KCK_ODP
Deep marine subsurface sediments: Bacterial and archaeal diversity and habitat preference
Bacteria and archaea thrive in deep marine subsurface sediments and constitute a major portion of Earths microbial biomass (Parkes et al. 2000).  Here we report pyrosequencing results of deep marine subsurface communities. Eight subsurface sediment samples were selected from Ocean Drilling Program Sites 1227, 1229 and 1231 on the Peru Margin, in the Peru Trench and in the Peru Basin, to represent a wide spectrum of geochemical regimes with different organic carbon sources and electron acceptors. The organic-rich sediments (TOC =~ 1-5%) of ODP sites 1227 and 1229 on the Peruvian continental shelf and continental slope are dominated by sulfate reduction, methanogenesis and sulfate-dependent methane oxidation (DHondt et al. 2004). The sampling horizons for the ICOMM survey include the sulfate-reducing upper sediments and the methane/sulfate interfaces at both sites, and the deep methanogenic zone at site 1229. In contrast, the far offshore Site 1231 in the Peru Basin is characterized by low organic carbon concentration (>0.4%TOC) and by microbial nitrate and metal reduction (DHondt et al. 2004).  Sampling depths are 7 to 40 m at ODP1227, 2 to 90m at OPD1229, and 43 m below sediment surface at ODP1231. Based on a total of ca. 494,000 V6-tag sequences and a 3% cutoff for OTU definition, we obtained on average 2835 bacterial and 1171 archaeal phylotypes per sample, a bacterial/archaeal phylotype ratio of 2.4. This ratio is more favorable to archaea than previous results; the bacterial/archaeal phylotype ratio from warm hydrothermal vent fluids was 13.4, based on 2754 archaeal and 36869 bacterial phylotypes (Huber et al. 2007). Thus, the carbon and energy limitations of deep subseafloor sediment appear to restrict bacterial diversity more severely than archaeal diversity. This result is consistent with Valentines (2007) inference that archaea are metabolically adapted for growth and survival under severe energy limitation in extreme environments. In agreement with 16S rRNA and 16S rDNA clone library analyses of the same sediments and sampling horizons (Parkes et al. 2005, Soensen and Teske 2006, Biddle et al. 2006, Inagaki et al. 2006), Proteobacteria and Chloroflexi were the most  abundant bacterial phyla; the uncultured Miscellaneous Crenarchaeal Group (within the Crenarchaetota) was the most abundant archaeal phylum-level group.  The V6-tag survey also detected smaller populations that were missing in 16S rRNA clone libraries.  For example, close relatives of sulfate-reducing Delta-proteobacteria (Desulfobacterium)  and of sulfate-dependent methane-oxidizing ANME archaea constituted ca. 1-2 % of the bacterial and archaeal V6 tags; their  distribution was largely congruent with sulfate-reducing and methane-oxidizing horizons in the sediment column.  The V6-tag survey also detected small numbers of bacterial phylotypes (ca, 10 - 100 per sediment sample)  that are closely related to cultured Proteobacteria, Firmicutes and Bacteroidetes that have been isolated from the same sediments (Batzke et al. 2007). However,  only a small subset of the V6-tags can be identified based on comparisons with cultured bacteria or with functionally constrained phylogenetic groups of archaea and bacteria;  the majority of the V6-tags is derived from uncultured subsurface bacteria and archaea that occur consistently in shallow and deep marine sediments.
Bacteria and archaea thrive in deep marine subsurface sediments and constitute a major portion of Earths microbial biomass (Parkes et al. 2000).  Here we report pyrosequencing results of deep marine subsurface communities. Eight subsurface sediment samples were selected from Ocean Drilling Program Sites 1227,  1229 and 1231 on the Peru Margin, in the Peru Trench and in the Peru Basin, to represent a wide spectrum of geochemical regimes with different organic carbon sources and  electron acceptors. The organic-rich sediments (TOC =~ 1-5%) of ODP sites 1227 and 1229 on the Peruvian continental shelf and continental slope are dominated by sulfate  reduction, methanogenesis and sulfate-dependent methane oxidation (DHondt et al. 2004). The sampling horizons for the ICOMM survey include the sulfate-reducing upper  sediments and the methane/sulfate interfaces at both sites, and the deep methanogenic zone at site 1229. In contrast, the far offshore Site 1231 in the Peru Basin is  characterized by low organic carbon concentration (>0.4%TOC) and by microbial nitrate and metal reduction (DHondt et al. 2004).  Sampling depths are 7 to 40 m at  ODP1227, 2 to 90m at OPD1229, and 43 m below sediment surface at ODP1231. Based on a total of ca. 494,000 V6-tag sequences and a 3% cutoff for OTU definition,  we obtained on average 2835 bacterial and 1171 archaeal phylotypes per sample, a bacterial/archaeal phylotype ratio of 2.4. This ratio is more favorable to archaea  than previous results; the bacterial/archaeal phylotype ratio from warm hydrothermal vent fluids was 13.4, based on 2754 archaeal and 36869 bacterial phylotypes  (Huber et al. 2007). Thus, the carbon and energy limitations of deep subseafloor sediment appear to restrict bacterial diversity more severely than archaeal diversity.  This result is consistent with Valentines (2007) inference that archaea are metabolically adapted for growth and survival under severe energy limitation in extreme  environments. In agreement with 16S rRNA and 16S rDNA clone library analyses of the same sediments and sampling horizons (Parkes et al. 2005, Soensen and Teske 2006,  Biddle et al. 2006, Inagaki et al. 2006), Proteobacteria and Chloroflexi were the most abundant bacterial phyla; the uncultured Miscellaneous Crenarchaeal Group  (within the Crenarchaetota) was the most abundant archaeal phylum-level group. The V6-tag survey also detected smaller populations that were missing in 16S rRNA clone  libraries. For example, close relatives of sulfate-reducing Delta-proteobacteria (Desulfobacterium) and of sulfate-dependent methane-oxidizing ANME archaea constituted  ca. 1-2 % of the bacterial and archaeal V6 tags; their distribution was largely congruent with sulfate-reducing and methane-oxidizing horizons in the sediment column.  The V6-tag survey also detected small numbers of bacterial phylotypes  (ca, 10 - 100 per sediment sample) that are closely related to cultured Proteobacteria,  Firmicutes and Bacteroidetes that have been isolated from the same  sediments (Batzke et al. 2007). However, only a small subset of the V6-tags can be identified based on  comparisons with cultured bacteria or with functionally constrained phylogenetic groups of archaea and bacteria;  the majority of the V6-tags is derived from uncultured subsurface  bacteria and archaea that occur consistently in  shallow and deep marine sediments.