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

White RA, Power IM, Dipple GM, Southam G, Suttle CA - Front Microbiol (2015)

Bottom Line: 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).

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology and Immunology, University of British Columbia Vancouver, BC, Canada.

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 (R (2) < 0.750) with freshwater microbial mats from Cuatro Ciénegas, Mexico, but are more similar to polar Arctic mats (R (2) > 0.900). These metagenomic profiles from an anthropogenic microbialite-forming ecosystem provide context to microbialite formation on a human-relevant timescale.

No MeSH data available.


Related in: MedlinePlus

Microbial community structure of Clinton Creek metagenomes. (A) Dot pot of representative taxonomic groups from Clinton Creek sediments and microbialites using RefSeq (protein coding ORFs) and M5RNA (rRNA, MG-RAST rRNA database) in log relative abundances. Samples were clustered (top) by ward clustering matrix using bootstraping of one thousand replications with Bray-Curtis distance cut-offs. “Other” denotes low abundance taxa that were < 1% of the total ORF or rRNA, individually, but were all combined here into one point. (B) PCAs of top 25 taxonomic groups from Clinton Creek sediments and microbialites by RefSeq (ORFs) and M5RNA (rRNA, MG-RAST rRNA database) classification using ward clustering matrix followed by bootstrapping of one thousand replications with Bray-Curtis distance cut-offs.
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Figure 2: Microbial community structure of Clinton Creek metagenomes. (A) Dot pot of representative taxonomic groups from Clinton Creek sediments and microbialites using RefSeq (protein coding ORFs) and M5RNA (rRNA, MG-RAST rRNA database) in log relative abundances. Samples were clustered (top) by ward clustering matrix using bootstraping of one thousand replications with Bray-Curtis distance cut-offs. “Other” denotes low abundance taxa that were < 1% of the total ORF or rRNA, individually, but were all combined here into one point. (B) PCAs of top 25 taxonomic groups from Clinton Creek sediments and microbialites by RefSeq (ORFs) and M5RNA (rRNA, MG-RAST rRNA database) classification using ward clustering matrix followed by bootstrapping of one thousand replications with Bray-Curtis distance cut-offs.

Mentions: The microbial communities within Clinton Creek are distinct from each other (Figure 2) and are dominated by differing compositions of Proteobacteria and Cyanobacteria. Proteobacteria comprised >50% of the ORFs and >35% of the 16S sequences recovered from the Clinton Creek sediments and microbialites (Figure 2). The microbialite contigs were dominated by anoxic photoheterotrophic Alphaproteobacteria (e.g., Rhodobacterales) (Figure 2A). In contrast, sediments contigs had greater abundance nitrogen-fixing Gammaproteobacteria (e.g., Pseudomonas spp.) (Figure 2A). Alphaproteobacteria are commonly found amongst, and are likely a critical component of, the microbialite-forming microbial consortium due to their role in nitrogen fixation, even in the presence of heterocystous cyanobacteria (Havemann and Foster, 2008). It has been suggested that prior to the evolution of cyanobacteria, anoxic phototrophs like Rhodobacterales could have had a role in the formation of Precambrian stromatolites (Bosak et al., 2007).


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

White RA, Power IM, Dipple GM, Southam G, Suttle CA - Front Microbiol (2015)

Microbial community structure of Clinton Creek metagenomes. (A) Dot pot of representative taxonomic groups from Clinton Creek sediments and microbialites using RefSeq (protein coding ORFs) and M5RNA (rRNA, MG-RAST rRNA database) in log relative abundances. Samples were clustered (top) by ward clustering matrix using bootstraping of one thousand replications with Bray-Curtis distance cut-offs. “Other” denotes low abundance taxa that were < 1% of the total ORF or rRNA, individually, but were all combined here into one point. (B) PCAs of top 25 taxonomic groups from Clinton Creek sediments and microbialites by RefSeq (ORFs) and M5RNA (rRNA, MG-RAST rRNA database) classification using ward clustering matrix followed by bootstrapping of one thousand replications with Bray-Curtis distance cut-offs.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4585152&req=5

Figure 2: Microbial community structure of Clinton Creek metagenomes. (A) Dot pot of representative taxonomic groups from Clinton Creek sediments and microbialites using RefSeq (protein coding ORFs) and M5RNA (rRNA, MG-RAST rRNA database) in log relative abundances. Samples were clustered (top) by ward clustering matrix using bootstraping of one thousand replications with Bray-Curtis distance cut-offs. “Other” denotes low abundance taxa that were < 1% of the total ORF or rRNA, individually, but were all combined here into one point. (B) PCAs of top 25 taxonomic groups from Clinton Creek sediments and microbialites by RefSeq (ORFs) and M5RNA (rRNA, MG-RAST rRNA database) classification using ward clustering matrix followed by bootstrapping of one thousand replications with Bray-Curtis distance cut-offs.
Mentions: The microbial communities within Clinton Creek are distinct from each other (Figure 2) and are dominated by differing compositions of Proteobacteria and Cyanobacteria. Proteobacteria comprised >50% of the ORFs and >35% of the 16S sequences recovered from the Clinton Creek sediments and microbialites (Figure 2). The microbialite contigs were dominated by anoxic photoheterotrophic Alphaproteobacteria (e.g., Rhodobacterales) (Figure 2A). In contrast, sediments contigs had greater abundance nitrogen-fixing Gammaproteobacteria (e.g., Pseudomonas spp.) (Figure 2A). Alphaproteobacteria are commonly found amongst, and are likely a critical component of, the microbialite-forming microbial consortium due to their role in nitrogen fixation, even in the presence of heterocystous cyanobacteria (Havemann and Foster, 2008). It has been suggested that prior to the evolution of cyanobacteria, anoxic phototrophs like Rhodobacterales could have had a role in the formation of Precambrian stromatolites (Bosak et al., 2007).

Bottom Line: 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).

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology and Immunology, University of British Columbia Vancouver, BC, Canada.

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 (R (2) < 0.750) with freshwater microbial mats from Cuatro Ciénegas, Mexico, but are more similar to polar Arctic mats (R (2) > 0.900). These metagenomic profiles from an anthropogenic microbialite-forming ecosystem provide context to microbialite formation on a human-relevant timescale.

No MeSH data available.


Related in: MedlinePlus