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Open Access Research article

Molecular analysis of meso- and thermophilic microbiota associated with anaerobic biowaste degradation

Jarmo Ritari1*, Kaisa Koskinen1, Jenni Hultman14, Jukka M Kurola2, Maritta Kymäläinen3, Martin Romantschuk2, Lars Paulin1 and Petri Auvinen1

Author Affiliations

1 Institute of Biotechnology, University of Helsinki, Viikinkaari 4, 00790, Helsinki, Finland

2 Department of Environmental Sciences, University of Helsinki, Niemenkatu 73 C, 15140, Lahti, Finland

3 HAMK University of Applied Sciences, P.O.Box 230, 13101, Hämeenlinna, Finland

4 Current address: Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Agnes Sjöbergin katu 2, 00790, Helsinki, Finland

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BMC Microbiology 2012, 12:121  doi:10.1186/1471-2180-12-121

Published: 22 June 2012



Microbial anaerobic digestion (AD) is used as a waste treatment process to degrade complex organic compounds into methane. The archaeal and bacterial taxa involved in AD are well known, whereas composition of the fungal community in the process has been less studied. The present study aimed to reveal the composition of archaeal, bacterial and fungal communities in response to increasing organic loading in mesophilic and thermophilic AD processes by applying 454 amplicon sequencing technology. Furthermore, a DNA microarray method was evaluated in order to develop a tool for monitoring the microbiological status of AD.


The 454 sequencing showed that the diversity and number of bacterial taxa decreased with increasing organic load, while archaeal i.e. methanogenic taxa remained more constant. The number and diversity of fungal taxa increased during the process and varied less in composition with process temperature than bacterial and archaeal taxa, even though the fungal diversity increased with temperature as well. Evaluation of the microarray using AD sample DNA showed correlation of signal intensities with sequence read numbers of corresponding target groups. The sensitivity of the test was found to be about 1%.


The fungal community survives in anoxic conditions and grows with increasing organic loading, suggesting that Fungi may contribute to the digestion by metabolising organic nutrients for bacterial and methanogenic groups. The microarray proof of principle tests suggest that the method has the potential for semiquantitative detection of target microbial groups given that comprehensive sequence data is available for probe design.