ena-STUDY-UNIVERSITY OF CALIFORNIA - SAN DIEGO-01-05-2015-22:34:03:216-87
Single-cell genomics of Prochlorococcus and SAR11 from the Red Sea
Among marine environments, the Red Sea is one of the most extreme, with year-round high solar irradiance, high temperature, high salinity, and low nutrient levels. To address whether the Red Sea harbors unique genetic adaptations to these extreme conditions, we sequenced the single-cell genomes of 5 Prochlorococcus cells and 21 SAR11 cells (including three SAR11 subclades without sequenced representatives) from a surface sample in the east-central Red Sea. We identified genes (clusters of orthologous genes) not found in genomes of these taxa from outside the Red Sea. The genes putatively exclusive to the Red Sea ("RS-only") encode functions involved in thermal stability of proteins and other functions, which can be implicated in an adaptive response to high temperature and high salinity. We showed that 67% of Prochlorococcus and 52% of SAR11 "RS-only" gene clusters are expressed in a surface metatranscriptome at some point over a 48-hour diel cycle, suggesting functional roles in the environment. However, of those same "RS-only" genes, 54% of Prochlorococcus and 77% of SAR11 genes are also found in one of the Global Ocean Sampling or several other surface metagenomes from other oceans. Remarkably, examining a metagenome from the surface Red Sea adds only 3 total additional genes not found in the other samples. These results suggest that most of the adaptations that seem endemic for a given region appear so only because of insufficient sequencing, and that not only most species but also most genes can be found provided sufficient sampling and sequecing effort.
Among marine environments, the Red Sea is one of the most extreme, with year-round high solar irradiance, high temperature, high salinity, and low nutrient levels. To address whether the Red Sea harbors unique genetic adaptations to these extreme conditions, we sequenced the single-cell genomes of 5 Prochlorococcus cells and 21 SAR11 cells (including three SAR11 subclades without sequenced representatives) from a surface sample in the east-central Red Sea. We identified genes (clusters of orthologous genes) not found in genomes of these taxa from outside the Red Sea. The genes putatively exclusive to the Red Sea ("RS-only") encode functions involved in thermal stability of proteins and other functions, which can be implicated in an adaptive response to high temperature and high salinity. We showed that 67% of Prochlorococcus and 52% of SAR11 "RS-only" gene clusters are expressed in a surface metatranscriptome at some point over a 48-hour diel cycle, suggesting functional roles in the environment. However, of those same "RS-only" genes, 54% of Prochlorococcus and 77% of SAR11 genes are also found in one of the Global Ocean Sampling or several other surface metagenomes from other oceans. Remarkably, examining a metagenome from the surface Red Sea adds only 3 total additional genes not found in the other samples. These results suggest that most of the adaptations that seem endemic for a given region appear so only because of insufficient sequencing, and that not only most species but also most genes can be found provided sufficient sampling and sequecing effort.