We observed similar rapid changes in the fungal

communities [22]. Estimations for real diversity of bacteria Estimations of coverage ranged between 15% and 67%, and all estimation models, the ACE model, Chao model and Simpson’s reciprocal index and diversity index, gave fairly similar results (Table 2). This suggests that they all give comparable and equally reliable approximations [33–35]. It can be argued that estimation models based on PCR NVP-HSP990 solubility dmso results are unreliable – some sequences are over-represented or that major OTUs mask the presence of minor OTUs. On the other hand PCR itself can favour one sequence over another [53]. However, although high amounts of sequences representing Lactobacillus spp. were observed in some samples, the method still revealed a high total diversity in the same samples. This study demonstrated that minor bacterial species could be amplified and cloned. Furthermore, the proportions of different bacteria were similar in comparison to results from earlier reports using other methods [5, 6, 8]. We can conclude that the bacterial community composition and the physical and chemical conditions in the composting mass were related. This observation is neither new nor surprising but to our knowledge, the bacterial

diversity present during the active phase of composting has not been NU7026 in vitro studied in such detail. The approach used here enabled us to include all the major phylotypes, as well as a wide range buy VX-661 of less abundant phylotypes in the comparison of microbial communities present during

composting. As a result, many phylotypes without reference sequences were found. oxyclozanide Amplification and cloning of ribosomal genes using universal bacterial primers does bring its own inherent biases, but these are likely to be much smaller than with other methods used in the past, particularly when over 1500 individual fragments have been sequenced. Conclusions Diagnosing a composting facility by microbial community structure analysis can be done, but with the approach used here, it becomes very expensive and time consuming. Rapid and relatively simple methods based on quantitative PCR or DNA micro-arrays may, however, become feasible in the near future. The utility of the comparison made in this study has been demonstrated after finishing the empirical phase of the study. Namely, by adjusting the conditions at the full-scale composting facility to mimic those of the pilot scale unit, the performance of the Kiertokapula composting plant has improved remarkably (data not shown). The main adjustments made were: (i) increasing the proportion of wood chips used as the matrix material (effect on bulk density), (ii) monitoring and adjusting the pH using wood ash, (iii) improving the internal aeration of the composting mass. The environmental burden in the form of noxious odours has disappeared, and no complaints from residents in the area have been received since early 2007.