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Librán-Embid F, Grass I, Emer C, Alarcón-Segura V, Behling H, Biagioni S, Ganuza C, Herrera-Krings C, Setyaningsih CA, Tscharntke T. Flower-bee versus pollen-bee metanetworks in fragmented landscapes. Proc Biol Sci 2024; 291:20232604. [PMID: 38807521 DOI: 10.1098/rspb.2023.2604] [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: 05/04/2023] [Accepted: 04/15/2024] [Indexed: 05/30/2024] Open
Abstract
Understanding the organization of mutualistic networks at multiple spatial scales is key to ensure biological conservation and functionality in human-modified ecosystems. Yet, how changing habitat and landscape features affect pollen-bee interaction networks is still poorly understood. Here, we analysed how bee-flower visitation and bee-pollen-transport interactions respond to habitat fragmentation at the local network and regional metanetwork scales, combining data from 29 fragments of calcareous grasslands, an endangered biodiversity hotspot in central Europe. We found that only 37% of the total unique pairwise species interactions occurred in both pollen-transport and flower visitation networks, whereas 28% and 35% were exclusive to pollen-transport and flower visitation networks, respectively. At local level, network specialization was higher in pollen-transport networks, and was negatively related to the diversity of land cover types in both network types. At metanetwork level, pollen transport data revealed that the proportion of single-fragment interactions increased with landscape diversity. Our results show that the specialization of calcareous grasslands' plant-pollinator networks decreases with landscape diversity, but network specialization is underestimated when only based on flower visitation information. Pollen transport data, more than flower visitation, and multi-scale analyses of metanetworks are fundamental for understanding plant-pollinator interactions in human-dominated landscapes.
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Affiliation(s)
- Felipe Librán-Embid
- Agroecology, University of Göttingen , Göttingen 37077, Germany
- Justus Liebig University of Gießen, Institute of Animal Ecology and Systematics, Heinrich-Buff-Ring 26 , Gießen 35390, Germany
| | - Ingo Grass
- Department of Ecology of Tropical Agricultural Systems, University of Hohenheim , Stuttgart 70599, Germany
- Center for Biodiversity and Integrative Taxonomy (KomBioTa), University of Hohenheim , Stuttgart 70599, Germany
| | - Carine Emer
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rua Pacheco Leão, 915, Jardim Botânico , Rio de Janeiro CEP22460-030, Brazil
| | - Viviana Alarcón-Segura
- Agroecology, University of Göttingen , Göttingen 37077, Germany
- Animal Ecology, Department of Biology, University of Marburg , Marburg 35037, Germany
| | - Hermann Behling
- Department of Palynology and Climate Dynamics, Albrecht-von-Haller-Institute for Plant Sciences, University of Göttingen , Göttingen 37077, Germany
| | - Siria Biagioni
- Department of Palynology and Climate Dynamics, Albrecht-von-Haller-Institute for Plant Sciences, University of Göttingen , Göttingen 37077, Germany
| | - Cristina Ganuza
- Department of Animal Ecology and Tropical Biology, University of Würzburg , Würzburg 97074, Germany
| | | | - Christina Ani Setyaningsih
- Department of Palynology and Climate Dynamics, Albrecht-von-Haller-Institute for Plant Sciences, University of Göttingen , Göttingen 37077, Germany
| | - Teja Tscharntke
- Agroecology, University of Göttingen , Göttingen 37077, Germany
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2
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San Martin G, Hautier L, Mingeot D, Dubois B. How reliable is metabarcoding for pollen identification? An evaluation of different taxonomic assignment strategies by cross-validation. PeerJ 2024; 12:e16567. [PMID: 38313030 PMCID: PMC10838070 DOI: 10.7717/peerj.16567] [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: 07/24/2023] [Accepted: 11/12/2023] [Indexed: 02/06/2024] Open
Abstract
Metabarcoding is a powerful tool, increasingly used in many disciplines of environmental sciences. However, to assign a taxon to a DNA sequence, bioinformaticians need to choose between different strategies or parameter values and these choices sometimes seem rather arbitrary. In this work, we present a case study on ITS2 and rbcL databases used to identify pollen collected by bees in Belgium. We blasted a random sample of sequences from the reference database against the remainder of the database using different strategies and compared the known taxonomy with the predicted one. This in silico cross-validation (CV) approach proved to be an easy yet powerful way to (1) assess the relative accuracy of taxonomic predictions, (2) define rules to discard dubious taxonomic assignments and (3) provide a more objective basis to choose the best strategy. We obtained the best results with the best blast hit (best bit score) rather than by selecting the majority taxon from the top 10 hits. The predictions were further improved by favouring the most frequent taxon among those with tied best bit scores. We obtained better results with databases containing the full sequences available on NCBI rather than restricting the sequences to the region amplified by the primers chosen in our study. Leaked CV showed that when the true sequence is present in the database, blast might still struggle to match the right taxon at the species level, particularly with rbcL. Classical 10-fold CV-where the true sequence is removed from the database-offers a different yet more realistic view of the true error rates. Taxonomic predictions with this approach worked well up to the genus level, particularly for ITS2 (5-7% of errors). Using a database containing only the local flora of Belgium did not improve the predictions up to the genus level for local species and made them worse for foreign species. At the species level, using a database containing exclusively local species improved the predictions for local species by ∼12% but the error rate remained rather high: 25% for ITS2 and 42% for rbcL. Foreign species performed worse even when using a world database (59-79% of errors). We used classification trees and GLMs to model the % of errors vs. identity and consensus scores and determine appropriate thresholds below which the taxonomic assignment should be discarded. This resulted in a significant reduction in prediction errors, but at the cost of a much higher proportion of unassigned sequences. Despite this stringent filtering, at least 1/5 sequences deemed suitable for species-level identification ultimately proved to be misidentified. An examination of the variability in prediction accuracy between plant families showed that rbcL outperformed ITS2 for only two of the 27 families examined, and that the % correct species-level assignments were much better for some families (e.g. 95% for Sapindaceae) than for others (e.g. 35% for Salicaceae).
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Affiliation(s)
- Gilles San Martin
- Life Sciences Department, Plant and Forest Health Unit, Walloon Agricultural Research Centre, Gembloux, Belgium
| | - Louis Hautier
- Life Sciences Department, Plant and Forest Health Unit, Walloon Agricultural Research Centre, Gembloux, Belgium
| | - Dominique Mingeot
- Life Sciences Department, Bioengineering Unit, Walloon Agricultural Research Centre, Gembloux, Belgium
| | - Benjamin Dubois
- Life Sciences Department, Bioengineering Unit, Walloon Agricultural Research Centre, Gembloux, Belgium
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3
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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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Pitteloud C, Defossez E, Albouy C, Descombes P, Rasmann S, Pellissier L. DNA-based networks reveal the ecological determinants of plant-herbivore interactions along environmental gradients. Mol Ecol 2023; 32:6436-6448. [PMID: 35620937 DOI: 10.1111/mec.16545] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 05/05/2022] [Accepted: 05/20/2022] [Indexed: 11/29/2022]
Abstract
Understanding the ecological rules structuring the organization of species interactions is a prerequisite to predicting how ecosystems respond to environmental changes. While the ecological determinants of single networks have been documented, it remains unclear whether network ecological rules are conserved along spatial and environmental gradients. To address this gap, we reconstructed 48 plant-herbivore interaction networks along six elevation gradients in the Central European Alps in Switzerland, using DNA metabarcoding on orthoptera faeces. We developed hypotheses on the ecological mechanisms expected to structure interaction networks, based on plant phylogeny, plant abundance, leaf toughness, leaf nitrogen content and plant metabolomics. We show that plant phylogenetic relationships and species abundance have the greatest explanatory power regarding the structure of the ecological networks. Moreover, we found that leaf nitrogen content is a key determinant of interactions in warmer environments, while phenolic compounds and tannins are more important in colder environments, suggesting that determinants of species interactions can shift along environmental gradients. With this work, we propose an approach to study the mechanisms that structure the way species interact with each other between bioregions and ecosystems.
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Affiliation(s)
- Camille Pitteloud
- Department of Environmental Systems Science, Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, ETH Zürich, Zürich, Switzerland
- Unit of Land Change Science, Swiss Federal Research Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Emmanuel Defossez
- Functional Ecology Laboratory, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Camille Albouy
- Department of Environmental Systems Science, Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, ETH Zürich, Zürich, Switzerland
- Unit of Land Change Science, Swiss Federal Research Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
- DECOD (Ecosystem Dynamics and Sustainability), IFREMER, INRAE, Institut Agro - Agrocampus Ouest, Nantes cedex 3, France
| | - Patrice Descombes
- Unit of Land Change Science, Swiss Federal Research Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Sergio Rasmann
- Functional Ecology Laboratory, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Loïc Pellissier
- Department of Environmental Systems Science, Ecosystems and Landscape Evolution, Institute of Terrestrial Ecosystems, ETH Zürich, Zürich, Switzerland
- Unit of Land Change Science, Swiss Federal Research Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
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5
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Bell KL, Turo KJ, Lowe A, Nota K, Keller A, Encinas‐Viso F, Parducci L, Richardson RT, Leggett RM, Brosi BJ, Burgess KS, Suyama Y, de Vere N. Plants, pollinators and their interactions under global ecological change: The role of pollen DNA metabarcoding. Mol Ecol 2023; 32:6345-6362. [PMID: 36086900 PMCID: PMC10947134 DOI: 10.1111/mec.16689] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 08/18/2022] [Accepted: 08/30/2022] [Indexed: 11/28/2022]
Abstract
Anthropogenic activities are triggering global changes in the environment, causing entire communities of plants, pollinators and their interactions to restructure, and ultimately leading to species declines. To understand the mechanisms behind community shifts and declines, as well as monitoring and managing impacts, a global effort must be made to characterize plant-pollinator communities in detail, across different habitat types, latitudes, elevations, and levels and types of disturbances. Generating data of this scale will only be feasible with rapid, high-throughput methods. Pollen DNA metabarcoding provides advantages in throughput, efficiency and taxonomic resolution over traditional methods, such as microscopic pollen identification and visual observation of plant-pollinator interactions. This makes it ideal for understanding complex ecological networks and their responses to change. Pollen DNA metabarcoding is currently being applied to assess plant-pollinator interactions, survey ecosystem change and model the spatiotemporal distribution of allergenic pollen. Where samples are available from past collections, pollen DNA metabarcoding has been used to compare contemporary and past ecosystems. New avenues of research are possible with the expansion of pollen DNA metabarcoding to intraspecific identification, analysis of DNA in ancient pollen samples, and increased use of museum and herbarium specimens. Ongoing developments in sequencing technologies can accelerate progress towards these goals. Global ecological change is happening rapidly, and we anticipate that high-throughput methods such as pollen DNA metabarcoding are critical for understanding the evolutionary and ecological processes that support biodiversity, and predicting and responding to the impacts of change.
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Affiliation(s)
- Karen L. Bell
- CSIRO Health & Biosecurity and CSIRO Land & WaterFloreatWAAustralia
- School of Biological SciencesUniversity of Western AustraliaCrawleyWAAustralia
| | - Katherine J. Turo
- Department of Ecology, Evolution, and Natural ResourcesRutgers UniversityNew BrunswickNew JerseyUSA
| | | | - Kevin Nota
- Department of Ecology and GeneticsEvolutionary Biology Centre, Uppsala UniversityUppsalaSweden
| | - Alexander Keller
- Organismic and Cellular Networks, Faculty of BiologyBiocenter, Ludwig‐Maximilians‐Universität MünchenPlaneggGermany
| | - Francisco Encinas‐Viso
- Centre for Australian National Biodiversity ResearchCSIROBlack MountainAustralian Capital TerritoryAustralia
| | - Laura Parducci
- Department of Ecology and GeneticsEvolutionary Biology Centre, Uppsala UniversityUppsalaSweden
- Department of Environmental BiologySapienza University of RomeRomeItaly
| | - Rodney T. Richardson
- Appalachian LaboratoryUniversity of Maryland Center for Environmental ScienceFrostburgMarylandUSA
| | | | - Berry J. Brosi
- Department of BiologyUniversity of WashingtonSeattleWashingtonUSA
| | - Kevin S. Burgess
- Department of BiologyCollege of Letters and Sciences, Columbus State University, University System of GeorgiaAtlantaGeorgiaUSA
| | - Yoshihisa Suyama
- Field Science CenterGraduate School of Agricultural Science, Tohoku UniversityOsakiMiyagiJapan
| | - Natasha de Vere
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
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6
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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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7
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Hassan S, Sabreena, Ganiee SA, Yaseen A, Zaman M, Shah AJ, Ganai BA. Unraveling the potential of environmental DNA for deciphering recent advances in plant-animal interactions: a systematic review. PLANTA 2023; 258:117. [PMID: 37957258 DOI: 10.1007/s00425-023-04267-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 10/18/2023] [Indexed: 11/15/2023]
Abstract
MAIN CONCLUSION Environmental DNA-based monitoring provides critical insights for enhancing our understanding of plant-animal interactions in the context of worldwide biodiversity decrease for developing a global framework for effective plant biodiversity conservation. To understand the ecology and evolutionary patterns of plant-animal interactions (PAI) and their pivotal roles in ecosystem functioning advances in molecular ecology tools such as Environmental DNA (eDNA) provide unprecedented research avenues. These methods being non-destructive in comparison to traditional biodiversity monitoring methods, enhance the discernment of ecosystem health, integrity, and complex interactions. This review intends to offer a systematic and critical appraisal of the prospective of eDNA for investigating PAI. The review thoroughly discusses and analyzes the recent reports (2015-2022) employing preferred reporting items for systematic reviews and meta-analyses (PRISMA) to outline the recent progression in eDNA approaches for elucidating PAI. The current review envisages that eDNA has a significant potential to monitor both plants and associated cohort of prospective pollinators (avian species and flowering plants, bees and plants, arthropods and plants, bats and plants, etc.). Furthermore, a brief description of the factors that influence the utility and interpretation of PAI eDNA is also presented. The review establishes that factors such as biotic and abiotic, primer selection and taxonomic resolution, and indeterminate spatio-temporal scales impact the availability and longevity of eDNA. The study also identified the limitations that influence PAI detection and suggested possible solutions for better execution of these molecular approaches. Overcoming these research caveats will augment the assortment of PAI analysis through eDNA that could be vital for ecosystem health and integrity. This review forms a critical guide and offers prominent insights for ecologists, environmental managers and researchers to assess and evaluate plant-animal interaction through environmental DNA.
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Affiliation(s)
- Shahnawaz Hassan
- Department of Environmental Science, University of Kashmir, Srinagar, 190006, India.
| | - Sabreena
- Department of Environmental Science, University of Kashmir, Srinagar, 190006, India
| | - Shahid Ahmad Ganiee
- Department of Environmental Science, University of Kashmir, Srinagar, 190006, India
| | - Aarif Yaseen
- Department of Environmental Science, University of Kashmir, Srinagar, 190006, India
| | - Muzafar Zaman
- Department of Environmental Science, University of Kashmir, Srinagar, 190006, India
| | - Abdul Jalil Shah
- Department of Pharmaceutical Sciences, University of Kashmir, Srinagar, 190006, India
| | - Bashir Ahmad Ganai
- Centre of Research for Development, University of Kashmir, Srinagar, 190006, India.
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8
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Wizenberg SB, Newburn LR, Pepinelli M, Conflitti IM, Richardson RT, Hoover SER, Currie RW, Giovenazzo P, Zayed A. Validating a multi-locus metabarcoding approach for characterizing mixed-pollen samples. PLANT METHODS 2023; 19:120. [PMID: 37925401 PMCID: PMC10625703 DOI: 10.1186/s13007-023-01097-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 10/21/2023] [Indexed: 11/06/2023]
Abstract
BACKGROUND The mutualistic interaction between entomophilous plants and pollinators is fundamental to the structure of most terrestrial ecosystems. The sensitive nature of this relationship has been disrupted by anthropogenic modifications to natural landscapes, warranting development of new methods for exploring this trophic interaction. Characterizing the composition of pollen collected by pollinators, e.g. Apis mellifera, is a common means of exploring this relationship, but traditional methods of microscopic pollen assessment are laborious and limited in their scope. The development of pollen metabarcoding as a method of rapidly characterizing the abundance and diversity of pollen within mixed samples presents a new frontier for this type of work, but metabarcoding may have limitations, and validation is warranted before any suite of primers can be confidently used in a research program. We set out to evaluate the utility of an integrative approach, using a set of established primers (ITS2 and rbcL) versus melissopalynological analysis for characterizing 27 mixed-pollen samples from agricultural sites across Canada. RESULTS Both individual markers performed well relative to melissopalynology at the family level with decreases in the strength of correlation and linear model fits at the genus level. Integrating data from both markers together via a multi-locus approach provided the best rank-based correlation between metagenetic and melissopalynological data at both the genus (ρ = 0.659; p < 0.001) and family level (ρ = 0.830; p < 0.001). Species accumulation curves indicated that, after controlling for sampling effort, melissopalynological characterization provides similar or higher species richness estimates than either marker. The higher number of plant species discovered via the metabarcoding approach simply reflects the vastly greater sampling effort in comparison to melissopalynology. CONCLUSIONS Pollen metabarcoding performed well at characterizing the composition of mixed pollen samples relative to a traditional melissopalynological approach. Limitations to the quantitative application of this method can be addressed by adopting a multi-locus approach that integrates information from multiple markers.
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Affiliation(s)
- Sydney B Wizenberg
- Department of Biology, York University, 4700 Keele St., Toronto, ON, M3J 1P3, Canada
| | - Laura R Newburn
- Department of Biology, York University, 4700 Keele St., Toronto, ON, M3J 1P3, Canada
| | - Mateus Pepinelli
- Department of Biology, York University, 4700 Keele St., Toronto, ON, M3J 1P3, Canada
| | - Ida M Conflitti
- Department of Biology, York University, 4700 Keele St., Toronto, ON, M3J 1P3, Canada
| | - Rodney T Richardson
- Appalachian Laboratory, University of Maryland Center for Environmental Science, Frostburg, MD, 21613, USA
| | - Shelley E R Hoover
- Department of Biological Sciences, University of Lethbridge, 4401 University Drive W, Lethbridge, AB, T1K3M4, Canada
| | - Robert W Currie
- Department of Entomology, University of Manitoba, 12 Dafoe Road, Winnipeg, MB, R3T2N2, Canada
| | - Pierre Giovenazzo
- Département de Biologie, Université Laval, 2325 Rue de l'Université, Québec City, Québec, G1V0A6, Canada
| | - Amro Zayed
- Department of Biology, York University, 4700 Keele St., Toronto, ON, M3J 1P3, Canada.
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9
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Streicher MB, Johnson SD, Willows‐Munro S. Effect of fuchsin fixation of pollen on DNA barcode recovery. Ecol Evol 2023; 13:e10475. [PMID: 37664513 PMCID: PMC10468989 DOI: 10.1002/ece3.10475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 07/12/2023] [Accepted: 07/21/2023] [Indexed: 09/05/2023] Open
Abstract
Pollen grains attached to insects are a valuable source of ecological information which can be used to reconstruct visitation networks. Morphological pollen identification relies on light microscopy with pollen usually stained and mounted in fuchsin jelly, which is also used to remove pollen from the bodies of insects. Pollen embedded in fuchsin jelly could potentially be used for DNA barcoding and metabarcoding (large-scale taxonomic identification of complex mixed samples) and thus provide additional information for pollination networks. In this study, we determine whether fuchsin-embedded pollen can be used for downstream molecular applications. We evaluate the quality of plant barcode (ITS) sequences amplified from DNA extracted from both fresh (untreated) pollen, and pollen which had been embedded in fuchsin jelly. We show that the addition of fuchsin to DNA extraction does not impact DNA barcode sequence quality during short-term storage. DNA extractions from both untreated and fuchsin-treated pollen produced reliable barcode sequences of high quality. Our findings suggest that pollen which has been collected, stained, and embedded in fuchsin jelly for preliminary microscopy work can be used within several days for downstream genetic analysis, though the quality of DNA from pollen stored in fuchsin jelly for extended periods is yet to be established.
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Affiliation(s)
- Melanie B. Streicher
- Centre for Functional Biodiversity, School of Life SciencesUniversity of KwaZulu‐NatalScottsvilleSouth Africa
| | - Steven D. Johnson
- Centre for Functional Biodiversity, School of Life SciencesUniversity of KwaZulu‐NatalScottsvilleSouth Africa
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10
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Westreich LR, Westreich ST, Tobin PC. Native solitary bee reproductive success depends on early season precipitation and host plant richness. Oecologia 2023; 201:965-978. [PMID: 36947272 DOI: 10.1007/s00442-023-05354-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/02/2023] [Indexed: 03/23/2023]
Abstract
Spring-emerging bees depend upon the synchronized bloom times of angiosperms that provide pollen and nectar for offspring. The emergence of such bees and bloom times are linked to weather but can be phenologically mismatched, which could limit bee developmental success. However, it remains unclear how such phenologically asynchrony could affect spring-emerging pollinators, and especially for those that forage over a relatively short time period. We examined the relationship between weather and host plant selection on the native spring-foraging solitary bee, Osmia lignaria, across 3 years at urban and rural sites in and around Seattle, Washington, USA. We used community science weather data to test the effects of precipitation, wind, and temperature on O. lignaria oviposition and developmental success. We also collected pollen data over two distinct foraging periods, early and late spring, and used Next-Generation Sequencing to identify plant genera from pollen. Among the weather variables, precipitation during the early foraging period adversely affected larval developmental success and adult bee emergence success, but not oviposition. Using DNA metabarcoding, we observed that increases in the number of plant genera in pollen increased adult emergence in both foraging periods, but not oviposition or larval development. We also observed that foraging bees consistently visited certain genera during each foraging period, especially Acer, Salix, and Rubus. However, pollen collected by O. lignaria over different years varied in the number of total genera visited, highlighting the importance of multi-year studies to ascertain bee foraging preferences and its link to developmental success.
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Affiliation(s)
- Lila R Westreich
- School of Environmental and Forest Sciences, University of Washington, 3715 W. Stevens Way NE, Seattle, WA, 98195, USA
| | | | - Patrick C Tobin
- School of Environmental and Forest Sciences, University of Washington, 3715 W. Stevens Way NE, Seattle, WA, 98195, USA.
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11
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Prudnikow L, Pannicke B, Wünschiers R. A primer on pollen assignment by nanopore-based DNA sequencing. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1112929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023] Open
Abstract
The possibility to identify plants based on the taxonomic information coming from their pollen grains offers many applications within various biological disciplines. In the past and depending on the application or research in question, pollen origin was analyzed by microscopy, usually preceded by chemical treatment methods. This procedure for identification of pollen grains is both time-consuming and requires expert knowledge of morphological features. Additionally, these microscopically recognizable features usually have a low resolution at species-level. Since a few decades, DNA has been used for the identification of pollen taxa, as sequencing technologies evolved both in their handling and affordability. We discuss advantages and challenges of pollen DNA analyses compared to traditional methods. With readers with little experience in this field in mind, we present a hands-on primer for genetic pollen analysis by nanopore sequencing. As our lab mainly works with pollen collected within agroecological research projects, we focus on pollen collected by pollinating insects. We briefly consider sample collection, storage and processing in the laboratory as well as bioinformatic aspects. Currently, pollen metabarcoding is mostly conducted with next-generation sequencing methods that generate short sequence reads (<1 kb). Increasingly, however, pollen DNA analysis is carried out using the long-read generating (several kb), low-budget and mobile MinION nanopore sequencing platform by Oxford Nanopore Technologies. Therefore, we are focusing on aspects for palynology with the MinION DNA sequencing device.
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12
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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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13
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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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14
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Crone MK, Biddinger DJ, Grozinger CM. Wild Bee Nutritional Ecology: Integrative Strategies to Assess Foraging Preferences and Nutritional Requirements. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.847003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Bees depend on flowering plants for their nutrition, and reduced availability of floral resources is a major driver of declines in both managed and wild bee populations. Understanding the nutritional needs of different bee species, and how these needs are met by the varying nutritional resources provided by different flowering plant taxa, can greatly inform land management recommendations to support bee populations and their associated ecosystem services. However, most bee nutrition research has focused on the three most commonly managed and commercially reared bee taxa—honey bees, bumble bees, and mason bees—with fewer studies focused on wild bees and other managed species, such as leafcutting bees, stingless bees, and alkali bees. Thus, we have limited information about the nutritional requirements and foraging preferences of the vast majority of bee species. Here, we discuss the approaches traditionally used to understand bee nutritional ecology: identification of floral visitors of selected focal plant species, evaluation of the foraging preferences of adults in selected focal bee species, evaluation of the nutritional requirements of focal bee species (larvae or adults) in controlled settings, and examine how these methods may be adapted to study a wider range of bee species. We also highlight emerging technologies that have the potential to greatly facilitate studies of the nutritional ecology of wild bee species, as well as evaluate bee nutritional ecology at significantly larger spatio-temporal scales than were previously feasible. While the focus of this review is on bee species, many of these techniques can be applied to other pollinator taxa as well.
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15
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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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16
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Lowe A, Jones L, Brennan G, Creer S, Vere N. Seasonal progression and differences in major floral resource use by bees and hoverflies in a diverse horticultural and agricultural landscape revealed by
DNA
metabarcoding. J Appl Ecol 2022. [DOI: 10.1111/1365-2664.14144] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Abigail Lowe
- National Botanic Garden of Wales, Llanarthne UK
- Molecular Ecology and Evolution Group, School of Natural Sciences Bangor University Bangor UK
| | - Laura Jones
- National Botanic Garden of Wales, Llanarthne UK
| | | | - Simon Creer
- Molecular Ecology and Evolution Group, School of Natural Sciences Bangor University Bangor UK
| | - Natasha Vere
- Natural History Museum of Denmark University of Copenhagen Denmark
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17
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Mitchell SR, DeBano SJ, Rowland MM, Burrows S. Feed the bees and shade the streams: riparian shrubs planted for restoration provide forage for native bees. Restor Ecol 2021. [DOI: 10.1111/rec.13525] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Scott R. Mitchell
- Department of Fisheries and Wildlife Oregon State University Corvallis OR 97330 U.S.A
- Hermiston Agricultural Research and Extension Center Oregon State University Hermiston OR 97838 U.S.A
| | - Sandra J. DeBano
- Department of Fisheries and Wildlife Oregon State University Corvallis OR 97330 U.S.A
- Hermiston Agricultural Research and Extension Center Oregon State University Hermiston OR 97838 U.S.A
| | - Mary M. Rowland
- United States Forest Service Pacific Northwest Research Station La Grande OR 97850‐3368 U.S.A
| | - Skyler Burrows
- Bee Biology and Systematics Laboratory Utah State University Logan UT 84322 U.S.A
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