PRJNA285514
Phylogenetic and Functional Substrate Specificity for Endolithic Microbial Communities from the Atacama Desert
Under extreme water deficit, rapid thermal fluctuation, and high solar radiation fluxes, endolithic (inhabiting rock) microbial ecosystems are considered environmental refuges for life in cold and hot deserts around the world. Metagenomics analysis of two rock substrates, calcite (calcium carbonate) and ignimbrite (volcanic glass), revealed that the communities were dominated by Cyanobacteria, Actinobacteria, and Chloroflexi, but that the relative distribution of these phyla was significantly different between the two substrates. Biodiversity estimates from 16S rRNA gene sequences and from the metagenome data all pointed to a higher taxonomic diversity for the calcite community. While the functional capabilities of the two communities appeared similar and tailored to the rock environment (photosynthetic-based), pathways for iron and Mn transport, and for osmoregulation were more diverse in the calcite community. These findings likely relate to the large cracks in the calcite rock favoring water retention, the assembly of a more diverse community, and increased interactions among community members. In contrast, the ignimbrite community was enriched in pathways for secondary metabolites, such as non-ribosomal peptides (NRPS) and polyketides (PKS), indicating a harsh competition for space in the narrow pores of the rock. Assemblies of the metagenome data produced population genomes for the major phyla found in both communities and revealed a greater phylogenetic diversity for the calcite Cyanobacteria population genomes. Draft genomes of the dominant Cyanobacteria in each community were constructed with more than 93% estimated completeness. The two annotated proteomes shared 64% amino acid identity but a significant higher number of clusters for NRPS and PKS were found in the ignimbrite draft genome. Together, these results indicate that the architecture of the rock substrate might be an essential element in determining the colonization, and the diversity, of the microbial communities in endolithic substrates at the dry limit for life.