Dataset complexity impacts both MOTU delimitation and biodiversity estimates in eukaryotic 18S rRNA metabarcoding studies

Santiago, Alejandro De; Pereira, Tiago José; Mincks, Sarah L.; Bik, Holly M.

doi:10.1002/edn3.255

Cited by 10 publications

(2 citation statements)

References 146 publications

(207 reference statements)

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“…ASVs are sequence clusters obtained by modelling study-speci c error rates to discriminate expected errors from rare diversity represented by sequence variants with low read counts (Callahan et al 2016). We chose ASVs over Operational Taxonomic Units (OTUs) because using a xed similarity threshold to determine taxonomic identity has been shown to in ate diversity estimates (Callahan et al 2017), and it is likely that lineages within Eukaryota have independent evolutionary identity rates (De Santiago et al 2021). The main parameters used in ASV parsing were 30% mismatch allowed for adapter and primer removal, average minimum quality of 30 (Phred 33), minimum sequence length before the alignment of 50 bp, and minimum sequence overlap of 40 bp with up to 2 mismatches (for complete parametrization see Table S2).…”

Section: Methods Edna Collection and Underwater Visual Surveysmentioning

confidence: 99%

eDNA metabarcoding warms up a hotspot of marine biodiversity: revealing underrepresented taxa in visual surveys and historical records from the Gulf of California

Mac Loughlin,

Valdivia-Carrillo,

Valenzuela-Quiñonez

et al. 2024

Mar. Biodivers.

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Environmental DNA (eDNA) metabarcoding is revolutionizing biodiversity monitoring, but comparisons against traditional data are uncommon. We targeted eukaryotes through the 18S barcode ampli ed from water samples at 20 sites from the Gulf of California (GC), and contrasted eDNA against 316 simultaneous visual surveys and a historical database with over 5k species. From 61k Ampli ed Sequence Variants, we identi ed 850 eukaryotic families, of which half represent new compiled records, including 174 families of planktonic, benthic, and parasitic invertebrates. eDNA revealed many overseen taxa, highlighting higher taxonomic ranks within micro invertebrates, microscopic fungi, and other micro eukaryotes from the supergroups Stramenopiles, Alveolata, and Rhizaria. The database combining all methods has doubled the number of distinct phyla, classes and orders compared to the historical baseline, indicating biodiversity levels in the GC are much higher than previously assumed. The estimated proportion of historical taxa included in public reference databases was only 18% for species, explaining the small portion of eDNA reads that were taxonomically assigned to species level (13%). Each method showed different taxonomic biases, with eDNA missing vertebrates, visual surveys targeting only seven phyla, and the historical records focusing on macroinvertebrates, sh and algae. Although all methods recovered the main known biogeographic regionalization, eDNA data did not support the historical pattern of higher diversity in the Central than Northern GC. While combining methods provides a novel view of biodiversity that is much more comprehensive than any individual approach, our study highlights many challenges in synthesizing biodiversity data from traditional and novel sources.

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Section: Methods Edna Collection and Underwater Visual Surveysmentioning

confidence: 99%

eDNA metabarcoding warms up a hotspot of marine biodiversity: revealing underrepresented taxa in visual surveys and historical records from the Gulf of California

Mac Loughlin,

Valdivia-Carrillo,

Valenzuela-Quiñonez

et al. 2024

Mar. Biodivers.

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“…Although denoising greatly lowers the fraction of spurious features (e.g. de Santiago et al, 2022), in some contexts it may be difficult to separate noise from a real signal in low abundant ASVs. For example, the denoising process might discard some rare taxa, that is, ASVs with a low number of sequences (Edgar, 2016b; Nearing et al, 2018).…”

Section: Basic Structure Of a Metabarcoding Pipelinementioning

confidence: 99%

A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses

Hakimzadeh,

Abdala Asbun,

Albanese

et al. 2023

Molecular Ecology Resources

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Environmental DNA (eDNA) metabarcoding has gained growing attention as a strategy for monitoring biodiversity in ecology. However, taxa identifications produced through metabarcoding require sophisticated processing of high‐throughput sequencing data from taxonomically informative DNA barcodes. Various sets of universal and taxon‐specific primers have been developed, extending the usability of metabarcoding across archaea, bacteria and eukaryotes. Accordingly, a multitude of metabarcoding data analysis tools and pipelines have also been developed. Often, several developed workflows are designed to process the same amplicon sequencing data, making it somewhat puzzling to choose one among the plethora of existing pipelines. However, each pipeline has its own specific philosophy, strengths and limitations, which should be considered depending on the aims of any specific study, as well as the bioinformatics expertise of the user. In this review, we outline the input data requirements, supported operating systems and particular attributes of thirty‐two amplicon processing pipelines with the goal of helping users to select a pipeline for their metabarcoding projects.

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Ebbs and Flows of Marine Biodiversity: Navigating Spatiotemporal Patterns of Environmental DNA in a Coastal Tidal Ecosystem

Scriver,

von Ammon,

Pochon

et al. 2024

Environmental DNA

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Environmental DNA (eDNA) offers an efficient approach to biodiversity monitoring and biosecurity surveillance in coastal ecosystems. Understanding eDNA dynamics in tidal areas is critical for guiding sampling strategy design and interpreting molecular detection results. In a field study conducted at Ōpua, Bay of Islands, Aotearoa, New Zealand, an international marina with a dynamic coastal environment, we investigated eDNA detection patterns across a local spatial and temporal gradient. Hourly samples were collected from six sampling stations around the marina, from artificial shore structures and a channel, over a 12‐h tidal cycle. Detected eukaryotic communities were assessed using eDNA metabarcoding analysis of the small‐subunit ribosomal RNA (18S rRNA) and mitochondrial Cytochrome C Oxidase subunit I (COI) genes. This core community was screened for marine nonindigenous species (NIS) using an online metabarcoding data screening app (ExPAT). Community composition varied significantly based on sampling location and time, with most of the core community captured around mid‐tide. The NIS community exhibited inconsistent detection for some species (e.g., the amphipod Monocorophium acherusicum) across space and time, whereas other NIS (e.g., the mussel Arcuatula senhousia) were consistently detected and behaved similar to the core community. Overall, species‐specific eDNA detection patterns may be linked to the biology and movement of the organism. The results indicated slightly higher NIS detection from artificial structures at the shore stations and within 2 h of low tide. For marine biosecurity applications, users may want to prioritize sampling near‐shore during low tide, while samples collected during mid‐tide may provide more comprehensive insights into the core community for biomonitoring. Further field studies across multiple tidal cycles and marinas may guide the standardization of molecular biomonitoring and biosurveillance sampling strategies and support their broader integration into marine biosecurity programs.

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Dataset complexity impacts both MOTU delimitation and biodiversity estimates in eukaryotic 18S rRNA metabarcoding studies

Abstract: This is an open access article under the terms of the Creat ive Commo ns Attri bution-NonCo mmercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.

Cited by 10 publications

References 146 publications

eDNA metabarcoding warms up a hotspot of marine biodiversity: revealing underrepresented taxa in visual surveys and historical records from the Gulf of California

eDNA metabarcoding warms up a hotspot of marine biodiversity: revealing underrepresented taxa in visual surveys and historical records from the Gulf of California

A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses

Ebbs and Flows of Marine Biodiversity: Navigating Spatiotemporal Patterns of Environmental DNA in a Coastal Tidal Ecosystem

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