The abundance of nitrogen cycle genes amoA and nifH depends on land-uses and soil types in South-Eastern Australia

Soil Biology and Biochemistry

Volumn 42, Issue 10, 2010, Pages 1774-1783

  Hayden, Helen L ^a   Drake, Judy ^a   Imhof, Mark ^b   Oxley, Andrew P A ^a   Norng, Sorn ^b   Mele, Pauline M ^a  

^a LA TROBE UNIVERSITY   (Australia)

^b DEPARTMENT OF PRIMARY INDUSTRIES   (Australia)

Author keywords

amoA; AOB; Bacteria; Management systems; nifH; Nitrogen cycle; Quantitative PCR; Remnant vegetation

Indexed keywords

AMOA; AOB; MANAGEMENT SYSTEMS; NIFH; NITROGEN CYCLE; QUANTITATIVE PCR; REMNANT VEGETATION;

BACTERIA; BACTERIOLOGY; BIOMASS; ELECTRIC CONDUCTIVITY; GENES; LAND USE; MANAGEMENT; MONITORING; NITROGEN; POLYMERASE CHAIN REACTION; POTASSIUM; VEGETATION;

SOILS;

ABUNDANCE; AGRICULTURAL LAND; BACTERIUM; BIOMASS; BIOMONITORING; CONSERVATION GENETICS; ECOSYSTEM FUNCTION; ELECTRICAL CONDUCTIVITY; GENE EXPRESSION; GEOMORPHOLOGY; LAND USE; NITROGEN CYCLE; PARAMETERIZATION; PH; POLYMERASE CHAIN REACTION; POPULATION DISTRIBUTION; POTASSIUM; PRIMARY PRODUCTION; QUANTITATIVE ANALYSIS; REGRESSION ANALYSIS; SOIL CARBON; SOIL MICROORGANISM; SOIL TYPE; VEGETATION TYPE;

AUSTRALIA; VICTORIA [AUSTRALIA];

BACTERIA (MICROORGANISMS);

EID: 77955921144     PISSN: 00380717     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.soilbio.2010.06.015     Document Type: Article

References (39)

1. Amato M., Ladd J.N. Assay for microbial biomass based on ninhydrin-reactive nitrogen in extracts of fumigated soils. Soil Biology and Biochemistry 1988, 20:107-114.
2. Amato M., Ladd J.N. Application of the ninhydrin-reactive N assay for microbial biomass in acid soils. Soil Biology and Biochemistry 1994, 26:1109-1115.
3. Bossio D.A., Scow K.M., Gunapala N., Graham K.J. Determinants of soil microbial communities: effects of agricultural management, season, and soil type on phospholipid fatty acid profiles. Microbial Ecology 1998, 36:1-12.
4. Breiman L., Friedman J., Olshen R.A., Stone C.J. Classification and Regression Trees 1984, Wadsworth International Group, Belmont.
5. Bruns M.A., Stephen J.R., Kowalchuk G.A., Prosser J.I., Paul E.A. Comparative diversity of ammonia oxidizer 16S rRNA gene sequences in native, tilled, and successional soils. Applied and Environmental Microbiology 1999, 65:2994-3000.
6. Bürgmann H., Widmer F., Sigler W.V., Zeyer J. mRNA extraction and reverse transcription-PCR protocol for detection of nifH gene expression by Azotobacter vinelandii in soil. Applied and Environmental Microbiology 2003, 69:1928-1935.
7. Cavagnaro T.R., Jackson L.E., Hristova K., Scow K.M. Short-term population dynamics of ammonia oxidizing bacteria in an agricultural soil. Applied Soil Ecology 2008, 40:13-18.
8. Colloff M.J., Wakelin S.A., Gomez D., Rogers S.L. Detection of nitrogen cycle genes in soils for measuring the effects of changes in land use and management. Soil Biology and Biochemistry 2008, 40:1637-1645.
9. De Boer W., Kowalchuk G.A. Nitrification in acid soils: micro-organisms and mechanisms. Soil Biology and Biochemistry 2001, 33:853-866.
10. He J.-Z., Shen J.-P., Zhang L.-M., Zhu Y.-G., Zheng Y.-M., Xu M.-G., Di H. Quantitative analyses of the abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea of a Chinese upland red soil under long-term fertilization practices. Environmental Microbiology 2007, 9:2364-2374.
11. Hermansson A., Lindgren P.-E. Quantification of ammonia-oxidizing bacteria in arable soil by real-time PCR. Applied and Environmental Microbiology 2001, 67:972-976.
12. Ihaka R., Gentleman R. R: A Language for data analysis and Graphics. Journal of Computational and Graphical Statistics 1996, 5:299-314.
13. Isbell R.F. The Australian Soil Classification 2002, CSIRO Publishing, Melbourne.
14. IUSS Working Group WRB World Reference Base for Soil Resources 2006, First Update 2007 2007, FAO, Rome, World Soil Resources Reports No. 103.
15. Jackson L.E., Calderon F.J., Steenwerth K.L., Scow K.M., Rolston D.E. Responses of soil microbial processes and community structure to tillage events and implications for soil quality. Geoderma 2003, 114:305-317.
16. Jangid K., Williams M.A., Franzluebbers A.J., Sanderlin J.S., Reeves J.H., Jenkins M.B., Endale D.M., Coleman D.C., Whitman W.B. Relative impacts of land-use, management intensity and fertilization upon soil microbial community structure in agricultural systems. Soil Biology and Biochemistry 2008, 40:2843-2853.
17. Kibblewhite M.G., Ritz K., Swift M.J. Soil health in agricultural systems. Philosophical Transactions of the Royal Society B: Biological Sciences 2008, 363:685-701.
18. Koops H.P., Möller U.C. The lithotrophic ammonia-oxidizing bacteria. The Prokaryotes 1992, 2625-2637. Springer-Verlag, New York. A. Balows, H.G. Trüper, M. Dworkin, W. Harder, K.H. Schleifer (Eds.).
19. Kowalchuk G.A., Stephen J.R. Ammonia-oxidising bacteria: a model for molecular microbial ecology. Annual Review of Microbiology 2001, 55:485-529.
20. Leininger S., Urich T., Schloter M., Schwark L., Qi J., Nicol G.W., Prosser J.I., Schuster S.C., Schleper C. Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 2006, 442:806-809.
21. Mele P.M., Crowley D.E. Application of self-organizing maps for assessing soil biological quality. Agriculture, Ecosystems & Environment 2008, 126:139-152.
22. Nicol G.W., Leininger S., Schleper C., Prosser J.I. The influence of soil pH on the diversity, abundance and transcriptional activity of ammonia oxidizing archaea and bacteria. Environmental Microbiology 2008, 10:2966-2978.
23. Okano Y., Hristova K.R., Leutenegger C.M., Jackson L.E., Denison R.F., Gebreyesus B., Lebauer D., Scow K.M. Application of real-time PCR to study effects of ammonium on population size of ammonia-oxidizing bacteria in soil. Applied and Environmental Microbiology 2004, 70:1008-1016.
24. Prosser J.L., Embley T.M. Cultivation-based and molecular approaches to characterisation of terrestrial and aquatic nitrifiers. Antoine Van Leeuwenhoek 2002, 81:165-179.
25. Prosser J.I., Nicol G.W. Relative contributions of archaea and bacteria to aerobic ammonia oxidation in the environment. Environmental Microbiology 2008, 10:2931-2941.
26. Ridley A.M., Mele P.M., Beverly C.R. Legume-based farming in Southern Australia: developing sustainable systems to meet environmental challenges. Soil Biology and Biochemistry 2004, 36:1213-1221.
27. Robertson G.P. Nitrification in forested ecosystems. Philosophical Transactions of the Royal Society of London 1982, 296B:445-457.
28. Rome S., Brunel B., Normand P., Fernandez M., Cleyet-Marel J. Evidence that two genomic species of Rhizobium are associated with Medicago truncatula. Archives of Microbiology 1996, 165:285-288.
29. Rösch C., Mergel A., Bothe H. Biodiversity of Denitrifying and dinitrogen-fixing bacteria in an acid forest soil. Applied and Environmental Microbiology 2002, 68:3818-3829.
30. Rotthauwe J.H., Witzel K.P., Liesack W. The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations. Applied and Environmental Microbiology 1997, 63:4704-4712.
31. Saleh-Lakha S., Miller M., Campbell R.G., Schneider K., Elahimanesh P., Hart M.M., Trevors J.T. Microbial gene expression in soil: methods, applications and challenges. Journal of Microbiological Methods 2005, 63:1-19.
32. Silgram M., Shepherd M.A. The effects of cultivation on soil nitrogen mineralization. Advances in Agronomy 1999, 65:267-311.
33. Smith C.J., Nedwell D.B., Dong L.F., Osborn A.M. Evaluation of quantitative polymerase chain reaction-based approaches for determining gene copy and gene transcript numbers in environmental samples. Environmental Microbiology 2006, 8:804-815.
34. Wakelin S.A., Colloff M.J., Harvey P.R., Marschner P., Gregg A.L., Rogers S.L. The effects of stubble retention and nitrogen application on soil microbial community structure and functional gene abundance under irrigated maize. FEMS Microbiology Ecology 2007, 59:661-670.
35. Wakelin S.A., Gregg A.L., Simpson R.J., Li G.D., Riley I.T., Mckay A.C. Pasture management clearly affects soil microbial community structure and N-cycling bacteria. Pedobiologia 2009, 52:237-251.
36. Wallenstein M.D., Vilgalys R.J. Quantitative analyses of nitrogen cycling genes in soils. Pedobiologia 2005, 49:665-672.
37. Yeates C., Gillings M. Rapid purification of DNA from soil for molecular biodiversity analysis. Letters in Applied Microbiology 1998, 27:49-53.
38. Zehr J.P., Jenkins B.D., Short S.M., Steward G.F. Nitrogenase gene diversity and microbial community structure: a cross-system comparison. Environmental Microbiology 2003, 5:539-554.
39. Zhang Y., Li D., Wang H., Xiao Q., Liu X. Molecular diversity of nitrogen-fixing bacteria from the Tibetan Plateau, China. FEMS Microbiology Letters 2006, 260:134-142.