Links among nitrification, nitrifier communities, and edaphic properties in contrasting soils receiving dairy slurry

Journal of Environmental Quality

Volumn 41, Issue 1, 2012, Pages 262-272

  Fortuna, Ann Marie ^a   Honeycutt, C Wayne ^b,d   Vandemark, George ^b   Griffin, Timothy S ^c   Larkin, Robert P ^b   He, Zhongqi ^b   Wienhold, Brian J ^b   Sistani, Karamat R ^b   Albrecht, Stephan L ^b   Woodbury, Bryan L ^b   Torbert, Henry A ^b   Powell, J Mark ^b   Hubbard, Robert K ^b   Eigenberg, Roger A ^b   Wright, Robert J ^b   Alldredge, J Richard ^a   Harsh, James B ^a  

^a WASHINGTON STATE UNIVERSITY   (United States)

^b AGRICULTURAL RESEARCH SERVICE   (United States)

^c TUFTS UNIVERSITY   (United States)

^d USDA NRCS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ABIOTIC FACTORS; AMMONIA OXIDIZING BACTERIA; ARCHAEA; BOS TAURUS; CATION EXCHANGE CAPACITIES; CLAY MINERALOGY; COPY NUMBER; DAIRY SLURRY; ENVIRONMENTAL CONDITIONS; GENE COPY NUMBER; N AVAILABILITY; NITRIFICATION RATES; NITROGEN MINERALIZATION; SOIL PROPERTY;

AMMONIUM COMPOUNDS; CLAY MINERALS; CRYSTALLOGRAPHY; DENITRIFICATION; GENES; MANURES; MINERALOGY; MINERALS; OXIDATION; POPULATION STATISTICS; SOILS;

NITRIFICATION;

AMMONIA; MINERAL; NITROGEN;

AGRICULTURAL SLURRY; ARCHAEBACTERIUM; ARTICLE; CATION EXCHANGE; CLAY; NITRIFICATION; NONHUMAN; SOIL; SOIL ANALYSIS; SOIL TREATMENT; VEGETATION; ANIMAL; BACTERIUM; CATTLE; CHEMISTRY; DAIRYING; ECOSYSTEM; ENVIRONMENTAL MONITORING; MANURE; METABOLISM; METHODOLOGY; OXIDATION REDUCTION REACTION; SEWAGE; SOIL POLLUTANT;

BOS TAURUS; NITROSOMONADALES;

AMMONIA; ANIMALS; ARCHAEA; BACTERIA; CATTLE; DAIRYING; ECOSYSTEM; ENVIRONMENTAL MONITORING; MANURE; NITRIFICATION; NITROGEN; OXIDATION-REDUCTION; SOIL; SOIL POLLUTANTS; WASTE DISPOSAL, FLUID;

EID: 84857092586     PISSN: 00472425     EISSN: 15372537     Source Type: Journal    
DOI: 10.2134/jeq2011.0202     Document Type: Article

References (54)

1. Aakra, Å., M. Hesselsøe, and L.R. Bakken. 2000. Surface attachment of ammonia-oxidising bacteria in soil. Microb. Ecol. 39:222-235.
2. Accoe, F., P. Boeckx, J. Busschaert, G. Hofman, and O. Van Cleemput. 2004. Gross N transformation rates and the net N mineralization rates related to the C and N contents of soil organic matter fractions in grassland soils of different age. Soil Biol. Biochem. 36:2075-2087. doi:10.1016/j. soilbio.2004.06.006
3. Bajwa, M.I. 1982. Soil clay mineralogies in relation to fertility management: Effect of clay mineral types on ammonium fixation under conditions of wetland rice culture. Agron. J. 74:143-144. doi:10.2134/agronj1982.0 0021962007400010037x
4. Belser, L.W. 1984. Bicarbonate uptake by nitrifiers: Effects of growth rate, pH, substrate concentration, and metabolic inhibitors. Appl. Environ. Microbiol. 48:1100-1104.
5. Blake, G.R., and K.H. Hartge. 1986. Bulk density. p. 363-375. In A. Klute (ed.) Methods of soil analysis. Part 1. 2nd ed. SSSA and ASA, Madison, WI.
6. Bosatta, E., and G.L. Agren. 1998. Theoretical analyses of soil texture effects on organic matter dynamics. Soil Biol. Biochem. 29:1633-1638. doi:10.1016/S0038-0717(97)00086-2
7. Boyle-Yarwood, S.A., P.J. Bottomley, and D.D. Myrold. 2008. Community composition of ammonia-oxidizing bacteria and archaea in soils under stands of red alder and Douglas fir in Oregon. Environ. Microbiol. 10:2956-2965. doi:10.1111/j.1462-2920.2008.01600.x
8. Burt, R. 2004. Soil Survey laboratory methods manual. Soil Survey Investigations Rep. 42. U.S. Gov. Print. Office, Washington, DC.
9. Curtin, D., and C.A. Campbell. 2008. Mineralizable nitrogen. p. 599-606. In M.R. Carter and E.G. Gregorich (ed.) Soil sampling and methods of analysis. 2nd ed. Canadian Society of Soil Science, Pinawa, Manitoba.
10. Di, H.J., K.C. Cameron, J.-P. Shen, C.S. Winefield, M. O'Callaghan, S. Bowatte, and J.-Z. He. 2010. Ammonia-oxidizing bacteria and archaea grown under contrasting soil nitrogen conditions. FEMS Microbiol. Ecol. 72:386-394. doi:10.1111/j.1574-6941.2010.00861.x
11. Di, H.J., K.C. Cameron, J.P. Shen, C.S. Winefield, M. O'Callaghan, S. Bowatte, and J.Z. He. 2009. Nitrification driven by bacteria and not archaea in nitrogen rich grassland soils. Nat. Geosci. 2:621-624. doi:10.1038/ngeo613
12. Drury, C.F., and E.G. Beauchamp. 1991. Ammonium fixation, release, nitrification, and immobilization in high-and low-fixing soils. Soil Sci. Soc. Am. J. 55:125-129. doi:10.2136/sssaj1991.03615995005500010022x
13. Gavlak, R.G., D.A. Horneck, and R.O. Miller. 1994. Plant, soil, and water reference methods for the western region. Western Regional Extension Publ. 125. Univ. of Alaska, Fairbanks.
14. Griffin, T.S., Z. He, and C.W. Honeycutt. 2005. Manure composition affects net transformation of nitrogen from dairy manures. Plant Soil 273:29- 38. doi:10.1007/s11104-004-6473-5
15. Hart, S.C., J.M. Stark, E.A. Davidson, and M.K. Firestone. 1994. Nitrogen mineralization, immobilization, and nitrification. p. 1011-1018. In R.W. Weaver, J.S. Angle, P.S. Bottomley, D. Bezdicek, S. Smith, M.A. Tabatabai, and A. Wollum (ed.) Methods of soil analysis. Part 2. Microbiological and biochemical properties. SSSA Book Ser. 5. SSSA and ASA, Madison, WI.
16. Herrmann, M., A.M. Saunders, and A. Schramm. 2008. Archaea dominate the ammonia-oxidizing community in the rhizosphere of the freshwater macrophyte Littorella uniflora. Appl. Environ. Microbiol. 74:3279- 3283. doi:10.1128/AEM.02802-07
17. Hermansson, A., and P.-E. Lindgren. 2002. Quantification of ammonia-oxidizing bacteria in arable soil by real-time PCR. Appl. Environ. Microbiol. 67:972-976. doi:10.1128/AEM.67.2.972-976.2001
18. Honeycutt, C.W., T.S. Griffin, B.J. Wienhold, B. Eghball, S.L. Albrecht, J.M. Powell, B.L. Woodbury, K.R. Sistani, R.K. Hubbard, and H.A. Torbert. 2005. Protocols for nationally coordinated laboratory and field research on manure nitrogen mineralization. Commun. Soil Sci. Plant Anal. 36:2807-2822. doi:10.1080/00103620500304184
19. Jia, Z., and R. Conrad. 2009. Bacteria rather than Archaea dominate microbial ammonia oxidation in an agricultural soil. Environ. Microbiol. 11:1658-1671. doi:10.1111/j.1462-2920.2009.01891.x
20. Koops, H. P., and A. Pommerening-Röser. 2001. Distribution and ecophysiology of the nitrifying bacteria emphasizing cultured species. FEMS Microbiol. Ecol. 37:1-9.
21. Laanbroek, H.J., and S. Gerards. 1991. Effects of organic manure on nitrification in arable soils. Biol. Fertil. Soils 12:147-153. doi:10.1007/BF00341492
22. Larkin, R.P., C.W. Honeycutt, and T.S. Griffin. 2006. Effect of swine and dairy manure amendments on microbial communities in three soils as influenced by environmental conditions. Biol. Fertil. Soils 43:51-61. doi:10.1007/s00374-005-0060-7
23. Lehtovirta, L.E., J.I. Prosser, and G.W. Nicol. 2009. Soil pH regulates the abundance and diversity of Group 1.1c Crenarchaeota. FEMS Microbiol. Ecol. 70:367-376. doi:10.1111/j.1574-6941.2009.00748.x
24. Leininger, S., T. Urich, M. Schloter, L. Schwark, J. Qi, G.W. Nicol, J.I. Prosser, S.C. Schuster, and C. Schleper. 2006. Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nat. Lett. 442:806-809. doi:10.1038/nature04983
25. Mamo, M., R.W. Taylor, and J.W. Shuford. 1993. Ammonia fixation by soil and pure minerals. Commun. Soil Sci. Plant Anal. 24:1115-1126. doi:10.1080/00103629309368864
26. Martens-Habbena, W., P.M. Berube, H. Urakawa, J.R. de la Torre, and D.A. Stahl. 2009. Ammonia oxidation kinetics determine niche separation of nitrifying archaea and bacteria. Nature 461:976-979. doi:10.1038/nature08465
27. McLean, E.O. 1982. Soil pH and lime requirement. p. 199-223. In A.L. Page, R.H. Miller, and D.R. Keeney (ed.) Methods of soil analysis. Part 2. Chemical and microbiological properties. 2nd ed. SSSA Book Ser. 5. SSSA and ASA, Madison, WI.
28. Mendum, T.A., R.E. Sockett, and P.R. Hirsch. 1999. Use of molecular and isotopic techniques to monitor the response of autotrophic ammonia-oxidizing populations of the β subdivision of the class Proteobacteria in arable soils to nitrogen fertilizer. Appl. Environ. Microbiol. 65:4155-4162.
29. Meunier, A., and B. Velde. 2004. Illite: Origins, evolution and metamorphism. Springer, Berlin.
30. Moore, D.M., and R.C. Reynolds. 1997. Sample preparation techniques for clay minerals. p. 204-226. In D.M. Moore and R.C. Reynolds (ed.) X-ray diffraction and the identification and analysis of clay minerals. 2nd ed. Oxford Univ. Press, New York.
31. Mulvaney, R.L. 1996. Nitrogen: Inorganic forms. p. 1123-1184. In D.L. Sparks et al. (ed.) Methods of Soil Analysis. Part 3. SSSA Book Ser. 5. SSSA and ASA, Madison, WI.
32. Nicol, G.W., G. Webster, L.A. Glover, and J.I. Prosser. 2004. Differential response of archaeal and bacterial communities to nitrogen inputs and pH changes in upland pasture rhizosphere soil. Environ. Microbiol. 6:861- 867. doi:10.1111/j.1462-2920.2004.00627.x
33. Norton, J.M., J.J. Alzerreca, Y. Suwa and M.G. Klotz. 2002. Diversity of ammonia monooxygenase operon in autotrophic ammonia-oxidizing bacteria. Arch. Microbiol. 177:139-149. doi:10.1007/s00203-001-0369-z
34. Okano, Y., K.R. Hristova, C.M. Leutenegger, L.E. Jackson, R.F. Denison, B. Gebreyesus, D. Lebauer, and K.M. Scow. 2004. Application of real-time PCR to study effects of ammonium on population size of ammonia-oxidizing bacteria in soil. Appl. Environ. Microbiol. 70:1008-1016. doi:10.1128/AEM.70.2.1008-1016.2004
35. Petersen, S.O., K. Henriksen, and T.H. Blackburn. 1991. Coupled nitrification-denitrification associated with liquid manure in a gel-stabilized model system. Biol. Fertil. Soils 12:19-27. doi:10.1007/BF00369383
36. Powell, S.J., and J.I. Prosser. 1991. Protection of Nitrosomonas europaea colonizing clay minerals from inhibition by nitrapyrin. J. Gen. Microbiol. 137:1923-1929.
37. Ross, D.S. 1995. Recommended methods for determining soil cation exchange capacity. p. 62-64. In Recommended soil testing procedures for the northeastern United States. 2nd ed. Northeastern Regional Publ. 493. Agriculture Experiment Station, Univ. of Delaware, Newark.
38. Russell, C.A., G.P. Robertson, E.A. Paul, and K.R. Kosola. 2004. Nitrogen cycling in popular stands defoliated by insects. Biogeochemistry 68:365- 381. doi:10.1023/B:BIOG.0000031038.70805.28
39. SAS Institute. 1997. SAS/STAT software changes and enhancements through release 6.12. SAS Inst., Cary, NC.
40. Sawhney, B.L. 1972. Selective sorption and fixation of cations by clay minerals: A review. Clays Clay Miner. 20:93-100. doi:10.1346/ CCMN.1972.0200208
41. Schauss, K., A. Focks, S. Leininger, A. Kotzerke, H. Heuer, S. Thiele-Bruhn, S. Sharma, B.-M. Wilke, M. Matthies, K. Smalla, J.C. Munch, W. Amelung, M. Kaupenjohann, M. Schloter, and C. Schleper. 2009. Dynamics and functional relevance of ammonia-oxidizing archaea in two agricultural soils. Environ. Microbiol. 11:446-456. doi:10.1111/j.1462-2920.2008.01783.x
42. Sistani, K.R., A. Adeli, S.L. McGowen, H. Tewolde, and G.E. Brink. 2008. Laboratory and field evaluation of broiler litter nitrogen mineralization. Bioresour. Technol. 99:2603-2611. doi:10.1016/j.biortech.2007.04.069
43. Smith, R.V., R.M. Doyle, L.C. Burns, and R.J. Stevens. 1997. A model for nitrite accumulation in soils. Soil Biol. Biochem. 29:1241-1247. doi:10.1016/S0038-0717(97)00028-X
44. Stanford, G., and S.J. Smith. 1972. Nitrogen mineralization potentials of soils. Soil Sci. Soc. Am. Proc. 36:465-472. doi:10.2136/sssaj1972.03615995003600030029x
45. Taylor, A.E., L.H. Zeglin, S. Dooley, D.D. Myrold, and P.J. Bottomley. 2010. Evidence for different contributions of archaea and bacteria to the ammonia-oxidizing potential of diverse Oregon soils. Appl. Environ. Microbiol. 76:7691-7698. doi:10.1128/AEM.01324-10
46. Thompson, R.B., B.F. Pain, and Y.J. Rees. 1990. Ammonia volatilization from cattle slurry following surface application to grassland: II. Influence of application rate, wind speed and applying slurry in narrow bands. Plant Soil 125:119-128.
47. USDA-ERS. 2001. Confined animal and manure nutrient data system. Available at http://www.ers.usda.gov/data/MANURE (verified 27 Sept. 2011).
48. USDA-NASS. 2004. 2002 census of agriculture. Available at http://www.nass.usda.gov/Census_of_Agriculture/index.asp (verified 27 Sept. 2011).
49. Whittig, L.D., and W.R. Allardice. 1986. X-ray diffraction techniques. p. 331-362. In A. Klute (ed.) Methods of soil analysis. Part 1. 2nd ed. SSSA Book Ser. 5. SSSA and ASA, Madison, WI.
50. Webster, G., T.M. Embley, T.E. Frietag, Z. Smith, and J.I. Prosser. 2005. Links among ammonia oxidizer species composition, functional diversity and nitrification kinetics in grassland soils. Environ. Microbiol. 7:676-684. doi:10.1111/j.1462-2920.2005.00740.x
51. Wolf, N. 2003. Determination of manure pH. p. 48-49. In John Peters (ed.) Recommended methods of manure analysis. Univ. of Wisconsin System, Madison.
52. Wuchter, C., B. Abbas, M.J. Coolen, L. Herfort, J. van Bleijswijk, P. Timmers, M. Strous, E. Teira, G.J. Herndl, J.J. Middelburg, S. Schouten, and J.S. Sinninghe Damsté. 2006. Archaeal nitrification in the ocean. Proc. Natl. Acad. Sci. USA 103:12317-12322. doi:10.1073/pnas.0600756103
53. You, J., A. Das, E.M. Dolan, and Z. Hu. 2009. Ammonia-oxidizing archaea involved in nitrogen removal. Water Res. 43:1801-1809. doi:10.1016/j.watres.2009.01.016
54. Zhang L.M., P.R. Offre, J.Z. He, D.T. Verhamme, G.W. Nicol, and J.I. Prosser. 2010. Autotrophic ammonia oxidation by soil thaumarchaea. Proc. Natl. Acad. Sci. USA 107:17240-17245.