Soil bacteria and archaea found in long-term corn (zea mays L.) agroecosystems in Quebec, Canada

Canadian Journal of Soil Science

Volumn 93, Issue 1, 2013, Pages 45-57

  Sheibani, Sara ^a   Yanni, Sandra F ^a   Wilhelm, Roland ^a   Whalen, Joann K ^a   Whyte, Lyle G ^a   Greer, Charles W ^a,b   Madramootoo, Chandra A ^a  

^a MCGILL UNIVERSITY   (Canada)

^b NATIONAL RESEARCH COUNCIL CANADA   (Canada)

Author keywords

Archaeal phylogeny; Conservation tillage; Corn agroecosystem; Residue management; Soil microbial biomass

Indexed keywords

AGRICULTURAL ECOSYSTEM; ASSESSMENT METHOD; BACTERIUM; BIOMASS; CELL ORGANELLE; CONSERVATION TILLAGE; FLUORESCENCE; MAIZE; PHYLOGENY; POLYMERASE CHAIN REACTION; SOIL MICROORGANISM; SPECIES DIVERSITY;

CANADA; QUEBEC [CANADA];

ACTINOBACTERIA; ARCHAEA; BACTERIA (MICROORGANISMS); CRENARCHAEOTA; FIRMICUTES; FUNGI; PROTEOBACTERIA; ZEA MAYS;

EID: 84873270037     PISSN: 00084271     EISSN: 19181841     Source Type: Journal    
DOI: 10.4141/CJSS2012-040     Document Type: Article

References (65)

1. Altschul, S., Gish, W., Miller, W., Myers, E. W. and Lipman, D. J. 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403-410.
2. Amann, R. I., Ludwig, W. and Schleifer, K. H. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59: 143-169.
3. Barns, S. M., Takala, S. L. and Kuske, C. R. 1999. Wide distribution and diversity of members of the bacterial kingdom acidobacterium in the environments. Appl. Environ. Microbiol. 65: 1731-1737.
4. Bhupathiraju, V. K., Hernandez, M., Krauter, P. and Alvarez- Cohen, L. 1999. A new direct microscopy based method for evaluating in-situ bioremediation. J. Hazard. Mater. 67: 299-312.
5. Bintrim, S. B., Donohue, T. J., Handelsman, J., Roberts, G. P. and Goodman, R. M. 1997. Molecular phylogeny of archaea from soil. Proc. Natl. Acad. Sci. USA. 94: 277-282.
6. Borneman, J., Skroch, P., O'Sullivan, K., Palus, J., Rumjanek, N., Jansen, J., Nienhuis, J. and Triplett, E. 1996. Molecular microbial diversity of an agricultural soil in Wisconsin. Appl. Environ. Microbiol. 62: 1935-1943.
7. Bottos, E., Vincent, W., Greer, C. and Whyte, L. 2008. Prokaryotic diversity of arctic ice shelf microbial mats. Environ. Microbiol. 10: 950-966.
8. Brochier-Armanet, C., Boussau, B., Gribaldo, S. and Forterre, P. 2008. Mesophilic crenarchaeota: Proposal for a third archaeal phylum, the Thaumarchaeota. Nat. Rev. Microbiol. 6: 245-252.
9. Buckley, D. and Schmidt, T. 2001. The structure of microbial communities in soil and the lasting impact of cultivation. Microb. Ecol. 42: 11-21.
10. Burgess, M. S., Madramootoo, C. A. and Mehuys, G. R. 1996. Tillage and crop residue effects on corn production in Quebec. Agron. J. 88: 792-797.
11. Cabrera, M. and Beare, M. 1993. Alkaline persulfate oxidation for determining total nitrogen in microbial biomass extracts. Soil Sci. Soc. Am. J. 57: 1007.
12. Cleveland, C. C., Nemergut, D. R., Schmidt, S. K. and Townsend, A. R. 2007. Increases in soil respiration following labile carbon additions linked to rapid shifts in soil microbial community composition. Biogeochemistry 82: 229-240.
13. Dam, R. F., Mehdi, B. B., Burgess, M. S. E., Madramootoo, C. A., Mehuys, G. R. and Callum, I. R. 2005. Soil bulk density and crop yield under eleven consecutive years of corn with different tillage and residue practices in a sandy loam soil in Central Canada. Soil Tillage Res. 84: 41-53.
14. Dijk, J. A., Breugelmans, P., Philips, J., Haest, P. J., Smolders, E. and Springael, D. 2008. Catalyzed reporter depositionfluorescent in situ hybridization (CARD-FISH) detection of dehalococcoides. J. Microbiol. Methods 73: 142-147.
15. Doran, J. W. and Zeiss, M. R. 2000. Soil health and suatnability: managing the biotic component of soil quality. Appl. Soil Ecol. 15: 3-11.
16. Environment Canada. 2010. Canadian climate normals 1970- 2000: Montreal/Pierre Elliott Trudeau International Airport. Environment Canada, Ottawa, ON. [Onlione] Available: http://climate.weatheroffice.gc.ca/climate-normals/index-e.html [2010 Oct. 22].
17. Feng, Y., Motta, A. C., Reeves, D. W., Burmester, C. H., van Santen, E. and Osborne, J. A. 2003. Soil microbial communities under conventional-till and no-till continuous cotton systems. Soil Biol. Biochem. 35: 1693-1703.
18. Forney, L. J., Zhou, X. and Brown, C. J. 2004. Molecular microbial ecology: land of the one-eyed king. Curr. Opin. Microbiol. 7: 210-220.
19. Furlong, M., Singleton, D., Coleman, D. and Whitman, W. 2002. Molecular and culture-based analyses of prokaryotic communities from an agricultural soil and the burrows and casts of the earthworm Lumbricus rubellus. Appl. Environ. Microbiol. 68: 1265-1279.
20. Garbeva, P., Postma, J., Van Veen, J. and Van Elsas, J. 2006. Effect of above ground plant species on soil microbial community structure and its impact on suppression of Rhizoctonia solani AG3. Environ. Microbiol. 8: 233-246.
21. Govaerts, B., Mezzalama, M., Unno, Y., Sayre, K., Luna- Guido, M., Vanherck, K., Dendooven, L. and Deckers, J. 2007. Influence of tillage, residue management, and crop rotation on soil microbial biomass and catabolic diversity. Appl. Soil Ecol. 37: 18-30.
22. Granatstein, D. M., Bezdicek, D. F., Cochran, V. L., Elliott, L. F. and Hammel, J. 1987. Long-term tillage and rotation effects on soil microbial biomass, carbon and nitrogen. Biol. Fertil. Soils 5: 265-270.
23. Halpern, M. T., Whalen, J. K. and Madramootoo, C. A. 2010. Long-term tillage and residue management influences soil carbon and nitrogen dynamics. Soil Sci. Soc. Am. J. 74: 1211-1217.
24. Helgason, B. L., Walley, F. L. and Germida, J. J. 2010. Longterm no-till management affects microbial biomass but not community composition in Canadian prairie agroecosystems. Soil Biol. Biochem 42: 2192-2202.
25. Huber, H., Huber, R. and Stetter, K. 2006. Thermoproteales. Pages 10-12 in M. Dworkin, S. Falkow, E. Rosenberg, K.-H. Schleifer, and E. Stackebrandt, eds. The Prokaryotes. Springer, New York, NY.
26. Huber, H. and Stetter, K. 2006. Desulfurococcales. Pages 52-68 in M. Dworkin, S. Falkow, E. Rosenberg, K.-H. Schleifer, and E. Stackebrandt, eds. The prokaryotes. 3rd ed. Vol. 5. Springer, New York, NY.
27. Joergensen, R. G. 1996. Quantification of the microbial biomass by determining ninhydrin-reactive N. Soil Biol. Biochem. 28: 301-306.
28. Joergensen, R. G. and Mueller, T. 1996. The fumigationextraction method to estimate soil microbial biomass: calibration of the kEN value. Soil Biol. Biochem. 28: 33-37.
29. Jones, R. T., Robeson, M. S., Lauber, C. L., Hamady, M., Knight, R. and Fierer, N. 2009. A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses. ISME J. 3: 442-453.
30. Kersters K., De Vos P., Gillis M., Swings J., Vandamme P. and Stackebrandt E. 2006. Introduction to the proteobacteria. Pages 3-37 in M. Dwarkin, S. Falkow, E. Rosenberg, K.-H. Schleifer, E. and Stackebrandt, eds. The prokaryotes. 3rd ed. Vol. 5. Springer, New York, NY.
31. Leininger, S., Urich, T., Schloter, M., Schwark, L., Qi, J. and Nicol, G. W. et al. 2006. Archaea predominate among ammonia-oxidizing prokaryotes in soils. Nature 442: 806-809.
32. Liu, Z.-Zh., Lozupone, C., Hamady, M., Bushman, F. D. and Knight, R. 2007. Short pyrosequencing reads suffice for accurate microbial community analysis. Nucleic Acid Res. 35: 1-10.
33. Ludwig, W., Schleifer, K.-H. and Whitman, W. B. 2009. Revised road map to the phylum Firmicutes. Pages 1-13 in P. De Vos, G. Garrity, D. Jones, N. R. Krieg, W. Ludwig, F. A. Rainey, K.-H. Schleifer, and W. B. Whitman, eds. Bergey's manual of systematic bacteriology. 2nd ed. Vol. 3. The firmicutes. Springer, New York, NY.
34. Lupwayi, N. Z., Lafond, G. P., Ziadi, N. and Grant, C. A. 2012. Soil microbial response to nitrogen fertilizer and tillage in barley and corn. Soil Tillage Res. 118: 139-146.
35. Lupwayi, N. Z., Clayton, G. W., O'Donovan, J. T., Harker, K. N., Turkington, T. K. and Rice, W. A. 2004. Soil microbiological properties during decomposition of crop residues under convemtional and zero tillage. Can. J. Soil Sci. 84: 411-419.
36. Lupwayi, N. Z., Rice, W. A. and Clayton, G. W. 1998. Soil microbial diversity and community structure under wheat as influenced by tillage and crop rotation. Soil Biol. Biochem. 30: 1733-1741.
37. Martens-Habbena, W., Berube, P. M., Urakawa, H., de la Torre, J. R. and Stahl, D. A. 2009. Ammonia oxidation kinetics determine niche separation of nitrifying archaea and cacteria. Nature 461: 976-979.
38. Metting, F. B. 1993. Structure and physiological ecology of soil microbial communities. Pages 3-24 in F. B. Metting, ed. Soil microbial ecology - Application in agricultural and environmental management. Marcel Dekker, New York, NY.
39. Muhling, M., Woolven-Allen, J., Murrell, J. C. and Joint, I. 2008. Improved group-specific PCR primers for denaturing gradient gel electrophoresis analysis of the genetic diversity of complex microbial communities. ISME J. 2: 379-392.
40. Niederberger, T. D., Perreault, N., Tille, S., Sherwood, L. B., Lacrampe-Couloume, G., Andersen, D., Greer, C. W., Pollard, W. and Whyte, L. G. 2010. Microbial characterization of a subzero, hypersaline methane seep in the Canadian high arctic. ISME J. 4: 784-798.
41. Patricia, B. B. and Gordon, V. W. 2006. Protist genetic diversity in the acidic hydrothermal environments of Lassen Volcanic National Park, USA. J. Eukaryotic Microbiol. 53: 420-431.
42. Paustian, K., Collins, H. P. and Paul, E. A. 1997. Management controls on soil organic carbon. Pages 15-51 in E. A. Paul, K. Paustian, E. T. Elliott, and C. V. Cole, eds. Soil organic matter in temperate agroecosystems: Long-term experiments in North America. CRC Press, Boca Raton, FL.
43. Peixoto, R., Coutinho, H., Madari, B., Machado, P., Rumjanek, N., Van Elsas, J., Seldin, L. and Rosado, A. 2006. Soil aggregation and bacterial community structure as affected by tillage and cover cropping in the Brazilian Cerrados. Soil Tillage Res. 90: 16-28.
44. Perreault, N. N., Andersen, D. T., Pollard, W. H., Greer, C. W. and Whyte, L. G. 2007. Characterization of the prokaryotic diversity in cold saline perennial springs of the Canadian high arctic. Appl. Environ. Microbiol. 73: 1532-1543.
45. Quaiser, A., Ochsenreiter, T., Lanz, C., Schuster, S. C., Treusch, A. H. and Schleper, C. 2003. Acidobacteria form a coherent but highly diverse group within the bacterial domain: evidence from environmental genomics. Mol. Microbiol. 50: 563-575.
46. Roesch, L. F. W., Fulthorpe, R. R., Rive, A., Casella, G., Hadwin, A. K. M., Kent, A. D., Daroub, S. H., Camargo, F. A. O., Farmerie, W. G. and Triplett, E. W. 2007. Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J. 1: 283-290.
47. SAS Institute, Inc. 2009. The SAS system for windows, release 9.2. SAS Institute, Inc., Campus Drive, Cary, NC.
48. Schloss, P. D. and Handelsman, J. 2005. Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl. Environ. Microbiol. 71: 1501-1506.
49. Spang, A., Hatzenpichler, R., Brochier-Armanet, C., Rattei, T., Tischler, P., Spieck, E., Streit, W., Stahl, D. A., Wagner, M. and Schleper, C. 2010. Distinct gene set in two different lineages of ammonia-oxidizing archaea supports the phylum Thaumarchaeota. Trends Microbiol. 18: 331-340.
50. Spedding, T. A., Hamel, C., Mehuys, G. R. and Madramootoo, C. A. 2004. Soil microbial dynamics in maize-growing soil under different tillage and residue management systems. Soil Biol. Biochem. 36: 499-512.
51. Statistics Canada. 2011a. CANSIM Table 001-0010 and 001- 0018: Estimated areas, yield, production, average farm price of principal field crops. Statistics Canada, Ottawa, ON.
52. Statistics Canada. 2011b. CANSIM Table 001-0018: Estimated areas, yield, production, average farm price and total farm value of selected principal field crops. Statistics Canada, Ottawa, ON.
53. Steven, B., Briggs, G., McKay, C. P., Pollard, W. H., Greer, C. W. and Whyte, L. G. 2007. Characterization of the microbial diversity in a permafrost sample from the Canadian high arctic using culture-dependent and culture-independent methods. FEMS Microbiol. Ecol. 59: 513-523.
54. Steven, B., Pollard, W. H., Greer, C. W. and Whyte, L. G. 2008. Microbial diversity and activity through a permafrost/ ground ice core profile from the Canadian high arctic. Environ. Microbiol. 10: 3388-3403.
55. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. and Kumar, S. 2011. MEGA5: Molecular Evolutionary Genetics Analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28: 2731-2739.
56. Tourna, M., Stieglmeier, M., Spang, A., Könneke, M., Schintlmeister, A., Urich, T., Engel, M., Schloter, M., Wagner, A., Richter, A. and Schleper, C. 2011. Nitrososphaera viennensis, an ammonia oxidizing archaeon from soil. PNAS 108: 8420-8425.
57. Upchurch, R., Chiu, C., Everett, K., Dyszynski, G., Coleman, D. and Whitman, W. 2008. Differences in the composition and diversity of bacterial communities from agricultural and forest soils. Soil Biol. Biochem. 40: 1294-1305.
58. Valinsky, L., Della Vedova, G., Scupham, A. J., Alvey, S., Figueroa, A., Yin, B., Hartin, R. J., Chrobak, M., Crowley, D. E., Jiang, T. and Borneman, J. 2002. Analysis of bacterial community composition by oligonucleotide fingerprinting of rRNA genes. Appl. Environ. Microbiol. 68: 3243-3250.
59. Van Groenigen, K. J., Bloem, J., Bââth, E., Boeckx, P., Rousk, J., Bode, S., Forristal, D. and Jones, M. B. 2010. Abundance, production and stabilization of microbial biomass under conventional and reduced tillage. Soil Biol. Biochem. 42: 48-55.
60. Voroney, R. P., Brookes, P. C. and Beyaert, R. P. 2008. Soil microbial biomass C, N, P and S. Pages 637-651 in M. R. Carter and E. G. Gregorich, eds. Soil sampling and methods of analysis. 2nd ed. CRC Press, Boca Raton, FL.
61. Vyn, T. J. and Raimbault, B. A. 1993. Long-term effect of five tillage systems on corn response and soil structure. Agron. J. 85: 1074-1079.
62. Whalen, J. K. and Sampedro, L. 2010. Soil ecology and management. CABI International, Oxfordshire, UK. 320 pp.
63. Whyte, L. G. and Greer, C. W. 2005. Molecular techniques for monitoring and assessing soil bioremediation. R. Margesin and F. Schinner, eds. Pages 201-231 in Manual for soil analysis - Monitoring and assessing soil bioremediation. Springer Verlag, Berlin, Germany.
64. Yin, C., Jones, K. L., Peterson, D. E., Garrett, K. A. and Hulbert, S. H. 2010. Members of soil bacterial communities sensitive to tillage and crop rotation. Soil Biol. Biochem. 42: 2111-2118.
65. Zhang, H., Parameswaran, P., Badalamenti, J., Rittmann, B. E. and Krajmalnik-Brown, R. 2011. Integrating high-throughput pyrosequencing and quantitative real-time PCR to analyze complex microbial communities. Methods Mol. Biol. 733: 107-128.