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Elwick KE, Damaso N, Robertson JM. DNA Barcoding and Metabarcoding Protocols for Species Identification. Methods Mol Biol 2024; 2744:155-169. [PMID: 38683317 DOI: 10.1007/978-1-0716-3581-0_9] [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
The article presents the several steps to be performed on a plant, fungal, insect, or soil sample to obtain DNA sequences for DNA barcode analysis. The chapter begins with a description of sample preparation including procedures for cleaning and proceeds to DNA extraction with methods adapted for the specific type of sample. Next, DNA quantification is described so the proper amount is used for the amplification of the selected barcode regions. Information is provided for reaction mixes and amplification conditions for several referenced barcode primer pairs tuned for the individual sample of interest. This is followed by a description of procedures to access the success of amplification, cleanup, and quantification of the product ready for either Sanger sequencing or library preparation for massive parallel sequencing (MPS). Finally, procedures are provided for Sanger sequencing, library preparation, and MPS sequencing. The chapter provides several references of barcode regions for different sample types.
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Affiliation(s)
- Kyleen E Elwick
- Research & Support Unit, Laboratory Division, Federal Bureau of Investigation, Quantico, VA, USA
| | - Natalie Damaso
- Counter WMD Systems, Massachusetts Institute of Technology, Lincoln Laboratory, Lexington, MA, USA
| | - James M Robertson
- Research & Support Unit, Laboratory Division, Federal Bureau of Investigation, Quantico, VA, USA.
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Çiftçi O, Wagemaker CAM, Mertens A, van Bodegom P, Pirovano W, Gravendeel B. Genotyping by sequencing for estimating relative abundances of diatom taxa in mock communities. BMC Ecol Evol 2023; 23:4. [PMID: 36747145 PMCID: PMC9903628 DOI: 10.1186/s12862-023-02104-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 01/13/2023] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Diatoms are present in all waters and are highly sensitive to pollution gradients. Therefore, they are ideal bioindicators for water quality assessment. Current indices used in these applications are based on identifying diatom species and counting their abundances using traditional light microscopy. Several molecular techniques have been developed to help automate different steps of this process, but obtaining reliable estimates of diatom community composition and species abundance remains challenging. RESULTS Here, we evaluated a recently developed quantification method based on Genotyping by Sequencing (GBS) for the first time in diatoms to estimate the relative abundances within a species complex. For this purpose, a reference database comprised of thousands of genomic DNA clusters was generated from cultures of Nitzschia palea. The sequencing reads from calibration and mock samples were mapped against this database for parallel quantification. We sequenced 25 mock diatom communities containing up to five taxa per sample in different abundances. Taxon abundances in these communities were also quantified by a diatom expert using manual counting of cells on light microscopic slides. The relative abundances of strains across mock samples were over- or under-estimated by the manual counting method, and a majority of mock samples had stronger correlations using GBS. Moreover, one previously recognized putative hybrid had the largest number of false positive detections demonstrating the limitation of the manual counting method when morphologically similar and/or phylogenetically close taxa are analyzed. CONCLUSIONS Our results suggest that GBS is a reliable method to estimate the relative abundances of the N. palea taxa analyzed in this study and outperformed traditional light microscopy in terms of accuracy. GBS provides increased taxonomic resolution compared to currently available quantitative molecular approaches, and it is more scalable in the number of species that can be analyzed in a single run. Hence, this is a significant step forward in developing automated, high-throughput molecular methods specifically designed for the quantification of [diatom] communities for freshwater quality assessments.
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Affiliation(s)
- Ozan Çiftçi
- Institute of Environmental Sciences (CML), Leiden University, P.O. Box 9518, 2300 RA, Leiden, The Netherlands. .,Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands. .,BaseClear B.V., Sylviusweg 74, 2333 BE, Leiden, The Netherlands. .,German Research Center for Geosciences, GFZ, 14473, Potsdam, Germany.
| | - Cornelis A. M. Wagemaker
- Radboud Institute for Biological and Environmental Sciences, Heyendaalseweg 135, 6500 GL Nijmegen, The Netherlands
| | - Adrienne Mertens
- Diatomella, IJkelaarstraat 3, 6611 KN Overasselt, The Netherlands
| | - Peter van Bodegom
- grid.5132.50000 0001 2312 1970Institute of Environmental Sciences (CML), Leiden University, P.O. Box 9518, 2300 RA Leiden, The Netherlands
| | - Walter Pirovano
- BaseClear B.V., Sylviusweg 74, 2333 BE Leiden, The Netherlands
| | - Barbara Gravendeel
- grid.425948.60000 0001 2159 802XNaturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands ,Radboud Institute for Biological and Environmental Sciences, Heyendaalseweg 135, 6500 GL Nijmegen, The Netherlands
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Alonso‐Crespo IM, Weidlich EWA, Temperton VM, Delory BM. Assembly history modulates vertical root distribution in a grassland experiment. OIKOS 2022. [DOI: 10.1111/oik.08886] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Griffiths M, Delory BM, Jawahir V, Wong KM, Bagnall GC, Dowd TG, Nusinow DA, Miller AJ, Topp CN. Optimisation of root traits to provide enhanced ecosystem services in agricultural systems: A focus on cover crops. PLANT, CELL & ENVIRONMENT 2022; 45:751-770. [PMID: 34914117 PMCID: PMC9306666 DOI: 10.1111/pce.14247] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 11/05/2021] [Accepted: 12/01/2021] [Indexed: 05/26/2023]
Abstract
Roots are the interface between the plant and the soil and play a central role in multiple ecosystem processes. With intensification of agricultural practices, rhizosphere processes are being disrupted and are causing degradation of the physical, chemical and biotic properties of soil. However, cover crops, a group of plants that provide ecosystem services, can be utilised during fallow periods or used as an intercrop to restore soil health. The effectiveness of ecosystem services provided by cover crops varies widely as very little breeding has occurred in these species. Improvement of ecosystem service performance is rarely considered as a breeding trait due to the complexities and challenges of belowground evaluation. Advancements in root phenotyping and genetic tools are critical in accelerating ecosystem service improvement in cover crops. In this study, we provide an overview of the range of belowground ecosystem services provided by cover crop roots: (1) soil structural remediation, (2) capture of soil resources and (3) maintenance of the rhizosphere and building of organic matter content. Based on the ecosystem services described, we outline current and promising phenotyping technologies and breeding strategies in cover crops that can enhance agricultural sustainability through improvement of root traits.
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Affiliation(s)
| | | | | | - Kong M. Wong
- Donald Danforth Plant Science CenterSt. LouisMissouriUSA
| | | | - Tyler G. Dowd
- Donald Danforth Plant Science CenterSt. LouisMissouriUSA
| | | | - Allison J. Miller
- Donald Danforth Plant Science CenterSt. LouisMissouriUSA
- Department of BiologySaint Louis UniversitySt. LouisMissouriUSA
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Narum S, News JK, Fountain-Jones N, Hooper Junior R, Ortiz-Barrientos D, O'Boyle B, Sibbett B. Editorial 2022. Mol Ecol Resour 2021; 22:1-8. [PMID: 34919782 DOI: 10.1111/1755-0998.13572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Yu RP, Lambers H, Callaway RM, Wright AJ, Li L. Belowground facilitation and trait matching: two or three to tango? TRENDS IN PLANT SCIENCE 2021; 26:1227-1235. [PMID: 34400074 DOI: 10.1016/j.tplants.2021.07.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 07/15/2021] [Accepted: 07/24/2021] [Indexed: 05/12/2023]
Abstract
High biodiversity increases ecosystem functions; however, belowground facilitation remains poorly understood in this context. Here, we explore mechanisms that operate via 'giving-receiving feedbacks' for belowground facilitation. These include direct effects via root exudates, signals, and root trait plasticity, and indirect biotic facilitation via the effects of root exudates on soil biota and feedback from biota to plants. We then highlight that these two- or three-way mechanisms must affect biodiversity-ecosystem function relationships via specific combinations of matching traits. To tango requires a powerful affinity and harmony between well-matched partners, and such matches link belowground facilitation to the effect of biodiversity on function. Such matching underpins applications in intercropping, forestry, and pasture systems, in which diversity contributes to greater productivity and sustainability.
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Affiliation(s)
- Rui-Peng Yu
- Key Laboratory of Plant-Soil Interactions, Ministry of Education, Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University, 2 Yuan Ming Yuan West Road, Beijing 100193, PR China
| | - Hans Lambers
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA 6009, Australia; National Academy of Agriculture Green Development, China Agricultural University, 2 Yuan Ming Yuan West Road, Beijing 100193, PR China
| | - Ragan M Callaway
- Division of Biological Sciences and Institute on Ecosystems, University of Montana, 32 Campus Drive, Missoula, MT 59812, USA
| | - Alexandra J Wright
- Department of Biological Sciences, California State University Los Angeles, 5151 State University Drive, Los Angeles, CA 90032, USA
| | - Long Li
- Key Laboratory of Plant-Soil Interactions, Ministry of Education, Beijing Key Laboratory of Biodiversity and Organic Farming, College of Resources and Environmental Sciences, China Agricultural University, 2 Yuan Ming Yuan West Road, Beijing 100193, PR China.
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Piñol J. Genotype by sequencing: An alternative new method to amplicon metabarcoding and shotgun metagenomics for the assessment of eukaryote biodiversity. Mol Ecol Resour 2021; 21:1001-1004. [PMID: 33423396 DOI: 10.1111/1755-0998.13320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/07/2020] [Accepted: 01/05/2021] [Indexed: 11/28/2022]
Abstract
The use of high-throughput DNA sequencing (HTS) has revolutionized the assessment of biodiversity in plant and animal communities. There are two main approaches to estimate the identity and the relative species abundance (RSA) in complex mixtures using HTS: amplicon metabarcoding and shotgun metagenomics. While amplicon metabarcoding targets one or a few genomic regions, shotgun metagenomics randomly explores the genome of the species. In this issue of Molecular Ecology Resources, Wagemaker et al. (2021) present a new method, multi-species Genotyping by Sequencing (msGBS), as an alternative middle ground between metabarcoding and metagenomics. They apply the technique to mixtures of plant roots and report the remarkable capacity of msGBS to estimate the RSA. If validated in other laboratories and biological communities, msGBS might become a third method to explore the biodiversity of biological communities, especially of plants, where current techniques are struggling to get sufficient taxonomic resolution.
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Affiliation(s)
- Josep Piñol
- Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.,CREAF, Cerdanyola del Vallès, Spain
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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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