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Metagenome-based diversity analyses suggest a significant contribution of non-cyanobacterial lineages to carbonate precipitation in modern microbialites.

Saghaï A, Zivanovic Y, Zeyen N, Moreira D, Benzerara K, Deschamps P, Bertolino P, Ragon M, Tavera R, López-Archilla AI, López-García P - Front Microbiol (2015)

Bottom Line: The associated microbial communities were mainly composed of bacteria, most of which seemed heterotrophic, whereas archaea were negligible.Although cyanobacteria were the most important bacterial group contributing to the carbonate precipitation potential, photosynthetic eukaryotes, anoxygenic photosynthesizers and sulfate reducers were also very abundant.Despite the previous identification of intracellularly calcifying cyanobacteria in Alchichica microbialites, most carbonate precipitation seems extracellular in this system.

View Article: PubMed Central - PubMed

Affiliation: Unité d'Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud Orsay, France.

ABSTRACT
Cyanobacteria are thought to play a key role in carbonate formation due to their metabolic activity, but other organisms carrying out oxygenic photosynthesis (photosynthetic eukaryotes) or other metabolisms (e.g., anoxygenic photosynthesis, sulfate reduction), may also contribute to carbonate formation. To obtain more quantitative information than that provided by more classical PCR-dependent methods, we studied the microbial diversity of microbialites from the Alchichica crater lake (Mexico) by mining for 16S/18S rRNA genes in metagenomes obtained by direct sequencing of environmental DNA. We studied samples collected at the Western (AL-W) and Northern (AL-N) shores of the lake and, at the latter site, along a depth gradient (1, 5, 10, and 15 m depth). The associated microbial communities were mainly composed of bacteria, most of which seemed heterotrophic, whereas archaea were negligible. Eukaryotes composed a relatively minor fraction dominated by photosynthetic lineages, diatoms in AL-W, influenced by Si-rich seepage waters, and green algae in AL-N samples. Members of the Gammaproteobacteria and Alphaproteobacteria classes of Proteobacteria, Cyanobacteria, and Bacteroidetes were the most abundant bacterial taxa, followed by Planctomycetes, Deltaproteobacteria (Proteobacteria), Verrucomicrobia, Actinobacteria, Firmicutes, and Chloroflexi. Community composition varied among sites and with depth. Although cyanobacteria were the most important bacterial group contributing to the carbonate precipitation potential, photosynthetic eukaryotes, anoxygenic photosynthesizers and sulfate reducers were also very abundant. Cyanobacteria affiliated to Pleurocapsales largely increased with depth. Scanning electron microscopy (SEM) observations showed considerable areas of aragonite-encrusted Pleurocapsa-like cyanobacteria at microscale. Multivariate statistical analyses showed a strong positive correlation of Pleurocapsales and Chroococcales with aragonite formation at macroscale, and suggest a potential causal link. Despite the previous identification of intracellularly calcifying cyanobacteria in Alchichica microbialites, most carbonate precipitation seems extracellular in this system.

No MeSH data available.


Related in: MedlinePlus

Lake Alchichica sampling sites and microbialite fragments collected. The two sampling sites AL-N and AL-W are indicated on the lake with stars. Photographs taken on site of the different samples are shown below. For AL-N samples, the correspondence with the depth gradient is schematically indicated on the (left). Upper views of microbialite fragments are shown on the left (AL-N) and upper (AL-W) part of the respective panels; downside views are on the right (AL-N) and lower (AL-W) part of the panels. The scale bar corresponds to 10 cm.
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Figure 1: Lake Alchichica sampling sites and microbialite fragments collected. The two sampling sites AL-N and AL-W are indicated on the lake with stars. Photographs taken on site of the different samples are shown below. For AL-N samples, the correspondence with the depth gradient is schematically indicated on the (left). Upper views of microbialite fragments are shown on the left (AL-N) and upper (AL-W) part of the respective panels; downside views are on the right (AL-N) and lower (AL-W) part of the panels. The scale bar corresponds to 10 cm.

Mentions: Microbialite samples were collected in January 2012 during the winter season when the lake is not stratified (Macek et al., 2009). Samples were collected in two different sites of the lake: the Western shore (19° 25′ 0.13″N; 97° 24′ 41.07″W) and the Northern shore (19° 25′ 12.49″N; 97° 24′ 12.35″W), which we termed AL-W and AL-N, respectively. The AL-W site was located at the steepest shore of the lake, where seepage activity was visible (active bubbling observed at the shore); the AL-W sample was collected at ca. 0.5–1 m depth with the help of a geologist’s hammer. At the AL-N site, samples were collected at different depths (1, 5, 10, and 15 m depth) by scuba diving. A portion of each microbialite fragment was removed and let dry for parallel chemical and mineralogical analysis. For metagenomic analysis, fragments of ca. 20 cm in diameter were picked up with gloves, photographed on site (Figure 1) and subsequently broken and manipulated with sterile chisels and/or forceps to minimize all possible contamination. For DNA purification, millimeter-sized microbialite grains were detached and collected from the total surface of those microbialite fragments down to a few millimeters deep in order to get predominantly the active microbialite community and to facilitate subsequent grinding prior to DNA purification. A large surface was sampled to limit local heterogeneity effects. AL-W samples were covered by a more glutinous and less mineralized biofilm, whereas AL-N samples were mineralized up to the surface (Figure 1). Subsampled grains were placed in sterile 50-ml Falcon tubes and transported to the UNAM laboratory (244 km away) at 4°C for immediate DNA purification. The remainder of the samples were frozen and stored at –20°C for subsequent use.


Metagenome-based diversity analyses suggest a significant contribution of non-cyanobacterial lineages to carbonate precipitation in modern microbialites.

Saghaï A, Zivanovic Y, Zeyen N, Moreira D, Benzerara K, Deschamps P, Bertolino P, Ragon M, Tavera R, López-Archilla AI, López-García P - Front Microbiol (2015)

Lake Alchichica sampling sites and microbialite fragments collected. The two sampling sites AL-N and AL-W are indicated on the lake with stars. Photographs taken on site of the different samples are shown below. For AL-N samples, the correspondence with the depth gradient is schematically indicated on the (left). Upper views of microbialite fragments are shown on the left (AL-N) and upper (AL-W) part of the respective panels; downside views are on the right (AL-N) and lower (AL-W) part of the panels. The scale bar corresponds to 10 cm.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4525015&req=5

Figure 1: Lake Alchichica sampling sites and microbialite fragments collected. The two sampling sites AL-N and AL-W are indicated on the lake with stars. Photographs taken on site of the different samples are shown below. For AL-N samples, the correspondence with the depth gradient is schematically indicated on the (left). Upper views of microbialite fragments are shown on the left (AL-N) and upper (AL-W) part of the respective panels; downside views are on the right (AL-N) and lower (AL-W) part of the panels. The scale bar corresponds to 10 cm.
Mentions: Microbialite samples were collected in January 2012 during the winter season when the lake is not stratified (Macek et al., 2009). Samples were collected in two different sites of the lake: the Western shore (19° 25′ 0.13″N; 97° 24′ 41.07″W) and the Northern shore (19° 25′ 12.49″N; 97° 24′ 12.35″W), which we termed AL-W and AL-N, respectively. The AL-W site was located at the steepest shore of the lake, where seepage activity was visible (active bubbling observed at the shore); the AL-W sample was collected at ca. 0.5–1 m depth with the help of a geologist’s hammer. At the AL-N site, samples were collected at different depths (1, 5, 10, and 15 m depth) by scuba diving. A portion of each microbialite fragment was removed and let dry for parallel chemical and mineralogical analysis. For metagenomic analysis, fragments of ca. 20 cm in diameter were picked up with gloves, photographed on site (Figure 1) and subsequently broken and manipulated with sterile chisels and/or forceps to minimize all possible contamination. For DNA purification, millimeter-sized microbialite grains were detached and collected from the total surface of those microbialite fragments down to a few millimeters deep in order to get predominantly the active microbialite community and to facilitate subsequent grinding prior to DNA purification. A large surface was sampled to limit local heterogeneity effects. AL-W samples were covered by a more glutinous and less mineralized biofilm, whereas AL-N samples were mineralized up to the surface (Figure 1). Subsampled grains were placed in sterile 50-ml Falcon tubes and transported to the UNAM laboratory (244 km away) at 4°C for immediate DNA purification. The remainder of the samples were frozen and stored at –20°C for subsequent use.

Bottom Line: The associated microbial communities were mainly composed of bacteria, most of which seemed heterotrophic, whereas archaea were negligible.Although cyanobacteria were the most important bacterial group contributing to the carbonate precipitation potential, photosynthetic eukaryotes, anoxygenic photosynthesizers and sulfate reducers were also very abundant.Despite the previous identification of intracellularly calcifying cyanobacteria in Alchichica microbialites, most carbonate precipitation seems extracellular in this system.

View Article: PubMed Central - PubMed

Affiliation: Unité d'Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud Orsay, France.

ABSTRACT
Cyanobacteria are thought to play a key role in carbonate formation due to their metabolic activity, but other organisms carrying out oxygenic photosynthesis (photosynthetic eukaryotes) or other metabolisms (e.g., anoxygenic photosynthesis, sulfate reduction), may also contribute to carbonate formation. To obtain more quantitative information than that provided by more classical PCR-dependent methods, we studied the microbial diversity of microbialites from the Alchichica crater lake (Mexico) by mining for 16S/18S rRNA genes in metagenomes obtained by direct sequencing of environmental DNA. We studied samples collected at the Western (AL-W) and Northern (AL-N) shores of the lake and, at the latter site, along a depth gradient (1, 5, 10, and 15 m depth). The associated microbial communities were mainly composed of bacteria, most of which seemed heterotrophic, whereas archaea were negligible. Eukaryotes composed a relatively minor fraction dominated by photosynthetic lineages, diatoms in AL-W, influenced by Si-rich seepage waters, and green algae in AL-N samples. Members of the Gammaproteobacteria and Alphaproteobacteria classes of Proteobacteria, Cyanobacteria, and Bacteroidetes were the most abundant bacterial taxa, followed by Planctomycetes, Deltaproteobacteria (Proteobacteria), Verrucomicrobia, Actinobacteria, Firmicutes, and Chloroflexi. Community composition varied among sites and with depth. Although cyanobacteria were the most important bacterial group contributing to the carbonate precipitation potential, photosynthetic eukaryotes, anoxygenic photosynthesizers and sulfate reducers were also very abundant. Cyanobacteria affiliated to Pleurocapsales largely increased with depth. Scanning electron microscopy (SEM) observations showed considerable areas of aragonite-encrusted Pleurocapsa-like cyanobacteria at microscale. Multivariate statistical analyses showed a strong positive correlation of Pleurocapsales and Chroococcales with aragonite formation at macroscale, and suggest a potential causal link. Despite the previous identification of intracellularly calcifying cyanobacteria in Alchichica microbialites, most carbonate precipitation seems extracellular in this system.

No MeSH data available.


Related in: MedlinePlus