Methanogenic population dynamics during semi‐continuous biogas fermentation and acidification by overloading

Aims: This study was to investigate the methanogenic community in a biogas reactor from start‐up to acidification conditions. Furthermore, reliability and accuracy of the applied quantitative real‐time PCR method (Q‐PCR) was briefly evaluated. Methods and Results: A mesophilic (37°C), maize silage fed, continuously stirred tank reactor was surveyed. It was operated semi‐continuously with increasing daily organic loading rates (OLRs) to reach acidification. Gas production and organic acid composition were measured. Methanogenic community structure was determined by 16S rDNA‐based Q‐PCR to estimate the abundance of key methanogenic micro‐organisms. 16S rDNA of hydrogenotrophic Methanobacteriales was most abundant at OLRs of ≥3·7 g dry organic matter (DOM) l^?1 day^?1. By contrast, that of aceticlastic Methanosaetaceae predominated at lower OLRs but disappeared at OLRs of ≥4·1 g DOM l^?1 day^?1. At the same OLR, the propionate concentration increased dramatically indicating the acidification of the digester. Application of internal standards to examine Q‐PCR’s accuracy revealed that the detected amount of 16S rDNA may vary within one log cycle. Conclusions: These results suggest that the absence of Methanosaetaceae might be taken as biological indicator for process’ instability. Inhibitory effects on Q‐PCR analyses could not be determined based on the spiking experiments. Significance and Impact of the Study: In this study, reactors’ microbiology was observed over time using Q‐PCR. Insights into the abundance of different methanogens might be used to improve the performance of biogas reactors.