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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

Mineral phases of Alchichica microbialites. (A) X-ray diffractograms of the Alchichica microbialite fragments sampled at different depths on the Northern shore (AL-N samples). (B–E) Scanning electron microscopy (SEM) images of the sample AL-N-10 (10 m depth) showing the most conspicuous mineral phases; hydromagnesite (H), aragonite (A), hydrotalcite (Ht), and illite (I) can be identified from the XRD patterns. (B) Hydromagnesite (light gray areas occupying most of the scanned surface) and aragonite (bright areas). (C) Micritic aragonite. (D,E) Large areas showing the encrustation of Pleurocapsa-like cyanobacteria in aragonite (the organic matter present in living cells appears in dark gray).
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Figure 2: Mineral phases of Alchichica microbialites. (A) X-ray diffractograms of the Alchichica microbialite fragments sampled at different depths on the Northern shore (AL-N samples). (B–E) Scanning electron microscopy (SEM) images of the sample AL-N-10 (10 m depth) showing the most conspicuous mineral phases; hydromagnesite (H), aragonite (A), hydrotalcite (Ht), and illite (I) can be identified from the XRD patterns. (B) Hydromagnesite (light gray areas occupying most of the scanned surface) and aragonite (bright areas). (C) Micritic aragonite. (D,E) Large areas showing the encrustation of Pleurocapsa-like cyanobacteria in aragonite (the organic matter present in living cells appears in dark gray).

Mentions: Concentrations of major elements, total organic carbon, and total sulfur were determined at the Service d’analyse des roches et minéraux (SARM), Centre de Recherches Pétrographiques et Géochimiques, Nancy, France (Table 1). Approximately 2 g of dry ground powder per sample were used for the analyses. Major elements were quantified using an ICP-AES ICap 6500 (Thermo Fischer) after an alkali fusion of rock powder with LiBO2 followed by dissolution with HNO3. The uncertainties of the major element measurements were between 1 and 25% depending on their concentrations. They were better than 2, 2, and 5% for Ca, Mg, and Si, respectively, which were considered for calculating the mineralogical composition of the microbialites. Total sulfur content was determined using the carbon/sulfur analyzer Horiba EMIA320V2. The uncertainties of these measurements were better than 15% for sulfur concentration values. The bulk mineralogical composition of all the samples was first analyzed by x-ray diffraction (XRD). About 1 g of each microbialite sample was crushed in an agate mortar and the powder was deposited on an aluminum sample holder. XRD measurements were performed using a PANalytical X’Pert diffractometer equipped with a cobalt anode (Co-Kα). Data were recorded at 40 kV and 35 mA in the continuous-scan mode between 4 and 120° (2θ) with a step of 0.0167° and a total counting time of around 2 h. XRD data were analyzed using the PANalytical X’Pert Highscore software for background subtraction, peak finding, and matching with XRD patterns of reference compounds from the International Crystal Structure Database (ICSD, Fachinformationszentrum, Karlsruhe, Germany; US Institute of Standards and Technology, USA). All samples were composed of two major carbonate phases: hydromagnesite [Mg5(CO3)4(OH)2.4H2O] and aragonite (CaCO3). In addition, we were able to identify hydrotalcite [(Mg 0.667 Al0.333)(OH)2 (CO3)0.167 (H2O)0.5] and illite (K4Al16Si8O48) as minor phases in some samples (Figure 2). Moreover, based on scanning electron microscopy (SEM) analyses (Zeyen et al., under review) and the present chemical analyses, we considered an additional silicate phase with a talc-like composition: Mg3Si4O10(OH)2. Based on this mineralogical assemblage and bulk chemical analyses of the samples, we could calculate the proportion of these three different phases. SEM observations of ultrathin sections coated with carbon were done in angle selected backscattered electron mode using a Zeiss Ultra 55 FEG-SEM operating at 15 kV at a working distance of 7.5 mm.


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)

Mineral phases of Alchichica microbialites. (A) X-ray diffractograms of the Alchichica microbialite fragments sampled at different depths on the Northern shore (AL-N samples). (B–E) Scanning electron microscopy (SEM) images of the sample AL-N-10 (10 m depth) showing the most conspicuous mineral phases; hydromagnesite (H), aragonite (A), hydrotalcite (Ht), and illite (I) can be identified from the XRD patterns. (B) Hydromagnesite (light gray areas occupying most of the scanned surface) and aragonite (bright areas). (C) Micritic aragonite. (D,E) Large areas showing the encrustation of Pleurocapsa-like cyanobacteria in aragonite (the organic matter present in living cells appears in dark gray).
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Related In: Results  -  Collection

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Figure 2: Mineral phases of Alchichica microbialites. (A) X-ray diffractograms of the Alchichica microbialite fragments sampled at different depths on the Northern shore (AL-N samples). (B–E) Scanning electron microscopy (SEM) images of the sample AL-N-10 (10 m depth) showing the most conspicuous mineral phases; hydromagnesite (H), aragonite (A), hydrotalcite (Ht), and illite (I) can be identified from the XRD patterns. (B) Hydromagnesite (light gray areas occupying most of the scanned surface) and aragonite (bright areas). (C) Micritic aragonite. (D,E) Large areas showing the encrustation of Pleurocapsa-like cyanobacteria in aragonite (the organic matter present in living cells appears in dark gray).
Mentions: Concentrations of major elements, total organic carbon, and total sulfur were determined at the Service d’analyse des roches et minéraux (SARM), Centre de Recherches Pétrographiques et Géochimiques, Nancy, France (Table 1). Approximately 2 g of dry ground powder per sample were used for the analyses. Major elements were quantified using an ICP-AES ICap 6500 (Thermo Fischer) after an alkali fusion of rock powder with LiBO2 followed by dissolution with HNO3. The uncertainties of the major element measurements were between 1 and 25% depending on their concentrations. They were better than 2, 2, and 5% for Ca, Mg, and Si, respectively, which were considered for calculating the mineralogical composition of the microbialites. Total sulfur content was determined using the carbon/sulfur analyzer Horiba EMIA320V2. The uncertainties of these measurements were better than 15% for sulfur concentration values. The bulk mineralogical composition of all the samples was first analyzed by x-ray diffraction (XRD). About 1 g of each microbialite sample was crushed in an agate mortar and the powder was deposited on an aluminum sample holder. XRD measurements were performed using a PANalytical X’Pert diffractometer equipped with a cobalt anode (Co-Kα). Data were recorded at 40 kV and 35 mA in the continuous-scan mode between 4 and 120° (2θ) with a step of 0.0167° and a total counting time of around 2 h. XRD data were analyzed using the PANalytical X’Pert Highscore software for background subtraction, peak finding, and matching with XRD patterns of reference compounds from the International Crystal Structure Database (ICSD, Fachinformationszentrum, Karlsruhe, Germany; US Institute of Standards and Technology, USA). All samples were composed of two major carbonate phases: hydromagnesite [Mg5(CO3)4(OH)2.4H2O] and aragonite (CaCO3). In addition, we were able to identify hydrotalcite [(Mg 0.667 Al0.333)(OH)2 (CO3)0.167 (H2O)0.5] and illite (K4Al16Si8O48) as minor phases in some samples (Figure 2). Moreover, based on scanning electron microscopy (SEM) analyses (Zeyen et al., under review) and the present chemical analyses, we considered an additional silicate phase with a talc-like composition: Mg3Si4O10(OH)2. Based on this mineralogical assemblage and bulk chemical analyses of the samples, we could calculate the proportion of these three different phases. SEM observations of ultrathin sections coated with carbon were done in angle selected backscattered electron mode using a Zeiss Ultra 55 FEG-SEM operating at 15 kV at a working distance of 7.5 mm.

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