Development and application of a PCR-denaturing gradient gel electrophoresis tool to study the diversity of Nitrobacter-like nxrA sequences in soil

FEMS Microbiology Ecology

Volumn 63, Issue 2, 2008, Pages 261-271

  Wertz, Sophie ^a,c   Poly, Franck ^a,b   Le Roux, Xavier ^a   Degrange, Valérie ^a  

^a University of Lyon   (France)

^b UMR 5557 Laboratoire d'Ecologie Microbienne ^*  (France)

^c UNIVERSITY OF NEW BRUNSWICK   (Canada)

Author keywords

Microbial diversity; Nitrification; Nitrite oxidoreductase; Nitrite oxidizing bacteria

Indexed keywords

NITRATE REDUCTASE;

ELECTROKINESIS; GRASSLAND SOIL; NITRIFICATION; NITRIFYING BACTERIUM; PHYLOGENETICS; POLYMERASE CHAIN REACTION; SOIL MICROORGANISM; SPECIES DIVERSITY;

ARTICLE; BACTERIAL GENE; DENATURING GRADIENT GEL ELECTROPHORESIS; GENE CLUSTER; GENE SEQUENCE; GENETIC VARIABILITY; NITROBACTER; NONHUMAN; NRXA GENE; PHYLOGENY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SOIL ANALYSIS;

NITROBACTER; NITROCOCCUS; NITROCOCCUS MOBILIS; NITROSPIRA; NITROSPIRA MARINA;

EID: 38049096119     PISSN: 01686496     EISSN: 15746941     Source Type: Journal    
DOI: 10.1111/j.1574-6941.2007.00416.x     Document Type: Article

References (50)

1. Acinas SG, Sarma-Rupavtarm R, Klepac-Ceraj V Polz MF (2005) PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample. Appl Environ Microbiol 71: 8966 8969.
2. Avrahami S, Liesack W Conrad R (2003) Effects of temperature and fertilizer on activity and community structure of soil ammonia-oxidizers. Environ Microbiol 5: 691 705.
3. Bock E, Sundermeyer-Klinger H Stackebrandt E (1983) New facultative lithoautotrophic nitrite-oxidizing bacteria. Arch Microbiol 136: 281 284.
4. Bock E, Koops HP Harms H (1986) Cell biology of nitrifying bacteria. Nitrification (Prosser JI, ed), pp. 17 38. Irl Press, Oxford, Washington DC.
5. Bock E, Koops HP, Möller UC Rudert M (1990) A new facultatively nitrite oxidizing bacterium, Nitrobacter vulgaris sp. nov. Arch Microbiol 153: 105 110.
6. Bürgmann H, Meier S, Bunge M, Widmer F Zeyer J (2005) Effect of model root exudates on structure and activity of a soil diazotroph community. Environ Microbiol 7: 1711 1724.
7. Daims H, Nielsen PH, Nielsen JL, Juretschko S Wagner M (2000) Novel Nitrospira-like bacteria as dominant nitrite-oxidizers in biofilms from wastewater treatment plants: diversity and in situ physiology. Water Sci Tech 41: 85 90.
8. Degrange V Bardin R (1995) Detection and counting of Nitrobacter populations in soil by PCR. Appl Environ Microbiol 61: 2093 2098.
9. DeJournett TD, Arnold WA LaPara TM (2007) The characterization and quantification of methanotrophic bacterial populations in constructed wetland sediments using PCR targeting 16S rRNA fragments. Appl Soil Ecol 35: 648 659.
10. Ehrich S, Behrens D, Lebedeva E, Ludwig W Bock E (1995) A new obligately chemolithoautotrophic, nitrite-oxidizing bacterium, Nitrospira moscoviensis sp. nov. and its phylogenetic relationship. Arch Microbiol 164: 16 23.
11. Felsenstein J (1993) PHYLIP (Phylogeny Inference Package. (), version 3.66, Department of Genome Science, University of Washington, Seattle.
12. Freitag TE Prosser JI (2003) Community structure of ammonia-oxidizing bacteria within anoxic marine sediments. Appl Environ Microbiol 69: 1359 1371.
13. Freitag T, Chang L, Clegg CD Prosser JI (2005) Influence of inorganic nitrogen regime on the diversity of nitrite-oxidizing bacteria in agricultural grassland soils. Appl Environ Microbiol 71: 8323 8334.
14. Galtier N, Gouy M Gautier C (1996) SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. CABIOS 12: 543 548.
15. Grundmann GL Normand P (2000) Microscale diversity of the genus Nitrobacter in soil on the basis of analysis of genes encoding rRNA. Appl Environ Microbiol 66: 4543 4546.
16. Guindon S Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696 704.
17. Hallin S, Throback IN, Dicksved J Pell M (2006) Metabolic profiles and genetic diversity of denitrifying communities in activated sludge after addition of methanol or ethanol. Appl Environ Microbiol 72: 5445 5452.
18. Hommes NG, Sayavedra-Soto LA Arp DJ (1998) Mutagenesis and expression of amo, which codes for ammonia monooxygenase in Nitrosomonas europaea. J Bacteriol 180: 3353 3359.
19. Kirstein K Bock E (1993) Close genetic relationship between Nitrobacter hamburgensis nitrite oxidoreductase and Escherichia coli nitrate reductase. Arch Microbiol 160: 447 453.
20. Klots MG, Alzerreca J Norton J (1997) A gene encoding a membrane protein exists upstream of the amoA/amoB genes in ammonia-oxidizing bacteria: a third member of the amo operon. FEMS Microbiol Lett 150: 65 73.
21. Kowalchuk G Stephen JR (2001) Ammonia-oxidizing bacteria: a model for molecular microbial ecology. Annu Rev Microbiol 55: 485 529.
22. Kowalchuk GA, Stephen JR, De Boer W, Prosser JI, Embley TM Woldendorp JW (1997) 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 Microb 63: 1489 1497.
23. Kowalchuk GA, Bodelier PLE, Heilig GHJ, Stephen JR Laanbroek HJ (1998) Community analysis of ammonia-oxidizing bacteria, in relation to oxygen availability in soils and root-oxygenated sediments, using PCR, DGGE, and oligonucleotide probe hybridisation. FEMS Microbiol Ecol 27: 339 350.
24. Kruskal JB Wish M (1978) Multidimensional Scaling. Sage Publications, Beverley Hills, CA.
25. Le Roux X, Bardy M, Loiseau P Louault F (2003) Stimulation of soil nitrification and denitrification by grazing in grasslands: do changes in plant species composition matter? Oecologia 137: 417 425.
26. Mahmood S Prosser JI (2006) The influence of synthetic sheep urine on ammonia oxidizing bacterial communities in grassland soil. FEMS Microbiol Ecol 56: 444 454.
27. Maixner F, Noguera DR, Anneser B, Stoecker K, Wegl G, Wagner M Daims H (2006) Nitrite concentration influences the population structure of Nitrospira-like bacteria. Env Microbiol 8: 1487 1495.
28. Muyzer G, De Waal EC Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microb 59: 695 700.
29. Navarro E, Fernandez MP, Grimont F, Clays Josserand A Bardin R (1992) Genomic heterogeneity of the genus Nitrobacter. Int J Syst Bacteriol 42: 554 560.
30. Nicolaisen MH Ramsing NB (2002) Denaturing gradient gel electrophoresis (DGGE) approaches to study the diversity of ammonia-oxidizing bacteria. J Microbiol Methods 50: 189 203.
31. Norton JM, Low JM Klotz MG (1996) The gene encoding ammonia monooxygenase subunit A exists in three nearly identical copies in Nitrosospira sp. NpAV. FEMS Microbiol Lett 139: 181 188.
32. Oksanen L (2004) The devil lies in details: reply to Stuart Hurlbert. Oikos 104: 598 605.
33. Orso S, Gouy M, Navarro E Normand P (1994) Molecular phylogenetic analysis of Nitrobacter spp. Int J Syst Bacteriol 44: 83 86.
34. Pan PHC (1971) Lack of distinction between Nitrobacter agilis and Nitrobacter winogradskyi. J Bacteriol 108: 1416 1418.
35. Patra AK, Abbadie L, Clays-Josserand A et al 2005) Effects of grazing on microbial functional groups involved in soil N dynamics. Ecol Monogr 75: 65 80.
36. Patra AK, Abbadie L, Clays-Josserand A et al 2006) Effects of management regime and plant species on the enzyme activity and genetic structure of N-fixing, denitrifying and nitrifying bacterial communities in grassland soils. Environ Microbiol 8: 1005 1016.
37. Perriere G Gouy M (1996) WWW-query: an on-line retrieval system for biological sequence banks. Biochimie 78: 364 369.
38. Phillips CJ, Harris D, Dollhopf SL, Gross KL, Prosser JI Paul EA (2000) Effects of agronomic treatments on structure and function of ammonia-oxidizing communities. Appl Environ Microbiol 66: 5410 5478.
39. Poly F, Wertz S, Brothier E Degrange V (2008) First exploration of Nitrobacter diversity in soils using functional gene nxrA encoding nitrite oxido-reductase. FEMS Microbiol Ecol 63: 132 140.
40. Prosser JI (1989) Autotrophic nitrification in bacteria. Adv Microbiol Physiol 30: 125 181.
41. Raymond J, Siefert JL, Staples CR Blankenship RE (2004) The natural history of nitrogen fixation. Mol Biol Evol 21: 541 554.
42. Rotthauwe JH, Witzel KP Liesack W (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.
43. Schmidt EL, Molina JAE Chiang C (1973) Isolation of chemoautotrophic nitrifiers from Moroccan soils. Bull Ecol Res Comm 17: 166 167.
44. Siripong S Rittmann BE (2007) Diversity study of nitrifying bacteria in full-scale municipal wastewater treatment plants. Water Res 41: 1110 1120.
45. Sorokin DY, Muyzer G, Brinkhoff T, Kuenen JG Jetten MSM (1998) Isolation and characterization of a novel facultatively alkaliphilic Nitrobacter species, N. alkalicus sp. nov. Arch Microbiol 170: 345 352.
46. Starkenburg SR, Chain PSG, Sayavedra-Soto LA et al 2006) Genome sequence of the chemolithoautotrophic nitrite-oxidizing bacterium Nitrobacter winogradskyi Nb-255. Appl Environ Microbiol 72: 2050 2063.
47. Teske A, Alm E, Regan JM, Toze S, Rittmann BE Stahl DA (1994) Evolutionary relationships among ammonia- and nitrite-oxidizing bacteria. J Bacteriol 176: 6623 6630.
48. Vanparys B, Spieck E, Heylen K, Wittebolle L, Geets J, Boon N De Vos P (2007) The phylogeny of the genus Nitrobacter based on comparative rep-PCR, 16S rRNA and nitrite oxidoreductase gene sequence analysis. Syst Appl Microbiol 30: 297 308.
49. Watson SW Waterbury JB (1971) Characteristics of two marine nitrite oxidizing bacteria, Nitrospira gracilis nov. gen. and Nitrococcus mobilis nov. sp. nov. sp. Arch Microbiol 77: 203 230.
50. Webster G, Embley TM, Freitag TE, Smith Z Prosser JI (2005) Links between ammonia-oxidizer species composition, functional diversity and nitrification kinetics in grassland soils. Environ Microbiol 5: 676 684.