| Title: |
Co-occurrence is associated with horizontal gene transfer across marine bacteria independent of phylogeny |
| Authors: |
Douglas, Gavin, M; Tromas, Nicolas; Gaudin, Marinna; Lypaczewski, Patrick; Bobay, Louis-Marie; Shapiro, B, Jesse; Chaffron, Samuel |
| Contributors: |
University of New Brunswick (UNB); North Carolina A&T State University; University of North Carolina System (UNC); McGill University = Université McGill Montréal, Canada; Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL); Université Savoie Mont Blanc (USMB Université de Savoie Université de Chambéry )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Observatoire des Sciences de l'Univers de Grenoble (Fédération OSUG); Laboratoire des Sciences du Numérique de Nantes (LS2N); Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique (IMT Atlantique); Institut Mines-Télécom Paris (IMT)-Institut Mines-Télécom Paris (IMT)-NANTES UNIVERSITÉ - École Centrale de Nantes (Nantes Univ - ECN); Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes université - UFR des Sciences et des Techniques (Nantes univ - UFR ST); Nantes Université - pôle Sciences et technologie; Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Nantes Université - pôle Sciences et technologie; Nantes Université (Nantes Univ); Global Oceans Systems Ecology & Evolution - Tara Oceans (GOSEE); Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE); Université Paris Sciences et Lettres (PSL)-Université Paris Sciences et Lettres (PSL)-Aix Marseille Université (AMU)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Université de Toulon (UTLN)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD Ile-de-France )-Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay)-European Molecular Biology Laboratory (EMBL)-NANTES UNIVERSITÉ - École Centrale de Nantes (Nantes Univ - ECN); Nantes Université (Nantes Univ)-Nantes Université (Nantes Univ)-Université australe du Chili |
| Source: |
ISSN: 1751-7362. |
| Publisher Information: |
CCSD; Nature Publishing Group |
| Publication Year: |
2026 |
| Collection: |
Université de Toulon: HAL |
| Subject Terms: |
co-occurrence; lateral gene transfer; horizontal gene transfer; metagenomics; bacteria; prokaryotes; ocean ecology; phylogenetics; lateral gene transferco-occurrence; [SDV.EE]Life Sciences [q-bio]/Ecology; environment |
| Description: |
International audience ; 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 15 339 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. |
| Document Type: |
article in journal/newspaper |
| Language: |
English |
| Relation: |
info:eu-repo/semantics/altIdentifier/pmid/41378915; PUBMED: 41378915; PUBMEDCENTRAL: PMC12815264; WOS: 001636460600001 |
| DOI: |
10.1093/ismejo/wraf275 |
| Availability: |
https://hal.inrae.fr/hal-05563160; https://hal.inrae.fr/hal-05563160v1/document; https://hal.inrae.fr/hal-05563160v1/file/2026_Douglas_ISME.pdf; https://doi.org/10.1093/ismejo/wraf275 |
| Rights: |
https://creativecommons.org/licenses/by/4.0/ ; info:eu-repo/semantics/OpenAccess |
| Accession Number: |
edsbas.41B1AFFC |
| Database: |
BASE |