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Tommasi N, Biella P, Maggioni D, Fallati L, Agostinetto G, Labra M, Galli P, Galimberti A. DNA metabarcoding unveils the effects of habitat fragmentation on pollinator diversity, plant-pollinator interactions, and pollination efficiency in Maldive islands. Mol Ecol 2023; 32:6394-6404. [PMID: 35651283 DOI: 10.1111/mec.16537] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 04/26/2022] [Accepted: 05/05/2022] [Indexed: 11/30/2022]
Abstract
Habitat fragmentation affects biodiversity, but with unclear effects on pollinators and their interactions with plants in anthropized landscapes. Islands could serve as open air laboratories, suitable to disentangle how land-use alteration impacts pollination ecology. In Maldive islands we investigated how pollinator richness, plant-pollinator interactions and pollination efficiency are influenced by the green area fragmentation (i.e., gardens and semi-natural patches). Moreover, we considered the mediating role of pollinator body size and the plant trait of being invasive in shaping interactions. To do this, we surveyed pollinator insects from 11 islands representing a gradient of green area fragmentation. A DNA metabarcoding approach was adopted to identify the pollen transported by pollinators and characterize the plant-pollinator interactions. We found that intermediate levels of green area fragmentation characterized pollinator communities and increased their species richness, while decreasing interaction network complexity. Invasive plants were more frequently found on pollinator bodies than native or exotic noninvasive ones, indicating a concerningly higher potential for pollen dispersal and reproduction of the former ones. Intriguingly, pollinator body size mediated the effect of landscape alteration on interactions, as only the largest bees expanded the foraging diet in terms of plant richness in the transported pollen at increasing fragmentation. In parallel, the pollination efficiency increased with pollinator species richness in two sentinel plants. This study shows that moderate landscape fragmentation of green areas shapes many aspects of the pollination ecosystem service, where despite interactions being less complex and mediated by pollinator body size, pollinator insect biodiversity and potential plant reproduction are supported.
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Affiliation(s)
- Nicola Tommasi
- ZooplantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
- INFN Sezione Milano Bicocca, Milan, Italy
| | - Paolo Biella
- ZooplantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Davide Maggioni
- Earth and Environmental Science Department, University of Milano Bicocca, Milan, Italy
- MaRHE Center (Marine Research and High Education Center), Magoodhoo, Maldives
| | - Luca Fallati
- Earth and Environmental Science Department, University of Milano Bicocca, Milan, Italy
- MaRHE Center (Marine Research and High Education Center), Magoodhoo, Maldives
| | - Giulia Agostinetto
- ZooplantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Massimo Labra
- ZooplantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
- INFN Sezione Milano Bicocca, Milan, Italy
| | - Paolo Galli
- Earth and Environmental Science Department, University of Milano Bicocca, Milan, Italy
- MaRHE Center (Marine Research and High Education Center), Magoodhoo, Maldives
| | - Andrea Galimberti
- ZooplantLab, Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
- INFN Sezione Milano Bicocca, Milan, Italy
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Marinchel N, Marchesini A, Nardi D, Girardi M, Casabianca S, Vernesi C, Penna A. Mock community experiments can inform on the reliability of eDNA metabarcoding data: a case study on marine phytoplankton. Sci Rep 2023; 13:20164. [PMID: 37978238 PMCID: PMC10656442 DOI: 10.1038/s41598-023-47462-5] [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: 04/29/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023] Open
Abstract
Environmental DNA metabarcoding is increasingly implemented in biodiversity monitoring, including phytoplankton studies. Using 21 mock communities composed of seven unicellular diatom and dinoflagellate algae, assembled with different composition and abundance by controlling the number of cells, we tested the accuracy of an eDNA metabarcoding protocol in reconstructing patterns of alpha and beta diversity. This approach allowed us to directly evaluate both qualitative and quantitative metabarcoding estimates. Our results showed non-negligible rates (17-25%) of false negatives (i.e., failure to detect a taxon in a community where it was included), for three taxa. This led to a statistically significant underestimation of metabarcoding-derived alpha diversity (Wilcoxon p = 0.02), with the detected species richness being lower than expected (based on cell numbers) in 8/21 mock communities. Considering beta diversity, the correlation between metabarcoding-derived and expected community dissimilarities was significant but not strong (R2 = 0.41), indicating suboptimal accuracy of metabarcoding results. Average biovolume and rDNA gene copy number were estimated for the seven taxa, highlighting a potential, though not exhaustive, role of the latter in explaining the recorded biases. Our findings highlight the importance of mock communities for assessing the reliability of phytoplankton eDNA metabarcoding studies and identifying their limitations.
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Affiliation(s)
- Nadia Marinchel
- Department of Pure and Applied Sciences, University of Urbino, Urbino, Italy.
- Department of Biomolecular Sciences, University of Urbino, Urbino, Italy.
| | - Alexis Marchesini
- Research Institute on Terrestrial Ecosystems (IRET), National Research Council (CNR), Porano, Italy
- National Biodiversity Future Center, Palermo, Italy
| | - Davide Nardi
- DAFNAE, University of Padova, Legnaro, PD, Italy
| | - Matteo Girardi
- Conservation Genomics Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige, Italy
| | - Silvia Casabianca
- Department of Biomolecular Sciences, University of Urbino, Urbino, Italy
- Fano Marine Center, Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, Fano, Italy
- CoNISMa, National Inter-University Consortium for Marine Sciences, Rome, Italy
| | - Cristiano Vernesi
- National Biodiversity Future Center, Palermo, Italy
- Forest Ecology Unit, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige, Italy
| | - Antonella Penna
- Department of Biomolecular Sciences, University of Urbino, Urbino, Italy.
- Fano Marine Center, Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, Fano, Italy.
- CoNISMa, National Inter-University Consortium for Marine Sciences, Rome, Italy.
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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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Ancillotto L, Falanga A, Agostinetto G, Tommasi N, Garonna AP, de Benedetta F, Bernardo U, Galimberti A, Conti P, Russo D. Predator-prey traits and foraging habitat shape the diet of a common insectivorous bat. ACTA OECOLOGICA 2023. [DOI: 10.1016/j.actao.2023.103890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Biella P, Tommasi N, Guzzetti L, Pioltelli E, Labra M, Galimberti A. City climate and landscape structure shape pollinators, nectar and transported pollen along a gradient of urbanization. J Appl Ecol 2022. [DOI: 10.1111/1365-2664.14168] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Paolo Biella
- ZooPlantLab, Department of Biotechnology and Biosciences University of Milano‐Bicocca Milan Italy
| | - Nicola Tommasi
- ZooPlantLab, Department of Biotechnology and Biosciences University of Milano‐Bicocca Milan Italy
- Istituto Nazionale di Fisica Nucleare ‐ Sez. Milano Bicocca Milan Italy
| | - Lorenzo Guzzetti
- ZooPlantLab, Department of Biotechnology and Biosciences University of Milano‐Bicocca Milan Italy
| | - Emiliano Pioltelli
- ZooPlantLab, Department of Biotechnology and Biosciences University of Milano‐Bicocca Milan Italy
| | - Massimo Labra
- ZooPlantLab, Department of Biotechnology and Biosciences University of Milano‐Bicocca Milan Italy
- Istituto Nazionale di Fisica Nucleare ‐ Sez. Milano Bicocca Milan Italy
| | - Andrea Galimberti
- ZooPlantLab, Department of Biotechnology and Biosciences University of Milano‐Bicocca Milan Italy
- Istituto Nazionale di Fisica Nucleare ‐ Sez. Milano Bicocca Milan Italy
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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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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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