Aquatic bacterial rhodopsin proton pumps harvest light energy for photoheterotrophic growth and are known to contain hydroxylated carotenoids that expand the wavelengths of light utilized, but these have not been characterized in marine archaea. Here, by combining a marine chromophore extract with purified archaeal rhodopsins identified in marine metagenomes, we show light energy transfer from diverse hydroxylated carotenoids to heimdallarchaeial rhodopsins (HeimdallRs) from uncultured marine planktonic members of 'Candidatus Kariarchaeaceae' ('Candidatus Asgardarchaeota'). These light-harvesting antennas absorb in the blue-light range and transfer energy to the green-light-absorbing retinal chromophore within HeimdallRs, enabling the use of light that is otherwise unavailable to the rhodopsin. Furthermore, we show elevated proton pumping by the antennas in HeimdallRs under white-light illumination, which better simulates the light conditions encountered by these archaea in their natural habitats. Our results indicate that light-harvesting antennas in microbial rhodopsins exist in families beyond xanthorhodopsins and proteorhodopsins and are present in both marine bacteria and archaea.

Centre Algatech Institute of Microbiology Czech Academy of Sciences Třeboň Czech Republic

Department of Biological Sciences Graduate School of Science The University of Tokyo Tokyo Japan

Department of Life Science and Applied Chemistry Nagoya Institute of Technology Nagoya Japan

Department of Physics Technische Universität Dortmund Germany

Faculty of Biology Technion Israel Institute of Technology Haifa Israel

Faculty of Science University of South Bohemia České Budějovice Czech Republic

Fritz Haber Center for Molecular Dynamics Research Institute of Chemistry The Hebrew University of Jerusalem Jerusalem Israel

Institute of Environmental Engineering ETH Zurich Switzerland

Laboratory of Biochemistry and Molecular Biology Faculty of Experimental Sciences Marine International Campus of Excellence University of Huelva Huelva Spain

OptoBioTechnology Research Center Nagoya Institute of Technology Nagoya Japan

Physical and Analytical Chemistry Department University of Jaén Jaén Spain

Research Center Chemical Sciences and Sustainability University Alliance Ruhr Bochum Germany

The Institute for Solid State Physics The University of Tokyo Kashiwa Japan

The Nancy and Stephen Grand Technion Energy Program Technion Israel Institute of Technology Haifa Israel

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Rozenberg, A., Inoue, K., Kandori, H. & Béjà, O. Microbial rhodopsins: the last two decades. Annu. Rev. Microbiol.75, 427–447 (2021). PubMed

Finkel, O. M., Béjà, O. & Belkin, S. Global abundance of microbial rhodopsins. ISME J.7, 448–451 (2013). PubMed PMC

DeLong, E. F. & Béjà, O. The light-driven proton pump proteorhodopsin enhances bacterial survival during tough times. PLoS Biol.8, e1000359 (2010). PubMed PMC

Munson-McGee, J. H. et al. Decoupling of respiration rates and abundance in marine prokaryoplankton. Nature612, 764–770 (2022). PubMed PMC

Balashov, S. P. et al. Xanthorhodopsin: a proton pump with a light-harvesting carotenoid antenna. Science309, 2061–2064 (2005). PubMed PMC

Imasheva, E. S., Balashov, S. P., Choi, A. R., Jung, K.-H. & Lanyi, J. K. Reconstitution of Gloeobacter violaceus rhodopsin with a light-harvesting carotenoid antenna. Biochemistry48, 10948–10955 (2009). PubMed PMC

Chazan, A. et al. Phototrophy by antenna-containing rhodopsin pumps in aquatic environments. Nature615, 535–540 (2023). PubMed

Luecke, H. et al. Crystallographic structure of xanthorhodopsin, the light-driven proton pump with a dual chromophore. Proc. Natl Acad. Sci. USA105, 16561–16565 (2008). PubMed PMC

Kopejtka, K. et al. A bacterium from a mountain lake harvests light using both proton-pumping xanthorhodopsins and bacteriochlorophyll-based photosystems. Proc. Natl Acad. Sci. USA119, e2211018119 (2022). PubMed PMC

Rinke, C. et al. A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.). ISME J.13, 663–675 (2019). PubMed PMC

Frigaard, N.-U., Martinez, A., Mincer, T. J. & DeLong, E. F. Proteorhodopsin lateral gene transfer between marine planktonic Bacteria and Archaea. Nature439, 847–850 (2006). PubMed

Iverson, V. et al. Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota. Science335, 587–590 (2012). PubMed

Pinhassi, J., DeLong, E. F., Béjà, O., González, J. M. & Pedrós-Alió, C. Marine bacterial and archaeal ion-pumping rhodopsins: genetic diversity, physiology, and ecology. Microbiol. Mol. Biol. Rev.80, 929–954 (2016). PubMed PMC

Tully, B. J. Metabolic diversity within the globally abundant Marine Group II Euryarchaea offers insight into ecological patterns. Nat. Commun.10, 271 (2019). PubMed PMC

Bulzu, P.-A. et al. Casting light on Asgardarchaeota metabolism in a sunlit microoxic niche. Nat. Microbiol.4, 1129–1137 (2019). PubMed

Inoue, K. et al. Schizorhodopsins: a family of rhodopsins from Asgard archaea that function as light-driven inward H+ pumps. Sci. Adv.6, eaaz2441 (2020). PubMed PMC

Eme, L. et al. Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes. Nature618, 992–999 (2023). PubMed PMC

Vosseberg, J. et al. The emerging view on the origin and early evolution of eukaryotic cells. Nature633, 295–305 (2024). PubMed

Liu, Y. et al. Expanded diversity of Asgard archaea and their relationships with eukaryotes. Nature593, 553–557 (2021). PubMed PMC

Varghese, N. J. et al. Microbial species delineation using whole genome sequences. Nucleic Acids Res.43, 6761–6771 (2015). PubMed PMC

Vernette, C. et al. The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes. Nucleic Acids Res.50, W516–W526 (2022). PubMed PMC

Ernst, O. P. et al. Microbial and animal rhodopsins: structures, functions, and molecular mechanisms. Chem. Rev.114, 126–163 (2014). PubMed PMC

Kirk, J. T. O. in Primary Productivity and Biogeochemical Cycles in the Sea (eds Falkowski, P. G. et al.) 9–29 (Springer, 1992).

Hirschi, S., Kalbermatter, D., Ucurum, Z., Lemmin, T. & Fotiadis, D. Cryo-EM structure and dynamics of the green-light absorbing proteorhodopsin. Nat. Commun.12, 4107 (2021). PubMed PMC

Gushchin, I. et al. Structural insights into the proton pumping by unusual proteorhodopsin from nonmarine bacteria. Proc. Natl Acad. Sci. USA110, 12631–12636 (2013). PubMed PMC

Balashov, S. P. et al. Breaking the carboxyl rule: lysine 96 facilitates reprotonation of the Schiff base in the photocycle of a retinal protein from Exiguobacterium sibiricum. J. Biol. Chem.288, 21254–21265 (2013). PubMed PMC

Field, M. J., Bash, P. A. & Karplus, M. A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations. J. Comput. Chem.11, 700–733 (1990).

Béjà, O., Spudich, E. N., Spudich, J. L., Leclerc, M. & DeLong, E. F. Proteorhodopsin phototrophy in the ocean. Nature411, 786–789 (2001). PubMed

Man, D. et al. Diversification and spectral tuning in marine proteorhodopsins. EMBO J.22, 1725–1731 (2003). PubMed PMC

Gómez-Consarnau, L. et al. Light stimulates growth of proteorhodopsin-containing marine Flavobacteria. Nature445, 210–213 (2007). PubMed

Liu, R. et al. Metagenomic insights into Heimdallarchaeia clades from the deep-sea cold seep and hydrothermal vent. Environ. Microbiome19, 43 (2024). PubMed PMC

Tully, B. J., Graham, E. D. & Heidelberg, J. F. The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans. Sci. Data5, 170203 (2018). PubMed PMC

Rodriguez-R, L. M., Tsementzi, D., Luo, C. & Konstantinidis, K. T. Iterative subtractive binning of freshwater chronoseries metagenomes identifies over 400 novel species and their ecologic preferences. Environ. Microbiol.22, 3394–3412 (2020). PubMed

Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods9, 357–359 (2012). PubMed PMC

Haro-Moreno, J. M. et al. Dysbiosis in marine aquaculture revealed through microbiome analysis: reverse ecology for environmental sustainability. FEMS Microbiol. Ecol.96, fiaa218 (2020). PubMed

Puente-Sánchez, F., Hoetzinger, M., Buck, M. & Bertilsson, S. Exploring environmental intra-species diversity through non-redundant pangenome assemblies. Mol. Ecol. Resour.23, 1724–1736 (2023). PubMed

Tatusova, T. et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res.44, 6614–6624 (2016). PubMed PMC

Nishimura, Y. & Yoshizawa, S. The OceanDNA MAG catalog contains over 50,000 prokaryotic genomes originated from various marine environments. Sci. Data9, 305 (2022). PubMed PMC

Paoli, L. et al. Biosynthetic potential of the global ocean microbiome. Nature607, 111–118 (2022). PubMed PMC

Parks, D. H. et al. A complete domain-to-species taxonomy for Bacteria and Archaea. Nat. Biotechnol.38, 1079–1086 (2020). PubMed

Asnicar, F. et al. Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0. Nat. Commun.11, 2500 (2020). PubMed PMC

Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics26, 2460–2461 (2010). PubMed

Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol.30, 772–780 (2013). PubMed PMC

Capella-Gutiérrez, S., Silla-Martínez, J. M. & Gabaldón, T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics25, 1972–1973 (2009). PubMed PMC

Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics30, 1312–1313 (2014). PubMed PMC

Camacho, C. et al. BLAST+: architecture and applications. BMC Bioinformatics10, 421 (2009). PubMed PMC

Darriba, D., Taboada, G. L., Doallo, R. & Posada, D. ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics27, 1164–1165 (2011). PubMed PMC

Matsen, F. A., Kodner, R. B. & Armbrust, E. V. pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics11, 538 (2010). PubMed PMC

Huson, D. H. & Bryant, D. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol.23, 254–267 (2006). PubMed

Abramson, J. et al. Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature630, 493–500 (2024). PubMed PMC

Fu, L., Niu, B., Zhu, Z., Wu, S. & Li, W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics28, 3150–3152 (2012). PubMed PMC

Tamura, K., Stecher, G. & Kumar, S. MEGA11: Molecular Evolutionary Genetics Analysis version 11. Mol. Biol. Evol.38, 3022–3027 (2021). PubMed PMC

Chen, I.-M. A. et al. IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes. Nucleic Acids Res.47, D666–D677 (2019). PubMed PMC

Steinegger, M. & Söding, J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat. Biotechnol.35, 1026–1028 (2017). PubMed

Eddy, S. R. A new generation of homology search tools based on probabilistic inference. Genome Inform.23, 205–211 (2009). PubMed

Chikhi, R., Raffestin, B., Korobeynikov, A., Edgar, R. & Babaian, A. Logan: planetary-scale genome assembly surveys life’s diversity. Preprint at bioRxiv10.1101/2024.07.30.605881 (2024).

Li, H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics34, 3094–3100 (2018). PubMed PMC

McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res.20, 1297–1303 (2010). PubMed PMC

Ahmed, F. et al. Profiling of carotenoids and antioxidant capacity of microalgae from subtropical coastal and brackish waters. Food Chem.165, 300–306 (2014). PubMed

Young, A. J., Orset, S. & Tsavalos, A. J. in Handbook of Photosynthesis (ed. Pessarakli, M.) 597–622 (Marcel Dekker, 1997).

Grote, A. et al. JCat: a novel tool to adapt codon usage of a target gene to its potential expression host. Nucleic Acids Res.33, W526–W531 (2005). PubMed PMC

Lakowicz, J. R. Principles of Fluorescence Spectroscopy (Springer, 2006).

Inoue, K. et al. A light-driven sodium ion pump in marine bacteria. Nat. Commun.4, 1678 (2013). PubMed

Wang, W.-W., Sineshchekov, O. A., Spudich, E. N. & Spudich, J. L. Spectroscopic and photochemical characterization of a deep ocean proteorhodopsin. J. Biol. Chem.278, 33985–33991 (2003). PubMed

Ihaka, R. & Gentleman, R. R: a language for data analysis and graphics. J. Comput. Graph. Stat.5, 299–314 (1996).

Bates, D., Mächler, M., Bolker, B. & Walker, S. Fitting linear mixed-effects models using lme4. J. Stat. Softw.67, 1–48 (2015).

Fox, J. & Weisberg, S. An R Companion to Applied Regression (Sage, 2019).

Shihoya, W. et al. Crystal structure of heliorhodopsin. Nature574, 132–136 (2019). PubMed

Hirata, K. et al. ZOO: an automatic data-collection system for high-throughput structure analysis in protein microcrystallography. Acta Crystallogr. D Struct. Biol.75, 138–150 (2019). PubMed PMC

Yamashita, K., Hirata, K. & Yamamoto, M. KAMO: towards automated data processing for microcrystals. Acta Crystallogr. D Struct. Biol.74, 441–449 (2018). PubMed PMC

Kabsch, W. XDS. Acta Crystallogr. D Biol. Crystallogr.66, 125–132 (2010). PubMed PMC

McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Crystallogr.40, 658–674 (2007). PubMed PMC

Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature596, 583–589 (2021). PubMed PMC

Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr.66, 486–501 (2010). PubMed PMC

Afonine, P. V. et al. Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallogr. D Biol. Crystallogr.68, 352–367 (2012). PubMed PMC

Bannwarth, C., Ehlert, S. & Grimme, S. GFN2-xTB—an accurate and broadly parametrized self-consistent tight-binding quantum chemical method with multipole electrostatics and density-dependent dispersion contributions. J. Chem. Theory Comput.15, 1652–1671 (2019). PubMed

Maier, J. A. et al. ff14SB: improving the accuracy of protein side chain and backbone parameters from ff99SB. J. Chem. Theory Comput.11, 3696–3713 (2015). PubMed PMC

Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W. & Klein, M. L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys.79, 926–935 (1983).

Steinbach, P. J. & Brooks, B. R. New spherical-cutoff methods for long-range forces in macromolecular simulation. J. Comput. Chem.15, 667–683 (1994).

Neese, F. Software update: the ORCA program system—version 5.0. WIREs Comput. Mol. Sci.12, e1606 (2022).

Hättig, C. in Advances in Quantum Chemistry Vol. 50 (ed. Jensen, H. J. Å.) 37–60 (Academic Press, 2005).

Dunning, T. Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen. J. Chem. Phys.90, 1007–1023 (1989).

Furche, F. et al. Turbomole. WIREs Comput. Mol. Sci.4, 91–100 (2014).

Rozenberg, A. Structural insights into light harvesting by antenna-containing rhodopsins in marine Asgard archaea. Bioinformatic Data. figshare10.6084/m9.figshare.26906593 (2025). PubMed PMC

Matsui, Y. et al. Specific damage induced by X-ray radiation and structural changes in the primary photoreaction of bacteriorhodopsin. J. Mol. Biol.324, 469–481 (2002). PubMed

Po, H. N. & Senozan, N. M. The Henderson–Hasselbalch equation: its history and limitations. J. Chem. Educ.78, 1499 (2001).

Larkin, M. A. et al. Clustal W and Clustal X version 2.0. Bioinformatics23, 2947–2948 (2007). PubMed

Robert, X. & Gouet, P. Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Res.42, W320–W324 (2014). PubMed PMC

Structural insights into light harvesting by antenna-containing rhodopsins in marine Asgard archaea