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Candidatus Pelagibacter ubique HIMB083 Genome sequencing
The heterotrophic alphaproteobacterial clade SAR11 accounts for approximately 25% of microbial plankton cells in the ocean surface layer, and may exceed 50% of the cells in temperate ocean gyres during the summer, making it a key to understanding the marine carbon cycle. The first SAR11 isolate, Pelagibacter, was reported in 2002. It is one of the smallest organisms known and was the first cultured cell shown to have proteorhodopsin. The complete genome sequences from three Pelagibacter isolates range from 1.31 to 1.46 Mbp, making them the smallest genomes known for heterotrophic bacteria that are not normally found associated with a living host in nature. Selection to minimize genome size, known as genome streamlining, has been implicated as an important factor in the evolution of SAR11 genomes, and multilocus sequence typing showed very high recombination rates in one Pelagibacter population, raising questions about how selection and recombination interact to shape SAR11 phenotypes. Ecological and genomic evidence suggest that at least three SAR11 ecotypes, each with a different seasonal and spatial distribution pattern, occupy the temperate ocean surface layer. Many important questions raised by these findings can be addressed by further genome sequencing. For example, what adaptations contribute to the dominance of this clade in the oxidation of marine dissolved organic carbon to CO2, what adaptations, particularly organic carbon substrate specificities, distinguish the SAR11 ecotypes, and what evolutionary models are appropriate for this clade? Part of the power of this investigation comes from the vast amount of SAR11 genomic DNA sequence in ocean metagenomic databases, which can be used to study natural variation in features that have been identified by complete genome sequencing.