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Crowe MA, Power JF, Morgan XC, Dunfield PF, Lagutin K, Rijpstra WIC, Vyssotski M, Damste JSS, Houghton KM, Ryan JLJ, Stott MB. Pyrinomonas methylaliphatogenes gen. nov., sp. nov., a novel group 4 thermophilic member of the phylum Acidobacteria from geothermal soils. Int J Syst Evol Microbiol 2014. [DOI: 10.1099/ijs.0.062836-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Crowe MA, Power JF, Morgan XC, Dunfield PF, Lagutin K, Rijpstra WIC, Vyssotski M, Sinninghe Damste JS, Houghton KM, Ryan JLJ, Stott MB. Pyrinomonas methylaliphatogenes gen. nov., sp. nov., a novel group 4 thermophilic member of the phylum Acidobacteria from geothermal soils. Int J Syst Evol Microbiol 2013; 64:220-227. [PMID: 24048862 DOI: 10.1099/ijs.0.055079-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An aerobic, thermophilic, moderately acidophilic non-spore-forming bacterium, strain K22(T), was isolated from geothermally heated soil at Mount Ngauruhoe, New Zealand. On the basis of 16S rRNA gene sequence similarity, K22(T) was shown to belong to subdivision 4 of the phylum Acidobacteria and to be most closely related to 'Candidatus Chloracidobacterium thermophilum' (86 %) and Blastocatella fastidiosa (86 %). Cells stained Gram-negative and were catalase and oxidase-positive. The major fatty acids detected were iso-C15 : 0, iso-C17 : 0, iso-C19 : 0 and iso-C21 : 0 when standard lipid extraction protocols were employed. Analysis of the total cell lipid acid hydrolysate also detected membrane-spanning and ether lipids, which made up approximately 40 % of the total membrane composition. These lipids included dicarboxylic (iso-diabolic) acid and the glyceryl ether of alkyl analogues of iso-C15 : 0 and iso-diabolic acid. The G+C content of the genomic DNA was 59.6 mol% and the primary respiratory quinone was MK-8. Strain K22(T) grew at 50-69 °C with an optimum temperature of 65 °C and at pH 4.1-7.8 with an optimum growth pH of 6.5. NaCl tolerance was up to 1 % (w/v). Cells displayed a chemoheterotrophic and obligately aerobic metabolism. Cells grew on nutrient broth, alginate, arabinose, Casamino acids, glucose, lactate, formate, mannose, sodium alginate, peptone, sucrose, tryptone, xanthan, xylan, xylose and yeast extract. Nitrogen sources included nitrate, ammonium, urea, yeast extract and Casamino acids, but not dinitrogen gas. The distinct phylogenetic position and the phenotypic characteristics separate strain K22(T) from all other members of the class Acidobacteria and indicate that it represents a novel species and genus, for which the name Pyrinomonas methylaliphatogenes gen. nov., sp. nov. is proposed. The type strain of the type species is K22(T) ( = DSM 25857(T) = ICMP 18710(T)).
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Affiliation(s)
- M A Crowe
- GNS Science, Extremophile Research Group, Private Bag 2000, Taupo 3352, New Zealand
| | - J F Power
- GNS Science, Extremophile Research Group, Private Bag 2000, Taupo 3352, New Zealand
| | - X C Morgan
- Department of Biostatistics, Harvard School of Public Health, 655 Huntington Ave., Boston MA 02115, USA
| | - P F Dunfield
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary T2N 1N4, Canada
| | - K Lagutin
- Callaghan Innovation, PO Box 31310, Lower Hutt 5040, New Zealand
| | - W I C Rijpstra
- Royal Netherlands Institute for Sea Research (NIOZ), Department of Marine Biogeochemistry and Toxicology, PO Box 59, 1790 AB Den Burg, The Netherlands
| | - M Vyssotski
- Callaghan Innovation, PO Box 31310, Lower Hutt 5040, New Zealand
| | - J S Sinninghe Damste
- Royal Netherlands Institute for Sea Research (NIOZ), Department of Marine Biogeochemistry and Toxicology, PO Box 59, 1790 AB Den Burg, The Netherlands
| | - K M Houghton
- GNS Science, Extremophile Research Group, Private Bag 2000, Taupo 3352, New Zealand
| | - J L J Ryan
- Callaghan Innovation, PO Box 31310, Lower Hutt 5040, New Zealand
| | - M B Stott
- GNS Science, Extremophile Research Group, Private Bag 2000, Taupo 3352, New Zealand
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Stott MB, Saito JA, Crowe MA, Dunfield PF, Hou S, Nakasone E, Daughney CJ, Smirnova AV, Mountain BW, Takai K, Alam M. Culture-independent characterization of a novel microbial community at a hydrothermal vent at Brothers volcano, Kermadec arc, New Zealand. ACTA ACUST UNITED AC 2008. [DOI: 10.1029/2007jb005477] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- M. B. Stott
- GNS Science, Extremophile Research Group; Taupo New Zealand
| | - J. A. Saito
- Department of Microbiology; University of Hawaii; Honolulu Hawaii USA
| | - M. A. Crowe
- GNS Science, Extremophile Research Group; Taupo New Zealand
| | - P. F. Dunfield
- GNS Science, Extremophile Research Group; Taupo New Zealand
| | - S. Hou
- Department of Microbiology; University of Hawaii; Honolulu Hawaii USA
| | - E. Nakasone
- Department of Microbiology; University of Hawaii; Honolulu Hawaii USA
| | - C. J. Daughney
- GNS Science, Extremophile Research Group; Taupo New Zealand
| | - A. V. Smirnova
- GNS Science, Extremophile Research Group; Taupo New Zealand
| | - B. W. Mountain
- GNS Science, Extremophile Research Group; Taupo New Zealand
| | - K. Takai
- Subground Animalcule Retrieval Program; Japan Agency for Marine-Earth Science and Technology; Yokosuka Japan
| | - M. Alam
- Department of Microbiology; University of Hawaii; Honolulu Hawaii USA
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Koch IH, Gich F, Dunfield PF, Overmann J. Edaphobacter modestus gen. nov., sp. nov., and Edaphobacter aggregans sp. nov., acidobacteria isolated from alpine and forest soils. Int J Syst Evol Microbiol 2008; 58:1114-22. [DOI: 10.1099/ijs.0.65303-0] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Dedysh SN, Horz HP, Dunfield PF, Liesack W. A novel pmoA lineage represented by the acidophilic methanotrophic bacterium Methylocapsa acidiphila [correction of acidophila] B2. Arch Microbiol 2001; 177:117-21. [PMID: 11797053 DOI: 10.1007/s00203-001-0362-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2001] [Revised: 09/14/2001] [Accepted: 09/25/2001] [Indexed: 10/27/2022]
Abstract
A fragment of the functional gene pmoA, which encodes the active-site polypeptide of particulate methane monooxygenase (pMMO), was PCR-amplified from DNA of the recently described acidophilic methanotrophic bacterium Methylocapsa acidiphila [corrected] B2. This methanotroph was isolated from an acidic Sphagnum peat bog and possesses a novel type III arrangement of intracytoplasmic membranes. Comparative sequence analysis revealed that the inferred peptide sequence of pmoA of Methylocapsa acidiphila [corrected] B2 belongs to a novel PmoA lineage. This lineage was only distantly related to the PmoA sequence cluster of type II methanotrophs, with identity values between 69.5% and 72%. The identity values between the PmoA of Methylocapsa acidiphila [corrected] B2 and PmoA sequences of type I methanotrophs ranged from 55.5 to 68%. However, the PmoA of this acidophilic methanotroph was more closely affiliated with the inferred peptide sequences of pmoA clones retrieved from various acidic upland soils showing atmospheric methane consumption. The PmoA identity values with these clones were 79.5-81%. Nonetheless, the apparent affinity for methane exhibited by Methylocapsa acidiphila [corrected] B2 was 1-2 microM, which is similar to values measured in other methanotrophic bacteria. This finding suggests that the pMMO of Methylocapsa acidiphila [corrected] B2 is not a novel enzyme specialized to have a high affinity for methane and that apparent "high-affinity" methane uptake is either the result of particular culture conditions or is performed by another pMMO type.
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Affiliation(s)
- S N Dedysh
- Institute of Microbiology of Russian Academy of Sciences, Prospect 60 Let Octyabrya, 7/2, Moscow 117811, Russia.
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Dunfield PF, Conrad R. Starvation alters the apparent half-saturation constant for methane in the type II methanotroph Methylocystis strain LR1. Appl Environ Microbiol 2000; 66:4136-8. [PMID: 10966442 PMCID: PMC92272 DOI: 10.1128/aem.66.9.4136-4138.2000] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
When cells of a type II methanotrophic bacterium (Methylocystis strain LR1) were starved of methane, both the K(m(app)) and the V(max(app)) for methane decreased. The specific affinity (a(o)(s)) remained nearly constant. Therefore, the decreased K(m(app)) in starved cells was probably not an adjustment to better utilize low-methane concentrations.
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Affiliation(s)
- P F Dunfield
- Max-Planck-Institut für terrestrische Mikrobiologie, Karl-von-Frisch Strasse, 35043 Marburg, Germany.
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Lukow1 T, Dunfield PF, Liesack W. Use of the T-RFLP technique to assess spatial and temporal changes in the bacterial community structure within an agricultural soil planted with transgenic and non-transgenic potato plants. FEMS Microbiol Ecol 2000; 32:241-247. [PMID: 10858583 DOI: 10.1111/j.1574-6941.2000.tb00717.x] [Citation(s) in RCA: 135] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The aim of this study was to examine whether the terminal restriction fragment length polymorphism (T-RFLP) analysis represents an appropriate technique for monitoring highly diverse soil bacterial communities, i.e. to assess spatial and/or temporal effects on bacterial community structure. The T-RFLP method, a recently described fingerprinting technique, is based on terminal restriction fragment length polymorphisms between distinct small-subunit rRNA gene sequence types. This technique permits an automated quantification of the fluorescence signal intensities of the individual terminal restriction fragments (T-RFs) in a given community fingerprint pattern. The indigenous bacterial communities of three soil plots located within an agricultural field of 110 m(2) were compared. The first site was planted with non-transgenic potato plants, while the other two were planted with transgenic GUS and Barnase/Barstar potato plants, respectively. Once prior to planting and three times after planting, seven parallel samples were taken from each of the three soil plots. The T-RFLP analysis resulted in very complex but highly reproducible community fingerprint patterns. The percentage abundance values of defined T-RFs were calculated for the seven parallel samples of the respective soil plot. A multivariate analysis of variance was used to test T-RFLP data sets for significant differences. The statistical treatments clearly revealed spatial and temporal effects, as well as spacextime interaction effects, on the structural composition of the bacterial communities. T-RFs which showed the highest correlations to the discriminant factors were not those T-RFs which showed the largest single variations between the seven-sample means of individual plots. In summary, the T-RFLP technique, although a polymerase chain reaction-based method, proved to be a suitable technique for monitoring highly diverse soil microbial communities for changes over space and/or time.
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Affiliation(s)
- T Lukow1
- Max-Planck-Institut für terrestrische Mikrobiologie, Karl-von-Frisch-Straße, D-35043, Marburg, Germany
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Dunfield PF, Liesack W, Henckel T, Knowles R, Conrad R. High-affinity methane oxidation by a soil enrichment culture containing a type II methanotroph. Appl Environ Microbiol 1999; 65:1009-14. [PMID: 10049856 PMCID: PMC91137 DOI: 10.1128/aem.65.3.1009-1014.1999] [Citation(s) in RCA: 143] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Methanotrophic bacteria in an organic soil were enriched on gaseous mixing ratios of <275 parts per million of volume (ppmv) of methane (CH4). After 4 years of growth and periodic dilution (>10(20) times the initial soil inoculum), a mixed culture was obtained which displayed an apparent half-saturation constant [Km(app)] for CH4 of 56 to 186 nM (40 to 132 ppmv). This value was the same as that measured in the soil itself and about 1 order of magnitude lower than reported values for pure cultures of methane oxidizers. However, the Km(app) increased when the culture was transferred to higher mixing ratios of CH4 (1,000 ppmv, or 1%). Denaturing gradient gel electrophoresis of the enrichment grown on <275 ppmv of CH4 revealed a single gene product of pmoA, which codes for a subunit of particulate methane monooxygenase. This suggested that only one methanotroph species was present. This organism was isolated from a sample of the enrichment culture grown on 1% CH4 and phylogenetically positioned based on its 16S rRNA, pmoA, and mxaF gene sequences as a type II strain of the Methylocystis/Methylosinus group. A coculture of this strain with a Variovorax sp., when grown on <275 ppmv of CH4, had a Km(app) (129 to 188 nM) similar to that of the initial enrichment culture. The data suggest that the affinity of methanotrophic bacteria for CH4 varies with growth conditions and that the oxidation of atmospheric CH4 observed in this soil is carried out by type II methanotrophic bacteria which are similar to characterized species.
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Affiliation(s)
- P F Dunfield
- Max-Planck-Institut für terrestrische Mikrobiologie, 35043 Marburg, Germany
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