Subsurface microbiology and biogeochemistry of a deep, cold-water carbonate mound from the Porcupine Seabight (IODP Expedition 307)

Abstract

The Porcupine Seabight Challenger Mound is the first carbonate mound to be drilled (approximately 270 m) and analyzed in detail microbiologically and biogeochemically. Two mound sites and a non-mound Reference site were analyzed with a range of molecular techniques [catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH), quantitative PCR (16S rRNA and functional genes, dsrA and mcrA), and 16S rRNA gene PCR-DGGE] to assess prokaryotic diversity, and this was compared with the distribution of total and culturable cell counts, radiotracer activity measurements and geochemistry. There was a significant and active prokaryotic community both within and beneath the carbonate mound. Although total cell numbers at certain depths were lower than the global average for other subseafloor sediments and prokaryotic activities were relatively low (iron and sulfate reduction, acetate oxidation, methanogenesis) they were significantly enhanced compared with the Reference site. In addition, there was some stimulation of prokaryotic activity in the deepest sediments (Miocene, > 10 Ma) including potential for anaerobic oxidation of methane activity below the mound base. Both Bacteria and Archaea were present, with neither dominant, and these were related to sequences commonly found in other subseafloor sediments. With an estimate of some 1600 mounds in the Porcupine Basin alone, carbonate mounds may represent a significant prokaryotic subseafloor habitat.

Fig. 1

a. Location of IODP Expedition 307 operations area in the Belgica Mound Province, Porcupine Seabight. b. Lithostratigraphy of three drilling sites (U1316, U1317 and U1318) projected on the seismic profile of Challenger Mound along a north-north-west to south-south-east transect.

Fig. 2

Depth profiles of prokaryotic cell numbers, prokaryotic activity and geochemical data for Reference site U1318. a. Prokaryotic cell numbers determined by AODC and qPCR of 16S rRNA genes, and bacterial CARD-FISH. The solid line shows Parkes and colleagues (2000) general model for prokaryotic cell distributions in deep marine sediments, and dotted lines represent 95% prediction limits. b. DNA copy numbers of the 16S rRNA genes determined by qPCR of Bacteria, Archaea and Geobacteraceae, mcrA and dsrA genes. c and d. Pore water concentrations of sulfate, alkalinity, dissolved Fe and acetate, and in situ methane. e. Potential rates of methanogenesis from H₂ : CO₂ and acetate. f. Rates of thymidine incorporation and acetate oxidation to CO₂. g. Culturable cells from MPN enrichments; heterotrophic, metal-reducing, sulfate-reducing and acetogenic bacteria.

Fig. 3

Depth profiles of prokaryotic cell numbers, prokaryotic activity and geochemical data for Mound site U1317. a. Prokaryotic cell numbers determined by AODC and qPCR of 16S rRNA genes, and bacterial CARD-FISH. The solid line shows Parkes and colleagues (2000) general model for prokaryotic cell distributions in deep marine sediments, and dotted lines represent 95% prediction limits. b. DNA copy numbers of the 16S rRNA genes determined by qPCR of Bacteria, Archaea and Geobacteraceae, and dsrA genes. c and d. Pore water concentrations of sulfate, alkalinity, dissolved Fe, sulfide and acetate, and in situ methane. e. Potential rates of methanogenesis from H₂ : CO₂ and acetate. f. Rates of thymidine incorporation and acetate oxidation to CO₂. g. Culturable cells from MPN enrichments; heterotrophic, metal-reducing, sulfate-reducing and acetogenic bacteria.

Fig. 4

Depth profiles of prokaryotic cell numbers, prokaryotic activity and geochemical data for Flank site U1316. a. Prokaryotic cell numbers determined by AODC and qPCR of 16S rRNA genes, and bacterial CARD-FISH. The solid line shows Parkes and colleagues (2000) general model for prokaryotic cell distributions in deep marine sediments, and dotted lines represent 95% prediction limits. b. DNA copy numbers of the 16S rRNA genes determined by qPCR of Bacteria, Archaea and Geobacteraceae, and dsrA genes. c and d. Pore water concentrations of sulfate, alkalinity, dissolved Fe and acetate, and in situ methane. e. Potential rates of methanogenesis from H₂ : CO₂ and acetate. f. Rates of thymidine incorporation and acetate oxidation to CO₂. g. Culturable cells from MPN enrichments; heterotrophic, metal-reducing, sulfate-reducing and acetogenic bacteria.

Fig. 5

Distribution of bacterial 16S rRNA gene sequences from Challenger Mound sites (U1316 and U1317) and the Reference site (U1318) at different sediment depths using nested PCR-DGGE analysis. a. Nested PCR-DGGE analysis with primer sets 27F-907R and 357F-518R. b. Nested PCR-DGGE analysis with primer sets 27F-1492R and 357F-518R. Numbers of DGGE bands at each depth are shown in parentheses.