Ecogenomics of the SAR11 clade

Members of the SAR11 clade, despite their high abundance, are often poorly represented by metagenome‐assembled genomes. This fact has hampered our knowledge about their ecology and genetic diversity. Here we examined 175 SAR11 genomes, including 47 new single‐amplified genomes. The presence of the first genomes associated with subclade IV suggests that, in the same way as subclade V, they might be outside the proposed Pelagibacterales order. An expanded phylogenomic classification together with patterns of metagenomic recruitment at a global scale have allowed us to define new ecogenomic units of classification (genomospecies), appearing at different, and sometimes restricted, metagenomic data sets. We detected greater microdiversity across the water column at a single location than in samples collected from similar depth across the global ocean, suggesting little influence of biogeography. In addition, pangenome analysis revealed that the flexible genome was essential to shape genomospecies distribution. In one genomospecies preferentially found within the Mediterranean, a set of genes involved in phosphonate utilization was detected. While another, with a more cosmopolitan distribution, was unique in having an aerobic purine degradation pathway. Together, these results provide a glimpse of the enormous genomic diversity within this clade at a finer resolution than the currently defined clades. This work was supported by grant ‘VIREVO’ CGL2016-76273-P [AEI/FEDER, EU] (cofounded with FEDER funds) from the Spanish Ministerio de Economía, Industria y Competitividad to FRV, and grants CGL2013-40564-R and SAF2013-49267-EXP from the Spanish Ministerio de Economía, Industria y Competitividad, grant ACIF/2015/332 from Generalitat Valenciana and grant 5334 from the Betty Moore Foundation to MMG. FRV was also a beneficiary of the 5top100-program of the Ministry for Science and Education of Russia. JHM was supported by a Ph.D. fellowship from the Spanish Ministerio de Economía y Competitividad (BES-2014-067828). MLP was supported by a postdoctoral fellowship from the Spanish Ministerio de Economía, Industria y Competitividad (IJCI-2017-34002).