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

Franke-Whittle, Ingrid H.; Knapp, Brigitte A.; Fuchs, Jacques; Kaufmann, Ruediger and Insam, Heribert (2009) Application of COMPOCHIP Microarray to Investigate the Bacterial Communities of Different Composts. Microbial Ecology, 57 (3), pp. 510-521.

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Online at: http://www.springerlink.com/content/n23016v15456l11p/

Summary

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.


EPrint Type:Journal paper
Keywords:COMPOCHIP microarray, bacterial communities, composts, Bodenwissenschaften, Bodenfruchtbarkeit, Kompost, Phytopathologie, Interaktion Boden-Pflanzenkrankheiten, Kompostqualität, BUWAL
Subjects: Crop husbandry > Composting and manuring
Research affiliation: Switzerland > FiBL - Research Institute of Organic Agriculture Switzerland > Soil Sciences
Switzerland > FiBL - Research Institute of Organic Agriculture Switzerland > Entomolgy
Austria > Other organizations
DOI:DOI 10.1007/s00248-008-9435-2
Related Links:http://www.ncbi.nlm.nih.gov/pubmed/18818861
Deposited By: Fuchs, Dr. Jacques G.
ID Code:18014
Deposited On:14 Nov 2010 19:23
Last Modified:10 Dec 2010 11:17
Document Language:English
Status:Published
Refereed:Peer-reviewed and accepted

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