The NSERC Canadian Lake Pulse Network: A national assessment of lake health providing science for water management in a changing climate

Huot, Yannick; Brown, Catherine; Potvin, Geneviève; Antoniades, Dermot; Baulch, Helen M.; Beisner, Beatrix E.; Bélanger, Simon; Brazeau, Stéphanie; Cabana, Hubert; Cardille, Jeffrey A.; Giorgio, Paul A. del; Gregory‐Eaves, Irene; Fortin, Marie‐Josée; Lang, Andrew S.; Laurion, Isabelle; Maranger, Roxane; Prairie, Yves T.; Rusak, James A.; Segura, Pedro A.; Siron, Robert; Smol, John P.; Vinebrooke, Rolf D.; Walsh, David A.

doi:10.1016/j.scitotenv.2019.133668

Cited by 80 publications

(117 citation statements)

References 150 publications

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“…The low-similarity alignment of sediment metagenomes and reference genomes representing genera detected in sediment metagenomes suggests that these contemporary reference genomes do not reflect historical microdiversity. Ecotypes could potentially be resolved if sets of genomes or metagenome-assembled genomes representative of local to regional pre-and postimpact diversity were made available, especially through largescale metagenomic lake surveys (59). Comparing the ecological dependencies reconstructed in ecotype time series could then retrace environmental change.…”

Section: Discussionmentioning

confidence: 99%

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Sediment Metagenomes as Time Capsules of Lake Microbiomes

Garner

Gregory‐Eaves

Walsh

2020

mSphere

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The reconstruction of ecological time series from lake sediment archives can retrace the environmental impact of human activities. Molecular genetic approaches in paleolimnology have provided unprecedented access to DNA time series, which record evidence of the microbial ecologies that underlaid historical lake ecosystems. Such studies often rely on single-gene surveys, and consequently, the full diversity of preserved microorganisms remains unexplored. In this study, we probed the diversity archived in contemporary and preindustrial sediments by comparative shotgun metagenomic analysis of surface water and sediment samples from three eastern Canadian lakes. In a strategy that was aimed at disentangling historical DNA from the indigenous sediment background, microbial preservation signals were captured by mapping sequence similarities between sediment metagenome reads and reference surface water metagenome assemblies. We detected preserved Cyanobacteria, diverse bacterioplankton, microeukaryotes, and viruses in sediment metagenomes. Among the preserved microorganisms were important groups never before reported in paleolimnological reconstructions, including bacteriophages (Caudovirales) and ubiquitous freshwater Betaproteobacteria (Polynucleobacter and Limnohabitans). In contrast, ultramicroscopic Actinobacteria (“Candidatus Nanopelagicales”) and Alphaproteobacteria (Pelagibacterales) were apparently not well preserved in sediment metagenomes even though they were numerically dominant in surface water metagenomes. Overall, our study explored a novel application of whole-metagenome shotgun sequencing for discovering the DNA remains of a broad diversity of microorganisms preserved in lake sediments. The recovery of diverse microbial time series supports the taxonomic expansion of microbiome reconstructions and the development of novel microbial paleoindicators. IMPORTANCE Lakes are critical freshwater resources under mounting pressure from climate change and other anthropogenic stressors. The reconstruction of ecological time series from sediment archives with paleolimnological techniques has been shown to be an effective means of understanding how humans are modifying lake ecosystems over extended timescales. In this study, we combined shotgun DNA sequencing with a novel comparative analysis of surface water and sediment metagenomes to expose the diversity of microorganisms preserved in lake sediments. The detection of DNA from a broad diversity of preserved microbes serves to more fully reconstruct historical microbiomes and describe preimpact lake conditions.

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Section: Discussionmentioning

confidence: 99%

“…1; Table 1). Lakes were selected by meeting the criteria of a maximum depth of at least 1 m and accessibility within 1 km from a road (59). At each lake, surface water and sediment cores were collected at the site of maximum depth, located by depth sounding and using bathymetric maps as guides when available.…”

Section: Methodsmentioning

confidence: 99%

Sediment Metagenomes as Time Capsules of Lake Microbiomes

Garner

Gregory‐Eaves

Walsh

2020

mSphere

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“…Similarly, the integration of ecological data at the national scale can stimulate a long-term collaborative vision in data sharing and water management and can allow for an increase in data accessibility to researchers, stakeholders, and policy makers. National-scale monitoring programs for inland waters are essential to achieve commitments under the 2030 Agenda for Sustainable Development and its 17 Sustainable Development Goals (Dickens et al 2019;Huot et al 2019).…”

Section: Discussionmentioning

confidence: 99%

“…With systematic and continuous nation-wide sampling, ecological variability across inland waters will be better understood (Soranno et al 2015), and gaps between fundamental ecological research and its application by managers will be greatly narrowed (Cadotte et al 2017). Current examples that provide a model for scaling up include the Natural Sciences and Engineering Research Council of Canada (NSERC) Canadian LakePulse Network in Canada (Huot et al 2019) and the National Lakes Assessment Program in the USA. Programs such as these will be instrumental in ensuring that Canada meets its commitments under the 2030 Agenda and the implementation of the associated UN Sustainable Development Goals.…”

Section: Opportunities From National Data Integrationmentioning

confidence: 99%

Horizon scan of conservation issues for inland waters in Canada

Pérez‐Jvostov

Sutherland

Barrett

et al. 2020

Can. J. Fish. Aquat. Sci.

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Horizon scanning is a systematic approach increasingly used to explore emerging trends, issues, opportunities, and threats in conservation. We present the results from one such exercise aimed at identifying emerging issues that could have important scientific, social, technological, and managerial implications for the conservation of inland waters in Canada in the proximate future. We recognized six opportunities and nine challenges, for which we provide research implications and policy options, such that scientists, policy makers, and the Canadian society as a whole can prepare for a potential growth in each of the topic areas we identified. The issues spanned a broad range of topics, from recognizing the opportunities and challenges of community-enabled science and the need to consider the legal rights of nature, to the likely increase of pharmaceuticals in wastewater due to an aging population. These issues represent a first baseline that could help decision makers identify and prioritize efforts while simultaneously stimulate new research avenues. We hope our horizon scan will pave the way for similar exercises related to the conservation of biodiversity in Canada.

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“…Dots represent lakes with bacterial loads beyond the whiskers. Lakes were sampled in six of the 18 terrestrial ecozones in Canada, and lakes were classified by size, where small lakes are ≥0.1 to <0.5 km 2 , medium lakes are ≥0.5 to <5 km 2 , and large lakes are ≥5 to <100 km 2(23).…”

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confidence: 99%

Microbiology in the Field: Construction and Validation of a Portable Incubator for Real-Time Quantification of Coliforms and Other Bacteria

Wight

Varin

Robertson

et al. 2020

Front. Public Health

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Performing microbiological assays on environmental samples in field settings poses logistical challenges with respect to the availability of suitable equipment or the ability to get samples to the laboratory in a timely fashion. For example, the viability of some bacteria can decrease greatly between sampling and arrival to the laboratory for processing. We developed and constructed rugged, reliable, and cost-effective portable incubators that were used by 10 independent field teams to perform microbiological assays on surface water samples from lakes across Canada. Rigorous testing and validation of our incubators ensured that incubation conditions were consistent within and across all 10 field teams and 2 sampling years. Samples from all sites were processed in duplicate and bacterial counts were highly repeatable within and across sampling teams. Bacterial counts were also found to be statistically equivalent to counts obtained with standard laboratory techniques using a conventional incubator. Using this method, thermotolerant coliforms (TTCs) and Escherichia coli were quantified from 432 lakes, allowing comparison to both historical datasets that relied on TTCs and those following current guidelines that use E. coli counts. We found higher loads at the shoreline than the middle of lakes and different patterns between ecozones. E. coli was not frequently detected, but many lakes exceeded Canadian guideline values for activities such as swimming and some even exceeded the guideline value for secondary recreational activities such as boating. To the best of our knowledge, this is the largest bacteriological water quality assessment of freshwater lakes to date in terms of both spatial scale and the number of lakes sampled. Our incubator design can be easily adapted for a wide variety of researcher goals and represents a robust platform for field studies and other applications, including those in remote or low-resources settings.

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The NSERC Canadian Lake Pulse Network: A national assessment of lake health providing science for water management in a changing climate

Cited by 80 publications

References 150 publications

Sediment Metagenomes as Time Capsules of Lake Microbiomes

Sediment Metagenomes as Time Capsules of Lake Microbiomes

Horizon scan of conservation issues for inland waters in Canada

Microbiology in the Field: Construction and Validation of a Portable Incubator for Real-Time Quantification of Coliforms and Other Bacteria

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