Rhodopsin-mediated nutrient uptake by cultivated photoheterotrophic Verrucomicrobiota

Rinat Bar-Shalom, Andrey Rozenberg, Matan Lahyani, Babak Hassanzadeh, Gobardhan Sahoo, Markus Haber, Ilia Burgsdorf, Xinyu Tang, Valeria Squatrito, Laura Gomez-Consarnau, Oded Béjà, Laura Steindler

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish
Number of pages11
JournalISME Journal
Issue number7
StatePublished - Jul 2023

Bibliographical note

Funding Information:
Funding for this project came from the Milgrom Foundation (to LS and OB) and from the United States National Science Foundation (NSF, OCE1924464 to L.G.-C) and the United States-Israel Binational Science Foundation (BSF, No. 2019612 to LS). We are very thankful to Prof. Aharon Oren for help with nomenclature. Thanks are due to Dr. Maya Ofek Lalzar, head of the Bioinformatics unit of University of Haifa, for help with the analysis performed on the 16S rRNA gene datasets. We would like to thank the captain and crew of EcoOcean for assistance on the MedEX research vessel.

Publisher Copyright:
© 2023, The Author(s).

ASJC Scopus subject areas

  • Microbiology
  • Ecology, Evolution, Behavior and Systematics


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