## 1 Introduction  
Biomass, such as activated sludge, biofilm, or digestate from anaerobic digesters, is considered to be a potential source of many valuable chemicals. However, ultimate success in obtaining valuable substances depends not only on the type of biomass and its content but also on the microorganisms engaged in its conversion. Therefore, gaining knowledge about microorganisms in biomass would be helpful in steering the metabolic processes towards efficient synthesis of valuable chemicals. Usually, the processes leading to the synthesis of valuable chemicals are not conducted by single strains of microorganisms, but by specialized microbial communities. Identification and characterization of the members of these communities is important, not only to understand the processes, but also to make it possible to construct synthetic microbial communities in the future [1]. Unfortunately, most microorganisms cannot be cultivated in laboratory conditions, but can only be identified by direct DNA analysis. Usually, the first stage of this approach is the extraction of metagenomic DNA, the efficiency of which affects the success of the entire analysis [2]. To ensure that the metagenomic DNA that is obtained will be representative of most of the microorganisms that inhabit the analyzed sample, the method of DNA extraction must be properly chosen and executed. The available methods should be examined for each habitat prior to beginning full-scale studies [3, 4]. Most investigators use commercial kits for extracting and purifyingnucleic acids for metagenomic analysis of samples from wastewater treatment plants. These DNA isolation kits have been successfully applied to study environmental samples, as well as samples from activated sludge and anaerobic digesters [5; 6]. Importantly, however, the microbial communities in soils, activated sludge, and anaerobic digesters differ in terms of their bacterial community compositions [7]. Moreover, wastewater habitats are not only heterogeneous in nature, but they tend to change over time, which could affect the performance of DNA isolation [3]. Despite these facts, extraction kits which proved suitable for one habitat are oftentimes used for other habitats without further validation [4]. However, to determine the diversity of wastewater communities, extraction methods must be appropriately selected and optimized for each individual habitat. DNA yield, purity, and bacterial diversity assessments vary depending on the DNA extraction methodology that is used [8; 9; 10; 11]. The method of DNA extraction chosen for an experiment should yield the highest possible number of OTUs (operational taxonomic units), while not excluding the detection of any taxonomic groups [4]. Such a method should provide high yield and purity and generate the most complete description possible of a community's diversity [4]. However, a difficulty lies in the fact that wastewater plants are designed to maximize nutrient recovery, which is accomplished by forcing communities to live closely together, for example, embedded in a self-produced matrix of extracellular polymeric substances (EPS). Because EPS contain considerable amounts of proteins, polysaccharides, lipids, and humic substances, which can strongly affect the purity and yield of extracted DNA, it can be difficult to obtain quality results with wastewater microorganisms. This is unfortunate because the purity of DNA is especially important for subsequent metagenomic procedures. Downstream procedures such as DNA amplification using polymerase chain reaction or preparation of DNA libraries are susceptible to contamination, which should be avoided or minimized [4]. ARISA has been widely used in metagenomic analysis and gives reproducible estimates of a bacterial community's diversity [12]. ARISA provides estimates of microbial richness and diversity based on the length heterogeneity of the 16S-23S internal transcribed spacer region (RIS) of bacterial rRNA [13; 14].