Biodiversity and biogeography of phages in modern stromatolites and thrombolites

Living fossils Stromatolites are living, layered structures formed in shallow waters by a combination of microbial biofilms — usually of blue-green algae — and granular deposits. They are rare today but for about 2 billion years, following their arrival in the fossil record 3.5 billion years ago, they are the main evidence of life on Earth. Modern stromatolites still look like their fossilized forebears. But are the modern microbes remnants of ancient ecosystems or just latecomers following a similar lifestyle? A metagenomic study of the bacteriophage communities in modern stromatolites and thrombolites (like stromatolites but with an irregular internal structure) shows that stromatolite-associated phages are very different from each other and from any other ecosystem studied so far. This finding strengthens the hypothesis that modern stromatolites are remnants of ancient ecosystems. Use of a comparative metagenomic approach suggests that phage communities in microbialites are endemic, and that marine and freshwater systems may share a common ancestral viral community. Viruses, and more particularly phages (viruses that infect bacteria), represent one of the most abundant living entities in aquatic and terrestrial environments. The biogeography of phages has only recently been investigated and so far reveals a cosmopolitan distribution of phage genetic material (or genotypes) 1 , 2 , 3 , 4 . Here we address this cosmopolitan distribution through the analysis of phage communities in modern microbialites, the living representatives of one of the most ancient life forms on Earth. On the basis of a comparative metagenomic analysis of viral communities associated with marine (Highborne Cay, Bahamas) and freshwater (Pozas Azules II and Rio Mesquites, Mexico) microbialites, we show that some phage genotypes are geographically restricted. The high percentage of unknown sequences recovered from the three metagenomes (>97%), the low percentage similarities with sequences from other environmental viral ( n = 42) and microbial ( n = 36) metagenomes, and the absence of viral genotypes shared among microbialites indicate that viruses are genetically unique in these environments. Identifiable sequences in the Highborne Cay metagenome were dominated by single-stranded DNA microphages that were not detected in any other samples examined, including sea water, fresh water, sediment, terrestrial, extreme, metazoan-associated and marine microbial mats. Finally, a marine signat