Tracking aquatic animals with sediment DNA records

Gregory‐Eaves, Irene; Eaves, Irene Gregory; Monchamp, Marie‐Ève; Taranu, Zofia E.

doi:10.22541/essoar.167287040.04332426/v1

Cited by 3 publications

(2 citation statements)

References 51 publications

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“…and Holopedium glacialis were relatively important in the water column samples, but rarely found in the sediments as subfossils (Figure S1), a pattern that has been observed previously (Çakıroğlu et al., 2014; Nykänen et al., 2009) and denotes poor preservation of those taxa. In the future, sediment DNA analyses could help bring forth more complete portrait of zooplankton assemblages in general (Gregory‐Eaves et al., in press).…”

Section: Discussionmentioning

confidence: 99%

Congruence of water column, contemporary and pre‐industrial sediment cladoceran assemblages in 85 Canadian lakes of contrasting human impact levels

Paquette,

Gregory‐Eaves,

Beisner

2023

Freshwater Biology

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Crustacean zooplankton occupy a key position as primary consumers within lake food webs, acting as early indicators of wider ecosystem shifts that can cascade to higher trophic levels. Their communities can be assessed via water column net hauls or via sediment samples containing preserved subfossil remnants from various time periods; the latter probably integrate multiple years of data, habitats within lakes, and seasonal patterns. The degree to which such samples do or do not correspond has never been assessed across a wide variety of lake types and gradients. As part of a larger sampling of over 600 lakes across lake‐rich Canada, 85 lakes were selected along a gradient of human impact, according to contemporary catchment land use, to analyse cladoceran zooplankton assemblage relatedness among snapshot water column, contemporary and pre‐industrial sediment samples. We used a combination of ordinations and matrix correlations (RV coefficients), along with partial redundancy analyses, to determine the degree to which the different sample types were comparable and whether they responded similarly to >30 environmental variables. We also compared conclusions obtained using the full cladoceran assemblages versus pelagic‐only taxa and whether our results varied according to degree of human impact. Overall, while all sample types were correlated, congruence was highest between contemporary and pre‐industrial sediment sample types. This result could arise from the under‐representation of littoral taxa in water column samples relative to those from the sediment. In high impacted catchments, however, we observed greater similarity between water column and contemporary sediment samples, as water quality stressors potentially structure assemblages in parallel directions over time. In these modern‐day sample types and among measured variables, we identified lake depth and pH as the most important structuring variables across Canada. In this first study comparing cladoceran assemblages in water column, contemporary and pre‐industrial sediments across many lakes, we conclude that water column and sediment samples respond similarly to environmental drivers but should not be considered entirely analogous or redundant.

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Section: Discussionmentioning

confidence: 99%

Congruence of water column, contemporary and pre‐industrial sediment cladoceran assemblages in 85 Canadian lakes of contrasting human impact levels

Paquette,

Gregory‐Eaves,

Beisner

2023

Freshwater Biology

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“…Unfortunately, many soft-bodied species, such as rotifers and microbial eukaryotes, do not leave behind diagnostic morphological features. Fish can leave remains like otoliths, scales, teeth, and bones that might be identifiable to broad groups (Sibert & Rubin, 2021), but these are often found in sparse quantities and have therefore been largely excluded from many reconstructive analyses used to infer past ecosystem changes (Gregory-Eaves et al, 2023). Indirect proxies, such as stable isotope analyses (Finney et al, 2000) or zooplankton-based transfer functions (Jeppesen et al, 1996(Jeppesen et al, , 2001, have been used to reconstruct past fish abundances, but often fail to provide definite information on species identification and community composition.…”

Section: Introductionmentioning

confidence: 99%

Detection of fish sedimentary DNA in aquatic systems: A review of methodological challenges and future opportunities

Huston,

Lopez,

Cheng

et al. 2023

Environmental DNA

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Environmental DNA studies have proliferated over the last decade, with promising data describing the diversity of organisms inhabiting aquatic and terrestrial ecosystems. The recovery of DNA present in the sediment of aquatic systems (sedDNA) has provided short‐ and long‐term data on a wide range of biological groups (e.g., photosynthetic organisms, zooplankton species) and has advanced our understanding of how environmental changes have affected aquatic communities. However, substantial challenges remain for recovering the genetic material of macro‐organisms (e.g., fish) from sediments, preventing complete reconstructions of past aquatic ecosystems, and limiting our understanding of historic, higher trophic level interactions. In this review, we outline the biotic and abiotic factors affecting the production, persistence, and transport of fish DNA from the water column to the sediments, and address questions regarding the preservation of fish DNA in sediment. We identify sources of uncertainties around the recovery of fish sedDNA arising during the sedDNA workflow. This includes methodological issues related to experimental design, DNA extraction procedures, and the selected molecular method (quantitative PCR, digital PCR, metabarcoding, metagenomics). By evaluating previous efforts (published and unpublished works) to recover fish sedDNA signals, we provide suggestions for future research and propose troubleshooting workflows for the effective detection and quantification of fish sedDNA. With further research, the use of sedDNA has the potential to be a powerful tool for inferring fish presence over time and reconstructing their population and community dynamics.

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Long-term environmental changes in the Canadian boreal zone: Synthesizing temporal trends from lake sediment archives to inform future sustainability

et al. 2023

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Covering 55% of Canada’s total surface area and stretching from coast to coast to coast, the Canadian boreal zone is crucial to the nation’s economic and ecological integrity. Although often viewed as relatively underdeveloped, it is vulnerable to numerous stressors such as mining, forestry, and anthropogenic climate change. Natural archives preserved in lake sediments can provide key insights by quantifying pre-disturbance conditions (pre-1850 CE) and the nature, magnitude, direction, and speed of environmental change induced by anthropogenic stressors over the past ~150 years. Here, we paired a review of paleolimnological literature of the Canadian boreal zone with analyses of published sediment core data to highlight the effects of climate change, catchment disturbances, and atmospheric deposition on boreal lakes. Specifically, we conducted quantitative syntheses of two lake health indicators: elemental lead (Pb) and chlorophyll <i>a</i>. Segmented regressions and Mann-Kendall trend analysis revealed a generally increasing trend in elemental Pb across the boreal zone until ~1970 CE, followed by a generally decreasing trend to the present. Snapshot comparisons of sedimentary chlorophyll <i>a</i> from recent and pre-industrial sediments (i.e., top-bottom sediment core design) revealed that a majority of sites have increased over time, suggesting a general enhancement in lake primary production across the boreal zone. Collectively, this body of work demonstrates that long-term sediment records offer a critical perspective on ecosystem change not accessible through routine monitoring programs. We advocate using modern datasets in tandem with paleolimnology to establish baseline conditions, measure ecosystem changes, and set meaningful management targets.

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Tracking aquatic animals with sediment DNA records

Abstract: Chapter 5 "Cyanobacterial DNA from lake sediments" Marie-Eve Monchamp and Frances Pick Chapter 6 "DNA archives of protists in lake sediments"

Cited by 3 publications

References 51 publications

Congruence of water column, contemporary and pre‐industrial sediment cladoceran assemblages in 85 Canadian lakes of contrasting human impact levels

Congruence of water column, contemporary and pre‐industrial sediment cladoceran assemblages in 85 Canadian lakes of contrasting human impact levels

Detection of fish sedimentary DNA in aquatic systems: A review of methodological challenges and future opportunities

Long-term environmental changes in the Canadian boreal zone: Synthesizing temporal trends from lake sediment archives to inform future sustainability

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