Abstract
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.
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Acknowledgments
The authors would like to thank Michael Rudnicki and his laboratory at the Department of Nephrology, Medical University of Innsbruck for the use of the Microarray scanning equipment. Thanks also go to Alice Wallner, Austrian Agency for Health and Food Safety, AGES, for providing bacterial strains and to Thomas Kupper and Rahel Brändli (Ecole Polytechnique Fédérale from Lausanne, EPFL, Switzerland) for their collection of compost samples. The critical reviewing of the manuscript by Marta Goberna is also acknowledged. The project was funded by the Fonds zur Förderung der wissenschaftlichen Forschung (FWF) Austria, P-15694, and by the Tiroler Wissenschaftsfonds.
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List of oligonucleotide probes and target organisms included on the microarray (DOC 859 KB)
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Franke-Whittle, I.H., Knapp, B.A., Fuchs, J. et al. Application of COMPOCHIP Microarray to Investigate the Bacterial Communities of Different Composts. Microb Ecol 57, 510–521 (2009). https://doi.org/10.1007/s00248-008-9435-2
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DOI: https://doi.org/10.1007/s00248-008-9435-2