In the fens of Ljubljana marsh we studied nitrogen and phosphorus mineralization/immobilization and potential denitrification in relation to soil organic matter (SOM) content, soil temperature and water and redox potential imposed by controlled water table levels. N and P losses from soil solution into ground water were also monitored. Results indicate that microbial biomass and activity (N, P mineralization, potential denitrification) are directly proportional to SOM content of differently degraded peat soils. P losses to ground water were also much higher in SOM rich soil, which can be attributed to low sorption capacity of peat soil for P. Soil water potential seldom limits microbial activity under natural conditions. Molecular population dynamics measurements of the genus Pseudomonas were performed for the first time in soil, food, intestine and faeces of the terrestrial isopode Porcellio scaber and found that number of these bacteria was reduced by 99% during passage through Porcellio scaber intestine. A joint study with dr. J. M.Tiedje, Michigan State University, USA, was conducted to elucidate the effects of standard agricultural management on the genetic heterogeneity of nitrous oxide reductase (nosZ) fragments from denitrifying prokaryotes and 16SrRNA genes of archaea and bacteria in native and cultivated soil. Molecular methods of cloning, sequencing and typing (T-RFLP) were used. Phylogenetic resolution was greatly enhanced by the use of multiple evolutionary models to resolve the consensus tree. The results show that there is a relationship between land use and richness, diversity, and phylogenetic position of nosZ sequences. Furthermore, these results indicate that agricultural use of soil caused a shift towards more diverse denitrifying community. In collaboration with dr. D. Dubnau's laboratory, PHRI, USA, regulation of genetic competence in Bacillus subtilis was studied. Using DNA microarrays representing approximately 95% of the protein coding ORFs in B. subtilis, the expression profiles of comK in various genetic background were determined. The results suggest that the ComK regulon defines a growth arrested state - "K-state", distinct from sporulation, of which competence for genetic transformation is only one of the ComK regulated processes. In addition, our structure-function analyses of MecA contributed significantly to the understanding of the MecA role as an adapter protein, targeting other proteins for regulated degradation. Using surface plasmon resonance it was determined that the N-terminal domain of MecA interacts with ComK and ComS and the C terminal domain with ClpC, stimulating its ATPase activity and thus degradation of ComK by the ClpCP protease. The MecA paralog, YpbH, was purified and shown that it acts as a regulator of genetic competence and sporulation in B. subtilis. Finally, the comQXP' loci of a set of natural Bacillus isolates were sequenced and a striking polymorphism that correlates with specific patterns of activation of the quorum sensing response was shown. The striking variability of this system might be important for the survival of these bacteria in nature as a sexual isolation mechanism to escape the inappropriate induction of competence by closely related strains. The impact of quality and quantity of bacteriophage host cells on latent period optimization was determined. A mathematical model for the simulation of spin labeled membrane proteins spectra was produced. A structural intermediates during bacteriophage M13 disassembly process was determined. In addition the impact of virus infection on host phosphorus and carbon metabolism was studied.