Home LiteratureArticle Details
PMID: 11526021 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Detection of methanotroph diversity on roots of submerged rice plants by molecular retrieval of pmoA, mmoX, mxaF, and 16S rRNA and ribosomal DNA, including pmoA-based terminal restriction fragment length polymorphism profiling.

Applied and environmental microbiology ·Vol. 67 ·No. 9 ·2001-09-00 ·Pages 4177-85

Horz HP, Yimga MT, Liesack W

Abstract

The diversity of methanotrophic bacteria associated with roots of submerged rice plants was assessed using cultivation-independent techniques. The research focused mainly on the retrieval of pmoA, which encodes the alpha subunit of the particulate methane monooxygenase. A novel methanotroph-specific community-profiling method was established using the terminal restriction fragment length polymorphism (T-RFLP) technique. The T-RFLP profiles clearly revealed a more complex root-associated methanotrophic community than did banding patterns obtained by pmoA-based denaturing gradient gel electrophoresis. The comparison of pmoA-based T-RFLP profiles obtained from rice roots and bulk soil of flooded rice microcosms suggested that there was a substantially higher abundance of type I methanotrophs on rice roots than in the bulk soil. These were affiliated to the genera Methylomonas, Methylobacter, Methylococcus, and to a novel type I methanotroph sublineage. By contrast, type II methanotrophs of the Methylocystis-Methylosinus group could be detected with high relative signal intensity in both soil and root compartments. Phylogenetic treeing analyses and a set of substrate-diagnostic amino acid residues provided evidence that a novel pmoA lineage was detected. This branched distinctly from all currently known methanotrophs. To examine whether the retrieval of pmoA provided a complete view of root-associated methanotroph diversity, we also assessed the diversity detectable by recovery of genes coding for subunits of soluble methane monooxygenase (mmoX) and methanol dehydrogenase (mxaF). In addition, both 16S rRNA and 16S ribosomal DNA (rDNA) were retrieved using a PCR primer set specific to type I methanotrophs. The overall methanotroph diversity detected by recovery of mmoX, mxaF, and 16S rRNA and 16S rDNA corresponded well to the diversity detectable by retrieval of pmoA.

MeSH Terms
Alcohol Oxidoreductases/genetics DNA, Ribosomal/genetics Ecosystem Genes, rRNA Methane/metabolism Micrococcaceae/classification,genetics Molecular Sequence Data Oryza/microbiology Oxygenases/genetics Plant Roots/microbiology Polymorphism, Restriction Fragment Length RNA, Ribosomal, 16S/genetics Reverse Transcriptase Polymerase Chain Reaction Rhizobiaceae/classification,genetics Sequence Analysis, DNA Water
Chemicals
DNA, Ribosomal RNA, Ribosomal, 16S Water Alcohol Oxidoreductases alcohol dehydrogenase (acceptor) Oxygenases methane monooxygenase Methane
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Horz H P
Max-Planck-Institut für terrestrische Mikrobiologie, D-35043 Marburg, Germany.
Yimga M T
Liesack W
References (39)
39 references, click to expand
  1. Aerobic and anaerobic starvation metabolism in methanotrophic bacteria.
    Appl Environ Microbiol. 1995 Apr;61(4):1563-70 PMID: 16535004
  2. The neighbor-joining method: a new method for reconstructing phylogenetic trees.
    Mol Biol Evol. 1987 Jul;4(4):406-25 PMID: 3447015
  3. 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 Jun 1;32(3):241-247 PMID: 10858583
  4. Soluble methane monooxygenase gene clusters from trichloroethylene-degrading Methylomonas sp. strains and detection of methanotrophs during in situ bioremediation.
    Appl Environ Microbiol. 1999 Dec;65(12):5198-206 PMID: 10583965
  5. Evidence that particulate methane monooxygenase and ammonia monooxygenase may be evolutionarily related.
    FEMS Microbiol Lett. 1995 Oct 15;132(3):203-8 PMID: 7590173
  6. Vertical distribution of the methanotrophic community after drainage of rice field soil.
    FEMS Microbiol Ecol. 2001 Jan;34(3):279-291 PMID: 11137607
  7. 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 Nov;65(11):4887-97 PMID: 10543800
  8. Analysis of 16S rRNA and methane monooxygenase gene sequences reveals a novel group of thermotolerant and thermophilic methanotrophs, Methylocaldum gen. nov.
    Arch Microbiol. 1997 Dec;168(6):493-503 PMID: 9385141
  9. Methanotrophic bacteria.
    Microbiol Rev. 1996 Jun;60(2):439-71 PMID: 8801441
  10. Direct ribosome isolation from soil to extract bacterial rRNA for community analysis.
    Appl Environ Microbiol. 1996 Nov;62(11):4162-7 PMID: 8900007
  11. Diversity and structure of the methanogenic community in anoxic rice paddy soil microcosms as examined by cultivation and direct 16S rRNA gene sequence retrieval.
    Appl Environ Microbiol. 1998 Mar;64(3):960-9 PMID: 9501436
  12. Molecular analyses of novel methanotrophic communities in forest soil that oxidize atmospheric methane.
    Appl Environ Microbiol. 2000 May;66(5):1801-8 PMID: 10788342
  13. Methylocella palustris gen. nov., sp. nov., a new methane-oxidizing acidophilic bacterium from peat bogs, representing a novel subtype of serine-pathway methanotrophs.
    Int J Syst Evol Microbiol. 2000 May;50 Pt 3:955-69 PMID: 10843033
  14. The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations.
    Appl Environ Microbiol. 1997 Dec;63(12):4704-12 PMID: 9406389
  15. Activity and Distribution of Methane-Oxidizing Bacteria in Flooded Rice Soil Microcosms and in Rice Plants (Oryza sativa).
    Appl Environ Microbiol. 1997 Apr;63(4):1199-207 PMID: 16535562
  16. Molecular characterization of functional and phylogenetic genes from natural populations of methanotrophs in lake sediments.
    Appl Environ Microbiol. 1999 Nov;65(11):5066-74 PMID: 10543824
  17. Molecular characterization of methanotrophic isolates from freshwater lake sediment.
    Appl Environ Microbiol. 2000 Dec;66(12):5259-66 PMID: 11097900
  18. Survival and Recovery of Methanotrophic Bacteria Starved under Oxic and Anoxic Conditions.
    Appl Environ Microbiol. 1994 Jul;60(7):2602-8 PMID: 16349336
  19. Methylosarcina fibrata gen. nov., sp. nov. and Methylosarcina quisquiliarum sp.nov., novel type 1 methanotrophs.
    Int J Syst Evol Microbiol. 2001 Mar;51(Pt 2):611-21 PMID: 11321107
  20. Methylosphaera hansonii gen. nov., sp. nov., a psychrophilic, group I methanotroph from Antarctic marine-salinity, meromictic lakes.
    Microbiology. 1997 Apr;143 ( Pt 4):1451-9 PMID: 9141708
  21. Characterization of methanotrophic bacterial populations in soils showing atmospheric methane uptake.
    Appl Environ Microbiol. 1999 Aug;65(8):3312-8 PMID: 10427012
  22. Molecular analyses of the methane-oxidizing microbial community in rice field soil by targeting the genes of the 16S rRNA, particulate methane monooxygenase, and methanol dehydrogenase
    Appl Environ Microbiol. 1999 May;65(5):1980-90 PMID: 10223989
  23. Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA.
    Appl Environ Microbiol. 1997 Nov;63(11):4516-22 PMID: 9361437
  24. Activity and species composition of aerobic methanotrophic communities in tundra soils.
    Curr Microbiol. 1993 Sep;27(3):181-4 PMID: 23835752
  25. Detection of methanotrophic bacteria in environmental samples with the PCR.
    Appl Environ Microbiol. 1995 Jan;61(1):116-21 PMID: 7887594
  26. High-affinity methane oxidation by a soil enrichment culture containing a type II methanotroph.
    Appl Environ Microbiol. 1999 Mar;65(3):1009-14 PMID: 10049856
  27. Factors affecting competition between type I and type II methanotrophs in two-organism, continuous-flow reactors.
    Microb Ecol. 1993 Jan;25(1):1-17 PMID: 24189703
  28. The particulate methane monooxygenase gene pmoA and its use as a functional gene probe for methanotrophs.
    FEMS Microbiol Lett. 1997 Nov 15;156(2):205-10 PMID: 9513266
  29. Acidophilic methanotrophic communities from Sphagnum peat bogs.
    Appl Environ Microbiol. 1998 Mar;64(3):922-9 PMID: 9501432
  30. The methanol dehydrogenase structural gene mxaF and its use as a functional gene probe for methanotrophs and methylotrophs.
    Appl Environ Microbiol. 1997 Aug;63(8):3218-24 PMID: 9251208
  31. Detection and Isolation of Methanotrophic Bacteria Possessing Soluble Methane Monooxygenase (sMMO) Genes Using the Polymerase Chain Reaction (PCR)
    Microb Ecol. 1997 Jan;33(1):21-31 PMID: 9039762
  32. An evaluation of terminal-restriction fragment length polymorphism (T-RFLP) analysis for the study of microbial community structure and dynamics.
    Environ Microbiol. 2000 Feb;2(1):39-50 PMID: 11243261
  33. Carbon-14 in methane sources and in atmospheric methane: the contribution from fossil carbon.
    Science. 1989 Jul 21;245(4915):286-90 PMID: 17834679
  34. Isolation of acidophilic methane-oxidizing bacteria from northern peat wetlands.
    Science. 1998 Oct 9;282(5387):281-4 PMID: 9765151
  35. Molecular analysis of the methane monooxygenase (MMO) gene cluster of Methylosinus trichosporium OB3b.
    Mol Microbiol. 1991 Feb;5(2):335-42 PMID: 1904125
  36. Stimulation by ammonium-based fertilizers of methane oxidation in soil around rice roots.
    Nature. 2000 Jan 27;403(6768):421-4 PMID: 10667792
  37. Spatial changes in the bacterial community structure along a vertical oxygen gradient in flooded paddy soil cores.
    Appl Environ Microbiol. 2000 Feb;66(2):754-62 PMID: 10653747
  38. Exospores and cysts formed by methane-utilizing bacteria.
    J Gen Microbiol. 1970 May;61(2):219-26 PMID: 5476892
  39. Effects of O2 and CH4 on presence and activity of the indigenous methanotrophic community in rice field soil.
    Environ Microbiol. 2000 Dec;2(6):666-79 PMID: 11214799
Article Info
Journal
Applied and environmental microbiology
Abbr.
Appl Environ Microbiol
ISSN
0099-2240
DOI
10.1128/AEM.67.9.4177-4185.2001
Published
2001-09-00
Pages
4177-85
Language
English
Region
United States
NLM ID
7605801
PMCID
PMC93145
Subset
IM
Databases
GENBANK
AJ299504, AJ299505, AJ299506, AJ299507, AJ299508, AJ299509, AJ299510, AJ299511, AJ299512, AJ299513, AJ299514, AJ299515, AJ299516, AJ299517, AJ299518, AJ299519, AJ299520, AJ299521, AJ299522, AJ299523, AJ299524, AJ299525, AJ299526, AJ299527, AJ299528, AJ299529, AJ299530, AJ299531, AJ299532, AJ299533, AJ299534, AJ299535, AJ299536, AJ299537, AJ299538, AJ299539, AJ299540, AJ299541, AJ299542, AJ299543, AJ299544, AJ299545, AJ299546, AJ299547, AJ299548, AJ299549, AJ299550, AJ299551, AJ299552, AJ299553, AJ299946, AJ299947, AJ299948, AJ299949, AJ299950, AJ299951, AJ299952, AJ299953, AJ299954, AJ299955, AJ299956, AJ299957, AJ299958, AJ299959, AJ299960, AJ299961, AJ299962, AJ299963, AJ299964, AJ299965, AJ299966, AJ299967, AJ299968, AJ299969, AJ299970, AJ299971, AJ299972, AJ299973, AJ299974, AJ299975, AJ299976, AJ299977, AJ299978, AJ299979, AJ299980, AJ299981, AJ299982, AJ299983, AJ299984, AJ299985, AJ299986, AJ299987, AJ299988, AJ299989
External Links
PubMed source DOI: 10.1128/AEM.67.9.4177-4185.2001 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2