What can’t be measured won’t be managed: Scientists and U.S. Environmental Protection Agency work together to conserve the Great Lakes

What can’t be measured won’t be managed: Scientists and U.S. Environmental Protection Agency work together to conserve the Great Lakes

What can’t be measured won’t be managed: Scientists and U.S. Environmental Protection Agency work together to conserve the Great Lakes

The Great Lakes DNA Barcoding project brings together several international partners to understand the aquatic invertebrate biodiversity in the Laurentian Great Lakes
The Laurentian Great Lakes from space.

The Laurentian Great Lakes provide extremely valuable ecosystem services to nearly 40 million citizens of Canada and the United States who inhabit the watershed and many other visitors. These lakes are important for commercial navigation and are one of the most valuable freshwater commercial and recreational fisheries in the world. Such heavy use makes them vulnerable to invasive species, of which there are about 180 known to have invaded the five lakes1. However, the lakes’ biodiversity remains startlingly unknown, especially at lower trophic levels, even with strong scientific communities on both sides of the border.

The Great Lakes DNA Barcoding Project is using new and scalable genetic approaches to fill in the gaps in our knowledge of the native aquatic biodiversity of the Great Lakes and to detect previously undiscovered biological invasions. It will provide a baseline against which to monitor future changes in response to unintentional anthropogenic impacts and quantify efforts to restore biodiversity in parts of the lakes where it has declined.
The Great Lakes
The Great Lakes contain 21% of the world’s surface freshwater and are an important resource for agriculture, fishing, recreation, and international shipping. IMAGE CREDIT: 2013 National Geographic Society; Watershed defined by Great Lakes Aquatic Habitat Framework.

Understanding the impacts of anthropogenic changes on freshwater biodiversity is a major challenge with direct relevance to human health and well-being2. Monitoring and managing aquatic biodiversity needs to involve both academic and government institutions as well as stakeholders spanning farmers, fishermen, global transport companies, and policymakers in order to better inform environmental risk assessment, policy development, and natural resource management. Additionally, evaluating and improving private or public efforts to protect biodiversity requires an ability to quantify biodiversity, beginning with species richness.

The lack of scalable tools for assessing biodiversity has been a major impediment when monitoring the health of freshwater ecosystems. These habitats are dominated by small organisms that are difficult to identify and preserve. Species-level identification based on morphology is often impractical or sometimes even impossible. The process involves expert taxonomists and the special treatment of specimens requires significant investments in money, time, and labour. Therefore, when we rely only on these traditional survey practices, many organisms are identified only to genus/subfamily or simply neglected3,4.

DNA barcoding is a useful tool in these situations because the necessary taxonomic resources can be invested in a more targeted approach once a large number of specimens have been assigned a digital species identifier based on its DNA—the DNA barcode—to create a standardized, reproducible, and scalable solution for monitoring, otherwise difficult to quantify species. By digitizing taxonomic information in the form of a barcode, one needs not taxonomic expertise but simply access to sequencing technology for future identification and monitoring requirements. These technologies are becoming more portable and affordable every day and these tools become even more exciting when we apply non-invasive water sampling to monitor entire fauna from the trace amounts of DNA they leave behind (called ‘environmental DNA’)5.

The Great Lakes Barcoding Project, funded by the United States Environmental Protection Agency (EPA), aims to build a comprehensive genetic barcode library for aquatic invertebrates in the Laurentian Great Lakes watershed. The goal is to improve biodiversity monitoring, provide early detection of non-indigenous species, and inform management efforts to protect biodiversity from threats including climate change, pollution, and invasive species.

At the beginning of the project, only limited genetic information was available for many of the Great Lakes species6. The scale of the Great Lakes and its relatively large invertebrate biodiversity requires this research to be highly collaborative. To this end, the project has brought together several taxonomic experts, molecular ecologists, and aquatic biologists across USA and Canada, from the EPA and research institutions including Cornell University, Buffalo State College, University of Notre Dame, Central Michigan University, and the Centre for Biodiversity Genomics at the University of Guelph.

The Great Lakes DNA Barcoding Project team

The Great Lakes DNA Barcoding Project Team: Bret Coggins, Lars Rudstam, Susan Daniel, Adam Frankiewicz, James Watkins, Beth Whitmore, Joe Connolly; bottom row left to right: Sara Westergaard, Michael Pfrender, Bilgenur Baloglu, Kristy Deiner, Ed DeWalt, Alexander Karatayev, Christopher Marshall, Lyubov Burlakova (top to bottom, left to right). In attendance but not pictured: David Lodge, Kara Andres, and Jose Andres. George Rogalskyj and Erik Pilgrim joined electronically.
PHOTO CREDIT: The Great Lakes DNA Barcoding Project

 

At the end of February 2020, scientists as well as EPA representatives managing or participating in the project gathered at the beautiful Biological Field Station at Cornell University in upstate New York. We shared the latest project updates—everything from taxonomy to biodiversity, from ecological analysis to portable DNA sequencing, and the future of DNA-based monitoring. While the project is still in progress with hundreds of more specimens awaiting analysis, so far, our collaboration has resulted in over 1,000 DNA barcodes spanning over 300 invertebrate species.

This diversity includes more than ten taxonomic classes of invertebrates and is a resource that will improve tracking of non-native and native aquatic species, as well as clarify taxonomic inconsistencies or misrepresentations. The project has stimulated collaborations both within and outside of the main group of researchers and the sharing of specimens, resources, and, most importantly, new ideas and research directions has been an extremely encouraging and productive outcome.

Each plate of specimens sent away for DNA barcode analysis also contains a mix of feelings: satisfaction from a job well done, anticipation of the eventual results, and excitement around the new discoveries that may unfold.

References:

1. Great Lakes Aquatic Nonindigenous Species Information System. Retrieved from: www.glerl.noaa.gov/glansis/index.html

2. IPBES (2019) Global assessment report on biodiversity and ecosystem services of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services. ES Brondizio, J Settele, S Díaz and HT Ngo (editors). IPBES secretariat, Bonn, Germany.

3. Baloğlu B, Clews E and Meier R (2018) NGS barcoding reveals high resistance of a hyperdiverse chironomid (Diptera) swamp fauna against invasion from adjacent freshwater reservoirs. Frontiers in Zoology, 15(1)

4. Srivathsan A, Baloğlu B, Wang W, Tan WX, Bertrand D, Ng AH, Boey EJ, Koh JJ, Nagarajan N and Meier R (2018) A MinION™‐based pipeline for fast and cost‐effective DNA barcoding. Molecular Ecology Resources, 18(5): 1035–1049.

5. Deiner K, Bik HM, Mächler E, Seymour M, Lacoursière‐Roussel A, Altermatt F, Creer S, Bista I, Lodge DM, De Vere N and Pfrender ME (2017) Environmental DNA metabarcoding: Transforming how we survey animal and plant communities. Molecular Ecology, 26(21): 5872–5895.

6. Trebitz A, Sykes M, Barge J (2019) A reference inventory for aquatic fauna of the Laurentian Great Lakes. J. Great Lakes Res.

this project is supported by the

Great Lakes Restoration Initiative

Written by

Bilgenur Baloğlu

Bilgenur Baloğlu

Centre for Biodiversity Genomics, Guelph, ON, Canada

Christopher C. Marshall

Christopher C. Marshall

Department of Natural Resources, Cornell University, Ithaca, New York, USA

Lars Rudstam

Department of Natural Resources, Cornell University, Ithaca, New York, USA

David M. Lodge

David M. Lodge

Cornell Atkinson Center for Sustainability and Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA

Edward DeWalt

Illinois Natural History Survey, Champaign, Illinois, USA

Paul W. Simonin

Paul W. Simonin

Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA

Elizabeth Whitmore

Elizabeth Whitmore

Department of Natural Resources, Cornell University, Ithaca, New York, USA

Lyubov Burlakova

Great Lakes Center, Buffalo State College, Buffalo, NY, USA

Kristy Deiner

Kristy Deiner

Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland

June 18, 2020

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Discovering a resilient and hyperdiverse midge fly fauna in a Singaporean swamp forest

Discovering a resilient and hyperdiverse midge fly fauna in a Singaporean swamp forest

Discovering a resilient and hyperdiverse midge fly fauna in a Singaporean swamp forest

Researchers uncover a highly unique and diverse chironomid community in a Singaporean swamp forest highlighting the importance of these ecosystems and the power of Next-Generation Sequencing for biomonitoring efforts.

Nee Soon Swamp Forest, Singapore

PHOTO CREDIT: Wang Luan Keng

Benthic macroinvertebrates – those animals that live at the bottoms of water bodies – are abundant, diverse, relatively immobile, and responsive to environmental stresses, and these traits make them ideal indicators of the quality of aquatic ecosystems. Our study demonstrates the utility of Next-Generation Sequencing (NGS) platforms as an efficient and rapid tool for monitoring efforts.

In freshwater ecosystems, non-biting midges (Diptera: Chironomidae) often constitute the majority of diversity and biomass with different chironomid species varying in their sensitivity to environmental changes. But, when monitoring these habitats, chironomids are either ignored entirely or not studied at a species-level because morphological assessments are expensive and laborious, and the identification literature is based on adults while larvae are most often collected.

Chironomid adults collected from Nee Soon Swamp Forest. Different chironomid species vary in their sensitivity to environmental parameters. PHOTO CREDIT: Bilgenur Baloglu
The solution? NGS platforms. They allow for fast and effective species-level assessments of large-scale samples at low cost (less than $0.40 USD/specimen). Moreover, there is a high congruence between molecular and morphological identification, enabling a detailed examination of the composition of taxonomically complex communities1,2. Freshwater swamp forests – the forested wetlands occurring along rivers and lakes – are home to various endemic and endangered species with 33% of birds and 45% of mammals either threatened or endangered on the IUCN Red List3, and with most of the insect fauna unknown. These ecosystems are under threat worldwide from habitat destruction, pollution, and climate crisis. Most of the world’s tropical swamp forests are found in Southeast Asia’s Indo-Malayan region collectively occupying more than 13 million ha4 among many geographically separated peninsulas and islands. Nee Soon swamp forest is the largest remnant (90 ha) of its kind in Singapore and thus of high national conservation value.

Bilge Baloglu sampling water DNA from Singapore’s largest swamp forest remnant.
PHOTO CREDIT: Dickson Ng

We generated DNA barcodes using NGS to study chironomids among the natural swamp forest Nee Soon and three adjacent man-made reservoirs. We wanted to understand the effects of urbanization and to know whether the chironomid fauna of Nee Soon is resistant to, that is, minimally impacted by, the adjacent reservoirs. We sampled >14,000 chironomid specimens (both adults and larvae) as part of a freshwater quality monitoring program, and quantified species richness and compositional changes using NGS and DNA barcoding.

Our study showed that Singapore’s biggest swamp forest remnant maintains a rich and largely unique fauna of about 350 species. The minimal species overlap between sites indicated that the Nee Soon swamp forest is resistant against the invasion of species from surrounding artificial reservoirs. 

These findings suggest that even small or fragmented swamp forests can be suitable habitats for chironomids, shedding light on many other swamp forests in Southeast Asia that collectively occupy a much larger area and that are threatened by destruction for oil palm plantations and paper pulp production. Overall, our study exposes the enormous power of NGS and DNA barcoding in ecological research to study ecosystem health, biological diversity, and habitat conservation.

References:

1. Brodin Y, Ejdung G, Strandberg J, Lyrholm T (2013) Improving environmental and biodiversity monitoring in the Baltic Sea using DNA barcoding of Chironomidae (Diptera). Molecular Ecology Resources 13:996–1004.

2. Montagna M, Mereghetti V, Lencioni V, Rossaro B (2016) Integrated taxonomy and DNA barcoding of alpine midges (Diptera: Chironomidae). PLoS One 11:e0149673

3. Posa MR (2011) Peat swamp forest avifauna of Central Kalimantan, Indonesia: Effects of habitat loss and degradation. Biological Conservation 144(10):2548-2556.

4. Hooijer A, Page S, Canadell JG, Silvius M, Kwadijk J, Wösten H, Jauhiainen J (2010) Current and future CO2 emissions from drained peatlands in Southeast Asia. Biogeosciences 7:1505–1514

For full details, please refer to the publication in Frontiers in Zoology.

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