Functional gene differences in soil microbial communities from conventional, low-input, and organic farmlands

Applied and Environmental Microbiology

Volumn 79, Issue 4, 2013, Pages 1284-1292

  Xue, Kai ^a   Wu, Liyou ^a   Deng, Ye ^a   He, Zhili ^a   Van Nostrand, Joy ^a   Robertson, Philip G ^b   Schmidt, Thomas M ^b,c   Zhou, Jizhong ^a  

^a UNIVERSITY OF OKLAHOMA   (United States)

^b MICHIGAN STATE UNIVERSITY   (United States)

^c NONE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AGRICULTURAL RESEARCH; AGRICULTURE MANAGEMENT; AVAILABLE PHOSPHORUS; AVAILABLE POTASSIUMS; BULK DENSITY; C/N RATIO; CANONICAL CORRELATION ANALYSIS; CATION EXCHANGE CAPACITIES; ECOLOGICAL FUNCTIONS; FUNCTIONAL GENES; GENES ENCODING ENZYMES; HIGH-THROUGHPUT; LIGNIN DEGRADATION; MANAGEMENT SYSTEMS; MICHIGAN; N AVAILABILITY; POTENTIAL FUNCTION; SOIL MICROBIAL COMMUNITY; SOIL MICROBIAL COMMUNITY COMPOSITIONS;

AGRICULTURE; DENITRIFICATION; METHANE; MICROORGANISMS; SOILS;

GENES;

CARBON; NITROGEN; PHOSPHORUS; SULFUR;

AGRICULTURAL LAND; AGRICULTURAL MANAGEMENT; AGRICULTURAL PRACTICE; AMMONIFICATION; BULK DENSITY; CANONICAL ANALYSIS; CARBON; COMMUNITY COMPOSITION; DEGRADATION; DENITRIFICATION; GENE; ION EXCHANGE; LIGNIN; MANAGEMENT PRACTICE; MICROBIAL COMMUNITY; ORGANIC FARMING; PHOSPHORUS; SOIL MICROORGANISM; SOIL NITROGEN; SULFUR;

AGRICULTURE; ARTICLE; BACTERIAL GENE; BIOTA; CHEMISTRY; GENETICS; METABOLISM; METAGENOME; METHODOLOGY; MICROARRAY ANALYSIS; MICROBIOLOGY; SOIL; UNITED STATES;

AGRICULTURE; BIOTA; CARBON; GENES, BACTERIAL; METABOLIC NETWORKS AND PATHWAYS; METAGENOME; MICHIGAN; MICROARRAY ANALYSIS; NITROGEN; PHOSPHORUS; SOIL; SOIL MICROBIOLOGY; SULFUR;

MICHIGAN; UNITED STATES;

EID: 84874682986     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.03393-12     Document Type: Article

References (59)

1. Jackson LE, Calderon FJ, Steenwerth KL, Scow KM, Rolston DE. 2003. Responses of soil microbial processes and community structure to tillage events and implications for soil quality. Geoderma 114:305-317.
2. van Bruggen AHC, Semenov AM. 2000. In search of biological indicators for soil health and disease suppression. Appl. Soil Ecol. 15:13-24.
3. Pimentel D, Hepperly P, Hanson J, Douds D, Seidel R. 2005. Environmental, energetic, and economic comparisons of organic and conventional farming systems. Bioscience 55:573-582.
4. Bossio DA, Scow KM, Gunapala N, Graham KJ. 1998. Determinants of soil microbial communities: effects of agricultural management, season, and soil type on phospholipid fatty acid profiles. Microb. Ecol. 36:1-12.
5. Buyer JS, Teasdale JR, Roberts DP, Zasada IA, Maul JE. 2010. Factors affecting soil microbial community structure in tomato cropping systems. Soil Biol. Biochem. 42:831- 841.
6. Heinze S, Raupp J, Joergensen RG. 2010. Effects of fertilizer and spatial heterogeneity in soil pH on microbial biomass indices in a long-term field trial of organic agriculture. Plant Soil 328:203-215.
7. Islam MR, Trivedi P, Palaniappan P, Reddy MS, Sa T. 2009. Evaluating the effect of fertilizer application on soil microbial community structure in rice based cropping system using fatty acid methyl esters (FAME) analysis. World J. Microbiol. Biotechnol. 25:1115-1117.
8. Jangid K, Williams MA, Franzluebbers AJ, Sanderlin JS, Reeves JH, Jenkins MB, Endale DM, Coleman DC, Whitman WB. 2008. Relative impacts of land-use, management intensity and fertilization upon soil microbial community structure in agricultural systems. Soil Biol. Biochem. 40:2843-2853.
9. Kong AYY, Scow KM, Cordova-Kreylos AL, Holmes WE, Six J. 2011. Microbial community composition and carbon cycling within soil microenvironments of conventional, low-input, and organic cropping systems. Soil Biol. Biochem. 43:20 -30.
10. Marschner P, Kandeler E, Marschner B. 2003. Structure and function of the soil microbial community in a long-term fertilizer experiment. Soil Biol. Biochem. 35:453- 461.
11. Patra AK, Le Roux X, Grayston SJ, Loiseau P, Louault F. 2008. Unraveling the effects of management regime and plant species on soil organic carbon and microbial phospholipid fatty acid profiles in grassland soils. Bioresour. Technol. 99:3545-3551.
12. Peacock AD, Mullen MD, Ringelberg DB, Tyler DD, Hedrick DB, Gale PM, White DC. 2001. Soil microbial community responses to dairy manure or ammonium nitrate applications. Soil Biol. Biochem. 33:1011- 1019.
13. Zhong WH, Gu T, Wang W, Zhang B, Lin XG, Huang QR, Shen WS. 2010. The effects of mineral fertilizer and organic manure on soil microbial community and diversity. Plant Soil 326:511-522.
14. Zhang NL, Wan SQ, Li LH, Bi J, Zhao MM, Ma KP. 2008. Impacts of urea N addition on soil microbial community in a semi-arid temperate steppe in northern China. Plant Soil 311:19 -28.
15. Chu HY, Lin XG, Fujii T, Morimoto S, Yagi K, Hu JL, Zhang JB. 2007. Soil microbial biomass, dehydrogenase activity, bacterial community structure in response to long-term fertilizer management. Soil Biol. Biochem. 39:2971-2976.
16. Blackwood CB, Dell CJ, Smucker AJM, Paul EA. 2006. Eubacterial communities in different soil macroaggregate environments and cropping systems. Soil Biol. Biochem. 38:720 -728.
17. Blackwood CB, Paul EA. 2003. Eubacterial community structure and population size within the soil light fraction, rhizosphere, and heavy fraction of several agricultural systems. Soil Biol. Biochem. 35:1245-1255.
18. Sessitsch A, Weilharter A, Gerzabek MH, Kirchmann H, Kandeler E. 2001. Microbial population structures in soil particle size fractions of a long-term fertilizer field experiment. Appl. Environ. Microbiol. 67:4215-4224.
19. Buckley DH, Schmidt TM. 2001. The structure of microbial communities in soil and the lasting impact of cultivation. Microb. Ecol. 42:11-21.
20. Levine UY, Teal TK, Robertson GP, Schmidt TM. 2011. Agriculture's impact on microbial diversity and associated fluxes of carbon dioxide and methane. ISME J. 5:1683-1691.
21. Ramirez KS, Lauber CL, Knight R, Bradford MA, Fierer N. 2010. Consistent effects of nitrogen fertilization on soil bacterial communities in contrasting systems. Ecology 91:3463-3470.
22. Cavigelli MA, Robertson GP. 2001. Role of denitrifier diversity in rates of nitrous oxide consumption in a terrestrial ecosystem. Soil Biol. Biochem. 33:297-310.
23. Phillips CJ, Harris D, Dollhopf SL, Gross KL, Prosser JI, Paul EA. 2000. Effects of agronomic treatments on structure and function of ammoniaoxidizing communities. Appl. Environ. Microbiol. 66:5410 -5418.
24. Morales SE, Cosart T, Holben WE. 2010. Bacterial gene abundances as indicators of greenhouse gas emission in soils. ISME J. 4:799-808.
25. He ZL, Deng Y, Van Nostrand JD, Tu QC, Xu MY, Hemme CL, Li XY, Wu LY, Gentry TJ, Yin YF, Liebich J, Hazen TC, Zhou JZ. 2010. GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity. ISME J. 4:1167-1179.
26. Reeve JR, Schadt CW, Carpenter-Boggs L, Kang S, Zhou JZ, Reganold JP. 2010. Effects of soil type and farm management on soil ecological functional genes and microbial activities. ISME J. 4:1099 -1107.
27. Robertson GP, Paul EA, Harwood RR. 2000. Greenhouse gases in intensive agriculture: contributions of individual gases to the radiative forcing of the atmosphere. Science 289:1922-1925.
28. Gelfand I, Snapp SS, Robertson GP. 2010. Energy efficiency of conventional, organic, and alternative cropping systems for food and fuel at a site in the US Midwest. Environ. Sci. Technol. 44:4006-4011.
29. Syswerda SP, Basso B, Hamilton SK, Tausig JB, Robertson GP. 2012. Long-term nitrate loss along an agricultural intensity gradient in the Upper Midwest USA. Agric. Ecosyst. Environ. 149:10 -19.
30. Grandy AS, Loecke TD, Parr S, Robertson GP. 2006. Long-term trends in nitrous oxide emissions, soil nitrogen, and crop yields of till and no-till cropping systems. J. Environ. Qual. 35:1487-1495.
31. Davis AS, Renner KA, Gross KL. 2005. Weed seedbank and community shifts in a long-term cropping systems experiment. Weed Sci. 53:296 -306.
32. Zhou JZ, Bruns MA, Tiedje JM. 1996. DNA recovery from soils of diverse composition. Appl. Environ. Microbiol. 62:316 -322.
33. Ahn SJ, Costa J, Emanuel JR. 1996. PicoGreen quantitation of DNA: effective evaluation of samples pre- or post-PCR. Nucleic Acids Res. 24: 2623-2625.
34. Wu LY, Liu X, Schadt CW, Zhou JZ. 2006. Microarray-based analysis of subnanogram quantities of microbial community DNAs by using wholecommunity genome amplification. Appl. Environ. Microbiol. 72:4931-4941.
35. Liang YT, He ZL, Wu LY, Deng Y, Li GH, Zhou JZ. 2010. Development of a common oligonucleotide reference standard for microarray data normalization and comparison across different microbial communities. Appl. Environ. Microbiol. 76:1088 -1094.
36. He ZL, Zhou JZ. 2008. Empirical evaluation of a new method for calculating signal-to-noise ratio for microarray data analysis. Appl. Environ. Microbiol. 74:2957-2966.
37. Holm S. 1979. A simple sequentially rejective multiple test procedure. Scand. J. Stat. 6:65-70.
38. Syswerda SP, Corbin AT, Mokma DL, Kravchenko AN, Robertson GP. 2011. Agricultural management and soil carbon storage in surface vs deep layers. Soil Sci. Soc. Am. J. 75:92-101.
39. Lal R, Griffin M, Apt J, Lave L, Morgan MG. 2004. Ecology. Managing soil carbon. Science 304:393.
40. Yang YH, Yao J, Hu S, Qi Y. 2000. Effects of agricultural chemicals on DNA sequence diversity of soil microbial community: a study with RAPD marker. Microb. Ecol. 39:72-79.
41. Sarathchandra SU, Ghani A, Yeates GW, Burch G, Cox NR. 2001. Effect of nitrogen and phosphate fertilisers on microbial and nematode diversity in pasture soils. Soil Biol. Biochem. 33:953-964.
42. Bobbink R. 1991. Effects of nutrient enrichment in Dutch chalk grassland. J. Appl. Ecol. 28:28-41.
43. Bobbink R, Hornung M, Roelofs JGM. 1998. The effects of air-borne nitrogen pollutants on species diversity in natural and semi-natural European vegetation. J. Ecol. 86:717-738.
44. Clark CM, Tilman D. 2008. Loss of plant species after chronic low-level nitrogen deposition to prairie grasslands. Nature 451:712-715.
45. Gough L, Osenberg CW, Gross KL, Collins SL. 2000. Fertilization effects on species density and primary productivity in herbaceous plant communities. Oikos 89:428-439.
46. Reich PB. 2009. Elevated CO2 reduces losses of plant diversity caused by nitrogen deposition. Science 326:1399 -1402.
47. Goldberg DE, Miller TE. 1990. Effects of different resource additions on species-diversity in an annual plant community. Ecology 71:213-225.
48. Suding KN, Collins SL, Gough L, Clark C, Cleland EE, Gross KL, Milchunas DG, Pennings S. 2005. Functional- and abundance-based mechanisms explain diversity loss due to N fertilization. Proc. Natl. Acad. Sci. U. S. A. 102:4387- 4392.
49. Vitousek PM, Aber JD, Howarth RW, Likens GE, Matson PA, Schindler DW, Schlesinger WH, Tilman D. 1997. Human alteration of the global nitrogen cycle: sources and consequences. Ecol. Appl. 7:737-750.
50. Mader P, Fliessbach A, Dubois D, Gunst L, Fried P, Niggli U. 2002. Soil fertility and biodiversity in organic farming. Science 296:1694 -1697.
51. Sun HY, Deng SP, Raun WR. 2004. Bacterial community structure and diversity in a century-old manure-treated agroecosystem. Appl. Environ. Microbiol. 70:5868 -5874.
52. Fontaine S, Bardoux G, Abbadie L, Mariotti A. 2004. Carbon input to soil may decrease soil carbon content. Ecol. Lett. 7:314 -320.
53. Fontaine S, Mariotti A, Abbadie L. 2003. The priming effect of organic matter: a question of microbial competition? Soil Biol. Biochem. 35:837-843.
54. Harper JL, Hawksworth DL. 1994. Biodiversity: measurement and estimation. Philos. Trans. R. Soc. Lond. B Biol. Sci. 345:5-12.
55. Fuhrman JA. 2009. Microbial community structure and its functional implications. Nature 459:193-199.
56. Elfstrand S, Bath B, Martensson A. 2007. Influence of various forms of green manure amendment on soil microbial community composition, enzyme activity and nutrient levels in leek. Appl. Soil Ecol. 36:70-82.
57. Sekiguchi H, Kushida A, Takenaka S. 2007. Effects of cattle manure and green manure on the microbial community structure in upland soil determined by denaturing gradient gel electrophoresis. Microbes Environ. 22: 327-335.
58. Cruz-Martinez K, Suttle KB, Brodie EL, Power ME, Andersen GL, Banfield JF. 2009. Despite strong seasonal responses, soil microbial consortia are more resilient to long-term changes in rainfall than overlying grassland. ISME J. 3:738 -744.
59. Xue K, Serohijos RC, Devare M, Thies JE. 2011. Decomposition rates and residue-colonizing microbial communities of Bacillus thuringiensis insecticidal protein Cry3Bb-expressing (Bt) and non-Bt corn hybrids in the field. Appl. Environ. Microbiol. 77:839-846.