Land-use and management practices affect soil ammonia oxidiser community structure, activity and connectedness

Soil Biology and Biochemistry

Volumn 78, Issue , 2014, Pages 138-148

  Bissett, Andrew ^a   Abell, Guy C J ^a   Brown, Mark ^b   Thrall, Peter H ^a   Bodrossy, Lev ^a   Smith, Matthew C ^c   Baker, Geoff H ^a   Richardsson, Alan E ^a  

^a CSIRO   (Australia)

^b UNIVERSITY OF NEW SOUTH WALES   (Australia)

^c UNIVERSITY OF WISCONSIN MILWAUKEE   (United States)

Author keywords

Ammonia oxidiser; Denitrification; Land use; Microarray; Nitrification

Indexed keywords

AMMONIA; DENITRIFICATION; ECOSYSTEMS; FORESTRY; MICROARRAYS; NITRIFICATION; SOCIAL SCIENCES; AGRICULTURE; BIOGEOCHEMISTRY; ECOLOGY; SOILS;

BIOGEOCHEMICAL CYCLE; BIOTIC INTERACTIONS; COMMUNITY STRUCTURES; ECOSYSTEM FUNCTIONS; FUNCTIONAL CAPACITY; MANAGEMENT PRACTICES; MICROBIAL COMMUNITIES; SYSTEM CONNECTIVITY; LAND USE AND MANAGEMENTS; MICROBIAL ECO SYSTEM;

LAND USE;

AMMONIA; COMMUNITY DYNAMICS; CONNECTIVITY; DENITRIFICATION; ECOSYSTEM SERVICE; LAND USE; MANAGEMENT PRACTICE; MICROBIAL ACTIVITY; MICROBIAL COMMUNITY; NITRIFICATION; NITROGEN CYCLE; OXIDATION; SOIL ECOSYSTEM; BIOGEOCHEMICAL CYCLE; COMMUNITY STRUCTURE; LAND MANAGEMENT; LAND USE CHANGE; SOIL CHEMISTRY; SOIL MICROORGANISM;

EID: 84907311951     PISSN: 00380717     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.soilbio.2014.07.020     Document Type: Article

References (51)

1. Abell G.C.J., Banks J., Ross D.J., Keane J.P., Robert S.S., Revill A.T., Volkman J.K. Effects of estuarine sediment hypoxia on nitrogen fluxes and ammonia oxidizer gene transcription. FEMS Microbiology Ecology 2011, 75:111-122.
2. Abell G.C.J., Robert S.S., Frampton D.M.F., Volkman J.K., Rizwi F., Csontos J.z., Bodrossy L. High-throughput analysis of ammonia oxidiser community composition via a novel, amoA-based functional gene array. PLoS ONE 2012, 7:e51542.
3. Bader G., Hogue C. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 2003, 4:2.
4. Bates S.T., Berg-Lyons D., Caporaso J.G., Walters W.A., Knight R., Fierer N. Examining the global distribution of dominant archaeal populations in soil. ISME Journal 2010, 5:908-917.
5. Benjamini Y., Yekutieli D. The control of the false discovery rate in multiple testing under dependency. The Annals of Statistics 2001, 29:1165-1188.
6. Bissett A., Brown M.V., Siciliano S.D., Thrall P.H. Microbial community responses to anthropogenically induced environmental change: towards a systems approach. Ecology Letters 2013, 16:128-139.
7. Bissett A., Richardson A.E., Baker G., Thrall P.H. Long-term land use effects on soil microbial community structure and function. Applied Soil Ecology 2011, 51:66-78.
8. 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.
9. Brussaard L., de Ruiter P.C., Brown G.G. Soil biodiversity for agricultural sustainability. Agriculture, Ecosystems & Environment 2007, 121:233-244.
10. 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.
11. Clarke K.R., Warwick R.M. Change in Marine Communties: an Approach to Statistical Analysis and Interpretation 2001, PRIMER-E, Plymouth, 178 pp. second ed.
12. 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.
13. Di H.J., Cameron K.C., Shen J.P., Winefield C.S., O'Callaghan M., Bowatte S., He J.Z. Nitrification driven by bacteria and not archaea in nitrogen-rich grassland soils. Nature Geoscience 2009, 2:621-624.
14. Di H.J., Cameron K.C., Shen J.P., Winefield C.S., O'Callaghan M., Bowatte S., He J.Z. Ammonia-oxidizing bacteria and archaea grow under contrasting soil nitrogen conditions. FEMS Microbiology Ecology 2010, 72:386-394.
15. Drury C.F., Myrold D.D., Beauchamp E.G., Reynolds W.D. Denitrification techniques for soils. Soil Sampling and Methods of Analysis 2008, 471-494. CRC Press, Boca Raton, Fl, U.S.A. second ed. M.R. Carter, E.G. Gregorich (Eds.).
16. Enwall K., Nyberg K., Bertilsson S., Cederlund H., Stenström J., Hallin S. Long-term impact of fertilization on activity and composition of bacterial communities and metabolic guilds in agricultural soil. Soil Biology and Biochemistry 2007, 39:106-115.
17. Francis C.A., Roberts K.J., Beman J.M., Santoro A.E., Oakley B.B. Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. Proceedings of the National Academy of Sciences of the United States of America 2005, 102:14683-14688.
18. Graham E.B., Wieder W.R., Leff J.W., Weintraub S.R., Townsend A.R., Cleveland C.C., Philippot L., Nemergut D.R. Do we need to understand microbial communities to predict ecosystem function? A comparison of statistical models of nitrogen cycling processes. Soil Biology and Biochemistry 2014, 68:279-282.
19. Hart S.C., Stark J.M., Davidson E.A., Firestone M.K. Nitrogen mineralization, immobilization, and nitrification. Part 2. Microbiological and Biochemical Properties 1994, 1011-1016. SSSA, Madison, WI. R.W. Weaver, J.S. Angle, B.S. Bottomley (Eds.).
20. Hayden H.L., Drake J., Imhof M., Oxley A.P.A., Norng S., Mele P.M. The abundance of nitrogen cycle genes amoA and nifH depends on land-uses and soil types in South-Eastern Australia. Soil Biology and Biochemistry 2010, 42:1774-1783.
21. 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.
22. Himes F.L. Nitrogen, sulfur, and phosphorus and the sequestering of carbon. Soil Processes and the Carbon Cycle 1998, 315-320. CRC Press, Boca Raton, FL. R. Lal, J.M. Kimble, R.F. Follett, B.A. Stewart (Eds.).
23. Horz H.-P., Barbrook A., Field C.B., Bohannan B.J.M. Ammonia-oxidizing bacteria respond to multifactorial global change. Proceedings of the National Academy of Sciences of the United States of America 2004, 101:15136-15141.
24. Johansson J.F., Paul L.R., Finlay R.D. Microbial interactions in the mycorrhizosphere and their significance for sustainable agriculture. FEMS Microbiology Ecology 2004, 48:1-13.
25. Kelly J.J., Policht K., Grancharova T., Hundal L.S. Distinct responses in ammonia-oxidizing archaea and bacteria after addition of biosolids to an agricultural soil. Applied and Environmental Microbiology 2011, 77:6551-6558.
26. Kirkby C.A., Kirkegaard J.A., Richardson A.E., Wade L.J., Blanchard C., Batten G. Stable soil organic matter: a comparison of C:N:P:S ratios in Australian and other world soils. Geoderma 2011, 163:197-208.
27. Kirkegaard J.A., Angus J.F., Gardner P.A., Mueller W. Reduced growth and yield of wheat with conservation cropping. I. Field studies in the first year of the cropping Phase. Australian Journal of Agricultural Research 1994, 45:511-528.
28. Lauber C.L., Strickland M.S., Bradford M.A., Fierer N. The influence of soil properties on the structure of bacterial and fungal communities across land-use types. Soil Biology and Biochemistry 2008, 40:2407-2415.
29. Martens-Habbena W., Berube P.M., Urakawa H., de la Torre J.R., Stahl D.A. Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria. Nature 2009, 461:976-979.
30. Navarrete A.c.A., Taketani R.G.a., Mendes L.W., Cannavan F.d.S., Moreira F.M.d.S., Tsai S.M. Land-use systems affect Archaeal community structure and functional diversity in western Amazon soils. Revista Brasileira de Ciência do Solo 2011, 35:1527-1540.
31. 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, 9999.
32. Nicol G.W., Prosser J.I., Martin G.K., Lisa Y.S. Chapter One - Strategies to Determine Diversity, Growth, and Activity of Ammonia-oxidizing Archaea in Soil, Methods in Enzymology 2011, 3-34. Academic Press.
33. Norton J.M., Stark J.M., Martin G.K. Chapter Fifteen - Regulation and Measurement of Nitrification in Terrestrial Systems, Methods in Enzymology 2011, 343-368. Academic Press.
34. Olsen S.R., Sommers L.E. Phosphorous. Methods of Soil Analysis 1982, 403-430. Soil Science Society of America, Madison, Wisconin, U.S.A. A.L. Page (Ed.).
35. Osborne C.A., Zwart A.B., Broadhurst L.M., Young A.G., Richardson A.E. The influence of sampling strategies and spatial variation on the detected soil bacterial communities under three different land-use types. FEMS Microbiology Ecology 2011, 78:70-79.
36. Osler G.H.R., Sommerkorn M. Toward a complete soil C and N cycle: incorporating the soil fauna. Ecology 2007, 88:1611-1621.
37. Prosser J.I., Nicol G.W. Archaeal and bacterial ammonia-oxidisers in soil: the quest for niche specialisation and differentiation. Trends in Microbiology 2012, 20:523-531.
38. Raes J., Bork P. Molecular eco-systems biology: towards an understanding of community function. Nature Reviews Microbiology 2008, 6:693-699.
39. Raison R.J., Connell M.J., Khanna P.K. Methodology for studying fluxes of soil mineral-N in situ. Soil Biology and Biochemistry 1987, 19:521-530.
40. Rayment G.E., Higginson F.R. Australian Laboratory Handbook of Soil and Water Chemical Methods 1992, Inkata Press, Melbourne, 330 pp.
41. Reshef D.N., Reshef Y.A., Finucane H.K., Grossman S.R., McVean G., Turnbaugh P.J., Lander E.S., Mitzenmacher M., Sabeti P.C. Detecting novel associations in large data sets. Science 2011, 334:1518-1524.
42. Reynolds H.L., Packer A., Bever J.D., Clay K. Grassroots ecology: plant-microbe-soil interactions as drivers of plant community structure and dynamics. Ecology 2003, 84:2281-2291.
43. Rice C.W., Smith M.S. Denitrification in no-till and plowed soils 1. Soil Science Society of America Journal 1982, 46:1168-1173.
44. 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.
45. Rowell D.L. Soil Science: Methods and Applications 1994, Longman Group Ltd, UK, London.
46. Santoro A.E., Casciotti K.L., Francis C.A. Activity, abundance and diversity of nitrifying archaea and bacteria in the central California Current. Environmental Microbiology 2010, 12:1989-2006.
47. Shannon P., Markiel A., Ozier O., Baliga N.S., Wang J.T., Ramage D., Amin N., Schwikowski B., Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research 2003, 13:2498-2504.
48. Sher Y., Zaady E., Nejidat A. Spatial and temporal diversity and abundance of ammonia oxidizers in semi-arid and arid soils: indications for a differential seasonal effect on archaeal and bacterial ammonia oxidizers. FEMS Microbiology Ecology 2013, 86:544-556.
49. Tiedje J.M. Denitrification. Methods of Soil Analysis, Part 2 1982, 10110-11026. ASA-SSSA, Madison, WI. A.L. Page (Ed.).
50. Wilhelm R., Abeliovich A., Nejidat A. Effect of long-term ammonia starvation on the oxidation of ammonia and hydroxylamine by Nitrosomonas europaea. Journal of Biochemistry 1998, 124:811-815.
51. Yeager C.M., Northup D.E., Grow C.C., Barns S.M., Kuske C.R. Changes in nitrogen-fixing and ammonia-oxidizing bacterial communities in soil of a mixed conifer forest after wildfire. Applied and Environmental Microbiology 2005, 71:2713-2722.