Structure and activity of soil-inhabiting methanotrophic communities in northern forest of Japan

Soil Biology and Biochemistry

Volumn 41, Issue 2, 2009, Pages 403-408

  Tsutsumi, Masazumi ^a   Kojima, Hisaya ^a   Uemura, Shigeru ^a   Ono, Kiyomi ^a   Sumida, Akihiro ^a   Hara, Toshihiko ^a   Fukui, Manabu ^a  

^a HOKKAIDO UNIVERSITY   (Japan)

Author keywords

DGGE; Methane; Methanotroph; Microbial community structure; Northern forest; pmoA; Undergrowth vegetation

Indexed keywords

COLLOIDS; ELECTROPHORESIS; FORESTRY; GELATION; GENE ENCODING; METHANE; VEGETATION;

DGGE; METHANOTROPH; MICROBIAL COMMUNITY STRUCTURE; NORTHERN FOREST; PMOA; UNDERGROWTH VEGETATION;

SOILS;

BAMBOO; COMMUNITY STRUCTURE; DOMINANCE; ENZYME ACTIVITY; FOREST SOIL; GENE EXPRESSION; LABORATORY METHOD; METHANE; MICROBIAL ACTIVITY;

COLLOIDS; ELECTROPHORESIS; FORESTRY; FORESTS; GELATION; GENETIC ENGINEERING; METHANE; MICROORGANISMS; PLANTS; SOIL ANALYSIS;

ASIA; EURASIA; FAR EAST; JAPAN;

SASA; SASA KURILENSIS; SASA SENANENSIS;

EID: 58149496081     PISSN: 00380717     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.soilbio.2008.12.005     Document Type: Article

References (38)

1. Amaral J.A., and Knowles R. Inhibition of methane consumption in forest soils and pure cultures of methanotrophs by aqueous forest soil extracts. Soil Biology & Biochemistry 29 (1997) 1713-1720
2. Bodelier P.L.E., and Laanbroek H.J. Nitrogen as a regulatory factor of methane oxidation in soils and sediments FEMS. Microbiology Ecology 47 (2004) 265-277
3. Bourne D.G., McDonald I.R., and Murrell J.C. Comparison of pmoA PCR primer sets as tools for investigating methanotroph diversity in three Danish soils. Applied and Environmental Microbiology 67 (2001) 3802-3809
4. Curry C.L. Modeling the soil consumption of atmospheric methane at the global scale. Global Biogeochemical Cycles 21 (2007) GB4012
5. Dunfield P.F., Liesack W., Henckel T., Knowles R., and Conrad R. High-affinity methane oxidation by a soil enrichment culture containing a type II methanotroph. Applied and Environmental Microbiology 65 (1999) 1009-1014
6. 4 sink. Global Biogeochemical Cycles 21 (2007) GB4013
7. Dörr H., Katruff L., and Levin I. Soil texture parameterization of the methane uptake in aerated soils. Chemosphere 26 (1993) 697-713
8. Hanson R.S., and Hanson T.E. Methanotrophic bacteria. Microbiological Reviews 60 (1996) 439-471
9. Henckel T., Jäckel U., Schnell S., and Conrad R. Molecular analyses of novel methanotrophic communities in forest soil that oxidize atmospheric methane. Applied and Environmental Microbiology 66 (2000) 1801-1808
10. Holmes A.J., Costello A., Lidstrom M.E., and Murrell J.C. Evidence that particulate methane monooxygenase and ammonia monooxygenase may be evolutionarily related. FEMS Microbiology Letters 132 (1995) 203-208
11. Holmes A.J., Roslev P., McDonald I.R., Iverson N., Henriksen K., and Murrell J.C. Characterization of methanotrophic bacterial populations in soils showing atmospheric methane uptake. Applied and Environmental Microbiology 65 (1999) 3312-3318
12. Ishii H.T., Kobayashi T., Uemura S., Takahashi K., Hanba Y.T., Sumida A., and Hara T. Removal of understory dwarf bamboo (Sasa kurilensis) induces changes in water-relations characteristics of overstory Betula ermanii trees. Journal of Forest Research 13 (2008) 101-109
13. Ishizuka S., Sakata T., and Ishizuka K. Methane oxidation in Japanese forest soils. Soil Biology & Biochemistry 32 (2000) 769-777
14. Kato K., Sumida A., Yoshida T., Akibayashi Y., and Hara T. Stand structure and light conditions of a conifer-hardwood mixed forest in northern Hokkaido, Japan. Transactions of the Meeting in Hokkaido Branch of the Japanese Forestry Society 53 (2005) 58-59 (in Japanese)
15. Knief C., Lipaki A., and Dunfield P.F. Diversity and activity of methanotrophic bacteria in different upland soils. Applied and Environmental Microbiology 69 (2003) 6703-6714
16. Knief C., Vanitchung S., Harvey N.W., Conrad R., Dunfield P.F., and Chidthaisong A. Diversity of methanotrophic bacteria in tropical upland soils under different land uses. Applied and Environmental Microbiology 71 (2005) 3826-3831
17. Knief C.A., Kolb S., Bodelier P.L.E., Lipski A., and Dunfield P.F. The active methanotrophic community in hydromorphic soils changes in response to changing methane concentration. Environmental Microbiology 8 (2006) 321-333
18. Kolb S., Knief C., Dunfield P.F., and Conrad R. Abundance and activity of uncultured methanotrophic bacteria involved in the consumption of atmospheric methane in two forest soils. Environmental Microbiology 7 (2005) 1150-1161
19. Lau E., Ahmad A., Steudler P.A., and Cavanaugh C.M. Molecular characterization of methanotrophic communities in forest soils that consume atmospheric methane. FEMS Microbiology Ecology 60 (2007) 490-500
20. Mancinelli R.L. The regulation of methane oxidation in soil. Annual Review of Microbiology 49 (1995) 581-605
21. Muyzer G., Hottenträger S., Teske A., and Wawer C. Denaturing gradient gel electrophoresis of PCR-amplified 16S rDNA - a new molecular approach to analyze the genetic diversity of mixed microbial communities. In: Akkermans A.D.L., Van Elsas J.D., and De Brujin F. (Eds). Molecular Microbial Ecology Manual (1996), Kluwer Academic, Dordrecht pp. 3.4.4/1-23
22. Nakano T., Inoue G., and Fukuda M. Methane consumption and soil respiration by a birch forest soil in West Siberia. Tellus 56B (2004) 223-229
23. Reay D.S., Radajewski S., Murrell J.C., McNamara N., and Nedwell D.B. Effects of land-use on the activity and diversity of methane oxidizing bacteria in forest soils. Soil Biology & Biochemistry 33 (2001) 1613-1623
24. Rodhe H. A comparison of the contribution of various gases to the greenhouse effect. Science 248 (1990) 1217-1219
25. 4 exchange, and microbial N turnover over a Mediterranean pine forest soil. Biogeosciences 3 (2006) 121-133
26. Singh J.S., Singh S., Raghubanshi A.S., Singh S., Kashyap A.K., and Reddy V.S. Effect of soil nitrogen, carbon and moisture on methane uptake by dry tropical forest soils. Plant and Soil 196 (1997) 115-121
27. Singh B.K., Tate K.R., Kolipaka G., Hedley C.B., Macdonald C.A., Millard P., and Murrell C. Effect of afforestation and reforestation of pastures on the activity and population dynamics of methanotrophic bacteria. Applied and Environmental Microbiology 73 (2007) 5153-5161
28. Smith K.A., Dobbie K.E., Ball B.C., Bakken L.R., Sitaula B.K., Hansen S., Brumme R., Borken W., Christensen S., Prieme A., Fowler D., Macdonald J.A., Skiba U., Klemedtsson L., Kasimir-Klemedtsson A., DegÓrska A., and Orlanski P. Oxidation of atmospheric methane in northern European soils, comparison with other ecosystems, and uncertainties in the global terrestrial sink. Global Change Biology 6 (2000) 791-803
29. Steinkamp R., Butterbach-Bahl K., and Papen H. Methane oxidation by soils of an N limited and N fertilized spruce forest in the Black Forest, Germany. Soil Biology & Biochemistry 33 (2001) 145-153
30. Steinkamp R., Zimmer W., and Papen H. Improved method for detection of methanotrophic bacteria in forest soils by PCR. Current Microbiology 42 (2001) 316-322
31. Takahashi K., Uemura S., and Hara T. Effect of understory dwarf bamboo on seasonal changes in soil temperature in a Betula ermanii forest, northern Japan. Eurasian Journal of Forest Research 5 (2002) 49-53
32. Takahashi K., Mitsuishi D., Uemura S., Suzuki J., and Hara T. Stand structure and dynamics during a 16-year period in a sub-boreal conifer-hardwood mixed forest, northern Japan. Forest Ecology and Management 174 (2003) 39-50
33. Tamai N., Takenaka C., Ishizuka S., and Tezuka T. Methane flux and regulatory variables in soils of three equal-aged Japanese cypress (Chamaecyparis obtusa) forests in central Japan. Soil Biology & Biochemistry 35 (2003) 633-641
34. Tamura K., Dulley J., Nei M., and Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24 (2007) 1596-1599
35. 2O in three subtropical forest ecosystems in southern China. Global Change Biology 12 (2006) 546-560
36. Tappeiner J.C., and Alm A.A. Undergrowth vegetation effects on the nutrient content of litterfall and soils in red pine and birch stands in northern Minnesota. Ecology 56 (1975) 1193-1200
37. Tripathi S.K., Sumida A., Shibata H., Uemura S., Ono K., and Hara T. Growth and substrate quality of fine root and soil nitrogen availability in a young Betula ermanii forest of northern Japan: effects of the removal of understory dwarf bamboo (Sasa kurilensis). Forest Ecology and Management 212 (2005) 278-290
38. Tripathi S.K., Sumida A., Ono K., Shibata H., Uemura S., Takahashi K., and Hara T. The effects of understorey dwarf bamboo (Sasa kurilensis) removal on soil fertility in a Betula ermanii forest of northern Japan. Ecological Research 21 (2006) 315-320