Metagenome recruitment of the global ocean survey dataset to four closely-related SAR11 genomes

Abstract

The free-living marine bacterial clade known as SAR11 is thought to be one of the most abundant lineages of organisms on our planet. It is also one of the smallest free-living organisms, and possibly the ancestor of the very successful endosymbiont, mitochondria. Members of this group of bacteria possess an incredibly small genome that displays a high degree of synteny and high DNA recombination rate, which represents the upper limit for bacteria. This study examines the global metagenomic read recruitment of the genomes of four closely related SAR11 strains, HIMB4, HIMB5, HIMB83, and HIMB140, in publicly available coastal and open ocean metagenome libraries. Recruitment plots were used to identify and analyze clusters of genes with unusual recruitment patterns, and utilized 2,797,042 open ocean and 2,131,159 coastal high quality reads. It was found that strain HIMB83 possessed the most highly recruited genome and had the highest coastal preference of the four. A hypervariable region previously identified in SAR11, HVR2, was identified in all four strains, and was characterized by a large number of genes coding for cell wall and membrane components as well as several enzymes involved in carbohydrate metabolism. HVR1 was also present in all examined genomes where it was dominated by 12 proteins involved in the type II secretion and type IV pilus pathway. The recruitment of the proteorhodopsin gene present in each of the strains was similar, with a greater degree of conservation on the 3' end of the gene. A phage integrase and extra DNA polymerase was found within the genome of HIMB4, suggesting a possible lysogenic virus present within the genome. This study adds to the current understanding of SAR11 subgroup 1a in a global context, and provides a workflow for generating metagenome recruitment plots for future studies.