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Sorwar E, Oliveira JIN, Malar C M, Krüger M, Corradi N. Assembly and comparative analyses of the Geosiphon pyriformis metagenome. Environ Microbiol 2024; 26:e16681. [PMID: 39054868 DOI: 10.1111/1462-2920.16681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 07/09/2024] [Indexed: 07/27/2024]
Abstract
Geosiphon pyriformis, a representative of the fungal sub-phylum Glomeromycotina, is unique in its endosymbiosis with cyanobacteria within a fungal cell. This symbiotic relationship occurs in bladders containing nuclei of G. pyriformis, Mollicutes-like bacterial endosymbionts (MRE), and photosynthetically active and dividing cells of Nostoc punctiforme. Recent genome analyses have shed light on the biology of G. pyriformis, but the genome content and biology of its endosymbionts remain unexplored. To fill this gap, we gathered and examined metagenomic data from the bladders of G. pyriformis, where N. punctiforme and MRE are located. This ensures that our analyses are focused on the organs directly involved in the symbiosis. By comparing this data with the genetic information of related cyanobacteria and MREs from other species of Arbuscular Mycorrhizal Fungi, we aimed to reveal the genetic content of these organisms and understand how they interact at a genetic level to establish a symbiotic relationship. Our analyses uncovered significant gene expansions in the Nostoc endosymbiont, particularly in mobile elements and genes potentially involved in xenobiotic degradation. We also confirmed that the MRE of Glomeromycotina are monophyletic and possess a highly streamlined genome. These genomes show dramatic differences in both structure and content, including the presence of enzymes involved in environmental sensing and stress response.
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Affiliation(s)
- Essam Sorwar
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Mathu Malar C
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Manuela Krüger
- Institute of Experimental Botany, The Czech Academy of Science, Prague, Czech Republic
| | - Nicolas Corradi
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
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2
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Han K, Hong U, Park S, Kwon S, Kim Y. In situ field method for evaluating biodegradation potential of BTEX by indigenous heterotrophic denitrifying microorganisms in a BTEX-contaminated fractured-rock aquifer. ENVIRONMENTAL TECHNOLOGY 2021; 42:1326-1335. [PMID: 31524076 DOI: 10.1080/09593330.2019.1668482] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 09/10/2019] [Indexed: 06/10/2023]
Abstract
Generally different anaerobic degradation potentials for benzene, toluene, ethylbenzene and xylene isomers (BTEX) has been reported due to site specific conditions, such as the indigenous microbial population, electron acceptors (EA) available and concentrations of each BTEX compound. It was of interest to estimate relative biodegradation potential of each BTEX compound during enhanced anaerobic bioremediation of a BTEX-contaminated aquifer. In this study, an in situ method for assessing the degradation potentials of each BTEX compound present as a mixture under NO3-injecting conditions by performing a series of single-well push-pull tests and well-to-well tests (WWTs) was developed. During the 1st and 2nd WWTs, biological heterotrophic dissimilative NO3- denitrification was confirmed by simultaneous detection of both NO2- and N2O and significant production of CO2 during the NO3- degradation. The biodegradation fractions of NO3- injected during the 1st and 2nd WWTs were 1.7% and 5.0%, respectively, with 7.18 and 8.85 mmol N/L/day of in situ zero-order denitrification rate coefficients. The concentrations of benzene, ethylbenzene, and xylenes measured were similar to values calculated when considering only dilution, but the measured concentrations of toluene were significantly lower than the values calculated were. These results indicate that in situ method presented in the study successfully evaluate anaerobic biodegradation potential of individual BTEX compounds by indigenous heterotrophic denitrifying microorganisms.
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Affiliation(s)
- Kyungjin Han
- Department of Environmental Engineering, Korea University, Sejong, Republic of Korea
| | - Uijeon Hong
- Department of Environmental Engineering, Korea University, Sejong, Republic of Korea
- KE Tech Incorporated, Daejeon, Republic of Korea
| | - Sunhwa Park
- National Institute of Environmental Research, Incheon, Republic of Korea
| | - Sooyoul Kwon
- Department of Environmental Health, Korea National Open University, Seoul, Republic of Korea
| | - Young Kim
- Department of Environmental Engineering, Korea University, Sejong, Republic of Korea
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Chang YT, Chen HC, Chou HL, Li H, Boyd SA. A coupled UV photolysis-biodegradation process for the treatment of decabrominated diphenyl ethers in an aerobic novel bioslurry reactor. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:6078-6089. [PMID: 32989696 PMCID: PMC7521767 DOI: 10.1007/s11356-020-10753-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 09/06/2020] [Indexed: 06/11/2023]
Abstract
The commercial flame retardant is an emerging contaminant (EC) commonly found in soils and sediments. A coupled UV-photolysis-biodegradation process was used to decompose decabromodiphenyl ether (BDE-209) in clay slurries. A novel bioslurry bioreactor (NBB) was employed in which BDE-209 degradation was maximized by the simultaneous application of LED UVA irradiation and biodegradation by a mixed bacterial culture. The rate of BDE-209 degradation decreased in the order: coupled UV photolysis-biodegradation (1.31 × 10-2 day-1) > UV photolysis alone (1.10 × 10-2 day-1) > biodegradation alone (1.00 × 10-2 day-1). Degradation intermediates detected included hydroxylated polybrominated diphenylethers, partially debrominated PBDE congeners and polybrominated dibenzofuran. The UV-resistant bacterial strains isolated that could utilize BDE-209 as a sole carbon source included Stenotrophomonas sp., Pseudomonas sp., and Microbacterium sp. These strains encoded important functional genes such as dioxygenase and reductive dehalogenases. Continuous UV irradiation during the NBB process affected various biochemical oxidative reactions during PBDEs biodegradation. Simultaneous photolysis and biodegradation in the NBB system described reduces operational time, energy, expense, and maintenance-demands required for the remediation of BDE-209 when compared to sequential UV-biodegradation process or to biodegradation alone.
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Affiliation(s)
- Yi-Tang Chang
- Department of Microbiology, Soochow University, Taipei, 11102, Taiwan.
- Department of Plant, Soil and Microbial Science, Michigan State University, East Lansing, MI, 48824, USA.
| | - Huei-Chen Chen
- Department of Microbiology, Soochow University, Taipei, 11102, Taiwan
| | - Hsi-Ling Chou
- Department of Microbiology, Soochow University, Taipei, 11102, Taiwan
| | - Hui Li
- Department of Plant, Soil and Microbial Science, Michigan State University, East Lansing, MI, 48824, USA
| | - Stephen A Boyd
- Department of Plant, Soil and Microbial Science, Michigan State University, East Lansing, MI, 48824, USA.
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A Comparison of the Microbial Community and Functional Genes Present in Free-Living and Soil Particle-Attached Bacteria from an Aerobic Bioslurry Reactor Treating High-Molecular-Weight PAHs. SUSTAINABILITY 2019. [DOI: 10.3390/su11041088] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
High-molecular-weight (HMW) polycyclic aromatic hydrocarbons (PAHs) contaminate a wide range of ecosystems, including soils, groundwater, rivers and harbor sediments. The effective removal of HMW PAHs is a difficult challenge if a rapid remediation time and low economic cost are required. Bioremediation provides a cheap and eco-friendly cleanup strategy for the removal of HMW PAHs. Previous studies have focused on removal efficiency during PAHs bioremediation. In such studies, only limited research has targeted the bacterial communities and functional genes present in such bioremediation systems, specifically those of free-living (aqueous) bacteria and soil particle-attached bacteria present. In this study, a high-level of HMW PAH (1992 mg/kg pyrene) was bioremediated in an aerobic bioslurry reactor (ABR) for 42 days. The results showed a pseudo first order constant rate for pyrene biodegradation of 0.0696 day−1. The microbial communities forming free-living bacteria and soil-attached bacteria in the ABR were found to be different. An analysis of the aqueous samples identified free-living Mycobacterium spp., Pseudomonas putida, Rhodanobacter spp. and Burkholderia spp.; these organisms would seem to be involved in pyrene biodegradation. Various biointermediates, including phenanthrene, catechol, dibenzothiophene, 4,4′-bipyrimidine and cyclopentaphenanthrene, were identified and measured in the aqueous samples. When a similar approach was taken with the soil particle samples, most of the attached bacterial species did not seem to be involved in pyrene biodegradation. Furthermore, community level physiological profiling resulted in significantly different results for the aqueous and soil particle samples. Nevertheless, these two bacterial populations both showed positive signals for the presence of various dioxygenases, including PAHs-RHDα dioxygenases, riesk iron-sulfur motif dioxygenases and catechol 2,3-dioxygenases. The present findings provide a foundation that should help environmental engineers when designing future HMW PAH bioremediation systems that use the ABR approach.
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Zhang S, Ying Z, You J, Ye J, Cheng Z, Chen D, Chen J. Superior performance and mechanism of chlorobenzene degradation by a novel bacterium. RSC Adv 2019; 9:15004-15012. [PMID: 35516324 PMCID: PMC9064227 DOI: 10.1039/c9ra01229j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 05/05/2019] [Indexed: 01/08/2023] Open
Abstract
A newly isolated strain was identified as Ochrobactrum sp. by 16S rRNA sequence analysis and named as ZJUTCB-1.
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Affiliation(s)
- Shihan Zhang
- College of Environment
- Zhejiang University of Technology
- Hangzhou
- China
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province
| | - Zanyun Ying
- College of Environment
- Zhejiang University of Technology
- Hangzhou
- China
| | - Juping You
- College of Environment
- Zhejiang University of Technology
- Hangzhou
- China
| | - Jiexu Ye
- College of Environment
- Zhejiang University of Technology
- Hangzhou
- China
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province
| | - Zhuowei Cheng
- College of Environment
- Zhejiang University of Technology
- Hangzhou
- China
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province
| | - Dongzhi Chen
- College of Environment
- Zhejiang University of Technology
- Hangzhou
- China
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province
| | - Jianmeng Chen
- College of Environment
- Zhejiang University of Technology
- Hangzhou
- China
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province
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6
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QM/MM study of the reaction mechanism of Cl-cis,cis-muconate with muconate lactonizing enzyme. Bioorg Chem 2018; 80:453-460. [DOI: 10.1016/j.bioorg.2018.05.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 05/09/2018] [Accepted: 05/10/2018] [Indexed: 11/18/2022]
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Nijenhuis I, Stollberg R, Lechner U. Anaerobic microbial dehalogenation and its key players in the contaminated Bitterfeld-Wolfen megasite. FEMS Microbiol Ecol 2018; 94:4828323. [PMID: 29385441 DOI: 10.1093/femsec/fiy012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 01/25/2018] [Indexed: 11/14/2022] Open
Abstract
The megasite Bitterfeld-Wolfen is highly contaminated as a result of accidents and because of dumping of wastes from local chemical industries in the last century. A variety of contaminants including chlorinated ethenes and benzenes, hexachlorohexanes and chlorinated dioxins can still be found in the groundwater and (river) sediments. Investigations of the in situ microbial transformation of organohalides have been performed only over the last two decades at this megasite. In this review, we summarise the research on the activity of anaerobic dehalogenating bacteria at the field site in Bitterfeld-Wolfen, focusing on chlorinated ethenes, monochlorobenzene and chlorinated dioxins. Various methods and concepts were applied including ex situ cultivation and isolation, and in situ analysis of hydrochemical parameters, compound-specific stable isotope analysis of contaminants, 13C-tracer studies and molecular markers. Overall, biotransformation of organohalides is ongoing at the field site and Dehalococcoides mccartyi species play an important role in the detoxification process in the Bitterfeld-Wolfen region.
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Affiliation(s)
- Ivonne Nijenhuis
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Reiner Stollberg
- Department of Groundwater Remediation, Helmholtz Centre for Environmental Research-UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Ute Lechner
- Institute of Biology/Microbiology Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle, Germany
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8
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Jastrzebski R, Quesne MG, Weckhuysen BM, de Visser SP, Bruijnincx PCA. Experimental and computational evidence for the mechanism of intradiol catechol dioxygenation by non-heme iron(III) complexes. Chemistry 2014; 20:15686-91. [PMID: 25322920 PMCID: PMC4497327 DOI: 10.1002/chem.201404988] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Indexed: 11/15/2022]
Abstract
Catechol intradiol dioxygenation is a unique reaction catalyzed by iron-dependent enzymes and non-heme iron(III) complexes. The mechanism by which these systems activate dioxygen in this important metabolic process remains controversial. Using a combination of kinetic measurements and computational modelling of multiple iron(III) catecholato complexes, we have elucidated the catechol cleavage mechanism and show that oxygen binds the iron center by partial dissociation of the substrate from the iron complex. The iron(III) superoxide complex that is formed subsequently attacks the carbon atom of the substrate by a rate-determining C-O bond formation step.
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Affiliation(s)
- Robin Jastrzebski
- Inorganic Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Utrecht UniversityUniversiteitsweg 99, 3584 CG Utrecht (The Netherlands)
- The Manchester Institute for Biotechnology and the School of Chemical Engineering and Analytical Science, The University of Manchester131 Princess Street, Manchester, M1 7DN (UK)
| | - Matthew G Quesne
- The Manchester Institute for Biotechnology and the School of Chemical Engineering and Analytical Science, The University of Manchester131 Princess Street, Manchester, M1 7DN (UK)
| | - Bert M Weckhuysen
- Inorganic Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Utrecht UniversityUniversiteitsweg 99, 3584 CG Utrecht (The Netherlands)
| | - Sam P de Visser
- The Manchester Institute for Biotechnology and the School of Chemical Engineering and Analytical Science, The University of Manchester131 Princess Street, Manchester, M1 7DN (UK)
| | - Pieter C A Bruijnincx
- Inorganic Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Utrecht UniversityUniversiteitsweg 99, 3584 CG Utrecht (The Netherlands)
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9
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Táncsics A, Szoboszlay S, Szabó I, Farkas M, Kovács B, Kukolya J, Mayer Z, Kriszt B. Quantification of subfamily I.2.C catechol 2,3-dioxygenase mRNA transcripts in groundwater samples of an oxygen-limited BTEX-contaminated site. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:232-40. [PMID: 22091737 DOI: 10.1021/es201842h] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Low dissolved oxygen concentration of subsurface environments is a limiting factor for microbial aromatic hydrocarbon degradation, and to date, there are only a limited number of available reports on functional genes and microbes that take part in the degradation of aromatic hydrocarbons under hypoxic conditions. Recent discoveries shed light on the prevalence of subfamily I.2.C catechol 2,3-dioxygenases in petroleum hydrocarbon contaminated hypoxic groundwaters, and their considerable environmental importance was suggested. Here, we report on a Hungarian aromatic hydrocarbon (methyl-substituted benzene derivatives, mostly xylenes) contaminated site where we investigated this presumption. Groundwater samples were taken from the center and the edge of the contaminant plume and beyond the plume. mRNA transcripts of subfamily I.2.C catechol 2,3-dioxygenases were detected in considerable amounts in the contaminated samples by qPCR analysis, while activity of subfamily I.2.A, which includes the largest group of extradiol dioxygenases described by culture-dependent studies and thought to be widely distributed in BTEX-contaminated environments, was not observed. Bacterial community structure analyses showed the predominance of genus Rhodoferax related species in the contaminated samples.
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Affiliation(s)
- András Táncsics
- Regional University Center of Excellence in Environmental Industry, Faculty of Agricultural and Environmental Sciences, Szent István University, Gödöllő, Hungary.
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Lillis L, Clipson N, Doyle E. Quantification of catechol dioxygenase gene expression in soil during degradation of 2,4-dichlorophenol. FEMS Microbiol Ecol 2010; 73:363-9. [PMID: 20533943 DOI: 10.1111/j.1574-6941.2010.00906.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The tfdC and C23O genes encode two catechol dioxygenases that catalyse ortho and meta cleavage of a key metabolite (chlorocatechol) of 2,4-dichlorophenol (2,4-DCP) metabolism, respectively. Primers were designed and a real-time PCR assay was developed to assess the abundance and expression of both tfdC and C23O genes in a soil amended with 2,4-DCP over a 21-day period. tfdC, the gene encoding the ortho cleaving dioxygenase, was significantly more abundant than the meta cleaving dioxygenase gene (C23O) throughout the experiment. The highest levels of tfdC were observed 2 days after amendment of soil with 2,4-DCP, at which stage the rate of 2,4-DCP degradation was at its maximum. In contrast, C230 copy numbers declined initially and peaked when degradation had slowed considerably. mRNA of the two chlorocatechol dioxygenase genes was not detected on day 0, but both genes were expressed after this time point. tfdC was expressed at a significantly higher level than C23O in 2,4-DCP-amended soil throughout the course of the microcosm, indicating the dominance of the ortho metabolic pathway. Phylogenetic analysis revealed a wide diversity of chlorocatechol dioxygenase genes in the 2,4-DCP-exposed soil examined.
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Affiliation(s)
- Lorraine Lillis
- School of Biology and Environmental Science, Ardmore House, University College Dublin, Dublin, Ireland
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Balcke GU, Paschke H, Vogt C, Schirmer M. Pulsed gas injection: a minimum effort approach for enhanced natural attenuation of chlorobenzene in contaminated groundwater. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2009; 157:2011-2018. [PMID: 19299054 DOI: 10.1016/j.envpol.2009.02.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2008] [Revised: 02/23/2009] [Accepted: 02/24/2009] [Indexed: 05/27/2023]
Abstract
Chlorobenzene-contaminated groundwater was used to assess pulsed gas sparging as a minimum effort aeration strategy to enhance intrinsic natural attenuation. In contrast to existing biosparging operations, oxygen was supplied at minimum rate by reducing the gas injection frequency to 0.33 day(-1). Field tests in a model aquifer were conducted in a 12 m long reactor, filled with indigenous aquifer material and continuously recharged with polluted groundwater over 3 years. The closed arrangement allowed yield balances, cost accounting as well as the investigation of spatial distributions of parameters which are sensitive to the biodegradation process. Depending on the injection frequency and on the gas chosen for injection (pure oxygen or air) oxygen-deficient conditions prevailed in the aquifer. Despite the limiting availability of dissolved oxygen in the groundwater, chlorobenzene degradation under oxygen-deficient conditions proved to be more effective than under conditions with dissolved oxygen being available in high concentrations.
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Affiliation(s)
- Gerd Ulrich Balcke
- Department of Hydrogeology, UFZ Helmholtz Centre for Environmental Research, Theodor-Lieser-Strasse 4, D-06120 Halle/Saale, Germany.
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12
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Jehmlich N, Schmidt F, Taubert M, Seifert J, von Bergen M, Richnow HH, Vogt C. Comparison of methods for simultaneous identification of bacterial species and determination of metabolic activity by protein-based stable isotope probing (Protein-SIP) experiments. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2009; 23:1871-1878. [PMID: 19449321 DOI: 10.1002/rcm.4084] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We developed a concept for analysing carbon and nitrogen fluxes in microbial communities by employing protein-based stable isotope probing (Protein-SIP) in metabolic labelling experiments with stable isotope labelled substrates. For identification of microbial species intact protein profiling (IPP) can be used, whereas the assessment of their metabolic activity is achieved by shotgun mass mapping (SMM). Microbial cultures were grown on substrates containing (13)C or (15)N. For identification of species we tested both the IPP and the SMM approaches. Mass spectra (MALDI-MS) were taken from mixtures of either intact proteins or peptides from tryptic digestion for generating species-specific peak patterns. In the case of SMM, the fragmentation of peptides was additionally used to obtain sequence information for species identification. Mass spectra of peptide sequences allow calculation of the amount of (13)C or (15)N incorporation within peptides for determining metabolic activity of the specific species. The comparison of IPP and SMM revealed a higher robustness of species identification by SMM. In addition, the assessment of incorporation levels of (13)C and (15)N into peptides by SMM revealed a lower uncertainty (0.5-0.8 atom %) compared to IPP (6.4-8.9 atom %). The determination of metabolic activity and function of individual species by Protein-SIP can help to analyse carbon and nitrogen fluxes within microbial communities.
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Affiliation(s)
- Nico Jehmlich
- Department of Proteomics, Helmholtz Centre for Environmental Research - UFZ, Permoserstr. 15, D-04318 Leipzig, Germany
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Rahm BG, Richardson RE. Dehalococcoides' gene transcripts as quantitative bioindicators of tetrachloroethene, trichloroethene, and cis-1,2-dichloroethene dehalorespiration rates. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2008; 42:5099-5105. [PMID: 18754354 DOI: 10.1021/es702912t] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Gene transcripts corresponding to 16S rRNA, the hydrogenase (H2ase) Hup, a sequence annotated asformate dehydrogenase (Fdh) and reductive dehalogenases (RDases) TceA, PceA, DET1559, and DET1545 in Dehalococcoides ethenogenes strain 195 (DET) hold promise as potential bioindicators of the dehalorespiration of chlorinated ethenes. Here, we present quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR) data taken from DET-containing mixed culture microcosms (4.4 x 10(8) DET 16S rRNA gene copies/mL) operated under continuous-feed conditions, with the aim of clarifying the relationships between pseudosteady-state abundances of bioindicator transcripts and respiration rate of various substrates: tetrachloroethene (PCE), trichloroethene (TCE), and cis-1,2-dichloroethene (cDCE). Results from PCE-fed microcosms suggested an induction threshold for transcription of some bioindicator genes between chloroethene respiration rates of 2.1 and 9.5 microeeq/L/hr. Putative RDase genes DET1559 and DET1545, however, were up-regulated at low PCE respiration rates and may be functionally significant when substrate levels are low. Data from PCE-fed microcosms operated at saturation kinetics indicated that a high respiration rate was not necessarily associated with a correspondingly high bioindicator transcript abundance. From these microcosms we calculated an approximate yield value of 1.6 x 10(8) 16S rRNA gene copies (cells) per micromol Cl- released and estimated a kmax of PCE respiration of 3 x 10(-9) micromol Cl- per 16S rRNA gene copy per day. TCE- and cDCE-fed microcosm studies indicated that Fdh, Hup, and TceA were the most abundant transcripts and could make suitable choices as bioindicators of activity for these substrates. Hup transcripts could be positively correlated to respiration rate (between approximately 8 and 45 microeeq/L/hr) regardless of chloroethene substrate, with transcript levels predicted to increase by 1.8 x 10(9) copies/mL culture for every/eeq/ L/hr increase in respiration rate (R2 = 0.90). Although RDase transcripts may provide information on substrate range, H2ase transcripts may be better indicators of per cell respiration rates.
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Affiliation(s)
- Brian G Rahm
- Cornell University, Department of Civil and Environmental Engineering, 220 Hollister Hall, Ithaca, New York 14853, USA
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Guerin TF. Ex-situ bioremediation of chlorobenzenes in soil. JOURNAL OF HAZARDOUS MATERIALS 2008; 154:9-20. [PMID: 17988797 DOI: 10.1016/j.jhazmat.2007.09.094] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2007] [Revised: 09/22/2007] [Accepted: 09/24/2007] [Indexed: 05/20/2023]
Abstract
Chlorinated benzenes, including chlorobenzene (CB) and 1,2-dichlorobenzene (DCB) are widely used as chemical intermediates and solvents across industry. Soil contaminated with these compounds was treated in a pilot-scale trial in 6 m3 cells. Air was drawn through each cell and exhausted via an activated carbon (GAC) filter system. The trial objective was to stimulate native microflora with nutrients and varying levels of organic amendments (0%, 12% and 35%). Initial soil DCB concentrations varied from <1 to 6 mg/kg in the three cells with an average of 2 mg/kg. Approximately 90% of the DCB mass present in the soil was removed over a period of 2-3 weeks. Up to 100-fold increases in total heterotrophs (THP), CB+ and DCB+ degraders were observed. Residual concentrations of chlorinated benzenes were generally below detection limits (0.2 mg/kg). Adding organic matter did not enhance the removal of CB and DCB under the trial conditions, which were set up to minimize losses from volatilization. Biodegradation estimation calculations indicated that <5% of the chlorinated benzenes were removed by volatilization and 90% removed by biodegradation. Laboratory shake flask trials confirmed that the soils in the pilot-scale treatment contained a microbial consortium capable of mineralizing CB and DCB. This consortium was capable of mineralizing both CB and DCB with up to 50% of carbon added as chlorinated benzene substrate being recovered as CO2 and up to 44% of organic chlorine being released as chloride ion in mineralization tests, further confirming these chlorinated benzenes were biodegraded. The study confirms that vented ex-situ biotreatment processes for chlorinated benzenes can be achieved without excessive losses from volatilization and that naturally occurring microflora can be readily stimulated with aeration and nutrients.
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Affiliation(s)
- Turlough F Guerin
- Telstra Corporation Limited, L33/242 Exhibition Street, Melbourne 3000, Australia.
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15
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Ciesielski S, Pokoj T, Klimiuk E. Molecular insight into activated sludge producing polyhydroxyalkanoates under aerobic–anaerobic conditions. J Ind Microbiol Biotechnol 2008; 35:805-14. [DOI: 10.1007/s10295-008-0352-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2007] [Accepted: 04/01/2008] [Indexed: 10/22/2022]
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Herrmann S, Kleinsteuber S, Neu TR, Richnow HH, Vogt C. Enrichment of anaerobic benzene-degrading microorganisms by in situ microcosms. FEMS Microbiol Ecol 2008; 63:94-106. [PMID: 18081593 DOI: 10.1111/j.1574-6941.2007.00401.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Microcosms filled with different solids (sand, lava, Amberlite XAD-7) were exposed for 67 days in the sulfidic part of a groundwater monitoring well downstream of the source zone of a benzene-contaminated aquifer and subsequently incubated in the laboratory. Benzene was repeatedly degraded in several microcosms accompanied by production of sulfide, leading to stable benzene-degrading enrichment cultures. In control microcosms without filling material, benzene was initially degraded, but the benzene-degrading capacity could not be sustained. The results indicate that long-term physiologically active benzene-degrading microorganisms were attached to surfaces of the solids. The biodiversity and attachment behavior of microorganisms in the in situ microcosms was assessed by confocal laser scanning microscopy and single-strand conformation polymorphism (SSCP) analysis, followed by sequencing of dominant SSCP bands. The microbial community was composed of several different Bacteria, representing members of Clostridia, Bacteroidales, all subgroups of the Proteobacteria, Verrucomicrobia, Nitrospira, Chloroflexi and Chlorobi. Only a few archaeal sequences could be retrieved from the communities. The majority of phylotypes were affiliated to bacterial groups with a possible functional relationship to the bacterial sulfur cycle, thus indicating that the microbial community in the investigated aquifer zone depends mainly on inorganic sulfur compounds as electron donors or acceptors, a finding that corresponds to the geochemical data.
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Affiliation(s)
- Steffi Herrmann
- Department of Isotope Biogeochemistry, UFZ-Helmholtz Centre for Environmental Research, Permoserstrasse 15, Leipzig, Germany
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Weiss JV, Cozzarelli IM. Biodegradation in contaminated aquifers: incorporating microbial/molecular methods. GROUND WATER 2008; 46:305-322. [PMID: 18194318 DOI: 10.1111/j.1745-6584.2007.00409.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
In order to evaluate natural attenuation in contaminated aquifers, there has been a recent recognition that a multidisciplinary approach, incorporating microbial and molecular methods, is required. Observed decreases in contaminant mass and identified footprints of biogeochemical reactions are often used as evidence of intrinsic bioremediation, but characterizing the structure and function of the microbial populations at contaminated sites is needed. In this paper, we review the experimental approaches and microbial methods that are available as tools to evaluate the controls on microbially mediated degradation processes in contaminated aquifers. We discuss the emerging technologies used in biogeochemical studies and present a synthesis of recent studies that serve as models of integrating microbiological approaches with more traditional geochemical and hydrogeologic approaches in order to address important biogeochemical questions about contaminant fate.
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Affiliation(s)
- Johanna V Weiss
- Biotechnology Program, Northern Virginia Community College, Manassas, VA 20109, USA
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Rahm BG, Richardson RE. Correlation of respiratory gene expression levels and pseudo-steady-state PCE respiration rates in Dehalococcoides ethenogenes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2008; 42:416-421. [PMID: 18284140 DOI: 10.1021/es071455s] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
DNA and RNA transcripts, particularly of genes of functional importance in the reductively dechlorinating microbe Dehalococcoides, are increasingly being studied as potential molecular bioindicators of reductive dechlorination. Ideally, mRNA bioindicators would be informative both qualitatively (with respect to dechlorination end point and substrate range) and quantitatively (with respectto activity rates). Here, we examined pseudo-steady-state mRNA levels in Dehalococcoides-containing microcosms continuously fed PCE at various loading rates. We characterized gene transcript abundance of potential Dehalococcoides bioindicators of reductive dechlorination, including 16S rRNA, and genes encoding an annotated formate dehydrogenase (Fdh), the hydrogenase (H2ase) Hup, and the reductive dehalogenases (RDases) TceA, DET1559, PceA, and DET1545. Increases in steady PCE loading rate led to corresponding increases in PCE respiration rate (1.5 +/- 0.1, 2.5 +/- 0.3, 4.8 +/- 0.1, and 9.2 +/- 0.5 micromol/L/hr). We also observed that pseudo-steady-state expression levels of most functional targets increase linearly over PCE respiration rates of 1.5-4.8 micromol/L/hr, with Fdh, Hup, and TceA transcripts increasing by approximately 2 x 10(10) copies per mL of culture for every micromol/L/hr increase in chloroethene respiration rate, and DET1559 and PceAtranscripts increasing by approximately9 x 10(9) copies per mL of culture, butthat increased respiration rates of 9.2 micromol/L/hr did not necessarily lead to corresponding increases in transcript levels.
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Affiliation(s)
- Brian G Rahm
- Department of Civil and Environmental Engineering, Cornell University, 220 Hollister Hall, Ithaca, New York 14853, USA
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Nicolaisen MH, Baelum J, Jacobsen CS, Sørensen J. Transcription dynamics of the functional tfdA gene during MCPA herbicide degradation by Cupriavidus necator AEO106 (pRO101) in agricultural soil. Environ Microbiol 2008; 10:571-9. [PMID: 18190516 DOI: 10.1111/j.1462-2920.2007.01476.x] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A modified protocol for simultaneous extraction of RNA and DNA, followed by real-time polymerase chain reaction quantification, was used to investigate tfdA gene expression during in situ degradation of the herbicide MCPA (4-chloro-2-methylphenoxy-acetic acid) in soil. tfdA encodes an alpha-ketoglutarate-dependent dioxygenase catalysing the first step in the degradation pathway of MCPA and 2,4-D (2,4-dichlorophenoxy-acetic acid). A linear recovery of tfdA mRNA over three orders of magnitude was shown, and the tfdA mRNA level was normalized using the tfdA mRNA/DNA ratio. The density of active cells required for tfdA mRNA detection was 10(5) cells g(-1) soil. Natural soil microcosms inoculated with Cupriavidus necator (formerly Ralstonia eutropha) AEO106 (pRO101) cells were amended with four different MCPA concentrations (2, 20, 50 and 150 mg kg(-1)). Mineralization rates were estimated by quantification of 14CO2 emission from degradation of 14C-MCPA. tfdA mRNA was detected 1 h after amendment at all four concentrations. In soils amended with 2 and 20 mg kg(-1), the mRNA/DNA ratio for tfdA demonstrated a sharp transient maximum of tfdA expression from no to full expression within 3 and 6 h respectively, followed by a decline and complete loss of expression after 19 and 43 h. A more complex pattern of tfdA expression was observed for the higher 50 and 150 mg kg(-1) amendments; this coincided with growth of C. necator AEO106 (pRO101) in the system. Repeated amendment with MCPA after 2 weeks in the 20 mg kg(-1) scenario revealed a sharp increase of tfdA mRNA, and absence of a mineralization lag phase. For all amendments, tfdA mRNA was detectable only during active mineralization, and thus revealed a direct correlation between tfdA mRNA presence and microbial degrader activity. The present study demonstrates that direct analysis of functional gene expression dynamics by quantification of mRNA can indeed be made in natural soil.
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Affiliation(s)
- Mette Haubjerg Nicolaisen
- Section of Genetics and Microbiology, Department of Ecology, University of Copenhagen, Thorvaldensvej 40, 1871 Frederiksberg C, Denmark.
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Dominguez RF, da Silva MLB, McGuire TM, Adamson D, Newell CJ, Alvarez PJJ. Aerobic bioremediation of chlorobenzene source-zone soil in flow-through columns: performance assessment using quantitative PCR. Biodegradation 2007; 19:545-53. [PMID: 17960485 DOI: 10.1007/s10532-007-9160-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2007] [Accepted: 10/08/2007] [Indexed: 11/25/2022]
Abstract
Flow-through aquifer columns were operated for 12 weeks to evaluate the benefits of aerobic biostimulation for the bioremediation of source-zone soil contaminated with chlorobenzenes (CBs). Quantitative Polymerase Chain Reaction (qPCR) was used to measure the concentration of total bacteria (16S rRNA gene) and oxygenase genes involved in the biodegradation of aromatic compounds (i.e., toluene dioxygenase, ring hydroxylating monooxygenase, naphthalene dioxygenase, phenol hydroxylase, and biphenyl dioxygenase). Monochlorobenzene, which is much more soluble than dichlorobenzenes, was primarily removed by flushing, and biostimulation showed little benefit. In contrast, dichlorobenzene removal was primarily due to biodegradation, and the removal efficiency was much higher in oxygen-amended columns compared to a control column. To our knowledge, this is the first report that oxygen addition can enhance CB source-zone soil bioremediation. Analysis by qPCR showed that whereas the biphenyl and toluene dioxygenase biomarkers were most abundant, increases in the concentration of the phenol hydroxylase gene reflected best the higher dichlorobenzene removal due to aerobic biostimulation. This suggests that quantitative molecular microbial ecology techniques could be useful to assess CB source-zone bioremediation performance.
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Affiliation(s)
- Rosa F Dominguez
- Department of Civil and Environmental Engineering, Rice University, Houston, TX, USA
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21
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Balcke GU, Wegener S, Kiesel B, Benndorf D, Schlömann M, Vogt C. Kinetics of chlorobenzene biodegradation under reduced oxygen levels. Biodegradation 2007; 19:507-18. [DOI: 10.1007/s10532-007-9156-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2007] [Accepted: 10/01/2007] [Indexed: 11/30/2022]
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22
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Winderl C, Schaefer S, Lueders T. Detection of anaerobic toluene and hydrocarbon degraders in contaminated aquifers using benzylsuccinate synthase (bssA) genes as a functional marker. Environ Microbiol 2007; 9:1035-46. [PMID: 17359274 DOI: 10.1111/j.1462-2920.2006.01230.x] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Benzylsuccinate synthase (Bss) is the key enzyme of anaerobic toluene degradation and has been found in all anaerobic toluene degrading bacterial isolates tested. However, only a few pure cultures capable of anaerobic toluene oxidation are available to date, and it is important to understand the relevance of these model organisms for in situ bioremediation of hydrocarbon-contaminated aquifers. Due to their phylogenetic dispersal, it is not possible to specifically target anaerobic toluene degraders using marker rRNA genes. We therefore established an assay targeting a approximately 794 bp fragment within the Bss alpha-subunit (bssA) gene, which allows for the specific detection and affiliation of both known and unknown anaerobic degraders. Three distinct tar-oil-contaminated aquifer sites were screened for intrinsic bssA gene pools in order to identify and compare the diversity of hydrocarbon degraders present at these selected sites. We were able to show that local diversity patterns of degraders were entirely distinct, apparently highly specialized and well-adapted to local biogeochemical settings. Discovered at one of the sites were bssA genes closely related to that of Geobacter spp., which provides evidence for an importance of iron reduction for toluene degradation in these sediments. Retrieved from the other two sites, dominated by sulfate reduction, were previously unidentified bssA genes and also deeply branching putative bssA homologues. We provide evidence for a previously unrecognized diversity of anaerobic toluene degraders and also of other hydrocarbon degraders using fumarate-adding key reactions in contaminated aquifers. These findings enhance our current understanding of intrinsic hydrocarbon-degrading microbial communities in perturbed aquifers and may have potential for the future assessment and prediction of natural attenuation based on degradation genes.
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Affiliation(s)
- Christian Winderl
- Institute of Groundwater Ecology, GSF - National Research Center for Environment and Health, Neuherberg, Germany
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23
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Nestler H, Kiesel B, Kaschabek SR, Mau M, Schlömann M, Balcke GU. Biodegradation of chlorobenzene under hypoxic and mixed hypoxic-denitrifying conditions. Biodegradation 2007; 18:755-67. [PMID: 17279449 DOI: 10.1007/s10532-007-9104-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2006] [Accepted: 01/16/2007] [Indexed: 10/23/2022]
Abstract
Pseudomonas veronii strain UFZ B549, Acidovorax facilis strain UFZ B530, and a community of indigenous groundwater bacteria, adapted to oxygen limitation, were cultivated on chlorobenzene and its metabolites 2-chloro-cis,cis-muconate and acetate/succinate under hypoxic and denitrifying conditions. Highly sensitive approaches were used to maintain defined low oxygen partial pressures in an oxygen-re-supplying headspace. With low amounts of oxygen available all cultures converted chlorobenzene, though the pure strains accumulated 3-chlorocatechol and 2-chloro-cis,cis-muconate as intermediates. Under strictly anoxic conditions no chlorobenzene transformation was observed, while 2-chloro-cis,cis-muconate, the fission product of oxidative ring cleavage, was readily degraded by the investigated chlorobenzene-degrading cultures at the expense of nitrate as terminal electron acceptor. Hence, we conclude that oxygen is an obligatory reactant for initial activation of chlorobenzene and fission of the aromatic ring, but it can be partially replaced by nitrate in respiration. The tendency to denitrify in the presence of oxygen during growth on chlorobenzene appeared to depend on the oxygen availability and the efficiency to metabolize chlorobenzene under oxygen limitation, which is largely regulated by the activity of the intradiol ring fission dioxygenase. Permanent cultivation of a groundwater consortium under reduced oxygen levels resulted in enrichment of a community almost exclusively composed of members of the beta-Proteobacteria and Bacteroidetes. Thus, it is deduced that these strains can still maintain high activities of oxygen-requiring enzymes that allow for efficient CB transformation under hypoxic conditions.
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Affiliation(s)
- Holger Nestler
- Department of Hydrogeology, Helmholtz Centre for Environmental Research-UFZ, Theodor-Lieser-Strasse 4, D-06120 Halle (Saale), Germany.
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24
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Lee PKH, Johnson DR, Holmes VF, He J, Alvarez-Cohen L. Reductive dehalogenase gene expression as a biomarker for physiological activity of Dehalococcoides spp. Appl Environ Microbiol 2006; 72:6161-8. [PMID: 16957242 PMCID: PMC1563655 DOI: 10.1128/aem.01070-06] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study characterizes the transcriptional expression of the reductive dehalogenase (RDase)-encoding tceA and vcrA genes and evaluates their applicability as potential biological markers of Dehalococcoides activity. When Dehalococcoides ethenogenes 195 was provided with trichloroethene (TCE) as the electron acceptor, the expression of the tceA gene increased by 90-fold relative to that in cells starved of chlorinated ethenes, demonstrating that tceA gene expression is indicative of the active physiological state of this strain. In a Dehalococcoides-containing enrichment culture that contains both the tceA and vcrA genes, the tceA gene was up-regulated in response to TCE and cis-1,2-dichloroethene (cDCE) exposure, while the vcrA gene was up-regulated in response to TCE, cDCE, and vinyl chloride (VC). When chlorinated ethenes were depleted, the RDase-encoding gene transcripts decayed exponentially, with a half-life between 4.8 and 6.1 h, until they reached a stable background level after 2 days. We found that while gene expression correlated generally to the presence of chlorinated ethenes, there was no apparent direct relationship between RDase-encoding transcript numbers and respective rates of TCE, cDCE, and VC dechlorination activities. However, elevated tceA and vcrA expression did correlate with chlorinated-ethene reduction beyond cDCE, suggesting that elevated RDase-encoding transcript numbers could serve as a biomarker for the physiological ability of Dehalococcoides spp. to dechlorinate beyond cDCE.
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Affiliation(s)
- Patrick K H Lee
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA 94720-1710, USA
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25
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Gödeke S, Richnow HH, Weiss H, Fischer A, Vogt C, Borsdorf H, Schirmer M. Multi tracer test for the implementation of enhanced in-situ bioremediation at a BTEX-contaminated megasite. JOURNAL OF CONTAMINANT HYDROLOGY 2006; 87:211-36. [PMID: 16844262 DOI: 10.1016/j.jconhyd.2006.05.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2004] [Revised: 05/10/2006] [Accepted: 05/15/2006] [Indexed: 05/10/2023]
Abstract
At the Centre for Environmental Research Leipzig-Halle (UFZ) research site in Zeitz, Germany, benzene contaminates the lower of two aquifers with concentrations of up to 20 mg/l. Since the benzene plume has a minimum length of approximately 1 km, enhanced natural attenuation measures are being considered as a remediation strategy. This study describes the performance and evaluation of a multi-species reactive tracer test using the tracers fluorescein and bromide as conservative tracers and toluene as reactive tracer. Sampling was performed over a period of six months using a detailed network of multilevel sampling wells. Toluene was only slightly retarded in comparison to bromide, whereas fluorescein was retarded considerably stronger. Therefore, it was not possible to use fluorescein as an in situ tracer for the determination of groundwater velocities. The ionic nature of fluorescein is assumed to be the major reason for its retardation. The results show that the infiltration conditions were suitable to produce a wide spreading of the tracer front along the full thickness of the aquifer. Thus, a large aquifer volume can be treated in future enhanced bioremediation measures. The total quantity of infiltrated toluene (24 l) was degraded under sulfate-reducing conditions over a flow path of 50 m. Benzylsuccinate was identified as a metabolite of toluene degradation under sulfate-reducing conditions at this site. The modelling results show that toluene degradation was described more accurately using Monod kinetics than first-order kinetics. Since toluene was only slightly retarded in comparison to bromide, sorption and desorption processes were considered to be negligible.
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Affiliation(s)
- Stefan Gödeke
- UFZ - Centre for Environmental Research Leipzig-Halle in the Helmholtz Association, Department of Groundwater Remediation, Permoserstr. 15, 04318 Leipzig, Germany
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26
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Vogt C, Lösche A, Kleinsteuber S, Müller S. Population profiles of a stable, commensalistic bacterial culture grown with toluene under sulphate-reducing conditions. Cytometry A 2005; 66:91-102. [PMID: 16003722 DOI: 10.1002/cyto.a.20158] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
BACKGROUND Most bacteria present in nature are not culturable in pure culture by means of classic cultivation methods (Pace NR, 1997, Science 276:734-740; Amann RI et al., 1995, Microbiol Rev 59:143-169.). However, it was recently shown that most aerobic heterotrophic bacteria could grow only on artificial media when other micro-organisms are present (Kaeberlein T et al., 2002, Science 296:1127-1129). Because the sulphate reducer Desulfobacula toluolica DSM 7467 and a bacterium (strain MV1) identified as Cellulosimicrobium sp. were not culturable unaccompanied, flow cytometry was used to highlight the strains' relation within the consortium. METHODS DNA patterns were used to provide strain-specific information about population proliferation dynamics. Cells were grown anaerobically and fed with toluene under sulphate-reducing conditions. RESULTS Oxidation of toluene occurred only in association with sulphate reduction and growth of D. toluolica. A characteristic chromosomal pattern, with at least six subpopulations of D. toluolica, appeared during the stationary phase, and asymmetric cell division was detected. The accompanying strain MV1 grew repeatedly to a high percentage of the culture only in certain growth phases of D. toluolica independently of the feeding substrate toluene. CONCLUSIONS A commensalistic relation between the two strains is suggested. The repeated rapid and frequent changes of the quantities within the community subsets are indicative of very flexible adaptations to changing environmental conditions, reflecting the need for modulated cell states and the ability to use every available source of carbon and energy for survival.
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Affiliation(s)
- Carsten Vogt
- Department of Environmental Microbiology, Centre for Environmental Research Leipzig-Halle, Leipzig, Germany
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27
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Scow KM, Hicks KA. Natural attenuation and enhanced bioremediation of organic contaminants in groundwater. Curr Opin Biotechnol 2005; 16:246-53. [PMID: 15961025 DOI: 10.1016/j.copbio.2005.03.009] [Citation(s) in RCA: 153] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2005] [Revised: 03/15/2005] [Accepted: 03/24/2005] [Indexed: 11/22/2022]
Abstract
An area of intense scientific and practical interest is the biogeochemical and microbial processes determining the success of natural attenuation, biostimulation and/or bioaugmentation treatments for organic contaminants in groundwater. Recent studies in this area have focused on the reductive dechlorination of chlorinated solvents, the degradation of the fuel additive methyl tert-butyl ether, and the removal of long-term hydrocarbon contamination. These studies have been facilitated by the use of stable isotope analysis to demonstrate in situ bioremediation and push-pull tests, in which isotopes are injected into aquifers and then quickly retrieved and analyzed, to measure in situ activity. Molecular tools such as quantitative PCR, the detection of mRNA expression, and numerous DNA fingerprinting methods have also proved valuable, being employed to identify and sometimes quantify environmentally important organisms or changes in communities. Methods to track bacteria and tools to characterize bacterial attachment properties have also offered insight into bacterial transport in situ.
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Affiliation(s)
- Kate M Scow
- Land, Air and Water Resources, University of California, 1 Shields Avenue Davis, California 95616, USA
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28
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Meckenstock RU, Morasch B, Griebler C, Richnow HH. Stable isotope fractionation analysis as a tool to monitor biodegradation in contaminated acquifers. JOURNAL OF CONTAMINANT HYDROLOGY 2004; 75:215-55. [PMID: 15610901 DOI: 10.1016/j.jconhyd.2004.06.003] [Citation(s) in RCA: 251] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2003] [Revised: 06/18/2004] [Accepted: 06/18/2004] [Indexed: 05/22/2023]
Abstract
The assessment of biodegradation in contaminated aquifers has become an issue of increasing importance in the recent years. To some extent, this can be related to the acceptance of intrinsic bioremediation or monitored natural attenuation as a means to manage contaminated sites. Among the few existing methods to detect biodegradation in the subsurface, stable isotope fractionation analysis (SIFA) is one of the most promising approaches which is pronounced by the drastically increasing number of applications. This review covers the recent laboratory and field studies assessing biodegradation of contaminants via stable isotope analysis. Stable isotope enrichment factors have been found that vary from no fractionation for dioxygenase reactions converting aromatic hydrocarbons over moderate fractionation by monooxygenase reactions (epsilon=-3 per thousand) and some anaerobic studies on microbial degradation of aromatic hydrocarbons (epsilon=-1.7 per thousand) to larger fractionations by anaerobic dehalogenation reactions of chlorinated solvents (epsilon=between -5 per thousand and -30 per thousand). The different isotope enrichment factors can be related to the respective biochemical reactions. Based on that knowledge, we discuss under what circumstances SIFA can be used for a qualitative or even a quantitative assessment of biodegradation in the environment. In a steadily increasing number of cases, it was possible to explain biodegradation processes in the field based on isotope enrichment factors obtained from laboratory experiments with pure cultures and measured isotope values from the field. The review will focus on the aerobic and anaerobic degradation of aromatic hydrocarbons and chlorinated solvents as the major contaminants of groundwater. Advances in the instrumental development for stable isotope analysis are only mentioned if it is important for the understanding of the application.
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Affiliation(s)
- Rainer U Meckenstock
- Institute of Groundwater Ecology, GSF-National Research Center for Environment and Health, Ingolstädter Landstrasse 1, D-85764 Neuherberg, Germany.
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29
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Sharkey FH, Banat IM, Marchant R. Detection and quantification of gene expression in environmental bacteriology. Appl Environ Microbiol 2004; 70:3795-806. [PMID: 15240248 PMCID: PMC444812 DOI: 10.1128/aem.70.7.3795-3806.2004] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Freddie H Sharkey
- School of Biomedical Sciences, University of Ulster, Coleraine, County Londonderry BT52 1SA, Northern Ireland
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30
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Küster E, Dorusch F, Vogt C, Weiss H, Altenburger R. On line biomonitors used as a tool for toxicity reduction evaluation of in situ groundwater remediation techniques. Biosens Bioelectron 2004; 19:1711-22. [PMID: 15142606 DOI: 10.1016/j.bios.2004.01.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2003] [Revised: 12/23/2003] [Accepted: 01/14/2004] [Indexed: 10/26/2022]
Abstract
Success of groundwater remediation is typically controlled via snapshot analysis of selected chemical substances or physical parameters. Biological parameters, i.e. ecotoxicological assays, are rarely employed. Hence the aim of the study was to develop a bioassay tool, which allows an on line monitoring of contaminated groundwater, as well as a toxicity reduction evaluation (TRE) of different remediation techniques in parallel and may furthermore be used as an additional tool for process control to supervise remediation techniques in a real time mode. Parallel testing of groundwater remediation techniques was accomplished for short and long time periods, by using the energy dependent luminescence of the bacterium Vibrio fischeri as biological monitoring parameter. One data point every hour for each remediation technique was generated by an automated biomonitor. The bacteria proved to be highly sensitive to the contaminated groundwater and the biomonitor showed a long standing time despite the highly corrosive groundwater present in Bitterfeld, Germany. The bacterial biomonitor is demonstrated to be a valuable tool for remediation success evaluation. Dose response relationships were generated for the six quantitatively dominant groundwater contaminants (2-chlortoluene, 1,2- and 1,4-dichlorobenzene, monochlorobenzene, ethylenbenzene and benzene). The concentrations of individual volatile organic chemicals (VOCs) could not explain the observed effects in the bacteria. An expected mixture toxicity was calculated for the six components using the concept of concentration addition. The calculated EC(50) for the mixture was still one order of magnitude lower than the observed EC(50) of the actual groundwater. The results pointed out that chemical analysis of the six most quantitative substances alone was not able to explain the effects observed with the bacteria. Thus chemical analysis alone may not be an adequate tool for remediation success evaluation in terms of toxicity reduction.
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Affiliation(s)
- Eberhard Küster
- Department of Chemical Ecotoxicology, UFZ Centre for Environmental Research Leipzig-Halle in the Helmholtz-Association, Permoserstr. 15, 04318 Leipzig, Germany.
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31
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Han JI, Semrau JD. Quantification of gene expression in methanotrophs by competitive reverse transcription-polymerase chain reaction. Environ Microbiol 2004; 6:388-99. [PMID: 15008816 DOI: 10.1111/j.1462-2920.2004.00572.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To improve the monitoring of methanotrophic activity, a competitive reverse transcription-polymerase chain reaction (RT-PCR) methodology was developed. Homologous internal RNA standards were created for mmoX and pmoA, genes encoding polypeptides of sMMO and pMMO, respectively. Using specific primer sets, expression of sMMO and pMMO could be quantified by means of competitive RT-PCR and capillary electrophoresis with uncoated bare-fused silica columns and UV detection. Using this technique, it was discovered that the amount of mRNA transcript for both mmoX and pmoA correlated well with whole-cell sMMO and pMMO activity respectively. A method for soil RNA extraction was also developed to utilize this RNA quantification technique for the monitoring of methanotrophic activity in situ. In a model soil slurry system with a background concentration of 2.9 micro M copper, it was found that only pmoA was transcribed by cells capable of expressing both forms of MMO. As pMMO and sMMO have very different substrate ranges and kinetics, this methodology may prove useful for optimizing in situ bioremediation by methanotrophs. Provided sufficient sequence information is available to create specific primer sets, these techniques can be applied for monitoring and measuring the activity of other microbial communities in situ.
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Affiliation(s)
- Jong-In Han
- Department of Civil and Environmental Engineering, The University of Michigan, 1351 Beal Avenue, Ann Arbor, Michigan 48109-2125, USA
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Vogt C, Alfreider A, Lorbeer H, Hoffmann D, Wuensche L, Babel W. Bioremediation of chlorobenzene-contaminated ground water in an in situ reactor mediated by hydrogen peroxide. JOURNAL OF CONTAMINANT HYDROLOGY 2004; 68:121-141. [PMID: 14698874 DOI: 10.1016/s0169-7722(03)00092-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
New in situ reactive barrier technologies were tested nearby a local aquifer in Bitterfeld, Saxonia-Anhalt, Germany, which is polluted mainly by chlorobenzene (CB), in concentrations up to 450 microM. A reactor filled with original aquifer sediment was designed for the microbiological remediation of the ground water by indigenous bacterial communities. Two remediation variants were examined: (a) the degradation of CB under anoxic conditions in the presence of nitrate; (b) the degradation of CB under mixed electron acceptor conditions (oxygen+nitrate) using hydrogen peroxide as the oxygen-releasing compound. Under anoxic conditions, no definite degradation of CB was observed. Adding hydrogen peroxide (2.94 mM) and nitrate (2 mM) led to the disappearance of CB (ca. 150 microM) in the lower part of the reactor, accompanied by a strong increase of the number of cultivable aerobic CB degrading bacteria in reactor water and sediment samples, indicating that CB was degraded mainly by productive bacterial metabolism. Several aerobic CB degrading bacteria, mostly belonging to the genera Pseudomonas and Rhodococcus, were isolated from reactor water and sediments. In laboratory experiments with reactor water, oxygen was rapidly released by hydrogen peroxide, whereas biotic-induced decomposition reactions of hydrogen peroxide were almost four times faster than abiotic-induced decomposition reactions. A clear chemical degradation of CB mediated by hydrogen peroxide was not observed. CB was also completely degraded in the reactor after reducing the hydrogen peroxide concentration to 880 microM. The CB degradation completely collapsed after reducing the hydrogen peroxide concentration to 440 microM. In the following, the hydrogen peroxide concentrations were increased again (to 880 microM, 2.94 mM, and 880 microM, respectively), but the oxygen demand for CB degradation was higher than observed before, indicating a shift in the bacterial population. During the whole experiment, nitrate was uniformly reduced during the flow path in the reactor.
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Affiliation(s)
- Carsten Vogt
- Department of Environmental Microbiology, UFZ Centre for Environmental Research Leipzig-Halle, Permoserstrasse 15, D-04318, Leipzig, Germany.
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Berselli S, Milone G, Canepa P, Di Gioia D, Fava F. Effects of cyclodextrins, humic substances, and rhamnolipids on the washing of a historically contaminated soil and on the aerobic bioremediation of the resulting effluents. Biotechnol Bioeng 2004; 88:111-20. [PMID: 15389483 DOI: 10.1002/bit.20218] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Nontoxic and biodegradable pollutant-mobilizing agents, instead of chemical surfactants, were tested in the washing of an actual-site chloroaromatic-contaminated soil. A soil historically contaminated by chlorinated anilines and benzenes, thiophenes and several polycyclic aromatic hydrocarbons was subjected to washing by suspending it (15% w/v) in water or in water with 1.0% (w/v) beta-clodextrin (beta-CD), hydroxypropyl-beta-cyclodextrin (HP-beta-CD), rhamnolipid (RL), dissolved humic substances (HS), or Triton X-100 (TX) in shaken batch reactors for 24 hr. The resulting wastewaters were amended with nutrients and treated aerobically in shaken reactors for 65 days. The biogenic agents markedly enhanced (by 237%, beta-CD; 265%, HP-beta-CD; 400%, RL; 566%, HS) the capability of water of eluting organic pollutants from the soil. TX enhanced the overall pollutant removal by about 660%; however, a lower depletion of the initial soil ecotoxicity, along with a more extensive impact on the soil organic matter, was observed. Furthermore, TX adversely affected the bioremediation of the resulting effluent by apparently inducing a premature decrease of specialized bacterial biomass. By contrast, the biogenic agents, and in particular HS and RL, sustained the biodegradation and dechlorination of pollutants by apparently enhancing the availability of specialized bacteria in the reactors. Thus, the biogenic agents proposed here seem to be promising nontoxic and nonaggressive soil washing agents for the integrated physicochemical (washing) and biological (aerobic posttreatment) restoration of poorly bioremediable (chloro) organics-contaminated soils.
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Affiliation(s)
- Sara Berselli
- Department of Applied Chemistry and Material Science, Faculty of Engineering, University of Bologna, Viale Risorgimento 2, I-40136 Bologna, Italy
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