The impact of the process parameters hydraulic retention time (HRT), organic loading rate (OLR) and substrate upon bacterial diversity was analyzed. Therefore, a controlled anaerobic fermentation (1755 days) of beet silage, only initially inoculated with manure, was monitored by the amplified "ribosomal DNA" restriction analysis. More than 85% of detected operational taxonomic units (OTUs) could not be assigned to described Bacteria. In contrast to studies analyzing the digestion of energy crops in the presence of manure, Chloroflexi were detected, whereas Clostridia and Chloroflexi were identified as persistent groups. Both groups are known as potential hydrogen producers or users. Species distribution patterns for Firmicutes, Bacteroidetes, Synergistetes and Thermotogae were not clearly linked to process parameters. The presence of Planctomycetes, Actinobacteria and Alcaligenaceae was related to long HRTs and short OLRs, while Acidobacteria were governed by short HRTs and high OLRs, respectively. The impact of substrate variations on diversity was minute. (C) 2011 Elsevier Ltd. All rights reserved.