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International audience; All living organisms contribute to the biogeochemical cycles, but microorganisms, due to their high abundance, their tremendous metabolic capacities and adaptation potential, play a key role in the functioning and the evolution of biogeochemical cycles. Consequently, they are keyplayers in adaptation, resistance and resilience of ecosystems. The role of microorganisms in the main biogeochemical cycles (carbon, nitrogen, sulfur, phosphorus, silicon, metals), in soils, freshwater and marine ecosystems is presented. Microbial processes involved in the turnover of biogeochemical cycles are discussed from gene to ecosystem (natural and anthropogenic ecosystems), at global, regional and local scales, as well as in targeted microenvironments (such as particles or microniches). The biodiversity of microorganisms is highlighted and their metabolic pathways on which are based exchanges and biotransformations of organic and mineral components within ecosystems are described in details. The impacts of human activities on the microbial actors and processes of biogeochemical cycles, and the cascading ecological effects (greenhouse gas emissions, acid rains, dystrophic crises, etc.), are also discussed.

A novel anaerobic, long-chain alkene-degrading, sulfate-reducing bacterium, strain LM2801T, was isolated from brackish sediment of a wastewater decantation facility of an oil refinery (Berre lagoon, France). Cells of strain LM2801T were Gram-negative, motile, slightly curved or vibrioid rods. Its optimum growth conditions were 30–36 °C, 6–10 g NaCl l−1 and pH 7.5. Strain LM2801T incompletely oxidized long-chain alkenes (from C14 to C23) and fatty acids (C14 to C24). The DNA G+C content was 45.5 mol%. Sequence analyses of the 16S rRNA and dsrAB genes indicated that the strain was a member of the family Desulfobacteraceae within the Deltaproteobacteria. This novel isolate possesses phenotypic and phylogenetic traits that do not allow its classification as a member of any previously described genus. Therefore, strain LM2801T is described as a member of a new genus, Desulfatiferula gen. nov., of which Desulfatiferula olefinivorans sp. nov. is the type species. The type strain of Desulfatiferula olefinivorans is LM2801T (=DSM 18843T =JCM 14469T).

This book is a treatise on microbial ecology that covers traditional and cutting-edge issues in the ecology of microbes in the biosphere. It emphasizes on study tools, microbial taxonomy and the fundamentals of microbial activities and interactions within their communities and environment as well as on the related food web dynamics and biogeochemical cycling. The work exceeds the traditional domain of microbial ecology by revisiting the evolution of cellular prokaryotes and eukaryotes and stressing the general principles of ecology. The overview of the topics, authored by more than 80 specialists, is one of the broadest in the field of environmental microbiology.

Resume En France, deux hydrophytes amphibies du genre Ludwigia (Onagraceae) posent, depuis une vingtaine d'annees, de tres graves problemes ecologiques et economiques : L. peploides (Kunth) Raven et L. grandiflora (Michaux) Greuter & Burdet. L'etude bacteriologique et physicochimique, realisee sur trois ecosystemes aquatiques mediterraneens differents, met en evidence, pour la premiere fois, une nuisance directe de l'invasion de ces taxons americains introduits. Au cours de la periode de fort developpement des plantes, en ete, on observe l'apparition dans la colonne d'eau de conditions anoxiques et la production de composes toxiques, notamment dans les populations a L. grandiflora. La toxicite est liee a une proliferation de bacteries sulfato-reductrices produisant des sulfures tres nocifs pour tous les organismes aquatiques. Pour citer cet article : S. Dandelot et al., C. R. Biologies 328 (2005).

A novel marine sulfate-reducing bacterium, strain CV2803T, which is able to oxidize aliphatic hydrocarbons, was isolated from a hydrocarbon-polluted marine sediment (Gulf of Fos, France). The cells were rod-shaped and slightly curved, measuring 0·6×2·2–5·5 μm. Strain CV2803Tstained Gram-negative and was non-motile and non-spore-forming. Optimum growth occurred in the presence of 24 g NaCl l−1, at pH 7·5 and at a temperature between 28 and 35 °C. Strain CV2803Toxidized alkanes (from C13to C18) and alkenes (from C7to C23). The DNA G+C content was 41·4 mol%. Comparative sequence analyses of the 16S rRNA gene and dissimilatory sulfite reductase (dsrAB) gene and those of other sulfate-reducing bacteria, together with its phenotypic properties, indicated that strain CV2803Twas a member of a distinct cluster that contained unnamed species. Therefore, strain CV2803T(=DSM 15576T=ATCC BAA-743T) is proposed as the type strain of a novel species in a new genus,Desulfatibacillum aliphaticivoransgen. nov., sp. nov.

Small-subunit (16S) ribosomal DNA clone libraries were constructed using DNA isolated from the anoxic sediments underlying the cyanobacterial mats from two sampling stations of different salinity (Station A, 150-200 per thousand salinity; Station B, 250-320 per thousand salinity) located in the Mediterranean salterns of Salin-de-Giraud (France). Previous studies have shown that the mats at these two sites differ greatly in physicochemical and microbial composition. Sequence analysis of the clone libraries indicated that prokaryotic diversity was high in the sediments from both stations, in both the Bacteria and Archaea domains. Clones related to the alpha- and delta-Proteobacteria (phylum Proteobacteria), the strictly anaerobic fermentative bacteria (phylum Firmicutes), and the Cytophaga-Flavobacterium-Bacteroides (CFB) group (phylum Bacteroidetes) were found in the libraries from both sediments and accounted for the majority of Bacteria domain clones. The results indicated that the populations of delta-Proteobacteria (principally sulfate-reducing bacteria) were significantly different in the two sediments. In addition, several clones from Station A were related either to the gamma-Proteobacteria (phylum Proteobacteria) or to the Spirochaeta, whereas the library from Station B contained several clones related to the uncultured, deep-branching 'KTK group' of Bacteria. Among the Archaea domain clones, all from Station B and the majority from Station A were related to the order Halobacteriales (phylum Euryarchaeota, class Halobacteria). In addition, 12% of the Archaea domain clones from Station A were related to the Methanococci group (phylum Euryarchaeota, class Methanobacteria) and 32% to the phylum Crenarchaeota. This study represents the first molecular analysis of the diversity of halophilic prokaryotes present in these sediments and the results are discussed in the light of our current knowledge of the microbial ecology of these hypersaline ecosystems.

Microbial mats developing in the hypersaline lagoons of a commercial saltern in the Salin-de-Giraud (Rhône delta) were found to contain a red layer fully dominated by spirilloid phototrophic purple bacteria underlying a cyanobacterial layer. From this layer four strains of spirilloid purple bacteria were isolated, all of which were extremely halophilic. All strains were isolated by using the same medium under halophilic photolithoheterotrophic conditions. One of them, strain SG 3105 was a purple non-sulfur bacterial strain closely related to Rhodovibrio sodomensis with a 16S rDNA sequence similarity of 98.8%. The three other isolated strains, SG 3301T, SG 3302 and SG 3304, were purple sulfur bacteria and were found to be very similar. The cells were motile by a polar tuft of flagella. Photosynthetic intracytoplasmic membranes of the lamellar stack type contained BChl a and spirilloxanthin as the major carotenoid. Phototrophic growth with sulfide as electron donor was poor; globules of elemental sulfur were present outside the cells. In the presence of sulfide and CO2 good growth occurred with organic substrates. Optimum growth occurred in the presence of 9-12% (w/v) NaCl at neutral pH (optimal pH 6.8-7) and at 30-35 degrees C. The DNA base composition of strains SG 3301T and SG 3304 were 74.5 and 74.1 mol% G + C, respectively. According to the 16S rDNA sequences, strains SG 3301T and SG 3304 belonged to the genus Halorhodospira, but they were sufficiently separated morphologically, physiologically and genetically from other recognized Halorhodospira species to be described as a new species of the genus. They are, therefore, described as Halorhodospira neutriphila sp. nov. with strain SG 3301T as the type strain (=DSM 15116T).

The cellular structures of prokaryotic and eukaryotic microorganisms and the characters distinguishing the three domains of life (Archaea, Bacteria, Eukarya) are first described. Then, the metabolic diversity of microorganisms is discussed, the knowledge of which is essential to understand the role of microorganisms in natural and anthropogenic environments. The different degradation pathways for mineral and organic compounds that provide cellular energy are described (aerobic and anaerobic respirations, fermentations) as well as the photosynthetic processes (aerobic and anaerobic photosynthesis). Finally, the mechanisms of biosynthesis are presented: autotrophy and heterotrophy, assimilation of C1, and assimilation of organic and inorganic compounds (mainly nitrogen and sulfur assimilation).

The large diversity of metabolic capacities and the high genetic plasticity of microorganisms allow them to degrade virtually all organic compounds of natural or anthropogenic (xenobiotics) origin including those that are sources of environmental pollution. Thus microorganisms are major actors to eliminate or alleviate pollutions in the environment. The natural attenuation processes due to microbial activities (biodegradation and/or biotransformation) as well as the possibilities of using microorganisms in preventive treatments and bioremediation – biostimulation, bioaugmentation, rhizostimulation, bioleaching, and bioimmobilization – are presented. The main methods for microbial treatment of pollution, the chemical structure and the origin of the major pollutants, as well as the mechanisms of degradation by microorganisms – on the basis of physiological, biochemical, and genetic approaches – are described. Examples of treatments are presented for urban wastewater (activated sludge, lagoons, and planted beds), solid wastes (aerobic treatment or composting, anaerobic treatment and methanization, discharges), gaseous effluents, pesticides, polychlorobiphenyls, and finally hydrocarbons and petroleum products in the marine environment.

A novel sulfate-reducing bacterium designated strain BE2801T was isolated from oil-polluted estuarine sediments (Berre Lagoon, France). Cells were Gram-stain-negative, motile, slightly curved or vibrioid rods. Optimal growth of strain BE2801T occurred at 30–32 °C, 0.5–1.5% NaCl (w/v) and pH 7.2–7.4. Strain BE2801T grew with C4 to C20 fatty acids or C12 to C20 n-alkenes as electron donors. Acetate and carbon dioxide were the oxidation products. The major cellular fatty acids were C16 : 0, C16 : 1ω7c and C18 : 1ω7. The DNA G+C content was 50.2 mol%. 16S rRNA and dsrAB gene sequence analysis indicated that strain BE2801T was a member of the family Desulfobacteraceae within the class Deltaproteobacteria . DNA–DNA hybridization with the most closely related taxon demonstrated 14.8 % relatedness. Based on phenotypic and phylogenetic evidence, strain BE2801T ( = DSM 25524T = JCM 18157T) is proposed to be a representative of a novel species of the genus Desulfatiferula , for which the name Desulfatiferula berrensis sp. nov. is suggested.

A high intensity direct current was applied for more than 10 min onto a bacterial suspension of Pseudomonas oleovorans ATCC 29347 suspended in silicone oil. The application of a gradually increased electric field from 0 to 2500 V x cm(-1) resulted in a decrease of the optical density of the bacterial suspension and the occurrence of a peak current of several hundred microA for living cells instead of a linear increase (few microA) for killed or lyophilised cells. This procedure is not only a rapid way of investigating the living state of cell cultures but also an efficient experimental tool to study the cellular effects of a controlled electrical stress.

International audience; Complete nucleotide sequences of the 16S rDNAs were determined from Thiocapsa and Amoebobacter species, including all available type strains and some additional isolates. The distance-matrix analysis and the dendrogram for estimating the genetic relationships revealed that the investigated strains were found in two major clusters within the Chromatiaceae. One cluster comprises all Amoebobacter species, Thiocapsa roseopersicina and several isolates related to Thiocapsa roseopersicina. Representatives of the species Amoebobacter roseus, Amoebobacter pendens and Thiocapsa roseopersicina, the so called 'Thiocapsa roseopersicina group', are very closely related, justifying their inclusion into one genus, Thiocapsa, for which an emended description is presented. Amoebobacter purpureus and Amoebobacter pedioformis formed two separate lines of descent with less than 93% (89.6-92-9%) similarity to strains of the 'Thiocapsa roseopersicina group'. Therefore, they will be considered as two separate genera. As a consequence, an emended description is presented for the genus Amoebobacter, with Amoebobacter purpureus as the new type species and A. pedioformis is transferred to Thiolamprovum pedioforme gen. nov., comb. nov. Two species, Thiocapsa pfennigii and Thiocapsa halophila, which have been classified with the genus Thiocapsa because of their morphological properties, were found within another major cluster of the Chromatiaceae and are only distantly phylogenetically related to the first cluster with 88.4-90.6% and 90.4-92.2% sequence similarity, respectively.

From the microbial mats that develop in Solar Lake, a new purple sulfur bacterium was isolated. This strain (Chromatium strain SL 3201) was morphologically similar to Chromatium gracile and Chromatium minutissimum. Chromatium SL 3201 was found to be a moderate halophile with a growth range between 2 and 20% NaCl (optimum 4-5% NaCl) and was able to grow photo-organotrophically using glycolate and glycerol. It is the first described phototrophic sulfur bacterium able to use glycolate. According to NaCl requirements and utilization of organic compounds, the strain is not related to any known species of the genus Chromatium. On the basis of its 16S rRNA gene sequence, it clusters with other Chromatium species and is most similar to Chromatium salexigens and Chr. gracile, but it is sufficiently separated to be considered as a new species of the genus. It is, therefore, described as Chromatium glycolicum sp. nov.

A microbial enrichment culture from brackish sediments was able to grow on octadec-1-ene (an unsaturated aliphatic hydrocarbon) as sole source of carbon and energy, under methanogenic conditions. Octadecene degradation is stopped either when bromoethanesulfonic acid, a selective inhibitor of methanogenesis is introduced, or when hydrogen is introduced. In the presence of bromoethanesulfonic acid, the degradation is restored by the addition of a hydrogenotrophic sulfate-reducing microorganism with sulfate. Results of molecular biodiversity, which revealed the presence of bacteria as well as of acetoclastic and hydrogenotrophic methanogens, are consistent with a syntrophic degradation involving Bacteria and Archaea. This is the first demonstration of syntrophic alkene degradation by microbial communities, showing that syntrophy is more widespread than we could have thought so far. These results highlight the need for a better understanding of microbial interactions and their role in the organic-matter degradation in polluted environments.

International audience

Microbial mats that develop in the gypsum crust of the hypersaline ponds of Salins-de-Giraud (Camargue, France) were carefully investigated between 1989 and 1991. During the warm seasons, when these mats were fully developed, analyses of microbial activities and microprofiles of oxygen and sulfide have shown a great activity of the different kinds of bacteria found in the mat below the gypsum crust. Oxygen production could amount to 2 μmol cm−3 h−1 during the maximum daylight whereas the oxidation of sulfide in the light was calculated to be 12.7 μmol cm−3 h−1, i.e. 300 to 180 mmol m−2 day−1 assuming 8–10 hours of constant daylight and a sulfide oxidation zone of 3 mm in thickness. This sulfide oxidation consumes about 65–95% of the diel sulfide production which has been estimated to be 400 to 450 mmol m−2 day−1 originating from sulfate reduction which takes place in the 6 cm depth horizon of sediment plus mat. According to the amounts of sulfate precipitated at the sediment surface in the form of gypsum, sulfate reduction is never limited and was found to be among the highest values reported in the literature (average value of 8200 nmols cm−3 day−1). Completely covered by the gypsum crust, this ecosystem has been found to react as a closed system. Consequently, the sulfide does not escape and accumulate below the crust. It was detected up to the top of the mat after a few hours of darkness. It is reoxidized during the day by the photosynthetic organisms that from the mats. These latter mats were composed of 2 to 3 laminated layers of phototrophic organisms: an upper brown layer of the cyanobacterium Aphanothece, an intermediate green layer of the cyanobacterium Phormidium and an underlying red layer of purple sulfur-oxidizing bacteria from which two new halophilic species were isolated (Chromatium salexigens and Thiocapsa halophila). It has been found that the accumulated sulfide is oxidized not only by the phototrophic bacteria in the sulfide oxidation zone but also by the oxygen produced by the cyanobacteria which are able to photosynthesize in the presence of sulfide.

A new phototrophic sulfur bacterium has been isolated from a red layer in a laminated mat occurring underneath a gypsum crust in the mediterranean salterns of Salin-de-Giraud (Camargue, France). Single cells were coccus-shaped, non motile, without gas vacuoles and contained sulfur globules. Bacteriochlorophyll a and okenone were present as major photosynthetic pigments. These properties and the G+C content of DNA (65.9–66.6 mol% G+C) are typical characteristics of the genus Thiocapsa. However, the new isolate differs from known species in the genus, particularly in NaCl requirement (optimum, 7% NaCl; range, 3–20% NaCl) and some physiological characteristics. Therefore, a new species is proposed, Thiocapsa halophila, sp. nov.

Summary From samples collected in the anoxic part of the photosynthetic microbial mat of Solar Lake, sulfate-reducing bacteria were enriched with lactate and sulfate in basal medium supplemented with 10% NaCl and 1% MgCl2.6H2O. A few strains were isolated and maintained in pure culture. Strain SL 8903 which showed the highest NaCl tolerance (up to 18%) consisted of motile non-sporulating vibrioid cells and resembled the genus Desulfovibrio. However, on the basis of physiological differences to all described species of this genus, strain SL 8903 was described as a new species and named Desulfovibrio halophilus, sp. nov.

A novel budding purple non-sulfur bacterium (strain AR2102T) was isolated in pure culture from a microbial mat that had developed in brackish-water ponds on the coral rim of the atoll of Rangiroa (Tuamotu Islands, French Polynesia). Single cells of this strain were rod-shaped and motile by means of polar flagella and divided by budding. Their intracellular photosynthetic membranes were of the lamellar type. Bacteriochlorophyll a and carotenoids of the normal spirilloxanthin series, with spirilloxanthin as the main carotenoid, were present as photosynthetic pigments. Bacteriochlorophyll a absorption in the infrared portion of the light spectrum exhibited an unusual in vivo absorption peak at 909 nm. The strain grew optimally under photoheterotrophic conditions, but could grow photolithotrophically on thiosulfate or chemo-organotrophically under micro-oxic conditions. Optimal growth occurred in the presence of 1–2 % NaCl. Comparative sequence analysis of the 16S rRNA gene placed strain AR2102T within the class Alphaproteobacteria, in a cluster with Rhodobium species. Representatives of this cluster form a closely related group of slightly to moderately halotolerant to halophilic, rod-shaped, purple non-sulfur bacteria that divide by budding. The new isolate exhibited some differences in physiology (no utilization of alcohols or carbohydrates) and genetic characteristics (low relatedness in DNA–DNA hybridization) as well as in its relation to light (differences in absorption wavelengths) from previously described Rhodobium species. Consequently, we propose that strain AR2102T (=DSM 17143T=ATCC BAA-1145T) should be considered as the type strain of a novel species within the genus Rhodobium, Rhodobium pfennigii sp. nov.

The alkane-degrading, sulfate-reducing bacterium Desulfatibacillum aliphaticivorans strain CV2803 T , recently isolated from marine sediments, was investigated for n -alkane metabolism. The total cellular fatty acids of this strain had predominantly odd numbers of carbon atoms (C odd) when the strain was grown on a C-odd alkane (pentadecane) and even numbers of carbon atoms (C even) when it was grown on a C-even alkane (hexadecane). Detailed analyses of those fatty acids by gas chromatography/mass spectrometry allowed us to identify saturated 2-, 4-, 6-, and 8-methyl- and monounsaturated 6-methyl-branched fatty acids, with chain lengths that specifically correlated with those of the alkane. Growth of D. aliphaticivorans on perdeuterated hexadecane demonstrated that those methyl-branched fatty acids were directly derived from the substrate. In addition, cultures on pentadecane and hexadecane produced (1-methyltetradecyl)succinate and (1-methylpentadecyl)succinate, respectively. These results indicate that D. aliphaticivorans strain CV2803 T oxidizes n -alkanes into fatty acids anaerobically, via the addition of fumarate at C-2. Based on our observations and on literature data, a pathway for anaerobic n -alkane metabolism by D. aliphaticivorans is proposed. This involves the transformation of the initial alkylsuccinate into a 4-methyl-branched fatty acid which, in addition to catabolic reactions, can alternatively undergo chain elongation and desaturation to form storage fatty acids.

In France, two amphibious hydrophytes of alien Ludwigia (Onagraceae) have for about the past twenty years been causing serious ecological and economic problems: L. peploides (Kunth) Raven et L. grandiflora (Michaux) GreuterBurdet. This bacteriological and physicochemical study, focused on three different Mediterranean aquatic ecosystems, reveals, for the first time, a direct negative impact of these American invaders. During summer, while plant growth is intensive, and the appearance in the water column of anoxic conditions and production of toxic compounds may be observed, notably in L. grandiflora stands. The toxicity is linked to a proliferation of sulphate-reducing bacteria producing sulphides that are very harmful for aquatic organisms.

International audience; Three new spirilloid phototrophic purple non-sulfur bacteria were isolated in pure culture from three different environments: strain CE2105 from a brackish lagoon in the Arcachon Bay (Atlantic coast, France), strain SE3104 from a saline sulfur spring in the Pyrenees (Navarra, Spain), and strain AT2115 a microbial mat (Tetiaroa Atoll, Society Islands). Single cells of the three strains were spiral-shaped and highly motile. Their intracellular photosynthetic membranes were of the vesicular type. Bacteriochlorophyll a and carotenoids of the normal spirilloxanthin series were present as photosynthetic pigments. Optimal growth occurred under photoheterotrophic conditions and in the presence of 0.5-4% w/v NaCl. These features are similar to those described for Roseospira mediosalina. Comparative sequence analysis of their 16S rRNA genes placed these strains within the α-subclass of Proteobacteria, in a cluster together with Roseospira mediosalina and Rhodospira trueperi. They form a closely related group of slightly to moderately halophilic spiral-shaped purple nonsulfur bacteria. However, the three new isolates exhibited some differences in their physiology and genetic characteristics. Consequently, we propose that they are members of three new species within the genus Roseospira, Roseospira marina sp. nov., Roseospira navarrensis sp. nov., and Roseospira thiosulfatophila sp. nov., with strains CE2105, SE3104, and AT2115 as the type strains, respectively. As a consequence, an emended description of the genus Roseospira is also given.

A diverse range of fermentative bacteria have been isolated from the commercial salterns of Salin-de-Giraud (Camargue, France). One of these isolates, strain SG 3902T, has many of the morphological and physiological characteristics of the genus Orenia, as was confirmed by a phylogenetic study based on 16S rRNA gene sequencing. The closest species is Orenia marismortui, with a similarity of only 95.1%. However, strain SG 3902T, unlike O. marismortui, does not ferment mannose, glycogen or starch. The G + C contents of the DNA also differ significantly, being 29.6 mol% for O. marismortui and 33.7 mol% for strain SG 3902T. On the basis of these physiological and genetic differences, it is proposed that strain SG 3902T should be considered as a representative of a new species belonging to the genus Orenia, under the name Orenia salinaria sp. nov. The type strain is SG 3902T (= ATCC 700911).

The Chromatiaceae observed to date in hypersaline environments were found in microbial mats which develop in solar salterns. These salterns are man-made structures based on a succession of shallow ponds in which seawater circulates and evaporates until the NaC1 concentration reaches saturation, with resulting precipitation and crystalisation. Consequently, a gradient of brines exists between the successive ponds. In the initial ponds, with salinities of 6-8%, most of the isolated phototrophs are marine or slightly halophilic bacteria, according to the classification of Triiper and Galinski [1].

A microbial enrichment culture from marine sediment was able to grow on hexadecan-2-one as the sole source of carbon and energy under sulfate-reducing conditions. Oxidation of the ketone involved carboxylation reactions and was coupled to sulfide production. This enrichment culture also grew on 6,10,14-trimethylpentadecan-2-one.

The Prevost lagoon (Mediterranean coast, France), was subject to annual dystrophic crises caused by the biodegradation of opportunistic macroalgae (Ulva lactuca) in the past. These crises result in anoxic waters with subsequent blooms of Purple Sulphur Bacteria (red waters) which, by oxidizing sulphide, contribute to the reestablishment of oxic conditions in the water column. Mechanical dredging of the macroalgal biomass has been carried out in the lagoon since 1991 with the aim of preventing the ecological and economic disturbances caused by such crises. Dredging began just before the phototrophic bloom when the water was already hypoxic (O-2 = 0.7 mg . L-1) and contained sulphilde (H2S = 7.3 mg . L-1) and purple patches of phototrophic bacteria (Thiocapsa sp.) that were beginning to develop on decaying macroalgae at the sediment surface. The dredging prevented red water formation and drastically modified both phototrophic community structure and activity and biogeochemical sulphur cycling. The dredging permitted the reestablishment of oxic conditions for a short period only (1-13 August). Resuspension of the superficial sediment layers disturbed the phototrophic bacterial community, whose numbers decreased by one order of magnitude (from 2 x 10(6) to 3.9 x 10(5) CFU.mL(-1)). The phototrophic community was no longer effective in reoxidizing the reduced sulphur compounds remaining its the sediments, as shown by a drastic sulphate depletion in the superficial sediment layers. Moreover, the increase in the specific bacteriochlorophyll a concentration of the phototrophic purple bacteria and the rapid development of Green Sulphur Bacteria (Prosthecochloris-like microorganisms) indicated that the phototrophic community was growing under severe light-limiting conditions due to the resuspension of sediment particles in the water. These conditions did not allow the phototrophic bacterial community to efficiently reoxidize the reduced sulphur compounds originating from the sediments. In consequence, hypoxic conditions (O-2 = 4.7 to 4.8 mg . L-1) and low sulphide concentrations (H2S = 0.4 to 0.7 mg . L-1) were detected in the water column until September. The ecological balance in the lagoon was reestablished only in October, whereas, in previous years it had been restored in August., L'étang du Prévost (côte méditerranéenne française) a été soumis périodiquement à des crises dystrophiques estivales provoquées par la biodégradation de grandes quantités de macroalgues (Ulva lactuca). Ces crises se traduisent par l'anoxie des eaux et la formation d'eaux rouges (malaïgues) dues au développement des bactéries phototrophes sulfureuses rouges ; par leur activité de réoxydation des composés soufrés toxiques, ces microorganismes contribuent à la restauration de conditions oxiques. Depuis 1991, afin d'éviter les nuisances écologiques et économiques causées par ces phénomènes, un programme de dragage des macroalgues a été mis en place dans l'étang. Le ramassage des algues est entrepris juste avant le développement de l'eau rouge, lorsque les eaux sont déjà hypoxiques (O2 = 0.4 to 0.7 mg·L−1) et contiennent du sulfure (H2S = 7,3 mg·L−1). Les bactéries phototrophes (Thiocapsa sp.) forment déjà des biofilms sur les macroalgues en décomposition à la surface des sédiments. Le dragage évite la formation de l'eau rouge et influe largement sur la communauté de bactéries phototrophes et donc sur le cycle du soufre. Le dragage ne restaure des conditions oxiques dans les eaux de l'étang que pour une courte durée. La mise en suspension des sédiments superficiels affecte la communauté de bactéries phototrophes dont les nombres ont chuté d'un facteur 10 (de 2 × 106 à 3,9 × 105 CFU.mL−1). Le déficit en sulfate des sédiments superficiels montre que cette communauté n'est plus capable de réoxyder les composés soufrés issus des sédiments. De plus, l'augmentation du contenu spécifique en Bchl.a des bactéries phototrophes rouges ainsi que le développement rapide des bactéries phototrophes vertes sulfureuses (Prosthecochloris sp.) indiquent que la lumière constitue un facteur limitant l'activité de ces microorganismes, facteur limitant par suite de la mise en suspension de particules sédimentaires. Cette communauté ne pouvant plus jouer son rôle dans la réoxydation des composés soufrés, les eaux redeviennent hypoxiques (O2 = 4,7 à 4,8 mg·L−1) alors que de faibles concentrations en sulfures y sont détectées (H2S = 0,4 à 0,7 mg·L−1). Les conditions normales ne sont rétablies dans l'étang du Prévost qu'en octobre alors que les années précédentes elles étaient atteintes plus tôt en été.

cited By 22; International audience; A new marine phototrophic purple sulfur bacterium (strain CE2203) was isolated in pure culture from a man-made coastal lagoon located on the Atlantic coast (Arcachon Bay, France). Single cells were coccus-shaped, did not contain gas vesicles, and were highly motile. Intracellular photosynthetic membranes were of the vesicular type. Bacteriochlorophyll a and carotenoids of the normal spirilloxanthin series were present us photosynthetic pigments. Hydrogen sulfide, thiosulfate, elemental sulfur, and molecular hydrogen were used as electron donors during photolithotrophic growth under anoxic conditions, while carbon dioxide was utilized as carbon source. Acetate, propionate, lactate, glycolate, pyruvate, fumarate, succinate, fructose, sucrose, ethanol, and propanol were photoassimilated in the presence of hydrogen sulfide. During growth on sulfide, elemental sulfur globules were stored inside the cells. Chemotrophic growth under microoxic conditions in the dark was possible. The DNA base composition was 66.9 mol% G+C. Comparative sequence analysis of the 16S rRNA gene confirmed the membership of strain CE2203 in the family Chromatiaceae. Morphological characteristics of strain CE2203 indicated a close affiliation to the genera Thiocystis and Thiocapsa. However, the phylogenetic treeing revealed no closer relationship to Thiocystis spp. than to Thiocapsa roseopersicina or other known members of the Chromatiaceae. Consequently, strain CE2203 is proposed as the type strain of a new genus and species, Thiorhodocccus minus gen. nov., sp. nov.

Sediment samples collected from coastal lagoons on the French Mediterranean (Prevost Lagoon) and Atlantic coasts (Arcachon Bay and Certes fishponds) have been studied in order to determine the population densities and the species diversity of the different groups of anoxygenic phototrophic bacteria (purple sulfur bacteria, purple nonsulfur bacteria and green sulfur bacteria) present in these ecosystems. Several strains of each group were isolated in pure culture and characterized by their physiological properties. The occurrence of purple nonsulfur bacteria in organic rich sediments of the Arcachon Bay and the dominance of purple sulfur bacteria in the Prevost lagoon and Certes fishponds are discussed with respect to their community structure and abundance. The diversity differences of the phototrophic bacterial strains isolated from both environments are also discussed.

Eight strains of Chromatiaceae isolated from marine sediments are cultivated under light intensities of 50–5000 lx. A decrease in the light intensity brings about an increase in the specific bacteriochlorophyll content and also in the length of development. In certain strains, the increase in pigment contents partly compensates for the loss in light intensity, up to the maximum concentration of bacteriochlorophyll. This mechanism is only a physiological compatibility which ensures the survival of these organisms under feeble light intensities.

Summary In the course of ecological studies in salinas and salt-works of Salin de Giraud (Camargue, France), a halophilic strain of the Chromatiaceae was isolated from a red layer below the gypsum crust. Because of its morphology, this strain (SG 3201) was assigned to the genus Chromatium , resembling Chromatium buderi and Chromatium vinosum . However it differed from these species in some physiological characteristics, in particular pigment composition, salinity range with 10% NaCl requirement for optimum growth, and utilization of some substrates. It is the first described Chromatium strain with high NaCl requirement. Therefore, a new species, Chromatium salexigens , is proposed.

In evergreen oak leaves collected at a western Mediterranean site (Var, France), the amounts of both hydrolyzable and condensed tannins decrease through the depth of the leaf litter. The decrease in condensed tannins could be partly explained by the cellular degradation of the lower epidermis and the mesophyll of leaves, as observed in histological sections. However, the condensed tannins may also be degraded by microbial enzymes because their average molecular weight decreased by about 50%. In contrast, the decrease in hydrolyzable tannins seems to be initiated by microbial enzymatic action, which is then followed by the same degradation process described above.

Bottles of medium were inoculated with both strains of Chromatiaceae and Chlorobiaceae (mixed cultures) and immersed at different depths in the marine coastal waters of the Marseilles basin (France). After development, the in vivo absorption characteristics of the cells show the effect of the daylight penetration on the selective growth of phototrophic sulfur bacteria. With depth, sunlight selects Chlorobiaceae rich in brown carotenoid pigments to the detriment of Chromatiaceae.

La possibilite de photoproduire de l'hydrogene a partir de soufre et de sulfure par des Chromatiaceae appartenant aux genres Chromatium, Thiocapsa, Thiocystis et Ectothiorhodospira a ete examiniee. Sur huit souches testees, six seulement liberent de l'hydrogene en presence de sulfure. Sur soufre, les Ectothiorhodospira forment du H2 alors que les autres souches excretent du sulfure. Des experiences manometriques avec une souche d'Ectothiorhodospira montrent que la photoproduction de H2 est etroitement correlee a l'assimilation du CO2 et que l'utilisation des substrats endogenes est exacerbee par le sulfure.

Experiments with mixed cultures ofEscherichia coli, Desulfovibrio vulgaris, andChromatium vinosum were conducted using a synthetic medium with glucose as the substrate. The bacterial number and the changes in the chemical factors were determined during the development of the mixed culture. (i) Fermentation of glucose byE. coli produces organic acids (formic, acetic, lactic, and succinic) and alcohol. The growth-yield constant K (cell dry weight per weight solid substrate) does not exceed 0.05. (ii) In the mixed culture ofE. coli andD. vulgaris, the reduction of sulfate is accompanied by a total consumption of formate, lactate, and alcohol and an increase in the sulfide and acetate content. (iii) When the three physiologically different species are allowed to grow simultaneously, there is no accumulation of catabolites in the medium and the growth yield constant increases to 0.46. Maximum phototrophic production requires the presence of bothE. coli andD. vulgaris. A low substrate concentration and the simultaneous growth of the three organisms are other factors that contribute towards a high output. The biochemical parameters of the medium are influenced to a large extent by the glucose level. The results suggest that the behavior of the strains is different in pure and mixed cultures.

In this work we tried to caractérisé biological activity of the formed litter into two QueAcut ilex ecosystems. The methods used showed that respiratory and alkaline phosphatase activities are different in the two ecosystems. The other enzymatic activities (acid phosphatases , ureases and catechol-oxygenases ) are very high in all ecosystems and do not allow to distinguish between them. No nitrogenasic activity could be revealed., Le but de ce travail a été de caractériser l 'activité biologique dans la litière de Chêne vert en deux stations. Les méthodes utilisées ont mis en évidence des différences dans les activités respiratoires et phosphatase alcalins. Les autres activités enzymatiques (phosphatases acides , uréases et catéchol-oxygénases) sont très élevées et ne permettent pas une distinction entre les stations. Aucune activité nitrogénasique n'a été décelée., Chabert Alain, Le Petit J., Loisel Roger, Matheron Robert, Tagger S. Dégradation biologique de la litière de chêne vert dans deux forêts de la région provençale (Var, France). In: Ecologia mediterranea, tome 10 n°1-2, 1984. pp. 171-181.

Dans les cultures mixtes, la fermentation du glucose par Escherichia coli fournit des sources de carbone et d'electrons au Desulfovibrio desulfuricans qui est a l'origine de la formation des substrats utilisables par la souche de Chlorobium.

International audience; The diversity of metabolic activities is a characteristic of the microbial world. This enormous diversity needs to be structured in order to be understood, and as a result, taxonomy and systematics are constantly changing since the beginning of the history of microbiology and particularly today with the introduction in the last 20 years of phylogeny as the core of systematics. The history of concepts in systematics and classification is presented. Classification is the science of ordering microorganism groups (taxa) based on their interrelationships. Taxonomy is the discipline that defines the principles and laws of classification. Nomenclature is the science of defining and naming the taxonomic categories (species, genera, families, orders, classes, divisions, phyla, kingdoms, domains), according to their hierarchical rank. In this way, different schools of classification and bacterial systematics were developed in the twentieth century. Today, there is an international consensus based on the classification of the Bergey’s Manual revisited with the concepts of phylogeny. Through this classification, the concept of the prokaryotic world organization has evolved. From the idea of a kingdom of prokaryotes, the concept of three domains in the organization of life supported by phylogenetic trees is fully accepted today. Among these three domains, two are prokaryotic: Bacteria and Archaea. In this chapter, the role of horizontal gene transfers in the evolution of life is discussed. The origin of eukaryotes with the primary, secondary, and tertiary endosymbioses is also presented. This allows to improve or to transform the concept of the tree of life from phylogeny to full genome study.

Originally, “genomics” was used only to describe a scientific discipline which consisted in mapping, sequencing, and analyzing genomes. Nowadays, this term is widely used by a growing number of people in a broader sense to describe global techniques for studying genomes including from a functional point of view. These include the analysis of messenger RNAs (transcriptomics), protein contents (proteomics), and metabolites (metabolomics). At a higher level of complexity, it also describes the so-called “meta” approaches that allow to investigate the ecology of microbial communities, including uncultured microorganisms. Based on the use of recent technological developments, the numerous examples provide an integrated view of how microorganisms adapt to particular ecological niches and participate in the dynamics of ecosystems.

International audience; Microorganisms to Physicochemical Conditions…?> live in a constantly changing environment and must modify their physiology and morphology to cope with these changes. The main systems for molecular adaptation to modifications of environmental conditions and the behavioral responses of prokaryotes in various habitats, excluding extreme habitats, are discussed. The main regulation systems that are described are transcription, signal transduction, and protein modifications. Three specialized systems are also presented in details: quorum sensing, phase variation, and antibiosis. Quorum sensing allows bacteria to trigger some responses when their density is high enough to permit the function to be successful. Phase variation is an adaptive process by which a bacterial subpopulation undergoes frequent, usually reversible phenotypic changes resulting from genetic or epigenetic alterations, allowing rapid modification of the cells physiology. Antibiosis is the ability to synthesize molecules that will impact other taxa and eventually provide a selective advantage to which some microbes respond by resisting to these molecules.Finally are described the physiological responses to various environmental parameters such as temperature, oxidants, salinity, acidity, pressure, desiccation, and how this translates in different biotopes such as soil, water bodies, sediments, biofilms, mats, air, and manmade biotopes.

Classification of prokaryotes is hierarchically organized into seven levels: kingdoms, phyla, classes, orders, families, genera, and species. In prokaryotes, because they reproduce by clonal fission, the species, considered as the basic unit of the biological diversity, faces several problems such as the definition of an individual. A bacterial strain can be recognized as an individual belonging to a species. However, many inconsistencies exist between phenotypic similarity levels and evolutionary relationships deduced from molecular phylogenies. Most taxonomic groups have been reconsidered through phylogenetic analysis in the 1980s, and a consensus has been reached on the need for coherence between taxonomy and phylogeny. Thus, the multiple revisions of species, genera, or higher taxonomic levels pose many complex problems that are solved gradually. Prokaryotic microorganisms correspond to two of the three domains of life: Archaea and Bacteria. Their systematics is described in the “Bergey’s Manual for Systematic Bacteriology, second edition” published in five volumes.

International audience; We present briefly, first, the history of the discovery of microorganisms and particularly bacteria with the pioneering works of Antoni van Leeuwenhoek, Louis Pasteur, and Robert Koch, essentially. In a second and more detailed part, the history of microbial ecology is presented with particularly the very important work of Sergei Winogradsky and his discoveries of the main bacterial groups active in biogeochemical cycles. It is followed by a description of the major microbial ecologists who have been very active in promoting and developing microbial ecology throughout the world. Their role in the advances of microbial ecology is presented and discussed.

All ecosystems are composed of multiple species performing numerous functions. This plurality identified as biodiversity has become a research topic of general importance for understanding how ecosystems function. The word “biodiversity” has subsequently received different interpretations we aim to describe. Microbial systems can be used to illustrate these definitions and to clarify paradigms that have emerged in general ecology. Microbial biodiversity can be characterized by the kind of biodiversity (taxa or functional groups present), the representativeness of samples, and the culturability of samples or taxa, in terms of genetic, functional, or physiological characteristics. Biodiversity is a major driver of ecosystem functioning, and this relation is described in the case of several biotopes. Several mathematical approaches have been used to quantify microbial diversity, and the various indices are described and discussed.