Review The microbiology and biochemistry of anaerobic bioreactors with relevance to domestic sewage treatment Vincent O’Flaherty*, Gavin Collins & The´re`se Mahony Microbial Ecology Laboratory, Department of Microbiology and Environmental Change Institute, National University of Ireland, Galway, Ireland (*author for correspondence: e-mail: vincent.oflaherty@nuigalway.ie; phone: +353-91-493734; fax: +353-91-525700) Key words: anaerobic digestion, domestic sewage, EGSB, Fluorescent in situ hybridisation, granular sludge, methanogenesis, methanogenic activity, PCR, psychrophilic, TRFLP, UASB, 16S rRNA Abstract Anaerobic granular and fixed-film reactors have been successfully operated for wastewater treatment at full scale for over two decades and represent a sustainable, energy-producing approach, which is increasingly being directed towards treatment of domestic sewage. Research over the past two decades, and significant operational experience, has demonstrated that there are no fundamental microbiological barriers to the implementation of AD for domestic sewage treatment in regions with warm and temperate climates. Despite this, the underlying microbiology of methanogenesis is not fully understood and novel groups of microbes have been identified in sludge, with unknown functions. The methanogenic process has recently been subject to systematic investigation using newly developed analytical and microbiological approaches. A combination of process monitoring, physiological, molecular microbiological and microscopic methods are beginning to generate a comprehensive, integrated data set at micro-organism, granule and reactor level and the current state of knowledge is reviewed here. Information on the formation of granules, on the relationship between reactor operating conditions and microbial consortia and on the impact of process changes on the microorganisms in reactors will, in future, enable the link between the processes occurring at microorganism level (scale ca. 1 lm–1 mm) and the processes occurring within reactors (scale >1 m), which will enhance the efficiency and applicability of anaerobic sewage treatment. 1. Introduction Despite the widespread harnessing of anaerobic digestion (AD) in engineered systems, knowledge gaps remain regarding the nature and function of the microbial populations involved in the process, including the mesophilic, sub-mesophilic or psy- chrophilic anaerobic digesters used for the treat- ment of domestic wastewaters (Lettinga et al. 2001; O’Flaherty & Lens 2003). Historically, knowledge gaps relating to the microbiology of AD have resulted in a lack of inte- gration of the fundamental processes occurring at microorganism level (scale ca. 1 lm–1 mm) into the processes occurring within bioreactors (scale >1 m). Anaerobic digesters are mostly operated as ‘‘black boxes’’, taking the effluent concentration as an output value that cannot be improved and the process control strategy, if applied at all, does not generally take into account processes occur- ring at microorganism level. The result is that reactors are mainly designed using empirical de- sign criteria, which can lead to over-dimensioning of reactor volumes and sub-optimal or unstable treatment, an important feature with respect to anaerobic treatment of domestic wastewater. In some cases, the principles of design and operation of reactors can be derived from, for example, Reviews in Environmental Science and Bio/Technology (2006) 5:39–55 Ó Springer 2006 DOI 10.1007/s11157-005-5478-8