Origin, dynamics, and implications of extracellular DNA pools in marine sediments

Torti, A.; Lever, Mark A.; Jørgensen, Bo Barker

doi:10.1016/j.margen.2015.08.007

Cited by 267 publications

(295 citation statements)

References 170 publications

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“…The number of chloroplast DNA copies results mainly from the number of chloroplasts per cell and the number of chloroplast genomes per chloroplast, which vary across diatom taxa (Bedoshvili et al 2009). Other aspects regarding taphonomy are the preservation potential of DNA Pedersen et al 2015) versus diatom valves (Ryves et al 2006) and the different representations of DNA versus valves in the various lake habitats, for example caused by different transport characteristics and adsorption of DNA to sediments (Torti et al 2015;Turner et al 2015).…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2016

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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.

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Section: Discussionmentioning

confidence: 99%

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

et al. 2016

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“…Since DNA can be retrieved from both living and senescent cells, and free DNA can persist in the environment (Torti et al, 2015), the RNA-sourced samples were used to investigate potential influence by local conditions. Based on rRNA reads, ciliates, and dinoflagellates were found in all samples (Figure 3, Supplementary Tables 4 and 5), with greater proportions during summer (ca.…”

Section: Seasonal Succession and Distributionmentioning

confidence: 99%

Seasonal and Interannual Changes in Ciliate and Dinoflagellate Species Assemblages in the Arctic Ocean (Amundsen Gulf, Beaufort Sea, Canada)

et al. 2017

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Recent studies have focused on how climate change could drive changes in phytoplankton communities in the Arctic. In contrast, ciliates and dinoflagellates that can contribute substantially to the mortality of phytoplankton have received less attention. Some dinoflagellate and ciliate species can also contribute to net photosynthesis, which suggests that species composition could reflect food web complexity. To identify potential seasonal and annual species occurrence patterns and to link species with environmental conditions, we first examined the seasonal pattern of microzooplankton and then performed an in-depth analysis of interannual species variability. We used high-throughput amplicon sequencing to identify ciliates and dinoflagellates to the lowest taxonomic level using a curated Arctic 18S rRNA gene database. DNA-and RNA-derived reads were generated from samples collected from the Canadian Arctic from November 2007 to July 2008. The proportion of ciliate reads increased in the surface toward summer, when salinity was lower and smaller phytoplankton prey were abundant, while chloroplastidic dinoflagellate species increased at the subsurface chlorophyll maxima (SCM), where inorganic nutrient concentrations were higher. Comparing communities collected in summer and fall from 2003 to 2010, we found that microzooplankton community composition change was associated with the record ice minimum in the summer of 2007. Specifically, reads from smaller predatory species like Laboea, Monodinium, and Strombidium and several unclassified ciliates increased in the summer after 2007, while the other usually summer-dominant dinoflagellate taxa decreased. The ability to exploit smaller prey, which are predicted to dominate the future Arctic, could be an advantage for these smaller ciliates in the wake of the changing climate.

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“…Constituting a significant fraction of the total DNA (Dell' Anno and Danovaro, 2005;Pietramellara et al, 2009;Torti et al, 2015), it is assumed that the taxonomic composition of the free DNA present in the environment reflects the biodiversity of the sample (Ficetola et al, 2008), which would simplify DNA extraction protocols (Pearman et al, 2016) and allow the detection of organisms that are even larger than the sample itself (Foote et al, 2012;Thomsen et al, 2012;Kelly et al, 2014;Davy et al, 2015). Thus, this method appears as a promising costeffective alternative for macroinvertebrate diversity monitoring, but no robust evidence that the entire macroinvertebrate community can be detected using extracellular DNA exists so far.…”

Section: Introductionmentioning

confidence: 99%

Benchmarking DNA Metabarcoding for Biodiversity-Based Monitoring and Assessment

2016

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Characterization of biodiversity has been extensively used to confidently monitor and assess environmental status. Yet, visual morphology, traditionally and widely used for species identification in coastal and marine ecosystem communities, is tedious and entails limitations. Metabarcoding coupled with high-throughput sequencing (HTS) represents an alternative to rapidly, accurately, and cost-effectively analyze thousands of environmental samples simultaneously, and this method is increasingly used to characterize the metazoan taxonomic composition of a wide variety of environments. However, a comprehensive study benchmarking visual and metabarcoding-based taxonomic inferences that validates this technique for environmental monitoring is still lacking. Here, we compare taxonomic inferences of benthic macroinvertebrate samples of known taxonomic composition obtained using alternative metabarcoding protocols based on a combination of different DNA sources, barcodes of the mitochondrial cytochrome oxidase I gene and amplification conditions. Our results highlight the influence of the metabarcoding protocol in the obtained taxonomic composition and suggest the better performance of an alternative 313 bp length barcode to the traditionally 658 bp length one used for metazoan metabarcoding. Additionally, we show that a biotic index inferred from the list of macroinvertebrate taxa obtained using DNA-based taxonomic assignments is comparable to that inferred using morphological identification. Thus, our analyses prove metabarcoding valid for environmental status assessment and will contribute to accelerating the implementation of this technique to regular monitoring programs.

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Origin, dynamics, and implications of extracellular DNA pools in marine sediments

Cited by 267 publications

References 170 publications

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

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

Seasonal and Interannual Changes in Ciliate and Dinoflagellate Species Assemblages in the Arctic Ocean (Amundsen Gulf, Beaufort Sea, Canada)

Benchmarking DNA Metabarcoding for Biodiversity-Based Monitoring and Assessment

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