Formerly, liquid cultivation of microorganisms was performed either by shaking flasks or fermenter containing nutrient rich medium. This method is useful for growing cells rapidly and high production of many bio-products. However, microoganisms in nature often attach to some solid surfaces and form biofilms. Biofilms are three dimensionally ordered structure containing microbial cells and extracellular polymeric matrices [Rev2](Fig. 1). Biofilms benefit the member cells to survive in harsh conditions mainly by specific gene expression and leading cells into dormant stage [95]. Aerobic microbes often form pellicles, floating biofilms, on the surface of liquid medium. We found that Bacillus subtilis forms pellicles using flagella for the binding of cells [76](Fig. 2, 3). Most unique biofilm dependent gene expression is under the control of quorum sensing systems. This system is initiated by accumulation of quorum sensing signal molecules that are almost constantly secreted by microbial cells. It is interesting that Gram-negative bacteria often use acyl homoserine lactones as signals while Gram-positive bacteria often use small peptides. There are cross talks between different microbial families and genera. Recently, a flanone compound containing boron was found commonly used in Gram-positive and Gram-negative bacteria. Several toxins and enzymes are produced in biofilm dependent manners [87]. A group of microbial cells gain a hundred to thousand times higher tolerance to antibiotics. Thus, elimination of harmful microbial biofilms is important issue to keep good health condition of the host living organisms including human body. However, our research interest is the beneficial biofilm formation by non-pathogenic bacteria and archaea. We believe that studying beneficial biofilms should contribute to develop novel environmental biotechnology [92, 95, 100].

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