Long term geological record of a global deep subsurface microbial habitat in sand injection complexes

Peer reviewedPublisher PD

Archaeal communities associated with shallow to deep subseafloor sediments of the New Caledonia Basin

The definitive version is available at ww3.interscience.wiley.com. En libre-accès sur Archimer : http://archimer.ifremer.fr/doc/2009/publication-6801.pdfInternational audienceThe distribution of the archaeal communities in deep subseafloor sediments [0-36 m below the seafloor (mbsf)] from the New Caledonia and Fairway Basins was investigated using DNA- and RNA-derived 16S rRNA clone libraries, functional genes and denaturing gradient gel electrophoresis (DGGE). A new method, Co-Migration DGGE (CM-DGGE), was developed to access selectively the active archaeal diversity. Prokaryotic cell abundances at the open-ocean sites were on average approximately 3.5 times lower than at a site under terrestrial influence. The sediment surface archaeal community (0-1.5 mbsf) was characterized by active Marine Group 1 (MG-1) Archaea that co-occurred with ammonia monooxygenase gene (amoA) sequences affiliated to a group of uncultured sedimentary Crenarchaeota. However, the anoxic subsurface methane-poor sediments (below 1.5 mbsf) were dominated by less active archaeal communities, such as the Thermoplasmatales, Marine Benthic Group D and other lineages probably involved in the methane cycle (Methanosarcinales, ANME-2 and DSAG/MBG-B). Moreover, the archaeal diversity of some sediment layers was restricted to only one lineage (Uncultured Euryarchaeota, DHVE6, MBG-B, MG-1 and SAGMEG). Sequences forming two clusters within the Thermococcales order were also present in these cold subseafloor sediments, suggesting that these uncultured putative thermophilic archaeal communities might have originated from a different environment. This study shows a transition between surface and subsurface sediment archaeal communities

Acetate bioavailability and turnover in an estuarine sediment

An enzymatic method for the determination of acetate in marine porewaters was cross-calibrated against a bioassay technique to investigate whether the enzymatic method directly measured the bioavailable acetate pool. Cells of the acetate-oxidising sulfate-reducing bacterium Desulfobacter sp. (DSM 2035) were added to sterile porewater from an intertidal estuarine sediment (Southdown, Tamar Estuary, UK), at three different depths. The porewater was inoculated with [1(2)-14C]acetate and incubated. Removal of [14C]acetate, production of 14CO2 and changes in acetate pool concentrations, measured by both chemical derivatisation and the enzyme method, were determined. [14C]acetate, total and bioavailable acetate were initially rapidly removed, but after depletion of bioavailable acetate a significant amount (20–50%) of the original acetate pool remained unmetabolised. After 18 h the samples were respiked with [14C]acetate, which was mineralised rapidly (at the same rate as initial depletion) although the total recalcitrant acetate pool remained constant. Decay rates at each depth for the initial removal of [14C]acetate and after respiking were the same. Degradation rates of acetate in sediments decreased with depth, corresponding with lower biologically available acetate concentrations deeper in the sediment. Although both bioavailable and total acetate methods result in an overestimate when compared to an independent measure of carbon flow within sediments (sulfate reduction), the overestimate is significantly smaller when data from the enzyme method are used, although still not wholly satisfactory (208%). The enzymatic assay offers advantages over chemical determinations of acetate in marine porewaters, although when used to directly predict the proportion of bioavailable acetate, results do not concur with those provided by the bioassay technique, and below 9 cm in the sediment a substantial sulfate reduction rate was measured but no bioavailable acetate was present. The bioassay technique indicates that bioavailable acetate decreases with increasing sediment depth, and that the pools are turned over at different rates: whether this has an effect on carbon flow within sediments requires further investigation

Acetate bioavailability and turnover in an estuarine sediment

An enzymatic method for the determination of acetate in marine porewaters was cross-calibrated against a bioassay technique to investigate whether the enzymatic method directly measured the bioavailable acetate pool. Cells of the acetate-oxidising sulfate-reducing bacterium Desulfobacter sp. (DSM 2035) were added to sterile porewater from an intertidal estuarine sediment (Southdown, Tamar Estuary, UK), at three different depths. The porewater was inoculated with [1(2)-14C]acetate and incubated. Removal of [14C]acetate, production of 14CO2 and changes in acetate pool concentrations, measured by both chemical derivatisation and the enzyme method, were determined. [14C]acetate, total and bioavailable acetate were initially rapidly removed, but after depletion of bioavailable acetate a significant amount (20–50%) of the original acetate pool remained unmetabolised. After 18 h the samples were respiked with [14C]acetate, which was mineralised rapidly (at the same rate as initial depletion) although the total recalcitrant acetate pool remained constant. Decay rates at each depth for the initial removal of [14C]acetate and after respiking were the same. Degradation rates of acetate in sediments decreased with depth, corresponding with lower biologically available acetate concentrations deeper in the sediment. Although both bioavailable and total acetate methods result in an overestimate when compared to an independent measure of carbon flow within sediments (sulfate reduction), the overestimate is significantly smaller when data from the enzyme method are used, although still not wholly satisfactory (208%). The enzymatic assay offers advantages over chemical determinations of acetate in marine porewaters, although when used to directly predict the proportion of bioavailable acetate, results do not concur with those provided by the bioassay technique, and below 9 cm in the sediment a substantial sulfate reduction rate was measured but no bioavailable acetate was present. The bioassay technique indicates that bioavailable acetate decreases with increasing sediment depth, and that the pools are turned over at different rates: whether this has an effect on carbon flow within sediments requires further investigation

Incorporation of methyl [3H] thymidine by obligate and facultative anerobic bacteria when grown under defined culture condition

Incorporation of [methyl-3H]thymidine into bacterial DNA was determined for a range of axenic anaerobic bacterial cultures: fermentative heterotrophs, sulphate-reducing bacteria, purple sulphur bacteria, acetogens and methanogens. Anaerobically growing Bacillus sp. and the obligate aerobe Thiobacillus ferrooxidans were also investigated. Actively growing cultures of sulphate-reducing bacteria belonging to the genera Desulfovibrio, Desulfotomaculum, Desulfobacter, Desulfobotulus and Desulfobulbus, purple sulphur bacteria (Chromatium vinosum OP2 and Thiocapsa roseopersicina OP1), methanogens (Methanococcus GS16 and Methanosarcina barkeri) and an acetogen (Acetobacterium woodii) did not incorporate [methyl-3H]thymidine into DNA. The only obligate anaerobes in which thymidine incorporation into DNA could be unequivocally demonstrated were members of the genus Clostridium. Anaerobically growing Bacillus sp. also incorporated thymidine. These data demonstrate that pure culture representatives of major groups of anaerobic bacteria involved in the terminal oxidation of organic carbon and anoxygenic phototrophs within sediments are unable to incorporate [methyl-3H]thymidine into DNA, although some obligate and facultative anaerobes can. Variability in thymidine incorporation amongst pure culture isolates indicates that unless existing techniques can be calibrated to take this into consideration then productivity estimates in both aerobic and anaerobic environments may be greatly underestimated using the [methyl-3H]thymidine technique