1
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Gaonkar CC, Campbell L. A full-length 18S ribosomal DNA metabarcoding approach for determining protist community diversity using Nanopore sequencing. Ecol Evol 2024; 14:e11232. [PMID: 38606340 PMCID: PMC11007259 DOI: 10.1002/ece3.11232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 03/21/2024] [Indexed: 04/13/2024] Open
Abstract
Protist diversity studies are frequently conducted using DNA metabarcoding methods. Currently, most studies have utilized short read sequences to assess protist diversity. One limitation of using short read sequences is the low resolution of the markers. For better taxonomic resolution longer sequences of the 18S rDNA are required because the full-length has both conserved and hypervariable regions. In this study, a new primer pair combination was used to amplify the full-length 18S rDNA and its efficacy was validated with a test community and then validated with field samples. Full-length sequences obtained with the Nanopore MinION for protist diversity from field samples were compared with Illumina MiSeq V4 and V8-V9 short reads. Sequences generated from the high-throughput sequencers are Amplicon Sequence Variants (ASVs). Metabarcoding results show high congruency among the long reads and short reads in taxonomic annotation at the major taxonomic group level; however, not all taxa could be successfully detected from sequences. Based on the criteria of ≥95% similarity and ≥1000 bp query length, 298 genera were identified by all markers in the field samples, 250 (84%) were detected by 18S, while only 226 (76%) by V4 and 213 (71%) by V8-V9. Of the total 85 dinoflagellate genera observed, 19 genera were not defined by 18S dinoflagellate ASVs compared to only three among the total 52 diatom genera. The discrepancy in this resolution is due to the lack of taxonomically available 18S reference sequences in particular for dinoflagellates. Overall, this preliminary investigation demonstrates that application of the full-length 18S rDNA approach can be successful in field studies.
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Affiliation(s)
- Chetan C. Gaonkar
- Department of OceanographyTexas A&M UniversityCollege StationTexasUSA
| | - Lisa Campbell
- Department of OceanographyTexas A&M UniversityCollege StationTexasUSA
- Department of BiologyTexas A&M UniversityCollege StationTexasUSA
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2
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Owens LA, Friant S, Martorelli Di Genova B, Knoll LJ, Contreras M, Noya-Alarcon O, Dominguez-Bello MG, Goldberg TL. VESPA: an optimized protocol for accurate metabarcoding-based characterization of vertebrate eukaryotic endosymbiont and parasite assemblages. Nat Commun 2024; 15:402. [PMID: 38195557 PMCID: PMC10776621 DOI: 10.1038/s41467-023-44521-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 12/15/2023] [Indexed: 01/11/2024] Open
Abstract
Protocols for characterizing taxonomic assemblages by deep sequencing of short DNA barcode regions (metabarcoding) have revolutionized our understanding of microbial communities and are standardized for bacteria, archaea, and fungi. Unfortunately, comparable methods for host-associated eukaryotes have lagged due to technical challenges. Despite 54 published studies, issues remain with primer complementarity, off-target amplification, and lack of external validation. Here, we present VESPA (Vertebrate Eukaryotic endoSymbiont and Parasite Analysis) primers and optimized metabarcoding protocol for host-associated eukaryotic community analysis. Using in silico prediction, panel PCR, engineered mock community standards, and clinical samples, we demonstrate VESPA to be more effective at resolving host-associated eukaryotic assemblages than previously published methods and to minimize off-target amplification. When applied to human and non-human primate samples, VESPA enables reconstruction of host-associated eukaryotic endosymbiont communities more accurately and at finer taxonomic resolution than microscopy. VESPA has the potential to advance basic and translational science on vertebrate eukaryotic endosymbiont communities, similar to achievements made for bacterial, archaeal, and fungal microbiomes.
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Affiliation(s)
- Leah A Owens
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA.
| | - Sagan Friant
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
- Department of Anthropology, The Pennsylvania State University, University Park, PA, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Bruno Martorelli Di Genova
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Microbiology and Molecular Genetics, Larner College of Medicine, The University of Vermont, Burlington, VT, USA
| | - Laura J Knoll
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Monica Contreras
- Center for Biophysics and Biochemistry, Venezuelan Institute of Scientific Research (IVIC), Caracas, Venezuela
| | - Oscar Noya-Alarcon
- Centro Amazónico de Investigación y Control de Enfermedades Tropicales-CAICET, Puerto Ayacucho, Amazonas, Venezuela
| | - Maria G Dominguez-Bello
- Department of Biochemistry and Microbiology, Rutgers University-New Brunswick, New Brunswick, NJ, USA
- Department of Anthropology, Rutgers University, New Brunswick, NJ, USA
- Institute for Food, Nutrition and Health, Rutgers University, New Brunswick, NJ, USA
- Canadian Institute for Advanced Research (CIFAR), Toronto, ON, Canada
| | - Tony L Goldberg
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA.
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3
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Latz MAC, Grujcic V, Brugel S, Lycken J, John U, Karlson B, Andersson A, Andersson AF. Short- and long-read metabarcoding of the eukaryotic rRNA operon: evaluation of primers and comparison to shotgun metagenomics sequencing. Mol Ecol Resour 2022; 22:2304-2318. [PMID: 35437888 DOI: 10.1111/1755-0998.13623] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 03/17/2022] [Accepted: 04/11/2022] [Indexed: 11/30/2022]
Abstract
High-throughput sequencing for analysis of microbial diversity has evolved vastly over the last decade. Currently the go-to method for studying microbial eukaryotes is short-read metabarcoding of variable regions of the 18S rRNA gene with <500 bp amplicons. However, there is a growing interest in applying long-read sequencing of amplicons covering the rRNA operon for improving taxonomic resolution. For both methods, the choice of primers is crucial. It determines if community members are covered, if they can be identified at a satisfactory taxonomic level, and if the obtained community profile is representative. Here, we designed new primers targeting 18S and 28S rRNA based on 177,934 and 21,072 database sequences, respectively. The primers were evaluated in silico along with published primers on reference sequence databases and marine metagenomics datasets. We further evaluated a subset of the primers for short- and long-read sequencing on environmental samples in vitro and compared the obtained community profile with primer-unbiased metagenomic sequencing. Of the short-read pairs, a new V6-V8 pair and the V4_Balzano pair used with a simplified PCR protocol provided good results in silico and in vitro. Fewer differences were observed between the long-read primer pairs. The long-read amplicons and ITS1 alone provided higher taxonomic resolution than V4. Together, our results represent a reference and guide for selection of robust primers for research on and environmental monitoring of microbial eukaryotes.
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Affiliation(s)
- Meike A C Latz
- KTH Royal Institute of Technology, Department of Gene Technology, Science for Life Laboratory, Stockholm, Sweden.,University of Copenhagen, Department of Plant and Environmental Sciences, Frederiksberg C, Denmark
| | - Vesna Grujcic
- KTH Royal Institute of Technology, Department of Gene Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Sonia Brugel
- Umeå University, Department of Ecology and Environmental Sciences, Umeå, Sweden
| | - Jenny Lycken
- Swedish Meteorological and Hydrological Institute, Oceanographic Research, Gothenburg, Sweden
| | - Uwe John
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany.,Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany
| | - Bengt Karlson
- Swedish Meteorological and Hydrological Institute, Oceanographic Research, Gothenburg, Sweden
| | - Agneta Andersson
- Umeå University, Department of Ecology and Environmental Sciences, Umeå, Sweden
| | - Anders F Andersson
- KTH Royal Institute of Technology, Department of Gene Technology, Science for Life Laboratory, Stockholm, Sweden
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4
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Raupach MJ, Rulik B, Spelda J. Surprisingly high genetic divergence of the mitochondrial DNA barcode fragment (COI) within Central European woodlice species (Crustacea, Isopoda, Oniscidea). Zookeys 2022; 1082:103-125. [PMID: 35115867 PMCID: PMC8794987 DOI: 10.3897/zookeys.1082.69851] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 12/20/2021] [Indexed: 11/12/2022] Open
Abstract
DNA barcoding has become the most popular approach for species identification in recent years. As part of the German Barcode of Life project, the first DNA barcode library for terrestrial and freshwater isopods from Germany is presented. The analyzed barcode library included 38 terrestrial (78% of the documented species of Germany) and five freshwater (63%) species. A total of 513 new barcodes was generated and 518 DNA barcodes were analyzed. This analysis revealed surprisingly high intraspecific genetic distances for numerous species, with a maximum of 29.4% for Platyarthrus hoffmannseggii Brandt, 1833. The number of BINs per species ranged from one (32 species, 68%) to a maximum of six for Trachelipus rathkii (Brandt, 1833). In spite of such high intraspecific variability, interspecific distances with values between 12.6% and 29.8% allowed a valid species assignment of all analyzed isopods. The observed high intraspecific distances presumably result from phylogeographic events, Wolbachia infections, atypical mitochondrial DNAs, heteroplasmy, or various combinations of these factors. Our study represents the first step in generating an extensive reference library of DNA barcodes for terrestrial and freshwater isopods for future molecular biodiversity assessment studies.
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5
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Phylogeography and genetic diversity of the commercially-collected Caribbean blue-legged hermit crab (Clibanarius tricolor). CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01348-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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6
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Laakmann S, Blanco-Bercial L, Cornils A. The crossover from microscopy to genes in marine diversity: from species to assemblages in marine pelagic copepods. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190446. [PMID: 33131432 PMCID: PMC7662206 DOI: 10.1098/rstb.2019.0446] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
An accurate identification of species and communities is a prerequisite for analysing and recording biodiversity and community shifts. In the context of marine biodiversity conservation and management, this review outlines past, present and forward-looking perspectives on identifying and recording planktonic diversity by illustrating the transition from traditional species identification based on morphological diagnostic characters to full molecular genetic identification of marine assemblages. In this process, the article presents the methodological advancements by discussing progress and critical aspects of the crossover from traditional to novel and future molecular genetic identifications and it outlines the advantages of integrative approaches using the strengths of both morphological and molecular techniques to identify species and assemblages. We demonstrate this process of identifying and recording marine biodiversity on pelagic copepods as model taxon. Copepods are known for their high taxonomic and ecological diversity and comprise a huge variety of behaviours, forms and life histories, making them a highly interesting and well-studied group in terms of biodiversity and ecosystem functioning. Furthermore, their short life cycles and rapid responses to changing environments make them good indicators and core research components for ecosystem health and status in the light of environmental change. This article is part of the theme issue 'Integrative research perspectives on marine conservation'.
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Affiliation(s)
- Silke Laakmann
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Ammerländer Heerstrasse 231, 26129 Oldenburg, Germany.,Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | | | - Astrid Cornils
- Alfred Wegener Institute Helmholtz Center for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
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7
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Schroeder A, Stanković D, Pallavicini A, Gionechetti F, Pansera M, Camatti E. DNA metabarcoding and morphological analysis - Assessment of zooplankton biodiversity in transitional waters. MARINE ENVIRONMENTAL RESEARCH 2020; 160:104946. [PMID: 32907716 DOI: 10.1016/j.marenvres.2020.104946] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 02/28/2020] [Accepted: 03/07/2020] [Indexed: 06/11/2023]
Abstract
Zooplankton biodiversity assessment is a crucial element in monitoring marine ecosystem processes and community responses to environmental alterations. In order to evaluate the suitability of metabarcoding for zooplankton biodiversity assessment and biomonitoring as a fast and more cost-effective method, seasonal zooplankton sampling was carried out in the Venice Lagoon and the nearby coastal area (Northern Adriatic Sea). The molecular analysis showed higher taxa richness compared to the classical morphological method (224 vs. 88 taxa), discriminating better the meroplanktonic component, morphologically identified only up to order level. Both methods revealed a similar spatio-temporal distribution pattern and the sequence abundances and individual counts were significantly correlated for various taxonomic groups. These results indicate that DNA metabarcoding is an efficient tool for biodiversity assessments in ecosystems with high spatial and temporal variability, where high sampling effort is required as well as fast alert systems for non-native species (NIS).
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Affiliation(s)
- Anna Schroeder
- National Research Council, Institute of Marine Sciences (CNR ISMAR) Venice, Arsenale Tesa 104, Castello 2737/F, 30122, Venice, Italy; University of Trieste, Department of Life Sciences, Via Licio Giorgieri 5, 34127, Trieste, Italy.
| | - David Stanković
- Marine Biology Station Piran, National Institute of Biology, Fornace 41, 6330, Piran, Slovenia.
| | - Alberto Pallavicini
- University of Trieste, Department of Life Sciences, Via Licio Giorgieri 5, 34127, Trieste, Italy; Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy; National Interuniversity Consortium For Marine Sciences (CoNISMa), Piazzale Flaminio 9, 00196, Rome, Italy.
| | - Fabrizia Gionechetti
- University of Trieste, Department of Life Sciences, Via Licio Giorgieri 5, 34127, Trieste, Italy.
| | - Marco Pansera
- National Research Council, Institute of Marine Sciences (CNR ISMAR) Venice, Arsenale Tesa 104, Castello 2737/F, 30122, Venice, Italy.
| | - Elisa Camatti
- National Research Council, Institute of Marine Sciences (CNR ISMAR) Venice, Arsenale Tesa 104, Castello 2737/F, 30122, Venice, Italy.
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8
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Li D, Olden JD, Lockwood JL, Record S, McKinney ML, Baiser B. Changes in taxonomic and phylogenetic diversity in the Anthropocene. Proc Biol Sci 2020; 287:20200777. [PMID: 32546087 PMCID: PMC7329034 DOI: 10.1098/rspb.2020.0777] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 05/20/2020] [Indexed: 12/21/2022] Open
Abstract
To better understand how ecosystems are changing, a multifaceted approach to measuring biodiversity that considers species richness (SR) and evolutionary history across spatial scales is needed. Here, we compiled 162 datasets for fish, bird and plant assemblages across the globe and measured how taxonomic and phylogenetic diversity changed at different spatial scales (within site α diversity and between sites spatial β diversity). Biodiversity change is measured from these datasets in three ways: across land use gradients, from species lists, and through sampling of the same locations across two time periods. We found that local SR and phylogenetic α diversity (Faith's PD (phylogenetic diversity)) increased for all taxonomic groups. However, when measured with a metric that is independent of SR (phylogenetic species variation, PSV), phylogenetic α diversity declined for all taxonomic groups. Land use datasets showed declines in SR, Faith's PD and PSV. For all taxonomic groups and data types, spatial taxonomic and phylogenetic β diversity decreased when measured with Sorensen dissimilarity and phylogenetic Sorensen dissimilarity, respectively, providing strong evidence of global biotic homogenization. The decoupling of α and β diversity, as well as taxonomic and phylogenetic diversity, highlights the need for a broader perspective on contemporary biodiversity changes. Conservation and environmental policy decisions thus need to consider biodiversity beyond local SR to protect biodiversity and ecosystem services.
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Affiliation(s)
- Daijiang Li
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL 32611, USA
| | - Julian D. Olden
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA 98105, USA
| | - Julie L. Lockwood
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, NJ 08901, USA
| | - Sydne Record
- Department of Biology, Bryn Mawr College, Bryn Mawr, PA 19010, USA
| | - Michael L. McKinney
- Department of Earth and Planetary Sciences, The University of Tennessee, Knoxville, TN 37996, USA
| | - Benjamin Baiser
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL 32611, USA
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9
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Hirakata Y, Hatamoto M, Oshiki M, Watari T, Kuroda K, Araki N, Yamaguchi T. Temporal variation of eukaryotic community structures in UASB reactor treating domestic sewage as revealed by 18S rRNA gene sequencing. Sci Rep 2019; 9:12783. [PMID: 31484981 PMCID: PMC6726610 DOI: 10.1038/s41598-019-49290-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 08/22/2019] [Indexed: 11/09/2022] Open
Abstract
Eukaryotes are important components of ecosystems in wastewater treatment processes. However, little is known about eukaryotic community in anaerobic wastewater treatment systems. In this study, eukaryotic communities in an up flow anaerobic sludge blanket (UASB) reactor treating domestic sewage during two years of operation were investigated using V4 and V9 regions of 18S rRNA gene for amplicon sequencing. In addition, activated sludge and influent sewage samples were also analyzed and used as the references for aerobic eukaryotic community to characterize anaerobic eukaryotes. The amplicon sequence V4 and V9 libraries detected different taxonomic groups, especially from the UASB samples, suggesting that commonly used V4 and V9 primer pairs could produce a bias for eukaryotic communities analysis. Eukaryotic community structures in the UASB reactor were influenced by the immigration of eukaryotes via influent sewage but were clearly different from the influent sewage and activated sludge. Multivariate statistics indicated that protist genera Cyclidium, Platyophrya and Subulatomonas correlated with chemical oxygen demand and suspended solid concentration, and could be used as bioindicators of treatment performance. Uncultured eukaryotes groups were dominant in the UASB reactor, and their physiological roles need to be examined to understand their contributions to anaerobic processes in future studies.
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Affiliation(s)
- Yuga Hirakata
- Department of Science of Technology Innovation, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, 940-2188, Japan
| | - Masashi Hatamoto
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, 940-2188, Japan.
| | - Mamoru Oshiki
- Department of Civil Engineering, National institute of Technology, Nagaoka College, 888 Nishikatakaimachi, Nagaoka, Niigata, 940-0834, Japan
| | - Takahiro Watari
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, 940-2188, Japan
| | - Kyohei Kuroda
- Department of Chemical Science and Engineering, National Institute of Technology, Miyakonojo College, 473-1 Yoshio-cho, Miyakonojo, Miyazaki, 885-8567, Japan
| | - Nobuo Araki
- Department of Civil Engineering, National institute of Technology, Nagaoka College, 888 Nishikatakaimachi, Nagaoka, Niigata, 940-0834, Japan
| | - Takashi Yamaguchi
- Department of Science of Technology Innovation, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, 940-2188, Japan.,Department of Civil and Environmental Engineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, 940-2188, Japan
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10
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Detection of introduced and resident marine species using environmental DNA metabarcoding of sediment and water. Sci Rep 2019; 9:11559. [PMID: 31399606 PMCID: PMC6689084 DOI: 10.1038/s41598-019-47899-7] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 07/25/2019] [Indexed: 12/12/2022] Open
Abstract
Environmental DNA (eDNA) surveys are increasingly being used for biodiversity monitoring, principally because they are sensitive and can provide high resolution community composition data. Despite considerable progress in recent years, eDNA studies examining how different environmental sample types can affect species detectability remain rare. Comparisons of environmental samples are especially important for providing best practice guidance on early detection and subsequent mitigation of non-indigenous species. Here we used eDNA metabarcoding of COI (cytochrome c oxidase subunit I) and 18S (nuclear small subunit ribosomal DNA) genes to compare community composition between sediment and water samples in artificial coastal sites across the United Kingdom. We first detected markedly different communities and a consistently greater number of distinct operational taxonomic units in sediment compared to water. We then compared our eDNA datasets with previously published rapid assessment biodiversity surveys and found excellent concordance among the different survey techniques. Finally, our eDNA surveys detected many non-indigenous species, including several newly introduced species, highlighting the utility of eDNA metabarcoding for both early detection and temporal / spatial monitoring of non-indigenous species. We conclude that careful consideration on environmental sample type is needed when conducting eDNA surveys, especially for studies assessing community change.
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11
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Metabarcoding of marine environmental DNA based on mitochondrial and nuclear genes. Sci Rep 2018; 8:14822. [PMID: 30287908 PMCID: PMC6172225 DOI: 10.1038/s41598-018-32917-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 09/17/2018] [Indexed: 11/17/2022] Open
Abstract
We establish the new approach of environmental DNA (eDNA) analyses for the North Sea. Our study uses a multigene approach, including the mitochondrial cytochrome-c-oxidase subunit I (COI) gene for analyzing species composition and the nuclear hypervariable region V8 of 18S rDNA for analyzing supraspecific biodiversity. A new minibarcode primer (124 bp) was created on the basis of a metazoan COI barcode library with 506 species and tested in silico, in vitro, and in situ. We applied high throughput sequencing to filtrates of 23 near-bottom water samples taken at three seasons from 14 stations. The set of COI primers allowed amplification of mitochondrial minibarcodes for diverse metazoan phyla and the differentiation at the species level for more than 99% of the specimens in the dataset. Our results revealed that the number of sequences is not consistent with proportions in the given DNA mixture. Altogether, environmental sequences could be assigned to 114 species and to 12 metazoan phyla. A spatial distribution of taxa recovered by eDNA was congruent with known distributions. Finally, the successful detection of species and biodiversity depends on a comprehensive sequence reference database. Our study offers a powerful tool for future biodiversity research, including the detection of nonnative species.
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12
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Hering D, Borja A, Jones JI, Pont D, Boets P, Bouchez A, Bruce K, Drakare S, Hänfling B, Kahlert M, Leese F, Meissner K, Mergen P, Reyjol Y, Segurado P, Vogler A, Kelly M. Implementation options for DNA-based identification into ecological status assessment under the European Water Framework Directive. WATER RESEARCH 2018; 138:192-205. [PMID: 29602086 DOI: 10.1016/j.watres.2018.03.003] [Citation(s) in RCA: 153] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 03/02/2018] [Accepted: 03/03/2018] [Indexed: 05/22/2023]
Abstract
Assessment of ecological status for the European Water Framework Directive (WFD) is based on "Biological Quality Elements" (BQEs), namely phytoplankton, benthic flora, benthic invertebrates and fish. Morphological identification of these organisms is a time-consuming and expensive procedure. Here, we assess the options for complementing and, perhaps, replacing morphological identification with procedures using eDNA, metabarcoding or similar approaches. We rate the applicability of DNA-based identification for the individual BQEs and water categories (rivers, lakes, transitional and coastal waters) against eleven criteria, summarised under the headlines representativeness (for example suitability of current sampling methods for DNA-based identification, errors from DNA-based species detection), sensitivity (for example capability to detect sensitive taxa, unassigned reads), precision of DNA-based identification (knowledge about uncertainty), comparability with conventional approaches (for example sensitivity of metrics to differences in DNA-based identification), cost effectiveness and environmental impact. Overall, suitability of DNA-based identification is particularly high for fish, as eDNA is a well-suited sampling approach which can replace expensive and potentially harmful methods such as gill-netting, trawling or electrofishing. Furthermore, there are attempts to replace absolute by relative abundance in metric calculations. For invertebrates and phytobenthos, the main challenges include the modification of indices and completing barcode libraries. For phytoplankton, the barcode libraries are even more problematic, due to the high taxonomic diversity in plankton samples. If current assessment concepts are kept, DNA-based identification is least appropriate for macrophytes (rivers, lakes) and angiosperms/macroalgae (transitional and coastal waters), which are surveyed rather than sampled. We discuss general implications of implementing DNA-based identification into standard ecological assessment, in particular considering any adaptations to the WFD that may be required to facilitate the transition to molecular data.
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Affiliation(s)
- Daniel Hering
- University of Duisburg-Essen, Aquatic Ecology, 45117 Essen, Germany.
| | - Angel Borja
- AZTI, Marine Research Division, 20110 Pasaia, Spain
| | - J Iwan Jones
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Didier Pont
- Association VigiLIFE, 17, rue du Lac Saint-André, Savoie Technolac - BP 274, 73375 Le Bourget-du-Lac Cedex, France and Institute of Hydrobiology and Aquatic Ecosystem Management, University of Natural Resources and Life Sciences, Gregor-Mendel-Strasse 33, 1180 Vienna, Austria
| | - Pieter Boets
- PCM, Provincial Centre of Environmental Research, Godshuizenlaan 95, 9000 Ghent, Belgium
| | | | - Kat Bruce
- NatureMetrics Ltd, Egham, TW20 9TY, UK
| | - Stina Drakare
- Swedish University of Agricultural Sciences, Department of Aquatic Sciences and Assessment, PO Box 7050, SE-750 07 Uppsala, Sweden
| | - Bernd Hänfling
- University of Hull, Evolutionary Biology Group, School of Environmental Sciences, Hull, HU6 7RX, UK
| | - Maria Kahlert
- Swedish University of Agricultural Sciences, Department of Aquatic Sciences and Assessment, PO Box 7050, SE-750 07 Uppsala, Sweden
| | - Florian Leese
- University of Duisburg-Essen, Aquatic Ecosystem Research, 45117 Essen, Germany
| | - Kristian Meissner
- Finnish Environment Institute, Freshwater Centre, FI-40500 Jyväskylä, Finland
| | - Patricia Mergen
- Botanic Garden Meise, Nieuwelaan, 38, 1860 Meise, Belgium; Royal Museum for Central Africa, Leuvensesteenweg, 13, 3080 Tervuren, Belgium
| | - Yorick Reyjol
- Agence Française pour la Biodiversité (AFB), 5 square Felix Nadar, 94300 Vincennes, France
| | - Pedro Segurado
- Forest Research Center, School of Agriculture, University of Lisbon, Tapada da Ajuda, 1349-017 Lisbon, Portugal
| | - Alfried Vogler
- Department of Life Sciences, Imperial College London, and Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Martyn Kelly
- Bowburn Consultancy, 11 Monteigne Drive, Bowburn, Durham DH6 5QB, UK
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13
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Leray M, Knowlton N. Censusing marine eukaryotic diversity in the twenty-first century. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0331. [PMID: 27481783 PMCID: PMC4971183 DOI: 10.1098/rstb.2015.0331] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2016] [Indexed: 11/12/2022] Open
Abstract
The ocean constitutes one of the vastest and richest biomes on our planet. Most recent estimations, all based on indirect approaches, suggest that there are millions of marine eukaryotic species. Moreover, a large majority of these are small (less than 1 mm), cryptic and still unknown to science. However, this knowledge gap, caused by the lack of diagnostic morphological features in small organisms and the limited sampling of the global ocean, is currently being filled, thanks to new DNA-based approaches. The molecular technique of PCR amplification of homologous gene regions combined with high-throughput sequencing, routinely used to census unculturable prokaryotes, is now also being used to characterize whole communities of marine eukaryotes. Here, we review how this methodological advancement has helped to better quantify the magnitude and patterns of marine eukaryotic diversity, with an emphasis on taxonomic groups previously largely overlooked. We then discuss obstacles remaining to achieve a global understanding of marine eukaryotic diversity. In particular, we argue that 18S variable regions do not provide sufficient taxonomic resolution to census marine life, and suggest combining broad eukaryotic surveys targeting the 18S rRNA region with more taxon-focused analyses of hypervariable regions to improve our understanding of the diversity of species, the functional units of marine ecosystems. This article is part of the themed issue ‘From DNA barcodes to biomes’.
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Affiliation(s)
- Matthieu Leray
- National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
| | - Nancy Knowlton
- National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
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14
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Sommer SA, Van Woudenberg L, Lenz PH, Cepeda G, Goetze E. Vertical gradients in species richness and community composition across the twilight zone in the North Pacific Subtropical Gyre. Mol Ecol 2017; 26:6136-6156. [PMID: 28792641 DOI: 10.1111/mec.14286] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 06/08/2017] [Accepted: 06/30/2017] [Indexed: 01/28/2023]
Abstract
Although metazoan animals in the mesopelagic zone play critical roles in deep pelagic food webs and in the attenuation of carbon in midwaters, the diversity of these assemblages is not fully known. A metabarcoding survey of mesozooplankton diversity across the epipelagic, mesopelagic and upper bathypelagic zones (0-1500 m) in the North Pacific Subtropical Gyre revealed far higher estimates of species richness than expected given prior morphology-based studies in the region (4,024 OTUs, 10-fold increase), despite conservative bioinformatic processing. Operational taxonomic unit (OTU) richness of the full assemblage peaked at lower epipelagic-upper mesopelagic depths (100-300 m), with slight shoaling of maximal richness at night due to diel vertical migration, in contrast to expectations of a deep mesopelagic diversity maximum as reported for several plankton groups in early systematic and zoogeographic studies. Four distinct depth-stratified species assemblages were identified, with faunal transitions occurring at 100 m, 300 m and 500 m. Highest diversity occurred in the smallest zooplankton size fractions (0.2-0.5 mm), which had significantly lower % OTUs classified due to poor representation in reference databases, suggesting a deep reservoir of poorly understood diversity in the smallest metazoan animals. A diverse meroplankton assemblage also was detected (350 OTUs), including larvae of both shallow and deep living benthic species. Our results provide some of the first insights into the hidden diversity present in zooplankton assemblages in midwaters, and a molecular reappraisal of vertical gradients in species richness, depth distributions and community composition for the full zooplankton assemblage across the epipelagic, mesopelagic and upper bathypelagic zones.
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Affiliation(s)
- Stephanie A Sommer
- Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Manoa, Honolulu, HI, USA
| | - Lauren Van Woudenberg
- Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Manoa, Honolulu, HI, USA
| | - Petra H Lenz
- Pacific Biosciences Research Center, School of Ocean and Earth Science and Technology, University of Hawai'i at Manoa, Honolulu, HI, USA
| | - Georgina Cepeda
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Instituto Nacional de Investigación y Desarrollo Pesquero (INIDEP), Mar del Plata, Argentina
| | - Erica Goetze
- Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawai'i at Manoa, Honolulu, HI, USA
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15
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Hirai J, Nagai S, Hidaka K. Evaluation of metagenetic community analysis of planktonic copepods using Illumina MiSeq: Comparisons with morphological classification and metagenetic analysis using Roche 454. PLoS One 2017; 12:e0181452. [PMID: 28715458 PMCID: PMC5513544 DOI: 10.1371/journal.pone.0181452] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Accepted: 06/30/2017] [Indexed: 12/22/2022] Open
Abstract
Metagenetics is a rapid and taxonomically comprehensive method for revealing community structures within environmental samples, based on large amounts of sequence data produced by high-throughput sequencers. Because community structures of planktonic copepods are important in the ocean owing to their high diversity and abundance, a metagenetic analysis of the 28S D2 region using Roche 454 was previously developed. However, the Illumina MiSeq platform with a high sequence output is being used more frequently in metagenetics, and non-calanoid copepods have not previously been fully evaluated. Here, we evaluated an Illumina MiSeq-based metagenetic analysis using a mock community and field-collected samples that were examined in a previous study using Roche 454, and the community structure, including non-calanoid copepods, was compared among morphological and metagenetic analyses. We removed a singleton read and applied an appropriate abundance threshold to remove erroneous Molecular Operational Taxonomic Units (MOTUs) with low-abundance sequences in the MiSeq-based analysis. Results showed that the copepod community was successfully characterized using Illumina MiSeq. Higher-quality sequences were obtained using MiSeq than by Roche 454, which reduced the overestimation of diversity, especially at a strict 99% similarity threshold for MOTU clustering. Taxonomic compositions in terms of both biomass and presence/absence of species, including non-calanoids, were more appropriately represented in the MiSeq- than in Roche 454-based analysis. Our data showed that metagenetic analysis using Illumina MiSeq is more useful for revealing copepod communities than Roche 454, owing to the lower cost and higher quality.
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Affiliation(s)
- Junya Hirai
- National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Satoshi Nagai
- National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Kiyotaka Hidaka
- National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
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16
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George KH. Phylogeny of the taxon Paralaophontodes Lang (Copepoda, Harpacticoida, Laophontodinae), including species descriptions, chorological remarks, and a key to species. ZOOSYST EVOL 2017. [DOI: 10.3897/zse.93.11314] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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17
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Clarke LJ, Beard JM, Swadling KM, Deagle BE. Effect of marker choice and thermal cycling protocol on zooplankton DNA metabarcoding studies. Ecol Evol 2017; 7:873-883. [PMID: 28168024 PMCID: PMC5288259 DOI: 10.1002/ece3.2667] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 11/02/2016] [Accepted: 11/08/2016] [Indexed: 02/06/2023] Open
Abstract
DNA metabarcoding is a promising approach for rapidly surveying biodiversity and is likely to become an important tool for measuring ecosystem responses to environmental change. Metabarcoding markers need sufficient taxonomic coverage to detect groups of interest, sufficient sequence divergence to resolve species, and will ideally indicate relative abundance of taxa present. We characterized zooplankton assemblages with three different metabarcoding markers (nuclear 18S rDNA, mitochondrial COI, and mitochondrial 16S rDNA) to compare their performance in terms of taxonomic coverage, taxonomic resolution, and correspondence between morphology‐ and DNA‐based identification. COI amplicons sequenced on separate runs showed that operational taxonomic units representing >0.1% of reads per sample were highly reproducible, although slightly more taxa were detected using a lower annealing temperature. Mitochondrial COI and nuclear 18S showed similar taxonomic coverage across zooplankton phyla. However, mitochondrial COI resolved up to threefold more taxa to species compared to 18S. All markers revealed similar patterns of beta‐diversity, although different taxa were identified as the greatest contributors to these patterns for 18S. For calanoid copepod families, all markers displayed a positive relationship between biomass and sequence reads, although the relationship was typically strongest for 18S. The use of COI for metabarcoding has been questioned due to lack of conserved primer‐binding sites. However, our results show the taxonomic coverage and resolution provided by degenerate COI primers, combined with a comparatively well‐developed reference sequence database, make them valuable metabarcoding markers for biodiversity assessment.
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Affiliation(s)
- Laurence J Clarke
- Antarctic Climate & Ecosystems Cooperative Research Centre University of Tasmania Hobart Tas. Australia; Australian Antarctic Division Kingston Tas. Australia
| | - Jason M Beard
- Institute for Marine and Antarctic Studies University of Tasmania Hobart Tas. Australia
| | - Kerrie M Swadling
- Antarctic Climate & Ecosystems Cooperative Research Centre University of Tasmania Hobart Tas. Australia; Institute for Marine and Antarctic Studies University of Tasmania Hobart Tas. Australia
| | - Bruce E Deagle
- Antarctic Climate & Ecosystems Cooperative Research Centre University of Tasmania Hobart Tas. Australia; Australian Antarctic Division Kingston Tas. Australia
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18
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Holovachov O. Metabarcoding of marine nematodes - evaluation of similarity scores used in alignment-based taxonomy assignment approach. Biodivers Data J 2016:e10647. [PMID: 27932928 PMCID: PMC5136674 DOI: 10.3897/bdj.4.e10647] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 11/11/2016] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND The diversity of organisms is being commonly accessed using metabarcoding of environmental samples. Reliable identification of barcodes is one of the critical steps in the process and several taxonomy assignment methods were proposed to accomplish this task, including alignment-based approach that uses Basic Local Alignment Search Tool (BLAST) algorithm. This publication evaluates the variability of 5' end of 18S rRNA barcoding region as expressed by similarity scores (alignment score and identity score) produced by BLAST, and its impact on barcode identification to family-level taxonomic categories. NEW INFORMATION In alignment-based taxonomy assignment approach, reliable identification of anonymous OTUs to supraspecific taxa depends on the correct application of similarity thresholds. Since various taxa show different level of genetic variation, practical application of alignment-based approach requires the determination and use of taxon-specific similarity thresholds.
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19
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Design and Evaluation of Illumina MiSeq-Compatible, 18S rRNA Gene-Specific Primers for Improved Characterization of Mixed Phototrophic Communities. Appl Environ Microbiol 2016; 82:5878-91. [PMID: 27451454 DOI: 10.1128/aem.01630-16] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 07/20/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The use of high-throughput sequencing technologies with the 16S rRNA gene for characterization of bacterial and archaeal communities has become routine. However, the adoption of sequencing methods for eukaryotes has been slow, despite their significance to natural and engineered systems. There are large variations among the target genes used for amplicon sequencing, and for the 18S rRNA gene, there is no consensus on which hypervariable region provides the most suitable representation of diversity. Additionally, it is unclear how much PCR/sequencing bias affects the depiction of community structure using current primers. The present study amplified the V4 and V8-V9 regions from seven microalgal mock communities as well as eukaryotic communities from freshwater, coastal, and wastewater samples to examine the effect of PCR/sequencing bias on community structure and membership. We found that degeneracies on the 3' end of the current V4-specific primers impact read length and mean relative abundance. Furthermore, the PCR/sequencing error is markedly higher for GC-rich members than for communities with balanced GC content. Importantly, the V4 region failed to reliably capture 2 of the 12 mock community members, and the V8-V9 hypervariable region more accurately represents mean relative abundance and alpha and beta diversity. Overall, the V4 and V8-V9 regions show similar community representations over freshwater, coastal, and wastewater environments, but specific samples show markedly different communities. These results indicate that multiple primer sets may be advantageous for gaining a more complete understanding of community structure and highlight the importance of including mock communities composed of species of interest. IMPORTANCE The quantification of error associated with community representation by amplicon sequencing is a critical challenge that is often ignored. When target genes are amplified using currently available primers, differential amplification efficiencies result in inaccurate estimates of community structure. The extent to which amplification bias affects community representation and the accuracy with which different gene targets represent community structure are not known. As a result, there is no consensus on which region provides the most suitable representation of diversity for eukaryotes. This study determined the accuracy with which commonly used 18S rRNA gene primer sets represent community structure and identified particular biases related to PCR amplification and Illumina MiSeq sequencing in order to more accurately study eukaryotic microbial communities.
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Lanzén A, Lekang K, Jonassen I, Thompson EM, Troedsson C. High-throughput metabarcoding of eukaryotic diversity for environmental monitoring of offshore oil-drilling activities. Mol Ecol 2016; 25:4392-406. [DOI: 10.1111/mec.13761] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 06/20/2016] [Accepted: 07/13/2016] [Indexed: 10/21/2022]
Affiliation(s)
- Anders Lanzén
- Department of Conservation of Natural Resources; NEIKER Tecnalia; Bizkaia Technology Park 48160 Derio Spain
| | - Katrine Lekang
- Department of Biology; University of Bergen; Box 7800 5020 Bergen Norway
| | - Inge Jonassen
- Computational Biology Unit; Department of Informatics; University of Bergen; Bergen Norway
| | - Eric M. Thompson
- Department of Biology; University of Bergen; Box 7800 5020 Bergen Norway
- Sars International Centre for Marine Molecular Biology; University of Bergen; Bergen Norway
- Uni Research Environment; Uni Research AS; 5020 Bergen Norway
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21
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Morinière J, Cancian de Araujo B, Lam AW, Hausmann A, Balke M, Schmidt S, Hendrich L, Doczkal D, Fartmann B, Arvidsson S, Haszprunar G. Species Identification in Malaise Trap Samples by DNA Barcoding Based on NGS Technologies and a Scoring Matrix. PLoS One 2016; 11:e0155497. [PMID: 27191722 PMCID: PMC4871420 DOI: 10.1371/journal.pone.0155497] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 04/30/2016] [Indexed: 11/23/2022] Open
Abstract
The German Barcoding initiatives BFB and GBOL have generated a reference library of more than 16,000 metazoan species, which is now ready for applications concerning next generation molecular biodiversity assessments. To streamline the barcoding process, we have developed a meta-barcoding pipeline: We pre-sorted a single malaise trap sample (obtained during one week in August 2014, southern Germany) into 12 arthropod orders and extracted DNA from pooled individuals of each order separately, in order to facilitate DNA extraction and avoid time consuming single specimen selection. Aliquots of each ordinal-level DNA extract were combined to roughly simulate a DNA extract from a non-sorted malaise sample. Each DNA extract was amplified using four primer sets targeting the CO1-5’ fragment. The resulting PCR products (150-400bp) were sequenced separately on an Illumina Mi-SEQ platform, resulting in 1.5 million sequences and 5,500 clusters (coverage ≥10; CD-HIT-EST, 98%). Using a total of 120,000 DNA barcodes of identified, Central European Hymenoptera, Coleoptera, Diptera, and Lepidoptera downloaded from BOLD we established a reference sequence database for a local CUSTOM BLAST. This allowed us to identify 529 Barcode Index Numbers (BINs) from our sequence clusters derived from pooled Malaise trap samples. We introduce a scoring matrix based on the sequence match percentages of each amplicon in order to gain plausibility for each detected BIN, leading to 390 high score BINs in the sorted samples; whereas 268 of these high score BINs (69%) could be identified in the combined sample. The results indicate that a time consuming presorting process will yield approximately 30% more high score BINs compared to the non-sorted sample in our case. These promising results indicate that a fast, efficient and reliable analysis of next generation data from malaise trap samples can be achieved using this pipeline.
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Affiliation(s)
- Jérôme Morinière
- SNSB, Bavarian State Collection of Zoology, Münchhausenstrasse 21, 81247, München, Germany
| | | | - Athena Wai Lam
- SNSB, Bavarian State Collection of Zoology, Münchhausenstrasse 21, 81247, München, Germany
| | - Axel Hausmann
- SNSB, Bavarian State Collection of Zoology, Münchhausenstrasse 21, 81247, München, Germany.,GeoBio-Center der LMU München, München, Germany
| | - Michael Balke
- SNSB, Bavarian State Collection of Zoology, Münchhausenstrasse 21, 81247, München, Germany.,GeoBio-Center der LMU München, München, Germany
| | - Stefan Schmidt
- SNSB, Bavarian State Collection of Zoology, Münchhausenstrasse 21, 81247, München, Germany
| | - Lars Hendrich
- SNSB, Bavarian State Collection of Zoology, Münchhausenstrasse 21, 81247, München, Germany
| | - Dieter Doczkal
- SNSB, Bavarian State Collection of Zoology, Münchhausenstrasse 21, 81247, München, Germany
| | - Berthold Fartmann
- LGC Genomics GmbH, Ostendstraße 25, TGS Haus 8, 12459, Berlin, Germany
| | - Samuel Arvidsson
- LGC Genomics GmbH, Ostendstraße 25, TGS Haus 8, 12459, Berlin, Germany
| | - Gerhard Haszprunar
- SNSB, Bavarian State Collection of Zoology, Münchhausenstrasse 21, 81247, München, Germany.,GeoBio-Center der LMU München, München, Germany
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Naupay AI, Cribillero NG, Lopez-Urbina MT, Gonzalez AE, Gomez-Puerta LA. Finding of pentastomes of genus Reighardia (Pentastomida) in the Belcher's gull (Larus belcheri). Parasitol Int 2016; 65:288-90. [PMID: 26892103 DOI: 10.1016/j.parint.2016.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 02/08/2016] [Accepted: 02/12/2016] [Indexed: 11/18/2022]
Abstract
This report describes the finding of Reighardia sp. (Pentastomida) infecting the air sac of two Belcher's gulls (Larus belcheri) found dead on the beaches of Pucusana, a district in southern Lima, Peru. Three pentastomes were collected from two Belcher's gulls. Then, they were morphologically and molecular analyzed. Molecular characterization of the parasite was achieved by amplifying a fragment of the small subunit ribosomal RNA gene (SSU rRNA). Based on both morphological and molecular data the pentastomes were identified as pentastomes of the genus Reighardia. This is the first report showing that the Belcher's gull is a new natural definitive host for this pentastome.
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Affiliation(s)
- Asucena I Naupay
- School of Biological Science, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Nelly G Cribillero
- School of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Maria T Lopez-Urbina
- School of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Armando E Gonzalez
- School of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Luis A Gomez-Puerta
- School of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Lima, Peru.
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