Comparative Analysis of Soil Microbial Communities between Conventional and Organic Farming Systems in Pepper Cultivation
![]() |
Kim, Yiseul
(농촌진흥청 국립농업과학원 농업미생물과)
Lee, Youngmi (농촌진흥청 국립농업과학원 유기농업과) Weon, Hang-Yeon (농촌진흥청 국립농업과학원 농업미생물과) Sang, Mee Kyung (농촌진흥청 국립농업과학원 농업미생물과) Song, Jaekyeong (국립농업과학원 농업미생물과) |
1 | Cole, J. R., Q. Wang, E. Cardenas, J. Fish, B. Chai, R. J. Farris, A. S. Kulam-Syed-Mohideen, D. M. McGarrell, T. Marsh, G. M. Garrity and J. M. Tiedje. 2009. The ribosomal database project: Improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 37: D141-D145. DOI |
2 | Esperschutz, J., A. Gattinger, P. Mader, M. Schloter, and A. Fliessbach. 2007. Response of soil microbial biomass and community structures to conventional and organic farming systems under identical crop rotations. FEMS. Microbiol. Ecol. 61: 26-37. DOI |
3 | Hartmann, M., B. Frey, J. Mayer, P. Mäder, and F. Widmer. 2015. Distinct soil microbial diversity under long-term organic and conventional farming. J. ISME. 9: 1177-1194. DOI |
4 | Hayat, R., S. Ali, U. Amara, R. Khalid, and I. Ahmed. 2010. Soil beneficial bacteria and their role in plant growth promotion: a review. Ann. Microbiol. 60: 579-598. DOI |
5 | Kirk, J. L., L. A. Beaudette, M. Hart, P. Moutoglis, J. N. Klironomos, H. Lee, and J. T. Trevors. 2004. Methods of studying soil microbial diversity. J. Microbiol. Methods. 58: 169-188. DOI |
6 | Lauber, C. L., M. Hamady, R. Knight, and N. Fierer. 2009. Pyrosequencing-based assessment of soil pH as a predictor of soil bacterial community structure at the continental scale. Appl. Environ. Microbiol. 75: 5111-5120. DOI |
7 | Lee, S. T., D. C. Seo, J. S. Cho, E. S. Kim, W. D. Song, and Y. H. Lee. 2011. Influence of cultivated regions in organic and conventional farming paddy field. Korean J. Soil Sci. Fert. 44(3): 408-414. DOI |
8 | Lee, Y., J. H. Ahn, Y. M. Choi, H. Y. Weon, J. H. Yoon, and J. Song. 2015. Bacterial core community in soybean rhizosphere. Korean J. Microbiol. 51(4): 347-354. DOI |
9 | Li, R., E. Khafipour, D. O. Krause, M. H. Entz, T. R. de Kievit, and W. G. Dilantha Fernando. 2012. Pyrosequencing reveals the influence of organic and conventional farming systems on bacterial communities. PLoS ONE. 7(12): e51897. DOI |
10 | Liao, J., Y. Liang, and D. Huang. 2018. Organic farming improves soil microbial abundance and diversity under greenhouse condition: a case study in shanghai (Eastern China). Sustainability. 10: 3825. DOI |
11 | Liu, B., C. Tu, S. Hu, M. Gumpertz, and J. B. Ristaino. 2007. Effect of organic, sustainable, and conventional management strategies in grower fields on soil physical, chemical, and biological factors and the incidence of Southern blight. Appl. Soil. Ecol. 37: 202-214. DOI |
12 | Lori, M., S. Symnaczik, P. Mäder, G. De Deyn, and A. Gattinger. 2017. Organic farming enhances soil microbial abundance and activity-a meta-analysis and meta-regression. PLoS One. 12: e0180442-e0180442. DOI |
13 | Lupatini, M., G. Korthals, M. de Hollander, T. Janssens, and E. Kuramae. 2017. Soil microbiome is more heterogeneous in organic than in conventional farming system. Front Microbiol. 7: 2064. |
14 | Mader, P., A. Fliessbach, D. Dubois, L. Gunst, P. Fried, and U. Niggli. 2002. Soil fertility and biodiversity in organic farming. Science. 296: 1694-1697. DOI |
15 | NIAST. 2002. Methods of soil chemical analysis. National Institute of Agricultural Science and Technology, RDA, Suwon, Korea. |
16 | Oehl, F., E. Sieverding, K. Ineichen, P. Mader, T. Boller, and A. Wiemken. 2003. Impact of land use intensity on the species diversity of arbuscular mycorrhizal fungi in agroecosystems of central Europe. Appl. Environ. Microbiol. 69: 2816-2824. DOI |
17 | Pruesse, E., J. Peplies, and F. O. Glockner. 2012. Sina: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 28: 1823-1829. DOI |
18 | Orr, C. H., A. James, C. Leifert, J. M. Cooper, and S. P. Cummings. 2011. Diversity and activity of free-living nitrogen-fixing bacteria and total bacteria in organic and conventionally managed soils. Appl. Environ. Microbiol. 77(3): 911-919. DOI |
19 | Pershina, E., J. Valkonen, P. Kurki, E. Ivanova, E. Chirak, I. Korvigo, N. Provorov, and E. Andronov. 2015. Comparative analysis of prokaryotic communities associated with organic and conventional farming systems. PLoS One. 10: e0145072-e0145072. DOI |
20 | Pimentel, D., P. Hepperly, J. Hanson, D. Douds, and R. Seidel. 2005. Environmental, energetic, and economic comparisons of organic and conventional farming systems. J. Biosci. 55: 573-582. DOI |
21 | Quince, C., A. Lanzen, R. J. Davenport, and P. J. Turnbaugh. 2011. Removing noise from pyrosequenced amplicons. BMC Bioinformatics 12: 38. DOI |
22 | Ramirez, K. S., C. L. Lauber, R. Knight, M. A. Bradford, and N. Fierer. 2010. Consistent effects of nitrogen fertilization on soil bacterial communities in contrasting systems. Ecology. 91: 3463-3470. DOI |
23 | RDA. 2013. Pepper. Agricultural technic guideline. RDA, Suwon, Korea. |
24 | RDA. 2009. Pepper. Organic cultivation manual. RDA, Suwon, Korea. |
25 | Schloss, P. D., S. L. Westcott, T. Ryabin, J. R. Hall, M. Hartmann, E. B. Hollister, R. A. Lesniewski, B. B. Oakley, D. H. Parks, and C. J. Robinson. 2009. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl. Environ. Microbiol. 75: 7537-7541. DOI |
26 | Wright, S. F., J. L. Starr, and I. C. Paltineanu. 1999. Changes in aggregate stability and concentration of glomalin during tillage management transition. J. Soil. Sci. Soc. Am. 63: 1825-1829. DOI |
27 | Shokralla, S., J. Spall, J. Gibson, and M. Hajibabaei. 2012. Next-generation sequencing technologies for enviromental DNA research. Mol. Ecol. 21: 1794-1805. DOI |
28 | Stagnari, F., G. Perpetuini, R. Tofalo, G. Campanelli, F. Leteo, U. Della Vella, M. Schirone, G. Suzzi, and M. Pisante. 2014. Long-term impact of farm management and crops on soil microorganisms assessed by combined DGGE and PLFA analyses. Front Microbiol. 5: 644-644. |
29 | Torjusen, H., G. Lieblein, M. Wandel, and C. A. Francis. 2001. Food system orientation and quality perception among consumers and producers of organic food in Hedmark County, Norway. Food Qual. Prefer. 12: 207-216. DOI |
30 | van Diepeningen, A. D., O. J. de Vos, G. W. Korthals, and A. H. C. van Bruggen. 2006. Effects of organic versus conventional management on chemical and biological parameters in agricultural soils. Appl. Soil. Ecol. 31: 120-135. DOI |
31 | Xue, K., L. Wu, Y. Deng, Z. He, J. V. Nostrand, P. G. Robertson, T. M. Schmidt, and J. Zhou. 2013. Functional gene differences in soil microbial communities from conventional, low-input, and organic farmlands. Appl. Environ. Microbiol. 79: 1284-1292. DOI |
32 | Zikeli, S., L. Deil, and K. Moller. 2017. The challenge of imbalanced nutrient flows in organic farming systems: a study of organic greenhouses in Southern Germany. Agric. Ecosyst. Environ. 244: 1-13. DOI |
33 | Chaudhry, V., A. Rehman, A. Mishra, P. Chauhan, and C. S. Nautiyal. 2012. Changes in bacterial community structure of agricultural land due to long-term organic and chemical amendments. Microb. Ecol. 64: 450-460. DOI |
34 | Ahn, J. H., B. Y. Kim, D. H. Kim, J. Song, and H. Y. Weon. 2012. Application of amplicon pyrosequencing in soil microbial ecology. Korean J. Soil Sci. Fert. 45(6): 1073-1085. DOI |
35 | Araujo A. S. F. and W. J. Melo. 2010. Soil microbial biomass in organic farming system. Ciencia Rural, Santa Maria. 40(11): 2419-2426. DOI |
36 | Barak, P., B. O. Jobe, A. R. Krueger, L. A. Peterson, and D. A. Laird. 1997. Effects of longterm soil acidification due to nitrogen fertilizer inputs in Wisconsin. Plant Soil. 197: 61-69. DOI |
37 | Cho, H. J., S. W. Hwang, K. H. Han, H. R. Cho, J. H. Shin, and L. Y. Kim. 2009. Physicochemical properties of upland soils under organic farming. Korean J. Soil Sci. Fert. 42(2): 98-102 |
38 | Choi, B. S., J. A. Jung, M. K. Oh, S. H. Jeon, H. G. Goh, Y. S. Ok, and J. K. Sung. 2010. Effects of green manure crops on improvement of chemical and biological properties in soil. Korean J. Soil Sci. Fert. 43(5): 650-658. |
39 | Chung, J. B., and Y. J. LEE. 2008. Comparison of soil nutrient status in conventional and organic apple farm. Korean. Soc. Soil Sci. Fert. 41(1): 26-33. |
![]() |