Microbial Ecology

, Volume 57, Issue 3, pp 510–521 | Cite as

Application of COMPOCHIP Microarray to Investigate the Bacterial Communities of Different Composts

  • Ingrid H. Franke-Whittle
  • Brigitte A. Knapp
  • Jacques Fuchs
  • Ruediger Kaufmann
  • Heribert Insam
Original Article


A microarray spotted with 369 different 16S rRNA gene probes specific to microorganisms involved in the degradation process of organic waste during composting was developed. The microarray was tested with pure cultures, and of the 30,258 individual probe-target hybridization reactions performed, there were only 188 false positive (0.62%) and 22 false negative signals (0.07%). Labeled target DNA was prepared by polymerase chain reaction amplification of 16S rRNA genes using a Cy5-labeled universal bacterial forward primer and a universal reverse primer. The COMPOCHIP microarray was applied to three different compost types (green compost, manure mix compost, and anaerobic digestate compost) of different maturity (2, 8, and 16 weeks), and differences in the microorganisms in the three compost types and maturity stages were observed. Multivariate analysis showed that the bacterial composition of the three composts was different at the beginning of the composting process and became more similar upon maturation. Certain probes (targeting Sphingobacterium, Actinomyces, Xylella/Xanthomonas/Stenotrophomonas, Microbacterium, Verrucomicrobia, Planctomycetes, Low G + C and Alphaproteobacteria) were more influential in discriminating between different composts. Results from denaturing gradient gel electrophoresis supported those of microarray analysis. This study showed that the COMPOCHIP array is a suitable tool to study bacterial communities in composts.

Supplementary material

248_2008_9435_MOESM1_ESM.doc (860 kb)
ESM Table 1List of oligonucleotide probes and target organisms included on the microarray (DOC 859 KB)


  1. 1.
    Alfreider A, Peters S, Tebbe CC, Rangger A, Insam H (2002) Microbial community dynamics during composting of organic matter as determined by 16S ribosomal DNA analysis. Compost Sci Util 10:303–312Google Scholar
  2. 2.
    Alm EW, Oerther DB, Larsen N, Stahl DA, Raskin L (1996) The oligonucleotide probe database. Appl Environ Microbiol 62:3557–3559PubMedGoogle Scholar
  3. 3.
    Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1991) Basic local alignment search tool. J Mol Bio 215:403–410Google Scholar
  4. 4.
    Amann R, Binder BJ, Olson RJ, Chisholm SW, Devereux R, Stahl DA (1990) Combination of 16S rRNA-targeted oligonucleotide probes with flow cytometry for analyzing mixed microbial populations. Appl Environ Microbiol 56:1919–1925PubMedGoogle Scholar
  5. 5.
    Barrett DM, Flaigel DO, Metz DC, Montone K, Furth EE (1997) In situ hybridization for Helicobacter pylori in gastric mucosal biopsy specimens: quantitative evaluation of test performance in comparison with the CLOtest and thiazine stain. J Clin Lab Anal 11:374–379PubMedCrossRefGoogle Scholar
  6. 6.
    Beffa T, Blanc M, Lyon P-F, Vogt G, Marchiani M, Lott Fischer J, Aragno M (1996) Isolation of Thermus strains from hot composts (60 to 80 °C). Appl Environ Microbiol 62:1723–1727PubMedGoogle Scholar
  7. 7.
    Blanc M, Marilley L, Beffa T, Aragno M (1999) Thermophilic bacterial communities in hot composts as revealed by most probable number counts and molecular (16S rDNA) methods. FEMS Microbiol Ecol 28:141–149CrossRefGoogle Scholar
  8. 8.
    Bodrossy L, Sessitsch A (2004) Oligonucleotide microarrays in microbial diagnostics. Curr Opin Microbiol 7:246–255CrossRefGoogle Scholar
  9. 9.
    Bodrossy L, Stralis-Pavese N, Murrell JC, Radajewski S, Weilharter A, Sessitsch A (2003) Development and validation of a diagnostic microbial microarray for methanotrophs. Environ Microbiol 5:566–582PubMedCrossRefGoogle Scholar
  10. 10.
    Breslauer KJ, Frank R, Blocker H, Marky LA (1986) Predicting DNA duplex stability from the base sequence. Proc Natl Acad Sci USA 83:3746–3750PubMedCrossRefGoogle Scholar
  11. 11.
    Buchholz-Cleven BEE, Rattunde B, Straub KL (1997) Screening for genetic diversity of isolates of anaerobic Fe(II)-oxidizing bacteria using DGGE and whole-cell hybridization. Syst Appl Microbiol 20:301–309Google Scholar
  12. 12.
    Daims H, Brühl A, Amann R, Schleiffer K-H, Wagner M (1999) The domain-specific probe EUB338 is insufficient for the detection of all Bacteria: development and evaluation of a more comprehensive probe set. Syst Appl Microbiol 22:434–444PubMedGoogle Scholar
  13. 13.
    Danon M, Franke-Whittle I, Insam H, Chen Y, Hadar Y (2008) Molecular analysis of bacterial community succession during prolonged compost curing. FEMS Microbiol Ecol 65:133–144PubMedCrossRefGoogle Scholar
  14. 14.
    Dees PM, Ghiorse WC (2001) Microbial diversity in hot synthetic compost as revealed by PCR-amplified rRNA sequences from cultivated isolates and extracted DNA. FEMS Microbiol Ecol 35:207–216PubMedCrossRefGoogle Scholar
  15. 15.
    Dionisi HM, Harms G, Layton AC, Gregory IR, Parker J, Hawkins SA, Robinson KG, Sayler GS (2003) Power analysis for real-time PCR quantification of genes in activated sludge and analysis of the variability introduced by DNA extraction. Appl Environ Microbiol 69:6597–6604PubMedCrossRefGoogle Scholar
  16. 16.
    Elorrieta MA, Suarez-Estrella F, Lopez MJ, Vargas-Garcia MC, Moreno J (2003) Survival of phytopathogenic bacteria during waste composting. Agric Ecosyst Environ 96:141–146Google Scholar
  17. 17.
    Eyers L, Stenuit B, El Fantroussi S, Agathos SN (2003) Microbial Ecology of TNT-contaminated soils and anaerobic TNT biodegradation processes. In: Proceedings of the 103rd general meeting of the American Society for Microbiology, Washington DCGoogle Scholar
  18. 18.
    Franke-Whittle IH, Klammer SH, Insam H (2005) Design and application of an oligonucleotide microarray for the investigation of compost microbial communities. J Microbiol Meth 62:37–56CrossRefGoogle Scholar
  19. 19.
    Franke-Whittle IH, Klammer SH, Mayrhofer S, Insam H (2006) Comparison of different methods for the production of labeled target DNA for microarray hybridization. J Microbiol Meth 65:117–126CrossRefGoogle Scholar
  20. 20.
    Fuchs JG (2002) Practical use of quality compost for plant health and vitality improvement. In: Insam H, Riddech N, Klammer S (eds) Microbiology of composting. Springer-Verlag, Berlin, pp 435–444Google Scholar
  21. 21.
    Guschin D, Mobarry B, Proudnikov D, Stahl D, Rittmann B, Mirzabekov A (1997) Oligonucleotide microchips as genosensors for determinative and environmental studies in microbiology. Appl Environ Microbiol 63:2397–2402PubMedGoogle Scholar
  22. 22.
    Haruta S, Kondo M, Nakamura K, Chanchitpricha C, Aiba H, Ishii M, Igarashi Y (2004) Succession of a microbial community during stable operation of a semi-continuous garbage-decomposing system. J Biosci Bioeng 98:20–27PubMedGoogle Scholar
  23. 23.
    Hogardt M, Trebesius K, Geiger AM, Hornef M, Rosenecker J, Heesemann J (2000) Specific and rapid detection by fluorescent in situ hybridisation of bacteria in clinical samples obtained from cystic fibrosis patients. J Clin Microbiol 38:818–825PubMedGoogle Scholar
  24. 24.
    Hoitink HAJ, Boehm MJ (1999) Biocontrol within the context of soil microbial communities: A substrate-dependent phenomenon. Annu Rev Phytopath 37:427–446CrossRefGoogle Scholar
  25. 25.
    Hoitink HAJ, Fahy PC (1986) Basis for the control of soilborne plant pathogens with composts. Annu Rev Phytopath 24:93–114CrossRefGoogle Scholar
  26. 26.
    Hoitink HAJ, Stone AG, Han DY (1997) Suppression of plant diseases by compost. HortScience 32:184–187Google Scholar
  27. 27.
    Kim K-H, Ten LN, Liu Q-M, Im W-T, Lee S-T (2006) Sphingobacterium daejeonense sp. nov., isolated from a compost sample. Int J Syst Evol Microbiol 56:2031–2036PubMedCrossRefGoogle Scholar
  28. 28.
    Koizumi Y, Kelly JJ, Nakagawa T, Urakawa H, El-Fantroussi S, Al-Muzaini S, Fukui M, Urushigawa Y, Stahl DA (2002) Parallel characterization of anaerobic toluene- and ethylbenzene-degrading microbial consortia by PCR-denaturing gradient gel electrophoresis, RNA-DNA membrane hybridization, and DNA microarray technology. Appl Environ Microbiol 68:3215–3225PubMedCrossRefGoogle Scholar
  29. 29.
    Lee D-Y, Shannon K, Beaudette LA (2006) Detection of bacterial pathogens in municipal wastewater using an oligonucleotide microarray and real-time quantitative PCR. J Microbiol Meth 65:453–467CrossRefGoogle Scholar
  30. 30.
    Legendre P, Legendre L (1998) Numerical ecology. Elsevier Science BV, AmsterdamGoogle Scholar
  31. 31.
    Liu W-T, Mirzabekov AD, Stahl DA (2001) Optimization of an oligonucleotide microchip for microbial identification studies: a non-equilibrium dissociation approach. Environ Microbiol 3:619–629PubMedCrossRefGoogle Scholar
  32. 32.
    Loy A, Horn M, Wagner M (2003) ProbeBase: an online resource for rRNA-targeted oligonucleotide probes. Nucleic Acids Res 31:514–516PubMedCrossRefGoogle Scholar
  33. 33.
    Loy A, Lehner A, Lee N, Adamczyk J, Meier H, Ernst J, Schleifer K-H, Wagner M (2002) Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment. Appl Environ Microbiol 68:5064–5081PubMedCrossRefGoogle Scholar
  34. 34.
    Ludwig L, Strunk O, Westram R, Richter L, Meier H, Yadhukumar A, Buchner A, Lai T, Steppi S, Jobb G, Foerster W, Brettske I, Gerber S, Ginhart AW, Gross O, Grumann S, Hermann S, Jost R, Koenig A, Liss T, Lussmann R, May M, Nonhoff B, Reichel B, Strehlow R, Stamatakis A, Stuckmann N, Vilbig A, Lenke M, Ludwig T, Bode A, Schleifer K-H (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32:1363–1371PubMedCrossRefGoogle Scholar
  35. 35.
    Muyzer G, de Waal EC, Uitterlinden AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analyses of polymerase chain reaction-amplified genes for 16S rRNA. Appl Environ Microbiol 59:695–700PubMedGoogle Scholar
  36. 36.
    Nakasaki K, Hiraoka S, Nagata H (1998) A new operation for producing disease-suppressive compost from grass clippings. Appl Environ Microbiol 64:4015–4020PubMedGoogle Scholar
  37. 37.
    Peplies J, Glockner FO, Amann R (2003) Optimization strategies for DNA microarray-based detection of bacteria with 16S rRNA-targeting oligonucleotide probes. Appl Environ Microbiol 69:1397–1407PubMedCrossRefGoogle Scholar
  38. 38.
    Ryckeboer J, Mergaert J, Vaes K, Klammer S, De Clercq D, Coosemans J, Insam H, Swings J (2003) A survey of bacteria and fungi occurring during composting and self-heating processes. Ann Microbiol 53:349–410Google Scholar
  39. 39.
    Sanguin H, Herrera A, Oger-Desfeux C, Dechesne A, Simonet P, Navarro E, Vogel T, Moenne-Loccoz Y, Xavier N, Grundmann GL (2006) Development and validation of a prototype 16S rRNA-based taxonomic microarray for Alphaproteobacteria. Environ Microbiol 8:289–307PubMedCrossRefGoogle Scholar
  40. 40.
    Schloss P, Hay AG, Wilson DB, Gossett JM, Walker LP (2005) Quantifying bacterial population dynamics in compost using 16S rRNA gene probes. Appl Microbiol Biotechnol 66:457–463PubMedCrossRefGoogle Scholar
  41. 41.
    Schwieger F, Tebbe CC (1998) A new approach to utilize PCR-single-strand conformation polymorphism for 16S rRNA gene-based microbial community analysis. Appl Environ Microbiol 64:4870–4876PubMedGoogle Scholar
  42. 42.
    Stahl DA, Amann R (1991) Development and application of nucleic acid probes in bacterial systematics. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. John Wiley, Sons, Chichester, England, pp 205–248Google Scholar
  43. 43.
    Stralis-Pavese N, Sessitsch A, Weilharter A, Reichenauer T, Riesing J, Csontos J, Murrell JC, Bodrossy L (2004) Optimization of diagnostic microarray for application in analysing landfill methanotroph communities under different plant covers. Environ Microbiol 6:347–363PubMedCrossRefGoogle Scholar
  44. 44.
    Suzuki MT, Giovannoni SJ (1996) Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol 62:625–630PubMedGoogle Scholar
  45. 45.
    Taroncher-Oldenburg G, Griner EM, Francis CA, Ward BB (2003) Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment. Appl Environ Microbiol 69:1159–1171PubMedCrossRefGoogle Scholar
  46. 46.
    ter Braak CJF, Šmilauer P (2002) CANOCO Reference Manual and CanoDraw for Windows User’s Guide: Software for Canonical Community Ordination (version 4.5). Microcomputer Power, IthacaGoogle Scholar
  47. 47.
    Tiquia SM (2005) Microbial community dynamics in manure composts based on 16S and 18S RDNA T-RFLP profiles. Environ Technol 26:1101–1113PubMedCrossRefGoogle Scholar
  48. 48.
    Tiquia SM, Wu L, Chong SC, Passovets S, Xu D, Xu Y, Zhou J (2004) Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples. Biotechniques 36:664–675PubMedGoogle Scholar
  49. 49.
    Urakawa H, Noble PA, El Fantroussi S, Kelly JJ, Stahl DA (2002) Single-base-pair discrimination of terminal mismatches by using oligonucleotide microarrays and neural network analyses. Appl Environ Microbiol 68:235–244PubMedCrossRefGoogle Scholar
  50. 50.
    Varani G (1995) Exceptionally stable nucleic acid hairpins. Annu Rev Biophys Biomol Struct 24:379–404PubMedCrossRefGoogle Scholar
  51. 51.
    von Wintzingerode F, Gobel UB, Stackebrandt E (1997) Determination of microbial diversity in environmental samples: Pitfalls of PCR-based rRNA analysis. FEMS Microbiol Rev 21:213–229CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2008

Authors and Affiliations

  • Ingrid H. Franke-Whittle
    • 1
  • Brigitte A. Knapp
    • 1
  • Jacques Fuchs
    • 2
  • Ruediger Kaufmann
    • 3
  • Heribert Insam
    • 1
  1. 1.Institute of MicrobiologyLeopold-Franzens-UniversitätInnsbruckAustria
  2. 2.Forschungsinstitut für Biologischen Landbau (FIBL)FrickSwitzerland
  3. 3.Institute for EcologyLeopold-Franzens-UniversitätInnsbruckAustria

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