MOLECULAR ECOLOGY OF MICROBES - A REVIEW OF PROMISES, PITFALLS AND TRUE PROGRESS

Ecosystems, including engineered ones, are complex systems in which mi croorganisms occur in heterogenous communities. Their behaviour in the environment is often unknown due to the lack of proper detection and identification techniques. Molecular ecology is a new field in which m icrobes can be recognized and their function can be understood at the DNA/RNA level without unreliable steps of cultivation of microbes. Dur ing the last few years genetically modified microbes have been constru cted by recombinant DNA techniques for putative use in the environment . The slow progress in this field is due to the lack of integration of microbial ecology and molecular biology. In the present review, examp les will be given of the use of DNA probes and marker genes in our stu dy on the ecology of genetically modified microbes and wild-type recal citrant microorganisms that are difficult to cultivate or even 'non-cu lturable'. Emphasis is given to the development and use of oligonucreo tide probes directed towards 16S rRNA, to detect microbes in various e ngineered ecosystems: (i) Frankia in root nodules, and (ii) propionate -oxidizing sulfate-reducing bacteria in anaerobic granular sludge. Exp ression of genes is demonstrated by studies on the localization of nif H transcripts in root nodules of Coriaria and Alnus. In addition we wi ll describe examples of the use of marker genes(gusA gene and aphV gen e) to study competition and genetic stability of released engineered R hizobium and Streptomyces strains.