Environmental DNA metabarcoding primers for freshwater fish detection and quantification: In silico and in tanks

Shu, Lu; Ludwig, Arne; Peng, Zuogang

doi:10.1002/ece3.7658

Cited by 34 publications

(29 citation statements)

References 90 publications

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“…systematically compared 22 fish metabarcoding primer sets using both those methods and found vastly different taxonomic coverages, amplification preferences, discrimination powers, and detected fish communities among the primers, thus providing general guidance for primer selection and also emphasizing the importance of case-by-case evaluation for specific systems. Other studies that have compared various subsets of universal fish primers generally agree that primer performance varies depending on the particular fish community Collins et al, 2019;Evans et al, 2016;Evans, Shirey, et al, 2017;Hänfling et al, 2016;Polanco Fernandez et al, 2021;Shaw et al, 2016;Shu et al, 2021). Joint use of multiple barcodes can help reduce amplification bias associated with individual primers and can generate a more comprehensive total biodiversity profile .…”

Section: How Effective Is Edna For Detecting Fish Diversity?mentioning

confidence: 99%

Fishing for fish environmental DNA: Ecological applications, methodological considerations, surveying designs, and ways forward

et al. 2022

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Vast global declines of freshwater and marine fish diversity and population abundance pose serious threats to both ecosystem sustainability and human livelihoods.Environmental DNA (eDNA)-based biomonitoring provides robust, efficient, and costeffective assessment of species occurrences and population trends in diverse aquatic environments. Thus, it holds great potential for improving conventional surveillance frameworks to facilitate fish conservation and fisheries management. However, the many technical considerations and rapid developments underway in the eDNA arena can overwhelm researchers and practitioners new to the field. Here, we systematically analysed 416 fish eDNA studies to summarize research trends in terms of investigated targets, research aims, and study systems, and reviewed the applications, rationales, methodological considerations, and limitations of eDNA methods with an emphasis on fish and fisheries research. We highlighted how eDNA technology may advance our knowledge of fish behaviour, species distributions, population genetics, community structures, and ecological interactions. We also synthesized the current knowledge of several important methodological concerns, including the qualitative and quantitative power eDNA has to recover fish biodiversity and abundance, and the spatial and temporal representations of eDNA with respect to its sources. To facilitate ecological applications implementing fish eDNA techniques, recent literature was summarized to generate guidelines for effective sampling in lentic, lotic, and marine habitats. Finally, we identified current gaps and limitations, and pointed out newly emerging research avenues for fish eDNA. As methodological optimization and standardization improve, eDNA technology should revolutionize fish monitoring and promote biodiversity conservation and fisheries management that transcends geographic and temporal boundaries.

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Section: How Effective Is Edna For Detecting Fish Diversity?mentioning

confidence: 99%

Fishing for fish environmental DNA: Ecological applications, methodological considerations, surveying designs, and ways forward

et al. 2022

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“…For example, 16S rRNA is most often employed to characterize bacterial communities, ITS is often used for fungi [63], and 18S rRNA is commonly employed for zooplankton [64]. For fishes, primers that amplify a portion of the 12S and 16S rRNA genes seem to provide a compromise between universality and specificity and are commonly used [65][66][67]. Incomplete reference databases also pose obstacles to taxonomic assignments [62,68].…”

Section: Reference Databases and Taxonomic Assignmentsmentioning

confidence: 99%

Comparing eDNA metabarcoding primers for assessing fish communities in a biodiverse estuary

et al. 2022

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Metabarcoding of environmental DNA is increasingly used for biodiversity assessments in aquatic communities. The efficiency and outcome of these efforts are dependent upon either de novo primer design or selecting an appropriate primer set from the dozens that have already been published. Unfortunately, there is a lack of studies that have directly compared the efficacy of different metabarcoding primers in marine and estuarine systems. Here we evaluate five commonly used primer sets designed to amplify rRNA barcoding genes in fishes and compare their performance using water samples collected from estuarine sites in the highly biodiverse Indian River Lagoon in Florida. Three of the five primer sets amplify a portion of the mitochondrial 12S gene (MiFish_12S, 171bp; Riaz_12S, 106 bp; Valentini_12S, 63 bp), one amplifies 219 bp of the mitochondrial 16S gene (Berry_16S), and the other amplifies 271 bp of the nuclear 18S gene (MacDonald_18S). The vast majority of the metabarcoding reads (> 99%) generated using the 18S primer set assigned to non-target (non-fish) taxa and therefore this primer set was omitted from most analyses. Using a conservative 99% similarity threshold for species level assignments, we detected a comparable number of species (55 and 49, respectively) and similarly high Shannon’s diversity values for the Riaz_12S and Berry_16S primer sets. Meanwhile, just 34 and 32 species were detected using the MiFish_12S and Valentini_12S primer sets, respectively. We were able to amplify both bony and cartilaginous fishes using the four primer sets with the vast majority of reads (>99%) assigned to the former. We detected the greatest number of elasmobranchs (six species) with the Riaz_12S primer set suggesting that it may be a suitable candidate set for the detection of sharks and rays. Of the total 76 fish species that were identified across all datasets, the combined three 12S primer sets detected 85.5% (65 species) while the combination of the Riaz_12S and Berry_16S primers detected 93.4% (71 species). These results highlight the importance of employing multiple primer sets as well as using primers that target different genomic regions. Moreover, our results suggest that the widely adopted MiFish_12S primers may not be the best choice, rather we found that the Riaz_12S primer set was the most effective for eDNA-based fish surveys in our system.

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“…The reference database presented herein represents a first step making DNA barcoding of Madagascar’s ichthyofauna widely applicable. By also including 16S sequences for 187 fish species occurring in Madagascar, 88 of which from freshwater habitats, our library also provides a preliminary resource for DNA metabarcoding of environmental DNA (eDNA) samples, for which primers for 12S and 16S rDNA often perform better than those for COI [ 64 ].…”

Section: Resultsmentioning

confidence: 99%

Towards a DNA barcode library for Madagascar’s threatened ichthyofauna

Vences¹,

Stützer²,

Raminosoa

et al. 2022

PLoS ONE

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In order to improve the molecular resources available for conservation management of Madagascar’s threatened ichthyofauna, we elaborated a curated database of 2860 mitochondrial sequences of the mitochondrial COI, 16S and ND2 genes of Malagasy fishes, of which 1141 sequences of freshwater fishes were newly sequenced for this data set. The data set is mostly composed of COI (2015 sequences) while 16S and ND2 sequences from partly the same samples were used to match the COI sequences to reliably identified reference sequences of these genes. We observed COI uncorrected pairwise genetic distances of 5.2‒31.0% (mean 20.6%) among species belonging to different genera, and 0.0‒22.4% (mean 6.4%) for species belonging to the same genus. Deeply divergent mitochondrial lineages of uncertain attribution were found among Malagasy freshwater eleotrids and gobiids, confirming these groups are in need of taxonomic revision. DNA barcodes assigned to introduced cichlids (tilapias) included Coptodon rendallii, C. zillii, Oreochromis aureus (apparently a new country record), O. cf. mossambicus, O. niloticus, and one undetermined species of Oreochromis, with sequences of up to three species found per location. In aplocheiloid killifishes of the genus Pachypanchax, most species from northern Madagascar had only low mitochondrial divergences, three of these species (P. omalonotus, P. patriciae, and P. varatraza) were not reciprocally monophyletic, and one genetically deviant lineage was discovered in a northern locality, suggesting a need for partial taxonomic revision of this genus. While the lack of voucher specimens for most of the samples sequenced herein precludes final conclusions, our first step towards a DNA barcoding reference library of Madagascar’s fishes already demonstrates the value of such a data set for improved taxonomic inventory and conservation management. We strongly suggest further exploration of Madagascar’s aquatic environments, which should include detailed photographic documentation and tissue sampling of large numbers of specimens, and collection of preserved voucher specimens as well as of living fish for the buildup of ex situ assurance populations of threatened species complying with the One Plan Approach proposed by the IUCN SSC Conservation Breeding Specialist Group (CBSG).

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Environmental DNA metabarcoding primers for freshwater fish detection and quantification: In silico and in tanks

Abstract: This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Cited by 34 publications

References 90 publications

Fishing for fish environmental DNA: Ecological applications, methodological considerations, surveying designs, and ways forward

Fishing for fish environmental DNA: Ecological applications, methodological considerations, surveying designs, and ways forward

Comparing eDNA metabarcoding primers for assessing fish communities in a biodiverse estuary

Towards a DNA barcode library for Madagascar’s threatened ichthyofauna

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