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Weinhold A, Grüner E, Keller A. Bumble bee microbiota shows temporal succession and increase of lactic acid bacteria when exposed to outdoor environments. Front Cell Infect Microbiol 2024; 14:1342781. [PMID: 38500505 PMCID: PMC10945022 DOI: 10.3389/fcimb.2024.1342781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/19/2024] [Indexed: 03/20/2024] Open
Abstract
Question The large earth bumble bee (Bombus terrestris) maintains a social core gut-microbiota, similar as known from the honey bee, which plays an important role for host health and resistance. Experiments under laboratory conditions with commercial hives are limited to vertically transmitted microbes and neglect influences of environmental factors or external acquisition of microbes. Various environmental and landscape-level factors may have an impact on the gut-microbiota of pollinating insects, with consequences for pollinator health and fitness in agroecosystems. Still, it is not fully clear whether access to different flower diversities will have a significant influence on the bumble bee microbiota. Here, we tested in a semi-field experiment if the bumble bee microbiota changes over time when exposed to different flower diversities within outdoor flight cages. We used commercial hives to distinguish between vertically and horizontally transmitted bacteria, respectively from the nest environment or the exposed outside environment. Result The sequential sampling of foraging workers over a period of 35 days indicated a temporal progression of the bumble bee microbiota when placed outside. The microbiota increased in diversity and changed in composition and variability over time. We observed a major increase in relative abundance of the families Lactobacillaceae, Bifidobacteriaceae and Weeksellaceae. In contrast, major core-taxa like Snodgrassella and Gilliamella declined in their relative abundance over time. The genus Lactobacillus showed a high diversity and strain specific turnover, so that only specific ASVs showed an increase over time, while others had a more erratic occurrence pattern. Exposure to different flower diversities had no significant influence on the progression of the bumble bee microbiota. Conclusion The bumble bee microbiota showed a dynamic temporal succession with distinct compositional changes and diversification over time when placed outdoor. The exposure of bumble bees to environmental conditions, or environmental microbes, increases dissimilarity and changes the gut-community composition. This shows the importance of environmental influences on the temporal dynamic and progression of the bumble bee microbiota.
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Affiliation(s)
- Arne Weinhold
- Cellular and Organismic Networks, Faculty of Biology, Center for Organismic Adaptation, Ludwig-Maximilians-Universität München, Munich, Germany
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2
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Quaresma A, Ankenbrand MJ, Garcia CAY, Rufino J, Honrado M, Amaral J, Brodschneider R, Brusbardis V, Gratzer K, Hatjina F, Kilpinen O, Pietropaoli M, Roessink I, van der Steen J, Vejsnæs F, Pinto MA, Keller A. Semi-automated sequence curation for reliable reference datasets in ITS2 vascular plant DNA (meta-)barcoding. Sci Data 2024; 11:129. [PMID: 38272945 PMCID: PMC10810873 DOI: 10.1038/s41597-024-02962-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 01/12/2024] [Indexed: 01/27/2024] Open
Abstract
One of the most critical steps for accurate taxonomic identification in DNA (meta)-barcoding is to have an accurate DNA reference sequence dataset for the marker of choice. Therefore, developing such a dataset has been a long-term ambition, especially in the Viridiplantae kingdom. Typically, reference datasets are constructed with sequences downloaded from general public databases, which can carry taxonomic and other relevant errors. Herein, we constructed a curated (i) global dataset, (ii) European crop dataset, and (iii) 27 datasets for the EU countries for the ITS2 barcoding marker of vascular plants. To that end, we first developed a pipeline script that entails (i) an automated curation stage comprising five filters, (ii) manual taxonomic correction for misclassified taxa, and (iii) manual addition of newly sequenced species. The pipeline allows easy updating of the curated datasets. With this approach, 13% of the sequences, corresponding to 7% of species originally imported from GenBank, were discarded. Further, 259 sequences were manually added to the curated global dataset, which now comprises 307,977 sequences of 111,382 plant species.
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Affiliation(s)
- Andreia Quaresma
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, S/N, Edifício FC4, 4169-007, Porto, Portugal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Vila do Conde, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Vila do Conde, Portugal
| | - Markus J Ankenbrand
- Center for Computational and Theoretical Biology, Faculty of Biology, Julius-Maximilians-Universität Würzburg, Klara-Oppenheimer-Weg 32, 97074, Würzburg, Germany
| | - Carlos Ariel Yadró Garcia
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
| | - José Rufino
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
- Research Centre in Digitalization and Intelligent Robotics (CeDRI), Instituto Politécnico de Bragança, Bragança, Portugal
| | - Mónica Honrado
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
| | - Joana Amaral
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
| | - Robert Brodschneider
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria
| | - Valters Brusbardis
- Latvian Beekeepers' Association (LBA), Rigas iela 22, LV-3004, Jelgava, Latvia
| | - Kristina Gratzer
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria
| | - Fani Hatjina
- Ellinikos Georgikos Organismos DIMITRA (ELGO- DIMITRA), Kourtidou 56-58, GR-11145, Athina, Greece
| | - Ole Kilpinen
- Danish Beekeepers Association (DBF), Fulbyvej 15, DK-4180, Sorø, Denmark
| | - Marco Pietropaoli
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana "M. Aleandri" (IZSLT), Via Appia Nuova 1411, IT-00178, Roma, Italy
| | - Ivo Roessink
- Wageningen Environmental Research, WageningenUniversity&Research, Droevendaalsesteeg 3, 6700 AA, Wageningen, Netherlands
| | | | - Flemming Vejsnæs
- Danish Beekeepers Association (DBF), Fulbyvej 15, DK-4180, Sorø, Denmark
| | - M Alice Pinto
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha (SusTEC), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
| | - Alexander Keller
- Cellular and Organismic Interactions, Biocenter, Faculty of Biology, Ludwig-Maximilians-Universität München, Großhaderner Str. 2-4, 82152, Planegg-Martinsried, Germany.
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3
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Wasti QZ, Sabar MF, Farooq A, Khan MU. Stepping towards pollen DNA metabarcoding: A breakthrough in forensic sciences. Forensic Sci Med Pathol 2023:10.1007/s12024-023-00770-8. [PMID: 38147285 DOI: 10.1007/s12024-023-00770-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2023] [Indexed: 12/27/2023]
Abstract
This review is engaged in determining the capability of plant pollen as a significant source of evidence for the linkage between suspects and crime location in forensic sciences. Research and review articles were collected from Google Scholar, the Web of Science, and PubMed. Articles were searched using specific keywords such as "Forensic Palynology," "Pollen metabarcoding," "Plant forensics," and "Pollen" AND "criminal investigation." Boolean logic was also utilized to narrow the articles to be included in this review article. Through the literature and exploratory research, it has been observed in the current study that with advancements in technology, forensic palynology has found its application in creating an association between the crime scene and suspected individuals to have a link to it, as pollen DNA is a long-lasting investigative tool that can effectively help forensic investigations. Moreover, the literature shows that the DNA of pollen and spores has helped forensic scientists link suspects to crime scenes, and the introduction of pollen DNA metabarcoding tools has eased the efforts of palynologists to analyze pollen DNA. The introduction of DNA metabarcoding techniques to analyze pollen from plants has helped identify the geological locations of the plants and ultimately identify the culprit.
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Affiliation(s)
- Qandeel Zaineb Wasti
- Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | | | - Abeera Farooq
- Punjab University College of Pharmacy, University of the Punjab, Lahore, Pakistan
| | - Muhammad Umer Khan
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan.
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4
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Encinas-Viso F, Bovill J, Albrecht DE, Florez-Fernandez J, Lessard B, Lumbers J, Rodriguez J, Schmidt-Lebuhn A, Zwick A, Milla L. Pollen DNA metabarcoding reveals cryptic diversity and high spatial turnover in alpine plant-pollinator networks. Mol Ecol 2023; 32:6377-6393. [PMID: 36065738 DOI: 10.1111/mec.16682] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 08/18/2022] [Accepted: 08/30/2022] [Indexed: 11/29/2022]
Abstract
Alpine plant-pollinator communities play an important role in the functioning of alpine ecosystems, which are highly threatened by climate change. However, we still have a poor understanding of how environmental factors and spatiotemporal variability shape these communities. Here, we investigate what drives structure and beta diversity in a plant-pollinator metacommunity from the Australian alpine region using two approaches: pollen DNA metabarcoding (MB) and observations. Individual pollinators often carry pollen from multiple plant species, and therefore we expected MB to reveal a more diverse and complex network structure. We used two gene regions (ITS2 and trnL) to identify plant species present in the pollen loads of 154 insect pollinator specimens from three alpine habitats and construct MB networks, and compared them to networks based on observations alone. We compared species and interaction turnover across space for both types of networks, and evaluated their differences for plant phylogenetic diversity and beta diversity. We found significant structural differences between the two types of networks; notably, MB networks were much less specialized but more diverse than observation networks, with MB detecting many cryptic plant species. Both approaches revealed that alpine pollination networks are very generalized, but we estimated a high spatial turnover of plant species (0.79) and interaction rewiring (0.6) as well as high plant phylogenetic diversity (0.68) driven by habitat differences based on the larger diversity of plant species and species interactions detected with MB. Overall, our findings show that habitat and microclimatic heterogeneity drives diversity and fine-scale spatial turnover of alpine plant-pollinator networks.
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Affiliation(s)
- Francisco Encinas-Viso
- Centre for Australian National Biodiversity Research, Australian Capital Territory, Canberra, Australia
| | - Jessica Bovill
- Centre for Australian National Biodiversity Research, Australian Capital Territory, Canberra, Australia
| | - David E Albrecht
- Centre for Australian National Biodiversity Research, Australian Capital Territory, Canberra, Australia
| | - Jaime Florez-Fernandez
- Australian National Insect Collection, Australian Capital Territory, Canberra, Australia
| | - Bryan Lessard
- Australian National Insect Collection, Australian Capital Territory, Canberra, Australia
| | - James Lumbers
- Australian National Insect Collection, Australian Capital Territory, Canberra, Australia
| | - Juanita Rodriguez
- Australian National Insect Collection, Australian Capital Territory, Canberra, Australia
| | - Alexander Schmidt-Lebuhn
- Centre for Australian National Biodiversity Research, Australian Capital Territory, Canberra, Australia
| | - Andreas Zwick
- Australian National Insect Collection, Australian Capital Territory, Canberra, Australia
| | - Liz Milla
- Centre for Australian National Biodiversity Research, Australian Capital Territory, Canberra, Australia
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5
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Jia H, Chen Y, Li X, Pan Y, Liu D, Liu Y, Wu K. Regional Pollination Activity by Moth Migration in Athetis lepigone. PLANTS (BASEL, SWITZERLAND) 2023; 12:3406. [PMID: 37836146 PMCID: PMC10574918 DOI: 10.3390/plants12193406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/23/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023]
Abstract
Nocturnal moths (Lepidoptera) are important pollinators of a wide range of plant species. Understanding the foraging preferences of these insects is essential for their scientific management. However, this information is lacking for most moth species. The present study was therefore conducted to delineate the host plant feeding and pollination ranges of an agriculturally important nocturnal moth species Athetis lepigone by identifying the pollen species adhering to their bodies during long-distance migration. Pollen grains were dislodged from 1871 A. lepigone migrants captured on Beihuang Island in the Bohai Strait between 2020 and 2021. This region is a key seasonal migration pathway for A. lepigone in northern China. Almost 20% of all moths sampled harbored pollens, providing direct evidences that this moth species may serve as pollinators. Moreover, at least 39 pollen taxa spanning 21 plant families and 31 genera were identified, with a preference for Asteraceae, Amaranthaceae, and Pinaceae. Additionally, the pollen adherence ratios and taxa varied with moth sex, inter-annual changes, and seasonal fluctuations. Most importantly, the pollen taxa were correlated with insect migration stages and indicated that A. lepigone bidirectionally migrates between central China (Shandong, Hebei, and Henan Provinces) and northeastern China (Liaoning Province). Overall, the findings of the present work provide valuable information on the pollination behavior, geographical origins, and pollination regions of A. lepigone moths and could facilitate the design and optimization of efficacious local and regional management strategies for this important insect.
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Affiliation(s)
- Huiru Jia
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.J.); (Y.C.); (X.L.); (Y.P.); (D.L.); (Y.L.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510640, China
| | - Yuchao Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.J.); (Y.C.); (X.L.); (Y.P.); (D.L.); (Y.L.)
| | - Xiaokang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.J.); (Y.C.); (X.L.); (Y.P.); (D.L.); (Y.L.)
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Yunfei Pan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.J.); (Y.C.); (X.L.); (Y.P.); (D.L.); (Y.L.)
| | - Dazhong Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.J.); (Y.C.); (X.L.); (Y.P.); (D.L.); (Y.L.)
| | - Yongqiang Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.J.); (Y.C.); (X.L.); (Y.P.); (D.L.); (Y.L.)
| | - Kongming Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (H.J.); (Y.C.); (X.L.); (Y.P.); (D.L.); (Y.L.)
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6
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Martins AC, Proença CEB, Vasconcelos TNC, Aguiar AJC, Farinasso HC, de Lima ATF, Faria JEQ, Norrana K, Costa MBR, Carvalho MM, Dias RL, Bustamante MMC, Carvalho FA, Keller A. Contrasting patterns of foraging behavior in neotropical stingless bees using pollen and honey metabarcoding. Sci Rep 2023; 13:14474. [PMID: 37660141 PMCID: PMC10475120 DOI: 10.1038/s41598-023-41304-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 08/24/2023] [Indexed: 09/04/2023] Open
Abstract
Stingless bees are major flower visitors in the tropics, but their foraging preferences and behavior are still poorly understood. Studying stingless bee interactions with angiosperms is methodologically challenging due to the high tropical plant diversity and inaccessibility of upper canopy flowers in forested habitats. Pollen DNA metabarcoding offers an opportunity of assessing floral visitation efficiently and was applied here to understand stingless bee floral resources spectra and foraging behavior. We analyzed pollen and honey from nests of three distantly related stingless bee species, with different body size and social behavior: Melipona rufiventris, Scaptotrigona postica and Tetragonisca angustula. Simultaneously, we evaluate the local floristic components through seventeen rapid botanical surveys conducted at different distances from the nests. We discovered a broad set of explored floral sources, with 46.3 plant species per bee species in honey samples and 53.67 in pollen samples. Plant families Myrtaceae, Asteraceae, Euphorbiaceae, Melastomataceae and Malpighiaceae dominated the records, indicating stingless bee preferences for abundant resources that flowers of these families provide in the region. Results also reinforce the preference of stingless bees for forest trees, even if only available at long distances. Our high-resolution results encourage future bee-plant studies using pollen and honey metabarcoding in hyper-diverse tropical environments.
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Affiliation(s)
- Aline C Martins
- Departamento de Ecologia, Universidade de Brasília, Brasília, DF, 70910-900, Brazil.
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA.
| | - Carolyn E B Proença
- Departamento de Botânica, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - Thais N C Vasconcelos
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Antonio J C Aguiar
- Laboratório de Abelhas, Departamento de Zoologia, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - Hannah C Farinasso
- Laboratório de Abelhas, Departamento de Zoologia, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - Aluisio T F de Lima
- Departamento de Botânica, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - Jair E Q Faria
- Departamento de Botânica, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - Krissya Norrana
- Laboratório de Abelhas, Departamento de Zoologia, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - Marcella B R Costa
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Matheus M Carvalho
- Laboratório de Abelhas, Departamento de Zoologia, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
- Laboratório de Biologia Comparada e Abelhas, Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, 14040-901, Brazil
| | - Rodrigo L Dias
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | | | - Fernanda A Carvalho
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-901, Brazil
| | - Alexander Keller
- Cellular and Organismic Networks, Faculty of Biology, Ludwig-Maximilians University, 82152, Munich, Germany
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7
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Kasprzyk I. Forensic botany: who?, how?, where?, when? Sci Justice 2023; 63:258-275. [PMID: 36870705 DOI: 10.1016/j.scijus.2023.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 01/09/2023] [Accepted: 01/15/2023] [Indexed: 01/19/2023]
Abstract
Plants are a good source of biological forensic evidence; this is due to their ubiquity, their ability to collect reference material, and their sensitivity to environmental changes. However, in many countries, botanical evidence is recognised as being scientifically. Botanical evidence is not mostly used for perpertration, instead it tends to serve as circumstantial evidence. Plant materials constitute the basis, among others, for linking a suspect or object to a crime scene or a victim, confirming or not confirming an alibi, determining the post-mortem interval, and determining the origin of food/object. Forensic botany entails field work, knowledge of plants, understanding ecosystem processes, and a basis understaning of geoscience. In this study, experiments with mammal cadavers were conducted to determine the occurence of an event. The simplest criterion characterising botanical evidence is its size. Therefore, macroremains include whole plants or their larger fragments (e.g. tree bark, leaves, seeds, prickles, and thorns), whereas microscopic evidence includes palynomorphs (spores and pollen grains), diatoms, and tissues. Botanical methods allow for an analysis to be repeated multiple times and the test material is easy to collect in the field. Forensic botany can be supplemented with molecular analyses, which, although specific and sensitive, still require validation.
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Affiliation(s)
- Idalia Kasprzyk
- Institute of Biology and Biotechnology, College of Natural Sciences, University of Rzeszów, Al. Rejtana 16c, 35-959 Rzeszów, Poland.
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8
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Verbeke S, Boeraeve M, Carpentier S, Jacquemyn H, Pozo MI. The impact of plant diversity and vegetation composition on bumblebee colony fitness. OIKOS 2023. [DOI: 10.1111/oik.09790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Affiliation(s)
- Sebastiaan Verbeke
- Ecology, Evolution and Biodiversity Conservation, KU Leuven Leuven Belgium
| | - Margaux Boeraeve
- Ecology, Evolution and Biodiversity Conservation, KU Leuven Leuven Belgium
| | - Sebastien Carpentier
- Division of Crop Biotechnics, Dept of Biosystems, KU Leuven Leuven Belgium
- SYBIOMA: Facility for Systems Biology Mass Spectrometry Leuven Belgium
| | - Hans Jacquemyn
- Ecology, Evolution and Biodiversity Conservation, KU Leuven Leuven Belgium
| | - María I. Pozo
- Ecology, Evolution and Biodiversity Conservation, KU Leuven Leuven Belgium
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9
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Johnson MD, Freeland JR, Parducci L, Evans DM, Meyer RS, Molano-Flores B, Davis MA. Environmental DNA as an emerging tool in botanical research. AMERICAN JOURNAL OF BOTANY 2023; 110:e16120. [PMID: 36632660 DOI: 10.1002/ajb2.16120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/03/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
Over the past quarter century, environmental DNA (eDNA) has been ascendant as a tool to detect, measure, and monitor biodiversity (species and communities), as a means of elucidating biological interaction networks, and as a window into understanding past patterns of biodiversity. However, only recently has the potential of eDNA been realized in the botanical world. Here we synthesize the state of eDNA applications in botanical systems with emphases on aquatic, ancient, contemporary sediment, and airborne systems, and focusing on both single-species approaches and multispecies community metabarcoding. Further, we describe how abiotic and biotic factors, taxonomic resolution, primer choice, spatiotemporal scales, and relative abundance influence the utilization and interpretation of airborne eDNA results. Lastly, we explore several areas and opportunities for further development of eDNA tools for plants, advancing our knowledge and understanding of the efficacy, utility, and cost-effectiveness, and ultimately facilitating increased adoption of eDNA analyses in botanical systems.
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Affiliation(s)
- Mark D Johnson
- Engineering Research and Development Center, Construction Engineering Research Laboratory (CERL), Champaign, IL, USA
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, IL, USA
| | - Joanna R Freeland
- Department of Biology, Trent University, 1600 West Bank Drive, Peterborough, ON, K9L 0G2, Canada
| | - Laura Parducci
- Department of Environmental Biology, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18D, SE-75236, Uppsala, Sweden
| | - Darren M Evans
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Rachel S Meyer
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Brenda Molano-Flores
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, IL, USA
| | - Mark A Davis
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois Urbana-Champaign, Champaign, IL, USA
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10
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Lee SK, Woo C, Lee EJ, Yamamoto N. Using high-throughput sequencing to investigate the dietary composition of the Korean water deer (Hydropotes inermis argyropus): a spatiotemporal comparison. Sci Rep 2022; 12:22271. [PMID: 36564425 PMCID: PMC9789119 DOI: 10.1038/s41598-022-26862-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022] Open
Abstract
The Korean water deer (Hydropotes inermis argyropus) is considered a vermin in Korea because it damages crops, but also listed as a vulnerable species on the IUCN's red list. Therefore, it is indispensable to manage them appropriately by understanding the ecology such as food habits. Here, we aimed to apply high-throughput sequencing (HTS), a sensitive and objective method, to investigate the dietary composition of the Korean water deer inhabiting the lowland and forest areas in summer and winter. We targeted the internal transcribed spacer 2 (ITS2) region for plant identification. From a total of 40 fecal samples analyzed, 63 plant genera were identified, with Morus being the most abundant, and some of the plant taxa identified by HTS were detected for the first time as the diets of Korean water deer. By type, woody plants (68.6%) were the most predominant, followed by forbs (7.0%) and graminoids (0.7%). We found that the deer in the forest area ate more woody plants (84.6%) than those in the lowland area (52.7%). It was also found that the type of woody plants that the deer ate changed by season. Overall, our results indicate that the Korean water deer is a browser that is seasonally adaptable and feeds on a wide variety of woody plants. We expect that the results and genetics methods reported here, by parallelly investigating their habitat range and reproductive behavior in the future, will help the management and conservation of the Korean water deer, which is in contradictory situations.
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Affiliation(s)
- Seung-Kyung Lee
- grid.31501.360000 0004 0470 5905School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Cheolwoon Woo
- grid.31501.360000 0004 0470 5905Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, 08826 South Korea
| | - Eun Ju Lee
- grid.31501.360000 0004 0470 5905School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Naomichi Yamamoto
- grid.31501.360000 0004 0470 5905Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, 08826 South Korea ,grid.31501.360000 0004 0470 5905Institute of Health and Environment, Seoul National University, Seoul, South Korea
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11
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Dubois B, Debode F, Hautier L, Hulin J, Martin GS, Delvaux A, Janssen E, Mingeot D. A detailed workflow to develop QIIME2-formatted reference databases for taxonomic analysis of DNA metabarcoding data. BMC Genom Data 2022; 23:53. [PMID: 35804326 PMCID: PMC9264521 DOI: 10.1186/s12863-022-01067-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 07/01/2022] [Indexed: 11/10/2022] Open
Abstract
Background The DNA metabarcoding approach has become one of the most used techniques to study the taxa composition of various sample types. To deal with the high amount of data generated by the high-throughput sequencing process, a bioinformatics workflow is required and the QIIME2 platform has emerged as one of the most reliable and commonly used. However, only some pre-formatted reference databases dedicated to a few barcode sequences are available to assign taxonomy. If users want to develop a new custom reference database, several bottlenecks still need to be addressed and a detailed procedure explaining how to develop and format such a database is currently missing. In consequence, this work is aimed at presenting a detailed workflow explaining from start to finish how to develop such a curated reference database for any barcode sequence. Results We developed DB4Q2, a detailed workflow that allowed development of plant reference databases dedicated to ITS2 and rbcL, two commonly used barcode sequences in plant metabarcoding studies. This workflow addresses several of the main bottlenecks connected with the development of a curated reference database. The detailed and commented structure of DB4Q2 offers the possibility of developing reference databases even without extensive bioinformatics skills, and avoids ‘black box’ systems that are sometimes encountered. Some filtering steps have been included to discard presumably fungal and misidentified sequences. The flexible character of DB4Q2 allows several key sequence processing steps to be included or not, and downloading issues can be avoided. Benchmarking the databases developed using DB4Q2 revealed that they performed well compared to previously published reference datasets. Conclusion This study presents DB4Q2, a detailed procedure to develop custom reference databases in order to carry out taxonomic analyses with QIIME2, but also with other bioinformatics platforms if desired. This work also provides ready-to-use plant ITS2 and rbcL databases for which the prediction accuracy has been assessed and compared to that of other published databases. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-022-01067-5.
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12
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Flower-Visiting Insect Assemblages on Fall-Blooming Native California Sage Scrub Shrubs. DIVERSITY 2022. [DOI: 10.3390/d14110958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Pollinator studies in the endangered California sage scrub ecosystem have focused on spring insect assemblages, when most plant species bloom. Consequently, the insect assemblages using common fall-blooming sage scrub shrubs Lepidospartum squamatum, Ericameria pinifolia, and Baccharis pilularis remain undescribed. Our study aimed to: (1) document flower-visiting insect assemblages on fall-blooming shrubs, (2) assess the efficacy of three sampling techniques in inventorying insect assemblages, and (3) explore, using DNA metabarcoding, which plants are utilized and the extent to which surrounding suburban habitats’ plants are also used. While elevated sampling is required to inventory flower-visiting insects, we describe a diverse assemblage consisting of 123 species. Insect assemblages differed between L. squamatum and B. pilularis, as well as, E. pinifolia and B. pilularis, but not between L. squamatum and E. pinifolia. Direct sampling approaches (netting and photo documentation) collected 115 species not collected by passive malaise traps, highlighting that active observations are required to describe flower-visiting insect assemblages. Sequencing the ITS2 region of pollen from abundant visitors revealed that a majority of pollen is from the sage scrub ecosystem, highlighting its value. Our results indicate that the presence of fall-blooming shrubs may be critical for maintaining diverse sage scrub insect and pollinator assemblages.
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Sofiev M, Sofieva S, Palamarchuk J, Šaulienė I, Kadantsev E, Atanasova N, Fatahi Y, Kouznetsov R, Kuula J, Noreikaite A, Peltonen M, Pihlajamäki T, Saarto A, Svirskaite J, Toiviainen L, Tyuryakov S, Šukienė L, Asmi E, Bamford D, Hyvärinen AP, Karppinen A. Bioaerosols in the atmosphere at two sites in Northern Europe in spring 2021: Outline of an experimental campaign. ENVIRONMENTAL RESEARCH 2022; 214:113798. [PMID: 35810819 DOI: 10.1016/j.envres.2022.113798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/07/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
A coordinated observational and modelling campaign targeting biogenic aerosols in the air was performed during spring 2021 at two locations in Northern Europe: Helsinki (Finland) and Siauliai (Lithuania), approximately 500 km from each other in north-south direction. The campaign started on March 1, 2021 in Siauliai (12 March in Helsinki) and continued till mid-May in Siauliai (end of May in Helsinki), thus recording the transition of the atmospheric biogenic aerosols profile from winter to summer. The observations included a variety of samplers working on different principles. The core of the program was based on 2- and 2.4--hourly sampling in Helsinki and Siauliai, respectively, with sticky slides (Hirst 24-h trap in Helsinki, Rapid-E slides in Siauliai). The slides were subsequently processed extracting the DNA from the collected aerosols, which was further sequenced using the 3-rd generation sequencing technology. The core sampling was accompanied with daily and daytime sampling using standard filter collectors. The hourly aerosol concentrations at the Helsinki monitoring site were obtained with a Poleno flow cytometer, which could recognize some of the aerosol types. The sampling campaign was supported by numerical modelling. For every sample, SILAM model was applied to calculate its footprint and to predict anthropogenic and natural aerosol concentrations, at both observation sites. The first results confirmed the feasibility of the DNA collection by the applied techniques: all but one delivered sufficient amount of DNA for the following analysis, in over 40% of the cases sufficient for direct DNA sequencing without the PCR step. A substantial variability of the DNA yield has been noticed, generally not following the diurnal variations of the total-aerosol concentrations, which themselves showed variability not related to daytime. An expected upward trend of the biological material amount towards summer was observed but the day-to-day variability was large. The campaign DNA analysis produced the first high-resolution dataset of bioaerosol composition in the North-European spring. It also highlighted the deficiency of generic DNA databases in applications to atmospheric biota: about 40% of samples were not identified with standard bioinformatic methods.
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Affiliation(s)
- Mikhail Sofiev
- Finnish Meteorological Institute, Helsinki, Finland; Vilnius University, Vilnius, Lithuania.
| | - Svetlana Sofieva
- Finnish Meteorological Institute, Helsinki, Finland; University of Helsinki, Helsinki, Finland
| | | | | | | | - Nina Atanasova
- Finnish Meteorological Institute, Helsinki, Finland; University of Helsinki, Helsinki, Finland
| | - Yalda Fatahi
- Finnish Meteorological Institute, Helsinki, Finland
| | | | - Joel Kuula
- Finnish Meteorological Institute, Helsinki, Finland
| | | | - Martina Peltonen
- Finnish Meteorological Institute, Helsinki, Finland; University of Helsinki, Helsinki, Finland
| | | | | | - Julija Svirskaite
- Finnish Meteorological Institute, Helsinki, Finland; University of Helsinki, Helsinki, Finland
| | | | | | | | - Eija Asmi
- Finnish Meteorological Institute, Helsinki, Finland
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14
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Boff S, Keller A, Raizer J, Lupi D. Decreased efficiency of pollen collection due to Sulfoxaflor exposure leads to a reduction in the size of bumble bee workers in late European summer. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.842563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Bumble bees (Bombus terrestris) are important pollinators of wild and crop plants. Despite their importance in the process of fruit and seed production on crop sites, their activity may be impaired due to exposure to pesticides. This species has a yearly life cycle and colony success may rely on effective foraging of workers on ruderal plants late in summer when most crops are no longer flowering. In the current study, we investigated the effect of chronic exposure to Sulfoxaflor on aspects of the foraging behavior of bumble bees and whether Sulfoxaflor influences the body size of workers of B. terrestris in a crop landscape. We found that 2 weeks of continuous exposure to Sulfoxaflor influenced workers’ foraging dynamics and collection of resources. However, there was no evidence that the 5 ppb dose of the pesticide impacted the ability of bees to handle flowers with different traits. Workers from colonies exposed to Sulfoxaflor were smaller. The effect on worker size may be explained as a consequence of the reduced pollen income per unit of worker foraging. Thus, if the effects of Sulfoxaflor applied directly to crops had the same effect as that observed on commercial bumble bees after our chronic exposure, it might negatively impact colony success due to the impact on pollen collection and the reduction in the size of workers.
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15
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Honey DNA metabarcoding revealed foraging resource partitioning between Korean native and introduced honey bees (Hymenoptera: Apidae). Sci Rep 2022; 12:14394. [PMID: 35999346 PMCID: PMC9399230 DOI: 10.1038/s41598-022-18465-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 08/12/2022] [Indexed: 11/08/2022] Open
Abstract
Honey DNA metabarcoding provides information of floral sources of honey and foraging plant preferences of honey bees. We evaluated the floral composition of honey from two different species of honey bees, Apis cerana honey (ACH) and A. mellifera honey (AMH) in a mixed apiary located in a semi-forest environment to understand the floral preference and level of interspecific competition on floral resource. Three honey samples were collected from different hives of each species in mid-August. In total, 56 plant taxa were identified across the honey samples and among them, 38 taxonomic units were found in ACH compared with a total of 33 in AMH. The number of major plants (> 1% of reads) in honey samples was 9 and 11 in ACH and AMH respectively indicating the higher diversity of plant taxa in AMH. 23 taxonomic units were found exclusively in ACH, 18 taxonomic units were found only in AMH and 15 taxonomic units were shared between ACH and AMH indicating that 73% of the taxonomic units were present only in honey originated from one of the honeybee species. Qualitative and quantitative analyses of the shared major plants revealed the division of floral resource between these co-existing honey bee species pointing to a low level of interspecific competition between these two important pollinators.
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16
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Klečka J, Mikát M, Koloušková P, Hadrava J, Straka J. Individual-level specialisation and interspecific resource partitioning in bees revealed by pollen DNA metabarcoding. PeerJ 2022; 10:e13671. [PMID: 35959478 PMCID: PMC9359135 DOI: 10.7717/peerj.13671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 06/12/2022] [Indexed: 01/17/2023] Open
Abstract
It is increasingly recognised that intraspecific variation in traits, such as morphology, behaviour, or diet is both ubiquitous and ecologically important. While many species of predators and herbivores are known to display high levels of between-individual diet variation, there is a lack of studies on pollinators. It is important to fill in this gap because individual-level specialisation of flower-visiting insects is expected to affect their efficiency as pollinators with consequences for plant reproduction. Accordingly, the aim of our study was to quantify the level of individual-level specialisation and foraging preferences, as well as interspecific resource partitioning, in three co-occurring species of bees of the genus Ceratina (Hymenoptera: Apidae: Xylocopinae), C. chalybea, C. nigrolabiata, and C. cucurbitina. We conducted a field experiment where we provided artificial nesting opportunities for the bees and combined a short-term mark-recapture study with the dissection of the bees' nests to obtain repeated samples from individual foraging females and complete pollen provisions from their nests. We used DNA metabarcoding based on the ITS2 locus to identify the composition of the pollen samples. We found that the composition of pollen carried on the bodies of female bees and stored in the brood provisions in their nests significantly differed among the three co-occurring species. At the intraspecific level, individual females consistently differed in their level of specialisation and in the composition of pollen carried on their bodies and stored in their nests. We also demonstrate that higher generalisation at the species level stemmed from larger among-individual variation in diets, as observed in other types of consumers, such as predators. Our study thus reveals how specialisation and foraging preferences of bees change from the scale of individual foraging bouts to complete pollen provisions accumulated in their nests over many days. Such a multi-scale view of foraging behaviour is necessary to improve our understanding of the functioning of plant-flower visitor communities.
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Affiliation(s)
- Jan Klečka
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Michael Mikát
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Pavla Koloušková
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Jiří Hadrava
- Institute of Entomology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic,Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jakub Straka
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
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17
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Swenson SJ, Eichler L, Hörren T, Kolter A, Köthe S, Lehmann GUC, Meinel G, Mühlethaler R, Sorg M, Gemeinholzer B. The potential of metabarcoding plant components of Malaise trap samples to enhance knowledge of plant-insect interactions. METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.85213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The worldwide rapid declines in insect and plant abundance and diversity that have occurred in the past decades have gained public attention and demand for political actions to counteract these declines are growing. Rapid large-scale biomonitoring can aid in observing these changes and provide information for decisions for land management and species protection. Malaise traps have long been used for insect sampling and when insects are captured in these traps, they carry traces of plants they have visited on the body surface or as digested food material in the gut contents. Metabarcoding offers a promising method for identifying these plant traces, providing insight into the plants with which insects are directly interacting at a given time. To test the efficacy of DNA metabarcoding with these sample types, 79 samples from 21 sites across Germany were analysed with the ITS2 barcode. This study, to our knowledge, is the first examination of metabarcoding plant DNA traces from Malaise trap samples. Here, we report on the feasibility of sequencing these sample types, analysis of the resulting taxa, the usage of cultivated plants by insects near nature conservancy areas and the detection of rare and neophyte species. Due to the frequency of contamination and false positive reads, isolation and PCR negative controls should be used in every reaction. Metabarcoding has advantages in efficiency and resolution over microscopic identification of pollen and is the only possible identification method for the other plant traces from Malaise traps and could provide a broad utility for future studies of plant-insect interactions.
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18
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Alexander JB, Marnane MJ, Elsdon TS, Bunce M, Songploy S, Sitaworawet P, Harvey ES. Complementary molecular and visual sampling of fish on oil and gas platforms provides superior biodiversity characterisation. MARINE ENVIRONMENTAL RESEARCH 2022; 179:105692. [PMID: 35785679 DOI: 10.1016/j.marenvres.2022.105692] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
Offshore oil and gas platforms have the potential to provide complex refugia for fish and benthic colonisers. We compare two methods of biodiversity assessment for fish and elasmobranchs at seven decommissioned oil and gas platforms as well as five sediment sites, located 5 km from platforms, in the Gulf of Thailand. Using surveys from stereo-video ROV transects, and data from Environmental DNA (eDNA) water-column samples, we detected fish and elasmobranch taxa from 39 families and 66 genera across both platform and sediment sites with eDNA, compared with 18 families and 29 genera by stereo-ROV with platforms yielding significantly greater species richness. This study demonstrates that the combination of stereo-video ROV and eDNA provide effective, non-extractive and complementary methods to enhance data capture. This approach sets new benchmarks for evaluating fish assemblages surrounding platforms and will enhance measurements of biota to inform decisions on the fate of oil/gas infrastructure.
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Affiliation(s)
- Jason B Alexander
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia.
| | | | - Travis S Elsdon
- Chevron Technical Center, Perth, Western Australia, Australia
| | - Michael Bunce
- Institute of Environmental Science and Research, New Zealand
| | - Se Songploy
- Aquatic Resources Research Institute, Chulalongkorn University, Bangkok, Thailand
| | | | - Euan S Harvey
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
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19
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Leonhardt SD, Peters B, Keller A. Do amino and fatty acid profiles of pollen provisions correlate with bacterial microbiomes in the mason bee Osmia bicornis? Philos Trans R Soc Lond B Biol Sci 2022; 377:20210171. [PMID: 35491605 DOI: 10.1098/rstb.2021.0171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Bee performance and well-being strongly depend on access to sufficient and appropriate resources, in particular pollen and nectar of flowers, which constitute the major basis of bee nutrition. Pollen-derived microbes appear to play an important but still little explored role in the plant pollen-bee interaction dynamics, e.g. through affecting quantities and ratios of important nutrients. To better understand how microbes in pollen collected by bees may affect larval health through nutrition, we investigated correlations between the floral, bacterial and nutritional composition of larval provisions and the gut bacterial communities of the solitary megachilid bee Osmia bicornis. Our study reveals correlations between the nutritional quality of pollen provisions and the complete bacterial community as well as individual members of both pollen provisions and bee guts. In particular pollen fatty acid profiles appear to interact with specific members of the pollen bacterial community, indicating that pollen-derived bacteria may play an important role in fatty acid provisioning. As increasing evidence suggests a strong effect of dietary fatty acids on bee performance, future work should address how the observed interactions between specific fatty acids and the bacterial community in larval provisions relate to health in O. bicornis. This article is part of the theme issue 'Natural processes influencing pollinator health: from chemistry to landscapes'.
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Affiliation(s)
- Sara Diana Leonhardt
- Plant-Insect Interactions, TUM School of Life Science Systems, Technical University of Munich, Freising, Germany
| | - Birte Peters
- Department for Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany.,Center for Computational and Theoretical Biology, University of Würzburg, Emil Fischer Strasse, 97074 Würzburg, Germany
| | - Alexander Keller
- Cellular and Organismic Networks, Faculty of Biology, Ludwig-Maximilians-Universität Munich, 82152 Planegg-Martinsried, Germany
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20
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Peters B, Keller A, Leonhardt SD. Diets maintained in a changing world: Does land‐use intensification alter wild bee communities by selecting for flexible generalists? Ecol Evol 2022; 12:e8919. [PMID: 35600696 PMCID: PMC9108308 DOI: 10.1002/ece3.8919] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 04/07/2022] [Accepted: 04/19/2022] [Indexed: 11/08/2022] Open
Affiliation(s)
- Birte Peters
- Department for Animal Ecology and Tropical Biology University of Würzburg Biocenter Würzburg Germany
- Department of Bioinformatics University of Würzburg Biocenter Würzburg Germany
- Center for Computational and Theoretical Biology University of Würzburg Würzburg Germany
| | - Alexander Keller
- Cellular and Organismic Networks Faculty of Biology Ludwig‐Maximilians‐Universität Munich Planegg‐Martinsried Germany
| | - Sara Diana Leonhardt
- Department for Animal Ecology and Tropical Biology University of Würzburg Biocenter Würzburg Germany
- Department of Life Science Systems Technical University of Munich Freising Germany
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21
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Bohmann K, Elbrecht V, Carøe C, Bista I, Leese F, Bunce M, Yu DW, Seymour M, Dumbrell AJ, Creer S. Strategies for sample labelling and library preparation in DNA metabarcoding studies. Mol Ecol Resour 2022; 22:1231-1246. [PMID: 34551203 PMCID: PMC9293284 DOI: 10.1111/1755-0998.13512] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 09/07/2021] [Accepted: 09/14/2021] [Indexed: 11/26/2022]
Abstract
Metabarcoding of DNA extracted from environmental or bulk specimen samples is increasingly used to profile biota in basic and applied biodiversity research because of its targeted nature that allows sequencing of genetic markers from many samples in parallel. To achieve this, PCR amplification is carried out with primers designed to target a taxonomically informative marker within a taxonomic group, and sample-specific nucleotide identifiers are added to the amplicons prior to sequencing. The latter enables assignment of the sequences back to the samples they originated from. Nucleotide identifiers can be added during the metabarcoding PCR and during "library preparation", that is, when amplicons are prepared for sequencing. Different strategies to achieve this labelling exist. All have advantages, challenges and limitations, some of which can lead to misleading results, and in the worst case compromise the fidelity of the metabarcoding data. Given the range of questions addressed using metabarcoding, ensuring that data generation is robust and fit for the chosen purpose is critically important for practitioners seeking to employ metabarcoding for biodiversity assessments. Here, we present an overview of the three main workflows for sample-specific labelling and library preparation in metabarcoding studies on Illumina sequencing platforms; one-step PCR, two-step PCR, and tagged PCR. Further, we distill the key considerations for researchers seeking to select an appropriate metabarcoding strategy for their specific study. Ultimately, by gaining insights into the consequences of different metabarcoding workflows, we hope to further consolidate the power of metabarcoding as a tool to assess biodiversity across a range of applications.
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Affiliation(s)
- Kristine Bohmann
- Faculty of Health and Medical SciencesSection for Evolutionary GenomicsGlobe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Vasco Elbrecht
- Department of Environmental Systems ScienceETH ZurichZürichSwitzerland
| | - Christian Carøe
- Faculty of Health and Medical SciencesSection for Evolutionary GenomicsGlobe InstituteUniversity of CopenhagenCopenhagenDenmark
| | - Iliana Bista
- Department of GeneticsUniversity of CambridgeCambridgeUK
- Tree of LifeWellcome Sanger InstituteHinxtonUK
| | - Florian Leese
- Aquatic Ecosystem ResearchFaculty of BiologyUniversity of Duisburg‐EssenEssenGermany
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) LaboratorySchool of Molecular and Life SciencesCurtin UniversityPerthWAAustralia
| | - Douglas W. Yu
- State Key Laboratory of Genetic Resources and EvolutionKunming Institute of ZoologyChinese Academy of SciencesKunmingChina
- School of Biological SciencesNorwich Research ParkUniversity of East AngliaNorwichUK
- Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunming YunnanChina
| | - Mathew Seymour
- Department of EcologySwedish University of Agricultural SciencesUppsalaSweden
| | | | - Simon Creer
- Molecular Ecology and Evolution GroupSchool of Natural SciencesBangor UniversityGwyneddUK
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Carneiro de Melo Moura C, Setyaningsih CA, Li K, Merk MS, Schulze S, Raffiudin R, Grass I, Behling H, Tscharntke T, Westphal C, Gailing O. Biomonitoring via DNA metabarcoding and light microscopy of bee pollen in rainforest transformation landscapes of Sumatra. BMC Ecol Evol 2022; 22:51. [PMID: 35473550 PMCID: PMC9040256 DOI: 10.1186/s12862-022-02004-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 04/07/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Intense conversion of tropical forests into agricultural systems contributes to habitat loss and the decline of ecosystem functions. Plant-pollinator interactions buffer the process of forest fragmentation, ensuring gene flow across isolated patches of forests by pollen transfer. In this study, we identified the composition of pollen grains stored in pot-pollen of stingless bees, Tetragonula laeviceps, via dual-locus DNA metabarcoding (ITS2 and rbcL) and light microscopy, and compared the taxonomic coverage of pollen sampled in distinct land-use systems categorized in four levels of management intensity (forest, shrub, rubber, and oil palm) for landscape characterization. RESULTS Plant composition differed significantly between DNA metabarcoding and light microscopy. The overlap in the plant families identified via light microscopy and DNA metabarcoding techniques was low and ranged from 22.6 to 27.8%. Taxonomic assignments showed a dominance of pollen from bee-pollinated plants, including oil-bearing crops such as the introduced species Elaeis guineensis (Arecaceae) as one of the predominant taxa in the pollen samples across all four land-use types. Native plant families Moraceae, Euphorbiaceae, and Cannabaceae appeared in high proportion in the analyzed pollen material. One-way ANOVA (p > 0.05), PERMANOVA (R² values range from 0.14003 to 0.17684, for all tests p-value > 0.5), and NMDS (stress values ranging from 0.1515 to 0.1859) indicated a lack of differentiation between the species composition and diversity of pollen type in the four distinct land-use types, supporting the influx of pollen from adjacent areas. CONCLUSIONS Stingless bees collected pollen from a variety of agricultural crops, weeds, and wild plants. Plant composition detected at the family level from the pollen samples likely reflects the plant composition at the landscape level rather than the plot level. In our study, the plant diversity in pollen from colonies installed in land-use systems with distinct levels of forest transformation was highly homogeneous, reflecting a large influx of pollen transported by stingless bees through distinct land-use types. Dual-locus approach applied in metabarcoding studies and visual pollen identification showed great differences in the detection of the plant community, therefore a combination of both methods is recommended for performing biodiversity assessments via pollen identification.
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Affiliation(s)
| | - Christina A Setyaningsih
- Department of Palynology and Climate Dynamics, Albrecht-von-Haller-Institute for Plant Sciences, University of Göttingen, 37073, Göttingen, Germany
| | - Kevin Li
- Agroecology, Department of Crop Sciences, University of Göttingen, Grisebachstrasse 6, 37077, Göttingen, Germany
| | - Miryam Sarah Merk
- Statistics and Econometrics, University of Göttingen, Göttingen, Germany
| | - Sonja Schulze
- Agroecology, Department of Crop Sciences, University of Göttingen, Grisebachstrasse 6, 37077, Göttingen, Germany
| | - Rika Raffiudin
- Department of Biology, IPB University ID, Bogor, West Java, 16880, Indonesia
| | - Ingo Grass
- Department of Ecology of Tropical Agricultural Systems, University of Hohenheim, 70599, Stuttgart, Germany
| | - Hermann Behling
- Department of Palynology and Climate Dynamics, Albrecht-von-Haller-Institute for Plant Sciences, University of Göttingen, 37073, Göttingen, Germany
| | - Teja Tscharntke
- Agroecology, Department of Crop Sciences, University of Göttingen, Grisebachstrasse 6, 37077, Göttingen, Germany
| | - Catrin Westphal
- Functional Agrobiodiversity, Department of Crop Sciences, University of Göttingen, Grisebachstrasse 6, 37077, Göttingen, Germany
| | - Oliver Gailing
- Department of Forest Genetics and Forest Tree Breeding, University of Göttingen, 37077, Göttingen, Germany. .,Centre of Biodiversity and Sustainable Land Use, University of Göttingen, 37077, Göttingen, Germany.
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23
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Abstract
The identification of floral visitation by pollinators provides an opportunity to improve our understanding of the fine-scale ecological interactions between plants and pollinators, contributing to biodiversity conservation and promoting ecosystem health. In this review, we outline the various methods which can be used to identify floral visitation, including plant-focused and insect-focused methods. We reviewed the literature covering the ways in which DNA metabarcoding has been used to answer ecological questions relating to plant use by pollinators and discuss the findings of this research. We present detailed methodological considerations for each step of the metabarcoding workflow, from sampling through to amplification, and finally bioinformatic analysis. Detailed guidance is provided to researchers for utilisation of these techniques, emphasising the importance of standardisation of methods and improving the reliability of results. Future opportunities and directions of using molecular methods to analyse plant–pollinator interactions are then discussed.
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24
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Quaresma A, Brodschneider R, Gratzer K, Gray A, Keller A, Kilpinen O, Rufino J, van der Steen J, Vejsnæs F, Pinto MA. Preservation methods of honey bee-collected pollen are not a source of bias in ITS2 metabarcoding. ENVIRONMENTAL MONITORING AND ASSESSMENT 2021; 193:785. [PMID: 34755261 DOI: 10.1007/s10661-021-09563-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/26/2021] [Indexed: 06/13/2023]
Abstract
Pollen metabarcoding is emerging as a powerful tool for ecological research and offers unprecedented scale in citizen science projects for environmental monitoring via honey bees. Biases in metabarcoding can be introduced at any stage of sample processing and preservation is at the forefront of the pipeline. While in metabarcoding studies pollen has been preserved at - 20 °C (FRZ), this is not the best method for citizen scientists. Herein, we compared this method with ethanol (EtOH), silica gel (SG) and room temperature (RT) for preservation of pollen collected from hives in Austria and Denmark. After ~ 4 months of storage, DNAs were extracted with a food kit, and their quality and concentration measured. Most DNA extracts exhibited 260/280 absorbance ratios close to the optimal 1.8, with RT samples from Austria performing slightly worse than FRZ and SG samples (P < 0.027). Statistical differences were also detected for DNA concentration, with EtOH samples producing lower yields than RT and FRZ samples in both countries and SG in Austria (P < 0.042). Yet, qualitative and quantitative assessments of floral composition obtained using high-throughput sequencing with the ITS2 barcode gave non-significant effects of preservation methods on richness, relative abundance and Shannon diversity, in both countries. While freezing and ethanol are commonly employed for archiving tissue for molecular applications, desiccation is cheaper and easier to use regarding both storage and transportation. Since SG is less dependent on ambient humidity and less prone to contamination than RT, we recommend SG for preserving pollen for metabarcoding. SG is straightforward for laymen to use and hence robust for widespread application in citizen science studies.
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Affiliation(s)
- Andreia Quaresma
- Centro de Investigação de Montanha, Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal
| | - Robert Brodschneider
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria
| | - Kristina Gratzer
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010, Graz, Austria
| | - Alison Gray
- Department of Mathematics and Statistics, University of Strathclyde, Glasgow, UK
| | - Alexander Keller
- Center for Computational and Theoretical Biology, Hubland Nord, Würzburg, Germany
- Department of Bioinformatics, University of Würzburg, Am Hubland, BiocenterWürzburg, Germany
| | | | - José Rufino
- Research Centre in Digitalization and Intelligent Robotics (CeDRI), Instituto Politécnico de Bragança, Bragança, Portugal
| | | | | | - M Alice Pinto
- Centro de Investigação de Montanha, Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253, Bragança, Portugal.
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25
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Landscapes with high amounts of mass-flowering fruit crops reduce the reproduction of two solitary bees. Basic Appl Ecol 2021. [DOI: 10.1016/j.baae.2021.07.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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26
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Bell KL, Petit RA, Cutler A, Dobbs EK, Macpherson JM, Read TD, Burgess KS, Brosi BJ. Comparing whole-genome shotgun sequencing and DNA metabarcoding approaches for species identification and quantification of pollen species mixtures. Ecol Evol 2021; 11:16082-16098. [PMID: 34824813 PMCID: PMC8601920 DOI: 10.1002/ece3.8281] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/04/2021] [Accepted: 10/08/2021] [Indexed: 12/12/2022] Open
Abstract
Molecular identification of mixed-species pollen samples has a range of applications in various fields of research. To date, such molecular identification has primarily been carried out via amplicon sequencing, but whole-genome shotgun (WGS) sequencing of pollen DNA has potential advantages, including (1) more genetic information per sample and (2) the potential for better quantitative matching. In this study, we tested the performance of WGS sequencing methodology and publicly available reference sequences in identifying species and quantifying their relative abundance in pollen mock communities. Using mock communities previously analyzed with DNA metabarcoding, we sequenced approximately 200Mbp for each sample using Illumina HiSeq and MiSeq. Taxonomic identifications were based on the Kraken k-mer identification method with reference libraries constructed from full-genome and short read archive data from the NCBI database. We found WGS to be a reliable method for taxonomic identification of pollen with near 100% identification of species in mixtures but generating higher rates of false positives (reads not identified to the correct taxon at the required taxonomic level) relative to rbcL and ITS2 amplicon sequencing. For quantification of relative species abundance, WGS data provided a stronger correlation between pollen grain proportion and sequence read proportion, but diverged more from a 1:1 relationship, likely due to the higher rate of false positives. Currently, a limitation of WGS-based pollen identification is the lack of representation of plant diversity in publicly available genome databases. As databases improve and costs drop, we expect that eventually genomics methods will become the methods of choice for species identification and quantification of mixed-species pollen samples.
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Affiliation(s)
- Karen L Bell
- Department of Environmental Sciences Emory University Atlanta Georgia USA
- Present address: School of Biological Sciences University of Western Australia Perth Australia
- Present address: CSIRO Land & Water and CSIRO Health & Biosecurity Floreat WA Australia
| | - Robert A Petit
- Division of Infectious Diseases Department of Medicine Emory University Atlanta Georgia USA
| | - Anya Cutler
- Department of Environmental Sciences Emory University Atlanta Georgia USA
| | - Emily K Dobbs
- Department of Environmental Sciences Emory University Atlanta Georgia USA
- Present address: Department of Biology Northern Kentucky University Highland Heights Kentucky USA
| | - J Michael Macpherson
- Department of Biology Chapman University Orange California USA
- Present address: 23andMe Mountain View California USA
| | - Timothy D Read
- Division of Infectious Diseases Department of Medicine Emory University Atlanta Georgia USA
| | - Kevin S Burgess
- Department of Biology Columbus State University Columbus Georgia USA
| | - Berry J Brosi
- Department of Environmental Sciences Emory University Atlanta Georgia USA
- Present address: Department of Biology University of Washington Seattle Washington USA
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27
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Casanelles‐Abella J, Müller S, Keller A, Aleixo C, Alós Orti M, Chiron F, Deguines N, Hallikma T, Laanisto L, Pinho P, Samson R, Tryjanowski P, Van Mensel A, Pellissier L, Moretti M. How wild bees find a way in European cities: Pollen metabarcoding unravels multiple feeding strategies and their effects on distribution patterns in four wild bee species. J Appl Ecol 2021. [DOI: 10.1111/1365-2664.14063] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Joan Casanelles‐Abella
- Biodiversity and Conservation Biology Swiss Federal Institute for Forest, Snow and Landscape Research WSL Birmensdorf Switzerland
- Institute of Terrestrial Ecosystems ETH Zurich Zurich Switzerland
| | - Stefanie Müller
- Biodiversity and Conservation Biology Swiss Federal Institute for Forest, Snow and Landscape Research WSL Birmensdorf Switzerland
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland
| | - Alexander Keller
- Organismic and Cellular Interactions Biocenter Faculty of Biology Ludwig‐Maximilians‐Universität München Martinsried Germany
| | - Cristiana Aleixo
- Centre for Ecology, Evolution and Environmental Changes (cE3c) Faculdade de Ciências Universidade de Lisboa Lisboa Portugal
| | - Marta Alós Orti
- Institute of Agricultural and Environmental Sciences Estonian University of Life Sciences Tartu Estonia
| | - François Chiron
- Université Paris‐SaclayCNRSAgroParisTechEcologie Systématique Evolution Orsay France
| | - Nicolas Deguines
- Université Paris‐SaclayCNRSAgroParisTechEcologie Systématique Evolution Orsay France
- Laboratoire Ecologie et Biologie des Interactions Equipe Ecologie Evolution Symbiose Université de PoitiersUMR CNRS Nouvelle‐Aquitaine France
| | - Tiit Hallikma
- Institute of Agricultural and Environmental Sciences Estonian University of Life Sciences Tartu Estonia
| | - Lauri Laanisto
- Institute of Agricultural and Environmental Sciences Estonian University of Life Sciences Tartu Estonia
| | - Pedro Pinho
- Centre for Ecology, Evolution and Environmental Changes (cE3c) Faculdade de Ciências Universidade de Lisboa Lisboa Portugal
| | - Roeland Samson
- Laboratory of Environmental and Urban Ecology Department of Bioscience Engineering University of Antwerp Antwerp Belgium
| | - Piotr Tryjanowski
- Department of Zoology Poznan University of Life Sciences Poznań Poland
| | - Anskje Van Mensel
- Laboratory of Environmental and Urban Ecology Department of Bioscience Engineering University of Antwerp Antwerp Belgium
| | - Loïc Pellissier
- Institute of Terrestrial Ecosystems ETH Zurich Zurich Switzerland
- Land Change Science Swiss Federal Institute for Forest, Snow and Landscape Research WSL Birmensdorf Switzerland
| | - Marco Moretti
- Biodiversity and Conservation Biology Swiss Federal Institute for Forest, Snow and Landscape Research WSL Birmensdorf Switzerland
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28
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Bumble Bee Foraged Pollen Analyses in Spring Time in Southern Estonia Shows Abundant Food Sources. INSECTS 2021; 12:insects12100922. [PMID: 34680691 PMCID: PMC8538635 DOI: 10.3390/insects12100922] [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: 08/02/2021] [Revised: 09/30/2021] [Accepted: 10/01/2021] [Indexed: 11/17/2022]
Abstract
Simple Summary Pollinators make a strong contribution to ecosystem stability. However, nowadays, they also need protection and sustainable habitat to live and develop. Not all regions can provide suitable habitats due to agricultural intensification, urbanization, climate changes and corresponding impacts. Our study was conducted in the late spring in south Estonia where arable lands were surrounded by forest patches and rural areas. For better performance, we used both light microscopy and DNA metabarcoding methods for pollen identification. We found that bumble bees foraged on the diverse food sources showing preferences for several main plant families. Additionally, in our case, land-use types did not show important effects on bumble bee food choices and foraging decisions. Various landscape features can provide diverse food sources at the early development stages and support nest longevity. Here, we can say that a better understanding of pollinators’ food preferences can help in the application of more suitable measures for their conservation. Abstract Agricultural landscapes usually provide higher quantities of single-source food, which are noticeably lacking in diversity and might thus have low nutrient value for bumble bee colony development. Here, in this study, we analysed the pollen foraging preferences over a large territory of a heterogeneous agricultural landscape: southern Estonia. We aimed to assess the botanical diversity of bumble bee food plants in the spring time there. We looked for preferences for some food plants or signs of food shortage that could be associated with any particular landscape features. For this purpose, we took Bombus terrestris commercial hives to the landscape, performed microscopy analyses and improved the results with the innovative DNA metabarcoding technique to determine the botanical origin of bumble bee-collected pollen. We found high variability of forage plants with no strong relationship with any particular landscape features. Based on the low number of plant species in single flights, we deduce that the availability of main forage plants is sufficient indicating rich forage availabilities. Despite specific limitations, we saw strong correlations between microscopy and DNA metabarcoding data usable for quantification analyses. As a conclusion, we saw that the spring-time vegetation in southern Estonia can support bumble bee colony development regardless of the detailed landscape structure. The absence of clearly dominating food preference by the tested generalist bumble bee species B. terrestris makes us suggest that other bumble bee species, at least food generalists, should also find plenty of forage in their early development phase.
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29
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Towards Integrated Pest and Pollinator Management in Intensive Pear Cultivation: A Case Study from Belgium. INSECTS 2021; 12:insects12100901. [PMID: 34680669 PMCID: PMC8539969 DOI: 10.3390/insects12100901] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 09/13/2021] [Accepted: 09/22/2021] [Indexed: 11/29/2022]
Abstract
Simple Summary Over the past decades, Integrated Pest Management (IPM) strategies have been widely adopted in commercial fruit production in Europe, supporting natural pest control as an ecosystem service. At the same time, there has been a growing awareness of the importance of pollinating insects, leading to the concept of Integrated Pest and Pollinator Management (IPPM). Here we present the outcomes of a 4-year case study as a valuable illustration of an IPPM strategy in a commercial intensive pear orchard. We show how the added-value of local biodiversity measures can be visualized in front of growers, linking ecological measures to economic benefits. This scientifically-based as well as practice-oriented demonstrative case study supports the acceptance and adoption of IPPM principles in commercial intensive pear production cultivation. Abstract Recently, the concept of Integrated Pest Management (IPM) was further extended into Integrated Pest and Pollinator Management (IPPM). Implementation of IPPM strategies entails the combination of actions for pest and pollinator management providing complementary or synergistic benefits for yield and/or quality of the harvest. The aim of this study was to examine IPPM elements (i.e., mixed hedgerow, nesting boxes for mason bees, Osmia spp.) and demonstrate their impact in the practical context of modern commercial fruit cultivation in a 4-year case study in an intensive ‘Conference’ pear orchard. The outcomes of visual observations during transect walks and molecular analysis of pollen collected by mason bees, showed the importance of additional floral resources for the presence of mason bees and other pollinating insects in the orchard environment. Pear quality assessments indicated that insect-mediated pollination had a significant positive impact, with a tendency for higher quality pears in the close vicinity of Osmia nesting boxes. However, despite the fact that pear pollen was also detected in Osmia spp. nest cells, the amount and frequency of pear pollen collection for their nest built-up turned out to be rather low. In the same intensive pear orchard studied for pollination effects, we simultaneously demonstrate the impact of a mixed hedgerow to enhance integrated pest control.
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30
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Chiara B, Francesco C, Fulvio B, Paola M, Annalisa G, Stefania S, Luigi AP, Simone P. Exploring the botanical composition of polyfloral and monofloral honeys through DNA metabarcoding. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.108175] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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31
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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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32
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Leontidou K, Vokou D, Sandionigi A, Bruno A, Lazarina M, De Groeve J, Li M, Varotto C, Girardi M, Casiraghi M, Cristofori A. Plant biodiversity assessment through pollen DNA metabarcoding in Natura 2000 habitats (Italian Alps). Sci Rep 2021; 11:18226. [PMID: 34521917 PMCID: PMC8440677 DOI: 10.1038/s41598-021-97619-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 08/02/2021] [Indexed: 01/28/2023] Open
Abstract
Monitoring biodiversity is of increasing importance in natural ecosystems. Metabarcoding can be used as a powerful molecular tool to complement traditional biodiversity monitoring, as total environmental DNA can be analyzed from complex samples containing DNA of different origin. The aim of this research was to demonstrate the potential of pollen DNA metabarcoding using the chloroplast trnL partial gene sequencing to characterize plant biodiversity. Collecting airborne biological particles with gravimetric Tauber traps in four Natura 2000 habitats within the Natural Park of Paneveggio Pale di San Martino (Italian Alps), at three-time intervals in 1 year, metabarcoding identified 68 taxa belonging to 32 local plant families. Metabarcoding could identify with finer taxonomic resolution almost all non-rare families found by conventional light microscopy concurrently applied. However, compared to microscopy quantitative results, Poaceae, Betulaceae, and Oleaceae were found to contribute to a lesser extent to the plant biodiversity and Pinaceae were more represented. Temporal changes detected by metabarcoding matched the features of each pollen season, as defined by aerobiological studies running in parallel, and spatial heterogeneity was revealed between sites. Our results showcase that pollen metabarcoding is a promising approach in detecting plant species composition which could provide support to continuous monitoring required in Natura 2000 habitats for biodiversity conservation.
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Affiliation(s)
- Kleopatra Leontidou
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, San Michele all' Adige, Trentino, Italy. .,Department of Ecology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece.
| | - Despoina Vokou
- Department of Ecology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Anna Sandionigi
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Antonia Bruno
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Maria Lazarina
- Department of Ecology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Johannes De Groeve
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, San Michele all' Adige, Trentino, Italy.,Department of Geography, Ghent University, Krijgslaan 281, 9000, Ghent, Belgium
| | - Mingai Li
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, San Michele all' Adige, Trentino, Italy
| | - Claudio Varotto
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, San Michele all' Adige, Trentino, Italy
| | - Matteo Girardi
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, San Michele all' Adige, Trentino, Italy
| | - Maurizio Casiraghi
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Antonella Cristofori
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, San Michele all' Adige, Trentino, Italy
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33
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Harnessing the Power of Metabarcoding in the Ecological Interpretation of Plant-Pollinator DNA Data: Strategies and Consequences of Filtering Approaches. DIVERSITY 2021. [DOI: 10.3390/d13090437] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Although DNA metabarcoding of pollen mixtures has been increasingly used in the field of pollination biology, methodological and interpretation issues arise due to its high sensitivity. Filtering or maintaining false positives, contaminants, and rare taxa or molecular features could lead to different ecological results. Here, we reviewed how this choice has been addressed in 43 studies featuring pollen DNA metabarcoding, which highlighted a very high heterogeneity of filtering methods. We assessed how these strategies shaped pollen assemblage composition, species richness, and interaction networks. To do so, we compared four processing methods: unfiltering, filtering with a proportional 1% of sample reads, a fixed threshold of 100 reads, and the ROC approach (Receiver Operator Characteristic). The results indicated that filtering impacted species composition and reduced species richness, with ROC emerging as a conservative approach. Moreover, in contrast to unfiltered networks, filtering decreased network Connectance and Entropy, and it increased Modularity and Connectivity, indicating that using cut-off thresholds better describes interactions. Overall, unfiltering might compromise reliable ecological interpretations, unless a study targets rare species. We discuss the suitability of each filtering type, plead for justifying filtering strategies on biological or methodological bases and for developing shared approaches to make future studies more comparable.
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34
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Oliver AE, Newbold LK, Gweon HS, Read DS, Woodcock BA, Pywell RF. Integration of DNA extraction, metabarcoding and an informatics pipeline to underpin a national citizen science honey monitoring scheme. MethodsX 2021; 8:101303. [PMID: 34434823 PMCID: PMC8374279 DOI: 10.1016/j.mex.2021.101303] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 03/05/2021] [Indexed: 01/04/2023] Open
Abstract
Worldwide honeybees (Apis mellifera L.) are one of the most widely kept domesticated animals, supporting domestic and commercial livelihoods through the production of honey and wax, as well as in the delivery of pollination services to crops. Quantifying which plant species are foraged upon by honeybees provides insights into their nutritional status as well as patterns of landscape scale habitat utilization. Here we outline a rapid and reproducible methodology for identifying environmental DNA (eDNA) originating principally from pollen grains suspended within honey. The process is based on a DNA extraction incorporating vacuum filtration prior to universal eukaryotic internal transcribed spacer 2 region (ITS2) amplicon generation, sequencing and identification. To provide a pre-cursor to sequence phylotyping, we outline systems for error-corrected processing amplicon sequence variant abundance tables that removes chimeras. This methodology underpins the new UK National Honey Monitoring Scheme.We compare the efficacy and speed of centrifugation and filtration systems for removing pollen from honey samples as a precursor to plant DNA barcoding. We introduce the ‘HONEYPI’ informatics pipeline, an open access resource implemented in python 2.7, to ensure long-term reproducibility during the process of amplicon sequence variant classification.
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Affiliation(s)
- Anna E Oliver
- UK Centre for Ecology and Hydrology, Wallingford, Oxfordshire OX10 8BB, UK
| | - Lindsay K Newbold
- UK Centre for Ecology and Hydrology, Wallingford, Oxfordshire OX10 8BB, UK
| | - Hyun S Gweon
- School of Biological Sciences, University of Reading, Reading RG6 6UR, UK
| | - Daniel S Read
- UK Centre for Ecology and Hydrology, Wallingford, Oxfordshire OX10 8BB, UK
| | - Ben A Woodcock
- UK Centre for Ecology and Hydrology, Wallingford, Oxfordshire OX10 8BB, UK
| | - Richard F Pywell
- UK Centre for Ecology and Hydrology, Wallingford, Oxfordshire OX10 8BB, UK
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35
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Arstingstall KA, DeBano SJ, Li X, Wooster DE, Rowland MM, Burrows S, Frost K. Capabilities and limitations of using DNA metabarcoding to study plant-pollinator interactions. Mol Ecol 2021; 30:5266-5297. [PMID: 34390062 DOI: 10.1111/mec.16112] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 11/29/2022]
Abstract
Many pollinator populations are experiencing declines, emphasizing the need for a better understanding of the complex relationship between bees and flowering plants. Using DNA metabarcoding to describe plant-pollinator interactions eliminates many challenges associated with traditional methods and has the potential to reveal a more comprehensive understanding of foraging behavior and pollinator life history. Here we use DNA metabarcoding of ITS2 and rbcL gene regions to identify plant species present in pollen loads of 404 bees from three habitats in eastern Oregon. Our specific objectives were to 1) determine whether plant species identified using DNA metabarcoding are consistent with plant species identified using observations, 2) compare characterizations of diet breadth derived from foraging observations to those based on plant species assignments obtained using DNA metabarcoding, and 3) compare plant species assignments produced by DNA metabarcoding using a "regional" reference database to those produced using a "local" database. At the three locations, 31-86% of foraging observations were consistent with DNA metabarcoding data, 8-50% of diet breadth characterizations based on observations differed from those based on DNA metabarcoding data, and 22-25% of plant species detected using the regional database were not known to occur in the study area in question. Plant-pollinator networks produced from DNA metabarcoding data had higher sampling completeness and significantly lower specialization than networks based on observations. Here, we examine some strengths and limitations of using DNA metabarcoding to identify plant species present in bee pollen loads, make ecological inferences about foraging behavior, and provide guidance for future research.
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Affiliation(s)
| | - Sandra J DeBano
- Department of Fisheries and Wildlife, Oregon State University, Corvallis.,Hermiston Agricultural Research and Extension Center, Oregon State University, Hermiston
| | - Xiaoping Li
- Hermiston Agricultural Research and Extension Center, Oregon State University, Hermiston
| | - David E Wooster
- Department of Fisheries and Wildlife, Oregon State University, Corvallis.,Hermiston Agricultural Research and Extension Center, Oregon State University, Hermiston
| | - Mary M Rowland
- United States Forest Service, Pacific Northwest Research Station, La Grande
| | - Skyler Burrows
- Bee Biology and Systematics Lab, Utah State University, Logan
| | - Kenneth Frost
- Hermiston Agricultural Research and Extension Center, Oregon State University, Hermiston.,Department of Botany and Plant Pathology, Oregon State University, Corvallis
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36
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Geographic source estimation using airborne plant environmental DNA in dust. Sci Rep 2021; 11:16238. [PMID: 34376726 PMCID: PMC8355115 DOI: 10.1038/s41598-021-95702-3] [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: 05/14/2021] [Accepted: 07/22/2021] [Indexed: 02/07/2023] Open
Abstract
Information obtained from the analysis of dust, particularly biological particles such as pollen, plant parts, and fungal spores, has great utility in forensic geolocation. As an alternative to manual microscopic analysis of dust components, we developed a pipeline that utilizes the airborne plant environmental DNA (eDNA) in settled dust to estimate geographic origin. Metabarcoding of settled airborne eDNA was used to identify plant species whose geographic distributions were then derived from occurrence records in the USGS Biodiversity in Service of Our Nation (BISON) database. The distributions for all plant species identified in a sample were used to generate a probabilistic estimate of the sample source. With settled dust collected at four U.S. sites over a 15-month period, we demonstrated positive regional geolocation (within 600 km2 of the collection point) with 47.6% (20 of 42) of the samples analyzed. Attribution accuracy and resolution was dependent on the number of plant species identified in a dust sample, which was greatly affected by the season of collection. In dust samples that yielded a minimum of 20 identified plant species, positive regional attribution was achieved with 66.7% (16 of 24 samples). For broader demonstration, citizen-collected dust samples collected from 31 diverse U.S. sites were analyzed, and trace plant eDNA provided relevant regional attribution information on provenance in 32.2% of samples. This showed that analysis of airborne plant eDNA in settled dust can provide an accurate estimate regional provenance within the U.S., and relevant forensic information, for a substantial fraction of samples analyzed.
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James ARM, Geber MA, Toews DPL. Molecular assays of pollen use consistently reflect pollinator visitation patterns in a system of flowering plants. Mol Ecol Resour 2021; 22:361-374. [PMID: 34260821 DOI: 10.1111/1755-0998.13468] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 06/21/2021] [Accepted: 07/07/2021] [Indexed: 11/28/2022]
Abstract
Determining how pollinators visit plants vs. how they carry and transfer pollen is an ongoing project in pollination ecology. The current tools for identifying the pollens that bees carry have different strengths and weaknesses when used for ecological inference. In this study we use three methods to better understand a system of congeneric, coflowering plants in the genus Clarkia and their bee pollinators: observations of plant-pollinator contact in the field, and two different molecular methods to estimate the relative abundance of each Clarkia pollen in samples collected from pollinators. We use these methods to investigate if observations of plant-pollinator contact in the field correspond to the pollen bees carry; if individual bees carry Clarkia pollens in predictable ways, based on previous knowledge of their foraging behaviors; and how the three approaches differ for understanding plant-pollinator interactions. We find that observations of plant-pollinator contact are generally predictive of the pollens that bees carry while foraging, and network topologies using the three different methods are statistically indistinguishable from each other. Results from molecular pollen analysis also show that while bees can carry multiple species of Clarkia at the same time, they often carry one species of pollen. Our work contributes to the growing body of literature aimed at resolving how pollinators use floral resources. We suggest our novel relative amplicon quantification method as another tool in the developing molecular ecology and pollination biology toolbox.
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Affiliation(s)
- Aubrie R M James
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Monica A Geber
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - David P L Toews
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA.,Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
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38
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Xu H, Li P, Ren G, Wang Y, Jiang D, Liu C. Authentication of Three Source Spices of Arnebiae Radix Using DNA Barcoding and HPLC. Front Pharmacol 2021; 12:677014. [PMID: 34276367 PMCID: PMC8281675 DOI: 10.3389/fphar.2021.677014] [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: 03/07/2021] [Accepted: 05/19/2021] [Indexed: 11/16/2022] Open
Abstract
Arnebia decumbens (Vent.) Coss. et Kralik, A. euchroma (Royle) Johnst and A. guttata Bunge, three commonly used traditional Chinese medicinal plants have been widely used for the clinical treatment of inflammatory diseases caused by fungal, bacterial, oxidation, and other related pathogens. However, precise identification at the similar species level is usually challenging due to the influence of the source of medicinal materials, traditional ethnic medicine and medicinal habits. Here we developed a comprehensive and efficient identification system for three source spices of Arnebiae Radix based on DNA barcoding and HPLC fingerprinting. A total of 599 samples from thirty-five wild populations were collected and identified by using DNA barcodes of ITS2 regions, and the chemotypes of seven naphthoquinoneswere revealed by HPLC quantitative analysis including principal component analysis and hierarchical clustering analysis. Our results showed that the ITS2 sequences can distinguish three source spices of Arnebiae Radix from adulterants. However, it was difficult to identify them by HPLC-specific chromatograms combined with chemometric analysis. These results indicated that DNA barcoding was a more powerful method than HPLC fingerprinting for the identification of related species that were genetically similar. DNA barcoding analysis could be a promising and reliable tool to accurately confirm the identities of medicinal materials, especially for those whose sources are multiple and difficult to be identified by conventional chromatography.
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Affiliation(s)
- Haiyan Xu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China.,College of Traditional Chinese Medicine, Xinjiang Medical University, Xinjiang, China
| | - Ping Li
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Guangxi Ren
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Yanjiao Wang
- Department of Basic Medical Sciences, Xinjiang Medical University, Xinjiang, China
| | - Dan Jiang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Chunsheng Liu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
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39
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Suanno C, Aloisi I, Fernández-González D, Del Duca S. Monitoring techniques for pollen allergy risk assessment. ENVIRONMENTAL RESEARCH 2021; 197:111109. [PMID: 33848553 DOI: 10.1016/j.envres.2021.111109] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 03/12/2021] [Accepted: 03/29/2021] [Indexed: 05/15/2023]
Abstract
Understanding airborne pollen allergens trends is of great importance for the high prevalence and the socio-economic impact that pollen-related respiratory diseases have on a global scale. Pursuing this aim, aeropalynology evolved as a broad and complex field, that requires multidisciplinary knowledge covering the molecular identity of pollen allergens, the nature of allergen-bearing particles (pollen grains, pollen sub-particles, and small airborne particles), and the distribution of their sources. To estimate the health hazard that urban vegetation and atmospheric pollen concentrations pose to allergic subjects, it is pivotal to develop efficient and rapid monitoring systems and reliable allergic risk indices. Here, we review different pollen allergens monitoring approaches, classifying them into I) vegetation-based, II) pollen-based, and III) allergen-based, and underlining their advantages and limits. Finally, we discuss the outstanding issues and directions for future research that will further clarify our understanding of pollen aeroallergens dynamics and allergen avoidance strategies.
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Affiliation(s)
- Chiara Suanno
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Via Irnerio 42, 40126, Bologna, Italy.
| | - Iris Aloisi
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Via Irnerio 42, 40126, Bologna, Italy.
| | - Delia Fernández-González
- Institute of Atmospheric Sciences and Climate, ISAC-CNR, Via Piero Gobetti 101, 40129, Bologna, Italy; Department Biodiversity and Environmental Management, University of León, 24071, Callejón Campus Vegazana, S/n, 24007, León, Spain
| | - Stefano Del Duca
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Via Irnerio 42, 40126, Bologna, Italy
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Mayr AV, Keller A, Peters MK, Grimmer G, Krischke B, Geyer M, Schmitt T, Steffan‐Dewenter I. Cryptic species and hidden ecological interactions of halictine bees along an elevational gradient. Ecol Evol 2021; 11:7700-7712. [PMID: 34188845 PMCID: PMC8216903 DOI: 10.1002/ece3.7605] [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: 10/26/2020] [Revised: 03/29/2021] [Accepted: 03/31/2021] [Indexed: 11/07/2022] Open
Abstract
Changes of abiotic and biotic conditions along elevational gradients represent serious challenges to organisms which may promote the turnover of species, traits and biotic interaction partners. Here, we used molecular methods to study cuticular hydrocarbon (CHC) profiles, biotic interactions and phylogenetic relationships of halictid bees of the genus Lasioglossum along a 2,900 m elevational gradient at Mt. Kilimanjaro, Tanzania. We detected a strong species turnover of morphologically indistinguishable taxa with phylogenetically clustered cryptic species at high elevations, changes in CHC profiles, pollen resource diversity, and a turnover in the gut and body surface microbiome of bees. At high elevations, increased proportions of saturated compounds in CHC profiles indicate physiological adaptations to prevent desiccation. More specialized diets with higher proportions of low-quality Asteraceae pollen imply constraints in the availability of food resources. Interactive effects of climatic conditions on gut and surface microbiomes, CHC profiles, and pollen diet suggest complex feedbacks among abiotic conditions, ecological interactions, physiological adaptations, and phylogenetic constraints as drivers of halictid bee communities at Mt. Kilimanjaro.
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Affiliation(s)
- Antonia V. Mayr
- Department of Animal Ecology and Tropical BiologyBiocenterUniversity of WürzburgWürzburgGermany
| | - Alexander Keller
- Department of Animal Ecology and Tropical BiologyBiocenterUniversity of WürzburgWürzburgGermany
- Center for Computational and Theoretical BiologyCampus NordUniversity of WürzburgWürzburgGermany
- Department of BioinformaticsBiocenterUniversity of WürzburgWürzburgGermany
| | - Marcell K. Peters
- Department of Animal Ecology and Tropical BiologyBiocenterUniversity of WürzburgWürzburgGermany
| | - Gudrun Grimmer
- Department of Animal Ecology and Tropical BiologyBiocenterUniversity of WürzburgWürzburgGermany
| | - Beate Krischke
- Department of Animal Ecology and Tropical BiologyBiocenterUniversity of WürzburgWürzburgGermany
| | - Mareen Geyer
- Department of Animal Ecology and Tropical BiologyBiocenterUniversity of WürzburgWürzburgGermany
| | - Thomas Schmitt
- Department of Animal Ecology and Tropical BiologyBiocenterUniversity of WürzburgWürzburgGermany
| | - Ingolf Steffan‐Dewenter
- Department of Animal Ecology and Tropical BiologyBiocenterUniversity of WürzburgWürzburgGermany
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41
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Piko J, Keller A, Geppert C, Batáry P, Tscharntke T, Westphal C, Hass AL. Effects of three flower field types on bumblebees and their pollen diets. Basic Appl Ecol 2021. [DOI: 10.1016/j.baae.2021.02.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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42
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Piot N, Eeraerts M, Pisman M, Claus G, Meeus I, Smagghe G. More is less: mass-flowering fruit tree crops dilute parasite transmission between bees. Int J Parasitol 2021; 51:777-785. [PMID: 33811913 DOI: 10.1016/j.ijpara.2021.02.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 01/28/2021] [Accepted: 02/01/2021] [Indexed: 11/16/2022]
Abstract
Parasites influence wild bee population dynamics and are regarded as one of the main drivers of wild bee decline. Most of these parasites are mainly transmitted between bee species via the use of shared floral resources. Disturbance of the plant-pollinator network at a location can hence disturb the transmission of these parasites. Expansion and intensification of agriculture, another major driver of wild bee decline, often disturbs local plant-pollinator networks by altering the availability and diversity of floral resources. Mass-flowering crops are an extreme example as they provide an abundance of floral resources for a short period of time, substantially altering the present plant-pollinator network. This likely has repercussions on parasite transmission in the pollinator community. Using the bloom of mass-flowering crops we tested the hypothesis that an increase in floral resources can dilute parasite transmission in the pollinator community. To test this, we analysed the presence of parasites in the pollen of the brood cell provisions of Osmia spp., collected from trap nests placed in apple and sweet cherry orchards. We collected pollen at several time intervals during and after mass bloom, and found that pollen collected during mass bloom had significantly lower parasite prevalence compared with pollen collected after mass bloom. Furthermore, using pollen barcoding data we found that the presence of MFCs in pollen was a good predictor for lower parasite prevalence. Taken together, our results indicate that an increase in flower availability can reduce parasite transmission between bees.
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Affiliation(s)
- Niels Piot
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Coupure links 653, Ghent University, Ghent, Belgium.
| | - Maxime Eeraerts
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Coupure links 653, Ghent University, Ghent, Belgium
| | - Matti Pisman
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Coupure links 653, Ghent University, Ghent, Belgium
| | - Gregor Claus
- Laboratory of Crop Protection Chemistry, Department of Plants and Crops, Faculty of Bioscience Engineering, Coupure links 653, Ghent University, Ghent, Belgium
| | - Ivan Meeus
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Coupure links 653, Ghent University, Ghent, Belgium
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Coupure links 653, Ghent University, Ghent, Belgium
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43
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Lobaton J, Andrew R, Duitama J, Kirkland L, Macfadyen S, Rader R. Using RNA-seq to characterize pollen-stigma interactions for pollination studies. Sci Rep 2021; 11:6635. [PMID: 33758263 PMCID: PMC7988043 DOI: 10.1038/s41598-021-85887-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 03/08/2021] [Indexed: 11/18/2022] Open
Abstract
Insects are essential for the reproduction of pollinator-dependent crops and contribute to the pollination of 87% of wild plants and 75% of the world’s food crops. Understanding pollen flow dynamics between plants and pollinators is thus essential to manage and conserve wild plants and ensure yields are maximized in food crops. However, the determination of pollen transfer in the field is complex and laborious. We developed a field experiment in a pollinator-dependent crop and used high throughput RNA sequencing (RNA-seq) to quantify pollen flow by measuring changes in gene expression between pollination treatments across different apple (Malus domestica Borkh.) cultivars. We tested three potential molecular indicators of successful pollination and validated these results with field data by observing single and multiple visits by honey bees (Apis mellifera) to apple flowers and measured fruit set in a commercial apple orchard. The first indicator of successful outcrossing was revealed via differential gene expression in the cross-pollination treatments after 6 h. The second indicator of successful outcrossing was revealed by the expression of specific genes related to pollen tube formation and defense response at three different time intervals in the stigma and the style following cross-pollination (i.e. after 6, 24, and 48 h). Finally, genotyping variants specific to donor pollen could be detected in cross-pollination treatments, providing a third indicator of successful outcrossing. Field data indicated that one or five flower visits by honey bees were insufficient and at least 10 honey bee flower visits were required to achieve a 25% probability of fruit set under orchard conditions. By combining the genotyping data, the differential expression analysis, and the traditional fruit set field experiments, it was possible to evaluate the pollination effectiveness of honey bee visits under orchards conditions. This is the first time that pollen-stigma-style mRNA expression analysis has been conducted after a pollinator visit (honey bee) to a plant (in vivo apple flowers). This study provides evidence that mRNA sequencing can be used to address complex questions related to stigma–pollen interactions over time in pollination ecology.
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Affiliation(s)
- Juan Lobaton
- School of Environmental and Rural Science, University of New England, Armidale, Australia. .,CSIRO, Clunies Ross St., Acton, ACT, Australia.
| | - Rose Andrew
- School of Environmental and Rural Science, University of New England, Armidale, Australia
| | - Jorge Duitama
- Systems and Computing, Engineering Department, Universidad de Los Andes, Bogota, Colombia
| | - Lindsey Kirkland
- School of Environmental and Rural Science, University of New England, Armidale, Australia
| | | | - Romina Rader
- School of Environmental and Rural Science, University of New England, Armidale, Australia
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Mousavi-Derazmahalleh M, Stott A, Lines R, Peverley G, Nester G, Simpson T, Zawierta M, De La Pierre M, Bunce M, Christophersen CT. eDNAFlow, an automated, reproducible and scalable workflow for analysis of environmental DNA sequences exploiting Nextflow and Singularity. Mol Ecol Resour 2021; 21:1697-1704. [PMID: 33580619 DOI: 10.1111/1755-0998.13356] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 01/29/2021] [Accepted: 02/08/2021] [Indexed: 12/18/2022]
Abstract
Metabarcoding of environmental DNA (eDNA) when coupled with high throughput sequencing is revolutionising the way biodiversity can be monitored across a wide range of applications. However, the large number of tools deployed in downstream bioinformatic analyses often places a challenge in configuration and maintenance of a workflow, and consequently limits the research reproducibility. Furthermore, scalability needs to be considered to handle the growing amount of data due to increase in sequence output and the scale of project. Here, we describe eDNAFlow, a fully automated workflow that employs a number of state-of-the-art applications to process eDNA data from raw sequences (single-end or paired-end) to generation of curated and noncurated zero-radius operational taxonomic units (ZOTUs) and their abundance tables. This pipeline is based on Nextflow and Singularity which enable a scalable, portable and reproducible workflow using software containers on a local computer, clouds and high-performance computing (HPC) clusters. Finally, we present an in-house Python script to assign taxonomy to ZOTUs based on user specified thresholds for assigning lowest common ancestor (LCA). We demonstrate the utility and efficiency of the pipeline using an example of a published coral diversity biomonitoring study. Our results were congruent with the aforementioned study. The scalability of the pipeline is also demonstrated through analysis of a large data set containing 154 samples. To our knowledge, this is the first automated bioinformatic pipeline for eDNA analysis using two powerful tools: Nextflow and Singularity. This pipeline addresses two major challenges in the analysis of eDNA data; scalability and reproducibility.
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Affiliation(s)
- Mahsa Mousavi-Derazmahalleh
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia.,WA Human Microbiome Collaboration Centre (WAHMCC), School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia.,eDNA Frontiers, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Audrey Stott
- Pawsey Supercomputing Centre, Kensington, WA, Australia
| | - Rose Lines
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia.,WA Human Microbiome Collaboration Centre (WAHMCC), School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia.,eDNA Frontiers, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Georgia Peverley
- eDNA Frontiers, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Georgia Nester
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Tiffany Simpson
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia.,eDNA Frontiers, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Michal Zawierta
- Department of Electrical, Electronic and Computer Engineering, The University of Western Australia, Nedlands, WA, Australia
| | | | - Michael Bunce
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia.,Environmental Protection Authority, Wellington, New Zealand
| | - Claus T Christophersen
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia.,WA Human Microbiome Collaboration Centre (WAHMCC), School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia.,School of Medical & Health Sciences, Edith Cowan University, Joondalup, WA, Australia
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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: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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Swenson SJ, Gemeinholzer B. Testing the effect of pollen exine rupture on metabarcoding with Illumina sequencing. PLoS One 2021; 16:e0245611. [PMID: 33529182 PMCID: PMC7853484 DOI: 10.1371/journal.pone.0245611] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 01/04/2021] [Indexed: 12/21/2022] Open
Abstract
Pollen metabarcoding has received much attention recently for its potential to increase taxonomic resolution of the identifications of pollen grains necessary for various public health, ecological and environmental inquiry. However, methodologies implemented are widely varied across studies confounding comparisons and casting uncertainty on the reliability of results. In this study, we investigated part of the methodology, the effects of level of exine rupture and lysis incubation time, on the performance of DNA extraction and Illumina sequencing. We examined 15 species of plants from 12 families with pollen that varies in size, shape, and aperture number to evaluate effort necessary for exine rupture. Then created mock communities of 14 of the species from DNA extractions at 4 levels of exine rupture (0, 33, 67, and 100%) and two levels of increased lysis incubation time without exine rupture (2 or 24 hours). Quantities of these DNA extractions displayed a positive correlation between increased rupture and DNA yield, however increasing time of lysis incubation was associated with decreased DNA yield. Illumina sequencing was performed with these artificial community treatments with three common plant DNA barcode regions (rbcL, ITS1, ITS2) with two different primer pairings for ITS2 and rbcL. We found decreased performance in treatments with 0% or 100% exine rupture compared to 33% and 67% rupture, based on deviation from expected proportions and species retrieval, and increased lysis incubation was found to be detrimental to results.
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47
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Elliott B, Wilson R, Shapcott A, Keller A, Newis R, Cannizzaro C, Burwell C, Smith T, Leonhardt SD, Kämper W, Wallace HM. Pollen diets and niche overlap of honey bees and native bees in protected areas. Basic Appl Ecol 2021. [DOI: 10.1016/j.baae.2020.12.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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48
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Gous A, Eardley CD, Johnson SD, Swanevelder DZH, Willows-Munro S. Floral hosts of leaf-cutter bees (Megachilidae) in a biodiversity hotspot revealed by pollen DNA metabarcoding of historic specimens. PLoS One 2021; 16:e0244973. [PMID: 33476342 PMCID: PMC7819603 DOI: 10.1371/journal.pone.0244973] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 12/21/2020] [Indexed: 11/18/2022] Open
Abstract
South Africa is a megadiverse country with three globally recognised biodiversity hotspots within its borders. Bees in particular show high diversity and endemism in the western part of the country. Not much is currently known about the floral host preferences of indigenous bees in South Africa, with data only available from observational studies. Pollen metabarcoding provides provenance information by utilising DNA analyses instead of floral visitation and traditional microscopic identification to identify pollinator food plants, which can be time consuming and imprecise. In this study, we sampled pollen from leaf-cutter bees (Megachilidae) specimens maintained in a historic insect collection (National Collection of Insects, South Africa) that were originally collected from two florally important areas in South Africa (Succulent Karoo and Savanna) and used metabarcoding to determine pollen provenance. We also sampled pollen from leafcutter bee species with wider distributions, that extend across many different biomes, to determine if these 'generalist' species show relaxed floral host specificity in some biomes. Metabarcoding involved sequencing of the nuclear internal transcribed spacer 2 (ITS2) region. Amplicons were compared to a sequence reference database to assign taxonomic classifications to family level. Sequence reads were also clustered to OTUs based on 97% sequence similarity to estimate numbers of plant species visited. We found no significant difference in the mean number of plant taxa visited in the Succulent Karoo and Savanna regions, but the widespread group visited significantly more floral hosts. Bees from the widespread group were also characterised by a significantly different composition in pollen assemblage. The time since specimens were collected did not have an effect on the mean number of taxa visited by any of the bee species studied. This study highlights national history collections as valuable sources of temporal and spatial biodiversity data.
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Affiliation(s)
- Annemarie Gous
- Biotechnology Platform, Agricultural Research Council, Pretoria, South Africa
- School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Connal D. Eardley
- School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Steven D. Johnson
- School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | | | - Sandi Willows-Munro
- School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
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Sobek CJ, Walker FM. Square salads: exploring the diet of the southern hairy-nosed wombat (Lasiorhinus latifrons) via DNA metabarcoding. AUSTRALIAN MAMMALOGY 2021. [DOI: 10.1071/am20021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Southern hairy-nosed wombats (Lasiorhinus latifrons) are large semi-fossorial marsupials that inhabit semiarid areas of southern South Australia and southeast Western Australia. Despite their size and prominence on the landscape, little is published about diet and foraging preferences. Further, it is unclear whether this wombat species’ diet overlaps with sympatric western grey kangaroos (Macropus fuliginosus), which are locally abundant across the southern hairy-nosed wombat’s distribution. Competition for food resources may be an added stressor in Murraylands populations where kangaroos are plentiful. Here, we identified diet items and dietary overlap of southern hairy-nosed wombats and western grey kangaroos. We accomplished this by opportunistically sampling fresh faecal pellets from both species at Brookfield Conservation Park in April 2017. We performed DNA metabarcoding via Illumina next generation sequencing of the faecal DNA using the plant ITS2 gene. We identified 10 genera in the wombat diet and 20 in the diet of kangaroos; diets of both species included native and introduced genera. Eight genera were shared between both marsupials. This work highlights the capabilities of non-invasive genetic sampling in concert with DNA metabarcoding to elucidate diet and dietary overlap between species.
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Adamchuk LO. IMPROVEMENT OF THE METHOD OF BOTANICAL IDENTIFICATION OF HONEY. FOOD SCIENCE AND TECHNOLOGY 2020. [DOI: 10.15673/fst.v14i4.1895] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The pollen spectrum of honey reflects the regional crops, forest plantations, all the diversity of the plant species near the apiary. That is why the use, adaptation, and improvement of various methods of pollen analysis and interpretation of its results are topical questions in the countries which produce original varieties of honey on the international market. Ukraine is a leader in manufacturing and exporting honey in Europe and worldwide. Usually, Ukrainian honey is exported not as a finished food product, but as a raw material. This is because the pollen spectrum of Ukrainian honeys is provided with no description characterising their botanical and geographical origin, which, in turn, is because there are no pollen analysis methods implemented in production laboratories. The purpose of this study was improving the pollen analysis method to identify the botanical origin of Ukrainian honeys. The research was conducted in the laboratory of the Department of Standardisation and Certification of Agricultural Products in the National University of Life and Environmental Science of Ukraine, and in the production laboratory of Ascania-Pack Company. The analysis of harmonised methods of melissopalynology and standardised pollen detection methods has allowed developing a botanical method of honey identification adapted to be introduced in Ukrainian laboratories. The method suggested is a complex of individual procedures, operations, and techniques. It has been detailed how to prepare solution to fix and stain pollen preparations obtained from honey. The method of preparing a suspension of pollen grains from honey has been improved: extra dissolution of crystals and a lower speed of the centrifuge reduce the time of making the preparation and improve its quality. The method of obtaining preparations of pollen grains from honey has been adapted to harmonised international melissopalynological methods. New methods have been developed to count pollen grains in prepared monofloral and polyfloral honey samples. It has been detailed how to identify step-by- step the botanical origin of honey by pollen grains using international databases. The method has been implemented in the production laboratories of leading enterprises in Ukraine and Belarus.
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