Denitrier abundance and activity across the San Francisco Bay estuary

Environmental Microbiology Reports

Volumn 2, Issue 5, 2010, Pages 667-676

  Mosier, Annika C ^a   Francis, Christopher A ^a  

^a STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 78649708202     PISSN: None     EISSN: 17582229     Source Type: Journal    
DOI: 10.1111/j.1758-2229.2010.00156.x     Document Type: Article

References (53)

1. Abell, G.C., Revill, A.T., Smith, C., Bissett, A.P., Volkman, J.K., and Robert, S.S. (2010) Archaeal ammonia oxidizers and nirS-type denitrifiers dominate sediment nitrifying and denitrifying populations in a subtropical macrotidal estuary. ISME J 4: 286-300.
2. ter Braak, C.J.F., and Smilauer, P. (2002) CANOCO Reference Manual and CanoDraw for Windows User's Guide: Software for Canonical Community Ordination (Version 4.5). Ithaca, NY, USA: Microcomputer Power.
3. Braker, G., Fesefeldt, A., and Witzel, K.P. (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.
4. Braker, G., Zhou, J.Z., Wu, L.Y., Devol, A.H., and Tiedje, J.M. (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.
5. Braker, G., Ayala-del-Rio, H.L., Devol, A.H., Fesefeldt, A., and Tiedje, J.M. (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.
6. Bricker, S.B., Clement, C.G., Pirhalla, D.E., Orlando, S.P., and Farrow, D.R.G. (1999) National Estuarine Eutrophication Assessment: Effects of Nutrient Enrichment in the Nation's Estuaries. Silver Spring, MD, USA: NOAA, National Ocean Service, Special Projects Office and the National Centers for Coastal Ocean Science.
7. Bulow, S.E., Francis, C.A., Jackson, G.A., and Ward, B.B. (2008) Sediment denitrifier community composition and nirS gene expression investigated with functional gene microarrays. Environ Microbiol 10: 3057-3069.
8. Christensen, P.B., Nielsen, L.P., Sorensen, J., and Revsbech, N.P. (1990) Denitrification in nitrate-rich streams: diurnal and seasonal variation related to benthic oxygen metabolism. Limnol Oceanogr 35: 640-652.
9. Cornwell, J.C., Kemp, W.M., and Kana, T.M. (1999) Denitrification in coastal ecosystems: methods, environmental controls, and ecosystem level controls, a review. Aquatic Ecol 33: 41-54.
10. Diaz, R.J., and Rosenberg, R. (2008) Spreading dead zones and consequences for marine ecosystems. Science 321: 926-929.
11. Dong, L.F., Thornton, D.C.O., Nedwell, D.B., and Underwood, G.J.C. (2000) Denitrification in sediments of the River Colne estuary, England. Mar Ecol Prog Ser 203: 109-122.
12. Francis, C.A., Beman, J.M., and Kuypers, M.M.M. (2007) New processes and players in the nitrogen cycle: the microbial ecology of anaerobic and archaeal ammonia oxidation. ISME J 1: 19-27.
13. Hager, S., and Schemel, L. (1996) Dissolved inorganic nitrogen, phosphorus and silicon in South San Francisco Bay; I. Major factors affecting distributions. In San Francisco Bay: The Ecosystem; Further Investigations into the Natural History of San Francisco Bay and Delta with Reference to the Influence of Man. Hollibaugh, J.T. (ed.). San Francisco, CA, USA: American Association for the Advancement of Science, p. 542.
14. Hallin, S., Throback, I.N., Dicksved, J., and 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.
15. Hamersley, M.R., Lavik, G., Woebken, D., Rattray, J.E., Lam, P., Hopmans, E.C., et al. (2007) Anaerobic ammonium oxidation in the Peruvian oxygen minimum zone. Limnol Oceanogr 52: 923-933.
16. Hannig, M., Braker, G., Dippner, J., and Jurgens, K. (2006) Linking denitrifier community structure and prevalent biogeochemical parameters in the pelagial of the central Baltic Proper (Baltic Sea). FEMS Microbiol Ecol 57: 260-271.
17. Henry, S., Baudoin, E., Lopez-Gutierrez, J.C., Martin-Laurent, F., Baumann, A., and Philippot, L. (2004) Quantification of denitrifying bacteria in soils by nirK gene targeted real-time PCR. J Microbiol Methods 59: 327-335.
18. Jayakumar, D.A., Francis, C.A., Naqvi, S.W.A., and Ward, B.B. (2004) Diversity of nitrite reductase genes (nirS) in the denitrifying water column of the coastal Arabian Sea. Aquat Microb Ecol 34: 69-78.
19. Jensen, M.M., Kuypers, M.M.M., Lavik, G., and Thamdrup, B. (2008) Rates and regulation of anaerobic ammonium oxidation and denitrification in the Black Sea. Limnol Oceanogr 53: 23-36.
20. Junier, P., Kim, O.S., Witzel, K.P., Imhoff, J.F., and Hadas, O. (2008) Habitat partitioning of denitrifying bacterial communities carrying nirS or nirK genes in the stratified water column of Lake Kinneret, Israel. Aquat Microb Ecol 51: 129-140.
21. Kemp, W.M., Sampou, P., Caffrey, J., Mayer, M., Henriksen, K., and Boynton, W.R. (1990) Ammonium recycling versus denitrification in Chesapeake Bay sediments. Limnol Oceanogr 35: 1545-1563.
22. Kimmerer, W.J. (2004) Open water processes of the San Francisco Estuary: from physical forcing to biological responses. San Francisco Estuary Watershed Sci 2: 1-147.
23. Koop-Jakobsen, K., and Giblin, A. (2009) Anammox in tidal marsh sediments: the role of salinity, nitrogen loading, and marsh vegetation. Estuaries Coasts 32: 238-245.
24. Kuypers, M.M., Lavik, G., Woebken, D., Schmid, M., Fuchs, B.M., Amann, R., et al. (2005) Massive nitrogen loss from the Benguela upwelling system through anaerobic ammonium oxidation. Proc Natl Acad Sci USA 102: 6478-6483.
25. Lam, P., Lavik, G., Jensen, M.M., van de Vossenberg, J., Schmid, M., Woebken, D., et al. (2009) Revising the nitrogen cycle in the Peruvian oxygen minimum zone. Proc Natl Acad Sci USA 106: 4752-4757.
26. Liu, X.D., Tiquia, S.M., Holguin, G., Wu, L.Y., Nold, S.C., Devol, A.H., et al. (2003) Molecular diversity of denitrifying genes in continental margin sediments within the oxygendeficient zone off the Pacific coast of Mexico. Appl Environ Microbiol 69: 3549-3560.
27. McCune, B., and Grace, J.B. (2002) Analysis of Ecological Communities. Gleneden Beach, OR, USA: MjM Software Design.
28. Mosier, A.C., and Francis, C.A. (2008) Relative abundance and diversity of ammonia-oxidizing archaea and bacteria in the San Francisco Bay estuary. Environ Microbiol 10: 3002-3016.
29. Nielsen, K., Nielsen, L.P., and Rasmussen, P. (1995) Estuarine nitrogen retention independently estimated by the denitrification rate and mass-balance method: a study of Norsminde Fjord, Denmark. Mar Ecol Prog Ser 119: 275-283.
30. Nogales, B., Timmis, K.N., Nedwell, D.B., and Osborn, A.M. (2002) Detection and diversity of expressed denitrification genes in estuarine sediments after reverse transcription-PCR amplification from mRNA. Appl Environ Microbiol 68: 5017-5025.
31. Oakley, B.B., Francis, C.A., Roberts, K.J., Fuchsman, C.A., Srinivasan, S., and Staley, J.T. (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.
32. Prieme, A., Braker, G., and Tiedje, J.M. (2002) Diversity of nitrite reductase (nirK and nirS) gene fragments in forested upland and wetland soils. Appl Environ Microbiol 68: 1893-1900.
33. Rabalais, N.N. (2002) Nitrogen in aquatic ecosystems. Ambio 31: 102-112.
34. Rich, J.J., Dale, O.R., Song, B., and Ward, B.B. (2008) Anaerobic ammonium oxidation (anammox) in Chesapeake Bay sediments. Microb Ecol 55: 311-320.
35. Risgaard-Petersen, N., Meyer, R.L., Schmid, M., Jetten, M.S.M., Enrich-Prast, A., Rysgaard, S., and Revsbech, N.P. (2004) Anaerobic ammonium oxidation in an estuarine sediment. Aquat Microb Ecol 36: 293-304.
36. + adsorption capacity, nitrification, and denitrification in Danish estuarine sediments. Estuaries 22: 21-30.
37. Saleh-Lakha, S., Shannon, K.E., Henderson, S.L., Goyer, C., Trevors, J.T., Zebarth, B.J., and Burton, D.L. (2009) Effect of pH and temperature on denitrification gene expression and activity in Pseudomonas mandelii. Appl Environ Microbiol 75: 3903-3911.
38. Santoro, A.E., Boehm, A.B., and Francis, C.A. (2006) Denitrifier community composition along a nitrate and salinity gradient in a coastal aquifer. Appl Environ Microbiol 72: 2102-2109.
39. Schloss, P.D., and Handelsman, J. (2006) Introducing SONS, a tool for operational taxonomic unit-based comparisons of microbial community memberships and structures. Appl Environ Microbiol 72: 6773-6779.
40. Seitzinger, S.P. (1988) Denitrification in freshwater and coastal marine ecosystems: ecological and geochemical significance. Limnol Oceanogr 33: 702-724.
41. Seitzinger, S., Harrison, J.A., Bohlke, J.K., Bouwman, A.F., Lowrance, R., Peterson, B., et al. (2006) Denitrification across landscapes and waterscapes: a synthesis. Ecol Appl 16: 2064-2090.
42. Shapleigh, J.P. (2006) The denitrifying prokaryotes. In The Prokaryotes. Dworkin, M., Falkow, S., Rosenberg, E., Schleifer, K.-H., and Stackebrandt, E. (eds). New York, NY, USA: Springer, pp. 769-792.
43. Sharma, S., Aneja, M.K., Mayer, J., Munch, J.C., and Schloter, M. (2005) Diversity of transcripts of nitrite reductase genes (nirK and nirS) in rhizospheres of grain legumes. Appl Environ Microbiol 71: 2001-2007.
44. Smith, C.J., Nedwell, D.B., Dong, L.F., and Osborn, A.M. (2007) Diversity and abundance of nitrate reductase genes (narG and napA), nitrite reductase genes (nirS and nrfA), and their transcripts in estuarine sediments. Appl Environ Microbiol 73: 3612-3622.
45. Smith, M.S., and Tiedje, J.M. (1979) Phases of denitrification following oxygen depletion in soil. Soil Biol Biochem 11: 261-267.
46. Sorensen, J. (1978) Denitrification rates in a marine sediment as measured by the acetylene inhibition technique. Appl Environ Microbiol 36: 139-143.
47. Tamegai, H., Aoki, R., Arakawa, S., and Kato, C. (2007) Molecular analysis of the nitrogen cycle in deep-sea microorganisms from the Nankai Trough: genes for nitrification and denitrification from deep-sea environmental DNA. Extremophiles 11: 269-275.
48. +) reduces denitrification and induces enrichment of novel nirK genotypes in soil. FEMS Microbiol Lett 270: 189-194.
49. Tiquia, S.M., Masson, S.A., and Devol, A. (2006) Vertical distribution of nitrite reductase genes (nirS) in continental margin sediments of the Gulf of Mexico. FEMS Microbiol Ecol 58: 464-475.
50. Trimmer, M., Nicholls, J.C., and Deflandre, B. (2003) Anaerobic ammonium oxidation measured in sediments along the Thames estuary, United Kingdom. Appl Environ Microbiol 69: 6447-6454.
51. Wankel, S.D., Kendall, C., Francis, C.A., and Paytan, A. (2006) Nitrogen sources and cycling in the San Francisco Bay Estuary: a nitrate dual isotopic composition approach. Limnol Oceanogr 51: 1654-1664.
52. Yan, T.F., Fields, M.W., Wu, L.Y., Zu, Y.G., Tiedje, J.M., and Zhou, J.Z. (2003) Molecular diversity and characterization of nitrite reductase gene fragments (nirK and nirS) from nitrate- and uranium-contaminated groundwater. Environ Microbiol 5: 13-24.
53. Zumft, W.G. (1997) Cell biology and molecular basis of denitrification. Microbiol Mol Biol Rev 61: 533-542.