The effect of tides on nearshore environmental DNA

Kelly, Ryan P.; Gallego, Ramón; Jacobs-Palmer, Emily

doi:10.7717/peerj.4521

Cited by 106 publications

(123 citation statements)

References 36 publications

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“…It has previously been suggested that many animal lineages remain unsampled and/or unsequenced, potentially even harboring novel phyla (López-escardó et al, 2018;Nguyen et al, 2019). All sampling methods are subject to methodological limitations, and different sampling methods will capture different subsets of biodiversity (Kelly et al, 2017;Shelton et al, 2016). Like more traditional survey methods, eDNA metabarcoding has a certain level of taxonomic selectivity, which may be the result of primer bias.…”

Section: Discussionmentioning

confidence: 99%

“…as of yet, been scarce (Cowart, Murphy, & Cheng, 2017;Djurhuus et al, 2017;Drummond et al, 2015;Günther, Knebelsberger, Neumann, Laakmann, & Martínez Arbizu, 2018;Kelly, Gallego, & Jacobs-Palmer, 2017;Villarino et al, 2018); the majority of these have relied on ribosomal markers, such as 18S Guardiola et al, 2015;Lindeque et al, 2013), 16S , and 12S (Miya et al, 2015), but due to their relatively conserved sequences, it is often impossible to distinguish taxa at the species, genus, or even family level (Tang et al, 2012), which represents a significant limitation to the evaluation of community changes and the biological and/or environmental mechanisms responsible for these changes (Mackas & Beaugrand, 2010).…”

Section: Studies Targeting Marine Eukaryotic Community Diversity Havementioning

confidence: 99%

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Biodiversity assessment of tropical shelf eukaryotic communities via pelagic eDNA metabarcoding

Bakker

Wangensteen

Baillie

et al. 2019

Ecology and Evolution

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Our understanding of marine communities and their functions in an ecosystem relies on the ability to detect and monitor species distributions and abundances. Currently, the use of environmental DNA (eDNA) metabarcoding is increasingly being applied for the rapid assessment and monitoring of aquatic species. Most eDNA metabarcoding studies have either focussed on the simultaneous identification of a few specific taxa/groups or have been limited in geographical scope. Here, we employed eDNA metabarcoding to compare beta diversity patterns of complex pelagic marine communities in tropical coastal shelf habitats spanning the whole Caribbean Sea. We screened 68 water samples using a universal eukaryotic COI barcode region and detected highly diverse communities, which varied significantly among locations, and proved good descriptors of habitat type and environmental conditions. Less than 15% of eukaryotic taxa were assigned to metazoans, most DNA sequences belonged to a variety of planktonic “protists,” with over 50% of taxa unassigned at the phylum level, suggesting that the sampled communities host an astonishing amount of micro‐eukaryotic diversity yet undescribed or absent from COI reference databases. Although such a predominance of micro‐eukaryotes severely reduces the efficiency of universal COI markers to investigate vertebrate and other metazoans from aqueous eDNA, the study contributes to the advancement of rapid biomonitoring methods and brings us closer to a full inventory of extant marine biodiversity.

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Section: Discussionmentioning

confidence: 99%

Section: Studies Targeting Marine Eukaryotic Community Diversity Havementioning

confidence: 99%

Biodiversity assessment of tropical shelf eukaryotic communities via pelagic eDNA metabarcoding

Bakker

Wangensteen

Baillie

et al. 2019

Ecology and Evolution

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“…Encouragingly, Harper et al (2018) demonstrated that Triturus cristatus (great crested newt) detection via metabarcoding with no threshold is equivalent to qPCR with a stringent detection threshold. eDNA metabarcoding has also been applied to large-scale investigations of spatial or temporal variation in marine and freshwater communities, with some studies indicating that communities can be distinguished from 100 m to 2 km due to stream discharge or tidal patterns Kelly, Gallego, & Jacobs-Palmer, 2018;Li, Evans, et al, 2018;O'Donnell et al, 2017;Port et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Limited dispersion and quick degradation of environmental DNA in fish ponds inferred by metabarcoding

Handley

Harper

et al. 2019

Environmental DNA

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Background Environmental DNA (eDNA) metabarcoding is a promising tool for rapid, non‐invasive biodiversity monitoring. Aims In this study, eDNA metabarcoding is applied to explore the spatial and temporal distribution of fish communities in two aquaculture ponds and to evaluate the detection sensitivity of this tool for low‐density species alongside highly abundant species. Materials & Methods This study was carried out at two artificially stocked ponds with a high fish density following the introduction and removal of two rare fish species. Results & Discussion When two rare species were introduced and kept at a fixed location in the ponds, eDNA concentration (i.e., proportional read counts abundance) of the introduced species typically peaked after two days. The increase in eDNA concentration of the introduced fish after 43 hrs may have been caused by increased eDNA shedding rates as a result of fish being stressed by handling, as observed in other studies. Thereafter, it gradually declined and stabilised after six days. These findings are supported by the highest community dissimilarity of different sampling positions being observed on the second day after introduction, which then gradually decreased over time. On the sixth day, there was no longer a significant difference in community dissimilarity between sampling days. The introduced species were no longer detected at any sampling positions on 48 hrs after removal from the ponds. eDNA is found to decay faster in the field than in controlled conditions, which can be attributed to the complex effects of environmental conditions on eDNA persistence or resulting in the vertical transport of intracellular DNA and the extracellular DNA absorbed by particles in the sediment. The eDNA signal and detection probability of the introduced species were strongest near the keepnets, resulting in the highest community variance of different sampling events at this position. Thereafter, the eDNA signal significantly decreased with increasing distance, although the signal increased slightly again at 85 m position away from the keepnets. Conclusions Collectively, these findings reveal that eDNA distribution in lentic ecosystems is highly localised in space and time, which adds to the growing weight of evidence that eDNA signal provides a good approximation of the presence and distribution of species in ponds. Moreover, eDNA metabarcoding is a powerful tool for detection of rare species alongside more abundant species due to the use of generic PCR primers, and can enable monitoring of spatial and temporal community variance.

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“…To counteract the inclusion of these organisms into our analysis, we specifically excluded from the analysis any aeDNA from groups with no marine representatives, since our primary interest was to describe the in situ coral reef community. However, lateral mixing may still occur through local currents that transport DNA across reef habitats or sites (Kelly, Gallego, & Jacobs-Palmer, 2018). Moreover, we have presented data from just two sediment cores as a proof of concept; given the different patterns exhibited by PAN1 and PAN3, more replication at the level of cores should increase confidence in the strength of our approach.…”

Section: Limitationsmentioning

confidence: 85%

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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The effect of tides on nearshore environmental DNA

Cited by 106 publications

References 36 publications

Biodiversity assessment of tropical shelf eukaryotic communities via pelagic eDNA metabarcoding

Biodiversity assessment of tropical shelf eukaryotic communities via pelagic eDNA metabarcoding

Limited dispersion and quick degradation of environmental DNA in fish ponds inferred by metabarcoding

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

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