Clifton, Ben E.Alcolombri, UriaUechi, Gen IchiroJackson, Colin J.Laurino, Paola2025-05-232025-05-230028-0836PubMed:39261732ORCID:/0000-0001-6150-3822/work/184102723http://www.scopus.com/inward/record.url?scp=85203524683&partnerID=8YFLogxKhttps://hdl.handle.net/1885/733752351SAR11 bacteria are the most abundant microorganisms in the surface ocean1 and have global biogeochemical importance2–4. To thrive in their competitive oligotrophic environment, these bacteria rely heavily on solute-binding proteins that facilitate uptake of specific substrates via membrane transporters5,6. The functions and properties of these transport proteins are key factors in the assimilation of dissolved organic matter and biogeochemical cycling of nutrients in the ocean, but they have remained largely inaccessible to experimental investigation. Here we performed genome-wide experimental characterization of all solute-binding proteins in a prototypical SAR11 bacterium, revealing specific functions and general trends in their properties that contribute to the success of SAR11 bacteria in oligotrophic environments. We found that the solute-binding proteins of SAR11 bacteria have extremely high binding affinity (dissociation constant >20 pM) and high binding specificity, revealing molecular mechanisms of oligotrophic adaptation. Our functional data have uncovered new carbon sources for SAR11 bacteria and enable accurate biogeographical analysis of SAR11 substrate uptake capabilities throughout the ocean. This study provides a comprehensive view of the substrate uptake capabilities of ubiquitous marine bacteria, providing a necessary foundation for understanding their contribution to assimilation of dissolved organic matter in marine ecosystems.B.E.C. was supported by a JSPS Postdoctoral Fellowship for Overseas Researchers from the Japan Society for the Promotion of Science. P.L. gratefully acknowledges funding from the Okinawa Institute of Science and Technology. U.A. gratefully acknowledges funding from Alon Scholarships (The Council for Higher Education, Israel). The synchrotron radiation experiments were performed at BL32XU of SPring-8 with the approval of the Japan Synchrotron Radiation Research Institute (JASRI) (proposal no. 2023A2731). We thank A. Vardi for critical reading of the initial manuscript; D. Kozome for assistance with X-ray data collection; P. Jain for assistance with synthesis and NMR; Y. Iinuma and O. Smith for assistance with GC\u2013MS; and the Instrumental Analysis Section and Sequencing Section at OIST for providing instrument access and training.8enPublisher Copyright: © The Author(s) 2024.2024-10-1710.1038/s41586-024-07924-w85203524683