Microbial populations in various paddy soils respond differently to denitrification-inducing conditions, albeit background bacterial populations are similar

Soil Science and Plant Nutrition

Volumn 56, Issue 2, 2010, Pages 220-224

  Ishii, Satoshi ^a   Yamamoto, Michihiro ^a   Tago, Kanako ^a   Otsuka, Shigeto ^a   Senoo, Keishi ^a  

^a UNIVERSITY OF TOKYO   (Japan)

Author keywords

Community structure; Denaturing gradient gel electrophoresis; Denitrification; Rice paddy soil

Indexed keywords

BACTERIA (MICROORGANISMS);

EID: 77953223441     PISSN: 00380768     EISSN: 17470765     Source Type: Journal    
DOI: 10.1111/j.1747-0765.2010.00453.x     Document Type: Article

References (17)

1. Akiyama H, Yan X, Yagi K. Estimations of emission factors for fertilizer-induced direct N2O emissions from agricultural soils in Japan: summary of available data. Soil Sci. Plant Nutr. 2006, 52:774-787.
2. Hayatsu M, Tago K, Saito M. Various players in the nitrogen cycle: diversity and functions of the microorganisms involved in nitrification and denitrification. Soil Sci. Plant Nutr. 2008, 54:33-45.
3. Hiramatsu M, Fujii T, Watanabe K. Bacterial communities in rice paddy soils with long-term application of organic fertilizers, as analyzed by PCR-DGGE. 2007, Abstracts of the Annual Meeting, Japanese Society of Soil Science and Plant Nutrition 53, 38 (in Japanese
4. Ishii S, Kadota K, Senoo K. Application of a clustering-based peak alignment algorithm to analyze various DNA fingerprinting data. J. Microbiol. Meth. 2009a, 78:344-350.
5. Ishii S, Yamamoto M, Kikuchi M. Microbial populations responsive to denitrification-inducing conditions in rice paddy soil, as revealed by comparative 16S rRNA gene analysis. Appl. Environ. Microbiol. 2009b, 75:7070-7078.
6. Loy A, Schulz C, Lücker S. 16S rRNA gene-based oligonucleotide microarray for environmental monitoring of the Betaproteobacterial order " Rhodocyclales" Appl. Environ. Microbiol. 2005, 71:1373-1386.
7. Morimoto S, Ogawa N, Hasebe A, Fujii T. Isolation of effective 3-chlorobenzoate-degraders in soil using community analyses by PCR-DGGE. Microbes Environ. 2008, 23:285-292.
8. Muyzer G, De Waal EC, Uitterlinden AG. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 1993, 59:695-700.
9. Nishimura S, Sawamoto T, Akiyama H, Sudo S, Cheng W, Yagi K. Continuous, automated nitrous oxide measurements from paddy soils converted to upland crops. Soil Sci. Soc. Am. J. 2005, 69:1977-1986.
10. Nishimura S, Sawamoto T, Akiyama H, Sudo S, Yagi K. Methane and nitrous oxide emissions from a paddy field with Japanese conventional water management and fertilizer application. Glob. Biogeochem. Cycles 2004, 18:GB2017.
11. Otsuka S, Sudiana I, Komori A. Community structure of soil bacteria in a tropical rainforest several years after fire. Microbes Environ. 2008, 23:49-56.
12. Philippot L, Hallin S, Schloter M. Ecology of denitrifying prokaryotes in agricultural soil. Adv. Agron. 2007, 96:249-305.
13. Ravishankara AR, Daniel JS, Portmann RW. Nitrous oxide (N2O): the dominant ozone-depleting substance emitted in the 21st century. Science 2009, 326:123-125.
14. Saito T, Ishii S, Otsuka S, Nishiyama M, Senoo K. Identification of novel Betaproteobacteria in a succinate-assimilating population in denitrifying rice paddy soil by using stable isotope probing. Microbes Environ. 2008, 23:192-200.
15. Suzuki C, Nagaoka K, Shimada A, Takenaka M. Bacterial communities are more dependent on soil type than fertilizer type, but the reverse is true for fungal communities. Soil Sci. Plant Nutr. 2009, 55:80-90.
16. Wang Q, Garrity GM, Tiedje JM, Cole JR. Naïve Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 2007, 73:5261-5267.
17. Yoshida M, Ishii S, Otsuka S, Senoo K. Temporal shifts in diversity and quantity of nirS and nirK in a rice paddy field soil. Soil Biol. Biochem. 2009, 41:2044-2051.