Quantifying biodiversity using eDNA from water bodies: General principles and recommendations for sampling designs

Altermatt, Florian; Carraro, Luca; Antonetti, Manuel; Albouy, Camille; Yan, Zhang; Lyet, Arnaud; Zhang, Xiaowei; Pellissier, Loïc

doi:10.1002/edn3.430

Cited by 18 publications

(15 citation statements)

References 73 publications

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“…Our study, while largely unsuccessful for detecting cetacean eDNA, did produce and optimize species-specific primer assays for an additional two cetacean species. Overall, 'one size fits all' is not the best avenue for cetacean eDNA monitoring, and further research should focus on pilot studies to optimize species-specific cetacean methods, including sample techniques, assay design, and analysis techniques (Altermatt et al, 2023). Additionally, as previously suggested…”

Section: Con Clus Ionmentioning

confidence: 94%

Seas the DNA? Limited detection of cetaceans by low‐volume environmental DNA transect surveys

Robinson,

Migneault,

Dracott

et al. 2023

Environmental DNA

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Environmental DNA (eDNA) has begun to show promise as a robust and reproducible tool for monitoring cetaceans in coastal and offshore waters. Some limiting factors preventing the wider application of eDNA for cetacean monitoring includes lack of species‐specific qPCR assays and limited in situ validation. In this study, we determined 15 monitoring stations within cetacean hotspots in Chatham Sound (British Columbia, Canada), from which we collected a combination of visual and acoustic data, and low‐volume eDNA samples (equivalent to ~250 mL seawater). We designed novel eDNA assays for gray whale and Dall's porpoise and validated existing assays for harbor porpoise, killer whale, and humpback whale. Overall, we collected a total of 120 paired eDNA samples across four sampling intervals, 60 preserved with absolute ethanol and 60 preserved with propylene glycol antifreeze. Positive rates for visual (18%) and acoustic (4%) detections were higher than the eDNA detection rate (<3%), with only one sample (antifreeze‐preserved) producing a positive detection for humpback whales at one of the stations. We discuss factors which could have influenced the lack of detections and highlight the need for higher sample volumes and species‐specific sample approaches to improve detection success and confidence in eDNA applicability for cetacean monitoring.

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Section: Con Clus Ionmentioning

confidence: 94%

Seas the DNA? Limited detection of cetaceans by low‐volume environmental DNA transect surveys

Robinson,

Migneault,

Dracott

et al. 2023

Environmental DNA

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“…However, their suitability for very large rivers has only been minimally studied and may be challenged by the sheer extent of river that must be sampled (see also Altermatt et al). 26 The sampling strategy is a fundamental aspect of any ecological research or monitoring procedure and may profoundly affect the results and interpretations. Specifically, the spatial sampling design is crucial in ensuring the accuracy and comprehensiveness of fish eDNA monitoring.…”

Section: ■ Introductionmentioning

confidence: 99%

“…eDNA methods have brought innovation to biomonitoring, − particularly for smaller streams, ponds, and lakes. However, their suitability for very large rivers has only been minimally studied and may be challenged by the sheer extent of river that must be sampled (see also Altermatt et al) . The sampling strategy is a fundamental aspect of any ecological research or monitoring procedure and may profoundly affect the results and interpretations.…”

Section: Introductionmentioning

confidence: 99%

“…Up until now, sampling efforts of eDNA have profoundly varied between studies, ranging from 15 mL to 60 L, , which hinders the comparability of biodiversity estimates. A recent paper proposed adjusting the sampling effort to the size or volume of the aquatic ecosystems with a spatial-explicit river flow model . Moreover, a still neglected aspect is the spatial allocation of sampling locations, especially in medium and large rivers.…”

Section: Introductionmentioning

confidence: 99%

“…A recent paper proposed adjusting the sampling effort to the size or volume of the aquatic ecosystems with a spatial-explicit river flow model. 26 Moreover, a still neglected aspect is the spatial allocation of sampling locations, especially in medium and large rivers. While many studies have started to sample in multiple locations within one site, such as combing samples from the left and right banks, 38,39 a systematic analysis of vertical layers and horizontal locations has not yet been done.…”

Section: ■ Introductionmentioning

confidence: 99%

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Fishing eDNA in One of the World’s Largest Rivers: A Case Study of Cross-Sectional and Depth Profile Sampling in the Yangtze

Zhang,

et al. 2023

Environ. Sci. Technol.

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The world's largest rivers are home to diverse, endemic, and threatened fish species. However, their sheer sizes make large-scale biomonitoring challenging. While environmental DNA (eDNA) metabarcoding has become an established monitoring approach in smaller freshwater ecosystems, its suitability for large rivers may be challenged by the sheer extent of their cross sections (>1 km wide and tens of meters deep). Here, we sampled fish eDNA from multiple vertical layers and horizontal locations from two cross sections of the lower reach of the Yangtze River in China. Over half of the ASVs (amplicon sequence variants) were detected in only a single combination of the vertical layers and horizontal locations, with ∼7% across all combinations. We estimated the need to sample >100 L of water across the cross-sectional profiles to achieve ASV richness saturation, which translates to ∼60 L of water at the species level. No consistent pattern emerged for prioritizing certain depth and horizontal samples, yet we underline the importance of sampling and integrating different layers and locations simultaneously. Our study highlights the significance of spatially stratified sampling and sampling volumes when using eDNA approaches. Specifically, we developed and tested a scalable and broadly applicable strategy that advances the monitoring and conservation of large rivers.

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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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Quantifying biodiversity using eDNA from water bodies: General principles and recommendations for sampling designs

Cited by 18 publications

References 73 publications

Seas the DNA? Limited detection of cetaceans by low‐volume environmental DNA transect surveys

Seas the DNA? Limited detection of cetaceans by low‐volume environmental DNA transect surveys

Fishing eDNA in One of the World’s Largest Rivers: A Case Study of Cross-Sectional and Depth Profile Sampling in the Yangtze

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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