1
|
Vigneron A, Guyoneaud R, Goñi-Urriza M. Genome-Centric Metatranscriptomics Reveals Multiple Co-occurring Routes for Hydrocarbon Degradation in Chronically Contaminated Marine Microbial Mats. Environ Sci Technol 2024; 58:1551-1562. [PMID: 38197744 DOI: 10.1021/acs.est.3c08386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Long-term hydrocarbon pollution is a devious threat to aquatic and marine ecosystems. However, microbial responses to chronic pollution remain poorly understood. Combining genome-centric metagenomic and metatranscriptomic analyses of microbial mat samples that experienced chronic hydrocarbon pollution for more than 80 years, we analyzed the transcriptomic activity of alkane and aromatic hydrocarbon degradation pathways at the population level. Consistent with the fluctuating and stratified redox conditions of the habitat, both aerobic and anaerobic hydrocarbon degradation pathways were expressed by taxonomically and metabolically contrasted lineages including members of Bacteroidiales, Desulfobacteraceae, Pseudomonadales; Alcanivoraceae and Halieaceae populations with (photo)-heterotrophic, sulfur- and organohalide-based metabolisms, providing evidence for the co-occurrence and activity of aerobic and anaerobic hydrocarbon degradation pathways in shallow marine microbial mats. In addition, our results suggest that aerobic alkane degradation in long-term pollution involved bacterial families that are naturally widely distributed in marine habitats, but hydrocarbon concentration and composition were found to be a strong structuring factor of their intrafamily diversity and transcriptomic activities.
Collapse
Affiliation(s)
- Adrien Vigneron
- Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau 64053, France
| | - Rémy Guyoneaud
- Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau 64053, France
| | - Marisol Goñi-Urriza
- Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau 64053, France
| |
Collapse
|
2
|
Scuvée D, Goñi-Urriza M, Gassie C, Khalfaoui-Hassani B, Guyoneaud R. Consortia cultivation of the Desulfobacterota from macrophyte periphyton: tool for increasing the cultivation of microorganisms involved in mercury methylation. Microbiol Res 2023; 273:127415. [PMID: 37247586 DOI: 10.1016/j.micres.2023.127415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/02/2023] [Accepted: 05/17/2023] [Indexed: 05/31/2023]
Abstract
Invasive macrophytes are a persistent environmental problem in aquatic ecosystems. They also cause potential health issues, since periphyton colonizing their aquatic roots are hot spot of mercury methylation. Because periphytons are at the base of the trophic chain, the produced methylmercury is bioamplified through the food webs. In this work, a consortia cultivation approach was applied in order to investigate methylators in the periphyton of Ludwigia sp., an invasive macrophyte. Five growth conditions were used in order to favor the growth of different sulfate reducers, the major mercury methylators in this periphyton. A total of 33 consortia containing putative Hg methylators were obtained. Based on the amino acid sequences of HgcA (essential enzyme for Hg methylation), the obtained consortia could be subdivided into five main clusters, affiliated with Desulfovibrionaceae, Desulfobulbaceae and Syntrophobacteraceae. The main cluster, related to Desulfovibrionaceae, showed the highest sequence diversity; notwithstanding most of the sequences of this cluster showed no close representatives. Through the consortia approach, species thus far uncultivated were cultivated. The successful cultivation of these species was probably possible through the metabolites produced by other members of the consortium. The analysis of the microbial composition of the consortia uncover certain microbial interactions that may exist within this complex environment.
Collapse
Affiliation(s)
- Diva Scuvée
- Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM UMR5254, Environmental Microbiology and Chemistry, 64000 Pau, France
| | - Marisol Goñi-Urriza
- Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM UMR5254, Environmental Microbiology and Chemistry, 64000 Pau, France
| | - Claire Gassie
- Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM UMR5254, Environmental Microbiology and Chemistry, 64000 Pau, France
| | - Bahia Khalfaoui-Hassani
- Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM UMR5254, Environmental Microbiology and Chemistry, 64000 Pau, France
| | - Rémy Guyoneaud
- Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM UMR5254, Environmental Microbiology and Chemistry, 64000 Pau, France.
| |
Collapse
|
3
|
Brito EMS, Guyoneaud R, Caretta CA, Joseph M, Goñi-Urriza M, Ollivier B, Hirschler-Réa A. Bacterial diversity of an acid mine drainage beside the Xichú River (Mexico) accessed by culture-dependent and culture-independent approaches. Extremophiles 2023; 27:5. [PMID: 36800123 DOI: 10.1007/s00792-023-01291-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 02/02/2023] [Indexed: 02/18/2023]
Abstract
Xichú River is a Mexican river located in an environmental preservation area called Sierra Gorda Biosphere Reserve. Around it, there are tons of abandoned mine residues that represent a serious environmental issue. Sediment samples of Xichú River, visibly contaminated by flows of an acid mine drainage, were collected to study their prokaryotic diversity. The study was based on both cultural and non-cultural approaches. The analysis of total 16S rRNA gene by MiSEQ sequencing allowed to identify 182 Operational Taxonomic Units. The community was dominated by Pseudomonadota, Bacteroidota, "Desulfobacterota" and Acidobacteriota (27, 21, 19 and 16%, respectively). Different culture conditions were used focusing on the isolation of anaerobic bacteria, including sulfate-reducing bacteria (SRB) and arsenate-reducing bacteria (ARB). Finally, 16 strains were isolated. Among them, 12 were phylogenetically identified, with two strains being SRB, belonging to the genus Solidesulfovibrio ("Desulfobacterota"), while ten are ARB belonging to the genera Azospira (Pseudomonadota), Peribacillus (Bacillota), Raineyella and Propionicimonas (Actinomycetota). The isolate representative of Raineyella genus probably corresponds to a new species, which, besides arsenate, also reduces nitrate, nitrite, and fumarate.
Collapse
Affiliation(s)
- Elcia Margareth Souza Brito
- Environmental Engineering Department, Laboratory of Environmental Microbiology and Applied Molecular Biology, DI-CGT, Universidad de Guanajuato, CP 36000, Guanajuato (Gto.), Mexico
| | - Rémy Guyoneaud
- UMR 5254, Environmental Microbiology Group, E2S-UPPA CNRS, IPREM, Université de Pau et des Pays de l'Adour, Pau, France
| | - César Augusto Caretta
- Astronomy Department, Universidad de Guanajuato, DCNE-CGT, CP 36023, Guanajuato (Gto.), Mexico.
| | - Manon Joseph
- UM 110, CNRS, IRD, Aix Marseille Université, Institut Méditerranéen d'Océanologie (MIO), Marseille, France
| | - Marisol Goñi-Urriza
- UMR 5254, Environmental Microbiology Group, E2S-UPPA CNRS, IPREM, Université de Pau et des Pays de l'Adour, Pau, France
| | - Bernard Ollivier
- UM 110, CNRS, IRD, Aix Marseille Université, Institut Méditerranéen d'Océanologie (MIO), Marseille, France
| | - Agnès Hirschler-Réa
- UM 110, CNRS, IRD, Aix Marseille Université, Institut Méditerranéen d'Océanologie (MIO), Marseille, France
| |
Collapse
|
4
|
Vigneron A, Cruaud P, Guyoneaud R, Goñi-Urriza M. Into the darkness of the microbial dark matter in situ activities through expression profiles of Patescibacteria populations. Front Microbiol 2023; 13:1073483. [PMID: 36699594 PMCID: PMC9868632 DOI: 10.3389/fmicb.2022.1073483] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 12/05/2022] [Indexed: 01/11/2023] Open
Abstract
Patescibacteria form a highly diverse and widespread superphylum of uncultured microorganisms representing a third of the global microbial diversity. Most of our knowledge on Patescibacteria putative physiology relies on metagenomic mining and metagenome-assembled genomes, but the in situ activities and the ecophysiology of these microorganisms have been rarely explored, leaving the role of Patescibacteria in ecosystems elusive. Using a genome-centric metatranscriptomic approach, we analyzed the diel and seasonal gene transcription profiles of 18 Patescibacteria populations in brackish microbial mats to test whether our understanding of Patescibacteria metabolism allows the extrapolation of their in situ activities. Although our results revealed a circadian cycle in Patescibacteria activities, a strong streamlined genetic expression characterized the Patescibacteria populations. This result has a major consequence for the extrapolation of their physiology and environmental function since most transcribed genes were uncharacterized, indicating that the ecophysiology of Patescibacteria cannot be yet reliably predicted from genomic data.
Collapse
Affiliation(s)
- Adrien Vigneron
- IBEAS, Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | | | - Rémy Guyoneaud
- IBEAS, Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Marisol Goñi-Urriza
- IBEAS, Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| |
Collapse
|
5
|
Barrouilhet S, Monperrus M, Tessier E, Khalfaoui-Hassani B, Guyoneaud R, Isaure MP, Goñi-Urriza M. Effect of exogenous and endogenous sulfide on the production and the export of methylmercury by sulfate-reducing bacteria. Environ Sci Pollut Res Int 2023; 30:3835-3846. [PMID: 35953752 DOI: 10.1007/s11356-022-22173-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
Mercury (Hg) is a global pollutant of environmental and health concern; its methylated form, methylmercury (MeHg), is a potent neurotoxin. Sulfur-containing molecules play a role in MeHg production by microorganisms. While sulfides are considered to limit Hg methylation, sulfate and cysteine were shown to favor this process. However, these two forms can be endogenously converted by microorganisms into sulfide. Here, we explore the effect of sulfide (produced by the cell or supplied exogenously) on Hg methylation. For this purpose, Pseudodesulfovibrio hydrargyri BerOc1 was cultivated in non-sulfidogenic conditions with addition of cysteine and sulfide as well as in sulfidogenic conditions. We report that Hg methylation depends on sulfide concentration in the culture and the sulfides produced by cysteine degradation or sulfate reduction could affect the Hg methylation pattern. Hg methylation was independent of hgcA expression. Interestingly, MeHg production was maximal at 0.1-0.5 mM of sulfides. Besides, a strong positive correlation between MeHg in the extracellular medium and the increase of sulfide concentrations was observed, suggesting a facilitated MeHg export with sulfide and/or higher desorption from the cell. We suggest that sulfides (exogenous or endogenous) play a key role in controlling mercury methylation and should be considered when investigating the impact of Hg in natural environments.
Collapse
Affiliation(s)
- Sophie Barrouilhet
- Universite de Pau Et Des Pays de L'Adour, E2S UPPA, CNRS, IPREM UMR 5254, Pau, France
| | - Mathilde Monperrus
- Universite de Pau Et Des Pays de L'Adour, E2S UPPA, CNRS, IPREM UMR 5254, Anglet, France
| | - Emmanuel Tessier
- Universite de Pau Et Des Pays de L'Adour, E2S UPPA, CNRS, IPREM UMR 5254, Pau, France
| | | | - Rémy Guyoneaud
- Universite de Pau Et Des Pays de L'Adour, E2S UPPA, CNRS, IPREM UMR 5254, Pau, France
| | - Marie-Pierre Isaure
- Universite de Pau Et Des Pays de L'Adour, E2S UPPA, CNRS, IPREM UMR 5254, Pau, France
| | - Marisol Goñi-Urriza
- Universite de Pau Et Des Pays de L'Adour, E2S UPPA, CNRS, IPREM UMR 5254, Pau, France.
| |
Collapse
|
6
|
Isaure MP, Albertelli M, Kieffer I, Tucoulou R, Petrel M, Gontier E, Tessier E, Monperrus M, Goñi-Urriza M. Relationship Between Hg Speciation and Hg Methylation/Demethylation Processes in the Sulfate-Reducing Bacterium Pseudodesulfovibrio hydrargyri: Evidences From HERFD-XANES and Nano-XRF. Front Microbiol 2020; 11:584715. [PMID: 33154741 PMCID: PMC7591507 DOI: 10.3389/fmicb.2020.584715] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 09/17/2020] [Indexed: 01/09/2023] Open
Abstract
Microorganisms are key players in the transformation of mercury into neurotoxic methylmercury (MeHg). Nevertheless, this mechanism and the opposite MeHg demethylation remain poorly understood. Here, we explored the impact of inorganic mercury (IHg) and MeHg concentrations from 0.05 to 50 μM on the production and degradation of MeHg in two sulfate-reducing bacteria, Pseudodesulfovibrio hydrargyri BerOc1 able to methylate and demethylate mercury and Desulfovibrio desulfuricans G200 only able to demethylate MeHg. MeHg produced by BerOc1 increased with increasing IHg concentration with a maximum attained for 5 μM, and suggested a saturation of the process. MeHg was mainly found in the supernatant suggesting its export from the cell. Hg L3-edge High- Energy-Resolution-Fluorescence-Detected-X-ray-Absorption-Near-Edge-Structure spectroscopy (HERFD-XANES) identified MeHg produced by BerOc1 as MeHg-cysteine2 form. A dominant tetracoordinated βHgS form was detected for BerOc1 exposed to the lowest IHg concentrations where methylation was detected. In contrast, at the highest exposure (50 μM) where Hg methylation was abolished, Hg species drastically changed suggesting a role of Hg speciation in the production of MeHg. The tetracoordinated βHgS was likely present as nano-particles as suggested by transmission electron microscopy combined to X-ray energy dispersive spectroscopy (TEM-X-EDS) and nano-X ray fluorescence (nano-XRF). When exposed to MeHg, the production of IHg, on the contrary, increased with the increase of MeHg exposure until 50 μM for both BerOc1 and G200 strains, suggesting that demethylation did not require intact biological activity. The formed IHg species were identified as various tetracoordinated Hg-S forms. These results highlight the important role of thiol ligands and Hg coordination in Hg methylation and demethylation processes.
Collapse
Affiliation(s)
- Marie-Pierre Isaure
- Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, MIRA, IPREM, Pau, France
| | - Marine Albertelli
- Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, MIRA, IPREM, Pau, France
| | - Isabelle Kieffer
- FAME-UHD, BM16 Beamline, European Synchrotron Radiation Facility (ESRF), BP220, Grenoble, France.,CNRS, IRD, Irstea, Météo France, OSUG, FAME, Université Grenoble Alpes, Grenoble, France
| | - Rémi Tucoulou
- ID16B Beamline, European Synchrotron Radiation Facility (ESRF), BP220, Grenoble, France
| | - Melina Petrel
- Bordeaux Imaging Center UMS 3420 CNRS - US4 INSERM, Université de Bordeaux, Pôle d'imagerie Électronique, Bordeaux, France
| | - Etienne Gontier
- Bordeaux Imaging Center UMS 3420 CNRS - US4 INSERM, Université de Bordeaux, Pôle d'imagerie Électronique, Bordeaux, France
| | - Emmanuel Tessier
- Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, MIRA, IPREM, Pau, France
| | - Mathilde Monperrus
- Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, MIRA, IPREM, Anglet, France
| | - Marisol Goñi-Urriza
- Université de Pau et des Pays de l'Adour, E2S UPPA, CNRS, MIRA, IPREM, Pau, France
| |
Collapse
|
7
|
Aubé J, Senin P, Bonin P, Pringault O, Jeziorski C, Bouchez O, Klopp C, Guyoneaud R, Goñi-Urriza M. Meta-omics Provides Insights into the Impact of Hydrocarbon Contamination on Microbial Mat Functioning. Microb Ecol 2020; 80:286-295. [PMID: 32076743 DOI: 10.1007/s00248-020-01493-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 02/04/2020] [Indexed: 06/10/2023]
Abstract
Photosynthetic microbial mats are stable, self-supported communities. Due to their coastal localization, these mats are frequently exposed to hydrocarbon contamination and are able to grow on it. To decipher how this contamination disturbs the functioning of microbial mats, we compared two mats: a contaminated mat exposed to chronic petroleum contamination and a reference mat. The taxonomic and metabolic structures of the mats in spring and fall were determined using metagenomic and metatranscriptomic approaches. Extremely high contamination disturbed the seasonal variations of the mat. ABC transporters, two-component systems, and type IV secretion system-related genes were overabundant in the contaminated mats. Xenobiotic degradation metabolism was minor in the metagenomes of both mats, and only the expression of genes involved in polycyclic aromatic hydrocarbon degradation was higher in the contaminated mat. Interestingly, the expression rates of genes involved in hydrocarbon activation decreased during the 1-year study period, concomitant with the decrease in easily degradable hydrocarbons, suggesting a transient effect of hydrocarbon contamination. Alteromonadales and Oceanospirillales hydrocarbonoclastic bacteria appeared to be key in hydrocarbon remediation in the contaminated mat. Overall, the contaminated microbial mat was able to cope with hydrocarbon contamination and displayed an adaptive functioning that modified seasonal behaviour.
Collapse
Affiliation(s)
- Johanne Aubé
- Environmental Microbiology, Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
- Laboratoire de Microbiologie des Environnements Extrêmes, UMR6197, IFREMER, CNRS, Université de Bretagne Occidentale, Plouzané, France
| | - Pavel Senin
- Environmental Microbiology, Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
- Plateforme Bioinformatique Genotoul, UR875 Biométrie et Intelligence Artificielle, INRA, Castanet-Tolosan, France
| | - Patricia Bonin
- Mediterranean Institute of Oceanography (MIO), Aix Marseille University, Université de Toulon, CNRS/INSU/IRD, UM 110, Marseille, France
| | - Olivier Pringault
- UMR 9190 MARBEC IRD-Ifremer-CNRS, Université de Montpellier, Place Eugène Bataillon, Montpellier, France
| | | | - Olivier Bouchez
- GeT-PlaGe, Genotoul, INRA Auzeville, Castanet-Tolosan, France
| | - Christophe Klopp
- Plateforme Bioinformatique Genotoul, UR875 Biométrie et Intelligence Artificielle, INRA, Castanet-Tolosan, France
| | - Rémy Guyoneaud
- Environmental Microbiology, Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Marisol Goñi-Urriza
- Environmental Microbiology, Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France.
| |
Collapse
|
8
|
Brito EMS, Rodríguez-Galván M, Hernández-Espino LG, Caretta CA, Goñi-Urriza M, Malm O, Torres JPM, Guyoneaud R. Prospecting bacterial consortia from a geothermal site for metals biotransformation. Biodegradation 2020; 31:235-247. [PMID: 32676947 DOI: 10.1007/s10532-020-09906-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 07/01/2020] [Indexed: 11/30/2022]
Abstract
Biomats that flourished in a fumarole located on the geothermal site Los Azufres (Mexico) were used as inocula to select aerobic and sulfate-reducing bacteria consortia for studying their capacity to reduce hexavalent chromium [Cr(VI)], aiming to use these consortia in biotransformation technologies. The sample site is characterized by slightly warm (nearly 27 [Formula: see text]C), acid (pH 3) and about hypoxic (1.8 mg L[Formula: see text] of dissolved oxygen) conditions. Four culture systems (2 aerobic and 2 anaerobic) were investigated, including their enzymatic activity, capacity to produce biofilms, and an analysis of the total bacterial populations. For the anaerobic condition (using sulfate and sulfur as electron acceptors), four pH values (from 2 to 8) and four carbon sources (pyruvate, glycerol, Na-lactate and Na-acetate) were probed. Significant biological Cr(VI) removal was observed for all the pH values probed, particularly during the first 12 h, being more effective at the most acid conditions. At a pH value of 4 and using pyruvate as carbon source, 100 mg L[Formula: see text] of Cr(VI) were completely depleted in less than 12 h, while the use of Na-lactate was less effective but still reasonable. These results indicate that sulfate-reducing bacteria consortia from geothermal sites like the one studied here are capable of biotransforming Cr(VI) and have the potential to provide metal bioremediation technologies.
Collapse
Affiliation(s)
- E M S Brito
- Environmental Microbiology and Applied Molecular Biology Lab., Dept. Environmental Eng., DI-CGT, Universidad de Guanajuato (UG), Guanajuato, Mexico
| | - M Rodríguez-Galván
- Environmental Microbiology and Applied Molecular Biology Lab., Dept. Environmental Eng., DI-CGT, Universidad de Guanajuato (UG), Guanajuato, Mexico
| | - L G Hernández-Espino
- Environmental Microbiology and Applied Molecular Biology Lab., Dept. Environmental Eng., DI-CGT, Universidad de Guanajuato (UG), Guanajuato, Mexico
| | - C A Caretta
- Dept. of Astronomy, DCNE-CGT, Universidad de Guanajuato (UG), Guanajuato, Mexico.
| | - M Goñi-Urriza
- Environmental Microbiology Group, EEM-UMR IPREM 5254, Université de Pau et des Pays de l'Adour (UPPA), Pau, France
| | - O Malm
- Radioisotopes Lab. (LREPF), IBCCF, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - J P M Torres
- Micropollutants Lab., IBCCF, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - R Guyoneaud
- Environmental Microbiology Group, EEM-UMR IPREM 5254, Université de Pau et des Pays de l'Adour (UPPA), Pau, France
| |
Collapse
|
9
|
Goñi-Urriza M, Klopp C, Ranchou-Peyruse M, Ranchou-Peyruse A, Monperrus M, Khalfaoui-Hassani B, Guyoneaud R. Genome insights of mercury methylation among Desulfovibrio and Pseudodesulfovibrio strains. Res Microbiol 2019; 171:3-12. [PMID: 31655199 DOI: 10.1016/j.resmic.2019.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 10/10/2019] [Accepted: 10/11/2019] [Indexed: 01/28/2023]
Abstract
Mercury methylation converts inorganic mercury into the toxic methylmercury, and the consequences of this transformation are worrisome for human health and the environment. This process is performed by anaerobic microorganisms, such as several strains related to Pseudodesulfovibrio and Desulfovibrio genera. In order to provide new insights into the molecular mechanisms of mercury methylation, we performed a comparative genomic analysis on mercury methylators and non-methylators from (Pseudo)Desulfovibrio strains. Our results showed that (Pseudo)Desulfovibrio species are phylogenetically and metabolically distant and consequently, these genera should be divided into various genera. Strains able to perform methylation are affiliated with one branch of the phylogenetic tree, but, except for hgcA and hgcB genes, no other specific genetic markers were found among methylating strains. hgcA and hgcB genes can be found adjacent or separated, but proximity between those genes does not promote higher mercury methylation. In addition, close examination of the non-methylator Pseudodesulfovibrio piezophilus C1TLV30 strain, showed a syntenic structure that suggests a recombination event and may have led to hgcB depletion. The genomic analyses identify also arsR gene coding for a putative regulator upstream hgcA. Both genes are cotranscribed suggesting a role of ArsR in hgcA expression and probably a role in mercury methylation.
Collapse
Affiliation(s)
- Marisol Goñi-Urriza
- Environmental Microbiology, CNRS/UNIV PAU & PAYS ADOUR/E2S UPPA, Institut des Sciences Analytiques et de Physicochimie pour l'Environnement et les Matériaux, IPREM, UMR5254, Pau, France.
| | - Christophe Klopp
- Plateforme Bioinformatique Genotoul, UR875 Biométrie et Intelligence Artificielle, INRA, Castanet-Tolosan, France.
| | - Magali Ranchou-Peyruse
- Environmental Microbiology, CNRS/UNIV PAU & PAYS ADOUR/E2S UPPA, Institut des Sciences Analytiques et de Physicochimie pour l'Environnement et les Matériaux, IPREM, UMR5254, Pau, France.
| | - Anthony Ranchou-Peyruse
- Environmental Microbiology, CNRS/UNIV PAU & PAYS ADOUR/E2S UPPA, Institut des Sciences Analytiques et de Physicochimie pour l'Environnement et les Matériaux, IPREM, UMR5254, Pau, France.
| | - Mathilde Monperrus
- CNRS/UNIV PAU & PAYS ADOUR/E2S UPPA, Institut des Sciences Analytiques et de Physicochimie pour l'Environnement et les Matériaux, IPREM, UMR5254, Anglet, France.
| | - Bahia Khalfaoui-Hassani
- Environmental Microbiology, CNRS/UNIV PAU & PAYS ADOUR/E2S UPPA, Institut des Sciences Analytiques et de Physicochimie pour l'Environnement et les Matériaux, IPREM, UMR5254, Pau, France.
| | - Rémy Guyoneaud
- Environmental Microbiology, CNRS/UNIV PAU & PAYS ADOUR/E2S UPPA, Institut des Sciences Analytiques et de Physicochimie pour l'Environnement et les Matériaux, IPREM, UMR5254, Pau, France.
| |
Collapse
|
10
|
Brito EMS, Romero-Núñez VM, Caretta CA, Bertin P, Valerdi-Negreros JC, Guyoneaud R, Goñi-Urriza M. The bacterial diversity on steam vents from Paricutín and Sapichu volcanoes. Extremophiles 2019; 23:249-263. [PMID: 30712189 DOI: 10.1007/s00792-019-01078-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Accepted: 01/22/2019] [Indexed: 01/30/2023]
Abstract
Vapor steam vents are prevailing structures on geothermal sites in which local geochemical conditions allow the development of extremophilic microorganisms. We describe the structure of the prokaryotic community able to grow on the walls and rocks of such microecosystems in two terrestrial Mexican volcanoes: Paricutín (PI and PII samples) and its satellite Sapichu (S sample). The investigated samples showed similar diversity indices, with few dominant OTUs (abundance > 1%): 21, 16 and 23, respectively for PI, PII and S. However, each steam vent showed a particular community profile: PI was dominated by photosynthetic bacteria (Cyanobacteria and Chloroflexia class), PII by Actinobacteria and Proteobacteria, and S by Ktedonobacteria class, Acidobacteria and Cyanobacteria phyla. Concerning the predicted metabolic potential, we found a dominance of cellular pathways, especially the ones for energy generation with metabolisms for sulfur respiration, nitrogen fixation, methanogenesis, carbon fixation, photosynthesis, and metals, among others. We suggest a different maturity stage for the three studied fumaroles, from the youngest (PI) to the oldest (S and PII), also influenced by the temperature and other geochemical parameters. Furthermore, four anaerobic strains were isolated, belonging to Clostridia class (Clostridium sphenoides, C. swellfunanium and Anaerocolumna cellulosilytica) and to Bacilli class (Paenibacillus azoreducens).
Collapse
Affiliation(s)
| | - Víctor Manuel Romero-Núñez
- Ingeniería Ambiental, División de Ingenierías (CGT), Universidad de Guanajuato, Guanajuato, Gto., Mexico
| | - César Augusto Caretta
- Departamento de Astronomía, División de Ciencias Naturales y Exactas (CGT), Universidad de Guanajuato, Guanajuato, Gto., Mexico
| | - Pierre Bertin
- Equipe Génomique, Structure et Traduction, Inst. Biologie Intégrative de la Cellule (I2BC) CNRS-UMR9198, Universitè Paris-Sud, 91405, Orsay Cedex, France
| | | | - Rémy Guyoneaud
- CNRS/Universitè de Pau et des Pays de l'Adour/E2S, Institut des Sciences Analytiques et de Physicochimie pour l'Environnement et les Matériaux, Environmental Microbiology Group, UMR 5254, 64000, Pau, France
| | - Marisol Goñi-Urriza
- CNRS/Universitè de Pau et des Pays de l'Adour/E2S, Institut des Sciences Analytiques et de Physicochimie pour l'Environnement et les Matériaux, Environmental Microbiology Group, UMR 5254, 64000, Pau, France
| |
Collapse
|
11
|
Bouchet S, Goñi-Urriza M, Monperrus M, Guyoneaud R, Fernandez P, Heredia C, Tessier E, Gassie C, Point D, Guédron S, Achá D, Amouroux D. Linking Microbial Activities and Low-Molecular-Weight Thiols to Hg Methylation in Biofilms and Periphyton from High-Altitude Tropical Lakes in the Bolivian Altiplano. Environ Sci Technol 2018; 52:9758-9767. [PMID: 30037219 DOI: 10.1021/acs.est.8b01885] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The sources and factors controlling concentrations of monomethylmercury (MMHg) in aquatic ecosystems need to be better understood. Here, we investigated Hg transformations in sediments, periphyton associated with green algae's or aquatic plants, and benthic biofilms from the Lake Titicaca hydrosystem and compared them to the occurrence of active methylating microorganisms and extracellular Hg ligands. Intense Hg methylation was found in benthic biofilms and green algae's periphyton, while it remained low in sediments and aquatic plants' periphyton. Demethylation varied between compartments but remained overall in the same range. Hg methylation was mainly carried out by sulfate reducers, although methanogens also played a role. Its variability between compartments was first explained by the presence or absence of the hgcAB genes. Next, both benthic biofilm and green algae's periphyton exhibited a great diversity of extracellular low-molecular-weight (LMW) thiols (13 or 14 compounds) present at a range of a few nmol L-1 or μmol L-1 but clearly dominated by cysteine and 3-mercaptopropionic acid. Hg methylation was overall positively correlated to the total thiol concentrations, albeit to different extents according to the compartment and conditions. This work is the first examining the interplay between active methylating bacterial communities and extracellular ligands in heterotrophic biofilms and supports the involvement of LMW thiols in Hg methylation in real aquatic systems.
Collapse
Affiliation(s)
- Sylvain Bouchet
- CNRS/Univ Pau & Pays Adour , Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux , UMR5254, 64000 , Pau , France
| | - Marisol Goñi-Urriza
- CNRS/Univ Pau & Pays Adour , Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux , UMR5254, 64000 , Pau , France
| | - Mathilde Monperrus
- CNRS/Univ Pau & Pays Adour , Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux , UMR5254, 64000 , Pau , France
| | - Rémy Guyoneaud
- CNRS/Univ Pau & Pays Adour , Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux , UMR5254, 64000 , Pau , France
| | - Pablo Fernandez
- Unidad de Calidad Ambiental (UCA) , Instituto de Ecologia, Universidad Mayor de San Andres, Campus Universitario de Cota Cota , Calle 27 , 00000 La Paz , Bolivia
| | - Carlos Heredia
- Unidad de Calidad Ambiental (UCA) , Instituto de Ecologia, Universidad Mayor de San Andres, Campus Universitario de Cota Cota , Calle 27 , 00000 La Paz , Bolivia
| | - Emmanuel Tessier
- CNRS/Univ Pau & Pays Adour , Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux , UMR5254, 64000 , Pau , France
| | - Claire Gassie
- CNRS/Univ Pau & Pays Adour , Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux , UMR5254, 64000 , Pau , France
| | - David Point
- Unidad de Calidad Ambiental (UCA) , Instituto de Ecologia, Universidad Mayor de San Andres, Campus Universitario de Cota Cota , Calle 27 , 00000 La Paz , Bolivia
- Géosciences Environnement Toulouse, UMR5563, IRD UR 234 , Université Paul Sabatier , 14 Avenue Edouard Belin , 31400 Toulouse , France
| | - Stéphane Guédron
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, IRD, IFSTTAR, ISTerre , 38000 Grenoble , France
- Laboratorio de Hidroquímica , Instituto de Investigaciones Químicas, Universidad Mayor de San Andrés, Campus Universitario de Cota-Cota , casilla 3161 , 00000 La Paz , Bolivia
| | - Dario Achá
- Unidad de Calidad Ambiental (UCA) , Instituto de Ecologia, Universidad Mayor de San Andres, Campus Universitario de Cota Cota , Calle 27 , 00000 La Paz , Bolivia
| | - David Amouroux
- CNRS/Univ Pau & Pays Adour , Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux , UMR5254, 64000 , Pau , France
- Unidad de Calidad Ambiental (UCA) , Instituto de Ecologia, Universidad Mayor de San Andres, Campus Universitario de Cota Cota , Calle 27 , 00000 La Paz , Bolivia
- Géosciences Environnement Toulouse, UMR5563, IRD UR 234 , Université Paul Sabatier , 14 Avenue Edouard Belin , 31400 Toulouse , France
| |
Collapse
|
12
|
Ranchou-Peyruse M, Goñi-Urriza M, Guignard M, Goas M, Ranchou-Peyruse A, Guyoneaud R. Pseudodesulfovibrio hydrargyri sp. nov., a mercury-methylating bacterium isolated from a brackish sediment. Int J Syst Evol Microbiol 2018. [PMID: 29533171 DOI: 10.1099/ijsem.0.002173] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The strain BerOc1T was isolated from brackish sediments contaminated with hydrocarbons and heavy metals. This strain has been used as a model strain of sulfate-reducer to study the biomethylation of mercury. The cells are vibrio-shaped, motile and not sporulated. Phylogeny and physiological traits placed this strain within the genus Pseudodesulfovibrio. Optimal growth was obtained at 30 °C, 1.5 % NaCl and pH 6.0-7.4. The estimated G+C content of the genomic DNA was 62.6 mol%. BerOc1T used lactate, pyruvate, fumarate, ethanol and hydrogen. Terminal electron acceptors used were sulfate, sulfite, thiosulfate and DMSO. Only pyruvate could be used without a terminal electron acceptor. The major fatty acids were C18 : 0, anteiso-C15 : 0, C16 : 0 and C18 : 1ω7. The name Pseudodesulfovibrio hydrargyri sp. nov. is proposed for the type strain BerOc1T (DSM 10384T=JCM 31820T).
Collapse
Affiliation(s)
- Magali Ranchou-Peyruse
- Université de Pau et des Pays de l'Adour, CNRS, Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux - MIRA, UMR 5254, 64000, Pau, France
| | - Marisol Goñi-Urriza
- Université de Pau et des Pays de l'Adour, CNRS, Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux - MIRA, UMR 5254, 64000, Pau, France
| | - Marion Guignard
- Université de Pau et des Pays de l'Adour, CNRS, Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux - MIRA, UMR 5254, 64000, Pau, France
| | - Marjorie Goas
- Université de Pau et des Pays de l'Adour, CNRS, Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux - MIRA, UMR 5254, 64000, Pau, France
| | - Anthony Ranchou-Peyruse
- Université de Pau et des Pays de l'Adour, CNRS, Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux - MIRA, UMR 5254, 64000, Pau, France
| | - Rémy Guyoneaud
- Université de Pau et des Pays de l'Adour, CNRS, Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux - MIRA, UMR 5254, 64000, Pau, France
| |
Collapse
|
13
|
Colin Y, Goñi-Urriza M, Gassie C, Carlier E, Monperrus M, Guyoneaud R. Distribution of Sulfate-Reducing Communities from Estuarine to Marine Bay Waters. Microb Ecol 2017; 73:39-49. [PMID: 27581035 DOI: 10.1007/s00248-016-0842-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 08/17/2016] [Indexed: 06/06/2023]
Abstract
Estuaries are highly dynamic ecosystems in which freshwater and seawater mix together. Depending on tide and river inflows, particles originating from rivers or from the remobilization of sediments accumulate in the water column. Due to the salinity gradient and the high heterotrophic activity in the estuarine plume, hypoxic and anoxic microniches may form in oxygenated waters, sustaining favorable conditions for resuspended anaerobic microorganisms. In this context, we tested the hypothesis that anaerobic sulfate-reducing prokaryotes may occur in the water column of the Adour River. Using 16S ribosomal RNA (rRNA) and dsrAB-based terminal restriction fragment length polymorphism (T-RFLP) techniques, we characterized total prokaryotic and sulfate-reducing communities along a gradient from estuarine to marine bay waters. Sulfate-reducing prokaryotes were further characterized by the description of dsrB genes and the cultivation of sulfidogenic anaerobic microorganisms. As a result, physical-chemical parameters had a significant effect on water bacterial diversity and community structure along the studied gradient. The concentration of cultured sulfidogenic microorganisms ranged from 1 to 60 × 103 cells l-1 in the water column. Sulfate-reducing prokaryotes occurring in estuarine waters were closely related to microorganisms previously detected in freshwater sediments, suggesting an estuarine origin, mainly by the remobilization of the sediments. In the marine bay station, sediment-derived sulfate-reducing prokaryotes were not cultured anymore, probably due to freshwater dilution, increasing salinity and extended oxic stress. Nevertheless, isolates related to the type strain Desulfovibrio oceani were cultured from the diluted plume and deep marine waters, indicating the occurrence of autochthonous sulfate-reducing bacteria offshore.
Collapse
Affiliation(s)
- Yannick Colin
- Equipe Environnement et Microbiologie, IPREM UMR CNRS 5254, Université de Pau et des Pays de l'Adour, IBEAS, BP 1155, 64013, Pau Cedex, France.
- INRA, UMR 1136 INRA/Université de Lorraine, Interactions Arbres Micro-organismes, Centre de Nancy, 54280, Champenoux, France.
| | - Marisol Goñi-Urriza
- Equipe Environnement et Microbiologie, IPREM UMR CNRS 5254, Université de Pau et des Pays de l'Adour, IBEAS, BP 1155, 64013, Pau Cedex, France
| | - Claire Gassie
- Equipe Environnement et Microbiologie, IPREM UMR CNRS 5254, Université de Pau et des Pays de l'Adour, IBEAS, BP 1155, 64013, Pau Cedex, France
| | - Elisabeth Carlier
- Equipe Environnement et Microbiologie, IPREM UMR CNRS 5254, Université de Pau et des Pays de l'Adour, IBEAS, BP 1155, 64013, Pau Cedex, France
| | - Mathilde Monperrus
- Laboratoire de Chimie Analytique Bio-Inorganique et Environnement (LCABIE), IPREM UMR CNRS 5254, Université de Pau et des Pays de l'Adour, Pau, France
| | - Rémy Guyoneaud
- Equipe Environnement et Microbiologie, IPREM UMR CNRS 5254, Université de Pau et des Pays de l'Adour, IBEAS, BP 1155, 64013, Pau Cedex, France
| |
Collapse
|
14
|
Aubé J, Senin P, Pringault O, Bonin P, Deflandre B, Bouchez O, Bru N, Biritxinaga-Etchart E, Klopp C, Guyoneaud R, Goñi-Urriza M. The impact of long-term hydrocarbon exposure on the structure, activity, and biogeochemical functioning of microbial mats. Mar Pollut Bull 2016; 111:115-125. [PMID: 27449831 DOI: 10.1016/j.marpolbul.2016.07.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 07/11/2016] [Accepted: 07/16/2016] [Indexed: 06/06/2023]
Abstract
Photosynthetic microbial mats are metabolically structured systems driven by solar light. They are ubiquitous and can grow in hydrocarbon-polluted sites. Our aim is to determine the impact of chronic hydrocarbon contamination on the structure, activity, and functioning of a microbial mat. We compared it to an uncontaminated mat harboring similar geochemical characteristics. The mats were sampled in spring and fall for 2years. Seasonal variations were observed for the reference mat: sulfur cycle-related bacteria dominated spring samples, while Cyanobacteria dominated in autumn. The contaminated mat showed minor seasonal variation; a progressive increase of Cyanobacteria was noticed, indicating a perturbation of the classical seasonal behavior. Hydrocarbon content was the main factor explaining the differences in the microbial community structure; however, hydrocarbonoclastic bacteria were among rare or transient Operational Taxonomic Units (OTUs) in the contaminated mat. We suggest that in long-term contaminated systems, hydrocarbonoclastic bacteria cannot be considered a sentinel of contamination.
Collapse
Affiliation(s)
- Johanne Aubé
- Equipe Environnement et Microbiologie, IPREM UMR CNRS 5254, Université de Pau et des Pays de l'Adour, IBEAS, BP 1155, 64013 Pau Cedex, France.
| | - Pavel Senin
- Equipe Environnement et Microbiologie, IPREM UMR CNRS 5254, Université de Pau et des Pays de l'Adour, IBEAS, BP 1155, 64013 Pau Cedex, France; Plateforme Bioinformatique Genotoul, UR875, Biométrie et Intelligence Artificielle, INRA, 31326 Castanet-Tolosan, France.
| | - Olivier Pringault
- UMR 9190 MARBEC IRD-Ifremer-CNRS, Université de Montpellier, Place Eugène Bataillon, Case 093, 34095 Montpellier Cedex 5, France.
| | - Patricia Bonin
- MIO, Institut Méditerranéen d'Océanologie, UMR 7294, F13288 Marseille, France.
| | - Bruno Deflandre
- EPOC, UMR 5805, Université de Bordeaux, F33615 Pessac, France.
| | - Olivier Bouchez
- GeT-PlaGe, Genotoul, INRA Auzeville, F31326 Castanet-Tolosan, France.
| | - Noëlle Bru
- Université de Pau et des Pays de l'Adour, Laboratoire de Mathématiques et de leurs Applications de Pau, UMR CNRS 5142, FED 4155 MIRA, Campus Montaury, 64600 Anglet, France.
| | - Edurne Biritxinaga-Etchart
- Université de Pau et des Pays de l'Adour, Laboratoire de Mathématiques et de leurs Applications de Pau, UMR CNRS 5142, FED 4155 MIRA, Campus Montaury, 64600 Anglet, France.
| | - Christophe Klopp
- Plateforme Bioinformatique Genotoul, UR875, Biométrie et Intelligence Artificielle, INRA, 31326 Castanet-Tolosan, France.
| | - Rémy Guyoneaud
- Equipe Environnement et Microbiologie, IPREM UMR CNRS 5254, Université de Pau et des Pays de l'Adour, IBEAS, BP 1155, 64013 Pau Cedex, France.
| | - Marisol Goñi-Urriza
- Equipe Environnement et Microbiologie, IPREM UMR CNRS 5254, Université de Pau et des Pays de l'Adour, IBEAS, BP 1155, 64013 Pau Cedex, France.
| |
Collapse
|
15
|
Goñi-Urriza M, Corsellis Y, Lanceleur L, Tessier E, Gury J, Monperrus M, Guyoneaud R. Relationships between bacterial energetic metabolism, mercury methylation potential, and hgcA/hgcB gene expression in Desulfovibrio dechloroacetivorans BerOc1. Environ Sci Pollut Res Int 2015; 22:13764-71. [PMID: 25772867 DOI: 10.1007/s11356-015-4273-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 02/23/2015] [Indexed: 05/16/2023]
Abstract
The proteins encoded by the hgcA and hgcB genes are currently the only ones known to be involved in the mercury methylation by anaerobic microorganisms. However, no studies have been published to determine the relationships between their expression level and the net/gross methylmercury production. This study aimed to decipher the effect of growth conditions on methylmercury production and the relationships between hgcA and hgcB expression levels and net methylation. Desulfovibrio dechloroacetivorans strain BerOc1 was grown under sulfidogenic conditions with different carbon sources and electron donors as well as under fumarate respiration. A good correlation was found between the biomass production and the methylmercury production when the strain was grown under sulfate-reducing conditions. Methylmercury production was much higher under fumarate respiration when no sulfide was produced. During exponential growth, hgcA and hgcB gene expression levels were only slightly higher in the presence of inorganic mercury, and it was difficult to conclude whether there was a significant induction of hgcA and hgcB genes by inorganic mercury. Besides, no relationships between hgcA and hgcB expression levels and net mercury methylation could be observed when the strain was grown either under sulfate reduction or fumarate respiration, indicating that environmental factors had more influence than expression levels.
Collapse
Affiliation(s)
- Marisol Goñi-Urriza
- EEM-UMR IPREM CNRS 5254, Equipe Environnement et Microbiologie, University of Pau, Pau, France,
| | | | | | | | | | | | | |
Collapse
|
16
|
Brito EMS, De la Cruz Barrón M, Caretta CA, Goñi-Urriza M, Andrade LH, Cuevas-Rodríguez G, Malm O, Torres JPM, Simon M, Guyoneaud R. Impact of hydrocarbons, PCBs and heavy metals on bacterial communities in Lerma River, Salamanca, Mexico: Investigation of hydrocarbon degradation potential. Sci Total Environ 2015; 521-522:1-10. [PMID: 25828406 DOI: 10.1016/j.scitotenv.2015.02.098] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 02/11/2015] [Accepted: 02/27/2015] [Indexed: 06/04/2023]
Abstract
Freshwater contamination usually comes from runoff water or direct wastewater discharges to the environment. This paper presents a case study which reveals the impact of these types of contamination on the sediment bacterial population. A small stretch of Lerma River Basin, heavily impacted by industrial activities and urban wastewater release, was studied. Due to industrial inputs, the sediments are characterized by strong hydrocarbon concentrations, ranging from 2 935 to 28 430μg·kg(-1) of total polyaromatic hydrocarbons (PAHs). These sediments are also impacted by heavy metals (e.g., 9.6μg·kg(-1) of Cd and 246μg·kg(-1) of Cu, about 8 times the maximum recommended values for environmental samples) and polychlorinated biphenyls (ranging from 54 to 123μg·kg(-1) of total PCBs). The bacterial diversity on 6 sediment samples, taken from upstream to downstream of the main industrial and urban contamination sources, was assessed through TRFLP. Even though the high PAH concentrations are hazardous to aquatic life, they are not the only factor driving bacterial community composition in this ecosystem. Urban discharges, leading to hypoxia and low pH, also strongly influenced bacterial community structure. The bacterial bioprospection of these samples, using PAH as unique carbon source, yielded 8 hydrocarbonoclastic strains. By sequencing the 16S rDNA gene, these were identified as similar to Mycobacterium goodii, Pseudomonas aeruginosa, Pseudomonas lundensis or Aeromonas veronii. These strains showed high capacity to degrade naphthalene (between 92 and 100% at 200mg·L(-1)), pyrene (up to 72% at 100mg·L(-1)) and/or fluoranthene (52% at 50mg·L(-1)) as their only carbon source on in vitro experiments. These hydrocarbonoclastic bacteria were detected even in the samples upstream of the city of Salamanca, suggesting chronical contamination, already in place longer before. Such microorganisms are clearly potential candidates for hydrocarbon degradation in the treatment of oil discharges.
Collapse
Affiliation(s)
- Elcia M S Brito
- Ingeniería Ambiental, Depto. Ing. Civil, DI-CGT, Universidad de Guanajuato, Guanajuato, Gto, Mexico.
| | - Magali De la Cruz Barrón
- Ingeniería Ambiental, Depto. Ing. Civil, DI-CGT, Universidad de Guanajuato, Guanajuato, Gto, Mexico
| | - César A Caretta
- Depto. Astronomía, DCNyE-CGT, Universidad de Guanajuato, Gto, Mexico
| | - Marisol Goñi-Urriza
- Equipe Environnement et Microbiologie (EEM-UMR-IPREM), Universitè de Pau et des Pays de l'Adour, Pau, France
| | - Leandro H Andrade
- Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Germán Cuevas-Rodríguez
- Ingeniería Ambiental, Depto. Ing. Civil, DI-CGT, Universidad de Guanajuato, Guanajuato, Gto, Mexico
| | - Olaf Malm
- Inst. Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - João P M Torres
- Inst. Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Maryse Simon
- Equipe Environnement et Microbiologie (EEM-UMR-IPREM), Universitè de Pau et des Pays de l'Adour, Pau, France
| | - Remy Guyoneaud
- Equipe Environnement et Microbiologie (EEM-UMR-IPREM), Universitè de Pau et des Pays de l'Adour, Pau, France
| |
Collapse
|
17
|
Colin Y, Goñi-Urriza M, Caumette P, Guyoneaud R. Contribution of enrichments and resampling for sulfate reducing bacteria diversity assessment by high-throughput cultivation. J Microbiol Methods 2015; 110:92-7. [PMID: 25578508 DOI: 10.1016/j.mimet.2015.01.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 01/07/2015] [Accepted: 01/07/2015] [Indexed: 10/24/2022]
Abstract
The development of new high-throughput cultivation methods aims to increase the isolation efficiency as compared to standard techniques that often require enrichment procedures to compensate the low microbial recovery. In the current study, estuarine sulfate-reducing bacteria were isolated using an anaerobic isolation procedure in 384-well microplates. Ninety-nine strains were recovered from initial sediments. Isolates were identified according to their partial 16S rRNA sequences and clustered into 13 phylotypes. Besides, the increase in species richness obtained through enrichments or resampling was investigated. Forty-four enrichment procedures were conducted and shifts in sulfate-reducing bacterial communities were investigated through dsrAB gene fingerprinting. Despite efforts in conducting numerous enrichment conditions only few of them were statistically different from initial sample. The cultural diversity obtained from 3 of the most divergent enrichments, as well as from resampled sediments equally contributed to raise the sulfate-reducing diversity up to 22 phylotypes. Enrichments (selection of metabolism) or resampling (transient populations and micro-heterogeneity) may still be helpful to assess new microbial phylotypes. Nevertheless, all the newly cultivated strains were all representatives of minor Operational Taxonomic Units and could eventually be recovered by maintaining high-throughput isolation effort from the initial sediments.
Collapse
Affiliation(s)
- Yannick Colin
- Equipe Environnement et Microbiologie, IPREM UMR CNRS 5254, Université de Pau et des Pays de l'Adour, IBEAS, BP 1155, 64013 Pau Cedex, France
| | - Marisol Goñi-Urriza
- Equipe Environnement et Microbiologie, IPREM UMR CNRS 5254, Université de Pau et des Pays de l'Adour, IBEAS, BP 1155, 64013 Pau Cedex, France
| | - Pierre Caumette
- Equipe Environnement et Microbiologie, IPREM UMR CNRS 5254, Université de Pau et des Pays de l'Adour, IBEAS, BP 1155, 64013 Pau Cedex, France
| | - Rémy Guyoneaud
- Equipe Environnement et Microbiologie, IPREM UMR CNRS 5254, Université de Pau et des Pays de l'Adour, IBEAS, BP 1155, 64013 Pau Cedex, France.
| |
Collapse
|
18
|
Brito EMS, Villegas-Negrete N, Sotelo-González IA, Caretta CA, Goñi-Urriza M, Gassie C, Hakil F, Colin Y, Duran R, Gutiérrez-Corona F, Piñón-Castillo HA, Cuevas-Rodríguez G, Malm O, Torres JPM, Fahy A, Reyna-López GE, Guyoneaud R. Microbial diversity in Los Azufres geothermal field (Michoacán, Mexico) and isolation of representative sulfate and sulfur reducers. Extremophiles 2014; 18:385-98. [DOI: 10.1007/s00792-013-0624-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2013] [Accepted: 12/29/2013] [Indexed: 11/28/2022]
|
19
|
Giloteaux L, Duran R, Casiot C, Bruneel O, Elbaz-Poulichet F, Goñi-Urriza M. Three-year survey of sulfate-reducing bacteria community structure in Carnoulès acid mine drainage (France), highly contaminated by arsenic. FEMS Microbiol Ecol 2012; 83:724-37. [PMID: 23057444 DOI: 10.1111/1574-6941.12028] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Revised: 09/27/2012] [Accepted: 10/03/2012] [Indexed: 11/29/2022] Open
Abstract
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.
Collapse
Affiliation(s)
- Ludovic Giloteaux
- Equipe Environnement et Microbiologie - UMR IPREM5254, Université de Pau et des Pays de l'Adour, Pau Cedex, France
| | | | | | | | | | | |
Collapse
|
20
|
Chronopoulou PM, Fahy A, Coulon F, Païssé S, Goñi-Urriza M, Peperzak L, Acuña Alvarez L, McKew BA, Lawson T, Timmis KN, Duran R, Underwood GJC, McGenity TJ. Impact of a simulated oil spill on benthic phototrophs and nitrogen-fixing bacteria in mudflat mesocosms. Environ Microbiol 2012; 15:242-52. [DOI: 10.1111/j.1462-2920.2012.02864.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Revised: 07/21/2012] [Accepted: 07/24/2012] [Indexed: 11/29/2022]
Affiliation(s)
| | - Anne Fahy
- School of Biological Sciences; University of Essex; Wivenhoe Park; Colchester; CO4 3SQ; UK
| | | | - Sandrine Païssé
- Equipe Environnement et Microbiologie; UMR CNRS-IPREM 5254; IBEAS; Université de Pau et des Pays de l'Adour; Pau; BP 1155 F-64013; France
| | - Marisol Goñi-Urriza
- Equipe Environnement et Microbiologie; UMR CNRS-IPREM 5254; IBEAS; Université de Pau et des Pays de l'Adour; Pau; BP 1155 F-64013; France
| | - Louis Peperzak
- Department of Biological Oceanography; Royal Netherlands Institute for Sea Research (NIOZ); PO Box 50; NL 1790; AB Den Burg; The Netherlands
| | - Laura Acuña Alvarez
- School of Biological Sciences; University of Essex; Wivenhoe Park; Colchester; CO4 3SQ; UK
| | - Boyd A. McKew
- School of Biological Sciences; University of Essex; Wivenhoe Park; Colchester; CO4 3SQ; UK
| | - Tracy Lawson
- School of Biological Sciences; University of Essex; Wivenhoe Park; Colchester; CO4 3SQ; UK
| | | | - Robert Duran
- Equipe Environnement et Microbiologie; UMR CNRS-IPREM 5254; IBEAS; Université de Pau et des Pays de l'Adour; Pau; BP 1155 F-64013; France
| | - Graham J. C. Underwood
- School of Biological Sciences; University of Essex; Wivenhoe Park; Colchester; CO4 3SQ; UK
| | - Terry J. McGenity
- School of Biological Sciences; University of Essex; Wivenhoe Park; Colchester; CO4 3SQ; UK
| |
Collapse
|
21
|
Colin Y, Goñi-Urriza M, Caumette P, Guyoneaud R. Combination of high throughput cultivation and dsrA sequencing for assessment of sulfate-reducing bacteria diversity in sediments. FEMS Microbiol Ecol 2012; 83:26-37. [PMID: 22809466 DOI: 10.1111/j.1574-6941.2012.01452.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Revised: 07/03/2012] [Accepted: 07/05/2012] [Indexed: 11/29/2022] Open
Abstract
Improving the knowledge on sulfate-reducing bacteria (SRB) diversity and ecophysiology will permit a better understanding on their key roles in aquatic ecosystems. Therefore, their diversity was evaluated in estuarine sediments by a polyphasic approach including dsrA gene cloning and sequencing (156 clones) and high-throughput isolations in 384-well microplates (177 strains). Using the related thresholds of 95% (DsrA amino acid sequences) and 97% (16S rRNA gene sequences) for sequence similarity, SRB were grouped into 60 and 22 operational taxonomic units, respectively. Both approaches poorly overlapped and rather complemented each other. The clone library was dominated by sequences related to the Desulfobacteraceae, while only one isolate belonged to this family. Most of the strains were affiliated to the genera Desulfopila and Desulfotalea within the Desulfobulbaceae. Desulfopila-related strains exhibited a high phylogenetic microdiversity and represented numerically significant populations. In contrast, Desulfovibrio isolates were less abundant but displayed a high phylogenetic diversity. Three hundred and eighty-four-well microplate isolations enhanced significantly the number of isolates handled. As a consequence, 15 new taxa sharing less than 98% sequence similarity (16S rRNA gene) with their closest relatives were obtained. This polyphasic approach allowed to obtain a high phylogenetic diversity and thus a better view of sulfate-reducing communities in intertidal sediments.
Collapse
Affiliation(s)
- Yannick Colin
- Equipe Environnement et Microbiologie, IPREM UMR CNRS 5254, Université de Pau et des Pays de l'Adour, IBEAS, Pau Cedex, France
| | | | | | | |
Collapse
|
22
|
Paissé S, Goñi-Urriza M, Stadler T, Budzinski H, Duran R. Ring-hydroxylating dioxygenase (RHD) expression in a microbial community during the early response to oil pollution. FEMS Microbiol Ecol 2012. [DOI: 10.1111/j.1574-6941.2012.01392.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Sandrine Paissé
- Equipe Environnement et Microbiologie; UMR CNRS IPREM 5254; Université de Pau; Pau Cedex; France
| | - Marisol Goñi-Urriza
- Equipe Environnement et Microbiologie; UMR CNRS IPREM 5254; Université de Pau; Pau Cedex; France
| | - Thibault Stadler
- Equipe Environnement et Microbiologie; UMR CNRS IPREM 5254; Université de Pau; Pau Cedex; France
| | - Hélène Budzinski
- Institut des Sciences Moléculaires; UMR CNRS 5255; Université Bordeaux; Talence; France
| | - Robert Duran
- Equipe Environnement et Microbiologie; UMR CNRS IPREM 5254; Université de Pau; Pau Cedex; France
| |
Collapse
|
23
|
Paissé S, Goñi-Urriza M, Stadler T, Budzinski H, Duran R. Ring-hydroxylating dioxygenase (RHD) expression in a microbial community during the early response to oil pollution. FEMS Microbiol Ecol 2012; 80:77-86. [DOI: 10.1111/j.1574-6941.2011.01270.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Revised: 11/08/2011] [Accepted: 11/24/2011] [Indexed: 11/27/2022] Open
Affiliation(s)
- Sandrine Paissé
- Equipe Environnement et Microbiologie; UMR CNRS IPREM 5254; Université de Pau; Pau Cedex; France
| | - Marisol Goñi-Urriza
- Equipe Environnement et Microbiologie; UMR CNRS IPREM 5254; Université de Pau; Pau Cedex; France
| | - Thibault Stadler
- Equipe Environnement et Microbiologie; UMR CNRS IPREM 5254; Université de Pau; Pau Cedex; France
| | - Hélène Budzinski
- Institut des Sciences Moléculaires; UMR CNRS 5255; Université Bordeaux; Talence; France
| | - Robert Duran
- Equipe Environnement et Microbiologie; UMR CNRS IPREM 5254; Université de Pau; Pau Cedex; France
| |
Collapse
|
24
|
Paisse S, Duran R, Coulon F, Goñi-Urriza M. Are alkane hydroxylase genes (alkB) relevant to assess petroleum bioremediation processes in chronically polluted coastal sediments? Appl Microbiol Biotechnol 2011; 92:835-44. [PMID: 21660544 DOI: 10.1007/s00253-011-3381-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Revised: 05/11/2011] [Accepted: 05/11/2011] [Indexed: 11/24/2022]
Abstract
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.
Collapse
Affiliation(s)
- Sandrine Paisse
- Equipe Environnement et Microbiologie-UMR IPREM5254, Université de Pau, BP 1155, 64013 Pau cedex, France
| | | | | | | |
Collapse
|
25
|
Piñón-Castillo H, Brito E, Goñi-Urriza M, Guyoneaud R, Duran R, Nevarez-Moorillon G, Gutiérrez-Corona J, Caretta C, Reyna-López G. Hexavalent chromium reduction by bacterial consortia and pure strains from an alkaline industrial effluent. J Appl Microbiol 2010; 109:2173-82. [DOI: 10.1111/j.1365-2672.2010.04849.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
26
|
Païssé S, Goñi-Urriza M, Coulon F, Duran R. How a bacterial community originating from a contaminated coastal sediment responds to an oil input. Microb Ecol 2010; 60:394-405. [PMID: 20652237 DOI: 10.1007/s00248-010-9721-7] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2010] [Accepted: 06/29/2010] [Indexed: 05/29/2023]
Abstract
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.
Collapse
Affiliation(s)
- Sandrine Païssé
- Equipe Environnement et Microbiologie-UMR CNRS IPREM 5254, Université de Pau, BP1155, 64013 Pau Cedex, France
| | | | | | | |
Collapse
|
27
|
Ben Said O, Goñi-Urriza M, El Bour M, Aissa P, Duran R. Bacterial community structure of sediments of the bizerte lagoon (Tunisia), a southern Mediterranean coastal anthropized lagoon. Microb Ecol 2010; 59:445-456. [PMID: 19789910 DOI: 10.1007/s00248-009-9585-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2009] [Accepted: 08/27/2009] [Indexed: 05/28/2023]
Abstract
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.
Collapse
Affiliation(s)
- Olfa Ben Said
- Equipe Environnement et Microbiologie-IPREM UMR 5254-IBEAS, Université de Pau et des Pays de l'Adour, Avenue de l'Université, BP 1155, 64013 Pau Cedex, France
| | | | | | | | | |
Collapse
|
28
|
Brito EMS, Duran R, Guyoneaud R, Goñi-Urriza M, García de Oteyza T, Crapez MAC, Aleluia I, Wasserman JCA. A case study of in situ oil contamination in a mangrove swamp (Rio De Janeiro, Brazil). Mar Pollut Bull 2009; 58:418-423. [PMID: 19185324 DOI: 10.1016/j.marpolbul.2008.12.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2008] [Revised: 11/24/2008] [Accepted: 12/10/2008] [Indexed: 05/27/2023]
Abstract
Mangroves are sensitive ecosystems of prominent ecological value that lamentably have lost much of their areas across the world. The vulnerability of mangroves grown in proximity to cities requires the development of new technologies for the remediation of acute oil spills and chronic contaminations. Studies on oil remediation are usually performed with in vitro microcosms whereas in situ experiments are rare. The aim of this work was to evaluate oil degradation on mangrove ecosystems using in situ microcosms seeded with an indigenous hydrocarbonoclastic bacterial consortium (HBC). Although the potential degradation of oil through HBC has been reported, their seeding directly on the sediment did not stimulate oil degradation during the experimental period. This is probably due to the availability of carbon sources that are easier to degrade than petroleum hydrocarbons. Our results emphasize the fragility of mangrove ecosystems during accidental oil spills and also the need for more efficient technologies for their remediation.
Collapse
Affiliation(s)
- Elcia M S Brito
- Departamento de Geoquímica Ambiental, Universidade Federal Fluminense, Niterói, RJ, Brazil.
| | | | | | | | | | | | | | | |
Collapse
|
29
|
Bordenave S, Goñi-Urriza M, Vilette C, Blanchard S, Caumette P, Duran R. Diversity of ring-hydroxylating dioxygenases in pristine and oil contaminated microbial mats at genomic and transcriptomic levels. Environ Microbiol 2008; 10:3201-11. [PMID: 18662307 DOI: 10.1111/j.1462-2920.2008.01707.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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.
Collapse
Affiliation(s)
- Sylvain Bordenave
- Equipe Environnement et Microbiologie, Institut Pluridisciplinaire de Recherche Environnement et Matériaux, UMR CNRS 5254, Université de Pau BP1155-64013 Pau cedex, France
| | | | | | | | | | | |
Collapse
|
30
|
Goñi-Urriza M, Arpin C, Capdepuy M, Dubois V, Caumette P, Quentin C. Type II topoisomerase quinolone resistance-determining regions of Aeromonas caviae, A. hydrophila, and A. sobria complexes and mutations associated with quinolone resistance. Antimicrob Agents Chemother 2002; 46:350-9. [PMID: 11796341 PMCID: PMC127024 DOI: 10.1128/aac.46.2.350-359.2002] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Most Aeromonas strains isolated from two European rivers were previously found to be resistant to nalidixic acid. In order to elucidate the mechanism of this resistance, 20 strains of Aeromonas caviae (n = 10), A. hydrophila (n = 5), and A. sobria (n = 5) complexes, including 3 reference strains and 17 environmental isolates, were investigated. Fragments of the gyrA, gyrB, parC, and parE genes encompassing the quinolone resistance-determining regions (QRDRs) were amplified by PCR and sequenced. Results obtained for the six sensitive strains showed that the GyrA, GyrB, ParC, and ParE QRDR fragments of Aeromonas spp. were highly conserved (> or =96.1% identity), despite some genetic polymorphism; they were most closely related to those of Vibrio spp., Pseudomonas spp., and members of the family Enterobacteriaceae (72.4 to 97.1% homology). All 14 environmental resistant strains carried a point mutation in the GyrA QRDR at codon 83, leading to the substitution Ser-83-->Ile (10 strains) or Ser-83-->Arg. In addition, seven strains harbored a mutation in the ParC QRDR either at position 80 (five strains), generating a Ser-80-->Ile (three strains) or Ser-80-->Arg change, or at position 84, yielding a Glu-84-->Lys modification. No amino acid alterations were discovered in the GyrB and ParE QRDRs. Double gyrA-parC missense mutations were associated with higher levels of quinolone resistance compared with the levels associated with single gyrA mutations. The most resistant strains probably had an additional mechanism(s) of resistance, such as decreased accumulation of the drugs. Our data suggest that, in mesophilic Aeromonas spp., as in other gram-negative bacteria, gyrase and topoisomerase IV are the primary and secondary targets for quinolones, respectively.
Collapse
Affiliation(s)
- Marisol Goñi-Urriza
- Laboratoire de Microbiologie, Université de Bordeaux 2, Bordeaux. Laboratoire d'Ecologie Moléculaire, Université de Pau, Pau, France
| | | | | | | | | | | |
Collapse
|
31
|
Goñi-Urriza M, Pineau L, Capdepuy M, Roques C, Caumette P, Quentin C. Antimicrobial resistance of mesophilic Aeromonas spp. isolated from two European rivers. J Antimicrob Chemother 2000; 46:297-301. [PMID: 10933657 DOI: 10.1093/jac/46.2.297] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The activity of 19 antibiotics and four antiseptics and/or disinfectants was studied against 138 non-redundant strains of Aeromonas spp. (104 Aeromonas caviae, 22 Aeromonas sobria and 12 Aeromonas hydrophila) isolated from two European rivers. Antibiotic resistance frequencies were: nalidixic acid, 59%; tetracycline, 14%; fosfomycin, 8%; tobramycin and cotrimoxazole, 7%; cefotaxime, 4%; chloramphenicol, 2%; gentamicin, 1%. Most of the nalidixic acid-resistant strains were susceptible to fluoroquinolones (54-98%). Antibiotic resistance rates varied according to the source of the strains. All Aeromonas spp. strains were killed by 50 ppm of chlorine, cetylpyridinium chloride and peracetic acid, and by 1600 ppm of glutaraldehyde.
Collapse
Affiliation(s)
- M Goñi-Urriza
- Laboratoire de Microbiologie, Faculté de Pharmacie, Université de Bordeaux 2, 146 rue Léo Saignat, 33076 Bordeaux cedex, France
| | | | | | | | | | | |
Collapse
|
32
|
Goñi-Urriza M, Capdepuy M, Arpin C, Raymond N, Caumette P, Quentin C. Impact of an urban effluent on antibiotic resistance of riverine Enterobacteriaceae and Aeromonas spp. Appl Environ Microbiol 2000; 66:125-32. [PMID: 10618213 PMCID: PMC91795 DOI: 10.1128/aem.66.1.125-132.2000] [Citation(s) in RCA: 268] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In order to evaluate the impact of an urban effluent on antibiotic resistance of freshwater bacterial populations, water samples were collected from the Arga river (Spain), upstream and downstream from the wastewater discharge of the city of Pamplona. Strains of Enterobacteriaceae (representative of the human and animal commensal flora) (110 isolates) and Aeromonas (typically waterborne bacteria) (118 isolates) were selected for antibiotic susceptibility testing. Most of the Aeromonas strains (72%) and many of the Enterobacteriaceae (20%) were resistant to nalidixic acid. Singly nalidixic acid-resistant strains were frequent regardless of the sampling site for Aeromonas, whereas they were more common upstream from the discharge for enterobacteria. The most common resistances to antibiotics other than quinolones were to tetracycline (24.3%) and beta-lactams (20.5%) for Enterobacteriaceae and to tetracycline (27.5%) and co-trimoxazole (26.6%) for Aeromonas. The rates of these antibiotic resistances increased downstream from the discharge at similar degrees for the two bacterial groups; it remained at high levels for enterobacteria but decreased along the 30-km study zone for Aeromonas. Genetic analysis of representative strains demonstrated that these resistances were mostly (enterobacteria) or exclusively (Aeromonas) chromosomally mediated. Moreover, a reference strain of Aeromonas caviae (CIP 7616) could not be transformed with conjugative R plasmids of enterobacteria. Thus, the urban effluent resulted in an increase of the rates of resistance to antibiotics other than quinolones in the riverine bacterial populations, despite limited genetic exchanges between enterobacteria and Aeromonas. Quinolone resistance probably was selected by heavy antibiotic discharges of unknown origin upstream from the urban effluent.
Collapse
Affiliation(s)
- M Goñi-Urriza
- Laboratoire de Microbiologie, Université de Bordeaux 2, France
| | | | | | | | | | | |
Collapse
|
33
|
Goñi-Urriza M, Capdepuy M, Raymond N, Quentin C, Caumette P. Impact of an urban effluent on the bacterial community structure in the Arga River (Spain), with special reference to culturable gram-negative rods. Can J Microbiol 1999; 45:826-32. [PMID: 10907419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
The Arga River is an interesting system in which to study the impact of urban effluent pollution because it receives a single effluent in the form of wastewater discharge from the city of Pamplona. To analyze the extent of this discharge, total bacteria, culturable heterotrophic bacteria, and Gram-negative heterotrophic bacteria were enumerated and 409 isolates of the latter were identified. One sampling station was located upstream from the inflow, while five were located up to 30 km downstream. Bacterial counts increased drastically downstream from the wastewater inflow. Total bacterial numbers decreased along the 30 km downstream, the last station attaining similar values to those recorded upstream from the discharge. However, culturable heterotrophic and Gram-negative heterotrophic bacteria levels generally remained significantly higher within the 30 km zone investigated. Among the 409 isolates identified, Aeromonas spp. were the most frequent both upstream and downstream from the discharge. In contrast, although strains belonging to different genera of Enterobacteriaceae were found in all stations, their occurrence was significantly higher just downstream from the polluted discharge. Acinetobacter spp., which were never found upstream, were detected in all stations below the discharge. Our results clearly show that the bacterial community structure changes definitively downstream from the discharge and that Aeromonas were common throughout the sampling zone. Thus they cannot be considered good indicators of pollution in this setting compared to some genera of Enterobacteriaceae or some species of Acinetobacter, the distribution of which correlated better with the distance from the wastewater discharge.
Collapse
Affiliation(s)
- M Goñi-Urriza
- Laboratoire de Microbiologie, Université de Bordeaux 2, France
| | | | | | | | | |
Collapse
|
34
|
Goñi-Urriza M, Capdepuy M, Raymond N, Quentin C, Caumette P. Impact of an urban effluent on the bacterial community structure in the Arga River (Spain), with special reference to culturable Gram-negative rods. Can J Microbiol 1999. [DOI: 10.1139/w99-073] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The Arga River is an interesting system in which to study the impact of urban effluent pollution because it receives a single effluent in the form of wastewater discharge from the city of Pamplona. To analyze the extent of this discharge, total bacteria, culturable heterotrophic bacteria, and Gram-negative heterotrophic bacteria were enumerated and 409 isolates of the latter were identified. One sampling station was located upstream from the inflow, while five were located up to 30 km downstream. Bacterial counts increased drastically downstream from the wastewater inflow. Total bacterial numbers decreased along the 30 km downstream, the last station attaining similar values to those recorded upstream from the discharge. However, culturable heterotrophic and Gram-negative heterotrophic bacteria levels generally remained significantly higher within the 30 km zone investigated. Among the 409 isolates identified, Aeromonas spp. were the most frequent both upstream and downstream from the discharge. In contrast, although strains belonging to different genera of Enterobacteriaceae were found in all stations, their occurrence was significantly higher just downstream from the polluted discharge. Acinetobacter spp., which were never found upstream, were detected in all stations below the discharge. Our results clearly show that the bacterial community structure changes definitively downstream from the discharge and that Aeromonas were common throughout the sampling zone. Thus they cannot be considered good indicators of pollution in this setting compared to some genera of Enterobacteriaceae or some species ofAcinetobacter, the distribution of which correlated better with the distance from the wastewater discharge.Key words: Aeromonas, Enterobacteriaceae, sewage, freshwater.
Collapse
|