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Tejerina J, Ryan J, Vyssotski M, Lagutin K, Lu Y, Visnovsky G. Labelling of eicosapentaenoic acid with stable isotope 13C in the marine bacterium Shewanella marinintestina. J Microbiol Methods 2023; 204:106633. [PMID: 36462663 DOI: 10.1016/j.mimet.2022.106633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 11/26/2022] [Accepted: 11/26/2022] [Indexed: 12/02/2022]
Abstract
Eicosapentaenoic acid (EPA) is an essential omega-3 polyunsaturated fatty acid that plays a critical role in marine life. It is present in several marine animals, including fish, but the primary producers of EPA are phytoplankton and specific marine bacteria. Although most of the EPA present in marine animals come from phytoplankton, the bacterial input into the marine EPA food web is still unknown. The labelling of EPA within a bacterial strain could be a viable strategy to help revealing this contribution. In this work, Shewanella marinintestina IRL 567, a marine bacterium isolated from fish guts and known to produce EPA, was labelled with the stable isotope 13C at small (250-mL shake flask), bench (2.5-L shake flask), and pilot scale (50-L stirred tank bioreactor). Growing the bacterium with 13C-acetate in the culture medium demonstrated that EPA was de-novo synthesized utilizing acetate as precursor. 13C incorporation into the EPA molecule resulted in values as high as 95.5% of the synthesized EPA being labelled in small scale, 95.9% in bench scale and 91.5% in pilot scale. This simple method to label EPA proved to be effective and therefore it could be a valuable tool to follow the fate of bacterial EPA into higher trophic levels.
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Affiliation(s)
- Jimena Tejerina
- Department of Chemical and Process Engineering, University of Canterbury, Private Bag, 4800 Christchurch, New Zealand.
| | - Jason Ryan
- Luinabio, 2806 Ipswich Rd, Brisbane, Queensland 4077, Australia
| | - Mikhail Vyssotski
- Callaghan Innovation, PO Box 31310, Lower Hutt 5040, Wellington, New Zealand
| | - Kirill Lagutin
- Callaghan Innovation, PO Box 31310, Lower Hutt 5040, Wellington, New Zealand
| | - Yinrong Lu
- Callaghan Innovation, PO Box 31310, Lower Hutt 5040, Wellington, New Zealand
| | - Gabriel Visnovsky
- Department of Chemical and Process Engineering, University of Canterbury, Private Bag, 4800 Christchurch, New Zealand
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Hidalgo KJ, Teramoto EH, Soriano AU, Valoni E, Baessa MP, Richnow HH, Vogt C, Chang HK, Oliveira VM. Taxonomic and functional diversity of the microbiome in a jet fuel contaminated site as revealed by combined application of in situ microcosms with metagenomic analysis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 708:135152. [PMID: 31812384 DOI: 10.1016/j.scitotenv.2019.135152] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 10/21/2019] [Accepted: 10/22/2019] [Indexed: 06/10/2023]
Abstract
Natural attenuation represents all processes that govern contaminant mass removal, which mainly occurs via microbial degradation in the environment. Although this process is intrinsic its rate and efficiency depend on multiple factors. This study aimed to characterize the microbial taxonomic and functional diversity in different aquifer sediments collected in the saturated zone and in situ microcosms (BACTRAP®s) amended with hydrocarbons (13C-labeled and non-labeled benzene, toluene and naphthalene) using 16S rRNA gene and "shotgun" Illumina high throughput sequencing at a jet-fuel contaminated site. The BACTRAP®s were installed to assess hydrocarbon metabolism by native bacteria. Results indicated that Proteobacteria, Actinobacteria and Firmicutes were the most dominant phyla (~98%) in the aquifer sediment samples. Meanwhile, in the benzene- and toluene-amended BACTRAP®s the phyla Firmicutes and Proteobacteria accounted for about 90% of total community. In the naphthalene-amended BACTRAP®, members of the SR-FBR-L83 family (Order Ignavibacteriales) accounted for almost 80% of bacterial community. Functional annotation of metagenomes showed that only the sediment sample located at the source zone border and with the lowest BTEX concentration, has metabolic potential to degrade hydrocarbons aerobically. On the other hand, in situ BACTRAP®s allowed enrichment of hydrocarbon-degrading bacteria. Metagenomic data suggest that fumarate addition is the main mechanism for hydrocarbon activation of toluene. Also, indications for methylation, hydroxylation and carboxylation as activation mechanisms for benzene anaerobic conversion were found. After 120 days of exposure in the contaminated groundwater, the isotopic analysis of fatty acids extracted from BACTRAP®s demonstrated the assimilation of isotopic labeled compounds in the cells of microbes expressed by strong isotopic enrichment. We propose that the microbiota in this jet-fuel contaminated site has metabolic potential to degrade benzene and toluene by a syntrophic process, between members of the families Geobacteraceae and Peptococcaceae (genus Pelotomaculum), coupled to nitrate, iron and/or sulfate reduction.
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Affiliation(s)
- K J Hidalgo
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato 255, Cidade Universitária, Campinas, SP. ZIP 13083-862, Brazil.
| | - E H Teramoto
- Laboratory of Basin Studies (LEBAC), São Paulo State University (UNESP), Rio Claro, Av. 24A, 1515 ZIP 13506-900, Brazil
| | - A U Soriano
- PETROBRAS/ R&D Center (CENPES), Av. Horácio Macedo, 950. ZIP 21941-915 Ilha do Fundão, Rio de Janeiro, Brazil
| | - E Valoni
- PETROBRAS/ R&D Center (CENPES), Av. Horácio Macedo, 950. ZIP 21941-915 Ilha do Fundão, Rio de Janeiro, Brazil
| | - M P Baessa
- PETROBRAS/ R&D Center (CENPES), Av. Horácio Macedo, 950. ZIP 21941-915 Ilha do Fundão, Rio de Janeiro, Brazil
| | - H H Richnow
- Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research (UFZ), Permoserstrasse 15 04318 Leipzig, Germany
| | - C Vogt
- Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research (UFZ), Permoserstrasse 15 04318 Leipzig, Germany
| | - H K Chang
- Laboratory of Basin Studies (LEBAC), São Paulo State University (UNESP), Rio Claro, Av. 24A, 1515 ZIP 13506-900, Brazil
| | - V M Oliveira
- Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas - UNICAMP, Paulínia, Brazil, Av. Alexandre Cazellato, 999, ZIP 13148-218, Brazil
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3
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Wilhelm RC, Hanson BT, Chandra S, Madsen E. Community dynamics and functional characteristics of naphthalene-degrading populations in contaminated surface sediments and hypoxic/anoxic groundwater. Environ Microbiol 2018; 20:3543-3559. [PMID: 30051558 DOI: 10.1111/1462-2920.14309] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 06/07/2018] [Indexed: 12/19/2022]
Abstract
Earlier research on the biogeochemical factors affecting natural attenuation in coal-tar contaminated groundwater, at South Glens Falls, NY, revealed the importance of anaerobic metabolism and trophic interactions between degrader and bacterivore populations. Field-based characterizations of both phenomena have proven challenging, but advances in stable isotope probing (SIP), single-cell imaging and shotgun metagenomics now provide cultivation-independent tools for their study. We tracked carbon from 13 C-labelled naphthalene through microbial populations in contaminated surface sediments over 6 days using respiration assays, secondary ion mass spectrometry imaging and shotgun metagenomics to disentangle the contaminant-based trophic web. Contaminant-exposed communities in hypoxic/anoxic groundwater were contrasted with those from oxic surface sediments to identify putative features of anaerobic catabolism of naphthalene. In total, six bacteria were responsible for naphthalene degradation. Cupriavidus, Ralstonia and Sphingomonas predominated at the earliest stages of SIP incubations and were succeeded in later stages by Stenotrophomonas and Rhodococcus. Metagenome-assembled genomes provided evidence for the ecological and functional characteristics underlying these temporal shifts. Identical species of Stenotrophomonas and Rhodococcus were abundant in the most contaminated, anoxic groundwater. Apparent increases in bacterivorous protozoa were observed following exposure to naphthalene, though insignificant amounts of carbon were transferred between bacterial degraders and populations of secondary feeders.
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Affiliation(s)
- Roland C Wilhelm
- Soil and Crop Sciences, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Buck T Hanson
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Subhash Chandra
- Cornell SIMS Laboratory, Department of Earth and Atmospheric Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Eugene Madsen
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
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Wegener G, Kellermann MY, Elvert M. Tracking activity and function of microorganisms by stable isotope probing of membrane lipids. Curr Opin Biotechnol 2016; 41:43-52. [PMID: 27179643 DOI: 10.1016/j.copbio.2016.04.022] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 04/27/2016] [Accepted: 04/27/2016] [Indexed: 12/17/2022]
Abstract
Microorganisms in soils and sediments are highly abundant and phylogenetically diverse, but their specific metabolic activity and function in the environment is often not well constrained. To address this critical aspect in environmental biogeochemistry, different methods involving stable isotope probing (SIP) and detection of the isotope label in a variety of molecular compounds have been developed. Here we review recent progress in lipid-SIP, a technique that combines the assimilation of specific 13C-labeled metabolic substrates such as inorganic carbon, methane, glucose and amino acids into diagnostic membrane lipid compounds. Using the structural characteristics of certain lipid types in combination with genetic molecular techniques, the SIP approach reveals the activity and function of distinct microbial groups in the environment. More recently, deuterium labeling in the form of deuterated water (D2O) extended the lipid-SIP portfolio. Since lipid biosynthetic pathways involve hydrogen (H+) uptake from water, lipid production can be inferred from the detection of D-assimilation into these compounds. Furthermore, by combining D2O and 13C-inorganic carbon (IC) labeling in a dual-SIP approach, rates of auto- and heterotrophic carbon fixation can be estimated. We discuss the design, analytical prerequisites, data processing and interpretation of single and dual-SIP experiments and highlight a case study on anaerobic methanotrophic communities inhabiting hydrothermally heated marine sediments.
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Affiliation(s)
- Gunter Wegener
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany; MARUM Center for Marine Environmental Sciences, Leobener Straße, 28359 Bremen, Germany.
| | - Matthias Y Kellermann
- Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, CA 93106, USA
| | - Marcus Elvert
- MARUM Center for Marine Environmental Sciences, Leobener Straße, 28359 Bremen, Germany
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5
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Cupples AM. Contaminant-Degrading Microorganisms Identified Using Stable Isotope Probing. Chem Eng Technol 2016. [DOI: 10.1002/ceat.201500479] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Bombach P, Nägele N, Rosell M, Richnow HH, Fischer A. Evaluation of ethyl tert-butyl ether biodegradation in a contaminated aquifer by compound-specific isotope analysis and in situ microcosms. JOURNAL OF HAZARDOUS MATERIALS 2015; 286:100-106. [PMID: 25559863 DOI: 10.1016/j.jhazmat.2014.12.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 12/07/2014] [Accepted: 12/17/2014] [Indexed: 06/04/2023]
Abstract
Ethyl tert-butyl ether (ETBE) is an upcoming groundwater pollutant in Europe whose environmental fate has been less investigated, thus far. In the present study, we investigated the in situ biodegradation of ETBE in a fuel-contaminated aquifer using compound-specific stable isotope analysis (CSIA), and in situ microcosms in combination with total lipid fatty acid (TLFA)-stable isotope probing (SIP). In a first field investigation, CSIA revealed insignificant carbon isotope fractionation, but low hydrogen isotope fractionation of up to +14‰ along the prevailing anoxic ETBE plume suggesting biodegradation of ETBE. Ten months later, oxygen injection was conducted to enhance the biodegradation of petroleum hydrocarbons (PH) at the field site. Within the framework of this remediation measure, in situ microcosms loaded with [(13)C6]-ETBE (BACTRAP(®)s) were exposed for 119 days in selected groundwater wells to assess the biodegradation of ETBE by TLFA-SIP under the following conditions: (i) ETBE as main contaminant; (ii) ETBE as main contaminant subjected to oxygen injection; (iii) ETBE plus other PH; (iv) ETBE plus other PH subjected to oxygen injection. Under all conditions investigated, significant (13)C-incorporation into microbial total lipid fatty acids extracted from the in situ microcosms was found, providing clear evidence of ETBE biodegradation.
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Affiliation(s)
- Petra Bombach
- UFZ - Helmholtz Centre for Environmental Research, Department of Isotope Biogeochemistry, Permoserstrasse 15, D-04318 Leipzig, Germany; Isodetect GmbH Leipzig, Deutscher Platz 5b, D-04103 Leipzig, Germany.
| | - Norbert Nägele
- Kuvier the Biotech Company S.L., Ctra. N-I, p.k. 234-P.E. INBISA 23ª, E-09001 Burgos, Spain
| | - Mònica Rosell
- UFZ - Helmholtz Centre for Environmental Research, Department of Isotope Biogeochemistry, Permoserstrasse 15, D-04318 Leipzig, Germany; Grup de Mineralogia Aplicada i Medi Ambient, Departament de Cristal·lografia, Mineralogia i Dipòsits Minerals, Facultat de Geologia, Universitat de Barcelona (UB), C/Martí i Franquès s/n, 08028 Barcelona, Spain
| | - Hans H Richnow
- UFZ - Helmholtz Centre for Environmental Research, Department of Isotope Biogeochemistry, Permoserstrasse 15, D-04318 Leipzig, Germany
| | - Anko Fischer
- Isodetect GmbH Leipzig, Deutscher Platz 5b, D-04103 Leipzig, Germany
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Bahr A, Fischer A, Vogt C, Bombach P. Evidence of polycyclic aromatic hydrocarbon biodegradation in a contaminated aquifer by combined application of in situ and laboratory microcosms using (13)C-labelled target compounds. WATER RESEARCH 2015; 69:100-109. [PMID: 25437342 DOI: 10.1016/j.watres.2014.10.045] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Revised: 10/17/2014] [Accepted: 10/20/2014] [Indexed: 05/21/2023]
Abstract
The number of approaches to evaluate the biodegradation of polycyclic aromatic hydrocarbons (PAHs) within contaminated aquifers is limited. Here, we demonstrate the applicability of a novel method based on the combination of in situ and laboratory microcosms using (13)C-labelled PAHs as tracer compounds. The biodegradation of four PAHs (naphthalene, fluorene, phenanthrene, and acenaphthene) was investigated in an oxic aquifer at the site of a former gas plant. In situ biodegradation of naphthalene and fluorene was demonstrated using in situ microcosms (BACTRAP(®)s). BACTRAP(®)s amended with either [(13)C6]-naphthalene or [(13)C5/(13)C6]-fluorene (50:50) were incubated for a period of over two months in two groundwater wells located at the contaminant source and plume fringe, respectively. Amino acids extracted from BACTRAP(®)-grown cells showed significant (13)C-enrichments with (13)C-fractions of up to 30.4% for naphthalene and 3.8% for fluorene, thus providing evidence for the in situ biodegradation and assimilation of those PAHs at the field site. To quantify the mineralisation of PAHs, laboratory microcosms were set up with BACTRAP(®)-grown cells and groundwater. Naphthalene, fluorene, phenanthrene, or acenaphthene were added as (13)C-labelled substrates. (13)C-enrichment of the produced CO2 revealed mineralisation of between 5.9% and 19.7% for fluorene, between 11.1% and 35.1% for acenaphthene, between 14.2% and 33.1% for phenanthrene, and up to 37.0% for naphthalene over a period of 62 days. Observed PAH mineralisation rates ranged between 17 μg L(-1) d(-1) and 1639 μg L(-1) d(-1). The novel approach combining in situ and laboratory microcosms allowed a comprehensive evaluation of PAH biodegradation at the investigated field site, revealing the method's potential for the assessment of PAH degradation within contaminated aquifers.
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Affiliation(s)
- Arne Bahr
- UFZ - Helmholtz Centre for Environmental Research, Department of Isotope Biogeochemistry, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Anko Fischer
- Isodetect GmbH, Deutscher Platz 5b, 04103 Leipzig, Germany
| | - Carsten Vogt
- UFZ - Helmholtz Centre for Environmental Research, Department of Isotope Biogeochemistry, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Petra Bombach
- UFZ - Helmholtz Centre for Environmental Research, Department of Isotope Biogeochemistry, Permoserstrasse 15, 04318 Leipzig, Germany; Isodetect GmbH, Deutscher Platz 5b, 04103 Leipzig, Germany.
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8
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Badia-Fabregat M, Rosell M, Caminal G, Vicent T, Marco-Urrea E. Use of stable isotope probing to assess the fate of emerging contaminants degraded by white-rot fungus. CHEMOSPHERE 2014; 103:336-342. [PMID: 24393565 DOI: 10.1016/j.chemosphere.2013.12.029] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 11/27/2013] [Accepted: 12/11/2013] [Indexed: 06/03/2023]
Abstract
The widespread of emerging contaminants in the environment and their potential impact on humans is a matter of concern. White-rot fungi are cosmopolitan organisms able to remove a wide range of pharmaceuticals and personal care products (PPCP) through cometabolism (i.e. laccases and peroxidases) or detoxification mechanisms (i.e. cytochrome P450 system). However, the use of PPCP as carbon source for these organisms is largely unexplored. Here, we used carbon stable isotope tracer experiments to assess the fate of anti-inflammatory diclofenac (DCF) and UV filter benzophenone-3 (BP3) during degradation by Trametes versicolor. The comparison between carbon isotopic composition of emitted carbon dioxide from 13C-labelled DCF ([acetophenyl ring-13C6]-DCF) and 13C-BP3 ([phenyl-13C6]-BP3) versus their 12C-homologue compounds showed mineralization of about 45% and 10% of the 13C contained in their respective molecules after 9 days of incubation. The carbon isotopic composition of the bulk biomass and the application of amino acid-stable isotope probing (SIP) allowed distinguishing between incorporation of 13C from BP3 into amino acids, which implies the use of this emerging contaminant as carbon source, and major intracellular accumulation of 13C from DCF without implying the transformation of its labelled phenyl ring into anabolic products. A mass balance of 13C in different compartments over time provided a comprehensive picture of the fate of DCF and BP3 across their different transformation processes. This is the first report assessing biodegradation of PPCP by SIP techniques and the use of emerging contaminants as carbon source for amino acid biosynthesis.
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Affiliation(s)
- Marina Badia-Fabregat
- Departament d'Enginyeria Química, Escola d'Enginyeria, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Mònica Rosell
- Grup de Mineralogia Aplicada i Medi Ambient, Departament de Cristal·lografia, Mineralogia i Dipòsits Minerals, Facultat de Geologia, Universitat de Barcelona, Martí Franquès s/n, 08028 Barcelona, Spain
| | - Glòria Caminal
- Institut de Química Avançada de Catalunya, IQAC-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Teresa Vicent
- Departament d'Enginyeria Química, Escola d'Enginyeria, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Ernest Marco-Urrea
- Departament d'Enginyeria Química, Escola d'Enginyeria, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
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Rakoczy J, Feisthauer S, Wasmund K, Bombach P, Neu TR, Vogt C, Richnow HH. Benzene and sulfide removal from groundwater treated in a microbial fuel cell. Biotechnol Bioeng 2013; 110:3104-13. [PMID: 23775304 DOI: 10.1002/bit.24979] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Revised: 06/03/2013] [Accepted: 06/07/2013] [Indexed: 11/11/2022]
Abstract
Sulfidic benzene-contaminated groundwater was used to fuel a two-chambered microbial fuel cell (MFC) over a period of 770 days. We aimed to understand benzene and sulfide removal processes in the anoxic anode chamber and describe the microbial community enriched over the operational time. Operated in batch feeding-like circular mode, supply of fresh groundwater resulted in a rapid increase in current production, accompanied by decreasing benzene and sulfide concentrations. The total electron recoveries for benzene and sulfide were between 18% and 49%, implying that benzene and sulfide were not completely oxidized at the anode. Pyrosequencing of 16S rRNA genes from the anode-associated bacterial community revealed the dominance of δ-Proteobacteria (31%), followed by β-Proteobacteria, Bacteroidetes, ϵ-Proteobacteria, Chloroflexi, and Firmicutes, most of which are known for anaerobic metabolism. Two-dimensional compound-specific isotope analysis demonstrated that benzene degradation was initiated by monohydroxylation, probably triggered by small amounts of oxygen which had leaked through the cation exchange membrane into the anode chamber. Experiments with [(13)C(6) ]-benzene revealed incorporation of (13)C into fatty acids of mainly Gram-negative bacteria, which are therefore candidates for benzene degradation. Our study demonstrated simultaneous benzene and sulfide removal by groundwater microorganisms which use an anode as artificial electron acceptor, thereby releasing an electrical current.
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Affiliation(s)
- Jana Rakoczy
- Department of Isotope Biogeochemistry, UFZ-Helmholtz Centre for Environmental Research, Permoserstraße 15, 04318, Leipzig, Germany
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Jechalke S, Franchini AG, Bastida F, Bombach P, Rosell M, Seifert J, von Bergen M, Vogt C, Richnow HH. Analysis of structure, function, and activity of a benzene-degrading microbial community. FEMS Microbiol Ecol 2013; 85:14-26. [DOI: 10.1111/1574-6941.12090] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 01/30/2013] [Accepted: 02/06/2013] [Indexed: 11/30/2022] Open
Affiliation(s)
- Sven Jechalke
- Department of Isotope Biogeochemistry; UFZ - Helmholtz Centre for Environmental Research; Leipzig; Germany
| | - Alessandro G. Franchini
- Department of Environmental Biotechnology; UFZ - Helmholtz Centre for Environmental Research; Leipzig; Germany
| | - Felipe Bastida
- Department of Isotope Biogeochemistry; UFZ - Helmholtz Centre for Environmental Research; Leipzig; Germany
| | - Petra Bombach
- Department of Isotope Biogeochemistry; UFZ - Helmholtz Centre for Environmental Research; Leipzig; Germany
| | - Mónica Rosell
- Department of Isotope Biogeochemistry; UFZ - Helmholtz Centre for Environmental Research; Leipzig; Germany
| | - Jana Seifert
- Department of Proteomics; UFZ - Helmholtz Centre for Environmental Research; Leipzig; Germany
| | | | - Carsten Vogt
- Department of Isotope Biogeochemistry; UFZ - Helmholtz Centre for Environmental Research; Leipzig; Germany
| | - Hans H. Richnow
- Department of Isotope Biogeochemistry; UFZ - Helmholtz Centre for Environmental Research; Leipzig; Germany
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Uhlik O, Leewis MC, Strejcek M, Musilova L, Mackova M, Leigh MB, Macek T. Stable isotope probing in the metagenomics era: a bridge towards improved bioremediation. Biotechnol Adv 2012; 31:154-65. [PMID: 23022353 DOI: 10.1016/j.biotechadv.2012.09.003] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 09/17/2012] [Accepted: 09/17/2012] [Indexed: 12/24/2022]
Abstract
Microbial biodegradation and biotransformation reactions are essential to most bioremediation processes, yet the specific organisms, genes, and mechanisms involved are often not well understood. Stable isotope probing (SIP) enables researchers to directly link microbial metabolic capability to phylogenetic and metagenomic information within a community context by tracking isotopically labeled substances into phylogenetically and functionally informative biomarkers. SIP is thus applicable as a tool for the identification of active members of the microbial community and associated genes integral to the community functional potential, such as biodegradative processes. The rapid evolution of SIP over the last decade and integration with metagenomics provide researchers with a much deeper insight into potential biodegradative genes, processes, and applications, thereby enabling an improved mechanistic understanding that can facilitate advances in the field of bioremediation.
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Affiliation(s)
- Ondrej Uhlik
- Institute of Chemical Technology Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Technicka 3, 166 28 Prague, Czech Republic.
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Ralebitso-Senior TK, Senior E, Di Felice R, Jarvis K. Waste gas biofiltration: advances and limitations of current approaches in microbiology. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:8542-8573. [PMID: 22746978 DOI: 10.1021/es203906c] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
As confidence in gas biofiltration efficacy grows, ever more complex malodorant and toxic molecules are ameliorated. In parallel, for many countries, emission control legislation becomes increasingly stringent to accommodate both public health and climate change imperatives. Effective gas biofiltration in biofilters and biotrickling filters depends on three key bioreactor variables: the support medium; gas molecule solubilization; and the catabolic population. Organic and inorganic support media, singly or in combination, have been employed and their key criteria are considered by critical appraisal of one, char. Catabolic species have included fungal and bacterial monocultures and, to a lesser extent, microbial communities. In the absence of organic support medium (soil, compost, sewage sludge, etc.) inoculum provision, a targeted enrichment and isolation program must be undertaken followed, possibly, by culture efficacy improvement. Microbial community process enhancement can then be gained by comprehensive characterization of the culturable and total populations. For all species, support medium attachment is critical and this is considered prior to filtration optimization by water content, pH, temperature, loadings, and nutrients manipulation. Finally, to negate discharge of fungal spores, and/or archaeal and/or bacterial cells, capture/destruction technologies are required to enable exploitation of the mineralization product CO(2).
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Siggins A, Gunnigle E, Abram F. Exploring mixed microbial community functioning: recent advances in metaproteomics. FEMS Microbiol Ecol 2012; 80:265-80. [PMID: 22225547 PMCID: PMC3491685 DOI: 10.1111/j.1574-6941.2011.01284.x] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Revised: 10/07/2011] [Accepted: 12/13/2011] [Indexed: 11/27/2022] Open
Abstract
System approaches to elucidate ecosystem functioning constitute an emerging area of research within microbial ecology. Such approaches aim at investigating all levels of biological information (DNA, RNA, proteins and metabolites) to capture the functional interactions occurring in a given ecosystem and track down characteristics that could not be accessed by the study of isolated components. In this context, the study of the proteins collectively expressed by all the microorganisms present within an ecosystem (metaproteomics) is not only crucial but can also provide insights into microbial functionality. Overall, the success of metaproteomics is closely linked to metagenomics, and with the exponential increase in the availability of metagenome sequences, this field of research is starting to experience generation of an overwhelming amount of data, which requires systematic analysis. Metaproteomics has been employed in very diverse environments, and this review discusses the recent advances achieved in the context of human biology, soil, marine and freshwater environments as well as natural and bioengineered systems.
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Affiliation(s)
- Alma Siggins
- Microbial Ecology Laboratory, Department of Microbiology and Ryan Institute, National University of IrelandGalway (NUI, Galway), Galway, Ireland
| | - Eoin Gunnigle
- Microbial Ecology Laboratory, Department of Microbiology and Ryan Institute, National University of IrelandGalway (NUI, Galway), Galway, Ireland
| | - Florence Abram
- Functional Environmental Microbiology, Department of Microbiology, National University of IrelandGalway (NUI, Galway), Galway, Ireland
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