**5. Biofilms**

Biofilms are surface attached structured bacterial communities that create a protective environment for bacterial cells [54]. Biofilm formation is a highly regulated process and is controlled by a number of environmental and genetic factors [55–57]. Biofilms are also induced by antimicrobial stress/SOS response. While biofilm formation is an integral part of the prokaryotic life cycle, biofilms also cause biofilm associated diseases that are difficult to treat, e.g. urinary tract infections (UTI), chronic infections in cystic fibrosis (CF) patients, colonization of medical devices and periodontal diseases [58].

A number of factors allow bacteria in biofilms to survive high dose antibiotic treatment [58, 59]. Antibiotic diffusion is prevented by a mechanical barrier formed by the extracellular matrix. Further, low oxygen and nutrient concentrations within biofilms create niches with low bacterial metabolic activity. In addtion, up to 1% of bacterial cells in biofilms may be dormant persister cells not affected by antimicrobials [60]. Furthermore, high cell density within biofilms enhances horizontal gene transfer and competition, that together with accumulation of metabolic products,

microaerobic areas and oxidative stress, incite DNA damage and provoke the SOS response. Starvation stress in biofilm bacteria was shown to increase the level of tolerance to the fluoroquinolone ofloxacin in *E. coli* biofilms and was dependent on the presence of a functional bacterial SOS response [59].

In biofilms, phenotypic variants e.g. small colony variants (SCV), that are slow growing and very tolerant to host defenses and antimicrobials have also been described. SCVs exhibit increased production of exopolysaccharides, can autoaggregate and attach stronly to surfaces [61–63]. They are potentially responsible for difficult to treat persistent infections, wherein bacteria persist in the host for prolonged periods of time despite antimicrobial therapy. Thus, recalcitrance of biofilms to antimicrobials can be due to tolerance, when dispersed biofilm cells exhibit antibiotic sensitivity and low MIC, as well as resistance, characterized by increased MICs and a resistant phenotype of dispersed biofilm bacteria. The SOS response plays a significant role in biofilm formation but in turn, in the dynamic biofilm environment, SOS inducing factors are generated that promote mutagenesis and diversification.
