Microarrays for investigating compost microflora

Composting is used in one breath with environmentally sound and economic organic waste recy-cling. Albeit microbial activity is the major process for compost production and utilization, little is known about the involved microflora. Beyond traditional cultivation , we aim at the characterisation of compost microflora with a nucleic acid based approach employing 16S and 18S rDNA and rRNA for bacteria and fungi, respectively. The project will have three parts: (i) screening of available databases to preselect microorganisms for provisional test-chips; (ii) molecular and conventional isolation of genes and microorganisms of compost samples, sequencing of their rDNA and design of a prototype chip; and (iii) validation of the prototype with compost samples of different sources, and by spiking with known strains. Results of the community characterization shall be matched with conventional (chemical) and microbiological compost analyses.

Composting is a process of considerable economic importance used around the world for the recycling of organic waste materials. In many aspects, Austria is among the world leaders in compost technology and application of compost teand thus scientific advancement in this field may keep Austria ahead. The process requires the presence of many different microorganisms and as a result, both beneficial and pathogenic microorganisms can be found in compost samples. A better knowledge of the microbial communities present and active in the composting process and a simple detection tool for different microorganisms would allow the fine- tuning of production processes so as to obtain specific qualities for that compost, such as the absence of pathogens, the presence of beneficial microorganisms, or plant disease suppressiveness. In this study, we have developed a microarray that will allow in a single test the presence of different microorganisms in a particular compost sample to be determined. In particular, we are interested in the presence of pathogenic and potentially beneficial microorganisms in mature composts, and the microarray allows this information to be obtained. Microorganisms of interest were selected, probes designed, and hybridization methods developed. The microarray has been tested on samples of different composts, and has revealed the presence of the different microbial communities in the particular composts. This test offers considerable potential for the compost industry, as it will allow composters to determine the quality of the end product, in terms of its safety, as well allowing a fine-tuning of the composting process in order to produce a better compost end product.