Ecogenomics of the SAR11 clade

Abstract

Members of the SAR11 clade, despite their high abundance, are often poorly represented by metagenomeassembled 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.Received

Microdiversity and phylogeographic diversification of bacterioplankton in pelagic freshwater systems revealed through long-read amplicon sequencing

“…The results demonstrated sympatric, allopatric, and temporal microdiversity in lake bacterioplankton and revealed phylogeographic patterns that could not be observed based on shortread amplicon sequencing or the MAG-based approach. Our results consistently supported genetic isolation between lakes in Japan and Europe, in contrast to previous reports of genomes sharing ANI>95% in freshwater habitats thousands of kilometers apart [40,43,44,46] as well as in distant marine [83,84] systems. The rapid accumulation of sequence data obtained from all over the world will allow for this topic to be revisited to draw broader conclusions about the global-scale dispersal and diversification processes of ubiquitous freshwater bacterioplankton lineages.…”

Metagenome Mining Reveals Hidden Genomic Diversity of Pelagimyophages in Aquatic Environments

“…Glycosyltransferases in bacteriophages are involved in the glycosylation of viral DNA to protect against the host restrictionmodification systems or in the modification of the O-antigen chain of the host to protect against coinfection by other phages (36). Considering that the glycosyltransferase family most represented in PMPs is GT8, which is mainly involved in LPS biosynthesis (78), and that only one SAR11 genome out of more than 100 sequenced thus far codes for a restriction-modification system (79), it seems likely that glycosyltransferases in this group are involved in the modification of the O-chain of their host.…”

The Evolutionary Success of the Marine Bacterium SAR11 Analyzed through a Metagenomic Perspective

“…Despite being the most abundant and successful marine microorganisms in the surface ocean (28), the study of SAR11 population structures and dynamics has lagged considerably due to the difficulty of culturing and isolating these organisms and the paradoxical difficulty of obtaining MAGs for this group, as demonstrated by several marine metagenomic studies around the world (8,29,30). Single-cell genomics overcame some of these limitations of metagenomic assembly and promoted the increase in the number of individual genomes sequenced of the SAR11 clade, thus disentangling part of the elusive genetic diversity among members of this taxon (24,(31)(32)(33)(34)(35)(36). Although the delimitation of populations within this clade is a controversial issue, in a recent study, an improved phylogenomic classification (enriched by single-cell genomes) based on whole-genome comparisons, together with a fine ecogenomic characterization of SAR11 at a global scale, allowed discerning novel operational taxonomic units, which were called genomospecies (33).…”