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Haas M, Baur H, Schweizer T, Monje JC, Moser M, Bigalk S, Krogmann L. Tiny wasps, huge diversity - A review of German Pteromalidae with new generic and species records (Hymenoptera: Chalcidoidea). Biodivers Data J 2021; 9:e77092. [PMID: 34916873 PMCID: PMC8671368 DOI: 10.3897/bdj.9.e77092] [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: 10/26/2021] [Accepted: 12/01/2021] [Indexed: 12/31/2022] Open
Abstract
Background Despite their ecological and economic importance, hymenopteran parasitoids are severely understudied. Even in countries with a long taxonomic history such as Germany, dating back to the 18th century and including prolific figures like Christian Gottfired Nees von Esenbeck and Otto Schmiedeknecht, those species-rich groups are seldom the subject of comprehensive research efforts, leaving their true diversity unknown. This is often due to their small size of a few millimetres on average, leading to difficulties in their identification and examination. The chalcidoid family Pteromalidae is no exception to this neglect. So far, 735 species have been reported from Germany. Estimating the diversity of this group is not possible, but it has to be assumed that many more species are still to be discovered in Germany. New information With this study, we improve the knowledge on pteromalid diversity and present new records of 17 genera and 41 species, previously unknown to occur in Germany. We also match and describe previously unknown sexes of two species, based on DNA barcode data. The results of this study were generated as part of the German Barcode of Life Project. The newly-recorded species are illustrated and notes on the biology and distribution are given. The ecological significance of Pteromalidae and potential value as indicators for nature conservation efforts are briefly discussed.
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Affiliation(s)
- Michael Haas
- Entomology, State Museum of Natural History, Stuttgart, Germany Entomology, State Museum of Natural History Stuttgart Germany.,Systematic Entomology (190n), University of Hohenheim, Stuttgart, Germany Systematic Entomology (190n), University of Hohenheim Stuttgart Germany
| | - Hannes Baur
- Department of Invertebrates, Natural History Museum Bern, Bern, Switzerland Department of Invertebrates, Natural History Museum Bern Bern Switzerland.,Institute of Ecology and Evolution, University of Bern, Bern, Switzerland Institute of Ecology and Evolution, University of Bern Bern Switzerland
| | - Tanja Schweizer
- Entomology, State Museum of Natural History, Stuttgart, Germany Entomology, State Museum of Natural History Stuttgart Germany
| | - Juan Carlos Monje
- Entomology, State Museum of Natural History, Stuttgart, Germany Entomology, State Museum of Natural History Stuttgart Germany
| | - Marina Moser
- Entomology, State Museum of Natural History, Stuttgart, Germany Entomology, State Museum of Natural History Stuttgart Germany.,Systematic Entomology (190n), University of Hohenheim, Stuttgart, Germany Systematic Entomology (190n), University of Hohenheim Stuttgart Germany
| | - Sonia Bigalk
- Entomology, State Museum of Natural History, Stuttgart, Germany Entomology, State Museum of Natural History Stuttgart Germany
| | - Lars Krogmann
- Entomology, State Museum of Natural History, Stuttgart, Germany Entomology, State Museum of Natural History Stuttgart Germany.,Systematic Entomology (190n), University of Hohenheim, Stuttgart, Germany Systematic Entomology (190n), University of Hohenheim Stuttgart Germany
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52
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Tay WT, Court LN, Macfadyen S, Jacomb F, Vyskočilová S, Colvin J, De Barro PJ. A high-throughput amplicon sequencing approach for population-wide species diversity and composition survey. Mol Ecol Resour 2021; 22:1706-1724. [PMID: 34918473 DOI: 10.1111/1755-0998.13576] [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: 11/28/2019] [Revised: 11/16/2021] [Accepted: 12/06/2021] [Indexed: 11/30/2022]
Abstract
Management of agricultural pests requires an understanding of pest species diversity, their interactions with beneficial insects and spatial-temporal patterns of pest abundance. Invasive and agriculturally important insect pests can build up very high populations, especially in cropping landscapes. Traditionally, sampling effort for species identification involves small sample sizes and is labour intensive. Here, we describe a multi-primer high throughput sequencing (HTS) metabarcoding method and associated analytical workflow for a rapid, intensive, high-volume survey of pest species compositions. We demonstrate our method using the taxonomically challenging Bemisia pest cryptic species complex as examples. The whiteflies Bemisia including the 'tabaci' species are agriculturally important capable of vectoring diverse plant viruses that cause diseases and crop losses. Our multi-primer metabarcoding HTS amplicon approach simultaneously process high volumes of whitefly individuals, with efficiency to detect rare (i.e., 1%) test-species, while our improved whitefly primers for metabarcoding also detected beneficial hymenopteran parasitoid species from whitefly nymphs. Field-testing our redesigned Bemisia metabarcoding primer sets across the Tanzania, Uganda and Malawi cassava cultivation landscapes, we identified the sub-Saharan Africa 1 Bemisia putative species as the dominant pest species, with other cryptic Bemisia species being detected at various abundances. We also provide evidence that Bemisia species compositions can be affected by host crops and sampling techniques that target either nymphs or adults. Our multi-primer HTS metabarcoding method incorporated two over-lapping amplicons of 472bp and 518bp that spanned the entire 657bp 3' barcoding region for Bemisia, and is particularly suitable to molecular diagnostic surveys of this highly cryptic insect pest species complex that also typically exhibited high population densities in heavy crop infestation episodes. Our approach can be adopted to understand species biodiversity across landscapes, with broad implications for improving trans-boundary biosecurity preparedness, thus contributing to molecular ecological knowledge and the development of control strategies for high-density, cryptic, pest-species complexes.
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Affiliation(s)
- W T Tay
- CSIRO Black Mountain Laboratories, Clunies Ross Street, ACT, 2601, Australia
| | - L N Court
- CSIRO Black Mountain Laboratories, Clunies Ross Street, ACT, 2601, Australia
| | - S Macfadyen
- CSIRO Black Mountain Laboratories, Clunies Ross Street, ACT, 2601, Australia
| | - F Jacomb
- CSIRO Black Mountain Laboratories, Clunies Ross Street, ACT, 2601, Australia
| | - S Vyskočilová
- CSIRO Black Mountain Laboratories, Clunies Ross Street, ACT, 2601, Australia.,Natural Resources Institute, University of Greenwich, Central Avenue, Chatham, Maritime Kent, ME4 4TB, United Kingdom
| | - J Colvin
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham, Maritime Kent, ME4 4TB, United Kingdom
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53
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Elbrecht V, Bourlat SJ, Hörren T, Lindner A, Mordente A, Noll NW, Schäffler L, Sorg M, Zizka VMA. Pooling size sorted Malaise trap fractions to maximize taxon recovery with metabarcoding. PeerJ 2021; 9:e12177. [PMID: 34707928 PMCID: PMC8500090 DOI: 10.7717/peerj.12177] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 08/29/2021] [Indexed: 12/22/2022] Open
Abstract
Background Small and rare specimens can remain undetected when metabarcoding is applied on bulk samples with a high specimen size heterogeneity. This is especially critical for Malaise trap samples, where most of the biodiversity is contributed by small taxa with low biomass. The separation of samples in different size fractions for downstream analysis is one possibility to increase detection of small and rare taxa. However, experiments systematically testing different size sorting approaches and subsequent proportional pooling of fractions are lacking, but would provide important information for the optimization of metabarcoding protocols. We set out to find a size sorting strategy for Malaise trap samples that maximizes taxonomic recovery but remains scalable and time efficient. Methods Three Malaise trap samples were sorted into four size classes using dry sieving. Each fraction was homogenized and lysed. The corresponding lysates were pooled to simulate unsorted samples. Pooling was additionally conducted in equal proportions and in four different proportions enriching the small size fraction of samples. DNA from the individual size classes as well as the pooled fractions was extracted and metabarcoded using the FwhF2 and Fol-degen-rev primer set. Additionally, alternative wet sieving strategies were explored. Results The small size fractions harboured the highest diversity and were best represented when pooling in favour of small specimens. Metabarcoding of unsorted samples decreases taxon recovery compared to size sorted samples. A size separation into only two fractions (below 4 mm and above) can double taxon recovery compared to not size sorting. However, increasing the sequencing depth 3- to 4-fold can also increase taxon recovery to levels comparable with size sorting, but remains biased towards biomass rich taxa in the sample. Conclusion We demonstrate that size fractionation of Malaise trap bulk samples can increase taxon recovery. While results show distinct patterns, the lack of statistical support due to the limited number of samples processed is a limitation. Due to increased speed and lower risk of cross-contamination as well as specimen damage we recommend wet sieving and proportional pooling of the lysates in favour of the small size fraction (80–90% volume). However, for large-scale projects with time constraints, increasing sequencing depth is an alternative solution.
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Affiliation(s)
- Vasco Elbrecht
- Centre for Biodiversity Monitoring, Zoological Research Museum Alexander Koenig, Bonn, Germany.,SimplexDNA AG, Winterthur, Switzerland
| | - Sarah J Bourlat
- Centre for Biodiversity Monitoring, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | | | - Angie Lindner
- Centre for Biodiversity Monitoring, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Adriana Mordente
- Centre for Biodiversity Monitoring, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Niklas W Noll
- Centre for Biodiversity Monitoring, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Livia Schäffler
- Centre for Biodiversity Monitoring, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Martin Sorg
- Entomological Society Krefeld, Krefeld, Germany
| | - Vera M A Zizka
- Centre for Biodiversity Monitoring, Zoological Research Museum Alexander Koenig, Bonn, Germany
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54
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Mammola S, Pétillon J, Hacala A, Monsimet J, Marti S, Cardoso P, Lafage D. Challenges and opportunities of species distribution modelling of terrestrial arthropod predators. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13434] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Stefano Mammola
- Laboratory for Integrative Biodiversity Research (LIBRe) Finnish Museum of Natural History (LUOMUS) University of Helsinki Helsinki Finland
- Molecular Ecology Group (MEG), Water Research Institute (RSA) National Research Council (CNR) Verbania Pallanza Italy
| | | | - Axel Hacala
- UMR ECOBIO Université de Rennes 1 Rennes France
| | - Jérémy Monsimet
- Inland Norway University of Applied Sciences, Campus Evenstad Koppang Norway
| | | | - Pedro Cardoso
- Laboratory for Integrative Biodiversity Research (LIBRe) Finnish Museum of Natural History (LUOMUS) University of Helsinki Helsinki Finland
| | - Denis Lafage
- UMR ECOBIO Université de Rennes 1 Rennes France
- Department of Environmental and Life Sciences/Biology Karlstad University Karlstad Sweden
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55
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Jones RAC, Sharman M, Trębicki P, Maina S, Congdon BS. Virus Diseases of Cereal and Oilseed Crops in Australia: Current Position and Future Challenges. Viruses 2021; 13:2051. [PMID: 34696481 PMCID: PMC8539440 DOI: 10.3390/v13102051] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/02/2021] [Accepted: 10/03/2021] [Indexed: 12/22/2022] Open
Abstract
This review summarizes research on virus diseases of cereals and oilseeds in Australia since the 1950s. All viruses known to infect the diverse range of cereal and oilseed crops grown in the continent's temperate, Mediterranean, subtropical and tropical cropping regions are included. Viruses that occur commonly and have potential to cause the greatest seed yield and quality losses are described in detail, focusing on their biology, epidemiology and management. These are: barley yellow dwarf virus, cereal yellow dwarf virus and wheat streak mosaic virus in wheat, barley, oats, triticale and rye; Johnsongrass mosaic virus in sorghum, maize, sweet corn and pearl millet; turnip yellows virus and turnip mosaic virus in canola and Indian mustard; tobacco streak virus in sunflower; and cotton bunchy top virus in cotton. The currently less important viruses covered number nine infecting nine cereal crops and 14 infecting eight oilseed crops (none recorded for rice or linseed). Brief background information on the scope of the Australian cereal and oilseed industries, virus epidemiology and management and yield loss quantification is provided. Major future threats to managing virus diseases effectively include damaging viruses and virus vector species spreading from elsewhere, the increasing spectrum of insecticide resistance in insect and mite vectors, resistance-breaking virus strains, changes in epidemiology, virus and vectors impacts arising from climate instability and extreme weather events, and insufficient industry awareness of virus diseases. The pressing need for more resources to focus on addressing these threats is emphasized and recommendations over future research priorities provided.
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Affiliation(s)
- Roger A. C. Jones
- UWA Institute of Agriculture, University of Western Australia, Crawley, WA 6009, Australia
| | - Murray Sharman
- Queensland Department of Agriculture and Fisheries, Ecosciences Precinct, P.O. Box 267, Brisbane, QLD 4001, Australia;
| | - Piotr Trębicki
- Grains Innovation Park, Agriculture Victoria, Department of Jobs, Precincts and Regions, Horsham, VIC 3400, Australia; (P.T.); (S.M.)
| | - Solomon Maina
- Grains Innovation Park, Agriculture Victoria, Department of Jobs, Precincts and Regions, Horsham, VIC 3400, Australia; (P.T.); (S.M.)
| | - Benjamin S. Congdon
- Department of Primary Industries and Regional Development, South Perth, WA 6151, Australia;
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56
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Buchner D, Macher TH, Beermann AJ, Werner MT, Leese F. Standardized high-throughput biomonitoring using DNA metabarcoding: Strategies for the adoption of automated liquid handlers. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2021; 8:100122. [PMID: 36156998 PMCID: PMC9488008 DOI: 10.1016/j.ese.2021.100122] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/26/2021] [Accepted: 08/26/2021] [Indexed: 05/11/2023]
Abstract
Reliable and comprehensive monitoring data are required to trace and counteract biodiversity loss. High-throughput metabarcoding using DNA extracted from community samples (bulk) or from water or sediment (environmental DNA) has revolutionized biomonitoring, given the capability to assess biodiversity across the tree of life rapidly with feasible effort and at a modest price. DNA metabarcoding can be upscaled to process hundreds of samples in parallel. However, while automated high-throughput analysis workflows are well-established in the medical sector, manual sample processing still predominates in biomonitoring laboratory workflows limiting the upscaling and standardization for routine monitoring applications. Here we present an automated, scalable, and reproducible metabarcoding workflow to extract DNA from bulk samples, perform PCR and library preparation on a liquid handler. Key features are the independent sample replication throughout the workflow and the use of many negative controls for quality assurance and quality control. We generated two datasets: i) a validation dataset consisting of 42 individual arthropod specimens of different species, and ii) a routine monitoring dataset consisting of 60 stream macroinvertebrate bulk samples. As a marker, we used the mitochondrial COI gene. Our results show that the developed single-deck workflow is free of laboratory-derived contamination and produces highly consistent results. Minor deviations between replicates are mostly due to stochastic differences for low abundant OTUs. Thus, we successfully demonstrated that robotic liquid handling can be used reliably from DNA extraction to final library preparation on a single deck, thereby substantially increasing throughput, reducing costs, and increasing data robustness for biodiversity assessments and monitoring.
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Affiliation(s)
- Dominik Buchner
- University of Duisburg-Essen, Aquatic Ecosystem Research, Universitätsstr. 5, 45141, Essen, Germany
| | - Till-Hendrik Macher
- University of Duisburg-Essen, Aquatic Ecosystem Research, Universitätsstr. 5, 45141, Essen, Germany
| | - Arne J. Beermann
- University of Duisburg-Essen, Aquatic Ecosystem Research, Universitätsstr. 5, 45141, Essen, Germany
- University of Duisburg-Essen, Centre for Water and Environmental Research (ZWU), Universitätsstr. 3, 45141, Essen, Germany
| | - Marie-Thérése Werner
- University of Duisburg-Essen, Aquatic Ecosystem Research, Universitätsstr. 5, 45141, Essen, Germany
| | - Florian Leese
- University of Duisburg-Essen, Aquatic Ecosystem Research, Universitätsstr. 5, 45141, Essen, Germany
- University of Duisburg-Essen, Centre for Water and Environmental Research (ZWU), Universitätsstr. 3, 45141, Essen, Germany
- Corresponding author. University of Duisburg-Essen, Aquatic Ecosystem Research, Universitätsstr. 5, 45141 Essen, Germany.
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57
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Paula DP. Next-Generation Sequencing and Its Impacts on Entomological Research in Ecology and Evolution. NEOTROPICAL ENTOMOLOGY 2021; 50:679-696. [PMID: 34374956 DOI: 10.1007/s13744-021-00895-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
The advent of NGS-based methods has been profoundly transforming entomological research. Through continual development and improvement of different methods and sequencing platforms, NGS has promoted mass elucidation of partial or whole genetic materials associated with beneficial insects, pests (of agriculture, forestry and animal, and human health), and species of conservation concern, helping to unravel ecological and evolutionary mechanisms and characterizing survival, trophic interactions, and dispersal. It is shifting the scale of biodiversity and environmental analyses from individuals and biodiversity indicator species to the large-scale study of communities and ecosystems using bulk samples of species or a mixed "soup" of environmental DNA. As the NGS-based methods have become more affordable, complexity demystified, and specificity and sensitivity proven, their use in entomological research has spread widely. This article presents several examples on how NGS-based methods have been used in entomology to provide incentives to apply them when appropriate and to open our minds to the expected advances in entomology that are yet to come.
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58
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Lopez MLD, Lin YY, Sato M, Hsieh CH, Shiah FK, Machida RJ. Using metatranscriptomics to estimate the diversity and composition of zooplankton communities. Mol Ecol Resour 2021; 22:638-652. [PMID: 34555254 PMCID: PMC9293175 DOI: 10.1111/1755-0998.13506] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 08/18/2021] [Accepted: 09/09/2021] [Indexed: 01/04/2023]
Abstract
DNA metabarcoding is a rapid, high‐resolution tool used for biomonitoring complex zooplankton communities. However, diversity estimates derived with this approach can be biased by the co‐detection of sequences from environmental DNA (eDNA), nuclear‐encoded mitochondrial (NUMT) pseudogene contamination, and taxon‐specific PCR primer affinity differences. To avoid these methodological uncertainties, we tested the use of metatranscriptomics as an alternative approach for characterizing zooplankton communities. Specifically, we compared metatranscriptomics with PCR‐based methods using genomic (gDNA) and complementary DNA (cDNA) amplicons, and morphology‐based data for estimating species diversity and composition for both mock communities and field‐collected samples. Mock community analyses showed that the use of gDNA mitochondrial cytochrome c oxidase I (mtCO1) amplicons inflates species richness due to the co‐detection of extra‐organismal eDNA. Significantly more amplicon sequence variants, nucleotide diversity, and indels were observed with gDNA amplicons than with cDNA, indicating the presence of putative NUMT pseudogenes. Moreover, PCR‐based methods failed to detect the most abundant species in mock communities due to priming site mismatch. Overall, metatranscriptomics provided estimates of species richness and composition that closely resembled those derived from morphological data. The use of metatranscriptomics was further tested using field‐collected samples, with the results showing consistent species diversity estimates among biological and technical replicates. Additionally, temporal zooplankton species composition changes could be monitored using different mitochondrial markers. These findings demonstrate the advantages of metatranscriptomics as an effective tool for monitoring diversity in zooplankton research.
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Affiliation(s)
- Mark Louie D Lopez
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan.,Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Ya-Ying Lin
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Mitsuhide Sato
- Department of Environment and Fisheries Resources, Nagasaki University, Nagasaki, Japan
| | - Chih-Hao Hsieh
- Institute of Oceanography, National Taiwan University, Taipei, Taiwan.,Environmental Change Research Center, Academia Sinica, Taipei, Taiwan
| | - Fuh-Kwo Shiah
- Environmental Change Research Center, Academia Sinica, Taipei, Taiwan
| | - Ryuji J Machida
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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Kolter A, Gemeinholzer B. Internal transcribed spacer primer evaluation for vascular plant metabarcoding. METABARCODING AND METAGENOMICS 2021. [DOI: 10.3897/mbmg.5.68155] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The unprecedented ongoing biodiversity decline necessitates scalable means of monitoring in order to fully understand the underlying causes. DNA metabarcoding has the potential to provide a powerful tool for accurate and rapid biodiversity monitoring. Unfortunately, in many cases, a lack of universal standards undermines the widespread application of metabarcoding. One of the most important considerations in metabarcoding of plants, aside from selecting a potent barcode marker, is primer choice. Our study evaluates published ITS primers in silico and in vitro, through mock communities and presents newly designed primers. We were able to show that a large proportion of previously available ITS primers have unfavourable attributes. Our combined results support the recommendation of the introduced primers ITS-3p62plF1 and ITS-4unR1 as the best current universal plant specific ITS2 primer combination. We also found that PCR optimisation, such as the addition of 5% DMSO, is essential to obtain meaningful results in ITS2 metabarcoding. Finally, we conclude that continuous quality assurance is indispensable for reliable metabarcoding results.
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60
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Lukic D, Eberle J, Thormann J, Holzschuh C, Ahrens D. Excluding spatial sampling bias does not eliminate oversplitting in DNA-based species delimitation analyses. Ecol Evol 2021; 11:10327-10337. [PMID: 34367578 PMCID: PMC8328443 DOI: 10.1002/ece3.7836] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/05/2021] [Accepted: 06/07/2021] [Indexed: 01/02/2023] Open
Abstract
DNA barcoding and DNA-based species delimitation are major tools in DNA taxonomy. Sampling has been a central debate in this context, because the geographical composition of samples affects the accuracy and performance of DNA barcoding. Performance of complex DNA-based species delimitation is to be tested under simpler conditions in absence of geographic sampling bias. Here, we present an empirical dataset sampled from a single locality in a Southeast-Asian biodiversity hotspot (Laos: Phou Pan mountain). We investigate the performance of various species delimitation approaches on a megadiverse assemblage of herbivorous chafer beetles (Coleoptera: Scarabaeidae) to infer whether species delimitation suffers in the same way from exaggerate infraspecific variation despite the lack of geographic genetic variation that led to inconsistencies between entities from DNA-based and morphology-based species inference in previous studies. For this purpose, a 658 bp fragment of the mitochondrial cytochrome c oxidase subunit 1 (cox1) was analyzed for a total of 186 individuals of 56 morphospecies. Tree-based and distance-based species delimitation methods were used. All approaches showed a rather limited match ratio (max. 77%) with morphospecies. Poisson tree process (PTP) and statistical parsimony network analysis (TCS) prevailingly over-splitted morphospecies, while 3% clustering and Automatic Barcode Gap Discovery (ABGD) also lumped several species into one entity. ABGD revealed the highest congruence between molecular operational taxonomic units (MOTUs) and morphospecies. Disagreements between morphospecies and MOTUs have to be explained by historically acquired geographic genetic differentiation, incomplete lineage sorting, and hybridization. The study once again highlights how important morphology still is in order to correctly interpret the results of molecular species delimitation.
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Affiliation(s)
- Daniel Lukic
- Zoologisches Forschungsmuseum Alexander KoenigZentrum für Taxonomie und EvolutionsforschungBonnGermany
| | - Jonas Eberle
- Zoologische EvolutionsbiologieParis‐Lodron‐UniversitätSalzburgAustria
| | - Jana Thormann
- Zoologisches Forschungsmuseum Alexander KoenigZentrum für Taxonomie und EvolutionsforschungBonnGermany
| | | | - Dirk Ahrens
- Zoologisches Forschungsmuseum Alexander KoenigZentrum für Taxonomie und EvolutionsforschungBonnGermany
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61
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A Rapid and Cost-Effective Identification of Invertebrate Pests at the Borders Using MinION Sequencing of DNA Barcodes. Genes (Basel) 2021; 12:genes12081138. [PMID: 34440312 PMCID: PMC8392835 DOI: 10.3390/genes12081138] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/23/2021] [Accepted: 07/24/2021] [Indexed: 12/12/2022] Open
Abstract
The rapid and accurate identification of invertebrate pests detected at the border is a challenging task. Current diagnostic methods used at the borders are mainly based on time consuming visual and microscopic examinations. Here, we demonstrate a rapid in-house workflow for DNA extraction, PCR amplification of the barcode region of the mitochondrial cytochrome oxidase subunit I (COI) gene and Oxford Nanopore Technologies (ONT) MinION sequencing of amplified products multiplexed after barcoding on ONT Flongle flow cells. A side-by-side comparison was conducted of DNA barcode sequencing-based identification and morphological identification of both large (>0.5 mm in length) and small (<0.5 mm in length) invertebrate specimens intercepted at the Australian border. DNA barcode sequencing results supported the morphological identification in most cases and enabled immature stages of invertebrates and their eggs to be identified more confidently. Results also showed that sequencing the COI barcode region using the ONT rapid sequencing principle is a cost-effective and field-adaptable approach for the rapid and accurate identification of invertebrate pests. Overall, the results suggest that MinION sequencing of DNA barcodes offers a complementary tool to the existing morphological diagnostic approaches and provides rapid, accurate, reliable and defendable evidence for identifying invertebrate pests at the border.
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Ferravante C, Memoli D, Palumbo D, Ciaramella P, Di Loria A, D'Agostino Y, Nassa G, Rizzo F, Tarallo R, Weisz A, Giurato G. HOME-BIO (sHOtgun MEtagenomic analysis of BIOlogical entities): a specific and comprehensive pipeline for metagenomic shotgun sequencing data analysis. BMC Bioinformatics 2021; 22:106. [PMID: 34225648 PMCID: PMC8256542 DOI: 10.1186/s12859-021-04004-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 02/08/2021] [Indexed: 12/12/2022] Open
Abstract
Background Next-Generation-Sequencing (NGS) enables detection of microorganisms present in biological and other matrices of various origin and nature, allowing not only the identification of known phyla and strains but also the discovery of novel ones. The large amount of metagenomic shotgun data produced by NGS require comprehensive and user-friendly pipelines for data analysis, that speed up the bioinformatics steps, relieving the users from the need to manually perform complex and time-consuming tasks. Results We describe here HOME-BIO (sHOtgun MEtagenomic analysis of BIOlogical entities), an exhaustive pipeline for metagenomics data analysis, comprising three independent analytical modules designed for an inclusive analysis of large NGS datasets. Conclusions HOME-BIO is a powerful and easy-to-use tool that can be run also by users with limited computational expertise. It allows in-depth analyses by removing low-complexity/ problematic reads, integrating the analytical steps that lead to a comprehensive taxonomy profile of each sample by querying different source databases, and it is customizable according to specific users’ needs.
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Affiliation(s)
- Carlo Ferravante
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Via S. Allende, 1, 84081, Baronissi, SA, Italy.,Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Via Delpino 1, 80137, Naples, Italy.,Genomix4Life, via S. Allende 43/L, 84081, Baronissi, SA, Italy
| | - Domenico Memoli
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Via S. Allende, 1, 84081, Baronissi, SA, Italy
| | - Domenico Palumbo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Via S. Allende, 1, 84081, Baronissi, SA, Italy
| | - Paolo Ciaramella
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Via Delpino 1, 80137, Naples, Italy
| | - Antonio Di Loria
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Via Delpino 1, 80137, Naples, Italy
| | - Ylenia D'Agostino
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Via S. Allende, 1, 84081, Baronissi, SA, Italy
| | - Giovanni Nassa
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Via S. Allende, 1, 84081, Baronissi, SA, Italy
| | - Francesca Rizzo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Via S. Allende, 1, 84081, Baronissi, SA, Italy
| | - Roberta Tarallo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Via S. Allende, 1, 84081, Baronissi, SA, Italy
| | - Alessandro Weisz
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Via S. Allende, 1, 84081, Baronissi, SA, Italy. .,CRGS - Genome Research Center for Health, University of Salerno Campus of Medicine, 84081, Baronissi, SA, Italy.
| | - Giorgio Giurato
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, Via S. Allende, 1, 84081, Baronissi, SA, Italy.
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63
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Sherpa S, Després L. The evolutionary dynamics of biological invasions: A multi-approach perspective. Evol Appl 2021; 14:1463-1484. [PMID: 34178098 PMCID: PMC8210789 DOI: 10.1111/eva.13215] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 02/22/2021] [Accepted: 03/02/2021] [Indexed: 01/02/2023] Open
Abstract
Biological invasions, the establishment and spread of non-native species in new regions, can have extensive economic and environmental consequences. Increased global connectivity accelerates introduction rates, while climate and land-cover changes may decrease the barriers to invasive populations spread. A detailed knowledge of the invasion history, including assessing source populations, routes of spread, number of independent introductions, and the effects of genetic bottlenecks and admixture on the establishment success, adaptive potential, and further spread, is crucial from an applied perspective to mitigate socioeconomic impacts of invasive species, as well as for addressing fundamental questions on the evolutionary dynamics of the invasion process. Recent advances in genomics together with the development of geographic information systems provide unprecedented large genetic and environmental datasets at global and local scales to link population genomics, landscape ecology, and species distribution modeling into a common framework to study the invasion process. Although the factors underlying population invasiveness have been extensively reviewed, analytical methods currently available to optimally combine molecular and environmental data for inferring invasive population demographic parameters and predicting further spreading are still under development. In this review, we focus on the few recent insect invasion studies that combine different datasets and approaches to show how integrating genetic, observational, ecological, and environmental data pave the way to a more integrative biological invasion science. We provide guidelines to study the evolutionary dynamics of invasions at each step of the invasion process, and conclude on the benefits of including all types of information and up-to-date analytical tools from different research areas into a single framework.
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Affiliation(s)
- Stéphanie Sherpa
- CNRSLECAUniversité Grenoble AlpesUniversité Savoie Mont BlancGrenobleFrance
| | - Laurence Després
- CNRSLECAUniversité Grenoble AlpesUniversité Savoie Mont BlancGrenobleFrance
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64
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Yang C, Bohmann K, Wang X, Cai W, Wales N, Ding Z, Gopalakrishnan S, Yu DW. Biodiversity Soup II: A bulk‐sample metabarcoding pipeline emphasizing error reduction. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13602] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Chunyan Yang
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of Sciences Kunming China
| | - Kristine Bohmann
- Section for Evolutionary Genomics Globe Institute Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
| | - Xiaoyang Wang
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of Sciences Kunming China
| | - Wang Cai
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of Sciences Kunming China
| | - Nathan Wales
- Section for Evolutionary Genomics Globe Institute Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
- Department of Archaeology University of York York UK
| | - Zhaoli Ding
- Biodiversity Genomics Center Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics Globe Institute Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
| | - Douglas W. Yu
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of Sciences Kunming China
- School of Biological Sciences University of East AngliaNorwich Research Park Norwich UK
- Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming China
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65
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Highly diverse and rapidly spreading: Melanagromyza sojae threatens the soybean belt of South America. Biol Invasions 2021. [DOI: 10.1007/s10530-020-02447-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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66
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Validation of an Effective Protocol for Culicoides Latreille (Diptera: Ceratopogonidae) Detection Using eDNA Metabarcoding. INSECTS 2021; 12:insects12050401. [PMID: 33946322 PMCID: PMC8146839 DOI: 10.3390/insects12050401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 04/20/2021] [Accepted: 04/27/2021] [Indexed: 11/16/2022]
Abstract
Simple Summary All organisms shed genetic material into the environment, which is known as environmental DNA. Current molecular technologies allow for sequencing molecular markers in complex environmental samples. The use of these methods permits an effective identification and monitoring of flighted insects such as Culicoides species. These biting midges are agricultural pests of significant economic concern. This study identified Culicoides species using a novel molecular-based approach for this group and compared these results to morphological identifications of the specimens collected. There were forty-two Culicoides specimens collected in total, using a saturated salt solution as a collection fluid. Molecular identification detected four species. Using morphological identification, we identified two out of these four taxonomic ranks at the species level and one at the subgenus level. The inconsistency in identifying Culicoides specimens to the species level indicates the need for curated DNA reference libraries for molecular-based identification. The saturated salt solution used in the traps preserved the morphological characteristics and the organisms’ environmental DNA, which is an essential contribution of this study. Abstract eDNA metabarcoding is an effective molecular-based identification method for the biosurveillance of flighted insects. An eDNA surveillance approach maintains specimens for secondary morphological identification useful for regulatory applications. This study identified Culicoides species using eDNA metabarcoding and compared these results to morphological identifications of trapped specimens. Insects were collected using ultraviolet (UV) lighted fan traps containing a saturated salt (NaCl) solution from two locations in Guelph, Ontario, Canada. There were forty-two Culicoides specimens collected in total. Molecular identification detected four species, C. biguttatus, C. stellifer, C. obsoletus, and C. mulrennani. Using morphological identification, two out of these four taxonomic ranks were confirmed at the species level (C. biguttatus and C. stellifer) and one was confirmed at the subgenus level (Avaritia [C. obsoletus]). No molecular detection of Culicoides species occurred in traps with an abundance of less than three individuals per taxon. The inconsistency in identifying Culicoides specimens to the species level punctuates the need for curated DNA reference libraries for Culicoides. In conclusion, the saturated salt (NaCl) solution preserved the Culicoides’ morphological characteristics and the eDNA.
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67
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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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68
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Maina S, Zheng L, Rodoni BC. Targeted Genome Sequencing (TG-Seq) Approaches to Detect Plant Viruses. Viruses 2021; 13:583. [PMID: 33808381 PMCID: PMC8066983 DOI: 10.3390/v13040583] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/22/2021] [Accepted: 03/27/2021] [Indexed: 12/18/2022] Open
Abstract
Globally, high-throughput sequencing (HTS) has been used for virus detection in germplasm certification programs. However, sequencing costs have impeded its implementation as a routine diagnostic certification tool. In this study, the targeted genome sequencing (TG-Seq) approach was developed to simultaneously detect multiple (four) viral species of; Pea early browning virus (PEBV), Cucumber mosaic virus (CMV), Bean yellow mosaic virus (BYMV) and Pea seedborne mosaic virus (PSbMV). TG-Seq detected all the expected viral amplicons within multiplex PCR (mPCR) reactions. In contrast, the expected PCR amplicons were not detected by gel electrophoresis (GE). For example, for CMV, GE only detected RNA1 and RNA2 while TG-Seq detected all the three RNA components of CMV. In an mPCR to amplify all four viruses, TG-Seq readily detected each virus with more than 732,277 sequence reads mapping to each amplicon. In addition, TG-Seq also detected all four amplicons within a 10-8 serial dilution that were not detectable by GE. Our current findings reveal that the TG-Seq approach offers significant potential and is a highly sensitive targeted approach for detecting multiple plant viruses within a given biological sample. This is the first study describing direct HTS of plant virus mPCR products. These findings have major implications for grain germplasm healthy certification programs and biosecurity management in relation to pathogen entry into Australia and elsewhere.
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Affiliation(s)
- Solomon Maina
- Microbial Sciences, Pests & Diseases, Agriculture Victoria, 110 Natimuk Road, Horsham, Victoria 3400, Australia
- Australian Grains Genebank, Agriculture Victoria, 110 Natimuk Road, Horsham, Victoria 3400, Australia
| | - Linda Zheng
- Microbial Sciences, Pests & Diseases, Agriculture Victoria, AgriBio, 5 Ring Road, Bundoora, Victoria 3083, Australia; (L.Z.); (B.C.R.)
| | - Brendan C. Rodoni
- Microbial Sciences, Pests & Diseases, Agriculture Victoria, AgriBio, 5 Ring Road, Bundoora, Victoria 3083, Australia; (L.Z.); (B.C.R.)
- School of Applied Systems Biology (SASB), La Trobe University, Bundoora, Victoria 3083, Australia
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69
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Wu X, Luo H, Xu F, Ge C, Li S, Deng X, Wiedmann M, Baker RC, Stevenson A, Zhang G, Tang S. Evaluation of Salmonella Serotype Prediction With Multiplex Nanopore Sequencing. Front Microbiol 2021; 12:637771. [PMID: 33776971 PMCID: PMC7987803 DOI: 10.3389/fmicb.2021.637771] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 02/08/2021] [Indexed: 12/13/2022] Open
Abstract
The use of whole genome sequencing (WGS) data generated by the long-read sequencing platform Oxford Nanopore Technologies (ONT) has been shown to provide reliable results for Salmonella serotype prediction in a previous study. To further meet the needs of industry for accurate, rapid, and cost-efficient Salmonella confirmation and serotype classification, we evaluated the serotype prediction accuracy of using WGS data from multiplex ONT sequencing with three, four, five, seven, or ten Salmonella isolates (each isolate represented one Salmonella serotype) pooled in one R9.4.1 flow cell. Each multiplexing strategy was repeated with five flow cells, and the loaded samples were sequenced simultaneously in a GridION sequencer for 48 h. In silico serotype prediction was performed using both SeqSero2 (for raw reads and genome assemblies) and SISTR (for genome assemblies) software suites. An average of 10.63 Gbp of clean sequencing data was obtained per flow cell. We found that the unevenness of data yield among each multiplexed isolate was a major barrier for shortening sequencing time. Using genome assemblies, both SeqSero2 and SISTR accurately predicted all the multiplexed isolates under each multiplexing strategy when depth of genome coverage ≥50× for each isolate. We identified that cross-sample barcode assignment was a major cause of prediction errors when raw sequencing data were used for prediction. This study also demonstrated that, (i) sequence data generated by ONT multiplex sequencing can be used to simultaneously predict serotype for three to ten Salmonella isolates, (ii) with three to ten Salmonella isolates multiplexed, genome coverage at ≥50× per isolate was obtained within an average of 6 h of ONT multiplex sequencing, and (iii) with five isolates multiplexed, the cost per isolate might be reduced to 23% of that incurred with single ONT sequencing. This study is a starting point for future validation of multiplex ONT WGS as a cost-efficient and rapid Salmonella confirmation and serotype classification tool for the food industry.
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Affiliation(s)
- Xingwen Wu
- Mars Global Food Safety Center, Beijing, China
| | - Hao Luo
- Mars Global Food Safety Center, Beijing, China
| | - Feng Xu
- Mars Global Food Safety Center, Beijing, China
| | - Chongtao Ge
- Mars Global Food Safety Center, Beijing, China
| | - Shaoting Li
- Center for Food Safety, University of Georgia, Griffin, GA, United States
| | - Xiangyu Deng
- Center for Food Safety, University of Georgia, Griffin, GA, United States
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, NY, United States
| | | | | | | | - Silin Tang
- Mars Global Food Safety Center, Beijing, China
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70
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Milián‐García Y, Young R, Madden M, Bullas‐Appleton E, Hanner RH. Optimization and validation of a cost-effective protocol for biosurveillance of invasive alien species. Ecol Evol 2021; 11:1999-2014. [PMID: 33717437 PMCID: PMC7920766 DOI: 10.1002/ece3.7139] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 11/23/2020] [Accepted: 11/26/2020] [Indexed: 01/30/2023] Open
Abstract
Environmental DNA (eDNA) metabarcoding has revolutionized biodiversity monitoring and invasive pest biosurveillance programs. The introduction of insect pests considered invasive alien species (IAS) into a non-native range poses a threat to native plant health. The early detection of IAS can allow for prompt actions by regulating authorities, thereby mitigating their impacts. In the present study, we optimized and validated a fast and cost-effective eDNA metabarcoding protocol for biosurveillance of IAS and characterization of insect and microorganism diversity. Forty-eight traps were placed, following the CFIA's annual forest insect trapping survey, at four locations in southern Ontario that are high risk for forest IAS. We collected insects and eDNA samples using Lindgren funnel traps that contained a saturated salt (NaCl) solution in the collection jar. Using cytochrome c oxidase I (COI) as a molecular marker, a modified Illumina protocol effectively identified 2,535 Barcode Index Numbers (BINs). BINs were distributed among 57 Orders and 304 Families, with the vast majority being arthropods. Two IAS (Agrilus planipennis and Lymantria dispar) are regulated by the Canadian Food Inspection Agency (CFIA) as plant health pests, are known to occur in the study area, and were identified through eDNA in collected traps. Similarly, using 16S ribosomal RNA and nuclear ribosomal internal transcribed spacer (ITS), five bacterial and three fungal genera, which contain species of regulatory concern across several Canadian jurisdictions, were recovered from all sampling locations. Our study results reaffirm the effectiveness and importance of integrating eDNA metabarcoding as part of identification protocols in biosurveillance programs.
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Affiliation(s)
| | - Robert Young
- Department of Integrative BiologyUniversity of GuelphGuelphONCanada
| | - Mary Madden
- Department of Integrative BiologyUniversity of GuelphGuelphONCanada
| | | | - Robert H. Hanner
- Department of Integrative BiologyUniversity of GuelphGuelphONCanada
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71
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Wirta H, Abrego N, Miller K, Roslin T, Vesterinen E. DNA traces the origin of honey by identifying plants, bacteria and fungi. Sci Rep 2021; 11:4798. [PMID: 33637887 PMCID: PMC7910293 DOI: 10.1038/s41598-021-84174-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 02/03/2021] [Indexed: 01/31/2023] Open
Abstract
The regional origin of a food product commonly affects its value. To this, DNA-based identification of tissue remains could offer fine resolution. For honey, this would allow the usage of not only pollen but all plant tissue, and also that of microbes in the product, for discerning the origin. Here we examined how plant, bacterial and fungal taxa identified by DNA metabarcoding and metagenomics differentiate between honey samples from three neighbouring countries. To establish how the taxonomic contents of honey reflect the country of origin, we used joint species distribution modelling. At the lowest taxonomic level by metabarcoding, with operational taxonomic units, the country of origin explained the majority of variation in the data (70-79%), with plant and fungal gene regions providing the clearest distinction between countries. At the taxonomic level of genera, plants provided the most separation between countries with both metabarcoding and metagenomics. The DNA-based methods distinguish the countries more than the morphological pollen identification and the removal of pollen has only a minor effect on taxonomic recovery by DNA. As we find good resolution among honeys from regions with similar biota, DNA-based methods hold great promise for resolving honey origins among more different regions.
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Affiliation(s)
- Helena Wirta
- Faculty of Agriculture and Forestry, University of Helsinki, P.O. Box 27, 00014, Helsinki, Finland.
| | - Nerea Abrego
- Faculty of Agriculture and Forestry, University of Helsinki, P.O. Box 27, 00014, Helsinki, Finland
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, 40014, Jyväskylä, Finland
| | - Kirsten Miller
- Department of Ecology, Swedish University of Agricultural Sciences, P.O. Box 7044, 750 07, Uppsala, Sweden
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
| | - Tomas Roslin
- Faculty of Agriculture and Forestry, University of Helsinki, P.O. Box 27, 00014, Helsinki, Finland
- Department of Ecology, Swedish University of Agricultural Sciences, P.O. Box 7044, 750 07, Uppsala, Sweden
| | - Eero Vesterinen
- Department of Ecology, Swedish University of Agricultural Sciences, P.O. Box 7044, 750 07, Uppsala, Sweden
- Department of Biology, University of Turku, Turku, Finland
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72
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Baloğlu B, Chen Z, Elbrecht V, Braukmann T, MacDonald S, Steinke D. A workflow for accurate metabarcoding using nanopore MinION sequencing. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13561] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Bilgenur Baloğlu
- Centre for Biodiversity Genomics University of Guelph Guelph ON Canada
| | - Zhewei Chen
- California Institute of Technology Pasadena CA USA
| | - Vasco Elbrecht
- Centre for Biodiversity Genomics University of Guelph Guelph ON Canada
- Centre for Biodiversity MonitoringZoological Research Museum Alexander Koenig Bonn Germany
| | - Thomas Braukmann
- Centre for Biodiversity Genomics University of Guelph Guelph ON Canada
| | - Shanna MacDonald
- Centre for Biodiversity Genomics University of Guelph Guelph ON Canada
| | - Dirk Steinke
- Centre for Biodiversity Genomics University of Guelph Guelph ON Canada
- Integrative Biology University of Guelph Guelph ON Canada
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73
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Martoni F, Valenzuela I, Blacket MJ. On the complementarity of DNA barcoding and morphology to distinguish benign endemic insects from possible pests: the case of Dirioxa pornia and the tribe Acanthonevrini (Diptera: Tephritidae: Phytalmiinae) in Australia. INSECT SCIENCE 2021; 28:261-270. [PMID: 32096585 PMCID: PMC7818419 DOI: 10.1111/1744-7917.12769] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 02/20/2020] [Accepted: 02/22/2020] [Indexed: 06/10/2023]
Abstract
Fruit flies are considered economically important insects due to some species being agricultural pests. However, morphological identification of fruit fly adults and larvae can be difficult requiring a high level of taxonomic expertise, with misidentifications causing problematic false-positive/negative results. While destructive molecular techniques can assist with the identification process, these often cannot be applied where it is mandatory to retain a voucher reference specimen. In this work, we non-destructively (and partial-destructively) processed larvae and adults mostly belonging to the species Dirioxa pornia (Walker, 1849), of the poorly studied nonpest fruit fly tribe Acanthonevrini (Tephritidae) from Australia, to enable molecular identifications whilst retaining morphological vouchers. By retaining the morphological features of specimens, we confirmed useful characters for genus/species-level identification, contributing to improved accuracy for future diagnostics using both molecular and morphological approaches. We provide DNA barcode information for three species of Acanthonevrini known from Australia, which prior to our study was only available for a single species, D. pornia. Our specimen examinations provide new distribution records for three nonpest species: Acanthonevroides variegatus Permkam and Hancock, 1995 in South Australia, Acanthonevroides basalis (Walker, 1853) and D. pornia in Victoria, Australia; as well as new host plant records for D. pornia, from kangaroo apple, apricot and loquat.
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Affiliation(s)
- Francesco Martoni
- Agriculture Victoria ResearchAgriBio Centre for AgriBioscienceBundooraVictoriaAustralia
| | - Isabel Valenzuela
- Agriculture Victoria ResearchAgriBio Centre for AgriBioscienceBundooraVictoriaAustralia
| | - Mark J. Blacket
- Agriculture Victoria ResearchAgriBio Centre for AgriBioscienceBundooraVictoriaAustralia
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74
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Montgomery GA, Belitz MW, Guralnick RP, Tingley MW. Standards and Best Practices for Monitoring and Benchmarking Insects. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2020.579193] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Benchmark studies of insect populations are increasingly relevant and needed amid accelerating concern about insect trends in the Anthropocene. The growing recognition that insect populations may be in decline has given rise to a renewed call for insect population monitoring by scientists, and a desire from the broader public to participate in insect surveys. However, due to the immense diversity of insects and a vast assortment of data collection methods, there is a general lack of standardization in insect monitoring methods, such that a sudden and unplanned expansion of data collection may fail to meet its ecological potential or conservation needs without a coordinated focus on standards and best practices. To begin to address this problem, we provide simple guidelines for maximizing return on proven inventory methods that will provide insect benchmarking data suitable for a variety of ecological responses, including occurrence and distribution, phenology, abundance and biomass, and diversity and species composition. To track these responses, we present seven primary insect sampling methods—malaise trapping, light trapping, pan trapping, pitfall trappings, beating sheets, acoustic monitoring, and active visual surveys—and recommend standards while highlighting examples of model programs. For each method, we discuss key topics such as recommended spatial and temporal scales of sampling, important metadata to track, and degree of replication needed to produce rigorous estimates of ecological responses. We additionally suggest protocols for scalable insect monitoring, from backyards to national parks. Overall, we aim to compile a resource that can be used by diverse individuals and organizations seeking to initiate or improve insect monitoring programs in this era of rapid change.
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75
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Ducotterd C, Crovadore J, Lefort F, Rubin JF, Ursenbacher S. A powerful long metabarcoding method for the determination of complex diets from faecal analysis of the European pond turtle (Emys orbicularis, L. 1758). Mol Ecol Resour 2020; 21:433-447. [PMID: 33047508 PMCID: PMC7821331 DOI: 10.1111/1755-0998.13277] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 08/31/2020] [Accepted: 10/01/2020] [Indexed: 01/16/2023]
Abstract
High‐throughput sequencing has become an accurate method for the identification of species present in soil, water, faeces, gut or stomach contents. However, information at the species level is limited due to the choice of short barcodes and based on the idea that DNA is too degraded to allow longer sequences to be amplified. We have therefore developed a long DNA metabarcoding method based on the sequencing of short reads followed by de novo assembly, which can precisely identify the taxonomic groups of organisms associated with complex diets, such as omnivorous individuals. The procedure includes 11 different primer pairs targeting the COI gene, the large subunit of the ribulose‐1,5‐bisphosphate carboxylase gene, the maturase K gene, the 28S rRNA and the trnL‐trnF chloroplastic region. We validated this approach using 32 faeces samples from an omnivorous reptile, the European pond turtle (Emys orbicularis, L. 1758). This metabarcoding approach was assessed using controlled experiments including mock communities and faecal samples from captive feeding trials. The method allowed us to accurately identify prey DNA present in the diet of the European pond turtles to the species level in most of the cases (82.4%), based on the amplicon lengths of multiple markers (168–1,379 bp, average 546 bp), and produced by de novo assembly. The proposed approach can be adapted to analyse various diets, in numerous conservation and ecological applications. It is consequently appropriate for detecting fine dietary variations among individuals, populations and species as well as for the identification of rare food items.
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Affiliation(s)
- Charlotte Ducotterd
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Centre Emys, Association de Protection et Récupération des Tortues, Chavornay, Switzerland.,La Maison de la Rivière, Tolochenaz, Switzerland.,HEPIA, HES-SO, University of Applied Sciences and Arts Western Switzerland, Jussy, Switzerland
| | - Julien Crovadore
- HEPIA, HES-SO, University of Applied Sciences and Arts Western Switzerland, Jussy, Switzerland
| | - François Lefort
- HEPIA, HES-SO, University of Applied Sciences and Arts Western Switzerland, Jussy, Switzerland
| | - Jean-François Rubin
- La Maison de la Rivière, Tolochenaz, Switzerland.,HEPIA, HES-SO, University of Applied Sciences and Arts Western Switzerland, Jussy, Switzerland
| | - Sylvain Ursenbacher
- Department of Environmental Sciences, Section of Conservation Biology, University of Basel, Basel, Switzerland.,info fauna - Centre Suisse de Cartographie de la Faune (CSCF) and Centre de coordination pour les reptiles et les amphibiens de Suisse (Karch), Neuchâtel, Switzerland
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76
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Djemiel C, Goulas E, Badalato N, Chabbert B, Hawkins S, Grec S. Targeted Metagenomics of Retting in Flax: The Beginning of the Quest to Harness the Secret Powers of the Microbiota. Front Genet 2020; 11:581664. [PMID: 33193706 PMCID: PMC7652851 DOI: 10.3389/fgene.2020.581664] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 09/21/2020] [Indexed: 12/13/2022] Open
Abstract
The mechanical and chemical properties of natural plant fibers are determined by many different factors, both intrinsic and extrinsic to the plant, during growth but also after harvest. A better understanding of how all these factors exert their effect and how they interact is necessary to be able to optimize fiber quality for use in different industries. One important factor is the post-harvest process known as retting, representing the first step in the extraction of bast fibers from the stem of species such as flax and hemp. During this process microorganisms colonize the stem and produce hydrolytic enzymes that target cell wall polymers thereby facilitating the progressive destruction of the stem and fiber bundles. Recent advances in sequencing technology have allowed researchers to implement targeted metagenomics leading to a much better characterization of the microbial communities involved in retting, as well as an improved understanding of microbial dynamics. In this paper we review how our current knowledge of the microbiology of retting has been improved by targeted metagenomics and discuss how related '-omics' approaches might be used to fully characterize the functional capability of the retting microbiome.
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Affiliation(s)
- Christophe Djemiel
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Estelle Goulas
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Nelly Badalato
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Brigitte Chabbert
- Université de Reims Champagne Ardenne, INRAE, UMR FARE A 614, Reims, France
| | - Simon Hawkins
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Sébastien Grec
- Univ. Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
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77
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Castle ST, Allan N, Clifford D, Aylward CM, Ramsey J, Fascetti AJ, Pesapane R, Roy A, Statham M, Sacks B, Foley J. Diet composition analysis provides new management insights for a highly specialized endangered small mammal. PLoS One 2020; 15:e0240136. [PMID: 33007017 PMCID: PMC7531790 DOI: 10.1371/journal.pone.0240136] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 09/20/2020] [Indexed: 01/04/2023] Open
Abstract
The critically endangered Amargosa vole (Microtus californicus scirpensis) is found only in rare marsh habitat near Tecopa, California in a plant community dominated by three-square bulrush (Schoenoplectus americanus). Since the earliest research on the Amargosa vole, the existing paradigm has been that these voles are obligatorily dependent on bulrush as their only food source and for the three-dimensional canopy and litter structure it provides for predator avoidance. However, no prior research has confirmed the diet of the Amargosa vole. In this study we characterized the Amargosa vole' nutritional needs, analyzed the quality of bulrush by forage analysis, and performed microhistological and metabarcoding analyses of vole feces to determine what foods were consumed in the wild. All bulrush plant tissues analyzed were low in fat (from 0.9% of dry matter in roots to 3.6% in seeds), high in neutral detergent fiber (from 5.9% in rhizomes to 33.6% in seeds), and low in protein (7.3-8.4%). These findings support the conclusion that bulrush alone is unlikely to support vole survival and reproduction. Fecal microhistology and DNA metabarcoding revealed relatively diverse diets including plants in 14 families, with rushes (Juncaceae), bulrushes (Cyperaceae), and grasses (Poaceae) being the most common diet items. On microhistology, all analyzed samples contained bulrush, sedges (Carex sp.), rushes (Juncus sp.), and beaked spikerush (Eleocharis rostrellata) even from marshes where non-bulrush plants were uncommon. There was evidence of insects at <1% in two marshes but none in the remaining marshes. Metabarcoding detected ten genera of plants. When considering non-Schoenoplectus targets, for which metabarcoding had poor sensitivity, saltgrass (Distichlis spicata) was the most commonly detected species, with prominent contributions from seaside arrowgrass (Triglochin concinna) and yerba mansa (Anemopsis californica) as well. Diversity of vole diets generally increased with increasing site plant diversity, but differences were not statistically significant. Confirming details about dietary behaviors is critical for informing appropriate conservation planning including habitat management and reintroduction of voles into new sites.
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Affiliation(s)
- Stephanie T. Castle
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, United States of America
- Wildlife Investigations Lab, California Department of Fish and Wildlife, Rancho Cordova, CA, United States of America
| | - Nora Allan
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, United States of America
| | - Deana Clifford
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, United States of America
- Wildlife Investigations Lab, California Department of Fish and Wildlife, Rancho Cordova, CA, United States of America
| | - Cody M. Aylward
- Department of Fish, Wildlife and Conservation Biology, University of California, Davis, CA, United States of America
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, Davis, CA, United States of America
| | - Jon Ramsey
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, CA, United States of America
| | - Andrea J. Fascetti
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, CA, United States of America
| | - Risa Pesapane
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, United States of America
| | - Austin Roy
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, United States of America
| | - Mark Statham
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, Davis, CA, United States of America
| | - Benjamin Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, Davis, CA, United States of America
- Department of Population Health, and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, United States of America
| | - Janet Foley
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, United States of America
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78
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Galimberti A, Assandri G, Maggioni D, Ramazzotti F, Baroni D, Bazzi G, Chiandetti I, Corso A, Ferri V, Galuppi M, Ilahiane L, La Porta G, Laddaga L, Landi F, Mastropasqua F, Ramellini S, Santinelli R, Soldato G, Surdo S, Casiraghi M. Italian odonates in the Pandora's box: A comprehensive DNA barcoding inventory shows taxonomic warnings at the Holarctic scale. Mol Ecol Resour 2020; 21:183-200. [PMID: 32755053 DOI: 10.1111/1755-0998.13235] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 12/20/2022]
Abstract
The Odonata are considered among the most endangered freshwater faunal taxa. Their DNA-based monitoring relies on validated reference data sets that are often lacking or do not cover important biogeographical centres of diversification. This study presents the results of a DNA barcoding campaign on Odonata, based on the standard 658-bp 5' end region of the mitochondrial COI gene, involving the collection of 812 specimens (409 of which barcoded) from peninsular Italy and its main islands (328 localities), belonging to all the 88 species (31 Zygoptera and 57 Anisoptera) known from the country. Additional BOLD and GenBank data from Holarctic samples expanded the data set to 1,294 DNA barcodes. A multi-approach species delimitation analysis involving two distance (OT and ABGD) and four tree-based (PTP, MPTP, GMYC and bGMYC) methods was used to explore these data. Of the 88 investigated morphospecies, 75 (85%) unequivocally corresponded to distinct molecular operational units, whereas the remaining ones were classified as 'warnings' (i.e. showing a mismatch between morphospecies assignment and DNA-based species delimitation). These results are in contrast with other DNA barcoding studies on Odonata showing up to 95% of identification success. The species causing warnings were grouped into three categories depending on if they showed low, high or mixed genetic divergence patterns. The analysis of haplotype networks revealed unexpected intraspecific complexity at the Italian, Palearctic and Holarctic scale, possibly indicating the occurrence of cryptic species. Overall, this study provides new insights into the taxonomy of odonates and a valuable basis for future DNA and eDNA-based monitoring studies.
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Affiliation(s)
- Andrea Galimberti
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano - Bicocca, Milan, Italy
| | - Giacomo Assandri
- Area per l'Avifauna Migratrice, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano Emilia, Italy
| | - Davide Maggioni
- Department of Environmental and Earth Sciences (DISAT), University of Milano - Bicocca, Milan, Italy.,Marine Research and High Education (MaRHE) Center, University of Milano - Bicocca, Faafu Magoodhoo, Maldives
| | - Fausto Ramazzotti
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano - Bicocca, Milan, Italy
| | - Daniele Baroni
- Section of Ecology, Department of Biology, University of Turku, Turku, Finland
| | | | | | | | - Vincenzo Ferri
- Department of Biology, University of Rome 2 - Tor Vergata, Rome, Italy
| | | | - Luca Ilahiane
- Department of Sciences and Technological Innovation (DISIT), University of Eastern Piedmont, Alessandria, Italy
| | - Gianandrea La Porta
- Department of Chemistry, Biology and Biotechnology (DCBB), University of Perugia, Perugia, Italy
| | - Lorenzo Laddaga
- Società di Scienze Naturali del Verbano Cusio Ossola, Natural Science Museum Collegio Mellerio Rosmini, Domodossola, Italy
| | | | | | - Samuele Ramellini
- Department of Ecology and Environmental Policies, University of Milan, Milan, Italy
| | | | | | - Salvatore Surdo
- Department of Agriculture, Food and Forest Sciences, University of Palermo, Palermo, Italy
| | - Maurizio Casiraghi
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano - Bicocca, Milan, Italy
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79
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Jactel H, Desprez-Loustau ML, Battisti A, Brockerhoff E, Santini A, Stenlid J, Björkman C, Branco M, Dehnen-Schmutz K, Douma JC, Drakulic J, Drizou F, Eschen R, Franco JC, Gossner MM, Green S, Kenis M, Klapwijk MJ, Liebhold AM, Orazio C, Prospero S, Robinet C, Schroeder M, Slippers B, Stoev P, Sun J, van den Dool R, Wingfield MJ, Zalucki MP. Pathologists and entomologists must join forces against forest pest and pathogen invasions. NEOBIOTA 2020. [DOI: 10.3897/neobiota.58.54389] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The world’s forests have never been more threatened by invasions of exotic pests and pathogens, whose causes and impacts are reinforced by global change. However, forest entomologists and pathologists have, for too long, worked independently, used different concepts and proposed specific management methods without recognising parallels and synergies between their respective fields. Instead, we advocate increased collaboration between these two scientific communities to improve the long-term health of forests.
Our arguments are that the pathways of entry of exotic pests and pathogens are often the same and that insects and fungi often coexist in the same affected trees. Innovative methods for preventing invasions, early detection and identification of non-native species, modelling of their impact and spread and prevention of damage by increasing the resistance of ecosystems can be shared for the management of both pests and diseases.
We, therefore, make recommendations to foster this convergence, proposing in particular the development of interdisciplinary research programmes, the development of generic tools or methods for pest and pathogen management and capacity building for the education and training of students, managers, decision-makers and citizens concerned with forest health.
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80
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Knot IE, Zouganelis GD, Weedall GD, Wich SA, Rae R. DNA Barcoding of Nematodes Using the MinION. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00100] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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81
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Kennedy SR, Prost S, Overcast I, Rominger AJ, Gillespie RG, Krehenwinkel H. High-throughput sequencing for community analysis: the promise of DNA barcoding to uncover diversity, relatedness, abundances and interactions in spider communities. Dev Genes Evol 2020; 230:185-201. [PMID: 32040713 PMCID: PMC7127999 DOI: 10.1007/s00427-020-00652-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 01/29/2020] [Indexed: 12/19/2022]
Abstract
Large-scale studies on community ecology are highly desirable but often difficult to accomplish due to the considerable investment of time, labor and, money required to characterize richness, abundance, relatedness, and interactions. Nonetheless, such large-scale perspectives are necessary for understanding the composition, dynamics, and resilience of biological communities. Small invertebrates play a central role in ecosystems, occupying critical positions in the food web and performing a broad variety of ecological functions. However, it has been particularly difficult to adequately characterize communities of these animals because of their exceptionally high diversity and abundance. Spiders in particular fulfill key roles as both predator and prey in terrestrial food webs and are hence an important focus of ecological studies. In recent years, large-scale community analyses have benefitted tremendously from advances in DNA barcoding technology. High-throughput sequencing (HTS), particularly DNA metabarcoding, enables community-wide analyses of diversity and interactions at unprecedented scales and at a fraction of the cost that was previously possible. Here, we review the current state of the application of these technologies to the analysis of spider communities. We discuss amplicon-based DNA barcoding and metabarcoding for the analysis of community diversity and molecular gut content analysis for assessing predator-prey relationships. We also highlight applications of the third generation sequencing technology for long read and portable DNA barcoding. We then address the development of theoretical frameworks for community-level studies, and finally highlight critical gaps and future directions for DNA analysis of spider communities.
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Affiliation(s)
- Susan R Kennedy
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology, Onna, Okinawa, Japan
| | - Stefan Prost
- LOEWE-Centre for Translational Biodiversity Genomics, Senckenberg Museum, Frankfurt, Germany
- National Zoological Garden, South African National Biodiversity Institute, Pretoria, South Africa
| | - Isaac Overcast
- Graduate Center of the City University New York, New York, NY, USA
- Ecole Normale Supérieure, Paris, France
| | | | - Rosemary G Gillespie
- Environmental Sciences Policy and Management, University of California Berkeley, Berkeley, CA, USA
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82
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Machado DDN, Costa EC, Guedes JVC, Barbosa LR, Martínez G, Mayorga SI, Ramos SO, Branco M, Garcia A, Vanegas-Rico JM, Jiménez-Quiroz E, Laudonia S, Novoselsky T, Hodel DR, Arakelian G, Silva H, Perini CR, Valmorbida I, Ugalde GA, Arnemann JA. One maternal lineage leads the expansion of Thaumastocoris peregrinus (Hemiptera: Thaumastocoridae) in the New and Old Worlds. Sci Rep 2020; 10:3487. [PMID: 32103053 PMCID: PMC7044308 DOI: 10.1038/s41598-020-60236-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 02/05/2020] [Indexed: 11/09/2022] Open
Abstract
The bronze bug, Thaumastocoris peregrinus, an Australian native insect, has become a nearly worldwide invasive pest in the last 16 years and has been causing significant damage to eucalypts (Myrtaceae), including Eucalyptus spp. and Corymbia spp. Its rapid expansion leads to new questions about pathways and routes that T. peregrinus used to invade other continents and countries. We used mtDNA to characterize specimens of T. peregrinus collected from 10 countries where this species has become established, including six recently invaded countries: Chile, Israel, Mexico, Paraguay, Portugal, and the United States of America. We then combined our mtDNA data with previous data available from South Africa, Australia, and Europe to construct a world mtDNA network of haplotypes. Haplotype A was the most common present in all specimens of sites sampled in the New World, Europe, and Israel, however from Australia second more frequently. Haplotype D was the most common one from native populations in Australia. Haplotype A differs from the two major haplotypes found in South Africa (D and G), confirming that at least two independent invasions occurred, one from Australia to South Africa, and the other one from Australia to South America (A). In conclusion, Haplotype A has an invasion success over many countries in the World. Additionally, analyzing data from our work and previous reports, it is possible to suggest some invasive routes of T. peregrinus to predict such events and support preventive control measures.
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Affiliation(s)
- Dayanna do N Machado
- Doutoranda pelo Programa de Pós-Graduação em Engenharia Florestal, Universidade Federal de Santa Maria, Santa Maria, Brasil.
- Departamento de Defesa Fitossanitária, Avenida Roraima n. 1000, prédio 42, sala 3223, 97105-900, Santa Maria, Rio Grande do Sul, Brasil.
| | - Ervandil C Costa
- Departamento de Defesa Fitossanitária, Avenida Roraima n. 1000, prédio 42, sala 3223, 97105-900, Santa Maria, Rio Grande do Sul, Brasil
| | - Jerson V C Guedes
- Departamento de Defesa Fitossanitária, Avenida Roraima n. 1000, prédio 42, sala 3223, 97105-900, Santa Maria, Rio Grande do Sul, Brasil
| | - Leonardo R Barbosa
- Empresa Brasileira de Pesquisa Agropecuária - Embrapa Florestas, Colombo, Paraná, 83411-000, Brazil
| | - Gonzalo Martínez
- Instituto Nacional de Investigación Agropecuaria (INIA), Ruta 5 Km 386, Tacuarembó, Uruguay
| | - Sandra I Mayorga
- Servicio Agrícola y Ganadero (SAG), Av. Presidente Bulnes 140, Santiago, Chile
| | - Sergio O Ramos
- Instituto Nacional de Tecnología Agropecuaria (INTA), Estación Yuquerí, Ruta Provincial 22 y vías del Ferrocarril 3200, Concordia, Entre Ríos, Argentina
| | - Manuela Branco
- Centro de Estudos Florestais, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - André Garcia
- Centro de Estudos Florestais, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal
| | - Juan Manuel Vanegas-Rico
- Laboratorio de Control de Plagas, Unidad de Morfología y Función (UMF), Facultad de Estudios Superiores Iztacala, UNAM. Av. de los barrios #1. Los Reyes Iztacala, Tlalnepantla de Baz, 54090, Mexico
| | - Eduardo Jiménez-Quiroz
- Laboratorio de Análisis y Referencia en Sanidad Forestal, Av. Progreso 3, 04100, Coyoacán, Ciudad de México, Mexico
| | - Stefania Laudonia
- Dipartimento di Agraria, Università degli Studi di Napoli Federico II, Portici, Italy
| | - Tania Novoselsky
- The Steinhardt Museum of Natural History, Israel National Center for Biodiversity Studies, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Donald R Hodel
- University of California, Cooperative Extension, 700 W. Main Street, Alhambra, California, 91801, United States of America
| | - Gevork Arakelian
- Entomologist, Los Angeles County Agricultural Commissioner, 11012 S. Garfield Ave, South Gate, CA, 90280, United States of America
| | - Horacio Silva
- Faculdad de Agronomía Universidad de la República Uruguay, Ruta 3 km 363, 60000, Paysandú, Uruguay
| | - Clérison R Perini
- Departamento de Defesa Fitossanitária, Avenida Roraima n. 1000, prédio 42, sala 3223, 97105-900, Santa Maria, Rio Grande do Sul, Brasil
| | - Ivair Valmorbida
- Department of Entomology, Iowa State University, Ames, Iowa, USA
| | - Gustavo A Ugalde
- Departamento de Defesa Fitossanitária, Avenida Roraima n. 1000, prédio 42, sala 3223, 97105-900, Santa Maria, Rio Grande do Sul, Brasil
| | - Jonas A Arnemann
- Departamento de Defesa Fitossanitária, Avenida Roraima n. 1000, prédio 42, sala 3223, 97105-900, Santa Maria, Rio Grande do Sul, Brasil
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83
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Batovska J, Mee PT, Lynch SE, Sawbridge TI, Rodoni BC. Sensitivity and specificity of metatranscriptomics as an arbovirus surveillance tool. Sci Rep 2019; 9:19398. [PMID: 31852942 PMCID: PMC6920425 DOI: 10.1038/s41598-019-55741-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 11/29/2019] [Indexed: 01/30/2023] Open
Abstract
The ability to identify all the viruses within a sample makes metatranscriptomic sequencing an attractive tool to screen mosquitoes for arboviruses. Practical application of this technique, however, requires a clear understanding of its analytical sensitivity and specificity. To assess this, five dilutions (1:1, 1:20, 1:400, 1:8,000 and 1:160,000) of Ross River virus (RRV) and Umatilla virus (UMAV) isolates were spiked into subsamples of a pool of 100 Culex australicus mosquitoes. The 1:1 dilution represented the viral load of one RRV-infected mosquito in a pool of 100 mosquitoes. The subsamples underwent nucleic acid extraction, mosquito-specific ribosomal RNA depletion, and Illumina HiSeq sequencing. The viral load of the subsamples was also measured using reverse transcription droplet digital PCR (RT-ddPCR) and quantitative PCR (RT-qPCR). Metatranscriptomic sequencing detected both RRV and UMAV in the 1:1, 1:20 and 1:400 subsamples. A high specificity was achieved, with 100% of RRV and 99.6% of UMAV assembled contigs correctly identified. Metatranscriptomic sequencing was not as sensitive as RT-qPCR or RT-ddPCR; however, it recovered whole genome information and detected 19 other viruses, including four first detections for Australia. These findings will assist arbovirus surveillance programs in utilising metatranscriptomics in routine surveillance activities to enhance arbovirus detection.
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Affiliation(s)
- Jana Batovska
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, Victoria, Australia.
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia.
| | - Peter T Mee
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, Victoria, Australia
| | - Stacey E Lynch
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, Victoria, Australia.
| | - Tim I Sawbridge
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, Victoria, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
| | - Brendan C Rodoni
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, Bundoora, Victoria, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
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84
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Naseem MT, Ashfaq M, Khan AM, Rasool A, Asif M, Hebert PDN. BIN overlap confirms transcontinental distribution of pest aphids (Hemiptera: Aphididae). PLoS One 2019; 14:e0220426. [PMID: 31821347 PMCID: PMC6903727 DOI: 10.1371/journal.pone.0220426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 11/24/2019] [Indexed: 11/25/2022] Open
Abstract
DNA barcoding is highly effective for identifying specimens once a reference sequence library is available for the species assemblage targeted for analysis. Despite the great need for an improved capacity to identify the insect pests of crops, the use of DNA barcoding is constrained by the lack of a well-parameterized reference library. The current study begins to address this limitation by developing a DNA barcode reference library for the pest aphids of Pakistan. It also examines the affinities of these species with conspecific populations from other geographic regions based on both conventional taxonomy and Barcode Index Numbers (BINs). A total of 809 aphids were collected from a range of plant species at sites across Pakistan. Morphological study and DNA barcoding allowed 774 specimens to be identified to one of 42 species while the others were placed to a genus or subfamily. Sequences obtained from these specimens were assigned to 52 BINs whose monophyly were supported by neighbor-joining (NJ) clustering and Bayesian inference. The 42 species were assigned to 41 BINs with 38 showing BIN concordance. These species were represented on BOLD by 7,870 records from 69 countries. Combining these records with those from Pakistan produced 60 BINs with 12 species showing a BIN split and three a BIN merger. Geo-distance correlations showed that intraspecific divergence values for 49% of the species were not affected by the distance between populations. Forty four of the 52 BINs from Pakistan had counterparts in 73 countries across six continents, documenting the broad distributions of pest aphids.
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Affiliation(s)
- Muhammad Tayyib Naseem
- National institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences, Islamabad, Pakistan
| | - Muhammad Ashfaq
- Centre for Biodiversity Genomics & Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
- * E-mail:
| | - Arif Muhammad Khan
- National institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
- Department of Biotechnology, University of Sargodha, Sargodha, Pakistan
| | - Akhtar Rasool
- National institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
- Department of Zoology, University of Swat, Swat, Pakistan
| | - Muhammad Asif
- National institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics & Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
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85
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Krehenwinkel H, Pomerantz A, Prost S. Genetic Biomonitoring and Biodiversity Assessment Using Portable Sequencing Technologies: Current Uses and Future Directions. Genes (Basel) 2019; 10:E858. [PMID: 31671909 PMCID: PMC6895800 DOI: 10.3390/genes10110858] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/18/2019] [Accepted: 10/25/2019] [Indexed: 12/12/2022] Open
Abstract
We live in an era of unprecedented biodiversity loss, affecting the taxonomic composition of ecosystems worldwide. The immense task of quantifying human imprints on global ecosystems has been greatly simplified by developments in high-throughput DNA sequencing technology (HTS). Approaches like DNA metabarcoding enable the study of biological communities at unparalleled detail. However, current protocols for HTS-based biodiversity exploration have several drawbacks. They are usually based on short sequences, with limited taxonomic and phylogenetic information content. Access to expensive HTS technology is often restricted in developing countries. Ecosystems of particular conservation priority are often remote and hard to access, requiring extensive time from field collection to laboratory processing of specimens. The advent of inexpensive mobile laboratory and DNA sequencing technologies show great promise to facilitate monitoring projects in biodiversity hot-spots around the world. Recent attention has been given to portable DNA sequencing studies related to infectious organisms, such as bacteria and viruses, yet relatively few studies have focused on applying these tools to Eukaryotes, such as plants and animals. Here, we outline the current state of genetic biodiversity monitoring of higher Eukaryotes using Oxford Nanopore Technology's MinION portable sequencing platform, as well as summarize areas of recent development.
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Affiliation(s)
| | - Aaron Pomerantz
- Department of Integrative Biology, University of California, Berkeley, CA-94720, USA.
- Marine Biology Laboratory, Woods Hole, MA-02543, USA.
| | - Stefan Prost
- LOEWE-Centre for Translational Biodiversity Genomics, Senckenberg Museum, 60325 Frankfurt, Germany.
- South African National Biodiversity Institute, National Zoological Garden, Pretoria 0002, South Africa.
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