Community structure of β-Proteobacterial ammonia-oxidizing bacteria in prawn farm sediment

Progress in Natural Science

Volumn 18, Issue 6, 2008, Pages 679-684

  Ma, Ying ^a   Wang, Lin ^a   Qian, Lumin ^b  

^a JIMEI UNIVERSITY   (China)

^b SOA Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources Key Laboratory of Marine Genetic   (China)

Author keywords

16S rRNA gene; Ammonia oxidizing bacteria; Phylogenetic diversity; Prawn farm sediment

Indexed keywords

AMMONIA; BACTERIA; CLONING; GENES; MARINE BIOLOGY; RNA; SHELLFISH;

16S RRNA GENE; AMMONIA OXIDIZING BACTERIA; COMMUNITY STRUCTURES; NITROSOMONAS; PHYLOGENETIC DIVERSITY; PRAWN FARM SEDIMENT; RESTRICTION FRAGMENT LENGTH POLYMORPHISM ANALYSIS; RESTRICTION FRAGMENT LENGTH POLYMORPHISMS; RRNA GENE LIBRARY; SPECIFIC PRIMERS;

SEDIMENTS;

EID: 46449104894     PISSN: 10020071     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.pnsc.2008.01.013     Document Type: Article

References (28)

1. T.H. Blackburn N.D. Blackburn Model of nitrification and denitrification in marine sediments FEMS Microbiol Lett 100 1–3 1992 517 522
2. U. Purkhold A. Pommerening-Röser S. Juretschko Phylogeny of all recognized species of ammonia oxidizers based on comparative 16S rRNA and amo A sequence analysis: implications for molecular diversity surveys Appl Environ Microbiol 66 12 2000 5368 5382
3. S. Juretschko G. Timmermann M. Schmid Combined molecular and conventional analyses of nitrifying bacterium diversity in activated sludge: Nitrosococcus mobilis and Nitrospira -like bacteria as dominant populations Appl Environ Microbiol 64 8 1998 3042 3051
4. J.R. Stephen G.A. Kowalchuk M.V. Bruns Analysis of β-subgroup proteobacterial ammonia oxidizer populations in soil by denaturing gradient gel electrophoresis analysis and hierarchical phylogenetic probing Appl Environ Microbiol 64 8 1998 2958 2965
5. G.A. Kowalchuk J.R. Stephen W. de Boer Analysis of ammonia-oxidizing bacteria of the β-subdivision of the class Proteobacteria in coastal sand dunes by denaturing gradient gel electrophoresis and sequencing of PCR-amplified 16S ribosomal DNA fragments Appl Environ Microbiol 63 4 1997 1489 1497
6. A. Schramm L.H. Larsen N.P. Revsbech Structure and function of a nitrifying biofilm as determined by in situ hybridization and the use of microelectrodes Appl Environ Microbiol 62 12 1996 4641 4647
7. A. Schramm D. de Beer M. Wagner Identification and activities in situ of Nitrosospira and Nitrospira spp. as dominant populations in a nitrifying fluidized bed reactor Appl Environ Microbiol 64 9 1998 3480 3485
8. W.D. Hiorns R.C. Hastings I.M. Head Amplification of 16S ribosomal RNA genes of autotrophic ammonia-oxidizing bacteria demonstrates the ubiquity of nitrosospiras in the environment Microbiology 141 1995 2793 2800
9. C.J. Phillips Z. Smith T.M. Embley Phylogenetic differences between particle-associated and planktonic ammonia-oxidizing bacteria of the β-subdivision of the class Proteobacteria in the northwestern Mediterranean Sea Appl Environ Microbiol 65 2 1999 779 786
10. P.C. Burrell C.M. Phalen T.A. Hovanec Identification of bacteria responsible for ammonia oxidation in freshwater aquaria Appl Environ Microbiol 67 12 2001 5791 5800
11. A.E. McCaig C.J. Phillips J.R. Stephen Nitrogen cycling and community structure of proteobacterial beta-subgroup ammonia-oxidizing bacteria within polluted marine fish farm sediments Appl Environ Microbiol 65 1 1999 213 220
12. Y.N. Wang B.J. Wang X. Dai Bacterial conversion of sulfur- and phosphorous-compounds and microbial diversity in sediments from a near-shore marine-cultural region Environ Sci 26 2 2005 157 162 (in Chinese)
13. P. Shao Y.Q. Chen H. Zhou Phylogenetic diversity of Archaea in prawn farm sediment Mar Biol 146 2004 133 142
14. J.R. Stephen A.E. McCaig Z. Smith Molecular diversity of soil and marine 16S rRNA gene sequences related to β-subgroup ammonia-oxidizing bacteria Appl Environ Microbiol 62 11 1996 4147 4154
15. J.M. Regan G.W. Harrington D.R. Noguera Ammonia- and nitrite-oxidizing bacterial communities in a pilot-scale chloraminated drinking water distribution system Appl Environ Microbiol 68 1 2002 73 81
16. M.A. Voytek B.B. Ward Detection of ammonium-oxidizing bacteria of the beta-subclass of the class Proteobacteria in aquatic samples with the PCR Appl Environ Microbiol 61 7 1995 1444 1450
17. T.D. Mullins T.B. Britschgi R.L. Krest Genetic comparisons reveal the same unknown bacterial lineages in Atlantic and Pacific bacterioplankton communities Limnol Oceanogr 40 1 1995 148 158
18. C.J. Krebs Ecological methodology 2nd ed. 1989 Harper Collins Publishers New York p. 654
19. B.L. Maidak J.R. Cole T.G. Lilburn The RDP-II (Ribosomal Database Project) Nucleic Acids Res 29 1 2001 173 174
20. J.D. Thompson T.J. Gibson F. Plewniak The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools Nucleic Acids Res 25 24 1997 4876 4882
21. S. Kumar K. Tamura M. Nei MEGA 3: integrated software for molecular evolutionary genetics analysis and sequence alignment Brief Bioinform 5 2 2004 150 163
22. U. Purkhold M. Wagner G. Timmermann 16S rRNA and amo A-based phylogeny of 12 novel betaproteobacterial ammonia-oxidizing isolates: extension of the dataset and proposal of a new lineage within the nitrosomonads Int J Syst Evol Micr 53 2003 1485 1494
23. Voytek MA. Relative abundance and species diversity of autotrophic ammonia-oxidizing bacteria in aquatic systems. Ph.D. Dissertation, University of California, Santa Cruz, 1996.
24. H. Urakawa H. Maki S. Kawabata Abundance and population structure of ammonia-oxidizing bacteria that inhabit canal sediments receiving effluents from municipal wastewater treatment plants Appl Environ Microbiol 72 10 2006 6845 6850
25. T.E. Freitag J.I. Prosser Community structure of ammonia-oxidizing bacteria within anoxic marine sediments Appl Environ Microbiol 69 3 2003 1359 1371
26. T.E. Freitag L. Chang J.I. Prosser Changes in the community structure and activity of betaproteobacterial ammonia-oxidizing sediment bacteria along a freshwater-marine gradient Environ Microbiol 8 4 2006 684 696
27. M. De Bie A. Speksnijder G. Kowalchuk Shifts in the dominant populations of ammonia-oxidizing β-subclass Proteobacteria along the eutrophic Schelde estuary Aquat Microb Ecol 23 2001 225 236
28. Y. Ma L.M. Qian Y.S. Wang Progress in molecular ecology of nitrifying bacteria J Fish Sci China 14 5 2007 872 879 (in Chinese)