Metabarcoding of marine zooplankton: prospects, progress and pitfalls

Bucklin, Ann; Lindeque, Penelope K.; Rodríguez-Ezpeleta, Naiara; Albaina, Aitor; Lehtiniemi, Maiju

doi:10.1093/plankt/fbw023

Cited by 171 publications

(183 citation statements)

References 53 publications

Supporting

Mentioning

179

Contrasting

Unclassified

Order By: Relevance

“…Each marker comes with advantages and drawbacks (Bucklin et al, 2016). 18S in general is known to underestimate the diversity present at the species level in metabarcoding studies (in metazoans in particular, Tang et al, 2012;Leray and Knowlton, 2016), and several species or even several genera can share the same sequence for the v7 region amplified (Guardiola et al, 2016).…”

Section: Discussionmentioning

confidence: 99%

“…It has been acknowledged that primer bias and differences in copy number of 18S (or mitochondrial abundance in the case of COI) hinder a direct quantitative relationship between number of reads (usually in the form of relative frequency within samples) and biomass of a given MOTU. Nevertheless, most studies analysing this relationship report a gross correlation, in the sense that more abundant species also tend to be represented by a higher relative or absolute number of reads (reviewed in Lejzerowicz et al, 2015;Barnes and Turner, 2016;Valentini et al, 2016;Bucklin et al, 2016). It can be added here that abundance estimation using traditional methods is not free of biases, either (Shelton et al, 2016).…”

Section: Discussionmentioning

confidence: 99%

“…This technique, albeit still subject to some limitations, will likely become a cornerstone in decision making of management bodies in the near future (Kelly et al, 2014a;Danovaro et al, 2016). In the marine realm, eukaryotic diversity has been analysed using metabarcoding in plankton and sediment communities (reviewed in Carugati et al, 2015;Bucklin et al, 2016;Sinniger et al, 2016). These studies aimed at diverse applications, including community description, beta-diversity patterns, impact assessment, or study of ecological interactions, among others (e.g., Bik et al, 2012;Fonseca et al, 2014;Pawlowski et al, 2016;Brannock et al, 2016;Guardiola et al, 2015Guardiola et al, , 2016.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Under the canopy: Community-wide effects of invasive algae in Marine Protected Areas revealed by metabarcoding

Wangensteen

Cebrián

Palacín

et al. 2018

Marine Pollution Bulletin

View full text Add to dashboard Cite

Running title: community-wide effects of invasive algae in MPAs Highlights  Hard-bottom communities dominated by invasive algae were studied with metabarcoding  A size-fractionation method is developed for the metabarcoding of complex samples  A modified primer set is used for the amplification of a COI fragment  A semiquantitave abundance index is proposed for statistical analyses  Results show effects of canopy-forming invasive algae on the underlying communities AbstractWe analysed with multigene (18S and COI) metabarcoding the effects of the proliferation of invasive seaweeds on rocky littoral communities in two Spanish Marine Protected Areas. The invasive algae studied were Caulerpa cylindracea, Lophocladia lallemandii and Asparagopsis armata. They are canopy-forming, landscape-dominant seaweeds, and we were interested in their effects on the underlying communities of meiobenthos and macrobenthos, separated in two size fractions through sieving. A new semiquantitative treatment of metabarcoding data is introduced. The results for both markers showed that the presence of the invasive seaweed had a significant effect on the understory communities for Lophocladia lallemandii and Asparagopsis armata but not for Caulerpa cylindracea. Likewise, changes in MOTU richness and diversity with invasion status varied in magnitude and direction depending on the alga considered. Our results showed that metabarcoding allows monitoring of the less conspicuous, but not least important, effects of the presence of dominant invasive seaweeds.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Under the canopy: Community-wide effects of invasive algae in Marine Protected Areas revealed by metabarcoding

Wangensteen

Cebrián

Palacín

et al. 2018

Marine Pollution Bulletin

View full text Add to dashboard Cite

show abstract

“…This causes a bottleneck in sample throughput because manual sorting and visual identification is labor-intensive and slow. Identification demands a high degree of specialized taxonomic knowledge, such expertise is required for each BQE target separately, and juvenile and cryptic species can nonetheless be misidentified (Bourlat et al, 2013;Aylagas et al, 2014Aylagas et al, , 2016Pawlowski et al, 2014;Carugati et al, 2015;Thomsen and Willerslev, 2015;Bowers et al, 2016;Bucklin et al, 2016;Danovaro et al, 2016). Estimates suggest that between 24 and 98% of marine eukaryotic species are yet to be described (Leray and Knowlton, 2016).…”

Section: Current Limitations In Marine Ecological Quality Assessmentmentioning

confidence: 99%

“…Amplification of 18S rRNA regions is used for a variety of communities, including phytoplankton and other microeukaryotes (Dunthorn et al, 2012;Hugerth et al, 2014;Johnson and Martiny, 2015;del Campo et al, 2016;Giner et al, 2016), and amplification of the 23S rRNA gene is used to classify organisms such as zooplankton (Hirai et al, 2015a;Bucklin et al, 2016). Amplification of mitochondrial DNA is used to identify an assortment of organisms, with cytochrome oxidase I (COI), cytochrome b, and mitochondrial 16S as examples of popularly employed target regions (Dauble et al, 2012;Pawlowski et al, 2014;Cowart et al, 2015;Guo et al, 2015;Harada et al, 2015;Johnson and Martiny, 2015;Aylagas et al, 2016;Bucklin et al, 2016;Creer et al, 2016;Leray and Knowlton, 2016;Thompson et al, 2016;Trivedi et al, 2016). Newer approaches are being used to identify fish (Miya et al, 2015) and marine mammals (Foote et al, 2012;Ma et al, 2016) from seawater samples.…”

Section: Dna Sequencing Applied To Marine Monitoring Technical Contextmentioning

confidence: 99%

DNA Sequencing as a Tool to Monitor Marine Ecological Status

et al. 2017

View full text Add to dashboard Cite

Many ocean policies mandate integrated, ecosystem-based approaches to marine monitoring, driving a global need for efficient, low-cost bioindicators of marine ecological quality. Most traditional methods to assess biological quality rely on specialized expertise to provide visual identification of a limited set of specific taxonomic groups, a time-consuming process that can provide a narrow view of ecological status. In addition, microbial assemblages drive food webs but are not amenable to visual inspection and thus are largely excluded from detailed inventory. Molecular-based assessments of biodiversity and ecosystem function offer advantages over traditional methods and are increasingly being generated for a suite of taxa using a "microbes to mammals" or "barcodes to biomes" approach. Progress in these efforts coupled with continued improvements in high-throughput sequencing and bioinformatics pave the way for sequence data to be employed in formal integrated ecosystem evaluation, including food web assessments, as called for in the European Union Marine Strategy Framework Directive. DNA sequencing of bioindicators, both traditional (e.g., benthic macroinvertebrates, ichthyoplankton) and emerging (e.g., microbial assemblages, fish via eDNA), promises to improve assessment of marine biological quality by increasing the breadth, depth, and throughput of information and by reducing costs and reliance on specialized taxonomic expertise.

show abstract

Divergent patterns of zooplankton connectivity in the epipelagic and mesopelagic zones of the eastern North Pacific

Matthews,

Blanco‐Bercial

2023

Ecology and Evolution

View full text Add to dashboard Cite

Due to historical under‐sampling of the deep ocean, the distributional ranges of mesopelagic zooplankton are not well documented, leading to uncertainty about the mechanisms that shape midwater zooplankton community composition. Using a combination of DNA metabarcoding (18S‐V4 and mtCOI) and trait‐based analysis, we characterized zooplankton diversity and community composition in the upper 1000 m of the northeast Pacific Ocean. We tested whether the North Pacific Transition Zone is a biogeographic boundary region for mesopelagic zooplankton. We also tested whether zooplankton taxa occupying different vertical habitats and exhibiting different ecological traits differed in the ranges of temperature, Chl‐a, and dissolved oxygen conditions inhabited. The depth of the maximum taxonomic richness deepened with increasing latitude in the North Pacific. Community similarity in the mesopelagic zone also increased in comparison with the epipelagic zone, and no evidence was found for a biogeographic boundary between previously delineated mesopelagic biogeochemical provinces. Epipelagic zooplankton exhibited broader temperature and Chl‐a ranges than mesopelagic taxa. Within the epipelagic, taxa with broader temperature and Chl‐a ranges also had broader distributional ranges. However, mesopelagic taxa were distributed across wider dissolved oxygen ranges, and within the mesopelagic, only oxygen ranges covaried with distributional ranges. Environmental and distributional ranges also varied among traits, both for epipelagic taxa and mesopelagic taxa. The strongest differences in both environmental and distributional ranges were observed for taxa with or without diel vertical migration behavior. Our results suggest that species traits can influence the differential effects of physical dispersal and environmental selection in shaping biogeographic distributions.

show abstract

Metabarcoding of marine zooplankton: prospects, progress and pitfalls

Cited by 171 publications

References 53 publications

Under the canopy: Community-wide effects of invasive algae in Marine Protected Areas revealed by metabarcoding

Under the canopy: Community-wide effects of invasive algae in Marine Protected Areas revealed by metabarcoding

DNA Sequencing as a Tool to Monitor Marine Ecological Status

Divergent patterns of zooplankton connectivity in the epipelagic and mesopelagic zones of the eastern North Pacific

Contact Info

Product

Resources

About