DNA Reveals Nature’s Hidden Pest Control Network

Overview

Hebert’s team at the Centre for Biodiversity Genomics enhances our understanding of complex ecological relationships by studying symbiomes (the complete ecosystem of organisms associated with a single specimen). Using advanced DNA sequencing and improved data platforms, the research reveals hidden interactions between species, particularly focusing on parasitic wasps and their roles in controlling pest populations. This work transforms how we discover and use natural pest control agents while advancing our understanding of biodiversity.

Application

The research by Hebert’s team revolutionizes pest management by identifying local, naturally occurring pest control agents through DNA analysis. Instead of relying on introduced species for pest control, scientists can now discover and utilize native species that already help regulate pest populations. For instance, in Finland, this approach led to discovering five previously unknown species of parasitic wasps that help control moth populations. This knowledge helps farmers and land managers develop more effective, environmentally friendly pest control strategies while better understanding and protecting beneficial species in their ecosystems.

Challenge

Understanding the complex ecological interactions between beneficial organisms, parasites, and their hosts is crucial for effective ecosystem management, pest control, and biodiversity conservation. However, traditional monitoring methods often miss tiny, hidden, or hard-to-identify species, creating significant gaps in our understanding of their roles in controlling pest populations and maintaining ecosystem health. This challenge is particularly pressing as insect communities face rapid, poorly documented changes, with decreases in their numbers and diversity potentially threatening the benefits they provide to ecosystems. While DNA metabarcoding (analyzing genetic material from multiple species simultaneously) offers a promising solution by enabling the detection of diverse species, current sequencing technologies must adapt to manage the vast data and ecological complexity involved. Despite its potential, the full scope of symbiome (the complete ecosystem of organisms associated with an individual) interactions remains underexplored, limiting our ability to track ecosystem health and develop effective pest management strategies.

Did You Know?

Symbiomes are the complete collection of organisms living in close association with an individual, including parasites, beneficial partners, and neutral organisms. While research often focuses on single species, analyzing symbiomes through DNA sequencing reveals entire networks of interacting organisms, providing a fuller picture of ecological relationships.

Research

Dr. Paul Hebert and the Centre for Biodiversity Genomics addressed critical gaps in biodiversity informatics by enhancing two key platforms: BOLD (Barcode of Life Data System) and mBRAVE (Multiplex Barcode Research and Visualization Environment). BOLD, which currently hosts over 16.8 million public records representing 1.5 million species, is being upgraded to support more complex data types from new sequencing technologies. Using advanced sequencing platforms like PacBio Sequel, the project analyzes DNA extracts containing genetic material not just from the target specimen but from all associated organisms, revealing complex ecological relationships from previously inaccessible or neglected species groups. Meanwhile, mBRAVE is being enhanced to process and analyze the vast amount of sequence data generated by high-speed sequencing, using multiple computers working together to handle large datasets efficiently.

Image of Formicidae Montana documented by the Centre for Biodiversity Genomics.

Results

This research project demonstrates the power of DNA sequencing and metabarcoding in advancing our understanding of biodiversity across vast geographic and species ranges. A key application has been studying parasitic Hymenoptera (wasps, bees, and ants), particularly wasps that parasitize and control pest species. By analyzing symbiomes from individual specimens, the project has uncovered hidden species, improved our knowledge of parasitic wasp-host relationships, and explored under-studied groups of parasitic wasps. For example, in Bangladesh, these methods revealed 25 species, 58 genera, 12 subfamilies, and 7 families of parasitic wasps previously unknown in the country. In Finland, combining DNA analysis with studying wasp gut contents led to discovering five previously unknown species and confirmed their parasitism of Xestia moths. The research also identified six new species of Lipolexis wasps, which help control aphid pests.

These findings not only demonstrate the significance of parasitic Hymenoptera in ecosystems but also show how DNA sequencing and metabarcoding can identify local biocontrol agents, offering a significant advantage over traditional pest management approaches, which often focus on introduced species.

Impact

This research has broad implications for both genetic studies and practical applications in agriculture and conservation. In genetics, the ability to analyze symbiomes represents a significant advance. By improving established genomic platforms like BOLD and mBRAVE, this project enhanced our ability to capture and process vast amounts of genetic data, revealing previously hidden species interactions. For agriculture and conservation, identifying local pest control agents through DNA sequencing offers promise for more sustainable pest management strategies. This could transform how beneficial organisms are discovered and used, expanding beyond parasitic wasps to include understudied groups like roundworms, fungi, and single-celled organisms. Such insights could provide critical solutions for managing invasive pests, such as the spotted lanternfly, which has caused billions in damage to North American agriculture. While traditional pest management methods have often focused on introduced species, the ability to identify and use local, naturally occurring beneficial organisms could offer a more effective, regionally tailored approach to pest control.

Learn More

Attiná, N., Núñez Bustos, E. O., Lijtmaer, D. A., Hebert, P. D. N., Tubaro, P. L., & Lavinia, P. D. (2021). Genetic variation in neotropical butterflies is associated with sampling scale, species distributions, and historical forest dynamics. Molecular Ecology Resources, 21(7), 2333–2349. https://doi.org/10.1111/1755-0998.13441

Basset, Y., Hajibabaei, M., Wright, M. T. G., Castillo, A. M., Donoso, D. A., Segar, S. T., Souto-Vilarós, D., Soliman, D. Y., Roslin, T., Smith, M. A., Lamarre, G. P. A., de León, L. F., Decaëns, T., Palacios-Vargas, J. G., Castaño-Meneses, G., Scheffrahn, R. H., Rivera, M., Perez, F., Bobadilla, R., … Barrios, H. (2022). Comparison of traditional and DNA metabarcoding samples for monitoring tropical soil arthropods (Formicidae, Collembola and Isoptera). Scientific Reports, 12(1). https://doi.org/10.1038/s41598-022-14915-2

Čkrkić, J., Petrović, A., Kocić, K., Ye, Z., Vollhardt, I. M. G., Hebert, P. D. N., Traugott, M., & Tomanović, Ž. (2019). Hidden in plain sight: phylogeography of an overlooked parasitoid species Trioxys sunnysidensis Fulbright & Pike (Hymenoptera: Braconidae: Aphidiinae). Agricultural and Forest Entomology, 21(3), 299–308. https://doi.org/10.1111/afe.12332

DeWaard, J. R., Levesque-Beaudin, V., DeWaard, S. L., Ivanova, N. v., McKeown, J. T. A., Miskie, R., Naik, S., Perez, K. H. J., Ratnasingham, S., Sobel, C. N., Sones, J. E., Steinke, C., Telfer, A. C., Young, A. D., Young, M. R., Zakharov, E. v., & Hebert, P. D. N. (2019). Expedited assessment of terrestrial arthropod diversity by coupling Malaise traps with DNA barcoding. Genome, 62(3), 85–95. https://doi.org/10.1139/gen-2018-0093

Dewaard, J. R., Ratnasingham, S., Zakharov, E. v, Borisenko, A. v, Steinke, D., Telfer, A. C., Perez, K. H. J., Sones, J. E., Young, M. R., Levesque-Beaudin, V., Sobel, C. N., Abrahamyan, A., Bessonov, K., Blagoev, G., Dewaard, S. L., Ho, C., Ivanova, N. v, Layton, K. K. S., Lu, L., … Hebert, P. D. N. (n.d.). A reference library for the identification of Canadian invertebrates: 1.5 million DNA barcodes, voucher specimens, and genomic samples.

Dincă, V., Dapporto, L., Somervuo, P., Vodă, R., Cuvelier, S., Gascoigne-Pees, M., Huemer, P., Mutanen, M., Hebert, P. D. N., & Vila, R. (2021). High resolution DNA barcode library for European butterflies reveals continental patterns of mitochondrial genetic diversity. Communications Biology, 4(1). https://doi.org/10.1038/s42003-021-01834-7

D’Souza, M. L., & Hebert, P. D. N. (2018). Stable baselines of temporal turnover underlie high beta diversity in tropical arthropod communities. Molecular Ecology, 27(10), 2447–2460. https://doi.org/10.1111/mec.14693

Hobern, D., & Hebert, P. (2019). BIOSCAN – Revealing Eukaryote Diversity, Dynamics, and Interactions. Biodiversity Information Science and Standards, 3. https://doi.org/10.3897/biss.3.37333

Huemer, P., Hebert, P. D. N., Mutanen, M., Wieser, C., Wiesmair, B., Hausmann, A., Yakovlev, R., Möst, M., Gottsberger, B., Strutzenberger, P., & Fiedler, K. (2018). Large geographic distance versus small DNA barcode divergence: Insights from a comparison of European to South Siberian Lepidoptera. PLoS ONE, 13(11). https://doi.org/10.1371/journal.pone.0206668

Kocić, K., Petrović, A., Čkrkić, J., Kavallieratos, N. G., Rakhshani, E., Arnó, J., Aparicio, Y., Hebert, P. D. N., & Tomanović, Ž. (2020). Resolving the taxonomic status of potential biocontrol agents belonging to the neglected genus lipolexis förster (hymenoptera, braconidae, aphidiinae) with descriptions of six new species. Insects, 11(10), 1–30. https://doi.org/10.3390/insects11100667

Mazumdar, S., David Neil Hebert, P., Amin Bhuiya, B., & Ismail Miah, M. (2019). Parasitic Hymenoptera Recovered by DNA Barcoding of Malaise Trap Collection at the Chittagong University Campus, Bangladesh. American Journal of BioScience, 7(6), 94. https://doi.org/10.11648/j.ajbio.20190706.12

Morinière, J., Balke, M., Doczkal, D., Geiger, M. F., Hardulak, L. A., Haszprunar, G., Hausmann, A., Hendrich, L., Regalado, L., Rulik, B., Schmidt, S., Wägele, J. W., & Hebert, P. D. N. (2019). A DNA barcode library for 5,200 German flies and midges (Insecta: Diptera) and its implications for metabarcoding-based biomonitoring. Molecular Ecology Resources, 19(4), 900–928. https://doi.org/10.1111/1755-0998.13022

Mutanen, M., Ovaskainen, O., Várkonyi, G., Itämies, J., Prosser, S. W. J., Hebert, P. D. N., & Hanski, I. (2020). Dynamics of a host–parasitoid interaction clarified by modelling and DNA sequencing. In Ecology Letters (Vol. 23, Issue 5, pp. 851–859). Blackwell Publishing Ltd. https://doi.org/10.1111/ele.13486

Pentinsaari, M., Blagoev, G. A., Hogg, I. D., Levesque-Beaudin, V., Perez, K., Sobel, C. N., Vandenbrink, B., & Borisenko, A. (2020). A DNA barcoding survey of an arctic arthropod community: Implications for future monitoring. Insects, 11(1). https://doi.org/10.3390/insects11010046

Pilgrim, J., Thongprem, P., Davison, H. R., Siozios, S., Baylis, M., Zakharov, E. v., Ratnasingham, S., Dewaard, J. R., Macadam, C. R., Smith, M. A., & Hurst, G. D. D. (2021). Torix Rickettsia are widespread in arthropods and reflect a neglected symbiosis. GigaScience, 10(3). https://doi.org/10.1093/gigascience/giab021

Steinke, D., Braukmann, T. W. A., Manerus, L., Woodhouse, A., & Elbrecht, V. (2021). Effects of Malaise trap spacing on species richness and composition of terrestrial arthropod bulk samples. Metabarcoding and Metagenomics, 5, 43–50. https://doi.org/10.3897/MBMG.5.59201

Principal Investigator

Collaborator

Dr. Sujeevan Ratnasingham

Research funding for Food from Thought is provided in part by the Canada First Research Excellence Fund

University of Guelph

50 Stone Road East,
Guelph, Ontario N1G 2W1

Call: 519-824-4120

Email: fft@uoguelph.ca

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