title: Selection Maintains Low Genomic GC Content in Marine SAR11 Lineages.
abstract: The genomic G+C content of ocean bacteria varies from below 30% to over 60%. This broad range of base composition is likely shaped by distinct mutational processes, recombination, effective population size, and selection driven by environmental factors. A number of studies have hypothesized that depletion of G/C in genomes of marine bacterioplankton cells is an adaptation to the nitrogen-poor pelagic oceans, but they failed to disentangle environmental factors from mutational biases and population history. Here, we reconstructed the evolutionary changes of bases at synonymous sites in genomes of two marine SAR11 populations and a freshwater counterpart with its evolutionary origin rooted in the marine lineage. Although they all have similar genome sizes, DNA repair gene repertoire, and base compositions, there is a stronger bias toward A/T changes, a reduced frequency of nitrogenous amino acids, and an exclusive occurrence of polyamine, opine, and taurine transport systems in the ocean populations, consistent with a greater nitrogen stress in surface oceans compared with freshwater lakes. Furthermore, the ratio of nonsynoymous to synonymous nucleotide diversity is not statistically distinguishable among these populations, suggesting that population history has a limited effect. Taken together, the ecological transition of SAR11 from ocean to freshwater habitats makes nitrogen more available to these organisms, and thus relaxation of purifying selection drove a genome-wide reduction in the frequency of G/C to A/T changes in the freshwater population.
authors.affiliation: Simon F. S. Li Marine Science Laboratory, School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China hluo2006@gmail.com.
authors.forename: Haiwei
authors.initials: H
authors.lastname: Luo
authors.affiliation: Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
authors.forename: Luke R
authors.initials: LR
authors.lastname: Thompson
authors.affiliation: Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
authors.forename: Ulrich
authors.initials: U
authors.lastname: Stingl
authors.affiliation: Department of Biological Sciences, University of South Carolina.
authors.forename: Austin L
authors.initials: AL
authors.lastname: Hughes
mesh_terms: D000222:Adaptation, Physiological / Q000187:drug effects / Q000235:genetics; D000596:Amino Acids / Q000235:genetics; D001482:Base Composition / Q000235:genetics*; D001483:Base Sequence; D005618:Fresh Water / Q000382:microbiology; D016680:Genome, Bacterial; D016013:Likelihood Functions; D009584:Nitrogen / Q000494:pharmacology; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012623:Seawater / Q000382:microbiology*; D012641:Selection, Genetic; D013312:Stress, Physiological / Q000187:drug effects
chemical_list: D000596:Amino Acids; D012336:RNA, Ribosomal, 16S; D009584:Nitrogen
keywords: GC content; LD12; SAR11; alphaproteobacteria; bacterioplankton evolution; genome streamlining; nitrogen limitation