1
|
Ranchou-Peyruse M, Guignard M, Haddad PG, Robin S, Boesch F, Lanot M, Carrier H, Dequidt D, Chiquet P, Caumette G, Cézac P, Ranchou-Peyruse A. A deep continental aquifer downhole sampler for microbiological studies. Front Microbiol 2023; 13:1012400. [PMID: 36687568 PMCID: PMC9846368 DOI: 10.3389/fmicb.2022.1012400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 12/06/2022] [Indexed: 01/06/2023] Open
Abstract
To be effective, microbiological studies of deep aquifers must be free from surface microbial contaminants and from infrastructures allowing access to formation water (wellheads, well completions). Many microbiological studies are based on water samples obtained after rinsing a well without guaranteeing the absence of contaminants from the biofilm development in the pipes. The protocol described in this paper presents the adaptation, preparation, sterilization and deployment of a commercial downhole sampler (PDSshort, Leutert, Germany) for the microbiological studying of deep aquifers. The ATEX sampler (i.e., explosive atmospheres) can be deployed for geological gas storage (methane, hydrogen). To validate our procedure and confirm the need to use such a device, cell counting and bacterial taxonomic diversity based on high-throughput sequencing for different water samples taken at the wellhead or at depth using the downhole sampler were compared and discussed. The results show that even after extensive rinsing (7 bore volumes), the water collected at the wellhead was not free of microbial contaminants, as shown by beta-diversity analysis. The downhole sampler procedure was the only way to ensure the purity of the formation water samples from the microbiological point of view. In addition, the downhole sampler allowed the formation water and the autochthonous microbial community to be maintained at in situ pressure for laboratory analysis. The prevention of the contamination of the sample and the preservation of its representativeness are key to guaranteeing the best interpretations and understanding of the functioning of the deep biosphere.
Collapse
Affiliation(s)
- Magali Ranchou-Peyruse
- E2S-UPPA, CNRS, IPREM, Universite de Pau & Pays Adour, Pau, France
- E2S-UPPA, LaTEP, Universite de Pau & Pays Adour, Pau, France
- Joint Laboratory SEnGA, E2S-UPPA-Teréga, Pau, France
| | - Marion Guignard
- E2S-UPPA, CNRS, IPREM, Universite de Pau & Pays Adour, Pau, France
| | - Perla G Haddad
- E2S-UPPA, LaTEP, Universite de Pau & Pays Adour, Pau, France
| | | | | | | | - Hervé Carrier
- Joint Laboratory SEnGA, E2S-UPPA-Teréga, Pau, France
- E2S-UPPA, CNRS, TOTAL, LFCR, Universite de Pau & Pays Adour, Pau, France
| | - David Dequidt
- STORENGY - Geosciences Department, Bois-Colombes, France
| | - Pierre Chiquet
- Joint Laboratory SEnGA, E2S-UPPA-Teréga, Pau, France
- Teréga, Pau, France
| | - Guilhem Caumette
- Joint Laboratory SEnGA, E2S-UPPA-Teréga, Pau, France
- Teréga, Pau, France
| | - Pierre Cézac
- E2S-UPPA, LaTEP, Universite de Pau & Pays Adour, Pau, France
- Joint Laboratory SEnGA, E2S-UPPA-Teréga, Pau, France
| | - Anthony Ranchou-Peyruse
- E2S-UPPA, CNRS, IPREM, Universite de Pau & Pays Adour, Pau, France
- Joint Laboratory SEnGA, E2S-UPPA-Teréga, Pau, France
| |
Collapse
|
2
|
Shrestha R, Cerna K, Spanek R, Bartak D, Cernousek T, Sevcu A. The effect of low-pH concrete on microbial community development in bentonite suspensions as a model for microbial activity prediction in future nuclear waste repository. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 808:151861. [PMID: 34838551 DOI: 10.1016/j.scitotenv.2021.151861] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 11/10/2021] [Accepted: 11/17/2021] [Indexed: 06/13/2023]
Abstract
Concrete as an important component of an engineered barrier system in deep geological repositories (DGR) for radioactive waste may come into contact with bentonite, or other clays, rich in indigenous microorganisms, with potentially harmful impacts on barrier integrity. Our study aimed to assess the effect of a concrete environment on indigenous bentonite and groundwater microbial communities as these particular conditions will select for the potentially harmful microorganisms to the concrete in the future DGR. The two-month experiment under anoxic conditions consisted of crushed, aged, low-pH concrete, Czech Ca-Mg bentonite, and anoxic groundwater, with control samples without concrete or with sterile groundwater. The microbial diversity and proliferation were estimated by qPCR and 16S rRNA gene amplicon sequencing. The presence of concrete had a strong effect on microbial diversity and reduced the increase in total microbial biomass, though low-pH concrete harbored indigenous bacteria. The growth of sulfate reducers was also limited in concrete samples. Several genera, such as Massilia, Citrifermentans, and Lacunisphaera, dominant in bentonite controls, were suppressed in concrete-containing samples. In contrast, genera such as Bacillus, Dethiobacter and Anaerosolibacter specifically proliferated in the presence of concrete. Genera such as Thermincola or Pseudomonas exhibited high versatility and proliferated well under both conditions. Because several of the detected bacterial genera are known to affect concrete integrity, further long-term studies are needed to estimate the effect of bentonite and groundwater microorganisms on concrete stability in future DGR.
Collapse
Affiliation(s)
- Rojina Shrestha
- Technical University of Liberec, Institute for Nanomaterials, Advanced Technologies and Innovations, Bendlova 1407/7, 461 17 Liberec 1, Czech Republic
| | - Katerina Cerna
- Technical University of Liberec, Institute for Nanomaterials, Advanced Technologies and Innovations, Bendlova 1407/7, 461 17 Liberec 1, Czech Republic.
| | - Roman Spanek
- Technical University of Liberec, Institute for Nanomaterials, Advanced Technologies and Innovations, Bendlova 1407/7, 461 17 Liberec 1, Czech Republic
| | - Deepa Bartak
- Technical University of Liberec, Institute for Nanomaterials, Advanced Technologies and Innovations, Bendlova 1407/7, 461 17 Liberec 1, Czech Republic
| | - Tomas Cernousek
- Research Centre Rez, Department of Nuclear Fuel Cycle, Husinec-Rez 130, 25068, Czech Republic
| | - Alena Sevcu
- Technical University of Liberec, Institute for Nanomaterials, Advanced Technologies and Innovations, Bendlova 1407/7, 461 17 Liberec 1, Czech Republic
| |
Collapse
|
3
|
Shrestha R, Černoušek T, Stoulil J, Kovářová H, Sihelská K, Špánek R, Ševců A, Steinová J. Anaerobic microbial corrosion of carbon steel under conditions relevant for deep geological repository of nuclear waste. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 800:149539. [PMID: 34392220 DOI: 10.1016/j.scitotenv.2021.149539] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 08/04/2021] [Accepted: 08/04/2021] [Indexed: 06/13/2023]
Abstract
We examined microbial corrosion of carbon steel in synthetic bentonite pore water inoculated with natural underground water containing microorganisms over a period of 780-days under sterile and anaerobic conditions. Corrosion behaviour was determined using the mass loss method, SEM-EDS analysis and Raman spectroscopy, while qualitative and quantitative changes in the microbial community were analysed using molecular-biological tools (16S rDNA amplicon sequencing and qPCR analysis, respectively). Corrosion rates were significantly higher in the biotic environment (compared with an abiotic environment), with significant localisation of corrosion attacks of up to 1 mm arising within 12-months. Nitrate reducing bacteria, such as Pseudomonas, Brevundimonas and Methyloversatilis, dominated the microbial consortium, the high abundance of Methyloversatilis correlating with periods of highest localised corrosion penetrations, suggesting that this bacterium plays an important role in microbially influenced corrosion. Our results indicate that nitrate-reducing bacteria could represent a potential threat to waste canisters under nuclear repository conditions.
Collapse
Affiliation(s)
- Rojina Shrestha
- Institute for Nanomaterials, Advanced Technologies and Innovations, Technical University of Liberec, Bendlova 1407/7, Liberec 1 461 17, Czech Republic
| | - Tomáš Černoušek
- Research Center Řež, Department of Nuclear Fuel Cycle, Husinec-Řež 130 25068, Czech Republic
| | - Jan Stoulil
- University of Chemistry and Technology, Department of Metals and Corrosion Engineering, Technická 5, Prague 166 28, Czech Republic
| | - Hana Kovářová
- Research Center Řež, Department of Nuclear Fuel Cycle, Husinec-Řež 130 25068, Czech Republic
| | - Kristína Sihelská
- Research Center Řež, Department of Nuclear Fuel Cycle, Husinec-Řež 130 25068, Czech Republic
| | - Roman Špánek
- Institute for Nanomaterials, Advanced Technologies and Innovations, Technical University of Liberec, Bendlova 1407/7, Liberec 1 461 17, Czech Republic
| | - Alena Ševců
- Institute for Nanomaterials, Advanced Technologies and Innovations, Technical University of Liberec, Bendlova 1407/7, Liberec 1 461 17, Czech Republic
| | - Jana Steinová
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Prague 128 01, Czech Republic; Institute for Nanomaterials, Advanced Technologies and Innovations, Technical University of Liberec, Bendlova 1407/7, Liberec 1 461 17, Czech Republic.
| |
Collapse
|
4
|
Grigoryan AA, Jalique DR, Stroes-Gascoyne S, Wolfaardt GM, Keech PG, Korber DR. Prediction of bacterial functional diversity in clay microcosms. Heliyon 2021; 7:e08131. [PMID: 34703919 PMCID: PMC8524152 DOI: 10.1016/j.heliyon.2021.e08131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/05/2021] [Accepted: 10/01/2021] [Indexed: 12/02/2022] Open
Abstract
Microorganisms in clay barriers could affect the long-term performance of waste containers in future deep geological repositories (DGR) for used nuclear fuel through production of corrosive metabolites (e.g., sulfide), which is why clay materials are highly compacted: to reduce both physical space and access to water for microorganisms to grow. However, the highly compacted nature of clays and the resulting low activity or dormancy of microorganisms complicate the extraction of biomarkers (i.e., PLFA, DNA etc.) from such barriers for predictive analysis of microbial risks. In order to overcome these challenges, we have combined culture- and 16S rRNA gene amplicon sequencing-based approaches to describe the functional diversity of microorganisms in several commercial clay products, including two different samples of Wyoming type MX-80 bentonite (Batch 1 and Batch 2), the reference clay for a future Canadian DGR, and Avonlea type Canaprill, a clay sample for comparison. Microorganisms from as-received bentonites were enriched in anoxic 10% w/v clay microcosms for three months at ambient temperature with addition of 10% hydrogen along with presumable indigenous organics and sulfate in the clay. High-throughput sequencing of 16S rRNA gene fragments indicated a high abundance of Gram-positive bacteria of the phylum Firmicutes (82%) in MX-80 Batch 1 incubations. Bacterial libraries from microcosms with MX-80 Batch 2 were enriched with Firmicutes (53%) and Chloroflexi (43%). Firmicutes also significantly contributed (<15%) to the bacterial community in Canaprill clay microcosm, which was dominated by Gram-negative Proteobacteria (>70%). Sequence analysis revealed presence of the bacterial families Peptostreptococcaceae, Clostridiaceae, Peptococcaceae, Bacillaceae, Enterobacteriaceae, Veillonellaceae, Tissierellaceae and Planococcaceae in MX-80 Batch 1 incubations; Bacillaceae, along with unidentified bacteria of the phylum Chloroflexi, in MX-80 Batch 2 clay microcosms, and Pseudomonadaceae, Hydrogenophilaceae, Bacillaceae, Desulfobacteraceae, Desulfobulbaceae, Peptococcaceae, Pelobacteraceae, Alcaligenaceae, Rhodospirillaceae in Canaprill microcosms. Exploration of potential metabolic pathways in the bacterial communities from the clay microcosms suggested variable patterns of sulfur cycling in the different clays with the possible prevalence of bacterial sulfate-reduction in MX-80 bentonite, and probably successive sulfate-reduction/sulfur-oxidation reactions in Canaprill microcosms. Furthermore, analysis of potential metabolic pathways in the bentonite enrichments suggested that bacteria with acid-producing capabilities (i.e., fermenters and acetogens) together with sulfide-producing prokaryotes might perhaps contribute to corrosion risks in clay systems. However, the low activity or dormancy of microorganisms in highly compacted bentonites as a result of severe environmental constraints (e.g., low water activity and high swelling pressure in the confined bentonite) in situ would be expected to largely inhibit bacterial activity in highly compacted clay-based barriers in a future DGR.
Collapse
Affiliation(s)
- Alexander A. Grigoryan
- Department of Food and Bioproducts Sciences, University of Saskatchewan, Saskatoon, Canada
- Saudi Arabian Oil Company, Dhahran, Saudi Arabia
| | - Daphne R. Jalique
- Department of Food and Bioproducts Sciences, University of Saskatchewan, Saskatoon, Canada
- Lallemand Inc., Saskatoon, Canada
| | - Simcha Stroes-Gascoyne
- Department of Food and Bioproducts Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Gideon M. Wolfaardt
- Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada
- Department of Microbiology, University of Stellenbosch, Cape Town, South Africa
| | | | - Darren R. Korber
- Department of Food and Bioproducts Sciences, University of Saskatchewan, Saskatoon, Canada
| |
Collapse
|
5
|
Nasser B, Saito Y, Alarawi M, Al-Humam AA, Mineta K, Gojobori T. Characterization of microbiologically influenced corrosion by comprehensive metagenomic analysis of an inland oil field. Gene 2021; 774:145425. [PMID: 33450352 DOI: 10.1016/j.gene.2021.145425] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 01/05/2021] [Indexed: 11/17/2022]
Abstract
Corrosion in pipelines and reservoir tanks in oil plants is a serious problem in the global energy industry because it causes substantial economic losses associated with frequent part replacement and can lead to potential damage to entire crude oil fields. Previous studies revealed that corrosion is mainly caused by microbial activities in a process currently termed microbiologically influenced corrosion or biocorrosion. Identifying the bacteria responsible for biocorrosion is crucial for its suppression. In this study, we analyzed the microbial communities present at corrosion sites in oil plant pipelines using comparative metagenomic analysis along with bioinformatics and statistics. We analyzed the microbial communities in pipelines in an oil field in which groundwater is used as injection water. We collected samples from four different facilities in the oil field. Metagenomic analysis revealed that the microbial community structures greatly differed even among samples from the same facility. Treatments such as biocide administration and demineralization at each location in the pipeline may have independently affected the microbial community structure. The results indicated that microbial inspection throughout the pipeline network is essential to prevent biocorrosion at industrial plants. By identifying the bacterial species responsible for biocorrosion, this study provides bacterial indicators to detect and classify biocorrosion. Furthermore, these species may serve as biomarkers to detect biocorrosion at an early stage. Then, appropriate management such as treatment with suitable biocides can be performed immediately and appropriately. Thus, our study will serve as a platform for obtaining microbial information related to biocorrosion to enable the development of a practical approach to prevent its occurrence.
Collapse
Affiliation(s)
- Badoor Nasser
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia; King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
| | - Yoshimoto Saito
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia; King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
| | - Mohammed Alarawi
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia; King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
| | | | - Katsuhiko Mineta
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia; King Abdullah University of Science and Technology (KAUST), Computer, Electrical, and Mathematical Sciences and Engineering Division (CEMSE), Thuwal, Saudi Arabia.
| | - Takashi Gojobori
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia; King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia; King Abdullah University of Science and Technology (KAUST), Computer, Electrical, and Mathematical Sciences and Engineering Division (CEMSE), Thuwal, Saudi Arabia.
| |
Collapse
|
6
|
Ruiz-Lopez S, Foster L, Boothman C, Cole N, Morris K, Lloyd JR. Identification of a Stable Hydrogen-Driven Microbiome in a Highly Radioactive Storage Facility on the Sellafield Site. Front Microbiol 2020; 11:587556. [PMID: 33329459 PMCID: PMC7732693 DOI: 10.3389/fmicb.2020.587556] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 10/26/2020] [Indexed: 11/29/2022] Open
Abstract
The use of nuclear power has been a significant part of the United Kingdom’s energy portfolio with the Sellafield site being used for power production and more recently reprocessing and decommissioning of spent nuclear fuel activities. Before being reprocessed, spent nuclear fuel is stored in water ponds with significant levels of background radioactivity and in high alkalinity (to minimize fuel corrosion). Despite these challenging conditions, the presence of microbial communities has been detected. To gain further insight into the microbial communities present in extreme environments, an indoor, hyper-alkaline, oligotrophic, and radioactive spent fuel storage pond (INP) located on the Sellafield site was analyzed. Water samples were collected from sample points within the INP complex, and also the purge water feeding tank (FT) that supplies water to the pond, and were screened for the presence of the 16S and 18S rRNA genes to inform sequencing requirements over a period of 30 months. Only 16S rRNA genes were successfully amplified for sequencing, suggesting that the microbial communities in the INP were dominated by prokaryotes. Quantitative Polymerase Chain Reaction (qPCR) analysis targeting 16S rRNA genes suggested that bacterial cells in the order of 104–106 mL–1 were present in the samples, with loadings rising with time. Next generation Illumina MiSeq sequencing was performed to identify the dominant microorganisms at eight sampling times. The 16S rRNA gene sequence analysis suggested that 70% and 91% from of the OTUs samples, from the FT and INP respectively, belonged to the phylum Proteobacteria, mainly from the alpha and beta subclasses. The remaining OTUs were assigned primarily to the phyla Acidobacteria, Bacteroidetes, and, Cyanobacteria. Overall the most abundant genera identified were Hydrogenophaga, Curvibacter, Porphyrobacter, Rhodoferax, Polaromonas, Sediminibacterium, Roseococcus, and Sphingomonas. The presence of organisms most closely related to Hydrogenophaga species in the INP areas, suggests the metabolism of hydrogen as an energy source, most likely linked to hydrolysis of water caused by the stored fuel. Isolation of axenic cultures using a range of minimal and rich media was also attempted, but only relatively minor components (from the phylum Bacteroidetes) of the pond water communities were obtained, emphasizing the importance of DNA-based, not culture-dependent techniques, for assessing the microbiome of nuclear facilities.
Collapse
Affiliation(s)
- Sharon Ruiz-Lopez
- Department of Earth and Environmental Sciences, University of Manchester (UoM), Manchester, United Kingdom
| | - Lynn Foster
- Department of Earth and Environmental Sciences, University of Manchester (UoM), Manchester, United Kingdom
| | - Chris Boothman
- Department of Earth and Environmental Sciences, University of Manchester (UoM), Manchester, United Kingdom
| | - Nick Cole
- Sellafield Ltd., Warrington, United Kingdom
| | - Katherine Morris
- Department of Earth and Environmental Sciences, University of Manchester (UoM), Manchester, United Kingdom
| | - Jonathan R Lloyd
- Department of Earth and Environmental Sciences, University of Manchester (UoM), Manchester, United Kingdom
| |
Collapse
|
7
|
Effect of Alkaline Artificial Seawater Environment on the Corrosion Behaviour of Duplex Stainless Steel 2205. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10155043] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Sulphate reducing bacteria (SRB) can be found in alkaline environments. Due to their metabolite products such as hydrogen sulphide, the corrosion behaviour of materials in alkaline environments may be affected by the presence of SRB. This study focuses on the investigation of corrosion behaviour of duplex stainless steel DSS 2205 in nutrient rich artificial seawater containing SRB species, Desulfovibrio vulgaris, at different alkaline conditions with pH range from 7 to 10. The open circuit potential value (OCP), sulphide level and pH were recorded daily. Confocal laser scanning microscopy (CLSM) was used to study the adhesion of SRB on the DSS 2205 surface. Electrochemical impedance spectroscopy (EIS) was used to study the properties of the biofilm. Potentiodynamic polarization was used to study the corrosion behaviour of material. Inductively coupled plasma mass was used to measure the concentration of cations Fe, Ni, Mo, Mn in the experimental solution after 28 days. Scanning electron microscopy (SEM) and energy dispersive X-ray spectroscopy (EDS) were used for surface analysis. The results showed that D. vulgaris are active in an alkaline environment with pH 7–9. However, at pH 10, D. vulgaris activity exhibited an 8-day lag. The corrosion rate of DSS 2205 at pH 9 was higher than at other pH environments due to a higher dissolved concentration of hydrogen sulphide.
Collapse
|
8
|
Lopes BC, Machado EC, Rodrigues HF, Leal CD, Araújo JCD, Teixeira de Matos A. Effect of alkaline treatment on pathogens, bacterial community and antibiotic resistance genes in different sewage sludges for potential agriculture use. ENVIRONMENTAL TECHNOLOGY 2020; 41:529-538. [PMID: 30051768 DOI: 10.1080/09593330.2018.1505960] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 07/22/2018] [Indexed: 06/08/2023]
Abstract
Alkaline treatment is widely used to reduce pathogens in sewage sludge in developing countries and guarantee that it is safe for use in agriculture. The aim of this study was to investigate the effect of alkaline treatment applied to waste-activated (WAS) and Upflow Anaerobic Sludge Blanket (UASB)-sludge on the bacterial community, pathogens (viable helminths eggs and Salmonella spp), and antibiotic resistance genes (ARG). The bacterial community structure was examined through denaturing gel gradient electrophoresis (DGGE), targeting 16S rRNA genes. Polymerase chain reaction (PCR) was applied to evaluate the presence of several ARGs. The conducted alkaline experiment consisted of adding hydrated lime (Ca(OH)2) to sewage sludges. Samples were taken before and after 2, 24, 48, and 72 hours of treatment. Alkaline treatment changed considerably the bacterial community structure and after 24 hours, shifts in bacterial profiles were more pronounced in the UASB sludge sample than in WAS. Some bacteria remained under extreme pH conditions (pH > 12), such as Azospira oryzae and Dechloromonas denitrificans in the WAS samples, and Geothrix and Geobacter in the UASB sludge samples. The values of pathogens and indicators in the sludge after 24 hours of alkaline treatment meet sanitary law regulations and thus the sludges could have the potential to agricultural distribution. It is important to highlight that ARG, which are not currently present in sanitary regulations, were detected in the sludge samples after the alkaline treatment, which could be a concern for human health.
Collapse
Affiliation(s)
- Bruna Coelho Lopes
- Department of Sanitary and Environmental Engineering, Faculty of Engineering, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Elayne Cristina Machado
- Department of Sanitary and Environmental Engineering, Faculty of Engineering, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Hortência Franco Rodrigues
- Department of Sanitary and Environmental Engineering, Faculty of Engineering, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Cintia Dutra Leal
- Department of Sanitary and Environmental Engineering, Faculty of Engineering, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Juliana Calábria de Araújo
- Department of Sanitary and Environmental Engineering, Faculty of Engineering, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Antonio Teixeira de Matos
- Department of Sanitary and Environmental Engineering, Faculty of Engineering, Federal University of Minas Gerais, Belo Horizonte, Brazil
| |
Collapse
|
9
|
Baltic Sea methanogens compete with acetogens for electrons from metallic iron. ISME JOURNAL 2019; 13:3011-3023. [PMID: 31444483 PMCID: PMC6864099 DOI: 10.1038/s41396-019-0490-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 07/17/2019] [Accepted: 08/02/2019] [Indexed: 01/05/2023]
Abstract
Microbially induced corrosion of metallic iron (Fe0)-containing structures is an environmental and economic hazard. Methanogens are abundant in low-sulfide environments and yet their specific role in Fe0 corrosion is poorly understood. In this study, Sporomusa and Methanosarcina dominated enrichments from Baltic Sea methanogenic sediments that were established with Fe0 as the sole electron donor and CO2 as the electron acceptor. The Baltic-Sporomusa was phylogenetically affiliated to the electroactive acetogen S. silvacetica. Baltic-Sporomusa adjusted rapidly to growth on H2. On Fe0, spent filtrate enhanced growth of this acetogen suggesting that it was using endogenous enzymes to retrieve electrons and produce acetate. Previous studies have proposed that acetate produced by acetogens can feed commensal acetoclastic methanogens such as Methanosarcina. However, Baltic-methanogens could not generate methane from acetate, plus the decrease or absence of acetogens stimulated their growth. The decrease in numbers of Sporomusa was concurrent with an upsurge in Methanosarcina and increased methane production, suggesting that methanogens compete with acetogens for electrons from Fe0. Furthermore, Baltic-methanogens were unable to use H2 (1.5 atm) for methanogenesis and were inhibited by spent filtrate additions, indicating that enzymatically produced H2 is not a favorable electron donor. We hypothesize that Baltic-methanogens retrieve electrons from Fe0 via a yet enigmatic direct electron uptake mechanism.
Collapse
|
10
|
Ding W, Zhang W, Wang R, Sun Y, Pei B, Gao Z, Qian PY. Distribution, diversity and functional dissociation of the mac genes in marine biofilms. BIOFOULING 2019; 35:230-243. [PMID: 30950294 DOI: 10.1080/08927014.2019.1593384] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Bacteria produce metamorphosis-associated contractile (MAC) structures to induce larval metamorphosis in Hydroides elegans. The distribution and diversity of mac gene homologs in marine environments are largely unexplored. In the present study mac genes were examined in marine environments by analyzing 101 biofilm and 91 seawater metagenomes. There were more mac genes in biofilms than in seawater, and substratum type, location, or sampling time did not affect the mac genes in biofilms. The mac gene clusters were highly diverse and often incomplete while the three MAC components co-occurred with other genes of different functions. Genomic analysis of four Pseudoalteromonas and two Streptomyces strains revealed the mac genes transfers among different microbial taxa. It is proposed that mac genes are more specific to biofilms; gene transfer among different microbial taxa has led to highly diverse mac gene clusters; and in most cases, the three MAC components function individually rather than forming a complex.
Collapse
Affiliation(s)
- Wei Ding
- a Department of Ocean Science and Division of Life Science , Hong Kong University of Science and Technology , Hong Kong , PR China
| | - Weipeng Zhang
- a Department of Ocean Science and Division of Life Science , Hong Kong University of Science and Technology , Hong Kong , PR China
| | - Ruojun Wang
- a Department of Ocean Science and Division of Life Science , Hong Kong University of Science and Technology , Hong Kong , PR China
| | - Yanan Sun
- a Department of Ocean Science and Division of Life Science , Hong Kong University of Science and Technology , Hong Kong , PR China
| | - Bite Pei
- a Department of Ocean Science and Division of Life Science , Hong Kong University of Science and Technology , Hong Kong , PR China
| | - Zhaoming Gao
- b Sanya Institute of Deep-sea Science and Engineering , Chinese Academy of Sciences , Hainan , PR China
| | - Pei-Yuan Qian
- a Department of Ocean Science and Division of Life Science , Hong Kong University of Science and Technology , Hong Kong , PR China
| |
Collapse
|
11
|
Bomberg M, Raulio M, Jylhä S, Mueller CW, Höschen C, Rajala P, Purkamo L, Kietäväinen R, Ahonen L, Itävaara M. CO 2 and carbonate as substrate for the activation of the microbial community in 180 m deep bedrock fracture fluid of Outokumpu Deep Drill Hole, Finland. AIMS Microbiol 2017; 3:846-871. [PMID: 31294193 PMCID: PMC6604968 DOI: 10.3934/microbiol.2017.4.846] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 10/17/2017] [Indexed: 01/22/2023] Open
Abstract
Microbial communities in deep subsurface environments comprise a large portion of Earth's biomass, but the metabolic activities in these habitats are largely unknown. Here the effect of CO2 and carbonate on the microbial community of an isolated groundwater fracture zone at 180 m depth of the Outokumpu Deep Scientific Drill Hole (Finland) was tested. Outokumpu groundwater at 180 m depth contains approximately 0.45 L L−1 dissolved gas of which methane contributes 76%. CO2, on the other hand, is scarce. The number of microbial cells with intracellular activity in the groundwater was low when examined with redox staining. Fluorescence Assisted Cell Sorting (FACS) analyses indicated that only 1% of the microbial community stained active with the redox sensing dye in the untreated groundwater after 4 weeks of starvation. However, carbon substrate and sulfate addition increased the abundance of fluorescent cells up to 7%. CO2 and CO2 + sulfate activated the greatest number of microbes, especially increasing the abundance of Pseudomonas sp., which otherwise was present at only low abundance in Outokumpu. Over longer exposure time (2 months) up to 50% of the bacterial cells in the groundwater were shown to incorporate inorganic carbon from carbonate into biomass. Carbon recapture is an important feature in this ecosystem since it may decrease the rate of carbon loss in form of CO2 released from cellular processes.
Collapse
Affiliation(s)
- Malin Bomberg
- VTT Technical Research Centre of Finland, P.O. Box 1000, FIN-02044 VTT, Finland
| | - Mari Raulio
- VTT Technical Research Centre of Finland, P.O. Box 1000, FIN-02044 VTT, Finland.,Tikkurila Oyj, P.O. Box 53, Kuninkaalantie 1, FI-01301 Vantaa, Finland
| | - Sirpa Jylhä
- VTT Technical Research Centre of Finland, P.O. Box 1000, FIN-02044 VTT, Finland
| | - Carsten W Mueller
- Lehrstuhl für Bodenkunde, Department Ecology and Ecosystem Management, Center of Life and Food Sciences Weihenstephan, Technische Universität München, D-85350, Freising-Weihenstephan, Germany
| | - Carmen Höschen
- Lehrstuhl für Bodenkunde, Department Ecology and Ecosystem Management, Center of Life and Food Sciences Weihenstephan, Technische Universität München, D-85350, Freising-Weihenstephan, Germany
| | - Pauliina Rajala
- VTT Technical Research Centre of Finland, P.O. Box 1000, FIN-02044 VTT, Finland
| | - Lotta Purkamo
- VTT Technical Research Centre of Finland, P.O. Box 1000, FIN-02044 VTT, Finland
| | | | - Lasse Ahonen
- Geological Survey of Finland (GTK), P.O. Box 96, 02151 Espoo, Finland
| | - Merja Itävaara
- VTT Technical Research Centre of Finland, P.O. Box 1000, FIN-02044 VTT, Finland
| |
Collapse
|
12
|
Bomberg M, Mäkinen J, Salo M, Arnold M. Microbial Community Structure and Functions in Ethanol-Fed Sulfate Removal Bioreactors for Treatment of Mine Water. Microorganisms 2017; 5:microorganisms5030061. [PMID: 28930182 PMCID: PMC5620652 DOI: 10.3390/microorganisms5030061] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 09/14/2017] [Accepted: 09/19/2017] [Indexed: 01/16/2023] Open
Abstract
Sulfate-rich mine water must be treated before it is released into natural water bodies. We tested ethanol as substrate in bioreactors designed for biological sulfate removal from mine water containing up to 9 g L−1 sulfate, using granular sludge from an industrial waste water treatment plant as inoculum. The pH, redox potential, and sulfate and sulfide concentrations were measured twice a week over a maximum of 171 days. The microbial communities in the bioreactors were characterized by qPCR and high throughput amplicon sequencing. The pH in the bioreactors fluctuated between 5.0 and 7.7 with the highest amount of up to 50% sulfate removed measured around pH 6. Dissimilatory sulfate reducing bacteria (SRB) constituted only between 1% and 15% of the bacterial communities. Predicted bacterial metagenomes indicated a high prevalence of assimilatory sulfate reduction proceeding to formation of l-cystein and acetate, assimilatory and dissimilatory nitrate reduction, denitrification, and oxidation of ethanol to acetaldehyde with further conversion to ethanolamine, but not to acetate. Despite efforts to maintain optimal conditions for biological sulfate reduction in the bioreactors, only a small part of the microorganisms were SRB. The microbial communities were highly diverse, containing bacteria, archaea, and fungi, all of which affected the overall microbial processes in the bioreactors. While it is important to monitor specific physicochemical parameters in bioreactors, molecular assessment of the microbial communities may serve as a tool to identify biological factors affecting bioreactor functions and to optimize physicochemical attributes for ideal bioreactor performance.
Collapse
Affiliation(s)
- Malin Bomberg
- VTT Technical Research Centre of Finland, P.O. Box 1000, FIN-02044 Espoo, Finland.
| | - Jarno Mäkinen
- VTT Technical Research Centre of Finland, P.O. Box 1000, FIN-02044 Espoo, Finland.
| | - Marja Salo
- VTT Technical Research Centre of Finland, P.O. Box 1000, FIN-02044 Espoo, Finland.
| | - Mona Arnold
- VTT Technical Research Centre of Finland, P.O. Box 1000, FIN-02044 Espoo, Finland.
| |
Collapse
|