World Journal of Microbiology and Biotechnology

, Volume 24, Issue 7, pp 1159–1167

Bacterial community diversity assessment in municipal solid waste compost amended soil using DGGE and ARISA fingerprinting methods

  • Hanene Cherif
  • Hadda Ouzari
  • Massimo Marzorati
  • Lorenzo Brusetti
  • Naceur Jedidi
  • Abdennaceur Hassen
  • Daniele Daffonchio
Original Paper

Abstract

Bacterial community structure and diversity of Tunisian agricultural soil treated with different amounts of municipal solid waste compost (MSWC) and other fertilizers were studied using DGGE and ARISA fingerprinting methods. Sequence analysis of dominant DGGE bands revealed the presence of three major clusters, Cytophaga/Flexibacter/Bacteroides (CFB) group, Proteobacteria and Acidobacteria group. Using ARISA profiles, dominant populations were assigned to low and high GC Gram positive bacteria, Cyanobacteria, Spirochetes and Cytophagales. The two methods revealed the absence of significant bacterial community shifts related to the different MSWC applications. Moreover, indigenous bacterial population of the used loam-clayey soil was observed to limit proliferation and survival of Proteobacteria, initially dominant in MSWC and farmyard manure. Effectiveness of the two methods for soil bacterial community studying was shown. While DGGE was more accurate for bacterial identification, ARISA was more practical for handling and rapid estimation of dominant bacteria.

Keywords

ARISA Bacterial community structure Compost DGGE 

References

  1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410Google Scholar
  2. Bouzaiane O, Cherif H, Saidi N, Jedidi N, Hassen A (2007) Effects of municipal solid waste compost application on the microbial biomass of cultivated and non-cultivated soil in a semi-arid zone. Waste Manage Res 25(4):334–342CrossRefGoogle Scholar
  3. Borin S, Marzorati M, Brusetti L, Zilli M, Cherif H, Hassen A, Converti A, Sorlini C, Daffonchio D (2006) Microbial succession in a compost-packed biofilter treating benzene-contaminated air. Biodegradation 17(2):79–89CrossRefGoogle Scholar
  4. Borneman J, Skroch PW, O’Sullivan KM, Palus JA, Rumjanek NG, Jansen JL, Nienhuis J, Triplett EW (1996) Molecular microbial diversity of an agricultural soil in Wisconsin. Appl Environ Microbiol 62:1935–1943Google Scholar
  5. Brusetti L, Francia P, Bertolini C, Pagluica A, Borin S, Sorlini C, Abruzzese A, Sacchi G, Viti C, Giovannetti L, Bazzicalupo M, Daffonchio D (2004) Bacterial communities assiciated with the rhizosphere of transgenic Bt 176 maize (Zea mays) and its non transgenic counterpart. Plant Soil 266:11–21CrossRefGoogle Scholar
  6. Cardinale M, Brusetti L, Quatrini P, Borin S, Maria Puglia A, Rizzi A, Zanardini E, Sorlini C, Corselli C, Daffonchio D (2004) Comparison of different primer sets for use in automated ribosomal intergenic spacer analysis of complex bacterial communities. Appl Environ Microbiol 70:6146–6156CrossRefGoogle Scholar
  7. Crecchio C, Curci M, Mininni R, Ricciuti P, Ruggiero P (2001) Short-term effects of municipal solid waste compost amendments on soil carbon and nitrogen content, some enzyme activities and genetic diversity. Biol Fert Soils 34:311–318CrossRefGoogle Scholar
  8. De Lipthay JR, Enzinger C, Johnsen K, Aamand J, Sørensen SJ (2004) Impact of DNA extraction method on bacterial community composition measured by denaturing gradient gel electrophoresis. Soil Biol Bioch 36:1607–1614CrossRefGoogle Scholar
  9. Duineveld BM, Rosado AS, Van Elsas JD, Van Veen JA (1998) Analysis of the dynamics of bacterial communities in the rhizosphere of the chrysanthemum via denaturing gradient gel electrophoresis and substrate utilization patterns. Appl Environ Microbiol 64:4950–4957Google Scholar
  10. Fisher MM, Triplett EW (1999) Automated approach for ribosomal intergenic spacer analysis of microbial diversity and its application to freshwater bacterial communities. Appl Environ Microbiol 65:4630–4636Google Scholar
  11. Girvan MS, Bullimore J, Pretty JN, Osborn AM, Ball AS (2003) Soil type is the primary determinant of the composition of the total and active bacterial communities in arable soils. Appl Environ Microbiol 69:1800–1809CrossRefGoogle Scholar
  12. Green SJ, Frederick C, Michel Jr, Hadar Y, Minz D (2004) Similarity of bacterial communities in sawdust-and straw-amended cow manure composts. FEMS Microbiol Lett 233:115–123CrossRefGoogle Scholar
  13. Hamdi H, Jedidi N, Ayari F, M’hiri A, Hassen A, Ghrabi A (2002) The effect of Tunis’ urban compost on soil properties, chemical composition of plant and yield. In: Proceedings of international symposium on environmental pollution control and waste management, January 2002, Tunis (EPCOWM’2002), pp 383–384Google Scholar
  14. Jedidi N, Van Cleemput O, M’hiri A (1993) Mineralization of organic amendments in a Tunisian soil. In: Muongoy K, Merckx R (eds) soil organic matter dynamics and sustainability of tropical agriculture, pp 163–169Google Scholar
  15. Jedidi N, Van Cleemput O, M’hiri A (1995) Quantification des processus de minéralisation et d’organisation de l’azote dans un sol en présence d’amendements organiques. Can J Soil Sci 75:85–91Google Scholar
  16. Li Z, Xu J, Tang C, Wu J, Muhammad A, Wang H (2005) Application of 16S rDNA-PCR amplification and DGGE fingerprinting for detection of shift in microbial community diversity in Cu-, Zn-, and Cd-contaminated paddy soils. Chemosphere 62:1374–1380CrossRefGoogle Scholar
  17. Marzorati M, Alma A, Sacchi L, Pajoro M, Palermo S, Brusetti L, Raddadi N, Balloi A, Tedeschi R, Clementi E, Corona S, Quaglino F, Bianco PA, Beninati T, Bandi C, Daffonchio D (2006) A Novel Bacteroidetes Symbiont is localized in Scaphoideus titanus, the insect vector of flavescence dore´e in Vitis vinifera. Appl Environ Microbiol 72:1467–1475CrossRefGoogle Scholar
  18. Muyzer G, de Wall EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes encoding for 16S rRNA. Appl Environ Microbiol 59:695–700Google Scholar
  19. Niemi RM, Heiskanen I, Wallenius K, Lindström K (2001) Extraction and purification of DNA in rhizophere soil samples for PCR-DGGE analysis of bacterial consortia. J Microbiol Methods 45:155–165CrossRefGoogle Scholar
  20. Norris TB, Wraith JM, Castenholz RW, McDermott TR (2002) Soil microbial community structure across a thermal gradient following a geothermal heating Event. Appl Environ Microbiol 68:6300–6309CrossRefGoogle Scholar
  21. Ranjard L, Poly F, Nazaret S (2000) Monitoring complex bacterial communities using culture-independent molecular techniques: application to soil environment. Res Microbiol 151:167–177CrossRefGoogle Scholar
  22. Ranjard L, Poly F, Lata JC, Mouguel C, Thioulouse J, Nazaret S (2001) Characterization of bacterial and fungal soil communities by automated ribosomal intergenic spacer analysis fingerprints: biological and methodological variability. Appl Environ Microbiol 67:4479–4487CrossRefGoogle Scholar
  23. Ranjard L, Lejon DP, Mougel C, Schehrer L, Merdinoglu D, Chaussod R (2003) Sampling strategy in molecular microbial ecology: influence of soil sample size on DNA fingerprinting analysis of fungal and bacterial communities. Environ Microbiol 5:1111–1120CrossRefGoogle Scholar
  24. Ros M, Klammer S, Knapp B, Aichberger K, Insam H (2006) Long-term effects of compost amendment of soil on functional and structural diversity and microbial activity. Soil Use Manage 22:209–218CrossRefGoogle Scholar
  25. Sass AM, Sass H, Coolen MJ, Cypionka H, Overmann J (2001) Microbial communities in the chemocline of a hypersaline deep-sea basin (Urania basin, Mediterranean Sea). Appl Environ Microbiol 67:5392–5402CrossRefGoogle Scholar
  26. Seghers D, Wittebolle L, Top EM, Verstraete W, Siciliano SD (2004) Impact of agricultural practices on the Zea mays L. endophytic community. Appl Environ Microbiol 70:1475–1482CrossRefGoogle Scholar
  27. 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 67:4215–4224CrossRefGoogle Scholar
  28. Smit E, Leeflang P, Gommans S, Van den Broek J, Van Mil S, Wernars K (2001) Diversity and seasonal fluctuations of the dominant members of the bacterial soil community in a wheat field as determined by cultivation and molecular methods. Appl Environ Microbiol 67:2284–2291CrossRefGoogle Scholar
  29. Steele JA, Ozis F, Fuhrman JA, Devinny JS (2005) Structure of microbial communities in ethanol biofilters. Chem Eng J 113:135–143CrossRefGoogle Scholar
  30. Sun HY, Deng SP, Raun WR (2004) Bacterial community structure and diversity in a century-old manure-treated agroecosystem. Appl Environ Microbiol 70:5868–5874CrossRefGoogle Scholar
  31. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 24:4876–4882CrossRefGoogle Scholar
  32. Yoshida M, Jedidi N, Hamdi H, Ayari F, Hassen A (2003) Magnetic susceptibility variation of MSW compost amended soils: in situ method for monitoring heavy metal contamination. Waste Manage Res 21:155–160CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2007

Authors and Affiliations

  • Hanene Cherif
    • 1
  • Hadda Ouzari
    • 1
  • Massimo Marzorati
    • 2
  • Lorenzo Brusetti
    • 2
  • Naceur Jedidi
    • 1
  • Abdennaceur Hassen
    • 1
  • Daniele Daffonchio
    • 2
  1. 1.Laboratoire Eau et EnvironnentInstitut National Recherche Scientifique & TechniqueTunisTunisia
  2. 2.Dipartimento di Scienze e Tecnologie Alimentari e MicrobiologicheUniversità degli Studi di MilanoMilanItaly

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