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Courtot É, Boisseau M, Dhorne-Pollet S, Serreau D, Gesbert A, Reigner F, Basiaga M, Kuzmina T, Lluch J, Annonay G, Kuchly C, Diekmann I, Krücken J, von Samson-Himmelstjerna G, Mach N, Sallé G. Comparison of two molecular barcodes for the study of equine strongylid communities with amplicon sequencing. PeerJ 2023; 11:e15124. [PMID: 37070089 PMCID: PMC10105562 DOI: 10.7717/peerj.15124] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 03/03/2023] [Indexed: 04/19/2023] Open
Abstract
Basic knowledge on the biology and epidemiology of equine strongylid species still needs to be improved to contribute to the design of better parasite control strategies. Nemabiome metabarcoding is a convenient tool to quantify and identify species in bulk samples that could overcome the hurdle that cyathostomin morphological identification represents. To date, this approach has relied on the internal transcribed spacer 2 (ITS-2) of the ribosomal RNA gene, with a limited investigation of its predictive performance for cyathostomin communities. Using DNA pools of single cyathostomin worms, this study aimed to provide the first elements to compare performances of the ITS-2 and a cytochrome c oxidase subunit I (COI) barcode newly developed in this study. Barcode predictive abilities were compared across various mock community compositions of two, five and 11 individuals from distinct species. The amplification bias of each barcode was estimated. Results were also compared between various types of biological samples, i.e., eggs, infective larvae or adults. Bioinformatic parameters were chosen to yield the closest representation of the cyathostomin community for each barcode, underscoring the need for communities of known composition for metabarcoding purposes. Overall, the proposed COI barcode was suboptimal relative to the ITS-2 rDNA region, because of PCR amplification biases, reduced sensitivity and higher divergence from the expected community composition. Metabarcoding yielded consistent community composition across the three sample types. However, imperfect correlations were found between relative abundances from infective larvae and other life-stages for Cylicostephanus species using the ITS-2 barcode. While the results remain limited by the considered biological material, they suggest that additional improvements are needed for both the ITS-2 and COI barcodes.
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Affiliation(s)
- Élise Courtot
- Animal Health, UMR1282 Infectiologie et Santé Publique, INRAE, Nouzilly, France
| | - Michel Boisseau
- Animal Health, UMR1282 Infectiologie et Santé Publique, INRAE, Nouzilly, France
- Animal Health, UMR1225 IHAP, Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Toulouse, France
| | | | - Delphine Serreau
- Animal Health, UMR1282 Infectiologie et Santé Publique, INRAE, Nouzilly, France
| | - Amandine Gesbert
- Animal Physiology, UEPAO, Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Nouzilly, France
| | - Fabrice Reigner
- Animal Physiology, UEPAO, Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Nouzilly, France
| | | | - Tetiana Kuzmina
- Schmalhausen Institute of Zoology NAS of Ukraine, Kyiv, Ukraine
- Institute of Parasitology, Slovak Academy of Sciences, Košice, Slovak Republic
| | - Jérôme Lluch
- GeT-PlaGe, Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Toulouse, France
| | - Gwenolah Annonay
- GeT-PlaGe, Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Toulouse, France
| | - Claire Kuchly
- GeT-PlaGe, Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Toulouse, France
| | - Irina Diekmann
- Institute for Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Jürgen Krücken
- Institute for Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | | | - Nuria Mach
- Animal Health, UMR1225 IHAP, Institut National de la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Toulouse, France
| | - Guillaume Sallé
- Animal Health, UMR1282 Infectiologie et Santé Publique, INRAE, Nouzilly, France
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2
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Striuchkova A, Malykh I, Potapov M, Kuznetsova N. Sympatry of genetic lineages of Parisotomanotabilis s. l. (Collembola, Isotomidae) in the East European Plain. Zookeys 2022; 1137:1-15. [PMID: 36760483 PMCID: PMC9836473 DOI: 10.3897/zookeys.1137.95769] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
Parisotomanotabilis (Schaeffer, 1896) is one of the most abundant eurytopic species of springtails in temperate regions of the northern hemisphere, and is often used as a model species for studies on the genetics of soil microarthropod populations. Six genetic lineages (L0, L1, L2, L3, L4-Saltzwedel, L4-Hebert) are known which are distributed mainly parapatrically in Western and Central Europe. Individuals of P.notabilis from 21 locations on the East European Plain were analyzed. Three genetic lineages were found: L1, L2, L4-Hebert. In contrast to Western and Central Europe, the coexistence of two or three lineages was revealed in about half of the locations on the East European Plain. The most diverse genetic composition of P.notabilis populations was noted in natural forests and slightly disturbed habitats, while the least diverse was in places with a high anthropogenic influence.
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Affiliation(s)
- Anastasia Striuchkova
- Department of Zoology and Ecology, Institute of Biology and Chemistry, Moscow State Pedagogical University, Moscow, RussiaMoscow State Pedagogical UniversityMoscowRussia
| | - Irina Malykh
- Department of Zoology and Ecology, Institute of Biology and Chemistry, Moscow State Pedagogical University, Moscow, RussiaMoscow State Pedagogical UniversityMoscowRussia
| | - Mikhail Potapov
- Department of Zoology and Ecology, Institute of Biology and Chemistry, Moscow State Pedagogical University, Moscow, RussiaMoscow State Pedagogical UniversityMoscowRussia
| | - Nataliya Kuznetsova
- Department of Zoology and Ecology, Institute of Biology and Chemistry, Moscow State Pedagogical University, Moscow, RussiaMoscow State Pedagogical UniversityMoscowRussia
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3
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Hu M, Li F, Qiao J, Yuan C, Yu H, Zhuang L. New Arsenite Oxidase Gene ( aioA) PCR Primers for Assessing Arsenite-Oxidizer Diversity in the Environment Using High-Throughput Sequencing. Front Microbiol 2021; 12:691913. [PMID: 34690945 PMCID: PMC8527091 DOI: 10.3389/fmicb.2021.691913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 09/16/2021] [Indexed: 11/13/2022] Open
Abstract
Gene encoding the large subunit of As(III) oxidase (AioA), an important component of the microbial As(III) oxidation system, is a widely used biomarker to characterize As(III)-oxidizing communities in the environment. However, many studies were restricted to a few sequences generated by clone libraries and Sanger sequencing, which may have underestimated the diversity of As(III)-oxidizers in natural environments. In this study, we designed a primer pair, 1109F (5'-ATC TGG GGB AAY RAC AAY TA-3') and 1548R (5'-TTC ATB GAS GTS AGR TTC AT-3'), targeting gene sequence encoding for the conserved molybdopterin center of the AioA protein, yielding amplicons approximately 450 bp in size that are feasible for highly parallel amplicon sequencing. By utilizing in silico analyses and the experimental construction of clone libraries using Sanger sequencing, the specificity and resolution of 1109F/1548R are approximated with two other previously published and commonly used primers, i.e., M1-2F/M3-2R and deg1F/deg1R. With the use of the 1109F/1548R primer pair, the taxonomic composition of the aioA genes was similar both according to the Sanger and next-generation sequencing (NGS) platforms. Furthermore, high-throughput amplicon sequencing using the primer pair, 1109F/1548R, successfully identified the well-known As(III)-oxidizers in paddy soils and sediments, and they also revealed the differences in the community structure and composition of As(III)-oxidizers in above two biotopes. The random forest analysis showed that the dissolved As(III) had the highest relative influence on the Chao1 index of the aioA genes. These observations demonstrate that the newly designed PCR primers enhanced the ability to detect the diversity of aioA-encoding microorganisms in environments using highly parallel short amplicon sequencing.
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Affiliation(s)
- Min Hu
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, China.,National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou, China
| | - Fangbai Li
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, China.,National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou, China
| | - Jiangtao Qiao
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, China.,National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou, China
| | - Chaolei Yuan
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin, China
| | - Huanyun Yu
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou, China.,National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou, China
| | - Li Zhuang
- School of Environment, Jinan University, Guangzhou, China
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Creedy TJ, Andújar C, Meramveliotakis E, Noguerales V, Overcast I, Papadopoulou A, Morlon H, Vogler AP, Emerson BC, Arribas P. Coming of age for COI metabarcoding of whole organism community DNA: Towards bioinformatic harmonisation. Mol Ecol Resour 2021; 22:847-861. [PMID: 34496132 PMCID: PMC9292290 DOI: 10.1111/1755-0998.13502] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 07/28/2021] [Accepted: 08/23/2021] [Indexed: 11/26/2022]
Abstract
Metabarcoding of DNA extracted from community samples of whole organisms (whole organism community DNA, wocDNA) is increasingly being applied to terrestrial, marine and freshwater metazoan communities to provide rapid, accurate and high resolution data for novel molecular ecology research. The growth of this field has been accompanied by considerable development that builds on microbial metabarcoding methods to develop appropriate and efficient sampling and laboratory protocols for whole organism metazoan communities. However, considerably less attention has focused on ensuring bioinformatic methods are adapted and applied comprehensively in wocDNA metabarcoding. In this study we examined over 600 papers and identified 111 studies that performed COI metabarcoding of wocDNA. We then systematically reviewed the bioinformatic methods employed by these papers to identify the state‐of‐the‐art. Our results show that the increasing use of wocDNA COI metabarcoding for metazoan diversity is characterised by a clear absence of bioinformatic harmonisation, and the temporal trends show little change in this situation. The reviewed literature showed (i) high heterogeneity across pipelines, tasks and tools used, (ii) limited or no adaptation of bioinformatic procedures to the nature of the COI fragment, and (iii) a worrying underreporting of tasks, software and parameters. Based upon these findings we propose a set of recommendations that we think the metabarcoding community should consider to ensure that bioinformatic methods are appropriate, comprehensive and comparable. We believe that adhering to these recommendations will improve the long‐term integrative potential of wocDNA COI metabarcoding for biodiversity science.
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Affiliation(s)
- Thomas J Creedy
- Department of Life Sciences, Natural History Museum, London, UK
| | - Carmelo Andújar
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), S.C. La Laguna, Spain
| | | | - Victor Noguerales
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), S.C. La Laguna, Spain.,Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Isaac Overcast
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieur, CNRS, INSERM, Université PSL, Paris, France
| | - Anna Papadopoulou
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Hélène Morlon
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieur, CNRS, INSERM, Université PSL, Paris, France
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, UK.,Department of Life Sciences, Imperial College London Silwood Park Campus, Ascot, UK
| | - Brent C Emerson
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), S.C. La Laguna, Spain
| | - Paula Arribas
- Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), S.C. La Laguna, Spain
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5
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Andújar C, Creedy TJ, Arribas P, López H, Salces-Castellano A, Pérez-Delgado AJ, Vogler AP, Emerson BC. Validated removal of nuclear pseudogenes and sequencing artefacts from mitochondrial metabarcode data. Mol Ecol Resour 2021; 21:1772-1787. [PMID: 33503286 DOI: 10.1111/1755-0998.13337] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 12/08/2020] [Accepted: 01/11/2021] [Indexed: 01/04/2023]
Abstract
Metabarcoding of Metazoa using mitochondrial genes may be confounded by both the accumulation of PCR and sequencing artefacts and the co-amplification of nuclear mitochondrial pseudogenes (NUMTs). The application of read abundance thresholds and denoising methods is efficient in reducing noise accompanying authentic mitochondrial amplicon sequence variants (ASVs). However, these procedures do not fully account for the complex nature of concomitant sequences and the highly variable DNA contribution of specimens in a metabarcoding sample. We propose, as a complement to denoising, the metabarcoding Multidimensional Abundance Threshold Evaluation (metaMATE) framework, a novel approach that allows comprehensive examination of multiple dimensions of abundance filtering and the evaluation of the prevalence of unwanted concomitant sequences in denoised metabarcoding datasets. metaMATE requires a denoised set of ASVs as input, and designates a subset of ASVs as being either authentic (mitochondrial DNA haplotypes) or nonauthentic ASVs (NUMTs and erroneous sequences) by comparison to external reference data and by analysing nucleotide substitution patterns. metaMATE (i) facilitates the application of read abundance filtering strategies, which are structured with regard to sequence library and phylogeny and applied for a range of increasing abundance threshold values, and (ii) evaluates their performance by quantifying the prevalence of nonauthentic ASVs and the collateral effects on the removal of authentic ASVs. The output from metaMATE facilitates decision-making about required filtering stringency and can be used to improve the reliability of intraspecific genetic information derived from metabarcode data. The framework is implemented in the metaMATE software (available at https://github.com/tjcreedy/metamate).
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Affiliation(s)
- Carmelo Andújar
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC, San Cristóbal de la Laguna, Spain
| | - Thomas J Creedy
- Department of Life Sciences, Natural History Museum, London, UK
| | - Paula Arribas
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC, San Cristóbal de la Laguna, Spain
| | - Heriberto López
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC, San Cristóbal de la Laguna, Spain
| | - Antonia Salces-Castellano
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC, San Cristóbal de la Laguna, Spain
| | - Antonio José Pérez-Delgado
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC, San Cristóbal de la Laguna, Spain
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, UK.,Department of Life Sciences, Imperial College London, Ascot, UK
| | - Brent C Emerson
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC, San Cristóbal de la Laguna, Spain
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6
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Andújar C, Arribas P, Yu DW, Vogler AP, Emerson BC. Why the COI barcode should be the community DNA metabarcode for the metazoa. Mol Ecol 2018; 27:3968-3975. [PMID: 30129071 DOI: 10.1111/mec.14844] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 07/21/2018] [Accepted: 08/03/2018] [Indexed: 12/25/2022]
Abstract
Metabarcoding of complex metazoan communities is increasingly being used to measure biodiversity in terrestrial, freshwater and marine ecosystems, revolutionizing our ability to observe patterns and infer processes regarding the origin and conservation of biodiversity. A fundamentally important question is which genetic marker to amplify, and although the mitochondrial cytochrome oxidase subunit I (COI) gene is one of the more widely used markers in metabarcoding for the Metazoa, doubts have recently been raised about its suitability. We argue that (a) the extensive coverage of reference sequence databases for COI; (b) the variation it presents; (c) the comparative advantages for denoising protein-coding genes; and (d) recent advances in DNA sequencing protocols argue in favour of standardizing for the use of COI for metazoan community samples. We also highlight where research efforts should focus to maximize the utility of metabarcoding.
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Affiliation(s)
- Carmelo Andújar
- Grupo de Ecología y Evolución en Islas, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de la Laguna, Spain
| | - Paula Arribas
- Grupo de Ecología y Evolución en Islas, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de la Laguna, Spain
| | - Douglas W Yu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- School of Biological Sciences, University of East Anglia, Norwich, Norfolk, UK
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming Yunnan, China
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, UK
- Department of Life Sciences, Imperial College London, Ascot, UK
| | - Brent C Emerson
- Grupo de Ecología y Evolución en Islas, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de la Laguna, Spain
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7
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Anslan S, Bahram M, Hiiesalu I, Tedersoo L. PipeCraft: Flexible open-source toolkit for bioinformatics analysis of custom high-throughput amplicon sequencing data. Mol Ecol Resour 2017; 17:e234-e240. [DOI: 10.1111/1755-0998.12692] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 04/24/2017] [Accepted: 05/18/2017] [Indexed: 11/28/2022]
Affiliation(s)
- Sten Anslan
- Institute of Ecology and Earth Sciences; University of Tartu; Tartu Estonia
| | - Mohammad Bahram
- Institute of Ecology and Earth Sciences; University of Tartu; Tartu Estonia
- Department of Organismal Biology; Evolutionary Biology Centre; Uppsala University; Uppsala Sweden
| | - Indrek Hiiesalu
- Institute of Ecology and Earth Sciences; University of Tartu; Tartu Estonia
| | - Leho Tedersoo
- Natural History Museum; University of Tartu; Tartu Estonia
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8
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Cicconardi F, Borges PAV, Strasberg D, Oromí P, López H, Pérez-Delgado AJ, Casquet J, Caujapé-Castells J, Fernández-Palacios JM, Thébaud C, Emerson BC. MtDNA metagenomics reveals large-scale invasion of belowground arthropod communities by introduced species. Mol Ecol 2017; 26:3104-3115. [PMID: 28139037 DOI: 10.1111/mec.14037] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 12/12/2016] [Accepted: 12/24/2016] [Indexed: 11/26/2022]
Abstract
Using a series of standardized sampling plots within forest ecosystems in remote oceanic islands, we reveal fundamental differences between the structuring of aboveground and belowground arthropod biodiversity that are likely due to large-scale species introductions by humans. Species of beetle and spider were sampled almost exclusively from single islands, while soil-dwelling Collembola exhibited more than tenfold higher species sharing among islands. Comparison of Collembola mitochondrial metagenomic data to a database of more than 80 000 Collembola barcode sequences revealed almost 30% of sampled island species are genetically identical, or near identical, to individuals sampled from often very distant geographic regions of the world. Patterns of mtDNA relatedness among Collembola implicate human-mediated species introductions, with minimum estimates for the proportion of introduced species on the sampled islands ranging from 45% to 88%. Our results call for more attention to soil mesofauna to understand the global extent and ecological consequences of species introductions.
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Affiliation(s)
- Francesco Cicconardi
- Institute of Ecology, University of Innsbruck, Technikerstrasse 25, a-6020, Innsbruck, Austria
| | - Paulo A V Borges
- CE3C - Centre for Ecology, Evolution and Environmental Changes/Azorean Biodiversity Group and Departamento de Ciências Agrárias e Ambiente, Universidade dos Açores, Rua Capitão João d'Ávila s/n, 9700-042, Angra do Heroísmo, Açores, Portugal
| | - Dominique Strasberg
- UMR PVBMT, Peuplements Végétaux et Bio-agresseurs en Milieu Tropical, Université de La Réunion, 15 avenue René Cassin, CS 93002, 97 744, Saint Denis Cedex 9, Reunion Island, France
| | - Pedro Oromí
- Departamento de Biología Animal y Edafología y Geología, Universidad de La Laguna, C/Astrofísico Francisco Sánchez, 38206, La Laguna, Tenerife, Canary Islands, Spain
| | - Heriberto López
- Island Ecology and Evolution Research Group, IPNA-CSIC, 38206, La Laguna, Tenerife, Canary Islands, Spain
| | - Antonio J Pérez-Delgado
- Island Ecology and Evolution Research Group, IPNA-CSIC, 38206, La Laguna, Tenerife, Canary Islands, Spain
| | - Juliane Casquet
- Laboratoire Evolution & Diversité Biologique, UMR 5174 CNRS-Université Paul Sabatier-ENFA, 31062, Toulouse Cedex 9, France
| | - Juli Caujapé-Castells
- Departamento de Biodiversidad Molecular y Banco de ADN, Jardín Botánico Canario 'Viera y Clavijo' - Unidad Asociada CSIC, Cabildo de Gran Canaria, Camino del Palmeral 15 de Tafira Alta, 35017, Las Palmas de Gran Canaria, Spain
| | - José María Fernández-Palacios
- Island Ecology and Biogeography Research Group, Instituto de Enfermedades Tropicales y Salud Pública de Canarias (IUETSPC), Universidad de La Laguna, Tenerife, Canary Islands, 38206, Spain
| | - Christophe Thébaud
- Laboratoire Evolution & Diversité Biologique, UMR 5174 CNRS-Université Paul Sabatier-ENFA, 31062, Toulouse Cedex 9, France
| | - Brent C Emerson
- Island Ecology and Evolution Research Group, IPNA-CSIC, 38206, La Laguna, Tenerife, Canary Islands, Spain.,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
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9
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Saitoh S, Aoyama H, Fujii S, Sunagawa H, Nagahama H, Akutsu M, Shinzato N, Kaneko N, Nakamori T. A quantitative protocol for DNA metabarcoding of springtails (Collembola). Genome 2017; 59:705-23. [PMID: 27611697 DOI: 10.1139/gen-2015-0228] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We developed a novel protocol with superior quantitative analysis results for DNA metabarcoding of Collembola, a major soil microarthropod order. Degenerate PCR primers were designed for conserved regions in the mitochondrial cytochrome c oxidase subunit I (mtCOI) and 16S ribosomal RNA (mt16S) genes based on published collembolan mitogenomes. The best primer pair was selected based on its ability to amplify each gene, irrespective of the species. DNA was extracted from 10 natural communities sampled in a temperate forest (with typically 25-30 collembolan species per 10 soil samples) and 10 mock communities (with seven cultured collembolan species). The two gene regions were then amplified using the selected primers, ligated with adapters for 454 technology, and sequenced. Examination of the natural community samples showed that 32 and 36 operational taxonomic units (defined at a 90% sequence similarity threshold) were recovered from the mtCOI and mt16S data, respectively, which were comparable to the results of the microscopic identification of 25 morphospecies. Further, sequence abundances for each collembolan species from the mtCOI and mt16S data of the mock communities, after normalization by using a species as the internal control, showed good correlation with the number of individuals in the samples (R = 0.91-0.99), although relative species abundances within a mock community sample estimated from sequences were skewed from community composition in terms of the number of individuals or biomass of the species. Thus, this protocol enables the comparison of collembolan communities in a quantitative manner by metabarcoding.
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Affiliation(s)
- Seikoh Saitoh
- a Tropical Biosphere Research Center, University of the Ryukyus, 1 Senbaru, Nishihara 903-0213, Japan
| | - Hiroaki Aoyama
- a Tropical Biosphere Research Center, University of the Ryukyus, 1 Senbaru, Nishihara 903-0213, Japan
| | - Saori Fujii
- b Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, Yokohama 240-8501, Japan
| | - Haruki Sunagawa
- c Okinawa Prefectural Agricultural Research Center, 820 Makabe, Itoman 901-0336, Japan
| | - Hideki Nagahama
- a Tropical Biosphere Research Center, University of the Ryukyus, 1 Senbaru, Nishihara 903-0213, Japan
| | - Masako Akutsu
- d Department of Electrical Engineering and Computer Science, School of Industrial and Welfare Engineering, Tokai University, Toroku 9-1-1, Higashi-ku, Kumamoto 862-8652, Japan
| | - Naoya Shinzato
- a Tropical Biosphere Research Center, University of the Ryukyus, 1 Senbaru, Nishihara 903-0213, Japan
| | - Nobuhiro Kaneko
- b Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, Yokohama 240-8501, Japan
| | - Taizo Nakamori
- b Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, Yokohama 240-8501, Japan
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Arribas P, Andújar C, Hopkins K, Shepherd M, Vogler AP. Metabarcoding and mitochondrial metagenomics of endogean arthropods to unveil the mesofauna of the soil. Methods Ecol Evol 2016. [DOI: 10.1111/2041-210x.12557] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Paula Arribas
- Department of Life Sciences Natural History Museum Cromwell Road London SW7 5BD UK
- Department of Life Sciences Imperial College London Silwood Park Campus Ascot SL5 7PY UK
| | - Carmelo Andújar
- Department of Life Sciences Natural History Museum Cromwell Road London SW7 5BD UK
- Department of Life Sciences Imperial College London Silwood Park Campus Ascot SL5 7PY UK
| | - Kevin Hopkins
- Department of Life Sciences Natural History Museum Cromwell Road London SW7 5BD UK
| | | | - Alfried P. Vogler
- Department of Life Sciences Natural History Museum Cromwell Road London SW7 5BD UK
- Department of Life Sciences Imperial College London Silwood Park Campus Ascot SL5 7PY UK
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Hug LA, Edwards EA. Diversity of reductive dehalogenase genes from environmental samples and enrichment cultures identified with degenerate primer PCR screens. Front Microbiol 2013; 4:341. [PMID: 24312087 PMCID: PMC3832961 DOI: 10.3389/fmicb.2013.00341] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 10/29/2013] [Indexed: 01/11/2023] Open
Abstract
Reductive dehalogenases are the critical enzymes for anaerobic organohalide respiration, a microbial metabolic process that has been harnessed for bioremediation efforts to resolve chlorinated solvent contamination in groundwater and is implicated in the global halogen cycle. Reductive dehalogenase sequence diversity is informative for the dechlorination potential of the site or enrichment culture. A suite of degenerate PCR primers targeting a comprehensive curated set of reductive dehalogenase genes was designed and applied to 12 DNA samples extracted from contaminated and pristine sites, as well as six enrichment cultures capable of reducing chlorinated compounds to non-toxic end-products. The amplified gene products from four environmental sites and two enrichment cultures were sequenced using Illumina HiSeq, and the reductive dehalogenase complement of each sample determined. The results indicate that the diversity of the reductive dehalogenase gene family is much deeper than is currently accounted for: one-third of the translated proteins have less than 70% pairwise amino acid identity to database sequences. Approximately 60% of the sequenced reductive dehalogenase genes were broadly distributed, being identified in four or more samples, and often in previously sequenced genomes as well. In contrast, 17% of the sequenced reductive dehalogenases were unique, present in only a single sample and bearing less than 90% pairwise amino acid identity to any previously identified proteins. Many of the broadly distributed reductive dehalogenases are uncharacterized in terms of their substrate specificity, making these intriguing targets for further biochemical experimentation. Finally, comparison of samples from a contaminated site and an enrichment culture derived from the same site 8 years prior allowed examination of the effect of the enrichment process.
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Affiliation(s)
- Laura A Hug
- Department of Cell and Systems Biology, University of Toronto Toronto, ON, Canada
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Cicconardi F, Fanciulli PP, Emerson BC. Collembola, the biological species concept and the underestimation of global species richness. Mol Ecol 2013; 22:5382-96. [DOI: 10.1111/mec.12472] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 07/10/2013] [Accepted: 07/17/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Francesco Cicconardi
- Department of Physics; University of Rome “La Sapienza”; P.le A. Moro 5 Rome 00185 Italy
- Smithsonian Tropical Research Institute; Apartado 0843-03092 Panamá, República de Panamá
| | - Pietro P. Fanciulli
- Department of Life Sciences; University of Siena; Via Aldo Moro 2 Siena 53100 Italy
| | - Brent C. Emerson
- Island Ecology and Evolution Research Group; IPNA-CSIC; La Laguna Tenerife 38206 Canary Islands Spain
- School of Biological Sciences; University of East Anglia; Norwich Research Park Norwich NR4 7TJ UK
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Deng W, Maust BS, Westfall DH, Chen L, Zhao H, Larsen BB, Iyer S, Liu Y, Mullins JI. Indel and Carryforward Correction (ICC): a new analysis approach for processing 454 pyrosequencing data. ACTA ACUST UNITED AC 2013; 29:2402-9. [PMID: 23900188 DOI: 10.1093/bioinformatics/btt434] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
MOTIVATION Pyrosequencing technology provides an important new approach to more extensively characterize diverse sequence populations and detect low frequency variants. However, the promise of this technology has been difficult to realize, as careful correction of sequencing errors is crucial to distinguish rare variants (∼1%) in an infected host with high sensitivity and specificity. RESULTS We developed a new approach, referred to as Indel and Carryforward Correction (ICC), to cluster sequences without substitutions and locally correct only indel and carryforward sequencing errors within clusters to ensure that no rare variants are lost. ICC performs sequence clustering in the order of (i) homopolymer indel patterns only, (ii) indel patterns only and (iii) carryforward errors only, without the requirement of a distance cutoff value. Overall, ICC removed 93-95% of sequencing errors found in control datasets. On pyrosequencing data from a PCR fragment derived from 15 HIV-1 plasmid clones mixed at various frequencies as low as 0.1%, ICC achieved the highest sensitivity and similar specificity compared with other commonly used error correction and variant calling algorithms. AVAILABILITY AND IMPLEMENTATION Source code is freely available for download at http://indra.mullins.microbiol.washington.edu/ICC. It is implemented in Perl and supported on Linux, Mac OS X and MS Windows.
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Affiliation(s)
- Wenjie Deng
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA
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