Reconstruction of 100-year dynamics in Daphnia spawning activity revealed by sedimentary DNA

Tsugeki, Narumi K.; Nakane, Kai; Doi, Hideyuki; Ochi, Natsuki; Kuwae, Michinobu

doi:10.1038/s41598-021-03899-0

Cited by 15 publications

(38 citation statements)

References 67 publications

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“…During the 1920s and 1940s, P. altivelis eDNA was relatively stable, but during the 1940s-1970s, almost no eDNA was detected. This period coincided with the period when many resting eggs of Daphnia were detected (Tsugeki et al, 2022). Daphnia and other zooplankton species produce resting eggs because of habitat deterioration or stress (Hairston, 1996).…”

Section: Discussionmentioning

confidence: 75%

“…In fact, the concentration of chlorophyll, adjusted for degradation, declined sharply in 1940, suggesting a major environmental change. Since in Lake Biwa, Daphnia were kept low abundance before the 1960s (Tsugeki et al , 2022), thus it is likely that highly limited food resources during the 1940s~1970s had been keeping the P. altivelis population low abundance, resulting to become undetectable of eDNA due to a low amount of eDNA. In addition, since eDNA of Eodiaptomus japonicus , one of the major food resources of P. altivelis , tends to be detected at relatively slightly higher concentrations before 1940 (Liu et al 2021; Nakane et al unpublished), the abundance of this food resource of P. altivelis may have this abundance may have contributed to the high biomass of P. altivelis during this period.…”

Section: Discussionmentioning

confidence: 99%

“…In addition, since eDNA of Eodiaptomus japonicus , one of the major food resources of P. altivelis , tends to be detected at relatively slightly higher concentrations before 1940 (Liu et al 2021; Nakane et al unpublished), the abundance of this food resource of P. altivelis may have this abundance may have contributed to the high biomass of P. altivelis during this period. P. altivelis eDNA concentrations have been increasing since the 1980s when Daphnia population were kept high abundance (Tsugeki et al , 2022). The zooplankton increases like Daphnia as food resources were assumed to provide an increase in the biomass of P. altivelis which resulted in an increase in eDNA concentrations.…”

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Fish environmental DNA in lake sediment overcomes the gap of reconstructing past fauna in lake ecosystems

Sakata

Tsugeki

Kuwae

et al. 2022

Preprint

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Underwater sediments are a natural archive of biological information. Reconstruction of past fauna has been conducted for various taxonomic groups using morphological remains and DNA derived from these remains. However, information on past occurrences of fish species, the top predator of lake ecosystems, could have been reproduced only in exceptional environments, and past quantitative information on fish, particularly in lake ecosystems, has been a knowledge gap in reconstructing past fauna. Tracking the quantitative fluctuations of fish is essential for reconstructing multiple trophic levels of organisms in lake ecosystems. To acquire past quantitative fish information from lake sediments, we collected approximately 30 cm-length of underwater sediments in Lake Biwa. We extracted sedimentary environmental DNA (eDNA) and measured temporal fluctuations in the eDNA concentration of the native and fishery target species Plecoglossus altivelis and Gymnogobius isaza. For P. altivelis, we examined the possibility of tracking quantitative fluctuations by comparing sedimentary eDNA with recorded catch per unit effort (CPUE). The chronology of the sediments allowed us to obtain information on sediments collected in Lake Biwa over the past 100 years. The deepest depths at which sedimentary eDNA was detected were 30 and 13 cm for P. altivelis and G. isaza from the surface, corresponding to approximately 100 and 30 years ago, respectively. In the comparison of sedimentary eDNA concentrations and biomass, we found a significant correlation between the CPUE of P. altivelis and its sedimentary eDNA concentration adjusted to compensate for DNA degradation. Sedimentary eDNA fluctuations were observed in P. altivelis, possibly reflecting the abundance fluctuation due to variations in the main food resources of zooplankton. Our findings provide essential pieces for the reconstruction of past fauna of lake ecosystems. The addition of quantitative information on fish species will reach a new phase, for instance, by investigating population shifts or biological interactions in the reconstruction of past fauna in lake ecosystems.

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Section: Discussionmentioning

confidence: 75%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Fish environmental DNA in lake sediment overcomes the gap of reconstructing past fauna in lake ecosystems

Sakata

Tsugeki

Kuwae

et al. 2022

Preprint

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“…DNA samples were quantified via real-time TaqMan quantitative PCR using the QuantStudio™ 1 Real-Time PCR System (Thermo Fisher Scientific, Waltham, MA, USA) in Center for Marine Environmental Studies, Ehime University. The qPCR method was followed according to a previous study (Tsugeki et al, 2022) on the developed preprint (which was not certified by peer review) is the author/funder. All rights reserved.…”

Section: Qpcrmentioning

confidence: 99%

Sedimentary DNA can reveal the past population dynamics of a pelagic copepod

Nakane

Liu

Doi

et al. 2022

Preprint

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Copepods play a key trophic role as secondary producers in transferring primary production to higher trophic levels such as fish. Copepod production significantly contributes to successful fish recruitment. Despite their importance, knowledge of their dynamics over several decades remains limited due to the difficulty to obtain long-term data series with exhaustive sampling and analysis. However, an understanding long-term copepod dynamic is urgently required to head toward better management for sustainable aquatic ecosystems and fish recruitment. Sedimentary DNA (sedDNA) has been developing a useful tool for reconstructing past plankton dynamics. This study evaluates whether sedDNA targeting the pelagic copepod, Eodiaptomus japonicus, in Lake Biwa (Japan) can be an effective tool for elucidating its past population dynamics. It was applied a quantitative polymerase chain reaction method targeting the mitochondrial cytochrome c oxidase subunit I gene on sediment cores and compared the detected sedDNA concentrations with the unique long-term dataset of demographic traits, biomass, specific growth rate, production, subitaneous eggs, and resting eggs of E. japonicus. The sedDNA concentration of E. japonicus recovered from sediment layers did not correlate significantly with its resting eggs and its specific growth rate but with in situ production, biomass, and subitaneous egg production. The results provided the evidence for the sedDNA as a tracking tool for assessing copepod past production dynamics.

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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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Reconstruction of 100-year dynamics in Daphnia spawning activity revealed by sedimentary DNA

Cited by 15 publications

References 67 publications

Fish environmental DNA in lake sediment overcomes the gap of reconstructing past fauna in lake ecosystems

Fish environmental DNA in lake sediment overcomes the gap of reconstructing past fauna in lake ecosystems

Sedimentary DNA can reveal the past population dynamics of a pelagic copepod

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

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