18S rRNA V9 metabarcoding for diet characterization: a critical evaluation with two sympatric zooplanktivorous fish species

Albaina, Aitor; Aguirre, Mikel; Abad, David; Santos, M.B.; Estonba, Andone

doi:10.1002/ece3.1986

Cited by 97 publications

(95 citation statements)

References 71 publications

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“…To circumvent this problem, we suggest here a method based on abundance ranks. The semiquantitative or rank-level value of metabarcoding data has been shown in several contexts (e.g., Kelly et al, 2014b;Sun et al, 2015;Abad et al, 2016;Albaina et al, 2016, Hänfling et al, 2016. Our method is expected to filter out potential biases, at the cost of partially sacrificing the quantitative information present.…”

Section: Discussionmentioning

confidence: 97%

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

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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.

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Section: Discussionmentioning

confidence: 97%

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

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“…Although there are methodological limitations (e.g., PCR bias, gene copy numbers), sequence reads provide semi-quantitative information for zooplankton biomass (Lindeque et al, 2013;Hirai et al, 2015a;Albaina et al, 2016;Clarke et al, 2017), which is not directly comparable with the number of individuals in morphological analysis. We nevertheless observed similar seasonal patterns in diversity indexes, abundance-based community structures, and taxonomic compositions between the metagenetic and morphological analyses.…”

Section: Seasonal Changes In Dominant Taxamentioning

confidence: 99%

Cryptic Zooplankton Diversity Revealed by a Metagenetic Approach to Monitoring Metazoan Communities in the Coastal Waters of the Okhotsk Sea, Northeastern Hokkaido

et al. 2017

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Monitoring zooplankton communities is important to understand dynamics in marine ecosystems. However, it is difficult to identify cryptic species and immature stages of zooplankton using morphological classification, which is time-consuming and requires high skill levels. Here, we conducted a metagenetic analysis of the 18S region in 101 zooplankton samples collected weekly throughout 2014 and 2015 at the Okhotsk Tower in Mombetsu, Hokkaido, Japan, and compared the results of this analysis with those provided by morphological analysis. The metagenetic analysis detected 561 molecular taxonomic units (MOTUs), whereas the morphological analysis detected 201 taxonomic groups. Zooplankton communities were dominated by copepods throughout the sampling period; however, non-copepod taxa, which comprised high proportions of both MOTUs (mean 51.1%) and sequence reads (mean 19.1%), were also important. Cryptic diversity detected by the metagenetic analysis was primarily driven by Copepoda and by the larvae of benthic taxa such as Bivalvia, Gastropoda, and Polychaeta. Community structure and diversity varied between periods of warm and cold water, indicating strong correlations with water temperature and thus seasonality. Furthermore, metagenetic analysis revealed detailed seasonal changes in dominant taxa, including larval stages of metazoans with high taxonomic resolutions; these included commercially important organisms such as Japanese scallops. The metagenetic analysis revealed that changes in both water mass and bentho-pelagic interactions sustain ecosystems rich in zooplankton diversity in this area. Metagenetic analysis provides novel insight into zooplankton diversity, and generates massive sequence data that may be used in future research; thus, it is considered an effective tool for monitoring zooplankton communities.

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“…The forward primer 1389F was used in combination with the reverse primer 1510R. This set of primers was developed as a standard marker of marine microbial eukaryotic diversity and has also shown reliable amplification of marine zooplankton assemblages (Pearman et al, 2014;de Vargas et al, 2015;Pearman and Irigoien, 2015;Albaina et al, 2016). All primers had a Roche 454 tag and a 10 bp barcode.…”

Section: Dna Isolation Amplification and Sequencingmentioning

confidence: 99%

Metabarcoding Reveals Seasonal and Temperature-Dependent Succession of Zooplankton Communities in the Red Sea

2017

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Very little is known about the composition and the annual cycle of zooplankton assemblages in the Red Sea, a confined water body characterized by a high biodiversity and endemism but at the same time one of the most understudied areas in the world in terms of marine biodiversity. This high diversity together with the lack of references for several of the groups poses a problem in obtaining basic information on zooplankton seasonal patterns. In the present work, we used high throughput sequencing to examine the temporal and spatial distribution of the zooplankton communities inhabiting the epipelagic zone in the central Red Sea. The analysis of zooplankton assemblages collected at two sites-coastal and offshore-twice a month at several depth strata by using MANTA, Bongo and WP2 nets provides baseline information of the seasonal patterns of the zooplankton community over 1 year. We show that the seasonal fluctuation of zooplankton communities living in the upper 100 m of the water column is driven mainly by the annual changes in seawater temperature. The 18S rRNA gene was used for metabarcoding of zooplankton assemblages revealing 630 metazoan OTUs (97% similarity) in five phyla, highlighting the richness of the Red Sea community. During colder months, communities were characterized by lower richness and higher biomass than communities found during the hot season. Throughout the year the zooplankton communities were dominated by the class Maxillopoda, mainly represented by copepods and class Hydrozoa. The rise in the water temperature favors the appearance of classes Malacostraca, Cephalopoda, Gastropoda, and Saggitoidea. The present study provides essential baseline information for future monitoring and improves our knowledge of the marine ecosystem in the Red Sea while reporting the main environmental variable structuring zooplankton assemblages in this region.

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18S rRNA V9 metabarcoding for diet characterization: a critical evaluation with two sympatric zooplanktivorous fish species

Cited by 97 publications

References 71 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

Cryptic Zooplankton Diversity Revealed by a Metagenetic Approach to Monitoring Metazoan Communities in the Coastal Waters of the Okhotsk Sea, Northeastern Hokkaido

Metabarcoding Reveals Seasonal and Temperature-Dependent Succession of Zooplankton Communities in the Red Sea

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