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Whitley BS, Li Z, Jones L, de Vere N. Mega-Barcoding Projects: Delivering National DNA Barcoding Initiatives for Plants. Methods Mol Biol 2024; 2744:445-473. [PMID: 38683335 DOI: 10.1007/978-1-0716-3581-0_27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
Plant DNA barcoding has a multitude of applications ranging from species detection and biomonitoring to investigating ecological networks and checking food quality. The ability to accurately identify species, using DNA barcoding, depends on the quality and comprehensiveness of the reference library that is used. This chapter describes how to create plant reference libraries using the rbcL, matK, and ITS2 DNA barcode regions. It covers the creation of species lists, the collection of specimens from the field and herbarium, DNA extraction, PCR amplification, and DNA sequencing. This methodology gives special attention to using samples from herbaria, as they represent important collections of easily accessible, taxonomically verified plant material.
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Affiliation(s)
- Brandon S Whitley
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Zhao Li
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Laura Jones
- National Botanic Garden of Wales, Llanarthne, UK
| | - Natasha de Vere
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
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2
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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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3
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Trujillo-Argueta S, del Castillo RF, Velasco-Murguía A. Testing the effectiveness of rbcLa DNA-barcoding for species discrimination in tropical montane cloud forest vascular plants (Oaxaca, Mexico) using BLAST, genetic distance, and tree-based methods. PeerJ 2022; 10:e13771. [PMID: 35990900 PMCID: PMC9390329 DOI: 10.7717/peerj.13771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 07/01/2022] [Indexed: 01/17/2023] Open
Abstract
DNA-barcoding is a species identification tool that uses a short section of the genome that provides a genetic signature of the species. The main advantage of this novel technique is that it requires a small sample of tissue from the tested organism. In most animal groups, this technique is very effective. However, in plants, the recommended standard markers, such as rbcLa, may not always work, and their efficacy remains to be tested in many plant groups, particularly from the Neotropical region. We examined the discriminating power of rbcLa in 55 tropical cloud forest vascular plant species from 38 families (Oaxaca, Mexico). We followed the CBOL criteria using BLASTn, genetic distance, and monophyly tree-based analyses (neighbor-joining, NJ, maximum likelihood, ML, and Bayesian inference, BI). rbcLa universal primers amplified 69.0% of the samples and yielded 91.3% bi-directional sequences. Sixty-three new rbcLa sequences were established. BLAST discriminates 80.8% of the genus but only 15.4% of the species. There was nil minimum interspecific genetic distances in Quercus, Oreopanax, and Daphnopsis. Contrastingly, Ericaceae (5.6%), Euphorbiaceae (4.6%), and Asteraceae (3.3%) species displayed the highest within-family genetic distances. According to the most recent angiosperm classification, NJ and ML trees successfully resolved (100%) monophyletic species. ML trees showed the highest mean branch support value (87.3%). Only NJ and ML trees could successfully discriminate Quercus species belonging to different subsections: Quercus martinezii (white oaks) from Q. callophylla and Q. laurina (red oaks). The ML topology could distinguish species in the Solanaceae clade with similar BLAST matches. Also, the BI topology showed a polytomy in this clade, and the NJ tree displayed low-support values. We do not recommend genetic-distance approaches for species discrimination. Severe shortages of rbcLa sequences in public databases of neotropical species hindered effective BLAST comparisons. Instead, ML tree-based analysis displays the highest species discrimination among the tree-based analyses. With the ML topology in selected genera, rbcLa helped distinguish infra-generic taxonomic categories, such as subsections, grouping affine species within the same genus, and discriminating species. Since the ML phylogenetic tree could discriminate 48 species out of our 55 studied species, we recommend this approach to resolve tropical montane cloud forest species using rbcLa, as an initial step and improve DNA amplification methods.
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Ampt EA, van Ruijven J, Zwart MP, Raaijmakers JM, Termorshuizen AJ, Mommer L. Plant neighbours can make or break the disease transmission chain of a fungal root pathogen. THE NEW PHYTOLOGIST 2022; 233:1303-1316. [PMID: 34787907 PMCID: PMC9300135 DOI: 10.1111/nph.17866] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 11/04/2021] [Indexed: 05/07/2023]
Abstract
Biodiversity can reduce or increase disease transmission. These divergent effects suggest that community composition rather than diversity per se determines disease transmission. In natural plant communities, little is known about the functional roles of neighbouring plant species in belowground disease transmission. Here, we experimentally investigated disease transmission of a fungal root pathogen (Rhizoctonia solani) in two focal plant species in combinations with four neighbour species of two ages. We developed stochastic models to test the relative importance of two transmission-modifying mechanisms: (1) infected hosts serve as nutrient supply to increase hyphal growth, so that successful disease transmission is self-reinforcing; and (2) plant resistance increases during plant development. Neighbouring plants either reduced or increased disease transmission in the focal plants. These effects depended on neighbour age, but could not be explained by a simple dichotomy between hosts and nonhost neighbours. Model selection revealed that both transmission-modifying mechanisms are relevant and that focal host-neighbour interactions changed which mechanisms steered disease transmission rate. Our work shows that neighbour-induced shifts in the importance of these mechanisms across root networks either make or break disease transmission chains. Understanding how diversity affects disease transmission thus requires integrating interactions between focal and neighbour species and their pathogens.
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Affiliation(s)
- Eline A. Ampt
- Plant Ecology and Nature Conservation GroupWageningen UniversityPO Box 47Wageningen6700 AAthe Netherlands
| | - Jasper van Ruijven
- Plant Ecology and Nature Conservation GroupWageningen UniversityPO Box 47Wageningen6700 AAthe Netherlands
| | - Mark P. Zwart
- Department of Microbial EcologyNetherlands Institute for Ecology (NIOO‐KNAW)PO Box 50Wageningen6700 ABthe Netherlands
| | - Jos M. Raaijmakers
- Department of Microbial EcologyNetherlands Institute for Ecology (NIOO‐KNAW)PO Box 50Wageningen6700 ABthe Netherlands
| | | | - Liesje Mommer
- Plant Ecology and Nature Conservation GroupWageningen UniversityPO Box 47Wageningen6700 AAthe Netherlands
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5
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Rajaniemi TK. Root allocation and foraging precision in heterogeneous soils. Basic Appl Ecol 2022. [DOI: 10.1016/j.baae.2022.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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6
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Pragmatic Applications and Universality of DNA Barcoding for Substantial Organisms at Species Level: A Review to Explore a Way Forward. BIOMED RESEARCH INTERNATIONAL 2022; 2022:1846485. [PMID: 35059459 PMCID: PMC8766189 DOI: 10.1155/2022/1846485] [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: 09/27/2021] [Accepted: 12/06/2021] [Indexed: 01/04/2023]
Abstract
DNA barcodes are regarded as hereditary succession codes that serve as a recognition marker to address several queries relating to the identification, classification, community ecology, and evolution of certain functional traits in organisms. The mitochondrial cytochrome c oxidase 1 (CO1) gene as a DNA barcode is highly efficient for discriminating vertebrate and invertebrate animal species. Similarly, different specific markers are used for other organisms, including ribulose bisphosphate carboxylase (rbcL), maturase kinase (matK), transfer RNA-H and photosystem II D1-ApbsArabidopsis thaliana (trnH-psbA), and internal transcribed spacer (ITS) for plant species; 16S ribosomal RNA (16S rRNA), elongation factor Tu gene (Tuf gene), and chaperonin for bacterial strains; and nuclear ITS for fungal strains. Nevertheless, the taxon coverage of reference sequences is far from complete for genus or species-level identification. Applying the next-generation sequencing approach to the parallel acquisition of DNA barcode sequences could greatly expand the potential for library preparation or accurate identification in biodiversity research. Overall, this review articulates on the DNA barcoding technology as applied to different organisms, its universality, applicability, and innovative approach to handling DNA-based species identification.
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7
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Luo W, Ni M, Wang Y, Lan R, Eissenstat DM, Cahill JF, Li B, Chu C. Limited evidence of vertical fine-root segregation in a subtropical forest. THE NEW PHYTOLOGIST 2021; 231:2308-2318. [PMID: 34110016 DOI: 10.1111/nph.17546] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 06/03/2021] [Indexed: 06/12/2023]
Abstract
Vertical root segregation and the resulting niche partitioning can be a key underpinning of species coexistence. This could result from substantial interspecific variations in root profiles and rooting plasticity in response to soil heterogeneity and neighbours, but they remain largely untested in forest communities. In a diverse forest in subtropical China, we randomly sampled > 4000 root samples from 625 0-30 cm soil profiles. Using morphological and DNA-based methods, we identified 109 woody plant species, determined the degree of vertical fine-root segregation, and examined rooting plasticity in response to soil heterogeneity and neighbour structure. We found no evidence of vertical fine-root segregation among cooccurring species. By contrast, root abundance of different species tended to be positively correlated within soil zones. Underlying these findings was a lack of interspecific variation in fine-root profiles with over 90% of species concentrated in the 0-10 cm soil zone with only one species dominating in the 10-20 cm soil zone. Root profiles exhibited low responsiveness to root neighbours but tended to be shallow in soils with low phosphorus and copper content. These findings suggest that if there is niche differentiation leading to coexistence in this diverse forest, it would be occurring by mechanisms other than vertical fine-root segregation.
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Affiliation(s)
- Wenqi Luo
- State Key Laboratory of Biocontrol, School of Life Sciences and School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Ming Ni
- State Key Laboratory of Biocontrol, School of Life Sciences and School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
- Département de Biologie, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada
| | - Youshi Wang
- State Key Laboratory of Biocontrol, School of Life Sciences and School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Runxuan Lan
- State Key Laboratory of Biocontrol, School of Life Sciences and School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - David M Eissenstat
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA, 16802, USA
| | - James F Cahill
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Buhang Li
- State Key Laboratory of Biocontrol, School of Life Sciences and School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Chengjin Chu
- State Key Laboratory of Biocontrol, School of Life Sciences and School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
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8
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Karunarathna A, Tibpromma S, Jayawardena RS, Nanayakkara C, Asad S, Xu J, Hyde KD, Karunarathna SC, Stephenson SL, Lumyong S, Kumla J. Fungal Pathogens in Grasslands. Front Cell Infect Microbiol 2021; 11:695087. [PMID: 34434901 PMCID: PMC8381356 DOI: 10.3389/fcimb.2021.695087] [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: 04/14/2021] [Accepted: 06/21/2021] [Indexed: 01/02/2023] Open
Abstract
Grasslands are major primary producers and function as major components of important watersheds. Although a concise definition of grasslands cannot be given using a physiognomic or structural approach, grasslands can be described as vegetation communities experiencing periodical droughts and with canopies dominated by grasses and grass-like plants. Grasslands have a cosmopolitan distribution except for the Antarctic region. Fungal interactions with grasses can be pathogenic or symbiotic. Herbivorous mammals, insects, other grassland animals, and fungal pathogens are known to play important roles in maintaining the biomass and biodiversity of grasslands. Although most pathogenicity studies on the members of Poaceae have been focused on economically important crops, the plant-fungal pathogenic interactions involved can extend to the full range of ecological circumstances that exist in nature. Hence, it is important to delineate the fungal pathogen communities and their interactions in man-made monoculture systems and highly diverse natural ecosystems. A better understanding of the key fungal players can be achieved by combining modern techniques such as next-generation sequencing (NGS) together with studies involving classic phytopathology, taxonomy, and phylogeny. It is of utmost importance to develop experimental designs that account for the ecological complexity of the relationships between grasses and fungi, both above and below ground. In grasslands, loss in species diversity increases interactions such as herbivory, mutualism, predation or infectious disease transmission. Host species density and the presence of heterospecific host species, also affect the disease dynamics in grasslands. Many studies have shown that lower species diversity increases the severity as well as the transmission rate of fungal diseases. Moreover, communities that were once highly diverse but have experienced decreased species richness and dominancy have also shown higher pathogenicity load due to the relaxed competition, although this effect is lower in natural communities. This review addresses the taxonomy, phylogeny, and ecology of grassland fungal pathogens and their interactions in grassland ecosystems.
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Affiliation(s)
- Anuruddha Karunarathna
- Centre for Mountain Futures, Kunming Institute of Botany, Kunming, China.,Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai, Thailand.,Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, Thailand
| | - Saowaluck Tibpromma
- Centre for Mountain Futures, Kunming Institute of Botany, Kunming, China.,CIFOR-ICRAF China Program, World Agroforestry (ICRAF), Kunming, China
| | - Ruvishika S Jayawardena
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, Thailand.,School of Science, Mae Fah Luang University, Chiang Rai, Thailand
| | | | - Suhail Asad
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Jianchu Xu
- Centre for Mountain Futures, Kunming Institute of Botany, Kunming, China.,CIFOR-ICRAF China Program, World Agroforestry (ICRAF), Kunming, China
| | - Kevin D Hyde
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, Thailand
| | - Samantha C Karunarathna
- Centre for Mountain Futures, Kunming Institute of Botany, Kunming, China.,CIFOR-ICRAF China Program, World Agroforestry (ICRAF), Kunming, China
| | - Steven L Stephenson
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Saisamorn Lumyong
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand.,Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand.,Academy of Science, The Royal Society of Thailand, Bangkok, Thailand
| | - Jaturong Kumla
- Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand.,Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
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Chen Y, Zhu X, Loukopoulos P, Weston LA, Albrecht DE, Quinn JC. Genotypic identification of Panicum spp. in New South Wales, Australia using DNA barcoding. Sci Rep 2021; 11:16055. [PMID: 34362980 PMCID: PMC8346583 DOI: 10.1038/s41598-021-95610-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 07/16/2021] [Indexed: 02/07/2023] Open
Abstract
Australia has over 30 Panicum spp. (panic grass) including several non-native species that cause crop and pasture loss and hepatogenous photosensitisation in livestock. It is critical to correctly identify them at the species level to facilitate the development of appropriate management strategies for efficacious control of Panicum grasses in crops, fallows and pastures. Currently, identification of Panicum spp. relies on morphological examination of the reproductive structures, but this approach is only useful for flowering specimens and requires significant taxonomic expertise. To overcome this limitation, we used multi-locus DNA barcoding for the identification of ten selected Panicum spp. found in Australia. With the exception of P. buncei, other native Australian Panicum were genetically separated at the species level and distinguished from non-native species. One nuclear (ITS) and two chloroplast regions (matK and trnL intron-trnF) were identified with varying facility for DNA barcode separation of the Panicum species. Concatenation of sequences from ITS, matK and trnL intron-trnF regions provided clear separation of eight regionally collected species, with a maximum intraspecific distance of 0.22% and minimum interspecific distance of 0.33%. Two of three non-native Panicum species exhibited a smaller genome size compared to native species evaluated, and we speculate that this may be associated with biological advantages impacting invasion of non-native Panicum species in novel locations. We conclude that multi-locus DNA barcoding, in combination with traditional taxonomic identification, provides an accurate and cost-effective adjunctive tool for further distinguishing Panicum spp. at the species level.
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Affiliation(s)
- Yuchi Chen
- grid.1037.50000 0004 0368 0777School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW Australia ,grid.1680.f0000 0004 0559 5189Graham Centre for Agricultural Innovation, Charles Sturt University and NSW Department of Primary Industries, Wagga Wagga, NSW Australia ,grid.1008.90000 0001 2179 088XMelbourne Veterinary School, The University of Melbourne, Werribee, VIC Australia
| | - Xiaocheng Zhu
- grid.1680.f0000 0004 0559 5189Graham Centre for Agricultural Innovation, Charles Sturt University and NSW Department of Primary Industries, Wagga Wagga, NSW Australia ,grid.1680.f0000 0004 0559 5189Wagga Wagga Agricultural Institute, NSW Department of Primary Industries, Wagga Wagga, NSW Australia
| | - Panayiotis Loukopoulos
- grid.1037.50000 0004 0368 0777School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW Australia ,grid.1008.90000 0001 2179 088XMelbourne Veterinary School, The University of Melbourne, Werribee, VIC Australia
| | - Leslie A. Weston
- grid.1037.50000 0004 0368 0777School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW Australia ,grid.1680.f0000 0004 0559 5189Graham Centre for Agricultural Innovation, Charles Sturt University and NSW Department of Primary Industries, Wagga Wagga, NSW Australia
| | - David E. Albrecht
- grid.467784.e0000 0001 2231 5722Australian National Herbarium, Centre for Australian National Biodiversity Research (a Joint Venture Between Parks Australia and CSIRO), Canberra, Australian Capital Territory, Australia
| | - Jane C. Quinn
- grid.1037.50000 0004 0368 0777School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW Australia ,grid.1680.f0000 0004 0559 5189Graham Centre for Agricultural Innovation, Charles Sturt University and NSW Department of Primary Industries, Wagga Wagga, NSW Australia
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10
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Isola D, Bartoli F, Langone S, Ceschin S, Zucconi L, Caneva G. Plant DNA Barcode as a Tool for Root Identification in Hypogea: The Case of the Etruscan Tombs of Tarquinia (Central Italy). PLANTS (BASEL, SWITZERLAND) 2021; 10:1138. [PMID: 34205139 PMCID: PMC8228792 DOI: 10.3390/plants10061138] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/30/2021] [Accepted: 06/01/2021] [Indexed: 11/21/2022]
Abstract
Roots can produce mechanical and chemical alterations to building structures, especially in the case of underground historical artifacts. In archaeological sites, where vegetation plays the dual role of naturalistic relevance and potential threat, trees and bushes are under supervision. No customized measures can be taken against herbaceous plants lacking fast and reliable root identification methods that are useful to assess their dangerousness. In this study, we aimed to test the efficacy of DNA barcoding in identifying plant rootlets threatening the Etruscan tombs of the Necropolis of Tarquinia. As DNA barcode markers, we selected two sections of the genes rbcL and matK, the nuclear ribosomal internal transcribed spacer (nrITS), and the intergenic spacer psbA-trnH. All fourteen root samples were successfully sequenced and identified at species (92.9%) and genus level (7.01%) by GenBank matching and reference dataset implementation. Some eudicotyledons with taproots, such as Echium italicum L., Foeniculum vulgare Mill., and Reseda lutea L. subsp. lutea, showed a certain recurrence. Further investigations are needed to confirm this promising result, increasing the number of roots and enlarging the reference dataset with attention to meso-Mediterranean perennial herbaceous species. The finding of herbaceous plants roots at more than 3 m deep confirms their potential risk and underlines the importance of vegetation planning, monitoring, and management on archaeological sites.
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Affiliation(s)
- Daniela Isola
- Department of Sciences, Roma Tre University, 00146 Rome, Italy; (F.B.); (S.L.); (S.C.); (G.C.)
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, 01100 Viterbo, Italy;
| | - Flavia Bartoli
- Department of Sciences, Roma Tre University, 00146 Rome, Italy; (F.B.); (S.L.); (S.C.); (G.C.)
| | - Simone Langone
- Department of Sciences, Roma Tre University, 00146 Rome, Italy; (F.B.); (S.L.); (S.C.); (G.C.)
| | - Simona Ceschin
- Department of Sciences, Roma Tre University, 00146 Rome, Italy; (F.B.); (S.L.); (S.C.); (G.C.)
| | - Laura Zucconi
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, 01100 Viterbo, Italy;
| | - Giulia Caneva
- Department of Sciences, Roma Tre University, 00146 Rome, Italy; (F.B.); (S.L.); (S.C.); (G.C.)
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11
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Luo W, Lan R, Chen D, Zhang B, Xi N, Li Y, Fang S, Valverde-Barrantes OJ, Eissenstat DM, Chu C, Wang Y. Limiting similarity shapes the functional and phylogenetic structure of root neighborhoods in a subtropical forest. THE NEW PHYTOLOGIST 2021; 229:1078-1090. [PMID: 32924174 DOI: 10.1111/nph.16920] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 08/10/2020] [Indexed: 06/11/2023]
Abstract
Environmental filtering and limiting similarity mechanisms can simultaneously structure community assemblages. However, how they shape the functional and phylogenetic structure of root neighborhoods remains unclear, hindering the understanding of belowground community assembly processes and diversity maintenance. In a 50-ha plot in a subtropical forest, China, we randomly sampled > 2700 root clusters from 625 soil samples. Focusing on 10 root functional traits measured on 76 woody species, we examined the functional and phylogenetic structure of root neighborhoods and linked their distributions with environmental cues. Functional overdispersion was pervasive among individual root traits (50% of the traits) and accentuated when different traits were combined. Functional clustering (20% of the traits) seemed to be associated with a soil nutrient gradient with thick roots dominating fertile areas whereas thin roots dominated infertile soils. Nevertheless, such traits also were sorted along other environmental cues, showing multidimensional adaptive trait syndromes. Species relatedness also was an important factor defining root neighborhoods, resulting in significant phylogenetic overdispersion. These results suggest that limiting similarity may drive niche differentiation of coexisting species to reduce competition, and that alternative root strategies could be crucial in promoting root neighborhood resource use and species coexistence.
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Affiliation(s)
- Wenqi Luo
- Department of Ecology, State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Runxuan Lan
- Department of Ecology, State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Dongxia Chen
- Department of Ecology, State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Bingwei Zhang
- Department of Ecology, State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Nianxun Xi
- Department of Ecology, State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yuanzhi Li
- Department of Ecology, State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Suqing Fang
- Department of Ecology, State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Oscar J Valverde-Barrantes
- International Center for Tropical Biodiversity, Department of Biological Sciences, Florida International University, Miami, FL, 33199, USA
| | - David M Eissenstat
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Chengjin Chu
- Department of Ecology, State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Youshi Wang
- Department of Ecology, State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
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12
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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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13
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Thu Ha TT, Khanh TD, Trung KH. Evaluation of Genetic Diversity and Identification of <i>Huperzia</i> Species Collected in Some Different Areas in Vietnam by Molecular Markers. INTERNATIONAL LETTERS OF NATURAL SCIENCES 2020. [DOI: 10.18052/www.scipress.com/ilns.80.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The objective of this study was to evaluate genetic diversity of 35 Huperzia samples collected from the different ecological areas in Vietnam by using rbcL markers. The results revealed that the samples were genetically diverse in high genetic similarity which ranged from 98.0 to 99.0%, respectively. Based on the Genbank data in comparison, it was ascertained that only one sample (BK3) is a member of H.phlegmarioides group, and others belonged H. squarrosa group as divided into two main groups by phylogenetic tree analyses. It suggests that some Huperzia samples may plausibly descend from the same origin, evolution and arising relations. This study has provided useful information for further identifying the high-quality genetic plant sources for propagation, development and conservation of the high-valued medicinal materials of Huperzia plants in this country.
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14
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Onipchenko VG, Kipkeev AM, Mommer L, van der Paauw JW, van Logtestijn RSP, Tekeev DK, Zernov AS, Akhmetzhanova AA, Kozhevnikova AD, Hiiesalu I, Makarov MI, Cornelissen JHC. Snow roots: Where are they and what are they for? Ecology 2020; 102:e03255. [PMID: 33222182 DOI: 10.1002/ecy.3255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 09/10/2020] [Accepted: 10/05/2020] [Indexed: 11/12/2022]
Affiliation(s)
- Vladimir G Onipchenko
- Faculty of Biology, Moscow State Lomonosov University, Leninskie Gory 1-12, Moscow, 119234, Russia
| | - Alii M Kipkeev
- Faculty of Biology, Moscow State Lomonosov University, Leninskie Gory 1-12, Moscow, 119234, Russia
| | - Liesje Mommer
- Plant Ecology & Nature Conservation Group, Department of Environmental Science, Wageningen University & Research Centre, Wageningen, The Netherlands
| | - Jan Willem van der Paauw
- Plant Ecology & Nature Conservation Group, Department of Environmental Science, Wageningen University & Research Centre, Wageningen, The Netherlands
| | - Richard S P van Logtestijn
- Systems Ecology, Department of Ecological Science, Faculty of Science, Vrije Universiteit, De Boelelaan 1085, Amsterdam, 1081 HV, The Netherlands
| | - Dzhamal K Tekeev
- Teberda State Reserve, Badukskii 1, Karachaevo-Cherkessian Republic, Teberda, 369210, Russia
| | - Alexander S Zernov
- Faculty of Biology, Moscow State Lomonosov University, Leninskie Gory 1-12, Moscow, 119234, Russia
| | - Asem A Akhmetzhanova
- Faculty of Biology, Moscow State Lomonosov University, Leninskie Gory 1-12, Moscow, 119234, Russia
| | - Anna D Kozhevnikova
- Timiryazev Institute of Plant Physiology RAS, Botanicheskaya ul. 35, Moscow, 127276, Russia
| | - Inga Hiiesalu
- Institute of Ecology and Earth Sciences, University of Tartu, Lai 40, Tartu, 51005, Estonia
| | - Mikhail I Makarov
- Faculty of Soil Science, Moscow State Lomonosov University, Leninskie Gory 1-12, Moscow, 119234, Russia
| | - Johannes H C Cornelissen
- Systems Ecology, Department of Ecological Science, Faculty of Science, Vrije Universiteit, De Boelelaan 1085, Amsterdam, 1081 HV, The Netherlands
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15
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Wagemaker CAM, Mommer L, Visser EJW, Weigelt A, van Gurp TP, Postuma M, Smit-Tiekstra AE, de Kroon H. msGBS: A new high-throughput approach to quantify the relative species abundance in root samples of multispecies plant communities. Mol Ecol Resour 2020; 21:1021-1036. [PMID: 33058506 PMCID: PMC8246947 DOI: 10.1111/1755-0998.13278] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [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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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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17
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Ghareb HES, Ibrahim SD, Hegazi GAEM. In vitro propagation and DNA barcode analysis of the endangered Silene schimperiana in Saint Katherine protectorate. J Genet Eng Biotechnol 2020; 18:41. [PMID: 32778978 PMCID: PMC7417468 DOI: 10.1186/s43141-020-00052-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 07/13/2020] [Indexed: 11/10/2022]
Abstract
BACKGROUND Anthropogenic activity, climate change, pollution, and exploitation of natural resources are some reasons that cause threatening of plant diversity. Silene schimperiana is an endangered plant species in Egypt and is endemic to the high mountain of Saint Katherine Protected Area in southern Sinai. The purpose of the study was the ex situ conservation of Silene schimperiana through in vitro propagation and DNA barcode analysis. RESULTS To develop an efficient ex situ conservation program of the plant, in vitro propagation protocol has been achieved from shoot tip and stem nodal segment explants of in vitro germinated seedlings. Explants were established in vitro on Murashige and Skoog (MS) medium supplemented with 2.89 μM gibberellic acid (GA3), 1.08 μM α-naphthaleneacetic acid (NAA), and 1.16 μM kinetin (Kin). The highest number of axillary shoots (9.27) was obtained when they were transferred to MS medium supplemented with 4.48 μM 6-benzyl adenine (BA). Hundred percent of multiple axillary shoots were rooted on quarter-strength MS medium supplemented with 4.92 μM indole-3-butyric acid (IBA) and 10.75 μM NAA. Rooted plants were transferred to pots containing a soil-peat mixture (1: 2 v/v) and successfully acclimatized in the greenhouse. Plant identification is a crucial aspect to understand and conserve plant diversity from extinction. DNA barcode analysis of Silene schimperiana was carried out using two chloroplast DNA markers (cpDNA): 1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) and RNA polymerase subunit (rpoC1) and a nuclear ribosome DNA marker (ncDNA), internal transcribed spacer (ITS). Phylogenetic analysis revealed a successful identification of Silene schimperiana on the species and genus levels and supported the inclusion of Silene schimperiana in genus Silene. CONCLUSIONS In this study, a relevant in vitro propagation method was established to facilitate the recovery of Silene schimperiana, in addition to DNA barcoding of the plant as a tool for effective management and conservation of plant genetic resources.
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Affiliation(s)
- Heba El-Sayed Ghareb
- Tissue Culture Unit, Department of Genetic Resources, Desert Research Center, 1 Mathaf El-Matareya Street, Cairo, El-Matareya, 11357, Egypt
| | | | - Ghada Abd El-Moneim Hegazi
- Tissue Culture Unit, Department of Genetic Resources, Desert Research Center, 1 Mathaf El-Matareya Street, Cairo, El-Matareya, 11357, Egypt.
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18
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Whitehurst LE, Cunard CE, Reed JN, Worthy SJ, Marsico TD, Lucardi RD, Burgess KS. Preliminary application of DNA barcoding toward the detection of viable plant propagules at an initial, international point-of-entry in Georgia, USA. Biol Invasions 2020. [DOI: 10.1007/s10530-020-02204-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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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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Metzler P, La Flèche M, Karst J. Expanding and testing fluorescent amplified fragment length polymorphisms for identifying roots of boreal forest plant species. APPLICATIONS IN PLANT SCIENCES 2019; 7:e01236. [PMID: 31024780 PMCID: PMC6476169 DOI: 10.1002/aps3.1236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 12/21/2018] [Indexed: 06/07/2023]
Abstract
PREMISE OF THE STUDY Identifying roots to species is challenging, but is a common problem in ecology. Fluorescent amplified fragment length polymorphisms (FAFLPs) can distinguish species within a mixed sample, are high throughput, and are inexpensive. To broaden the use of this tool across ecosystems, unique size profiles must be established for species, and its limits identified. METHODS Fragments of three noncoding cpDNA regions were used to create size profiles for 193 species common to the western Canadian boreal forest. We compared detection success among congeners using FAFLPs and Sanger sequencing of the trnL intron. We also simulated and experimentally created communities to test the influence of species richness, cpDNA regions used, and extraction/amplification biases on detection success. RESULTS Of the 193 species, 54% had unique size profiles. This value decreased when fewer cpDNA regions were used. In simulated communities, ambiguous species identifications were positively related to the species richness of the community. In mock communities, some species evaded detection owing to poor extraction or amplification. Sequencing did not increase detection success compared to FAFLPs for a subset of 24 species across nine genera. DISCUSSION We recommend FAFLPs are best suited to confirm rather than discover species occurring belowground.
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Affiliation(s)
- Paul Metzler
- Department of Renewable ResourcesUniversity of AlbertaEdmontonT6G 2E3AlbertaCanada
| | - Marc La Flèche
- Department of Renewable ResourcesUniversity of AlbertaEdmontonT6G 2E3AlbertaCanada
| | - Justine Karst
- Department of Renewable ResourcesUniversity of AlbertaEdmontonT6G 2E3AlbertaCanada
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21
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Above- and belowground overyielding are related at the community and species level in a grassland biodiversity experiment. ADV ECOL RES 2019. [DOI: 10.1016/bs.aecr.2019.05.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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22
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Tan S, Luo Y, Hollingsworth PM, Burgess KS, Xu K, Li D, Gao L. DNA barcoding herbaceous and woody plant species at a subalpine forest dynamics plot in Southwest China. Ecol Evol 2018; 8:7195-7205. [PMID: 30073078 PMCID: PMC6065341 DOI: 10.1002/ece3.4254] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 03/05/2018] [Accepted: 05/14/2018] [Indexed: 01/13/2023] Open
Abstract
Although DNA barcoding has been widely used to identify plant species composition in temperate and tropical ecosystems, relatively few studies have used DNA barcodes to document both herbaceous and woody components of forest plot. A total of 201 species (72 woody species and 129 herbaceous species) representing 135 genera distributed across 64 families of seed plants were collected in a 25 ha CForBio subalpine forest dynamics plot. In total, 491 specimens were screened for three DNA regions of the chloroplast genome (rbcL, matK, and trnH-psbA) as well as the internal transcribed spacers (ITS) of nuclear ribosomal DNA. We quantified species resolution for each barcode separately or in combination using a ML tree-based method. Amplification and sequencing success were highest for rbcL, followed by trnH-psbA, which performed better than ITS and matK. The rbcL + ITS barcode had slightly higher species resolution rates (88.60%) compared with rbcL + matK (86.60%) and rbcL + trnH-psbA (86.01%). The addition of trnH-psbA or ITS to the rbcL + matK barcode only marginally increased species resolution rates, although in combination the four barcodes had the highest discriminatory power (90.21%). The situations where DNA barcodes did not discriminate among species were typically associated with higher numbers of co-occurring con-generic species. In addition, herbaceous species were much better resolved than woody species. Our study represents one of the first applications of DNA barcodes in a subalpine forest dynamics plot and contributes to our understanding of patterns of genetic divergence among woody and herbaceous plant species.
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Affiliation(s)
- Shao‐Lin Tan
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunming, YunnanChina
- Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunming, YunnanChina
- College of Life SciencesUniversity of Chinese Academy of SciencesKunming, YunnanChina
| | - Ya‐Huang Luo
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunming, YunnanChina
| | | | - Kevin S. Burgess
- Department of BiologyCollege of Letters and SciencesColumbus State UniversityUniversity System of GeorgiaColumbusGeorgia
| | - Kun Xu
- Lijiang Forest Ecosystem Research StationKunming Institute of BotanyChinese Academy of SciencesLijiangChina
| | - De‐Zhu Li
- Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunming, YunnanChina
- College of Life SciencesUniversity of Chinese Academy of SciencesKunming, YunnanChina
| | - Lian‐Ming Gao
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of SciencesKunming, YunnanChina
- Lijiang Forest Ecosystem Research StationKunming Institute of BotanyChinese Academy of SciencesLijiangChina
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Mommer L, Cotton TEA, Raaijmakers JM, Termorshuizen AJ, van Ruijven J, Hendriks M, van Rijssel SQ, van de Mortel JE, van der Paauw JW, Schijlen EGWM, Smit‐Tiekstra AE, Berendse F, de Kroon H, Dumbrell AJ. Lost in diversity: the interactions between soil-borne fungi, biodiversity and plant productivity. THE NEW PHYTOLOGIST 2018; 218:542-553. [PMID: 29468690 PMCID: PMC5887887 DOI: 10.1111/nph.15036] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 01/03/2018] [Indexed: 05/17/2023]
Abstract
There is consensus that plant species richness enhances plant productivity within natural grasslands, but the underlying drivers remain debated. Recently, differential accumulation of soil-borne fungal pathogens across the plant diversity gradient has been proposed as a cause of this pattern. However, the below-ground environment has generally been treated as a 'black box' in biodiversity experiments, leaving these fungi unidentified. Using next generation sequencing and pathogenicity assays, we analysed the community composition of root-associated fungi from a biodiversity experiment to examine if evidence exists for host specificity and negative density dependence in the interplay between soil-borne fungi, plant diversity and productivity. Plant species were colonised by distinct (pathogenic) fungal communities and isolated fungal species showed negative, species-specific effects on plant growth. Moreover, 57% of the pathogenic fungal operational taxonomic units (OTUs) recorded in plant monocultures were not detected in eight plant species plots, suggesting a loss of pathogenic OTUs with plant diversity. Our work provides strong evidence for host specificity and negative density-dependent effects of root-associated fungi on plant species in grasslands. Our work substantiates the hypothesis that fungal root pathogens are an important driver of biodiversity-ecosystem functioning relationships.
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Affiliation(s)
- Liesje Mommer
- Plant Ecology and Nature Conservation GroupWageningen UniversityPO Box 47Wageningen6700 AAthe Netherlands
| | - T. E. Anne Cotton
- School of Biological SciencesUniversity of EssexWivenhoe ParkColchesterCO4 3SQUK
- Department of Animal and Plant SciencesUniversity of SheffieldSouth YorkshireS10 2TNUK
| | - Jos M. Raaijmakers
- Department of Microbial EcologyNetherlands Institute for Ecology (NIOO‐KNAW)PO Box 50Wageningen6700 ABthe Netherlands
| | | | - Jasper van Ruijven
- Plant Ecology and Nature Conservation GroupWageningen UniversityPO Box 47Wageningen6700 AAthe Netherlands
| | - Marloes Hendriks
- Institute for Water and Wetland ResearchExperimental Plant EcologyRadboud University NijmegenPO Box 9010Nijmegen6500 GLthe Netherlands
| | - Sophia Q. van Rijssel
- Plant Ecology and Nature Conservation GroupWageningen UniversityPO Box 47Wageningen6700 AAthe Netherlands
| | - Judith E. van de Mortel
- HAS University of Applied SciencesDepartment of Applied BiologyUniversity of Applied SciencesSpoorstraat 62Venlo5911 KJthe Netherlands
| | - Jan Willem van der Paauw
- Plant Ecology and Nature Conservation GroupWageningen UniversityPO Box 47Wageningen6700 AAthe Netherlands
| | - Elio G. W. M. Schijlen
- Wageningen University and Research BU BiosciencePO Box 16Wageningen6700 AAthe Netherlands
| | - Annemiek E. Smit‐Tiekstra
- Institute for Water and Wetland ResearchExperimental Plant EcologyRadboud University NijmegenPO Box 9010Nijmegen6500 GLthe Netherlands
| | - Frank Berendse
- Plant Ecology and Nature Conservation GroupWageningen UniversityPO Box 47Wageningen6700 AAthe Netherlands
| | - Hans de Kroon
- Institute for Water and Wetland ResearchExperimental Plant EcologyRadboud University NijmegenPO Box 9010Nijmegen6500 GLthe Netherlands
| | - Alex J. Dumbrell
- School of Biological SciencesUniversity of EssexWivenhoe ParkColchesterCO4 3SQUK
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24
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Subrahmaniam HJ, Libourel C, Journet EP, Morel JB, Muños S, Niebel A, Raffaele S, Roux F. The genetics underlying natural variation of plant-plant interactions, a beloved but forgotten member of the family of biotic interactions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:747-770. [PMID: 29232012 DOI: 10.1111/tpj.13799] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 12/02/2017] [Accepted: 12/06/2017] [Indexed: 05/22/2023]
Abstract
Despite the importance of plant-plant interactions on crop yield and plant community dynamics, our understanding of the genetic and molecular bases underlying natural variation of plant-plant interactions is largely limited in comparison with other types of biotic interactions. By listing 63 quantitative trait loci (QTL) mapping and global gene expression studies based on plants directly challenged by other plants, we explored whether the genetic architecture and the function of the candidate genes underlying natural plant-plant interactions depend on the type of interactions between two plants (competition versus commensalism versus reciprocal helping versus asymmetry). The 16 transcriptomic studies are unevenly distributed between competitive interactions (n = 12) and asymmetric interactions (n = 4, all focusing on response to parasitic plants). By contrast, 17 and 30 QTL studies were identified for competitive interactions and asymmetric interactions (either weed suppressive ability or response to parasitic plants), respectively. Surprisingly, no studies have been carried out on the identification of genetic and molecular bases underlying natural variation in positive interactions. The candidate genes underlying natural plant-plant interactions can be classified into seven categories of plant function that have been identified in artificial environments simulating plant-plant interactions either frequently (photosynthesis, hormones), only recently (cell wall modification and degradation, defense pathways against pathogens) or rarely (ABC transporters, histone modification and meristem identity/life history traits). Finally, we introduce several avenues that need to be explored in the future to obtain a thorough understanding of the genetic and molecular bases underlying plant-plant interactions within the context of realistic community complexity.
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Affiliation(s)
| | - Cyril Libourel
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Etienne-Pascal Journet
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
- AGIR, Université de Toulouse, INRA, INPT, INP-EI PURPAN, Castanet-Tolosan, France
| | - Jean-Benoît Morel
- BGPI, INRA, CIRAD, SupAgro, Université de Montpellier, Montpellier, France
| | - Stéphane Muños
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Andreas Niebel
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Sylvain Raffaele
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Fabrice Roux
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
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Valverde-Barrantes OJ, Smemo KA, Feinstein LM, Kershner MW, Blackwood CB. Patterns in spatial distribution and root trait syndromes for ecto and arbuscular mycorrhizal temperate trees in a mixed broadleaf forest. Oecologia 2017; 186:731-741. [DOI: 10.1007/s00442-017-4044-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 12/10/2017] [Indexed: 11/25/2022]
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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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Birch JL, Walsh NG, Cantrill DJ, Holmes GD, Murphy DJ. Testing efficacy of distance and tree-based methods for DNA barcoding of grasses (Poaceae tribe Poeae) in Australia. PLoS One 2017; 12:e0186259. [PMID: 29084279 PMCID: PMC5662090 DOI: 10.1371/journal.pone.0186259] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 09/28/2017] [Indexed: 01/09/2023] Open
Abstract
In Australia, Poaceae tribe Poeae are represented by 19 genera and 99 species, including economically and environmentally important native and introduced pasture grasses [e.g. Poa (Tussock-grasses) and Lolium (Ryegrasses)]. We used this tribe, which are well characterised in regards to morphological diversity and evolutionary relationships, to test the efficacy of DNA barcoding methods. A reference library was generated that included 93.9% of species in Australia (408 individuals, [Formula: see text] = 3.7 individuals per species). Molecular data were generated for official plant barcoding markers (rbcL, matK) and the nuclear ribosomal internal transcribed spacer (ITS) region. We investigated accuracy of specimen identifications using distance- (nearest neighbour, best-close match, and threshold identification) and tree-based (maximum likelihood, Bayesian inference) methods and applied species discovery methods (automatic barcode gap discovery, Poisson tree processes) based on molecular data to assess congruence with recognised species. Across all methods, success rate for specimen identification of genera was high (87.5-99.5%) and of species was low (25.6-44.6%). Distance- and tree-based methods were equally ineffective in providing accurate identifications for specimens to species rank (26.1-44.6% and 25.6-31.3%, respectively). The ITS marker achieved the highest success rate for specimen identification at both generic and species ranks across the majority of methods. For distance-based analyses the best-close match method provided the greatest accuracy for identification of individuals with a high percentage of "correct" (97.6%) and a low percentage of "incorrect" (0.3%) generic identifications, based on the ITS marker. For tribe Poeae, and likely for other grass lineages, sequence data in the standard DNA barcode markers are not variable enough for accurate identification of specimens to species rank. For recently diverged grass species similar challenges are encountered in the application of genetic and morphological data to species delimitations, with taxonomic signal limited by extensive infra-specific variation and shared polymorphisms among species in both data types.
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Affiliation(s)
- Joanne L. Birch
- Royal Botanic Gardens Victoria, Melbourne, Victoria, Australia
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Weisser WW, Roscher C, Meyer ST, Ebeling A, Luo G, Allan E, Beßler H, Barnard RL, Buchmann N, Buscot F, Engels C, Fischer C, Fischer M, Gessler A, Gleixner G, Halle S, Hildebrandt A, Hillebrand H, de Kroon H, Lange M, Leimer S, Le Roux X, Milcu A, Mommer L, Niklaus PA, Oelmann Y, Proulx R, Roy J, Scherber C, Scherer-Lorenzen M, Scheu S, Tscharntke T, Wachendorf M, Wagg C, Weigelt A, Wilcke W, Wirth C, Schulze ED, Schmid B, Eisenhauer N. Biodiversity effects on ecosystem functioning in a 15-year grassland experiment: Patterns, mechanisms, and open questions. Basic Appl Ecol 2017. [DOI: 10.1016/j.baae.2017.06.002] [Citation(s) in RCA: 212] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Hollingsworth PM, Li DZ, van der Bank M, Twyford AD. Telling plant species apart with DNA: from barcodes to genomes. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150338. [PMID: 27481790 PMCID: PMC4971190 DOI: 10.1098/rstb.2015.0338] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/01/2016] [Indexed: 12/17/2022] Open
Abstract
Land plants underpin a multitude of ecosystem functions, support human livelihoods and represent a critically important component of terrestrial biodiversity-yet many tens of thousands of species await discovery, and plant identification remains a substantial challenge, especially where material is juvenile, fragmented or processed. In this opinion article, we tackle two main topics. Firstly, we provide a short summary of the strengths and limitations of plant DNA barcoding for addressing these issues. Secondly, we discuss options for enhancing current plant barcodes, focusing on increasing discriminatory power via either gene capture of nuclear markers or genome skimming. The former has the advantage of establishing a defined set of target loci maximizing efficiency of sequencing effort, data storage and analysis. The challenge is developing a probe set for large numbers of nuclear markers that works over sufficient phylogenetic breadth. Genome skimming has the advantage of using existing protocols and being backward compatible with existing barcodes; and the depth of sequence coverage can be increased as sequencing costs fall. Its non-targeted nature does, however, present a major informatics challenge for upscaling to large sample sets.This article is part of the themed issue 'From DNA barcodes to biomes'.
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Affiliation(s)
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Heilongtan, Kunming, Yunnan 650201, People's Republic of China
| | - Michelle van der Bank
- Department of Botany and Plant Biotechnology, University of Johannesburg, Auckland park, Johannesburg PO Box 524, South Africa
| | - Alex D Twyford
- Ashworth Laboratories, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
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Bell KL, de Vere N, Keller A, Richardson RT, Gous A, Burgess KS, Brosi BJ. Pollen DNA barcoding: current applications and future prospects. Genome 2016; 59:629-40. [DOI: 10.1139/gen-2015-0200] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Identification of the species origin of pollen has many applications, including assessment of plant–pollinator networks, reconstruction of ancient plant communities, product authentication, allergen monitoring, and forensics. Such applications, however, have previously been limited by microscopy-based identification of pollen, which is slow, has low taxonomic resolution, and has few expert practitioners. One alternative is pollen DNA barcoding, which could overcome these issues. Recent studies demonstrate that both chloroplast and nuclear barcoding markers can be amplified from pollen. These recent validations of pollen metabarcoding indicate that now is the time for researchers in various fields to consider applying these methods to their research programs. In this paper, we review the nascent field of pollen DNA barcoding and discuss potential new applications of this technology, highlighting existing limitations and future research developments that will improve its utility in a wide range of applications.
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Affiliation(s)
- Karen L. Bell
- Emory University, School of Environmental Sciences, Atlanta, GA, USA
| | - Natasha de Vere
- National Botanic Garden of Wales, Llanarthne, United Kingdom
| | - Alexander Keller
- Department of Animal Ecology and Tropical Biology, University of Würzburg, Würzburg, Germany
| | | | - Annemarie Gous
- Biotechnology Platform, Agricultural Research Council, Pretoria, South Africa
- School of Life Science, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | | | - Berry J. Brosi
- Emory University, School of Environmental Sciences, Atlanta, GA, USA
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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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Building a Plant DNA Barcode Reference Library for a Diverse Tropical Flora: An Example from Queensland, Australia. DIVERSITY 2016. [DOI: 10.3390/d8010005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Porter TM, Shokralla S, Baird D, Golding GB, Hajibabaei M. Ribosomal DNA and Plastid Markers Used to Sample Fungal and Plant Communities from Wetland Soils Reveals Complementary Biotas. PLoS One 2016; 11:e0142759. [PMID: 26731732 PMCID: PMC4712138 DOI: 10.1371/journal.pone.0142759] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 10/22/2015] [Indexed: 11/19/2022] Open
Abstract
Though the use of metagenomic methods to sample below-ground fungal communities is common, the use of similar methods to sample plants from their underground structures is not. In this study we use high throughput sequencing of the ribulose-bisphosphate carboxylase large subunit (rbcL) plastid marker to study the plant community as well as the internal transcribed spacer and large subunit ribosomal DNA (rDNA) markers to investigate the fungal community from two wetland sites. Observed community richness and composition varied by marker. The two rDNA markers detected complementary sets of fungal taxa and total fungal composition clustered according to primer rather than by site. The composition of the most abundant plants, however, clustered according to sites as expected. We suggest that future studies consider using multiple genetic markers, ideally generated from different primer sets, to detect a more taxonomically diverse suite of taxa compared with what can be detected by any single marker alone. Conclusions drawn from the presence of even the most frequently observed taxa should be made with caution without corroborating lines of evidence.
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Affiliation(s)
| | - Shadi Shokralla
- Biodiversity Institute of Ontario & Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Donald Baird
- Environment Canada @ Canadian Rivers Institute, University of New Brunswick, Fredericton, NB, E3B 6E1, Canada
| | - G. Brian Golding
- McMaster University, Biology Department, Hamilton, ON, L8S 4K1, Canada
| | - Mehrdad Hajibabaei
- Biodiversity Institute of Ontario & Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
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Bolson M, Smidt EDC, Brotto ML, Silva-Pereira V. ITS and trnH-psbA as Efficient DNA Barcodes to Identify Threatened Commercial Woody Angiosperms from Southern Brazilian Atlantic Rainforests. PLoS One 2015; 10:e0143049. [PMID: 26630282 PMCID: PMC4704546 DOI: 10.1371/journal.pone.0143049] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 10/30/2015] [Indexed: 01/10/2023] Open
Abstract
The Araucaria Forests in southern Brazil are part of the Atlantic Rainforest, a key hotspot for global biodiversity. This habitat has experienced extensive losses of vegetation cover due to commercial logging and the intense use of wood resources for construction and furniture manufacturing. The absence of precise taxonomic tools for identifying Araucaria Forest tree species motivated us to test the ability of DNA barcoding to distinguish species exploited for wood resources and its suitability for use as an alternative testing technique for the inspection of illegal timber shipments. We tested three cpDNA regions (matK, trnH-psbA, and rbcL) and nrITS according to criteria determined by The Consortium for the Barcode of Life (CBOL). The efficiency of each marker and selected marker combinations were evaluated for 30 commercially valuable woody species in multiple populations, with a special focus on Lauraceae species. Inter- and intraspecific distances, species discrimination rates, and ability to recover species-specific clusters were evaluated. Among the regions and different combinations, ITS was the most efficient for identifying species based on the 'best close match' test; similarly, the trnH-psbA + ITS combination also demonstrated satisfactory results. When combining trnH-psbA + ITS, Maximum Likelihood analysis demonstrated a more resolved topology for internal branches, with 91% of species-specific clusters. DNA barcoding was found to be a practical and rapid method for identifying major threatened woody angiosperms from Araucaria Forests such as Lauraceae species, presenting a high confidence for recognizing members of Ocotea. These molecular tools can assist in screening those botanical families that are most targeted by the timber industry in southern Brazil and detecting certain species protected by Brazilian legislation and could be a useful tool for monitoring wood exploitation.
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Affiliation(s)
- Mônica Bolson
- Departamento de Botânica, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Eric de Camargo Smidt
- Departamento de Botânica, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | | | - Viviane Silva-Pereira
- Departamento de Botânica, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
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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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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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Abstract
DNA barcoding uses specific regions of DNA in order to identify species. Initiatives are taking place around the world to generate DNA barcodes for all groups of living organisms and to make these data publically available in order to help understand, conserve, and utilize the world's biodiversity. For land plants the core DNA barcode markers are two sections of coding regions within the chloroplast, part of the genes, rbcL and matK. In order to create high quality databases, each plant that is DNA barcoded needs to have a herbarium voucher that accompanies the rbcL and matK DNA sequences. The quality of the DNA sequences, the primers used, and trace files should also be accessible to users of the data. Multiple individuals should be DNA barcoded for each species in order to check for errors and allow for intraspecific variation. The world's herbaria provide a rich resource of already preserved and identified material and these can be used for DNA barcoding as well as by collecting fresh samples from the wild. These protocols describe the whole DNA barcoding process, from the collection of plant material from the wild or from the herbarium, how to extract and amplify the DNA, and how to check the quality of the data after sequencing.
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Affiliation(s)
- Natasha de Vere
- National Botanic Garden of Wales, Llanarthne, Carmarthenshire, SA32 8HG, UK,
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DNA barcodes for ecology, evolution, and conservation. Trends Ecol Evol 2015; 30:25-35. [DOI: 10.1016/j.tree.2014.10.008] [Citation(s) in RCA: 284] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 10/23/2014] [Accepted: 10/28/2014] [Indexed: 01/28/2023]
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Valverde-Barrantes OJ, Smemo KA, Feinstein LM, Kershner MW, Blackwood CB. Aggregated and complementary: symmetric proliferation, overyielding, and mass effects explain fine-root biomass in soil patches in a diverse temperate deciduous forest landscape. 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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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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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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Ravenek JM, Bessler H, Engels C, Scherer-Lorenzen M, Gessler A, Gockele A, De Luca E, Temperton VM, Ebeling A, Roscher C, Schmid B, Weisser WW, Wirth C, de Kroon H, Weigelt A, Mommer L. Long-term study of root biomass in a biodiversity experiment reveals shifts in diversity effects over time. OIKOS 2014. [DOI: 10.1111/oik.01502] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Janneke M. Ravenek
- Dept of Experimental Plant Ecology; Inst. for Water and Wetland Research, Radboud Univ.; Heyendaalseweg 135 NL-6525 AJ Nijmegen the Netherlands
| | - Holger Bessler
- Faculty of Agriculture and Horticulture, Humboldt Univ.; Unter den Linden 6 DE-10099 Berlin Germany
| | - Christof Engels
- Faculty of Agriculture and Horticulture, Humboldt Univ.; Unter den Linden 6 DE-10099 Berlin Germany
| | - Michael Scherer-Lorenzen
- Faculty of Biology, Dept of Geobotany; Univ. of Freiburg; Schänzlestrasse 1 DE-79104 Freiburg Germany
| | - Arthur Gessler
- Faculty of Agriculture and Horticulture, Humboldt Univ.; Unter den Linden 6 DE-10099 Berlin Germany
- Research Unit Forest Dynamics, Swiss Federal Inst. for Forest, Snow and Landscape Reserach WSL; Zürcherstr. 111 CH-8903 Birmensdorf Switzerland
| | - Annette Gockele
- Faculty of Biology, Dept of Geobotany; Univ. of Freiburg; Schänzlestrasse 1 DE-79104 Freiburg Germany
| | - Enrica De Luca
- Inst. of Evolutionary Biology and Environmental Studies, Univ. of Zürich; Winterthurerstrasse 190 CH-8057 Zürich Switzerland
| | - Vicky M. Temperton
- Plant Sciences, Inst. for Bio- and Geosciences (IBG-2); Forschungszentrum Jülich GmbH DE-52425 Jülich Germany
| | - Anne Ebeling
- Inst. of Ecology, Friedrich Schiller Univ.; Dornburger Strasse 159 DE-07743 Jena Germany
| | - Christiane Roscher
- UFZ, Dept of Community Ecology; Helmholtz Centre for Environmental Research; Theodor-Lieser-Strasse 4 DE-06120 Halle Germany
| | - Bernhard Schmid
- Inst. of Evolutionary Biology and Environmental Studies, Univ. of Zürich; Winterthurerstrasse 190 CH-8057 Zürich Switzerland
| | - Wolfgang W. Weisser
- Dept of Ecology and Ecosystem Management; Center for Food and Life Sciences Weihenstephan, Technische Univ. München; Hans-Carl-von-Carlowitz-Platz 2 DE-85350 Freising-Weihenstephan Germany
| | - Christian Wirth
- Dept of Systematic Botany and Functional Biodiversity; Inst. of Biology, Univ. of Leipzig; Johannisallee 21 DE04103 Leipzig Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig; Leipzig Germany
| | - Hans de Kroon
- Dept of Experimental Plant Ecology; Inst. for Water and Wetland Research, Radboud Univ.; Heyendaalseweg 135 NL-6525 AJ Nijmegen the Netherlands
| | - Alexandra Weigelt
- Dept of Systematic Botany and Functional Biodiversity; Inst. of Biology, Univ. of Leipzig; Johannisallee 21 DE04103 Leipzig Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig; Leipzig Germany
| | - Liesje Mommer
- Nature Conservation and Plant Ecology group, Wageningen Univ.; PO box 47, NL-6700 AA Wageningen the Netherlands
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Gundel PE, Pierik R, Mommer L, Ballaré CL. Competing neighbors: light perception and root function. Oecologia 2014; 176:1-10. [DOI: 10.1007/s00442-014-2983-x] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 05/24/2014] [Indexed: 11/24/2022]
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Elliott TL, Jonathan Davies T. Challenges to barcoding an entire flora. Mol Ecol Resour 2014; 14:883-91. [PMID: 24813242 DOI: 10.1111/1755-0998.12277] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 04/12/2014] [Accepted: 04/20/2014] [Indexed: 12/01/2022]
Abstract
DNA barcodes are species-specific genetic markers that allow taxonomic identification of biological samples. The promise of DNA barcoding as a rapid molecular tool for conducting biodiversity inventories has catalysed renewed efforts to document and catalogue the diversity of life, parallel to the large-scale sampling conducted by Victorian naturalists. The unique contribution of DNA barcode data is in its ability to identify biotic material that would be impossible to classify using traditional taxonomic keys. However, the utility of DNA barcoding relies upon the construction of accurate barcode libraries that provide a reference database to match to unidentified samples. Whilst there has been much debate in the literature over the choice and efficacy of barcode markers, there has been little consideration of the practicalities of generating comprehensive barcode reference libraries for species-rich floras. Here, we discuss several challenges to the generation of such libraries and present a case study from a regional biodiversity hotspot in southern Quebec. We suggest that the key challenges include (i) collection of specimens for rare or ephemeral species, (ii) limited access to taxonomic expertise necessary for reliable identification of reference specimens and (iii) molecular challenges in amplifying and matching barcode data. To be most effective, we recommend that sampling must be both flexible and opportunistic and conducted across the entire growing season by expert taxonomists. We emphasize that the success of the global barcoding initiative will depend upon the close collaboration of taxonomists, plant collectors, and molecular biologists.
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Affiliation(s)
- Tammy L Elliott
- Department of Biology, McGill University, 1205 Docteur Penfield Avenue, Montreal, Quebec H3A 1B1, Canada
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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 that 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 Greeks and Romans (e.g., Theophrastus, Pliny the Elder, and Dioscorides). In the fifteenth to 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 enters 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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Mankga LT, Yessoufou K, Moteetee AM, Daru BH, van der Bank M. Efficacy of the core DNA barcodes in identifying processed and poorly conserved plant materials commonly used in South African traditional medicine. Zookeys 2013; 365:215-33. [PMID: 24453559 PMCID: PMC3890679 DOI: 10.3897/zookeys.365.5730] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Accepted: 10/25/2013] [Indexed: 11/12/2022] Open
Abstract
Medicinal plants cover a broad range of taxa, which may be phylogenetically less related but morphologically very similar. Such morphological similarity between species may lead to misidentification and inappropriate use. Also the substitution of a medicinal plant by a cheaper alternative (e.g. other non-medicinal plant species), either due to misidentification, or deliberately to cheat consumers, is an issue of growing concern. In this study, we used DNA barcoding to identify commonly used medicinal plants in South Africa. Using the core plant barcodes, matK and rbcLa, obtained from processed and poorly conserved materials sold at the muthi traditional medicine market, we tested efficacy of the barcodes in species discrimination. Based on genetic divergence, PCR amplification efficiency and BLAST algorithm, we revealed varied discriminatory potentials for the DNA barcodes. In general, the barcodes exhibited high discriminatory power, indicating their effectiveness in verifying the identity of the most common plant species traded in South African medicinal markets. BLAST algorithm successfully matched 61% of the queries against a reference database, suggesting that most of the information supplied by sellers at traditional medicinal markets in South Africa is correct. Our findings reinforce the utility of DNA barcoding technique in limiting false identification that can harm public health.
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Affiliation(s)
- Ledile T. Mankga
- African Centre for DNA Barcoding, Department of Botany and Plant Biotechnology, University of Johannesburg, PO Box 524, Auckland Park 2006, Johannesburg, South Africa
| | - Kowiyou Yessoufou
- African Centre for DNA Barcoding, Department of Botany and Plant Biotechnology, University of Johannesburg, PO Box 524, Auckland Park 2006, Johannesburg, South Africa
| | - Annah M. Moteetee
- African Centre for DNA Barcoding, Department of Botany and Plant Biotechnology, University of Johannesburg, PO Box 524, Auckland Park 2006, Johannesburg, South Africa
| | - Barnabas H. Daru
- African Centre for DNA Barcoding, Department of Botany and Plant Biotechnology, University of Johannesburg, PO Box 524, Auckland Park 2006, Johannesburg, South Africa
| | - Michelle van der Bank
- African Centre for DNA Barcoding, Department of Botany and Plant Biotechnology, University of Johannesburg, PO Box 524, Auckland Park 2006, Johannesburg, South Africa
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Saarela JM, Sokoloff PC, Gillespie LJ, Consaul LL, Bull RD. DNA barcoding the Canadian Arctic flora: core plastid barcodes (rbcL + matK) for 490 vascular plant species. PLoS One 2013; 8:e77982. [PMID: 24348895 PMCID: PMC3865322 DOI: 10.1371/journal.pone.0077982] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 09/08/2013] [Indexed: 01/16/2023] Open
Abstract
Accurate identification of Arctic plant species is critical for understanding potential climate-induced changes in their diversity and distributions. To facilitate rapid identification we generated DNA barcodes for the core plastid barcode loci (rbcL and matK) for 490 vascular plant species, representing nearly half of the Canadian Arctic flora and 93% of the flora of the Canadian Arctic Archipelago. Sequence recovery was higher for rbcL than matK (93% and 81%), and rbcL was easier to recover than matK from herbarium specimens (92% and 77%). Distance-based and sequence-similarity analyses of combined rbcL + matK data discriminate 97% of genera, 56% of species, and 7% of infraspecific taxa. There is a significant negative correlation between the number of species sampled per genus and the percent species resolution per genus. We characterize barcode variation in detail in the ten largest genera sampled (Carex, Draba, Festuca, Pedicularis, Poa, Potentilla, Puccinellia, Ranunculus, Salix, and Saxifraga) in the context of their phylogenetic relationships and taxonomy. Discrimination with the core barcode loci in these genera ranges from 0% in Salix to 85% in Carex. Haplotype variation in multiple genera does not correspond to species boundaries, including Taraxacum, in which the distribution of plastid haplotypes among Arctic species is consistent with plastid variation documented in non-Arctic species. Introgression of Poa glauca plastid DNA into multiple individuals of P. hartzii is problematic for identification of these species with DNA barcodes. Of three supplementary barcode loci (psbA-trnH, psbK-psbI, atpF-atpH) collected for a subset of Poa and Puccinellia species, only atpF-atpH improved discrimination in Puccinellia, compared with rbcL and matK. Variation in matK in Vaccinium uliginosum and rbcL in Saxifraga oppositifolia corresponds to variation in other loci used to characterize the phylogeographic histories of these Arctic-alpine species.
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Affiliation(s)
- Jeffery M. Saarela
- Botany Section, Research and Collections Services, Canadian Museum of Nature, Ottawa, Ontario, Canada
| | - Paul C. Sokoloff
- Botany Section, Research and Collections Services, Canadian Museum of Nature, Ottawa, Ontario, Canada
| | - Lynn J. Gillespie
- Botany Section, Research and Collections Services, Canadian Museum of Nature, Ottawa, Ontario, Canada
| | - Laurie L. Consaul
- Botany Section, Research and Collections Services, Canadian Museum of Nature, Ottawa, Ontario, Canada
| | - Roger D. Bull
- Botany Section, Research and Collections Services, Canadian Museum of Nature, Ottawa, Ontario, Canada
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Joly S, Davies TJ, Archambault A, Bruneau A, Derry A, Kembel SW, Peres-Neto P, Vamosi J, Wheeler TA. Ecology in the age of DNA barcoding: the resource, the promise and the challenges ahead. Mol Ecol Resour 2013; 14:221-32. [DOI: 10.1111/1755-0998.12173] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Revised: 09/03/2013] [Accepted: 09/16/2013] [Indexed: 12/29/2022]
Affiliation(s)
- Simon Joly
- Institut de recherche en biologie végétale; Département de sciences biologiques; Université de Montréal; 4101 Sherbrooke East Montréal Quebec, Canada H1X 2B2
- Montreal Botanical Garden; 4101 Sherbrooke East Montréal Quebec, Canada H1X 2B2
| | - T. Jonathan Davies
- Biology Department; McGill University; 1205 Dr Penfield Montréal Quebec, Canada H3A 1B1
| | - Annie Archambault
- Québec Centre for Biodiversity Science; 1205 Dr Penfield Montréal Quebec, Canada H3A 1B1
| | - Anne Bruneau
- Institut de recherche en biologie végétale; Département de sciences biologiques; Université de Montréal; 4101 Sherbrooke East Montréal Quebec, Canada H1X 2B2
| | - Alison Derry
- Département des sciences biologiques; Université du Québec à Montréal; 141 Avenue du Président-Kennedy Montréal Quebec, Canada H2X 1Y4
| | - Steven W. Kembel
- Département des sciences biologiques; Université du Québec à Montréal; 141 Avenue du Président-Kennedy Montréal Quebec, Canada H2X 1Y4
| | - Pedro Peres-Neto
- Département des sciences biologiques; Université du Québec à Montréal; 141 Avenue du Président-Kennedy Montréal Quebec, Canada H2X 1Y4
| | - Jana Vamosi
- Department of Biological Sciences; University of Calgary; 2500 University Drive NW Calgary Alberta, Canada T2N 1N4
| | - Terry A. Wheeler
- Department of Natural Resources Sciences; McGill University; Macdonald Campus Ste. Anne de Bellevue Quebec, Canada H9X 3V9
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Chen CW, Huang YM, Kuo LY, Nguyen QD, Luu HT, Callado JR, Farrar DR, Chiou WL. trnL-F is a powerful marker for DNA identification of field vittarioid gametophytes (Pteridaceae). ANNALS OF BOTANY 2013; 111:663-73. [PMID: 23380240 PMCID: PMC3605945 DOI: 10.1093/aob/mct004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2012] [Accepted: 12/11/2012] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS The gametophyte phase of ferns plays an important role in habitat selection, dispersal, adaptation and evolution. However, ecological studies on fern gametophytes have been impeded due to the difficulty of species identification of free-living gametophytes. DNA barcoding provides an alternative approach to identifying fern gametophytes but is rarely applied to field studies. In this study, an example of field vittarioid gametophyte identification using DNA barcoding, which has not been done before, is given. METHODS A combination of distance-based and tree-based approaches was performed to evaluate the discriminating power of three candidate barcodes (matK, rbcL and trnL-F) on 16 vittarioid sporophytes. Sequences of the trnL-F region were generated from 15 fern gametophyte populations by tissue-direct PCR and were compared against the sporophyte dataset, using BLAST. KEY RESULTS trnL-F earns highest primer universality and discriminatory ability scores, whereas PCR success rates were very low for matK and rbcL regions (10·8 % and 41·3 %, respectively). BLAST analyses showed that all the sampled field gametophytes could be successfully identified to species level. Three gametophyte populations were also discovered to be living beyond the known occurrence of their sporophyte counterparts. CONCLUSIONS This study demonstrates that DNA barcoding (i.e. reference databasing, tissue-direct PCR and molecular analysis), especially the trnL-F region, is an efficient tool to identify field gametophytes, and has considerable potential in exploring the ecology of fern gametophytes.
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Affiliation(s)
- Cheng Wei Chen
- Division of Silviculture, Taiwan Forestry Research Institute, Taipei 10066, Taiwan
| | - Yao Moan Huang
- Division of Silviculture, Taiwan Forestry Research Institute, Taipei 10066, Taiwan
| | - Li Yaung Kuo
- Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Quoc Dat Nguyen
- Southern Institute of Ecology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Hong Truong Luu
- Southern Institute of Ecology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | | | - Donald R. Farrar
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa 50011-1020 USA
| | - Wen Liang Chiou
- Division of Botanical Garden, Taiwan Forestry Research Institute, Taipei 10066, Taiwan
- For correspondence. E-mail
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