Stratified communities of active Archaea in deep marine subsurface sediments

Abstract

Archaeal 16S rRNA was extracted from samples of deep marine subsurface sediments from Peru Margin site 1227, Ocean Drilling Program leg 201. The amounts of archaeal 16S rRNA in each extract were quantified by serial dilution and reverse transcription (RT)-PCR. The results indicated a 1,000-fold variation in rRNA content with depth in the sediment, with the highest concentrations found near the sediment surface and in the sulfate-methane transition zone (SMTZ). The phylogenetic composition of the active archaeal population revealed by cloning and sequencing of RT-PCR products changed with depth. Several phylotypes affiliated with marine benthic group B (MBGB) dominated clone libraries from the upper part of the SMTZ and were detected only in this layer. Members of the miscellaneous crenarchaeotal group (MCG) dominated clone libraries from the other layers. These results demonstrate that archaeal communities change in activity and community composition over short distances in geochemically distinct zones of deep subseafloor sediments and that these changes are traceable in the rRNA pool. It was shown for the first time that members of both the MCG and MBGB Archaea are more active in the SMTZ than in layers above and below. This indicates that they benefit either directly or indirectly from the anaerobic oxidation of methane. They also appear to be ecophysiologically flexible, as they have been retrieved from a wide range of marine sediments of various geochemical properties.

FIG. 1.

Concentration profiles of sulfate (black squares) and methane (open triangles) at site 1227 (redrawn from reference 17).

FIG. 2.

Results of 16S rRNA extraction and analysis. (a) Relative amounts of 16S rRNA in extracts from different depths (black squares). A value of 1 corresponds to the detection limit. The data are compared with the amounts of archaeal genes for 16S rRNA extracted from similar depths in the sediment and quantified by Q-PCR (open circles) (redrawn from reference 42). These numbers were normalized such that the amount of DNA found at 37.75 mbsf corresponds to a value of 1. The SMTZ is indicated in the figure by the stippled lines. (b) Phylogenetic composition of RT-PCR clone libraries from each depth. The sample from 37.75 mbsf was extracted twice; the second extract was amplified with two primer sets, yielding three independent clone libraries. Groups shown include MBGB (54), MCG (17), and SAGMEG-1 (51).

FIG. 3.

Neighbor-joining tree showing phylogenetic positions of the crenarchaeotal phylotypes retrieved during this study. Phylotype names refer to sample 1H-5 (6.55 mbsf), 2H-2 (7.35 mbsf), 3H-5 (21.35 mbsf), 5H-2 (37.75 mbsf), 5H-3 (37.35 mbsf), 5H-5 (40.35 mbsf), or 6H-2 (45.35 mbsf). Some phylotypes were retrieved from several layers, as indicated. Numbers in parentheses indicates the number of times found in clone libraries. The three numbers given at each phylotype from sample 5H-2 refer to the first extraction, second extraction, and second extraction using an alternative reverse primer for PCR. Bootstrap values equal to or larger than 0.5 are indicated. The values were determined using 1,000 replicates.

FIG. 4.

Neighbor-joining tree indicating the phylogenetic positions of the euryarchaeotal phylotypes found during this study.

FIG. 5.

S_Chao1 estimates of total numbers of phylotypes in clone libraries from cores 1H-5, from 6.55 mbsf (squares); 2H-2, from 7.35 mbsf (circles); and 3H-5, from 21.35 mbsf (triangles). Estimators were calculated from randomly sampled subsets as well as from the entire data set from each sample (22). Error bars indicate standard deviations in richness estimates for four resamplings.