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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.


Scatter plots of functional gene annotations using SEED subsystem level III. One sided G-test (w/Yates' + Fisher's) with asymptomatic confidence intervals (0.95) using Benjamini-Hochberg FDR procedure in STAMP. Each dot represents a unique functional classification gene.
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Figure 6: Scatter plots of functional gene annotations using SEED subsystem level III. One sided G-test (w/Yates' + Fisher's) with asymptomatic confidence intervals (0.95) using Benjamini-Hochberg FDR procedure in STAMP. Each dot represents a unique functional classification gene.

Mentions: Clinton Creek microbialite and sediment metagenomes are more functionally related to polar mats than microbialites isolated from marine or tropical ecosystems. Using SEED subsystem level III, PCA indicates better clustering to polar mats and sediments from the Arctic and Antarctica (Figure 5). The Clinton Creek samples cluster most closely Markham Ice shelf and Ward Hunt Ice shelf mats isolated from the Canadian High Arctic (Figure 5; Varin et al., 2012). Markham mats are functionally the most similar based on strong correlation to Clinton Creek microbialites based on SEED subsystem level III (Figure 6, R2 = 0.952). Overall, polar mats (e.g., Markham, Ward Hunt, and McMurdo) had strong correlation of pathways in SEED than other ecosystems (Figure 6, R2 > 0.900). Markham mats like Clinton Creek microbialites are dominated by Proteobacteria, and have Gemmatimonadetes present at 3% of the total 16S clones (Bottos et al., 2008). Polar mats, whether on microbialites or on ice shelves, appear to have functional gene similarities; this likely relates to handling shifts in temperature, including temperatures well below freezing (−10°C; Varin et al., 2012).


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)

Scatter plots of functional gene annotations using SEED subsystem level III. One sided G-test (w/Yates' + Fisher's) with asymptomatic confidence intervals (0.95) using Benjamini-Hochberg FDR procedure in STAMP. Each dot represents a unique functional classification gene.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 6: Scatter plots of functional gene annotations using SEED subsystem level III. One sided G-test (w/Yates' + Fisher's) with asymptomatic confidence intervals (0.95) using Benjamini-Hochberg FDR procedure in STAMP. Each dot represents a unique functional classification gene.
Mentions: Clinton Creek microbialite and sediment metagenomes are more functionally related to polar mats than microbialites isolated from marine or tropical ecosystems. Using SEED subsystem level III, PCA indicates better clustering to polar mats and sediments from the Arctic and Antarctica (Figure 5). The Clinton Creek samples cluster most closely Markham Ice shelf and Ward Hunt Ice shelf mats isolated from the Canadian High Arctic (Figure 5; Varin et al., 2012). Markham mats are functionally the most similar based on strong correlation to Clinton Creek microbialites based on SEED subsystem level III (Figure 6, R2 = 0.952). Overall, polar mats (e.g., Markham, Ward Hunt, and McMurdo) had strong correlation of pathways in SEED than other ecosystems (Figure 6, R2 > 0.900). Markham mats like Clinton Creek microbialites are dominated by Proteobacteria, and have Gemmatimonadetes present at 3% of the total 16S clones (Bottos et al., 2008). Polar mats, whether on microbialites or on ice shelves, appear to have functional gene similarities; this likely relates to handling shifts in temperature, including temperatures well below freezing (−10°C; Varin et al., 2012).

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.