Inès Barrenechea Angeles

UiT The Arctic University of Norway

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Jan Pawłowski

University of Geneva

Ngoc‐Loi Nguyen

Polish Academy of Sciences

Franck Lejzerowicz

University of Oslo

Tristan Cordier

NORCE Norwegian Research Centre

Maria Holzmann

University of Geneva

Raphaël Morard

University of Bremen

Andrew J. Gooday

National Oceanography Centre

Daniel Arizteguí

University of Geneva

Ewa Demianiuk

Institute of Paleobiology

Wojciech Majewski

Polish Academy of Sciences

Cooperative Institutions

Centre National de la Recherche Scientifique

University of Geneva

Stazione Zoologica Anton Dohrn

University of Urbino

UiT The Arctic University of Norway

Polish Academy of Sciences

Universität Hamburg

National Agency for New Technologies, Energy and Sustainable Economic Development

Station Biologique de Roscoff

Sorbonne Université

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Metabarcoding reveals high diversity of benthic foraminifera linked to water masses circulation at coastal Svalbard

Geobiology (2022)

Ngoc‐Loi Nguyen Joanna Pawłowska Inès Barrenechea Angeles Marek Zajączkowski Jan Pawłowski

Arctic marine biodiversity is undergoing rapid changes due to global warming and modifications of oceanic water masses circulation. These changes have been demonstrated in the case of mega- and macrofauna, but much less is known about their impact on the biodiversity of smaller size organisms, such as foraminifera that represent a main component of meiofauna in the Arctic. Several studies analyzed the distribution and diversity of Arctic foraminifera. However, all these studies are based exclusively on the morphological identification of specimens sorted from sediment samples. Here, we present the first assessment of Arctic foraminifera diversity based on metabarcoding of sediment DNA samples collected in fjords and open sea areas in the Svalbard Archipelago. We obtained a total of 5,968,786 reads that represented 1384 amplicon sequence variants (ASVs). More than half of the ASVs (51.7%) could not be assigned to any group in the reference database suggesting a high genetic novelty of Svalbard foraminifera. The sieved and unsieved samples resolved comparable communities, sharing 1023 ASVs, comprising over 97% of reads. Our analyses show that the foraminiferal assemblage differs between the localities, with communities distinctly separated between fjord and open sea stations. Each locality was characterized by a specific assemblage, with only a small overlap in the case of open sea areas. Our study demonstrates a clear pattern of the influence of water masses on the structure of foraminiferal communities. The stations situated on the western coast of Svalbard that are strongly influenced by warm and salty Atlantic water (AW) are characterized by much higher diversity than stations in the northern and eastern part, where the impact of AW is less pronounced. This high diversity and specificity of Svalbard foraminifera associated with water mass distribution indicate that the foraminiferal metabarcoding data can be very useful for inferring present and past environmental conditions in the Arctic.

Circulation (fluid dynamics)

10.1111/gbi.12530

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Citations (8)

Distribution patterns of foraminifera of Northwest Atlantic analyzed using metabarcoding and morphological approaches

EGU General Assembly Conference Abstracts (2019)

Inès Barrenechea Angeles Raphaël Morard Franck Lejzerowicz Tristan Cordier Stephan Mulitza

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BFR2: a curated ribosomal reference dataset for benthic foraminifera

Scientific Data (2024)

Maria Holzmann Ngoc‐Loi Nguyen Inès Barrenechea Angeles Jan Pawłowski

Abstract Benthic foraminifera are one of the major groups of marine protists that also occur in freshwater and terrestrial habitats. They are widely used to monitor current and past environmental conditions. Over the last three decades, thousands of DNA sequences have been obtained from benthic foraminiferal isolates. The results of this long-term effort are compiled here in the form of the first curated benthic foraminiferal ribosomal reference dataset (BFR2). The present dataset contains over 5000 sequences of a fragment of the 18S rDNA gene, which is recognized as the DNA barcode of foraminifera. The sequences represent 279 species and 204 genera belonging to 91 families. Thirteen percent of these sequences have not been assigned to any morphologically described group and may represent species new to science. Furthermore, forty-five percent of the sequences have not been previously published. The BFR 2 dataset aims to collect all DNA barcodes of benthic foraminifera and to provide a much-needed reference dataset for the rapidly developing field of molecular foraminiferal studies.

Barcode

DNA Barcoding

Environmental DNA

Benthic Habitat

10.1038/s41597-024-04137-8

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Citations (1)

Assessing the ecological quality status of the highly polluted Bagnoli area (Tyrrhenian Sea, Italy) using foraminiferal eDNA metabarcoding

The Science of The Total Environment (2021)

M. Cavaliere Inès Barrenechea Angeles Marina Montresor Carla Bucci Lorenzo Brocani

Bioindicator

Environmental DNA

10.1016/j.scitotenv.2021.147871

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Citations (35)

Assigning the unassigned: A signature-based classification of rDNA metabarcodes reveals new deep-sea diversity

PLoS ONE (2024)

Inès Barrenechea Angeles Ngoc‐Loi Nguyen Mattia Greco Koh Siang Tan Jan Pawłowski

Environmental DNA metabarcoding reveals a vast genetic diversity of marine eukaryotes. Yet, most of the metabarcoding data remain unassigned due to the paucity of reference databases. This is particularly true for the deep-sea meiofauna and eukaryotic microbiota, whose hidden diversity is largely unexplored. Here, we tackle this issue by using unique DNA signatures to classify unknown metabarcodes assigned to deep-sea foraminifera. We analyzed metabarcoding data obtained from 311 deep-sea sediment samples collected in the Clarion-Clipperton Fracture Zone, an area of potential polymetallic nodule exploitation in the Eastern Pacific Ocean. Using the signatures designed in the 37F hypervariable region of the 18S rRNA gene, we were able to classify 802 unassigned metabarcodes into 61 novel lineages, which have been placed in 27 phylogenetic clades. The comparison of new lineages with other foraminiferal datasets shows that most novel lineages are widely distributed in the deep sea. Five lineages are also present in the shallow-water datasets; however, phylogenetic analysis of these lineages separates deep-sea and shallow-water metabarcodes except in one case. While the signature-based classification does not solve the problem of gaps in reference databases, this taxonomy-free approach provides insight into the distribution and ecology of deep-sea species represented by unassigned metabarcodes, which could be useful in future applications of metabarcoding for environmental monitoring.

Environmental DNA

Phylogenetic diversity

10.1371/journal.pone.0298440

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An Integrative Taxonomic Survey of Benthic Foraminiferal Species (Protista, Rhizaria) from the Eastern Clarion-Clipperton Zone

Journal of Marine Science and Engineering (2023)

Oceanne Himmighofen Maria Holzmann Inès Barrenechea Angeles Jan Pawłowski Andrew J. Gooday

The abyssal Pacific Clarion Clipperton Zone (CCZ) hosts vast, commercially valuable seafloor deposits of polymetallic nodules. Foraminifera (testate protists) dominate benthic communities in this region. Here, we present a taxonomic survey, combining morphological and genetic data and focussing on mainly meiofauna-sized Foraminifera from the eastern CCZ. Sequences obtained from >100 specimens, the majority photographically documented, were analysed phylogenetically. Most were single-chambered Monothalamea (‘monothalamids’), a high percentage of them squatters inhabiting empty tests of mainly multi-chambered Foraminifera. The first sequences for the monothalamid genus Storthosphaera were obtained, while specimens assigned to Gloiogullmia, Hippocrepinella and Vanhoeffenella yielded new sequences. Among multichambered taxa, high-throughput Illumina sequencing (HTS) revealed a second haplotype of the calcareous rotaliid Oridorsalis umbonatus, possibly representing a distinct species. Additional HTS sequences were obtained from the rotaliids Nuttallides umbonifer and Globocassidulina subglobosa, confirming their wide distributions. We also obtained the first sequences for Cribrostomoides subglobosa, showing that it branches separately from other members of this genus. The fact that many sequences did not correspond to known morphospecies reflects the scarcity of reference barcodes for deep-sea Foraminifera, particularly the poorly known but highly diverse monothalamids. We recommend using HTS of single specimens to reveal further unknown species. Despite extensive research, much remains to be learnt about the true scale of foraminiferal biodiversity in the CCZ.

Incertae sedis

10.3390/jmse11112038

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New xenophyophores (Foraminifera, Monothalamea) from the eastern Clarion-Clipperton Zone (equatorial Pacific)

Zootaxa (2024)

Andrew J. Gooday Maria Holzmann Inès Barrenechea Angeles S. L. Lim Jan Pawłowski

Xenophyophores are large, agglutinated foraminifera that dominate the benthic megafauna in some parts of the deep sea. Here, we describe an assemblage of largely fragmentary specimens from the Clarion-Clipperton Zone (CCZ), an area of the eastern abyssal Pacific hosting large, commercially significant deposits of polymetallic nodules. We recognised 18 morphospecies of which eight yielded DNA sequences. These include two new genera and three new species, Claraclippia seminuda gen. & sp. nov., Stereodiktyoma mollis gen. & sp. nov., and Aschemonella tani sp. nov., three that are assigned to known species, Abyssalia foliformis, Aschemonella monilis and Shinkaiya contorta, and two assigned to open nomenclature forms Abyssalia aff. foliformis and Stannophyllum aff. granularium. An additional ten forms are represented only by morphology. The following seven are placed in known genera, species and open-nomenclature forms: Aschemonella? sp., Homogammina sp., Psammina multiloculata, P. aff. multiloculata, P. aff. limbata form 1 sensu Gooday et al., 2018, P. aff. limbata form 2 sensu Gooday et al., 2018, and Stannophyllum spp. The other three could not be identified to genus level. This new collection brings the total of described and undescribed species and morphotypes from the CCZ to 27 and 70, respectively, reinforcing the already high diversity of xenophyophores known from this part of the Pacific.

Sensu

Incertae sedis

Abyssal zone

10.11646/zootaxa.5419.2.1

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Citations (2)

Supplementary material to "Sedimentary ancient DNA insights into foraminiferal diversity near the grounding line in the western Ross Sea, Antarctica"

Ewa Demianiuk Mateusz Baca Danijela Popović Inès Barrenechea Angeles Ngoc‐Loi Nguyen

10.5194/egusphere-2024-2824-supplement

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Benthic foraminiferal DNA metabarcodes significantly vary along a gradient from abyssal to hadal depths and between each side of the Kuril-Kamchatka trench

Progress In Oceanography (2019)

Tristan Cordier Inès Barrenechea Angeles Franck Lejzerowicz Emanuela Reo Jan Pawłowski

Abyssal zone

Benthos

Abyssal plain

10.1016/j.pocean.2019.102175

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Citations (27)

Encapsulated in sediments: eDNA deciphers the ecosystem history of one of the most polluted European marine sites

Environment International (2023)

Inès Barrenechea Angeles Maria Lorena Romero-Martínez Marco Cavaliere Stefano Varrella Fabio Francescangeli

The Anthropocene is characterized by dramatic ecosystem changes driven by human activities. The impact of these activities can be assessed by different geochemical and paleontological proxies. However, each of these proxies provides only a fragmentary insight into the effects of anthropogenic impacts. It is highly challenging to reconstruct, with a holistic view, the state of the ecosystems from the preindustrial period to the present day, covering all biological components, from prokaryotes to multicellular eukaryotes. Here, we used sedimentary ancient DNA (sedaDNA) archives encompassing all trophic levels of biodiversity to reconstruct the two century-natural history in Bagnoli-Coroglio (Gulf of Pozzuoli, Tyrrhenian Sea), one of the most polluted marine-coastal sites in Europe. The site was characterized by seagrass meadows and high eukaryotic diversity until the beginning of the 20th century. Then, the ecosystem completely changed, with seagrasses and associated fauna as well as diverse groups of planktonic and benthic protists being replaced by low diversity biota dominated by dinophyceans and infaunal metazoan species. The sedaDNA analysis revealed a five-phase evolution of the area, where changes appear as the result of a multi-level cascade effect of impacts associated with industrial activities, urbanization, water circulation and land-use changes. The sedaDNA allowed to infer reference conditions that must be considered when restoration actions are to be implemented.

Biota

Anthropocene

Marine ecosystem

10.1016/j.envint.2023.107738

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Citations (25)