Ecogenomics of the SAR11 clade.

Jose M Haro‐Moreno,Mario López‐Pérez,Francisco Rodriguez‐Valera,Monica Lluesma Gomez,Juan J Roda‐Garcia,Riccardo Rosselli,Manuel Martinez‐Garcia,Francisco Martinez‐Hernandez,Oscar Fornas

doi:10.1111/1462-2920.14896

Abstract

SummaryMembers 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.

Highlights

The SAR11 clade, as originally defined by 16S rRNA sequences (Giovannoni et al, 1990), is a group of extremely successful pelagic bacteria, among the most abundant in aquatic environments, accounting for about 25% of the plankton cells in upper regions of the ocean photic zone (Morris et al, 2002; Rappé et al, 2002; Thorpe et al, 2007; Salcher et al, 2011)
A comparison of this classification with the phylogenetic reconstruction based on rRNA internal transcribed spacer (ITS) (Fig. S1) showed that both trees have almost the same topology, with the exception of subclade Ia.2, which appeared as part of phylotype Ia.3 in the phylogenomic classification (Fig. 1), as it has been recently suggested (Delmont et al, 2019)
We have found a remarkable degree of diversity despite the relative conservation of the 16S rRNA sequences or the overall synteny

Summary

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. 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. 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

Introduction

Results and discussion

Conclusions

Experimental procedures