## 1 Introduction  
The extraction of sucrose from sugar beets takes place in several steps. In Austrian plants, a combination of a countercurrent mixer and an extraction tower is employed. First, sugar beets are sliced into cossettes, which are treated in a solid-liquid extraction process using the countercurrent principle to extract sucrose (Figure 1). In this area of the tower extraction system, the temperatures vary from 20 \({}^{\circ}\)C in raw juice to 72 \({}^{\circ}\)C in the tower end of the countercurrent mixer. In the next step, juice purification, temperatures of over 90 \({}^{\circ}\)C and pH values of up to 12 are necessary to reduce non-sugars and to stabilize the juice. Then, water from the so-called thin juice is evaporated, and the resulting thick juice is used to crystallize white sugar in a multistage crystallization process [1]. Due to the conditions of high pH values and high temperatures in these processing steps, the growth of microorganisms was not considered to be of any technological relevance for a long time. This assumption changed in 1930 with the observation of microorganisms influencing the storage of beets [2]. In addition to technological challenges, microorganisms can cause financial losses due to sucrose losses, as sucrose may be metabolized into different microbiological metabolites. The total sucrose losses caused by microorganisms are calculated to range between 0.02% and 0.66% of processed beets [3, 4]. Since 1930, various methods have been employed to determine the microbiota present during sugar beet production to obtain a better understanding of the process and to limit microbial activity. For example, a large set of different antimicrobialagents have been applied to combat microorganisms in different processing steps. Most investigations have been carried out using culture-based methods [5; 6; 7; 8]. These methods are limited because many species are difficult to culture or are even not culturable due to special growth requirements. Furthermore, culture-based methods require preselection of media and cultivation conditions [9]; this preselection of incubation conditions may subsequently influence the identification of microorganisms, which is undesired. Characterizing the whole bacterial community and its diversity is therefore quite difficult. This difficulty led to the use of molecular-based methods mostly based on DNA analysis that are more sensitive, more accurate and more specific and may even be faster [10]. Despite this progress, microscopic or cultural methods are most often used to identify microorganisms. Some methods, which have also been applied in the sugar industry, combine culture-based methods with molecular biological methods, such as 16S rDNA sequencing or Matrix Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS), to identify isolates [11; 12; 13]. The advantages of these combined molecular biological methods include identifying microorganisms with greater sensitivity and accuracy. However, these methods still have the disadvantage of requiring pure cultures. Further applicable culture-independent methods could include real-time polymerase chain reaction (PCR) or specific microscopic techniques such as transmission electron microscopy (TEM) or scanning electron microscopy (SEM) [10]. Detecting and characterizing all occurring microorganisms in one sample is very challenging and almost impossible with the methods mentioned above, as the interactions between microorganisms may interfere with the detectability of the microbiota. A possible time and cost saving solution for characterizing a complex bacterial community is utilizing high-throughput sequencing techniques. These techniques provide qualitative and semi-quantitative data about the composition of the bacterial community. Flow cytometric analyses can help to normalize these data and additionally provide information about the physiological state of the microorganisms.