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Metagenomic and genomic analyses of modern freshwater microbialites : unmasking a community of complex metabolic potential White III, Richard Allen

Abstract

Microbialites represent the oldest known persistent ecosystems and potentially the earliest evidence of life on the planet, having existed for ~85% of the geologic history of Earth (Dupraz et al., 2009). Despite over one hundred years of active research, little is known about modern freshwater microbialite ecosystems with regards to metabolic potential and microbialite-specific community structure. We performed metagenomic analysis of freshwater thrombolithic clotted microbialites from Pavilion Lake (British Columbia, Canada) and Clinton Creek (Yukon, Canada). In addition, metagenomes were obtained from the surrounding water and sediments to sort out which members of the microbial community were microbialite-specific. Pavilion Lake microbialites are distinct from the surrounding environments in microbial community structure and metabolic potential. The microbialites are dominated by heterotrophic processes with high abundances of heavy metal, antibiotic resistance, and alcohol fermentation pathways from the numerically dominant Proteobacteria. Clinton Creek houses the northern-most and fastest growing microbialites, which have a high proportion of photosynthetic genes, supporting isotopic data that photosynthesis drives microbialite formation. Clinton Creek has distinct communities, with microbialites dominated by Alphaproteobacteria (photoheterotrophs) and sediments dominated by Gammaproteobacteria (mainly heterotrophic nitrogen-fixers). To complement the metagenomic study of Pavilion Lake, a culturing based study was performed that yielded over one hundred new bacterial isolates. The new bacterial isolates were further screened for pigment containing strains that were non-photosynthetic. Amongst these pigment containing bacteria two new isolates were found and designated as an Exiguobacterium and an Agrococcus. Polyphasic analysis revealed that both are new species, which were named Agrococcus pavilionensis strain RW1 and Exiguobacterium pavilionensis strain RW2. Genome sequencing of both strain RW1 and iii RW2 was completed and a comparative genomic and phylogenetic study was performed to evaluate their evolutionary placement and metabolic potential. Both isolates have low abundance in the Pavilion Lake microbialites, although they contribute heavy metal resistance genes that are found amongst the microbialite metagenomes. Hypothetical carotenoid biosynthesis pathways are also described which may be responsible for the coloration in Agrococcus and Exiguobacterium and may be related to photo-protection.

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