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Kar M, Jahan SH, Rahman MA, Datta SD. Molecular identification and eco-friendly management of rice brown planthoppers in Bangladesh. Heliyon 2024; 10:e35514. [PMID: 39166075 PMCID: PMC11334857 DOI: 10.1016/j.heliyon.2024.e35514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 07/24/2024] [Accepted: 07/30/2024] [Indexed: 08/22/2024] Open
Abstract
Infestation by various insect pests is the main constraint for growing rice where rice brown planthopper (Nilaparvata lugens Stål) can severely damage rice plants directly through feeding. Therefore, the study aims to detect rice brown planthoppers (BPH) and provide environment-friendly management tactics to mitigate the problem which caused by brown planthoppers. The BPH samples were collected from rice fields of different locations in the Patuakhali of Bangladesh for molecular identification. A molecularly single species of rice brown planthopper, Nilaparavata lugens was identified using mitochondrial cytochrome oxidase subunit I (mtCOI) universal marker. The nucleotide sequences of collected samples were compared with other nucleotide sequences from the GenBank database of NCBI, which make single clades in the phylogenetic tree at an insignificant distance. Moreover, brown planthopper management observations were recorded in laboratory conditions after providing an artificial diet with different treatments of plant-based insecticides Neem oil (1 %, 5 %, and 10 %), Castor oil (1 %, 5 %, and 10 %) where only 20 % sucrose solution was used as negative control and Abamectin (1 %, 5 % and 10 %) were also used as a positive control for comparing the efficacy of plant-based insecticides on rice brown planthoppers. The results showed the highest mortality (100 %) of rice brown planthoppers was recorded by Abamectin 10 %, followed by Abamectin 5 %. Neem 10 % performed better than Abamectin 1 % during 1st hour. Initial after exposure of 2nd hour for Abamectin 1 % revealed greater mortality (59 %) than Neem 10 %. Neem 5 % showed less effect on mortality in brown planthopper than Neem 10 % but was higher than Neem 1 % during 6 h of observation. The Castor oil of 10 % caused higher mortality than the Castor of 5 % but not up to the marks of Abamectin and different concentrations of Neem oil. Castor oil of 1 % and control have shown no mortality of brown planthopper for 6 h of observation.
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Affiliation(s)
- Moumita Kar
- Department of Entomology, Patuakhali Science and Technology University, Dumki, 8602, Patuakhali, Bangladesh
| | - S.M. Hemayet Jahan
- Department of Entomology, Patuakhali Science and Technology University, Dumki, 8602, Patuakhali, Bangladesh
| | - Mohammad Atikur Rahman
- Department of Entomology, Patuakhali Science and Technology University, Dumki, 8602, Patuakhali, Bangladesh
| | - Shuvo Dip Datta
- Department of Building Engineering and Construction Management, Khulna University of Engineering & Technology, Khulna, 9203, Bangladesh
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2
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Canelo T, Marquina D, Chozas S, Bergsten J, Gaytán Á, Pérez-Izquierdo C, Bonal R. Effects of livestock on arthropod biodiversity in Iberian holm oak savannas revealed by metabarcoding. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 365:121619. [PMID: 38963962 DOI: 10.1016/j.jenvman.2024.121619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 06/12/2024] [Accepted: 06/24/2024] [Indexed: 07/06/2024]
Abstract
Increasing food production while avoiding negative impacts on biodiversity constitutes one of the main challenges of our time. Traditional silvopastoral systems like Iberian oak savannas ("dehesas") set an example, where free-range livestock has been reared for centuries while preserving a high natural value. Nevertheless, factors decreasing productivity need to be addressed, one being acorn losses provoked by pest insects. An increased and focalized grazing by livestock on infested acorns would kill the larvae inside and decrease pest numbers, but increased livestock densities could have undesired side effects on ground arthropod communities as a whole. We designed an experimental setup including areas under trees with livestock exclosures of different ages (short-term: 1-year exclusion, long-term: 10-year exclusion), along with controls (continuous grazing), using DNA metabarcoding (mitochondrial markers COI and 16S) to rapidly assess arthropod communities' composition. Livestock removal quickly increased grass cover and arthropod taxonomic richness and diversity, which was already higher in short-term (1-year exclosures) than beneath the canopies of control trees. Interestingly, arthropod diversity was not highest at long-term exclosures (≥10 years), although their community composition was the most distinct. Also, regardless of treatment, we found that functional diversity strongly correlated with the vegetation structure, being higher at trees beneath which there was higher grass cover and taller herbs. Overall, the taxonomic diversity peak at short term exclosures would support the intermediate disturbance hypothesis, which relates it with the higher microhabitat heterogeneity at moderately disturbed areas. Thus, we propose a rotatory livestock management in dehesas: plots with increased grazing should co-exist with temporal short-term exclosures. Ideally, a few long-term excluded areas should be also kept for the singularity of their arthropod communities. This strategy would make possible the combination of biological pest control and arthropod conservation in Iberian dehesas.
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Affiliation(s)
- Tara Canelo
- Dpto. Ingeniería del Medio Agronómico y Forestal. Grupo de Investigación Forestal, INDEHESA, Centro Universitario de Plasencia, Universidad de Extremadura, Avda. Virgen del Puerto 2, 10600, Plasencia, Cáceres, Spain; Centro de Ecologia Aplicada "Prof. Baeta Neves" (CEABN), Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisboa, Portugal.
| | - Daniel Marquina
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden; Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Sergio Chozas
- cE3c - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute. FCUL: Sciences Faculty of the University of Lisbon Campo Grande, Portugal
| | - Johannes Bergsten
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Álvaro Gaytán
- Instituto de Recursos Naturales y Agrobiología de Sevilla, Consejo Superior de Investigaciones Científicas (IRNAS-CSIC), Sevilla, Spain
| | - Carlos Pérez-Izquierdo
- Dpto. Ingeniería del Medio Agronómico y Forestal. Grupo de Investigación Forestal, INDEHESA, Centro Universitario de Plasencia, Universidad de Extremadura, Avda. Virgen del Puerto 2, 10600, Plasencia, Cáceres, Spain
| | - Raúl Bonal
- Dpto. Ingeniería del Medio Agronómico y Forestal. Grupo de Investigación Forestal, INDEHESA, Centro Universitario de Plasencia, Universidad de Extremadura, Avda. Virgen del Puerto 2, 10600, Plasencia, Cáceres, Spain; Department of Biodiversity, Ecology and Evolution. Complutense University of Madrid, Spain
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3
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Girard EB, Didaskalou EA, Pratama AMA, Rattner C, Morard R, Renema W. Quantitative assessment of reef foraminifera community from metabarcoding data. Mol Ecol Resour 2024:e14000. [PMID: 39041197 DOI: 10.1111/1755-0998.14000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 06/20/2024] [Accepted: 07/15/2024] [Indexed: 07/24/2024]
Abstract
Describing living community compositions is essential to monitor ecosystems in a rapidly changing world, but it is challenging to produce fast and accurate depiction of ecosystems due to methodological limitations. Morphological methods provide absolute abundances with limited throughput, whereas metabarcoding provides relative abundances of genes that may not correctly represent living communities from environmental DNA assessed with morphological methods. However, it has the potential to deliver fast descriptions of living communities provided that it is interpreted with validated species-specific calibrations and reference databases. Here, we developed a quantitative approach to retrieve from metabarcoding data the assemblages of living large benthic foraminifera (LBF), photosymbiotic calcifying protists, from Indonesian coral reefs that are under increasing anthropogenic pressure. To depict the diversity, we calculated taxon-specific correction factors to reduce biological biases by comparing surface area, biovolume and calcite volume, and the number of mitochondrial gene copies in seven common LBF species. To validate the approach, we compared calibrated datasets of morphological communities from mock samples with bulk reef sediment; both sample types were metabarcoded. The calibration of the data significantly improved the estimations of genus relative abundance, with a difference of ±5% on average, allowing for comparison of past morphological datasets with future molecular ones. Our results also highlight the application of our quantitative approach to support reef monitoring operations by capturing fine-scale processes, such as seasonal and pollution-driven dynamics, that require high-throughput sampling treatment.
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Affiliation(s)
- Elsa B Girard
- Naturalis Biodiversity Center, Leiden, The Netherlands
- IBED, University of Amsterdam, Amsterdam, The Netherlands
| | | | - Andi M A Pratama
- Marine Science Department, Faculty of Marine Science and Fisheries, Hasanuddin University, Makassar, Indonesia
| | | | | | - Willem Renema
- Naturalis Biodiversity Center, Leiden, The Netherlands
- IBED, University of Amsterdam, Amsterdam, The Netherlands
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4
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Kurata S, Mano S, Nakahama N, Hirota SK, Suyama Y, Ito M. Development of mitochondrial DNA cytochrome c oxidase subunit I primer sets to construct DNA barcoding library using next-generation sequencing. Biodivers Data J 2024; 12:e117014. [PMID: 38933488 PMCID: PMC11199957 DOI: 10.3897/bdj.12.e117014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 05/25/2024] [Indexed: 06/28/2024] Open
Abstract
Insects are one of the most diverse eukaryotic groups on the planet, with one million or more species present, including those yet undescribed. The DNA barcoding system has been developed, which has aided in the identification of cryptic species and undescribed species. The mitochondrial cytochrome c oxidase I region (mtDNA COI) has been utilised for the barcoding analysis of insect taxa. Thereafter, next-generation sequencing (NGS) technology has been developed, allowing for rapid acquisition of massive amounts of sequence data for genetic analyses. Although NGS-based PCR primers designed to amplify the mtDNA COI region have been developed, their target regions were only a part of COI region and/or there were taxonomic bias for PCR amplification. As the mtDNA COI region is a traditional DNA marker for the DNA barcoding system, modified primers for this region would greatly contribute to taxonomic studies. In this study, we redesigned previously developed PCR primer sets that targetted the mtDNA COI barcoding region to improve amplification efficiency and to enable us to conduct sequencing analysis on NGS. As a result, the redesigned primer sets achieved a high success rate (> 85%) for species examined in this study, covering four insect orders (Coleoptera, Lepidoptera, Orthoptera and Odonata). Thus, by combining the primers with developed primer sets for 12S or 16S rRNA regions, we can conduct more detailed taxonomic, phylogeographic and conservation genetic studies using NGS.
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Affiliation(s)
- Seikan Kurata
- Tomakomai Experimental Forest, Hokkaido University, Tomakomai, JapanTomakomai Experimental Forest, Hokkaido UniversityTomakomaiJapan
| | - Shota Mano
- Faculty of Bioresource Sciences, Akita Prefectural University, Akita, JapanFaculty of Bioresource Sciences, Akita Prefectural UniversityAkitaJapan
| | - Naoyuki Nakahama
- Institute of Natural and Environmental Sciences, University of Hyogo, hyogo, JapanInstitute of Natural and Environmental Sciences, University of HyogohyogoJapan
| | - Shun K Hirota
- Botanical Gardens, Osaka Metropolitan University, Osaka, JapanBotanical Gardens, Osaka Metropolitan UniversityOsakaJapan
| | - Yoshihisa Suyama
- Graduate School of Agricultural Science, Tohoku University, Miyagi, JapanGraduate School of Agricultural Science, Tohoku UniversityMiyagiJapan
| | - Motomi Ito
- Komaba museum, University of Tokyo, Tokyo, JapanKomaba museum, University of TokyoTokyoJapan
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5
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Giusti A, Spatola G, Mancini S, Nuvoloni R, Armani A. Novel foods, old issues: Metabarcoding revealed mislabeling in insect-based products sold by e-commerce on the EU market. Food Res Int 2024; 184:114268. [PMID: 38609245 DOI: 10.1016/j.foodres.2024.114268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/14/2024]
Abstract
Insects intended for human consumption are considered Novel Foods according to EU legislation. marketed in form of powders, bars, snacks are increasingly available on the EU market, especially on e-commerce. The commercial form and the way of distribution make IBPs particularly prone to mislabeling. Literature concerning the mislabeling occurrence in IBPs is extremely scarce. In this study, 46 processed IBPs were collected on nine EU e-commerce platforms (e-CO) to be authenticated by metabarcoding. A 200 bp region from 16S rRNA gene was used as molecular target. Sequencing data were processed using DADA2 R package, and sequences were taxonomically assigned through BLAST analysis against GenBank. Procedural blanks and positive controls were included in the analysis, and threshold values were established to filter the final data. The mislabeling rate (i. e. the mismatch between the species declared on the IBP label and the species identified by metabarcoding) was calculated. Overall, a high mislabeling rate (33.3 %) was observed, although this percentage is influenced by the e-CO platform and the insect species, with A. domesticus particularly involved. The use of species not listed in authorized Novel Food (e. g. Gryllus locorojo), and/or the partial replacement of high value species with lower value species was highlighted for the first time in processed IBPs. The presence of insect pests was also detected. Metabarcoding was confirmed as an effective tool for IBPs authentication. Also, outcomes from this study can provide useful data on the main issues involving the EU IBPs' market, that can represent an incentive to reinforce both official controls and FBO's self-controls on these poorly investigated products.
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Affiliation(s)
- Alice Giusti
- Department of Veterinary Sciences, University of Pisa, 56124 Pisa, Italy
| | - Gabriele Spatola
- Department of Veterinary Sciences, University of Pisa, 56124 Pisa, Italy
| | - Simone Mancini
- Department of Veterinary Sciences, University of Pisa, 56124 Pisa, Italy
| | - Roberta Nuvoloni
- Department of Veterinary Sciences, University of Pisa, 56124 Pisa, Italy
| | - Andrea Armani
- Department of Veterinary Sciences, University of Pisa, 56124 Pisa, Italy.
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Ficetola GF, Guerrieri A, Cantera I, Bonin A. In silico assessment of 18S rDNA metabarcoding markers for the characterization of nematode communities. PLoS One 2024; 19:e0298905. [PMID: 38578734 PMCID: PMC10997105 DOI: 10.1371/journal.pone.0298905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 01/31/2024] [Indexed: 04/07/2024] Open
Abstract
Nematodes are keystone actors of soil, freshwater and marine ecosystems, but the complexity of morphological identification has limited broad-scale monitoring of nematode biodiversity. DNA metabarcoding is increasingly used to assess nematode diversity but requires universal primers with high taxonomic coverage and high taxonomic resolution. Several primers have been proposed for the metabarcoding of nematode diversity, many of which target the 18S rRNA gene. In silico analyses have a great potential to assess key parameters of primers, including taxonomic coverage, resolution and specificity. Based on a recently-available reference database, we tested in silico the performance of fourteen commonly used and one newly optimized primer for nematode metabarcoding. Most primers showed very good coverage, amplifying most of the sequences in the reference database, while four markers showed limited coverage. All primers showed good taxonomic resolution. Resolution was particularly good if the aim was the identification of higher-level taxa, such as genera or families. Overall, species-level resolution was higher for primers amplifying long fragments. None of the primers was highly specific for nematodes as, despite some variation, they all amplified a large number of other eukaryotes. Differences in performance across primers highlight the complexity of the choice of markers appropriate for the metabarcoding of nematodes, which depends on a trade-off between taxonomic resolution and the length of amplified fragments. Our in silico analyses provide new insights for the identification of the most appropriate primers, depending on the study goals and the origin of DNA samples. This represents an essential step to design and optimize metabarcoding studies assessing nematode diversity.
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Affiliation(s)
- Gentile Francesco Ficetola
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
- LECA, Laboratoire d’Ecologie Alpine, Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, Grenoble, France
| | | | - Isabel Cantera
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
| | - Aurelie Bonin
- Argaly, Bâtiment Cleanspace, Sainte-Hélène-du-Lac, France
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7
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Rodrigues Jardim B, Gambley C, Tran-Nguyen LTT, Webster C, Kehoe M, Kinoti WM, Bond S, Davis R, Jones L, Pathania N, Sharman M, Chapman T, Rodoni BC, Constable FE. A metagenomic investigation of phytoplasma diversity in Australian vegetable growing regions. Microb Genom 2024; 10:001213. [PMID: 38446015 PMCID: PMC10999746 DOI: 10.1099/mgen.0.001213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 02/21/2024] [Indexed: 03/07/2024] Open
Abstract
In this study, metagenomic sequence data was used to investigate the phytoplasma taxonomic diversity in vegetable-growing regions across Australia. Metagenomic sequencing was performed on 195 phytoplasma-positive samples, originating either from historic collections (n=46) or during collection efforts between January 2015 and June 2022 (n=149). The sampled hosts were classified as crop (n=155), weed (n=24), ornamental (n=7), native plant (n=6), and insect (n=3) species. Most samples came from Queensland (n=78), followed by Western Australia (n=46), the Northern Territory (n=32), New South Wales (n=17), and Victoria (n=10). Of the 195 draft phytoplasma genomes, 178 met our genome criteria for comparison using an average nucleotide identity approach. Ten distinct phytoplasma species were identified and could be classified within the 16SrII, 16SrXII (PCR only), 16SrXXV, and 16SrXXXVIII phytoplasma groups, which have all previously been recorded in Australia. The most commonly detected phytoplasma taxa in this study were species and subspecies classified within the 16SrII group (n=153), followed by strains within the 16SrXXXVIII group ('Ca. Phytoplasma stylosanthis'; n=6). Several geographic- and host-range expansions were reported, as well as mixed phytoplasma infections of 16SrII taxa and 'Ca. Phytoplasma stylosanthis'. Additionally, six previously unrecorded 16SrII taxa were identified, including five putative subspecies of 'Ca. Phytoplasma australasiaticum' and a new putative 16SrII species. PCR and sequencing of the 16S rRNA gene was a suitable triage tool for preliminary phytoplasma detection. Metagenomic sequencing, however, allowed for higher-resolution identification of the phytoplasmas, including mixed infections, than was afforded by only direct Sanger sequencing of the 16S rRNA gene. Since the metagenomic approach theoretically obtains sequences of all organisms in a sample, this approach was useful to confirm the host family, genus, and/or species. In addition to improving our understanding of the phytoplasma species that affect crop production in Australia, the study also significantly expands the genomic sequence data available in public sequence repositories to contribute to phytoplasma molecular epidemiology studies, revision of taxonomy, and improved diagnostics.
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Affiliation(s)
- Bianca Rodrigues Jardim
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
- Agriculture Victoria Research, Department of Energy, Environment and Climate Action, AgriBio, Bundoora, Victoria, Australia
| | - Cherie Gambley
- Horticulture and Forestry Science, Department of Agriculture and Fisheries Maroochy Research Facility, Nambour, Queensland, Australia
| | | | - Craig Webster
- Diagnostic Laboratory Services, Department of Primary Industries and Regional Development, South Perth, Western Australia, Australia
| | - Monica Kehoe
- Diagnostic Laboratory Services, Department of Primary Industries and Regional Development, South Perth, Western Australia, Australia
| | - Wycliff M. Kinoti
- Agriculture Victoria Research, Department of Energy, Environment and Climate Action, AgriBio, Bundoora, Victoria, Australia
| | - Samantha Bond
- Biosecurity and Animal Welfare, Department of Industry, Tourism and Trade, Darwin, Northern Territory, Australia
| | - Richard Davis
- Northern Australia Quarantine Strategy, Department of Agriculture, Fisheries and Forestry, Canberra, Australian Capital Territory, 2601, Australia
| | - Lynne Jones
- Northern Australia Quarantine Strategy, Department of Agriculture, Fisheries and Forestry, Canberra, Australian Capital Territory, 2601, Australia
| | - Nandita Pathania
- Department of Agriculture and Fisheries, Mareeba, Queensland, Australia
| | - Murray Sharman
- Department of Agriculture and Fisheries, Ecosciences Precinct, Dutton Park, Queensland 4102, Australia
| | - Toni Chapman
- Biosecurity and Food Safety, New South Wales Department of Primary Industries, Elizabeth Macarthur Agricultural Institute (EMAI), Menangle, New South Wales, 2567, Australia
| | - Brendan C. Rodoni
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
- Agriculture Victoria Research, Department of Energy, Environment and Climate Action, AgriBio, Bundoora, Victoria, Australia
| | - Fiona E. Constable
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
- Agriculture Victoria Research, Department of Energy, Environment and Climate Action, AgriBio, Bundoora, Victoria, Australia
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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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Suzuki SS, Baba YG, Toju H. Dynamics of species-rich predator-prey networks and seasonal alternations of core species. Nat Ecol Evol 2023; 7:1432-1443. [PMID: 37460838 DOI: 10.1038/s41559-023-02130-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 06/16/2023] [Indexed: 09/08/2023]
Abstract
In nature, entangled webs of predator-prey interactions constitute the backbones of ecosystems. Uncovering the network architecture of such trophic interactions has been recognized as the essential step for exploring species with great impacts on ecosystem-level phenomena and functions. However, it has remained a major challenge to reveal how species-rich networks of predator-prey interactions are continually reshaped through time in the wild. Here, we show that dynamics of species-rich predator-prey interactions can be characterized by remarkable network structural changes and alternations of species with greatest impacts on community processes. On the basis of high-throughput detection of prey DNA from 1,556 spider individuals collected in a grassland ecosystem, we reconstructed dynamics of interaction networks involving, in total, 50 spider species and 974 prey species and strains through 8 months. The networks were compartmentalized into modules (groups) of closely interacting predators and prey in each month. Those modules differed in detritus/grazing food chain properties, forming complex fission-fusion dynamics of belowground and aboveground energy channels across the seasons. The substantial shifts of network structure entailed alternations of spider species located at the core positions within the entangled webs of interactions. These results indicate that knowledge of dynamically shifting food webs is crucial for understanding temporally varying roles of 'core species' in ecosystem processes.
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Affiliation(s)
- Sayaka S Suzuki
- Center for Ecological Research, Kyoto University, Otsu, Japan.
| | - Yuki G Baba
- Institute for Agro-Environmental Sciences, NARO, Tsukuba, Japan
| | - Hirokazu Toju
- Center for Ecological Research, Kyoto University, Otsu, Japan.
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10
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Murphy R, Strube ML. RibDif2: expanding amplicon analysis to full genomes. BIOINFORMATICS ADVANCES 2023; 3:vbad111. [PMID: 37655178 PMCID: PMC10466081 DOI: 10.1093/bioadv/vbad111] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/10/2023] [Accepted: 08/18/2023] [Indexed: 09/02/2023]
Abstract
Motivation As previously described, amplicon analysis of the bacterial 16S gene has several limitations owing to fundamental characteristics of both the 16S gene and technological restrictions. Previously, RibDif was introduced to help quantify these limitations by detailed analysis of a given genera and the 16S gene profile of its members, notably multiplicity and divergence of 16S alleles within genomes as well as shared alleles between species. Apart from using amplicon analysis for only the 16S gene, amplicons derived from genus-specific genes or even functional genes are increasingly being utilized. Moreover, long-read technologies are progressively being used to sequence longer amplicons, and since these inherently contain more information, they may likely alleviate the issues proposed in RibDif. Results Taking these phenomena into account, we here propose RibDif2. RibDif2 retains the 16S-optimized functionality of the original RibDif but can now run any set of primers on any part of the genome in any set of organisms, be it prokaryote, eukaryote, or archaea. We demonstrate this new functionality by showing full species resolution of Pseudoalteromonas using complete rRNA-operon amplicons, as well as selection of optimally discriminatory primers for Staphylococcus and Pseudomonas. Moreover, we show a potential bias toward terrestrial bacteria relative to marine ones for primers amplifying biosynthetic gene clusters and lastly suggest optimal primers to differentiate the members of the insect genus Drosophila. We believe that RibDif2 will facilitate the work of all scientists using amplicon sequencing, especially in the era of long-read sequencing. Availability and implementation Ribdif2 is freely available at https://github.com/Rob-murphys/ribdif.
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Affiliation(s)
- Robert Murphy
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby 2800, Denmark
| | - Mikael Lenz Strube
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby 2800, Denmark
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11
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Terra MT, Macklin KS, Burleson M, Jeon A, Beckmann JF, Hauck R. Mapping the poultry insectome in and around broiler breeder pullet farms identifies new potential Dipteran vectors of Histomonas meleagridis. Parasit Vectors 2023; 16:244. [PMID: 37475041 PMCID: PMC10360274 DOI: 10.1186/s13071-023-05833-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 06/09/2023] [Indexed: 07/22/2023] Open
Abstract
BACKGROUND Histomonas meleagridis can infect chickens and turkeys. It uses the eggs of the cecal worm Heterakis gallinarum as a vector and reservoir. Litter beetles (Alphitobius diaperinus) and other arthropod species have been implicated as potential vectors, but little information about other arthropod species as potential vectors is known. METHODS Four broiler breeder pullet farms were sampled every 4 months. On each farm, three types of traps were set inside and outside two houses. Trapped arthropod specimens were morphologically identified at order level and grouped into families/types when possible. Selected specimens from abundant types found both inside and outside barns were screened for H. meleagridis and H. gallinarum by qPCR. RESULTS A total of 4743 arthropod specimens were trapped. The three most frequently encountered orders were Diptera (38%), Coleoptera (17%), and Hymenoptera (7%). Three hundred seventeen discrete types were differentiated. More arthropods were trapped outside than inside. Alpha diversity was greater outside than inside but not significantly influenced by season. The composition of the arthropod populations, including the insectome, varied significantly between trap location and seasons. Up to 50% of litter beetles tested positive for H. meleagridis DNA 4 months after an observed histomonosis outbreak. Sporadically litter beetles were positive for H. gallinarum DNA. Thirteen further arthropod types were tested, and specimens of four Dipteran families tested positive for either one or both parasites. CONCLUSIONS This study describes the insectome in and around broiler breeder pullet farms and identifies new potential vectors of H. meleagridis through qPCR. The results show a limited but present potential of arthropods, especially flies, to transmit histomonosis between farms.
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Affiliation(s)
| | - Kenneth S Macklin
- Department of Poultry Science, Mississippi State University, Mississippi State, MS, US
| | | | - Alan Jeon
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, US
| | - John F Beckmann
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, US.
| | - Ruediger Hauck
- Department of Poultry Science, Auburn University, Auburn, AL, US.
- Department of Pathobiology, Auburn University, Auburn, AL, US.
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12
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Tsz Long Wong D, Norman H, Creedy TJ, Jordaens K, Moran KM, Young A, Mengual X, Skevington JH, Vogler AP. The phylogeny and evolutionary ecology of hoverflies (Diptera: Syrphidae) inferred from mitochondrial genomes. Mol Phylogenet Evol 2023; 184:107759. [PMID: 36921697 DOI: 10.1016/j.ympev.2023.107759] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 03/01/2023] [Accepted: 03/08/2023] [Indexed: 03/16/2023]
Abstract
Hoverflies (Diptera: Syrphidae) are a diverse group of pollinators and a major research focus in ecology, but their phylogenetic relationships remain incompletely known. Using a genome skimming approach we generated mitochondrial genomes for 91 species, capturing a wide taxonomic diversity of the family. To reduce the required amount of input DNA and overall cost of the library construction, sequencing and assembly was conducted on mixtures of specimens, which raises the problem of chimera formation of mitogenomes. We present a novel chimera detection test based on gene tree incongruence, but identified only a single mitogenome of chimeric origin. Together with existing data for a final set of 127 taxa, phylogenetic analysis on nucleotide and amino acid sequences using Maximum Likelihood and Bayesian Inference revealed a basal split of Microdontinae from all other syrphids. The remainder consists of several deep clades assigned to the subfamily Eristalinae in the current classification, including a clade comprising the subfamily Syrphinae (plus Pipizinae). These findings call for a re-definition of subfamilies, but basal nodes had insufficient support to allow such action. Molecular-clock dating placed the origin of the Syrphidae crown group in the mid-Cretaceous while the Eristalinae-Syrphinae clade likely originated near the K/Pg boundary. Transformation of larval life history characters on the tree suggests that Syrphidae initially had sap feeding larvae, which diversified greatly in diet and habitat association during the Eocene and Oligocene, coinciding with the diversification of angiosperms and the evolution of various insect groups used as larval host, prey, or mimicry models. Mitogenomes proved to be a powerful phylogenetic marker for studies of Syrphidae at subfamily and tribe levels, allowing dense taxon sampling that provided insight into the great ecological diversity and rapid evolution of larval life history traits of the hoverflies.
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Affiliation(s)
- Daniel Tsz Long Wong
- Department of Life Sciences, Imperial College London, Exhibition Road, London, SW7 2BX, U.K; Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, U.K.
| | - Hannah Norman
- Department of Life Sciences, Imperial College London, Exhibition Road, London, SW7 2BX, U.K; Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, U.K.
| | - Thomas J Creedy
- Department of Life Sciences, Imperial College London, Exhibition Road, London, SW7 2BX, U.K; Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, U.K.
| | - Kurt Jordaens
- Department of Biology-Invertebrates Unit, Royal Museum for Central Africa, Joint Experimental Molecular Unit Leuvensesteenweg 13, B-3080 Tervuren, Belgium.
| | - Kevin M Moran
- Canadian National Collection of Insects, Arachnids and Nematodes, Agriculture and Agri-Food Canada, K.W. Neatby Building, 960 Carling Avenue, Ottawa, Ontario, ON K1A 0C6, Canada; Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, ON K1S 5B6, Canada.
| | - Andrew Young
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, ON N1G 2W1, Canada.
| | - Ximo Mengual
- Zoologisches Forschungsmuseum Alexander Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Adenauerallee 127, 53113 Bonn, Germany.
| | - Jeffrey H Skevington
- Canadian National Collection of Insects, Arachnids and Nematodes, Agriculture and Agri-Food Canada, K.W. Neatby Building, 960 Carling Avenue, Ottawa, Ontario, ON K1A 0C6, Canada; Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, ON K1S 5B6, Canada.
| | - Alfried P Vogler
- Department of Life Sciences, Imperial College London, Exhibition Road, London, SW7 2BX, U.K; Department of Life Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, U.K.
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13
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Development of a DNA Metabarcoding Method for the Identification of Insects in Food. Foods 2023; 12:foods12051086. [PMID: 36900603 PMCID: PMC10001320 DOI: 10.3390/foods12051086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/20/2023] [Accepted: 03/01/2023] [Indexed: 03/08/2023] Open
Abstract
Insects have the potential to become an efficient and reliable food source for humans in the future and could contribute to solving problems with the current food chain. Analytical methods to verify the authenticity of foods are essential for consumer acceptance. We present a DNA metabarcoding method that enables the identification and differentiation of insects in food. The method, developed on Illumina platforms, is targeting a 200 bp mitochondrial 16S rDNA fragment, which we found to be suitable for distinguishing more than 1000 insect species. We designed a novel universal primer pair for a singleplex PCR assay. Individual DNA extracts from reference samples, DNA extracts from model foods and food products commercially available were investigated. In all of the samples investigated, the insect species were correctly identified. The developed DNA metabarcoding method has a high potential to identify and differentiate insect DNA in the context of food authentication in routine analysis.
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14
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Rongier G, Sagne A, Etienne S, Petitclerc F, Jaouen G, Murienne J, Orivel J. Ants of French Guiana: 16S rRNA sequence dataset. Biodivers Data J 2023; 11:e91577. [PMID: 38327367 PMCID: PMC10848834 DOI: 10.3897/bdj.11.e91577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 11/30/2022] [Indexed: 02/10/2023] Open
Abstract
This dataset represents a reference library of DNA sequences for ants from French Guiana. A total of 3931 new sequences from the 16S rRNA gene has been generated. The reference library covers 344 species distributed in 57 genera. Overall, 3920 sequences have been assigned at the species level and 11 at the genus level. All these sequences were submitted to DDBJ/EMBL/GenBank databases in the Bioproject: PRJNA779056: 16S French Guiana Ants (Hymenoptera: Formicidae), sequence identifier KFFS00000000.
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Affiliation(s)
- Gaëtan Rongier
- UMR Écologie des Forêts de Guyane (AgroParisTech, CIRAD, CNRS, INRAE, Université de Guyane, Université des Antilles), Kourou, French GuianaUMR Écologie des Forêts de Guyane (AgroParisTech, CIRAD, CNRS, INRAE, Université de Guyane, Université des Antilles)KourouFrench Guiana
| | - Audrey Sagne
- UMR Écologie des Forêts de Guyane (AgroParisTech, CIRAD, CNRS, INRAE, Université de Guyane, Université des Antilles), Kourou, French GuianaUMR Écologie des Forêts de Guyane (AgroParisTech, CIRAD, CNRS, INRAE, Université de Guyane, Université des Antilles)KourouFrench Guiana
| | - Sandrine Etienne
- UMR Écologie des Forêts de Guyane (AgroParisTech, CIRAD, CNRS, INRAE, Université de Guyane, Université des Antilles), Kourou, French GuianaUMR Écologie des Forêts de Guyane (AgroParisTech, CIRAD, CNRS, INRAE, Université de Guyane, Université des Antilles)KourouFrench Guiana
| | - Frederic Petitclerc
- UMR Écologie des Forêts de Guyane (AgroParisTech, CIRAD, CNRS, INRAE, Université de Guyane, Université des Antilles), Kourou, French GuianaUMR Écologie des Forêts de Guyane (AgroParisTech, CIRAD, CNRS, INRAE, Université de Guyane, Université des Antilles)KourouFrench Guiana
| | - Gaelle Jaouen
- UMR Écologie des Forêts de Guyane (AgroParisTech, CIRAD, CNRS, INRAE, Université de Guyane, Université des Antilles), Kourou, French GuianaUMR Écologie des Forêts de Guyane (AgroParisTech, CIRAD, CNRS, INRAE, Université de Guyane, Université des Antilles)KourouFrench Guiana
| | - Jerome Murienne
- Laboratoire Evolution et Diversité Biologique (EDB UMR5174) CNRS, Université Paul Sabatier Toulouse 3, IRD, Toulouse, FranceLaboratoire Evolution et Diversité Biologique (EDB UMR5174) CNRS, Université Paul Sabatier Toulouse 3, IRDToulouseFrance
| | - Jerome Orivel
- UMR Écologie des Forêts de Guyane (AgroParisTech, CIRAD, CNRS, INRAE, Université de Guyane, Université des Antilles), Kourou, French GuianaUMR Écologie des Forêts de Guyane (AgroParisTech, CIRAD, CNRS, INRAE, Université de Guyane, Université des Antilles)KourouFrench Guiana
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15
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Martoni F, Smith RL, Piper AM, Nancarrow N, Aftab M, Trebicki P, Kimber RBE, Rodoni BC, Blacket MJ. Non-destructive insect metabarcoding as a surveillance tool for the Australian grains industry: a first trial for the iMapPESTS smart trap. METABARCODING AND METAGENOMICS 2023. [DOI: 10.3897/mbmg.7.95650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Surveillance and long-term monitoring of insect pest populations are of paramount importance to limit dispersal and inform pest management. Molecular methods have been employed in diagnostics, surveillance and monitoring for the past few decades, often paired with more traditional techniques relying on morphological examinations. Within this context, the ‘iMapPESTS: Sentinel Surveillance for Agriculture’ project was conceptualised to enhance on-farm pest management decision-making via development and deployment of smart traps, able to collect insects, as well as recording associated environmental data. Here, we compared an iMapPESTS ‘Sentinel’ smart trap to an alternative suction trap over a 10-week period. We used a non-destructive insect metabarcoding approach complemented by insect morphological diagnostics to assess and compare aphid species presence and diversity across trap samples and time. Furthermore, we paired this with environmental data recorded throughout the sampling period. This methodology recorded a total of 497 different taxa from 70 traps over a 10-week period in the grain-growing region in western Victoria. This included not only the 14 aphid target species, but an additional 12 aphid species, including a new record for Victoria. Ultimately, with more than 450 bycatch species detected, this highlighted the value of insect metabarcoding, not only for pest surveillance, but also at a broader ecosystem level, with potential applications in integrated pest management and biocontrol.
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16
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Pathiraja D, Cho J, Kim J, Choi IG. Metabarcoding of eDNA for tracking the floral and geographical origins of bee honey. Food Res Int 2023; 164:112413. [PMID: 36737994 DOI: 10.1016/j.foodres.2022.112413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 12/11/2022] [Accepted: 12/25/2022] [Indexed: 12/31/2022]
Abstract
Authentic honey products have a high commercial value and are often falsified via adulteration. Metabarcoding of environmental DNA (eDNA) from bacterial, floral, and entomological sources has recently been proposed as a useful tool for identifying and authenticating floral and geographical origins of bee honey. In this study, eDNA metabarcoding was applied to reveal the bacterial, plant, and honey bee DNA signatures of 48 commercial honey products from six different geographical origins. Bacterial DNA composition in commercial honey showed different relative abundance of Paenibacillus and Bacillus in geographically different samples, and high abundance of Methylobacterium in chestnut honey implying potential use of bacterial DNA composition for honey authentication. Using the chloroplast trnL (UAA) as a DNA marker, floral origins of commercial honey were investigated. Based on floral DNA signatures, 12 monofloral honey samples were identified among the 45 samples tested. Targeted amplicon sequencing of cytochrome oxidase I (COI) gene from entomological DNA identified three different Apis mellifera sequence variants, specific to geographic origin of honey, suggesting that COI can be implemented as a DNA marker to trace the origin of honey. Therefore, the current study demonstrated the potential of eDNA based metabarcoding as a robust tool for evaluating commercial bee honey by exploring their floral and geographical origins.
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Affiliation(s)
- Duleepa Pathiraja
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Junghwan Cho
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Junsung Kim
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - In-Geol Choi
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea.
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17
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Rahman MM, Nam H, Choi N, Kim J. Development of Molecular-Based Species Identification and Optimization of Reaction Conditions for Molecular Diagnosis of Three Major Asian Planthoppers (Hemiptera: Delphacidae). INSECTS 2023; 14:124. [PMID: 36835693 PMCID: PMC9962309 DOI: 10.3390/insects14020124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/21/2023] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Asian planthoppers (Hemiptera: Delphacidae) that include brown planthoppers (BPH, Nilaparvata lugens, Stål), white-backed planthoppers (WBPH, Sogatella furcifera, Horváth), and small brown planthoppers (SBPH, Laodelphax striatellus, Fallén) are the primary sucking-type pests of rice. These three insects share morphological and sequence similarities. As insecticide resistance patterns and control strategies vary according to species, the accurate discrimination of these species is important. Here, we developed six species-specific primers based on partial mitochondrial genome sequences. The primers were successfully used in multiplex PCR, loop-mediated isothermal amplification (LAMP) assays, and conventional PCR. Here, we used genomic DNA obtained using the DNA-releasing technique (tissue samples were incubated at 95 °C for 5 min with 30 μL nuclease-free water, and the supernatant was used). We showed that multiplex PCR could analyze the density of each species following a mass collection in the field; the LAMP assay can diagnose the species within 40 min; conventional PCR can be widely applied to a large number of field samples, as well as individuals or mass collections. In conclusion, these results demonstrate the potential of the species-specific primers and DNA-releasing technique for accurate multiplex PCR and LAMP assays, which may assist the intensive field monitoring of integrated management of these species.
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Affiliation(s)
- Md-Mafizur Rahman
- Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon 24341, Republic of Korea
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Science, Islamic University, Kushtia 7003, Bangladesh
| | - Hwayeun Nam
- Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon 24341, Republic of Korea
- Incheon International Airport Regional Office, Animal and Plant Quarantine Agency, Incheon 22382, Republic of Korea
| | - Nakjung Choi
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Juil Kim
- Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon 24341, Republic of Korea
- Program of Applied Biology, Division of Bio-Resource Sciences, College of Agriculture and Life Science, Kangwon National University, Chuncheon 24341, Republic of Korea
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18
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Metabarcoding Approaches for Soil Eukaryotes, Protists, and Microfauna. Methods Mol Biol 2022; 2605:1-16. [PMID: 36520386 DOI: 10.1007/978-1-0716-2871-3_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
There have been major developments in the molecular characterization of soil protist and micrometazoan diversity, leading to a better understanding of these minute soil eukaryotes. Like in all newly developing research fields, several approaches are currently used in parallel to study these organisms. Here, we synthesize these various approaches and propose a best practice manual that should help researchers to efficiently target soil eukaryotic diversity as a whole. We cover the whole working pipeline, ranging from sampling to nucleic acids extraction to bioinformatic processing and sequence identification. Synchronous approaches to molecularly survey microbial-sized eukaryotes and other soil biodiversity groups are needed in order to provide a cumulative knowledge of soil biodiversity, as here shown for the soil eukaryome. This will be crucial in understanding the important ecosystem functions provided by soil biodiversity.
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19
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Comparative environmental RNA and DNA metabarcoding analysis of river algae and arthropods for ecological surveys and water quality assessment. Sci Rep 2022; 12:19828. [PMID: 36400924 PMCID: PMC9674700 DOI: 10.1038/s41598-022-23888-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 11/07/2022] [Indexed: 11/19/2022] Open
Abstract
Environmental DNA (eDNA) metabarcoding is widely used for species analysis, while the use of environmental RNA (eRNA) metabarcoding is more limited. We conducted comparative eDNA/eRNA metabarcoding of the algae and arthropods (aquatic insects) in water samples from Naka River, Japan, to evaluate their potential for biological monitoring and water quality assessment. Both methods detected various algae and arthropod species; however, their compositions were remarkably different from those in traditional field surveys (TFSs), indicating low sensitivity. For algae, the species composition derived from eDNA and eRNA metabarcoding was equivalent. While TFSs focus on attached algae, metabarcoding analysis theoretically detects both planktonic and attached algae. A recently expanded genomic database for aquatic insects significantly contributed to the sensitivity and positive predictivity for arthropods. While the sensitivity of eRNA was lower than that of eDNA, the positive predictivity of eRNA was higher. The eRNA of terrestrial arthropods indicated extremely high or low read numbers when compared with eDNA, suggesting that eRNA could be an effective indicator of false positives. Arthropod and algae eDNA/eRNA metabarcoding analysis enabled water quality estimates from TFSs. The eRNA of algae and arthropods could thus be used to evaluate biodiversity and water quality and provide insights from ecological surveys.
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20
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Kirse A, Bourlat SJ, Langen K, Zapke B, Zizka VMA. Comparison of destructive and non-destructive DNA extraction methods for the metabarcoding of arthropod bulk samples. Mol Ecol Resour 2022; 23:92-105. [PMID: 35932285 DOI: 10.1111/1755-0998.13694] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 07/07/2022] [Accepted: 07/25/2022] [Indexed: 11/28/2022]
Abstract
DNA metabarcoding is routinely used for biodiversity assessment, especially targeting highly diverse groups for which limited taxonomic expertise is available. Various protocols are currently in use, although standardization is key to its application in large-scale monitoring. DNA metabarcoding of arthropod bulk samples can be either conducted destructively from sample tissue, or non-destructively from sample fixative or lysis buffer. Non-destructive methods are highly desirable for the preservation of sample integrity but have yet to be experimentally evaluated in detail. Here, we compare diversity estimates from 14 size sorted Malaise trap samples processed consecutively with three non-destructive approaches (one using fixative ethanol and two using lysis buffers) and one destructive approach (using homogenized tissue). Extraction from commercial lysis buffer yielded comparable species richness and high overlap in species composition to the ground tissue extracts. A significantly divergent community was detected from preservative ethanol-based DNA extraction. No consistent trend in species richness was found with increasing incubation time in lysis buffer. These results indicate that non-destructive DNA extraction from incubation in lysis buffer could provide a comparable alternative to destructive approaches with the added advantage of preserving the specimens for post-metabarcoding taxonomic work but at a higher cost per sample.
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Affiliation(s)
- Ameli Kirse
- LIB/Zoological Research Museum Alexander Koenig (ZFMK), Centre for Biodiversity Monitoring, Bonn, Germany
| | - Sarah J Bourlat
- LIB/Zoological Research Museum Alexander Koenig (ZFMK), Centre for Biodiversity Monitoring, Bonn, Germany
| | - Kathrin Langen
- LIB/Zoological Research Museum Alexander Koenig (ZFMK), Centre for Biodiversity Monitoring, Bonn, Germany
| | - Björn Zapke
- LIB/Zoological Research Museum Alexander Koenig (ZFMK), Centre for Biodiversity Monitoring, Bonn, Germany
| | - Vera M A Zizka
- LIB/Zoological Research Museum Alexander Koenig (ZFMK), Centre for Biodiversity Monitoring, Bonn, Germany
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21
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van Klink R, August T, Bas Y, Bodesheim P, Bonn A, Fossøy F, Høye TT, Jongejans E, Menz MHM, Miraldo A, Roslin T, Roy HE, Ruczyński I, Schigel D, Schäffler L, Sheard JK, Svenningsen C, Tschan GF, Wäldchen J, Zizka VMA, Åström J, Bowler DE. Emerging technologies revolutionise insect ecology and monitoring. Trends Ecol Evol 2022; 37:872-885. [PMID: 35811172 DOI: 10.1016/j.tree.2022.06.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/26/2022] [Accepted: 06/07/2022] [Indexed: 12/30/2022]
Abstract
Insects are the most diverse group of animals on Earth, but their small size and high diversity have always made them challenging to study. Recent technological advances have the potential to revolutionise insect ecology and monitoring. We describe the state of the art of four technologies (computer vision, acoustic monitoring, radar, and molecular methods), and assess their advantages, current limitations, and future potential. We discuss how these technologies can adhere to modern standards of data curation and transparency, their implications for citizen science, and their potential for integration among different monitoring programmes and technologies. We argue that they provide unprecedented possibilities for insect ecology and monitoring, but it will be important to foster international standards via collaboration.
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Affiliation(s)
- Roel van Klink
- German Centre for Integrative Biodiversity Research (iDiv) Halle Jena Leipzig, Puschstrasse 4, 04103, Leipzig, Germany; Martin Luther University-Halle Wittenberg, Department of Computer Science, 06099, Halle (Saale), Germany.
| | - Tom August
- UK Centre for Ecology & Hydrology, Benson Lane, Wallingford, OX10 8BB, UK
| | - Yves Bas
- Centre d'Écologie et des Sciences de la Conservation, Muséum National d'Histoire Naturelle, Paris, France; CEFE, Université Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Paul Bodesheim
- Friedrich Schiller University Jena, Computer Vision Group, Ernst-Abbe-Platz 2, 07743, Jena, Germany
| | - Aletta Bonn
- German Centre for Integrative Biodiversity Research (iDiv) Halle Jena Leipzig, Puschstrasse 4, 04103, Leipzig, Germany; Helmholtz - Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318, Leipzig, Germany; Friedrich Schiller University Jena, Institute of Biodiversity, Dornburger Strasse 159, 07743, Jena, Germany
| | - Frode Fossøy
- Norwegian Institute for Nature Research, P.O. Box 5685 Torgarden, 7485, Trondheim, Norway
| | - Toke T Høye
- Aarhus University, Department of Ecoscience and Arctic Research Centre, C.F. Møllers Allé 8, 8000, Aarhus, Denmark
| | - Eelke Jongejans
- Radboud University, Animal Ecology and Physiology, Heyendaalseweg 135, 6525, AJ, Nijmegen, The Netherlands; Netherlands Institute of Ecology, Animal Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Myles H M Menz
- Max Planck Institute for Animal Behaviour, Department of Migration, Am Obstberg 1, 78315, Radolfzell, Germany; College of Science and Engineering, James Cook University, Townsville, Qld, Australia
| | - Andreia Miraldo
- Swedish Museum of Natural Sciences, Department of Bioinformatics and Genetics, Frescativägen 40, 114 18, Stockholm, Sweden
| | - Tomas Roslin
- Swedish University of Agricultural Sciences (SLU), Department of Ecology, Ulls väg 18B, 75651, Uppsala, Sweden
| | - Helen E Roy
- UK Centre for Ecology & Hydrology, Benson Lane, Wallingford, OX10 8BB, UK
| | - Ireneusz Ruczyński
- Mammal Research Institute, Polish Academy of Sciences, Stoczek 1, 17-230, Białowieża, Poland
| | - Dmitry Schigel
- Global Biodiversity Information Facility (GBIF), Universitetsparken 15, 2100, Copenhagen, Denmark
| | - Livia Schäffler
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn, Adenauerallee 127, 53113, Bonn, Germany
| | - Julie K Sheard
- German Centre for Integrative Biodiversity Research (iDiv) Halle Jena Leipzig, Puschstrasse 4, 04103, Leipzig, Germany; Helmholtz - Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318, Leipzig, Germany; Friedrich Schiller University Jena, Institute of Biodiversity, Dornburger Strasse 159, 07743, Jena, Germany; University of Copenhagen, Centre for Macroecology, Evolution and Climate, Globe Institute, Universitetsparken 15, bld. 3, 2100, Copenhagen, Denmark
| | - Cecilie Svenningsen
- University of Copenhagen, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | - Georg F Tschan
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn, Adenauerallee 127, 53113, Bonn, Germany
| | - Jana Wäldchen
- German Centre for Integrative Biodiversity Research (iDiv) Halle Jena Leipzig, Puschstrasse 4, 04103, Leipzig, Germany; Max Planck Institute for Biogeochemistry, Department of Biogeochemical Integration, Hans-Knoell-Str. 10, 07745, Jena, Germany
| | - Vera M A Zizka
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn, Adenauerallee 127, 53113, Bonn, Germany
| | - Jens Åström
- Norwegian Institute for Nature Research, P.O. Box 5685 Torgarden, 7485, Trondheim, Norway
| | - Diana E Bowler
- German Centre for Integrative Biodiversity Research (iDiv) Halle Jena Leipzig, Puschstrasse 4, 04103, Leipzig, Germany; UK Centre for Ecology & Hydrology, Benson Lane, Wallingford, OX10 8BB, UK; Helmholtz - Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318, Leipzig, Germany; Friedrich Schiller University Jena, Institute of Biodiversity, Dornburger Strasse 159, 07743, Jena, Germany
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22
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Magoga G, Forni G, Brunetti M, Meral A, Spada A, De Biase A, Montagna M. Curation of a reference database of COI sequences for insect identification through DNA metabarcoding: COins. Database (Oxford) 2022; 2022:baac055. [PMID: 35796594 PMCID: PMC9261288 DOI: 10.1093/database/baac055] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/19/2022] [Accepted: 06/17/2022] [Indexed: 11/15/2022]
Abstract
DNA metabarcoding is a widespread approach for the molecular identification of organisms. While the associated wet-lab and data processing procedures are well established and highly efficient, the reference databases for taxonomic assignment can be implemented to improve the accuracy of identifications. Insects are among the organisms for which DNA-based identification is most commonly used; yet, a DNA-metabarcoding reference database specifically curated for their species identification using software requiring local databases is lacking. Here, we present COins, a database of 5' region cytochrome c oxidase subunit I sequences (COI-5P) of insects that includes over 532 000 representative sequences of >106 000 species specifically formatted for the QIIME2 software platform. Through a combination of automated and manually curated steps, we developed this database starting from all COI sequences available in the Barcode of Life Data System for insects, focusing on sequences that comply with several standards, including a species-level identification. COins was validated on previously published DNA-metabarcoding sequences data (bulk samples from Malaise traps) and its efficiency compared with other publicly available reference databases (not specific for insects). COins can allow an increase of up to 30% of species-level identifications and thus can represent a valuable resource for the taxonomic assignment of insects' DNA-metabarcoding data, especially when species-level identification is needed https://doi.org/10.6084/m9.figshare.19130465.v1.
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Affiliation(s)
- Giulia Magoga
- Department of Agricultural and Environmental Sciences, University of Milan, Via Celoria 2, Milano 20133, Italy
| | - Giobbe Forni
- Department of Agricultural and Environmental Sciences, University of Milan, Via Celoria 2, Milano 20133, Italy
| | - Matteo Brunetti
- Department of Agricultural and Environmental Sciences, University of Milan, Via Celoria 2, Milano 20133, Italy
| | - Aycan Meral
- Department of Agricultural and Environmental Sciences, University of Milan, Via Celoria 2, Milano 20133, Italy
| | - Alberto Spada
- Department of Agricultural and Environmental Sciences, University of Milan, Via Celoria 2, Milano 20133, Italy
| | - Alessio De Biase
- Department of Biology and Biotechnology ‘Charles Darwin’, Sapienza University of Rome, Viale dell’Università 32, Rome 00185, Italy
| | - Matteo Montagna
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, Portici 80055, Italy
- Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology (BAT Center), University of Naples Federico II, Via Università 100, Naples 80055, Italy
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23
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Comparing eDNA metabarcoding primers for assessing fish communities in a biodiverse estuary. PLoS One 2022; 17:e0266720. [PMID: 35714082 PMCID: PMC9205523 DOI: 10.1371/journal.pone.0266720] [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: 05/07/2021] [Accepted: 03/26/2022] [Indexed: 12/21/2022] Open
Abstract
Metabarcoding of environmental DNA is increasingly used for biodiversity assessments in aquatic communities. The efficiency and outcome of these efforts are dependent upon either de novo primer design or selecting an appropriate primer set from the dozens that have already been published. Unfortunately, there is a lack of studies that have directly compared the efficacy of different metabarcoding primers in marine and estuarine systems. Here we evaluate five commonly used primer sets designed to amplify rRNA barcoding genes in fishes and compare their performance using water samples collected from estuarine sites in the highly biodiverse Indian River Lagoon in Florida. Three of the five primer sets amplify a portion of the mitochondrial 12S gene (MiFish_12S, 171bp; Riaz_12S, 106 bp; Valentini_12S, 63 bp), one amplifies 219 bp of the mitochondrial 16S gene (Berry_16S), and the other amplifies 271 bp of the nuclear 18S gene (MacDonald_18S). The vast majority of the metabarcoding reads (> 99%) generated using the 18S primer set assigned to non-target (non-fish) taxa and therefore this primer set was omitted from most analyses. Using a conservative 99% similarity threshold for species level assignments, we detected a comparable number of species (55 and 49, respectively) and similarly high Shannon’s diversity values for the Riaz_12S and Berry_16S primer sets. Meanwhile, just 34 and 32 species were detected using the MiFish_12S and Valentini_12S primer sets, respectively. We were able to amplify both bony and cartilaginous fishes using the four primer sets with the vast majority of reads (>99%) assigned to the former. We detected the greatest number of elasmobranchs (six species) with the Riaz_12S primer set suggesting that it may be a suitable candidate set for the detection of sharks and rays. Of the total 76 fish species that were identified across all datasets, the combined three 12S primer sets detected 85.5% (65 species) while the combination of the Riaz_12S and Berry_16S primers detected 93.4% (71 species). These results highlight the importance of employing multiple primer sets as well as using primers that target different genomic regions. Moreover, our results suggest that the widely adopted MiFish_12S primers may not be the best choice, rather we found that the Riaz_12S primer set was the most effective for eDNA-based fish surveys in our system.
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Marquina D, Roslin T, Łukasik P, Ronquist F. Evaluation of non-destructive DNA extraction protocols for insect metabarcoding: gentler and shorter is better. METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.78871] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
DNA metabarcoding can accelerate research on insect diversity, as it is cheap and fast compared to manual sorting and identification. Most metabarcoding protocols require homogenisation of the sample, preventing further work on the specimens. Mild digestion of the tissue by incubation in a lysis buffer has been proposed as an alternative, and, although some mild lysis protocols have already been presented, they have so far not been evaluated against each other. Here, we analyse how two mild lysis buffers (one more aggressive, one gentler in terms of tissue degradation), two different incubation times, and two DNA purification methods (a manual precipitation and an automated protocol) affect the accuracy of retrieving the true composition of mock communities using two mitochondrial markers (COI and 16S). We found that protocol-specific variation in concentration and purity of the DNA extracts produced had little effect on the recovery of species. However, the two lysis treatments differed in quantification of species abundances. Digestion in the gentler buffer and for a shorter time yielded better representation of original sample composition. Digestion in a more aggressive buffer or longer incubation time yielded lower alpha diversity values and increased differences between metabarcoding results and the true species-abundance distribution. We conclude that the details of non-destructive protocols can have a significant effect on metabarcoding performance. A short and mild lysis treatment appears the best choice for recovering the true composition of the sample. This not only improves accuracy, but also comes with a faster processing time than the other treatments.
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25
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Hintikka S, Carlsson JE, Carlsson J. The bacterial hitchhiker’s guide to COI: Universal primer-based COI capture probes fail to exclude bacterial DNA, but 16S capture leaves metazoa behind. METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.80416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Environmental DNA (eDNA) metabarcoding from water samples has, in recent years, shown great promise for biodiversity monitoring. However, universal primers targeting the cytochrome oxidase I (COI) marker gene popular in metazoan studies have displayed high levels of nontarget amplification. To date, enrichment methods bypassing amplification have not been able to match the detection levels of conventional metabarcoding. This study evaluated the use of universal metabarcoding primers as capture probes to either isolate target DNA or to remove nontarget DNA, prior to amplification, by using biotinylated versions of universal metazoan and bacterial barcoding primers, namely metazoan COI (mlCOIintF) and bacterial 16S (515F). Additionally, each step of the protocol was assessed by amplifying for both metazoan COI (mlCOIintF/jgHCO2198) and bacterial 16S (515F/806R) to investigate the effect on the metazoan and bacterial communities. Bacterial read abundance increased significantly in response to the captures (COI library), while the quality of the captured DNA was also improved. The metazoan-oriented probe captured bacterial DNA in a range that was also amplifiable with the 16S primers, demonstrating the ability of capture probes to isolate fragments of DNA spanning over a longer distance than perhaps expected, from eDNA. Although the use of the tested COI probe cannot be recommended for metazoan enrichment, based on the experimental results, the concept of capturing these longer fragments could be applied to metazoan metabarcoding. By using a truly conserved site without a high-level taxonomic resolution as a target for capture, it may be possible to isolate DNA fragments large enough to span over a nearby barcoding region (e.g., COI), which can then be processed through a conventional metabarcoding-by-amplification protocol.
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26
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Ghonche-Golan S, Nazemi-Rafie J, Rezapanah M. The relationship study among Apis spp. using mitochondrial markers, Procrustes coordinates and residuals of geometric morphometric method. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01123-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Fonseca VG, Kirse A, Giebner H, Vause BJ, Drago T, Power DM, Peck LS, Clark MS. Metabarcoding the Antarctic Peninsula biodiversity using a multi-gene approach. ISME COMMUNICATIONS 2022; 2:37. [PMID: 37938273 PMCID: PMC9723778 DOI: 10.1038/s43705-022-00118-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 03/16/2022] [Accepted: 03/21/2022] [Indexed: 07/04/2023]
Abstract
Marine sediment communities are major contributors to biogeochemical cycling and benthic ecosystem functioning, but they are poorly described, particularly in remote regions such as Antarctica. We analysed patterns and drivers of diversity in metazoan and prokaryotic benthic communities of the Antarctic Peninsula with metabarcoding approaches. Our results show that the combined use of mitochondrial Cox1, and 16S and 18S rRNA gene regions recovered more phyla, from metazoan to non-metazoan groups, and allowed correlation of possible interactions between kingdoms. This higher level of detection revealed dominance by the arthropods and not nematodes in the Antarctic benthos and further eukaryotic diversity was dominated by benthic protists: the world's largest reservoir of marine diversity. The bacterial family Woeseiaceae was described for the first time in Antarctic sediments. Almost 50% of bacteria and 70% metazoan taxa were unique to each sampled site (high alpha diversity) and harboured unique features for local adaptation (niche-driven). The main abiotic drivers measured, shaping community structure were sediment organic matter, water content and mud. Biotic factors included the nematodes and the highly abundant bacterial fraction, placing protists as a possible bridge for between kingdom interactions. Meiofauna are proposed as sentinels for identifying anthropogenic-induced changes in Antarctic marine sediments.
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Affiliation(s)
- V G Fonseca
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth, UK.
| | - A Kirse
- Zoological Research Museum Alexander Koenig (ZFMK), Bonn, Germany
| | - H Giebner
- Zoological Research Museum Alexander Koenig (ZFMK), Bonn, Germany
| | - B J Vause
- British Antarctic Survey, Natural Environment Research Council, Cambridge, UK
| | - T Drago
- Portuguese Institute for Sea and Atmosphere (IPMA), Tavira, Portugal
- Institute Dom Luiz (IDL), University of Lisbon, Lisbon, Portugal
| | - D M Power
- Centre of Marine Sciences (CCMAR), Faro, Portugal
| | - L S Peck
- British Antarctic Survey, Natural Environment Research Council, Cambridge, UK
| | - M S Clark
- British Antarctic Survey, Natural Environment Research Council, Cambridge, UK
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Piper AM, Cunningham JP, Cogan NOI, Blacket MJ. DNA Metabarcoding Enables High-Throughput Detection of Spotted Wing Drosophila (Drosophila suzukii) Within Unsorted Trap Catches. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.822648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The spotted wing drosophila (Drosophila suzukii, Matsumara) is a rapidly spreading global pest of soft and stone fruit production. Due to the similarity of many of its life stages to other cosmopolitan drosophilids, surveillance for this pest is currently bottlenecked by the laborious sorting and morphological identification of large mixed trap catches. DNA metabarcoding presents an alternative high-throughput sequencing (HTS) approach for multi-species identification, which may lend itself ideally to rapid and scalable diagnostics of D. suzukii within unsorted trap samples. In this study, we compared the qualitative (identification accuracy) and quantitative (bias toward each species) performance of four metabarcoding primer pairs on D. suzukii and its close relatives. We then determined the sensitivity of a non-destructive metabarcoding assay (i.e., which retains intact specimens) by spiking whole specimens of target species into mock communities of increasing specimen number, as well as 29 field-sampled communities from a cherry and a stone fruit orchard. Metabarcoding successfully detected D. suzukii and its close relatives Drosophila subpulchrella and Drosophila biarmipes in the spiked communities with an accuracy of 96, 100, and 100% respectively, and identified a further 57 non-target arthropods collected as bycatch by D. suzukii surveillance methods in a field scenario. While the non-destructive DNA extraction retained intact voucher specimens, dropouts of single species and entire technical replicates suggests that these protocols behave more similarly to environmental DNA than homogenized tissue metabarcoding and may require increased technical replication to reliably detect low-abundance taxa. Adoption of high-throughput metabarcoding assays for screening bulk trap samples could enable a substantial increase in the geographic scale and intensity of D. suzukii surveillance, and thus likelihood of detecting a new introduction. Trap designs and surveillance protocols will, however, need to be optimized to adequately preserve specimen DNA for molecular identification.
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29
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Martoni F, Piper AM, Rodoni BC, Blacket MJ. Disentangling bias for non-destructive insect metabarcoding. PeerJ 2022; 10:e12981. [PMID: 35228909 PMCID: PMC8881911 DOI: 10.7717/peerj.12981] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 02/01/2022] [Indexed: 01/11/2023] Open
Abstract
A fast and reliable method for obtaining a species-level identification is a fundamental requirement for a wide range of activities, from plant protection and invasive species management to biodiversity assessments and ecological studies. For insects, novel molecular techniques such as DNA metabarcoding have emerged as a rapid alternative to traditional morphological identification, reducing the dependence on limited taxonomic experts. Until recently, molecular techniques have required a destructive DNA extraction, precluding the possibility of preserving voucher specimens for future studies, or species descriptions. Here we paired insect metabarcoding with two recent non-destructive DNA extraction protocols, to obtain a rapid and high-throughput taxonomic identification of diverse insect taxa while retaining a physical voucher specimen. The aim of this work was to explore how non-destructive extraction protocols impact the semi-quantitative nature of metabarcoding, which alongside species presence/absence also provides a quantitative, but biased, representation of their relative abundances. By using a series of mock communities representing each stage of a typical metabarcoding workflow we were able to determine how different morphological (i.e., insect biomass and exoskeleton hardness) and molecular traits (i.e., primer mismatch and amplicon GC%), interact with different protocol steps to introduce quantitative bias into non-destructive metabarcoding results. We discuss the relevance of taxonomic bias to metabarcoding identification of insects and potential approaches to account for it.
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Affiliation(s)
- Francesco Martoni
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, State Government Victoria, Bundoora, Victoria, Australia
| | - Alexander M. Piper
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, State Government Victoria, Bundoora, Victoria, Australia,School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
| | - Brendan C. Rodoni
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, State Government Victoria, Bundoora, Victoria, Australia,School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
| | - Mark J. Blacket
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, State Government Victoria, Bundoora, Victoria, Australia
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Pragmatic Applications and Universality of DNA Barcoding for Substantial Organisms at Species Level: A Review to Explore a Way Forward. BIOMED RESEARCH INTERNATIONAL 2022; 2022:1846485. [PMID: 35059459 PMCID: PMC8766189 DOI: 10.1155/2022/1846485] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/06/2021] [Indexed: 01/04/2023]
Abstract
DNA barcodes are regarded as hereditary succession codes that serve as a recognition marker to address several queries relating to the identification, classification, community ecology, and evolution of certain functional traits in organisms. The mitochondrial cytochrome c oxidase 1 (CO1) gene as a DNA barcode is highly efficient for discriminating vertebrate and invertebrate animal species. Similarly, different specific markers are used for other organisms, including ribulose bisphosphate carboxylase (rbcL), maturase kinase (matK), transfer RNA-H and photosystem II D1-ApbsArabidopsis thaliana (trnH-psbA), and internal transcribed spacer (ITS) for plant species; 16S ribosomal RNA (16S rRNA), elongation factor Tu gene (Tuf gene), and chaperonin for bacterial strains; and nuclear ITS for fungal strains. Nevertheless, the taxon coverage of reference sequences is far from complete for genus or species-level identification. Applying the next-generation sequencing approach to the parallel acquisition of DNA barcode sequences could greatly expand the potential for library preparation or accurate identification in biodiversity research. Overall, this review articulates on the DNA barcoding technology as applied to different organisms, its universality, applicability, and innovative approach to handling DNA-based species identification.
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Govender A, Singh S, Groeneveld J, Pillay S, Willows-Munro S. Experimental validation of taxon-specific mini-barcode primers for metabarcoding of zooplankton. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2022; 32:e02469. [PMID: 34626511 DOI: 10.1002/eap.2469] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 04/23/2021] [Accepted: 05/20/2021] [Indexed: 06/13/2023]
Abstract
Metabarcoding to determine the species composition and diversity of marine zooplankton communities is a fast-developing field in which the standardization of methods is yet to be fully achieved. The selection of genetic markers and primer choice are particularly important because they substantially influence species detection rates and accuracy. Validation is therefore an important step in the design of metabarcoding protocols. We developed taxon-specific mini-barcode primers for the cytochrome c oxidase subunit I (COI) gene region and used an experimental approach to test species detection rates and primer accuracy of the newly designed primers for prawns, shrimps and crabs and published primers for marine lobsters and fish. Artificially assembled mock communities (with known species ratios) and unsorted coastal tow-net zooplankton samples were sequenced and the detected species were compared with those seeded in mock communities to test detection rates. Taxon-specific primers increased detection rates of target taxa compared with a universal primer set. Primer cocktails (multiple primer sets) significantly increased species detection rates compared with single primer pairs and could detect up to 100% of underrepresented target taxa in mock communities. Taxon-specific primers recovered fewer false-positive or false-negative results than the universal primer. The methods used to design taxon-specific mini-barcodes and the experimental mock community validation protocols shown here can easily be applied to studies on other groups and will allow for a level of standardization among studies undertaken in different ecosystems or geographic locations.
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Affiliation(s)
- Ashrenee Govender
- School of Life Sciences, University of KwaZulu-Natal, Carbis Road, Pietermaritzburg, KwaZulu-Natal, 3201, South Africa
- Oceanographic Research Institute, King Shaka Avenue, Point, Durban, KwaZulu-Natal, 4001, South Africa
| | - Sohana Singh
- Oceanographic Research Institute, King Shaka Avenue, Point, Durban, KwaZulu-Natal, 4001, South Africa
| | - Johan Groeneveld
- School of Life Sciences, University of KwaZulu-Natal, Carbis Road, Pietermaritzburg, KwaZulu-Natal, 3201, South Africa
- Oceanographic Research Institute, King Shaka Avenue, Point, Durban, KwaZulu-Natal, 4001, South Africa
| | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Department of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Umbilo Rd, Durban, KwaZulu-Natal, 4001, South Africa
| | - Sandi Willows-Munro
- School of Life Sciences, University of KwaZulu-Natal, Carbis Road, Pietermaritzburg, KwaZulu-Natal, 3201, South Africa
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32
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A Comprehensive Evaluation of Enterobacteriaceae Primer Sets for Analysis of Host-Associated Microbiota. Pathogens 2021; 11:pathogens11010017. [PMID: 35055964 PMCID: PMC8780275 DOI: 10.3390/pathogens11010017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 12/17/2021] [Accepted: 12/20/2021] [Indexed: 12/12/2022] Open
Abstract
Enterobacteriaceae is one of the most important bacterial groups within the Proteobacteria phylum. This bacterial group includes pathogens, commensal and beneficial populations. Numerous 16S rRNA gene PCR-based assays have been designed to analyze Enterobacteriaceae diversity and relative abundance, and, to the best of our knowledge, 16 primer pairs have been validated, published and used since 2003. Nonetheless, a comprehensive performance analysis of these primer sets has not yet been carried out. This information is of particular importance due to the recent taxonomic restructuration of Enterobacteriaceae into seven bacterial families. To overcome this lack of information, the identified collection of primer pairs (n = 16) was subjected to primer performance analysis using multiple bioinformatics tools. Herein it was revealed that, based on specificity and coverage of the 16S rRNA gene, these 16 primer sets could be divided into different categories: Enterobacterales-, multi-family-, multi-genus- and Enterobacteriaceae-specific primers. These results highlight the impact of taxonomy changes on performance of molecular assays and data interpretation. Moreover, they underline the urgent need to revise and update the molecular tools used for molecular microbial analyses.
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Ollivier M, Lesieur V, Tavoillot J, Bénetière F, Tixier M, Martin J. An innovative approach combining metabarcoding and ecological interaction networks for selecting candidate biological control agents. J Appl Ecol 2021. [DOI: 10.1111/1365-2664.14016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mélodie Ollivier
- CBGP Montpellier SupAgro INRAE CIRAD IRD Univ Montpellier Montpellier France
| | - Vincent Lesieur
- CBGP Montpellier SupAgro INRAE CIRAD IRD Univ Montpellier Montpellier France
- CSIRO Health and Biosecurity European Laboratory Montferrier sur Lez France
| | - Johannes Tavoillot
- CBGP IRD CIRAD INRAE Montpellier SupAgro Univ Montpellier Montpellier France
| | - Fanny Bénetière
- CBGP Montpellier SupAgro INRAE CIRAD IRD Univ Montpellier Montpellier France
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Kirse A, Bourlat SJ, Langen K, Fonseca VG. Unearthing the Potential of Soil eDNA Metabarcoding—Towards Best Practice Advice for Invertebrate Biodiversity Assessment. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.630560] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Metabarcoding has proven to be a powerful tool to assess ecological patterns and diversity from different habitats. Terrestrial invertebrate diversity is frequently based on bulk samples, which require comparatively high sampling effort. With environmental DNA (eDNA) metabarcoding, field sampling effort can be reduced while increasing the number of recovered organism groups. However, a proof of concept is missing for several invertebrate groups, hampering the development of best-practice advice for these groups. This study aims to provide recommendations on key aspects for the processing of soil samples, from sampling effort to choice of DNA extraction method and marker genes. This study uses eDNA metabarcoding as a tool for assessing invertebrate biodiversity in soil samples, specifically comparing two DNA extraction methods (with and without a lysis step) and two genes, 18S and COI markers. The results show that the choice of marker and DNA extraction method (including a lysis step) significantly affect species detection rates and concomitantly observed invertebrate community composition. Combining methods, by using larger amounts of starting material and including a lysis step resulted in an increase of invertebrate species numbers. Together, these methods improved the detection of species with known lower population densities and allowed the assessment of temporary mesofauna. Furthermore, the choice of marker significantly influenced the diversity levels found. The 18S marker allowed the detection of a higher number of annelid and nematode OTUs, while the COI marker was more suitable for detecting changes in arthropod community structure, especially at the species level. This study makes significant advances to the field of invertebrate biodiversity assessment, particularly using metabarcoding tools by addressing several methodological considerations that are key for accurate ecological appraisals.
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35
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Kirse A, Bourlat SJ, Langen K, Fonseca VG. Metabarcoding Malaise traps and soil eDNA reveals seasonal and local arthropod diversity shifts. Sci Rep 2021; 11:10498. [PMID: 34006991 PMCID: PMC8131643 DOI: 10.1038/s41598-021-89950-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/23/2021] [Indexed: 02/03/2023] Open
Abstract
Forest habitats host enormous diversity, but little is known about the seasonal turnover of arthropod species between the above- and below ground forest layers. In this study, we used metabarcoding approaches to uncover arthropod diversity in different forest types and seasons. Our study shows that metabarcoding soil eDNA and Malaise trap bulk samples can provide valuable insights into the phenology and life cycles of arthropods. We found major differences in arthropod species diversity between soil samples and Malaise traps, with only 11.8% species overlap. Higher diversity levels were found in Malaise traps in summer whereas soil samples showed a diversity peak in winter, highlighting the seasonal habitat preferences and life strategies of arthropods. We conclude that collecting time series of bulk arthropod samples and eDNA in the same locations provides a more complete picture of local arthropod diversity and turnover rates and may provide valuable information on climate induced phenological shifts for long-term monitoring.
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Affiliation(s)
- Ameli Kirse
- Centre for Biodiversity Monitoring, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113, Bonn, Germany.
| | - Sarah J Bourlat
- Centre for Biodiversity Monitoring, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113, Bonn, Germany
| | - Kathrin Langen
- Centre for Biodiversity Monitoring, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113, Bonn, Germany
| | - Vera G Fonseca
- Centre for Biodiversity Monitoring, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113, Bonn, Germany.
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, The Nothe, Weymouth, Dorset, DT4 8UB, UK.
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36
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Batovska J, Piper AM, Valenzuela I, Cunningham JP, Blacket MJ. Developing a non-destructive metabarcoding protocol for detection of pest insects in bulk trap catches. Sci Rep 2021; 11:7946. [PMID: 33846382 PMCID: PMC8041782 DOI: 10.1038/s41598-021-85855-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/02/2021] [Indexed: 01/04/2023] Open
Abstract
Metabarcoding has the potential to revolutionise insect surveillance by providing high-throughput and cost-effective species identification of all specimens within mixed trap catches. Nevertheless, incorporation of metabarcoding into insect diagnostic laboratories will first require the development and evaluation of protocols that adhere to the specialised regulatory requirements of invasive species surveillance. In this study, we develop a multi-locus non-destructive metabarcoding protocol that allows sensitive detection of agricultural pests, and subsequent confirmation using traditional diagnostic techniques. We validate this protocol for the detection of tomato potato psyllid (Bactericera cockerelli) and Russian wheat aphid (Diuraphis noxia) within mock communities and field survey traps. We find that metabarcoding can reliably detect target insects within mixed community samples, including specimens that morphological identification did not initially detect, but sensitivity appears inversely related to community size and is impacted by primer biases, target loci, and sample indexing strategy. While our multi-locus approach allowed independent validation of target detection, lack of reference sequences for 18S and 12S restricted its usefulness for estimating diversity in field samples. The non-destructive DNA extraction proved invaluable for resolving inconsistencies between morphological and metabarcoding identification results, and post-extraction specimens were suitable for both morphological re-examination and DNA re-extraction for confirmatory barcoding.
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Affiliation(s)
- Jana Batovska
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC, 3083, Australia. .,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3086, Australia.
| | - Alexander M Piper
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC, 3083, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Isabel Valenzuela
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC, 3083, Australia
| | - John Paul Cunningham
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC, 3083, Australia.,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Mark J Blacket
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC, 3083, Australia
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Arribas P, Andújar C, Bidartondo MI, Bohmann K, Coissac É, Creer S, deWaard JR, Elbrecht V, Ficetola GF, Goberna M, Kennedy S, Krehenwinkel H, Leese F, Novotny V, Ronquist F, Yu DW, Zinger L, Creedy TJ, Meramveliotakis E, Noguerales V, Overcast I, Morlon H, Vogler AP, Papadopoulou A, Emerson BC. Connecting high-throughput biodiversity inventories: Opportunities for a site-based genomic framework for global integration and synthesis. Mol Ecol 2021; 30:1120-1135. [PMID: 33432777 PMCID: PMC7986105 DOI: 10.1111/mec.15797] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 12/21/2020] [Accepted: 01/05/2021] [Indexed: 01/03/2023]
Abstract
High-throughput sequencing (HTS) is increasingly being used for the characterization and monitoring of biodiversity. If applied in a structured way, across broad geographical scales, it offers the potential for a much deeper understanding of global biodiversity through the integration of massive quantities of molecular inventory data generated independently at local, regional and global scales. The universality, reliability and efficiency of HTS data can potentially facilitate the seamless linking of data among species assemblages from different sites, at different hierarchical levels of diversity, for any taxonomic group and regardless of prior taxonomic knowledge. However, collective international efforts are required to optimally exploit the potential of site-based HTS data for global integration and synthesis, efforts that at present are limited to the microbial domain. To contribute to the development of an analogous strategy for the nonmicrobial terrestrial domain, an international symposium entitled "Next Generation Biodiversity Monitoring" was held in November 2019 in Nicosia (Cyprus). The symposium brought together evolutionary geneticists, ecologists and biodiversity scientists involved in diverse regional and global initiatives using HTS as a core tool for biodiversity assessment. In this review, we summarize the consensus that emerged from the 3-day symposium. We converged on the opinion that an effective terrestrial Genomic Observatories network for global biodiversity integration and synthesis should be spatially led and strategically united under the umbrella of the metabarcoding approach. Subsequently, we outline an HTS-based strategy to collectively build an integrative framework for site-based biodiversity data generation.
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Affiliation(s)
- Paula Arribas
- Island Ecology and Evolution Research GroupInstituto de Productos Naturales y Agrobiología (IPNA‐CSIC)San Cristóbal de la LagunaSpain
| | - Carmelo Andújar
- Island Ecology and Evolution Research GroupInstituto de Productos Naturales y Agrobiología (IPNA‐CSIC)San Cristóbal de la LagunaSpain
| | - Martin I. Bidartondo
- Department of Life SciencesImperial College LondonLondonUK
- Comparative Plant and Fungal BiologyRoyal Botanic GardensLondonUK
| | - Kristine Bohmann
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, Globe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Éric Coissac
- Université Grenoble Alpes, CNRS, Université Savoie Mont BlancLECA, Laboratoire d’Ecologie AlpineGrenobleFrance
| | - Simon Creer
- School of Natural SciencesBangor UniversityGwyneddUK
| | - Jeremy R. deWaard
- Centre for Biodiversity GenomicsUniversity of GuelphGuelphCanada
- School of Environmental SciencesUniversity of GuelphGuelphCanada
| | - Vasco Elbrecht
- Centre for Biodiversity Monitoring (ZBM)Zoological Research Museum Alexander KoenigBonnGermany
| | - Gentile F. Ficetola
- Université Grenoble Alpes, CNRS, Université Savoie Mont BlancLECA, Laboratoire d’Ecologie AlpineGrenobleFrance
- Department of Environmental Sciences and PolicyUniversity of MilanoMilanoItaly
| | - Marta Goberna
- Department of Environment and AgronomyINIAMadridSpain
| | - Susan Kennedy
- Biodiversity and Biocomplexity UnitOkinawa Institute of Science and Technology Graduate UniversityOnna‐sonJapan
- Department of BiogeographyTrier UniversityTrierGermany
| | | | - Florian Leese
- Aquatic Ecosystem Research, Faculty of BiologyUniversity of Duisburg‐EssenEssenGermany
- Centre for Water and Environmental Research (ZWU) EssenUniversity of Duisburg‐EssenEssenGermany
| | - Vojtech Novotny
- Biology Centre, Institute of EntomologyCzech Academy of SciencesCeske BudejoviceCzech Republic
- Faculty of ScienceUniversity of South BohemiaCeske BudejoviceCzech Republic
| | - Fredrik Ronquist
- Department of Bioinformatics and GeneticsSwedish Museum of Natural HistoryStockholmSweden
| | - Douglas W. Yu
- State Key Laboratory of Genetic Resources and EvolutionKunming Institute of Zoology, Chinese Academy of SciencesKunmingChina
- Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunmingChina
- School of Biological SciencesUniversity of East AngliaNorwichUK
| | - Lucie Zinger
- Institut de Biologie de l’ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERMUniversité PSLParisFrance
| | | | | | | | - Isaac Overcast
- Institut de Biologie de l’ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERMUniversité PSLParisFrance
- Division of Vertebrate ZoologyAmerican Museum of Natural HistoryNew YorkUSA
| | - Hélène Morlon
- Institut de Biologie de l’ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERMUniversité PSLParisFrance
| | - Alfried P. Vogler
- Department of Life SciencesImperial College LondonLondonUK
- Department of Life SciencesNatural History MuseumLondonUK
| | | | - Brent C. Emerson
- Island Ecology and Evolution Research GroupInstituto de Productos Naturales y Agrobiología (IPNA‐CSIC)San Cristóbal de la LagunaSpain
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38
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Subrata SA, Siregar SRT, André A, Michaux JR. Identifying prey of the Javan mongoose (Urva javanica) in Java from fecal samples using next-generation sequencing. Mamm Biol 2020. [DOI: 10.1007/s42991-020-00086-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Zhou X, Chen Y, Nong X, Wang L, Liu Y, Yu H, Xie Y. Sequencing and characterization of the complete mitochondrial genome of Pseudoregma bambucicola (Hemiptera: Hormaphidinae) from Guizhou, China. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:3756-3758. [PMID: 33367089 PMCID: PMC7671660 DOI: 10.1080/23802359.2020.1835579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The bamboo aphids, Pseudoregma spp., are the commonest insect pests found in ornamental bamboos throughout southeastern Asia. In this study, the mitochondrial genome of a representative of Pseudoregma bambucicola isolated from the bamboo Bambusa multiplexcv in Guizhou of China was determined through Illumina MiSeq platform. The entire genome was 16,705 bp in length and encoded 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes. The phylogeneric analysis showed that the P. bambucicola (Guizhou isolate) clustered together with another two isolates from Sichuan and Fujian of China, respectively, and together formed a monophyletic relationship with Hormaphis betulae in Hormaphidinae. The mitochondrial DNA data presented here should contribute to future molecular identification, population genetic, and evolutionary biological studies of P. bambucicola.
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Affiliation(s)
- Xuan Zhou
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China.,Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yijun Chen
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Xiang Nong
- Bamboo Diseases and Pest Control and Resources Development Key Laboratory of Sichuan Province, Leshan, China.,College of Life Science, Leshan Normal University, Leshan, China
| | - Lidan Wang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yunjian Liu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Hua Yu
- Sichuan Entry-Exit Inspection and Quarantine Bureau, Chengdu, China
| | - Yue Xie
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
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40
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Ficetola GF, Boyer F, Valentini A, Bonin A, Meyer A, Dejean T, Gaboriaud C, Usseglio-Polatera P, Taberlet P. Comparison of markers for the monitoring of freshwater benthic biodiversity through DNA metabarcoding. Mol Ecol 2020; 30:3189-3202. [PMID: 32920861 DOI: 10.1111/mec.15632] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 08/16/2020] [Accepted: 08/27/2020] [Indexed: 12/22/2022]
Abstract
Metabarcoding of bulk or environmental DNA has great potential for biomonitoring of freshwater environments. However, successful application of metabarcoding to biodiversity monitoring requires universal primers with high taxonomic coverage that amplify highly variable, short metabarcodes with high taxonomic resolution. Moreover, reliable and extensive reference databases are essential to match the outcome of metabarcoding analyses with available taxonomy and biomonitoring indices. Benthic invertebrates, particularly insects, are key taxa for freshwater bioassessment. Nevertheless, few studies have so far assessed markers for metabarcoding of freshwater macrobenthos. Here we combined in silico and laboratory analyses to test the performance of different markers amplifying regions in the 18S rDNA (Euka02), 16S rDNA (Inse01) and COI (BF1_BR2-COI) genes, and developed an extensive database of benthic macroinvertebrates of France and Europe, with a particular focus on key insect orders (Ephemeroptera, Plecoptera and Trichoptera). Analyses on 1,514 individuals representing different taxa of benthic macroinvertebrates showed very different amplification success across primer combinations. The Euka02 marker showed the highest universality, while the Inse01 marker showed excellent performance for the amplification of insects. BF1_BR2-COI showed the highest resolution, while the resolution of Euka02 was often limited. By combining our data with GenBank information, we developed a curated database including sequences representing 822 genera. The heterogeneous performance of the different primers highlights the complexity in identifying the best markers, and advocates for the integration of multiple metabarcodes for a more comprehensive and accurate understanding of ecological impacts on freshwater biodiversity.
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Affiliation(s)
- Gentile Francesco Ficetola
- LECA, Laboratoire d'Ecologie Alpine, Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, Grenoble, France.,Department of Environmental Sciences and Policy, University of Milano, Milano, Italy
| | - Frédéric Boyer
- LECA, Laboratoire d'Ecologie Alpine, Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, Grenoble, France
| | | | - Aurélie Bonin
- LECA, Laboratoire d'Ecologie Alpine, Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, Grenoble, France.,Department of Environmental Sciences and Policy, University of Milano, Milano, Italy
| | - Albin Meyer
- Université de Lorraine, CNRS, LIEC, Metz, France
| | | | | | | | - Pierre Taberlet
- LECA, Laboratoire d'Ecologie Alpine, Univ. Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, Grenoble, France.,UiT - The Arctic University of Norway, Tromsø Museum, Tromsø, Norway
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41
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Tournayre O, Leuchtmann M, Filippi‐Codaccioni O, Trillat M, Piry S, Pontier D, Charbonnel N, Galan M. In silico and empirical evaluation of twelve metabarcoding primer sets for insectivorous diet analyses. Ecol Evol 2020; 10:6310-6332. [PMID: 32724515 PMCID: PMC7381572 DOI: 10.1002/ece3.6362] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/20/2020] [Accepted: 04/22/2020] [Indexed: 12/28/2022] Open
Abstract
During the most recent decade, environmental DNA metabarcoding approaches have been both developed and improved to minimize the biological and technical biases in these protocols. However, challenges remain, notably those relating to primer design. In the current study, we comprehensively assessed the performance of ten COI and two 16S primer pairs for eDNA metabarcoding, including novel and previously published primers. We used a combined approach of in silico, in vivo-mock community (33 arthropod taxa from 16 orders), and guano-based analyses to identify primer sets that would maximize arthropod detection and taxonomic identification, successfully identify the predator (bat) species, and minimize the time and financial costs of the experiment. We focused on two insectivorous bat species that live together in mixed colonies: the greater horseshoe bat (Rhinolophus ferrumequinum) and Geoffroy's bat (Myotis emarginatus). We found that primer degeneracy is the main factor that influences arthropod detection in silico and mock community analyses, while amplicon length is critical for the detection of arthropods from degraded DNA samples. Our guano-based results highlight the importance of detecting and identifying both predator and prey, as guano samples can be contaminated by other insectivorous species. Moreover, we demonstrate that amplifying bat DNA does not reduce the primers' capacity to detect arthropods. We therefore recommend the simultaneous identification of predator and prey. Finally, our results suggest that up to one-third of prey occurrences may be unreliable and are probably not of primary interest in diet studies, which may decrease the relevance of combining several primer sets instead of using a single efficient one. In conclusion, this study provides a pragmatic framework for eDNA primer selection with respect to scientific and methodological constraints.
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Affiliation(s)
- Orianne Tournayre
- CBGPINRAECIRADIRDMontpellier SupAgroUniversité de MontpellierMontpellierFrance
| | | | - Ondine Filippi‐Codaccioni
- LabEx ECOFECT “Ecoevolutionary Dynamics of Infectious DiseasesUniversité de LyonLyonFrance
- CNRSLaboratoire de Biométrie et Biologie ÉvolutiveUMR5558Université de LyonUniversité Lyon 1VilleurbanneFrance
| | - Marine Trillat
- CBGPINRAECIRADIRDMontpellier SupAgroUniversité de MontpellierMontpellierFrance
| | - Sylvain Piry
- CBGPINRAECIRADIRDMontpellier SupAgroUniversité de MontpellierMontpellierFrance
| | - Dominique Pontier
- LabEx ECOFECT “Ecoevolutionary Dynamics of Infectious DiseasesUniversité de LyonLyonFrance
- CNRSLaboratoire de Biométrie et Biologie ÉvolutiveUMR5558Université de LyonUniversité Lyon 1VilleurbanneFrance
| | - Nathalie Charbonnel
- CBGPINRAECIRADIRDMontpellier SupAgroUniversité de MontpellierMontpellierFrance
| | - Maxime Galan
- CBGPINRAECIRADIRDMontpellier SupAgroUniversité de MontpellierMontpellierFrance
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From Nucleotides to Satellite Imagery: Approaches to Identify and Manage the Invasive Pathogen Xylella fastidiosa and Its Insect Vectors in Europe. SUSTAINABILITY 2020. [DOI: 10.3390/su12114508] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Biological invasions represent some of the most severe threats to local communities and ecosystems. Among invasive species, the vector-borne pathogen Xylella fastidiosa is responsible for a wide variety of plant diseases and has profound environmental, social and economic impacts. Once restricted to the Americas, it has recently invaded Europe, where multiple dramatic outbreaks have highlighted critical challenges for its management. Here, we review the most recent advances on the identification, distribution and management of X. fastidiosa and its insect vectors in Europe through genetic and spatial ecology methodologies. We underline the most important theoretical and technological gaps that remain to be bridged. Challenges and future research directions are discussed in the light of improving our understanding of this invasive species, its vectors and host–pathogen interactions. We highlight the need of including different, complimentary outlooks in integrated frameworks to substantially improve our knowledge on invasive processes and optimize resources allocation. We provide an overview of genetic, spatial ecology and integrated approaches that will aid successful and sustainable management of one of the most dangerous threats to European agriculture and ecosystems.
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43
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Nong X, Liu Y, Wang L, Zhong S, Yu X, Xie Y. Mitochondrial genome of Hormaphis betulae and its comparative analysis with Pseudoregma bambucicola (Hemiptera: Hormaphidinae). Mitochondrial DNA B Resour 2020; 5:906-907. [PMID: 33426278 PMCID: PMC7755318 DOI: 10.1080/23802359.2020.1715878] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 01/07/2020] [Indexed: 10/25/2022] Open
Abstract
Hormaphis betulae (Hemiptera: Hormaphidinae) is a common aphid of birch plants. Here, the complete mitochondrial genome sequence of a representative of this aphid from China was determined using next generation sequencing platform. The genome was 15,129 bp in length and encoded 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes. The phylogeny revealed that two Chinese isolates of H. betulae clustered together and formed a monophyletic relationship with Pseudoregma bambucicola in the subfamily Hormaphidinae, supporting their species validity in Aphididae. The cumulative mitochondrial DNA data provides a better understanding of the phylogenetic relationship of this species in plant aphids.
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Affiliation(s)
- Xiang Nong
- Bamboo Diseases and Pest control and Resources Development Key Laboratory of Sichuan Province, Leshan, China
- College of Life Science, Leshan Normal University, Leshan, China
| | - Yunjian Liu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Lidan Wang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shengnan Zhong
- Bamboo Diseases and Pest control and Resources Development Key Laboratory of Sichuan Province, Leshan, China
- College of Life Science, Leshan Normal University, Leshan, China
- College of Food and Biological Engineering, Xihua University, Chengdu, China
| | - Xiaobo Yu
- Bamboo Diseases and Pest control and Resources Development Key Laboratory of Sichuan Province, Leshan, China
- College of Life Science, Leshan Normal University, Leshan, China
| | - Yue Xie
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
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44
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Nong X, Wang L, Liu Y, Zhong S, Yu X, Xie Y. The complete mitochondrial genome of the bamboo aphid Pseudoregma bambucicola and its phylogenetic position. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:642-643. [PMID: 33366683 PMCID: PMC7748661 DOI: 10.1080/23802359.2019.1711225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The bamboo aphid, Pseudoregma bambucicola, is a terrible insect pest of bamboos. Herein, the complete mitochondrial genome of a representative of this aphid from China was determined through next generation sequencing platform. The whole genome was 16,651 bp in size and encoded 13 protein-coding genes, 22 tRNA genes, and two rRNA genes. The phylogeny showed that two Chinese isolates of P. bambucicola clustered together and formed a monophyletic relationship with Hormaphis betulae in Hormaphidinae, supporting their species validity among the family Aphididae. The cumulative mitochondrial DNA data should contribute to a better understanding of the phylogenetic relationship of this aphid species.
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Affiliation(s)
- Xiang Nong
- Bamboo Diseases and Pest control and Resources Development Key Laboratory of Sichuan Province, Leshan, China.,College of Life Science, Leshan Normal University, Leshan, China
| | - Lidan Wang
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Yunjian Liu
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Shengnan Zhong
- Bamboo Diseases and Pest control and Resources Development Key Laboratory of Sichuan Province, Leshan, China.,College of Life Science, Leshan Normal University, Leshan, China.,College of Food and Biological Engineering, Xihua University, Chengdu, China
| | - Xiaobo Yu
- Bamboo Diseases and Pest control and Resources Development Key Laboratory of Sichuan Province, Leshan, China.,College of Life Science, Leshan Normal University, Leshan, China
| | - Yue Xie
- Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
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45
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Elbrecht V, Braukmann TW, Ivanova NV, Prosser SW, Hajibabaei M, Wright M, Zakharov EV, Hebert PD, Steinke D. Validation of COI metabarcoding primers for terrestrial arthropods. PeerJ 2019; 7:e7745. [PMID: 31608170 PMCID: PMC6786254 DOI: 10.7717/peerj.7745] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 08/25/2019] [Indexed: 01/08/2023] Open
Abstract
Metabarcoding can rapidly determine the species composition of bulk samples and thus aids biodiversity and ecosystem assessment. However, it is essential to use primer sets that minimize amplification bias among taxa to maximize species recovery. Despite this fact, the performance of primer sets employed for metabarcoding terrestrial arthropods has not been sufficiently evaluated. This study tests the performance of 36 primer sets on a mock community containing 374 insect species. Amplification success was assessed with gradient PCRs and the 21 most promising primer sets selected for metabarcoding. These 21 primer sets were also tested by metabarcoding a Malaise trap sample. We identified eight primer sets, mainly those including inosine and/or high degeneracy, that recovered more than 95% of the species in the mock community. Results from the Malaise trap sample were congruent with the mock community, but primer sets generating short amplicons produced potential false positives. Taxon recovery from both mock community and Malaise trap sample metabarcoding were used to select four primer sets for additional evaluation at different annealing temperatures (40-60 °C) using the mock community. The effect of temperature varied by primer pair but overall it only had a minor effect on taxon recovery. This study reveals the weak performance of some primer sets employed in past studies. It also demonstrates that certain primer sets can recover most taxa in a diverse species assemblage. Thus, based our experimental set up, there is no need to employ several primer sets targeting the same gene region. We identify several suitable primer sets for arthropod metabarcoding, and specifically recommend BF3 + BR2, as it is not affected by primer slippage and provides maximal taxonomic resolution. The fwhF2 + fwhR2n primer set amplifies a shorter fragment and is therefore ideal when targeting degraded DNA (e.g., from gut contents).
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Affiliation(s)
- Vasco Elbrecht
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | | | - Natalia V. Ivanova
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Sean W.J. Prosser
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Mehrdad Hajibabaei
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Michael Wright
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Evgeny V. Zakharov
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Paul D.N. Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Dirk Steinke
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
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46
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Collins RA, Bakker J, Wangensteen OS, Soto AZ, Corrigan L, Sims DW, Genner MJ, Mariani S. Non‐specific amplification compromises environmental DNA metabarcoding with COI. Methods Ecol Evol 2019. [DOI: 10.1111/2041-210x.13276] [Citation(s) in RCA: 132] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
| | - Judith Bakker
- Department of Biological Sciences Florida International University Miami FL USA
- Ecosystems & Environment Research Centre, School of Environment & Life Sciences University of Salford Salford UK
| | - Owen S. Wangensteen
- Ecosystems & Environment Research Centre, School of Environment & Life Sciences University of Salford Salford UK
- Norwegian College of Fishery Science, UiT The Arctic University of Norway Tromsø Norway
| | - Ana Z. Soto
- Ecosystems & Environment Research Centre, School of Environment & Life Sciences University of Salford Salford UK
| | - Laura Corrigan
- Environment Agency Tyneside House Newcastle upon Tyne UK
| | - David W. Sims
- The Laboratory Marine Biological Association of the United Kingdom Plymouth UK
- Ocean and Earth Science, National Oceanography Centre Southampton University of Southampton Southampton UK
| | | | - Stefano Mariani
- Ecosystems & Environment Research Centre, School of Environment & Life Sciences University of Salford Salford UK
- School of Natural Sciences & Psychology Liverpool John Moores University Liverpool UK
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Marquina D, Esparza-Salas R, Roslin T, Ronquist F. Establishing arthropod community composition using metabarcoding: Surprising inconsistencies between soil samples and preservative ethanol and homogenate from Malaise trap catches. Mol Ecol Resour 2019; 19:1516-1530. [PMID: 31379089 PMCID: PMC6899807 DOI: 10.1111/1755-0998.13071] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 06/26/2019] [Accepted: 07/03/2019] [Indexed: 11/29/2022]
Abstract
DNA metabarcoding allows the analysis of insect communities faster and more efficiently than ever before. However, metabarcoding can be conducted through several approaches, and the consistency of results across methods has rarely been studied. We compare the results obtained by DNA metabarcoding of the same communities using two different markers – COI and 16S – and three different sampling methods: (a) homogenized Malaise trap samples (homogenate), (b) preservative ethanol from the same samples, and (c) soil samples. Our results indicate that COI and 16S offer partly complementary information on Malaise trap samples, with each marker detecting a significant number of species not detected by the other. Different sampling methods offer highly divergent estimates of community composition. The community recovered from preservative ethanol of Malaise trap samples is significantly different from that recovered from homogenate. Small and weakly sclerotized insects tend to be overrepresented in ethanol while strong and large taxa are overrepresented in homogenate. For soil samples, highly degenerate COI primers pick up large amounts of nontarget DNA and only 16S provides adequate analyses of insect diversity. However, even with 16S, very little overlap in molecular operational taxonomic unit (MOTU) content was found between the trap and the soil samples. Our results demonstrate that none of the tested sampling approaches is satisfactory on its own. For instance, DNA extraction from preservative ethanol is not a valid replacement for destructive bulk extraction but a complement. In future metabarcoding studies, both should ideally be used together to achieve comprehensive representation of the target community.
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Affiliation(s)
- Daniel Marquina
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Rodrigo Esparza-Salas
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Tomas Roslin
- Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, Finland.,Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Fredrik Ronquist
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
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Piper AM, Batovska J, Cogan NOI, Weiss J, Cunningham JP, Rodoni BC, Blacket MJ. Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance. Gigascience 2019; 8:giz092. [PMID: 31363753 PMCID: PMC6667344 DOI: 10.1093/gigascience/giz092] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 06/25/2019] [Accepted: 07/09/2019] [Indexed: 12/21/2022] Open
Abstract
Trap-based surveillance strategies are widely used for monitoring of invasive insect species, aiming to detect newly arrived exotic taxa as well as track the population levels of established or endemic pests. Where these surveillance traps have low specificity and capture non-target endemic species in excess of the target pests, the need for extensive specimen sorting and identification creates a major diagnostic bottleneck. While the recent development of standardized molecular diagnostics has partly alleviated this requirement, the single specimen per reaction nature of these methods does not readily scale to the sheer number of insects trapped in surveillance programmes. Consequently, target lists are often restricted to a few high-priority pests, allowing unanticipated species to avoid detection and potentially establish populations. DNA metabarcoding has recently emerged as a method for conducting simultaneous, multi-species identification of complex mixed communities and may lend itself ideally to rapid diagnostics of bulk insect trap samples. Moreover, the high-throughput nature of recent sequencing platforms could enable the multiplexing of hundreds of diverse trap samples on a single flow cell, thereby providing the means to dramatically scale up insect surveillance in terms of both the quantity of traps that can be processed concurrently and number of pest species that can be targeted. In this review of the metabarcoding literature, we explore how DNA metabarcoding could be tailored to the detection of invasive insects in a surveillance context and highlight the unique technical and regulatory challenges that must be considered when implementing high-throughput sequencing technologies into sensitive diagnostic applications.
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Affiliation(s)
- Alexander M Piper
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora 3083, VIC, Australia
| | - Jana Batovska
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora 3083, VIC, Australia
| | - Noel O I Cogan
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora 3083, VIC, Australia
| | - John Weiss
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
| | - John Paul Cunningham
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
| | - Brendan C Rodoni
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora 3083, VIC, Australia
| | - Mark J Blacket
- Agriculture Victoria Research, AgriBio Centre, 5 Ring Road, Bundoora 3083, VIC, Australia
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49
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Marquina D, Andersson AF, Ronquist F. New mitochondrial primers for metabarcoding of insects, designed and evaluated using in silico methods. Mol Ecol Resour 2018; 19:90-104. [PMID: 30226026 PMCID: PMC7379581 DOI: 10.1111/1755-0998.12942] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 08/27/2018] [Accepted: 09/07/2018] [Indexed: 11/29/2022]
Abstract
Insect metabarcoding has been mainly based on PCR amplification of short fragments within the “barcoding region” of the gene cytochrome oxidase I (COI). However, because of the variability of this gene, it has been difficult to design good universal PCR primers. Most primers used today are associated with gaps in the taxonomic coverage or amplification biases that make the results less reliable and impede the detection of species that are present in the sample. We identify new primers for insect metabarcoding using computational approaches (ecoprimers and degeprime) applied to the most comprehensive reference databases of mitochondrial genomes of Hexapoda assembled to date. New primers are evaluated in silico against previously published primers in terms of taxonomic coverage and resolution of the corresponding amplicons. For the latter criterion, we propose a new index, exclusive taxonomic resolution, which is a more biologically meaningful measure than the standard index used today. Our results show that the best markers are found in the ribosomal RNA genes (12S and 16S); they resolve about 90% of the genetically distinct species in the reference database. Some markers in protein‐coding genes provide similar performance but only at much higher levels of primer degeneracy. Combining two of the best individual markers improves the effective taxonomic resolution with up to 10%. The resolution is strongly dependent on insect taxon: COI primers detect 40% of Hymenoptera, while 12S primers detect 12% of Collembola. Our results indicate that amplicon‐based metabarcoding of insect samples can be improved by choosing other primers than those commonly used today.
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Affiliation(s)
- Daniel Marquina
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Anders F Andersson
- Science for Life Laboratory, Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Fredrik Ronquist
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
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