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Söllinger A, Schwab C, Weinmaier T, Loy A, Tveit AT, Schleper C, Urich T. Phylogenetic and genomic analysis of Methanomassiliicoccales in wetlands and animal intestinal tracts reveals clade-specific habitat preferences. FEMS Microbiol Ecol 2016; 92:fiv149. [PMID: 26613748 DOI: 10.1093/femsec/fiv149] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/24/2015] [Indexed: 01/30/2023] Open
Abstract
Methanogenic Thermoplasmata of the novel order Methanomassiliicoccales were recently discovered in human and animal gastro-intestinal tracts (GITs). However, their distribution in other methanogenic environments has not been addressed systematically. Here, we surveyed Methanomassiliicoccales presence in wetland soils, a globally important source of methane emissions to the atmosphere, and in the GITs of different animals by PCR targeting their 16S rRNA and methyl:coenzyme M reductase (α-subunit) genes. We detected Methanomassiliicoccales in all 16 peat soils investigated, indicating their wide distribution in these habitats. Additionally, we detected their genes in various animal faeces. Methanomassiliicoccales were subdivided in two broad phylogenetic clades designated 'environmental' and 'GIT' clades based on differential, although non-exclusive, habitat preferences of their members. A well-supported cluster within the environmental clade comprised more than 80% of all wetland 16S rRNA gene sequences. Metagenome assembly from bovine rumen fluid enrichments resulted in two almost complete genomes of both Methanomassiliicoccales clades. Comparative genomics revealed that members of the environmental clade contain larger genomes and a higher number of genes encoding anti-oxidative enzymes than animal GIT clade representatives. This study highlights the wide distribution of Methanomassiliicoccales in wetlands, which suggests that they contribute to methane emissions from these climate-relevant ecosystems.
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Affiliation(s)
- Andrea Söllinger
- Department of Ecogenomics and Systems Biology, University of Vienna, 1090 Vienna, Austria
| | - Clarissa Schwab
- Institute of Food, Nutrition and Health, ETH Zürich, 8092 Zurich, Switzerland
| | - Thomas Weinmaier
- Department of Microbiology and Ecosystem Science, University of Vienna, 1090 Vienna, Austria
| | - Alexander Loy
- Department of Microbiology and Ecosystem Science, University of Vienna, 1090 Vienna, Austria
| | - Alexander T Tveit
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Christa Schleper
- Department of Ecogenomics and Systems Biology, University of Vienna, 1090 Vienna, Austria
| | - Tim Urich
- Department of Ecogenomics and Systems Biology, University of Vienna, 1090 Vienna, Austria Institute for Microbiology, Ernst-Moritz-Arndt University Greifswald, 17489 Greifswald, Germany
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2
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Hawkins AN, Johnson KW, Bräuer SL. Southern Appalachian peatlands support high archaeal diversity. MICROBIAL ECOLOGY 2014; 67:587-602. [PMID: 24419541 DOI: 10.1007/s00248-013-0352-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 12/12/2013] [Indexed: 06/03/2023]
Abstract
Mid-latitude peatlands with a temperate climate are sparsely studied and as such represent a gap in the current knowledge base regarding archaeal populations present and their roles in these environments. Phylogenetic analysis of the archaeal populations among three peatlands in the Southern Appalachians reveal not only methanogenic species but also significant populations of thaumarchaeal and crenarchaeal-related organisms of the uncultured miscellaneous crenarchaeotal group (MCG) and the terrestrial group 1.1c, as well as deep-branching Euryarchaeota primarily within the Lake Dagow sediment and rice cluster V lineages. The Thaum/Crenarchaea and deep-branching Euryarchaea represented approximately 24-83% and 2-18%, respectively, of the total SSU rRNA clones retrieved in each library, and methanogens represented approximately 14-72% of the clones retrieved. Several taxa that are either rare or novel to acidic peatlands were detected including the euryarchaeal SM1K20 cluster and thaumarchaeal/crenarchaeal-related clusters 1.1a, C3, SAGMCG-1, pSL12, and AK59. All three major groups (methanogens, Thaumarchaea/Crenarchaea, and deep-branching Euryarchaea) were detected in the RNA library, suggesting at least a minimum level of maintenance activity. Compared to their northern counterparts, Southern Appalachian peatlands appear to harbor a relatively high diversity of Archaea and exhibit a high level of intra-site heterogeneity.
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Affiliation(s)
- A N Hawkins
- Department of Biology, Appalachian State University, 572 Rivers Street, Boone, NC, 28608, USA
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3
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Mostofa KMG, Liu CQ, Minakata D, Wu F, Vione D, Mottaleb MA, Yoshioka T, Sakugawa H. Photoinduced and Microbial Degradation of Dissolved Organic Matter in Natural Waters. PHOTOBIOGEOCHEMISTRY OF ORGANIC MATTER 2013. [DOI: 10.1007/978-3-642-32223-5_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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4
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Reeb V, Kolel A, McDermott TR, Bhattacharya D. Good to the bone: microbial community thrives within bone cavities of a bison carcass at Yellowstone National Park. Environ Microbiol 2010; 13:2403-15. [PMID: 21044237 DOI: 10.1111/j.1462-2920.2010.02359.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The discovery of unanticipated microbial diversity in remote, often hostile environments has led to a greater appreciation of the complexity and richness of the natural world. Yellowstone National Park (YNP) has long been a focus of work on taxa that inhabit extreme environments. Here we report the finding of microbial flora that inhabit an unexpected niche: the cavities of bone remnants from a bison carcass in Norris Geyser Basin in YNP. Although bleached white on the surface, the bone cavities are bright green due to the presence of Stichococcus-like trebouxiophyte green algae. The cavities also harbour different fungi and bacteria. Stichococcus species are common lichen photobionts and the Thelebolales fungi present in the bone cavities have previously been found in association with animal remains. Scanning electron microscope analysis suggests the fungi and algae do not form lichen-like associations in the bone. Rather these taxa and the bacteria appear to be opportunists that have colonized an isolated oasis that provides nutrients and protection from desiccation and UV radiation.
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Affiliation(s)
- Valérie Reeb
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA
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5
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Galand PE, Saarnio S, Fritze H, Yrjälä K. Depth related diversity of methanogen Archaea in Finnish oligotrophic fen. FEMS Microbiol Ecol 2009; 42:441-9. [PMID: 19709303 DOI: 10.1111/j.1574-6941.2002.tb01033.x] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The annual rate of CH4 release and potential CH4 production has recently been studied in the Salmisuo fen in eastern Finland but the microbiota responsible for the CH4 production has not been examined. The diversity of the methane producing Archaea was analysed, at different depths, in the most representative microsite (Eriophorum lawn) of the fen. Methanogen populations were studied using primers amplifying a region of the methyl-coenzyme M reductase gene. PCR products were analysed by denaturing gradient gel electrophoresis and restriction fragment length polymorphism (RFLP) analysis of clone libraries. A representative of each RFLP group was sequenced. The study revealed a change of the methanogen populations with depth. Sequences from the upper layers of the fen grouped in a novel 'Fen cluster' and were related to Methanomicrobiales. Sequences retrieved from the deeper layers of the fen were related to Methanosarcinales via the Rice Cluster-I.
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Affiliation(s)
- Pierre E Galand
- Department of Biosciences, Division of General Microbiology, P.O. Box 56, University of Helsinki, FIN-00014 Helsinki, Finland
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6
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Talbot G, Topp E, Palin MF, Massé DI. Evaluation of molecular methods used for establishing the interactions and functions of microorganisms in anaerobic bioreactors. WATER RESEARCH 2008; 42:513-37. [PMID: 17719078 DOI: 10.1016/j.watres.2007.08.003] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2006] [Revised: 07/31/2007] [Accepted: 08/01/2007] [Indexed: 05/16/2023]
Abstract
Molecular techniques have unveiled the complexity of the microbial consortium in anaerobic bioreactors and revealed the presence of several uncultivated species. This paper presents a review of the panoply of classical and recent molecular approaches and multivariate analyses that have been, or might be used to establish the interactions and functions of these anaerobic microorganisms. Most of the molecular approaches used so far are based on the analysis of small subunit ribosomal RNA but recent studies also use quantification of functional gene expressions. There are now several studies that have developed quantitative real-time PCR assays to investigate methanogens. With a view to improving the stability and performance of bioreactors, monitoring with molecular methods is also discussed. Advances in metagenomics and proteomics will lead to the development of promising lab-on chip technologies for cost-effective monitoring.
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Affiliation(s)
- G Talbot
- Dairy and Swine Research and Development Centre, Agriculture and Agri-Food Canada, 2000 College Street, Sherbrooke, Quebec, Canada J1M 0C8.
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7
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Kotsyurbenko OR, Friedrich MW, Simankova MV, Nozhevnikova AN, Golyshin PN, Timmis KN, Conrad R. shift from acetoclastic to H2-dependent methanogenesis in a west Siberian peat bog at low pH values and isolation of an acidophilic Methanobacterium strain. Appl Environ Microbiol 2007; 73:2344-8. [PMID: 17277200 PMCID: PMC1855669 DOI: 10.1128/aem.02413-06] [Citation(s) in RCA: 160] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Methane production and archaeal community composition were studied in samples from an acidic peat bog incubated at different temperatures and pH values. H(2)-dependent methanogenesis increased strongly at the lowest pH, 3.8, and Methanobacteriaceae became important except for Methanomicrobiaceae and Methanosarcinaceae. An acidophilic and psychrotolerant Methanobacterium sp. was isolated using H(2)-plus-CO(2)-supplemented medium at pH 4.5.
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Affiliation(s)
- O R Kotsyurbenko
- Institut für Mikrobiologie, Carolo-Wilhelmina Technische Universität zu Braunschweig, Biozentrum, Braunschweig, Germany.
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Morales SE, Mouser PJ, Ward N, Hudman SP, Gotelli NJ, Ross DS, Lewis TA. Comparison of bacterial communities in New England Sphagnum bogs using terminal restriction fragment length polymorphism (T-RFLP). MICROBIAL ECOLOGY 2006; 52:34-44. [PMID: 16729225 DOI: 10.1007/s00248-005-0264-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2004] [Accepted: 05/10/2005] [Indexed: 05/09/2023]
Abstract
Wetlands are major sources of carbon dioxide, methane, and other greenhouse gases released during microbial degradation. Despite the fact that decomposition is mainly driven by bacteria and fungi, little is known about the taxonomic diversity of bacterial communities in wetlands, particularly Sphagnum bogs. To explore bacterial community composition, 24 bogs in Vermont and Massachusetts were censused for bacterial diversity at the surface (oxic) and 1 m (anoxic) regions. Bacterial diversity was characterized by a terminal restriction fragment length (T-RFLP) fingerprinting technique and a cloning strategy that targeted the 16S rRNA gene. T-RFLP analysis revealed a high level of diversity, and a canonical correspondence analysis demonstrated marked similarity among bogs, but consistent differences between surface and subsurface assemblages. 16S rDNA sequences derived from one of the sites showed high numbers of clones belonging to the Deltaproteobacteria group. Several other phyla were represented, as well as two Candidate Division-level taxonomic groups. These data suggest that bog microbial communities are complex, possibly stratified, and similar among multiple sites.
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Affiliation(s)
- Sergio E Morales
- Department of Microbiology and Molecular Genetics, University of Vermont, 95 Carrigan Drive, Burlington, VT 05405, USA
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9
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Crocetti G, Murto M, Björnsson L. An update and optimisation of oligonucleotide probes targeting methanogenic Archaea for use in fluorescence in situ hybridisation (FISH). J Microbiol Methods 2006; 65:194-201. [PMID: 16126291 DOI: 10.1016/j.mimet.2005.07.007] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2005] [Revised: 07/08/2005] [Accepted: 07/08/2005] [Indexed: 11/22/2022]
Abstract
Fluorescence in situ hybridisation (FISH) is a common and popular method used to investigate microbial populations in natural and engineered environments. DNA oligonucleotide probes require accurate determination of the optimal experimental conditions for their use in FISH. Oligonucleotides targeting the rRNA of methanogenic Archaea at various taxonomic levels have previously been published, although when applied in FISH, no optimisation data has been presented. In this study, 3000 Euryarchaeota 16S rRNA gene sequences were phylogenetically analysed and previously published oligonucleotides were evaluated for target group accuracy. Where necessary, modifications were introduced or new probes were designed. The updated set of probes was optimised for use in FISH for a more accurate detection of methanogenic Archaea.
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Affiliation(s)
- Gregory Crocetti
- Department of Biotechnology, Lund University, PO Box 124, SE-22100 Lund, Sweden
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10
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Earl J, Pickup RW, Ritchie DA, Edwards C. Development of temporal temperature gradient electrophoresis for characterising methanogen diversity. MICROBIAL ECOLOGY 2005; 50:327-36. [PMID: 16328656 DOI: 10.1007/s00248-005-0192-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2004] [Accepted: 01/11/2005] [Indexed: 05/05/2023]
Abstract
Temporal temperature gradient electrophoretic (TTGE) analysis of 16S rDNA sequences was optimized to monitor the methanogen population present in water and sediments of a small eutrophic lake, Priest Pot, in the English Lake district. The production of nonrepresentative TTGE profiles due to the generation of polymerase chain reaction (PCR) artifacts initially proved problematical. The use of a proofreading polymerase in the PCR was found to be essential and fully optimized protocols were established and tested to ensure confidence that the TTGE profiles truly reflected sequence diversity. TTGE analysis revealed the methanogen population to be less diverse in water than in sediment. The most genetic diversity was observed in TTGE profiles of sediment DNA isolated in winter and the least was in sediment DNA isolated in summer. DNA sequencing analysis of bands recovered from TTGE gels revealed the presence of two methanogen communities. One clustered with Methanosaeta species and the other with the Methanomicrobiales. Many sequences showed low DNA sequence similarity to known methanogens, suggesting that Priest Pot harbors previously undescribed methanogen species.
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Affiliation(s)
- Julie Earl
- School of Biological Sciences, University of Liverpool, Liverpool, L69 7ZB, UK
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11
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Galand PE, Fritze H, Conrad R, Yrjälä K. Pathways for methanogenesis and diversity of methanogenic archaea in three boreal peatland ecosystems. Appl Environ Microbiol 2005; 71:2195-8. [PMID: 15812059 PMCID: PMC1082526 DOI: 10.1128/aem.71.4.2195-2198.2005] [Citation(s) in RCA: 147] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The main objectives of this study were to uncover the pathways used for methanogenesis in three different boreal peatland ecosystems and to describe the methanogenic populations involved. The mesotrophic fen had the lowest proportion of CH4 produced from H2-CO2. The oligotrophic fen was the most hydrogenotrophic, followed by the ombrotrophic bog. Each site was characterized by a specific group of methanogenic sequences belonging to Methanosaeta spp. (mesotrophic fen), rice cluster-I (oligotrophic fen), and fen cluster (ombrotrophic bog).
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Affiliation(s)
- P E Galand
- Department of Biological and Environmental Sciences, General Microbilogy, University of Helsinki, Finland.
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12
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Galand PE, Juottonen H, Fritze H, Yrjälä K. Methanogen communities in a drained bog: effect of ash fertilization. MICROBIAL ECOLOGY 2005; 49:209-17. [PMID: 15965727 DOI: 10.1007/s00248-003-0229-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2003] [Accepted: 12/18/2003] [Indexed: 05/03/2023]
Abstract
Forestry practises such has drainage have been shown to decrease emissions of the greenhouse gas methane (CH(4)) from peatlands. The aim of the study was to examine the methanogen populations in a drained bog in northern Finland, and to assess the possible effect of ash fertilization on potential methane production and methanogen communities. Peat samples were collected from control and ash fertilized (15,000 kg/ha) plots 5 years after ash application, and potential CH(4) production was measured. The methanogen community structure was studied by DNA isolation, PCR amplification of the methyl coenzyme-M reductase (mcr) gene, denaturing gradient gel electrophoresis (DGGE), and restriction fragment length polymorphism (RFLP) analysis. The drained peatland showed low potential methane production and methanogen diversity in both control and ash-fertilized plots. Samples from both upper and deeper layers of peat were dominated by three groups of sequences related to Rice cluster-I hydrogenotroph methanogens. Even though pH was marginally greater in the ash-treated site, the occurrence of those sequences was not affected by ash fertilization. Interestingly, a less common group of sequences, related to the Fen cluster, were found only in the fertilized plots. The study confirmed the depth related change of methanogen populations in peatland.
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Affiliation(s)
- P E Galand
- Department of Biological and Environmental Sciences, Division of General Microbiology, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland.
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13
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Koizumi Y, Takii S, Fukui M. Depth-related change in archaeal community structure in a freshwater lake sediment as determined with denaturing gradient gel electrophoresis of amplified 16S rRNA genes and reversely transcribed rRNA fragments. FEMS Microbiol Ecol 2004; 48:285-92. [DOI: 10.1016/j.femsec.2004.02.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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14
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Earl J, Hall G, Pickup RW, Ritchie DA, Edwards C. Analysis of methanogen diversity in a hypereutrophic lake using PCR-RFLP analysis of mcr sequences. MICROBIAL ECOLOGY 2003; 46:270-8. [PMID: 14708751 DOI: 10.1007/s00248-003-2003-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The incidence and diversity of methanogens in Priest Pot, a dynamic and active lake, were monitored by analysing mcrA gene sequences generated from total DNA samples obtained at different times of the year and amplified using the polymerase chain reaction. A number of mcrA clones were analysed by developing an RFLP-based protocol to generate a number of restriction patterns that were assigned to a number of classes. The RFLP patterns for each class were compared with published sequence information for mcrA from cultured methanogens as well as with those from other experimental studies. They could be used to assign tentative identification for some of the Priest Pot clones and also revealed the presence of a number of clones that could not be affiliated to any known methanogens. The limitations of using RFLP profiles of mcrA gene sequences for studying methanogen ecology are discussed.
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Affiliation(s)
- J Earl
- School of Biological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
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15
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Lloyd D. Noninvasive methods for the investigation of organisms at low oxygen levels. ADVANCES IN APPLIED MICROBIOLOGY 2003; 51:155-83. [PMID: 12236057 DOI: 10.1016/s0065-2164(02)51005-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- David Lloyd
- School of Biosciences (Microbiology), Main Building, Cardiff University, P. O. Box 915, Cardiff CF10 3TL, Wales, United Kingdom
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