Rhodopsin photosystems convert light energy into electrochemical gradients used by the cell to produce ATP, or for other energy-demanding processes. While these photosystems are widespread in the ocean and have been identified in diverse microbial taxonomic groups, their physiological role in vivo has only been studied in few marine bacterial strains. Recent metagenomic studies revealed the presence of rhodopsin genes in the understudied Verrucomicrobiota phylum, yet their distribution within different Verrucomicrobiota lineages, their diversity, and function remain unknown. In this study, we show that more than 7% of Verrucomicrobiota genomes (n = 2916) harbor rhodopsins of different types. Furthermore, we describe the first two cultivated rhodopsin-containing strains, one harboring a proteorhodopsin gene and the other a xanthorhodopsin gene, allowing us to characterize their physiology under laboratory-controlled conditions. The strains were isolated in a previous study from the Eastern Mediterranean Sea and read mapping of 16S rRNA gene amplicons showed the highest abundances of these strains at the deep chlorophyll maximum (source of their inoculum) in winter and spring, with a substantial decrease in summer. Genomic analysis of the isolates suggests that motility and degradation of organic material, both energy demanding functions, may be supported by rhodopsin phototrophy in Verrucomicrobiota. Under culture conditions, we show that rhodopsin phototrophy occurs under carbon starvation, with light-mediated energy generation supporting sugar transport into the cells. Overall, this study suggests that photoheterotrophic Verrucomicrobiota may occupy an ecological niche where energy harvested from light enables bacterial motility toward organic matter and supports nutrient uptake.

Centro de Investigación Científica y de Educación Superior de Ensenada Ensenada BC México

Department of Biological Sciences University of Southern California Los Angeles CA 90089 USA

Department of Ecology and Environmental Sciences School of Life Sciences Pondicherry University Puducherry 605014 India

Department of Marine Biology Leon H Charney School of Marine Sciences University of Haifa Haifa 3498838 Israel

Faculty of Biology Technion Israel Institute of Technology Haifa 3200003 Israel

Institute of Hydrobiology Biology Centre CAS Na Sadkach 7 37005 Ceske Budejovice Czechia

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Beja O, Aravind L, Koonin EV, Suzuki MT, Hadd A, Nguyen LP, et al. Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science. 2000;289:1902–6. doi: 10.1126/science.289.5486.1902. PubMed DOI

Beja O, Spudich EN, Spudich JL, Leclerc M, DeLong EF. Proteorhodopsin phototrophy in the ocean. Nature. 2001;411:786–9. doi: 10.1038/35081051. PubMed DOI

Martinez A, Bradley AS, Waldbauer JR, Summons RE, DeLong EF. Proteorhodopsin photosystem gene expression enables photophosphorylation in a heterologous host. Proc Natl Acad Sci USA. 2007;104:5590–5. doi: 10.1073/pnas.0611470104. PubMed DOI PMC

Gomez-Consarnau L, Gonzalez JM, Coll-Llado M, Gourdon P, Pascher T, Neutze R, et al. Light stimulates growth of proteorhodopsin-containing marine Flavobacteria. Nature. 2007;445:210–3. doi: 10.1038/nature05381. PubMed DOI

Gomez-Consarnau L, Gonzalez JM, Riedel T, Jaenicke S, Wagner-Dobler I, Sanudo-Wilhelmy SA, et al. Proteorhodopsin light-enhanced growth linked to vitamin-B1 acquisition in marine Flavobacteria. ISME J. 2016;10:1102–12. doi: 10.1038/ismej.2015.196. PubMed DOI PMC

Steindler L, Schwalbach MS, Smith DP, Chan F, Giovannoni SJ. Energy starved Candidatus Pelagibacter ubique substitutes light-mediated ATP production for endogenous carbon respiration. PLoS ONE. 2011;6:e19725. doi: 10.1371/journal.pone.0019725. PubMed DOI PMC

Wang Z, O’Shaughnessy TJ, Soto CM, Rahbar AM, Robertson KL, Lebedev N, et al. Function and regulation of Vibrio campbellii proteorhodopsin: acquired phototrophy in a classical organoheterotroph. PLoS ONE. 2012;7:e38749. doi: 10.1371/journal.pone.0038749. PubMed DOI PMC

Finkel OM, Beja O, Belkin S. Global abundance of microbial rhodopsins. ISME J. 2013;7:448–51. doi: 10.1038/ismej.2012.112. PubMed DOI PMC

Gomez-Consarnau L, Raven JA, Levine NM, Cutter LS, Wang D, Seegers B, et al. Microbial rhodopsins are major contributors to the solar energy captured in the sea. Sci Adv. 2019;5:eaaw8855. doi: 10.1126/sciadv.aaw8855. PubMed DOI PMC

Campbell BJ, Waidner LA, Cottrell MT, Kirchman DL. Abundant proteorhodopsin genes in the North Atlantic Ocean. Environ Microbiol. 2008;10:99–109. PubMed

Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, Yooseph S, et al. The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol. 2007;5:e77. doi: 10.1371/journal.pbio.0050077. PubMed DOI PMC

Sabehi G, Massana R, Bielawski JP, Rosenberg M, Delong EF, Beja O. Novel proteorhodopsin variants from the Mediterranean and Red Seas. Environ Microbiol. 2003;5:842–9. doi: 10.1046/j.1462-2920.2003.00493.x. PubMed DOI

Sieradzki ET, Fuhrman JA, Rivero-Calle S, Gomez-Consarnau L. Proteorhodopsins dominate the expression of phototrophic mechanisms in seasonal and dynamic marine picoplankton communities. PeerJ. 2018;6:e5798. doi: 10.7717/peerj.5798. PubMed DOI PMC

Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science. 2004;304:66–74. doi: 10.1126/science.1093857. PubMed DOI

Dubinsky V, Haber M, Burgsdorf I, Saurav K, Lehahn Y, Malik A, et al. Metagenomic analysis reveals unusually high incidence of proteorhodopsin genes in the ultraoligotrophic Eastern Mediterranean Sea. Environ Microbiol. 2017;19:1077–90. doi: 10.1111/1462-2920.13624. PubMed DOI

Vollmers J, Voget S, Dietrich S, Gollnow K, Smits M, Meyer K, et al. Poles apart: Arctic and Antarctic Octadecabacter strains share high genome plasticity and a new type of xanthorhodopsin. PLoS ONE. 2013;8:e63422. doi: 10.1371/journal.pone.0063422. PubMed DOI PMC

Sharma AK, Spudich JL, Doolittle WF. Microbial rhodopsins: functional versatility and genetic mobility. Trends Microbiol. 2006;14:463–9. doi: 10.1016/j.tim.2006.09.006. PubMed DOI

Gomez-Consarnau L, Akram N, Lindell K, Pedersen A, Neutze R, Milton DL, et al. Proteorhodopsin phototrophy promotes survival of marine bacteria during starvation. PLoS Biol. 2010;8:e1000358. doi: 10.1371/journal.pbio.1000358. PubMed DOI PMC

Gonzalez JM, Fernandez-Gomez B, Fernandez-Guerra A, Gomez-Consarnau L, Sanchez O, Coll-Llado M, et al. Genome analysis of the proteorhodopsin-containing marine bacterium Polaribacter sp. MED152 (Flavobacteria) Proc Natl Acad Sci USA. 2008;105:8724–9. doi: 10.1073/pnas.0712027105. PubMed DOI PMC

Kimura H, Young CR, Martinez A, Delong EF. Light-induced transcriptional responses associated with proteorhodopsin-enhanced growth in a marine flavobacterium. ISME J. 2011;5:1641–51. doi: 10.1038/ismej.2011.36. PubMed DOI PMC

Riedel T, Tomasch J, Buchholz I, Jacobs J, Kollenberg M, Gerdts G, et al. Constitutive expression of the proteorhodopsin gene by a flavobacterium strain representative of the proteorhodopsin-producing microbial community in the North Sea. Appl Environ Microbiol. 2010;76:3187–97. doi: 10.1128/AEM.02971-09. PubMed DOI PMC

Stingl U, Desiderio RA, Cho JC, Vergin KL, Giovannoni SJ. The SAR92 clade: an abundant coastal clade of culturable marine bacteria possessing proteorhodopsin. Appl Environ Microbiol. 2007;73:2290–6. doi: 10.1128/AEM.02559-06. PubMed DOI PMC

Yoshizawa S, Kawanabe A, Ito H, Kandori H, Kogure K. Diversity and functional analysis of proteorhodopsin in marine Flavobacteria. Environ Microbiol. 2012;14:1240–8. doi: 10.1111/j.1462-2920.2012.02702.x. PubMed DOI

Giovannoni S, Stingl U. The importance of culturing bacterioplankton in the ‘omics’ age. Nat Rev Microbiol. 2007;5:820–6. doi: 10.1038/nrmicro1752. PubMed DOI

Haro-Moreno JM, Lopez-Perez M, de la Torre JR, Picazo A, Camacho A, Rodriguez-Valera F. Fine metagenomic profile of the Mediterranean stratified and mixed water columns revealed by assembly and recruitment. Microbiome. 2018;6:128. doi: 10.1186/s40168-018-0513-5. PubMed DOI PMC

Freitas S, Hatosy S, Fuhrman JA, Huse SM, Welch DB, Sogin ML, et al. Global distribution and diversity of marine Verrucomicrobia. ISME J. 2012;6:1499–505. doi: 10.1038/ismej.2012.3. PubMed DOI PMC

Herlemann DP, Lundin D, Labrenz M, Jurgens K, Zheng Z, Aspeborg H, et al. Metagenomic de novo assembly of an aquatic representative of the verrucomicrobial class Spartobacteria. mBio. 2013;4:e00569–00512. doi: 10.1128/mBio.00569-12. PubMed DOI PMC

Landry ZC, Vergin K, Mannenbach C, Block S, Yang Q, Blainey P, et al. Optofluidic single-cell genome amplification of sub-micron bacteria in the ocean subsurface. Front Microbiol. 2018;9:1152. doi: 10.3389/fmicb.2018.01152. PubMed DOI PMC

Sichert A, Corzett CH, Schechter MS, Unfried F, Markert S, Becher D, et al. Verrucomicrobia use hundreds of enzymes to digest the algal polysaccharide fucoidan. Nat Microbiol. 2020;5:1026–39. doi: 10.1038/s41564-020-0720-2. PubMed DOI

Yoon J, Yasumoto-Hirose M, Matsuo Y, Nozawa M, Matsuda S, Kasai H, et al. Pelagicoccus mobilis gen. nov., sp. nov., Pelagicoccus albus sp. nov. and Pelagicoccus litoralis sp. nov., three novel members of subdivision 4 within the phylum ‘Verrucomicrobia’, isolated from seawater by in situ cultivation. Int J Syst Evol. 2007;57:1377–85. doi: 10.1099/ijs.0.64970-0. PubMed DOI

Crespo BG, Pommier T, Fernandez-Gomez B, Pedros-Alio C. Taxonomic composition of the particle-attached and free-living bacterial assemblages in the Northwest Mediterranean Sea analyzed by pyrosequencing of the 16S rRNA. Microbiologyopen. 2013;2:541–52. doi: 10.1002/mbo3.92. PubMed DOI PMC

Connon SA, Giovannoni SJ. High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates. Appl Environ Microbiol. 2002;68:3878–85. doi: 10.1128/AEM.68.8.3878-3885.2002. PubMed DOI PMC

Sizikov S, Burgsdorf I, Handley KM, Lahyani M, Haber M, Steindler L. Characterization of sponge-associated Verrucomicrobia: microcompartment-based sugar utilization and enhanced toxin-antitoxin modules as features of host-associated Opitutales. Environ Microbiol. 2020;22:4669–88. doi: 10.1111/1462-2920.15210. PubMed DOI

Stingl U, Tripp HJ, Giovannoni SJ. Improvements of high-throughput culturing yielded novel SAR11 strains and other abundant marine bacteria from the Oregon coast and the Bermuda Atlantic Time Series study site. ISME J. 2007;1:361–71. doi: 10.1038/ismej.2007.49. PubMed DOI

Olm MR, Brown CT, Brooks B, Banfield JF. dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J. 2017;11:2864–8. doi: 10.1038/ismej.2017.126. PubMed DOI PMC

Asnicar F, Thomas AM, Beghini F, Mengoni C, Manara S, Manghi P, et al. Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0. Nat Commun. 2020;11:2500. doi: 10.1038/s41467-020-16366-7. PubMed DOI PMC

Hassanzadeh B, Thomson B, Deans F, Wenley J, Lockwood S, Currie K, et al. Microbial rhodopsins are increasingly favoured over chlorophyll in High Nutrient Low Chlorophyll waters. Environ Microbiol Rep. 2021;13:401–6. doi: 10.1111/1758-2229.12948. PubMed DOI

Roth Rosenberg D, Haber M, Goldford J, Lalzar M, Aharonovich D, Al-Ashhab A, et al. Particle-associated and free-living bacterial communities in an oligotrophic sea are affected by different environmental factors. Environ Microbiol. 2021;23:4295–308. doi: 10.1111/1462-2920.15611. PubMed DOI

Salazar G, Paoli L, Alberti A, Huerta-Cepas J, Ruscheweyh HJ, Cuenca M, et al. Gene expression changes and community turnover differentially shape the global ocean metatranscriptome. Cell. 2019;179:1068–83.e1021. doi: 10.1016/j.cell.2019.10.014. PubMed DOI PMC

Mende DR, Sunagawa S, Zeller G, Bork P. Accurate and universal delineation of prokaryotic species. Nat Methods. 2013;10:881–4. doi: 10.1038/nmeth.2575. PubMed DOI

Besemer J, Lomsadze A, Borodovsky M. GeneMarkS. a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res. 2001;29:2607–18. doi: 10.1093/nar/29.12.2607. PubMed DOI PMC

Eddy SR. Profile hidden Markov models. Bioinformatics. 1998;14:755–63. doi: 10.1093/bioinformatics/14.9.755. PubMed DOI

Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. BLAST+: architecture and applications. BMC Bioinform. 2009;10:421. doi: 10.1186/1471-2105-10-421. PubMed DOI PMC

Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006;22:1658–9. doi: 10.1093/bioinformatics/btl158. PubMed DOI

Katoh K, Misawa K, Kuma K, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002;30:3059–66. doi: 10.1093/nar/gkf436. PubMed DOI PMC

Capella-Gutierrez S, Silla-Martinez JM, Gabaldon T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009;25:1972–3. doi: 10.1093/bioinformatics/btp348. PubMed DOI PMC

Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015;32:268–74. doi: 10.1093/molbev/msu300. PubMed DOI PMC

Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics. 2010;26:2460–1. doi: 10.1093/bioinformatics/btq461. PubMed DOI

Barco RA, Garrity GM, Scott JJ, Amend JP, Nealson KH, Emerson D. A genus definition for bacteria and archaea based on a standard genome relatedness index. mBio. 2020;11:e02475-19. doi: 10.1128/mBio.02475-19. PubMed DOI PMC

Pushkarev A, Beja O. Functional metagenomic screen reveals new and diverse microbial rhodopsins. ISME J. 2016;10:2331–5. doi: 10.1038/ismej.2016.7. PubMed DOI PMC

Sabehi G, Loy A, Jung KH, Partha R, Spudich JL, Isaacson T, et al. New insights into metabolic properties of marine bacteria encoding proteorhodopsins. PLoS Biol. 2005;3:e273. doi: 10.1371/journal.pbio.0030273. PubMed DOI PMC

Iwasaka H, Koyanagi R, Satoh R, Nagano A, Watanabe K, Hisata K, et al. A possible trifunctional beta-carotene synthase gene identified in the draft genome of Aurantiochytrium sp. strain KH105. Genes. 2018;9:200. doi: 10.3390/genes9040200. PubMed DOI PMC

Rabeharindranto H, Castano-Cerezo S, Lautier T, Garcia-Alles LF, Treitz C, Tholey A, et al. Enzyme-fusion strategies for redirecting and improving carotenoid synthesis in S. cerevisiae. Metab Eng Commun. 2019;8:e00086. doi: 10.1016/j.mec.2019.e00086. PubMed DOI PMC

Cabello-Yeves PJ, Ghai R, Mehrshad M, Picazo A, Camacho A, Rodriguez-Valera F. Reconstruction of diverse verrucomicrobial genomes from metagenome datasets of freshwater reservoirs. Front Microbiol. 2017;8:2131. doi: 10.3389/fmicb.2017.02131. PubMed DOI PMC

Martinez-Garcia M, Swan BK, Poulton NJ, Gomez ML, Masland D, Sieracki ME, et al. High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton. ISME J. 2012;6:113–23. doi: 10.1038/ismej.2011.84. PubMed DOI PMC

Orellana LH, Francis TB, Ferraro M, Hehemann JH, Fuchs BM, Amann RI. Verrucomicrobiota are specialist consumers of sulfated methyl pentoses during diatom blooms. ISME J. 2022;16:630–41. doi: 10.1038/s41396-021-01105-7. PubMed DOI PMC

Haber M, Rosenberg DR, Lalzar M, Burgsdorf I, Saurav K, Lionheart R, et al. Spatiotemporal variation of microbial communities in the ultraoligotrophic Eastern Mediterranean Sea. Front Microbiol. 2022;13:867694. doi: 10.3389/fmicb.2022.867694. PubMed DOI PMC

Giovannoni SJ, Bibbs L, Cho JC, Stapels MD, Desiderio R, Vergin KL, et al. Proteorhodopsin in the ubiquitous marine bacterium SAR11. Nature. 2005;438:82–85. doi: 10.1038/nature04032. PubMed DOI

Walter JM, Greenfield D, Bustamante C, Liphardt J. Light-powering Escherichia coli with proteorhodopsin. Proc Natl Acad Sci USA. 2007;104:2408–12. doi: 10.1073/pnas.0611035104. PubMed DOI PMC

Vidal-Melgosa S, Sichert A, Francis TB, Bartosik D, Niggemann J, Wichels A, et al. Diatom fucan polysaccharide precipitates carbon during algal blooms. Nat Commun. 2021;12:1150. doi: 10.1038/s41467-021-21009-6. PubMed DOI PMC

Cardman Z, Arnosti C, Durbin A, Ziervogel K, Cox C, Steen AD, et al. Verrucomicrobia are candidates for polysaccharide-degrading bacterioplankton in an arctic fjord of Svalbard. Appl Environ Microbiol. 2014;80:3749–56. doi: 10.1128/AEM.00899-14. PubMed DOI PMC

Martinez-Garcia M, Brazel DM, Swan BK, Arnosti C, Chain PS, Reitenga KG, et al. Capturing single cell genomes of active polysaccharide degraders: an unexpected contribution of Verrucomicrobia. PLoS ONE. 2012;7:e35314. doi: 10.1371/journal.pone.0035314. PubMed DOI PMC

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