Limits...
Microbial communities in dark oligotrophic volcanic ice cave ecosystems of Mt. Erebus, Antarctica.

Tebo BM, Davis RE, Anitori RP, Connell LB, Schiffman P, Staudigel H - Front Microbiol (2015)

Bottom Line: Erebus (Antarctica) offer DOVEs in a polar alpine environment that is starved in organics and with oxygenated hydrothermal circulation in highly reducing host rock.The bacterial communities from these ice caves display low phylogenetic diversity, but with a remarkable diversity of RubisCO genes including new deeply branching Form I clades, implicating the Calvin-Benson-Bassham (CBB) cycle as a pathway of CO2 fixation.Our work casts a first glimpse at Mt.

View Article: PubMed Central - PubMed

Affiliation: Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University Portland, OR, USA.

ABSTRACT
The Earth's crust hosts a subsurface, dark, and oligotrophic biosphere that is poorly understood in terms of the energy supporting its biomass production and impact on food webs at the Earth's surface. Dark oligotrophic volcanic ecosystems (DOVEs) are good environments for investigations of life in the absence of sunlight as they are poor in organics, rich in chemical reactants and well known for chemical exchange with Earth's surface systems. Ice caves near the summit of Mt. Erebus (Antarctica) offer DOVEs in a polar alpine environment that is starved in organics and with oxygenated hydrothermal circulation in highly reducing host rock. We surveyed the microbial communities using PCR, cloning, sequencing and analysis of the small subunit (16S) ribosomal and Ribulose-1,5-bisphosphate Carboxylase/Oxygenase (RubisCO) genes in sediment samples from three different caves, two that are completely dark and one that receives snow-filtered sunlight seasonally. The microbial communities in all three caves are composed primarily of Bacteria and fungi; Archaea were not detected. The bacterial communities from these ice caves display low phylogenetic diversity, but with a remarkable diversity of RubisCO genes including new deeply branching Form I clades, implicating the Calvin-Benson-Bassham (CBB) cycle as a pathway of CO2 fixation. The microbial communities in one of the dark caves, Warren Cave, which has a remarkably low phylogenetic diversity, were analyzed in more detail to gain a possible perspective on the energetic basis of the microbial ecosystem in the cave. Atmospheric carbon (CO2 and CO), including from volcanic emissions, likely supplies carbon and/or some of the energy requirements of chemoautotrophic microbial communities in Warren Cave and probably other Mt. Erebus ice caves. Our work casts a first glimpse at Mt. Erebus ice caves as natural laboratories for exploring carbon, energy and nutrient sources in the subsurface biosphere and the nutritional limits on life.

No MeSH data available.


Related in: MedlinePlus

Pie chart showing the percentage of the major phyla identified in each cave by 16S rDNA analysis. The identification of the other, minor phyla are given in Tables 4–6.
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Figure 2: Pie chart showing the percentage of the major phyla identified in each cave by 16S rDNA analysis. The identification of the other, minor phyla are given in Tables 4–6.

Mentions: We used molecular phylogenetic analysis to examine the microbial communities in the three caves. The bacterial small subunit (SSU) ribosomal RNA gene was PCR amplified using domain specific primers (Table 1). PCR amplifications using Archaea-specific primers were negative for all three caves. Bacterial numbers for the cave samples determined by quantitative PCR (Q-PCR) of small subunit ribosomal genes (Einen et al., 2008) were 1.6–40 × 106 cells/g sediment (Table 3), or up to about 10 fold higher than found in the glassy rind of seafloor basalts (Einen et al., 2008). The PCR products were cloned and sequenced (results for the Eukarya are reported elsewhere, Connell and Staudigel, 2013). For Harry's Dream, Warren Cave, and Hubert's Nightmare we sequenced 102, 82, and 78 clones which grouped into, respectively, 34, 11, and 18 Operational Taxonomic Units (OTUs; 97% sequence identity cutoff) (Tables 4–6) and Chao1 indices of 70.1, 35.5, and 58.5. Distinct Bacterial communities were identified in each cave (Figure 2). The phylogeny of the organisms found in the clone libraries was frequently similar to cultured organisms or 16S rRNA gene sequences from other volcanic, cave, sediment or cold environments (Figure 3).


Microbial communities in dark oligotrophic volcanic ice cave ecosystems of Mt. Erebus, Antarctica.

Tebo BM, Davis RE, Anitori RP, Connell LB, Schiffman P, Staudigel H - Front Microbiol (2015)

Pie chart showing the percentage of the major phyla identified in each cave by 16S rDNA analysis. The identification of the other, minor phyla are given in Tables 4–6.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4356161&req=5

Figure 2: Pie chart showing the percentage of the major phyla identified in each cave by 16S rDNA analysis. The identification of the other, minor phyla are given in Tables 4–6.
Mentions: We used molecular phylogenetic analysis to examine the microbial communities in the three caves. The bacterial small subunit (SSU) ribosomal RNA gene was PCR amplified using domain specific primers (Table 1). PCR amplifications using Archaea-specific primers were negative for all three caves. Bacterial numbers for the cave samples determined by quantitative PCR (Q-PCR) of small subunit ribosomal genes (Einen et al., 2008) were 1.6–40 × 106 cells/g sediment (Table 3), or up to about 10 fold higher than found in the glassy rind of seafloor basalts (Einen et al., 2008). The PCR products were cloned and sequenced (results for the Eukarya are reported elsewhere, Connell and Staudigel, 2013). For Harry's Dream, Warren Cave, and Hubert's Nightmare we sequenced 102, 82, and 78 clones which grouped into, respectively, 34, 11, and 18 Operational Taxonomic Units (OTUs; 97% sequence identity cutoff) (Tables 4–6) and Chao1 indices of 70.1, 35.5, and 58.5. Distinct Bacterial communities were identified in each cave (Figure 2). The phylogeny of the organisms found in the clone libraries was frequently similar to cultured organisms or 16S rRNA gene sequences from other volcanic, cave, sediment or cold environments (Figure 3).

Bottom Line: Erebus (Antarctica) offer DOVEs in a polar alpine environment that is starved in organics and with oxygenated hydrothermal circulation in highly reducing host rock.The bacterial communities from these ice caves display low phylogenetic diversity, but with a remarkable diversity of RubisCO genes including new deeply branching Form I clades, implicating the Calvin-Benson-Bassham (CBB) cycle as a pathway of CO2 fixation.Our work casts a first glimpse at Mt.

View Article: PubMed Central - PubMed

Affiliation: Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University Portland, OR, USA.

ABSTRACT
The Earth's crust hosts a subsurface, dark, and oligotrophic biosphere that is poorly understood in terms of the energy supporting its biomass production and impact on food webs at the Earth's surface. Dark oligotrophic volcanic ecosystems (DOVEs) are good environments for investigations of life in the absence of sunlight as they are poor in organics, rich in chemical reactants and well known for chemical exchange with Earth's surface systems. Ice caves near the summit of Mt. Erebus (Antarctica) offer DOVEs in a polar alpine environment that is starved in organics and with oxygenated hydrothermal circulation in highly reducing host rock. We surveyed the microbial communities using PCR, cloning, sequencing and analysis of the small subunit (16S) ribosomal and Ribulose-1,5-bisphosphate Carboxylase/Oxygenase (RubisCO) genes in sediment samples from three different caves, two that are completely dark and one that receives snow-filtered sunlight seasonally. The microbial communities in all three caves are composed primarily of Bacteria and fungi; Archaea were not detected. The bacterial communities from these ice caves display low phylogenetic diversity, but with a remarkable diversity of RubisCO genes including new deeply branching Form I clades, implicating the Calvin-Benson-Bassham (CBB) cycle as a pathway of CO2 fixation. The microbial communities in one of the dark caves, Warren Cave, which has a remarkably low phylogenetic diversity, were analyzed in more detail to gain a possible perspective on the energetic basis of the microbial ecosystem in the cave. Atmospheric carbon (CO2 and CO), including from volcanic emissions, likely supplies carbon and/or some of the energy requirements of chemoautotrophic microbial communities in Warren Cave and probably other Mt. Erebus ice caves. Our work casts a first glimpse at Mt. Erebus ice caves as natural laboratories for exploring carbon, energy and nutrient sources in the subsurface biosphere and the nutritional limits on life.

No MeSH data available.


Related in: MedlinePlus