1
|
May T, Polag D, Keppler F, Greule M, Müller L, König H. Methane oxidation in industrial biogas plants—Insights in a novel methanotrophic environment evidenced by pmoA gene analyses and stable isotope labelling studies. J Biotechnol 2018; 270:77-84. [DOI: 10.1016/j.jbiotec.2018.01.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Revised: 01/24/2018] [Accepted: 01/31/2018] [Indexed: 02/05/2023]
|
2
|
Isolation of methanotrophic bacteria from termite gut. Microbiol Res 2015; 179:29-37. [DOI: 10.1016/j.micres.2015.06.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 05/08/2015] [Accepted: 06/06/2015] [Indexed: 11/20/2022]
|
3
|
Rajala P, Bomberg M, Kietäväinen R, Kukkonen I, Ahonen L, Nyyssönen M, Itävaara M. Rapid Reactivation of Deep Subsurface Microbes in the Presence of C-1 Compounds. Microorganisms 2015; 3:17-33. [PMID: 27682076 PMCID: PMC5023232 DOI: 10.3390/microorganisms3010017] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 01/26/2015] [Accepted: 01/29/2015] [Indexed: 11/30/2022] Open
Abstract
Microorganisms in the deep biosphere are believed to conduct little metabolic activity due to low nutrient availability in these environments. However, destructive penetration to long-isolated bedrock environments during construction of underground waste repositories can lead to increased nutrient availability and potentially affect the long-term stability of the repository systems, Here, we studied how microorganisms present in fracture fluid from a depth of 500 m in Outokumpu, Finland, respond to simple carbon compounds (C-1 compounds) in the presence or absence of sulphate as an electron acceptor. C-1 compounds such as methane and methanol are important intermediates in the deep subsurface carbon cycle, and electron acceptors such as sulphate are critical components of oxidation processes. Fracture fluid samples were incubated in vitro with either methane or methanol in the presence or absence of sulphate as an electron acceptor. Metabolic response was measured by staining the microbial cells with fluorescent dyes that indicate metabolic activity and transcriptional response with RT-qPCR. Our results show that deep subsurface microbes exist in dormant states but rapidly reactivate their transcription and respiration systems in the presence of C-1 substrates, particularly methane. Microbial activity was further enhanced by the addition of sulphate as an electron acceptor. Sulphate- and nitrate-reducing microbes were particularly responsive to the addition of C-1 compounds and sulphate. These taxa are common in deep biosphere environments and may be affected by conditions disturbed by bedrock intrusion, as from drilling and excavation for long-term storage of hazardous waste.
Collapse
Affiliation(s)
- Pauliina Rajala
- Technical Research Centre of Finland (VTT), Kemistintie 3/Tietotie 2, FI-02044, Espoo, Finland.
| | - Malin Bomberg
- Technical Research Centre of Finland (VTT), Kemistintie 3/Tietotie 2, FI-02044, Espoo, Finland.
| | - Riikka Kietäväinen
- Geological Survey of Finland (GTK), P.O. Box 96, FI-02151, Espoo, Finland.
| | - Ilmo Kukkonen
- University of Helsinki, P.O. Box 33, University of Helsinki, FI-00014, Helsinki, Finland.
| | - Lasse Ahonen
- Geological Survey of Finland (GTK), P.O. Box 96, FI-02151, Espoo, Finland.
| | - Mari Nyyssönen
- Technical Research Centre of Finland (VTT), Kemistintie 3/Tietotie 2, FI-02044, Espoo, Finland.
| | - Merja Itävaara
- Technical Research Centre of Finland (VTT), Kemistintie 3/Tietotie 2, FI-02044, Espoo, Finland.
| |
Collapse
|
4
|
Purkamo L, Bomberg M, Nyyssönen M, Kukkonen I, Ahonen L, Itävaara M. Heterotrophic communities supplied by ancient organic carbon predominate in deep fennoscandian bedrock fluids. MICROBIAL ECOLOGY 2015; 69:319-332. [PMID: 25260922 DOI: 10.1007/s00248-014-0490-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 08/29/2014] [Indexed: 06/03/2023]
Abstract
The deep subsurface hosts diverse life, but the mechanisms that sustain this diversity remain elusive. Here, we studied microbial communities involved in carbon cycling in deep, dark biosphere and identified anaerobic microbial energy production mechanisms from groundwater of Fennoscandian crystalline bedrock sampled from a deep drill hole in Outokumpu, Finland, by using molecular biological analyses. Carbon cycling pathways, such as carbon assimilation, methane production and methane consumption, were studied with cbbM, rbcL, acsB, accC, mcrA and pmoA marker genes, respectively. Energy sources, i.e. the terminal electron accepting processes of sulphate-reducing and nitrate-reducing communities, were assessed with detection of marker genes dsrB and narG, respectively. While organic carbon is scarce in deep subsurface, the main carbon source for microbes has been hypothesized to be inorganic carbon dioxide. However, our results demonstrate that carbon assimilation is performed throughout the Outokumpu deep scientific drill hole water column by mainly heterotrophic microorganisms such as Clostridia. The source of carbon for the heterotrophic microbial metabolism is likely the Outokumpu bedrock, mainly composed of serpentinites and metasediments with black schist interlayers. In addition to organotrophic metabolism, nitrate and sulphate are other possible energy sources. Methanogenic and methanotrophic microorganisms are scarce, but our analyses suggest that the Outokumpu deep biosphere provides niches for these organisms; however, they are not very abundant.
Collapse
Affiliation(s)
- Lotta Purkamo
- VTT Technical Research Centre of Finland, PL1000, 02044, Espoo, Finland,
| | | | | | | | | | | |
Collapse
|
5
|
Functional gene analysis of freshwater iron-rich flocs at circumneutral pH and isolation of a stalk-forming microaerophilic iron-oxidizing bacterium. Appl Environ Microbiol 2013; 79:5283-90. [PMID: 23811518 DOI: 10.1128/aem.03840-12] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Iron-rich flocs often occur where anoxic water containing ferrous iron encounters oxygenated environments. Culture-independent molecular analyses have revealed the presence of 16S rRNA gene sequences related to diverse bacteria, including autotrophic iron oxidizers and methanotrophs in iron-rich flocs; however, the metabolic functions of the microbial communities remain poorly characterized, particularly regarding carbon cycling. In the present study, we cultivated iron-oxidizing bacteria (FeOB) and performed clone library analyses of functional genes related to carbon fixation and methane oxidization (cbbM and pmoA, respectively), in addition to bacterial and archaeal 16S rRNA genes, in freshwater iron-rich flocs at groundwater discharge points. The analyses of 16S rRNA, cbbM, and pmoA genes strongly suggested the coexistence of autotrophic iron oxidizers and methanotrophs in the flocs. Furthermore, a novel stalk-forming microaerophilic FeOB, strain OYT1, was isolated and characterized phylogenetically and physiologically. The 16S rRNA and cbbM gene sequences of OYT1 are related to those of other microaerophilic FeOB in the family Gallionellaceae, of the Betaproteobacteria, isolated from freshwater environments at circumneutral pH. The physiological characteristics of OYT1 will help elucidate the ecophysiology of microaerophilic FeOB. Overall, this study demonstrates functional roles of microorganisms in iron flocs, suggesting several possible linkages between Fe and C cycling.
Collapse
|
6
|
Shukla AK, Upadhyay SN, Dubey SK. Current trends in trichloroethylene biodegradation: a review. Crit Rev Biotechnol 2012; 34:101-14. [PMID: 23057686 DOI: 10.3109/07388551.2012.727080] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Over the past few years biodegradation of trichloroethylene (TCE) using different microorganisms has been investigated by several researchers. In this review article, an attempt has been made to present a critical summary of the recent results related to two major processes--reductive dechlorination and aerobic co-metabolism used for TCE biodegradation. It has been shown that mainly Clostridium sp. DC-1, KYT-1, Dehalobacter, Dehalococcoides, Desulfuromonas, Desulfitobacterium, Propionibacterium sp. HK-1, and Sulfurospirillum bacterial communities are responsible for the reductive dechlorination of TCE. Efficacy of bacterial communities like Nitrosomonas, Pseudomonas, Rhodococcus, and Xanthobacter sp. etc. for TCE biodegradation under aerobic conditions has also been examined. Mixed cultures of diazotrophs and methanotrophs have been used for TCE degradation in batch and continuous cultures (biofilter) under aerobic conditions. In addition, some fungi (Trametes versicolor, Phanerochaete chrysosporium ME-446) and Actinomycetes have also been used for aerobic biodegradation of TCE. The available information on kinetics of biofiltration of TCE and its degradation end-products such as CO2 are discussed along with the available results on the diversity of bacterial community obtained using molecular biological approaches. It has emerged that there is a need to use metabolic engineering and molecular biological tools more intensively to improve the robustness of TCE degrading microbial species and assess their diversity.
Collapse
Affiliation(s)
- Awadhesh Kumar Shukla
- Department of Botany, Faculty of Science, Banaras Hindu University , Varanasi , India and
| | | | | |
Collapse
|
7
|
Fukuba T, Miyaji A, Okamoto T, Yamamoto T, Kaneda S, Fujii T. Integrated in situ genetic analyzer for microbiology in extreme environments. RSC Adv 2011. [DOI: 10.1039/c1ra00490e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
8
|
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.
Collapse
Affiliation(s)
- Johanna V Weiss
- Biotechnology Program, Northern Virginia Community College, Manassas, VA 20109, USA
| | | |
Collapse
|
9
|
Molecular ecology techniques for the study of aerobic methanotrophs. Appl Environ Microbiol 2007; 74:1305-15. [PMID: 18165358 DOI: 10.1128/aem.02233-07] [Citation(s) in RCA: 199] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
10
|
Chen Y, Dumont MG, Cébron A, Murrell JC. Identification of active methanotrophs in a landfill cover soil through detection of expression of 16S rRNA and functional genes. Environ Microbiol 2007; 9:2855-69. [DOI: 10.1111/j.1462-2920.2007.01401.x] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
11
|
Vigliotta G, Nutricati E, Carata E, Tredici SM, De Stefano M, Pontieri P, Massardo DR, Prati MV, De Bellis L, Alifano P. Clonothrix fusca Roze 1896, a filamentous, sheathed, methanotrophic gamma-proteobacterium. Appl Environ Microbiol 2007; 73:3556-65. [PMID: 17416684 PMCID: PMC1932688 DOI: 10.1128/aem.02678-06] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Crenothrix polyspora Cohn 1870 and Clonothrix fusca Roze 1896 are two filamentous, sheathed microorganisms exhibiting complex morphological differentiation, whose phylogeny and physiology have been obscure for a long time due to the inability to cultivate them. Very recently, DNA sequencing data from uncultured C. polyspora-enriched material have suggested that Crenothrix is a methane-oxidizing gamma-proteobacterium (39). In contrast, the possible ecological function of C. fusca, originally considered a developmental stage of C. polyspora, is unknown. In this study, temporal succession of two filamentous, sheathed microorganisms resembling Cohn's Crenothrix and Roze's Clonothrix was observed by analyzing the microbial community of an artesian well by optical microscopy. Combined culture-based and culture-independent approaches enabled us to assign C. fusca to a novel subgroup of methane-oxidizing gamma-proteobacteria distinct from that of C. polyspora. This assignment was supported by (i) methane uptake and assimilation experiments, (ii) ultrastructural data showing the presence in C. fusca cytoplasm of an elaborate membrane system resembling that of methanotrophic gamma-proteobacteria, and (iii) sequencing data demonstrating the presence in its genome of a methanol dehydrogenase alpha subunit-encoding gene (mxaF) and a conventional particulate methane mono-oxygenase alpha subunit-encoding gene (pmoA) that is different from the unusual pmoA (u-pmoA) of C. polyspora.
Collapse
Affiliation(s)
- Giovanni Vigliotta
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università degli Studi di Lecce, Via Monteroni, 73100 Lecce, Italy
| | | | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Pester M, Brune A. Expression profiles of fhs (FTHFS) genes support the hypothesis that spirochaetes dominate reductive acetogenesis in the hindgut of lower termites. Environ Microbiol 2006; 8:1261-70. [PMID: 16817934 DOI: 10.1111/j.1462-2920.2006.01020.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Reductive acetogenesis is an important metabolic process in the hindgut of wood-feeding termites. We analysed diversity and expression profiles of the bacterial fhs gene, a marker gene encoding a key enzyme of reductive acetogenesis, formyl tetrahydrofolate synthetase (FTHFS), to identify the active homoacetogenic populations in representatives of three different termite families. Clone libraries of polymerase chain reaction-amplified fhs genes from hindgut contents of Reticulitermes santonensis (Rhinotermitidae) and Cryptotermes secundus (Kalotermitidae) were compared with previously published fhs gene sequences obtained from Zootermopsis nevadensis (Termopsidae). Most of the clones clustered among the 'Termite Treponemes', which comprise also the fhs genes of the two strains of the homoacetogenic spirochaete Treponema primitia. The high abundance of treponemal fhs genes in all clone libraries was in agreement with the results of DNA-based terminal-restriction fragment length polymorphism (T-RFLP) analysis. Moreover, in mRNA-based T-RFLP profiles of the three termites, only expression of fhs genes of 'Termite Treponemes' was detected, albeit at different levels. In C. secundus, only one of the dominating phylotypes was transcribed, while in R. santonensis, the apparently less abundant fhs genes were the most actively expressed. Our results strongly support the hypothesis that spirochaetes are responsible for reductive acetogenesis in the hindgut of lower, wood-feeding termites.
Collapse
Affiliation(s)
- Michael Pester
- Max Planck Institute for Terrestrial Microbiology, Department of Biogeochemistry, Karl-von-Frisch-Strasse, 35043 Marburg, Germany
| | | |
Collapse
|
13
|
Stoecker K, Bendinger B, Schöning B, Nielsen PH, Nielsen JL, Baranyi C, Toenshoff ER, Daims H, Wagner M. Cohn's Crenothrix is a filamentous methane oxidizer with an unusual methane monooxygenase. Proc Natl Acad Sci U S A 2006; 103:2363-7. [PMID: 16452171 PMCID: PMC1413686 DOI: 10.1073/pnas.0506361103] [Citation(s) in RCA: 144] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
135 years ago Ferdinand Cohn, the founder of bacteriology, microscopically observed a conspicuous filamentous bacterium with a complex life cycle and described it as Crenothrix polyspora. This uncultured bacterium is infamous for mass developments in drinking water systems, but its phylogeny and physiology remained unknown. We show that C. polyspora is a gammaproteobacterium closely related to methanotrophs and capable of oxidizing methane. We discovered that C. polyspora encodes a phylogenetically very unusual particulate methane monooxygenase whose expression is strongly increased in the presence of methane. Our findings demonstrate a previously unrecognized complexity of the evolutionary history and cell biology of methane-oxidizing bacteria.
Collapse
Affiliation(s)
- Kilian Stoecker
- *Department für Mikrobielle Ökologie, Universität Wien, A-1090 Wien, Austria
| | - Bernd Bendinger
- Deutsche Vereinigung des Gas- und Wasserfaches-Forschungsstelle, Technische Universität Hamburg, D-21073 Hamburg, Germany; and
| | - Björn Schöning
- Deutsche Vereinigung des Gas- und Wasserfaches-Forschungsstelle, Technische Universität Hamburg, D-21073 Hamburg, Germany; and
| | - Per H. Nielsen
- Department of Life Sciences, Aalborg University, DK-9000 Aalborg, Denmark
| | - Jeppe L. Nielsen
- Department of Life Sciences, Aalborg University, DK-9000 Aalborg, Denmark
| | - Christian Baranyi
- *Department für Mikrobielle Ökologie, Universität Wien, A-1090 Wien, Austria
| | - Elena R. Toenshoff
- *Department für Mikrobielle Ökologie, Universität Wien, A-1090 Wien, Austria
| | - Holger Daims
- *Department für Mikrobielle Ökologie, Universität Wien, A-1090 Wien, Austria
| | - Michael Wagner
- *Department für Mikrobielle Ökologie, Universität Wien, A-1090 Wien, Austria
- To whom correspondence should be addressed at:
Department for Mikrobielle Ökologie, Universität Wien, Althanstrasse 14, A-1090 Wien, Austria. E-mail:
| |
Collapse
|
14
|
Anderson RT. DOE genomics: Applications toin situ subsurface bioremediation. ACTA ACUST UNITED AC 2006. [DOI: 10.1002/rem.20110] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
15
|
Watanabe K, Baker PW. Environmentally relevant microorganisms. J Biosci Bioeng 2005; 89:1-11. [PMID: 16232691 DOI: 10.1016/s1389-1723(00)88043-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/1999] [Accepted: 12/03/1999] [Indexed: 11/19/2022]
Abstract
The development of molecular microbial ecology in the 1990s has allowed scientists to realize that microbial populations in the natural environment are much more diverse than microorganisms so far isolated in the laboratory. This finding has exerted a significant impact on environmental biotechnology, since knowledge in this field has been largely dependent on studies with pollutant-degrading bacteria isolated by conventional culture methods. Researchers have thus started to use molecular ecological methods to analyze microbial populations relevant to pollutant degradation in the environment (called environmentally relevant microorganisms, ERMs), although further effort is needed to gain practical benefits from these studies. This review highlights the utility and limitations of molecular ecological methods for understanding and advancing environmental biotechnology processes. The importance of the combined use of molecular ecological and physiological methods for identifying ERMs is stressed.
Collapse
Affiliation(s)
- K Watanabe
- Marine Biotechnology Institute, Kamaishi Laboratories, 3-75-1 Heita, Kamaishi, Iwate 026-0001, Japan
| | | |
Collapse
|
16
|
Sharma S, Aneja MK, Mayer J, Munch JC, Schloter M. Diversity of transcripts of nitrite reductase genes (nirK and nirS) in rhizospheres of grain legumes. Appl Environ Microbiol 2005; 71:2001-7. [PMID: 15812032 PMCID: PMC1082563 DOI: 10.1128/aem.71.4.2001-2007.2005] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2004] [Accepted: 10/28/2004] [Indexed: 11/20/2022] Open
Abstract
Transcription of the nirK and nirS genes coding for dissimilatory bacterial nitrite reductases was analyzed by reverse transcription PCR (RT-PCR) of mRNA isolated from rhizosphere samples of three economically important grain legumes at maturity: Vicia faba, Lupinus albus, and Pisum sativum. The nirK gene and transcripts could be detected in all the rhizosphere samples. In contrast, nirS could not be detected. Sampling variations were analyzed by comparing denaturing gradient gel electrophoresis profiles derived from nirK RT-PCR products. High similarity was observed between the replicates, and so one representative product per legume was cloned. Clones with the correct insert size were screened by restriction fragment length polymorphism by using the restriction enzyme MspI. The clones could be distributed into 12 different patterns. Patterns 1, 3, 4, 5, and 7 were common in clone libraries of the three rhizosphere types under study. Patterns 2, 9, 10, and 11 were absent from Pisum rhizospheres, while patterns 6, 8, and 12 were absent from the Vicia library. Pattern 1, which was the most dominant in the Vicia and Lupinus libraries, constituted about 25% of all clones. The Lupinus library had clones representing all 12 patterns, indicating it to be the most diverse among the three. Clones representative of each pattern were sequenced. All patterns grouped together forming a distinct cluster, which was divergent from previously described nirK sequences in the database. The study revealed a hitherto unknown diversity of denitrifiers in legume rhizospheres. A plant-dependent rhizosphere effect on the transcripts of a gene was evident.
Collapse
Affiliation(s)
- Shilpi Sharma
- Institute of Soil Ecology, GSF-National Research Center for Environment and Health, P.O. Box 1129, D-85764 Neuherberg, Germany.
| | | | | | | | | |
Collapse
|
17
|
Holmes DE, Nevin KP, Lovley DR. In situ expression of nifD in Geobacteraceae in subsurface sediments. Appl Environ Microbiol 2005; 70:7251-9. [PMID: 15574924 PMCID: PMC535187 DOI: 10.1128/aem.70.12.7251-7259.2004] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In order to determine whether the metabolic state of Geobacteraceae involved in bioremediation of subsurface sediments might be inferred from levels of mRNA for key genes, in situ expression of nifD, a highly conserved gene involved in nitrogen fixation, was investigated. When Geobacter sulfurreducens was grown without a source of fixed nitrogen in chemostats with acetate provided as the limiting electron donor and Fe(III) as the electron acceptor, levels of nifD transcripts were 4 to 5 orders of magnitude higher than in chemostat cultures provided with ammonium. In contrast, the number of transcripts of recA and the 16S rRNA gene were slightly lower in the absence of ammonium. The addition of acetate to organic- and nitrogen-poor subsurface sediments stimulated the growth of Geobacteraceae and Fe(III) reduction, as well as the expression of nifD in Geobacteraceae. Levels of nifD transcripts in Geobacteraceae decreased more than 100-fold within 2 days after the addition of 100 microM ammonium, while levels of recA and total bacterial 16S rRNA in Geobacteraceae remained relatively constant. Ammonium amendments had no effect on rates of Fe(III) reduction in acetate-amended sediments or toluene degradation in petroleum-contaminated sediments, suggesting that other factors, such as the rate that Geobacteraceae could access Fe(III) oxides, limited Fe(III) reduction. These results demonstrate that it is possible to monitor one aspect of the in situ metabolic state of Geobacteraceae species in subsurface sediments via analysis of mRNA levels, which is the first step toward a more global analysis of in situ gene expression related to nutrient status and stress response during bioremediation by Geobacteraceae.
Collapse
Affiliation(s)
- Dawn E Holmes
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA.
| | | | | |
Collapse
|
18
|
Abstract
Aerobic methane-oxidizing bacteria (methanotrophs) are a diverse group of bacteria that are currently represented by 13 recognized genera. They play a major role in the global methane cycle and are widespread in nature with representatives found in soils, freshwater, seawater, freshwater and marine sediments, peat bogs and at extremes of temperature, salinity, and pH. There has been an interest in methanotrophs for their potential in bioremediation processes. Methanotroph diversity and ecology are often studied using the "functional" genes pmoA, mmoX, and mxaF, encoding subunits of the particulate methane monooxygenase, soluble methane monooxygenase, and the methanol dehydrogenase, respectively. This chapter describes methods used to detect and analyze these functional genes.
Collapse
Affiliation(s)
- Marc G Dumont
- Department of Biological Sciences, University of Warwick, Coventry, United Kingdom
| | | |
Collapse
|
19
|
Abstract
AIMS This paper demonstrates a rapid, simple method for the detection of Helicobacter pylori in water that eliminates the need for recovery of cells or DNA extraction prior to PCR. METHODS AND RESULTS Direct polymerase chain reaction (DPCR) with primers specific for H. pylori ureA (urease, subunit A) were used to detect H. pylori added to groundwater. DPCR also detected H. pylori in a naturally contaminated water sample. CONCLUSIONS DPCR should provide an improved method to assess contamination of water by H. pylori. SIGNIFICANCE AND IMPACT OF THE STUDY This simple, rapid method for detection of H. pylori in water will provide an improved means to investigate the possible role of water as a disease vector.
Collapse
Affiliation(s)
- J A Benson
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53201, USA
| | | | | |
Collapse
|
20
|
|
21
|
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.
Collapse
Affiliation(s)
- Jong-In Han
- Department of Civil and Environmental Engineering, The University of Michigan, 1351 Beal Avenue, Ann Arbor, Michigan 48109-2125, USA
| | | |
Collapse
|
22
|
Fode-Vaughan KA, Maki JS, Benson JA, Collins MLP. Direct PCR detection of Escherichia coli O157:H7. Lett Appl Microbiol 2003; 37:239-43. [PMID: 12904226 DOI: 10.1046/j.1472-765x.2003.01386.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
AIMS This paper reports a simple, rapid approach for the detection of Shiga toxin (Stx)-producing Escherichia coli (STEC). METHODS AND RESULTS Direct PCR (DPCR) obviates the need for the recovery of cells from the sample or DNA extraction prior to PCR. Primers specific for Stx-encoding genes stx1 and stx2 were used in DPCR for the detection of E. coli O157:H7 added to environmental water samples and milk. CONCLUSIONS PCR reactions containing one cell yielded a DPCR product. SIGNIFICANCE AND IMPACT OF THE STUDY This should provide an improved method to assess contamination of environmental and other samples by STEC and other pathogens.
Collapse
Affiliation(s)
- K A Fode-Vaughan
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | | | | | | |
Collapse
|
23
|
Nogales B, Timmis KN, Nedwell DB, Osborn AM. Detection and diversity of expressed denitrification genes in estuarine sediments after reverse transcription-PCR amplification from mRNA. Appl Environ Microbiol 2002; 68:5017-25. [PMID: 12324352 PMCID: PMC126436 DOI: 10.1128/aem.68.10.5017-5025.2002] [Citation(s) in RCA: 162] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2002] [Accepted: 07/07/2002] [Indexed: 11/20/2022] Open
Abstract
The expression of five denitrification genes coding for two nitrate reductases (narG and napA), two nitrite reductases (nirS and nirK), and nitrous oxide reductase (nosZ) was analyzed by reverse transcription (RT)-PCR of mRNA extracted from two sediment samples obtained in the River Colne estuary (United Kingdom), which receives high nitrogen inputs and for which high denitrification rates have been observed. The presence of all five genes in both sediment samples was confirmed by PCR amplification from extracted DNA prior to analysis of gene expression. Only nirS and nosZ mRNAs were detected; nirS was detected directly as an RT-PCR amplification product, and nosZ was detected following Southern blot hybridization. This indicated that active expression of at least the nirS and nosZ genes was occurring in the sediments at the time of sampling. Amplified nirS RT-PCR products were cloned and analyzed by sequencing, and they were compared with amplified nirS gene sequences from isolates obtained from the same sediments. A high diversity of nirS sequences was observed. Most of the cloned nirS sequences retrieved were specific to one site or the other, which underlines differences in the compositions of the bacterial communities involved in denitrifrification in the two sediments analyzed.
Collapse
Affiliation(s)
- Balbina Nogales
- Department of Biological Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, United Kingdom.
| | | | | | | |
Collapse
|
24
|
Baker PW, Futamata H, Harayama S, Watanabe K. Molecular diversity of pMMO and sMMO in a TCE-contaminated aquifer during bioremediation. FEMS Microbiol Ecol 2001. [DOI: 10.1111/j.1574-6941.2001.tb00894.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
|
25
|
Baker P, Futamata H, Harayama S, Watanabe K. Bacterial populations occuring in a trichloroethylene-contaminated aquifer during methane injection. Environ Microbiol 2001; 3:187-93. [PMID: 11321535 DOI: 10.1046/j.1462-2920.2001.00178.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Soil core samples were obtained from a trichloroethylene (TCE)-contaminated aquifer before and after the start of methane biostimulation. DNA was extracted directly from the soil samples, and denaturing gradient gel electrophoresis (DGGE) was used to analyse bacterial 16S ribosomal DNA fragments that were PCR amplified from these DNA samples. This analysis consistently detected two phylotypes in the methane-injected samples. These phylotypes were closely related to Methylobacter and Methylomonas, both belonging to type I methanotrophs. A competitive DGGE analysis using Methylosinus trichosporium OB3b cells as an internal quantitative standard showed that these populations accounted for 10(8)-10(9) cells g(-1) soil. These results showed that type I methanotrophs formed a significant proportion of the bacterial community during methane biostimulation. The implications of this finding for TCE bioremediation were discussed.
Collapse
Affiliation(s)
- P Baker
- Marine Biotechnology Institute, Kamaishi Laboratories, Iwate, Japan.
| | | | | | | |
Collapse
|
26
|
Hashimoto A, Iwasaki K, Nakajima M, Yagi O. Quantitative Detection of Trichloroethylene-Degrading Mycobacterium sp. TA27 with a Real-time PCR Product Detection System. Microbes Environ 2001. [DOI: 10.1264/jsme2.2001.109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Akiko Hashimoto
- National Institute for Environmental Studies and CREST, Japan Science and Technology Corporation
| | - Kazuhiro Iwasaki
- National Institute for Environmental Studies and CREST, Japan Science and Technology Corporation
| | - Mutsuyasu Nakajima
- Research Center for Water Environment Technology, the University of Tokyo
| | - Osami Yagi
- Research Center for Water Environment Technology, the University of Tokyo
| |
Collapse
|
27
|
Abstract
Methane-oxidizing bacteria (methanotrophs) have attracted considerable attention over the past 30 years. They have the unique ability to use methane as sole carbon and energy source, they are found in a wide variety of environments and play a crucial role in the global methane cycle. Methanotrophs also show considerable potential for bioremediation processes such as degradation of ground water pollutants, and for production of bulk chemicals from cheap substrates. We review here the cultivation-independent molecular biological methods that are available for the detection and characterization of methanotrophs in the natural environment.
Collapse
Affiliation(s)
- J C Murrell
- Department of Biological Sciences, University of Warwick, Coventry, UK.
| | | |
Collapse
|
28
|
Lemos SS, Perille Collins ML, Eaton SS, Eaton GR, Antholine WE. Comparison of EPR-visible Cu(2+) sites in pMMO from Methylococcus capsulatus (Bath) and Methylomicrobium album BG8. Biophys J 2000; 79:1085-94. [PMID: 10920038 PMCID: PMC1301004 DOI: 10.1016/s0006-3495(00)76362-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
X-band (9.1 GHz) and S-band (3.4 GHz) electron paramagnetic resonance (EPR) spectra for particulate methane monooxygenase (pMMO) in whole cells from Methylococcus capsulatus (Bath) grown on (63)Cu and (15)N were obtained and compared with previously reported spectra for pMMO from Methylomicrobium album BG8. For both M. capsulatus (Bath) and M. album BG8, two nearly identical Cu(2+) EPR signals with resolved hyperfine coupling to four nitrogens are observed. The EPR parameters for pMMO from M. capsulatus (Bath) (g( parallel) = 2.244, A( parallel) = 185 G, and A(N) = 19 G for signal one; g( parallel) = 2.246, A( parallel) = 180 G, and A(N) = 19 G for signal two) and for pMMO from M. album BG8 (g( parallel) = 2.243, A( parallel) = 180 G, and A(N) = 18 G for signal one; g( parallel) = 2. 251, A( parallel) = 180 G, and A(N) = 18 G for signal two) are very similar and are characteristic of type 2 Cu(2+) in a square planar or square pyramidal geometry. In three-pulse electron spin echo envelope modulation (ESEEM) data for natural-abundance samples, nitrogen quadrupolar frequencies due to the distant nitrogens of coordinated histidine imidazoles were observed. The intensities of the quadrupolar combination bands indicate that there are three or four coordinated imidazoles, which implies that most, if not all, of the coordinated nitrogens detected in the continuous wave spectra are from histidine imidazoles.
Collapse
Affiliation(s)
- S S Lemos
- Instituto de Química, Universidade de Brasília, Brasília-DF 70919-970, Brazil
| | | | | | | | | |
Collapse
|
29
|
Wise MG, McArthur JV, Shimkets LJ. Methanotroph diversity in landfill soil: isolation of novel type I and type II methanotrophs whose presence was suggested by culture-independent 16S ribosomal DNA analysis. Appl Environ Microbiol 1999; 65:4887-97. [PMID: 10543800 PMCID: PMC91658 DOI: 10.1128/aem.65.11.4887-4897.1999] [Citation(s) in RCA: 142] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The diversity of the methanotrophic community in mildly acidic landfill cover soil was assessed by three methods: two culture-independent molecular approaches and a traditional culture-based approach. For the first of the molecular studies, two primer pairs specific for the 16S rRNA gene of validly published type I (including the former type X) and type II methanotrophs were identified and tested. These primers were used to amplify directly extracted soil DNA, and the products were used to construct type I and type II clone libraries. The second molecular approach, based on denaturing gradient gel electrophoresis (DGGE), provided profiles of the methanotrophic community members as distinguished by sequence differences in variable region 3 of the 16S ribosomal DNA. For the culturing studies, an extinction-dilution technique was employed to isolate slow-growing but numerically dominant strains. The key variables of the series of enrichment conditions were initial pH (4. 8 versus 6.8), air/CH(4)/CO(2) headspace ratio (50:45:5 versus 90:9:1), and concentration of the medium (1x nitrate minimal salts [NMS] versus 0.2x NMS). Screening of the isolates showed that the nutrient-rich 1x NMS selected for type I methanotrophs, while the nutrient-poor 0.2x NMS tended to enrich for type II methanotrophs. Partial sequencing of the 16S rRNA gene from selected clones and isolates revealed some of the same novel sequence types. Phylogenetic analysis of the type I clone library suggested the presence of a new phylotype related to the Methylobacter-Methylomicrobium group, and this was confirmed by isolating two members of this cluster. The type II clone library also suggested the existence of a novel group of related species distinct from the validly published Methylosinus and Methylocystis genera, and two members of this cluster were also successfully cultured. Partial sequencing of the pmoA gene, which codes for the 27-kDa polypeptide of the particulate methane monooxygenase, reaffirmed the phylogenetic placement of the four isolates. Finally, not all of the bands separated by DGGE could be accounted for by the clones and isolates. This polyphasic assessment of community structure demonstrates that much diversity among the obligate methane oxidizers has yet to be formally described.
Collapse
Affiliation(s)
- M G Wise
- Department of Microbiology, University of Georgia, Athens, Georgia 30602-2605, USA
| | | | | |
Collapse
|