Loss of diversity of ammonia-oxidizing bacteria correlates with increasing salinity in an estuary system

Environmental Microbiology

Volumn 7, Issue 9, 2005, Pages 1289-1297

  Bernhard, Anne E ^a,c   Donn, Thomas ^a   Giblin, Anne E ^b   Stahl, David A ^a  

^a University of Washington   (United States)

^b ECOSYSTEMS CENTER   (United States)

^c The Holleran Center for Community Action and Public Policy   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMMONIA; AMMONIA MONOOXYGENASE; BACTERIAL DNA; FRESH WATER; INORGANIC SALT; OXIDOREDUCTASE;

ARTICLE; BACTERIAL GENE; CHEMISTRY; CLASSIFICATION; ENZYMOLOGY; GENETICS; MICROBIOLOGY; NITROSOMONADACEAE; OXIDATION REDUCTION REACTION; PHYLOGENY; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SEASON; SEDIMENT; UNITED STATES;

AMMONIA; DNA, BACTERIAL; FRESH WATER; GENES, BACTERIAL; GEOLOGIC SEDIMENTS; MASSACHUSETTS; NITROSOMONADACEAE; OXIDATION-REDUCTION; OXIDOREDUCTASES; PHYLOGENY; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; SALTS; SEASONS;

NITROSOMONADALES; NITROSOMONAS; NITROSOMONAS SP. NM143; NITROSOMONAS UREAE; NITROSOSPIRA; OLIGOTROPHA; PRUNUS DOMESTICA;

EID: 23944433934     PISSN: 14622912     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2005.00808.x     Document Type: Article

References (40)

1. Bernhard, A.E., and Peele, E.R. (1997) Nitrogen limitation of phytoplankton in a shallow embayment in northern Puget Sound. Estuaries 20: 759-769.
2. de Bie, M.J.M., Speksnijder, A., Kowalchuk, G.A., Schuurman, T., Zwart, G., Stephen, J.R., et al. (2001) Shifts in the dominant populations of ammonia-oxidizing beta-sub-class proteobacteria along the eutrophic Scheide Estuary. Aquat Microb Ecol 23: 225-236.
3. Boatman, C.D., and Murray, J.W. (1982) Modeling exchangeable NH4+ adsorption in marine-sediments - process and controls of adsorption. Limnol Oceanogr 27: 99-110.
4. Bollmann, A., and Laanbroek, H.J. (2002) Influence of oxygen partial pressure and salinity on the community composition of ammonia-oxidizing bacteria in the Scheide Estuary. Aquat Microb Ecol 28: 239-247.
5. Boynton, W.R., and Kemp, W.M. (1985) Nutrient regeneration and oxygen-consumption by sediments along an estuarine salinity gradient. Mar Ecol Prog Ser 23: 45-55.
6. Caffrey, J.M., Harrington, N., Solem, I., and Ward, B.B. (2003) Biogeochemical processes in a small California estuary. 2. Nitrification activity, community structure and role in nitrogen budgets. Mar Ecol Prog Ser 248: 27-40.
7. Cebron, A., Berthe, T., and Garnier, J. (2003) Nitrification and nitrifying bacteria in the lower Seine River and Estuary (France). Appl Environ Microbiol 69: 7091-7100.
8. Francis, C.A., O'Mullan, G.D., and Ward, B.B. (2003) Diversity of ammonia monooxygenase (amoA) genes across environmental gradients in Chesapeake Bay sediments. Geobiology 1: 129-140.
9. Hastings, R.C., Saunders, J.R., Hall, G.H., Pickup, R.W., and McCarthy, A.J. (1998) Application of molecular biological techniques to a seasonal study of ammonia oxidation in a eutrophic freshwater lake. Appl Environ Microbiol 64: 3674-3682.
10. Head, I.M., Hiorns, W.D., Embley, T.M., McCarthy, A.J., and Saunders, J.R. (1993) The phylogeny of autotrophic ammonia-oxidizing bacteria as determined by analysis of 16s ribosomal-RNA gene-sequences. J Gen Microbiol 139: 1147-1153.
11. Hiorns, W.D., Hastings, R.C., Head, I.M., McCarthy, A.J., Saunders, J.R., Pickup, R.W., and Hall, G.H. (1995) Amplification of 16S ribosomal RNA genes of autotrophic ammonia-oxidizing bacteria demonstrates the ubiquity of nitrosospiras in the environment. Microbiology 141: 2793-2800.
12. Hopkinson, C.S.J., Giblin, A.E., Tucker, J., and Garritt, R.H. (1999) Benthic metabolism and nutrient cycling along an estuarine salinity gradient. Estuaries 22: 863-881.
13. Horz, H.P., Rotthauwe, J.H., Lukow, T., and Liesack, W. (2000) Identification of major subgroups of ammonia-oxidizing bacteria in environmental samples by T-RFLP analysis of amoA PCR products. J Microbiol Methods 39: 197-204.
14. Howarth, R.W. (1988) Nutrient limitation of net primary production in marine ecosystems. Annu Rev Ecol 19: 89-110.
15. Hughes, J.B., Hellmann, J.J., Ricketts, T.H., and Bohannan, B.J. (2001) Counting the uncountable: statistical approaches to estimating microbial diversity. Appl Environ Microbiol 67: 4399-4406.
16. Huston, M. (1979) A general hypothesis of species diversity. Am Nat 75: 406-418.
17. Koops, H.P., and Pommerening-Roser, A. (2001) Distribution and ecophysiology of the nitrifying bacteria emphasizing cultured species. FEMS Microbiol Ecol 37: 1-9.
18. Kopczynski, E.D., Bateson, M.M., and Ward, D.M. (1994) Recognition of chimeric small-subunit ribosomal DNAs composed of genes from uncultivated microorganisms. Appl Environ Microbiol 60: 746-748.
19. Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, Yadhukumar, H., Buchner, A., et al. (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32: 1363-1371.
20. McCune, B., and Mefford, M.J. (1999) PC-ORD, Multivariate Analysis of Ecological Data. Gleneden Beach, OR, USA: MjM Software.
21. Mackey, R.L., and Currie, D.J. (2000) A re-examination of the expected effects of disturbance on diversity. Oikos 88: 483-493.
22. Nicolaisen, M.H., and Ramsing, N.B. (2002) Denaturing gradient gel electrophoresis (DGGE) approached to study the diversity of ammonia-oxidizing bacteria. J Microbiol Methods 50: 189-203.
23. Nixon, S.W. (1995) Coastal marine eutrophication: a definition, social causes, and future concerns. Ophelia 41: 199-219.
24. Nold, S.C., Zhou, J.Z., Devol, A.H., and Tiedje, J.M. (2000) Pacific northwest marine sediments contain ammonia-oxidizing bacteria in the beta subdivision of the proteobacteria. Appl Environ Microbiol 66: 4532-4535.
25. Phillips, C.J., Smith, Z., Embley, T.M., and Prosser, J.I. (1999) Phylogenetic differences between particle-associated and planktonic ammonia-oxidizing bacteria of the beta subdivision of the class proteobacteria in the northwestern Mediterranean Sea. Appl Environ Microbiol 65: 779-786.
26. Prosser, J.I. (1989) Autotrophic nitrification bacteria. Adv Microb Physiol 30: 125-181.
27. Purkhold, U., Pommerening-Roser, A., Juretschko, S., Schmid, M.C., Koops, H.P., and Wagner, M. (2000) Phylogeny of all recognized species of ammonia oxidizers based on comparative 16S rRNA and amoA sequence analysis: implications for molecular diversity surveys. Appl Environ Microbiol 66: 5368-5382.
28. Purkhold, U., Wagner, M., Timmermann, G., Pommerening-Roser, A., and Koops, H.-P. (2003) 16S rRNA and amoA-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 Microbiol 53: 1485-1494.
29. Rotthauwe, J.H., Witzel, K.P., and 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.
30. + adsorption capacity, nitrification, and denitrification in Danish estuarine sediments. Estuaries 22: 21-30.
31. Seitzinger, S.P. (1988) Denitrification in fresh-water and coastal marine ecosystems - ecological and geochemical significance. Limnol Oceanogr 33: 702-724.
32. Solorzano, L. (1969) Determination of ammonia in natural waters by the phenolhypochlorite method. Limnol Oceanogr 14: 799-801.
33. Speksnijder, A., Kowalchuk, G.A., Roest, K., and Laanbroek, H.J. (1998) Recovery of a Nitrosomonas-like 16S rDNA sequence group from freshwater habitats. Syst Appl Microbiol 21: 321-330.
34. Stehr, G., Bottcher, B., Dittberner, P., Rath, G., and Koops, H.P. (1995) The ammonia-oxidizing nitrifying population of the River Elbe estuary. FEMS Microbiol Ecol 17: 177-186.
35. Stephen, J.R., McCaig, A.E., Smith, Z., Prosser, J.I., and Embley, T.M. (1996) Molecular diversity of soil and marine 16S rRNA gene sequences related to beta-subgroup ammonia-oxidizing bacteria. Appl Environ Microbiol 62: 4147-4154.
36. Swofford, D.L. (1991) PAUP: Phylogenetic Analysis Using Parsimony. Fitchberg, MA, USA: Sinauer Associates.
37. Tobias, C.R., Cieri, M., Peterson, B.J., Deegan, L.A., Vallino, J., and Hughes, J. (2003) Processing watershed-derived nitrogen in a well-flushed New England estuary. Limnol Oceanogr 48: 1766-1778.
38. Vallino, J.J., and Hopkinson, C.S. (1998) Estimation of dispersion and characteristic mixing times in Plum Island Sound estuary. Estuar Coastal Shelf Sci 46: 333-350.
39. Vorosmarty, C.J., and Loder, T.C. (1994) Spring-neap tidal contrasts and nutrient dynamics in a marsh-dominated estuary. Estuaries 17: 537-551.
40. Ysebaert, T., Herman, P.M.J., Meire, P., Craeymeersch, J., Verbeek, H., and Heip, C.H.R. (2003) Large-scale patterns in estuaries: estuarine macrobenthic communities in the Scheide Estuary, NW Europe. Estuar Coastal Shelf Sci 57: 335-355.