Phylogenetic study on CTO primer-amplified ammonia-oxidizing bacteria and β-Proteobacteria associated with rice roots grown in a flooded paddy soil

Soil Science and Plant Nutrition

Volumn 49, Issue 5, 2003, Pages 719-727

  Ikenaga, Makoto ^a   Asakawa, Susumu ^a   Muraoka, Yoshitetsu ^a   Kimura, Makoto ^a  

^a NAGOYA UNIVERSITY   (Japan)

Author keywords

Ammonia oxidizing bacteria; Cto primer; Pcr dgge; Rice root

Indexed keywords

BACTERIA (MICROORGANISMS); METHYLOPHILUS; NEGIBACTERIA; NITROSOMONADALES; NITROSOSPIRA; PROTEOBACTERIA; RHODOCYCLUS;

EID: 0142038908     PISSN: 00380768     EISSN: 17470765     Source Type: Journal    
DOI: 10.1080/00380768.2003.10410330     Document Type: Article

References (32)

1. Aakra A, Hesselsoe M, and Bakken LR 2000: Surface attachment of ammonia oxidizing bacteria in soil. Microb. Ecol., 39,222-235
2. Aakra A, IMker JB, Prommerenmg-Roser A, Koops HP, and Nes IF 2001: Detailed phyogeny of ammonia-oxidizing bacteria determined by rDNA sequences and DNA homology values. Int. J Syst Evol. Mirobiol,51, 2021-2030
3. Abichandani CT and Patnaik S 1955: Mineralizing action of lime on soil nitrogen in waterlogged nee soils. Int. Rice Commun. Newslett., 13. 11-13
4. Alfreider A, Vogt C, and Babel W 2002: Microbiol diversity in an in situ reactor system treating monochlorobenzene contaminated groundwater as revealed by 16S ribosoma! DNA analysis. Syst Appl. Microbiol., 25, 232-240
5. Arth I, Frenzel P, and Conrad R 1998: Denitrification coupled to nitrification in the rhizosphere of rice. Soil Biol. Biochem., 30,509-515
6. Boer WD, Gubbewiek PJAK, and Troelstra SR 1990: Nitrification in Dutch heathland soils. II. Characteristics of nitrate production. Plant Sod, 127, 193-200
7. Bruns MA, Stephen JR, Kowalchuk GA, Prosser JI, and Paul EA 1999: Comparative diversity of ammonia oxidizer 16S rRNA gene sequences in native, tilled, and successional soils. Appl. Environ. Microbiol., 65, 2994-3000
8. Coates JD, Chakraborty R, Lack JG, O'Connor SM, and Cole KA 2001: Anaerobic benzene oxidation coupled to nitrate reduction in pure culture by two strains of Dechloromonas. Nature, 411, 1039-1043
9. Coates JD, Michaelidou U, Bruce RA, O'Conner SM, Crespi JM, and Achenbach LA 1999: Ubiquity and diversity of dis-similatory (per) chlorate-reducing bacteria. Appl Environ. Microbiol., 65, 5234-5241
10. Craswell ET and Vlek PLG 1979: Fate of fertilizer nitrogen applied to wetland rice. In Nitrogen and Rice, p. 175-192, International Rice Research Institute, Los Banos, Philippines
11. Haleem DAE, Wintzingerode FV, Moter A, Moawad H, and Gobel UB 2000: Phylogenetic analysis of rhizosphere-asso-ciated /3-subclass proteobactenal ammonia oxidizers in a municipal wastewater treatment plant based on rhizoremedi-ation technology. Lett. Appl. Microbial., 31, 34-38
12. Heuer H and Smalla K 1997: Application of denaturing gradient gel electrophoresis and temperature gradient gel electrophoresis for studying soil microbial communities. In Modem Soil Microbiology, Ed. JD van Elsas, JT Trevors, and F.MH Wellington, p. 353-373, Dekker, New York
13. Hoshikawa K 1975: The Growing Rice Plant-An Anatomical Monograph, p. 87-101, Nobunkyo, Tokyo
14. Hurek T, Wagner B, and Reinhold-Hurek B 1997: Identification of N7-fixmg plant- and fungus-associated Azoarcus species by PCR-based genomic fingerprints. Appl Environ. Microbiol., 62,4311-4339
15. Ikenaga M, Asakawa S, Muraoka Y, and Kimura M 2003: Bacterial communities associated with nodal roots of rice plants along with the growth stages: Estimation by PCR-DGGE and sequence analyses. Soil Set. Plant Nutr., 49, 591-602
16. Ikenaga M, Muraoka Y, Toyota K, and Kimura M 2002: Community structure of the microbiota associated with nodal roots of rice plants along with the growth stages: estimation by PCR-RFLP analysis. Biol. Fertil Soils, 36, 397-404
17. Keeney DR and Sahrawat KL 1986: 2. Nitrogen transformations in flooded rice soils. Fertil. Res., 9, 15-38
18. Kimura M, Wada H, and Takai Y 1979: The studies on the rhizosphere of paddy rice. IV. The effects of anaerobiosis on microbes. Soil Sci. Plant Nutr., 25, 145-153
19. Kowalchuk GA, Bodelier PLE, Heilig GHJ, Stephen JR, and Laanbroek HJ 1998: Community analysis of ammonia-oxidizing bacteria, in relation to oxygen availability m soils and root-oxygenated sediments, using PCR, DGGE and oligonucleotide probe hybridisation. FEMS Microbiol. Ecol., 27, 339-350
20. Kowalchuk GA, Naoumenko ZS, Derikx PJL, Felske A, Stephen JR, and Arkhipchenko IA 1999: Molecular analysis of ammonia-oxidizing bacteria of the /3 subdivision of the class Proteobacteria in compost and compost materials. Appl. Environ. Microbiol., 65, 396-403
21. Kowalchuk GA and Stephen JR 2001: Ammonia-oxidizing bacteria: A model for molecular microbial ecology. Annu. Rev. Microbiol, 55, 458-529
22. Kowaichuk GA, Stephen JR, Boer WD, Prosser JI, Embley TM, and Woldendorp JW 1997: Analysis of ammonia-oxidizing bacteria of the /? subdivision of the class proteobacteria in coastal sand dunes by denaturing gradient gel electrophore
23. sis and sequencing of PCR amplified 16S ribosomal DNA fragments. Appl. Environ Microbiol., 63, 1489-1497
24. McCaig AE, Phillips CJ, Stephen JR, Kowalchuk GA, Harvey SM, Herbert RA, Embley TM, and Prosser JI 1999: Nitrogen cycling and community structure of proteobacterial (3-subgroup ammonia-oxidizing bacteria within polluted marine fish farm sediments. Appl. Environ. Microbiol., 65, 213-220
25. Mendum TA, Sockett RE, and Hirsch PR 1999: Use of molecular and isotopic techniques to monitor the response of auto-trophic ammonia-oxidizing population of the beta subdivision of the class proteobacteria in arable soils to nitrogen fertilizer. Appl Environ. Microbiol., 65, 4155-4162
26. Mitsui S 1955: Inorganic Nutation, Fertilization and Soil Amelioration for Lowland Rice, p. 107, Yokendo, Tokyo
27. Nicolaisen MH and Ramsing NB 2002: Denaturing gradient gel electrophoresis (DGGE) approaches to study the diversity of ammonia-oxidizing bacteria. J. Microbiol Methods, 50, 189-203
28. Rotthauwe JH, Witzel KJP, and Liesack E 1997: The ammonia monooxygenase structural gene amoA as a functional marker: Molecular fine-scale analysis of natural ammonia-oxidizing populations. Appl. Environ Microbiol., 63, 4704 4712
29. Savant NK and Datta SKD 1982: Nitrogen transformations in wetland rice soils. AJv Agron., 35, 241-302
30. Stephen JR, Chang YJ, Macnaughton SJ, Kowalchuk GA, Leung KT, Flemming CA, and White DC 1999: Effect of toxic metals on indigenous soil /3-subgroup proteobacterium ammonia oxidizer community structure and protection against toxicity by inoculated metal-resistant bacteria. Appl. Environ. Microbiol., 65, 95-101
31. Stephen JR, Kowalchuk GA, Bruns MA, McCaig AE, Phillips CJ, Embley TM, and Prosser JI 1998: Analysis of /3-sub-group proteobacterial ammonia oxidizer population in soil by denaturing gradient gel electrophoresis analysis and hierarchical phylogenetic probing. Appl. Environ Microbiol., 64, 2958-2965
32. Yang CH and Crowley DE 2000: Rhizosphere microbial community structure in relation to root location and plant iron nutritional status. Appl Environ Microbiol., 66, 345-351