Thiocapsa marina sp. nov., a new purple sulfur bacterium containing okenone isolated from several brackish and marine environments

Four marine, phototrophic, purple sulfur bacteria (strains 5811T, 5812, BM-3 and BS-1) were isolated in pure culture from different brackish to marine sediments in the Mediterranean Sea, the White Sea and the Black Sea. Single cells of these strains were coccus-shaped, non-motile and did not contain gas vesicles. The colour of cell suspensions that were grown in the light was purple–red. Bacteriochlorophyll a and carotenoids of the okenone series were present as photosynthetic pigments. Photosynthetic membrane systems were of the vesicular type. Hydrogen sulfide, thiosulfate, elemental sulfur and molecular hydrogen were used as electron donors during photolithotrophic growth under anoxic conditions; carbon dioxide was utilized as the carbon source. During growth on sulfide, elemental sulfur globules were stored inside the cells. In the presence of hydrogen sulfide, several organic substances could be photoassimilated. Comparative 16S rDNA sequence analysis revealed an affiliation of these four strains to the genus Thiocapsa. Both phylogenetic analysis and the results of DNA–DNA hybridization studies revealed that these strains formed a separate cluster within the genus Thiocapsa. Thus, according to phenotypic characteristics and mainly the carotenoid composition, 16S rDNA sequence analysis and DNA–DNA hybridization data, it is proposed that these strains should be classified as a novel species, Thiocapsa marina sp. nov., with strain 5811T (=DSM 5653T=ATCC 43172T) as the type strain

Sulfide fluxes in a microbial mat from the Ebro Delta, Spain

The sulfur cycle of Ebro Delta microbial mats was studied in order to determine sulfide production and sulfide consumption. Vertical distribution of two major functional groups involved in the sulfur cycle, anoxygenic phototrophic bacteria and dissimilatory sulfate-reducing bacteria (SRB), was also studied. The former reached up to 2.2 ×108 cfu cm-3 sediment in the purple layer, and the latter reached about 1.8×105 SRB cm-3 sediment in the black layer. From the changes in sulfide concentrations under light-dark cycles it can be inferred that the rate of H2S production was 6.2 μmol H2S cm-3 day-1 at 2.6 mm, and 7.6 μmol H2S cm-3 day-1 at 6 mm. Furthermore, sulfide consumption was also assessed, determining rates of 0.04, 0.13 and 0.005 mmol l-1 of sulfide oxidized at depths of 2.6, 3 and 6 mm, respectively

Distribution of phototrophic populations and primary production in a microbial mat from the Ebro Delta, Spain

Microbial mats arising in the sand flats of the Ebro Delta (Tarragona, Spain) were investigated during the summer season, when the community was highly developed. These mats are composed of three pigmented layers of phototrophic organisms, an upper brown layer mainly composed of Lyngbya aestuarii and diatoms, an intermediate green layer of the cyanobacterium Microcoleus chthonoplastes, and an underlying pink layer of a so-far unidentified purple sulfur bacterium. In the photic zone, oxygenic phototrophs constitute about 58% of total photosynthetic biomass, measured as biovolume, and anoxygenic phototrophs represent 42%. Diatoms constitute 11.8% of the oxygenic biomass, M. chthonoplastes 61.2%, and L. aestuarii and coccoid cyanobacteria 20.6 and 6.4%, respectively. In this laminated community, organic matter has an autochthonous origin, and photosynthesis is the most important source of organic carbon. Oxygen production reaches up to 27.2 mmol O2 m–2 h–1, measured at 1000 μE m–2 s–1 light intensity, whereas oxidation of sulfide in the light has been calculated to be 18.6 mmol S m–2 h–1. This amount represents 26% of the total photosynthetic production in terms of photoassimilated carbon, demonstrating the important role of anoxygenic phototrophs as primary producers in the pink layer of Ebro Delta microbial mats. [Int Microbiol 2004; 7(1):19–25

Experimental simulation of H2 coinjection via a high-pressure reactor with natural gas in a low-salinity deep aquifer used for current underground gas storage

If dihydrogen (H2) becomes a major part of the energy mix, massive storage in underground gas storage (UGS), such as in deep aquifers, will be needed. The development of H2 requires a growing share of H2 in natural gas (and its current infrastructure), which is expected to reach approximately 2% in Europe. The impact of H2 in aquifers is uncertain, mainly because its behavior is site dependent. The main concern is the consequences of its consumption by autochthonous microorganisms, which, in addition to energy loss, could lead to reservoir souring and alter the petrological properties of the aquifer. In this work, the coinjection of 2% H2 in a natural gas blend in a low-salinity deep aquifer was simulated in a three-phase (aquifer rock, formation water, and natural gas/H2 mix) high-pressure reactor for 3 months with autochthonous microorganisms using a protocol described in a previous study. This protocol was improved by the addition of protocol coupling experimental measures and modeling to calculate the pH and redox potential of the reactor. Modeling was performed to better analyze the experimental data. As in previous experiments, sulfate reduction was the first reaction to occur, and sulfate was quickly consumed. Then, formate production, acetogenesis, and methanogenesis occurred. Overall, H2 consumption was mainly caused by methanogenesis. Contrary to previous experiments simulating H2 injection in aquifers of higher salinity using the same protocol, microbial H2 consumption remained limited, probably because of nutrient depletion. Although calcite dissolution and iron sulfide mineral precipitation likely occurred, no notable evolution of the rock phase was observed after the experiment. Overall, our results suggested that H2 can be stable in this aquifer after an initial loss. More generally, aquifers with low salinity and especially low electron acceptor availability should be favored for H2 costorage with natural gas

Recommended standards for the description of new species of anoxygenic phototrophic bacteria

Recommended standards for the description of new species of the anoxygenic phototrophic bacteria are proposed in accordance with Recommendation 30b of the International Code of Nomenclature of Bacteria. These standards include information on the natural habitat, ecology and phenotypic properties including morphology, physiology and pigments and on genetic information and nucleic acid data. The recommended standards were supported by the Subcommittee on the taxonomy of phototrophic bacteria of the International Committee on Systematics of Prokaryotes. They are considered as guidelines for authors to prepare descriptions of new specie

Activités microbiennes anaérobies et écodynamique des contaminants métalliques et organométalliques (cas de l étain et du mercure)

Le tributylétain (TBT) et le mercure (Hg) ainsi que leurs dérivés organiques sont des micropolluants métalliques, ubiquistes et persistants à l état de traces dans les écosystèmes aquatiques. Les processus microbiologiques d alkylation et de déalkylation des formes organiques plus toxiques de l étain et du mercure (méthyl-mercure, tributyl-étain ou méthylétains), en conditions oxiques ou anoxiques, sont peu connus. Ce travail porte dans une première partie sur l étude de la biodégradation du TBT par des communautés bactériennes simplifiées en culture continue. Les potentiels de dégradation du TBT et de méthylation de l étain inorganique, e.g. Sn(IV), des souches isolées de ce réacteur, tout comme ceux de différents microorganismes aérobies et/ou anaérobies, ont été caractérisés grâce à l utilisation de traceurs isotopiques stables et ont permis de définir certaines voies d alkylation et de déalkylation. Le second volet de ce document est consacré à l étude des capacités de microorganismes sulfato-réducteurs (MSR) à méthyler et à déméthyler le Hg et le méthylmercure. L utilisation de traceurs isotopiques stables du Hg a permis d étudier l aspect systématique du phénomène pour des microorganismes isolés de l environnement et sous différentes conditions physiologiques (fermentation, respiration nitrate, sulfato-réduction, limitation en substrat carboné). Finalement, l étude du fractionnement isotopique du Hg lors de sa méthylation par un MSR (Desulfobulbus propionicus, DSM6523) souligne l importance qu il y a à mieux comprendre le fonctionnement de ces deux mécanismes co-occurrents, dans la régulation de la production nette de méthylmercure dans les écosystèmes aquatiques.Tributyltin (TBT) and mercury (Hg) as well as their organic derivatives are ubiquitous and persistent metallic micro-pollutants present at trace level in aquatic ecosystems. The microbiological alkylation and dealkylation processes of the more toxic organic forms of tin and mercury (methylmercury, tributyltin or methyltin) under oxic and anoxic conditions are poorly understood. The first part of this study reports on TBT biotransformations in simplified bacterial communities under continuous culture. The potential for TBT biodegradation and inorganic tin methylation, e.g. Sn(IV), of strains isolated from this reactor as well as various aerobic and anaerobic microorganisms were simultaneously characterized by means of stable isotopic tracers, allowing to define some alkylation and dealkylation pathways. The second section of this document is dedicated to the investigation of the capacities of sulphate-reducing prokaryotes (SRP) for mercury methylation and demethylation. The use of Hg stable isotopic tracers allowed the systematic study of this phenomenon in environmental organisms under different physiological conditions (fermentation, nitrate respiration, sulphate respiration and substrate starvation). In conclusion, the study of isotopic fractionation of Hg during its methylation by a SRM (Desulfobulbus propionicus, DSM6523) highlighted the need to better understand the functioning of the co-occurring mechanisms implied in the regulation of net methylmercury production in aquatic ecosystems.PAU-BU Sciences (644452103) / SudocSudocFranceF

Analyse de la biodiversité bactérienne des sédiments anoxiques de milieux hypersales (marais salants de Salin-de-Giraud, France)

PAU-BU Sciences (644452103) / SudocSudocFranceF

Etude de populations bactériennes anaérobies d'un écosystème lagunaire impliquées dans la dégradation des hydrocarbures

Les milieux côtiers sont régulièrement exposés à des pollutions pétrolières ; une part importante des composés de ce pétrole se retrouve piégée dans les sédiments et tend à persister en conditions anoxiques. Parmi les communautés bactériennes colonisant ces milieux, certains microorganismes sont capables de dégrader les hydrocarbures pétroliers et participent ainsi à la biorémédiation de ces écosystèmes. L'objectif de ce travail était de comprendre le rôle et la coopération des différents groupes métaboliques bactériens anaérobies lors de la dégradation de molécules d'hydrocarbures modèles (alcanes, HAPs). Pour cela, des communautés bactériennes anaérobies dégradant des hydrocarbures ont été sélectionnées en conditions anoxiques et de lumière (cultures batch et continue) à partir de biofilms photosynthétiques se développant à la surface de sédiments lagunaires contaminées par des hydrocarbures pétroliers (Etang de Berre, France). L'association de techniques moléculaires (T-RFLP, clonage et séquençage) et culturales (enrichissement, isolement et caractérisation de souches bactériennes) a permis de déterminer la composition de ces communautés bactériennes ainsi que les interactions entre les différentes populations. La même composition en terme de groupes fonctionnels bactériens, à savoir les bactéries sulfato-réductrices, nitrate-réductrices, phototrophes anoxygéniques pourpres et fermentatives, a été systématiquement retrouvée quelle que soit la molécule d'hydrocarbure modèle. La culture continue a permis de sélectionner plus rapidement qu'en culture d'enrichissements les bactéries d'intérêt. Plusieurs souches bactériennes, appartenant à la communauté bactérienne capable de dégrader les hydrocarbures, ont été isolées ; leur étude a montré un lien entre la présence de bactéries dénitrifiantes proches de l'espèce Pseudomonas balearica et la dégradation de ce type de molécules. Des phénomènes de coopération entre les groupes fonctionnels, notamment entre les bactéries dénitrifiantes et les bactéries anoxygéniques pourpres, ont été mis en évidence tant du point de vue métabolique que de celui de la production d'émulsifiants. Une étude de diversité des bactéries phototrophes anoxygéniques pourpres directement réalisée à partir de sédiments chroniquement contaminés a montré la dominance de microorganismes proche du clade des Roseobacter (bactéries phototrophes anoxygéniques pourpres aérobies). Des membres de ce groupe des Roseobacter sont régulièrement retrouvés parmi les communautés bactériennes aérobies dégradant les hydrocarbures. Deux souches bactériennes proche de ce clade ont été isolées et se sont révélées capables de croître photosynthétiquement en conditions anoxiques.Coastal ecosystems are frequently exposed to oil contamination; a major part of compounds is trapped in sediments and tends to persist in anoxic conditions. Among the bacterial communities from these ecosystems, some microorganisms may degrade oil hydrocarbons and participate in the bioremediation of these ecosystems. The aim of this work was to increase our knowledge about the role and the cooperation of these different metabolic anaerobic bacterial groups during model hydrocarbons molecules degradation (alkanes, PAH). Anaerobic bacterial communities able to degrade hydrocarbons were selected in anoxic and light conditions (batch and continuous cultures) from a photosynthetic biofilm growing on a lagoon sediment surface contaminated with oil hydrocarbons (Etang de Berre, France). Both molecular (T-RFLP, cloning and sequencing) and cultural approaches (enrichment cultures, isolation and characterization) allowed determining bacterial communities diversity and the interactions. The identical composition in term of functional bacterial groups was systematically found such as sulfate-reducing, nitrate-reducing, purple anoxygenic phototrophic and fermentative bacteria, whatever the hydrocarbon molecule model used. The continuous culture allowed the select of bacteria implied in the hydrocarbon degradation faster than batch cultures. Several isolated bacterial strains from the community able to degrade hydrocarbons were isolated. The study of this bacterial community allowed associating the alkane degradation to denitrifying bacteria belonging to Pseudomonas balearica. Cooperation phenomena between the different bacterial functional groups, in particular between denitrifying bacteria and purple anoxygenic phototrophic bacteria, were highlighted. A diversity study of the purple phototrophic anoxygenic bacteria from sediments chronically contaminated showed the dominance of microorganisms closed to the Roseobacter clade (Purple phototrophic anoxygenic aerobic bacteria). This Roseobacter group is regularly found among the bacterial aerobic community able to degrade hydrocarbons. Two bacterial strains closed to this clade were isolated and were able to grow photosynthetically in anoxic conditions.PAU-BU Sciences (644452103) / SudocSudocFranceF