Ancient plant <scp>DNA</scp> in lake sediments

Parducci, Laura; Bennett, K. D.; Ficetola, Gentile Francesco; Alsos, Inger Greve; Suyama, Yoshihisa; Wood, Jamie R.; Pedersen, Mikkel Winther

doi:10.1111/nph.14470

Cited by 239 publications

(214 citation statements)

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“…In the case of thorough environmental studies, it requires stringent extraction protocol lysing all cells in order to recover the entire pool of ancient DNA and specific primer pairs to improve detection limits (Coolen, 2011; Coolen et al, 2013). The same applies to ancient 18S rRNA sequences (e.g., seeds, pollens, dinocysts, and frustules) (Parducci et al, 2005, 2017; Boere et al, 2011b). …”

Section: Discussionmentioning

confidence: 99%

“…Genetic material directly extracted from environmental samples without obvious biological sources is increasingly employed to study organisms that live or lived in the catchment, water column or sediment (Coolen et al, 2004, 2013; Boere et al, 2009; Ariztegui et al, 2015; Thomsen and Willerslev, 2015; Parducci et al, 2017). In ancient records, it is often best preserved within intact resting stages (Domaizon et al, 2017), such as pollens, planktonic cysts or endospores, which can then be used to trace past environmental changes (Coolen and Overmann, 1998, 2007; Parducci et al, 2005; Coolen et al, 2013) and complement other molecular indicators (Coolen et al, 2008, 2009; Boere et al, 2009; Vuillemin et al, 2014b, 2016a).…”

Section: Introductionmentioning

confidence: 99%

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Preservation and Significance of Extracellular DNA in Ferruginous Sediments from Lake Towuti, Indonesia

et al. 2017

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Extracellular DNA is ubiquitous in soil and sediment and constitutes a dominant fraction of environmental DNA in aquatic systems. In theory, extracellular DNA is composed of genomic elements persisting at different degrees of preservation produced by processes occurring on land, in the water column and sediment. Extracellular DNA can be taken up as a nutrient source, excreted or degraded by microorganisms, or adsorbed onto mineral matrices, thus potentially preserving information from past environments. To test whether extracellular DNA records lacustrine conditions, we sequentially extracted extracellular and intracellular DNA from anoxic sediments of ferruginous Lake Towuti, Indonesia. We applied 16S rRNA gene Illumina sequencing on both fractions to discriminate exogenous from endogenous sources of extracellular DNA in the sediment. Environmental sequences exclusively found as extracellular DNA in the sediment originated from multiple sources. For instance, Actinobacteria, Verrucomicrobia, and Acidobacteria derived from soils in the catchment. Limited primary productivity in the water column resulted in few sequences of Cyanobacteria in the oxic photic zone, whereas stratification of the water body mainly led to secondary production by aerobic and anaerobic heterotrophs. Chloroflexi and Planctomycetes, the main degraders of sinking organic matter and planktonic sequences at the water-sediment interface, were preferentially preserved during the initial phase of burial. To trace endogenous sources of extracellular DNA, we used relative abundances of taxa in the intracellular DNA to define which microbial populations grow, decline or persist at low density with sediment depth. Cell lysis became an important additional source of extracellular DNA, gradually covering previous genetic assemblages as other microbial genera became more abundant with depth. The use of extracellular DNA as nutrient by active microorganisms led to selective removal of sequences with lowest GC contents. We conclude that extracellular DNA preserved in shallow lacustrine sediments reflects the initial environmental context, but is gradually modified and thereby shifts from its stratigraphic context. Discrimination of exogenous and endogenous sources of extracellular DNA allows simultaneously addressing in-lake and post-depositional processes. In deeper sediments, the accumulation of resting stages and sequences from cell lysis would require stringent extraction and specific primers if ancient DNA is targeted.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Preservation and Significance of Extracellular DNA in Ferruginous Sediments from Lake Towuti, Indonesia

et al. 2017

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“…Bulk sediments contain a complex set of genetic material from many different types of organisms, as encountered in environmental DNA analyses (e.g., Anderson‐Carpenter et al ; Pansu et al ). Recent technological developments, such as next generation sequencing, may create opportunities for seda DNA to provide complementary information to existing proxies, especially with regard to biodiversity (Boessenkool et al ) and long‐term ecosystem dynamics (e.g., Anderson‐Carpenter et al ; Pansu et al ), although technical uncertainties remain (Parducci et al ).…”

Section: Future Research Opportunities In Ancient Lakesmentioning

confidence: 99%

Recent ecological change in ancient lakes

Hampton

McGowan

Ozersky

et al. 2018

Limnology & Oceanography

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Ancient lakes are among the best archivists of past environmental change, having experienced more than one full glacial cycle, a wide range of climatic conditions, tectonic events, and long association with human settlements. These lakes not only record long histories of environmental variation and human activity in their sediments, but also harbor very high levels of biodiversity and endemism. Yet, ancient lakes are faced with a familiar suite of anthropogenic threats, which may degrade the unusual properties that make them especially valuable to science and society. In all ancient lakes for which data exist, significant warming of surface waters has occurred, with a broad range of consequences. Eutrophication threatens both native species assemblages and regional economies reliant on clean surface water, fisheries, and tourism. Where sewage contributes nutrients and heavy metals, one can anticipate the occurrence of less understood emerging contaminants, such as pharmaceuticals, personal care products, and microplastics that negatively affect lake biota and water quality. Human populations continue to increase in most of the ancient lakes’ watersheds, which will exacerbate these concerns. Further, human alterations of hydrology, including those produced through climate change, have altered lake levels. Co‐occurring with these impacts have been intentional and unintentional species introductions, altering biodiversity. Given that the distinctive character of each ancient lake is strongly linked to age, there may be few options to remediate losses of species or other ecosystem damage associated with modern ecological change, heightening the imperative for understanding these systems.

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“…However, the eradication took place more than 6 years ago and eDNA from fish carcasses in lake systems has been suggested not to be detectable in water form more than 70 days (Dunker et al, 2016). Yet, while vertical migration (leaching) of DNA from sediments to the surrounding aquatic environment has not previously been observed in pond or lake sediments (Parducci et al, 2017;Sjögren et al, 2017), it cannot be completely ruled out as a DNA source in this study, as the persistence of eDNA in sediment depends largely on the origin of the DNA, its concentration and the nature of the sediment (Pietramellara et al, 2009). Sediment can have a higher content of eDNA than water (Pietramellara et al, 2009), and consequently longer temporal resolution (annual to decadal-centennial; Bálint et al, 2018).…”

Section: Discussionmentioning

confidence: 87%

Monitoring the eradication of the highly invasive topmouth gudgeon (Pseudorasbora parva) using a novel eDNA assay

Robinson

2019

Environmental DNA

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This is an open access article under the terms of the Creat ive Commo ns Attri butio n-NonCo mmerc ial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made. AbstractAquatic invasive species (AIS) represent an important threat for Biodiversity and are one of the factors determining the ecological integrity of water bodies under the Water Framework Directive. Eradication is one of the most effective tools for the management of invasive species but has important economic and ecological tradeoffs and its success needs to be carefully monitored. We assessed the eradication success of the topmouth gudgeon (Pseudorasbora parva), an invasive fish that poses significant risks to endemic aquatic fauna, in four ponds previously treated with the piscicide Rotenone using a novel qPCR-based environmental DNA (eDNA) assay. We validated the assay through successfully detecting DNA from topmouth gudgeon in two reservoirs with physically confirmed topmouth gudgeon populations. Topmouth gudgeon were detected in all four treated ponds using 750 ml water samples and in three of the ponds using 15 ml samples, despite the eradication treatment and lack of successful detection using conventional trapping methods. Our results highlight the difficulties of eradicating invasive fish and the need to incorporate reliable monitoring methods as part of a risk management strategy under the water framework directive (WFD). K E Y W O R D Saquatic invasive species, environmental DNA, invasion biology, water framework directive | 75 ROBINSON et al.

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Ancient plant DNA in lake sediments

Cited by 239 publications

References 182 publications

Preservation and Significance of Extracellular DNA in Ferruginous Sediments from Lake Towuti, Indonesia

Preservation and Significance of Extracellular DNA in Ferruginous Sediments from Lake Towuti, Indonesia

Recent ecological change in ancient lakes

Monitoring the eradication of the highly invasive topmouth gudgeon (Pseudorasbora parva) using a novel eDNA assay

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