 35% of variation in EC50 values based on Fv/Fm, showing differential sensivity among genotypes. Significant differences in EC50 values were found for RGR based on length for M. spicatum, with up to 72% of variation. Finally, C. demersum demonstrated significant sensitivity differences among genotypes with up to 78% variation for EC50 based on length. Overall, interspecific variation was higher than intraspecific variation, and explained 77% of the variation found among genotypes for RGR based on biomass, and 99% of the variation found for Fv/Fm. Our results highlight that depending on the endpoint, sensitivity can vary greatly within a species, and that pollutant- and species-specific endpoints should be considered in ERA.
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Affiliation(s)
| | - Camille Larue
- ECOLAB, Université de Toulouse, CNRS, INPT, UPS, France
| | - Sophie Lorber
- Toxalim, Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Hervé Gryta
- Laboratoire Evolution & Diversité Biologique (EDB UMR 5174), Université de Toulouse, CNRS, IRD, UPS, 118 route de Narbonne, Bat 4R1, 31062, Toulouse, France
| | - Elise Billoir
- LIEC, Université de Lorraine, CNRS, UMR 7360, Metz, Lorraine, France
| | | | - Arnaud Elger
- ECOLAB, Université de Toulouse, CNRS, INPT, UPS, France
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17
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Alexander JM, Levine JM. Earlier phenology of a nonnative plant increases impacts on native competitors. Proc Natl Acad Sci U S A 2019; 116:6199-6204. [PMID: 30850526 PMCID: PMC6442642 DOI: 10.1073/pnas.1820569116] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Adaptation to climate is expected to increase the performance of invasive species and their community-level impacts. However, while the fitness gains from adaptation should, in general, promote invader competitive ability, empirical demonstrations of this prediction are scarce. Furthermore, climate adaptation, in the form of altered timing of life cycle transitions, should affect the phenological overlap between nonnative and native competitors, with potentially large, but poorly tested, impacts on native species persistence. We evaluated these predictions by growing native California grassland plants in competition with nonnative Lactuca serriola, a species that flowers earlier in parts of its nonnative range that are drier than its putative European source region. In common garden experiments in southern California with L. serriola populations differing in phenology, plants originating from arid climates bolted up to 48 d earlier than plants from more mesic climates, and selection favored early flowering, supporting an adaptive basis for the phenology cline. The per capita competitive effects of L. serriola from early flowering populations on five early flowering native species were greater than the effects of L. serriola from later flowering populations. Consequently, the ability of the native species to increase when rare in competition with L. serriola, as inferred from field-parameterized competition models, declined with earlier L. serriola phenology. Indeed, changes to L. serriola phenology affected whether or not one native species was predicted to persist in competition with L. serriola Our results suggest that evolution in response to new climatic conditions can have important consequences for species interactions, and enhance the impacts of biological invasions on natural communities.
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Affiliation(s)
- Jake M Alexander
- Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland
| | - Jonathan M Levine
- Institute of Integrative Biology, ETH Zurich, 8092 Zurich, Switzerland
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18
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Ehlers BK, Bilde T. Inclusive fitness, asymmetric competition and kin selection in plants. OIKOS 2019. [DOI: 10.1111/oik.06390] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Bodil K. Ehlers
- Section for Plant and Insect Ecology, Dept of Bioscience, Aarhus Univ Vejlsøvej 25, DK‐8600 Silkeborg Denmark
| | - Trine Bilde
- Section for Genetics and Evolution, Dept of Bioscience, Aarhus Univ Århus Denmark
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19
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Peters K, Gorzolka K, Bruelheide H, Neumann S. Seasonal variation of secondary metabolites in nine different bryophytes. Ecol Evol 2018; 8:9105-9117. [PMID: 30271570 PMCID: PMC6157681 DOI: 10.1002/ece3.4361] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 06/12/2018] [Accepted: 06/22/2018] [Indexed: 12/27/2022] Open
Abstract
Bryophytes occur in almost all land ecosystems and contribute to global biogeochemical cycles, ecosystem functioning, and influence vegetation dynamics. As growth and biochemistry of bryophytes are strongly dependent on the season, we analyzed metabolic variation across seasons with regard to ecological characteristics and phylogeny. Using bioinformatics methods, we present an integrative and reproducible approach to connect ecology with biochemistry. Nine different bryophyte species were collected in three composite samples in four seasons. Untargeted liquid chromatography coupled with mass spectrometry (LC/MS) was performed to obtain metabolite profiles. Redundancy analysis, Pearson's correlation, Shannon diversity, and hierarchical clustering were used to determine relationships among species, seasons, ecological characteristics, and hierarchical clustering. Metabolite profiles of Marchantia polymorpha and Fissidens taxifolius which are species with ruderal life strategy (R-selected) showed low seasonal variability, while the profiles of the pleurocarpous mosses and Grimmia pulvinata which have characteristics of a competitive strategy (C-selected) were more variable. Polytrichum strictum and Plagiomnium undulatum had intermediary life strategies. Our study revealed strong species-specific differences in metabolite profiles between the seasons. Life strategies, growth forms, and indicator values for light and soil were among the most important ecological predictors. We demonstrate that untargeted Eco-Metabolomics provide useful biochemical insight that improves our understanding of fundamental ecological strategies.
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Affiliation(s)
- Kristian Peters
- Leibniz Institute of Plant Biochemistry, Stress and Developmental BiologyHalleGermany
| | - Karin Gorzolka
- Leibniz Institute of Plant Biochemistry, Stress and Developmental BiologyHalleGermany
| | - Helge Bruelheide
- Institute of Biology/Geobotany and Botanical GardenMartin Luther University Halle WittenbergHalleGermany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
| | - Steffen Neumann
- Leibniz Institute of Plant Biochemistry, Stress and Developmental BiologyHalleGermany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
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20
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Browne L, Karubian J. Rare genotype advantage promotes survival and genetic diversity of a tropical palm. THE NEW PHYTOLOGIST 2018; 218:1658-1667. [PMID: 29603256 DOI: 10.1111/nph.15107] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 02/13/2018] [Indexed: 06/08/2023]
Abstract
Negative density dependence, where survival decreases as density increases, is a well-established driver of species diversity at the community level, but the degree to which a similar process might act on the density or frequency of genotypes within a single plant species to maintain genetic diversity has not been well studied in natural systems. In this study, we determined the maternal genotype of naturally dispersed seeds of the palm Oenocarpus bataua within a tropical forest in northwest Ecuador, tracked the recruitment of each seed, and assessed the role of individual-level genotypic rarity on survival. We demonstrate that negative frequency-dependent selection within this species conferred a survival advantage to rare maternal genotypes and promoted population-level genetic diversity. The strength of the observed rare genotype survival advantage was comparable to the effect of conspecific density regardless of genotype. These findings corroborate an earlier, experimental study and implicate negative frequency-dependent selection of genotypes as an important, but currently underappreciated, determinant of plant recruitment and within-species genetic diversity. Incorporating intraspecific genetic variation into studies and theory of forest dynamics may improve our ability to understand and manage forests, and the processes that maintain their diversity.
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Affiliation(s)
- Luke Browne
- Department of Ecology and Evolutionary Biology, Tulane University, 400 Lindy Boggs, New Orleans, LA, 70118, USA
- Foundation for the Conservation of the Tropical Andes, Quito, Ecuador
- UCLA La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Jordan Karubian
- Department of Ecology and Evolutionary Biology, Tulane University, 400 Lindy Boggs, New Orleans, LA, 70118, USA
- Foundation for the Conservation of the Tropical Andes, Quito, Ecuador
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21
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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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22
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Jiang X, Michalet R, Chen S, Zhao L, Wang X, Wang C, An L, Xiao S. Phenotypic effects of the nurseThylacospermum caespitosumon dependent plant species along regional climate stress gradients. OIKOS 2017. [DOI: 10.1111/oik.04512] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xingpei Jiang
- State Key Laboratory of Grassland and Agro-ecosystems, School of Life Sciences, Lanzhou Univ., 222 Tianshuinan Road; CN-730000 Lanzhou PR China
| | - Richard Michalet
- Univ. of Bordeaux, U.M.R. CNRS, Allée Geoffroy Saint-Hilaire; Pessac France
| | - Shuyan Chen
- Ministry of Education Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Chongqing Univ.; Chongqing PR China
| | - Liang Zhao
- Ministry of Education Key Laboratory of Three Gorges Reservoir Region's Eco-Environment, Chongqing Univ.; Chongqing PR China
| | - Xiangtai Wang
- State Key Laboratory of Grassland and Agro-ecosystems, School of Life Sciences, Lanzhou Univ., 222 Tianshuinan Road; CN-730000 Lanzhou PR China
| | - Chenyue Wang
- State Key Laboratory of Grassland and Agro-ecosystems, School of Life Sciences, Lanzhou Univ., 222 Tianshuinan Road; CN-730000 Lanzhou PR China
| | - Lizhe An
- State Key Laboratory of Grassland and Agro-ecosystems, School of Life Sciences, Lanzhou Univ., 222 Tianshuinan Road; CN-730000 Lanzhou PR China
| | - Sa Xiao
- State Key Laboratory of Grassland and Agro-ecosystems, School of Life Sciences, Lanzhou Univ., 222 Tianshuinan Road; CN-730000 Lanzhou PR China
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23
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Lamy T, Laroche F, David P, Massol F, Jarne P. The contribution of species-genetic diversity correlations to the understanding of community assembly rules. OIKOS 2017. [DOI: 10.1111/oik.03997] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Thomas Lamy
- Dépt de sciences biologiques; Univ. de Montréal; C.P. 6128, Succursale Centre-ville, Montréal, QC, H3C 3J7, Canada, and: Marine Science Inst., Univ. of California Santa Barbara CA USA
| | - Fabien Laroche
- Centre d'Ecologie Fonctionnelle et Evolutive, CNRS - Univ. de Montpellier - Univ. P. Valéry Montpellier - EPHE, Montpellier 5, France. FL also at: AgroParisTech, Paris, France, and: Irstea, Domaine des Barres; Nogent sur Vernisson France
| | - Patrice David
- Centre d'Ecologie Fonctionnelle et Evolutive, CNRS - Univ. de Montpellier - Univ. P. Valéry Montpellier - EPHE, Montpellier 5, France. FL also at: AgroParisTech, Paris, France, and: Irstea, Domaine des Barres; Nogent sur Vernisson France
| | | | - Philippe Jarne
- Centre d'Ecologie Fonctionnelle et Evolutive, CNRS - Univ. de Montpellier - Univ. P. Valéry Montpellier - EPHE, Montpellier 5, France. FL also at: AgroParisTech, Paris, France, and: Irstea, Domaine des Barres; Nogent sur Vernisson France
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Michalet R, Maalouf JP, Hayek PA. Direct litter interference and indirect soil competitive effects of two contrasting phenotypes of a spiny legume shrub drive the forb composition of an oromediterranean community. OIKOS 2017. [DOI: 10.1111/oik.03800] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Richard Michalet
- Univ. of Bordeaux, UMR CNRS 5805 EPOC, avenue Geoffroy Saint-Hilaire, FR-33615 Pessac Cedex; France
| | | | - Patrick Al Hayek
- Univ. of Bordeaux, UMR CNRS 5805 EPOC, avenue Geoffroy Saint-Hilaire, FR-33615 Pessac Cedex; France
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25
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Grady KC, Wood TE, Kolb TE, Hersch-Green E, Shuster SM, Gehring CA, Hart SC, Allan GJ, Whitham TG. Local biotic adaptation of trees and shrubs to plant neighbors. OIKOS 2016. [DOI: 10.1111/oik.03240] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Kevin C. Grady
- School of Forestry; Northern Arizona University; Flagstaff AZ 86011 USA
| | - Troy E. Wood
- US Geological Survey; Southwest Biological Science Center; Flagstaff AZ 86011 USA
| | - Thomas E. Kolb
- School of Forestry; Northern Arizona University; Flagstaff AZ 86011 USA
| | - Erika Hersch-Green
- Dept of Biological Sciences; Michigan Technological University; Houghton MI USA
| | - Stephen M. Shuster
- Dept of Biological Sciences; Northern Arizona University; Flagstaff AZ USA
| | | | - Stephen C. Hart
- Life and Environmental Sciences Dept; Univ. of California; Merced CA USA
| | - Gerard J. Allan
- Dept of Biological Sciences; Northern Arizona University; Flagstaff AZ USA
| | - Thomas G. Whitham
- Dept of Biological Sciences; Northern Arizona University; Flagstaff AZ USA
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26
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Tree species, tree genotypes and tree genotypic diversity levels affect microbe-mediated soil ecosystem functions in a subtropical forest. Sci Rep 2016; 6:36672. [PMID: 27857198 PMCID: PMC5114573 DOI: 10.1038/srep36672] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 10/18/2016] [Indexed: 11/29/2022] Open
Abstract
Tree species identity and tree genotypes contribute to the shaping of soil microbial communities. However, knowledge about how these two factors influence soil ecosystem functions is still lacking. Furthermore, in forest ecosystems tree genotypes co-occur and interact with each other, thus the effects of tree genotypic diversity on soil ecosystem functions merit attention. Here we investigated the effects of tree species, tree genotypes and genotypic diversity levels, alongside soil physicochemical properties, on the overall and specific soil enzyme activity patterns. Our results indicate that tree species identity, tree genotypes and genotypic diversity level have significant influences on overall and specific soil enzyme activity patterns. These three factors influence soil enzyme patterns partly through effects on soil physicochemical properties and substrate quality. Variance partitioning showed that tree species identity, genotypic diversity level, pH and water content all together explained ~30% variations in the overall patterns of soil enzymes. However, we also found that the responses of soil ecosystem functions to tree genotypes and genotypic diversity are complex, being dependent on tree species identity and controlled by multiple factors. Our study highlights the important of inter- and intra-specific variations in tree species in shaping soil ecosystem functions in a subtropical forest.
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27
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Browne L, Karubian J. Frequency‐dependent selection for rare genotypes promotes genetic diversity of a tropical palm. Ecol Lett 2016; 19:1439-1447. [DOI: 10.1111/ele.12692] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 06/02/2016] [Accepted: 09/08/2016] [Indexed: 01/17/2023]
Affiliation(s)
- Luke Browne
- Department of Ecology and Evolutionary Biology Tulane University New Orleans Louisiana
- Foundation for the Conservation of the Tropical Andes Quito Ecuador
| | - Jordan Karubian
- Department of Ecology and Evolutionary Biology Tulane University New Orleans Louisiana
- Foundation for the Conservation of the Tropical Andes Quito Ecuador
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