Precambrian phototrophic microbial mats were important drivers of Earth's biogeochemical cycles, but their impact on Archean atmospheric CO2 concentrations orders of magnitude larger than today is poorly understood. Modern microbial mats serve as models for interpreting Precambrian stromatolite fossils and for studying modern microbial ecology. It is unclear how the genetic and metabolic diversity of microbial communities that are dominated by phototrophic bacteria in Yellowstone National Park (Wyoming, USA) is distributed, so we applied comparative metagenomic techniques to better understand how differences in community composition are related to the functional repertoires among their constituent organisms, and how this is influenced by geographic distribution. We obtained 2,355 16S rRNA clone sequences and 320 Mbp of whole genome shotgun (WGS) sequence from six high-temperature (33-60°C) springs. Community structure differences among springs were determined with 16S rRNA sequences, and these differences correlated with geochemical parameters. Overlapping metagenomic sequences were assembled into contiguous genomic scaffolds and predicted genes were annotated. Phylogenetic marker genes and annotations for genes putatively involved in phototrophy, carbon fixation, and sulfur cycling were identified. Metagenomic sequences were taxonomically grouped according to their similarity to reference genomes and also using the phylogenetic signatures inherent in the oligonucleotide frequencies of assembled scaffolds.
Different phototrophic bacteria encompassing a wide range of metabolic functional strategies were found to inhabit these springs, including oxygenic cyanobacteria, filamentous anoxygenic phototrophs (Kingdom Chloroflexi), green-sulfur bacteria (Order Chlorobiales), purple phototrophic proteobacteria, and recently discovered phototrophic acidobacteria. Springs exhibited large differences in community structure marked by the presence or absence of cyanobacteria and different lineages of anoxygenic phototrophic organisms. Many 16S rRNA-defined clades within the Chloroflexi exhibited site-specificity, suggesting that some organisms are uniquely associated with particular springs. There was correspondence between community profiles obtained from the 16S rRNA and WGS metagenomes, as shown by the abundance of particular 16S rRNA-defined taxonomic groups compared to the abundance of other phylogenetic marker genes. Scaffolds containing genes putatively involved in phototrophy, autotrophy, and sulfur cycling provide support for functional differences among guilds of anoxygenic and oxygenic phototrophs in these springs and provide further evidence for the existence of currently undescribed and uncultured phototrophic microorganisms. The combination of 16S rRNA and WGS sequencing has revealed the relative abundance of uncultivated microorganisms and their respective functional roles in these communities, leading to hypotheses regarding the primary factors controlling community structure.