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Bulka O, Webb J, Dworatzek S, Mahadevan R, Edwards EA. A Multifunctional Dehalobacter? Tandem Chloroform and Dichloromethane Degradation in a Mixed Microbial Culture. Environ Sci Technol 2023; 57:19912-19920. [PMID: 37962431 DOI: 10.1021/acs.est.3c06686] [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: 11/15/2023]
Abstract
Chloroform (CF) and dichloromethane (DCM) contaminate groundwater sites around the world but can be cleaned up through bioremediation. Although several strains of Dehalobacter restrictus can reduce CF to DCM and multiple Peptococcaceae can ferment DCM, these processes cannot typically happen simultaneously due to CF sensitivity in the known DCM-degraders or electron donor competition. Here, we present a mixed microbial culture that can simultaneously metabolize CF and DCM and create an additional enrichment culture fed only DCM. Through genus-specific quantitative polymerase chain reaction, we find that Dehalobacter grows while either CF alone or DCM alone is converted, indicating its involvement in both metabolic steps. Additionally, the culture was maintained for over 1400 days without the addition of an exogenous electron donor, and through electron balance calculations, we show that DCM metabolism would produce sufficient reducing equivalents (likely hydrogen) for CF respiration. Together, these results suggest intraspecies electron transfer could occur to continually reduce CF in the culture. Minimizing the addition of electron donor reduces the cost of bioremediation, and "self-feeding" could prolong bioremediation activity long after donor addition ends. Overall, understanding this mechanism informs strategies for culture maintenance and scale-up and benefits contaminated sites where the culture is employed for remediation worldwide.
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Affiliation(s)
- Olivia Bulka
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Jennifer Webb
- SiREM, 130 Stone Road West, Guelph, Ontario N1G 3Z2, Canada
| | | | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Elizabeth A Edwards
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
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Giannari D, Ho CH, Mahadevan R. A gap-filling algorithm for prediction of metabolic interactions in microbial communities. PLoS Comput Biol 2021; 17:e1009060. [PMID: 34723959 PMCID: PMC8584699 DOI: 10.1371/journal.pcbi.1009060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 11/11/2021] [Accepted: 10/05/2021] [Indexed: 11/24/2022] Open
Abstract
The study of microbial communities and their interactions has attracted the interest of the scientific community, because of their potential for applications in biotechnology, ecology and medicine. The complexity of interspecies interactions, which are key for the macroscopic behavior of microbial communities, cannot be studied easily experimentally. For this reason, the modeling of microbial communities has begun to leverage the knowledge of established constraint-based methods, which have long been used for studying and analyzing the microbial metabolism of individual species based on genome-scale metabolic reconstructions of microorganisms. A main problem of genome-scale metabolic reconstructions is that they usually contain metabolic gaps due to genome misannotations and unknown enzyme functions. This problem is traditionally solved by using gap-filling algorithms that add biochemical reactions from external databases to the metabolic reconstruction, in order to restore model growth. However, gap-filling algorithms could evolve by taking into account metabolic interactions among species that coexist in microbial communities. In this work, a gap-filling method that resolves metabolic gaps at the community level was developed. The efficacy of the algorithm was tested by analyzing its ability to resolve metabolic gaps on a synthetic community of auxotrophic Escherichia coli strains. Subsequently, the algorithm was applied to resolve metabolic gaps and predict metabolic interactions in a community of Bifidobacterium adolescentis and Faecalibacterium prausnitzii, two species present in the human gut microbiota, and in an experimentally studied community of Dehalobacter and Bacteroidales species of the ACT-3 community. The community gap-filling method can facilitate the improvement of metabolic models and the identification of metabolic interactions that are difficult to identify experimentally in microbial communities.
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Affiliation(s)
- Dafni Giannari
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | | | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
- The Institute of Biomaterials & Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
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3
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Chen G, Jiang N, Villalobos Solis MI, Kara Murdoch F, Murdoch RW, Xie Y, Swift CM, Hettich RL, Löffler FE. Anaerobic Microbial Metabolism of Dichloroacetate. mBio 2021; 12:e00537-21. [PMID: 33906923 PMCID: PMC8092247 DOI: 10.1128/mbio.00537-21] [Citation(s) in RCA: 6] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 03/17/2021] [Indexed: 12/23/2022] Open
Abstract
Dichloroacetate (DCA) commonly occurs in the environment due to natural production and anthropogenic releases, but its fate under anoxic conditions is uncertain. Mixed culture RM comprising "Candidatus Dichloromethanomonas elyunquensis" strain RM utilizes DCA as an energy source, and the transient formation of formate, H2, and carbon monoxide (CO) was observed during growth. Only about half of the DCA was recovered as acetate, suggesting a fermentative catabolic route rather than a reductive dechlorination pathway. Sequencing of 16S rRNA gene amplicons and 16S rRNA gene-targeted quantitative real-time PCR (qPCR) implicated "Candidatus Dichloromethanomonas elyunquensis" strain RM in DCA degradation. An (S)-2-haloacid dehalogenase (HAD) encoded on the genome of strain RM was heterologously expressed, and the purified HAD demonstrated the cofactor-independent stoichiometric conversion of DCA to glyoxylate at a rate of 90 ± 4.6 nkat mg-1 protein. Differential protein expression analysis identified enzymes catalyzing the conversion of DCA to acetyl coenzyme A (acetyl-CoA) via glyoxylate as well as enzymes of the Wood-Ljungdahl pathway. Glyoxylate carboligase, which catalyzes the condensation of two molecules of glyoxylate to form tartronate semialdehyde, was highly abundant in DCA-grown cells. The physiological, biochemical, and proteogenomic data demonstrate the involvement of an HAD and the Wood-Ljungdahl pathway in the anaerobic fermentation of DCA, which has implications for DCA turnover in natural and engineered environments, as well as the metabolism of the cancer drug DCA by gut microbiota.IMPORTANCE Dichloroacetate (DCA) is ubiquitous in the environment due to natural formation via biological and abiotic chlorination processes and the turnover of chlorinated organic materials (e.g., humic substances). Additional sources include DCA usage as a chemical feedstock and cancer drug and its unintentional formation during drinking water disinfection by chlorination. Despite the ubiquitous presence of DCA, its fate under anoxic conditions has remained obscure. We discovered an anaerobic bacterium capable of metabolizing DCA, identified the enzyme responsible for DCA dehalogenation, and elucidated a novel DCA fermentation pathway. The findings have implications for the turnover of DCA and the carbon and electron flow in electron acceptor-depleted environments and the human gastrointestinal tract.
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Affiliation(s)
- Gao Chen
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Nannan Jiang
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee, USA
- University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | | | - Fadime Kara Murdoch
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Robert Waller Murdoch
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
| | - Yongchao Xie
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Cynthia M Swift
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Robert L Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Frank E Löffler
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, USA
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Biosystems Engineering & Soil Science, University of Tennessee, Knoxville, Tennessee, USA
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee, USA
- Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, USA
- University of Tennessee and Oak Ridge National Laboratory (UT-ORNL) Joint Institute for Biological Sciences (JIBS), Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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Habe H, Sato Y, Aoyagi T, Inaba T, Hori T, Hamai T, Hayashi K, Kobayashi M, Sakata T, Sato N. Design, application, and microbiome of sulfate-reducing bioreactors for treatment of mining-influenced water. Appl Microbiol Biotechnol 2020; 104:6893-6903. [PMID: 32556398 DOI: 10.1007/s00253-020-10737-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/01/2020] [Accepted: 06/07/2020] [Indexed: 11/26/2022]
Abstract
Sulfate-reducing bioreactors, also called biochemical reactors, represent a promising option for passive treatment of mining-influenced water (MIW) based on similar technology to aerobic/anaerobic-constructed wetlands and vertical-flow wetlands. MIW from each mine site has a variety of site-specific properties related to its treatment; therefore, design factors, including the organic substrates and inorganic materials packed into the bioreactor, must be tested and evaluated before installation of full-scale sulfate-reducing bioreactors. Several full-scale sulfate-reducing bioreactors operating at mine sites provide examples, but holistic understanding of the complex treatment processes occurring inside the bioreactors is lacking. With the recent introduction of high-throughput DNA sequencing technologies, microbial processes within bioreactors may be clarified based on the relationships between operational parameters and key microorganisms identified using high-resolution microbiome data. In this review, the test design procedures and precedents of full-scale bioreactor application for MIW treatment are briefly summarized, and recent knowledge on the sulfate-reducing microbial communities of field-based bioreactors from fine-scale monitoring is presented.Key points• Sulfate-reducing bioreactors are promising for treatment of mining-influenced water.• Various design factors should be tested for application of full-scale bioreactors.• Introduction of several full-scale passive bioreactor systems at mine sites.• Desulfosporosinus spp. can be one of the key bacteria within field-based bioreactors.
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Affiliation(s)
- Hiroshi Habe
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki, 305-8569, Japan.
| | - Yuya Sato
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki, 305-8569, Japan
| | - Tomo Aoyagi
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki, 305-8569, Japan
| | - Tomohiro Inaba
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki, 305-8569, Japan
| | - Tomoyuki Hori
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki, 305-8569, Japan
| | - Takaya Hamai
- Japan Oil, Gas and Metals National Corporation (JOGMEC), 2-10-1 Toranomon, Minato-ku, Tokyo, 105-0001, Japan.
| | - Kentaro Hayashi
- JOGMEC Metals Technology Center, 9-3 Furudate, Kosakakozan, Kosaka, Akita, 017-0202, Japan
| | - Mikio Kobayashi
- Japan Oil, Gas and Metals National Corporation (JOGMEC), 2-10-1 Toranomon, Minato-ku, Tokyo, 105-0001, Japan
| | - Takeshi Sakata
- JOGMEC Metals Technology Center, 9-3 Furudate, Kosakakozan, Kosaka, Akita, 017-0202, Japan
| | - Naoki Sato
- Japan Oil, Gas and Metals National Corporation (JOGMEC), 2-10-1 Toranomon, Minato-ku, Tokyo, 105-0001, Japan
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Siddique T, Semple K, Li C, Foght JM. Methanogenic biodegradation of iso-alkanes and cycloalkanes during long-term incubation with oil sands tailings. Environ Pollut 2020; 258:113768. [PMID: 31864926 DOI: 10.1016/j.envpol.2019.113768] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 06/28/2019] [Revised: 12/07/2019] [Accepted: 12/07/2019] [Indexed: 06/10/2023]
Abstract
Microbes indigenous to oil sands tailings ponds methanogenically biodegrade certain hydrocarbons, including n-alkanes and monoaromatics, whereas other hydrocarbons such as iso- and cycloalkanes are more recalcitrant. We tested the susceptibility of iso- and cycloalkanes to methanogenic biodegradation by incubating them with mature fine tailings (MFT) collected from two depths (6 and 31 m below surface) of a tailings pond, representing different lengths of exposure to hydrocarbons. A mixture of five iso-alkanes and three cycloalkanes was incubated with MFT for 1700 d. Iso-alkanes were completely biodegraded in the order 3-methylhexane > 4-methylheptane > 2-methyloctane > 2-methylheptane, whereas 3-ethylhexane and ethylcyclopentane were only partially depleted and methylcyclohexane and ethylcyclohexane were not degraded during incubation. Pyrosequencing of 16S rRNA genes showed enrichment of Peptococcaceae (Desulfotomaculum) and Smithella in amended cultures with acetoclastic (Methanosaeta) and hydrogenotrophic methanogens (Methanoregula and Methanoculleus). Bioaugmentation of MFT by inoculation with MFT-derived enrichment cultures reduced the lag phase before onset of iso-alkane and cycloalkane degradation. However, the same enrichment culture incubated without MFT exhibited slower biodegradation kinetics and less CH4 production, implying that the MFT solid phase (clay minerals) enhanced methanogenesis. These results help explain and predict continued emissions of CH4 from oil sands tailings repositories in situ.
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Affiliation(s)
- Tariq Siddique
- Department of Renewable Resources, University of Alberta, Edmonton, AB T6G 2G7, Canada.
| | - Kathleen Semple
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Carmen Li
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Julia M Foght
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
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6
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Němeček J, Nechanická M, Špánek R, Eichler F, Zeman J, Černík M. Engineered in situ biogeochemical transformation as a secondary treatment following ISCO - A field test. Chemosphere 2019; 237:124460. [PMID: 31374391 DOI: 10.1016/j.chemosphere.2019.124460] [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: 02/14/2019] [Revised: 06/13/2019] [Accepted: 07/25/2019] [Indexed: 06/10/2023]
Abstract
ISCO using activated sodium persulphate is a widely used technology for treating chlorinated solvent source zones. In sensitive areas, however, high groundwater sulphate concentrations following treatment may be a drawback. In situ biogeochemical transformation, a technology that degrades contaminants via reduced iron minerals formed by microbial activity, offers a potential solution for such sites, the bioreduction of sulphate and production of iron sulphides that abiotically degrade chlorinated ethenes acting as a secondary technology following ISCO. This study assesses this approach in the field using hydrochemical and molecular tools, solid phase analysis and geochemical modelling. Following a neutralisation and bioaugmentation, favourable conditions for iron- and sulphate-reducers were created, resulting in a remarkable increase in their relative abundance. The abundance of dechlorinating bacteria (Dehalococcoides mccartyi, Dehalobacter sp. and Desulfitobacterium spp.) remained low throughout this process. The activity of iron- and sulphate-reducers was further stimulated through application of magnetite plus starch and microiron plus starch, resulting in an increase in ferrous iron concentration (from <LOQ to 337 mg/l), a decrease in sulphate concentration by 74-95% and production of hydrogen sulphide (from <LOQ to 25.9 mg/l). At the same time, a gradual revival of dechlorinators and an increase in ethene concentration was also observed. Tetrachloroethene and trichloroethene concentrations decreased by 98.5-99.98% and 75.4-98.5%, respectively. A decline in chlorine number indicated that biological dechlorination contributed to CVOC removal. This study brings new insights into biogeochemical processes that, when properly engineered, could provide a viable solution for secondary treatment.
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Affiliation(s)
- Jan Němeček
- ENACON s.r.o., Krčská 16, 140 00, Prague 4, Czech Republic; Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic.
| | - Magda Nechanická
- Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic
| | - Roman Špánek
- Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic
| | - František Eichler
- Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic
| | - Josef Zeman
- Masaryk University, Žerotínovo nám. 617/9, 601 77, Brno, Czech Republic
| | - Miroslav Černík
- Technical University of Liberec, Studentská 2, 461 17, Liberec, Czech Republic
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Laskar M, Awata T, Kasai T, Katayama A. Anaerobic Dechlorination by a Humin-Dependent Pentachlorophenol-Dechlorinating Consortium under Autotrophic Conditions Induced by Homoacetogenesis. Int J Environ Res Public Health 2019; 16:E2873. [PMID: 31405258 PMCID: PMC6720667 DOI: 10.3390/ijerph16162873] [Citation(s) in RCA: 12] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 08/03/2019] [Accepted: 08/09/2019] [Indexed: 11/16/2022]
Abstract
Anoxic aquifers suffer from energy limitations due to the unavailability of organic substrates, as dictated by hydrogen (H2) for various electron-accepting processes. This deficiency often results in the accumulation of persistent organic pollutants, where bioremediation using organic compounds often leads to secondary contamination. This study involves the reductive dechlorination of pentachlorophenol (PCP) by dechlorinators that do not use H2 directly, but rather through a reduced state of humin-a solid-phase humic substance-as the extracellular electron donor, which requires an organic donor such as formate, lactate, etc. This shortcoming was addressed by the development of an anaerobic mixed culture that was capable of reductively dechlorinating PCP using humin under autotrophic conditions induced by homoacetogenesis. Here, H2 was used for carbon-dioxide fixation to acetate; the acetate produced was used for the reduction of humin; and consequently used for dechlorination through reduced humin. The 16SrRNA gene sequencing analysis showed Dehalobacter and Dehalobacterium as the possible dechlorinators, while Clostridium and Oxobacter were identified as the homoacetogens. Thus, this work contributes to the development of an anaerobic consortium that balanced H2 dependency, where efficiency of humin reduction extends the applicability of anaerobic microbial remediation in aquifers through autotrophy, syntrophy, and reductive dechlorination.
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Affiliation(s)
- Mahasweta Laskar
- Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - Takanori Awata
- National Institute for Land and Infrastructure Management, Tsukuba 305-0804, Japan
| | - Takuya Kasai
- Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
- Institute of Materials and Systems for Sustainability, Nagoya University, Nagoya 464-8603, Japan
| | - Arata Katayama
- Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan.
- Institute of Materials and Systems for Sustainability, Nagoya University, Nagoya 464-8603, Japan.
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Fukuyama Y, Omae K, Yoshida T, Sako Y. Transcriptome analysis of a thermophilic and hydrogenogenic carboxydotroph Carboxydothermus pertinax. Extremophiles 2019; 23:389-398. [PMID: 30941583 PMCID: PMC6557876 DOI: 10.1007/s00792-019-01091-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 03/21/2019] [Indexed: 12/16/2022]
Abstract
A thermophilic and hydrogenogenic carboxydotroph, Carboxydothermus pertinax, performs hydrogenogenic CO metabolism in which CODH-II couples with distally encoded ECH. To enhance our knowledge of its hydrogenogenic CO metabolism, we performed whole transcriptome analysis of C. pertinax grown under 100% CO or 100% N2 using RNA sequencing. Of the 2577 genes, 36 and 64 genes were differentially expressed genes (DEGs) with false discovery rate adjusted P value < 0.05 when grown under 100% CO or 100% N2, respectively. Most of the DEGs were components of 23 gene clusters, suggesting switch between metabolisms via intensive expression changes in a relatively low number of gene clusters. Of the 9 significantly expressed gene clusters under 100% CO, CODH-II and ECH gene clusters were found. Only the ECH gene cluster was regulated by the CO-responsive transcriptional factor CooA, suggesting that others were separately regulated in the same transcriptional cascade as the ECH gene cluster. Of the 14 significantly expressed gene clusters under 100% N2, ferrous iron transport gene cluster involved in anaerobic respiration and prophage region were found. Considering that the expression of the temperate phage was strictly repressed under 100% CO, hydrogenogenic CO metabolism might be stable for C. pertinax.
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Affiliation(s)
- Yuto Fukuyama
- Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Kimiho Omae
- Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Takashi Yoshida
- Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Yoshihiko Sako
- Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan.
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Narihiro T, Nobu MK, Bocher BTW, Mei R, Liu WT. Co-occurrence network analysis reveals thermodynamics-driven microbial interactions in methanogenic bioreactors. Environ Microbiol Rep 2018; 10:673-685. [PMID: 30136425 DOI: 10.1111/1758-2229.12689] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 08/13/2018] [Accepted: 08/15/2018] [Indexed: 06/08/2023]
Abstract
Methanogenic bioreactors have been applied to treat purified terephthalic acid (PTA) wastewater containing complex aromatic compounds, such as terephthalic acid, para-toluic acid and benzoic acid. This study characterized the interaction of microbial populations in 42 samples obtained from 10 PTA-degrading methanogenic bioreactors. Approximately, 54 dominant populations (11 methanogens, 8 syntrophs and 35 functionally unknown clades) that represented 73.9% of total 16S rRNA gene iTag sequence reads were identified. Co-occurrence analysis based on the abundance of dominant OTUs showed two non-overlapping networks centred around aromatic compound- (group AR: Syntrophorhabdaceae, Syntrophus and Pelotomaculum) and fatty acid- (group FA: Smithella and Syntrophobacter) degrading syntrophs. Group AR syntrophs have no direct correlation with hydrogenotrophic methanogens, while those from group FA do. As degradation of aromatic compounds has a wider thermodynamic window than fatty acids, Group AR syntrophs may be less influenced by fluctuations in hydrogenotrophic methanogen abundance or may non-specifically interact with diverse methanogens. In both groups, network analysis reveals full-scale- and lab-scale-specific uncultivated taxa that may mediate interactions between syntrophs and methanogens, suggesting that those uncultivated taxa may support the degradation of aromatic compounds through uncharted ecophysiological traits. These observations suggest that organisms from multiple niches orchestrate their metabolic capacity in multiple interaction networks to effectively degrade PTA wastewater.
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Affiliation(s)
- Takashi Narihiro
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, 305-8566, Japan
| | - Masaru K Nobu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Ben T W Bocher
- Petrochemicals Technology, BP America, Naperville, IL, 60563, USA
| | - Ran Mei
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Wen-Tso Liu
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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Vargas-Rodriguez O, Englert M, Merkuryev A, Mukai T, Söll D. Recoding of the selenocysteine UGA codon by cysteine in the presence of a non-canonical tRNA Cys and elongation factor SelB. RNA Biol 2018; 15:471-479. [PMID: 29879865 PMCID: PMC6103700 DOI: 10.1080/15476286.2018.1474074] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 06/01/2018] [Accepted: 05/01/2018] [Indexed: 12/12/2022] Open
Abstract
In many organisms, the UGA stop codon is recoded to insert selenocysteine (Sec) into proteins. Sec incorporation in bacteria is directed by an mRNA element, known as the Sec-insertion sequence (SECIS), located downstream of the Sec codon. Unlike other aminoacyl-tRNAs, Sec-tRNASec is delivered to the ribosome by a dedicated elongation factor, SelB. We recently identified a series of tRNASec-like tRNA genes distributed across Bacteria that also encode a canonical tRNASec. These tRNAs contain sequence elements generally recognized by cysteinyl-tRNA synthetase (CysRS). While some of these tRNAs contain a UCA Sec anticodon, most have a GCA Cys anticodon. tRNASec with GCA anticodons are known to recode UGA codons. Here we investigate the clostridial Desulfotomaculum nigrificans tRNASec-like tRNACys, and show that this tRNA is acylated by CysRS, recognized by SelB, and capable of UGA recoding with Cys in Escherichia coli. We named this non-canonical group of tRNACys as 'tRNAReC' (Recoding with Cys). We performed a comprehensive survey of tRNAReC genes to establish their phylogenetic distribution, and found that, in a particular lineage of clostridial Pelotomaculum, the Cys identity elements of tRNAReC had mutated. This novel tRNA, which contains a UCA anticodon, is capable of Sec incorporation in E. coli, albeit with lower efficiency relative to Pelotomaculum tRNASec. We renamed this unusual tRNASec derived from tRNAReC as 'tRNAReU' (Recoding with Sec). Together, our results suggest that tRNAReC and tRNAReU may serve as safeguards in the production of selenoproteins and - to our knowledge - they provide the first example of programmed codon-anticodon mispairing in bacteria.
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Affiliation(s)
- Oscar Vargas-Rodriguez
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Markus Englert
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Anna Merkuryev
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Takahito Mukai
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Dieter Söll
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Department of Chemistry, Yale University, New Haven, CT, USA
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11
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Keller AH, Kleinsteuber S, Vogt C. Anaerobic Benzene Mineralization by Nitrate-Reducing and Sulfate-Reducing Microbial Consortia Enriched From the Same Site: Comparison of Community Composition and Degradation Characteristics. Microb Ecol 2018; 75:941-953. [PMID: 29124312 DOI: 10.1007/s00248-017-1100-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [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: 04/13/2017] [Accepted: 10/26/2017] [Indexed: 05/22/2023]
Abstract
Benzene mineralization under nitrate-reducing conditions was successfully established in an on-site reactor continuously fed with nitrate and sulfidic, benzene-containing groundwater extracted from a contaminated aquifer. Filling material from the reactor columns was used to set up anoxic enrichment cultures in mineral medium with benzene as electron donor and sole organic carbon source and nitrate as electron acceptor. Benzene degradation characteristics and community composition under nitrate-reducing conditions were monitored and compared to those of a well-investigated benzene-mineralizing consortium enriched from the same column system under sulfate-reducing conditions. The nitrate-reducing cultures degraded benzene at a rate of 10.1 ± 1.7 μM d-1, accompanied by simultaneous reduction of nitrate to nitrite. The previously studied sulfate-reducing culture degraded benzene at similar rates. Carbon and hydrogen stable isotope enrichment factors determined for nitrate-dependent benzene degradation differed significantly from those of the sulfate-reducing culture (ΛH/C nitrate = 12 ± 3 compared to ΛH/C sulfate = 28 ± 3), indicating different benzene activation mechanisms under the two conditions. The nitrate-reducing community was mainly composed of Betaproteobacteria, Ignavibacteria, and Anaerolineae. Azoarcus and a phylotype related to clone Dok59 (Rhodocyclaceae) were the dominant genera, indicating an involvement in nitrate-dependent benzene degradation. The primary benzene degrader of the sulfate-reducing consortium, a phylotype belonging to the Peptococcaceae, was absent in the nitrate-reducing consortium.
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Affiliation(s)
- Andreas H Keller
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318, Leipzig, Germany
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318, Leipzig, Germany
| | - Sabine Kleinsteuber
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318, Leipzig, Germany
| | - Carsten Vogt
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstraße 15, 04318, Leipzig, Germany.
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12
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van der Waals MJ, Atashgahi S, da Rocha UN, van der Zaan BM, Smidt H, Gerritse J. Benzene degradation in a denitrifying biofilm reactor: activity and microbial community composition. Appl Microbiol Biotechnol 2017; 101:5175-5188. [PMID: 28321487 PMCID: PMC5486827 DOI: 10.1007/s00253-017-8214-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 02/27/2017] [Accepted: 03/04/2017] [Indexed: 11/26/2022]
Abstract
Benzene is an aromatic compound and harmful for the environment. Biodegradation of benzene can reduce the toxicological risk after accidental or controlled release of this chemical in the environment. In this study, we further characterized an anaerobic continuous biofilm culture grown for more than 14 years on benzene with nitrate as electron acceptor. We determined steady state degradation rates, microbial community composition dynamics in the biofilm, and the initial anaerobic benzene degradation reactions. Benzene was degraded at a rate of 0.15 μmol/mg protein/day and a first-order rate constant of 3.04/day which was fourfold higher than rates reported previously. Bacteria belonging to the Peptococcaceae were found to play an important role in this anaerobic benzene-degrading biofilm culture, but also members of the Anaerolineaceae were predicted to be involved in benzene degradation or benzene metabolite degradation based on Illumina MiSeq analysis of 16S ribosomal RNA genes. Biomass retention in the reactor using a filtration finger resulted in reduction of benzene degradation capacity. Detection of the benzene carboxylase encoding gene, abcA, and benzoic acid in the culture vessel indicated that benzene degradation proceeds through an initial carboxylation step.
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Affiliation(s)
- Marcelle J van der Waals
- Deltares, Subsurface and Groundwater Systems, Princetonlaan 6, 3584 CB, Utrecht, The Netherlands.
- Wageningen University & Research, Laboratory of Microbiology, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
| | - Siavash Atashgahi
- Wageningen University & Research, Laboratory of Microbiology, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Ulisses Nunes da Rocha
- VU University of Amsterdam, Department of Molecular Cell Physiology, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - Bas M van der Zaan
- Deltares, Subsurface and Groundwater Systems, Princetonlaan 6, 3584 CB, Utrecht, The Netherlands
| | - Hauke Smidt
- Wageningen University & Research, Laboratory of Microbiology, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Jan Gerritse
- Deltares, Subsurface and Groundwater Systems, Princetonlaan 6, 3584 CB, Utrecht, The Netherlands
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13
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Ranchou‐Peyruse M, Gasc C, Guignard M, Aüllo T, Dequidt D, Peyret P, Ranchou‐Peyruse A. The sequence capture by hybridization: a new approach for revealing the potential of mono-aromatic hydrocarbons bioattenuation in a deep oligotrophic aquifer. Microb Biotechnol 2017; 10:469-479. [PMID: 27766749 PMCID: PMC5328808 DOI: 10.1111/1751-7915.12426] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 09/15/2016] [Accepted: 09/18/2016] [Indexed: 01/04/2023] Open
Abstract
The formation water of a deep aquifer (853 m of depth) used for geological storage of natural gas was sampled to assess the mono-aromatic hydrocarbons attenuation potential of the indigenous microbiota. The study of bacterial diversity suggests that Firmicutes and, in particular, sulphate-reducing bacteria (Peptococcaceae) predominate in this microbial community. The capacity of the microbial community to biodegrade toluene and m- and p-xylenes was demonstrated using a culture-based approach after several hundred days of incubation. In order to reveal the potential for biodegradation of these compounds within a shorter time frame, an innovative approach named the solution hybrid selection method, which combines sequence capture by hybridization and next-generation sequencing, was applied to the same original water sample. The bssA and bssA-like genes were investigated as they are considered good biomarkers for the potential of toluene and xylene biodegradation. Unlike a PCR approach which failed to detect these genes directly from formation water, this innovative strategy demonstrated the presence of the bssA and bssA-like genes in this oligotrophic ecosystem, probably harboured by Peptococcaceae. The sequence capture by hybridization shows significant potential to reveal the presence of genes of functional interest which have low-level representation in the biosphere.
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Affiliation(s)
- Magali Ranchou‐Peyruse
- Université de Pau et des Pays de l'AdourEquipe Environnement et Microbiologie, IPREM‐CNRS 5254F‐64013PauFrance
| | - Cyrielle Gasc
- Université d'AuvergneEA 4678 CIDAM63001Clermont‐FerrandFrance
| | - Marion Guignard
- Université de Pau et des Pays de l'AdourEquipe Environnement et Microbiologie, IPREM‐CNRS 5254F‐64013PauFrance
| | - Thomas Aüllo
- TIGF – Transport et Infrastructures Gaz France40 Avenue de l'Europe, CS2052264000PauFrance
| | - David Dequidt
- STORENGY – Geosciences DepartmentBois‐ColombesFrance
| | - Pierre Peyret
- Université d'AuvergneEA 4678 CIDAM63001Clermont‐FerrandFrance
| | - Anthony Ranchou‐Peyruse
- Université de Pau et des Pays de l'AdourEquipe Environnement et Microbiologie, IPREM‐CNRS 5254F‐64013PauFrance
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14
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Trueba-Santiso A, Parladé E, Rosell M, Lliros M, Mortan SH, Martínez-Alonso M, Gaju N, Martín-González L, Vicent T, Marco-Urrea E. Molecular and carbon isotopic characterization of an anaerobic stable enrichment culture containing Dehalobacterium sp. during dichloromethane fermentation. Sci Total Environ 2017; 581-582:640-648. [PMID: 28063652 DOI: 10.1016/j.scitotenv.2016.12.174] [Citation(s) in RCA: 9] [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: 11/03/2016] [Revised: 12/27/2016] [Accepted: 12/28/2016] [Indexed: 06/06/2023]
Abstract
UNLABELLED Biodegradation of dichloromethane (DCM) under reducing conditions is of major concern due to its widespread detection in contaminated groundwaters. Here, we report an anaerobic enrichment culture derived from a membrane bioreactor operating in an industrial wastewater treatment plant, capable of fermenting DCM and the brominated analogue dibromomethane (DBM). Comparative analysis of bacterial 16S rDNA-DGGE profiles from fresh liquid medium inoculated with single colonies picked from serial dilution-to-extinction agar vials showed that cultures degrading DCM contained a predominant band belonging to Dehalobacterium, however this band was absent in cultures unable to degrade DCM. Analysis of the microbial composition of the enrichment by bacterial 16S rRNA gene amplicon paired-end sequencing confirmed the presence of Dehalobacterium together with three additional phylotypes belonging to Acetobacterium, Desulfovibrio, and Wolinella, representing all four operational taxonomic units >99.9% of the retrieved sequences. The carbon isotopic fractionation (ε) determined for DCM degradation in this culture was -27±2‰. This value differs from the ε previously reported for the DCM-fermentative bacteria Dehalobacter (-15.5±1.5‰) but they are both significantly different from those reported for facultative methylotrophic organisms (ranging from -45 to -61‰). This significant difference in the ε allows differentiating between hydrolytic transformation of DCM via glutathione-dependent dehalogenases and fermentation pathway. CAPSULE The carbon isotopic fractionation of dichloromethane by an enriched Dehalobacterium-containing culture has significant potential to monitor biodegradation of DCM in groundwaters.
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Affiliation(s)
- Alba Trueba-Santiso
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Carrer de les Sitges s/n, 08193 Bellaterra, Spain
| | - Eloi Parladé
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Mònica Rosell
- Grup de Mineralogia Aplicada i Geoquímica de Fluids, Departament de Mineralogia, Petrologia i Geologia Aplicada, Facultat de Ciències de la Terra, Universitat de Barcelona (UB), Martí Franquès s/n, 08028 Barcelona, Spain
| | - Marc Lliros
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Siti Hatijah Mortan
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Carrer de les Sitges s/n, 08193 Bellaterra, Spain
| | - Maira Martínez-Alonso
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Nuria Gaju
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Lucía Martín-González
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Carrer de les Sitges s/n, 08193 Bellaterra, Spain
| | - Teresa Vicent
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Carrer de les Sitges s/n, 08193 Bellaterra, Spain
| | - Ernest Marco-Urrea
- Departament d'Enginyeria Química, Biològica i Ambiental, Universitat Autònoma de Barcelona (UAB), Carrer de les Sitges s/n, 08193 Bellaterra, Spain.
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15
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Lu Y, Ramiro-Garcia J, Vandermeeren P, Herrmann S, Cichocka D, Springael D, Atashgahi S, Smidt H. Dechlorination of three tetrachlorobenzene isomers by contaminated harbor sludge-derived enrichment cultures follows thermodynamically favorable reactions. Appl Microbiol Biotechnol 2017; 101:2589-2601. [PMID: 27909745 PMCID: PMC5320011 DOI: 10.1007/s00253-016-8004-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 11/09/2016] [Accepted: 11/11/2016] [Indexed: 01/27/2023]
Abstract
Dechlorination patterns of three tetrachlorobenzene isomers, 1,2,3,4-, 1,2,3,5-, and 1,2,4,5-TeCB, were studied in anoxic microcosms derived from contaminated harbor sludge. The removal of doubly, singly, and un-flanked chlorine atoms was noted in 1,2,3,4- and 1,2,3,5-TeCB fed microcosms, whereas only singly flanked chlorine was removed in 1,2,4,5-TeCB microcosms. The thermodynamically more favorable reactions were selectively followed by the enriched cultures with di- and/or mono-chlorobenzene as the main end products of the reductive dechlorination of all three isomers. Based on quantitative PCR analysis targeting 16S rRNA genes of known organohalide-respiring bacteria, the growth of Dehalococcoides was found to be associated with the reductive dechlorination of all three isomers, while growth of Dehalobacter, another known TeCB dechlorinator, was only observed in one 1,2,3,5-TeCB enriched microcosm among biological triplicates. Numbers of Desulfitobacterium and Geobacter as facultative dechlorinators were rather stable suggesting that they were not (directly) involved in the observed TeCB dechlorination. Bacterial community profiling suggested bacteria belonging to the phylum Bacteroidetes and the order Clostridiales as well as sulfate-reducing members of the class Deltaproteobacteria as putative stimulating guilds that provide electron donor and/or organic cofactors to fastidious dechlorinators. Our results provide a better understanding of thermodynamically preferred TeCB dechlorinating pathways in harbor environments and microbial guilds enriched and active in anoxic TeCB dechlorinating microcosms.
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Affiliation(s)
- Yue Lu
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- College of Environmental Science and Engineering, Hunan University, Changsha, People's Republic of China
| | - Javier Ramiro-Garcia
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- Laboratory of Systems and Synthetic Biology, Wageningen University, Wageningen, The Netherlands
| | | | - Steffi Herrmann
- Division of Soil and Water Management, KU Leuven, Leuven, Belgium
| | - Danuta Cichocka
- Division of Soil and Water Management, KU Leuven, Leuven, Belgium
| | - Dirk Springael
- Division of Soil and Water Management, KU Leuven, Leuven, Belgium
| | - Siavash Atashgahi
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.
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16
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Siddique T, Mohamad Shahimin MF, Zamir S, Semple K, Li C, Foght JM. Long-Term Incubation Reveals Methanogenic Biodegradation of C5 and C6 iso-Alkanes in Oil Sands Tailings. Environ Sci Technol 2015; 49:14732-14739. [PMID: 26571341 DOI: 10.1021/acs.est.5b04370] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
iso-Alkanes are major components of petroleum and have been considered recalcitrant to biodegradation under methanogenic conditions. However, indigenous microbes in oil sands tailings ponds exposed to solvents rich in 2-methylbutane, 2-methylpentane, 3-methylpentane, n-pentane, and n-hexane produce methane in situ. We incubated defined mixtures of iso- or n-alkanes with mature fine tailings from two tailings ponds of different ages historically exposed to different solvents: one, ~10 years old, receiving C5-C6 paraffins and the other, ~35 years old, receiving naphtha. A lengthy incubation (>6 years) revealed iso-alkane biodegradation after lag phases of 900-1800 and ~280 days, respectively, before the onset of methanogenesis, although lag phases were shorter with n-alkanes (~650-1675 and ~170 days, respectively). 2-Methylpentane and both n-alkanes were completely depleted during ~2400 days of incubation, whereas 2-methylbutane and 3-methylpentane were partially depleted only during active degradation of 2-methylpentane, suggesting co-metabolism. In both cases, pyrotag sequencing of 16S rRNA genes showed codominance of Peptococcaceae with acetoclastic (Methanosaeta) and hydrogenotrophic (Methanoregula and Methanolinea) methanogens. These observations are important for predicting long-term greenhouse-gas emissions from oil sands tailings ponds and extend the known range of hydrocarbons susceptible to methanogenic biodegradation in petroleum-impacted anaerobic environments.
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Affiliation(s)
- Tariq Siddique
- Department of Renewable Resources, University of Alberta , Edmonton, AB T6G 2G7, Canada
| | | | - Saima Zamir
- Department of Renewable Resources, University of Alberta , Edmonton, AB T6G 2G7, Canada
| | - Kathleen Semple
- Department of Biological Sciences, University of Alberta , Edmonton, AB T6G 2E9, Canada
| | - Carmen Li
- Department of Biological Sciences, University of Alberta , Edmonton, AB T6G 2E9, Canada
| | - Julia M Foght
- Department of Biological Sciences, University of Alberta , Edmonton, AB T6G 2E9, Canada
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17
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Zhuang L, Tang J, Wang Y, Hu M, Zhou S. Conductive iron oxide minerals accelerate syntrophic cooperation in methanogenic benzoate degradation. J Hazard Mater 2015; 293:37-45. [PMID: 25827267 DOI: 10.1016/j.jhazmat.2015.03.039] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [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: 01/16/2015] [Revised: 03/15/2015] [Accepted: 03/18/2015] [Indexed: 06/04/2023]
Abstract
Recent studies have suggested that conductive iron oxide minerals can facilitate syntrophic metabolism of the methanogenic degradation of organic matter, such as ethanol, propionate and butyrate, in natural and engineered microbial ecosystems. This enhanced syntrophy involves direct interspecies electron transfer (DIET) powered by microorganisms exchanging metabolic electrons through electrically conductive minerals. Here, we evaluated the possibility that conductive iron oxides (hematite and magnetite) can stimulate the methanogenic degradation of benzoate, which is a common intermediate in the anaerobic metabolism of aromatic compounds. The results showed that 89-94% of the electrons released from benzoate oxidation were recovered in CH4 production, and acetate was identified as the only carbon-bearing intermediate during benzoate degradation. Compared with the iron-free controls, the rates of methanogenic benzoate degradation were enhanced by 25% and 53% in the presence of hematite and magnetite, respectively. This stimulatory effect probably resulted from DIET-mediated methanogenesis in which electrons transfer between syntrophic partners via conductive iron minerals. Phylogenetic analyses revealed that Bacillaceae, Peptococcaceae, and Methanobacterium are potentially involved in the functioning of syntrophic DIET. Considering the ubiquitous presence of iron minerals within soils and sediments, the findings of this study will increase the current understanding of the natural biological attenuation of aromatic hydrocarbons in anaerobic environments.
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Affiliation(s)
- Li Zhuang
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650, China
| | - Jia Tang
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650, China
| | - Yueqiang Wang
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650, China
| | - Min Hu
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650, China
| | - Shungui Zhou
- Guangdong Key Laboratory of Agricultural Environment Pollution Integrated Control, Guangdong Institute of Eco-Environmental and Soil Sciences, Guangzhou 510650, China.
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18
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Lee M, Wells E, Wong YK, Koenig J, Adrian L, Richnow HH, Manefield M. Relative contributions of Dehalobacter and zerovalent iron in the degradation of chlorinated methanes. Environ Sci Technol 2015; 49:4481-4489. [PMID: 25764054 DOI: 10.1021/es5052364] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The role of bacteria and zerovalent iron (Fe(0)) in the degradation of chlorinated solvents in subsurface environments is of interest to researchers and remediation practitioners alike. Fe(0) used in reactive iron barriers for groundwater remediation positively interacted with enrichment cultures containing Dehalobacter strains in the transformation of halogenated methanes. Chloroform transformation and dichloromethane formation was up to 8-fold faster and 14 times higher, respectively, when a Dehalobacter-containing enrichment culture was combined with Fe(0) compared with Fe(0) alone. The dichloromethane-fermenting culture transformed dichloromethane up to three times faster with Fe(0) compared to without. Compound-specific isotope analysis was employed to compare abiotic and biotic chloroform and dichloromethane degradation. The isotope enrichment factor for the abiotic chloroform/Fe(0) reaction was large at -29.4 ± 2.1‰, while that for chloroform respiration by Dehalobacter was minimal at -4.3 ± 0.45‰. The combined abiotic/biotic dechlorination was -8.3 ± 0.7‰, confirming the predominance of biotic dechlorination. The enrichment factor for dichloromethane fermentation was -15.5 ± 1.5‰; however, in the presence of Fe(0) the factor increased to -23.5 ± 2.1‰, suggesting multiple mechanisms were contributing to dichloromethane degradation. Together the results show that chlorinated methane-metabolizing organisms introduced into reactive iron barriers can have a significant impact on trichloromethane and dichloromethane degradation and that compound-specific isotope analysis can be employed to distinguish between the biotic and abiotic reactions involved.
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Affiliation(s)
- Matthew Lee
- †School of Biotechnology and Biomolecular Science, University of New South Wales, Kensington, Sydney 2052, Australia
| | - Eliza Wells
- †School of Biotechnology and Biomolecular Science, University of New South Wales, Kensington, Sydney 2052, Australia
| | - Yie Kuan Wong
- †School of Biotechnology and Biomolecular Science, University of New South Wales, Kensington, Sydney 2052, Australia
| | - Joanna Koenig
- †School of Biotechnology and Biomolecular Science, University of New South Wales, Kensington, Sydney 2052, Australia
| | - Lorenz Adrian
- ‡Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Permoser Strasse 15, Leipzig 04318, Germany
| | - Hans H Richnow
- ‡Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Permoser Strasse 15, Leipzig 04318, Germany
| | - Mike Manefield
- †School of Biotechnology and Biomolecular Science, University of New South Wales, Kensington, Sydney 2052, Australia
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19
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Sutton NB, Atashgahi S, van der Wal J, Wijn G, Grotenhuis T, Smidt H, Rijnaarts HHM. Microbial dynamics during and after in situ chemical oxidation of chlorinated solvents. Ground Water 2015; 53:261-270. [PMID: 24898385 DOI: 10.1111/gwat.12209] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 03/13/2014] [Indexed: 06/03/2023]
Abstract
In situ chemical oxidation (ISCO) followed by a bioremediation step is increasingly being considered as an effective biphasic technology. Information on the impact of chemical oxidants on organohalide respiring bacteria (OHRB), however, is largely lacking. Therefore, we used quantitative PCR (qPCR) to monitor the abundance of OHRB (Dehalococcoides mccartyi, Dehalobacter, Geobacter, and Desulfitobacterium) and reductive dehalogenase genes (rdh; tceA, vcrA, and bvcA) at a field location contaminated with chlorinated solvents prior to and following treatment with sodium persulfate. Natural attenuation of the contaminants tetrachloroethene (PCE) and trichloroethene (TCE) observed prior to ISCO was confirmed by the distribution of OHRB and rdh genes. In wells impacted by persulfate treatment, a 1 to 3 order of magnitude reduction in the abundances of OHRB and complete absence of rdh genes was observed 21 days after ISCO. Groundwater acidification (pH<3) and increase in the oxidation reduction potential (>500 mV) due to persulfate treatment were significant and contributed to disruption of the microbial community. In wells only mildly impacted by persulfate, a slight stimulation of the microbial community was observed, with more than 1 order of magnitude increase in the abundance of Geobacter and Desulfitobacterium 36 days after ISCO. After six months, regeneration of the OHRB community occurred, however, neither D. mccartyi nor any rdh genes were observed, indicating extended disruption of biological natural attenuation (NA) capacity following persulfate treatment. For full restoration of biological NA activity, additional time may prove sufficient; otherwise addition electron donor amendment or bioaugmentation may be required.
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Affiliation(s)
- Nora B Sutton
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands
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20
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Li Z, Yoshida N, Wang A, Nan J, Liang B, Zhang C, Zhang D, Suzuki D, Zhou X, Xiao Z, Katayama A. Anaerobic mineralization of 2,4,6-tribromophenol to CO2 by a synthetic microbial community comprising Clostridium, Dehalobacter, and Desulfatiglans. Bioresour Technol 2015; 176:225-232. [PMID: 25461007 DOI: 10.1016/j.biortech.2014.10.097] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [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: 07/02/2014] [Revised: 10/13/2014] [Accepted: 10/18/2014] [Indexed: 06/04/2023]
Abstract
Anaerobic mineralization of 2,4,6-tribromophenol (2,4,6-TBP) was achieved by a synthetic anaerobe community comprising a highly enriched culture of Dehalobacter sp. phylotype FTH1 acting as a reductive debrominator; Clostridium sp. strain Ma13 acting as a hydrogen supplier via glucose fermentation; and a novel 4-chlorophenol-degrading anaerobe, Desulfatiglans parachlorophenolica strain DS. 2,4,6-TBP was debrominated to phenol by the combined action of Ma13 and FTH1, then mineralized into CO2 by sequential introduction of DS, confirmed using [ring-(14)C(U)] phenol. The optimum concentrations of glucose, SO4(2-), and inoculum densities were 0.5 or 2.5mM, 1.0 or 2.5mM, and the densities equivalent to 10(4)copiesmL(-1) of the 16S rRNA genes, respectively. This resulted in the complete mineralization of 23μM 2,4,6-TBP within 35days (0.58μmolL(-1)d(-1)). Thus, using a synthetic microbial community of isolates or highly enriched cultures would be an efficient, optimizable, low-cost strategy for anaerobic bioremediation of halogenated aromatics.
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Affiliation(s)
- Zhiling Li
- State Key Laboratory of Urban Water Resources and Environment, Harbin Institute of Technology (SKLUWRE, HIT), Harbin 150090, China; EcoTopia Science Institute, Nagoya University, Chikusa, Nagoya 464-8603, Japan
| | - Naoko Yoshida
- Center for Fostering Young and Innovative Researchers, Nagoya Institute of Technology, Syowa, Nagoya 466-8555, Japan
| | - Aijie Wang
- State Key Laboratory of Urban Water Resources and Environment, Harbin Institute of Technology (SKLUWRE, HIT), Harbin 150090, China; Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jun Nan
- State Key Laboratory of Urban Water Resources and Environment, Harbin Institute of Technology (SKLUWRE, HIT), Harbin 150090, China
| | - Bin Liang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Chunfang Zhang
- EcoTopia Science Institute, Nagoya University, Chikusa, Nagoya 464-8603, Japan
| | - Dongdong Zhang
- Graduate School of Engineering, Nagoya University, Chikusa, Nagoya 464-8603, Japan
| | - Daisuke Suzuki
- EcoTopia Science Institute, Nagoya University, Chikusa, Nagoya 464-8603, Japan
| | - Xue Zhou
- Graduate School of Environmental Studies, Nagoya University, Nagoya 464-8601, Japan
| | - Zhixing Xiao
- Graduate School of Engineering, Nagoya University, Chikusa, Nagoya 464-8603, Japan
| | - Arata Katayama
- EcoTopia Science Institute, Nagoya University, Chikusa, Nagoya 464-8603, Japan; Graduate School of Engineering, Nagoya University, Chikusa, Nagoya 464-8603, Japan; Graduate School of Environmental Studies, Nagoya University, Nagoya 464-8601, Japan.
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21
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Nelson JL, Jiang J, Zinder SH. Dehalogenation of chlorobenzenes, dichlorotoluenes, and tetrachloroethene by three Dehalobacter spp. Environ Sci Technol 2014; 48:3776-3782. [PMID: 24593835 DOI: 10.1021/es4044769] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Three enrichment cultures containing Dehalobacter spp. were developed that dehalogenate each of the dichlorobenzene (DCB) isomers to monochlorobenzene (MCB), and the strains using 1,2-DCB (12DCB1) or 1,3-DCB (13DCB1) are now considered isolated, whereas the strain using 1,4-DCB (14DCB1) is considered highly enriched. In this study, we examined the dehalogenation capability of each strain to use chlorobenzenes with three or more chlorines, tetrachloroethene (PCE), or dichlorotoluene (DCT) isomers. Strain 12DCB1 preferentially dehalogenated singly flanked chlorines, but not doubly flanked or unflanked chlorines. It dehalogenated pentachlorobenzene to MCB with little buildup of intermediates. Strain 13DCB1, which could use either 1,3-DCB or 1,2-DCB, demonstrated the widest dehalogenation spectrum of electron acceptors tested, and dehalogenated every chlorobenzene isomer except 1,4-DCB. Notably, strain 13DCB1 dehalogenated the recalcitrant 1,3,5-trichlorobenzene isomer to MCB, and qPCR of 16S rRNA genes indicated that strain 13DCB1 grew. Strain 14DCB1 exhibited the narrowest range of substrate utilization, but was the only strain to dehalogenate para-substituted chlorines. Strains 12DCB1 and 13DCB1 dehalogenated PCE to cis-dichloroethene, and all strains dehalogenated 3,4-DCT to monochlorotoluene. These findings show that Dehalobacter spp., like Dehalococcoides spp., are versatile dehalogenators and should be considered when determining the fate of chlorinated organics at contaminated sites.
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Affiliation(s)
- Jennifer L Nelson
- Department of Microbiology, 270 Wing Hall, Cornell University , Ithaca, New York 14853, United States
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22
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Kumar N, Omoregie EO, Rose J, Masion A, Lloyd JR, Diels L, Bastiaens L. Inhibition of sulfate reducing bacteria in aquifer sediment by iron nanoparticles. Water Res 2014; 51:64-72. [PMID: 24388832 DOI: 10.1016/j.watres.2013.09.042] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [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: 05/12/2013] [Revised: 09/18/2013] [Accepted: 09/21/2013] [Indexed: 05/20/2023]
Abstract
Batch microcosms were setup to determine the impact of different sized zero valent iron (Fe(0)) particles on microbial sulfate reduction during the in situ bio-precipitation of metals. The microcosms were constructed with aquifer sediment and groundwater from a low pH (3.1), heavy-metal contaminated aquifer. Nano (nFe(0)), micro (mFe(0)) and granular (gFe(0)) sized Fe(0) particles were added to separate microcosms. Additionally, selected microcosms were also amended with glycerol as a C-source for sulfate-reducing bacteria. In addition to metal removal, Fe(0) in microcosms also raised the pH from 3.1 to 6.5, and decreased the oxidation redox potential from initial values of 249 to -226 mV, providing more favorable conditions for microbial sulfate reduction. mFe(0) and gFe(0) in combination with glycerol were found to enhance microbial sulfate reduction. However, no sulfate reduction occurred in the controls without Fe(0) or in the microcosm amended with nFe(0). A separate dose test confirmed the inhibition for sulfate reduction in presence of nFe(0). Hydrogen produced by Fe(0) was not capable of supporting microbial sulfate reduction as a lone electron donor in this study. Microbial analysis revealed that the addition of Fe(0) and glycerol shifted the microbial community towards Desulfosporosinus sp. from a population initially dominated by low pH and metal-resisting Acidithiobacillus ferrooxidans.
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Affiliation(s)
- Naresh Kumar
- Flemish Institute for Technological Research (VITO), Mol, Belgium; CEREGE-UMR-7330, CNRS - Aix Marseille University, Aix-en-Provence, France; GDRi-iCEINT, International Consortium for the Environmental Implication of Nano Technology, France.
| | - Enoma O Omoregie
- Flemish Institute for Technological Research (VITO), Mol, Belgium; School of Earth, Atmosphere and Environmental Sciences, University of Manchester, UK
| | - Jerome Rose
- CEREGE-UMR-7330, CNRS - Aix Marseille University, Aix-en-Provence, France; GDRi-iCEINT, International Consortium for the Environmental Implication of Nano Technology, France
| | - Armand Masion
- CEREGE-UMR-7330, CNRS - Aix Marseille University, Aix-en-Provence, France; GDRi-iCEINT, International Consortium for the Environmental Implication of Nano Technology, France
| | - Jonathan R Lloyd
- School of Earth, Atmosphere and Environmental Sciences, University of Manchester, UK
| | - Ludo Diels
- Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Leen Bastiaens
- Flemish Institute for Technological Research (VITO), Mol, Belgium
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23
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Justicia-Leon SD, Higgins S, Mack EE, Griffiths DR, Tang S, Edwards EA, Löffler FE. Bioaugmentation with distinct Dehalobacter strains achieves chloroform detoxification in microcosms. Environ Sci Technol 2014; 48:1851-1858. [PMID: 24392834 DOI: 10.1021/es403582f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Chloroform (CF) is a widespread groundwater contaminant not susceptible to aerobic degradation. Under anoxic conditions, CF can undergo abiotic and cometabolic transformation but detoxification is generally not achieved. The recent discovery of distinct Dehalobacter strains that respire CF to dichloromethane (DCM) and ferment DCM to nonchlorinated products promises that bioremediation of CF plumes is feasible. To track both strains, 16S rRNA gene-based qPCR assays specific for either Dehalobacter strain were designed and validated. A laboratory treatability study explored the value of bioaugmentation and biostimulation to achieve CF detoxification using anoxic microcosms established with aquifer material from a CF-contaminated site. Microcosms that received 6% (v/v) of the CF-to-DCM-dechlorinating culture Dhb-CF to achieve an initial Dehalobacter cell titer of 1.6 ± 0.9 × 10(4) mL(-1) dechlorinated CF to stoichiometric amounts of DCM. Subsequent augmentation with 3% (v/v) of the DCM-degrading consortium RM to an initial Dehalobacter cell abundance of 1.2 ± 0.2 × 10(2) mL(-1) achieved complete DCM degradation in microcosms amended with 10 mM bicarbonate. Growth of the CF-respiring and the DCM-degrading Dehalobacter populations and detoxification were also observed in microcosms that received both inocula simultaneously. These findings suggest that anaerobic bioremediation (e.g., bioaugmentation) is a possible remedy at CF- and DCM-contaminated sites without CT, which strongly inhibited CF organohalide respiration and DCM organohalide fermentation.
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Wang S, He J. Dechlorination of commercial PCBs and other multiple halogenated compounds by a sediment-free culture containing Dehalococcoides and Dehalobacter. Environ Sci Technol 2013; 47:10526-10534. [PMID: 23964900 DOI: 10.1021/es4017624] [Citation(s) in RCA: 13] [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] [Indexed: 06/02/2023]
Abstract
At the contaminated sites, polychlorinated biphenyls (PCBs) frequently coexist with other halogenated compounds, such as polybrominated diphenyl ethers (PBDEs), chloroethanes, and chloroethenes. The presence of multiple halogenated compounds usually poses toxicity to dehalogenating microbes, because few cultures are capable of detoxifying a broad spectrum of halogenated compounds. In this study, a sediment-free culture, designed as AD14, is able to sequentially remove halogens from PCBs and other cocontaminants. Culture AD14 dechlorinated the commercial PCB mixture-Aroclor 1260-mainly by removing flanked para- and doubly flanked meta-chlorines. It also dehalogenated octa-brominated diphenyl ether mixture predominantly to tetra-BDEs, 2,4,6-trichlorophenol (2,4,6-TCP) to 4-CP, and tetrachloroethene (PCE)/1,2-dichloroethane (1,2-DCA) completely to ethene. When applied to a mixture of the above-mentioned compounds, culture AD14 stepwise removed halogens from 2,4,6-TCP, 1,2-DCA, PCE, PBDEs, and PCBs. Illumina sequencing analysis of 16S rRNA genes showed that only two known dechlorinating genera, Dehalococcoides and Dehalobacter, were present in culture AD14. Quantitative real-time PCR analysis showed that the 16S rRNA gene copies of Dehalococcoides and Dehalobacter increased from 1.14 × 10(5) to 7.04 × 10(6) copies mL(-1) and from 1.15 × 10(5) to 8.20 × 10(6) copies mL(-1) after removing 41.13 μM of total chlorine from PCBs. The above results suggest that both Dehalobacter and Dehalococcoides could be responsible for PCB dechlorination. Although two Dehalococoides mccartyi strains with identical 16S rRNA genes were isolated from the PCBs-dechlorinating mixed culture using trichloroethene (TCE) and vinyl chloride (VC) as alternatives to PCBs, the two isolates are incapable of dechlorinating PCBs. In all, culture AD14 is promising for bioremediation applications at sites cocontaminated with PCBs and other halogenated compounds.
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Affiliation(s)
- Shanquan Wang
- Department of Civil and Environmental Engineering, National University of Singapore , Block E2-02-13, 1 Engineering Drive 3, Singapore 117576, Singapore
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Zhang C, Li Z, Suzuki D, Ye L, Yoshida N, Katayama A. A humin-dependent Dehalobacter species is involved in reductive debromination of tetrabromobisphenol A. Chemosphere 2013; 92:1343-1348. [PMID: 23769323 DOI: 10.1016/j.chemosphere.2013.05.051] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [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: 03/04/2013] [Revised: 05/19/2013] [Accepted: 05/20/2013] [Indexed: 06/02/2023]
Abstract
Tetrabromobisphenol A (TBBPA) is the most widely used brominated flame retardant on the market. It has been detected in various environmental samples, and a growing body of evidence has demonstrated its toxic effects on living organisms. In this study, we report the enrichment and phylogenetic identification of bacteria that debrominate TBBPA to bisphenol A in the presence of humin. Incubation experiments indicated that humin was required for this debromination activity. Of the five compounds examined for inclusion in the TBBPA-debrominating culture, formate was the optimal electron donor. A 16S rRNA gene library showed that the culture was dominated by three known dehalogenator genera: Dehalobacter, Geobacter, and Sulfurospirillum. Further investigation indicated that Dehalobacter was responsible for the debromination of TBBPA. PCR-denaturing gradient gel electrophoresis analysis showed that Dehalobacter grew in the culture by utilizing TBBPA. Moreover, the copy number of the Dehalobacter 16S rRNA genes increased by about two orders of magnitude in the cultures without the addition of TBBPA, whereas it increased by approximately four orders of magnitude when TBBPA was present. The incubation experiments showed that Dehalobacter was reliant on humin for its debromination activity, indicating a new type of metabolism in Dehalobacter that is linked to humin respiration.
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Affiliation(s)
- Chunfang Zhang
- Graduate School of Engineering, Nagoya University, Nagoya 464-8603, Japan
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26
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Chan CCH, Mundle SOC, Eckert T, Liang X, Tang S, Lacrampe-Couloume G, Edwards EA, Lollar BS. Large carbon isotope fractionation during biodegradation of chloroform by Dehalobacter cultures. Environ Sci Technol 2012; 46:10154-10160. [PMID: 22900494 DOI: 10.1021/es3010317] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Compound specific isotope analysis (CSIA) has been applied to monitor bioremediation of groundwater contaminants and provide insight into mechanisms of transformation of chlorinated ethanes. To date there is little information on its applicability for chlorinated methanes. Moreover, published enrichment factors (ε) observed during the biotic and abiotic degradation of chlorinated alkanes, such as carbon tetrachloride (CT); 1,1,1-trichloroethane (1,1,1-TCA); and 1,1-dichloroethane (1,1-DCA), range from -26.5‰ to -1.8‰ and illustrate a system where similar C-Cl bonds are cleaved but significantly different isotope enrichment factors are observed. In the current study, biotic degradation of chloroform (CF) to dichloromethane (DCM) was carried out by the Dehalobacter containing culture DHB-CF/MEL also shown to degrade 1,1,1-TCA and 1,1-DCA. The carbon isotope enrichment factor (ε) measured during biodegradation of CF was -27.5‰ ± 0.9‰, consistent with the theoretical maximum kinetic isotope effect for C-Cl bond cleavage. Unlike 1,1,1-TCA and 1,1-DCA, reductive dechlorination of CF by the Dehalobacter-containing culture shows no evidence of suppression of the intrinsic maximum kinetic isotope effect. Such a large fractionation effect, comparable to those published for cis-1,2-dichloroethene (cDCE) and vinyl chloride (VC) suggests CSIA has significant potential to identify and monitor biodegradation of CF, as well as important implications for recent efforts to fingerprint natural versus anthropogenic sources of CF in soils and groundwater.
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Affiliation(s)
- Calvin C H Chan
- Department of Earth Sciences, University of Toronto, Toronto, ON, Canada
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Nelson JL, Fung JM, Cadillo-Quiroz H, Cheng X, Zinder SH. A role for Dehalobacter spp. in the reductive dehalogenation of dichlorobenzenes and monochlorobenzene. Environ Sci Technol 2011; 45:6806-13. [PMID: 21732639 DOI: 10.1021/es200480k] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Previously, we demonstrated the reductive dehalogenation of dichlorobenzene (DCB) isomers to monochlorobenzene (MCB), and MCB to benzene in sediment microcosms derived from a chlorobenzene-contaminated site. In this study, enrichment cultures were established for each DCB isomer and each produced MCB and trace amounts of benzene as end products. MCB dehalogenation activity could only be transferred in sediment microcosms. The 1,2-DCB-dehalogenating culture was studied the most intensively. Whereas Dehalococcoides spp. were not detected in any of the microcosms or cultures, Dehalobacter spp. were detected in 16S rRNA gene clone libraries from 1,2-DCB enrichment cultures, and by PCR using Dehalobacter-specific primers in 1,3-DCB and 1,4-DCB enrichments and MCB-dehalogenating microcosms. Quantitative PCR showed Dehalobacter 16S rRNA gene copies increased up to 3 orders of magnitude upon dehalogenation of DCBs or MCB, and that nearly all of bacterial 16S rRNA genes in a 1,2-DCB-dehalogenating culture belonged to Dehalobacter spp. Dehalobacter 16S rRNA genes from DCB enrichment cultures and MCB-dehalogenating microcosms showed considerable diversity, implying that 16S rRNA sequences do not predict dehalogenation-spectra of Dehalobacter spp. These studies support a role for Dehalobacter spp. in the reductive dehalogenation of DCBs and MCB, and this genus should be considered for its potential impact on chlorobenzene fate at contaminated sites.
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Affiliation(s)
- Jennifer L Nelson
- Department of Microbiology, Wing Hall, Cornell University, Ithaca, New York 14853, USA
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Lollar BS, Hirschorn S, Mundle SOC, Grostern A, Edwards EA, Lacrampe-Couloume G. Insights into enzyme kinetics of chloroethane biodegradation using compound specific stable isotopes. Environ Sci Technol 2010; 44:7498-7503. [PMID: 20831217 DOI: 10.1021/es101330r] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
While compound specific isotope analysis (CSIA) has been used extensively to investigate remediation of chlorinated ethenes, to date considerably less information is available on its applicability to chlorinated ethanes. In this study, biodegradation of 1,1,1-trichloroethane (1,1,1-TCA) and 1,1-dichloroethane (1,1-DCA) was carried out by a Dehalobacter-containing mixed culture. Carbon isotope fractionation factors (ε) measured during whole cell degradation demonstrated that values for 1,1,1-TCA and 1,1-DCA (-1.8‰ and -10.5‰, respectively) were significantly smaller than values reported for abiotic reductive dechlorination of these same compounds. Similar results were found in experiments degrading these two priority pollutants by cell free extracts (CFE) where values of -0.8‰ and -7.9‰, respectively, were observed. For 1,1,1-TCA in particular, the large kinetic isotope effect expected for cleavage of a C-Cl bond was almost completely masked during biodegradation by both whole cells and CFE. Comparison to previous studies demonstrates that these patterns of isotopic fractionation are not attributable to transport effects across the cell membrane, as had been seen for other compounds such as PCE. In contrast these results reflect significant differences in the kinetics of the enzymes catalyzing chlorinated ethane degradation.
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Lee YJ, Romanek CS, Wiegel J. Desulfosporosinus youngiae sp. nov., a spore-forming, sulfate-reducing bacterium isolated from a constructed wetland treating acid mine drainage. Int J Syst Evol Microbiol 2009; 59:2743-6. [PMID: 19625426 DOI: 10.1099/ijs.0.007336-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Yong-Jin Lee
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
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Karnachuk OV, Gerasimchuk AL, Banks D, Frengstad B, Stykon GA, Kaksonen AH, Puhakka JA, Ianenko AS, Pimenov NV. [Sulfur metabolite bacteria from waste water of gold miner tale-depot in Kuzbass]. Mikrobiologiia 2009; 78:535-544. [PMID: 19827719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
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Imachi H, Sakai S, Ohashi A, Harada H, Hanada S, Kamagata Y, Sekiguchi Y. Pelotomaculum propionicicum sp. nov., an anaerobic, mesophilic, obligately syntrophic, propionate-oxidizing bacterium. Int J Syst Evol Microbiol 2007; 57:1487-1492. [PMID: 17625181 DOI: 10.1099/ijs.0.64925-0] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [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: 11/18/2022] Open
Abstract
An anaerobic, mesophilic, syntrophic, propionate-oxidizing bacterium, strain MGP(T), was isolated as a defined co-culture with Methanospirillum hungatei from the methanogenic sludge of a mesophilic upflow anaerobic sludge blanket (UASB) reactor. The strain grew in the presence of propionate, but only in co-culture with methanogens, suggesting that it is an obligately syntrophic bacterium. The optimum temperature for growth was 37 degrees C, and the optimum pH was between 6.5 and 7.2. Based on comparative 16S rRNA gene sequence analysis, strain MGP(T) was affiliated with subcluster Ih of 'Desulfotomaculum cluster I', in which it was found to be moderately related to known species of the genera Pelotomaculum and Cryptanaerobacter. Similar to known species of the genus Pelotomaculum, strain MGP(T) could degrade propionate in syntrophy, but had no ability to reduce sulfate, sulfite and thiosulfate. Further phenotypic and genetic studies supported the affiliation of the strain as a novel species in this genus, for which the name Pelotomaculum propionicicum sp. nov. is proposed. The type strain is MGP(T) (=DSM 15578(T)=JCM 11929(T)). The strain has been deposited in the DSM and JCM culture collections as a defined co-culture with Methanospirillum hungatei.
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MESH Headings
- Anaerobiosis
- Bacterial Typing Techniques
- Coculture Techniques
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Genes, rRNA
- Hydrogen-Ion Concentration
- Methanospirillum/growth & development
- Microscopy, Electron, Transmission
- Molecular Sequence Data
- Oxidation-Reduction
- Peptococcaceae/classification
- Peptococcaceae/genetics
- Peptococcaceae/isolation & purification
- Peptococcaceae/metabolism
- Phylogeny
- Propionates/metabolism
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Sewage/microbiology
- Sulfates/metabolism
- Sulfites/metabolism
- Temperature
- Thiosulfates/metabolism
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Affiliation(s)
- Hiroyuki Imachi
- Subground Animalcule Retrieval (SUGAR) Program, Extremobiosphere Research Center, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan
- Department of Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Sanae Sakai
- Department of Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Akiyoshi Ohashi
- Department of Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Hideki Harada
- Department of Civil Engineering, Tohoku University, Sendai 980-8579, Japan
- Department of Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Satoshi Hanada
- Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
| | - Yoichi Kamagata
- Research Institute of Genome-Based Biofactory, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Hokkaido 062-8517, Japan
- Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
- Department of Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
| | - Yuji Sekiguchi
- Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8566, Japan
- Department of Environmental Systems Engineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188, Japan
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Abstract
Stable carbon isotope fractionation during the reductive dechlorination of chloroethenes by two bacterial strains that dechlorinate to ethene, Dehalococcoides ethenogenes 195 and Dehalococcoides sp. strain BAV1 as well as Sulfurospirillum multivorans and Dehalobacter restrictus strain PER-K23, isolates that do not dechlorinate past DCE, are reported. Fractionation by a Dehalococcoides-containing enrichment culture is also measured for comparison to the isolates. All data adequately fit the Rayleigh model and results are presented as enrichment factors. For strain 195, the measured enrichment factors were -9.6 +/- 0.4, -21.1 +/- 1.8, and -5.8 +/- 0.5 when degrading TCE, cDCE, and 1,1-DCE, respectively. Strain BAV1 exhibited enrichment factors of -16.9 +/- 1.4, -8.4 +/- 0.3, -21.4 +/- 0.9, and -24.0 +/- 2.0 for cDCE, 1,1-DCE, tDCE, and VC, respectively. The surprisingly large differences in enrichment factors caused by individual reductases (RDases) reducing different chloroethenes is likely the result of chemical structure differences among the chloroethenes. For TCE reduction, S. multivorans and D. restrictus strain PER-K23 exhibited enrichment factors of -16.4 +/- 1.5 and -3.3 +/- 0.3, respectively. While all of the organisms studied here utilize RDases that require corrinoid cofactors, the biotic TCE enrichment factors varied widely from those reported for the abiotic cobalamin-catalyzed reaction, indicating that additional factors affect the extent of fractionation in these biological systems. The enrichment factors measured for the Dehalococcoides-containing enrichment culture did not match well with those from any of the isolates, demonstrating the inherent difficulties in predicting fractionation factors of undefined communities. Although compound-specific isotope fractionation is a powerful tool for evaluating the progress of in situ bioremediation in the field, given the wide range of enrichment factors associated with functionally similar and phylogenetically diverse organisms, caution must be exercised when applying enrichment factors for the interpretation of dechlorination data.
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Affiliation(s)
- Patrick K H Lee
- Department of Civil and Environmental Engineering, University of California, Berkeley, California 94720, USA
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Komori H, Inagaki S, Yoshioka S, Aono S, Higuchi Y. Crystal Structure of CO-sensing Transcription Activator CooA Bound to Exogenous Ligand Imidazole. J Mol Biol 2007; 367:864-71. [PMID: 17292914 DOI: 10.1016/j.jmb.2007.01.043] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2006] [Revised: 01/11/2007] [Accepted: 01/17/2007] [Indexed: 10/23/2022]
Abstract
CooA is a CO-dependent transcriptional activator and transmits a CO-sensing signal to a DNA promoter that controls the expression of the genes responsible for CO metabolism. CooA contains a b-type heme as the active site for sensing CO. CO binding to the heme induces a conformational change that switches CooA from an inactive to an active DNA-binding form. Here, we report the crystal structure of an imidazole-bound form of CooA from Carboxydothermus hydrogenoformans (Ch-CooA). In the resting form, Ch-CooA has a six-coordinate ferrous heme with two endogenous axial ligands, the alpha-amino group of the N-terminal amino acid and a histidine residue. The N-terminal amino group of CooA that is coordinated to the heme iron is replaced by CO. This substitution presumably triggers a structural change leading to the active form. The crystal structure of Ch-CooA reveals that imidazole binds to the heme, which replaces the N terminus, as does CO. The dissociated N terminus is positioned approximately 16 A from the heme iron in the imidazole-bound form. In addition, the heme plane is rotated by 30 degrees about the normal of the porphyrin ring compared to that found in the inactive form of Rhodospirillum rubrum CooA. Even though the ligand exchange, imidazole-bound Ch-CooA remains in the inactive form for DNA binding. These results indicate that the release of the N terminus resulting from imidazole binding is not sufficient to activate CooA. The structure provides new insights into the structural changes required to achieve activation.
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Affiliation(s)
- Hirofumi Komori
- Department of Life Science, Graduate School of Life Science, University of Hyogo and Himeji Institute of Technology, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan
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Shimoyama T, Rajashekhara E, Ohmori D, Kosaka T, Watanabe K. MmcBC in Pelotomaculum thermopropionicum represents a novel group of prokaryotic fumarases. FEMS Microbiol Lett 2007; 270:207-13. [PMID: 17319878 DOI: 10.1111/j.1574-6968.2007.00665.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [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: 11/30/2022] Open
Abstract
The overall amino-acid sequence of MmcBC in Pelotomaculum thermopropionicum was substantially homologous (33%) to fumarase A in Escherichia coli, although its possible subunit structure was different from known fumarases and it lacked the fumarate-lyase signature sequence. Here, MmcBC in E. coli is expressed and characterized. The purified enzyme catalyzed reversible conversion of fumarate to L-malate at an optimum temperature of 70 degrees C. Its molecular size was 64.2 kDa, indicating that it consisted of one MmcB and one MmcC. EPR spectra revealed that it had an oxygen-sensitive [4Fe-4S] cluster. We propose that MmcBC represents a novel group of prokaryotic fumarases.
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Grostern A, Edwards EA. A 1,1,1-trichloroethane-degrading anaerobic mixed microbial culture enhances biotransformation of mixtures of chlorinated ethenes and ethanes. Appl Environ Microbiol 2006; 72:7849-56. [PMID: 17056695 PMCID: PMC1694251 DOI: 10.1128/aem.01269-06] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [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
1,1,1-trichloroethane (1,1,1-TCA) is a common groundwater pollutant as a result of improper disposal and accidental spills. It is often found as a cocontaminant with trichloroethene (TCE) and inhibits some TCE-degrading microorganisms. 1,1,1-TCA removal is therefore required for effective bioremediation of sites contaminated with mixed chlorinated organics. This study characterized MS, a 1,1,1-TCA-degrading, anaerobic, mixed microbial culture derived from a 1,1,1-TCA-contaminated site in the northeastern United States. MS reductively dechlorinated 1,1,1-TCA to 1,1-dichloroethane (1,1-DCA) and then to monochloroethane (CA) but not further. Cloning of bacterial 16S rRNA genes revealed among other organisms the presence of a Dehalobacter sp. and a Desulfovibrio sp., which are both phylogenetically related to known dehalorespiring strains. Monitoring of these populations with species-specific quantitative PCR during degradation of 1,1,1-TCA and 1,1-DCA showed that Dehalobacter proliferated during dechlorination. Dehalobacter growth was dechlorination dependent, whereas Desulfovibrio growth was dechlorination independent. Experiments were also performed to test whether MS could enhance TCE degradation in the presence of inhibiting levels of 1,1,1-TCA. Dechlorination of cis-dichloroethene (cDCE) and vinyl chloride (VC) in KB-1, a chloroethene-degrading culture used for bioaugmentation, was inhibited with 1,1,1-TCA present. When KB-1 and MS were coinoculated, degradation of cDCE and VC to ethene proceeded as soon as the 1,1,1-TCA was dechlorinated to 1,1-DCA by MS. This demonstrated the potential application of the MS and KB-1 cultures for cobioaugmentation of sites cocontaminated with 1,1,1-TCA and TCE.
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Affiliation(s)
- Ariel Grostern
- Department of cell and Systems Biology, University of Toronto, 200 College St., Toronto, ON M5S 3E5, Canada
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Slobodkin AI, Sokolova TG, Lysenko AM, Wiegel J. Reclassification of Thermoterrabacterium ferrireducens as Carboxydothermus ferrireducens comb. nov., and emended description of the genus Carboxydothermus. Int J Syst Evol Microbiol 2006; 56:2349-2351. [PMID: 17012560 DOI: 10.1099/ijs.0.64503-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [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: 11/18/2022] Open
Abstract
Similarities in phylogeny and metabolic properties between the type species of two monospecific genera of thermophilic anaerobic bacteria, Carboxydothermus hydrogenoformans and Thermoterrabacterium ferrireducens, and analysis of their recently available 16S rRNA gene sequences warranted clarification of their taxonomic positions. We have determined that the value of DNA–DNA hybridization between the type strains is 53 %. Additional physiological studies revealed that C. hydrogenoformans Z-2901T is capable of Fe(III) reduction with H2 as an electron donor and ferrihydrite as an electron acceptor. T. ferrireducens JW/AS-Y7T is able to grow and utilize CO with ferrihydrite as an electron acceptor without hydrogen or acetate production. We therefore reclassify Thermoterrabacterium ferrireducens as Carboxydothermus ferrireducens comb. nov. (type strain JW/AS-Y7T=DSM 11255T=VKM B-2392T). The description of the genus Carboxydothermus is emended to include such important physiological properties as growth on organic compounds and capacity for Fe(III) reduction.
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Affiliation(s)
- A I Slobodkin
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117 312 Moscow, Russia
| | - T G Sokolova
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117 312 Moscow, Russia
| | - A M Lysenko
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117 312 Moscow, Russia
| | - J Wiegel
- Department of Microbiology, University of Georgia, Athens, GA 30602, USA
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Zavarzina DG, Sokolova TG, Tourova TP, Chernyh NA, Kostrikina NA, Bonch-Osmolovskaya EA. Thermincola ferriacetica sp. nov., a new anaerobic, thermophilic, facultatively chemolithoautotrophic bacterium capable of dissimilatory Fe(III) reduction. Extremophiles 2006; 11:1-7. [PMID: 16988758 DOI: 10.1007/s00792-006-0004-7] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2005] [Accepted: 05/23/2006] [Indexed: 11/25/2022]
Abstract
A moderately thermophilic, sporeforming bacterium able to reduce amorphous Fe(III)-hydroxide was isolated from ferric deposits of a terrestrial hydrothermal spring, Kunashir Island (Kurils), and designated as strain Z-0001. Cells of strain Z-0001 were straight, Gram-positive rods, slowly motile. Strain Z-0001 was found to be an obligate anaerobe. It grew in the temperature range from 45 to 70 degrees C with an optimum at 57-60 degrees C, in a pH range from 5.9 to 8.0 with an optimum at 7.0-7.2, and in NaCl concentration range 0-3.5% with an optimum at 0%. Molecular hydrogen, acetate, peptone, yeast and beef extracts, glycogen, glycolate, pyruvate, betaine, choline, N-acetyl-D-glucosamine and casamino acids were used as energy substrates for growth in presence of Fe(III) as an electron acceptor. Sugars did not support growth. Magnetite, Mn(IV) and anthraquinone-2,6-disulfonate served as the alternative electron acceptors, supporting the growth of isolate Z-0001 with acetate as electron donor. Formation of magnetite was observed when amorphous Fe(III) hydroxide was used as electron acceptor. Yeast extract, if added, stimulated growth, but was not required. Isolate Z-0001 was able to grow chemolithoautotrophicaly with molecular hydrogen as the only energy substrate, Fe(III) as electron acceptor and CO(2) as the carbon source. Isolate Z-0001 was able to grow with 100% CO as the sole energy source, producing H(2) and CO(2), requiring the presence of 0.2 g l(-1) of acetate as the carbon source. The G+C content of strain Z-0001(T )DNA G+C was 47.8 mol%. Based on 16S rRNA sequence analyses strain Z-0001 fell into the cluster of family Peptococcaceae, within the low G+C content Gram-Positive bacteria, clustering with Thermincola carboxydophila (98% similarity). DNA-DNA hybridization with T. carboxydophila was 27%. On the basis of physiological and phylogenetic data it is proposed that strain Z-0001(T) (=DSMZ 14005, VKM B-2307) should be placed in the genus Thermincola as a new species Thermincola ferriacetica sp. nov.
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Affiliation(s)
- Daria G Zavarzina
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-letiya Oktyabrya 7/2, 117312, Moscow, Russia.
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Abstract
The Florida Everglades is one of the largest freshwater marshes in North America and has been subject to eutrophication for decades. A gradient in P concentrations extends for several kilometers into the interior of the northern regions of the marsh, and the structure and function of soil microbial communities vary along the gradient. In this study, stable isotope probing was employed to investigate the fate of carbon from the fermentation products propionate and butyrate in soils from three sites along the nutrient gradient. For propionate microcosms, 16S rRNA gene clone libraries from eutrophic and transition sites were dominated by sequences related to previously described propionate oxidizers, such as Pelotomaculum spp. and Syntrophobacter spp. Significant representation was also observed for sequences related to Smithella propionica, which dismutates propionate to butyrate. Sequences of dominant phylotypes from oligotrophic samples did not cluster with known syntrophs but with sulfate-reducing prokaryotes (SRP) and Pelobacter spp. In butyrate microcosms, sequences clustering with Syntrophospora spp. and Syntrophomonas spp. dominated eutrophic microcosms, and sequences related to Pelospora dominated the transition microcosm. Sequences related to Pelospora spp. and SRP dominated clone libraries from oligotrophic microcosms. Sequences from diverse bacterial phyla and primary fermenters were also present in most libraries. Archaeal sequences from eutrophic microcosms included sequences characteristic of Methanomicrobiaceae, Methanospirillaceae, and Methanosaetaceae. Oligotrophic microcosms were dominated by acetotrophs, including sequences related to Methanosarcina, suggesting accumulation of acetate.
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Affiliation(s)
- Ashvini Chauhan
- Soil and Water Science Department, University of Florida, P.O. Box 110290, Gainesville, FL 32611-0290, USA
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Imachi H, Sekiguchi Y, Kamagata Y, Loy A, Qiu YL, Hugenholtz P, Kimura N, Wagner M, Ohashi A, Harada H. Non-sulfate-reducing, syntrophic bacteria affiliated with desulfotomaculum cluster I are widely distributed in methanogenic environments. Appl Environ Microbiol 2006; 72:2080-91. [PMID: 16517657 PMCID: PMC1393244 DOI: 10.1128/aem.72.3.2080-2091.2006] [Citation(s) in RCA: 143] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The classical perception of members of the gram-positive Desulfotomaculum cluster I as sulfate-reducing bacteria was recently challenged by the isolation of new representatives lacking the ability for anaerobic sulfate respiration. For example, the two described syntrophic propionate-oxidizing species of the genus Pelotomaculum form the novel Desulfotomaculum subcluster Ih. In the present study, we applied a polyphasic approach by using cultivation-independent and culturing techniques in order to further characterize the occurrence, abundance, and physiological properties of subcluster Ih bacteria in low-sulfate, methanogenic environments. 16S rRNA (gene)-based cloning, quantitative fluorescence in situ hybridization, and real-time PCR analyses showed that the subcluster Ih population composed a considerable part of the Desulfotomaculum cluster I community in almost all samples examined. Additionally, five propionate-degrading syntrophic enrichments of subcluster Ih bacteria were successfully established, from one of which the new strain MGP was isolated in coculture with a hydrogenotrophic methanogen. None of the cultures analyzed, including previously described Pelotomaculum species and strain MGP, consumed sulfite, sulfate, or organosulfonates. In accordance with these phenotypic observations, a PCR-based screening for dsrAB (key genes of the sulfate respiration pathway encoding the alpha and beta subunits of the dissimilatory sulfite reductase) of all enrichments/(co)cultures was negative with one exception. Surprisingly, strain MGP contained dsrAB, which were transcribed in the presence and absence of sulfate. Based on these and previous findings, we hypothesize that members of Desulfotomaculum subcluster Ih have recently adopted a syntrophic lifestyle to thrive in low-sulfate, methanogenic environments and thus have lost their ancestral ability for dissimilatory sulfate/sulfite reduction.
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Affiliation(s)
- Hiroyuki Imachi
- Department of Environmental Systems Engineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan.
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Kosaka T, Uchiyama T, Ishii SI, Enoki M, Imachi H, Kamagata Y, Ohashi A, Harada H, Ikenaga H, Watanabe K. Reconstruction and regulation of the central catabolic pathway in the thermophilic propionate-oxidizing syntroph Pelotomaculum thermopropionicum. J Bacteriol 2006; 188:202-10. [PMID: 16352836 PMCID: PMC1317604 DOI: 10.1128/jb.188.1.202-210.2006] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [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
Obligate anaerobic bacteria fermenting volatile fatty acids in syntrophic association with methanogenic archaea share the intermediate bottleneck step in organic-matter decomposition. These organisms (called syntrophs) are biologically significant in terms of their growth at the thermodynamic limit and are considered to be the ideal model to address bioenergetic concepts. We conducted genomic and proteomic analyses of the thermophilic propionate-oxidizing syntroph Pelotomaculum thermopropionicum to obtain the genetic basis for its central catabolic pathway. Draft sequencing and subsequent targeted gap closing identified all genes necessary for reconstructing its propionate-oxidizing pathway (i.e., methylmalonyl coenzyme A pathway). Characteristics of this pathway include the following. (i) The initial two steps are linked to later steps via transferases. (ii) Each of the last three steps can be catalyzed by two different types of enzymes. It was also revealed that many genes for the propionate-oxidizing pathway, except for those for propionate coenzyme A transferase and succinate dehydrogenase, were present in an operon-like cluster and accompanied by multiple promoter sequences and a putative gene for a transcriptional regulator. Proteomic analysis showed that enzymes in this pathway were up-regulated when grown on propionate; of these enzymes, regulation of fumarase was the most stringent. We discuss this tendency of expression regulation based on the genetic organization of the open reading frame cluster. Results suggest that fumarase is the central metabolic switch controlling the metabolic flow and energy conservation in this syntroph.
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Affiliation(s)
- Tomoyuki Kosaka
- Laboratory of Applied Microbiology, Marine Biotechnology Institute, Heita, Kamaishi, Iwate 026-0001, Japan.
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Abstract
Mixed anaerobic microbial subcultures enriched from a multilayered aquifer at a former chlorinated solvent disposal facility in West Louisiana were examined to determine the organism(s) involved in the dechlorination of the toxic compounds 1,2-dichloroethane (1,2-DCA) and 1,1,2-trichloroethane (1,1,2-TCA) to ethene. Sequences phylogenetically related to Dehalobacter and Dehalococcoides, two genera of anaerobic bacteria that are known to respire with chlorinated ethenes, were detected through cloning of bacterial 16S rRNA genes. Denaturing gradient gel electrophoresis analysis of 16S rRNA gene fragments after starvation and subsequent reamendment of culture with 1,2-DCA showed that the Dehalobacter sp. grew during the dichloroelimination of 1,2-DCA to ethene, implicating this organism in degradation of 1,2-DCA in these cultures. Species-specific real-time quantitative PCR was further used to monitor proliferation of Dehalobacter and Dehalococcoides during the degradation of chlorinated ethanes and showed that in fact both microorganisms grew simultaneously during the degradation of 1,2-DCA. Conversely, Dehalobacter grew during the dichloroelimination of 1,1,2-TCA to vinyl chloride (VC) but not during the subsequent reductive dechlorination of VC to ethene, whereas Dehalococcoides grew only during the reductive dechlorination of VC but not during the dichloroelimination of 1,1,2-TCA. This demonstrated that in mixed cultures containing multiple dechlorinating microorganisms, these organisms can have either competitive or complementary dechlorination activities, depending on the chloro-organic substrate.
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Affiliation(s)
- Ariel Grostern
- Department of Botany, University of Toronto, 200 College St., Toronto, ON M5S 3E5, Canada
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Clark RW, Lanz ND, Lee AJ, Kerby RL, Roberts GP, Burstyn JN. Unexpected NO-dependent DNA binding by the CooA homolog from Carboxydothermus hydrogenoformans. Proc Natl Acad Sci U S A 2006; 103:891-6. [PMID: 16410360 PMCID: PMC1347970 DOI: 10.1073/pnas.0505919103] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
CooA, the CO-sensing heme protein from Rhodospirillum rubrum, regulates the expression of genes that encode a CO-oxidation system, allowing R. rubrum to use CO as a sole energy source. To better understand the gas-sensing regulation mechanism used by R. rubrum CooA and its homologs in other organisms, we characterized spectroscopically and functionally the Fe(II), Fe(II)-NO, and Fe(II)-CO forms of CooA from Carboxydothermus hydrogenoformans. Surprisingly, and unlike R. rubrum CooA, C. hydrogenoformans CooA binds NO to form a six-coordinate Fe(II)-NO heme that is active for DNA binding in vitro and in vivo. In contrast, R. rubrum CooA, which is exquisitely specific for CO, forms a five-coordinate Fe(II)-NO adduct that is inactive for DNA binding. Based on analyses of protein variants and temperature studies, NO-dependent DNA binding by C. hydrogenoformans CooA is proposed to result from a greater apparent stability of the six-coordinate Fe(II)-NO adduct at room temperature. Results from the present study strengthen the proposal that CO specificity in the CooA activation mechanism is based on the requirement for a small, neutral distal ligand, which in turn affects the relative positioning of the ligand-bound heme.
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Affiliation(s)
- Robert W Clark
- Departments of Chemistry and Bacteriology, University of Wisconsin, Madison, WI 53706, USA
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Qiu YL, Sekiguchi Y, Hanada S, Imachi H, Tseng IC, Cheng SS, Ohashi A, Harada H, Kamagata Y. Pelotomaculum terephthalicum sp. nov. and Pelotomaculum isophthalicum sp. nov.: two anaerobic bacteria that degrade phthalate isomers in syntrophic association with hydrogenotrophic methanogens. Arch Microbiol 2006; 185:172-82. [PMID: 16404568 DOI: 10.1007/s00203-005-0081-5] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2005] [Revised: 12/14/2005] [Accepted: 12/20/2005] [Indexed: 10/25/2022]
Abstract
An anaerobic phthalate isomer-degrading strain (JT(T)) that we previously isolated was characterized. In addition, a strictly anaerobic, mesophilic, syntrophic phthalate isomer-degrading bacterium, designated strain JI(T), was isolated and characterized in this study. Both were non-motile rods that formed spores. In both strains, the optimal growth was observed at temperatures around 37 degrees C and neutral pH. In syntrophic co-culture with the hydrogenotrophic methanogen Methanospirillum hungatei, both strains could utilize two or three phthalate isomers for growth, and produce acetate and methane as end products. Strain JT(T) was able to grow on isophthalate, terephthalate, and a number of low-molecular weight aromatic compounds, such as benzoate, hydroquinone, 2-hydroxybenzoate, 3-hydroxybenzoate, 2,5-dihydroxybenzoate, 3-phenylpropionate in co-culture with M. hungatei. It could also grow on crotonate, hydroquinone and 2,5-dihydroxybenzoate in pure culture. Strain JI(T) utilized all of the three phthalate isomers as well as benzoate and 3-hydroxybenzoate for growth in co-culture with M. hungatei. No substrates were, however, found to support the axenic growth of strain JI(T). Neither strain JT(T) nor strain JI(T) could utilize sulfate, sulfite, thiosulfate, nitrate, fumarate, Fe (III) or 4-hydroxybenzoate as electron acceptor. Phylogenetically, strains JT(T) and JI(T) were relatively close to the members of the genera Pelotomaculum and Cryptanaerobacter in 'Desulfotomaculum lineage I'. Physiological and chemotaxonomic characteristics indicated that the two isolates should be classified into the genus Pelotomaculum, creating two novel species for them. Here, we propose Pelotomaculum terephthalicum sp. nov. and Pelotomaculum isophthalicum sp. nov. for strain JT(T) and strain JI(T), respectively. The type strains are strains JT(T) (= DSM 16121(T )= JCM 11824(T )= NBRC 100523(T)) and JI(T) (= JCM 12282(T) = BAA-1053(T)) for P. terephthalicum and P. isophthalicum, respectively.
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Affiliation(s)
- Yan-Ling Qiu
- Institute of Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology, 305-8566 Tsukuba, Ibaraki, Japan
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Abstract
H2 maintains an important role in bacterial metabolism in anaerobic environments. The ability to measure and analyze H2 concentrations in biological systems is often useful for determining the physiological state of the microbiota. Methods for precisely analyzing H2 in bacterial cultures and environmental samples are now available. This chapter discusses H2 measurements from both the theoretical and practical methodology perspective of the analysis and the interpretation of data.
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Affiliation(s)
- Frank E Löffler
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta 30332-0512, USA
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Khijniak TV, Slobodkin AI, Coker V, Renshaw JC, Livens FR, Bonch-Osmolovskaya EA, Birkeland NK, Medvedeva-Lyalikova NN, Lloyd JR. Reduction of uranium(VI) phosphate during growth of the thermophilic bacterium Thermoterrabacterium ferrireducens. Appl Environ Microbiol 2005; 71:6423-6. [PMID: 16204572 PMCID: PMC1265970 DOI: 10.1128/aem.71.10.6423-6426.2005] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.8] [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
The thermophilic, gram-positive bacterium Thermoterrabacterium ferrireducens coupled organotrophic growth to the reduction of sparingly soluble U(VI) phosphate. X-ray powder diffraction and X-ray absorption spectroscopy analysis identified the electron acceptor in a defined medium as U(VI) phosphate [uramphite; (NH4)(UO2)(PO4) . 3H2O], while the U(IV)-containing precipitate formed during bacterial growth was identified as ningyoite [CaU(PO4)2 . H2O]. This is the first report of microbial reduction of a largely insoluble U(VI) compound.
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Affiliation(s)
- T V Khijniak
- The Williamson Research Centre for Molecular Environmental Science and The School of Earth, Atmospheric and Environmental Sciences, The University of Manchester, Manchester M13 9PL, United Kingdom
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Pawłowska-Cwiek L, Pado R. The role of benzoate secreted by Desulfotomaculum acetoxidans DSM 771 in sulfate uptake. Acta Biochim Pol 2005; 52:797-802. [PMID: 16265594] [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] [Received: 01/30/2004] [Revised: 03/24/2005] [Accepted: 10/13/2005] [Indexed: 05/05/2023]
Abstract
This work was designed to find the cause of the delay in hydrogen sulfide dissimilation in Desulfotomaculum acetoxidans DSM 771, which is dependent on the sulfate uptake. This bacterium grown without addition of any aromatic compound was shown by spectrum analysis with the methylene method to contain hydroxy-benzoate derivatives. The presence of these compounds was confirmed by HPLC in fractions obtained from cell walls after 15 days of culture. The test with 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt seemed to indicate the presence of peroxidase, which probably oxidized benzoate to its hydroxy derivatives. The test with 5-sulfo-salicylic acid proved the ability of the investigated strain to utilize arylsulfates and to reduce sulfate group to hydrogen sulfide. On the basis of the above data, we propose the following sequence of reactions: 1, benzoate secretion; 2, benzoate hydroxylation; 3, sulfonation of hydroxy-benzoate derivatives.
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Juteau P, Côté V, Duckett MF, Beaudet R, Lépine F, Villemur R, Bisaillon JG. Cryptanaerobacter phenolicus gen. nov., sp. nov., an anaerobe that transforms phenol into benzoate via 4-hydroxybenzoate. Int J Syst Evol Microbiol 2005; 55:245-250. [PMID: 15653882 DOI: 10.1099/ijs.0.02914-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [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: 11/18/2022] Open
Abstract
An anaerobic bacterium that transforms phenol and 4-hydroxybenzoate (4-OHB) into benzoate, strain LR7.2T, was isolated from a culture originating from a mixture of swamp water, sewage sludge, swine waste and soil. Cells of strain LR7.2T are Gram-positive short rods (1×2 μm) that are electron-dense when observed by electron microscopy. The optimum pH and temperature for growth and transformation activity of 4-OHB are 7·5–8·0 and 30–37 °C, respectively. The bacterium does not use sulphate, thiosulphate, nitrate, nitrite, FeCl3, fumarate or arsenate as an electron acceptor. It does not normally use sulphite, although stimulation of growth and 4-OHB transformation activity at a low concentration (up to 2 mM) has been reported previously under different culture conditions. The presence of 4-OHB or phenol is essential for growth; transformation of 4-OHB or phenol into benzoate is used to produce energy for growth. Using [6D]-phenol, 4-OHB was shown to be an intermediate in the transformation of phenol into benzoate. No spore was observed. The bacterium has a DNA G+C content of 51 mol% and its major membrane fatty acid is anteiso-C15 : 0. The 16S rRNA gene sequence of strain LR7.2T shows only 90 % similarity to its closest relative (Pelotomaculum thermopropionicum). From these results, a new taxon is proposed: Cryptanaerobacter phenolicus gen. nov., sp. nov. The type strain is LR7.2T (=ATCC BAA-820T=DSM 15808T).
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Affiliation(s)
- Pierre Juteau
- INRS - Institut Armand-Frappier, Université du Québec, 531 boulevard des Prairies, Laval, Quebec, Canada H7V 1B7
| | - Valérie Côté
- INRS - Institut Armand-Frappier, Université du Québec, 531 boulevard des Prairies, Laval, Quebec, Canada H7V 1B7
| | - Marie-France Duckett
- INRS - Institut Armand-Frappier, Université du Québec, 531 boulevard des Prairies, Laval, Quebec, Canada H7V 1B7
| | - Réjean Beaudet
- INRS - Institut Armand-Frappier, Université du Québec, 531 boulevard des Prairies, Laval, Quebec, Canada H7V 1B7
| | - François Lépine
- INRS - Institut Armand-Frappier, Université du Québec, 531 boulevard des Prairies, Laval, Quebec, Canada H7V 1B7
| | - Richard Villemur
- INRS - Institut Armand-Frappier, Université du Québec, 531 boulevard des Prairies, Laval, Quebec, Canada H7V 1B7
| | - Jean-Guy Bisaillon
- INRS - Institut Armand-Frappier, Université du Québec, 531 boulevard des Prairies, Laval, Quebec, Canada H7V 1B7
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Zuo R, Wood TK. Inhibiting mild steel corrosion from sulfate-reducing and iron-oxidizing bacteria using gramicidin-S-producing biofilms. Appl Microbiol Biotechnol 2004; 65:747-53. [PMID: 15278311 DOI: 10.1007/s00253-004-1651-1] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2003] [Revised: 04/08/2004] [Accepted: 04/23/2004] [Indexed: 11/29/2022]
Abstract
A gramicidin-S-producing Bacillus brevis 18-3 biofilm was shown to reduce corrosion rates of mild steel by inhibiting both the sulfate-reducing bacterium Desulfosporosinus orientis and the iron-oxidizing bacterium Leptothrix discophora SP-6. When L. discophora SP-6 was introduced along with D. orientis to a non-antimicrobial-producing biofilm control, Paenibacillus polymyxa ATCC 10401, a corrosive synergy was created and mild steel coupons underwent more severe corrosion than when only D. orientis was present, showing a 2.3-fold increase via electrochemical impedance spectroscopy (EIS) and a 1.8-fold difference via mass-loss measurements. However, when a gramicidin-S-producing, protective B. brevis 18-3 biofilm was established on mild steel, the metal coupons were protected against the simultaneous attack of D. orientis and L. discophora SP-6. EIS data showed that the protective B. brevis 18-3 biofilm decreased the corrosion rate about 20-fold compared with the non-gramicidin-producing P. polymyxa ATCC 10401 biofilm control. The mass loss for the protected mild steel coupons was also significantly lower than that for the unprotected ones (4-fold decrease). Scanning electron microscope images corroborated the corrosion inhibition by the gramicidin-S-producing B. brevis biofilm on mild steel by showing that the metal surface remained untarnished, i.e., the polishing grooves were still visible after exposure to the simultaneous attack of the sulfate-reducing bacterium and the iron-oxidizing bacterium.
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Affiliation(s)
- Rongjun Zuo
- Department of Chemical Engineering, University of Connecticut, Storrs, CT 06269-3222, USA
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Abstract
We examined the potential use of natural-abundance stable carbon isotope ratios of lipids for determining substrate usage by sulfate-reducing bacteria (SRB). Four SRB were grown under autotrophic, mixotrophic, or heterotrophic growth conditions, and the delta13C values of their individual fatty acids (FA) were determined. The FA were usually 13C depleted in relation to biomass, with Deltadelta13C(FA - biomass) of -4 to -17 per thousand; the greatest depletion occurred during heterotrophic growth. The exception was Desulfotomaculum acetoxidans, for which substrate limitation resulted in biomass and FA becoming isotopically heavier than the acetate substrate. The delta13C values of FA in Desulfotomaculum acetoxidans varied with the position of the double bond in the monounsaturated C16 and C18 FA, with FA becoming progressively more 13C depleted as the double bond approached the methyl end. Mixotrophic growth of Desulfovibrio desulfuricans resulted in little depletion of the i17:1 biomarker relative to biomass or acetate, whereas growth with lactate resulted in a higher proportion of i17:1 with a greater depletion in 13C. The relative abundances of 10Me16:0 in Desulfobacter hydrogenophilus and Desulfobacterium autotrophicum were not affected by growth conditions, yet the Deltadelta13C(FA - substrate) values of 10Me16:0 were considerably greater during autotrophic growth. These experiments indicate that FA delta13C values can be useful for interpreting carbon utilization by SRB in natural environments.
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Affiliation(s)
- K L Londry
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada.
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