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Sheard JK, Adriaens T, Bowler DE, Büermann A, Callaghan CT, Camprasse ECM, Chowdhury S, Engel T, Finch EA, von Gönner J, Hsing PY, Mikula P, Rachel Oh RY, Peters B, Phartyal SS, Pocock MJO, Wäldchen J, Bonn A. Emerging technologies in citizen science and potential for insect monitoring. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230106. [PMID: 38705194 PMCID: PMC11070260 DOI: 10.1098/rstb.2023.0106] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 03/29/2024] [Indexed: 05/07/2024] Open
Abstract
Emerging technologies are increasingly employed in environmental citizen science projects. This integration offers benefits and opportunities for scientists and participants alike. Citizen science can support large-scale, long-term monitoring of species occurrences, behaviour and interactions. At the same time, technologies can foster participant engagement, regardless of pre-existing taxonomic expertise or experience, and permit new types of data to be collected. Yet, technologies may also create challenges by potentially increasing financial costs, necessitating technological expertise or demanding training of participants. Technology could also reduce people's direct involvement and engagement with nature. In this perspective, we discuss how current technologies have spurred an increase in citizen science projects and how the implementation of emerging technologies in citizen science may enhance scientific impact and public engagement. We show how technology can act as (i) a facilitator of current citizen science and monitoring efforts, (ii) an enabler of new research opportunities, and (iii) a transformer of science, policy and public participation, but could also become (iv) an inhibitor of participation, equity and scientific rigour. Technology is developing fast and promises to provide many exciting opportunities for citizen science and insect monitoring, but while we seize these opportunities, we must remain vigilant against potential risks. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.
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Affiliation(s)
- Julie Koch Sheard
- Department of Ecosystem Services, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Straße 159, 07743 Jena, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
| | - Tim Adriaens
- Research Institute for Nature and Forest (INBO), Havenlaan 88 bus 73, 1000 Brussels, Belgium
| | - Diana E. Bowler
- UK Centre for Ecology & Hydrology, Wallingford, Oxfordshire, OX10 8BB, UK
| | - Andrea Büermann
- Department of Ecosystem Services, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
| | - Corey T. Callaghan
- Department of Wildlife Ecology and Conservation, Fort Lauderdale Research and Education Center, University of Florida, FL 33314, USA
| | - Elodie C. M. Camprasse
- School of Life and Environmental Sciences, Deakin University, Melbourne Burwood Campus, 221 Burwood Highway, Burwood, Victoria 3125, Australia
| | - Shawan Chowdhury
- Department of Ecosystem Services, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Straße 159, 07743 Jena, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
| | - Thore Engel
- Department of Ecosystem Services, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Straße 159, 07743 Jena, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
| | - Elizabeth A. Finch
- Department of Ecosystem Services, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Straße 159, 07743 Jena, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
| | - Julia von Gönner
- Department of Ecosystem Services, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Straße 159, 07743 Jena, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
| | - Pen-Yuan Hsing
- Faculty of Life Sciences, University of Bristol, 12a Priory Road, Bristol BS8 1TU, UK
| | - Peter Mikula
- TUM School of Life Sciences, Ecoclimatology, Technical University of Munich, Hans-Carl-von-Carlowitz-Platz 2, 85354 Freising, Germany
- Institute for Advanced Study, Technical University of Munich, Lichtenbergstraße 2a, 85748 Garching, Germany
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 16500 Prague, Czech Republic
| | - Rui Ying Rachel Oh
- Department of Ecosystem Services, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
| | - Birte Peters
- Department of Ecosystem Services, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
| | - Shyam S. Phartyal
- School of Ecology and Environment Studies, Nalanda University, Rajgir 803116, India
| | | | - Jana Wäldchen
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
- Department of Biogeochemical Integration, Max Planck Institute for Biogeochemistry, Hans-Knöll-Straße 10, 07745 Jena, Germany
| | - Aletta Bonn
- Department of Ecosystem Services, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, 04318 Leipzig, Germany
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Straße 159, 07743 Jena, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
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2
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Li M, Runemark A, Hernandez J, Rota J, Bygebjerg R, Brydegaard M. Discrimination of Hover Fly Species and Sexes by Wing Interference Signals. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2304657. [PMID: 37847885 DOI: 10.1002/advs.202304657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/08/2023] [Indexed: 10/19/2023]
Abstract
Remote automated surveillance of insect abundance and diversity is poised to revolutionize insect decline studies. The study reveals spectral analysis of thin-film wing interference signals (WISs) can discriminate free-flying insects beyond what can be accomplished by machine vision. Detectable by photonic sensors, WISs are robust indicators enabling species and sex identification. The first quantitative survey of insect wing thickness and modulation through shortwave-infrared hyperspectral imaging of 600 wings from 30 hover fly species is presented. Fringy spectral reflectance of WIS can be explained by four optical parameters, including membrane thickness. Using a Naïve Bayes Classifier with five parameters that can be retrieved remotely, 91% is achieved accuracy in identification of species and sexes. WIS-based surveillance is therefore a potent tool for remote insect identification and surveillance.
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Affiliation(s)
- Meng Li
- Department of Physics, Lund University, Sölvegatan 14c, Lund, 22363, Sweden
| | - Anna Runemark
- Department of Biology, Lund University, Sölvegatan 35, Lund, 22362, Sweden
| | | | - Jadranka Rota
- Biological Museum, Department of Biology, Lund University, Sölvegatan 37, Lund, 22362, Sweden
| | - Rune Bygebjerg
- Biological Museum, Department of Biology, Lund University, Sölvegatan 37, Lund, 22362, Sweden
| | - Mikkel Brydegaard
- Department of Physics, Lund University, Sölvegatan 14c, Lund, 22363, Sweden
- Department of Biology, Lund University, Sölvegatan 35, Lund, 22362, Sweden
- Norsk Elektro Optikk, Østensjøveien 34, Oslo, 0667, Norway
- FaunaPhotonics, Støberigade 14, Copenhagen, 2450, Denmark
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3
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Meyer R, Appeltans W, Duncan WD, Dimitrova M, Gan YM, Stjernegaard Jeppesen T, Mungall C, Paul DL, Provoost P, Robertson T, Schriml L, Suominen S, Walls R, Sweetlove M, Ung V, Van de Putte A, Wallis E, Wieczorek J, Buttigieg PL. Aligning Standards Communities for Omics Biodiversity Data: Sustainable Darwin Core-MIxS Interoperability. Biodivers Data J 2023; 11:e112420. [PMID: 37829294 PMCID: PMC10565567 DOI: 10.3897/bdj.11.e112420] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 10/02/2023] [Indexed: 10/14/2023] Open
Abstract
The standardization of data, encompassing both primary and contextual information (metadata), plays a pivotal role in facilitating data (re-)use, integration, and knowledge generation. However, the biodiversity and omics communities, converging on omics biodiversity data, have historically developed and adopted their own distinct standards, hindering effective (meta)data integration and collaboration. In response to this challenge, the Task Group (TG) for Sustainable DwC-MIxS Interoperability was established. Convening experts from the Biodiversity Information Standards (TDWG) and the Genomic Standards Consortium (GSC) alongside external stakeholders, the TG aimed to promote sustainable interoperability between the Minimum Information about any (x) Sequence (MIxS) and Darwin Core (DwC) specifications. To achieve this goal, the TG utilized the Simple Standard for Sharing Ontology Mappings (SSSOM) to create a comprehensive mapping of DwC keys to MIxS keys. This mapping, combined with the development of the MIxS-DwC extension, enables the incorporation of MIxS core terms into DwC-compliant metadata records, facilitating seamless data exchange between MIxS and DwC user communities. Through the implementation of this translation layer, data produced in either MIxS- or DwC-compliant formats can now be efficiently brokered, breaking down silos and fostering closer collaboration between the biodiversity and omics communities. To ensure its sustainability and lasting impact, TDWG and GSC have both signed a Memorandum of Understanding (MoU) on creating a continuous model to synchronize their standards. These achievements mark a significant step forward in enhancing data sharing and utilization across domains, thereby unlocking new opportunities for scientific discovery and advancement.
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Affiliation(s)
- Raïssa Meyer
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Reserach, Bremerhaven, GermanyAlfred Wegener Institute, Helmholtz Centre for Polar and Marine ReserachBremerhavenGermany
- Max Planck Institute for Marine Microbiology, Bremen, GermanyMax Planck Institute for Marine MicrobiologyBremenGermany
- University of Bremen, Faculty of Geosciences, Bremen, GermanyUniversity of Bremen, Faculty of GeosciencesBremenGermany
| | - Ward Appeltans
- Intergovernmental Oceanographic Commission of UNESCO, Ocean Biodiversity Information System (OBIS), Oostende, BelgiumIntergovernmental Oceanographic Commission of UNESCO, Ocean Biodiversity Information System (OBIS)OostendeBelgium
| | - William D. Duncan
- University of Florida, Gainesville, United States of AmericaUniversity of FloridaGainesvilleUnited States of America
| | - Mariya Dimitrova
- Bulgarian Academy of Sciences, Sofia, BulgariaBulgarian Academy of SciencesSofiaBulgaria
- Pensoft Publishers, Sofia, BulgariaPensoft PublishersSofiaBulgaria
| | - Yi-Ming Gan
- Royal Belgian Institute of Natural Sciences, Brussels, BelgiumRoyal Belgian Institute of Natural SciencesBrusselsBelgium
| | - Thomas Stjernegaard Jeppesen
- Global Biodiversity Information Facility (GBIF), Copenhagen, DenmarkGlobal Biodiversity Information Facility (GBIF)CopenhagenDenmark
| | - Christopher Mungall
- Lawrence Berkeley National Laboratory, National Microbiome Data Collaborative (NMDC), Berkeley, United States of AmericaLawrence Berkeley National Laboratory, National Microbiome Data Collaborative (NMDC)BerkeleyUnited States of America
| | - Deborah L Paul
- University of Illinois, Illinois Natural History Survey, Species File Group, Champaign-Urbana, United States of AmericaUniversity of Illinois, Illinois Natural History Survey, Species File GroupChampaign-UrbanaUnited States of America
| | - Pieter Provoost
- Intergovernmental Oceanographic Commission of UNESCO, Ocean Biodiversity Information System (OBIS), Oostende, BelgiumIntergovernmental Oceanographic Commission of UNESCO, Ocean Biodiversity Information System (OBIS)OostendeBelgium
| | - Tim Robertson
- Global Biodiversity Information Facility (GBIF), Copenhagen, DenmarkGlobal Biodiversity Information Facility (GBIF)CopenhagenDenmark
| | - Lynn Schriml
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, USA, Baltimore, United States of AmericaDepartment of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, USABaltimoreUnited States of America
| | - Saara Suominen
- Intergovernmental Oceanographic Commission of UNESCO, Ocean Biodiversity Information System (OBIS), Oostende, BelgiumIntergovernmental Oceanographic Commission of UNESCO, Ocean Biodiversity Information System (OBIS)OostendeBelgium
| | - Ramona Walls
- Critical Path Institute, Tucson, United States of AmericaCritical Path InstituteTucsonUnited States of America
| | - Maxime Sweetlove
- Royal Belgian Institute of Natural Sciences, Brussels, BelgiumRoyal Belgian Institute of Natural SciencesBrusselsBelgium
| | - Visotheary Ung
- UMR 7205 CNRS-MNHN-SU-EPHE-UA, Paris, FranceUMR 7205 CNRS-MNHN-SU-EPHE-UAParisFrance
| | - Anton Van de Putte
- Royal Belgian Institute of Natural Sciences, Université Libre de Bruxelles, Brussels, BelgiumRoyal Belgian Institute of Natural Sciences, Université Libre de BruxellesBrusselsBelgium
| | - Elycia Wallis
- Atlas of Living Australia, CSIRO, Melbourne, AustraliaAtlas of Living Australia, CSIROMelbourneAustralia
| | - John Wieczorek
- University of California, Berkeley, United States of AmericaUniversity of CaliforniaBerkeleyUnited States of America
| | - Pier Luigi Buttigieg
- Helmholtz Metadata Collaboration, GEOMAR Helmholtz Centre for Ocean Research, Kiel, GermanyHelmholtz Metadata Collaboration, GEOMAR Helmholtz Centre for Ocean ResearchKielGermany
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Müller L, Li M, Månefjord H, Salvador J, Reistad N, Hernandez J, Kirkeby C, Runemark A, Brydegaard M. Remote Nanoscopy with Infrared Elastic Hyperspectral Lidar. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2207110. [PMID: 36965063 DOI: 10.1002/advs.202207110] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 02/17/2023] [Indexed: 05/27/2023]
Abstract
Monitoring insects of different species to understand the factors affecting their diversity and decline is a major challenge. Laser remote sensing and spectroscopy offer promising novel solutions to this. Coherent scattering from thin wing membranes also known as wing interference patterns (WIPs) have recently been demonstrated to be species specific. The colors of WIPs arise due to unique fringy spectra, which can be retrieved over long distances. To demonstrate this, a new concept of infrared (950-1650 nm) hyperspectral lidar with 64 spectral bands based on a supercontinuum light source using ray-tracing and 3D printing is developed. A lidar with an unprecedented number of spectral channels, high signal-to-noise ratio, and spatio-temporal resolution enabling detection of free-flying insects and their wingbeats. As proof of principle, coherent scatter from a damselfly wing at 87 m distance without averaging (4 ms recording) is retrieved. The fringed signal properties are used to determine an effective wing membrane thickness of 1412 nm with ±4 nm precision matching laboratory recordings of the same wing. Similar signals from free flying insects (2 ms recording) are later recorded. The accuracy and the method's potential are discussed to discriminate species by capturing coherent features from free-flying insects.
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Affiliation(s)
- Lauro Müller
- Department of Physics, Lund University, Sölvegatan 14c, Lund, 22363, Sweden
| | - Meng Li
- Department of Physics, Lund University, Sölvegatan 14c, Lund, 22363, Sweden
| | - Hampus Månefjord
- Department of Physics, Lund University, Sölvegatan 14c, Lund, 22363, Sweden
| | - Jacobo Salvador
- Department of Physics, Lund University, Sölvegatan 14c, Lund, 22363, Sweden
| | - Nina Reistad
- Department of Physics, Lund University, Sölvegatan 14c, Lund, 22363, Sweden
- Centre for Environmental and Climate Science, Lund University, Sölvegatan 37, Lund, SE-223 62, Sweden
| | - Julio Hernandez
- Norsk Elektro Optikk A/S, Østensjøveien 34, Oslo, 0667, Norway
| | - Carsten Kirkeby
- Department of Veterinary and Animal Sciences, Copenhagen University, Frederiksberg, 1870, Denmark
- FaunaPhotonics, Støberigade 14, Copenhagen, 2450, Denmark
| | - Anna Runemark
- Department of Biology, Lund University, Sölvegatan 35, Lund, 22362, Sweden
| | - Mikkel Brydegaard
- Department of Physics, Lund University, Sölvegatan 14c, Lund, 22363, Sweden
- Norsk Elektro Optikk A/S, Østensjøveien 34, Oslo, 0667, Norway
- FaunaPhotonics, Støberigade 14, Copenhagen, 2450, Denmark
- Department of Biology, Lund University, Sölvegatan 35, Lund, 22362, Sweden
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5
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Santos V, Costa-Vera C, Rivera-Parra P, Burneo S, Molina J, Encalada D, Salvador J, Brydegaard M. Dual-Band Infrared Scheimpflug Lidar Reveals Insect Activity in a Tropical Cloud Forest. APPLIED SPECTROSCOPY 2023:37028231169302. [PMID: 37072925 DOI: 10.1177/00037028231169302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
We describe an entomological dual-band 808 and 980 nm lidar system which has been implemented in a tropical cloud forest (Ecuador). The system was successfully tested at a sample rate of 5 kHz in a cloud forest during challenging foggy conditions (extinction coefficients up to 20 km-1). At times, the backscattered signal could be retrieved from a distance of 2.929 km. We present insect and bat observations up to 200 m during a single night with an emphasis on fog aspects, potentials, and benefits of such dual-band systems. We demonstrate that the modulation contrast between insects and fog is high in the frequency domain compared to intensity in the time domain, thus allowing for better identification and quantification in misty forests. Oscillatory lidar extinction effects are shown in this work for the first time, caused by the combination of dense fog and large moths partially obstructing the beam. We demonstrate here an interesting case of a moth where left- and right-wing movements induced oscillations in both intensity and pixel spread. In addition, we were able to identify the dorsal and ventral sides of the wings by estimating the corresponding melanization with the dual-band lidar. We demonstrate that the wing beat trajectories in the dual-band parameter space are complementary rather than covarying or redundant, thus a dual-band entomological lidar approach to biodiversity studies is feasible in situ and endows species specificity differentiation. Future improvements are discussed. The introduction of these methodologies opens the door to a wealth of possible experiments to monitor, understand, and safeguard the biological resources of one of the most biodiverse countries on Earth.
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Affiliation(s)
- Victor Santos
- Departmento de Física, Escuela Politécnica Nacional, Quito
| | | | | | | | - Juan Molina
- Departmento de Física, Escuela Politécnica Nacional, Quito
| | - Diana Encalada
- Departmento de Economía, Universidad Técnica Particular de Loja, San Cayetano Alto, Loja, Ecuador
| | | | - Mikkel Brydegaard
- Department of Physics, Lund University, Lund, Sweden
- Norsk Elektro Optikk AS, Oslo, Norway
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6
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Genoud AP, Saha T, Williams GM, Thomas BP. Insect biomass density: measurement of seasonal and daily variations using an entomological optical sensor. APPLIED PHYSICS. B, LASERS AND OPTICS 2023; 129:26. [PMID: 36685802 PMCID: PMC9845170 DOI: 10.1007/s00340-023-07973-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 01/09/2023] [Indexed: 05/06/2023]
Abstract
Insects are major actors in Earth's ecosystems and their recent decline in abundance and diversity is alarming. The monitoring of insects is paramount to understand the cause of this decline and guide conservation policies. In this contribution, an infrared laser-based system is used to remotely monitor the biomass density of flying insects in the wild. By measuring the optical extinction caused by insects crossing the 36-m long laser beam, the Entomological Bistatic Optical Sensor System used in this study can evaluate the mass of each specimen. At the field location, between July and December 2021, the instrument made a total of 262,870 observations of insects for which the average dry mass was 17.1 mg and the median 3.4 mg. The daily average mass of flying insects per meter cube of air at the field location has been retrieved throughout the season and ranged between near 0 to 1.2 mg/m3. Thanks to its temporal resolution in the minute range, daily variations of biomass density have been observed as well. These measurements show daily activity patterns changing with the season, as large increases in biomass density were evident around sunset and sunrise during Summer but not during Fall.
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Affiliation(s)
- Adrien P. Genoud
- Department of Physics, New Jersey Institute of Technology, Newark, NJ USA
| | - Topu Saha
- Department of Physics, New Jersey Institute of Technology, Newark, NJ USA
| | | | - Benjamin P. Thomas
- Department of Physics, New Jersey Institute of Technology, Newark, NJ USA
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7
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Zizka VMA, Geiger MF, Hörren T, Kirse A, Noll NW, Schäffler L, Scherges AM, Sorg M. Repeated subsamples during
DNA
extraction reveal increased diversity estimates in
DNA
metabarcoding of Malaise traps. Ecol Evol 2022; 12:e9502. [PMCID: PMC9702565 DOI: 10.1002/ece3.9502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 10/11/2022] [Accepted: 10/18/2022] [Indexed: 11/29/2022] Open
Affiliation(s)
- Vera M. A. Zizka
- Leibniz Institute for the Analysis of Biodiversity Change (LIB), Zoological Research Museum Alexander Koenig (ZFMK) Centre for Biodiversity Monitoring and Conservation Science Bonn Germany
| | - Matthias F. Geiger
- Leibniz Institute for the Analysis of Biodiversity Change (LIB), Zoological Research Museum Alexander Koenig (ZFMK) Centre for Biodiversity Monitoring and Conservation Science Bonn Germany
| | | | - Ameli Kirse
- Leibniz Institute for the Analysis of Biodiversity Change (LIB), Zoological Research Museum Alexander Koenig (ZFMK) Centre for Biodiversity Monitoring and Conservation Science Bonn Germany
| | - Niklas W. Noll
- Leibniz Institute for the Analysis of Biodiversity Change (LIB), Zoological Research Museum Alexander Koenig (ZFMK) Centre for Biodiversity Monitoring and Conservation Science Bonn Germany
| | - Livia Schäffler
- Leibniz Institute for the Analysis of Biodiversity Change (LIB), Zoological Research Museum Alexander Koenig (ZFMK) Centre for Biodiversity Monitoring and Conservation Science Bonn Germany
| | - Alice M. Scherges
- Leibniz Institute for the Analysis of Biodiversity Change (LIB), Zoological Research Museum Alexander Koenig (ZFMK) Centre for Biodiversity Monitoring and Conservation Science Bonn Germany
| | - Martin Sorg
- Entomological Society Krefeld (EVK) Krefeld Germany
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8
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Kirse A, Bourlat SJ, Langen K, Zapke B, Zizka VMA. Comparison of destructive and non-destructive DNA extraction methods for the metabarcoding of arthropod bulk samples. Mol Ecol Resour 2022; 23:92-105. [PMID: 35932285 DOI: 10.1111/1755-0998.13694] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 07/07/2022] [Accepted: 07/25/2022] [Indexed: 11/28/2022]
Abstract
DNA metabarcoding is routinely used for biodiversity assessment, especially targeting highly diverse groups for which limited taxonomic expertise is available. Various protocols are currently in use, although standardization is key to its application in large-scale monitoring. DNA metabarcoding of arthropod bulk samples can be either conducted destructively from sample tissue, or non-destructively from sample fixative or lysis buffer. Non-destructive methods are highly desirable for the preservation of sample integrity but have yet to be experimentally evaluated in detail. Here, we compare diversity estimates from 14 size sorted Malaise trap samples processed consecutively with three non-destructive approaches (one using fixative ethanol and two using lysis buffers) and one destructive approach (using homogenized tissue). Extraction from commercial lysis buffer yielded comparable species richness and high overlap in species composition to the ground tissue extracts. A significantly divergent community was detected from preservative ethanol-based DNA extraction. No consistent trend in species richness was found with increasing incubation time in lysis buffer. These results indicate that non-destructive DNA extraction from incubation in lysis buffer could provide a comparable alternative to destructive approaches with the added advantage of preserving the specimens for post-metabarcoding taxonomic work but at a higher cost per sample.
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Affiliation(s)
- Ameli Kirse
- LIB/Zoological Research Museum Alexander Koenig (ZFMK), Centre for Biodiversity Monitoring, Bonn, Germany
| | - Sarah J Bourlat
- LIB/Zoological Research Museum Alexander Koenig (ZFMK), Centre for Biodiversity Monitoring, Bonn, Germany
| | - Kathrin Langen
- LIB/Zoological Research Museum Alexander Koenig (ZFMK), Centre for Biodiversity Monitoring, Bonn, Germany
| | - Björn Zapke
- LIB/Zoological Research Museum Alexander Koenig (ZFMK), Centre for Biodiversity Monitoring, Bonn, Germany
| | - Vera M A Zizka
- LIB/Zoological Research Museum Alexander Koenig (ZFMK), Centre for Biodiversity Monitoring, Bonn, Germany
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9
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van Klink R, August T, Bas Y, Bodesheim P, Bonn A, Fossøy F, Høye TT, Jongejans E, Menz MHM, Miraldo A, Roslin T, Roy HE, Ruczyński I, Schigel D, Schäffler L, Sheard JK, Svenningsen C, Tschan GF, Wäldchen J, Zizka VMA, Åström J, Bowler DE. Emerging technologies revolutionise insect ecology and monitoring. Trends Ecol Evol 2022; 37:872-885. [PMID: 35811172 DOI: 10.1016/j.tree.2022.06.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/26/2022] [Accepted: 06/07/2022] [Indexed: 12/30/2022]
Abstract
Insects are the most diverse group of animals on Earth, but their small size and high diversity have always made them challenging to study. Recent technological advances have the potential to revolutionise insect ecology and monitoring. We describe the state of the art of four technologies (computer vision, acoustic monitoring, radar, and molecular methods), and assess their advantages, current limitations, and future potential. We discuss how these technologies can adhere to modern standards of data curation and transparency, their implications for citizen science, and their potential for integration among different monitoring programmes and technologies. We argue that they provide unprecedented possibilities for insect ecology and monitoring, but it will be important to foster international standards via collaboration.
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Affiliation(s)
- Roel van Klink
- German Centre for Integrative Biodiversity Research (iDiv) Halle Jena Leipzig, Puschstrasse 4, 04103, Leipzig, Germany; Martin Luther University-Halle Wittenberg, Department of Computer Science, 06099, Halle (Saale), Germany.
| | - Tom August
- UK Centre for Ecology & Hydrology, Benson Lane, Wallingford, OX10 8BB, UK
| | - Yves Bas
- Centre d'Écologie et des Sciences de la Conservation, Muséum National d'Histoire Naturelle, Paris, France; CEFE, Université Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Paul Bodesheim
- Friedrich Schiller University Jena, Computer Vision Group, Ernst-Abbe-Platz 2, 07743, Jena, Germany
| | - Aletta Bonn
- German Centre for Integrative Biodiversity Research (iDiv) Halle Jena Leipzig, Puschstrasse 4, 04103, Leipzig, Germany; Helmholtz - Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318, Leipzig, Germany; Friedrich Schiller University Jena, Institute of Biodiversity, Dornburger Strasse 159, 07743, Jena, Germany
| | - Frode Fossøy
- Norwegian Institute for Nature Research, P.O. Box 5685 Torgarden, 7485, Trondheim, Norway
| | - Toke T Høye
- Aarhus University, Department of Ecoscience and Arctic Research Centre, C.F. Møllers Allé 8, 8000, Aarhus, Denmark
| | - Eelke Jongejans
- Radboud University, Animal Ecology and Physiology, Heyendaalseweg 135, 6525, AJ, Nijmegen, The Netherlands; Netherlands Institute of Ecology, Animal Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Myles H M Menz
- Max Planck Institute for Animal Behaviour, Department of Migration, Am Obstberg 1, 78315, Radolfzell, Germany; College of Science and Engineering, James Cook University, Townsville, Qld, Australia
| | - Andreia Miraldo
- Swedish Museum of Natural Sciences, Department of Bioinformatics and Genetics, Frescativägen 40, 114 18, Stockholm, Sweden
| | - Tomas Roslin
- Swedish University of Agricultural Sciences (SLU), Department of Ecology, Ulls väg 18B, 75651, Uppsala, Sweden
| | - Helen E Roy
- UK Centre for Ecology & Hydrology, Benson Lane, Wallingford, OX10 8BB, UK
| | - Ireneusz Ruczyński
- Mammal Research Institute, Polish Academy of Sciences, Stoczek 1, 17-230, Białowieża, Poland
| | - Dmitry Schigel
- Global Biodiversity Information Facility (GBIF), Universitetsparken 15, 2100, Copenhagen, Denmark
| | - Livia Schäffler
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn, Adenauerallee 127, 53113, Bonn, Germany
| | - Julie K Sheard
- German Centre for Integrative Biodiversity Research (iDiv) Halle Jena Leipzig, Puschstrasse 4, 04103, Leipzig, Germany; Helmholtz - Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318, Leipzig, Germany; Friedrich Schiller University Jena, Institute of Biodiversity, Dornburger Strasse 159, 07743, Jena, Germany; University of Copenhagen, Centre for Macroecology, Evolution and Climate, Globe Institute, Universitetsparken 15, bld. 3, 2100, Copenhagen, Denmark
| | - Cecilie Svenningsen
- University of Copenhagen, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350, Copenhagen, Denmark
| | - Georg F Tschan
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn, Adenauerallee 127, 53113, Bonn, Germany
| | - Jana Wäldchen
- German Centre for Integrative Biodiversity Research (iDiv) Halle Jena Leipzig, Puschstrasse 4, 04103, Leipzig, Germany; Max Planck Institute for Biogeochemistry, Department of Biogeochemical Integration, Hans-Knoell-Str. 10, 07745, Jena, Germany
| | - Vera M A Zizka
- Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn, Adenauerallee 127, 53113, Bonn, Germany
| | - Jens Åström
- Norwegian Institute for Nature Research, P.O. Box 5685 Torgarden, 7485, Trondheim, Norway
| | - Diana E Bowler
- German Centre for Integrative Biodiversity Research (iDiv) Halle Jena Leipzig, Puschstrasse 4, 04103, Leipzig, Germany; UK Centre for Ecology & Hydrology, Benson Lane, Wallingford, OX10 8BB, UK; Helmholtz - Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318, Leipzig, Germany; Friedrich Schiller University Jena, Institute of Biodiversity, Dornburger Strasse 159, 07743, Jena, Germany
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10
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Kaczmarek M, Entling MH, Hoffmann C. Using Malaise Traps and Metabarcoding for Biodiversity Assessment in Vineyards: Effects of Weather and Trapping Effort. INSECTS 2022; 13:insects13060507. [PMID: 35735844 PMCID: PMC9224819 DOI: 10.3390/insects13060507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 11/16/2022]
Abstract
Metabarcoding is a powerful tool for ecological studies and monitoring that might provide a solution to the time-consuming taxonomic identification of the vast diversity of insects. Here, we assess how ambient weather conditions during Malaise trap exposure and the effort of trapping affect biomass and taxa richness in vineyards. Biomass varied by more than twofold with weather conditions. It increased with warmer and drier weather but was not significantly related with wind or precipitation. Taxa richness showed a saturating relationship with increasing trapping duration and was influenced by environmental and seasonal effects. Taxa accumulation was high, increasing fourfold from three days of monthly trap exposure compared to continuous trapping and nearly sixfold from sampling at a single site compared to 32 sites. The limited saturation was mainly due to a large number of singletons, such as rare species, in the metabarcoding dataset. Metabarcoding can be key for long-term insect monitoring. We conclude that single traps operated for up to ten days per month are suitable to monitor the presence of common species. However, more intensive trapping is necessary for a good representation of rare species in biodiversity monitoring. The data collected here can potentially guide the design of monitoring studies.
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Affiliation(s)
- Marvin Kaczmarek
- Julius Kühn Institute—Federal Research Institute for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Geilweilerhof, D-76833 Siebeldingen, Germany;
- Institute for Environmental Sciences—iES Landau, University of Koblenz-Landau, Fortstraße 7, D-76829 Landau in der Pfalz, Germany;
- Correspondence:
| | - Martin H. Entling
- Institute for Environmental Sciences—iES Landau, University of Koblenz-Landau, Fortstraße 7, D-76829 Landau in der Pfalz, Germany;
| | - Christoph Hoffmann
- Julius Kühn Institute—Federal Research Institute for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Geilweilerhof, D-76833 Siebeldingen, Germany;
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11
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Svenningsen CS, Bowler DE, Hecker S, Bladt J, Grescho V, Dam NM, Dauber J, Eichenberg D, Ejrnæs R, Fløjgaard C, Frenzel M, Frøslev TG, Hansen AJ, Heilmann‐Clausen J, Huang Y, Larsen JC, Menger J, Nayan NLBM, Pedersen LB, Richter A, Dunn RR, Tøttrup AP, Bonn A. Flying insect biomass is negatively associated with urban cover in surrounding landscapes. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
| | - Diana E. Bowler
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Friedrich Schiller University Jena Institute of Biodiversity Jena Germany
- Department of Ecosystem Services Helmholtz Centre for Environmental Research – UFZ Leipzig Germany
| | - Susanne Hecker
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Department of Ecosystem Services Helmholtz Centre for Environmental Research – UFZ Leipzig Germany
| | - Jesper Bladt
- Department of Bioscience – Biodiversity and Conservation Aarhus University Aarhus Denmark
| | - Volker Grescho
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Department of Ecosystem Services Helmholtz Centre for Environmental Research – UFZ Leipzig Germany
| | - Nicole M. Dam
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Friedrich Schiller University Jena Institute of Biodiversity Jena Germany
| | - Jens Dauber
- Thünen‐Institute of Biodiversity Braunschweig Germany
| | - David Eichenberg
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Department of Ecosystem Services Helmholtz Centre for Environmental Research – UFZ Leipzig Germany
| | - Rasmus Ejrnæs
- Department of Bioscience – Biodiversity and Conservation Aarhus University Aarhus Denmark
| | - Camilla Fløjgaard
- Department of Bioscience – Biodiversity and Conservation Aarhus University Aarhus Denmark
| | - Mark Frenzel
- Department of Community Ecology Helmholtz Centre for Environmental Research – UFZ Halle Germany
| | - Tobias G. Frøslev
- Centre for GeoGenetics GLOBE Institute University of Copenhagen Copenhagen Denmark
| | - Anders J. Hansen
- Centre for GeoGenetics GLOBE Institute University of Copenhagen Copenhagen Denmark
| | - Jacob Heilmann‐Clausen
- Centre for Macroecology, Evolution and Climate GLOBE Institute University of Copenhagen Copenhagen Denmark
| | - Yuanyuan Huang
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Department of Ecosystem Services Helmholtz Centre for Environmental Research – UFZ Leipzig Germany
| | - Jonas C. Larsen
- Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Juliana Menger
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Department of Ecosystem Services Helmholtz Centre for Environmental Research – UFZ Leipzig Germany
- Coordenação de Biodiversidade Instituto Nacional de Pesquisas da Amazônia Manaus Brazil
| | - Nur L. B. M. Nayan
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Department of Ecosystem Services Helmholtz Centre for Environmental Research – UFZ Leipzig Germany
| | - Lene B. Pedersen
- Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Anett Richter
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Department of Ecosystem Services Helmholtz Centre for Environmental Research – UFZ Leipzig Germany
- Thünen‐Institute of Biodiversity Braunschweig Germany
| | - Robert R. Dunn
- Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
- Department of Applied Ecology North Carolina State University Raleigh North Carolina USA
| | - Anders P. Tøttrup
- Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Aletta Bonn
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
- Friedrich Schiller University Jena Institute of Biodiversity Jena Germany
- Department of Ecosystem Services Helmholtz Centre for Environmental Research – UFZ Leipzig Germany
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12
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Kjærandsen J. Current State of DNA Barcoding of Sciaroidea (Diptera)—Highlighting the Need to Build the Reference Library. INSECTS 2022; 13:insects13020147. [PMID: 35206721 PMCID: PMC8879535 DOI: 10.3390/insects13020147] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/18/2022] [Accepted: 01/27/2022] [Indexed: 12/10/2022]
Abstract
Simple Summary DNA barcoding is a method by which a specific region of the mitochondrial genome is used to quantify genetic distances within and between animal species. Most DNA barcodes of the world are assembled on the Barcode of Life online database BoldSystems (BOLD). There, machine-generated barcode index numbers (BINs) are automatically assigned to clusters of specimens thought to represent species. I review the current state of DNA barcoding of the superfamily Sciaroidea, a diverse insect group consisting of close to 16,000 described fly species in eight families. To date, over 1.2 million specimens of Sciaroidea have been barcoded and the 56,648 assigned BINs on BOLD already represent 3.5 times the number of described species. Still, 95% of the BINs have currently no associated scientific name and very little effort has been put into building a quality-checked reference library where named species are linked to the BINs on BOLD. In the Nordic region, however, substantial progress is made towards building a complete reference library. While DNA barcoding has tremendous potential for advancing the knowledge for many diverse groups of insects, its potential will never be fully reached absent more engagement of trained taxonomists to build voucher collections, curate the reference libraries, and describe new species. Abstract DNA barcoding has tremendous potential for advancing species knowledge for many diverse groups of insects, potentially paving way for machine identification and semi-automated monitoring of whole insect faunas. Here, I review the current state of DNA barcoding of the superfamily Sciaroidea (Diptera), a diverse group consisting of eight understudied fly families where the described species in the world makes up some 10% (≈16,000 species) of all Diptera. World data of Sciaroidea were extracted from the Barcode of Life online database BoldSystems (BOLD) and contrasted with results and experiences from a Nordic project to build the reference library. Well over 1.2 million (1,224,877) Sciaroidea specimens have been submitted for barcoding, giving barcode-compliant sequences resulting in 56,648 so-called barcode index numbers (BINs, machine-generated proxies for species). Although the BINs on BOLD already represent 3.5 times the number of described species, merely some 2850 named species (described or interim names, 5% of the BINs) currently have been assigned a BIN. The other 95% remain as dark taxa figuring in many frontier publications as statistics representing proxies for species diversity within a family. In the Nordic region, however, substantial progress has been made towards building a complete reference library, currently making up 55% of all named Sciaroidea BINs on BOLD. Another major source (31%) of named Sciaroidea BINs on BOLD comes from COI sequences mined from GenBank, generated through phylogenetic and integrative studies outside of BOLD. Building a quality reference library for understudied insects such as Sciaroidea requires heavy investment, both pre sequence and post sequence, by trained taxonomists to build and curate voucher collections, to continually improve the quality of the data and describe new species. Only when the BINs are properly calibrated by a rigorously quality-checked reference library can the great potential of both classical taxonomic barcoding, metabarcoding, and eDNA ecology be realized.
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Affiliation(s)
- Jostein Kjærandsen
- The Arctic University Museum of Norway, UiT-The Arctic University of Norway, P.O. Box 6050 Langnes, NO-9037 Tromsø, Norway
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