Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods

Pawłowski, Jan; Bruce, Kat; Panksep, Kristel; Aguirre, F.I.; Amafitano, S.; Apothéloz-Perret-Gentil, Laure; Baussant, Thierry; Bouchez, Agnès; Carugati, Laura; Cermakova, Kristina; Cordier, Tristan; Corinaldesi, Cinzia; Costa, Filipe O.; Danovaro, Roberto; Dell’Anno, Antonio; Duarte, Sofia Alexandra Ferreira; Eisendle, Ursula; Ferrari, B.; Frontalini, Fabrizio; Frühe, Larissa; Haegerbaeumer, Arne; Kisand, Veljo; Królicka, Adriana; Lanzén, Anders; Leese, Florian; Lejzerowicz, Franck; Lyautey, Émilie; Maček, Irena; Ságová-Marečková, Markéta; Pearman, John K.; Pochon, Xavier; Stoeck, Thorsten; Vivien, Régis; Weigand, Alexander; Fazi, Stefano

doi:10.1016/j.scitotenv.2021.151783

Cited by 87 publications

(59 citation statements)

References 238 publications

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“…First, it could be related to a faster degradation and/or turn-over rates of eDNA in the sediment, which are determined by the soil and eDNA characteristics, as well as enzymatic and microbial activities (Levy-Booth et al, 2007; Pietramellara et al, 2009; Torti et al, 2015). The overall lower abundance of eDNA in the sediments could also be driven by increased inhibition (Buxton et al, 2017; Pawlowski et al, 2022). Even though we used a specific soil extraction kit for both sediment and filtered water samples, the purification steps in the protocol could still not have been enough to reduce inhibition in the sediment as well as for the water samples.…”

Section: Discussionmentioning

confidence: 99%

Different approaches to processing environmental DNA samples in turbid waters have distinct effects for fish, bacterial and archaea communities

Turba

Thai

Jacobs

2022

Preprint

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Coastal lagoons are an important habitat for endemic and threatened species in California that have suffered impacts from urbanization and increased drought. Environmental DNA has been promoted as a way to aid in the monitoring of biological communities, but much remains to be understood on the biases introduced by different protocols meant to overcome challenges presented by unique systems under study. Turbid water is one methodologic challenge to eDNA recovery in these systems as it quickly clogs filters, preventing timely processing of samples. We investigated biases in community composition produced by two solutions to overcome slow filtration due to turbidity: freezing of water prior to filtration (for storage purposes and long-term processing), and use of sediment (as opposed to water samples). Bias assessments of community composition in downstream eDNA analysis was conducted for two sets of primers, 12S (fish) and 16S (bacteria and archaea). Our results show that freezing water prior to filtration had no effects on community composition for either primer, even when using a filter of larger pore size (3 μm), and therefore it is a viable approach in this system for comparison of water borne fish, bacteria and archaea. However, the 16S primer showed significantly different community composition in sediments compared to water samples, although still recovering eDNA of organisms from the water column. Sediment sample replicates were heterogeneous, and therefore increasing the number of replicates would be recommended for similar habitats.

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Section: Discussionmentioning

confidence: 99%

Different approaches to processing environmental DNA samples in turbid waters have distinct effects for fish, bacterial and archaea communities

Turba

Thai

Jacobs

2022

Preprint

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“…Marine organisms leave traces of their DNA in seawater or sediments, so that the detection of species-specific environmental DNA (eDNA) fragments may represent a noninvasive and sensitive tool to investigate the whole marine biota, from microorganisms to vertebrates [5,[57][58][59]. A major advantage of the eDNA approach is that sampling water or sediments is rapid and easier than other methodologies currently used for assessing biodiversity, and can routinely applied on a large scale [60].…”

Section: Monitoring As An Inventorymentioning

confidence: 99%

Biodiversity Monitoring in Mediterranean Marine Protected Areas: Scientific and Methodological Challenges

et al. 2022

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Biodiversity is a portmanteau word to indicate the variety of life at all levels from genes to ecosystems, but it is often simplistically equated to species richness; the word ecodiversity has thus been coined to address habitat variety. Biodiversity represents the core of the natural capital, and as such needs to be quantified and followed over time. Marine Protected Areas (MPAs) are a major tool for biodiversity conservation at sea. Monitoring of both species and habitat diversity in MPAs is therefore mandatory and must include both inventory and periodic surveillance activities. In the case of inventories, the ideal would be to census all species and all habitats, but while the latter goal can be within reach, the former seems unattainable. Species inventory should be commeasured to investigation effort, while habitat inventory should be based on mapping. Both inventories may profit from suitability spatial modelling. Periodic surveillance actions should privilege conspicuous species and priority habitats. Efficient descriptor taxa and ecological indices are recommended to evaluate environmental status. While it seems obvious that surveillance activities should be carried out with regular recurrence, diachronic inventories and mapping are rarely carried out. Time series are of prime importance to detect marine ecosystem change even in the absence of direct human impacts.

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“…Despite established protocols for sediment DNA-based biodiversity assessments (Fonseca and Lallias, 2016;Fonseca, 2018;Pawlowski et al, 2022) there remain technical considerations when conducting a marine carbon study. eDNA biodiversity assessments require the collection of a sediment sample, extracting the DNA from the sediment with no prior organism separation, followed by polymerase chain reaction (PCR) to create copies of the eDNA (called amplicons).…”

Section: Biomarkersmentioning

confidence: 99%

Sedimentary carbon on the continental shelf: Emerging capabilities and research priorities for Blue Carbon

et al. 2022

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Continental shelf sediments store large amounts of organic carbon. Protecting this carbon from release back into the marine system and managing the marine environment to maximize its rate of accumulation could both play a role in mitigating climate change. For these reasons, in the context of an expanding “Blue Carbon” concept, research interest in the quantity and vulnerability of carbon stored in continental shelf, slope, and deep ocean sediments is increasing. In these systems, carbon storage is physically distant from carbon sources, altered between source and sink, and disturbed by anthropogenic activities. The methodological approaches needed to obtain the evidence to assess shelf sea sediment carbon manageability and vulnerability within an evolving blue carbon framework cannot be transferred directly from those applied in coastal vegetated “traditional” blue carbon habitats. We present a toolbox of methods which can be applied in marine sediments to provide the evidence needed to establish where and when marine carbon in offshore sediments can contribute to climate mitigation, focusing on continental shelf sediments. These methods are discussed in the context of the marine carbon cycle and how they provide evidence on: (i) stock: how much carbon is there and how is it distributed? (ii) accumulation: how rapidly is carbon being added or removed? and (iii) anthropogenic pressures: is carbon stock and/or accumulation vulnerable to manageable human activities? Our toolbox provides a starting point to inform choice of techniques for future studies alongside consideration of their specific research questions and available resources. Where possible, a stepwise approach to analyses should be applied in which initial parameters are analysed to inform which samples, if any, will provide information of interest from more resource-intensive analyses. As studies increasingly address the knowledge gaps around continental shelf carbon stocks and accumulation – through both sampling and modelling – the management of this carbon with respect to human pressures will become the key question for understanding where it fits within the blue carbon framework and within the climate mitigation discourse.

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Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods

Cited by 87 publications

References 238 publications

Different approaches to processing environmental DNA samples in turbid waters have distinct effects for fish, bacterial and archaea communities

Different approaches to processing environmental DNA samples in turbid waters have distinct effects for fish, bacterial and archaea communities

Biodiversity Monitoring in Mediterranean Marine Protected Areas: Scientific and Methodological Challenges

Sedimentary carbon on the continental shelf: Emerging capabilities and research priorities for Blue Carbon

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