Metabarcoding improves detection of eukaryotes from early biofouling communities: implications for pest monitoring and pathway management

Zaiko, Anastasija; Schimanski, Kate B.; Pochon, Xavier; Hopkins, Grant A.; Goldstien, Sharyn J.; Floerl, Oliver; Wood, Susanna A.

doi:10.1080/08927014.2016.1186165

Cited by 56 publications

(63 citation statements)

References 54 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Most of the past attempts on using metabarcoding for port monitoring have relied on a single sampling method (Borrell et al, 2017;Brown et al, 2016;Grey et al, 2018;Lacoursière-Roussel et al, 2018;Zaiko et al, 2016) and only one evaluated the importance of using different sampling methods (Koziol et al, 2019). In agreement with the latter, our metabarcoding analysis shows that each sampling method recovered a distinct subset of the port community, and that, despite some taxa being expectedly associated with a given sampling F I G U R E 5 Principal component analyses of Hellinger-transformed abundances of OTUs included in the PBBS targeted taxa dataset for COI (a, b) and 18S (c, d).…”

Section: Metabarcoding-based Port Baseline Surveys Require a Combinmentioning

confidence: 99%

“…Recent studies have highlighted the potential of metabarcoding applied to eDNA to perform port biodiversity surveys (Borrell, Miralles, Huu, Mohammed-Geba, & Garcia-Vazquez, 2017;Grey et al, 2018;Lacoursière-Roussel et al, 2018). Yet, very few studies have performed port surveys based on additional sampling substrates (Brown, Chain, Zhan, MacIsaac, & Cristescu, 2016;Zaiko et al, 2016) and only one has compared biodiversity assessments obtained by the different substrates (Koziol et al, 2019). Additionally, few studies have considered the spatial and temporal variability of ports (e.g., eDNA in arctic ports Lacoursière-Roussel et al (2018) and settlement plates in austral temperate port Zaiko et al (2016)) but none has fully evaluated the impact of spatial and temporal variability on all the different communities of a port, which is critical to ensure maximum biodiversity recovery in PBBS.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Considerations for metabarcoding‐based port biological baseline surveys aimed at marine nonindigenous species monitoring and risk assessments

Rey

Basurko

Rodríguez-Ezpeleta

2020

Ecology and Evolution

View full text Add to dashboard Cite

Monitoring introduction and spread of nonindigenous species via maritime transport and performing risk assessments require port biological baseline surveys. Yet, the comprehensiveness of these surveys is often compromised by the large number of habitats present in a port, the seasonal variability, and the time‐consuming morphological approach used for taxonomic identification. Metabarcoding represents a promising alternative for rapid comprehensive port biological baseline surveys, but its application in this context requires further assessments. We applied metabarcoding (based on barcodes of the cytochrome c oxidase subunit I and of the 18S ribosomal RNA gene) to 192 port samples collected (a) from diverse habitats (water column—including environmental DNA and zooplankton, sediment, and fouling structures), (b) at different sites (from inner to outer estuary), and iii) during the four seasons of the year. By comparing the biodiversity metrics derived from each sample group, we show that each sampling method resulted in a distinct community profile and that environmental DNA alone cannot substitute for organismal sampling, and that, although sampling at different seasons and locations resulted in higher observed biodiversity, operational results can be obtained by sampling selected locations and seasons. By assessing the taxonomic composition of the samples, we show that metabarcoding data allowed the detection of previously recorded nonindigenous species as well as to reveal presence of new ones, even if in low abundance. Synthesis and application. Our comprehensive assessment of metabarcoding for port biological baseline surveys sets the basics for cost‐effective, standardized, and comprehensive monitoring of nonindigenous species and for performing risk assessments in ports. This development will contribute to the implementation of the recently entered into force International Convention for the Control and Management of Ships' Ballast Water and Sediments.

show abstract

Section: Metabarcoding-based Port Baseline Surveys Require a Combinmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Considerations for metabarcoding‐based port biological baseline surveys aimed at marine nonindigenous species monitoring and risk assessments

Rey

Basurko

Rodríguez-Ezpeleta

2020

Ecology and Evolution

View full text Add to dashboard Cite

show abstract

“…An increasing number of studies are using metabarcoding to characterize species diversity, or to detect rare or invasive species in environmental samples (Aylagas, Borja, Irigoien, & Rodríguez‐Ezpeleta, ; Brown, Chain, Zhan, MacIsaac, & Cristescu, ; de Vargas et al, ; Pochon, Zaiko, Fletcher, Laroche, & Wood, ; Zaiko et al, ). Unlike targeted approaches, metabarcoding enables many species to be identified simultaneously, and dependent on the approaches used, the taxa may represent multiple trophic levels (Keeley, Wood, & Pochon, ).…”

Section: Introductionmentioning

confidence: 99%

A comparison of droplet digital polymerase chain reaction (PCR), quantitative PCR and metabarcoding for species‐specific detection in environmental DNA

Wood

Pochon

Laroche

et al. 2019

Molecular Ecology Resources

Self Cite

100

View full text Add to dashboard Cite

Targeted species‐specific and community‐wide molecular diagnostics tools are being used with increasing frequency to detect invasive or rare species. Few studies have compared the sensitivity and specificity of these approaches. In the present study environmental DNA from 90 filtered seawater and 120 biofouling samples was analyzed with quantitative PCR (qPCR), droplet digital PCR (ddPCR) and metabarcoding targeting the cytochrome c oxidase I (COI) and 18S rRNA genes for the Mediterranean fanworm Sabella spallanzanii. The qPCR analyses detected S. spallanzanii in 53% of water and 85% of biofouling samples. Using ddPCR S. spallanzanii was detected in 61% of water of water and 95% of biofouling samples. There were strong relationships between COI copy numbers determined via qPCR and ddPCR (water R2 = 0.81, p < .001, biofouling R2 = 0.68, p < .001); however, qPCR copy numbers were on average 125‐fold lower than those measured using ddPCR. Using metabarcoding there was higher detection in water samples when targeting the COI (40%) compared to 18S rRNA (5.4%). The difference was less pronounced in biofouling samples (25% COI, 29% 18S rRNA). Occupancy modelling showed that although the occupancy estimate was higher for biofouling samples (ψ = 1.0), higher probabilities of detection were derived for water samples. Detection probabilities of ddPCR (1.0) and qPCR (0.93) were nearly double metabarcoding (0.57 to 0.27 marker dependent). Studies that aim to detect specific invasive or rare species in environmental samples should consider using targeted approaches until a detailed understanding of how community and matrix complexity, and primer biases affect metabarcoding data.

show abstract

“…In marine environments, some metabarcoding studies have analysed ecological patterns looking for drivers of biodiversity (e.g., Dafforn et al, 2014; Fonseca et al, 2010; Fonseca et al, 2014; Chariton et al, 2015; Lallias et al, 2015; Brannock et al, 2016), while others have explored assessment of human impacts or early surveillance of introduced species (e.g., Bik et al, 2012b; Brannock et al, 2014; Pawlowski et al, 2014b; Lejzerowicz et al, 2015; Pochon et al, 2015; Zaiko et al, 2016). …”

Section: Introductionmentioning

confidence: 99%

Spatio-temporal monitoring of deep-sea communities using metabarcoding of sediment DNA and RNA

Guardiola

Wangensteen

Taberlet

et al. 2016

PeerJ

104

View full text Add to dashboard Cite

We assessed spatio-temporal patterns of diversity in deep-sea sediment communities using metabarcoding. We chose a recently developed eukaryotic marker based on the v7 region of the 18S rRNA gene. Our study was performed in a submarine canyon and its adjacent slope in the Northwestern Mediterranean Sea, sampled along a depth gradient at two different seasons. We found a total of 5,569 molecular operational taxonomic units (MOTUs), dominated by Metazoa, Alveolata and Rhizaria. Among metazoans, Nematoda, Arthropoda and Annelida were the most diverse. We found a marked heterogeneity at all scales, with important differences between layers of sediment and significant changes in community composition with zone (canyon vs slope), depth, and season. We compared the information obtained from metabarcoding DNA and RNA and found more total MOTUs and more MOTUs per sample with DNA (ca. 20% and 40% increase, respectively). Both datasets showed overall similar spatial trends, but most groups had higher MOTU richness with the DNA template, while others, such as nematodes, were more diverse in the RNA dataset. We provide metabarcoding protocols and guidelines for biomonitoring of these key communities in order to generate information applicable to management efforts.

show abstract

Metabarcoding improves detection of eukaryotes from early biofouling communities: implications for pest monitoring and pathway management

Cited by 56 publications

References 54 publications

Considerations for metabarcoding‐based port biological baseline surveys aimed at marine nonindigenous species monitoring and risk assessments

Considerations for metabarcoding‐based port biological baseline surveys aimed at marine nonindigenous species monitoring and risk assessments

A comparison of droplet digital polymerase chain reaction (PCR), quantitative PCR and metabarcoding for species‐specific detection in environmental DNA

Spatio-temporal monitoring of deep-sea communities using metabarcoding of sediment DNA and RNA

Contact Info

Product

Resources

About