Abstract
Modern microbialites are complex microbial communities that interface with abiotic factors to form carbonate-rich organosedimentary structures whose ancestors provide the earliest evidence of life. Past studies primarily on marine microbialites have inventoried diverse taxa and metabolic pathways, but it is unclear which of these are members of the microbialite community and which are introduced from adjacent environments. Here we control for these factors by sampling the surrounding water and nearby sediment, in addition to the microbialites and use a metagenomics approach to interrogate the microbial community. Our findings suggest that the Pavilion Lake microbialite community profile, metabolic potential and pathway distributions are distinct from those in the neighboring sediments and water. Based on RefSeq classification, members of the Proteobacteria (e.g., alpha and delta classes) were the dominant taxa in the microbialites, and possessed novel functional guilds associated with the metabolism of heavy metals, antibiotic resistance, primary alcohol biosynthesis and urea metabolism; the latter may help drive biomineralization. Urea metabolism within Pavilion Lake microbialites is a feature not previously associated in other microbialites. The microbialite communities were also significantly enriched for cyanobacteria and acidobacteria, which likely play an important role in biomineralization. Additional findings suggest that Pavilion Lake microbialites are under viral selection as genes associated with viral infection (e.g CRISPR-Cas, phage shock and phage excision) are abundant within the microbialite metagenomes. The morphology of Pavilion Lake microbialites changes dramatically with depth; yet, metagenomic data did not vary significantly by morphology or depth, indicating that microbialite morphology is altered by other factors, perhaps transcriptional differences or abiotic conditions. This work provides a comprehensive metagenomic perspective of the interactions and differences between microbialites and their surrounding environment, and reveals the distinct nature of these complex communities.
Highlights
Microbialites are a specialized group of microbial mats that lithify carbonate-rich structures, and include thrombolites that consist of structures with unlaminated clots and stromatolites that have laminated layers (Burne and Moore, 1987; Perry et al, 2007)
We examine the novel metabolic potential associated with Pavilion Lake microbialites and investigate whether metabolic potential, not solely taxa, changes as a function of microbialite morphology
ANOVA using statistical analysis of metagenomic profiles (STAMP) on the highest level classification in the SEED database indicates that membrane transport, aromatic metabolism, motility, potassium metabolism, cell signaling and virulence genes are significantly enriched in microbialites over the surrounding environment (Table 3, p < 0.05)
Summary
Microbialites are a specialized group of microbial mats that lithify carbonate-rich structures, and include thrombolites that consist of structures with unlaminated clots and stromatolites that have laminated layers (Burne and Moore, 1987; Perry et al, 2007). Exploring the genetic differences between microbialite communities and those in the surrounding habitats requires identifying the relative abundance of taxa and their metabolic potential. To avoid distorting these ratios, DNA was extracted and unlike in other metagenomic studies of microbialites (Breitbart et al, 2009), sequenced without amplification. We sequenced total genomic DNA from cold temperate freshwater microbialites, as well as from the nearby sediment and water, to identify constituent taxa and infer their metabolic functional potential. We explore whether heterotrophic or phototrophic pathways dominate the microbialite functional metabolic potential in association with carbonate precipitation, and examine virus-host whole community interactions.
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