Wanted not, wasted not: Searching for non-target taxa in environmental DNA metabarcoding by-catch

Ritter, Camila Duarte; Pont, Giorgi Dal; Stika, Paula Valeska; Horodesky, Aline; Cozer, Nathieli; Netto, Otto Samuel Mader; Henn, Caroline; Ostrensky, Antônio; Pie, Márcio R.

doi:10.1016/j.envadv.2022.100169

Cited by 8 publications

(3 citation statements)

References 35 publications

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“…As with several metabarcoding primers, the MiFish primers are known to amplify other nontarget organismal groups, including mammal and bird species (Ritter et al, 2022). In our study, we further examined those zOTUs that received a poor taxonomic annotation.…”

Section: Reference Database Construction: Specific Considerationsmentioning

confidence: 99%

General principles for assignments of communities from eDNA: Open versus closed taxonomic databases

et al. 2022

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Metabarcoding of environmental DNA (eDNA) is a powerful tool for describing biodiversity, such as finding keystone species or detecting invasive species in environmental samples. Continuous improvements in the method and the advances in sequencing platforms over the last decade have meant this approach is now widely used in biodiversity sciences and biomonitoring. For its general use, the method hinges on a correct identification of taxa. However, past studies have shown how this crucially depends on important decisions during sampling, sample processing, and subsequent handling of sequencing data. With no clear consensus as to the best practice, particularly the latter has led to varied bioinformatic approaches and recommendations for data preparation and taxonomic identification. In this study, using a large freshwater fish eDNA sequence dataset, we compared the frequently used zero-radius Operational Taxonomic Unit (zOTU) approach of our raw reads and assigned it taxonomically (i) in combination with publicly available reference sequences (open databases) or (ii) with an OSU (Operational Sequence Units) database approach, using a curated database of reference sequences generated from specimen barcoding (closed database). We show both approaches gave comparable results for common species. However, the commonalities between the approaches decreased with read abundance and were thus less reliable and not comparable for rare species. The success of the zOTU approach depended on the suitability, rather than the size, of a reference database.Contrastingly, the OSU approach used reliable DNA sequences and thus often enabled species-level identifications, yet this resolution decreased with the recent phylogenetic age of the species. We show the need to include target group coverage, outgroups and full taxonomic annotation in reference databases to avoid misleading annotations that can occur when using short amplicon sizes as commonly used in eDNA metabarcoding studies. Finally, we make general suggestions to improve the construction and use of reference databases for metabarcoding studies in the future.

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Section: Reference Database Construction: Specific Considerationsmentioning

confidence: 99%

General principles for assignments of communities from eDNA: Open versus closed taxonomic databases

et al. 2022

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“…Development of environmental DNA (eDNA) methods and the related bioinformatics analyses has provided researchers with the ability to explore the biodiversity of aquatic communities via eDNA metabarcoding or to detect individual species via quantitative PCR (qPCR) (Cantera et al., 2022; Lacoursière‐Roussel et al., 2016; Laporte et al., 2021; Pilliod et al., 2013; Yang et al., 2021). These approaches, especially eDNA metabarcoding—the sequencing and characterization of all DNA of a given taxonomic group in an environmental sample—are now routinely applied in biodiversity and ecological studies across all types of ecosystems (Boivin‐Delisle et al., 2021; Closek et al., 2019; Czeglédi et al., 2021; Evans et al., 2016; Gamage et al., 2020; García Machado et al., 2022; Golpour et al., 2022; Harper et al., 2019; Hashemzadeh Segherloo, Tabatabaei, Abdolahi‐Mousavi, et al., 2022; McColl‐Gausden et al., 2021; Mena et al., 2021; Newton et al., 2023; Ritter et al., 2022; Roger et al., 2022; Sales et al., 2020; Yonezawa et al., 2020; Zhang et al., 2023). Among its advantages, eDNA is very sensitive, nondestructive, and noninvasive compared to conventional methods.…”

Section: Introductionmentioning

confidence: 99%

eDNA metabarcoding as a means to track distributions of different fish species in a protected area

Tabatabaei,

Hashemzadeh Segherloo,

Abdoli

et al. 2024

Environmental DNA

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In Lar National Park (Caspian Sea basin, Iran), the Caspian trout (Salmo caspius) population faces different threats, including introduced fish species. Due to the harsh environmental conditions and limited accessibility, monitoring of fish species via conventional approaches proves difficult. Hence, environmental DNA metabarcoding may prove an appropriate tool for monitoring fishes within the park. Environmental DNA samples from eight stream sites in the National Park were sequenced via metabarcoding of the 12S rRNA gene, and the species identified via eDNA metabarcoding were compared to the results of electrofishing performed at the same localities on the same day. No significant difference in the number of Caspian Sea trout DNA sequence reads was detected among the collection sites (p > 0.05). The highest number of reads was detected in Dalichay Stream, but the highest population density determined via electrofishing was in Siahpalas Stream. The discrepancy between the eDNA read count and trout population density, as well as the limited sampling scheme within this study, limit our ability to provide a robust conclusion about the application of environmental DNA metabarcoding for assessment of fish density in Lar National Park. Environmental DNA metabarcoding detected more species than electrofishing, but no significant differences in the composition of the local fish community were observed. Introduced fish species were all observed or detected in Siahpalas Stream, which is characterized by high water temperature, muddy substrate, and lower flow rate. A significant effect of flow rate and total dissolved solids on the presence of introduced fish species (p = 0.02) and of flow rate alone on relative abundance of introduced fish species (p = 0.03) was detected. To standardize the application of eDNA metabarcoding as a biodiversity assessment tool in Lar National Park, future studies should characterize the parameters that affect eDNA persistence and detectability in the system.

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“…However, an understanding of the history of environmental DNA analysis by investigators and researchers is required [ 62 ]. Species can be clearly detected in areas where they are not actually present [ 63 ]. Controlling false positives remains a major challenge in environmental DNA analysis [ 64 ].…”

Section: Introductionmentioning

confidence: 99%

Improving the efficiency of adaptive management methods in multiple fishways using environmental DNA

Nakai,

Masumoto,

Asaeda

et al. 2024

PLoS ONE

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Dams and weirs impede the continuity of rivers and transit of migratory fish. To overcome this obstacle, fishways are installed worldwide; however, management after installation is important. The Miyanaka Intake Dam has three fish ladders with different flow velocities and discharges and has been under adaptive management since 2012. Fish catch surveys, conducted as an adaptive management strategy, place a heavy burden on fish. Furthermore, a large number of investigators must be mobilized during the 30-day investigation period. Thus, a monitoring method using environmental DNA that exerts no burden on fish and requires only a few surveyors (to obtain water samples) and an in-house analyst was devised; however, its implementation in a fishway away from the point of analysis and with limited flow space and its effective water sampling frequency have not been reported. Therefore, in 2019, we started a trial aiming to evaluate the methods and application conditions of environmental DNA surveys for the continuous and long-term monitoring of various fish fauna upstream and downstream of the Miyanaka Intake Dam. To evaluate the fish fauna, the results of an environmental DNA survey (metabarcoding method) for 2019 to 2022 were compared to those of a catch survey in the fishway from 2012 to 2022. The results confirmed the use of environmental DNA surveys in evaluating the contribution of fishways to biodiversity under certain conditions and introduced a novel method for sample collection.

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Wanted not, wasted not: Searching for non-target taxa in environmental DNA metabarcoding by-catch

Cited by 8 publications

References 35 publications

General principles for assignments of communities from eDNA: Open versus closed taxonomic databases

General principles for assignments of communities from eDNA: Open versus closed taxonomic databases

eDNA metabarcoding as a means to track distributions of different fish species in a protected area

Improving the efficiency of adaptive management methods in multiple fishways using environmental DNA

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