Skip to main content
Log in

Changes in microbial community of agricultural soils subjected to organic farming system in korean paddy fields with no-till management

  • Environmental Science
  • Article
  • Published:
Journal of the Korean Society for Applied Biological Chemistry Submit manuscript

Abstract

Soil management for organic farming depends on the effects of soil microbial activities and aggregation. The seasonal changes were evaluated in the soil microbial community by fatty acid methyl ester (FAME) and total glomalin analysis in an organic farming system (OFS) with no-till management compared to those in a conventional farming system (CFS) with tillage and chemical amendments in a flooded paddy. The average concentrations of individual FAMEs and glomalin in the OFS were significantly higher than those in the CFS during rice-growing stages (p<0.001). OFS had significantly lower ratio of cy17:0/16:1ω7c and higher ratio of monounsaturated fatty acids to saturated fatty acids compared with those of CFS (p<0.001), indicating that microbial stress decreased due to organic soil inputs and the lack of chemical amendments, whereas communities of Gram-negative bacteria in OFS soils were significantly larger than those in CFS soils (p<0.001). Gram-negative bacteria should be considered as potential factor responsible for the clear microbial community differentiation observed between the OFS and the CFS in flooded paddy fields.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others

References

  • Altieri MA (2002) Agroecology: The sceience of natural resource managemen for poor farmers in marginal environments. Agric Ecosyst Environ 93, 1–24.

    Article  Google Scholar 

  • Balser T, Treseder KK, and Ekenler M (2005) Using lipid analysis and hyphal length to quantify AM and saprotrophic fungal abundance along a soil chronosequence. Soil Biol Biochem 37, 601–604.

    Article  CAS  Google Scholar 

  • Beare MH, Hendrix PF, and Coleman DC (1994) Water-stable aggregates and organic matter fractions in conventional-and no-tillage soils. Soil Sci Soc Am J 58, 777–786.

    Article  Google Scholar 

  • Bossio DA and Scow KM (1998) Impacts of carbon and flooding on soil microbial communities: Phospholipid fatty acid profiles and substrate utilization patterns. Microb Ecol 35, 265–278.

    Article  CAS  Google Scholar 

  • Bossio DA, Scow KM, Gunapala N, and Graham KJ (1998) Determinants of soil microbial communities: Effects of management, season and soil type on phospholipid fatty acid profiles. Microb Ecol 36, 1–12.

    Article  CAS  Google Scholar 

  • Bradleya K, Rhae A, Drijberb RA, and Knopsc J (2006) Increased N availability in grassland soils modifies their microbial communities and decreases the abundance of arbuscular mycorrhizal fungi. Soil Biol Biochem 38, 1583–1595.

    Article  Google Scholar 

  • Buyer JS and Drinkwater LE (1997) Comparison of substrate utilization assay and fatty acid analysis of soil microbial communities. J Microbiol Meth 30, 3–11.

    Article  CAS  Google Scholar 

  • Drenovsky RE, Vo D, Graham KJ, and Scow KM (2004) Soil water content and organic carbon availability are major determinants of soil microbial community composition. Microb Ecol 48, 424–430.

    Article  CAS  Google Scholar 

  • Frey SD, Elliott ET, and Paustian K (1999) Bacterial and fungal abundance and biomass in conventional and no-tillage agroecosystems along two climatic gradients. Soil Biol Biochem 31, 573–585.

    Article  CAS  Google Scholar 

  • Frostegård Å and Bååth E (1996) The use of phospholipid fatty acid analysis to estimate bacterial and fungal biomass in soil. Biol Fertil Soils 22, 59–65.

    Article  Google Scholar 

  • Frostegård Å, Tunlid A, and Bååth E (1993) Phospholipid fatty acid composition, biomass and activity of microbial communities from two soil types experimentally exposed to different heavy metals. Appl Environ Microbiol 59, 3605–3617.

    Google Scholar 

  • Graham JH, Hodge NC, and Morton JB (1995) Fatty acid methyl ester profiles for characterization of glomalean fungi and their endomycorrhizae. Appl Environ Microbiol 61, 58–64.

    CAS  Google Scholar 

  • Guckert JB, Hood MA, and White DC (1986) Phospholipid ester-linked fatty acid profile changes during nutrient deprivation of Vibrio cholerae: Increases in cis/trans ratio and proportions of cyclopropyl fatty acid. Appl Environ Microbial 52, 794–801.

    CAS  Google Scholar 

  • Hamman ST, Burke IC, and Strombeerger ME (2007) Relationships between microbial community structure and soil environmental conditions in a recently burned system. Soil Biol Biochem 39, 1703–1711.

    Article  CAS  Google Scholar 

  • Helgason BL, Walley FL, and Germida JJ (2007) Fungal and bacterial abundance in long-term no-till and intensive-till soils of the Northern Great Plains. Soil Sci Soc Am J 73, 120–127.

    Article  Google Scholar 

  • Johnson CK, Doran JW, Duke HR, Wienhold BJ, Eskridge KM, and Shanahan JF (2001) Field-scale electrical conductivity mapping for delineating soil condition. Soil Sci Soc Am J 65, 1829–1837.

    Article  CAS  Google Scholar 

  • Kieft TL, Wilch E, O’connor K, Ringelberg DB, and White DC (1997) Survival and phospholipid fatty acid profiles of surface and subsurface bacteria in natural sediment microcosms. Appl Environ Microbiol 63, 1531–1542.

    CAS  Google Scholar 

  • Lundquist EJ, Scow KM, Jackson LE, Uesugi SL, and Johnson CR (1999) Rapid response of soil microbial communities from conventional, low input, and organic farming systems to a wet/dry cycle. Soil Biol Biochem 31, 1661–1675.

    Article  CAS  Google Scholar 

  • Macalady JL, Fuller ME, and Scow KM (1998) Effects of metam sodium fumigation on soil microbial activity and community structure. J Environ Qual 27, 54–63.

    Article  CAS  Google Scholar 

  • Mäder P, Flieâbach A, Dubois D, Gunst L, Fried P, and Niggli U (2002) Soil fertility and biodiversity in organic farming. Science 296, 1694–1697.

    Article  Google Scholar 

  • Mamilov AS and Dilly OM (2002) Soil microbial ecophysiology as affected by short-term variations in environmental conditions. Soil Biol Biochem 34, 1283–1290.

    Article  CAS  Google Scholar 

  • Mechri B, Chehab H, Attia F, Mariem FB, Braham M, and Hammami M (2010) Olive mill wastewater effects on the microbial communities as studied in the field of olive trees by analysis of fatty acid signatures. Eur J Soil Biol 46, 312–318.

    Article  Google Scholar 

  • Meriles JM, Vargas Gil S, Conforto C, Figoni G, Lovera E, March GJ, and Guzmán CA (2009) Soil microbial communities under different soybean cropping systems: Characterization of microbial population dynamics, soil microbial activity, microbial biomass, and fatty acid profiles. Soil Till Res 103, 271–281.

    Article  Google Scholar 

  • Pennanen T (2001) Microbial communities in boreal coniferous forest humus exposed to heavy metals and changes in soil pH-a summary of the use of phospholipids fatty acids, Biolog® and 3H-Thymidine incorporation methods in field studies. Geoderma 100, 91–126.

    Article  CAS  Google Scholar 

  • Rilling MC, Lutgen ER, Ramsey PW, Klironomos JN, and Gannon JE (2005) Microbiota accompanying different arbuscular mycorrhizal fungal isolates influence soil aggregation. Pedobiologis 49, 251–259.

    Article  Google Scholar 

  • Rillig MC, Ramsey PW, Morris S, and Paul EA (2003) Glomalin, an arbuscular-mycorrhizal fungal soil protein, responds to land-use change. Plant Soil 253, 293–299.

    Article  CAS  Google Scholar 

  • Rillig MC, Wright SF, Nichols KA, Schmidt WF, and Torn MS (2001) Large contribution of arbuscular mycorrhizal fungi to soil carbon pools in tropical forest soils. Plant Soil 233, 167–177.

    Article  CAS  Google Scholar 

  • Rotenberg D, Joshi R, Benítez M, Chapin LG, Camp A, Zumpetta C, Osborne A, Dick WA, and McSpadden Gardener BB (2007) Farm management effects on rhizosphere colonization by native populations of 2,4-diacetylphloroglucinol-producing Pseudomonas spp. and their contributions to crop health. Phytopathology 97, 756–766.

    Article  CAS  Google Scholar 

  • Schutter ME and Dick RP (2000) Comparison of fatty acid methyl ester (FAME) methods for characterizing microbial communities. Soil Sci Soc Am J 64, 1659–1668.

    Article  CAS  Google Scholar 

  • Stark C, Condron LM, Stewart A, Di HJ, and O’Callaghan M (2007) Influence of organic and mineral amendments on microbial soil properties and processes. Appl Soil Ecol 35, 79–93.

    Article  Google Scholar 

  • Wang MC, Liu YH, Wang Q, Gong M, Hua XM, Pang YJ, Hu S, and Yang YH (2008) Impact of methamidophos on the biochemical, catabolic, and genetic characteristics of soil microbial communities. Soil Biol Biochem 40, 778–788.

    Article  CAS  Google Scholar 

  • Wright SF and Upadhyaya A (1998) A survey of soils for aggregate stability and glomalin, a glycoprotein produced by hyphae of arbuscular mycorrhizal fungi. Plant Soil 198, 97–107.

    Article  CAS  Google Scholar 

  • Wright SF, Franke-Snyder M, Morton JB, and Upadhyaya A (1996) Time-course study and partial characterization of a protein on hyphae of arbuscular mycorrhizal fungi during active colonization of roots. Plant Soil 181, 193–203.

    Article  CAS  Google Scholar 

  • Wright SF, Nichols KA, and Schmidt WF (2006) Comparison of efficacy of three extractants to solubilize glomalin on hyphae and in soil. Chemosphere 64, 1219–1224.

    Article  CAS  Google Scholar 

  • Wright SF, Starr JL, and Paltineanu IC (1999) Changes in aggregate stability and concentration of glomalin during tillage management transition. Soil Sci Soc Am J 63, 1825–1829.

    Article  CAS  Google Scholar 

  • Zelles L (1997) Phospholipid fatty acid profiles in selected members of soil microbial communities. Chemosphere 35, 275–294.

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Han Dae Yun.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Lee, Y.H., Yun, H.D. Changes in microbial community of agricultural soils subjected to organic farming system in korean paddy fields with no-till management. J. Korean Soc. Appl. Biol. Chem. 54, 434–441 (2011). https://doi.org/10.3839/jksabc.2011.067

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.3839/jksabc.2011.067

Key words

Navigation