To what extent is the DNA of microbial eukaryotes modified during burying into lake sediments? A repeat-coring approach on annually laminated sediments

Capo, Eric; Domaizon, Isabelle; Maier, Dominique Béatrice; Debroas, Didier; Bigler, Christian

doi:10.1007/s10933-017-0005-9

Cited by 21 publications

(21 citation statements)

References 71 publications

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“…This is coherent with the knowledge of the relationships between P concentration and Chlorophyta abundance (Naselli-Flores and Barone, 2000;Soares et al, 2013). Furthermore, using sed-DNA analysis, Capo et al (2017a) showed significant correlations between high P concentrations (up to 80 µg.L −1 ) and Chlorophyta abundance and more particularly within the Chlamydomonaceae family. Despite the correlations between PC3 geo scores (reflecting changes in P concentrations in sediments) and biological parameters (e.g., diversity metrics of protistan communities), the effects of this local anthropogenic pressures on aquatic communities appear to be overshadowed by the effects of terrestrial inputs in Nylandssjön.…”

Section: Effects Of Inter-annual Environmental Variability On Aquaticsupporting

confidence: 86%

“…For instance, Capo et al (2016) showed that protistan communities were driven by the large climatic fluctuations over the last 2000 years, including the Medieval Warm Period, the Little Ice Age and current warming. The longterm effects of an increasing warming trend on phytoplanktonic groups was also shown for several peri-alpines lakes at a centennial timescale (Capo et al, 2017a;Monchamp et al, 2018). However, our findings suggest that the high inter-annual variability of key environmental variables (e.g., weather, snow and ice phenology, terrestrial inputs) may dominate relative to those from global climatic pressures in the Nylandssjön 40-year record.…”

Section: Effects Of Inter-annual Environmental Variability On Aquaticmentioning

confidence: 69%

“…Adjusted p-values were not determined for correlations with PC1 geo -scores and transformed Shannon index values due to two low effective sample size for these variables. Finally, an analysis using generalized additive models (GAMs) (Hastie and Tibshirani, 1986) was performed to investigate when and to what extent environmental parameters contribute to the changes in biological parameters (structure, richness and diversity of protistan communities, richness and relative abundance of the 11 most abundant protistan groups and the abundance of Cyanobacteria), as detailed by Capo et al (2017a). The response variables that do not follow Gaussian distribution were log-transformed prior to modeling.…”

Section: Discussionmentioning

confidence: 99%

“…Application of DNA-based analysis to sedimentary archives can be a powerful tool to extract long-term data on lake aquatic communities (see Domaizon et al, 2017 for review). These archives can reveal the responses of key components of aquatic food webs to environmental changes over longer timeframes (Capo et al, 2016(Capo et al, , 2017aMonchamp et al, 2018;Tse et al, 2018;Vuillemin et al, 2018). For example, sedimentary DNA (sed-DNA) was used to identify the responses of protistan communities over centennial to millennial timescales to longterm forcing factors such as eutrophication and climate change (Capo et al, 2016(Capo et al, , 2017a.…”

Section: Introductionmentioning

confidence: 99%

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How Does Environmental Inter-annual Variability Shape Aquatic Microbial Communities? A 40-Year Annual Record of Sedimentary DNA From a Boreal Lake (Nylandssjön, Sweden)

et al. 2019

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To assess the sensitivity of lakes to anthropogenically-driven environmental changes (e.g., nutrient supply, climate change), it is necessary to first isolate the effects of between-year variability in weather conditions. This variability can strongly impact a lake's biological community especially in boreal and arctic areas where snow phenology play an important role in controlling the input of terrestrial matter to the lake. Identifying the importance of this inherent variability is difficult without time series that span at least several decades. Here, we applied a molecular approach (metabarcoding on eukaryotic 18S rRNA genes and qPCR on cyanobacterial 16S rRNA genes) to sedimentary DNA (sed-DNA) to unravel the annual variability of microbial community in 40 years' sediment record from the boreal lake Nylandssjön which preserve annually-laminated sediments. Our comparison between seasonal meteorological data, sediment inorganic geochemistry (X-ray fluorescence analyses) and organic biomarkers (pyrolysis-gas chromatography/mass spectrometry analyses), demonstrated that inter-annual variability strongly influence the sediment composition in Nylandssjön. Spring temperature, snow and ice phenology (e.g., the percentage of snow loss in spring, the timing of lake ice-off) were identified as important drivers for the inputs of terrestrial material to the lake, and were therefore also important for shaping the aquatic biological community. Main changes were detected in the late-80s/mid-90s and mid-2000s associated with increases in algal productivity, in total richness of the protistan community and in relative abundances of Chlorophyta, Dinophyceae as well as Cyanobacteria abundance. These changes could be linked to a decline in terrestrial inputs to the lake during the snow melt and runoff period, which in turn was driven by warmer winter temperatures. Even if our data shows that meteorological factors do affect the sediment composition and microbial communities, they only explain part of the variability. Capo et al. Inter-annual Variability in Lake Ecosystems This is most likely a consequence of the high inter-annual variability in abiotic and biotic parameters highlighting the difficulty to draw firm conclusions concerning drivers of biological changes at an annual or sub-annual resolution even with the 40-year varved sediment record from Nylandssjön. Hence, it is necessary to have an even longer time perspective in order to reveal the full implications of climate change.

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Section: Effects Of Inter-annual Environmental Variability On Aquaticsupporting

confidence: 86%

Section: Effects Of Inter-annual Environmental Variability On Aquaticmentioning

confidence: 69%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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How Does Environmental Inter-annual Variability Shape Aquatic Microbial Communities? A 40-Year Annual Record of Sedimentary DNA From a Boreal Lake (Nylandssjön, Sweden)

et al. 2019

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“…For mammal bones, the propensity for tissues and environments to create closed systems appears to be of greater importance than the absolute age of the aeDNA (Kistler, Ware, Smith, Collins, & Allaby, 2017). To date, there is little knowledge of how taphonomic processes affect the preservation of aeDNA from aquatic habitats, though assemblages derived from aeDNA have been shown to be stable over decadal timescales in lake sediments (Capo, Domaizon, Maier, Debroas, & Bigler, 2017).…”

Section: Limitationsmentioning

confidence: 99%

Broadening the taxonomic scope of coral reef palaeoecological studies using ancient DNA

et al. 2019

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Marine environments face acute pressures from human impacts, often resulting in substantial changes in community structure. On the inshore Great Barrier Reef (GBR), palaeoecological studies show the collapse of the previously dominant coral Acropora from the impacts of degraded water quality associated with European colonization. Even more dramatic impacts can result in the replacement of corals by fleshy macroalgae on modern reefs, but their past distribution is unknown because they leave no fossil record. Here, we apply DNA metabarcoding and high‐throughput sequencing of the 18S rDNA gene on palaeoenvironmental DNA (aeDNA) derived from sediment cores at two sites on Pandora Reef (GBR), to enhance palaeoecological studies by incorporating key soft‐bodied taxa, including macroalgae. We compared temporal trends in this aeDNA record with those of coral genera derived from macrofossils. Multivariate analysis of 12 eukaryotic groups from the aeDNA community showed wide variability over the past 750 years. The occurrence of brown macroalgae was negatively correlated only with the dominant coral at both sites. The occurrence of coralline and green macroalgae was positively correlated with only the dominant coral at one of the sites, where we also observed a significant association between the whole coral community and the occurrence of each of the three macroalgae groups. Our results demonstrate that reef sediments can provide a valuable archive for understanding the past distribution and occurrence of important soft‐bodied reef dwellers. Combining information from fossils and aeDNA provides an enhanced understanding of temporal changes of reefs ecosystems at decadal to millennial timescales.

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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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To what extent is the DNA of microbial eukaryotes modified during burying into lake sediments? A repeat-coring approach on annually laminated sediments

Cited by 21 publications

References 71 publications

How Does Environmental Inter-annual Variability Shape Aquatic Microbial Communities? A 40-Year Annual Record of Sedimentary DNA From a Boreal Lake (Nylandssjön, Sweden)

How Does Environmental Inter-annual Variability Shape Aquatic Microbial Communities? A 40-Year Annual Record of Sedimentary DNA From a Boreal Lake (Nylandssjön, Sweden)

Broadening the taxonomic scope of coral reef palaeoecological studies using ancient DNA

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

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