Distribution of denitrifying bacterial communities in the stratified water column and sediment-water interface in two freshwater lakes and the Baltic Sea

Aquatic Ecology

Volumn 45, Issue 1, 2011, Pages 99-112

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

^a Seoul National University   (South Korea)

^b MAX PLANCK INSTITUTE FOR EVOLUTIONARY BIOLOGY   (Germany)

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

^d UNIVERSITY OF NEUCHÂTEL   (Switzerland)

^e EPFL   (Switzerland)

Author keywords

Baltic Sea; Denitrifying bacteria; nirK, nirS; Plu see, Sch hsee; Sediment water interface; Water column

Indexed keywords

BACTERIUM; BIOMARKER; DENITRIFICATION; GENETIC ANALYSIS; MARINE ENVIRONMENT; MICROBIAL COMMUNITY; PHYLOGENETICS; POLYMERASE CHAIN REACTION; SEDIMENT-WATER INTERFACE; WATER COLUMN;

ATLANTIC OCEAN; BALTIC SEA; GERMANY; PLUSSEE; SCHLESWIG-HOLSTEIN; SCHOHSEE;

BACTERIA (MICROORGANISMS);

EID: 79651470126     PISSN: 13862588     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10452-010-9335-7     Document Type: Article

References (38)

1. Aberle N, Wiltshire KH (2006) Seasonality and diversity patterns of microphytobenthos in a mesotrophic lake. Arch Hydrobiol 167: 447-465.
2. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang ZWM, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
3. 2O release and on the community structure of ammonia oxidizers and denitrifiers. Appl Environ Microbiol 68: 5685-5692.
4. 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 community. Appl Environ Microbiol 66: 2096-2104.
5. Brettar I, Moore ERB, Höfle MG (2001) Phylogeny and abundance of novel denitrifying bacteria isolated from the water column of the central Baltic Sea. Microb Ecol 42: 295-305.
6. Castro-González M, Braker G, Farías 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.
7. Coyne MS, Arunakumari A, Averill BA, Tiedje JM (1989) Immunological identification and distribution of dissimilatory heme cd1 and non-heme copper nitrite reductases in denitrifying bacteria. Appl Environ Microbiol 55: 2924-2931.
8. 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.
9. Falk S, Hannig M, Gliesche C, Wardenga R, Koster M, Jürgens K, Braker G (2007) nirS-containing denitrifiers communities in the water column and sediment of the Baltic Sea. Biogeosciences 4: 255-268.
10. Hallin S, Lindgren PE (1999) PCR detection of genes encoding nitrite reductase in denitrifying bacteria. Appl Environ Microbiol 65.
11. Hannig M, Braker G, Dppner J, Jürgens K (2006) Linking denitrifier community structure and prevalent biogeochemical parameters in the pelagial of the central Baltic Sea Proper (Baltic Sea). FEMS Microbiol Ecol 57: 260-271.
12. 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.
13. Junier P, Junier T, Witzel KP (2008a) TRiFLe, a program for in silico terminal restriction fragment length polymorphism analysis with user-defined sequence sets. Appl Environ Microbiol 74: 6452-6456.
14. Junier P, Kim O-S, Witzel K-P, Imhoff JF, Hadas O (2008b) Habitat-partitioning of denitrifying bacterial communities carrying nirS/nirK genes in the stratified water column of Lake Kinneret, Israel. Aquatic Microb Ecol 51: 129-140.
15. Kim OS, Junier P, Imhoff JF, Witzel KP (2008) Comparative analysis of ammonia monooxygenase (amoA) genes in the water column and sediment-water interface of two lakes and the Baltic Sea. FEMS Microbiol Ecol 66: 367-378.
16. Knowles R (1982) Denitrification. Microbio Rev 46: 43-70.
17. Liu X, Tiquia SM, Holguin G, Wu L, Nold SC, Devol AH, Luo K, Palumbo AV, Tiedje JM, Zhou J (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.
18. Michotey V, Mejean V, Bonin P (2000) Comparison of methods for quantification of cytochrome cd1-denitrifying bacteria in environmental marine samples. Appl Environ Microbiol 66: 1564-1571.
19. 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.
20. 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.
21. Overbeck J, Chróst RJ (1994) Microbial ecology of Lake Plußsee. Ecol Studies 105: 1-44.
22. Philippot L (2002) Denitrifying genes in bacterial and archaeal genomes. Biochim Biophys Acta 1577: 355-376.
23. Priemé 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.
24. Rai H, Arts MT, Wainman BC, Dockal N, Krambeck HJ (1997) Lipid production in natural phytoplankton communities in a small freshwater Baltic lake, Lake Schöhsee, Germany. Freshw Biol 38: 581-590.
25. 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.
26. 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.
27. Satoh T, Hoshino Y, Kitamura H (1976) Rhodopseudomonas sphaeroides forma sp. denitrificans, a denitrifying strain as a subspecies of Rhodopseudomonas sphaeroides. Arch Microbiol 108: 265-269.
28. Schäfer H, McDonald IR, Nightingale PD, Murrell JC (2005) Evidence for the presence of a CmuA methyltransferase pathway in novel marine methyl halide-oxidizing bacteria. Environ Microbiol 7: 839-852.
29. Schloss PD, Handelsman J (2005) Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71: 1501-1506.
30. Sharma S, Aneja MK, Mayer J, Munch JC, Schloter M (2005) Diversity of transcripts of nitrite reductase genes (nirK and nirS) in rhizospheres of grain legumes. Appl Environ Microbiol 71: 2001-2007.
31. 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.
32. Throbäck IN, Enwall K, Jarvis Å, 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.
33. +) reduces denitrification and induces enrichment of novel nirK genotypes in soil. FEMS Microbiol Lett 270: 189-194.
34. Tuomainen JM, Hietanen S, Kuparinen J, Martikainen PJ, Servomaa K (2003) Baltic Sea cyanobacterial bloom contains denitrification and nitrification genes, but has negligible denitrification activity. FEMS Microbiol Ecol 45: 83-96.
35. Wolsing M, Priemé A (2004) Observation of high seasonal variation in community sturucture 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.
36. 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.
37. Yoshie S, Noda N, Tsuneda S, Hirata A, Inamori Y (2004) Salinity decreases nitrite reductase gene diversity in denitrifying bacteria of wastewater treatment systems. Appl Environ Microbiol 70: 3152-3157.
38. Zumft WG (1997) Cell biology and molecular basis of denitrification. Microbiol Mol Biol Rev 61: 533-616.