Urea production and turnover following the addition of AMP, CMP, RNA and a protein mixture to a marine sediment

The potential of adenosine 5′-monophosphate (AMP), cytidine 5′-monophosphate (CMP), 16S ribosomal RNA, and a protein (bovine serum albumin) to serve as substrates for bacterial urea production was evaluated in a defaunated, anoxic marine sediment. AMP, CMP and RNA stimulated urea production and urea turnover, but CMP to a lesser degree than AMP and RNA. The increase in urea production and turnover rates took place immediately after AMP, CMP, and RNA were added to the sediment. The rapid response in urea production and turnover rates suggests that the necessary uptake mechanisms and enzymes to utilize the substrates were present constitutively. Addition of the protein mixture did not result in any measurable changes in the urea pool size, urea turnover rate, or urea production rate during the 165 h of incubation. However, an increased and continuous net NH4+ production in the protein-amended sediment relative to the control sediment indicated that the added protein mixture was accessible for bacterial degradation. The results showed that purines and pyrimidines were substrates for the bacterial urea production in the marine sediment, whereas protein was not important for urea production

La messe est dite

Auteur d’une thèse remarquable et remarquée sur La conversion des intellectuels au catholicisme en France, 1885-1935 (Paris, CNRS Éditions, 1998, réédition en 2010), Frédéric Gugelot s’est intéressé plus particulièrement depuis à la figure de l’écrivain catholique. Il a dirigé notamment, avec Alain Dierkens, Fabrice Preyat et Cécile Vanderpelen-Diagre, le précieux ouvrage collectif La Croix et la bannière. L’écrivain catholique en francophonie (xviie-xxie siècles), paru en 2007 aux Éditions d..

Formate, acetate and propionate as substrates for sulfate reduction in sub-arctic sediments of Southwest Greenland.

Volatile fatty acids (VFAs) are key intermediates in the anaerobic mineralization of organic matter in marine sediments. We studied the role of VFAs in the carbon and energy turnover in the sulfate reduction zone of sediments from the sub-arctic Godthåbsfjord (SW Greenland) and the adjacent continental shelf in the NE Labrador Sea. VFA porewater concentrations were measured by a new two-dimensional ion chromatography-mass spectrometry method that enabled the direct analysis of VFAs without sample pretreatment. VFA concentrations were low and surprisingly constant (4-6 µmol L-1 for formate and acetate, and 0.5 µmol L-1 for propionate) throughout the sulfate reduction zone. Hence, VFAs are turned over while maintaining a stable concentration that is suggested to be under a strong microbial control. Estimated mean diffusion times of acetate between neighboring cells were <1 second, whereas VFA turnover times increased from several hours at the sediment surface to several years at the bottom of the sulfate reduction zone. Thus, diffusion was not limiting the VFA turnover. Despite constant VFA concentrations, the Gibbs energies (Gr) of VFA-dependent sulfate reduction decreased downcore, from -28 to -16 kJ (mol formate)-1, -68 to -31 kJ (mol acetate)-1, and -124 to -65 kJ (mol propionate)-1. Thus, Gr i

Size and Carbon Content of Sub-seafloor Microbial Cells at Landsort Deep, Baltic Sea

The discovery of a microbial ecosystem in ocean sediments has evoked interest in life under extreme energy limitation and its role in global element cycling. However, fundamental parameters such as the size and the amount of biomass of sub-seafloor microbial cells are poorly constrained. Here we determined the volume and the carbon content of microbial cells from a marine sediment drill core retrieved by the Integrated Ocean Drilling Program (IODP), Expedition 347, at Landsort Deep, Baltic Sea. To determine their shape and volume, cells were separated from the sediment matrix by multi-layer density centrifugation and visualized via epifluorescence microscopy (FM) and scanning electron microscopy (SEM). Total cell-carbon was calculated from amino acid-carbon, which was analyzed by high-performance liquid chromatography (HPLC) after cells had been purified by fluorescence-activated cell sorting (FACS). The majority of microbial cells in the sediment have coccoid or slightly elongated morphology. From the sediment surface to the deepest investigated sample (similar to 60 m below the seafloor), the cell volume of both coccoid and elongated cells decreased by an order of magnitude from similar to 0.05 to 0.005 mu m(3). The cell-specific carbon content was 19-31 fg C cell(-1), which is at the lower end of previous estimates that were used for global estimates of microbial biomass. The cell specific carbon density increased with sediment depth from about 200 to 1000 fg C mu m(-3), suggesting that cells decrease their water content and grow small cell sizes as adaptation to the long-term subsistence at very low energy availability in the deep biosphere. We present for the first time depth-related data on the cell volume and carbon content of sedimentary microbial cells buried down to 60 m below the seafloor. Our data enable estimates of volume-and biomass-specific cellular rates of energy metabolism in the deep biosphere and will improve global estimates of microbial biomass

D:L-Amino Acid Modeling Reveals Fast Microbial Turnover of Days to Months in the Subsurface Hydrothermal Sediment of Guaymas Basin

We investigated the impact of temperature on the microbial turnover of organic matter (OM) in a hydrothermal vent system in Guaymas Basin, by calculating microbial bio- and necromass turnover times based on the culture-independent D:L-amino acid model. Sediments were recovered from two stations near hydrothermal mounds (&lt;74°C) and from one cold station (&lt;9°C). Cell abundance at the two hydrothermal stations dropped from 108 to 106 cells cm-3 within ∼5 m of sediment depth resulting in a 100-fold lower cell number at this depth than at the cold site where numbers remained constant at 108 cells cm-3 throughout the recovered sediment. There were strong indications that the drop in cell abundance was controlled by decreasing OM quality. The quality of the sedimentary OM was determined by the diagenetic indicators %TAAC (percentage of total organic carbon present as amino acid carbon), %TAAN (percentage of total nitrogen present as amino acid nitrogen), aspartic acid:β-alanine ratios, and glutamic acid:γ-amino butyric acid ratios. All parameters indicated that the OM became progressively degraded with increasing sediment depth, and the OM in the hydrothermal sediment was more degraded than in the uniformly cold sediment. Nonetheless, the small community of microorganisms in the hydrothermal sediment demonstrated short turnover times. The modeled turnover times of microbial bio- and necromass in the hydrothermal sediments were notably faster (biomass: days to months; necromass: up to a few hundred years) than in the cold sediments (biomass: tens of years; necromass: thousands of years), suggesting that temperature has a significant influence on the microbial turnover rates. We suggest that short biomass turnover times are necessary for maintance of essential cell funtions and to overcome potential damage caused by the increased temperature.The reduced OM quality at the hyrothemal sites might thus only allow for a small population size of microorganisms

Competition between Ammonia-Oxidizing Bacteria and Benthic Microalgae

The abundance, activity, and diversity of ammonia-oxidizing bacteria (AOB) were studied in prepared microcosms with and without microphytobenthic activity. In the microcosm without alga activity, both AOB abundance, estimated by real-time PCR, and potential nitrification increased during the course of the experiment. AOB present in the oxic zone of these sediments were able to fully exploit their nitrification potential because NH(4)(+) did not limit growth. In contrast, AOB in the alga-colonized sediments reached less than 20% of their potential activity, suggesting starvation of cells. Starvation resulted in a decrease with time in the abundance of AOB as well as in nitrification potential. This decrease was correlated with an increase in alga biomass, suggesting competitive exclusion of AOB by microalgae. Induction of N limitation in the oxic zone of the alga-colonized sediments and O(2) limitation of the majority of AOB in darkness were major mechanisms by which microalgae suppressed the growth and survival of AOB. The competition pressure from the algae seemed to act on the entire population of AOB, as no differences were observed by denaturing gradient gel electrophoresis of amoA fragments during the course of the experiment. Enumeration of bacteria based on 16S rRNA gene copies and d-amino acids suggested that the algae also affected other bacterial groups negatively. Our data indicate that direct competitive interaction takes place between algae and AOB and that benthic algae are superior competitors because they have higher N uptake rates and grow faster than AOB