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Chemical distributions, respiration rates, and bacterial distributions were measured in 1994 in the water column and sediments of a small, tropical, anoxic basin (Golfo Dulce, Pacific coast of Costa Rica) to examine the biogeochemical controls on anoxia, sulfide, dissolved inorganic nitrogen, and organic carbon consumption. As reported previously, the deepest 100 m of the water column were anoxic, and sulfide concentrations in the bottom waters were less than 7 μM and then only transiently. Both free-swimming sulfide-oxidizing bacteria and Beggiatoa sp. (containing large vacuoles) were observed in the anoxic bottom waters or at the sediment-water interface. Aerobic respiration dominated the decomposition of organic matter in the surface waters and pycnocline, whereas sulfate reduction was principally restricted to the sediments. Bacteria were distributed in discrete zones and exhibited the highest densities where oxygen decreased below 1 μM around 100 m depth, and near the sediment-water interface. The sub-oxic, sub-pycnocline water column was characterized by a dissolved inorganic nitrogen (DIN) deficit of 2.9 mole m-2. With a water residence time of 35 – 57 d, estimated from a salt balance, this deficit corresponded to a DIN loss of 51 – 85 mmol m-2 d-1, comparable to the sub-pycnocline oxygen consumption. Sulfide in the water column was maintained at low concentrations by frequent inputs of oxygenated water from the Pacific Ocean. Sulfide production in the sediments due to bacterial sulfate reduction was scavenged by frequent deposition of iron-rich turbidites. Based on 210Pb distributions, the most recent emplacement of a turbidite in the basin sediments was determined to have occurred between 1989 and 1992. Rev. Biol. Trop. 54 (Suppl. 1): 171-191. Epub 2006 Sept. 30. En el Golfo Dulce, que es un pequeño ecosistema marino anóxico tropical en Costa Rica, se evaluaron, en la columna de agua y los sedimentos, las distribuciones de parámetros químicos, las tasas de respiración, y las distribuciones de bacterias, con el propósito de examinar los controles biológicos de la anoxia, sulfuro, nitrógeno inorgánico disuelto y consumo de carbón orgánico. Tal como fue informado en otros estudios, la columna de agua más profunda de 100 m es anóxica y las concentraciones de sulfuro en las aguas de fondo fue menor a 7 μM (y en forma transitoria). Tanto las bacterias nadadoras libres oxidadoras de sulfuro, como Beggiatoa sp. (con grandes vacuolas) fueron observadas en las aguas anóxicas del fondo o en la interfase agua-sedimento. La respiración aeróbica dominó la descomposición de la materia orgánica en las aguas superficiales y en la picnoclina, mientras que la reducción del sulfato estuvo restringida a los sedimentos. La distribución de las bacterias fue en zonas discretas en la zona anóxica y exhibió las densidades más grandes donde el oxígeno decreció por debajo de 1μM alrededor de los 100m de profundidad, y cerca de la interfase agua-sedimento. La columna de agua bajo la picnoclina fue sub-óxica y caracterizada por un déficit de nitrógeno inorgánico disuelto (DIN) de 2.9 mol.m-2. Con un tiempo de residencia de 35 a 57 días, estimado a partir del balance de sal, este déficit corresponde a una pérdida de DIN de 51-85 mmol.m-2.d-1, comparable con el consumo de oxígeno en la sub-picnoclina. El sulfuro en la columna de agua fue mantenido a concentraciones bajas por la frecuente entrada de agua con oxígeno proveniente del Océano Pacífico. La producción de sulfuro en los sedimentos debida a la reducción bacterial del sulfato fue entorpecida por la frecuente deposición de turbiditas ricas en hierro. Con base en la distribución de 210P, se calcula que la más reciente llegada de turbiditas a los sedimentos de la cuenca tuvo lugar entre 1989 y 1992.

Desulfotomaculum kuznetsovii is a moderately thermophilic member of the polyphyletic spore-forming genus Desulfotomaculum in the family Peptococcaceae. This species is of interest because it originates from deep subsurface thermal mineral water at a depth of about 3000 m. D. kuznetsovii is a rather versatile bacterium as it can grow with a large variety of organic substrates, including short-chain and long-chain fatty acids, which are degraded completely to carbon dioxide coupled to the reduction of sulfate. It can grow methylotrophically with methanol and sulfate and autotrophically with H2 + CO2 and sulfate. For growth it does not require any vitamins. Here, we describe the features of D. kuznetsovii together with the genome sequence and annotation. The chromosome has 3,601,386 bp organized in one contig. A total of 3567 candidate protein-encoding genes and 58 RNA genes were identified. Genes of the acetyl-CoA pathway possibly involved in heterotrophic growth with acetate and methanol, and in CO2 fixation during autotrophic growth are presented. Genomic comparison revealed that D. kuznetsovii shows a large similarity with Pelotomaculum thermopropionicum. Genes involved in propionate metabolism of these two strains show a strong similarity. However, main differences are found in genes involved in the electron acceptor metabolism.

International audience; Lake Pavin is a meromictic crater lake located in the French Massif Central area. In this ecosystem, most methane (CH(4)) produced in high quantity in the anoxic bottom layers, and especially in sediments, is consumed in the water column, with only a small fraction of annual production reaching the atmosphere. This study assessed the diversity of methanogenic and methanotrophic populations along the water column and in sediments using PCR and reverse transcription-PCR-based approaches targeting functional genes, i.e. pmoA (α-subunit of the particulate methane monooxygenase) for methanotrophy and mcrA (α-subunit of the methyl-coenzyme M reductase) for methanogenesis as well as the phylogenetic 16S rRNA genes. Although methanogenesis rates were much higher in sediments, our results confirm that CH(4) production also occurs in the water column where methanogens were almost exclusively composed of hydrogenotrophic methanogens, whereas both hydrogenotrophs and acetotrophs were almost equivalent in the sediments. Sequence analysis of markers, pmoA and the 16S rRNA gene, suggested that Methylobacter may be an important group actively involved in CH(4) oxidation in the water column. Two main phylotypes were characterized, one of which could consume CH(4) under conditions where the oxygen amount is undetectable.