{"id":209,"date":"2023-03-31T09:28:19","date_gmt":"2023-03-31T07:28:19","guid":{"rendered":"https:\/\/tara-gosee.fr\/publications\/"},"modified":"2023-05-10T15:05:53","modified_gmt":"2023-05-10T13:05:53","slug":"publications","status":"publish","type":"page","link":"https:\/\/tara-gosee.fr\/en\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"<div id=\"blocAffichPublis\">Number of results : 249<div class=\"blocFlexSDG\"><div class=\"blocPublication\"><h5>Co-occurrence is associated with horizontal gene transfer across marine bacteria independent of phylogeny<\/h5><div class=\"displayPubli\"><p>Gavin M Douglas, Nicolas Tromas, Marinna Gaudin, Patrick Lypaczewski, Louis-Marie Bobay, B Jesse Shapiro, Samuel Chaffron.<\/p><div class=\"txtPublis\"><div class=\"halDateformat\"><span>The International Society of Microbiologial Ecology Journal, 2026<\/span><\/div><div id=\"typeHalIconsBloc\"><div class=\"typeHal\"><span>Journal articles<\/span><\/div><div class=\"iconsBlocPublis\"> <span class=\"doiIcon\"><a href=\"https:\/\/dx.doi.org\/10.1093\/ismejo\/wraf275\">doi<\/a><\/span><a target=\"_blank\" class=\"lienIconHal\" href=\"https:\/\/hal.inrae.fr\/hal-05563160\/document\"><i class=\"fa-regular fa-file-pdf\"><\/i><\/a><a target=\"_blank\" class=\"lienIconHal\" href=\"https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC12815264\"><i class=\"fa-solid fa-unlock-keyhole\"><\/i><\/a><\/div><\/div><\/div><\/div><\/div><div class=\"sdg-wheel\" data-wheel-height=\"200\" data-model=\"aurora-sdg-multi\" data-text=\"Understanding the drivers and consequences of horizontal gene transfer (HGT) is a key goal of microbial evolution research. Although co-occurring taxa have long been appreciated to undergo HGT more often, this association is confounded with other factors, most notably their phylogenetic relatedness. To disentangle these factors, we analyzed 15\u2009339 marine prokaryotic genomes (mainly bacteria) and their distribution in the global ocean. We identified HGT events across these genomes and enrichments for functions previously shown to be prone to HGT. By mapping metagenomic reads from 1862 ocean samples to these genomes, we also identified co-occurrence patterns and environmental associations. Although we observed an expected negative association between HGT rates and phylogenetic distance, we only detected an association between co-occurrence and phylogenetic distance for closely related taxa. This observation refines the previously reported trend to closely related taxa, rather than a consistent pattern across all taxonomic levels, at least here within marine environments. In addition, we identified a significant association between co-occurrence and HGT, which remains even after controlling for phylogenetic distance and measured environmental variables. In a subset of samples with extended environmental data, we identified higher HGT levels associated with particle-attached prokaryotes and associations of varying directions with specific environmental variables, such as chlorophyll a and photosynthetically available radiation. Overall, our findings demonstrate the significant influence of ecological associations in shaping marine prokaryotic evolution through HGT.\"><\/div><\/div><div class=\"blocFlexSDG\"><div class=\"blocPublication\"><h5>Genomic analysis of <i>Ostreococcus tauri<\/i>-infecting viruses reveals a hypervariable region associated with host\u2013virus interactions<\/h5><div class=\"displayPubli\"><p>Julie Thomy, Julien Henri, David Demory, Frederic Sanchez, Marie-Line Escande, Gilles Mirambeau, Nigel Grimsley, Sheree Yau.<\/p><div class=\"txtPublis\"><div class=\"halDateformat\"><span>Virus Evolution, 2026<\/span><\/div><div id=\"typeHalIconsBloc\"><div class=\"typeHal\"><span>Journal articles<\/span><\/div><div class=\"iconsBlocPublis\"> <span class=\"doiIcon\"><a href=\"https:\/\/dx.doi.org\/10.1093\/ve\/veaf096\">doi<\/a><\/span><a target=\"_blank\" class=\"lienIconHal\" href=\"https:\/\/hal.sorbonne-universite.fr\/hal-05370419\/document\"><i class=\"fa-regular fa-file-pdf\"><\/i><\/a><\/div><\/div><\/div><\/div><\/div><div class=\"sdg-wheel\" data-wheel-height=\"200\" data-model=\"aurora-sdg-multi\" data-text=\"\"><\/div><\/div><div class=\"blocFlexSDG\"><div class=\"blocPublication\"><h5>Oceanography, biogeochemical cycles, and biodiversity in the Central Arctic Ocean: current state of knowledge and directions for future<\/h5><div class=\"displayPubli\"><p>Maxime Geoffroy, Igor Polyakov, Marit Reigstad, Silvia G Acinas, R\u00e9mi Amiraux, H\u00e9l\u00e8ne Angot, Mathieu Ardyna, Marcel Babin, Chris Bowler, Douglas Couet, Tyler D Eddy, Angela Falciatore, Lionel Guidi, Mario Hoppmann, Marie-No\u00eblle Houssais, Lee Karp, Connie Lovejoy, Eric Marechal, Eric Pelletier, Eva Ortega, Jean-Fran\u00e7ois Ghiglione, Georg Pohnert, Benjamin Rabe, Guillem Salazar, Julia Schmale, Nina Schuback, Matt Sullivan, Sandra Tippenhauer, Romain Troubl\u00e9, Emilia Trudnowska, Assaf Vardi, Flora Vincent.<\/p><div class=\"txtPublis\"><div class=\"halDateformat\"><span>Elementa: Science of the Anthropocene, 2026<\/span><\/div><div id=\"typeHalIconsBloc\"><div class=\"typeHal\"><span>Journal articles<\/span><\/div><div class=\"iconsBlocPublis\"><a target=\"_blank\" class=\"lienIconHal\" href=\"https:\/\/hal.science\/hal-05480562\/document\"><i class=\"fa-regular fa-file-pdf\"><\/i><\/a><\/div><\/div><\/div><\/div><\/div><div class=\"sdg-wheel\" data-wheel-height=\"200\" data-model=\"aurora-sdg-multi\" data-text=\"<div><p>Climatic changes in the physical environment modulate biogeochemical cycles, biodiversity, and trophic interactions in the Central Arctic Ocean (CAO). Physical processes and sea-ice conditions are highly seasonal in the CAO and dependent on interactions that occur throughout the evolution of the upper ocean-sea ice-lower atmosphere system. Understanding these seasonal interactions is critical to comprehending and predicting the long-term trends as the CAO moves towards ice-free summers and to informing future policy decisions at the core of ongoing discussions concerning the CAO Fisheries agreement, e.g., at the Arctic Council and International Council for Exploration of the Sea working group on the CAO. Here, we review current knowledge of the physical environment, biogeochemical cycles, and biodiversity in the waters of the CAO, identify emerging research questions, and introduce the science plan for the first Tara Polaris drift onboard the Tara Polar Station to advance knowledge and address these questions. Despite increased observational programs in the CAO over the past years, e.g., the Nansen and Amundsen Basin Observational System (NABOS) and Multidisciplinary drifting Observatory for the Study of Arctic Climate (MOSAiC), extensive knowledge gaps remain in relation to ocean stratification, sea ice and lightscape, nitrogen fixation and nutrient fluxes, carbon export and transfer, sympagic-pelagic coupling, aerosol production, contaminant transport and transformation, chronobiology, and fish distribution. Further knowledge on overall CAO biodiversity, ecosystem functionality and interannual variability is also critically needed.<\/p><p>We describe a way forward to address these knowledge gaps using ice-tethered and profiling instruments coupled with multi-omics, culturing, and imagery approaches deployed from Tara Polar Station during the first of ten Tara Polaris drifts designed to facilitate detection of interannual variability and change over time.<\/p><\/div>\"><\/div><\/div><div class=\"blocFlexSDG\"><div class=\"blocPublication\"><h5>Tara Polaris expeditions: seasonal and long-term contaminant monitoring in the changing central Arctic<\/h5><div class=\"displayPubli\"><p>Jean-Fran\u00e7ois Ghiglione, Lars-Eric Heimb\u00fcrger-Boavida, Marion Fourquez, Ian Hough, Jeroen E. Sonke, Alexandra ter Halle, Kathy S. Law, Julia Schmale, J. Michel Flores, Julien Gigault, Mathieu Ardyna, Stephen Kohler, Zhiyong Xie, Jay Cullen, Maxime Geoffroy, Cl\u00e9mentine Moulin, Romain Troubl\u00e9, Lee Karp-Boss, Chris Bowler, Marcel Babin, H\u00e9l\u00e8ne Angot.<\/p><div class=\"txtPublis\"><div class=\"halDateformat\"><span>2026<\/span><\/div><div id=\"typeHalIconsBloc\"><div class=\"typeHal\"><span>Preprints, Working Papers...<\/span><\/div><div class=\"iconsBlocPublis\"><a target=\"_blank\" class=\"lienIconHal\" href=\"https:\/\/hal.science\/hal-05466231\/document\"><i class=\"fa-regular fa-file-pdf\"><\/i><\/a><\/div><\/div><\/div><\/div><\/div><div class=\"sdg-wheel\" data-wheel-height=\"200\" data-model=\"aurora-sdg-multi\" data-text=\"The central Arctic atmosphere, cryosphere, hydrosphere and biosphere, is heavily impacted by anthropogenic activities. While some contaminants originate from local activities, the majority are transported over long distances via rivers, ocean currents, and atmospheric pathways. Contaminants can have adverse effects on the environment, ecosystems, and human health, which are expected to intensify with continued emissions and warming climate. This article outlines the objectives for new studies on contaminants in the Arctic Ocean, in particular during the Tara Polaris expedition, with an emphasis on year-round long-term contaminant dynamics and associated ecotoxicological risks. Mercury contamination remains a major concern in the Arctic, especially in the form of methylmercury, which is primarily produced by marine microbes. Methylmercury bioconcentrates, bioaccumulates and biomagnifies to harmful levels in Arctic wildlife and threatens indigenous communities. Anthropogenic lead (Pb), though low in Arctic waters, remains toxic and may be remobilized by climate change. Plastic pollution, from nano-to macro-scales, is widespread across all Arctic compartments, closely interacting with planktonic communities and posing ingestion risks to invertebrates, fish, seabirds and mammals (including humans). Chemicals of Emerging Arctic Concern (CEAC), including newly recognized persistent organic pollutants inherited from past industrial activities (e.g., per-and polyfluoroalkyl substances (PFAS)), are more recalcitrant in the environment than many other synthetic compounds, raising serious questions about their long-term ecological and health effects. In this context, the Tara Polaris expeditions aim to produce high-resolution, year-round observational data in the central Arctic to deepen our understanding of contaminant sources, transport, internal cycling and environmental fate. These data will also support the development and refinement of numerical models for contaminant dynamics in the context of both Arctic and global environmental change.\"><\/div><\/div><div class=\"blocFlexSDG\"><div class=\"blocPublication\"><h5>Tara Polaris expeditions: Sustained decadal observations of the coupled Arctic system in rapid transition<\/h5><div class=\"displayPubli\"><p>Mathieu Ardyna, Marcel Nicolaus, Marie-No\u00eblle Houssais, Jean-Christophe Raut, H\u00e9l\u00e8ne Angot, Kelsey Bisson, Kristina A Brown, J Michel Flores, Jean-Fran\u00e7ois Ghiglione, Maxime Geoffroy, Lars-Eric Heimb\u00fcrger-Boavida, Kathy S. Law, Fran\u00e7ois Ravetta, Julia Schmale, Nina Schuback, Jeroen E Sonke, Martin Vancoppenolle, Jean\u2010\u00e9ric Tremblay, Marcel Babin, Chris Bowler, Lee Karp-Boss, Lovejoy Connie, Rysgaard S\u00f8ren, Romain Troubl\u00e9.<\/p><div class=\"txtPublis\"><div class=\"halDateformat\"><span>2026<\/span><\/div><div id=\"typeHalIconsBloc\"><div class=\"typeHal\"><span>Preprints, Working Papers...<\/span><\/div><div class=\"iconsBlocPublis\"><a target=\"_blank\" class=\"lienIconHal\" href=\"https:\/\/hal.science\/hal-05453026\/document\"><i class=\"fa-regular fa-file-pdf\"><\/i><\/a><a target=\"_blank\" class=\"lienIconHal\" href=\"http:\/\/arxiv.org\/pdf\/2601.08370\"><i class=\"fa-solid fa-unlock-keyhole\"><\/i><\/a><\/div><\/div><\/div><\/div><\/div><div class=\"sdg-wheel\" data-wheel-height=\"200\" data-model=\"aurora-sdg-multi\" data-text=\"<div><p>The coupled Arctic system is in rapid transition and is set to undergo further dramatic changes over the coming decades. These changes will lead most likely to an ice-free ocean in summer, expected before mid-century. The Arctic will become more strongly influenced by atmospheric and oceanographic processes characteristic of mid-latitudes, increasing the prevalence of contaminants and new biological species. This ongoing transition of the Arctic to a new state necessitates systematic monitoring of all sentinels (variables that make an essential contribution to characterizing the Earth's state) to improve our understanding of the system, enhance forecasting and support knowledge-based decisions. Here, we describe a sustained multi-decadal observation program to be implemented on the Tara Polar Station between 2026 and 2046. The monitoring program is designed as a series of year-long drift expeditions, called Tara Polaris, in the central Arctic Ocean, covering all seasons. The multidisciplinary data will bridge ecological, geochemical, biological, and physical parameters and processes in the atmosphere, sea ice and ocean. In addition, data collected with consistent methodologies over a 20-year period will make it possible to distinguish long-term trends from seasonal and interannual variability. In this paper, we discuss specific measurement challenges in each compartment (i.e., atmosphere, sea ice and ocean) along key sentinels and the most pressing scientific questions to be addressed. The expected outcomes of the Tara Polaris program will enable us to understand and quantify the main feedbacks of the coupled Arctic system, with their seasonal and interannual trends and spatial variability.<\/p><\/div>\"><\/div><\/div><div class=\"blocFlexSDG\"><div class=\"blocPublication\"><h5>A new deep-branching environmental lineage of algae<\/h5><div class=\"displayPubli\"><p>Mahwash Jamy, Thomas Huber, Thibault Antoine, Hans-Joachim Ruscheweyh, Lucas Paoli, Eric Pelletier, Tom Delmont, Fabien Burki.<\/p><div class=\"txtPublis\"><div class=\"halDateformat\"><span>2025<\/span><\/div><div id=\"typeHalIconsBloc\"><div class=\"typeHal\"><span>Preprints, Working Papers...<\/span><\/div><div class=\"iconsBlocPublis\"> <span class=\"doiIcon\"><a href=\"https:\/\/dx.doi.org\/10.1101\/2025.01.16.633336\">doi<\/a><\/span><a target=\"_blank\" class=\"lienIconHal\" href=\"https:\/\/doi.org\/10.1101\/2025.01.16.633336\"><i class=\"fa-solid fa-unlock-keyhole\"><\/i><\/a><\/div><\/div><\/div><\/div><\/div><div class=\"sdg-wheel\" data-wheel-height=\"200\" data-model=\"aurora-sdg-multi\" data-text=\"Abstract Marine algae support the entire ocean ecosystem and beyond. Algae in culture poorly represents their large environmental diversity, and we still have a limited understanding of their convoluted evolution by endosymbiosis. Here, we performed a phylogeny-guided plastid genome-resolved metagenomic survey of Tara Oceans expeditions. We present a curated resource of 660 new non-redundant plastid genomes of environmental pelagic algae. This catalogue vastly expands the plastid genome diversity within major algal groups, often corresponding to algae without closely related reference genomes. Notably, we recovered four plastid genomes, including one near complete, forming a deep-branching plastid lineage of nano-size algae that we informally named leptophytes. This group is globally distributed and generally rare, although it can reach relatively high abundance at least in the Arctic. A mitochondrial contig including 62 genes showing strong read coverage correlation with leptophytes was also recovered from these Arctic samples and assigned to this group. Leptophytes encompass the enigmatic marine plastid group DPL2, one of the very few known plastid groups not clearly belonging to any major algal groups and for which only 16S rDNA amplicon data is available. Extensive gene content comparison and organellar phylogenomics support the view that leptophytes are sister to haptophytes, and raise the intriguing possibility that cryptophytes acquired their plastids from haptophytes. Collectively, our study demonstrates that metagenomics can reveal currently hidden diversity of organellar genomes, and shows the importance of including this diversity to improve models for plastid evolution.\"><\/div><\/div><div class=\"blocFlexSDG\"><div class=\"blocPublication\"><h5>A Pan-European study of the bacterial plastisphere diversity along river-to-sea continuums<\/h5><div class=\"displayPubli\"><p>L\u00e9na Philip, Leila Chapron, Val\u00e9rie Barbe, Ga\u00ebtan Burgaud, Isabelle Calv\u00e8s, Ika Paul-Pont, Odon Thi\u00e9beauld, Brice Sperandio, Lionel Navarro, Alexandra ter Halle, Boris Eyheraguibel, Wolfgang Ludwig, Maialen Palazot, Mikael Kedzierski, Anne-Leila Meistertzheim, Jean-Fran\u00e7ois Ghiglione.<\/p><div class=\"txtPublis\"><div class=\"halDateformat\"><span>Environmental Science and Pollution Research, 2025<\/span><\/div><div id=\"typeHalIconsBloc\"><div class=\"typeHal\"><span>Journal articles<\/span><\/div><div class=\"iconsBlocPublis\"> <span class=\"doiIcon\"><a href=\"https:\/\/dx.doi.org\/10.1007\/s11356-024-35658-9\">doi<\/a><\/span><a target=\"_blank\" class=\"lienIconHal\" href=\"https:\/\/hal.sorbonne-universite.fr\/hal-04828355\/document\"><i class=\"fa-regular fa-file-pdf\"><\/i><\/a><\/div><\/div><\/div><\/div><\/div><div class=\"sdg-wheel\" data-wheel-height=\"200\" data-model=\"aurora-sdg-multi\" data-text=\"Microplastics provide a persistent substrate that can facilitate the transport of microbes from one ecosystem to another. Since most marine plastic debris originates from land and is carried to the ocean by rivers, a significant concern about the plastisphere is the potential dispersal of freshwater bacteria into the sea. To address this question, we explored the plastisphere on microplastic debris (MPs) and on pristine microplastics (pMPs) as well as the bacteria living in surrounding waters, along the river-sea continuum in nine major European rivers sampled during the seven months of the Tara Microplastics mission. In both marine and riverine waters, we found a clear niche partitioning among MPs and pMPs plastispheres when compared to the bacteria living in the surrounding waters. Among the large dataset, we found a clear gradient of bacterial community structure from the freshwater to the sea, with a complete segregation in plastisphere composition between the two ecosystems. We also described for the first time a virulent human pathogenic bacteria on MPs (Shewanella putrefaciens) able to infect human intestinal epithelial cells, that was only detected in river. Our results reinforce the major role played by the environmental conditions in shaping plastisphere biodiversity, that is not consistent with a critical transfer of pathogens between freshwater and seawater ecosystems.\"><\/div><\/div><div class=\"blocFlexSDG\"><div class=\"blocPublication\"><h5>Biodiversity Genomic Data Management an IFB Initiative<\/h5><div class=\"displayPubli\"><p>Clara Emery, Lucas Lecl\u00e8re, Eric Pelletier, Vincent Lefort, Yvan Le Bras, Erwan Corre.<\/p><div class=\"txtPublis\"><div class=\"halDateformat\"><span>2025<\/span><\/div><div id=\"typeHalIconsBloc\"><div class=\"typeHal\"><span>Poster communications<\/span><\/div><div class=\"iconsBlocPublis\"><a target=\"_blank\" class=\"lienIconHal\" href=\"https:\/\/hal.science\/hal-05135435\/document\"><i class=\"fa-regular fa-file-pdf\"><\/i><\/a><\/div><\/div><\/div><\/div><\/div><div class=\"sdg-wheel\" data-wheel-height=\"200\" data-model=\"aurora-sdg-multi\" data-text=\"Biodiversity encompasses all living organisms, the ecosystems they inhabit, and the intricate interactions among species and with their environment. Biodiversity observatories, positioned at the interface of a given ecosystem, are crucial for assessing biodiversity. Beyond their direct role in conservation, these observatories enhance coordination and facilitate knowledge exchange among diverse institutions and the scientific community. Within the IFB, PNDB biodiversity community, and the PIA MUDILS4LS IS2's marine genomics data management initiative, we aim to establish FAIR (Findable, Accessible, Interoperable, and Reusable) data management recommendations. Our initial focus is an enhanced genomic observatory for marine biodiversity.\"><\/div><\/div><div class=\"blocFlexSDG\"><div class=\"blocPublication\"><h5>Co-occurrence drives horizontal gene transfer among marine prokaryotes<\/h5><div class=\"displayPubli\"><p>Gavin M Douglas, Nicolas Tromas, Marinna Gaudin, Patrick Lypaczewksi, Louis-Marie Bobay, B Jesse Shapiro, Samuel Chaffron.<\/p><div class=\"txtPublis\"><div class=\"halDateformat\"><span>2025<\/span><\/div><div id=\"typeHalIconsBloc\"><div class=\"typeHal\"><span>Preprints, Working Papers...<\/span><\/div><div class=\"iconsBlocPublis\"> <span class=\"doiIcon\"><a href=\"https:\/\/dx.doi.org\/10.1101\/2025.03.25.645238\">doi<\/a><\/span><a target=\"_blank\" class=\"lienIconHal\" href=\"https:\/\/hal.science\/hal-05027411\/document\"><i class=\"fa-regular fa-file-pdf\"><\/i><\/a><\/div><\/div><\/div><\/div><\/div><div class=\"sdg-wheel\" data-wheel-height=\"200\" data-model=\"aurora-sdg-multi\" data-text=\"Understanding the drivers of horizontal gene transfer (HGT) is a key question in microbial evolution. While co-occurring taxa have long been appreciated to undergo HGT more often, this association is confounded with other factors, most notably their phylogenetic distance.<p>To disentangle these factors, we analyzed 15,339 isolate and metagenome-assembled marine genomes. We identified HGT events across these genomes, and identified enrichments for functions previously shown to be prone to HGT. By mapping metagenomic reads from 1,862 ocean samples to these genomes, we also identified co-occurrence patterns and environmental associations. Although we observed an expected negative association between phylogenetic distance and HGT rates, we only detected the association between cooccurrence and phylogenetic distance when restricted to closely related taxa. This observation refines the previously reported trend to closely related taxa, rather than a consistent pattern across all taxonomic levels, at least within marine environments. In addition, we identified a significant association between co-occurrence and HGT, which remains even after controlling for phylogenetic distance and measured environmental variables. Overall, our findings demonstrate the significant influence of ecological associations in shaping marine bacterial evolution through HGT.<\/p>\"><\/div><\/div><div class=\"blocFlexSDG\"><div class=\"blocPublication\"><h5>Comparison of sedimentary ancient DNA (sedaDNA) extraction and shotgun metagenomic library preparation techniques<\/h5><div class=\"displayPubli\"><p>Mathilde Bourreau, Prashasti Singh, Linda Armbrecht, Jose Utge, Chris Bowler, Manon Sabourdy, Carlota Escutia, Juliane M\u00fcller, Fernando Bohoyo, Xavier Crosta, Johan Etourneau.<\/p><div class=\"txtPublis\"><div class=\"halDateformat\"><span>Marine Micropaleontology, 2025<\/span><\/div><div id=\"typeHalIconsBloc\"><div class=\"typeHal\"><span>Journal articles<\/span><\/div><div class=\"iconsBlocPublis\"> <span class=\"doiIcon\"><a href=\"https:\/\/dx.doi.org\/10.1016\/j.marmicro.2025.102498\">doi<\/a><\/span><\/div><\/div><\/div><\/div><\/div><div class=\"sdg-wheel\" data-wheel-height=\"200\" data-model=\"aurora-sdg-multi\" data-text=\"Sedimentary ancient DNA (sedaDNA) is an emerging field, increasingly being applied to the study of past aquatic ecosystems. However, several sedaDNA extraction methods from deep-ocean sediment matrices and sequencing library preparation have recently been developed, which may complexify results comparison and interpretations. We present a sedaDNA interlaboratory comparison study to assess the impact of extraction and library preparation protocols on metagenomic results. We applied three extraction protocols to four samples from two sediment cores from the Northern Antarctic Peninsula: (1) a \u2018combined\u2019 protocol using ethylenediaminetetraacetic acid (EDTA) and silica-in-solution to isolate DNA, (2) a high-guanidine protocol involving long cold centrifugation to remove polymerase chain reaction (PCR) inhibitors, and (3) a commercial kit, the DNeasy PowerSoil Pro Kit. We also compared two library preparation protocols, both optimised versions from Meyer and Kircher (2010). Using a blind approach relying on k-mer similarity assessment, greater variability was observed between individual samples than between protocols. An in-depth analysis of eukaryotic and (highly abundant) diatom community composition revealed that all protocols recovered eukaryotic sedaDNA, with minor differences between extraction and library protocols on sequence composition. However, the different DNA extraction and library preparations influenced the DNA read length, potentially resulting in selective targeting of organisms with variable sedaDNA preservation. This study highlights the importance of selection and standardisation of protocols to ensure reproducibility and comparability of past ecosystem reconstructions, particularly at lower taxonomic levels, e.g. diatoms. Although complete standardisation across research projects is challenging, this study shows that data remain reasonably comparable when processed consistently.\"><\/div><\/div><div id='paginationPubs' class='page-nav-container'>Pages - <span class=\"page-numbers current\">1 - <\/span><span class=\"page-numbers\">2 - <\/span><span class=\"page-numbers\">3 - <\/span><span class=\"page-numbers\">4 - <\/span><span class=\"page-numbers\">5 - <\/span><span class=\"page-numbers\">6 - <\/span><span class=\"page-numbers\">7 - <\/span><span class=\"page-numbers\">8 - <\/span><span class=\"page-numbers\">9 - <\/span><span class=\"page-numbers\">10 - <\/span><span class=\"page-numbers\">11 - <\/span><span class=\"page-numbers\">12 - <\/span><span class=\"page-numbers\">13 - <\/span><span class=\"page-numbers\">14 - <\/span><span class=\"page-numbers\">15 - <\/span><span class=\"page-numbers\">16 - <\/span><span class=\"page-numbers\">17 - <\/span><span class=\"page-numbers\">18 - <\/span><span class=\"page-numbers\">19 - <\/span><span class=\"page-numbers\">20 - <\/span><span class=\"page-numbers\">21 - <\/span><span class=\"page-numbers\">22 - <\/span><span class=\"page-numbers\">23 - <\/span><span class=\"page-numbers\">24 - <\/span><span class=\"page-numbers\">25<\/span><\/div><\/div>\n\n\n\n<div class=\"wp-block-group has-global-padding is-layout-constrained wp-block-group-is-layout-constrained\" style=\"margin-top:var(--wp--preset--spacing--40);margin-bottom:var(--wp--preset--spacing--40);padding-bottom:var(--wp--preset--spacing--50)\">\n<figure class=\"wp-block-image aligncenter size-full\"><img loading=\"lazy\" decoding=\"async\" width=\"735\" height=\"694\" src=\"https:\/\/tara-gosee.fr\/wp-content\/uploads\/sites\/3\/2023\/05\/fin_publication.png\" alt=\"\" class=\"wp-image-442\" srcset=\"https:\/\/tara-gosee.fr\/wp-content\/uploads\/sites\/3\/2023\/05\/fin_publication.png 735w, https:\/\/tara-gosee.fr\/wp-content\/uploads\/sites\/3\/2023\/05\/fin_publication-300x283.png 300w\" sizes=\"auto, (max-width: 735px) 100vw, 735px\" \/><\/figure>\n<\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"wp-custom-template-publications-2","meta":{"footnotes":""},"class_list":["post-209","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/tara-gosee.fr\/en\/wp-json\/wp\/v2\/pages\/209","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/tara-gosee.fr\/en\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/tara-gosee.fr\/en\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/tara-gosee.fr\/en\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/tara-gosee.fr\/en\/wp-json\/wp\/v2\/comments?post=209"}],"version-history":[{"count":3,"href":"https:\/\/tara-gosee.fr\/en\/wp-json\/wp\/v2\/pages\/209\/revisions"}],"predecessor-version":[{"id":584,"href":"https:\/\/tara-gosee.fr\/en\/wp-json\/wp\/v2\/pages\/209\/revisions\/584"}],"wp:attachment":[{"href":"https:\/\/tara-gosee.fr\/en\/wp-json\/wp\/v2\/media?parent=209"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}