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

Our plain-English summary of Metagenomic analysis reveals that modern microbialites and polar microbial mats have similar taxonomic and functional potential, by R.A. White, I.M. Power, G.M. Dipple, et al (Frontiers in Microbiology, 2015).

The study

• Authors: R.A. White, I.M. Power, G.M. Dipple, G. Southam, C.A. Suttle
• Journal: Frontiers in Microbiology
• Published: 2015;6:966
• Cited by: 33 articles, as counted by NIH iCite
• Read it: PubMed · Publisher · Free full text

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.

In plain English

This study examined microbes living in a flooded, abandoned open-pit asbestos mine at Clinton Creek, Yukon, Canada, where rock-like mounds called microbialites are forming. It studied microbes, not people, and did not look at asbestos-related disease. In July 2011 the authors took triplicate samples of microbialites and of the surrounding pond sediments, which contain chrysotile among other minerals, and sequenced the DNA in them. Proteobacteria made up more than 50% of the protein-coding sequences. Alphaproteobacteria dominated the microbialites, while Gammaproteobacteria dominated the sediments. Cyanobacteria made up 6.1% of protein-coding sequences in the microbialites and 1.4% in the sediments. The microbialites had more genes for photosynthesis. The microbialites' gene functions correlated closely with mats from the Canadian High Arctic and Antarctica (R2 = 0.952 for Markham Ice Shelf mats; R2 is a measure of correlation). They correlated more weakly with Cuatro Ciénegas, Mexico microbialites (R2 = 0.702 and 0.633) and were distinct from Yellowstone mats. The authors concluded that photosynthesis-induced alkalinization appears to drive microbialite formation there. They also suggested that Arctic mats may have the metabolic potential to form microbialites under favorable chemistry.

We wrote this plain-English summary from the full article with the help of AI, and a second AI model checked each sentence against the article. It is not the authors' wording; the abstract and the article are their own account.

What the study did and found

• Design: Environmental metagenomic study: DNA sequencing of microbial communities in microbialites and adjacent sediments, compared with published metagenomes from other sites
• Who was studied: Microbial communities in microbialites and sediments from the open-pit pond of the abandoned Clinton Creek asbestos mine, Yukon, Canada; triplicate samples of each collected in July 2011 (replicate DNA was pooled before sequencing)
• Exposure: No human exposure was studied. The site is a flooded asbestos mine pit, and the pond sediments contain chrysotile along with other minerals
• Main results:
  • Proteobacteria made up more than 50% of protein-coding sequences (ORFs) and more than 35% of 16S sequences in both the sediments and the microbialites
  • Alphaproteobacteria dominated the microbialites; Gammaproteobacteria dominated the sediments
  • Cyanobacteria accounted for 6.1% of protein-coding sequences in the microbialites versus 1.4% in the sediments
  • Gemmatimonadetes made up 7–8% of protein-coding sequences, in both sediments and microbialites
  • Photosynthetic pathways were more abundant in the microbialites than in the sediments (FDR p less than 0.01)
  • Of predicted MetaCyc pathways, 13 were found only in sediments, 240 were identified in microbialites, and 358 were shared
  • Clinton Creek microbialite gene functions correlated most strongly with Markham Ice Shelf mats from the Canadian High Arctic (R2 = 0.952)
  • Correlations were weaker with Cuatro Ciénegas microbialites (Pozas Azules II R2 = 0.702; Rio Mesquites R2 = 0.633) and lowest with the Highbourne Cay marine stromatolite (R2 = 0.018)
  • Clinton Creek samples were distinct from non-lithifying mats from Yellowstone hot springs
• The authors' conclusion: The authors concluded that the high proportion of photosynthetic genes implies microbialite formation at Clinton Creek is driven by photosynthesis-induced alkalinization. They also suggested that, under favorable chemistry, Arctic mats have the metabolic potential to form microbialites.
• Limitations the authors state:
  • The estimated abundance of Gemmatimonadetes may be low partly because few of their genomes are in reference databases, and their role remains unclear
  • Further work is needed to establish the influence of specific microbes on how fast microbialites form

Related studies

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