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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 CiƩnegas, 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.


Extended error plots for functional gene annotations for Clinton Creek metagenomes in STAMP using SEED subsystems. (A) SEED subsystem level I (highest level classification in SEED). (B) SEED subsystem level III (3rd lowest classification in SEED out of four levels). Extended error plots used a one sided G-test (w/Yates' + Fisher's) with asymptomatic confidence intervals (0.95) using Benjamini-Hochberg FDR procedure. *Red asterisks are significant photosynthetic pathways.
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Figure 3: Extended error plots for functional gene annotations for Clinton Creek metagenomes in STAMP using SEED subsystems. (A) SEED subsystem level I (highest level classification in SEED). (B) SEED subsystem level III (3rd lowest classification in SEED out of four levels). Extended error plots used a one sided G-test (w/Yates' + Fisher's) with asymptomatic confidence intervals (0.95) using Benjamini-Hochberg FDR procedure. *Red asterisks are significant photosynthetic pathways.

Mentions: The metabolic potential of the Clinton Creek microbialite metagenome predicts photosynthetic dominance, whereas the sediment metagenomes contained more heterotrophic metabolism (e.g., respiration) (Figure 3A). SEED subsystem level I (i.e., highest functional classification group) annotations indicated that carbohydrate metabolism relating to carbon fixation, DNA metabolism and photosynthesis pathways were significantly more abundant in the microbialites than sediments (Figure 4A, FDR p < 0.01). Lower level SEED subsystem predictions (level III) further revealed a higher abundance of photosynthetic pathways (e.g., photosystem II reaction centers and carotenoids and chlorophyll biosynthesis) in microbialites than sediments (Figure 3B, FDR p < 0.01). These photosynthetic pathways in microbialites were annotated as filamentous cyanobacteria genera such as Microcoleus, Lyngbya, Nodularia, and Anabaena, which were not found in the sediments.


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)

Extended error plots for functional gene annotations for Clinton Creek metagenomes in STAMP using SEED subsystems. (A) SEED subsystem level I (highest level classification in SEED). (B) SEED subsystem level III (3rd lowest classification in SEED out of four levels). Extended error plots used a one sided G-test (w/Yates' + Fisher's) with asymptomatic confidence intervals (0.95) using Benjamini-Hochberg FDR procedure. *Red asterisks are significant photosynthetic pathways.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 3: Extended error plots for functional gene annotations for Clinton Creek metagenomes in STAMP using SEED subsystems. (A) SEED subsystem level I (highest level classification in SEED). (B) SEED subsystem level III (3rd lowest classification in SEED out of four levels). Extended error plots used a one sided G-test (w/Yates' + Fisher's) with asymptomatic confidence intervals (0.95) using Benjamini-Hochberg FDR procedure. *Red asterisks are significant photosynthetic pathways.
Mentions: The metabolic potential of the Clinton Creek microbialite metagenome predicts photosynthetic dominance, whereas the sediment metagenomes contained more heterotrophic metabolism (e.g., respiration) (Figure 3A). SEED subsystem level I (i.e., highest functional classification group) annotations indicated that carbohydrate metabolism relating to carbon fixation, DNA metabolism and photosynthesis pathways were significantly more abundant in the microbialites than sediments (Figure 4A, FDR p < 0.01). Lower level SEED subsystem predictions (level III) further revealed a higher abundance of photosynthetic pathways (e.g., photosystem II reaction centers and carotenoids and chlorophyll biosynthesis) in microbialites than sediments (Figure 3B, FDR p < 0.01). These photosynthetic pathways in microbialites were annotated as filamentous cyanobacteria genera such as Microcoleus, Lyngbya, Nodularia, and Anabaena, which were not found in the sediments.

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 CiƩnegas, 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.