Metagenomic analysis reveals that modern microbialites and polar microbial mats have similar taxonomic and functional potential

Abstract

Within the subarctic climate of Clinton Creek, Yukon, Canada, lies an abandoned and flooded open-pit asbestos mine that harbors rapidly growing microbialites. To understand their formation we completed a metagenomic community profile of the microbialites and their surrounding sediments. Assembled metagenomic data revealed that bacteria within the phylum Proteobacteria numerically dominated this system, although the relative abundances of taxa within the phylum varied among environments. Bacteria belonging to Alphaproteobacteria and Gammaproteobacteria were dominant in the microbialites and sediments, respectively. The microbialites were also home to many other groups associated with microbialite formation including filamentous cyanobacteria and dissimilatory sulfate-reducing Deltaproteobacteria, consistent with the idea of a shared global microbialite microbiome. Other members were present that are typically not associated with microbialites including Gemmatimonadetes and iron-oxidizing Betaproteobacteria, which participate in carbon metabolism and iron cycling. Compared to the sediments, the microbialite microbiome has significantly more genes associated with photosynthetic processes (e.g., photosystem II reaction centers, carotenoid, and chlorophyll biosynthesis) and carbon fixation (e.g., CO dehydrogenase). The Clinton Creek microbialite communities had strikingly similar functional potentials to non-lithifying microbial mats from the Canadian High Arctic and Antarctica, but are functionally distinct, from non-lithifying mats or biofilms from Yellowstone. Clinton Creek microbialites also share metabolic genes (R2 < 0.750) with freshwater microbial mats from Cuatro Ciénegas, Mexico, but are more similar to polar Arctic mats (R2 > 0.900). These metagenomic profiles from an anthropogenic microbialite-forming ecosystem provide context to microbialite formation on a human-relevant timescale.

Comparative metagenomics of microbial mats from hypersaline lakes at Rottnest Island (WA, Australia), advancing our understanding of the effect of mat community and functional genes on microbialite accretion

“…Non‐lithifying mats had a higher abundance ( p < 0.01) of Firmicutes, particularly Bacilli and Clostridia, when compared to lithifying mats. Similar results were observed in Highborne Cay, Clifton Creek (Yukon, Canada) and Cuatro Ciénegas Basin, where the non‐lithifying mats analyzed also had higher relative abundance of Bacilli and Clostridia, in comparison to microbialite‐associated mats (Bonilla‐Rosso et al ; Khodadad and Foster ; White et al ). Bacilli and Clostridia taxa are known to influence carbonate precipitation via EPS degradation—which creates mineral nucleation points for precipitation—and urease decomposition—which provides a source of CO 2 to the environment (Schneider et al ; Zhu and Dittrich ).…”

A Study of the Microbial Spatial Heterogeneity of Bahamian Thrombolites Using Molecular, Biochemical, and Stable Isotope Analyses

“…These carbonate structures are formed via the metabolic activity of microbes, which influence and drive biological processes associated with sediment capture and microbiologically induced organomineralization. Microbialites have been found in a wide range of habitats including brackish (e.g., Laval et al, 2000;Breitbart et al, 2009;White et al, 2015;Chagas et al, 2016), marine (e.g., Dravis, 1983;Reid et al, 2000;Stolz et al, 2009;Casaburi et al, 2016), and hypersaline (e.g., Logan, 1961;Glunk et al, 2011;Wong et al, 2015;Paul et al, 2016;Ruvindy et al, 2016;Suosaari et al, 2016) environments and are classified based on their internal micro-fabrics (Burne and Moore, 1987;Dupraz et al, 2009). Two of the most well-studied types of microbialites are stromatolites, which exhibit laminated internal fabrics (Walter, 1994;Reid et al, 2000), and thrombolites with irregular clotted fabrics (Aitken, 1967;Kennard and James, 1986).…”

Comparative metagenomics unveils functions and genome features of microbialite‐associated communities along a depth gradient

“…Other moderately abundant groups in AL‐N, such as Chloroflexi and Nitrospirae, remained constant along the depth gradient. Consistent with other studies (Khodadad and Foster, ; Saghaï et al ., ; White III et al ., ; Ruvindy et al ., ), the presence of Archaea was negligible (0.1–0.9% of the single‐copy genes). Archaeal sequences consisted mostly of Euryarchaeota, except in AL‐N‐5 where Thaumarchaeota dominated.…”

“…Many of these studies have mainly focused on the prokaryotic component; e.g., in marine stromatolites from Shark Bay, Australia (Burns et al, 2004;Papineau et al, 2005;Leuko et al, 2007;Allen et al, 2009;Wong et al, 2015;Suosaari et al, 2016) and Highborne Cay, Bahamas (Baumgartner et al, 2009;Foster et al, 2009;Myshrall et al, 2010;Mobberley et al, 2012), but also in non-marine microbialites, such as those of Cuatro Ci enegas (Mexico, Nitti et al, 2012), Lake Van (Turkey, L opez-Garc ıa et al, 2005), Lake Alchichica (Mexico, Couradeau et al, 2011;Sagha€ ı et al, 2015), and several other freshwater systems (Santos et al, 2010;Centeno et al, 2012;Russell et al, 2014) or hypersaline lakes (Far ıas et al, 2013;Schneider et al, 2013). In all these systems, bacteria are highly diverse and clearly dominate microbial communities, archaea being scarce (Mobberley et al, 2013;Sagha€ ı et al, 2015;White III et al, 2015;Ruvindy et al, 2016). Comparatively, microbial eukaryotes are less-well studied.…”