Comparing environmental DNA collection methods for sampling community composition on marine infrastructure

Alexander, Jason B.; Marnane, Michael J.; McDonald, Justin I.; Lukehurst, Sherralee; Elsdon, Travis S.; Simpson, TiffanyJ. S.; Hinz, Shawn; Bunce, Michael; Harvey, Euan S.

doi:10.1016/j.ecss.2023.108283

Cited by 6 publications

(5 citation statements)

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“…This genetic material includes organismal and extra-organismal DNA from microorganisms and macroorganisms in the form of faeces, shed skin or hair, carcasses and living bodies ( Stewart 2019 ). Using genomic approaches to detect these ‘genetic footprints’ of organism life from environmental samples, for example, water, snow, soil, air or leaf swabs ( Stewart 2019 ), provides an opportunity to increase the detection rate ( Goldberg et al 2016 ) and increase temporal resolution ( Ogram et al 1987 , Pawlowski et al 2020 , Taberlet et al 2012 , Alexander et al 2023 Taberlet et al 2012,) of biological studies. Notably, eDNA analyses surpass conventional methods in terms of precision and resolution (e.g.…”

Section: Introductionmentioning

confidence: 99%

“…The application of eDNA for species composition assessments is flexible depending on the organisms of interest and may function as a general or targeted instrument (e.g. Thomas et al (2019) , Beng and Corlett (2020) , Burian et al (2021) , Carvalho et al (2021) , Alexander et al (2023) ). Targeted analyses aim to identify the presence or absence of a specific focal species (i.e.…”

Section: Introductionmentioning

confidence: 99%

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Environmental DNA-based biodiversity profiling along the Houdong River in north-eastern Taiwan

Lin,

Huang,

Padgett

et al. 2024

BDJ

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This paper describes two datasets: species occurrences, which were determined by environmental DNA (eDNA) metabarcoding and their associated DNA sequences, originating from a research project which was carried out along the Houdong River (猴洞坑), Jiaoxi Township, Yilan, Taiwan. The Houdong River begins at an elevation of 860 m and flows for approximately 9 km before it empties into the Pacific Ocean. Meandering through mountains, hills, plains and alluvial valleys, this short river system is representative of the fluvial systems in Taiwan. The primary objective of this study was to determine eukaryotic species occurrences in the riverine ecosystem through the use of the eDNA analysis. The second goal was, based on the current dataset, to establish a metabarcoding eDNA data template that will be useful and replicable for all users, particularly the Taiwan community. The species occurrence data are accessible at the Global Biodiversity Information Facility (GBIF) portal and its associated DNA sequences have been deposited in the European Nucleotide Archive (ENA) at EMBL-EBI, respectively. A total of 12 water samples from the study yielded an average of 1.5 million reads. The subsequent species identification from the collected samples resulted in the classification of 432 Operational Taxonomic Units (OTUs) out of a total of 2,734. Furthermore, a total of 1,356 occurrences with taxon matches in GBIF were documented (excluding 4,941 incertae sedis, accessed 05-12-2023). These data will be of substantial importance for future species and habitat monitoring within the short river, such as assessment of biodiversity patterns across different elevations, zonations and time periods and its correlation to water quality, land uses and anthropogenic activities. Further, these datasets will be of importance for regional ecological studies, in particular the freshwater ecosystem and its status in the current global change scenarios. The datasets are the first species diversity description of the Houdong River system using either eDNA or traditional monitoring processes.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Environmental DNA-based biodiversity profiling along the Houdong River in north-eastern Taiwan

Lin,

Huang,

Padgett

et al. 2024

BDJ

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“…Port ecosystems have different compartments (water, hard artificial substrates, sediment) that provide different windows on the biodiversity present. 44 , 45 , 46 , 47 , 48 Substrate selection is thus of crucial importance when designing metabarcoding surveys, and the need of analyzing multiple substrates has been proposed. 45 , 47 , 48 However, this is not always logistically feasible or cost-effective, and operational compromises should be sought.…”

Section: Introductionmentioning

confidence: 99%

“… 44 , 45 , 46 , 47 , 48 Substrate selection is thus of crucial importance when designing metabarcoding surveys, and the need of analyzing multiple substrates has been proposed. 45 , 47 , 48 However, this is not always logistically feasible or cost-effective, and operational compromises should be sought. Environmental DNA (eDNA) metabarcoding of filtered water has often been used in these environments 49 , 50 and has proven effective in detecting particular species with specific primers.…”

Section: Introductionmentioning

confidence: 99%

A new sampling device for metabarcoding surveillance of port communities and detection of non-indigenous species

Zarcero,

Antich,

Rius

et al. 2024

iScience

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“…Similarly, the protocol used for barcoding or metabarcoding studies affects the detection and quantification of biodiversity (Deiner et al., 2015). Conclusions based on eDNA studies may be further influenced by a combination of sampling effort (Bessey et al., 2020), sampling depth (Alexander et al., 2023; Andruszkiewicz et al., 2017; Jeunen et al., 2020), sample substrate (Alexander et al., 2023), and the efficiency of the capture, storage, extraction, amplification, and sequencing protocol (Goldberg et al., 2011). These steps may act either singularly or in combination, and the effect of each step can be difficult to disentangle.…”

Section: Introductionmentioning

confidence: 99%

Enhancing environmental DNA metabarcoding from marine ecosystems: Impact of filter type, storage method, and storage time on the assessment of fish alpha and beta diversity

Bizzozzero,

Altermatt,

Cicciarella

et al. 2024

Environmental DNA

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The collection of environmental DNA (eDNA) and subsequent metabarcoding are useful tools for assessing marine fish biodiversity noninvasively. It is of particular importance to evaluate biodiversity in regions that are hard to access and thus less well studied. Sampling and preservation methods tailored to the specific circumstances are required. Aquatic eDNA is often captured on filters made of different materials and pore sizes, and subsequently stored under divergent conditions for varying periods of time. Previous studies on multispecies detection in marine systems have primarily focused on capture and extraction effects. Our study, in contrast, examined the effects of filter type, storage method, and storage time on DNA yield, alpha (i.e., ZOTU richness) and beta diversity (i.e., ZOTU composition) recovered from a marine ecosystem in Shark Bay, Western Australia. We compared two different filter types (cellulose‐nitrate filters with pore sizes of 0.45 μm; glass‐fiber filters with pore sizes of 0.1 μm), two storage methods (preservation in Longmire's solution and drying, respectively), various storage times (30–68 days) on two metabarcoding assays using different fish‐specific primers. Our results showed that storage time decreased DNA yield and affected alpha and beta diversity estimates. Cellulose‐nitrate filters stored in Longmire's solution proved to be the best combination with the smallest decrease in DNA yield, no effect on alpha diversity and consistent community compositions. Storing glass‐fiber filters in Longmire's solution led to a decrease in eDNA yield and alpha diversity estimates with increasing storage time. Furthermore, the largest change in beta diversity for each metabarcode was found for glass‐fiber filters regardless of storage method. Our results highlight the importance of considering storage time and interactions between storage method and filter when analyzing eDNA results, especially when storing samples for an extended time period or comparison of samples stored for different durations.

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Comparing environmental DNA collection methods for sampling community composition on marine infrastructure

Cited by 6 publications

References 50 publications

Environmental DNA-based biodiversity profiling along the Houdong River in north-eastern Taiwan

Environmental DNA-based biodiversity profiling along the Houdong River in north-eastern Taiwan

A new sampling device for metabarcoding surveillance of port communities and detection of non-indigenous species

Enhancing environmental DNA metabarcoding from marine ecosystems: Impact of filter type, storage method, and storage time on the assessment of fish alpha and beta diversity

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