Molecular diversity of nitrite reductase genes (nirK) in nitrifying bacteria

被引:102
作者
Cantera, J. Jason L. [1 ]
Stein, Lisa Y. [1 ]
机构
[1] Univ Calif Riverside, Dept Environm Sci, Riverside, CA 92521 USA
关键词
D O I
10.1111/j.1462-2920.2006.01198.x
中图分类号
Q93 [微生物学];
学科分类号
071005 ; 100705 ;
摘要
Sequences of copper-containing nitrite reductase (nirK) genes obtained from completed nitrifier genome sequences were used to design polymerase chain reaction (PCR) primers to amplify partial nirK sequences from one Nitrosomonas and four Nitrosospira isolates. Deduced NirK protein sequences were highly similar to other copper-containing nitrite reductases including conserved motifs. Phylogenetic comparisons of NirK protein sequences placed orthologues from Nitrosomonas, Nitrosospira and Nitrobacter species into multiple distinct clades. Products related to nirK genes were not amplified from seven additional Nitrosomonas and Nitrosospira isolates by PCR with nirK-specific primers; however, DNA extracted from four of these isolates produced detectable signals in low-stringency Southern hybridizations probed with nirK gene fragments from ammonia-oxidizers with known nirK gene sequences. Analysis of promoter regions of nitrifier nirK genes revealed conserved binding motifs for the NsrR transcription factor in only one clade; other available nitrifier nirK gene promoters lacked characterized transcription factor binding motifs. Taken together, these results indicate that the sequences and regulation of nirK genes are diverse among nitrifiers. This study provides insight to the use of nirK genes for molecular diversity studies, establishes a framework to resolve the origins and diversification of nitrite reduction among the nitrifiers, and expands the database of nirK orthologues.
引用
收藏
页码:765 / 776
页数:12
相关论文
共 47 条
[1]  
[Anonymous], 1989, Cladistics, DOI DOI 10.1111/J.1096-0031.1989.TB00562.X
[2]  
Ausubel FM, 1995, CURRENT PROTOCOLS MO
[3]   Effect of soil ammonium concentration on N2O release and on the community structure of ammonia oxidizers and denitrifiers [J].
Avrahami, S ;
Conrad, R ;
Braker, G .
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2002, 68 (11) :5685-5692
[4]   Expression of nitrite reductase in Nitrosomonas europaea involves NsrR, a novel nitrite-sensitive transcription repressor [J].
Beaumont, HJE ;
Lens, SI ;
Reijnders, WNM ;
Westerhoff, HV ;
van Spanning, RJM .
MOLECULAR MICROBIOLOGY, 2004, 54 (01) :148-158
[5]   Novel nirK cluster genes in Nitrosomonas europaea are required for NirK-dependent tolerance to nitrite [J].
Beaumont, HJE ;
Lens, SI ;
Westerhoff, HV ;
van Spanning, RJA .
JOURNAL OF BACTERIOLOGY, 2005, 187 (19) :6849-6851
[6]   Nitrite reductase of Nitrosomonas europaea is not essential for production of gaseous nitrogen oxides and confers tolerance to nitrite [J].
Beaumont, HJE ;
Hommes, NG ;
Sayavedra-Soto, LA ;
Arp, DJ ;
Arciero, DM ;
Hooper, AB ;
Westerhoff, HV ;
van Spanning, RJM .
JOURNAL OF BACTERIOLOGY, 2002, 184 (09) :2557-+
[7]   GROWTH OF NITROBACTER IN THE ABSENCE OF DISSOLVED-OXYGEN [J].
BOCK, E ;
WILDERER, PA ;
FREITAG, A .
WATER RESEARCH, 1988, 22 (02) :245-250
[8]   NITROGEN LOSS CAUSED BY DENITRIFYING NITROSOMONAS CELLS USING AMMONIUM OR HYDROGEN AS ELECTRON-DONORS AND NITRITE AS ELECTRON-ACCEPTOR [J].
BOCK, E ;
SCHMIDT, I ;
STUVEN, R ;
ZART, D .
ARCHIVES OF MICROBIOLOGY, 1995, 163 (01) :16-20
[9]   The yjeB (nsrR) gene of Escherichia coli encodes a nitric oxide-sensitive transcriptional regulator [J].
Bodenmiller, DM ;
Spiro, S .
JOURNAL OF BACTERIOLOGY, 2006, 188 (03) :874-881
[10]   Nitrite reductase genes (nirK and nirS) as functional markers to investigate diversity of denitrifying bacteria in Pacific northwest marine sediment communities [J].
Braker, G ;
Zhou, JZ ;
Wu, LY ;
Devol, AH ;
Tiedje, JM .
APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2000, 66 (05) :2096-2104