Distribution and expression of microbial rhodopsins in the Baltic Sea and adjacent waters.
Rhodopsins are light-driven ion-pumping membrane proteins found in many organisms and are proposed to be of global importance for oceanic microbial energy generation. Several studies have focused on marine environments, with less exploration of rhodopsins in brackish waters. We investigated microbial rhodopsins in the Baltic Sea using size-fractionated metagenomic and metatranscriptomic datasets collected along a salinity gradient spanning from ∼0 to 35 PSU. The normalised genomic abundance of rhodopsins in Bacteria, as well as rhodopsin gene expression, was highest in the smallest size fraction (0.1-0.8 μm), relative to the medium (0.8-3.0 μm) and large (>3.0 μm) size fractions. The abundance of rhodopsins in the two smaller size fractions displayed a positive correlation with salinity. Proteobacteria and Bacteroidetes rhodopsins were the most abundant while Actinobacteria rhodopsins, or actinorhodopsins, were common at lower salinities. Phylogenetic analysis indicated that rhodopsins have adapted independently to the marine-brackish transition on multiple occasions, giving rise to green light-adapted variants from ancestral blue light-adapted ones. A notable diversity of viral-like rhodopsins was also detected in the dataset and potentially linked with eukaryotic phytoplankton blooms. Finally, a new clade of likely proton-pumping rhodopsin with non-canonical amino acids in the spectral tuning and proton accepting site was identified.
Department of Ecology, Environment and Plant Sciences, Stockholm University, Science for Life Laboratory, Solna, SE-17121, Sweden.
Björn
B
Brindefalk
Department of Ecology, Environment and Plant Sciences, Stockholm University, Science for Life Laboratory, Solna, SE-17121, Sweden.
Martin
M
Ekman
Department of Ecology, Environment and Plant Sciences, Stockholm University, Science for Life Laboratory, Solna, SE-17121, Sweden.
Karolina
K
Ininbergs
Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, CA, 92037, USA.
Christopher L
CL
Dupont
Informatics Group, J. Craig Venter Institute, San Diego, CA, 92037, USA.
Shibu
S
Yooseph
Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, SE-391 82, Sweden.
Jarone
J
Pinhassi
Department of Ecology, Environment and Plant Sciences, Stockholm University, Science for Life Laboratory, Solna, SE-17121, Sweden.
Birgitta
B
Bergman
D000222:Adaptation, Physiological / Q000235:genetics; D001419:Bacteria / Q000235:genetics* / Q000378:metabolism*; D015964:Gene Expression Regulation, Bacterial / Q000502:physiology; D008027:Light; D009792:Oceans and Seas; D010802:Phylogeny; D010839:Phytoplankton / Q000378:metabolism; D025604:Rhodopsins, Microbial / Q000737:chemistry* / Q000235:genetics*; D014871:Water Microbiology
D025604:Rhodopsins, Microbial