Advances in metabarcoding techniques bring us closer to reliable monitoring of the marine benthos

Abstract

1. Reliable and accurate biodiversity census methods are essential for monitoring ecosystem health and assessing potential ecological impacts of future development projects. Although metabarcoding is increasingly used to study biodiversity across ecological research, morphology-based identification remains the preferred approach for marine ecological impact assessments. Comparing metabarcoding to morphology-based protocols currently used by ecological surveyors is essential to determine whether this DNA-based approach is suitable for long-term monitoring of the marine ecosystems. 2. We compared metabarcoding and morphology-based approaches for the analysis of invertebrates in low diversity intertidal marine sediment samples. We used a recently developed bioinformatics pipeline and two taxonomic assignment methods to resolve and assign amplicon sequence variants (ASVs) from Illumina amplicon data. We analysed the community composition recovered by both methods and tested the effects, on the levels of diversity detected by the metabarcoding method, of sieving samples prior to DNA extraction. 3. Metabarcoding of the mitochondrial marker cytochrome c oxidase I (COI) gene recovers the presence of more taxonomic groups than the morphological approach. We found that sieving samples results in lower alpha diversity detected and suggests a community composition that differs significantly from that suggested by un-sieved samples in our metabarcoding analysis. We found that while metabarcoding and morphological approaches detected similar numbers of species, they are unable to identify the same set of species across samples. 4. Synthesis and applications. We show that metabarcoding using the cytochrome c oxidase I (COI) marker provides a more holistic, community-based, analysis of benthic invertebrate diversity than a traditional morphological approach. We also highlight current gaps in reference databases and bioinformatic pipelines for the identification of intertidal benthic invertebrates that need to be addressed before metabarcoding can replace traditional methods. Ultimately, with these limitations taken into consideration, resolving community-wide diversity patterns with metabarcoding could improve the management of non-protected marine habitats in the United Kingdom.

To denoise or to cluster? That is not the question. Optimizing pipelines for COI metabarcoding and metaphylogeography

“…The idea that denoising should be used instead of clustering has been followed by some (e.g., Tapolczai et al 2019, Steyaert et al 2020, Zamora-Terol et al 2020, Pearman et al 2020, while other authors have combined the two approaches (e.g., Brandt et al 2020, Nguyen et al 2020, Laroche et al 2020. Indeed, denoising has the advantages of reducing the dataset and to ease pooling or comparing studies, which is necessary in long term biomonitoring applications.…”

eDNA metabarcoding of small plankton samples to detect fish larvae and their preys from Atlantic and Pacific waters

“…In the past decade, there has been a growing interest in the use of high throughput sequencing (HTS) techniques that obtain millions of DNA sequences from water samples (environmental DNA or eDNA) representing the biota inhabiting those waters. The new methods of HTS on environmental samples, generically called metabarcoding, can help in species detection and inventory, as has been proven for Polarstern ballast water 13 – 15 , open waters 16 , estuaries 17 , marine benthos 18 and biofouling communities 19 , among others. They are employed for prokaryotes and some specific taxonomic groups like ciliates, in large oceanic expeditions like Tara Oceans 20 , 21 , but have been less applied for whole eukaryotic communities, and very little to target zooplankton fish prey, to our knowledge.…”

Combining Traditional Taxonomy and Metabarcoding: Assemblage Structure of Nematodes in the Shelf Sediments of the Eastern Antarctic Peninsula

“…While morphological identification is still a common practice used in meiofauna diversity assessments, the development of molecular techniques as high throughput sequencing (HTS) has opened the possibility to analyze a larger set of samples in a much shorter timeframe, often resulting in faster and more reliable analysis (Brannock et al, 2018;Steyaert et al, 2020). Molecular approaches can overcome some of the limitations of microscope-based identification: for example, the detection of cryptic species (i.e., individuals with same morphological features but different DNA sequences) is not possible based solely on morphological identification.…”

“…Disadvantages of the molecular analysis for species identification mainly lie in the incompleteness of online databases used to assign the taxonomical label to a specific DNA sequence and the need to find the right marker for a specific community (Ahmed et al, 2015). Nevertheless, many studies of the last decade have proven this approach to be particularly useful when dealing with such abundant organisms as nematodes, particularly by means of DNA metabarcoding and the use of Amplicon Sequence Variants (ASVs) (Macheriotou et al, 2020;Steyaert et al, 2020).…”