Habitat partitioning of denitrifying bacterial communities carrying nirS or nirK genes in the stratified water column of Lake Kinneret, Israel

Aquatic Microbial Ecology

Volumn 51, Issue 2, 2008, Pages 129-140

  Junier, Pilar ^a,b   Kim, Ok Sun ^b   Witzel, Karl Paul ^b   Imhoff, Johannes F ^c   Hadas, Ora ^d  

^a EPFL   (Switzerland)

^b MAX PLANCK INSTITUTE FOR EVOLUTIONARY BIOLOGY   (Germany)

^c GEOMAR HELMHOLTZ CENTRE FOR OCEAN RESEARCH KIEL   (Germany)

^d ISRAEL OCEANOGRAPHIC AND LIMNOLOGICAL RESEARCH   (Israel)

Author keywords

Lake Kinneret; nirK; nirS; T RFLP

Indexed keywords

BACTERIA (MICROORGANISMS);

EID: 46949105559     PISSN: 09483055     EISSN: None     Source Type: Journal    
DOI: 10.3354/ame01186     Document Type: Article

References (33)

1. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-3402
2. 2O release and on the community structure of ammonia oxidizers and denitrifiers. Appl Environ Microbiol 68:5685-5692
3. Beaumont HJ, Lens SI, Westerhoff HV, van Spanning RJ (2005) Novel nirK cluster genes in Nitrosomonas europaea are required for NirK-dependent tolerance to nitrite. J Bacteriol 187:6849-6851
4. Braker G, Fesefeldt A, Witzel KP (1998) Development of PCR primer systems for amplification of nitrite reductase genes (nirK and nirS) to detect denitrifying bacteria in environmental samples. Appl Environ Microbiol 64:3769-3775
5. Braker G, Zhou J, Wu L, Devol AH, Tiedje JM (2000) Nitrite reductase genes (nirK and nirS) as functional markers to investigate diversity of denitrifying bacteria in Pacific Northwest marine sediment communities. Appl Environ Microbiol 66:2096-2104
6. Braker G, Ayala del Rio HL, Devol AH, Fesefeldt A, Tiedje JM (2001) Community structure of denitrifiers, bacteria, and archaea along redox gradients in Pacific Northwest marine sediments by terminal restriction fragment length polymorphism analysis of amplified nitrite reductase (nirS) and 16S rRNA genes. Appl Environ Microbiol 67:1893-1901
7. Casciotti KL, Ward BB (2001) Dissimilatory nitrite reductase genes from autotrophic ammonia-oxidizing bacteria. Appl Environ Microbiol 67:2213-2221
8. Castro-Gonzalez M, Braker G, Farias L, Ulloa O (2005) Communities of nirS-type denitrifiers in the water column of the oxygen minimum zone in the eastern South Pacific. Environ Microbiol 7:1298-1306
9. 1 and non-heme copper nitrite reductases in denitrifying bacteria. Appl Environ Microbiol 55: 2924-2931
10. Eckert W, Imberger J, Saggio A (2002) Biogeochemical response to physical forcing in the water column of a warm monomictic lake. Biogeochemistry 61:291-307
11. Francis CA, Roberts KJ, Beman JM, Santoro AE, Oakley BB (2005) Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. Proc Natl Acad Sci USA 102:14683-14688
12. Hadas O, Pinkas R (1995) Sulphate reduction in the hypolimnion and sediments of Lake Kinneret, Israel. Freshw Biol 33:63-72
13. Hallin S, Lindgren PE (1999) PCR detection of genes encoding nitrite reductase in denitrifying bacteria. Appl Environ Microbiol 6:1652-1657
14. Jayakumar DA, Francis CA, Naqvi SWA, Ward BB (2004) Diversity of nitrite reductase genes (nirS) in the denitrifying water column of the coastal Arabian Sea. Aquat Microb Ecol 34:69-78
15. Kaplan CW, Kitts CL (2003) Variation between observed and true terminal restriction fragment length is dependent on true TRF length and purine content. J Microbiol Methods 54:121-125
16. Kitts CL (2001) Terminal restriction fragment patterns: a tool for comparing microbial communities and assessing community dynamics. Curr Issues Intest Microbiol 2:17-25
17. Knowles R (1982) Denitrification. Microbiol Rev 46:43-70
18. Liu X, Tiquia SM, Holguin G, Wu L and others (2003) Molecular diversity of denitrifying genes in continental margin sediments within the oxygen-deficient zone off the Pacific coast of Mexico. Appl Environ Microbiol 69:3549-3560
19. Lueders T, Friedrich MW (2003) Evaluation of PCR amplification bias by terminal restriction fragment length polymorphism analysis of small-subunit rRNA and mcrA genes by using defined template mixtures of methanogenic pure cultures and soil DNA extracts. Appl Environ Microbiol 69:320-326
20. 1-denitrifying bacteria in environmental marine samples. Appl Environ Microbiol 66:1564-1571
21. Nogales B, Timmis KN, Nedwell DB, Osborn AM (2002) Detection and diversity of expressed denitrification genes in estuarine sediments after reverse transcription-PCR amplification from mRNA. Appl Environ Microbiol 68:5017-5025
22. Oakley BB, Francis CA, Roberts KJ, Fuchsman CA, Srinivasan S, Staley JT (2007) Analysis of nitrite reductase (nirK and nirS) genes and cultivation reveal depauperate community of denitrifying bacteria in the Black Sea suboxic zone. Environ Microbiol 9:118-130
23. Philippot L (2002) Denitrifying genes in bacterial and Archaeal genomes. Biochim Biophys Acta 1577:355-376
24. Polz MF, Cavanaugh CM (1998) Bias in template-to-product ratios in multitemplate PCR. Appl Environ Microbiol 64:3724-3730
25. Prieme A, Braker G, Tiedje JM (2002) Diversity of nitrite reductase (nirK and nirS) gene fragments in forested upland and wetland soils. Appl Environ Microbiol 68:1893-1900
26. Rösch C, Mergel A, Bothe H (2002) Biodiversity of denitrifying and dinitrogen-fixing bacteria in an acid forest soil. Appl Environ Microbiol 68:3818-3829
27. Santoro AE, Boehm AB, Francis CA (2006) Denitrifier community composition along a nitrate and salinity gradient in a coastal aquifer. Appl Environ Microbiol 72:2102-2109
28. Shaked Y, Erel Y, Sukenik A (2004) The biogeochemical cycle of iron and associated elements in Lake Kinneret. Geochim Cosmochim Acta 68:1439-1451
29. Taroncher-Oldenburg G, Griner EM, Francis CA, Ward BB (2003) Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment. Appl Environ Microbiol 69:1159-1171
30. Throbäck IN, Enwall K, Jarvis A, Hallin S (2004) Reassessing PCR primers targeting nirS, nirK and nosZ genes for community surveys of denitrifying bacteria with DGGE. FEMS Microbiol Ecol 49:401-417
31. Wolsing M, Prieme A (2004) Observation of high seasonal variation in community structure of denitrifying bacteria in arable soil receiving artificial fertilizer and cattle manure by determining T-RFLP of nir gene fragments. FEMS Microbiol Ecol 48:261-271
32. Yan T, Fields MW, Wu L, Zu Y, Tiedje JM, Zhou J (2003) Molecular diversity and characterization of nitrite reductase gene fragments (nirK and nirS) from nitrate- and uranium-contaminated groundwater. Environ Microbiol 5:13-24
33. Zumft WG (1997) Cell biology and molecular basis of denitrification. Microbiol Mol Biol Rev 61:533-616