Innovation in biomonitoring using environmental genomics

Overview

Dr. Melania Cristescu’s research advances the use of environmental RNA (eRNA, genetic material released by organisms into their surroundings) as a powerful, non-invasive tool for monitoring biodiversity and ecosystem health in water environments, particularly those affected by farming. Her work demonstrates that eRNA can reveal unique insights—such as organisms’ metabolic activity and physical traits—that cannot be detected through environmental DNA alone, challenging earlier concerns about eRNA stability in the environment.

Application

Cristescu’s team’s findings support the growing potential of genetic tools like eRNA and eDNA for cost-effective, real-time environmental monitoring and improved management of agricultural watersheds (areas of land that drain into water bodies). These genetic tools offer several advantages over traditional methods, including minimal disruption to wildlife, broad coverage of species, and high sensitivity that allows detection of rare or hard-to-find species.

Challenge

Effective monitoring is crucial for properly managing water systems. In agricultural areas, the complex effects of farming on aquatic species’ health and functioning aren’t fully understood. Recent advances in environmental genomics (the study of genetic material from environmental samples) have transformed monitoring practices, allowing researchers to track biodiversity changes over time and better understand how farming practices affect water systems and species.
The development of DNA metabarcoding (a technique that identifies multiple species from a single environmental sample) has encouraged researchers to explore other genetic markers, such as eRNA. However, eRNA’s potential remains underexplored, largely due to skepticism about its stability, as it breaks down more quickly than eDNA. While recent research has shown promise for both eDNA and eRNA as monitoring tools, more study is needed to fully understand how these materials are produced, moved through the environment, and detected, especially in disturbed environments.

Did You Know?

Both eDNA and eRNA are used to monitor biodiversity in water environments by analyzing genetic material. While eDNA shows which species are present or were recently in the area, eRNA indicates which species are currently active and how they’re responding to their environment. When used together, these tools provide comprehensive information about ecosystem health.

Research

In collaboration with partner institutions in Québec, Dr. Melania Cristescu’s team has developed and validated eRNA-based methods as an effective tool for assessing biodiversity and gathering functional information about organisms in aquatic systems. Her ongoing work focuses on creating non-invasive genomic tools to monitor ecosystem health and connect species’ genetic responses to environmental stressors. Building on earlier research, Cristescu’s findings show that eRNA can provide similar insights to eDNA—and in some cases, reveal patterns that eDNA alone cannot detect. During earlier phases of the FfT project, her team studied the impacts of agricultural land use on freshwater ecosystems and investigated how these ecosystems adapt to environmental changes. More recent research has advanced experimental genomic techniques to better understand the effects of agriculture on watersheds and rivers, while also developing powerful eRNA-based tools to assess ecosystem health and trace biological responses back to specific environmental pressures.

Results

Cristescu’s team explored the potential of environmental DNA (eDNA) and RNA (eRNA) for biodiversity monitoring and assessment in aquatic environments, challenging previous assumptions about eRNA’s limitations. Studies by Cristescu’s team revealed that despite concerns about rapid degradation, eRNA can be successfully filtered from water samples and meta barcoded similarly to eDNA. Her work shows that eRNA is abundantly secreted by aquatic species and provides unique insights into gender, age, and phenotype differences between sampled species, while also reflecting metabolically active organisms, making it particularly valuable for real-time monitoring of environmental stress responses. Though eRNA is theoretically expected to degrade faster than eDNA due to its single-stranded structure and RNase susceptibility, comparative studies have yielded mixed results regarding degradation rates. The studies identified key factors that affect genetic detection in environmental samples, including the type of genetic marker used and the impact of environmental disturbances; the choice of different markers can influence which species are detected more than whether DNA or RNA is used, suggesting that using multiple markers may give a more complete picture of biodiversity.

Impact

Whether the sample is eRNA or eDNA, genomic analysis with eNA sampling provides a novel suite of methods for assessing biodiversity in a sensitive and non-invasive ways, often capturing information on hard-to-reach species or areas. Rather than interacting directly with wildlife, scientists can glean important information over periods of time using samples from the environment including water, soil, Genomic analysis is also cost effective, allowing for biodiversity monitoring based on repeated, accessible samples. Repeated analysis of eRNA samples can be used to assess the effectiveness of implemented conservation strategies across time, leading to better management informed by valuable, cost-effective monitoring data. For agricultural watersheds, this will be important to implement and improve upon strategies to manage agricultural pollution in freshwater systems. Finally, Cristescu’s work linking biodiversity data to environmental stressors using e-sampling generates helpful insights as to the impact of human activity on agricultural watersheds.

Learn More

arbosa Da Costa, N., Fugère, V., Hébert, M., Xu, C. C. Y., Barrett, R. D. H., Beisner, B. E., Bell, G., Yargeau, V., Fussmann, G. F., Gonzalez, A., & Shapiro, B. J. (2021). Resistance, resilience, and functional redundancy of freshwater bacterioplankton communities facing a gradient of agricultural stressors in a mesocosm experiment. Molecular Ecology, 30(19), 4771–4788. https://doi.org/10.1111/mec.16100

Barbosa Da Costa, N., Hébert, M.-P., Fugère, V., Terrat, Y., Fussmann, G. F., Gonzalez, A., & Shapiro, B. J. (2022). A glyphosate-based herbicide cross-selects for antibiotic resistance genes in bacterioplankton communities. mSystems, 7(2), e01482-21. https://doi.org/10.1128/msystems.01482-21

Bell, G., Fugère, V., Barrett, R., Beisner, B., Cristescu, M., Fussmann, G., Shapiro, J., & Gonzalez, A. (2019). Trophic structure modulates community rescue following acidification. Proceedings of the Royal Society B: Biological Sciences, 286(1904), 20190856. https://doi.org/10.1098/rspb.2019.0856

Cristescu, M. E., & Hebert, P. D. N. (2018). Uses and misuses of environmental DNA in biodiversity science and conservation. Annual Review of Ecology, Evolution, and Systematics, 49(1), 209–230. https://doi.org/10.1146/annurev-ecolsys-110617-062306

Firkowski, C. R., Schwantes, A. M., Fortin, M.-J., & Gonzalez, A. (2021). Monitoring social–ecological networks for biodiversity and ecosystem services in human-dominated landscapes. FACETS, 6, 1670–1692. https://doi.org/10.1139/facets-2020-0114

Fugère, V., Hébert, M.-P., Da Costa, N. B., Xu, C. C. Y., Barrett, R. D. H., Beisner, B. E., Bell, G., Fussmann, G. F., Shapiro, B. J., Yargeau, V., & Gonzalez, A. (2020). Community rescue in experimental phytoplankton communities facing severe herbicide pollution. Nature Ecology & Evolution, 4(4), 578–588. https://doi.org/10.1038/s41559-020-1134-5

Hébert, M., Fugère, V., Beisner, B. E., Barbosa Da Costa, N., Barrett, R. D. H., Bell, G., Shapiro, B. J., Yargeau, V., Gonzalez, A., & Fussmann, G. F. (2021). Widespread agrochemicals differentially affect zooplankton biomass and community structure. Ecological Applications, 31(7), e02423. https://doi.org/10.1002/eap.2423

Hébert, M., Fugère, V., & Gonzalez, A. (2019). The overlooked impact of rising glyphosate use on phosphorus loading in agricultural watersheds. Frontiers in Ecology and the Environment, 17(1), 48–56. https://doi.org/10.1002/fee.1985

Hébert, M.-P., Beisner, B. E., Rautio, M., & Fussmann, G. F. (2021). Warming winters in lakes: Later ice onset promotes consumer overwintering and shapes springtime planktonic food webs. Proceedings of the National Academy of Sciences, 118(48), e2114840118. https://doi.org/10.1073/pnas.2114840118

Hechler, R. M., Yates, M. C., Chain, F. J. J., & Cristescu, M. E. (2023). Environmental transcriptomics under heat stress: Can environmental RNA reveal changes in gene expression of aquatic organisms? Molecular Ecology. https://doi.org/10.1111/mec.17152

Hechler, R. M., & Cristescu, M. E. (2024). Revealing population demographics with environmental RNA. Molecular Ecology Resources, 24(4), e13951-n/a. https://doi.org/10.1111/1755-0998.1395
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Hleap, J. S., Cristescu, M. E., & Steinke, D. (2020). A 2 G2: A Python wrapper to perform very large alignments in semi-conserved regions. Bioinformatics. https://doi.org/10.1101/2020.05.21.109009

Hleap, J. S., Littlefair, J. E., Steinke, D., Hebert, P. D. N., & Cristescu, M. E. (2021). Assessment of current taxonomic assignment strategies for metabarcoding eukaryotes. Molecular Ecology Resources, 21(7), 2190–2203. https://doi.org/10.1111/1755-0998.13407

Kagzi, K., Hechler, R. M., Fussmann, G. F., & Cristescu, M. E. (2022). Environmental RNA degrades more rapidly than environmental DNA across a broad range of pH conditions. Molecular Ecology Resources, 22(7), 2640–2650. https://doi.org/10.1111/1755-0998.13655

Kagzi, K., Millette, K. L., Littlefair, J. E., Pochon, X., Wood, S. A., Fussmann, G. F., & Cristescu, M. E. (2023). Assessing the degradation of environmental DNA and RNA based on genomic origin in a metabarcoding context. Environmental DNA, 5(5), 1016–1031. https://doi.org/10.1002/edn3.437

Littlefair, J. E., Rennie, M. D., & Cristescu, M. E. (2022). Environmental nucleic acids: A field‐based comparison for monitoring freshwater habitats using eDNA and eRNA. Molecular Ecology Resources, 22(8), 2928–2940. https://doi.org/10.1111/1755-0998.13671

McCann, K. S., Cazelles, K., MacDougall, A. S., Fussmann, G. F., Bieg, C., Cristescu, M., Fryxell, J. M., Gellner, G., Lapointe, B., & Gonzalez, A. (2021). Landscape modification and nutrient‐driven instability at a distance. Ecology Letters, 24(3), 398–414. https://doi.org/10.1111/ele.13644

Millette, K. L., Gonzalez, A., & Cristescu, M. E. (2020). Breaking ecological barriers: Anthropogenic disturbance leads to habitat transitions, hybridization, and high genetic diversity. Science of The Total Environment, 740, 140046. https://doi.org/10.1016/j.scitotenv.2020.140046

Mitchell, M. G. E., Hartley, E., Tsuruda, M., Gonzalez, A., & Bennett, E. M. (2022). Contrasting responses of soybean aphids, primary parasitoids, and hyperparasitoids to forest fragments and agricultural landscape structure. Agriculture, Ecosystems & Environment, 326, 107752. https://doi.org/10.1016/j.agee.2021.107752

O’Connor, M. I., Mori, A. S., Gonzalez, A., Dee, L. E., Loreau, M., Avolio, M., Byrnes, J. E. K., Cheung, W., Cowles, J., Clark, A. T., Hautier, Y., Hector, A., Komatsu, K., Newbold, T., Outhwaite, C. L., Reich, P. B., Seabloom, E., Williams, L., Wright, A., & Isbell, F. (2021). Grand challenges in biodiversity–ecosystem functioning research in the era of science–policy platforms require explicit consideration of feedbacks. Proceedings of the Royal Society B: Biological Sciences, 288(1960), 20210783. https://doi.org/10.1098/rspb.2021.0783

Tadiri, C. P., Negrín Dastis, J. O., Cristescu, M. E., Gonzalez, A., & Fussmann, G. F. (2024). Ecosystem connectivity and configuration can mediate instability at a distance in metaecosystems. Functional Ecology, 38(1), 153–164. https://doi.org/10.1111/1365-2435.14455

Yates, M. C., Derry, A. M., & Cristescu, M. E. (2021). Environmental RNA: A revolution in ecological resolution? Trends in Ecology & Evolution, 36(7), 601–609. https://doi.org/10.1016/j.tree.2021.03.001

Principal Investigator

Collaborators

Dr. Gregor Fussmann, Dr. Andy Gonzalez, Dr. Graham Bell, Dr. Rowan Barrett, Dr. Dirk Steinke, Dr. Paul Hebert, Dr. Kevin McCann, Dr. John Fryxell, Vincent Fugère, Jesse Shapiro

Students and Post-doctoral fellows

Kaushar Kagzi, Robert Heckler, Wendy Morgado, Aleksey Sychterz, Patricia Hummer, Gabrielle Pellegrin, Michelle Gros, Christopher Hempel, Julien Beaulieu, Weller Elizabeth, Dr. Egor Katkov, Dr. Takahiro Maruki, Dr. Xiaoping He

Partners

McGill University, Université du Québec à Montréal

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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