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Cusack DF, Christoffersen B, Smith-Martin CM, Andersen KM, Cordeiro AL, Fleischer K, Wright SJ, Guerrero-Ramírez NR, Lugli LF, McCulloch LA, Sanchez-Julia M, Batterman SA, Dallstream C, Fortunel C, Toro L, Fuchslueger L, Wong MY, Yaffar D, Fisher JB, Arnaud M, Dietterich LH, Addo-Danso SD, Valverde-Barrantes OJ, Weemstra M, Ng JC, Norby RJ. Toward a coordinated understanding of hydro-biogeochemical root functions in tropical forests for application in vegetation models. New Phytol 2024; 242:351-371. [PMID: 38416367 DOI: 10.1111/nph.19561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 01/10/2024] [Indexed: 02/29/2024]
Abstract
Tropical forest root characteristics and resource acquisition strategies are underrepresented in vegetation and global models, hampering the prediction of forest-climate feedbacks for these carbon-rich ecosystems. Lowland tropical forests often have globally unique combinations of high taxonomic and functional biodiversity, rainfall seasonality, and strongly weathered infertile soils, giving rise to distinct patterns in root traits and functions compared with higher latitude ecosystems. We provide a roadmap for integrating recent advances in our understanding of tropical forest belowground function into vegetation models, focusing on water and nutrient acquisition. We offer comparisons of recent advances in empirical and model understanding of root characteristics that represent important functional processes in tropical forests. We focus on: (1) fine-root strategies for soil resource exploration, (2) coupling and trade-offs in fine-root water vs nutrient acquisition, and (3) aboveground-belowground linkages in plant resource acquisition and use. We suggest avenues for representing these extremely diverse plant communities in computationally manageable and ecologically meaningful groups in models for linked aboveground-belowground hydro-nutrient functions. Tropical forests are undergoing warming, shifting rainfall regimes, and exacerbation of soil nutrient scarcity caused by elevated atmospheric CO2. The accurate model representation of tropical forest functions is crucial for understanding the interactions of this biome with the climate.
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Affiliation(s)
- Daniela F Cusack
- Department of Ecosystem Science and Sustainability, Warner College of Natural Resources, Colorado State University, 1231 Libbie Coy Way, A104, Fort Collins, CO, 80523-1476, USA
- Smithsonian Tropical Research Institute, Apartado, Balboa, 0843-03092, Panama
| | - Bradley Christoffersen
- School of Integrative Biological and Chemical Sciences, The University of Texas Rio Grande Valley, Edinburg, TX, 78539, USA
| | - Chris M Smith-Martin
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, 55108, USA
| | | | - Amanda L Cordeiro
- Department of Ecosystem Science and Sustainability, Warner College of Natural Resources, Colorado State University, 1231 Libbie Coy Way, A104, Fort Collins, CO, 80523-1476, USA
- Smithsonian Tropical Research Institute, Apartado, Balboa, 0843-03092, Panama
| | - Katrin Fleischer
- Department Biogeochemical Signals, Max-Planck-Institute for Biogeochemistry, Hans-Knöll-Straße 10, Jena, 07745, Germany
| | - S Joseph Wright
- Smithsonian Tropical Research Institute, Apartado, Balboa, 0843-03092, Panama
| | - Nathaly R Guerrero-Ramírez
- Silviculture and Forest Ecology of Temperate Zones, Faculty of Forest Sciences and Forest Ecology, University of Göttingen, Gottingen, 37077, Germany
- Centre of Biodiversity and Sustainable Land Use (CBL), University of Göttingen, Gottingen, 37077, Germany
| | - Laynara F Lugli
- School of Life Sciences, Technical University of Munich, Freising, 85354, Germany
| | - Lindsay A McCulloch
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St., Cambridge, MA, 02138, USA
- National Center for Atmospheric Research, National Oceanographic and Atmospheric Agency, 1850 Table Mesa Dr., Boulder, CO, 80305, USA
| | - Mareli Sanchez-Julia
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, 70118, USA
| | - Sarah A Batterman
- Smithsonian Tropical Research Institute, Apartado, Balboa, 0843-03092, Panama
- Cary Institute of Ecosystem Studies, Millbrook, NY, 12545, USA
- School of Geography, University of Leeds, Leeds, LS2 9JT, UK
| | - Caroline Dallstream
- Department of Biology, McGill University, 1205 Av. du Docteur-Penfield, Montreal, QC, H3A 1B1, Canada
| | - Claire Fortunel
- AMAP (Botanique et Modélisation de l'Architecture des Plantes et des Végétations), Université de Montpellier, CIRAD, CNRS, INRAE, IRD, Montpellier, 34398, France
| | - Laura Toro
- Yale Applied Science Synthesis Program, The Forest School at the Yale School of the Environment, Yale University, New Haven, CT, 06511, USA
| | - Lucia Fuchslueger
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, 1030, Austria
| | - Michelle Y Wong
- Cary Institute of Ecosystem Studies, Millbrook, NY, 12545, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06511, USA
| | - Daniela Yaffar
- Functional Forest Ecology, Universität Hamburg, Barsbüttel, 22885, Germany
| | - Joshua B Fisher
- Schmid College of Science and Technology, Chapman University, 1 University Drive, Orange, CA, 92866, USA
| | - Marie Arnaud
- Institute of Ecology and Environmental Sciences (IEES), UMR 7618, CNRS-Sorbonne University-INRAE-UPEC-IRD, Paris, 75005, France
- School of Geography, Earth and Environmental Sciences & BIFOR, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Lee H Dietterich
- Department of Ecosystem Science and Sustainability, Warner College of Natural Resources, Colorado State University, 1231 Libbie Coy Way, A104, Fort Collins, CO, 80523-1476, USA
- U.S. Army Engineer Research and Development Center, Environmental Laboratory, Vicksburg, MS, 39180, USA
- Department of Biology, Haverford College, Haverford, PA, 19003, USA
| | - Shalom D Addo-Danso
- Forests and Climate Change Division, CSIR-Forestry Research Institute of Ghana, P.O Box UP 63 KNUST, Kumasi, Ghana
| | - Oscar J Valverde-Barrantes
- Department of Biological Sciences, International Center for Tropical Biodiversity, Florida International University, Miami, FL, 33199, USA
| | - Monique Weemstra
- Department of Biological Sciences, International Center for Tropical Biodiversity, Florida International University, Miami, FL, 33199, USA
| | - Jing Cheng Ng
- Nanyang Technological University, Singapore, 639798, Singapore
| | - Richard J Norby
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, 37996, USA
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Luo W, Wang Y, Cahill JF, Luan F, Zhong Y, Li Y, Li B, Chu C. Root-centric β diversity reveals functional homogeneity while phylogenetic heterogeneity in a subtropical forest. Ecology 2024; 105:e4189. [PMID: 37877169 DOI: 10.1002/ecy.4189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 08/25/2023] [Indexed: 10/26/2023]
Abstract
Root-centric studies have revealed fast taxonomic turnover across root neighborhoods, but how such turnover is accompanied by changes in species functions and phylogeny (i.e., β diversity) remains largely unknown. As β diversity can reflect the degree of community-wide biotic homogenization, such information is crucial for better inference of below-ground assembly rules, community structuring, and ecosystem processes. We collected 2480 root segments from 625 0-30 cm soil profiles in a subtropical forest in China. Root segments were identified into 138 species with DNA-barcoding with six root morphological and architectural traits measured per species. By using the mean pairwise (Dpw ) and mean nearest neighbor distance (Dnn ) to quantify species ecological differences, we first tested the non-random functional and phylogenetic turnover of root neighborhoods that would lend more support to deterministic over stochastic community assembly processes. Additionally, we examined the distance-decay pattern of β diversity, and finally partitioned β diversity into geographical and environmental components to infer their potential drivers of environmental filtering, dispersal limitation, and biotic interactions. We found that functional turnover was often lower than expected given the taxonomic turnover, whereas phylogenetic turnover was often higher than expected. Phylogenetic Dpw (e.g., interfamily species) turnover exhibited a distance-decay pattern, likely reflecting limited dispersal or abiotic filtering that leads to the spatial aggregation of specific plant lineages. Conversely, both functional and phylogenetic Dnn (e.g., intrageneric species) exhibited an inverted distance-decay pattern, likely reflecting strong biotic interactions among spatially and phylogenetically close species leading to phylogenetic and functional divergence. While the spatial distance was generally a better predictor of β diversity than environmental distance, the joint effect of environmental and spatial distance usually overrode their respective pure effects. These findings suggest that root neighborhood functional homogeneity may somewhat increase forest resilience after disturbance by exhibiting an insurance effect. Likewise, root neighborhood phylogenetic heterogeneity may enhance plant fitness by hindering the transmission of host-specific pathogens through root networks or by promoting interspecific niche complementarity not captured by species functions. Our study highlights the potential role of root-centric β diversity in mediating community structures and functions largely ignored in previous studies.
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Affiliation(s)
- Wenqi Luo
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Youshi Wang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - James F Cahill
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Fucheng Luan
- Guangdong Chebaling National Nature Reserve, Shaoguan, China
| | - Yonglin Zhong
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yuanzhi Li
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Buhang Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Chengjin Chu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, China
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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López-Angulo J, Matesanz S, Illuminati A, Pescador DS, Sánchez AM, Pías B, Chacón-Labella J, de la Cruz M, Escudero A. Ecological drivers of fine-scale distribution of arbuscular mycorrhizal fungi in a semiarid Mediterranean scrubland. Ann Bot 2023; 131:1107-1119. [PMID: 36976581 PMCID: PMC10457037 DOI: 10.1093/aob/mcad050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 03/27/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND AND AIMS Arbuscular mycorrhizal (AM) fungi enhance the uptake of water and minerals by the plant hosts, alleviating plant stress. Therefore, AM fungal-plant interactions are particularly important in drylands and other stressful ecosystems. We aimed to determine the combined and independent effects of above- and below-ground plant community attributes (i.e. diversity and composition), soil heterogeneity and spatial covariates on the spatial structure of the AM fungal communities in a semiarid Mediterranean scrubland. Furthermore, we evaluated how the phylogenetic relatedness of both plants and AM fungi shapes these symbiotic relationships. METHODS We characterized the composition and diversity of AM fungal and plant communities in a dry Mediterranean scrubland taxonomically and phylogenetically, using DNA metabarcoding and a spatially explicit sampling design at the plant neighbourhood scale. KEY RESULTS The above- and below-ground plant community attributes, soil physicochemical properties and spatial variables explained unique fractions of AM fungal diversity and composition. Mainly, variations in plant composition affected the AM fungal composition and diversity. Our results also showed that particular AM fungal taxa tended to be associated with closely related plant species, suggesting the existence of a phylogenetic signal. Although soil texture, fertility and pH affected AM fungal community assembly, spatial factors had a greater influence on AM fungal community composition and diversity than soil physicochemical properties. CONCLUSIONS Our results highlight that the more easily accessible above-ground vegetation is a reliable indicator of the linkages between plant roots and AM fungi. We also emphasize the importance of soil physicochemical properties in addition to below-ground plant information, while accounting for the phylogenetic relationships of both plants and fungi, because these factors improve our ability to predict the relationships between AM fungal and plant communities.
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Affiliation(s)
- Jesús López-Angulo
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, 28933, Móstoles, Madrid, Spain
- Department of Environmental Systems Science, Swiss Federal Institute of Technology Zurich (ETH), 8092 Zurich, Switzerland
| | - Silvia Matesanz
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, 28933, Móstoles, Madrid, Spain
| | - Angela Illuminati
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, 28933, Móstoles, Madrid, Spain
| | - David S Pescador
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, 28933, Móstoles, Madrid, Spain
- Departamento de Farmacología, Farmacognosia y Botánica, Facultad de Farmacia, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Ana M Sánchez
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, 28933, Móstoles, Madrid, Spain
| | - Beatriz Pías
- Departamento de Biodiversidad, Ecología y Evolución, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | | | - Marcelino de la Cruz
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, 28933, Móstoles, Madrid, Spain
| | - Adrián Escudero
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, 28933, Móstoles, Madrid, Spain
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Jones A. Molecular identification and mapping of mixed root samples to species and individuals. New Phytol 2023; 238:924-925. [PMID: 36906881 DOI: 10.1111/nph.18817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Affiliation(s)
- Andy Jones
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97330, USA
- Smithsonian Tropical Research Institute, Apartado Postal 0843-03092, Panamá, Panamá
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Osborne OG, Dobreva MP, Papadopulos AST, de Moura MSB, Brunello AT, de Queiroz LP, Pennington RT, Lloyd J, Savolainen V. Mapping the root systems of individual trees in a natural community using genotyping-by-sequencing. New Phytol 2023; 238:1305-1317. [PMID: 36444527 DOI: 10.1111/nph.18645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 11/11/2022] [Indexed: 06/16/2023]
Abstract
The architecture of root systems is an important driver of plant fitness, competition and ecosystem processes. However, the methodological difficulty of mapping roots hampers the study of these processes. Existing approaches to match individual plants to belowground samples are low throughput and species specific. Here, we developed a scalable sequencing-based method to map the root systems of individual trees across multiple species. We successfully applied it to a tropical dry forest community in the Brazilian Caatinga containing 14 species. We sequenced all 42 individual shrubs and trees in a 14 × 14 m plot using double-digest restriction site-associated sequencing (ddRADseq). We identified species-specific markers and individual-specific haplotypes from the data. We matched these markers to the ddRADseq data from 100 mixed root samples from across the centre (10 × 10 m) of the plot at four different depths using a newly developed R package. We identified individual root samples for all species and all but one individual. There was a strong significant correlation between belowground and aboveground size measurements, and we also detected significant species-level root-depth preference for two species. The method is more scalable and less labour intensive than the current techniques and is broadly applicable to ecology, forestry and agricultural biology.
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Affiliation(s)
- Owen G Osborne
- Department of Life Sciences, Georgina Mace Centre for the Living Planet, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, SL5 7PY, UK
- Molecular Ecology and Evolution Bangor, School of Natural Sciences, Bangor University, Environment Centre Wales, Deiniol Road, Bangor, LL57 2UW, UK
| | - Mariya P Dobreva
- Department of Life Sciences, Georgina Mace Centre for the Living Planet, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, SL5 7PY, UK
| | - Alexander S T Papadopulos
- Molecular Ecology and Evolution Bangor, School of Natural Sciences, Bangor University, Environment Centre Wales, Deiniol Road, Bangor, LL57 2UW, UK
| | - Magna S B de Moura
- Empresa Brasileira de Pesquisa Agropecuária, 56302-970, Petrolina, PE, Brazil
| | - Alexandre T Brunello
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes, 3900, Monte Alegre, 14040-901, Ribeirão Preto, SP, Brazil
| | - Luciano P de Queiroz
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Av. Transnordestina s.n., Novo Horizonte, 44036-900, Feira de Santana, BA, Brazil
| | - R Toby Pennington
- Geography, University of Exeter, Amory Building, Rennes Drive, Exeter, EX4 4RJ, UK
- Royal Botanic Garden Edinburgh, 20a Inverleith Row, Edinburgh, EH3 5LR, UK
| | - Jon Lloyd
- Department of Life Sciences, Georgina Mace Centre for the Living Planet, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, SL5 7PY, UK
- School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA, 6009, Australia
| | - Vincent Savolainen
- Department of Life Sciences, Georgina Mace Centre for the Living Planet, Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, SL5 7PY, UK
- Royal Botanic Gardens, Kew, Richmond, TW9 3AB, UK
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Affiliation(s)
- Pramod Kumar
- National Institute of Cancer Prevention and Research Indian Council for Medical Research (ICMR‐NICPR) Noida India
| | - Alka Rani
- National Institute of Cancer Prevention and Research Indian Council for Medical Research (ICMR‐NICPR) Noida India
| | - Shalini Singh
- National Institute of Cancer Prevention and Research Indian Council for Medical Research (ICMR‐NICPR) Noida India
| | - Anuj Kumar
- National Institute of Cancer Prevention and Research Indian Council for Medical Research (ICMR‐NICPR) Noida India
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Palmer CM, Wershoven NL, Martinson SJ, ter Hofstede HM, Kress WJ, Symes LB. Patterns of Herbivory in Neotropical Forest Katydids as Revealed by DNA Barcoding of Digestive Tract Contents. Diversity (Basel) 2022; 14. [PMID: 35369669 PMCID: PMC8974511 DOI: 10.3390/d14020152] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Many well-studied animal species use conspicuous, repetitive signals that attract both mates and predators. Orthopterans (crickets, katydids, and grasshoppers) are renowned for their acoustic signals. In Neotropical forests, however, many katydid species produce extremely short signals, totaling only a few seconds of sound per night, likely in response to predation by acoustically orienting predators. The rare signals of these katydid species raises the question of how they find conspecific mates in a structurally complex rainforest. While acoustic mechanisms, such as duetting, likely facilitate mate finding, we test the hypothesis that mate finding is further facilitated by colocalization on particular host plant species. DNA barcoding allows us to identify recently consumed plants from katydid stomach contents. We use DNA barcoding to test the prediction that katydids of the same species will have closely related plant species in their stomach. We do not find evidence for dietary specialization. Instead, katydids consumed a wide mix of plants within and across the flowering plants (27 species in 22 genera, 16 families, and 12 orders) with particular representation in the orders Fabales and Laurales. Some evidence indicates that katydids may gather on plants during a narrow window of rapid leaf out, but additional investigations are required to determine whether katydid mate finding is facilitated by gathering at transient food resources.
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Affiliation(s)
- Christine M. Palmer
- Natural Sciences Department, Castleton University, 233 South Street, Castleton, VT 05735, USA
- Correspondence:
| | - Nicole L. Wershoven
- Natural Sciences Department, Castleton University, 233 South Street, Castleton, VT 05735, USA
| | - Sharon J. Martinson
- Department of Biological Sciences, Dartmouth College, 78 College Street, Hanover, NH 03755, USA
- Smithsonian Tropical Research Institute, Balboa, Ancón, Apartado 0843-03092, Panama
- K. Lisa Yang Center for Conservation Bioacoustics, Cornell Lab of Ornithology, Cornell University, 159 Sapsucker Woods Road, Ithaca, NY 14850, USA
| | - Hannah M. ter Hofstede
- Department of Biological Sciences, Dartmouth College, 78 College Street, Hanover, NH 03755, USA
- Smithsonian Tropical Research Institute, Balboa, Ancón, Apartado 0843-03092, Panama
- Graduate Program in Ecology, Evolution, Environment and Society, Dartmouth College, 64 College Street, Suite 102, Hanover, NH 03755, USA
| | - W. John Kress
- Department of Biological Sciences, Dartmouth College, 78 College Street, Hanover, NH 03755, USA
- Department of Botany, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, Washington, DC 20013, USA
| | - Laurel B. Symes
- Department of Biological Sciences, Dartmouth College, 78 College Street, Hanover, NH 03755, USA
- Smithsonian Tropical Research Institute, Balboa, Ancón, Apartado 0843-03092, Panama
- K. Lisa Yang Center for Conservation Bioacoustics, Cornell Lab of Ornithology, Cornell University, 159 Sapsucker Woods Road, Ithaca, NY 14850, USA
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Ahmed S, Ibrahim M, Nantasenamat C, Nisar MF, Malik AA, Waheed R, Ahmed MZ, Ojha SC, Alam MK, Khan S. Pragmatic Applications and Universality of DNA Barcoding for Substantial Organisms at Species Level: A Review to Explore a Way Forward. BioMed Research International 2022; 2022:1-19. [PMID: 35059459 PMCID: PMC8766189 DOI: 10.1155/2022/1846485] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/06/2021] [Indexed: 01/04/2023]
Abstract
DNA barcodes are regarded as hereditary succession codes that serve as a recognition marker to address several queries relating to the identification, classification, community ecology, and evolution of certain functional traits in organisms. The mitochondrial cytochrome c oxidase 1 (CO1) gene as a DNA barcode is highly efficient for discriminating vertebrate and invertebrate animal species. Similarly, different specific markers are used for other organisms, including ribulose bisphosphate carboxylase (rbcL), maturase kinase (matK), transfer RNA-H and photosystem II D1-ApbsArabidopsis thaliana (trnH-psbA), and internal transcribed spacer (ITS) for plant species; 16S ribosomal RNA (16S rRNA), elongation factor Tu gene (Tuf gene), and chaperonin for bacterial strains; and nuclear ITS for fungal strains. Nevertheless, the taxon coverage of reference sequences is far from complete for genus or species-level identification. Applying the next-generation sequencing approach to the parallel acquisition of DNA barcode sequences could greatly expand the potential for library preparation or accurate identification in biodiversity research. Overall, this review articulates on the DNA barcoding technology as applied to different organisms, its universality, applicability, and innovative approach to handling DNA-based species identification.
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Freschet GT, Pagès L, Iversen CM, Comas LH, Rewald B, Roumet C, Klimešová J, Zadworny M, Poorter H, Postma JA, Adams TS, Bagniewska‐Zadworna A, Bengough AG, Blancaflor EB, Brunner I, Cornelissen JHC, Garnier E, Gessler A, Hobbie SE, Meier IC, Mommer L, Picon‐Cochard C, Rose L, Ryser P, Scherer‐Lorenzen M, Soudzilovskaia NA, Stokes A, Sun T, Valverde‐Barrantes OJ, Weemstra M, Weigelt A, Wurzburger N, York LM, Batterman SA, Gomes de Moraes M, Janeček Š, Lambers H, Salmon V, Tharayil N, McCormack ML. A starting guide to root ecology: strengthening ecological concepts and standardising root classification, sampling, processing and trait measurements. New Phytol 2021; 232:973-1122. [PMID: 34608637 PMCID: PMC8518129 DOI: 10.1111/nph.17572] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 03/22/2021] [Indexed: 05/17/2023]
Abstract
In the context of a recent massive increase in research on plant root functions and their impact on the environment, root ecologists currently face many important challenges to keep on generating cutting-edge, meaningful and integrated knowledge. Consideration of the below-ground components in plant and ecosystem studies has been consistently called for in recent decades, but methodology is disparate and sometimes inappropriate. This handbook, based on the collective effort of a large team of experts, will improve trait comparisons across studies and integration of information across databases by providing standardised methods and controlled vocabularies. It is meant to be used not only as starting point by students and scientists who desire working on below-ground ecosystems, but also by experts for consolidating and broadening their views on multiple aspects of root ecology. Beyond the classical compilation of measurement protocols, we have synthesised recommendations from the literature to provide key background knowledge useful for: (1) defining below-ground plant entities and giving keys for their meaningful dissection, classification and naming beyond the classical fine-root vs coarse-root approach; (2) considering the specificity of root research to produce sound laboratory and field data; (3) describing typical, but overlooked steps for studying roots (e.g. root handling, cleaning and storage); and (4) gathering metadata necessary for the interpretation of results and their reuse. Most importantly, all root traits have been introduced with some degree of ecological context that will be a foundation for understanding their ecological meaning, their typical use and uncertainties, and some methodological and conceptual perspectives for future research. Considering all of this, we urge readers not to solely extract protocol recommendations for trait measurements from this work, but to take a moment to read and reflect on the extensive information contained in this broader guide to root ecology, including sections I-VII and the many introductions to each section and root trait description. Finally, it is critical to understand that a major aim of this guide is to help break down barriers between the many subdisciplines of root ecology and ecophysiology, broaden researchers' views on the multiple aspects of root study and create favourable conditions for the inception of comprehensive experiments on the role of roots in plant and ecosystem functioning.
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Affiliation(s)
- Grégoire T. Freschet
- CEFEUniv Montpellier, CNRS, EPHE, IRD1919 route de MendeMontpellier34293France
- Station d’Ecologie Théorique et ExpérimentaleCNRS2 route du CNRS09200MoulisFrance
| | - Loïc Pagès
- UR 1115 PSHCentre PACA, site AgroparcINRAE84914Avignon cedex 9France
| | - Colleen M. Iversen
- Environmental Sciences Division and Climate Change Science InstituteOak Ridge National LaboratoryOak RidgeTN37831USA
| | - Louise H. Comas
- USDA‐ARS Water Management Research Unit2150 Centre Avenue, Bldg D, Suite 320Fort CollinsCO80526USA
| | - Boris Rewald
- Department of Forest and Soil SciencesUniversity of Natural Resources and Life SciencesVienna1190Austria
| | - Catherine Roumet
- CEFEUniv Montpellier, CNRS, EPHE, IRD1919 route de MendeMontpellier34293France
| | - Jitka Klimešová
- Department of Functional EcologyInstitute of Botany CASDukelska 13537901TrebonCzech Republic
| | - Marcin Zadworny
- Institute of DendrologyPolish Academy of SciencesParkowa 562‐035KórnikPoland
| | - Hendrik Poorter
- Plant Sciences (IBG‐2)Forschungszentrum Jülich GmbHD‐52425JülichGermany
- Department of Biological SciencesMacquarie UniversityNorth RydeNSW2109Australia
| | | | - Thomas S. Adams
- Department of Plant SciencesThe Pennsylvania State UniversityUniversity ParkPA16802USA
| | - Agnieszka Bagniewska‐Zadworna
- Department of General BotanyInstitute of Experimental BiologyFaculty of BiologyAdam Mickiewicz UniversityUniwersytetu Poznańskiego 661-614PoznańPoland
| | - A. Glyn Bengough
- The James Hutton InstituteInvergowrie, Dundee,DD2 5DAUK
- School of Science and EngineeringUniversity of DundeeDundee,DD1 4HNUK
| | | | - Ivano Brunner
- Forest Soils and BiogeochemistrySwiss Federal Research Institute WSLZürcherstr. 1118903BirmensdorfSwitzerland
| | - Johannes H. C. Cornelissen
- Department of Ecological ScienceFaculty of ScienceVrije Universiteit AmsterdamDe Boelelaan 1085Amsterdam1081 HVthe Netherlands
| | - Eric Garnier
- CEFEUniv Montpellier, CNRS, EPHE, IRD1919 route de MendeMontpellier34293France
| | - Arthur Gessler
- Forest DynamicsSwiss Federal Research Institute WSLZürcherstr. 1118903BirmensdorfSwitzerland
- Institute of Terrestrial EcosystemsETH Zurich8092ZurichSwitzerland
| | - Sarah E. Hobbie
- Department of Ecology, Evolution and BehaviorUniversity of MinnesotaSt PaulMN55108USA
| | - Ina C. Meier
- Functional Forest EcologyUniversity of HamburgHaidkrugsweg 122885BarsbütelGermany
| | - Liesje Mommer
- Plant Ecology and Nature Conservation GroupDepartment of Environmental SciencesWageningen University and ResearchPO Box 476700 AAWageningenthe Netherlands
| | | | - Laura Rose
- Station d’Ecologie Théorique et ExpérimentaleCNRS2 route du CNRS09200MoulisFrance
- Senckenberg Biodiversity and Climate Research Centre (BiK-F)Senckenberganlage 2560325Frankfurt am MainGermany
| | - Peter Ryser
- Laurentian University935 Ramsey Lake RoadSudburyONP3E 2C6Canada
| | | | - Nadejda A. Soudzilovskaia
- Environmental Biology DepartmentInstitute of Environmental SciencesCMLLeiden UniversityLeiden2300 RAthe Netherlands
| | - Alexia Stokes
- INRAEAMAPCIRAD, IRDCNRSUniversity of MontpellierMontpellier34000France
| | - Tao Sun
- Institute of Applied EcologyChinese Academy of SciencesShenyang110016China
| | - Oscar J. Valverde‐Barrantes
- International Center for Tropical BotanyDepartment of Biological SciencesFlorida International UniversityMiamiFL33199USA
| | - Monique Weemstra
- CEFEUniv Montpellier, CNRS, EPHE, IRD1919 route de MendeMontpellier34293France
| | - Alexandra Weigelt
- Systematic Botany and Functional BiodiversityInstitute of BiologyLeipzig UniversityJohannisallee 21-23Leipzig04103Germany
| | - Nina Wurzburger
- Odum School of EcologyUniversity of Georgia140 E. Green StreetAthensGA30602USA
| | - Larry M. York
- Biosciences Division and Center for Bioenergy InnovationOak Ridge National LaboratoryOak RidgeTN37831USA
| | - Sarah A. Batterman
- School of Geography and Priestley International Centre for ClimateUniversity of LeedsLeedsLS2 9JTUK
- Cary Institute of Ecosystem StudiesMillbrookNY12545USA
| | - Moemy Gomes de Moraes
- Department of BotanyInstitute of Biological SciencesFederal University of Goiás1974690-900Goiânia, GoiásBrazil
| | - Štěpán Janeček
- School of Biological SciencesThe University of Western Australia35 Stirling HighwayCrawley (Perth)WA 6009Australia
| | - Hans Lambers
- School of Biological SciencesThe University of Western AustraliaCrawley (Perth)WAAustralia
| | - Verity Salmon
- Environmental Sciences Division and Climate Change Science InstituteOak Ridge National LaboratoryOak RidgeTN37831USA
| | - Nishanth Tharayil
- Department of Plant and Environmental SciencesClemson UniversityClemsonSC29634USA
| | - M. Luke McCormack
- Center for Tree ScienceMorton Arboretum, 4100 Illinois Rt. 53LisleIL60532USA
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10
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Freschet GT, Pagès L, Iversen CM, Comas LH, Rewald B, Roumet C, Klimešová J, Zadworny M, Poorter H, Postma JA, Adams TS, Bagniewska-Zadworna A, Bengough AG, Blancaflor EB, Brunner I, Cornelissen JHC, Garnier E, Gessler A, Hobbie SE, Meier IC, Mommer L, Picon-Cochard C, Rose L, Ryser P, Scherer-Lorenzen M, Soudzilovskaia NA, Stokes A, Sun T, Valverde-Barrantes OJ, Weemstra M, Weigelt A, Wurzburger N, York LM, Batterman SA, Gomes de Moraes M, Janeček Š, Lambers H, Salmon V, Tharayil N, McCormack ML. A starting guide to root ecology: strengthening ecological concepts and standardising root classification, sampling, processing and trait measurements. New Phytol 2021. [PMID: 34608637 DOI: 10.1111/nph.17572.hal-03379708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
In the context of a recent massive increase in research on plant root functions and their impact on the environment, root ecologists currently face many important challenges to keep on generating cutting-edge, meaningful and integrated knowledge. Consideration of the below-ground components in plant and ecosystem studies has been consistently called for in recent decades, but methodology is disparate and sometimes inappropriate. This handbook, based on the collective effort of a large team of experts, will improve trait comparisons across studies and integration of information across databases by providing standardised methods and controlled vocabularies. It is meant to be used not only as starting point by students and scientists who desire working on below-ground ecosystems, but also by experts for consolidating and broadening their views on multiple aspects of root ecology. Beyond the classical compilation of measurement protocols, we have synthesised recommendations from the literature to provide key background knowledge useful for: (1) defining below-ground plant entities and giving keys for their meaningful dissection, classification and naming beyond the classical fine-root vs coarse-root approach; (2) considering the specificity of root research to produce sound laboratory and field data; (3) describing typical, but overlooked steps for studying roots (e.g. root handling, cleaning and storage); and (4) gathering metadata necessary for the interpretation of results and their reuse. Most importantly, all root traits have been introduced with some degree of ecological context that will be a foundation for understanding their ecological meaning, their typical use and uncertainties, and some methodological and conceptual perspectives for future research. Considering all of this, we urge readers not to solely extract protocol recommendations for trait measurements from this work, but to take a moment to read and reflect on the extensive information contained in this broader guide to root ecology, including sections I-VII and the many introductions to each section and root trait description. Finally, it is critical to understand that a major aim of this guide is to help break down barriers between the many subdisciplines of root ecology and ecophysiology, broaden researchers' views on the multiple aspects of root study and create favourable conditions for the inception of comprehensive experiments on the role of roots in plant and ecosystem functioning.
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Affiliation(s)
- Grégoire T Freschet
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, 1919 route de Mende, Montpellier, 34293, France
- Station d'Ecologie Théorique et Expérimentale, CNRS, 2 route du CNRS, 09200, Moulis, France
| | - Loïc Pagès
- UR 1115 PSH, Centre PACA, site Agroparc, INRAE, 84914, Avignon cedex 9, France
| | - Colleen M Iversen
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Louise H Comas
- USDA-ARS Water Management Research Unit, 2150 Centre Avenue, Bldg D, Suite 320, Fort Collins, CO, 80526, USA
| | - Boris Rewald
- Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences, Vienna, 1190, Austria
| | - Catherine Roumet
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, 1919 route de Mende, Montpellier, 34293, France
| | - Jitka Klimešová
- Department of Functional Ecology, Institute of Botany CAS, Dukelska 135, 37901, Trebon, Czech Republic
| | - Marcin Zadworny
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035, Kórnik, Poland
| | - Hendrik Poorter
- Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, D-52425, Jülich, Germany
- Department of Biological Sciences, Macquarie University, North Ryde, NSW, 2109, Australia
| | - Johannes A Postma
- Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, D-52425, Jülich, Germany
| | - Thomas S Adams
- Department of Plant Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Agnieszka Bagniewska-Zadworna
- Department of General Botany, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - A Glyn Bengough
- The James Hutton Institute, Invergowrie, Dundee,, DD2 5DA, UK
- School of Science and Engineering, University of Dundee, Dundee,, DD1 4HN, UK
| | - Elison B Blancaflor
- Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Ivano Brunner
- Forest Soils and Biogeochemistry, Swiss Federal Research Institute WSL, Zürcherstr. 111, 8903, Birmensdorf, Switzerland
| | - Johannes H C Cornelissen
- Department of Ecological Science, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1085, Amsterdam, 1081 HV, the Netherlands
| | - Eric Garnier
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, 1919 route de Mende, Montpellier, 34293, France
| | - Arthur Gessler
- Forest Dynamics, Swiss Federal Research Institute WSL, Zürcherstr. 111, 8903, Birmensdorf, Switzerland
- Institute of Terrestrial Ecosystems, ETH Zurich, 8092, Zurich, Switzerland
| | - Sarah E Hobbie
- Department of Ecology, Evolution and Behavior, University of Minnesota, St Paul, MN, 55108, USA
| | - Ina C Meier
- Functional Forest Ecology, University of Hamburg, Haidkrugsweg 1, 22885, Barsbütel, Germany
| | - Liesje Mommer
- Plant Ecology and Nature Conservation Group, Department of Environmental Sciences, Wageningen University and Research, PO Box 47, 6700 AA, Wageningen, the Netherlands
| | | | - Laura Rose
- Station d'Ecologie Théorique et Expérimentale, CNRS, 2 route du CNRS, 09200, Moulis, France
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Peter Ryser
- Laurentian University, 935 Ramsey Lake Road, Sudbury, ON, P3E 2C6, Canada
| | | | - Nadejda A Soudzilovskaia
- Environmental Biology Department, Institute of Environmental Sciences, CML, Leiden University, Leiden, 2300 RA, the Netherlands
| | - Alexia Stokes
- INRAE, AMAP, CIRAD, IRD, CNRS, University of Montpellier, Montpellier, 34000, France
| | - Tao Sun
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
| | - Oscar J Valverde-Barrantes
- International Center for Tropical Botany, Department of Biological Sciences, Florida International University, Miami, FL, 33199, USA
| | - Monique Weemstra
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, 1919 route de Mende, Montpellier, 34293, France
| | - Alexandra Weigelt
- Systematic Botany and Functional Biodiversity, Institute of Biology, Leipzig University, Johannisallee 21-23, Leipzig, 04103, Germany
| | - Nina Wurzburger
- Odum School of Ecology, University of Georgia, 140 E. Green Street, Athens, GA, 30602, USA
| | - Larry M York
- Biosciences Division and Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Sarah A Batterman
- School of Geography and Priestley International Centre for Climate, University of Leeds, Leeds, LS2 9JT, UK
- Cary Institute of Ecosystem Studies, Millbrook, NY, 12545, USA
| | - Moemy Gomes de Moraes
- Department of Botany, Institute of Biological Sciences, Federal University of Goiás, 19, 74690-900, Goiânia, Goiás, Brazil
| | - Štěpán Janeček
- School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley (Perth), WA 6009, Australia
| | - Hans Lambers
- School of Biological Sciences, The University of Western Australia, Crawley (Perth), WA, Australia
| | - Verity Salmon
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Nishanth Tharayil
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, 29634, USA
| | - M Luke McCormack
- Center for Tree Science, Morton Arboretum, 4100 Illinois Rt. 53, Lisle, IL, 60532, USA
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11
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Luo W, Ni M, Wang Y, Lan R, Eissenstat DM, Cahill JF, Li B, Chu C. Limited evidence of vertical fine-root segregation in a subtropical forest. New Phytol 2021; 231:2308-2318. [PMID: 34110016 DOI: 10.1111/nph.17546] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 06/03/2021] [Indexed: 06/12/2023]
Abstract
Vertical root segregation and the resulting niche partitioning can be a key underpinning of species coexistence. This could result from substantial interspecific variations in root profiles and rooting plasticity in response to soil heterogeneity and neighbours, but they remain largely untested in forest communities. In a diverse forest in subtropical China, we randomly sampled > 4000 root samples from 625 0-30 cm soil profiles. Using morphological and DNA-based methods, we identified 109 woody plant species, determined the degree of vertical fine-root segregation, and examined rooting plasticity in response to soil heterogeneity and neighbour structure. We found no evidence of vertical fine-root segregation among cooccurring species. By contrast, root abundance of different species tended to be positively correlated within soil zones. Underlying these findings was a lack of interspecific variation in fine-root profiles with over 90% of species concentrated in the 0-10 cm soil zone with only one species dominating in the 10-20 cm soil zone. Root profiles exhibited low responsiveness to root neighbours but tended to be shallow in soils with low phosphorus and copper content. These findings suggest that if there is niche differentiation leading to coexistence in this diverse forest, it would be occurring by mechanisms other than vertical fine-root segregation.
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Affiliation(s)
- Wenqi Luo
- State Key Laboratory of Biocontrol, School of Life Sciences and School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Ming Ni
- State Key Laboratory of Biocontrol, School of Life Sciences and School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada
| | - Youshi Wang
- State Key Laboratory of Biocontrol, School of Life Sciences and School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Runxuan Lan
- State Key Laboratory of Biocontrol, School of Life Sciences and School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - David M Eissenstat
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA, 16802, USA
| | - James F Cahill
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Buhang Li
- State Key Laboratory of Biocontrol, School of Life Sciences and School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Chengjin Chu
- State Key Laboratory of Biocontrol, School of Life Sciences and School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
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12
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Chitra‐Tarak R, Xu C, Aguilar S, Anderson‐Teixeira KJ, Chambers J, Detto M, Faybishenko B, Fisher RA, Knox RG, Koven CD, Kueppers LM, Kunert N, Kupers SJ, McDowell NG, Newman BD, Paton SR, Pérez R, Ruiz L, Sack L, Warren JM, Wolfe BT, Wright C, Wright SJ, Zailaa J, McMahon SM. Hydraulically-vulnerable trees survive on deep-water access during droughts in a tropical forest. New Phytol 2021; 231:1798-1813. [PMID: 33993520 PMCID: PMC8457149 DOI: 10.1111/nph.17464] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 04/29/2021] [Indexed: 05/24/2023]
Abstract
Deep-water access is arguably the most effective, but under-studied, mechanism that plants employ to survive during drought. Vulnerability to embolism and hydraulic safety margins can predict mortality risk at given levels of dehydration, but deep-water access may delay plant dehydration. Here, we tested the role of deep-water access in enabling survival within a diverse tropical forest community in Panama using a novel data-model approach. We inversely estimated the effective rooting depth (ERD, as the average depth of water extraction), for 29 canopy species by linking diameter growth dynamics (1990-2015) to vapor pressure deficit, water potentials in the whole-soil column, and leaf hydraulic vulnerability curves. We validated ERD estimates against existing isotopic data of potential water-access depths. Across species, deeper ERD was associated with higher maximum stem hydraulic conductivity, greater vulnerability to xylem embolism, narrower safety margins, and lower mortality rates during extreme droughts over 35 years (1981-2015) among evergreen species. Species exposure to water stress declined with deeper ERD indicating that trees compensate for water stress-related mortality risk through deep-water access. The role of deep-water access in mitigating mortality of hydraulically-vulnerable trees has important implications for our predictive understanding of forest dynamics under current and future climates.
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13
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Isola D, Bartoli F, Langone S, Ceschin S, Zucconi L, Caneva G. Plant DNA Barcode as a Tool for Root Identification in Hypogea: The Case of the Etruscan Tombs of Tarquinia (Central Italy). Plants (Basel) 2021; 10:1138. [PMID: 34205139 PMCID: PMC8228792 DOI: 10.3390/plants10061138] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/30/2021] [Accepted: 06/01/2021] [Indexed: 11/21/2022]
Abstract
Roots can produce mechanical and chemical alterations to building structures, especially in the case of underground historical artifacts. In archaeological sites, where vegetation plays the dual role of naturalistic relevance and potential threat, trees and bushes are under supervision. No customized measures can be taken against herbaceous plants lacking fast and reliable root identification methods that are useful to assess their dangerousness. In this study, we aimed to test the efficacy of DNA barcoding in identifying plant rootlets threatening the Etruscan tombs of the Necropolis of Tarquinia. As DNA barcode markers, we selected two sections of the genes rbcL and matK, the nuclear ribosomal internal transcribed spacer (nrITS), and the intergenic spacer psbA-trnH. All fourteen root samples were successfully sequenced and identified at species (92.9%) and genus level (7.01%) by GenBank matching and reference dataset implementation. Some eudicotyledons with taproots, such as Echium italicum L., Foeniculum vulgare Mill., and Reseda lutea L. subsp. lutea, showed a certain recurrence. Further investigations are needed to confirm this promising result, increasing the number of roots and enlarging the reference dataset with attention to meso-Mediterranean perennial herbaceous species. The finding of herbaceous plants roots at more than 3 m deep confirms their potential risk and underlines the importance of vegetation planning, monitoring, and management on archaeological sites.
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Affiliation(s)
- Daniela Isola
- Department of Sciences, Roma Tre University, 00146 Rome, Italy; (F.B.); (S.L.); (S.C.); (G.C.)
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, 01100 Viterbo, Italy;
| | - Flavia Bartoli
- Department of Sciences, Roma Tre University, 00146 Rome, Italy; (F.B.); (S.L.); (S.C.); (G.C.)
| | - Simone Langone
- Department of Sciences, Roma Tre University, 00146 Rome, Italy; (F.B.); (S.L.); (S.C.); (G.C.)
| | - Simona Ceschin
- Department of Sciences, Roma Tre University, 00146 Rome, Italy; (F.B.); (S.L.); (S.C.); (G.C.)
| | - Laura Zucconi
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, 01100 Viterbo, Italy;
| | - Giulia Caneva
- Department of Sciences, Roma Tre University, 00146 Rome, Italy; (F.B.); (S.L.); (S.C.); (G.C.)
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14
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Luo W, Lan R, Chen D, Zhang B, Xi N, Li Y, Fang S, Valverde-Barrantes OJ, Eissenstat DM, Chu C, Wang Y. Limiting similarity shapes the functional and phylogenetic structure of root neighborhoods in a subtropical forest. New Phytol 2021; 229:1078-1090. [PMID: 32924174 DOI: 10.1111/nph.16920] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 08/10/2020] [Indexed: 06/11/2023]
Abstract
Environmental filtering and limiting similarity mechanisms can simultaneously structure community assemblages. However, how they shape the functional and phylogenetic structure of root neighborhoods remains unclear, hindering the understanding of belowground community assembly processes and diversity maintenance. In a 50-ha plot in a subtropical forest, China, we randomly sampled > 2700 root clusters from 625 soil samples. Focusing on 10 root functional traits measured on 76 woody species, we examined the functional and phylogenetic structure of root neighborhoods and linked their distributions with environmental cues. Functional overdispersion was pervasive among individual root traits (50% of the traits) and accentuated when different traits were combined. Functional clustering (20% of the traits) seemed to be associated with a soil nutrient gradient with thick roots dominating fertile areas whereas thin roots dominated infertile soils. Nevertheless, such traits also were sorted along other environmental cues, showing multidimensional adaptive trait syndromes. Species relatedness also was an important factor defining root neighborhoods, resulting in significant phylogenetic overdispersion. These results suggest that limiting similarity may drive niche differentiation of coexisting species to reduce competition, and that alternative root strategies could be crucial in promoting root neighborhood resource use and species coexistence.
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Affiliation(s)
- Wenqi Luo
- Department of Ecology, State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Runxuan Lan
- Department of Ecology, State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Dongxia Chen
- Department of Ecology, State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Bingwei Zhang
- Department of Ecology, State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Nianxun Xi
- Department of Ecology, State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yuanzhi Li
- Department of Ecology, State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Suqing Fang
- Department of Ecology, State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Oscar J Valverde-Barrantes
- International Center for Tropical Biodiversity, Department of Biological Sciences, Florida International University, Miami, FL, 33199, USA
| | - David M Eissenstat
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Chengjin Chu
- Department of Ecology, State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Youshi Wang
- Department of Ecology, State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
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15
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Wagemaker CAM, Mommer L, Visser EJW, Weigelt A, van Gurp TP, Postuma M, Smit-Tiekstra AE, de Kroon H. msGBS: A new high-throughput approach to quantify the relative species abundance in root samples of multispecies plant communities. Mol Ecol Resour 2020; 21:1021-1036. [PMID: 33058506 PMCID: PMC8246947 DOI: 10.1111/1755-0998.13278] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 08/25/2020] [Accepted: 09/23/2020] [Indexed: 12/11/2022]
Abstract
Plant interactions are as important belowground as aboveground. Belowground plant interactions are however inherently difficult to quantify, as roots of different species are difficult to disentangle. Although for a couple of decades molecular techniques have been successfully applied to quantify root abundance, root identification and quantification in multispecies plant communities remains particularly challenging. Here we present a novel methodology, multispecies genotyping by sequencing (msGBS), as a next step to tackle this challenge. First, a multispecies meta‐reference database containing thousands of gDNA clusters per species is created from GBS derived High Throughput Sequencing (HTS) reads. Second, GBS derived HTS reads from multispecies root samples are mapped to this meta‐reference which, after a filter procedure to increase the taxonomic resolution, allows the parallel quantification of multiple species. The msGBS signal of 111 mock‐mixture root samples, with up to 8 plant species per sample, was used to calculate the within‐species abundance. Optional subsequent calibration yielded the across‐species abundance. The within‐ and across‐species abundances highly correlated (R2 range 0.72–0.94 and 0.85–0.98, respectively) to the biomass‐based species abundance. Compared to a qPCR based method which was previously used to analyse the same set of samples, msGBS provided similar results. Additional data on 11 congener species groups within 105 natural field root samples showed high taxonomic resolution of the method. msGBS is highly scalable in terms of sensitivity and species numbers within samples, which is a major advantage compared to the qPCR method and advances our tools to reveal hidden belowground interactions. see also the Perspective by Josep Piñol
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Affiliation(s)
- Cornelis A M Wagemaker
- Department of Experimental Plant Ecology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Liesje Mommer
- Plant Ecology and Nature Conservation Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Eric J W Visser
- Department of Experimental Plant Ecology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Alexandra Weigelt
- Systematic Botany and Functional Biodiversity, Faculty of Life Sciences, University of Leipzig, Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | | | - Maarten Postuma
- Plant Ecology and Nature Conservation Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Annemiek E Smit-Tiekstra
- Department of Experimental Plant Ecology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Hans de Kroon
- Department of Experimental Plant Ecology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
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16
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López-Angulo J, de la Cruz M, Chacón-Labella J, Illuminati A, Matesanz S, Pescador DS, Pías B, Sánchez AM, Escudero A. The role of root community attributes in predicting soil fungal and bacterial community patterns. New Phytol 2020; 228:1070-1082. [PMID: 32557640 DOI: 10.1111/nph.16754] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 06/04/2020] [Indexed: 06/11/2023]
Abstract
Roots are assumed to play a major role in structuring soil microbial communities, but most studies exploring the relationships between microbes and plants at the community level have only used aboveground plant distribution as a proxy. However, a decoupling between belowground and aboveground plant components may occur due to differential spreading of plant canopies and root systems. Thus, soil microbe-plant links are not completely understood. Using a combination of DNA metabarcoding and spatially explicit sampling at the plant neighbourhood scale, we assessed the influence of the plant root community on soil bacterial and fungal diversity (species richness, composition and β-diversity) in a dry Mediterranean scrubland. We found that root composition and biomass, but not richness, predict unique fractions of variation in microbial richness and composition. Moreover, bacterial β-diversity was related to root β-diversity, while fungal β-diversity was related to aboveground plant β-diversity, suggesting that plants differently influence both microbial groups. Our study highlights the role of plant distribution both belowground and aboveground, soil properties and other spatially structured factors in explaining the heterogeneity in soil microbial diversity. These results also show that incorporating data on both plant community compartments will further our understanding of the relationships between soil microbial and plant communities.
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Affiliation(s)
- Jesús López-Angulo
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, Móstoles, Madrid, 28933, Spain
| | - Marcelino de la Cruz
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, Móstoles, Madrid, 28933, Spain
| | - Julia Chacón-Labella
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Angela Illuminati
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, Móstoles, Madrid, 28933, Spain
| | - Silvia Matesanz
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, Móstoles, Madrid, 28933, Spain
| | - David S Pescador
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, Móstoles, Madrid, 28933, Spain
| | - Beatriz Pías
- Departamento de Biodiversidad, Ecología y Evolución, Universidad Complutense de Madrid, Madrid, 28040, Spain
| | - Ana M Sánchez
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, Móstoles, Madrid, 28933, Spain
| | - Adrián Escudero
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, Móstoles, Madrid, 28933, Spain
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17
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Zeng W, Xiang W, Zhou B, Ouyang S, Zeng Y, Chen L, Freschet GT, Valverde‐Barrantes OJ, Milcu A. Positive tree diversity effect on fine root biomass: via density dependence rather than spatial root partitioning. OIKOS 2020. [DOI: 10.1111/oik.07777] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Weixian Zeng
- Faculty of Life Science and Technology, Central South Univ. of Forestry and Technology CN‐410004 Changsha Hunan Province PR China
| | - Wenhua Xiang
- Faculty of Life Science and Technology, Central South Univ. of Forestry and Technology CN‐410004 Changsha Hunan Province PR China
- Huitong National Station for Scientific Observation and Research of Chinese Fir Plantation Ecosystem in Hunan Province CN‐438107 Huitong PR China
| | - Bo Zhou
- Faculty of Life Science and Technology, Central South Univ. of Forestry and Technology CN‐410004 Changsha Hunan Province PR China
| | - Shuai Ouyang
- Faculty of Life Science and Technology, Central South Univ. of Forestry and Technology CN‐410004 Changsha Hunan Province PR China
- Huitong National Station for Scientific Observation and Research of Chinese Fir Plantation Ecosystem in Hunan Province CN‐438107 Huitong PR China
| | - Yelin Zeng
- Faculty of Life Science and Technology, Central South Univ. of Forestry and Technology CN‐410004 Changsha Hunan Province PR China
- Huitong National Station for Scientific Observation and Research of Chinese Fir Plantation Ecosystem in Hunan Province CN‐438107 Huitong PR China
| | - Liang Chen
- Faculty of Life Science and Technology, Central South Univ. of Forestry and Technology CN‐410004 Changsha Hunan Province PR China
- Huitong National Station for Scientific Observation and Research of Chinese Fir Plantation Ecosystem in Hunan Province CN‐438107 Huitong PR China
| | - Grégoire T. Freschet
- Centre Ecologie Fonctionnelle Evolutive, Univ. Montpellier, CNRS, Univ. Paul Valéry, EPHE, IRD Montpellier France
| | | | - Alexandru Milcu
- Centre Ecologie Fonctionnelle Evolutive, Univ. Montpellier, CNRS, Univ. Paul Valéry, EPHE, IRD Montpellier France
- Ecotron Européen de Montpellier, Univ. Montpellier, CNRS Montferrier sur Lez France
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18
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Zinger L, Donald J, Brosse S, Gonzalez MA, Iribar A, Leroy C, Murienne J, Orivel J, Schimann H, Taberlet P, Lopes CM. Advances and prospects of environmental DNA in neotropical rainforests. Tropical Ecosystems in the 21st Century. Elsevier; 2020. pp. 331-73. [DOI: 10.1016/bs.aecr.2020.01.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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19
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Gaut BS, Miller AJ, Seymour DK. Living with Two Genomes: Grafting and Its Implications for Plant Genome-to-Genome Interactions, Phenotypic Variation, and Evolution. Annu Rev Genet 2019; 53:195-215. [PMID: 31424971 DOI: 10.1146/annurev-genet-112618-043545] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Plant genomes interact when genetically distinct individuals join, or are joined, together. Individuals can fuse in three contexts: artificial grafts, natural grafts, and host-parasite interactions. Artificial grafts have been studied for decades and are important platforms for studying the movement of RNA, DNA, and protein. Yet several mysteries about artificial grafts remain, including the factors that contribute to graft incompatibility, the prevalence of genetic and epigenetic modifications caused by exchanges between graft partners, and the long-term effects of these modifications on phenotype. Host-parasite interactions also lead to the exchange of materials, and RNA exchange actively contributes to an ongoing arms race between parasite virulence and host resistance. Little is known about natural grafts except that they can be frequent and may provide opportunities for evolutionary innovation through genome exchange. In this review, we survey our current understanding about these three mechanisms of contact, the genomic interactions that result, and the potential evolutionary implications.
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Affiliation(s)
- Brandon S Gaut
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697, USA;
| | - Allison J Miller
- Department of Biology, Saint Louis University, Saint Louis, Missouri 63103, USA.,Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | - Danelle K Seymour
- Department of Botany and Plant Sciences, University of California, Riverside, California 92521, USA
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20
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Matesanz S, Pescador DS, Pías B, Sánchez AM, Chacón‐Labella J, Illuminati A, Cruz M, López‐Angulo J, Marí‐Mena N, Vizcaíno A, Escudero A. Estimating belowground plant abundance with DNA metabarcoding. Mol Ecol Resour 2019; 19:1265-1277. [DOI: 10.1111/1755-0998.13049] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 06/01/2019] [Accepted: 06/12/2019] [Indexed: 01/02/2023]
Affiliation(s)
- Silvia Matesanz
- Área de Biodiversidad y Conservación Universidad Rey Juan Carlos Móstoles Spain
| | - David S. Pescador
- Área de Biodiversidad y Conservación Universidad Rey Juan Carlos Móstoles Spain
| | - Beatriz Pías
- Departamento de Biodiversidad Ecología y Evolución Universidad Complutense de Madrid Madrid Spain
| | - Ana M. Sánchez
- Área de Biodiversidad y Conservación Universidad Rey Juan Carlos Móstoles Spain
| | - Julia Chacón‐Labella
- Departamento de Medio Ambiente Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) Madrid Spain
| | - Angela Illuminati
- Área de Biodiversidad y Conservación Universidad Rey Juan Carlos Móstoles Spain
| | - Marcelino Cruz
- Área de Biodiversidad y Conservación Universidad Rey Juan Carlos Móstoles Spain
| | - Jesús López‐Angulo
- Área de Biodiversidad y Conservación Universidad Rey Juan Carlos Móstoles Spain
| | | | | | - Adrián Escudero
- Área de Biodiversidad y Conservación Universidad Rey Juan Carlos Móstoles Spain
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21
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Träger S, Öpik M, Vasar M, Wilson SD. Belowground plant parts are crucial for comprehensively estimating total plant richness in herbaceous and woody habitats. Ecology 2019; 100:e02575. [PMID: 30516275 DOI: 10.1002/ecy.2575] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 10/04/2018] [Accepted: 10/24/2018] [Indexed: 11/08/2022]
Abstract
Most studies consider aboveground plant species richness as a representative biodiversity measure. This approach inevitably assumes that the partitioning of total plant species richness into above- and belowground components is constant or at least consistent within and across vegetation types. However, with studies considering belowground plant richness still scarce and completely absent along vegetation gradients, this assumption lacks experimental support. Novel DNA sequencing techniques allow economical, high-throughput species identification of belowground environmental samples, enabling the measurement of the contributions of both above- and belowground plant components to total plant richness. We investigated above- and belowground plant species richness in four vegetation types (birch forest, heath, low alpine tundra, high alpine tundra) at the scale of herbaceous plant neighborhoods (dm) using 454 sequencing of the chloroplast trnL (UAA) intron to determine the plant species richness of environmental root samples and combined it with aboveground data from vegetation surveys to obtain total plant species richness. We correlated the measured plant species richness components with each other and with their respective plant biomass components within and across vegetation types. Total plant species richness exceeded aboveground richness twice on average and by as much as three times in low alpine tundra, indicating that a significant fraction of belowground plant richness cannot be recorded aboveground. More importantly, no consistent relationship among richness components (above- and belowground) was found within or across vegetation types, indicating that aboveground richness alone cannot predict total plant richness in contrasting vegetation types. Finally, no consistent relationship between plant richness and the corresponding biomass component was found. Our results clearly show that aboveground plant richness alone is a poor estimator of total plant species richness within and across different vegetation types. Consequently, it is crucial to account for belowground plant richness in future plant ecological studies in order to validate currently accepted plant richness patterns, as well as to measure potential changes in plant community composition in a changing environment.
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Affiliation(s)
- Sabrina Träger
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia.,Department of Biology, University of Regina, 3737 Wascana Parkway, Regina, Saskatchewan, S4S 0A2, Canada
| | - Maarja Öpik
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
| | - Martti Vasar
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
| | - Scott D Wilson
- Department of Biology, University of Regina, 3737 Wascana Parkway, Regina, Saskatchewan, S4S 0A2, Canada.,Climate Impacts Research Centre, Department of Ecology and Environmental Science, Umeå University, Abisko, 981 07, Sweden
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22
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Winbourne JB, Harrison MT, Sullivan BW, Alvarez-Clare S, Lins SR, Martinelli L, Nasto M, Piotto D, Rolim S, Wong M, Porder S. A New Framework for Evaluating Estimates of Symbiotic Nitrogen Fixation in Forests. Am Nat 2018; 192:618-629. [PMID: 30332582 DOI: 10.1086/699828] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Symbiotic nitrogen fixation (SNF) makes atmospheric nitrogen biologically available and regulates carbon storage in many terrestrial ecosystems. Despite its global importance, estimates of SNF rates are highly uncertain, particularly in tropical forests where rates are assumed to be high. Here we provide a framework for evaluating the uncertainty of sample-based SNF estimates and discuss its implications for quantifying SNF and thus understanding of forest function. We apply this framework to field data sets from six lowland tropical rainforests (mature and secondary) in Brazil and Costa Rica. We use this data set to estimate parameters influencing SNF estimation error, notably the root nodule abundance and variation in SNF rates among soil cores containing root nodules. We then use simulations to gauge the relationship between sampling effort and SNF estimation accuracy for a combination of parameters. Field data illuminate a highly right-skewed lognormal distribution of SNF rates among soil cores containing root nodules that were rare and spanned five orders of magnitude. Consequently, simulations demonstrated that sample sizes of hundreds to even thousands of soil cores are needed to obtain estimates of SNF that are within, for example, a factor of 2 of the actual rate with 75% probability. This represents sample sizes that are larger than most studies to date. As a result of this previously undescribed uncertainty, we suggest that current estimates of SNF in tropical forests are not sufficiently constrained to elucidate forest stand-level controls of SNF, which hinders our understanding of the impact of SNF on tropical forest ecosystem processes.
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23
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Craig ME, Turner BL, Liang C, Clay K, Johnson DJ, Phillips RP. Tree mycorrhizal type predicts within-site variability in the storage and distribution of soil organic matter. Glob Chang Biol 2018; 24:3317-3330. [PMID: 29573504 DOI: 10.1111/gcb.14132] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 02/08/2018] [Indexed: 05/14/2023]
Abstract
Forest soils store large amounts of carbon (C) and nitrogen (N), yet how predicted shifts in forest composition will impact long-term C and N persistence remains poorly understood. A recent hypothesis predicts that soils under trees associated with arbuscular mycorrhizas (AM) store less C than soils dominated by trees associated with ectomycorrhizas (ECM), due to slower decomposition in ECM-dominated forests. However, an incipient hypothesis predicts that systems with rapid decomposition-e.g. most AM-dominated forests-enhance soil organic matter (SOM) stabilization by accelerating the production of microbial residues. To address these contrasting predictions, we quantified soil C and N to 1 m depth across gradients of ECM-dominance in three temperate forests. By focusing on sites where AM- and ECM-plants co-occur, our analysis controls for climatic factors that covary with mycorrhizal dominance across broad scales. We found that while ECM stands contain more SOM in topsoil, AM stands contain more SOM when subsoil to 1 m depth is included. Biomarkers and soil fractionations reveal that these patterns are driven by an accumulation of microbial residues in AM-dominated soils. Collectively, our results support emerging theory on SOM formation, demonstrate the importance of subsurface soils in mediating plant effects on soil C and N, and indicate that shifts in the mycorrhizal composition of temperate forests may alter the stabilization of SOM.
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Affiliation(s)
- Matthew E Craig
- Department of Biology, Indiana University, Bloomington, IN, USA
| | | | - Chao Liang
- Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Keith Clay
- Department of Biology, Indiana University, Bloomington, IN, USA
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24
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Tan S, Luo Y, Hollingsworth PM, Burgess KS, Xu K, Li D, Gao L. DNA barcoding herbaceous and woody plant species at a subalpine forest dynamics plot in Southwest China. Ecol Evol 2018; 8:7195-7205. [PMID: 30073078 PMCID: PMC6065341 DOI: 10.1002/ece3.4254] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 03/05/2018] [Accepted: 05/14/2018] [Indexed: 01/13/2023] Open
Abstract
Although DNA barcoding has been widely used to identify plant species composition in temperate and tropical ecosystems, relatively few studies have used DNA barcodes to document both herbaceous and woody components of forest plot. A total of 201 species (72 woody species and 129 herbaceous species) representing 135 genera distributed across 64 families of seed plants were collected in a 25 ha CForBio subalpine forest dynamics plot. In total, 491 specimens were screened for three DNA regions of the chloroplast genome (rbcL, matK, and trnH-psbA) as well as the internal transcribed spacers (ITS) of nuclear ribosomal DNA. We quantified species resolution for each barcode separately or in combination using a ML tree-based method. Amplification and sequencing success were highest for rbcL, followed by trnH-psbA, which performed better than ITS and matK. The rbcL + ITS barcode had slightly higher species resolution rates (88.60%) compared with rbcL + matK (86.60%) and rbcL + trnH-psbA (86.01%). The addition of trnH-psbA or ITS to the rbcL + matK barcode only marginally increased species resolution rates, although in combination the four barcodes had the highest discriminatory power (90.21%). The situations where DNA barcodes did not discriminate among species were typically associated with higher numbers of co-occurring con-generic species. In addition, herbaceous species were much better resolved than woody species. Our study represents one of the first applications of DNA barcodes in a subalpine forest dynamics plot and contributes to our understanding of patterns of genetic divergence among woody and herbaceous plant species.
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Affiliation(s)
- Shao‐Lin Tan
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunming, YunnanChina
- Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunming, YunnanChina
- College of Life SciencesUniversity of Chinese Academy of SciencesKunming, YunnanChina
| | - Ya‐Huang Luo
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunming, YunnanChina
| | | | - Kevin S. Burgess
- Department of BiologyCollege of Letters and SciencesColumbus State UniversityUniversity System of GeorgiaColumbusGeorgia
| | - Kun Xu
- Lijiang Forest Ecosystem Research StationKunming Institute of BotanyChinese Academy of SciencesLijiangChina
| | - De‐Zhu Li
- Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunming, YunnanChina
- College of Life SciencesUniversity of Chinese Academy of SciencesKunming, YunnanChina
| | - Lian‐Ming Gao
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunming, YunnanChina
- Lijiang Forest Ecosystem Research StationKunming Institute of BotanyChinese Academy of SciencesLijiangChina
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25
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Subrahmaniam HJ, Libourel C, Journet EP, Morel JB, Muños S, Niebel A, Raffaele S, Roux F. The genetics underlying natural variation of plant-plant interactions, a beloved but forgotten member of the family of biotic interactions. Plant J 2018; 93:747-770. [PMID: 29232012 DOI: 10.1111/tpj.13799] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 12/02/2017] [Accepted: 12/06/2017] [Indexed: 05/22/2023]
Abstract
Despite the importance of plant-plant interactions on crop yield and plant community dynamics, our understanding of the genetic and molecular bases underlying natural variation of plant-plant interactions is largely limited in comparison with other types of biotic interactions. By listing 63 quantitative trait loci (QTL) mapping and global gene expression studies based on plants directly challenged by other plants, we explored whether the genetic architecture and the function of the candidate genes underlying natural plant-plant interactions depend on the type of interactions between two plants (competition versus commensalism versus reciprocal helping versus asymmetry). The 16 transcriptomic studies are unevenly distributed between competitive interactions (n = 12) and asymmetric interactions (n = 4, all focusing on response to parasitic plants). By contrast, 17 and 30 QTL studies were identified for competitive interactions and asymmetric interactions (either weed suppressive ability or response to parasitic plants), respectively. Surprisingly, no studies have been carried out on the identification of genetic and molecular bases underlying natural variation in positive interactions. The candidate genes underlying natural plant-plant interactions can be classified into seven categories of plant function that have been identified in artificial environments simulating plant-plant interactions either frequently (photosynthesis, hormones), only recently (cell wall modification and degradation, defense pathways against pathogens) or rarely (ABC transporters, histone modification and meristem identity/life history traits). Finally, we introduce several avenues that need to be explored in the future to obtain a thorough understanding of the genetic and molecular bases underlying plant-plant interactions within the context of realistic community complexity.
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Affiliation(s)
| | - Cyril Libourel
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Etienne-Pascal Journet
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
- AGIR, Université de Toulouse, INRA, INPT, INP-EI PURPAN, Castanet-Tolosan, France
| | - Jean-Benoît Morel
- BGPI, INRA, CIRAD, SupAgro, Université de Montpellier, Montpellier, France
| | - Stéphane Muños
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Andreas Niebel
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Sylvain Raffaele
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Fabrice Roux
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
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26
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Valverde-Barrantes OJ, Smemo KA, Feinstein LM, Kershner MW, Blackwood CB. Patterns in spatial distribution and root trait syndromes for ecto and arbuscular mycorrhizal temperate trees in a mixed broadleaf forest. Oecologia 2017; 186:731-741. [DOI: 10.1007/s00442-017-4044-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 12/10/2017] [Indexed: 11/25/2022]
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27
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Menge DNL, Levin SA. Spatial heterogeneity can resolve the nitrogen paradox of tropical forests. Ecology 2017; 98:1049-1061. [DOI: 10.1002/ecy.1733] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Revised: 11/20/2016] [Accepted: 01/03/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Duncan N. L. Menge
- Department of Ecology, Evolution, and Environmental Biology Columbia University 1200 Amsterdam Avenue, Schermerhorn Ex 1014A New York New York 10027 USA
| | - Simon A. Levin
- Department of Ecology and Evolutionary Biology Princeton University 106A Guyot Hall Princeton New Jersey 08544 USA
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28
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Becklund K, Powers J, Kinkel L. Tree species effects on pathogen-suppressive capacities of soil bacteria across two tropical dry forests in Costa Rica. Oecologia 2016; 182:789-802. [PMID: 27573616 DOI: 10.1007/s00442-016-3702-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 08/08/2016] [Indexed: 10/21/2022]
Abstract
Antibiotic-producing bacteria in the genus Streptomyces can inhibit soil-borne plant pathogens, and have the potential to mediate the impacts of disease on plant communities. Little is known about how antibiotic production varies among soil communities in tropical forests, despite a long history of interest in the role of soil-borne pathogens in these ecosystems. Our objective was to determine how tree species and soils influence variation in antibiotic-mediated pathogen suppression among Streptomyces communities in two tropical dry forest sites (Santa Rosa and Palo Verde). We targeted tree species that co-occur in both sites and used a culture-based functional assay to quantify pathogen-suppressive capacities of Streptomyces communities beneath 50 focal trees. We also measured host-associated litter and soil element concentrations as potential mechanisms by which trees may influence soil microbes. Pathogen-suppressive capacities of Streptomyces communities varied within and among tree species, and inhibitory phenotypes were significantly related to soil and litter element concentrations. Average proportions of inhibitory Streptomyces in soils from the same tree species varied between 1.6 and 3.3-fold between sites. Densities and proportions of pathogen-suppressive bacteria were always higher in Santa Rosa than Palo Verde. Our results suggest that spatial heterogeneity in the potential for antibiotic-mediated disease suppression is shaped by tree species, site, and soil characteristics, which could have significant implications for understanding plant community composition and diversity in tropical dry forests.
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29
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Warschefsky EJ, Klein LL, Frank MH, Chitwood DH, Londo JP, von Wettberg EJB, Miller AJ. Rootstocks: Diversity, Domestication, and Impacts on Shoot Phenotypes. Trends Plant Sci 2016; 21:418-437. [PMID: 26698413 DOI: 10.1016/j.tplants.2015.11.008] [Citation(s) in RCA: 142] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 10/16/2015] [Accepted: 11/11/2015] [Indexed: 05/18/2023]
Abstract
Grafting is an ancient agricultural practice that joins the root system (rootstock) of one plant to the shoot (scion) of another. It is most commonly employed in woody perennial crops to indirectly manipulate scion phenotype. While recent research has focused on scions, here we investigate rootstocks, the lesser-known half of the perennial crop equation. We review natural grafting, grafting in agriculture, rootstock diversity and domestication, and developing areas of rootstock research, including molecular interactions and rootstock microbiomes. With growing interest in perennial crops as valuable components of sustainable agriculture, rootstocks provide one mechanism by which to improve and expand woody perennial cultivation in a range of environmental conditions.
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Affiliation(s)
- Emily J Warschefsky
- Florida International University, Department of Biological Sciences, 11200 Southwest 8th Street, Miami, FL 33199-2156, USA; Fairchild Tropical Botanic Garden, Kushlan Tropical Science Institute, 10901 Old Cutler Road, Coral Gables, FL 33156-4233, USA
| | - Laura L Klein
- Saint Louis University, Department of Biology, 3507 Laclede Avenue, St. Louis, MO 63103-2010, USA; Missouri Botanical Garden, 4344 Shaw Boulevard, St. Louis, MO 63110-2226, USA
| | - Margaret H Frank
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132-2918, USA
| | - Daniel H Chitwood
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132-2918, USA
| | - Jason P Londo
- United States Department of Agriculture, Agriculture Research Service: Grape Genetics Research Unit, 630 West North Street, Geneva, NY 14456-1371, USA
| | - Eric J B von Wettberg
- Florida International University, Department of Biological Sciences, 11200 Southwest 8th Street, Miami, FL 33199-2156, USA; Fairchild Tropical Botanic Garden, Kushlan Tropical Science Institute, 10901 Old Cutler Road, Coral Gables, FL 33156-4233, USA; Florida International University, International Center for Tropical Botany, 11200 Southwest 8th Street, Miami, FL 33199-2156, USA
| | - Allison J Miller
- Saint Louis University, Department of Biology, 3507 Laclede Avenue, St. Louis, MO 63103-2010, USA; Missouri Botanical Garden, 4344 Shaw Boulevard, St. Louis, MO 63110-2226, USA.
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30
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Barberán A, McGuire KL, Wolf JA, Jones FA, Wright SJ, Turner BL, Essene A, Hubbell SP, Faircloth BC, Fierer N. Relating belowground microbial composition to the taxonomic, phylogenetic, and functional trait distributions of trees in a tropical forest. Ecol Lett 2015; 18:1397-405. [PMID: 26472095 DOI: 10.1111/ele.12536] [Citation(s) in RCA: 134] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 08/25/2015] [Accepted: 09/23/2015] [Indexed: 12/17/2022]
Abstract
The complexities of the relationships between plant and soil microbial communities remain unresolved. We determined the associations between plant aboveground and belowground (root) distributions and the communities of soil fungi and bacteria found across a diverse tropical forest plot. Soil microbial community composition was correlated with the taxonomic and phylogenetic structure of the aboveground plant assemblages even after controlling for differences in soil characteristics, but these relationships were stronger for fungi than for bacteria. In contrast to expectations, the species composition of roots in our soil core samples was a poor predictor of microbial community composition perhaps due to the patchy, ephemeral, and highly overlapping nature of fine root distributions. Our ability to predict soil microbial composition was not improved by incorporating information on plant functional traits suggesting that the most commonly measured plant traits are not particularly useful for predicting the plot-level variability in belowground microbial communities.
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Affiliation(s)
- Albert Barberán
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA
| | - Krista L McGuire
- Department of Biology, Barnard College, Columbia University, New York, NY, USA.,Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA
| | - Jeffrey A Wolf
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, USA.,Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - F Andrew Jones
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA.,Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panama
| | - Stuart Joseph Wright
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panama
| | - Benjamin L Turner
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panama
| | - Adam Essene
- Department of Biological Sciences, Fordham University, New York, NY, USA
| | - Stephen P Hubbell
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA.,Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Panama
| | - Brant C Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, USA
| | - Noah Fierer
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA.,Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
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31
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Frank DA, Pontes AW, Maine EM, Fridley JD. Fine-scale belowground species associations in temperate grassland. Mol Ecol 2015; 24:3206-16. [PMID: 25951537 DOI: 10.1111/mec.13232] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 05/01/2015] [Accepted: 05/05/2015] [Indexed: 12/01/2022]
Abstract
Evaluating how belowground processes contribute to plant community dynamics is hampered by limited information on the spatial structure of root communities at the scale that plants interact belowground. In this study, roots were mapped to the nearest one mm and molecularly identified by species on vertical (0-15 cm deep) surfaces of soil blocks excavated from dry and mesic grasslands in Yellowstone National Park (YNP) to examine the spatial relationships among species at the scale that roots interact. Our results indicated that average interspecific root - root distances for the majority of species were within a distance (3 mm) that roots have been shown to compete for resources. Most species placed their roots at random, although low root numbers for many species probably led to overestimating the occurrence of random patterns. According to theory, we expected that most of the remaining species would segregate their root systems to avoid competition. Instead we found that more species aggregated than segregated from others. Based on previous investigations, we hypothesize that species aggregate to increase uptake of water, nitrogen and/or phosphorus made available by neighbouring roots, or as a consequence of a reduction in the pathogenicity of soil biota growing in multispecies mixtures. Our results indicate that YNP grassland root communities are organized as closely interdigitating networks of species that potentially can support strong interactions among many species combinations. Future root research should address the prevalence and functional consequences of species aggregation across plant communities.
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Affiliation(s)
- Douglas A Frank
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA
| | - Alyssa W Pontes
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA
| | - Eleanor M Maine
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA
| | - Jason D Fridley
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA
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Dybzinski R, Farrior CE, Pacala SW. Increased forest carbon storage with increased atmospheric CO2 despite nitrogen limitation: a game-theoretic allocation model for trees in competition for nitrogen and light. Glob Chang Biol 2015; 21:1182-96. [PMID: 25392967 DOI: 10.1111/gcb.12783] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 06/26/2014] [Accepted: 09/22/2014] [Indexed: 05/22/2023]
Abstract
Changes in resource availability often cause competitively driven changes in tree allocation to foliage, wood, and fine roots, either via plastic changes within individuals or through turnover of individuals with differing strategies. Here, we investigate how optimally competitive tree allocation should change in response to elevated atmospheric CO2 along a gradient of nitrogen and light availability, together with how those changes should affect carbon storage in living biomass. We present a physiologically-based forest model that includes the primary functions of wood and nitrogen. From a tree's perspective, wood is an offensive and defensive weapon used against neighbors in competition for light. From a biogeochemical perspective, wood is the primary living reservoir of stored carbon. Nitrogen constitutes a tree's photosynthetic machinery and the support systems for that machinery, and its limited availability thus reduces a tree's ability to fix carbon. This model has been previously successful in predicting allocation to foliage, wood, and fine roots along natural productivity gradients. Using game theory, we solve the model for competitively optimal foliage, wood, and fine root allocation strategies for trees in competition for nitrogen and light as a function of CO2 and nitrogen mineralization rate. Instead of down-regulating under nitrogen limitation, carbon storage under elevated CO2 relative to carbon storage at ambient CO2 is approximately independent of the nitrogen mineralization rate. This surprising prediction is a consequence of both increased competition for nitrogen driving increased fine root biomass and increased competition for light driving increased allocation to wood under elevated CO2 .
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Affiliation(s)
- Ray Dybzinski
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
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33
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Anderson-Teixeira KJ, Davies SJ, Bennett AC, Gonzalez-Akre EB, Muller-Landau HC, Wright SJ, Abu Salim K, Almeyda Zambrano AM, Alonso A, Baltzer JL, Basset Y, Bourg NA, Broadbent EN, Brockelman WY, Bunyavejchewin S, Burslem DFRP, Butt N, Cao M, Cardenas D, Chuyong GB, Clay K, Cordell S, Dattaraja HS, Deng X, Detto M, Du X, Duque A, Erikson DL, Ewango CEN, Fischer GA, Fletcher C, Foster RB, Giardina CP, Gilbert GS, Gunatilleke N, Gunatilleke S, Hao Z, Hargrove WW, Hart TB, Hau BCH, He F, Hoffman FM, Howe RW, Hubbell SP, Inman-Narahari FM, Jansen PA, Jiang M, Johnson DJ, Kanzaki M, Kassim AR, Kenfack D, Kibet S, Kinnaird MF, Korte L, Kral K, Kumar J, Larson AJ, Li Y, Li X, Liu S, Lum SKY, Lutz JA, Ma K, Maddalena DM, Makana JR, Malhi Y, Marthews T, Mat Serudin R, McMahon SM, McShea WJ, Memiaghe HR, Mi X, Mizuno T, Morecroft M, Myers JA, Novotny V, de Oliveira AA, Ong PS, Orwig DA, Ostertag R, den Ouden J, Parker GG, Phillips RP, Sack L, Sainge MN, Sang W, Sri-Ngernyuang K, Sukumar R, Sun IF, Sungpalee W, Suresh HS, Tan S, Thomas SC, Thomas DW, Thompson J, Turner BL, Uriarte M, Valencia R, Vallejo MI, Vicentini A, Vrška T, Wang X, Wang X, Weiblen G, Wolf A, Xu H, Yap S, Zimmerman J. CTFS-ForestGEO: a worldwide network monitoring forests in an era of global change. Glob Chang Biol 2015; 21:528-49. [PMID: 25258024 DOI: 10.1111/gcb.12712] [Citation(s) in RCA: 267] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Accepted: 07/06/2014] [Indexed: 05/10/2023]
Abstract
Global change is impacting forests worldwide, threatening biodiversity and ecosystem services including climate regulation. Understanding how forests respond is critical to forest conservation and climate protection. This review describes an international network of 59 long-term forest dynamics research sites (CTFS-ForestGEO) useful for characterizing forest responses to global change. Within very large plots (median size 25 ha), all stems ≥ 1 cm diameter are identified to species, mapped, and regularly recensused according to standardized protocols. CTFS-ForestGEO spans 25 °S-61 °N latitude, is generally representative of the range of bioclimatic, edaphic, and topographic conditions experienced by forests worldwide, and is the only forest monitoring network that applies a standardized protocol to each of the world's major forest biomes. Supplementary standardized measurements at subsets of the sites provide additional information on plants, animals, and ecosystem and environmental variables. CTFS-ForestGEO sites are experiencing multifaceted anthropogenic global change pressures including warming (average 0.61 °C), changes in precipitation (up to ± 30% change), atmospheric deposition of nitrogen and sulfur compounds (up to 3.8 g N m(-2) yr(-1) and 3.1 g S m(-2) yr(-1)), and forest fragmentation in the surrounding landscape (up to 88% reduced tree cover within 5 km). The broad suite of measurements made at CTFS-ForestGEO sites makes it possible to investigate the complex ways in which global change is impacting forest dynamics. Ongoing research across the CTFS-ForestGEO network is yielding insights into how and why the forests are changing, and continued monitoring will provide vital contributions to understanding worldwide forest diversity and dynamics in an era of global change.
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Affiliation(s)
- Kristina J Anderson-Teixeira
- Center for Tropical Forest Science-Forest Global Earth Observatory, Smithsonian Tropical Research Institute, Panama, Republic of Panama; Conservation Ecology Center, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA, USA
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Affiliation(s)
- Andy Jones
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA; Smithsonian Tropical Research Institute, Balboa, Ancon, Panama City, Republic of Panama
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Kress WJ, García-robledo C, Uriarte M, Erickson DL. DNA barcodes for ecology, evolution, and conservation. Trends Ecol Evol 2015; 30:25-35. [DOI: 10.1016/j.tree.2014.10.008] [Citation(s) in RCA: 284] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 10/23/2014] [Accepted: 10/28/2014] [Indexed: 01/28/2023]
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Valverde-Barrantes OJ, Smemo KA, Feinstein LM, Kershner MW, Blackwood CB. Aggregated and complementary: symmetric proliferation, overyielding, and mass effects explain fine-root biomass in soil patches in a diverse temperate deciduous forest landscape. New Phytol 2015; 205:731-742. [PMID: 25441303 DOI: 10.1111/nph.13179] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 10/12/2014] [Indexed: 06/04/2023]
Abstract
Few studies describe root distributions at the species level in diverse forests, although belowground species interactions and traits are often assumed to affect fine-root biomass (FRB). We used molecular barcoding to study how FRB of trees relates to soil characteristics, species identity, root diversity, and root traits, and how these relationships are affected by proximity to ecotones in a temperate forest landscape. We found that soil patch root biomass increased in response to soil resources across all species, and there was little belowground vertical or horizontal spatial segregation among species. Root traits and species relative abundance did not explain significant variation in FRB after correcting for soil fertility. A positive relationship between phylogenetic diversity and FRB indicated significant belowground overyielding attributable to local root diversity. Finally, variation in FRB explained by soil fertility and diversity was reduced near ecotones, but only because of a reduction in biomass in periodically anoxic areas. These results suggest that symmetric responses to soil properties are coupled with complementary species traits and interactions to explain variation in FRB among soil patches. In addition, landscape-level dispersal among habitats and across ecotones helps explain variation in the strength of these relationships in complex landscapes.
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Zeng W, Zhou B, Lei P, Zeng Y, Liu Y, Liu C, Xiang W. A molecular method to identify species of fine roots and to predict the proportion of a species in mixed samples in subtropical forests. Front Plant Sci 2015; 6:313. [PMID: 25999977 PMCID: PMC4422015 DOI: 10.3389/fpls.2015.00313] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 04/20/2015] [Indexed: 05/17/2023]
Abstract
Understanding of belowground interactions among tree species and the fine root (≤2 mm in diameter) contribution of a species to forest ecosystem production are mostly restricted by experimental difficulties in the quantification of the species composition. The available approaches have various defects. By contrast, DNA-based methods can avoid these drawbacks. Quantitative real-time polymerase chain reaction (PCR) is an advanced molecular technology, but it is difficult to develop specific primer sets. The method of next-generation sequencing has several limitations, such as inaccurate sequencing of homopolymer regions, as well as being time-consuming, and requiring special knowledge for data analysis. This study evaluated the potential of the DNA-sequence-based method to identify tree species and to quantify the relative proportion of each species in mixed fine root samples. We discriminated the species by isolating DNA from individual fine roots and amplifying the plastid trnL(UAA; i.e., tRNA-Leu-UAA) intron using the PCR. To estimate relative proportions, we extracted DNA from fine root mixtures. After the plastid trnL(UAA) intron amplification and TA-cloning, we sequenced the positive clones from each mixture. Our results indicated that the plastid trnL(UAA) intron spacer successfully distinguished tree species of fine roots in subtropical forests. In addition, the DNA-sequence-based approach could reliably estimate the relative proportion of each species in mixed fine root samples. To our knowledge, this is the first time that the DNA-sequence-based method has been used to quantify tree species proportions in mixed fine root samples in Chinese subtropical forests. As the cost of DNA-sequencing declines and DNA-sequence-based methods improve, the molecular method will be more widely used to determine fine root species and abundance.
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Affiliation(s)
- Weixian Zeng
- Faculty of Life Science and Technology, Central South University of Forestry and TechnologyChangsha, China
- National Engineering Laboratory of Applied Technology for Forestry and Ecology in Southern ChinaChangsha, China
| | - Bo Zhou
- Faculty of Life Science and Technology, Central South University of Forestry and TechnologyChangsha, China
| | - Pifeng Lei
- Faculty of Life Science and Technology, Central South University of Forestry and TechnologyChangsha, China
- National Engineering Laboratory of Applied Technology for Forestry and Ecology in Southern ChinaChangsha, China
| | - Yeling Zeng
- Faculty of Life Science and Technology, Central South University of Forestry and TechnologyChangsha, China
- Huitong National Field Station for Scientific Observation and Research of Chinese Fir Plantation Ecosystem in Hunan ProvinceHuitong, China
| | - Yan Liu
- Faculty of Life Science and Technology, Central South University of Forestry and TechnologyChangsha, China
- National Engineering Laboratory of Applied Technology for Forestry and Ecology in Southern ChinaChangsha, China
| | - Cong Liu
- Faculty of Life Science and Technology, Central South University of Forestry and TechnologyChangsha, China
- National Engineering Laboratory of Applied Technology for Forestry and Ecology in Southern ChinaChangsha, China
| | - Wenhua Xiang
- Faculty of Life Science and Technology, Central South University of Forestry and TechnologyChangsha, China
- Huitong National Field Station for Scientific Observation and Research of Chinese Fir Plantation Ecosystem in Hunan ProvinceHuitong, China
- *Correspondence: Wenhua Xiang, Faculty of Life Science and Technology, Central South University of Forestry and Technology, No. 498 Southern Shaoshan Road, Changsha 410004, Hunan, China
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Erickson DL, Jones FA, Swenson NG, Pei N, Bourg NA, Chen W, Davies SJ, Ge XJ, Hao Z, Howe RW, Huang CL, Larson AJ, Lum SKY, Lutz JA, Ma K, Meegaskumbura M, Mi X, Parker JD, Fang-Sun I, Wright SJ, Wolf AT, Ye W, Xing D, Zimmerman JK, Kress WJ. Comparative evolutionary diversity and phylogenetic structure across multiple forest dynamics plots: a mega-phylogeny approach. Front Genet 2014; 5:358. [PMID: 25414723 PMCID: PMC4220724 DOI: 10.3389/fgene.2014.00358] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 09/26/2014] [Indexed: 11/13/2022] Open
Abstract
Forest dynamics plots, which now span longitudes, latitudes, and habitat types across the globe, offer unparalleled insights into the ecological and evolutionary processes that determine how species are assembled into communities. Understanding phylogenetic relationships among species in a community has become an important component of assessing assembly processes. However, the application of evolutionary information to questions in community ecology has been limited in large part by the lack of accurate estimates of phylogenetic relationships among individual species found within communities, and is particularly limiting in comparisons between communities. Therefore, streamlining and maximizing the information content of these community phylogenies is a priority. To test the viability and advantage of a multi-community phylogeny, we constructed a multi-plot mega-phylogeny of 1347 species of trees across 15 forest dynamics plots in the ForestGEO network using DNA barcode sequence data (rbcL, matK, and psbA-trnH) and compared community phylogenies for each individual plot with respect to support for topology and branch lengths, which affect evolutionary inference of community processes. The levels of taxonomic differentiation across the phylogeny were examined by quantifying the frequency of resolved nodes throughout. In addition, three phylogenetic distance (PD) metrics that are commonly used to infer assembly processes were estimated for each plot [PD, Mean Phylogenetic Distance (MPD), and Mean Nearest Taxon Distance (MNTD)]. Lastly, we examine the partitioning of phylogenetic diversity among community plots through quantification of inter-community MPD and MNTD. Overall, evolutionary relationships were highly resolved across the DNA barcode-based mega-phylogeny, and phylogenetic resolution for each community plot was improved when estimated within the context of the mega-phylogeny. Likewise, when compared with phylogenies for individual plots, estimates of phylogenetic diversity in the mega-phylogeny were more consistent, thereby removing a potential source of bias at the plot-level, and demonstrating the value of assessing phylogenetic relationships simultaneously within a mega-phylogeny. An unexpected result of the comparisons among plots based on the mega-phylogeny was that the communities in the ForestGEO plots in general appear to be assemblages of more closely related species than expected by chance, and that differentiation among communities is very low, suggesting deep floristic connections among communities and new avenues for future analyses in community ecology.
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Affiliation(s)
- David L. Erickson
- Department of Botany, Museum Routing Code-166, National Museum of Natural History, Smithsonian InstitutionWashington, DC, USA
| | - Frank A. Jones
- Department of Botany and Plant Pathology, Oregon State UniversityCorvallis, OR, USA
- Smithsonian Tropical Research Institute, PanamáPanamá
| | - Nathan G. Swenson
- Department of Plant Biology, Michigan State UniversityEast Lansing, MI, USA
| | - Nancai Pei
- Forest Ecosystem Station of the Pearl River Delta, State Forestry Administration, Research Institute of Tropical Forestry, Chinese Academy of ForestryGuangzhou, China
| | - Norman A. Bourg
- Conservation Ecology Center, Smithsonian Conservation Biology Institute, Smithsonian InstitutionFront Royal, VA, USA
| | - Wenna Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, The Chinese Academy of SciencesGuangzhou, China
| | - Stuart J. Davies
- Center for Tropical Forest Science-Forest Global Earth Observatory, Smithsonian Tropical Research InstituteWashington, DC, USA
| | - Xue-jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, The Chinese Academy of SciencesGuangzhou, China
| | - Zhanqing Hao
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of ScienceShenyang, China
| | - Robert W. Howe
- Department of Natural and Applied Sciences, Biology Program, University of Wisconsin-Green BayGreen Bay, WI, USA
| | - Chun-Lin Huang
- Laboratory of Molecular Phylogenetics, Department of Biology, National Museum of Natural ScienceTaichung, Taiwan
| | - Andrew J. Larson
- Department of Forest Management, The University of MontanaMissoula, MT, USA
| | - Shawn K. Y. Lum
- National Institute of Education, Nanyang Technological University, SingaporeSingapore
| | - James A. Lutz
- Wildland Resources, Utah State UniversityLogan, UT, USA
| | - Keping Ma
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Madhava Meegaskumbura
- Department of Zoology, Faculty of Science, University of PeradeniyaPeradeniya, Sri Lanka
| | - Xiangcheng Mi
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - John D. Parker
- Smithsonian Environmental Research Center, Smithsonian InstitutionEdgewater, MD, USA
| | - I. Fang-Sun
- Department of Natural Resources and Environmental Studies, National Dong Hwa UniversityHualien, Taiwan
| | | | - Amy T. Wolf
- Department of Natural and Applied Sciences, Biology Program, University of Wisconsin-Green BayGreen Bay, WI, USA
| | - W. Ye
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, The Chinese Academy of SciencesGuangzhou, China
| | - Dingliang Xing
- State Key Laboratory of Forest and Soil Ecology, Institute of Applied Ecology, Chinese Academy of ScienceShenyang, China
| | - Jess K. Zimmerman
- Institute for Tropical Ecosystem Studies, University of Puerto RicoSan Juan, PR, USA
| | - W. John Kress
- Department of Botany, Museum Routing Code-166, National Museum of Natural History, Smithsonian InstitutionWashington, DC, USA
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Miller AC, Woeste KE, Anagnostakis SL, Jacobs DF. Exploration of a rare population of Chinese chestnut in North America: stand dynamics, health and genetic relationships. AoB Plants 2014; 6:plu065. [PMID: 25336337 PMCID: PMC4243075 DOI: 10.1093/aobpla/plu065] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Accepted: 10/01/2014] [Indexed: 06/04/2023]
Abstract
With the transport of plants around the globe, exotic species can readily spread disease to their native relatives; however, they can also provide genetic resistance to those relatives through hybrid breeding programmes. American chestnut (Castanea dentata) was an abundant tree species in North America until its decimation by introduced chestnut blight. To restore chestnut in North America, efforts are ongoing to test putative blight-resistant hybrids of Castanea dentata and Chinese chestnut (Castanea mollissima), but little is known about the ecology of C. mollissima. In a forest in northeastern USA in which C. mollissima has become established, we explored questions of stand dynamics, health and genetic relationships of C. mollissima offspring to an adjacent parent orchard. We found that C. mollissima was adapted and randomly distributed among native species in this relatively young forest. The genetics of the C. mollissima population compared with its parents indicated little effect of selection pressure as each of the parent trees contributed at least one offspring. The ease with which this exotic species proliferated calls to question why C. mollissima is rare elsewhere in forests of North America. It is likely that a time window of low animal predation allowed seedlings to establish, and the shallow soil at this site limited the maximum forest canopy height, permitting the characteristically short-statured C. mollissima to avoid suppression. Our results indicate that because C. mollissima exhibited pioneer species characteristics, hybrids between C. mollissima and C. dentata have the potential to be successful pioneer species of future forests in North America, and we challenge the paradigm that exotic tree species are wholly detrimental to native biodiversity. We contend that exotic tree species should be assessed not only by their level of threat to native species, but also by their potential positive impacts on ecosystems via hybrid breeding programmes.
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Affiliation(s)
- Amy C Miller
- Department of Forestry and Natural Resources, Hardwood Tree Improvement and Regeneration Center, Purdue University, 715 West State St., West Lafayette, IN 47907, USA
| | - Keith E Woeste
- USDA Forest Service, Northern Research Station, Hardwood Tree Improvement and Regeneration Center, 715 West State St., West Lafayette, IN 47907, USA
| | | | - Douglass F Jacobs
- Department of Forestry and Natural Resources, Hardwood Tree Improvement and Regeneration Center, Purdue University, 715 West State St., West Lafayette, IN 47907, USA
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Gundel PE, Pierik R, Mommer L, Ballaré CL. Competing neighbors: light perception and root function. Oecologia 2014; 176:1-10. [DOI: 10.1007/s00442-014-2983-x] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 05/24/2014] [Indexed: 11/24/2022]
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41
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Papadopoulou A, Chesters D, Coronado I, De la Cadena G, Cardoso A, Reyes JC, Maes JM, Rueda RM, Gómez-Zurita J. Automated DNA-based plant identification for large-scale biodiversity assessment. Mol Ecol Resour 2014; 15:136-52. [PMID: 24666885 DOI: 10.1111/1755-0998.12256] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 02/17/2014] [Accepted: 02/22/2014] [Indexed: 11/29/2022]
Abstract
Rapid degradation of tropical forests urges to improve our efficiency in large-scale biodiversity assessment. DNA barcoding can assist greatly in this task, but commonly used phenetic approaches for DNA-based identifications rely on the existence of comprehensive reference databases, which are infeasible for hyperdiverse tropical ecosystems. Alternatively, phylogenetic methods are more robust to sparse taxon sampling but time-consuming, while multiple alignment of species-diagnostic, typically length-variable, markers can be problematic across divergent taxa. We advocate the combination of phylogenetic and phenetic methods for taxonomic assignment of DNA-barcode sequences against incomplete reference databases such as GenBank, and we developed a pipeline to implement this approach on large-scale plant diversity projects. The pipeline workflow includes several steps: database construction and curation, query sequence clustering, sequence retrieval, distance calculation, multiple alignment and phylogenetic inference. We describe the strategies used to establish these steps and the optimization of parameters to fit the selected psbA-trnH marker. We tested the pipeline using infertile plant samples and herbivore diet sequences from the highly threatened Nicaraguan seasonally dry forest and exploiting a valuable purpose-built resource: a partial local reference database of plant psbA-trnH. The selected methodology proved efficient and reliable for high-throughput taxonomic assignment, and our results corroborate the advantage of applying 'strict' tree-based criteria to avoid false positives. The pipeline tools are distributed as the scripts suite 'BAGpipe' (pipeline for Biodiversity Assessment using GenBank data), which can be readily adjusted to the purposes of other projects and applied to sequence-based identification for any marker or taxon.
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Affiliation(s)
- Anna Papadopoulou
- Animal Biodiversity and Evolution, Institut de Biologia Evolutiva (CSIC-Univ. Pompeu Fabra), 08003, Barcelona, Spain
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Pearse WD, Jones FA, Purvis A. Barro Colorado Island's phylogenetic assemblage structure across fine spatial scales and among clades of different ages. Ecology 2013; 94:2861-72. [DOI: 10.1890/12-1676.1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Farrior CE, Dybzinski R, Levin SA, Pacala SW. Competition for water and light in closed-canopy forests: a tractable model of carbon allocation with implications for carbon sinks. Am Nat 2013; 181:314-30. [PMID: 23448882 DOI: 10.1086/669153] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Abstract The dependence of forest productivity and community composition on rainfall is the result of complex interactions at multiple scales, from the physiology of carbon gain and water loss to competition among individuals and species. In an effort to understand the role of these multiscale interactions in the dependence of forest structure on rainfall, we build a tractable model of individual plant competition for water and light. With game-theoretic analyses, we predict the dominant plant allocation strategy, forest productivity, and carbon storage. We find that the amount and timing of rainfall are critical to forest structure. Comparing two forests that differ only in the total time plants spend in water saturation, the model predicts that the wetter forest has fewer fine roots, more leaves, and more woody biomass than the drier forest. In contrast, if two forests differ only in the amount of water available during water limitation, the model predicts that the wetter forest has more fine roots than the drier forest and equivalent leaves and woody biomass. The difference in these responses to increases in water availability has significant implications for potential carbon sinks with rising atmospheric CO2. We predict that enhanced productivity from increased leaf-level water-use efficiency during water limitation will be allocated to fine roots if plants respond competitively, producing only a small and short-lived carbon sink.
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Affiliation(s)
- Caroline E Farrior
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.
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Affiliation(s)
- Meelis Pärtel
- Institute of Ecology and Earth Sciences; University of Tartu; Lai 40; 51005; Tartu; Estonia
| | - Inga Hiiesalu
- Institute of Ecology and Earth Sciences; University of Tartu; Lai 40; 51005; Tartu; Estonia
| | - Maarja Öpik
- Institute of Ecology and Earth Sciences; University of Tartu; Lai 40; 51005; Tartu; Estonia
| | - Scott D. Wilson
- Department of Biology; University of Regina; Regina; Saskatchewan; S4S 0A2; Canada
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Hiiesalu I, Opik M, Metsis M, Lilje L, Davison J, Vasar M, Moora M, Zobel M, Wilson SD, Pärtel M. Plant species richness belowground: higher richness and new patterns revealed by next-generation sequencing. Mol Ecol 2011; 21:2004-16. [PMID: 22168247 DOI: 10.1111/j.1365-294x.2011.05390.x] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Variation in plant species richness has been described using only aboveground vegetation. The species richness of roots and rhizomes has never been compared with aboveground richness in natural plant communities. We made direct comparisons of grassland plant richness in identical volumes (0.1 × 0.1 × 0.1 m) above and below the soil surface, using conventional species identification to measure aboveground richness and 454 sequencing of the chloroplast trnL(UAA) intron to measure belowground richness. We described above- and belowground richness at multiple spatial scales (from a neighbourhood scale of centimetres to a community scale of hundreds of metres), and related variation in richness to soil fertility. Tests using reference material indicated that 454 sequencing captured patterns of species composition and abundance with acceptable accuracy. At neighbourhood scales, belowground richness was up to two times greater than aboveground richness. The relationship between above- and belowground richness was significantly different from linear: beyond a certain level of belowground richness, aboveground richness did not increase further. Belowground richness also exceeded that of aboveground at the community scale, indicating that some species are temporarily dormant and absent aboveground. Similar to other grassland studies, aboveground richness declined with increasing soil fertility; in contrast, the number of species found only belowground increased significantly with fertility. These results indicate that conventional aboveground studies of plant richness may overlook many coexisting species, and that belowground richness becomes relatively more important in conditions where aboveground richness decreases. Measuring plant belowground richness can considerably alter perceptions of biodiversity and its responses to natural and anthropogenic factors.
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Affiliation(s)
- Inga Hiiesalu
- Department of Botany, University of Tartu, Tartu, Estonia.
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