Analysis of DGGE profiles to explore the relationship between prokaryotic community composition and biogeochemical processes in deep subseafloor sediments from the Peru Margin

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Fry, John Christopher ; Webster, Gordon ; Cragg, Barry Andrew ; Weightman, Andrew John ; Parkes, Ronald John (2006)

The aim of this work was to relate depth profiles of prokaryotic community composition with geochemical processes in the deep subseafloor biosphere at two shallow-water sites on the Peru Margin in the Pacific Ocean (ODP Leg 201, sites 1228 and 1229). Principal component analysis of denaturing gradient gel electrophoresis banding patterns of deep-sediment Bacteria, Archaea, Euryarchaeota and the novel candidate division JS1, followed by multiple regression, showed strong relationships with prokaryotic activity and geochemistry (R2=55–100%). Further correlation analysis, at one site, between the principal components from the community composition profiles for Bacteria and 12 other variables quantitatively confirmed their relationship with activity and geochemistry, which had previously only been implied. Comparison with previously published cell counts enumerated by fluorescent in situ hybridization with rRNA-targeted probes confirmed that these denaturing gradient gel electrophoresis profiles described an active prokaryotic community
  • References (43)
    43 references, page 1 of 5

    Abell GCJ & Bowman JP (2005a) Colonization and community dynamics of class Flavobacteria on diatom detritus in experimental mesocosms based on Southern Ocean seawater. FEMS Microbiol Ecol 53: 379-391.

    Abell GCJ & Bowman JP (2005b) Ecological and biogeographic relationships of class Flavobacteria in the Southern Ocean. FEMS Microbiol Ecol 51: 265-277.

    Dar SA, Kuenen JG & Muyzer G (2005) Nested PCR-denaturing gradient gel electrophoresis approach to determine the diversity of sulfate-reducing bacteria in complex microbial communities. Appl Environ Microbiol 71: 2325-2330.

    DeLong EF (2004) Microbial life breathes deep. Science 306: 2198-2200.

    D'Hondt S, J rgensen BB, Miller DJ, Batzke A, Blake R, Cragg BA, et al. (2004) Distributions of microbial activities in deep subseafloor sediments. Science 306: 2216-2221.

    Fromin N, Hamelin J, Tarnawski S, Roesti D, Jourdain-Miserez K, Forestier N, Teyssier-Cuvelle S, Gillet F, Aragno M & Rossi P (2002) Statistical analysis of denaturing gel electrophoresis (DGE) fingerprinting patterns. Environ Microbiol 4: 634-643.

    Gremion F, Chatzinotas A, Kaufmann K, Sigler WV & Harms H (2004) Impacts of heavy metal contamination and phytoremediation on a microbial community during a twelvemonth microcosm experiment. FEMS Microbiol Ecol 48: 273-283.

    Hoj L, Olsen RA & Torsvik VL (2005) Archaeal communities in high arctic wetlands at Spitsbergen, Norway (78 degrees N) as characterized by 16S rRNA gene fingerprinting. FEMS Microbiol Ecol 53: 89-101.

    Iles TC (1993) Multiple regression. Biological Data Analysis (Fry JC, ed), pp. 127-172. Oxford University Press, Oxford.

    J rgensen BB (2000) Bacteria and marine biogeochemistry. Marine Geochemistry (Schultz HD & Zabel M, eds), pp. 173-207. Springer-Verlag, Berlin.

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