Effects of heavy fuel oil on the bacterial community structure of a pristine microbial mat

Potential of the microbial community present in an unimpacted beach sediment to remediate petroleum hydrocarbons

The potential of the microbial communities present in the intertidal zone of an unimpacted beach (a beach that did not suffer any significant oil spill) to degrade hydrocarbons was investigated. For that, laboratory-based microcosms (50-ml flasks) were set up with sandy beach sediment spiked with crude oil and incubated with local seawater for 15 days in the dark. Three bioremediation treatments were tested (biostimulation (BS), autochthonous bioaugmentation (AB), and combined treatment of biostimulation + bioaugmentation (BS + AB)) and the results were compared with natural attenuation (NA). Visual inspection showed clearly an oil solubility increase (confirmed by a higher hydrocarbons concentration in supernatant solutions) for all tested treatments when compared to NA. Significant degradation of the oil, shown by different profiles of petroleum hydrocarbons, was also observed for the different treatments particularly for BS + AB. Therefore, the microbial community of this unimpacted beach sediment could respond to an oil spill, degrading hydrocarbons. But to increase the natural attenuation pace, obtained results indicated that BS + AB is an appropriate approach for the bioremediation of beaches recently impacted by an oil spill. The autochthonous microbial cultures can be obtained "before" or "after" the contamination of the target site, being inoculated into the site right after it contamination.

Incidence of invasive macrophytes on methylmercury budget in temperate lakes: central role of bacterial periphytic communities

Several studies demonstrated high mercury (Hg) methylation and demethylation in the periphyton associated with floating roots in tropical ecosystems. The importance of aquatic plants on methylmercury production in three temperate ecosystems from south-western France was evaluated through Hg species concentrations, and Hg methylation/demethylation activities by using stable isotopic tracers ((199)Hg(II), Me(201)Hg). Hg accumulation and high methylation and demethylation yields were detected in plant roots and periphyton, whereas results for sediment and water were low to insignificant. The presence of sulfate reducing prokaryotes was detected in all compartments (T-RFLP based on dsrAB amplified through nested PCR) and their main role in Hg methylation could be demonstrated. In turn, sulfate reduction inhibition did not affect demethylation activities. The estimation of net MeHg budgets in these ecosystems suggested that aquatic rhizosphere is the principal location for methylmercury production and may represent an important source for the contamination of the aquatic food chain.

Impact of long-term diesel contamination on soil microbial community structure

Microbial community composition and diversity at a diesel-contaminated railway site were investigated by pyrosequencing of bacterial and archaeal 16S rRNA gene fragments to understand the interrelationships among microbial community composition, pollution level, and soil geochemical and physical properties. To this end, 26 soil samples from four matrix types with various geochemical characteristics and contaminant concentrations were investigated. The presence of diesel contamination significantly impacted microbial community composition and diversity, regardless of the soil matrix type. Clean samples showed higher diversity than contaminated samples (P < 0.001). Bacterial phyla with high relative abundances in all samples included Proteobacteria, Firmicutes, Actinobacteria, Acidobacteria, and Chloroflexi. High relative abundances of Archaea, specifically of the phylum Euryarchaeota, were observed in contaminated samples. Redundancy analysis indicated that increased relative abundances of the phyla Chloroflexi, Firmicutes, and Euryarchaeota correlated with the presence of contamination. Shifts in the chemical composition of diesel constituents across the site and the abundance of specific operational taxonomic units (OTUs; defined using a 97% sequence identity threshold) in contaminated samples together suggest that natural attenuation of contamination has occurred. OTUs with sequence similarity to strictly anaerobic Anaerolineae within the Chloroflexi, as well as to Methanosaeta of the phylum Euryarchaeota, were detected. Anaerolineae and Methanosaeta are known to be associated with anaerobic degradation of oil-related compounds; therefore, their presence suggests that natural attenuation has occurred under anoxic conditions. This research underscores the usefulness of next-generation sequencing techniques both to understand the ecological impact of contamination and to identify potential molecular proxies for detection of natural attenuation.

Three-year survey of sulfate-reducing bacteria community structure in Carnoulès acid mine drainage (France), highly contaminated by arsenic

A 3-year survey on sulfate-reducing bacteria (SRB) was conducted in the waters of the arsenic-rich acid mine drainage (AMD) located at Carnoulès (France) to determine the influence of environmental parameters on their community structure. The source (S5 station) exhibited most extreme conditions with pH lowering to ~1.2; iron, sulfate, and arsenic concentrations reaching 6843, 29 593, and 638 mg L(-1), respectively. The conditions were less extreme at the downstream stations S1 (pH ~3.7; iron, sulfate, and arsenic concentrations of 1114, 4207, and 167 mg L(-1), respectively) and COWG (pH ~3.4; iron, sulfate, and arsenic concentrations of 854, 3134, and 110 mg L(-1), respectively). SRB community structures were characterized by terminal restriction fragment length polymorphism and library analyses based on dsrAB genes. The predominant dsrAB sequences detected were most similar to the family Desulfobulbaceae. Additionally, certain phylotypes could be related to spatio-temporal fluctuations of pH, iron, and arsenic species. For example, Desulfohalobiaceae-related sequences were detected at the most acidic sample (pH 1.4) with high iron and arsenic concentrations (6379 and 524 mg L(-1), respectively). New dsrAB sequences, with no isolated representatives, were found exclusively in COWG. This study gives new insights on SRB community dynamics in AMD systems.

Homologous recombination is facilitated in starving populations of Pseudomonas putida by phenol stress and affected by chromosomal location of the recombination target

Homologous recombination (HR) has a major impact in bacterial evolution. Most of the knowledge about the mechanisms and control of HR in bacteria has been obtained in fast growing bacteria. However, in their natural environment bacteria frequently meet adverse conditions which restrict the growth of cells. We have constructed a test system to investigate HR between a plasmid and a chromosome in carbon-starved populations of the soil bacterium Pseudomonas putida restoring the expression of phenol monooxygenase gene pheA. Our results show that prolonged starvation of P. putida in the presence of phenol stimulates HR. The emergence of recombinants on selective plates containing phenol as an only carbon source for the growth of recombinants is facilitated by reactive oxygen species and suppressed by DNA mismatch repair enzymes. Importantly, the chromosomal location of the HR target influences the frequency and dynamics of HR events. In silico analysis of binding sites of nucleoid-associated proteins (NAPs) revealed that chromosomal DNA regions which flank the test system in bacteria exhibiting a lower HR frequency are enriched in binding sites for a subset of NAPs compared to those which express a higher frequency of HR. We hypothesize that the binding of these proteins imposes differences in local structural organization of the genome that could affect the accessibility of the chromosomal DNA to HR processes and thereby the frequency of HR.

Influence of pollution history on the response of coastal bacterial and nanoeukaryote communities to crude oil and biostimulation assays

Pollution history has often been proposed to explain site-dependent bioremediation efficiencies, but this hypothesis has been poorly explored. Here, bacteria and their heterotrophic nanoflagellates (HNF) predators originating from pristine and chronically oil-polluted coastal sites were subjected to crude oil ± nutrients or emulsifier amendments. The addition of crude oil had a more visible effect on bacteria originating from the pristine site with a higher increase in the activity of given OTU and inactivation of other petroleum-sensitive bacteria, as revealed by DNA and RNA-based comparison. Such changes resulted in a delay in microbial growth and in a lower bacterial degradation of the more complex hydrocarbons. Biostimulation provoked a selection of different bacterial community assemblages and stirred metabolically active bacteria. This resulted in a clear increase of the peak of bacteria and their HNF predators and higher oil degradation, irrespective of the pollution history of the site.

Interactions between Zn and bacteria in marine tropical coastal sediments

PURPOSE

The main goals of this study were (1) to examine the effects of zinc on the microbial community structure of anthropogenically impacted sediments in a tropical coastal ecosystem and (2) to determine whether these microbial benthic communities may enhance the adsorption of zinc.

METHODS

The interactions between zinc and bacteria in tropical sediments were studied in sediment microcosms amended with 2.5 mg L⁻¹ of Zn in the water phase and incubated for 8 days under different environmental conditions, oxic/anoxic and glucose addition. At the end of incubation, microbial structure was assessed by molecular fingerprints (T-RFLP) analysis and Zn speciation in the sediment was determined by sequential extraction.

RESULTS

In the three studied sediments, Zn spiking resulted in only slight changes in bacterial community structure. In contrast, the addition of low concentrations of glucose (5 mM) strongly modified the bacterial community structure: <20% of similarity with the initial structure concomitant with a strong diminution of the specific richness. Overall, these results suggest that highly labile organic matter has a larger impact on microbial structure than heavy metal. These weak impacts of Zn on bacteria diversity might be partly explained by (1) the strong adsorption of Zn in the presence of bacteria and/or (2) the incorporation of Zn into a nonbioavailable fraction. Nevertheless, Zn spiking resulted in significant changes in nutrient cycles, suggesting that bacterial metabolisms were impacted by the heavy metal. This led to an increase in nutrient supplies to the water column, potentially enhancing eutrophication in a nutrient-limited, oligotrophic ecosystem.

Detection by denaturing gradient gel electrophoresis of ammonia-oxidizing bacteria in microcosms of crude oil-contaminated mangrove sediments

Currently, the effect of crude oil on ammonia-oxidizing bacterium communities from mangrove sediments is little understood. We studied the diversity of ammonia-oxidizing bacteria in mangrove microcosm experiments using mangrove sediments contaminated with 0.1, 0.5, 1, 2, and 5% crude oil as well as non-contaminated control and landfarm soil from near an oil refinery in Camamu Bay in Bahia, Brazil. The evolution of CO(2) production in all crude oil-contaminated microcosms showed potential for mineralization. Cluster analysis of denaturing gradient gel electrophoresis-derived samples generated with primers for gene amoA, which encodes the functional enzyme ammonia monooxygenase, showed differences in the sample contaminated with 5% compared to the other samples. Principal component analysis showed divergence of the non-contaminated samples from the 5% crude oil-contaminated sediment. A Venn diagram generated from the banding pattern of PCR-denaturing gradient gel electrophoresis was used to look for operational taxonomic units (OTUs) in common. Eight OTUs were found in non-contaminated sediments and in samples contaminated with 0.5, 1, or 2% crude oil. A Jaccard similarity index of 50% was found for samples contaminated with 0.1, 0.5, 1, and 2% crude oil. This is the first study that focuses on the impact of crude oil on the ammonia-oxidizing bacterium community in mangrove sediments from Camamu Bay.

Influence of depth and time on diversity of free-living microbial community in the variably saturated zone of a granitic aquifer

We investigated the temporal and vertical changes in the microbial communities related to hydrological variations an aquifer (Brittany, France). Five water samplings were carried out, spanning three hydrological cycles in the variably and the permanently saturated zones. Seasonal variations in the major anion concentrations (NO3 -, SO4 2- and Cl(-) ) indicated that different physical processes occurred during the recharge process in the two zones. The variably saturated zone is mainly dominated by diffusion and advection processes from the soil, whereas the permanently saturated zone is controlled by moderate advective transfer from the variably saturated zone. Bacterial diversity was investigated by flow cytometry, 16S rRNA and narG genes analyses. Part of this diversity was new in that 6 of the 27 16S rRNA gene sequence phylotypes were unknown even at the class or phylum level. The narG gene analysis did not reveal any clear variation in time or depth within the nitrate reducers' community. In contrast, 16S rRNA gene analyses showed modifications of community composition that could be related to the hydrologic and chemical contrast between the two zones. It was concluded that the physical processes of water transfer could influence bacterial diversity at the soil-aquifer interface.

[Emerging Acinetobacter baumannii infections and factors favouring their occurrence]

During the last decade, Acinetobacter baumannii (AB) has been increasingly responsible for infections occurring in three particular contexts (in terms of patients and environment). Community AB pneumonia is severe infections, mainly described around the Indian Ocean, and which mainly concern patients with major co-morbidities. AB is also responsible for infections occurring among soldiers wounded in action during operations conducted in Iraq or Afghanistan. Lastly, this bacterium is responsible for infections occurring among casualties from natural disasters like earthquakes and tsunamis. Those infections are often due to multidrug-resistant strains, which can be implicated in nosocomial outbreaks when patients are hospitalized in a local casualty department or during their repatriation thereafter. The source of the contaminations which lead to AB infections following injuries (warfare or natural disasters) is still poorly known. Three hypotheses are usually considered: a contamination of wounds with environmental bacteria, a wound contamination from a previous cutaneous or oropharyngeal endogenous reservoir, or hospital acquisition. The implication of telluric or agricultural primary reservoirs in human AB infections is a common hypothesis which remains to be demonstrated by further specifically designed studies.

Microbial gene functions enriched in the Deepwater Horizon deep-sea oil plume

The Deepwater Horizon oil spill in the Gulf of Mexico is the deepest and largest offshore spill in the United State history and its impacts on marine ecosystems are largely unknown. Here, we showed that the microbial community functional composition and structure were dramatically altered in a deep-sea oil plume resulting from the spill. A variety of metabolic genes involved in both aerobic and anaerobic hydrocarbon degradation were highly enriched in the plume compared with outside the plume, indicating a great potential for intrinsic bioremediation or natural attenuation in the deep sea. Various other microbial functional genes that are relevant to carbon, nitrogen, phosphorus, sulfur and iron cycling, metal resistance and bacteriophage replication were also enriched in the plume. Together, these results suggest that the indigenous marine microbial communities could have a significant role in biodegradation of oil spills in deep-sea environments.

Are alkane hydroxylase genes (alkB) relevant to assess petroleum bioremediation processes in chronically polluted coastal sediments?

The diversity of alkB-related alkane hydroxylase sequences and the relationship between alkB gene expression and the hydrocarbon contamination level have been investigated in the chronically polluted Etang-de-Berre sediments. For this purpose, these sediments were maintained in microcosms and submitted to a controlled oil input miming an oil spill. New degenerated PCR primers targeting alkB-related alkane hydroxylase sequences were designed to explore the diversity and the expression of these genes using terminal restriction fragment length polymorphism fingerprinting and gene library analyses. Induction of alkB genes was detected immediately after oil addition and their expression detected only during 2 days, although the n-alkane degradation was observed throughout the 14 days of incubation. The alkB gene expression within triplicate microcosms was heterogeneous probably due to the low level of alkB transcripts. Moreover, the alkB gene expression of dominant OTUs has been observed in unoiled microcosms indicating that the expression of this gene cannot be directly related to the oil contamination. Although the dominant alkB genes and transcripts detected were closely related to the alkB of Marinobacter aquaeolei isolated from an oil-producing well, and to alkB genes related to the obligate alkanotroph Alcanivorax borkumensis, no clear relationship between the oil contamination and the expression of the alkB genes could be established. This finding suggests that in such coastal environments, alkB gene expression is not a function relevant enough to monitor bacterial response to oil contamination.

Bacterial diversity dynamics in a long-term petroleum-contaminated soil

Bacterial diversity dynamics were investigated in the soil samples in different distances and depths from/at a long-term petroleum-contaminated site. Microbial activity in the soil samples showed ATP values closely correlated with organic matter content (OC) and total petroleum hydrocarbon (TPH). Bacterial community diversity (H) and evenness (J) using PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis) and PCR-T-RFLP (terminal restriction fragment length polymorphism) results showed positive correlation with concentration of TPH or OC, but tmoA (toluene monooxygenase gene)-based bacterial H and J using a PCR-T-RFLP result did not. No significant difference of H and J values in the bacterial and the tmoA communities was observed. The bacterial community structure characterized by PCR-DGGE and PCR-T-RFLP techniques showed similarity according to soil sampling distance rather than soil sampling depth. Canonical correspondence analysis demonstrated that OC including TPH had the most significant effect on the bacterial community diversity at the long-term petroleum-contaminated site.

Optimisation research of petroleum hydrocarbon biodegradation in weathered drilling wastes from waste pits

The aim of this article is to discuss the problem of drilling waste remediation. Analyses and research showed that material stored in waste pits could be classified as soil with a high level of petroleum impurities (total petroleum hydrocarbons [TPH] = 102,417-132,472 mg kg(-1) dry mass). While preparing the complex technology of soil decontamination (which included primary reclamation, basic bioremediation and inoculation with biopreparations based on indigenous bacteria and fungi), laboratory tests indicated the use of an ex-situ method was fundamental. Remediation was controlled with a chromatographic method of qualitative and quantitative determination of petroleum hydrocarbons. Based on analytical data, there was the possibility to determine the effectiveness of consecutive purifying phases. Laboratory tests, following 135 days of basic bioremediation stimulated by optimum conditions to activate the growth of indigenous micro-organisms, resulted in a decrease in the TPH content, which was in the range of 52.3-72.5%. The next phase of soil decontamination lasted 135 days and involved the use of inoculation with biopreparations based on indigenous micro-organisms and fungi. This process enabled a TPH decrease of 93.8- 94.3%. Laboratory biodegradation research was done with the use of the biomarker C30-17α(H)21β(H)-hopane to normalize analyte (TPH, Σn-C8-n-C22 and Σn-C23-n-C36) concentrations. The calculated first-order biodegradation constants enable estimation of the purification stage dynamics and the effectiveness of the applied biopreparations. Furthermore, they represent the biodegradation degree of individual n-alkanes in subsequent stages of the soil purification process.

Diuron biotransformation and its effects on biofilm bacterial community structure

The effect of realistic environmental contamination of diuron on natural epilithic biofilms dwelling bacterial communities and their transformation capacities were investigated by using microcosm experiments. Cobbles carrying biofilms from two sites ("Pau" and "Lacq") located in areas of contrasting pesticide use (urban and agricultural) on the Gave de Pau river (South-West France) were analysed. The water of the upstream site, Pau, was characterised by fewer pesticides than the water of Lacq, whereas concentrations were higher at Pau. The sampled cobbles were exposed to diuron (10 μg L(-1)) in microcosms. After 3 weeks of exposure, pesticides were analysed and bacterial community structures were assessed with terminal-restriction fragment length polymorphism (T-RFLP). Diuron was biotransformed during contact with biofilms, revealing that these communities contribute to the production of DCPMU (1-(3,4-dichlorophenyl)-3-methylurea) and DCPU metabolites (1-(3,4-dichlorophenyl) urea) in the river ecosystems. Bacterial communities from the most contaminated site appeared to be more resistant to diuron exposure. Correlation analyses combining chemical data with molecular fingerprinting showed that past in situ exposure drove the response of the bacterial communities.

How a bacterial community originating from a contaminated coastal sediment responds to an oil input

Bacterial communities inhabiting coastal sediments are subjected to oil spills. In order to examine the early structural response of a complex bacterial community to oil pollution, a kinetic study of the crude oil impact on bacterial communities inhabiting sediments from the contaminated Etang-de-Berre lagoon was performed. The sediments were maintained in slurries in presence or absence of crude oil and the kinetic study was carried out 14 days. During this period, 54% of crude oil was biodegraded showing the importance of the early degradation step. The metabolically active community (16S rRNA transcript analysis) was immediately impacted by the oil input, observed as an apparent decrease of species richness in the first hour of incubation. Nevertheless, this shift was quickly reversed, highlighting a fast, adaptative and efficient response of the metabolically active bacterial population. The high proportion of sequences related to hydrocarbonoclastic strains or petroleum-associated clones in active oiled community was consistent with significant increasing numbers of cultivable hydrocarbonoclastic bacteria at the end of the experiment. We concluded that "Etang-de-Berre" bacterial communities inhabiting oiled sediments for decades adopted a specific structure depending on oil presence and were able to face hydrocarbon contamination quickly and efficiently.

Influence of microorganisms on the removal of nickel in tropical marine sediments (New Caledonia)

The removal of nickel in marine tropical sediments (New Caledonia) was studied in microcosms. Removal of Ni(2+) was strongly enhanced by the presence of bacteria, with rates up to twofold higher than those observed under sterilized conditions. After 8 days of incubation, Ni(2+) concentration in the water column ranged from 30% to 50% of the initial concentration according to sediment origin. Addition of glucose stimulated bacterial processes and resulted in a complete disappearance of Ni(2+) in the water phase. Incubation under anoxic conditions slightly affects the microbial structure inferred from T-RFLP analysis irrespective of Ni(2+) spiking, whereas incubation under oxic conditions resulted to moderate modification of the microbial structure, changes that might be more marked in the presence of Ni(2+). Five different T-RFs were observed in almost all microcosms with relative abundance between 5% and 30%. Incubation with glucose resulted in the dominance of a common T-RF, with relative abundance up to 39%.

Bacterial community structure of sediments of the bizerte lagoon (Tunisia), a southern Mediterranean coastal anthropized lagoon

In order to estimate how pollution affects the bacterial community structure and composition of sediments, chemical and molecular approaches were combined to investigate eight stations around the Bizerte lagoon. Terminal restriction fragment length polymorphism (T-RFLP) analysis of PCR-amplified 16S rRNA genes revealed that each station was characterized by a specific bacterial community structure. The combination of this data with those of chemical analysis showed a correlation between the bacterial fingerprint and the pollutant content, principally with hydrocarbon pollution. The composition of the bacterial community of two contrasted stations related to the pollution revealed sequences affiliated to alpha, beta, gamma, delta, epsilon subclass of the Proteobacteria, Actinobacteria, and Acidobacteria in both stations although in different extent. Gamma and delta subclass of the Proteobacteria were dominant and represent 70% of clones in the heavy-metal-contaminated station and 47% in the polyaromatic hydrocarbon (PAH)-contaminated. Nevertheless, most of the sequences found were unaffiliated to cultured bacteria. The adaptation of the bacterial community mainly to PAH compounds demonstrated here and the fact that these bacterial communities are mainly unknown suggest that the Bizerte lagoon is an interesting environment to understand the capacity of bacteria to cope with some pollutants.

Nested PCR and new primers for analysis of sulfate-reducing bacteria in low-cell-biomass environments

New primers were designed for the amplification of dsrAB genes by nested PCR to investigate the diversity of sulfate-reducing prokaryotes (SRP) in environments with low bacterial cell density. The success of the nested PCR for the determination of SRP diversity was estimated by terminal-restriction fragment length polymorphism analysis in the Reigous, a small creek at an inactive mine (Carnoulès, France), which constitutes an extreme acidic arsenic-rich environment. Nested PCR limits were evaluated in dsrAB-rich sediments, and this technique was compared to direct PCR using either known primers (DSR1F/DSR4R) or new primers (dsr619AF/dsr1905BR). The comparison of clone libraries revealed that, even if the levels of diversity observed were not identical, nested PCR did not reduce the diversity compared to that of direct DSR1F/DSR4R PCR. Clone sequences were affiliated mainly with the Desulfobacteraceae and Desulfohalobiaceae families. Many sequences (approximately 30%) were related to a deeply branching lineage unaffiliated with any cultured SRP. Although this dsrAB cluster was found in all libraries, the new primers better amplified this lineage, providing more information on this unknown bacterial group. Thanks to these new primers in nested PCR, the SRP community from Carnoulès could be characterized. Specific SRP populations were obtained according to environmental characteristics. Desulfomicrobiaceae-related sequences were recovered in samples with low pH, low levels of dissolved oxygen, and high As content, while sequences belonging to the deeply branching group were found in a less extreme sample. Furthermore, for the first time, dsrAB sequences related to the latter group were recovered from freshwater.

Effects of temperature and fertilization on total vs. active bacterial communities exposed to crude and diesel oil pollution in NW Mediterranean Sea

The dynamics of total and active microbial communities were studied in seawater microcosms amended with crude or diesel oil at different temperatures (25, 10 and 4 degrees C) in the presence/absence of organic fertilization (Inipol EAP 22). Total and hydrocarbon-degrading microbes were enumerated by fluorescence microscopy and Most Probable Number (MPN) method, respectively. Total (16S rDNA-based) vs. active (16S rRNA) bacterial community structure was monitored by Capillary-Electrophoresis Single Strand Conformation Polymorphism (CE-SSCP) fingerprinting. Hydrocarbons were analyzed after 12 weeks of incubation by gas chromatography-mass spectrometry. Total and hydrocarbon-degrading microbial counts were highly influenced by fertilization while no important differences were observed between temperatures. Higher biodegradation levels were observed in fertilized microcosms. Temperature and fertilization induced changes in structure of total bacterial communities. However, fertilization showed a more important effect on active bacterial structure. The calculation of Simpson's diversity index showed similar trends among temperatures whereas fertilization reduced diversity index of both total and active bacterial communities.

Phylogenetic diversity and temporal variation in the Spirochaeta populations from two Mediterranean microbial mats

Spirochetes are among the bacterial groups often observed in hydrogen-sulfide-rich layers of coastal microbial mats. However, relatively few spirochetes from these microbial mats have been described and characterized. We used 16S rDNA phylogenetic analysis to investigate the spirochetal diversity of microbial mats from two locations in the western Mediterranean (Ebro Delta, Spain, and Camargue, France). Samples from each location were monitored in the spring and winter over a period of 1 to 2 years. In the sequence analysis of 332 clones derived from samples of both locations, 42 novel phylotypes of not-yet-cultivated spirochetes belonging to the genus Spirochaeta were detected. None of the phylotypes were identified as known culturable species of Spirochaeta or previously identified phylotypes cloned from other hypersaline microbial mat such as Guerrero Negro, Mexico. Eight of the phylotypes were common to Ebro and Camargue mats, and two (IF058 and LL066) were present both in spring and winter. Some phylotypes appeared to show seasonal variation, i.e., they were found only in the spring, but not in the winter. Ebro and Camargue phylotypes, like phylotypes from Guerrero Negro, grouped according to the vertical gradient of oxygen and sulfide in the mat. Some phylotypes, such as LH073, IE028, LH042, or LG013 were harbored in low H2S or H2S-O2 interface zone. In contrast, major phylotypes were detected in deeper layers and they were likely strict anaerobes and high tolerant to H2S. The presence of spirochetes in differently located microbial mats suggests that they constitute very diverse and stable populations involved in a well-integrated metabolic symbiosis (i.e., permanent physiological cooperation) with other guild populations in the mats, where they maintain a coordinated functional and stable community.

Mercury methylation by a microbial community from sediments of the Adour Estuary (Bay of Biscay, France)

In order to study the influence of microorganisms on the mercury biogeochemistry, the metal content and the structure of microbial communities were determined in sediments from stations along the Adour Estuary. The comparison of the bacterial communities and their distribution in function of the environmental parameters by Canonical Correspondence Analysis (CCA) revealed the influence of metals on the bacterial communities structure. Sediments where the bacterial communities are mostly influenced by methylmercury were incubated in slurries with or without mercury, under oxic and anoxic conditions. Methylmercury production was detected in the anoxic biotic slurries with a net methylation yield of 0.3% after 24 h. CCA based on T-RFLP profiles revealed the impact of mercury addition on the bacterial communities structure. In addition, 17 bacterial strains, mainly sulphate-reducing bacteria involved in mercury methylation, were isolated and identified.

Diversity of ring-hydroxylating dioxygenases in pristine and oil contaminated microbial mats at genomic and transcriptomic levels

The aim of this work was to characterize bacterial ring-hydroxylating dioxygenase (RHD) diversity in a pristine microbial mat and follow their diversity changes in response to heavy fuel oil contamination. In order to describe the RHDs diversity, new degenerate primers were designed and a nested-PCR approach was developed to gain sensitivity and wider diversity. RHD diversity in artificially contaminated mats maintained in microcosms and in chronically contaminated mats was analysed by clone libraries and terminal restriction fragment length polymorphism (T-RFLP) at genomic and transcriptomic levels. The RHD diversity in the pristine microbial mat was represented by Pseudomonas putida nahAc-like genes and no increase of diversity was detected after 1 year of oil contamination. The diversity observed in a 30 year chronically polluted microbial mat was represented by four main RHD clusters and two new genes revealing higher polyaromatic hydrocarbon (PAH) degradation capacity. This study illustrates that a single petroleum contamination (such as oil spill) is not enough to involve a detectable modification of RHD diversity. The new degenerate primers described here allowed RHD gene amplification from pristine and contaminated samples thereby showing their diversity. The proposed approach solves one of the main problems of functional gene analysis providing effective amplification of the environmental diversity of the targeted genes.