Research ArticleMICROBIAL ECOLOGY

Macroecological drivers of archaea and bacteria in benthic deep-sea ecosystems

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Science Advances  29 Apr 2016:
Vol. 2, no. 4, e1500961
DOI: 10.1126/sciadv.1500961
  • Fig. 1 Sampling areas and locations of the sampling stations.
  • Fig. 2 Bathymetric patterns of the different microbial components in surface deep-sea sediments.

    (A to D) Depth-related patterns of the abundances of bacteria (A), archaea (B), MG-I Thaumarchaeota (C), and MG-II Euryarchaeota (D) in the top 1 cm of sediments collected in the different oceanic regions. Means and SDs (n = 3) are reported.

  • Fig. 3 Benthic bacterial and archaeal abundances in relation to food availability and bottom water temperature.

    (A and B) Relationships between benthic bacterial and archaeal abundances and food availability (expressed as biopolymeric C concentrations in the top 1 cm of sediments) (A) and between benthic bacterial and archaeal abundances and bottom water temperature (B). (A) The color-coded fitted curves show the correlations for bacterial abundances (Y = 8 × 107 X + 2 × 108; n = 54; R2 = 0.360; P < 0.01) and archaeal abundances (Y = 6 × 107 X − 2 × 107; n = 54; R2 = 0.432; P < 0.01) versus food availability. (B) The color-coded fitted curves show the correlations for bacterial abundances (Y = −1 × 107 X + 4 × 109; n = 53; R2 = 0.151; P < 0.05) and archaeal abundances (Y = −9 × 106 X + 3 × 109; n = 53; R2 = 0.194; P < 0.05) versus bottom water temperature.

  • Fig. 4 Changes of the different benthic microbial components in relation to latitude.

    (A and B) Latitudinal patterns of bacterial and archaeal abundances (A) and MG-I Thaumarchaeota and MG-II Euryarchaeota abundances (B) in the top 1 cm of sediments collected in the different oceanic regions at similar depths. The color-coded fitted curves show the correlations for bacteria (Y = 8.42 × 106 X − 8.1 × 107; n = 45; R2 = 0.679; P < 0.01), archaea (Y = 6.56 × 106 X − 2.2 × 108; n = 45; R2 = 0.679; P < 0.01), MG-I Thaumarchaeota (Y = 3.54 × 106 X − 1.2 × 108; n = 45; R2 = 0.747; P < 0.01), and MG-II Euryarchaeota (Y = 1.26 × 106 X − 3.5 × 107; n = 45; R2 = 0.629; P < 0.01).

  • Fig. 5 Distribution of the different microbial components along the vertical profiles of the sediments.

    (A to D) Abundances of bacteria (A), archaea (B), MG-I Thaumarchaeota (C), and MG-II Euryarchaeota (D) along the vertical profiles of sediments (down to 15-cm depth) collected in the different oceanic regions. Means and SDs (n = 3) are reported.

  • Fig. 6 Output of the regression tree analysis carried out to identify environmental factors explaining the distribution of bacterial abundances in the top 1 cm of sediments collected in the different oceanic regions.

    The significance level and the percentage of the explained variance of each predictor variable are reported along with the number of sampling sites for each oceanic region at the terminal nodes. OC flux, organic C that reaches the sea floor through particle sinking (expressed as mg C m−2 day−1); BPC, biopolymeric C concentrations in the sediment (expressed as mg C g−1); PRT/CHO, protein-to-carbohydrate ratio in the sediment (adimensional).

  • Fig. 7 Output of the regression tree analysis carried out to identify environmental factors explaining the distribution of archaeal abundances in the top 1 cm of sediments collected in the different oceanic regions.

    The significance level and the percentage of the explained variance of each predictor variable are reported along with the number of sampling sites for each oceanic region at the terminal nodes. OC flux, organic C that reaches the sea floor through particle sinking (expressed as mg C m−2 day−1); PRT/CHO, protein-to-carbohydrate ratio in the sediment (adimensional).

Supplementary Materials

  • Supplementary material for this article is available at http://advances.sciencemag.org/cgi/content/full/2/4/e1500961/DC1

    Supplementary Materials and Methods

    table S1. Details of the station locations, temperature, and salinity of bottom waters, total phytopigment (CPE) and biopolymeric C (BPC) concentrations, and protein-to-carbohydrate ratio (PRT/CHO) in surface sediments (0 to 1 cm), net photosynthetic primary production (NPP), and organic C fluxes (OC fluxes).

    table S2. Output of the in silico analysis dealing with the coverage of probes targeting 16S rRNA used in the present study.

    table S3. Statistical analysis testing for differences in the distribution of the different microbial components.

    fig. S1. Depth-related patterns of total prokaryotic abundances (obtained using SYBR Green I) in the top 1 cm of sediments collected in the different oceanic regions.

    fig. S2. Comparison of the abundances of bacteria and archaea obtained by CARD-FISH, with the number of 16S rDNA copies of bacteria and archaea obtained in surface sediments of different oceanic regions.

    fig. S3. Output of the regression tree analysis carried out to identify environmental factors explaining the distribution of MG-I Thaumarchaeota in the top 1 cm of sediments collected in the different oceanic regions.

    fig. S4. Output of the regression tree analysis carried out to identify environmental factors explaining the distribution of MG-II Euryarchaeota in the top 1 cm of sediments collected in the different oceanic regions.

  • Supplementary Materials

    This PDF file includes:

    • Supplementary Materials and Methods
    • table S1. Details of the station locations, temperature, and salinity of bottom waters, total phytopigment (CPE) and biopolymeric C (BPC) concentrations, and protein-to-carbohydrate ratio (PRT/CHO) in surface sediments (0 to 1 cm), net photosynthetic primary production (NPP), and organic C fluxes (OC fluxes).
    • table S2. Output of the in silico analysis dealing with the coverage of probes targeting 16S rRNA used in the present study.
    • table S3. Statistical analysis testing for differences in the distribution of the different microbial components.
    • fig. S1. Depth-related patterns of total prokaryotic abundances (obtained using SYBR Green I) in the top 1 cm of sediments collected in the different oceanic regions.
    • fig. S2. Comparison of the abundances of bacteria and archaea obtained by CARD-FISH, with the number of 16S rDNA copies of bacteria and archaea obtained in surface sediments of different oceanic regions.
    • fig. S3. Output of the regression tree analysis carried out to identify environmental factors explaining the distribution of MG-I Thaumarchaeota in the top 1 cm of sediments collected in the different oceanic regions.
    • fig. S4. Output of the regression tree analysis carried out to identify environmental factors explaining the distribution of MG-II Euryarchaeota in the top 1 cm of sediments collected in the different oceanic regions.

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