A comparative study of ancient environmental DNA to pollen and macrofossils from lake sediments reveals taxonomic overlap and additional plant taxa

Pedersen, Mikkel Winther; Ginolhac, Aurélien; Orlando, Ludovic; Olsen, Jesper; Andersen, Kenneth Geving; Holm, Jakob; Funder, Svend; Willerslev, Eske; Kjær, Kurt H.

doi:10.1016/j.quascirev.2013.06.006

Cited by 106 publications

(115 citation statements)

References 38 publications

Supporting

Mentioning

108

Contrasting

Order By: Relevance

“…During the PCR, the DNA of planktonic foraminifera might well be outcompeted by the autochthonous DNA of benthic foraminifera, which is potentially more abundant, less damaged and more easily extracted from cells than when tightly absorbed to sediment particles (Ceccherini et al, 2009;Torti et al, 2015). It is noteworthy that the relative proportion of sequence reads may reflect the relative proportion of DNA molecules -but not necessarily that of cells -as shown in the case of a mock foraminiferal DNA community amplified using foraminiferal-specific primers (Esling et al, 2015) Consistent with earlier studies (Capo et al, 2015;Lejzerowicz et al, 2013;Pawłowska et al, 2014;Pedersen et al, 2013), the taxonomic diversity revealed by the analyzed eDNA barcodes overlaps only partly with the diversity based on fossils present in the sediment. One part of the observed difference could be ascribed to the limited coverage of the reference database.…”

Section: Discussionsupporting

confidence: 81%

“…Recently, Kirkpatrick et al (2016) showed that the abundance of planktonic DNA was decreasing within 100-200 ka in sediments of the Bering Sea but traces were still detected in sediments up to 1.4 Ma. Direct comparison with co-occurring fossils showed that the sequenced eDNA pool exceeds the taxonomic spectrum of the fossils, but many of the taxa preserved as fossils were not identified in the eDNA (Pawłowska et al, 2014;Pedersen et al, 2013). This raises the question of how well the sedimentary DNA pool reflects the autochthonous (in situ origin) or allochthonous (external origin) community composition, whether there is any differential DNA preservation across taxa and whether the metabarcode marker selected is fully representative of the entire taxonomical diversity, regardless of its origin.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Planktonic foraminifera-derived environmental DNA extracted from abyssal sediments preserves patterns of plankton macroecology

et al. 2017

Self Cite

View full text Add to dashboard Cite

Abstract. Deep-sea sediments constitute a unique archive of ocean change, fueled by a permanent rain of mineral and organic remains from the surface ocean. Until now, paleoecological analyses of this archive have been mostly based on information from taxa leaving fossils. In theory, environmental DNA (eDNA) in the sediment has the potential to provide information on non-fossilized taxa, allowing more comprehensive interpretations of the fossil record. Yet, the process controlling the transport and deposition of eDNA onto the sediment and the extent to which it preserves the features of past oceanic biota remains unknown. Planktonic foraminifera are the ideal taxa to allow an assessment of the eDNA signal modification during deposition because their fossils are well preserved in the sediment and their morphological taxonomy is documented by DNA barcodes. Specifically, we re-analyze foraminiferal-specific metabarcodes from 31 deep-sea sediment samples, which were shown to contain a small fraction of sequences from planktonic foraminifera. We confirm that the largest portion of the metabarcode originates from benthic bottom-dwelling foraminifera, representing the in situ community, but a small portion (< 10 %) of the metabarcodes can be unambiguously assigned to planktonic taxa. These organisms live exclusively in the surface ocean and the recovered barcodes thus represent an allochthonous component deposited with the rain of organic remains from the surface ocean. We take advantage of the planktonic foraminifera portion of the metabarcodes to establish to what extent the structure of the surface ocean biota is preserved in sedimentary eDNA. We show that planktonic foraminifera DNA is preserved in a range of marine sediment types, the composition of the recovered eDNA metabarcode is replicable and that both the similarity structure and the diversity pattern are preserved. Our results suggest that sedimentary eDNA could preserve the ecological structure of the entire pelagic community, including nonfossilized taxa, thus opening new avenues for paleoceanographic and paleoecological studies.

show abstract

Section: Discussionsupporting

confidence: 81%

Section: Introductionmentioning

confidence: 99%

Planktonic foraminifera-derived environmental DNA extracted from abyssal sediments preserves patterns of plankton macroecology

et al. 2017

Self Cite

View full text Add to dashboard Cite

show abstract

“…Although the detection of ancient DNA in terrestrial (Willerslev et al 2003;Lydolph et al 2005;Haile et al 2009;Hebsgaard et al 2009;Jørgensen et al 2012) and aquatic (Matisoo-Smith et al 2008;Anderson-Carpenter et al 2011;Pedersen et al 2013;Stager et al 2015) sediments as well as frozen ice cores (Willerslev et al 2007) testifies to the fact that eDNA from diverse taxa can remain in the environment for a very long period of time under certain conditions, DNA possesses limited chemical stability (Lindahl 1993); in most cases, as soon as it is shed from an organism eDNA begins to degrade (Fig. 1d).…”

Section: Fate: What Factors Influence Edna Persistence?mentioning

confidence: 99%

The ecology of environmental DNA and implications for conservation genetics

2015

View full text Add to dashboard Cite

Environmental DNA (eDNA) refers to the genetic material that can be extracted from bulk environmental samples such as soil, water, and even air. The rapidly expanding study of eDNA has generated unprecedented ability to detect species and conduct genetic analyses for conservation, management, and research, particularly in scenarios where collection of whole organisms is impractical or impossible. While the number of studies demonstrating successful eDNA detection has increased rapidly in recent years, less research has explored the ''ecology'' of eDNA-myriad interactions between extraorganismal genetic material and its environment-and its influence on eDNA detection, quantification, analysis, and application to conservation and research. Here, we outline a framework for understanding the ecology of eDNA, including the origin, state, transport, and fate of extraorganismal genetic material. Using this framework, we review and synthesize the findings of eDNA studies from diverse environments, taxa, and fields of study to highlight important concepts and knowledge gaps in eDNA study and application. Additionally, we identify frontiers of conservation-focused eDNA application where we see the most potential for growth, including the use of eDNA for estimating population size, population genetic and genomic analyses via eDNA, inclusion of other indicator biomolecules such as environmental RNA or proteins, automated sample collection and analysis, and consideration of an expanded array of creative environmental samples. We discuss how a more complete understanding of the ecology of eDNA is integral to advancing these frontiers and maximizing the potential of future eDNA applications in conservation and research.

show abstract

“…Sedimentary DNA can be used to characterise recent and past biodiversity and thus is suitable to reveal information about past environmental change (Jørgensen et al 2012;Parducci et al 2012;Pedersen et al 2013). A metabarcoding approach to environmental DNA and subsequent DNA sequencing is commonly applied to characterise the composition of communities in environmental samples (Taberlet et al 2012a;Pedersen et al 2015).…”

Section: Introductionmentioning

confidence: 99%

Sedimentary DNA versus morphology in the analysis of diatom-environment relationships

et al. 2016

View full text Add to dashboard Cite

The Arctic treeline ecotone is characterised by a steep vegetation gradient from arctic tundra to northern taiga forests, which is thought to influence the water chemistry of thermokarst lakes in this region. Environmentally sensitive diatoms respond to such ecological changes in terms of variation in diatom diversity and richness, which so far has only been documented by microscopic surveys. We applied next-generation sequencing to analyse the diatom composition of lake sediment DNA extracted from 32 lakes across the treeline in the Khatanga region, Siberia, using a short fragment of the rbcL chloroplast gene as a genetic barcode. We compared diatom richness and diversity obtained from the genetic approach with diatom counts from traditional microscopic analysis. Both datasets were employed to investigate diversity and relationships with environmental variables, using ordination methods. After effective filtering of the raw data, the two methods gave similar results for diatom richness and composition at the genus level (DNA 12 taxa; morphology 19 taxa), even though there was a much higher absolute number of sequences obtained per genetic sample (median 50,278), compared with microscopic counts (median 426). Dissolved organic carbon explained the highest percentage of variance in both datasets (14.2 % DNA; 18.7 % morphology), reflecting the compositional turnover of diatom assemblages along the tundra-taiga transition. Differences between the two approaches are mostly a consequence of the filtering process of genetic data and limitations of genetic references in the database, which restricted the determination of genetically identified sequence types to the genus level. The morphological approach, however, allowed identifications mostly to species level, which permits better ecological interpretation of the diatom data. Nevertheless, because of a rapidly increasing reference database, the genetic approach with sediment DNA will, in the future, enable reliable Electronic supplementary material The online version of this article (doi:10.1007/s10933-016-9926-y) contains supplementary material, which is available to authorized users. 123J Paleolimnol DOI 10.1007/s10933-016-9926-y investigations of diatom composition from lake sediments that will have potential applications in both paleoecology and environmental monitoring.

show abstract

A comparative study of ancient environmental DNA to pollen and macrofossils from lake sediments reveals taxonomic overlap and additional plant taxa

Cited by 106 publications

References 38 publications

Planktonic foraminifera-derived environmental DNA extracted from abyssal sediments preserves patterns of plankton macroecology

Planktonic foraminifera-derived environmental DNA extracted from abyssal sediments preserves patterns of plankton macroecology

The ecology of environmental DNA and implications for conservation genetics

Sedimentary DNA versus morphology in the analysis of diatom-environment relationships

Contact Info

Product

Resources

About