A comparative whole-genome approach identifies bacterial traits for marine microbial interactions

Luca Zoccarato, Daniel Sher, Takeshi Miki, Daniel Segrè, Hans Peter Grossart

Research output: Contribution to journalArticlepeer-review

Abstract

Microbial interactions shape the structure and function of microbial communities with profound consequences for biogeochemical cycles and ecosystem health. Yet, most interaction mechanisms are studied only in model systems and their prevalence is unknown. To systematically explore the functional and interaction potential of sequenced marine bacteria, we developed a trait-based approach, and applied it to 473 complete genomes (248 genera), representing a substantial fraction of marine microbial communities. We identified genome functional clusters (GFCs) which group bacterial taxa with common ecology and life history. Most GFCs revealed unique combinations of interaction traits, including the production of siderophores (10% of genomes), phytohormones (3–8%) and different B vitamins (57–70%). Specific GFCs, comprising Alpha- and Gammaproteobacteria, displayed more interaction traits than expected by chance, and are thus predicted to preferentially interact synergistically and/or antagonistically with bacteria and phytoplankton. Linked trait clusters (LTCs) identify traits that may have evolved to act together (e.g., secretion systems, nitrogen metabolism regulation and B vitamin transporters), providing testable hypotheses for complex mechanisms of microbial interactions. Our approach translates multidimensional genomic information into an atlas of marine bacteria and their putative functions, relevant for understanding the fundamental rules that govern community assembly and dynamics.

Original languageEnglish
Article number276
JournalCommunications Biology
Volume5
Issue number1
DOIs
StatePublished - Dec 2022

Bibliographical note

Funding Information:
This work was supported by the Human Frontier Science Program (HFSP) through the grant number RGB 0020/2016. D.Sh and D.Se also acknowledge support by the National Science Foundation through grant NSFOCE-BSF 1635070. We thank Anna Godhe (who unexpectedly and sadly passed away during our studies), Mats Töpel and Oskar Johansson for providing early access to some of the genomes included in the analysis. We thank the entire IAMM team (Dikla Aharonovich, David Bernstein, Falk Eigemann, Elena Forchielli, Tal Luzzatto-Knaan, Shany Ofaim, Melissa Osborne, Solvig Pinnow, Dalit Roth-Rosenberg, Angela Vogts and Maren Voss) for the constructive discussions and ideas that led us to shape this manuscript, as well as Osnat Weissberg and Minoru Kasada for their feedbacks on debugging the code. A sincere thank you to Silvia Munari for her diligent proofreading of this manuscript.

Publisher Copyright:
© 2022, The Author(s).

ASJC Scopus subject areas

  • Medicine (miscellaneous)
  • Biochemistry, Genetics and Molecular Biology (all)
  • Agricultural and Biological Sciences (all)

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