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Blackman R, Couton M, Keck F, Kirschner D, Carraro L, Cereghetti E, Perrelet K, Bossart R, Brantschen J, Zhang Y, Altermatt F. Environmental DNA: The next chapter. Mol Ecol 2024; 33:e17355. [PMID: 38624076 DOI: 10.1111/mec.17355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 04/17/2024]
Abstract
Molecular tools are an indispensable part of ecology and biodiversity sciences and implemented across all biomes. About a decade ago, the use and implementation of environmental DNA (eDNA) to detect biodiversity signals extracted from environmental samples opened new avenues of research. Initial eDNA research focused on understanding population dynamics of target species. Its scope thereafter broadened, uncovering previously unrecorded biodiversity via metabarcoding in both well-studied and understudied ecosystems across all taxonomic groups. The application of eDNA rapidly became an established part of biodiversity research, and a research field by its own. Here, we revisit key expectations made in a land-mark special issue on eDNA in Molecular Ecology in 2012 to frame the development in six key areas: (1) sample collection, (2) primer development, (3) biomonitoring, (4) quantification, (5) behaviour of DNA in the environment and (6) reference database development. We pinpoint the success of eDNA, yet also discuss shortfalls and expectations not met, highlighting areas of research priority and identify the unexpected developments. In parallel, our retrospective couples a screening of the peer-reviewed literature with a survey of eDNA users including academics, end-users and commercial providers, in which we address the priority areas to focus research efforts to advance the field of eDNA. With the rapid and ever-increasing pace of new technical advances, the future of eDNA looks bright, yet successful applications and best practices must become more interdisciplinary to reach its full potential. Our retrospect gives the tools and expectations towards concretely moving the field forward.
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Affiliation(s)
- Rosetta Blackman
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Marjorie Couton
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - François Keck
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Dominik Kirschner
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, Ecosystems and Landscape Evolution, ETH Zürich, Zürich, Switzerland
- Department of Landscape Dynamics & Ecology, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Luca Carraro
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Eva Cereghetti
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Kilian Perrelet
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
- Department of Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
- Department of Urban Water Management, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Raphael Bossart
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Jeanine Brantschen
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Yan Zhang
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, China
| | - Florian Altermatt
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
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Davison J, Gerz M, Hiiesalu I, Moora M, Semchenko M, Zobel M. Niche types and community assembly. Ecol Lett 2024; 27:e14327. [PMID: 37819920 DOI: 10.1111/ele.14327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 10/13/2023]
Abstract
Studies of niche differentiation and biodiversity often focus on a few niche dimensions due to the methodological challenge of describing hyperdimensional niche space. However, this may limit our understanding of community assembly processes. We used the full spectrum of realized niche types to study arbuscular mycorrhizal fungal communities: distinguishing abiotic and biotic, and condition and resource, axes. Estimates of differentiation in relation to different niche types were only moderately correlated. However, coexisting taxon niches were consistently less differentiated than expected, based on a regional null model, indicating the importance of habitat filtering at that scale. Nonetheless, resource niches were relatively more differentiated than condition niches, which is consistent with the effect of a resource niche-based coexistence mechanism. Considering niche types, and in particular distinguishing resource and condition niches, provides a more complete understanding of community assembly, compared with studying individual niche axes or the full niche.
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Affiliation(s)
- John Davison
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Maret Gerz
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Inga Hiiesalu
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Mari Moora
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Marina Semchenko
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Martin Zobel
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
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Wipulasena AYAP, Davison J, Helm A, Kasari L, Moora M, Prangel E, Reitalu T, Vahter T, Vasar M, Zobel M. Soil community composition in dynamic stages of semi-natural calcareous grassland. PLoS One 2023; 18:e0292425. [PMID: 37847721 PMCID: PMC10581465 DOI: 10.1371/journal.pone.0292425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/20/2023] [Indexed: 10/19/2023] Open
Abstract
European dry thin-soil calcareous grasslands (alvars) are species-rich semi-natural habitats. Cessation of traditional management, such as mowing and grazing, leads to shrub and tree encroachment and the local extinction of characteristic alvar species. While soil microbes are known to play a critical role in driving vegetation and ecosystem dynamics, more information is needed about their composition and function in grasslands of different dynamic stages. Here we assess the composition of soil fungal, prokaryotic, and plant communities using soil environmental DNA from restored alvar grasslands in Estonia. The study areas included grasslands that had experienced different degrees of woody encroachment prior to restoration (woody plant removal and grazing), as well as unmanaged open grasslands. We found that, in general, different taxonomic groups exhibited correlated patterns of between-community variation. Previous forest sites, which had prior to restoration experienced a high degree of woody encroachment by ectomycorrhizal Scots pine, were compositionally most distinct from managed open grasslands, which had little woody vegetation even prior to restoration. The functional structure of plant and fungal communities varied in ways that were consistent with the representation of mycorrhizal types in the ecosystems prior to restoration. Compositional differences between managed and unmanaged open grasslands reflecting the implementation of grazing without further management interventions were clearer among fungal, and to an extent prokaryotic, communities than among plant communities. While previous studies have shown that during woody encroachment of alvar grassland, plant communities change first and fungal communities follow, our DNA-based results suggest that microbial communities reacted faster than plant communities during the restoration of grazing management in alvar grassland. We conclude that while the plant community responds faster to cessation of management, the fungal community responds faster to restoration of management. This may indicate hysteresis, where the eventual pathway back to the original state (grazed ecosystem) differs from the pathway taken towards the alternative state (abandoned semi-natural grassland ecosystem).
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Affiliation(s)
- A. Y. Ayesh Piyara Wipulasena
- Department of Botany, Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - John Davison
- Department of Botany, Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Aveliina Helm
- Department of Botany, Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Liis Kasari
- Department of Botany, Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Mari Moora
- Department of Botany, Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Elisabeth Prangel
- Department of Botany, Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Triin Reitalu
- Department of Botany, Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Tanel Vahter
- Department of Botany, Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Martti Vasar
- Department of Botany, Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Martin Zobel
- Department of Botany, Institute of Ecology and Earth Sciences, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
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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. ANNALS OF BOTANY 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] [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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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. THE NEW PHYTOLOGIST 2023; 238:1305-1317. [PMID: 36444527 DOI: 10.1111/nph.18645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 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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González-Toral C, Nava HS, Fernández Prieto JA, Cires E. What Hides in the Heights? The Case of the Iberian Endemism Bromus picoeuropeanus. PLANTS (BASEL, SWITZERLAND) 2023; 12:1531. [PMID: 37050157 PMCID: PMC10096826 DOI: 10.3390/plants12071531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/28/2023] [Accepted: 03/30/2023] [Indexed: 06/19/2023]
Abstract
Bromus picoeuropeanus is a recently described species belonging to a complex genus of grasses. It inhabits stony soils at heights ranging from 1600 to 2200 m in Picos de Europa (Cantabrian Mountains, northern Spain). This species is morphologically very similar to B. erectus, partially sharing its presumed distribution range. We aim to determine the relationship between these species and their altitudinal ranges in Picos de Europa and the Cantabrian Mountains by conducting phylogenetic analyses based on nuclear (ETS and ITS) and chloroplastic (trnL) markers. Phylogenetic trees were inferred by Maximum Likelihood and Bayesian Inference. Haplotype networks were estimated based on the plastid marker. Although the ITS topologies could not generate exclusive clades for these species, the ETS analyses generated highly supported B. picoeuropeanus exclusive clades, which included locations outside its altitudinal putative range. The ETS-ITS and ETS-ITS-trnL topologies generated B. picoeuropeanus exclusive clades, whereas the trnL-based trees and haplotype networks were unable to discriminate B. erectus and B. picoeuropeanus. This evidence suggests that B. picoeuropeanus is a separate species with a larger distribution than previously thought, opening new questions regarding the evolution of B. erectus and other similar species in European mountainous systems. However, more information is needed regarding B. picoeuropeanus susceptibility to temperature rises.
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Affiliation(s)
- Claudia González-Toral
- Department of Organisms and Systems Biology, University of Oviedo, C/Catedrático Rodrigo Uría s/n, 33071 Oviedo, Spain
| | - Herminio S. Nava
- Department of Organisms and Systems Biology, University of Oviedo, C/Catedrático Rodrigo Uría s/n, 33071 Oviedo, Spain
| | - José Antonio Fernández Prieto
- Department of Organisms and Systems Biology, University of Oviedo, C/Catedrático Rodrigo Uría s/n, 33071 Oviedo, Spain
- Institute of Natural Resources and Territorial Planning (INDUROT), Campus de Mieres, C/Gonzalo Gutiérrez Quirós s/n, 33600 Mieres, Spain
| | - Eduardo Cires
- Department of Organisms and Systems Biology, University of Oviedo, C/Catedrático Rodrigo Uría s/n, 33071 Oviedo, Spain
- Institute of Natural Resources and Territorial Planning (INDUROT), Campus de Mieres, C/Gonzalo Gutiérrez Quirós s/n, 33600 Mieres, Spain
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Vasar M, Davison J, Moora M, Sepp SK, Anslan S, Al-Quraishy S, Bahram M, Bueno CG, Cantero JJ, Fabiano EC, Decocq G, Drenkhan R, Fraser L, Oja J, Garibay-Orijel R, Hiiesalu I, Koorem K, Mucina L, Öpik M, Põlme S, Pärtel M, Phosri C, Semchenko M, Vahter T, Doležal J, Palacios AMV, Tedersoo L, Zobel M. Metabarcoding of soil environmental DNA to estimate plant diversity globally. FRONTIERS IN PLANT SCIENCE 2023; 14:1106617. [PMID: 37143888 PMCID: PMC10151745 DOI: 10.3389/fpls.2023.1106617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 04/03/2023] [Indexed: 05/06/2023]
Abstract
Introduction Traditional approaches to collecting large-scale biodiversity data pose huge logistical and technical challenges. We aimed to assess how a comparatively simple method based on sequencing environmental DNA (eDNA) characterises global variation in plant diversity and community composition compared with data derived from traditional plant inventory methods. Methods We sequenced a short fragment (P6 loop) of the chloroplast trnL intron from from 325 globally distributed soil samples and compared estimates of diversity and composition with those derived from traditional sources based on empirical (GBIF) or extrapolated plant distribution and diversity data. Results Large-scale plant diversity and community composition patterns revealed by sequencing eDNA were broadly in accordance with those derived from traditional sources. The success of the eDNA taxonomy assignment, and the overlap of taxon lists between eDNA and GBIF, was greatest at moderate to high latitudes of the northern hemisphere. On average, around half (mean: 51.5% SD 17.6) of local GBIF records were represented in eDNA databases at the species level, depending on the geographic region. Discussion eDNA trnL gene sequencing data accurately represent global patterns in plant diversity and composition and thus can provide a basis for large-scale vegetation studies. Important experimental considerations for plant eDNA studies include using a sampling volume and design to maximise the number of taxa detected and optimising the sequencing depth. However, increasing the coverage of reference sequence databases would yield the most significant improvements in the accuracy of taxonomic assignments made using the P6 loop of the trnL region.
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Affiliation(s)
- Martti Vasar
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
- *Correspondence: Martti Vasar,
| | - John Davison
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Mari Moora
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Siim-Kaarel Sepp
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Sten Anslan
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Saleh Al-Quraishy
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad Bahram
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - C. Guillermo Bueno
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Juan José Cantero
- Instituto Multidisciplinario de Biología Vegetal, Universidad Nacional de Córdoba, CONICET, Córdoba, Argentina
- Departamento de Biología Agrícola, Facultad de Agronomía y Veterinaria, Universidad Nacional de Río Cuarto, Córdoba, Argentina
| | | | - Guillaume Decocq
- Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN, UMR CNRS 7058), Jules Verne, University of Picardie, Amiens, France
| | - Rein Drenkhan
- Institute of Forestry and Engineering, Estonian University of Life Sciences, Tartu, Estonia
| | - Lauchlan Fraser
- Department of Natural Resource Sciences, Thompson Rivers University, Kamloops, BC, Canada
| | - Jane Oja
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Roberto Garibay-Orijel
- Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Inga Hiiesalu
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Kadri Koorem
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Ladislav Mucina
- Iluka Chair in Vegetation Science and Biogeography, Harry Butler Institute, Murdoch University, Perth, WA, Australia
- Department of Geography & Environmental Studies, Stellenbosch University, Stellenbosch, South Africa
| | - Maarja Öpik
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Sergei Põlme
- Center of Mycology and Microbiology, University of Tartu, Tartu, Estonia
| | - Meelis Pärtel
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Cherdchai Phosri
- Department of Biology, Nakhon Phanom University, Nakhon Phanom, Thailand
| | - Marina Semchenko
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Tanel Vahter
- Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Jiři Doležal
- Institute of Botany, The Czech Academy of Sciences, Třeboň, Czechia
- Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Aida M. Vasco Palacios
- Grupo de Microbiología Ambiental y Grupo BioMicro, Escuela de Microbiología, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Leho Tedersoo
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Center of Mycology and Microbiology, University of Tartu, Tartu, Estonia
| | - Martin Zobel
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Botany, University of Tartu, Tartu, Estonia
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8
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Hodžić J, Pearse I, Beaury EM, Corbin JD, Bakker JD. Root hemiparasitic plants are associated with more even communities across North America. Ecology 2022; 103:e3837. [PMID: 36178041 PMCID: PMC10077900 DOI: 10.1002/ecy.3837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 05/23/2022] [Indexed: 11/08/2022]
Abstract
Root hemiparasitic plants both compete with and extract resources from host plants. By reducing the abundance of dominant plants and releasing subordinates from competitive exclusion, they can have an outsized impact on plant communities. Most research on the ecological role of hemiparasites is manipulative and focuses on a small number of hemiparasitic taxa. Here, we ask whether patterns in natural plant communities match the expectation that hemiparasites affect the structure of plant communities. Our data were collected on 129 national park units spanning the continental United States. The most common hemiparasite genera were Pedicularis, Castilleja, Krameria, and Comandra. We used null models and linear mixed models to determine whether hemiparasites were associated with changes in community richness and evenness. Hemiparasite presence did not affect community metrics. Hemiparasite abundance was positively associated with increasing evenness of herbaceous species, but not with species richness. The associations that we observed on a continental scale are consistent with evidence that the impacts of root hemiparasitic plants on evenness can be substantial and abundance dependent but that effects on richness are less pronounced. Hemiparasites mediate competitive exclusion in communities to facilitate species coexistence and merit consideration of inclusion in ecological theories of coexistence.
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Affiliation(s)
- Jasna Hodžić
- School of Environmental and Forest Sciences University of Washington Seattle WA
| | - Ian Pearse
- U.S. Geological Survey, Fort Collins Science Center Fort Collins CO
| | - Evelyn M. Beaury
- Organismic and Evolutionary Biology Graduate Program University of Massachusetts Amherst Amherst MA
| | | | - Jonathan D. Bakker
- School of Environmental and Forest Sciences University of Washington Seattle WA
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9
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A Critical Assessment of the Congruency between Environmental DNA and Palaeoecology for the Biodiversity Monitoring and Palaeoenvironmental Reconstruction. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19159445. [PMID: 35954801 PMCID: PMC9368151 DOI: 10.3390/ijerph19159445] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 02/01/2023]
Abstract
The present study suggests that standardized methodology, careful site selection, and stratigraphy are essential for investigating ancient ecosystems in order to evaluate biodiversity and DNA-based time series. Based on specific keywords, this investigation reviewed 146 publications using the SCOPUS, Web of Science (WoS), PUBMED, and Google Scholar databases. Results indicate that environmental deoxyribose nucleic acid (eDNA) can be pivotal for assessing and conserving ecosystems. Our review revealed that in the last 12 years (January 2008–July 2021), 63% of the studies based on eDNA have been reported from aquatic ecosystems, 25% from marine habitats, and 12% from terrestrial environments. Out of studies conducted in aquatic systems using the environmental DNA (eDNA) technique, 63% of the investigations have been reported from freshwater ecosystems, with an utmost focus on fish diversity (40%). Further analysis of the literature reveals that during the same period, 24% of the investigations using the environmental DNA technique were carried out on invertebrates, 8% on mammals, 7% on plants, 6% on reptiles, and 5% on birds. The results obtained clearly indicate that the environmental DNA technique has a clear-cut edge over other biodiversity monitoring methods. Furthermore, we also found that eDNA, in conjunction with different dating techniques, can provide better insight into deciphering eco-evolutionary feedback. Therefore, an attempt has been made to offer extensive information on the application of dating methods for different taxa present in diverse ecosystems. Last, we provide suggestions and elucidations on how to overcome the caveats and delineate some of the research avenues that will likely shape this field in the near future. This paper aims to identify the gaps in environmental DNA (eDNA) investigations to help researchers, ecologists, and decision-makers to develop a holistic understanding of environmental DNA (eDNA) and its utility as a palaeoenvironmental contrivance.
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10
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Ariza M, Fouks B, Mauvisseau Q, Halvorsen R, Alsos IG, de Boer H. Plant biodiversity assessment through soil
eDNA
reflects temporal and local diversity. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- María Ariza
- Universitetet i Oslo, Naturhistorisk Museum Oslo Norway
| | - Bertrand Fouks
- Westfälische Wilhelms‐Universität Institute for Evolution and Biodiversity Molecular Evolution and Bioinformatics. Hüfferstraße 1 Münster Germany
| | | | | | - Inger Greve Alsos
- The Arctic University Museum of Norway UiT ‐ The Arctic University of Norway Norway
| | - Hugo de Boer
- Universitetet i Oslo, Naturhistorisk Museum Oslo Norway
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11
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Plastid Genome of Equisetum xylochaetum from the Atacama Desert, Chile and the Relationships of Equisetum Based on Frequently Used Plastid Genes and Network Analysis. PLANTS 2022; 11:plants11071001. [PMID: 35406981 PMCID: PMC9002811 DOI: 10.3390/plants11071001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 04/02/2022] [Accepted: 04/04/2022] [Indexed: 11/22/2022]
Abstract
The modern pteridophyte genus Equisetum is the only survivor of Sphenopsida, an ancient clade known from the Devonian. This genus, of nearly worldwide distribution, comprises approximately 15 extant species. However, genomic information is limited. In this study, we assembled the complete chloroplast genome of the giant species Equisetum xylochaetum from a metagenomic sequence and compared the plastid genome structure and protein-coding regions with information available for two other Equisetum species using network analysis. Equisetum chloroplast genomes showed conserved traits of quadripartite structure, gene content, and gene order. Phylogenetic analysis based on plastome protein-coding regions corroborated previous reports that Equisetum is monophyletic, and that E. xylochaetum is more closely related to E. hyemale than to E. arvense. Single-gene phylogenetic estimation and haplotype analysis showed that E. xylochaetum belonged to the subgenus Hippochaete. Single-gene haplotype analysis revealed that E. arvense, E. hyemale, E. myriochaetum, and E. variegatum resolved more than one haplotype per species, suggesting the presence of a high diversity or a high mutation rate of the corresponding nucleotide sequence. Sequences from E. bogotense appeared as a distinct group of haplotypes representing the subgenus Paramochaete that diverged from Hippochaete and Equisetum. In addition, the taxa that were frequently located at the joint region of the map were E. scirpoides and E. pratense, suggesting the presence of some plastome characters among the Equiseum subgenera.
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12
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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. THE NEW PHYTOLOGIST 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] [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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13
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Osathanunkul M, Sawongta N, Pheera W, Pechlivanis N, Psomopoulos F, Madesis P. Exploring plant diversity through soil DNA in Thai national parks for influencing land reform and agriculture planning. PeerJ 2021; 9:e11753. [PMID: 34414025 PMCID: PMC8340909 DOI: 10.7717/peerj.11753] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 06/21/2021] [Indexed: 11/20/2022] Open
Abstract
Background The severe deforestation, as indicated in national forest data, is a recurring problem in many areas of Northern Thailand, including Doi Suthep-Pui National Park. Agricultural expansion in these areas, is one of the major drivers of deforestation, having adverse consequences on local plant biodiversity. Conserving biodiversity is mainly dependent on the biological monitoring of species distribution and population sizes. However, the existing conventional approaches for monitoring biodiversity are rather limited. Methods Here, we explored soil DNA at four forest types in Doi Suthep-Pui National Park in Northern Thailand. Three soil samples, composed of different soil cores mixed together, per sampling location were collected. Soil biodiversity was investigated through eDNA metabarcoding analysis using primers targeting the P6 loop of the plastid DNA trnL (UAA) intron. Results The distribution of taxa for each sample was found to be similar between replicates. A strong congruence between the conventional morphology- and eDNA-based data of plant diversity in the studied areas was observed. All species recorded by conventional survey with DNA data deposited in the GenBank were detected through the eDNA analysis. Moreover, traces of crops, such as lettuce, maize, wheat and soybean, which were not expected and were not visually detected in the forest area, were identified. It is noteworthy that neighboring land and areas in the studied National Park were once used for crop cultivation, and even to date there is still agricultural land within a 5-10 km radius from the forest sites where the soil samples were collected. The presence of cultivated area near the forest may suggest that we are now facing agricultural intensification leading to deforestation. Land reform for agriculture usage necessitates coordinated planning in order to preserve the forest area. In that context, the eDNA-based data would be useful for influencing policies and management towards this goal.
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Affiliation(s)
- Maslin Osathanunkul
- Research Center in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, Chiang Mai, Thailand.,Faculty of Science, Department of Biology, Chiang Mai University, Chiang Mai, Thailand
| | - Nipitpong Sawongta
- Faculty of Science, Department of Biology, Chiang Mai University, Chiang Mai, Thailand
| | - Wittaya Pheera
- Faculty of Science, Department of Biology, Chiang Mai University, Chiang Mai, Thailand
| | - Nikolaos Pechlivanis
- Institute of Applied Biosciences (INAB), Centre for Research & Technology Hellas (CERTH), Thessaloniki, Greece.,Development and Molecular Biology, School of Biology, Department of Genetics, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Fotis Psomopoulos
- Institute of Applied Biosciences (INAB), Centre for Research & Technology Hellas (CERTH), Thessaloniki, Greece
| | - Panagiotis Madesis
- Institute of Applied Biosciences (INAB), Centre for Research & Technology Hellas (CERTH), Thessaloniki, Greece.,Crop Production and Rural Environment, Laboratory of Molecular Biology of Plants, Department of Agriculture, University of Thessaly, Volos, Magnesia, Greece
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14
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Rucińska A, Olszak M, Świerszcz S, Nobis M, Zubek S, Kusza G, Boczkowska M, Nowak A. Looking for Hidden Enemies of Metabarcoding: Species Composition, Habitat and Management Can Strongly Influence DNA Extraction while Examining Grassland Communities. Biomolecules 2021; 11:318. [PMID: 33669773 PMCID: PMC7921978 DOI: 10.3390/biom11020318] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/15/2021] [Accepted: 02/17/2021] [Indexed: 12/02/2022] Open
Abstract
Despite the raising preoccupation, the critical question of how the plant community is composed belowground still remains unresolved, particularly for the conservation priority types of vegetation. The usefulness of metabarcoding analysis of the belowground parts of the plant community is subjected to a considerable bias, that often impedes detection of all species in a sample due to insufficient DNA quality or quantity. In the presented study we have attempted to find environmental factors that determine the amount and quality of DNA extracted from total plant tissue from above- and belowground samples (1000 and 10,000 cm2). We analyzed the influence of land use intensity, soil properties, species composition, and season on DNA extraction. The most important factors for DNA quality were vegetation type, soil conductometry (EC), and soil pH for the belowground samples. The species that significantly decreased the DNA quality were Calamagrostis epigejos, Coronilla varia, and Holcus lanatus. For the aboveground part of the vegetation, the season, management intensity, and certain species-with the most prominent being Centaurea rhenana and Cirsium canum-have the highest influence. Additionally, we found that sample size, soil granulation, MgO, organic C, K2O, and total soil N content are important for DNA extraction effectiveness. Both low EC and pH reduce significantly the yield and quality of DNA. Identifying the potential inhibitors of DNA isolation and predicting difficulties of sampling the vegetation plots for metabarcoding analysis will help to optimize the universal, low-cost multi-stage DNA extraction procedure in molecular ecology studies.
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Affiliation(s)
- Anna Rucińska
- Polish Academy of Sciences Botanical Garden, Center for Biological Diversity Conservation in Powsin, Prawdziwka 2, 02-976 Warszawa, Poland; (A.R.); (M.O.); (M.B.); (A.N.)
| | - Marcin Olszak
- Polish Academy of Sciences Botanical Garden, Center for Biological Diversity Conservation in Powsin, Prawdziwka 2, 02-976 Warszawa, Poland; (A.R.); (M.O.); (M.B.); (A.N.)
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warszawa, Poland
| | - Sebastian Świerszcz
- Polish Academy of Sciences Botanical Garden, Center for Biological Diversity Conservation in Powsin, Prawdziwka 2, 02-976 Warszawa, Poland; (A.R.); (M.O.); (M.B.); (A.N.)
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239 Kraków, Poland
| | - Marcin Nobis
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387 Kraków, Poland; (M.N.); (S.Z.)
- Research Laboratory ‘Herbarium’, National Research Tomsk State University, 634050 Tomsk, Russia
| | - Szymon Zubek
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387 Kraków, Poland; (M.N.); (S.Z.)
| | - Grzegorz Kusza
- Institute of Biology, University of Opole, Oleska 22, 45-052 Opole, Poland;
| | - Maja Boczkowska
- Polish Academy of Sciences Botanical Garden, Center for Biological Diversity Conservation in Powsin, Prawdziwka 2, 02-976 Warszawa, Poland; (A.R.); (M.O.); (M.B.); (A.N.)
- National Centre for Plant Genetic Resources, Plant Breeding and Acclimatization Institute (IHAR)–National Research Institute, Radzików, 05-870 Błonie, Poland
| | - Arkadiusz Nowak
- Polish Academy of Sciences Botanical Garden, Center for Biological Diversity Conservation in Powsin, Prawdziwka 2, 02-976 Warszawa, Poland; (A.R.); (M.O.); (M.B.); (A.N.)
- Institute of Biology, University of Opole, Oleska 22, 45-052 Opole, Poland;
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15
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Vasar M, Davison J, Neuenkamp L, Sepp SK, Young JPW, Moora M, Öpik M. User-friendly bioinformatics pipeline gDAT (graphical downstream analysis tool) for analysing rDNA sequences. Mol Ecol Resour 2021; 21:1380-1392. [PMID: 33527735 DOI: 10.1111/1755-0998.13340] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 01/19/2021] [Accepted: 01/21/2021] [Indexed: 01/04/2023]
Abstract
High-throughput sequencing (HTS) of multiple organisms in parallel (metabarcoding) has become a routine and cost-effective method for the analysis of microbial communities in environmental samples. However, careful data treatment is required to identify potential errors in HTS data, and the large volume of data generated by HTS requires in-house experience with command line tools for downstream analysis. This paper introduces a pipeline that incorporates the most common command line tools into an easy-to-use graphical interface-gDAT. By using the Python scripting language, the pipeline is compatible with the latest Windows, macOS and Linux operating systems. The pipeline supports analysis of Sanger, 454, IonTorrent, Illumina and PacBio sequences, allows custom modification of quality filtering steps, and implements both open and closed-reference operational taxonomic unit-picking for sequence identification. Predefined parameters are optimized for analysis of small subunit (SSU) rRNA gene amplicons from arbuscular mycorrhizal fungi, but the pipeline is widely applicable to metabarcoding studies targeting a broad range of organisms. The pipeline was additionally tested with data using general eukaryotic primers from the SSU gene region and fungal primers from the internal transcribed spacer (ITS) marker region. We describe the pipeline design and evaluate its performance and speed by conducting analysis of example data sets using different marker regions sequenced on Illumina platforms. The graphical interface, with the option to use the command line if needed, provides an accessible tool for rapid data analysis with repeatability and logging capabilities. Keeping the software open-source maximizes code accessibility, allowing scrutiny and bug fixes by the community.
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Affiliation(s)
- Martti Vasar
- Department of Botany, University of Tartu, Tartu, Estonia
| | - John Davison
- Department of Botany, University of Tartu, Tartu, Estonia
| | - Lena Neuenkamp
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | | | | | - Mari Moora
- Department of Botany, University of Tartu, Tartu, Estonia
| | - Maarja Öpik
- Department of Botany, University of Tartu, Tartu, Estonia
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16
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Abstract
Taxonomy is the science that explores, describes, names, and classifies all organisms. In this introductory chapter, we highlight the major historical steps in the elaboration of this science, which provides baseline data for all fields of biology and plays a vital role for society but is also an independent, complex, and sound hypothesis-driven scientific discipline.In a first part, we underline that plant taxonomy is one of the earliest scientific disciplines that emerged thousands of years ago, even before the important contributions of the Greeks and Romans (e.g., Theophrastus, Pliny the Elder, and Dioscorides). In the fifteenth-sixteenth centuries, plant taxonomy benefited from the Great Navigations, the invention of the printing press, the creation of botanic gardens, and the use of the drying technique to preserve plant specimens. In parallel with the growing body of morpho-anatomical data, subsequent major steps in the history of plant taxonomy include the emergence of the concept of natural classification , the adoption of the binomial naming system (with the major role of Linnaeus) and other universal rules for the naming of plants, the formulation of the principle of subordination of characters, and the advent of the evolutionary thought. More recently, the cladistic theory (initiated by Hennig) and the rapid advances in DNA technologies allowed to infer phylogenies and to propose true natural, genealogy-based classifications.In a second part, we put the emphasis on the challenges that plant taxonomy faces nowadays. The still very incomplete taxonomic knowledge of the worldwide flora (the so-called taxonomic impediment) is seriously hampering conservation efforts that are especially crucial as biodiversity has entered its sixth extinction crisis. It appears mainly due to insufficient funding, lack of taxonomic expertise, and lack of communication and coordination. We then review recent initiatives to overcome these limitations and to anticipate how taxonomy should and could evolve. In particular, the use of molecular data has been era-splitting for taxonomy and may allow an accelerated pace of species discovery. We examine both strengths and limitations of such techniques in comparison to morphology-based investigations, we give broad recommendations on the use of molecular tools for plant taxonomy, and we highlight the need for an integrative taxonomy based on evidence from multiple sources.
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Affiliation(s)
- Germinal Rouhan
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, Sorbonne Université, Ecole Pratique des Hautes Etudes, Université des Antilles, CNRS, Paris, France.
| | - Myriam Gaudeul
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, Sorbonne Université, Ecole Pratique des Hautes Etudes, Université des Antilles, CNRS, Paris, France
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17
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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] [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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18
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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. THE NEW PHYTOLOGIST 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] [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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19
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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] [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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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] [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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Sun YQ, Wang J, Shen C, He JZ, Ge Y. Plant evenness modulates the effect of plant richness on soil bacterial diversity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 662:8-14. [PMID: 30682712 DOI: 10.1016/j.scitotenv.2019.01.211] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 01/17/2019] [Accepted: 01/17/2019] [Indexed: 06/09/2023]
Abstract
Understanding the relationships between aboveground and belowground biodiversity will help to expand our knowledge on how ecological communities and processes are interactively determined, and thus provide new perspectives for the conservation of biodiversity. Despite the theoretical analyses generally predicting a positive relationship between plant richness and soil microbial diversity, the results from empirical studies have been mixed, probably due to the effect of plant evenness. To investigate this relationship, we conducted field experiments in two geographically distinct sites (Linhai and Shenmu, >1400km apart), by simultaneously manipulating plant richness (2, 4, and 8 species) and evenness (homogeneous versus non-homogeneous). After one year, the bacterial response to plant richness with different plant evenness levels was evaluated using terminal restriction fragment length polymorphism (T-RFLP) analysis. Our results showed that plant evenness modulated plant richness effects on bacterial community, as reflected by the more pronounced positive correlations between bacterial richness and plant richness in homogeneous plant community than in the non-homogeneous treatment. Additionally, plant community structure significantly affected bacterial communities only in the homogeneous treatment in Shenmu, but not in the non-homogeneous treatments. Our results demonstrate that plant evenness could regulate plant richness effects on bacterial alpha- and beta-diversity and thus provide valuable insights into the association between aboveground and belowground biodiversity.
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Affiliation(s)
- Yao-Qin Sun
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiang Wang
- School of Life Sciences, Taizhou University, Taizhou 318000, China
| | - Congcong Shen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ji-Zheng He
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuan Ge
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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22
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Structural equation modeling of a winnowed soil microbiome identifies how invasive plants re-structure microbial networks. ISME JOURNAL 2019; 13:1988-1996. [PMID: 30926920 DOI: 10.1038/s41396-019-0407-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 01/28/2019] [Accepted: 03/13/2019] [Indexed: 12/14/2022]
Abstract
The development of microbial networks is central to ecosystem functioning and is the hallmark of complex natural systems. Characterizing network development over time and across environmental gradients is hindered by the millions of potential interactions among community members, limiting interpretations of network evolution. We developed a feature selection approach using data winnowing that identifies the most ecologically influential microorganisms within a network undergoing change. Using a combination of graph theory, leave-one-out analysis, and statistical inference, complex microbial communities are winnowed to identify the core organisms responding to external gradients or functionality, and then network development is evaluated against these externalities. In a plant invasion case study, the winnowed microbial network became more influential as the plant invasion progressed as a result of direct plant-microbe links rather than the expected indirect plant-soil-microbe links. This represents the first use of structural equation modeling to predict microbial network evolution, which requires identification of keystone taxa and quantification of the ecological processes underpinning community structure and function patterns.
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23
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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] [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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24
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Rasmussen PU, Hugerth LW, Blanchet FG, Andersson AF, Lindahl BD, Tack AJM. Multiscale patterns and drivers of arbuscular mycorrhizal fungal communities in the roots and root-associated soil of a wild perennial herb. THE NEW PHYTOLOGIST 2018; 220:1248-1261. [PMID: 29573431 PMCID: PMC6282561 DOI: 10.1111/nph.15088] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 02/11/2018] [Indexed: 05/12/2023]
Abstract
Arbuscular mycorrhizal (AM) fungi form diverse communities and are known to influence above-ground community dynamics and biodiversity. However, the multiscale patterns and drivers of AM fungal composition and diversity are still poorly understood. We sequenced DNA markers from roots and root-associated soil from Plantago lanceolata plants collected across multiple spatial scales to allow comparison of AM fungal communities among neighbouring plants, plant subpopulations, nearby plant populations, and regions. We also measured soil nutrients, temperature, humidity, and community composition of neighbouring plants and nonAM root-associated fungi. AM fungal communities were already highly dissimilar among neighbouring plants (c. 30 cm apart), albeit with a high variation in the degree of similarity at this small spatial scale. AM fungal communities were increasingly, and more consistently, dissimilar at larger spatial scales. Spatial structure and environmental drivers explained a similar percentage of the variation, from 7% to 25%. A large fraction of the variation remained unexplained, which may be a result of unmeasured environmental variables, species interactions and stochastic processes. We conclude that AM fungal communities are highly variable among nearby plants. AM fungi may therefore play a major role in maintaining small-scale variation in community dynamics and biodiversity.
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Affiliation(s)
- Pil U. Rasmussen
- Department of EcologyEnvironment and Plant SciencesStockholm UniversitySE‐106 91StockholmSweden
| | - Luisa W. Hugerth
- School of BiotechnologyScience for Life LaboratoryKTH Royal Institute of TechnologyPO Box 1031SE‐171 21SolnaSweden
- Centre for Translational Microbiome ResearchDepartment of Molecular, Tumor and Cell BiologyScience for Life LaboratoryKarolinska Institutet171 65SolnaSweden
| | - F. Guillaume Blanchet
- Département de BiologieFaculté des SciencesUniversité de Sherbrooke2500 Boulevard UniversitéSherbrookeQCJ1K 2R1Canada
| | - Anders F. Andersson
- School of BiotechnologyScience for Life LaboratoryKTH Royal Institute of TechnologyPO Box 1031SE‐171 21SolnaSweden
| | - Björn D. Lindahl
- Department of Soil and EnvironmentSwedish University of Agricultural SciencesBox 7014SE‐750 07UppsalaSweden
| | - Ayco J. M. Tack
- Department of EcologyEnvironment and Plant SciencesStockholm UniversitySE‐106 91StockholmSweden
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25
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Hutchinson MC, Bramon Mora B, Pilosof S, Barner AK, Kéfi S, Thébault E, Jordano P, Stouffer DB. Seeing the forest for the trees: Putting multilayer networks to work for community ecology. Funct Ecol 2018. [DOI: 10.1111/1365-2435.13237] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Matthew C. Hutchinson
- Department of Ecology and Evolutionary Biology Princeton University Princeton New Jersey
| | - Bernat Bramon Mora
- Centre for Integrative Ecology, School of Biological Sciences University of Canterbury Christchurch New Zealand
| | - Shai Pilosof
- Department of Ecology & Evolution University of Chicago Chicago Illinois
| | - Allison K. Barner
- Department of Environmental Science, Policy, and Management University of California Berkeley Berkeley California
| | - Sonia Kéfi
- ISEM, CNRS, Univ. Montpellier, IRD, EPHE Montpellier France
| | - Elisa Thébault
- CNRS, Sorbonne Université Institute of Ecology and Environmental Sciences of Paris Paris France
| | - Pedro Jordano
- Department of Integrative Ecology Estación Biológica de Doñana (EBD‐CSIC) Seville Spain
| | - Daniel B. Stouffer
- Centre for Integrative Ecology, School of Biological Sciences University of Canterbury Christchurch New Zealand
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26
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Klimešová J, Martínková J, Ottaviani G. Belowground plant functional ecology: Towards an integrated perspective. Funct Ecol 2018. [DOI: 10.1111/1365-2435.13145] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jitka Klimešová
- Department of Functional EcologyInstitute of BotanyCzech Academy of Sciences Třeboň Czech Republic
- Department of BotanyFaculty of ScienceCharles University Praha Czech Republic
| | - Jana Martínková
- Department of Functional EcologyInstitute of BotanyCzech Academy of Sciences Třeboň Czech Republic
| | - Gianluigi Ottaviani
- Department of Functional EcologyInstitute of BotanyCzech Academy of Sciences Třeboň Czech Republic
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27
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Leff JW, Bardgett RD, Wilkinson A, Jackson BG, Pritchard WJ, De Long JR, Oakley S, Mason KE, Ostle NJ, Johnson D, Baggs EM, Fierer N. Predicting the structure of soil communities from plant community taxonomy, phylogeny, and traits. THE ISME JOURNAL 2018; 12:1794-1805. [PMID: 29523892 PMCID: PMC6004312 DOI: 10.1038/s41396-018-0089-x] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 01/14/2018] [Accepted: 01/20/2018] [Indexed: 01/01/2023]
Abstract
There are numerous ways in which plants can influence the composition of soil communities. However, it remains unclear whether information on plant community attributes, including taxonomic, phylogenetic, or trait-based composition, can be used to predict the structure of soil communities. We tested, in both monocultures and field-grown mixed temperate grassland communities, whether plant attributes predict soil communities including taxonomic groups from across the tree of life (fungi, bacteria, protists, and metazoa). The composition of all soil community groups was affected by plant species identity, both in monocultures and in mixed communities. Moreover, plant community composition predicted additional variation in soil community composition beyond what could be predicted from soil abiotic characteristics. In addition, analysis of the field aboveground plant community composition and the composition of plant roots suggests that plant community attributes are better predictors of soil communities than root distributions. However, neither plant phylogeny nor plant traits were strong predictors of soil communities in either experiment. Our results demonstrate that grassland plant species form specific associations with soil community members and that information on plant species distributions can improve predictions of soil community composition. These results indicate that specific associations between plant species and complex soil communities are key determinants of biodiversity patterns in grassland soils.
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Affiliation(s)
- Jonathan W Leff
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, 80309, USA
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
| | - Richard D Bardgett
- School of Earth and Environmental Sciences, Michael Smith Building, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Anna Wilkinson
- School of Earth and Environmental Sciences, Michael Smith Building, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Benjamin G Jackson
- School of Geosciences, Grant Institute, The King's Buildings, James Hutton Road, Edinburgh, EH9 3FE, UK
| | - William J Pritchard
- School of Earth and Environmental Sciences, Michael Smith Building, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Jonathan R De Long
- School of Earth and Environmental Sciences, Michael Smith Building, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Simon Oakley
- Centre for Ecology & Hydrology, Lancaster Environment Centre, Library Avenue, Bailrigg, Lancaster, LA1 4AP, UK
| | - Kelly E Mason
- Centre for Ecology & Hydrology, Lancaster Environment Centre, Library Avenue, Bailrigg, Lancaster, LA1 4AP, UK
| | - Nicholas J Ostle
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - David Johnson
- School of Earth and Environmental Sciences, Michael Smith Building, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Elizabeth M Baggs
- The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus Buildings, Midlothian, EH25 9RG, UK
| | - Noah Fierer
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, 80309, USA.
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA.
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28
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Alsos IG, Lammers Y, Yoccoz NG, Jørgensen T, Sjögren P, Gielly L, Edwards ME. Plant DNA metabarcoding of lake sediments: How does it represent the contemporary vegetation. PLoS One 2018; 13:e0195403. [PMID: 29664954 PMCID: PMC5903670 DOI: 10.1371/journal.pone.0195403] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/21/2018] [Indexed: 11/18/2022] Open
Abstract
Metabarcoding of lake sediments have been shown to reveal current and past biodiversity, but little is known about the degree to which taxa growing in the vegetation are represented in environmental DNA (eDNA) records. We analysed composition of lake and catchment vegetation and vascular plant eDNA at 11 lakes in northern Norway. Out of 489 records of taxa growing within 2 m from the lake shore, 17–49% (mean 31%) of the identifiable taxa recorded were detected with eDNA. Of the 217 eDNA records of 47 plant taxa in the 11 lakes, 73% and 12% matched taxa recorded in vegetation surveys within 2 m and up to about 50 m away from the lakeshore, respectively, whereas 16% were not recorded in the vegetation surveys of the same lake. The latter include taxa likely overlooked in the vegetation surveys or growing outside the survey area. The percentages detected were 61, 47, 25, and 15 for dominant, common, scattered, and rare taxa, respectively. Similar numbers for aquatic plants were 88, 88, 33 and 62%, respectively. Detection rate and taxonomic resolution varied among plant families and functional groups with good detection of e.g. Ericaceae, Roseaceae, deciduous trees, ferns, club mosses and aquatics. The representation of terrestrial taxa in eDNA depends on both their distance from the sampling site and their abundance and is sufficient for recording vegetation types. For aquatic vegetation, eDNA may be comparable with, or even superior to, in-lake vegetation surveys and may therefore be used as an tool for biomonitoring. For reconstruction of terrestrial vegetation, technical improvements and more intensive sampling is needed to detect a higher proportion of rare taxa although DNA of some taxa may never reach the lake sediments due to taphonomical constrains. Nevertheless, eDNA performs similar to conventional methods of pollen and macrofossil analyses and may therefore be an important tool for reconstruction of past vegetation.
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Affiliation(s)
- Inger Greve Alsos
- Tromsø Museum, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
- * E-mail:
| | - Youri Lammers
- Tromsø Museum, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
| | - Nigel Giles Yoccoz
- Department of Arctic and Marine Biology, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
| | - Tina Jørgensen
- Tromsø Museum, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
| | - Per Sjögren
- Tromsø Museum, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
| | - Ludovic Gielly
- University Grenoble Alpes, LECA, Grenoble, France
- CNRS, LECA, Grenoble, France
| | - Mary E. Edwards
- Tromsø Museum, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
- Geography and Environment, University of Southampton, Highfield, Southampton, United Kingdom
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29
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Smith JA, Thomas AC, Levi T, Wang Y, Wilmers CC. Human activity reduces niche partitioning among three widespread mesocarnivores. OIKOS 2018. [DOI: 10.1111/oik.04592] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Justine A. Smith
- Dept of Environmental Sciences, Policy and Management; Univ. of California; Berkeley CA 94720 USA
- Center for Integrated Spatial Research, Environmental Studies Dept; Univ. of California; Santa Cruz, Santa Cruz CA USA
| | | | - Taal Levi
- Dept of Fisheries and Wildlife; Oregon State Univ.; Corvallis OR USA
| | - Yiwei Wang
- San Francisco Bay Bird Observatory; Milpitas CA USA
| | - Christopher C. Wilmers
- Center for Integrated Spatial Research, Environmental Studies Dept; Univ. of California; Santa Cruz, Santa Cruz CA USA
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30
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Li Z, Lamb EG, Piper CL, Siciliano SD. Plant belowground diversity and species segregation by depth in a semi-arid grassland. ECOSCIENCE 2017. [DOI: 10.1080/11956860.2017.1403242] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Zhi Li
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Eric G. Lamb
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Candace L. Piper
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
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31
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Mamet SD, Lamb EG, Piper CL, Winsley T, Siciliano SD. Archaea and bacteria mediate the effects of native species root loss on fungi during plant invasion. THE ISME JOURNAL 2017; 11:1261-1275. [PMID: 28140393 PMCID: PMC5437935 DOI: 10.1038/ismej.2016.205] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 11/16/2016] [Accepted: 12/15/2016] [Indexed: 01/21/2023]
Abstract
Although invasive plants can drive ecosystem change, little is known about the directional nature of belowground interactions between invasive plants, native roots, bacteria, archaea and fungi. We used detailed bioinformatics and a recently developed root assay on soils collected in fescue grassland along a gradient of smooth brome (Bromus inermis Leyss) invasion to examine the links between smooth brome shoot litter and root, archaea, bacteria and fungal communities. We examined (1) aboveground versus belowground influences of smooth brome on soil microbial communities, (2) the importance of direct versus microbe-mediated impacts of plants on soil fungal communities, and (3) the web of roots, shoots, archaea, bacteria and fungi interactions across the A and B soil horizons in invaded and non-invaded sites. Archaea and bacteria influenced fungal composition, but not vice versa, as indicated by redundancy analyses. Co-inertia analyses suggested that bacterial-fungal variance was driven primarily by 12 bacterial operational taxonomic units (OTUs). Brome increased bacterial diversity via smooth brome litter in the A horizon and roots in the B horizon, which then reduced fungal diversity. Archaea increased abundance of several bacterial OTUs, and the key bacterial OTUs mediated changes in the fungi's response to invasion. Overall, native root diversity loss and bacterial mediation were more important drivers of fungal composition than were the direct effects of increases in smooth brome. Critically, native plant species displacement and root loss appeared to be the most important driver of fungal composition during invasion. This causal web likely gives rise to the plant-fungi feedbacks, which are an essential factor determining plant diversity in invaded grassland ecosystems.
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Affiliation(s)
- Steven D Mamet
- Department of Soil Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Eric G Lamb
- Department of Plant Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Candace L Piper
- Department of Plant Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Tristrom Winsley
- Department of Soil Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Steven D Siciliano
- Department of Soil Science, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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Groendahl S, Kahlert M, Fink P. The best of both worlds: A combined approach for analyzing microalgal diversity via metabarcoding and morphology-based methods. PLoS One 2017; 12:e0172808. [PMID: 28234997 PMCID: PMC5325584 DOI: 10.1371/journal.pone.0172808] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 02/09/2017] [Indexed: 11/19/2022] Open
Abstract
An increasing number of studies use next generation sequencing (NGS) to analyze complex communities, but is the method sensitive enough when it comes to identification and quantification of species? We compared NGS with morphology-based identification methods in an analysis of microalgal (periphyton) communities. We conducted a mesocosm experiment in which we allowed two benthic grazer species to feed upon benthic biofilms, which resulted in altered periphyton communities. Morphology-based identification and 454 (Roche) pyrosequencing of the V4 region in the small ribosomal unit (18S) rDNA gene were used to investigate the community change caused by grazing. Both the NGS-based data and the morphology-based method detected a marked shift in the biofilm composition, though the two methods varied strongly in their abilities to detect and quantify specific taxa, and neither method was able to detect all species in the biofilms. For quantitative analysis, we therefore recommend using both metabarcoding and microscopic identification when assessing the community composition of eukaryotic microorganisms.
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Affiliation(s)
- Sophie Groendahl
- University of Cologne, Zoological Institute, Aquatic Chemical Ecology, Cologne, Germany
| | - Maria Kahlert
- Swedish University of Agricultural Sciences, Department of Aquatic Sciences and Assessment, Uppsala, Sweden
| | - Patrick Fink
- University of Cologne, Zoological Institute, Aquatic Chemical Ecology, Cologne, Germany
- University of Duesseldorf, Institute for Cell Biology and Zoology, Duesseldorf, Germany
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Fahner NA, Shokralla S, Baird DJ, Hajibabaei M. Large-Scale Monitoring of Plants through Environmental DNA Metabarcoding of Soil: Recovery, Resolution, and Annotation of Four DNA Markers. PLoS One 2016; 11:e0157505. [PMID: 27310720 PMCID: PMC4911152 DOI: 10.1371/journal.pone.0157505] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 05/31/2016] [Indexed: 12/25/2022] Open
Abstract
In a rapidly changing world we need methods to efficiently assess biodiversity in order to monitor ecosystem trends. Ecological monitoring often uses plant community composition to infer quality of sites but conventional aboveground surveys only capture a snapshot of the actively growing plant diversity. Environmental DNA (eDNA) extracted from soil samples, however, can include taxa represented by both active and dormant tissues, seeds, pollen, and detritus. Analysis of this eDNA through DNA metabarcoding provides a more comprehensive view of plant diversity at a site from a single assessment but it is not clear which DNA markers are best used to capture this diversity. Sequence recovery, annotation, and sequence resolution among taxa were evaluated for four established DNA markers (matK, rbcL, ITS2, and the trnL P6 loop) in silico using database sequences and in situ using high throughput sequencing of 35 soil samples from a remote boreal wetland. Overall, ITS2 and rbcL are recommended for DNA metabarcoding of vascular plants from eDNA when not using customized or geographically restricted reference databases. We describe a new framework for evaluating DNA metabarcodes and, contrary to existing assumptions, we found that full length DNA barcode regions could outperform shorter markers for surveying plant diversity from soil samples. By using current DNA barcoding markers rbcL and ITS2 for plant metabarcoding, we can take advantage of existing resources such as the growing DNA barcode database. Our work establishes the value of standard DNA barcodes for soil plant eDNA analysis in ecological investigations and biomonitoring programs and supports the collaborative development of DNA barcoding and metabarcoding.
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Affiliation(s)
- Nicole A. Fahner
- Department of Integrative Biology and Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Shadi Shokralla
- Department of Integrative Biology and Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Donald J. Baird
- Environment Canada at Canadian Rivers Institute and Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Mehrdad Hajibabaei
- Department of Integrative Biology and Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
- * E-mail:
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Drummond AJ, Newcomb RD, Buckley TR, Xie D, Dopheide A, Potter BC, Heled J, Ross HA, Tooman L, Grosser S, Park D, Demetras NJ, Stevens MI, Russell JC, Anderson SH, Carter A, Nelson N. Evaluating a multigene environmental DNA approach for biodiversity assessment. Gigascience 2015; 4:46. [PMID: 26445670 PMCID: PMC4595072 DOI: 10.1186/s13742-015-0086-1] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 09/15/2015] [Indexed: 12/30/2022] Open
Abstract
Background There is an increasing demand for rapid biodiversity assessment tools that have a broad taxonomic coverage. Here we evaluate a suite of environmental DNA (eDNA) markers coupled with next generation sequencing (NGS) that span the tree of life, comparing them with traditional biodiversity monitoring tools within ten 20×20 meter plots along a 700 meter elevational gradient. Results From six eDNA datasets (one from each of 16S, 18S, ITS, trnL and two from COI) we identified sequences from 109 NCBI taxonomy-defined phyla or equivalent, ranging from 31 to 60 for a given eDNA marker. Estimates of alpha and gamma diversity were sensitive to the number of sequence reads, whereas beta diversity estimates were less sensitive. The average within-plot beta diversity was lower than between plots for all markers. The soil beta diversity of COI and 18S markers showed the strongest response to the elevational variation of the eDNA markers (COI: r=0.49, p<0.001; 18S: r=0.48, p<0.001). Furthermore pairwise beta diversities for these two markers were strongly correlated with those calculated from traditional vegetation and invertebrate biodiversity measures. Conclusions Using a soil-based eDNA approach, we demonstrate that standard phylogenetic markers are capable of recovering sequences from a broad diversity of eukaryotes, in addition to prokaryotes by 16S. The COI and 18S eDNA markers are the best proxies for aboveground biodiversity based on the high correlation between the pairwise beta diversities of these markers and those obtained using traditional methods. Electronic supplementary material The online version of this article (doi:10.1186/s13742-015-0086-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexei J Drummond
- Allan Wilson Centre, University of Auckland, Auckland, New Zealand ; Department of Computer Science, University of Auckland, Private Bag 92019, Auckland, 1142 New Zealand
| | - Richard D Newcomb
- Allan Wilson Centre, University of Auckland, Auckland, New Zealand ; School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142 New Zealand ; The Institute for Plant and Food Research, Private Bag 92169, Auckland, 1142 New Zealand
| | - Thomas R Buckley
- Allan Wilson Centre, University of Auckland, Auckland, New Zealand ; School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142 New Zealand ; Landcare Research, Private Bag 92170, Auckland, 1142 New Zealand
| | - Dong Xie
- Allan Wilson Centre, University of Auckland, Auckland, New Zealand ; Department of Computer Science, University of Auckland, Private Bag 92019, Auckland, 1142 New Zealand
| | - Andrew Dopheide
- Allan Wilson Centre, University of Auckland, Auckland, New Zealand ; School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142 New Zealand ; The Institute for Plant and Food Research, Private Bag 92169, Auckland, 1142 New Zealand
| | - Benjamin Cm Potter
- Allan Wilson Centre, University of Auckland, Auckland, New Zealand ; School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142 New Zealand
| | - Joseph Heled
- Allan Wilson Centre, University of Auckland, Auckland, New Zealand ; Department of Computer Science, University of Auckland, Private Bag 92019, Auckland, 1142 New Zealand
| | - Howard A Ross
- Allan Wilson Centre, University of Auckland, Auckland, New Zealand ; School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142 New Zealand
| | - Leah Tooman
- Allan Wilson Centre, University of Auckland, Auckland, New Zealand ; The Institute for Plant and Food Research, Private Bag 92169, Auckland, 1142 New Zealand
| | - Stefanie Grosser
- Allan Wilson Centre, University of Auckland, Auckland, New Zealand ; Landcare Research, Private Bag 92170, Auckland, 1142 New Zealand
| | - Duckchul Park
- Landcare Research, Private Bag 92170, Auckland, 1142 New Zealand
| | - Nicholas J Demetras
- Department of Biological Sciences, University of Waikato, Private Bag 3105, Hamilton, 3240 New Zealand
| | - Mark I Stevens
- South Australian Museum, North Terrace, Adelaide, SA 5000 Australia ; School of Pharmacy and Medical Sciences, University of South Australia, GPO Box 2471, Adelaide, SA 5001 Australia
| | - James C Russell
- Allan Wilson Centre, University of Auckland, Auckland, New Zealand ; School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142 New Zealand ; Department of Statistics, University of Auckland, Private Bag 92019, Auckland, 1142 New Zealand
| | - Sandra H Anderson
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142 New Zealand
| | - Anna Carter
- Allan Wilson Centre, University of Auckland, Auckland, New Zealand ; School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, 6140 New Zealand
| | - Nicola Nelson
- Allan Wilson Centre, University of Auckland, Auckland, New Zealand ; School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington, 6140 New Zealand
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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] [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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Hendriks M, Ravenek JM, Smit-Tiekstra AE, van der Paauw JW, de Caluwe H, van der Putten WH, de Kroon H, Mommer L. Spatial heterogeneity of plant-soil feedback affects root interactions and interspecific competition. THE NEW PHYTOLOGIST 2015; 207:830-840. [PMID: 25871977 DOI: 10.1111/nph.13394] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Accepted: 03/02/2015] [Indexed: 06/04/2023]
Abstract
Plant-soil feedback is receiving increasing interest as a factor influencing plant competition and species coexistence in grasslands. However, we do not know how spatial distribution of plant-soil feedback affects plant below-ground interactions. We investigated the way in which spatial heterogeneity of soil biota affects competitive interactions in grassland plant species. We performed a pairwise competition experiment combined with heterogeneous distribution of soil biota using four grassland plant species and their soil biota. Patches were applied as quadrants of 'own' and 'foreign' soils from all plant species in all pairwise combinations. To evaluate interspecific root responses, species-specific root biomass was quantified using real-time PCR. All plant species suffered negative soil feedback, but strength was species-specific, reflected by a decrease in root growth in own compared with foreign soil. Reduction in root growth in own patches by the superior plant competitor provided opportunities for inferior competitors to increase root biomass in these patches. These patterns did not cascade into above-ground effects during our experiment. We show that root distributions can be determined by spatial heterogeneity of soil biota, affecting plant below-ground competitive interactions. Thus, spatial heterogeneity of soil biota may contribute to plant species coexistence in species-rich grasslands.
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Affiliation(s)
- Marloes Hendriks
- Department of Experimental Plant Ecology, Institute for Water and Wetland Research, Radboud University Nijmegen, PO Box 9100, 6500, GL Nijmegen, the Netherlands
| | - Janneke M Ravenek
- Department of Experimental Plant Ecology, Institute for Water and Wetland Research, Radboud University Nijmegen, PO Box 9100, 6500, GL Nijmegen, the Netherlands
| | - Annemiek E Smit-Tiekstra
- Department of Experimental Plant Ecology, Institute for Water and Wetland Research, Radboud University Nijmegen, PO Box 9100, 6500, GL Nijmegen, the Netherlands
| | - Jan Willem van der Paauw
- Department of Experimental Plant Ecology, Institute for Water and Wetland Research, Radboud University Nijmegen, PO Box 9100, 6500, GL Nijmegen, the Netherlands
- Nature Conservation and Plant Ecology, Wageningen University, PO Box 47, 6700 AA, Wageningen, the Netherlands
| | - Hannie de Caluwe
- Department of Experimental Plant Ecology, Institute for Water and Wetland Research, Radboud University Nijmegen, PO Box 9100, 6500, GL Nijmegen, the Netherlands
| | - Wim H van der Putten
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, PO Box 50, 6700 AB, Wageningen, the Netherlands
- Laboratory of Nematology, Wageningen University, PO Box 8123, 6700 ES, Wageningen, the Netherlands
| | - Hans de Kroon
- Department of Experimental Plant Ecology, Institute for Water and Wetland Research, Radboud University Nijmegen, PO Box 9100, 6500, GL Nijmegen, the Netherlands
| | - Liesje Mommer
- Nature Conservation and Plant Ecology, Wageningen University, PO Box 47, 6700 AA, Wageningen, the Netherlands
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37
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Lawson Handley L. How will the ‘molecular revolution’ contribute to biological recording? Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12516] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Lori Lawson Handley
- Evolutionary Biology Group; School of Biological, Biomedical and Environmental Sciences; University of Hull; Cottingham Road Hull HU6 7RX UK
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Karst J, Chow P, Landhäusser SM. Biases underlying species detection using fluorescent amplified-fragment length polymorphisms yielded from roots. PLANT METHODS 2015; 11:36. [PMID: 26113872 PMCID: PMC4480983 DOI: 10.1186/s13007-015-0079-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 06/12/2015] [Indexed: 05/12/2023]
Abstract
BACKGROUND Roots of different plant species are typically morphologically indistinguishable. Of the DNA-based techniques, fluorescent amplified-fragment length polymorphisms (FAFLPs) are considered reliable, high throughput, inexpensive methods to identify roots from mixed species samples. False-negatives, however, are not uncommon and their underlying causes are poorly understood. We investigated several sources of potential biases originating in DNA extraction and amplification. Specifically, we examined the effects of sample storage, tissue, and species on DNA yield and purity, and the effects of DNA concentration and fragment size on amplification of three non-coding chloroplast regions (trnT-trnL intergenic spacer, trnL intron, and trnL-trnF intergenic spacer). RESULTS We found that sample condition, tissue and species all affected DNA yield. A single freeze-thaw reduces DNA yield, DNA yield is less for roots than shoots, and species vary in the amount of DNA yielded from extractions. The effects of template DNA concentration, species identity, and their interaction on amplicon yield differed across the three chloroplast regions tested. We found that the effect of species identity on amplicon production was generally more pronounced than that of DNA concentration. Though these factors influenced DNA yield, they likely do not have a pronounced effect on detection success of fragments and only underscore the restriction on the use of FAFLPs for measuring species presence rather than their abundance. However, for two of the regions tested-the trnT-trnL intergenic spacer and the trnL intron-size-based fragment competition occurred and the likelihood of detection was higher for smaller than larger fragments. This result reveals a methodological bias when using FAFLPs. CONCLUSIONS To avoid potential bias with the use of FAFLPs, we recommend users check for the disproportionate absence of species detected belowground versus aboveground as a function of fragment size, and explore other regions, aside from the trnT-trnL intergenic spacer and trnL intron, for amplification.
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Affiliation(s)
- Justine Karst
- Department of Renewable Resources, University of Alberta, 442 Earth Sciences Building, Edmonton, AB T6G 2E3 Canada
| | - Pak Chow
- Department of Renewable Resources, University of Alberta, 442 Earth Sciences Building, Edmonton, AB T6G 2E3 Canada
| | - Simon M Landhäusser
- Department of Renewable Resources, University of Alberta, 442 Earth Sciences Building, Edmonton, AB T6G 2E3 Canada
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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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40
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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. THE NEW PHYTOLOGIST 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] [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. FRONTIERS IN PLANT SCIENCE 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] [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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42
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Piñol J, Mir G, Gomez-Polo P, Agustí N. Universal and blocking primer mismatches limit the use of high-throughput DNA sequencing for the quantitative metabarcoding of arthropods. Mol Ecol Resour 2014; 15:819-30. [PMID: 25454249 DOI: 10.1111/1755-0998.12355] [Citation(s) in RCA: 248] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 11/17/2014] [Accepted: 11/21/2014] [Indexed: 11/29/2022]
Abstract
The quantification of the biological diversity in environmental samples using high-throughput DNA sequencing is hindered by the PCR bias caused by variable primer-template mismatches of the individual species. In some dietary studies, there is the added problem that samples are enriched with predator DNA, so often a predator-specific blocking oligonucleotide is used to alleviate the problem. However, specific blocking oligonucleotides could coblock nontarget species to some degree. Here, we accurately estimate the extent of the PCR biases induced by universal and blocking primers on a mock community prepared with DNA of twelve species of terrestrial arthropods. We also compare universal and blocking primer biases with those induced by variable annealing temperature and number of PCR cycles. The results show that reads of all species were recovered after PCR enrichment at our control conditions (no blocking oligonucleotide, 45 °C annealing temperature and 40 cycles) and high-throughput sequencing. They also show that the four factors considered biased the final proportions of the species to some degree. Among these factors, the number of primer-template mismatches of each species had a disproportionate effect (up to five orders of magnitude) on the amplification efficiency. In particular, the number of primer-template mismatches explained most of the variation (~3/4) in the amplification efficiency of the species. The effect of blocking oligonucleotide concentration on nontarget species relative abundance was also significant, but less important (below one order of magnitude). Considering the results reported here, the quantitative potential of the technique is limited, and only qualitative results (the species list) are reliable, at least when targeting the barcoding COI region.
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Affiliation(s)
- J Piñol
- Universitat Autònoma Barcelona, Cerdanyola del Vallès, 08193, Spain.,CREAF, Cerdanyola del Vallès, 08193, Spain
| | - G Mir
- CRAG CSIC IRTA UAB UB, Cerdanyola del Vallès, 08193, Spain.,The Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia
| | - P Gomez-Polo
- IRTA, Carretera de Cabrils, Km. 2, E-08348 Cabrils, Barcelona, Spain
| | - N Agustí
- IRTA, Carretera de Cabrils, Km. 2, E-08348 Cabrils, Barcelona, Spain
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43
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Bardgett RD, Mommer L, De Vries FT. Going underground: root traits as drivers of ecosystem processes. Trends Ecol Evol 2014; 29:692-9. [PMID: 25459399 DOI: 10.1016/j.tree.2014.10.006] [Citation(s) in RCA: 375] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 09/30/2014] [Accepted: 10/23/2014] [Indexed: 10/24/2022]
Abstract
Ecologists are increasingly adopting trait-based approaches to understand how community change influences ecosystem processes. However, most of this research has focussed on aboveground plant traits, whereas it is becoming clear that root traits are important drivers of many ecosystem processes, such as carbon (C) and nutrient cycling, and the formation and structural stability of soil. Here, we synthesise emerging evidence that illustrates how root traits impact ecosystem processes, and propose a pathway to unravel the complex roles of root traits in driving ecosystem processes and their response to global change. Finally, we identify research challenges and novel technologies to address them.
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Affiliation(s)
- Richard D Bardgett
- Faculty of Life Sciences, Michael Smith Building, The University of Manchester, Oxford Road, Manchester M13 9PT, UK.
| | - Liesje Mommer
- Nature Conservation and Plant Ecology Group, Wageningen University, PO Box 47, 6700 AA, Wageningen, The Netherlands
| | - Franciska T De Vries
- Faculty of Life Sciences, Michael Smith Building, The University of Manchester, Oxford Road, Manchester M13 9PT, UK
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Randall MJ, Karst J, Pec GJ, Davis CS, Hall JC, Cahill JF. A molecular identification protocol for roots of boreal forest tree species. APPLICATIONS IN PLANT SCIENCES 2014; 2:apps1400069. [PMID: 25383267 PMCID: PMC4222544 DOI: 10.3732/apps.1400069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 09/15/2014] [Indexed: 05/12/2023]
Abstract
PREMISE OF THE STUDY Roots play a key role in many ecological processes, yet our ability to identify species from bulk root samples is limited. Molecular tools may be used to identify species from root samples, but they have not yet been developed for most systems. Here we present a PCR-based method previously used to identify roots of grassland species, modified for use in boreal forests. • METHODS We used repeatable interspecific size differences in fluorescent amplified fragment length polymorphisms of three noncoding chloroplast DNA regions to identify seven woody species common to boreal forests in Alberta, Canada. • RESULTS Abies balsamea, Alnus crispa, Betula papyrifera, Pinus contorta, and Populus tremuloides were identifiable to species, while Picea glauca and Picea mariana were identifiable to genus. In mixtures of known composition of foliar DNA, species were identified with 98% accuracy using one region. Mixed root samples of unknown composition were identified with 100% accuracy; four species were identified using one region, while three species were identified using two regions. • DISCUSSION This methodology is accurate, efficient, and inexpensive, and thus a valuable approach for ecological studies of roots. Furthermore, this method has now been validated for both grassland and boreal forest systems, and thus may also have applications in any plant community.
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Affiliation(s)
- Morgan J. Randall
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
- Author for correspondence:
| | - Justine Karst
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
- Department of Renewable Resources, University of Alberta, Edmonton, Alberta, T6G 2H1, Canada
| | - Gregory J. Pec
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
| | - Corey S. Davis
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
| | - Jocelyn C. Hall
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
| | - James F. Cahill
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada
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Reinhart KO, Anacker BL. More closely related plants have more distinct mycorrhizal communities. AOB PLANTS 2014; 6:plu051. [PMID: 25165062 PMCID: PMC4172195 DOI: 10.1093/aobpla/plu051] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 08/18/2014] [Indexed: 05/29/2023]
Abstract
Neighbouring plants are known to vary from having similar to dissimilar arbuscular mycorrhizal fungal (AMF) communities. One possibility is that closely related plants have more similar AMF communities than more distantly related plants, an indication of phylogenetic host specificity. Here, we investigated the structure of AMF communities among dominant grassland plants at three sites in the Northern Great Plains to test whether the pairwise phylogenetic distance among plant species was correlated with pairwise AMF community dissimilarity. For eight dominant and co-occurring grassland plant species, we reconstructed a phylogeny based on DNA data and characterized the AMF communities of their roots at each site. Community analyses revealed that AMF communities varied among sites and among plant species. Contrary to expectations for phylogenetic host specificity, we found that within a site more closely related plants had more distinct AMF communities despite their having similar phenologies. Associations with unique AMF communities may enhance the functional complementarity of related species and promote their coexistence.
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Affiliation(s)
- Kurt O Reinhart
- United States Department of Agriculture-Agricultural Research Service, Fort Keogh Livestock & Range Research Laboratory, 243 Fort Keogh Road, Miles City, MT 59301-4016, USA
| | - Brian L Anacker
- Department of Evolution and Ecology, University of California, Davis, CA, USA
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Williams AV, Nevill PG, Krauss SL. Next generation restoration genetics: applications and opportunities. TRENDS IN PLANT SCIENCE 2014; 19:529-537. [PMID: 24767982 DOI: 10.1016/j.tplants.2014.03.011] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Revised: 03/18/2014] [Accepted: 03/26/2014] [Indexed: 06/03/2023]
Abstract
Restoration ecology is a young scientific discipline underpinning improvements in the rapid global expansion of ecological restoration. The application of molecular tools over the past 20 years has made an important contribution to understanding genetic factors influencing ecological restoration success. Here we illustrate how recent advances in next generation sequencing (NGS) methods are revolutionising the practical contribution of genetics to restoration. Novel applications include a dramatically enhanced capacity to measure adaptive variation for optimal seed sourcing, high-throughput assessment and monitoring of natural and restored biological communities aboveground and belowground, and gene expression analysis as a measure of genetic resilience of restored populations. Challenges remain in data generation, handling and analysis, and how best to apply NGS for practical outcomes in restoration.
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Affiliation(s)
- Anna V Williams
- School of Plant Biology, The University of Western Australia, Crawley, WA 6009, Australia; Kings Park and Botanic Garden, Botanic Gardens and Parks Authority, West Perth, WA 6005, Australia
| | - Paul G Nevill
- School of Plant Biology, The University of Western Australia, Crawley, WA 6009, Australia; Kings Park and Botanic Garden, Botanic Gardens and Parks Authority, West Perth, WA 6005, Australia
| | - Siegfried L Krauss
- School of Plant Biology, The University of Western Australia, Crawley, WA 6009, Australia; Kings Park and Botanic Garden, Botanic Gardens and Parks Authority, West Perth, WA 6005, Australia.
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Hiiesalu I, Pärtel M, Davison J, Gerhold P, Metsis M, Moora M, Öpik M, Vasar M, Zobel M, Wilson SD. Species richness of arbuscular mycorrhizal fungi: associations with grassland plant richness and biomass. THE NEW PHYTOLOGIST 2014; 203:233-244. [PMID: 24641509 DOI: 10.1111/nph.12765] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 02/13/2014] [Indexed: 06/03/2023]
Abstract
Although experiments show a positive association between vascular plant and arbuscular mycorrhizal fungal (AMF) species richness, evidence from natural ecosystems is scarce. Furthermore, there is little knowledge about how AMF richness varies with belowground plant richness and biomass. We examined relationships among AMF richness, above- and belowground plant richness, and plant root and shoot biomass in a native North American grassland. Root-colonizing AMF richness and belowground plant richness were detected from the same bulk root samples by 454-sequencing of the AMF SSU rRNA and plant trnL genes. In total we detected 63 AMF taxa. Plant richness was 1.5 times greater belowground than aboveground. AMF richness was significantly positively correlated with plant species richness, and more strongly with below- than aboveground plant richness. Belowground plant richness was positively correlated with belowground plant biomass and total plant biomass, whereas aboveground plant richness was positively correlated only with belowground plant biomass. By contrast, AMF richness was negatively correlated with belowground and total plant biomass. Our results indicate that AMF richness and plant belowground richness are more strongly related with each other and with plant community biomass than with the plant aboveground richness measures that have been almost exclusively considered to date.
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Affiliation(s)
- Inga Hiiesalu
- Department of Botany, University of Tartu, 40 Lai St, 51005, Tartu, Estonia; Institute of Botany, Czech Academy of Sciences, 135 Dukelská St, 37982, Třeboň, Czech Republic
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Clarke LJ, Soubrier J, Weyrich LS, Cooper A. Environmental metabarcodes for insects: in silico PCR reveals potential for taxonomic bias. Mol Ecol Resour 2014; 14:1160-70. [PMID: 24751203 DOI: 10.1111/1755-0998.12265] [Citation(s) in RCA: 174] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 04/10/2014] [Accepted: 04/11/2014] [Indexed: 10/25/2022]
Abstract
Studies of insect assemblages are suited to the simultaneous DNA-based identification of multiple taxa known as metabarcoding. To obtain accurate estimates of diversity, metabarcoding markers ideally possess appropriate taxonomic coverage to avoid PCR-amplification bias, as well as sufficient sequence divergence to resolve species. We used in silico PCR to compare the taxonomic coverage and resolution of newly designed insect metabarcodes (targeting 16S) with that of existing markers [16S and cytochrome oxidase c subunit I (COI)] and then compared their efficiency in vitro. Existing metabarcoding primers amplified in silico <75% of insect species with complete mitochondrial genomes available, whereas new primers targeting 16S provided >90% coverage. Furthermore, metabarcodes targeting COI appeared to introduce taxonomic PCR-amplification bias, typically amplifying a greater percentage of Lepidoptera and Diptera species, while failing to amplify certain orders in silico. To test whether bias predicted in silico was observed in vitro, we created an artificial DNA blend containing equal amounts of DNA from 14 species, representing 11 insect orders and one arachnid. We PCR-amplified the blend using five primer sets, targeting either COI or 16S, with high-throughput amplicon sequencing yielding more than 6 million reads. In vitro results typically corresponded to in silico PCR predictions, with newly designed 16S primers detecting 11 insect taxa present, thus providing equivalent or better taxonomic coverage than COI metabarcodes. Our results demonstrate that in silico PCR is a useful tool for predicting taxonomic bias in mixed template PCR and that researchers should be wary of potential bias when selecting metabarcoding markers.
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Affiliation(s)
- Laurence J Clarke
- Australian Centre for Ancient DNA, University of Adelaide, Adelaide, SA, 5005, Australia
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Schultz NL, Reid N, Lodge G, Hunter JT. Seasonal and interannual variation in vegetation composition: Implications for survey design and data interpretation. AUSTRAL ECOL 2014. [DOI: 10.1111/aec.12141] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Nick L. Schultz
- Ecosystem Management, School of Environmental and Rural Science; University of New England; Armidale New South Wales Australia
| | - Nick Reid
- Ecosystem Management, School of Environmental and Rural Science; University of New England; Armidale New South Wales Australia
| | - Greg Lodge
- Department of Primary Industries; Tamworth Agricultural Institute; Calala New South Wales Australia
| | - John T. Hunter
- School of Behavioural, Cognitive and Social Sciences; University of New England; Armidale New South Wales Australia
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Öpik M, de Bello F, Price JN, Fraser LH. New insights into vegetation patterns and processes. THE NEW PHYTOLOGIST 2014; 201:383-387. [PMID: 26013049 DOI: 10.1111/nph.12606] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Affiliation(s)
- Maarja Öpik
- Department of Botany, University of Tartu, 40 Lai Str., 51005, Tartu, Estonia
| | - Francesco de Bello
- Biology Centre of Czech Academy of Sciences, Institute of Entomology, 37005, České Budějovice, Czech Republic
- Institute of Botany, Czech Academy of Sciences, Dukelská 135, 379 82, Třeboň, Czech Republic
| | - Jodi N Price
- School of Plant Biology, University of Western Australia, Crawley, Perth, WA 6009, Australia
| | - Lauchlan H Fraser
- Departments of Natural Resource Sciences and Biological Sciences, Thompson Rivers University, Kamloops, BC, V2C 0C8, Canada
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