Publication Details

Category Text Publication
Reference Category Journals
DOI 10.1186/s12934-017-0793-7
Title (Primary) Flow cytometric quantification, sorting and sequencing of methanogenic archaea based on F420 autofluorescence
Author Lambrecht, J.; Cichocki, N.; Hübschmann, T.; Koch, C.; Harms, H.; Müller, S.
Source Titel Microbial Cell Factories
Year 2017
Department UMB
Volume 16
Page From art. 180
Language englisch
Keywords Single cell analytics; F420 AutofluorescenceMethanogenic archaeaAnaerobic digestionBiogas16S rDNA sequencingProcess monitoring
UFZ wide themes RU4;


The widely established production of CH4 from renewable biomass in industrial scale anaerobic reactors may play a major role in the future energy supply. It relies on methanogenic archaea as key organisms which represent the bottleneck in the process. The quantitative analysis of these organisms can help to maximize process performance, uncover disturbances before failure, and may ultimately lead to community-based process control schemes. Existing qPCR and fluorescence microscopy-based methods are very attractive but can be cost-intensive and laborious.


In this study we present an autofluorescence-based, flow cytometric method for the fast low-cost quantification of methanogenic archaea in complex microbial communities and crude substrates. The method was applied to a methanogenic enrichment culture (MEC) and digester samples (DS). The methanogenic archaea were quantified using the distinct fluorescence of their cofactor F420 in a range from 3.7 × 108 (± 3.3 × 106) cells mL−1 and 1.8 x 109 (± 1.1 × 108) cells mL−1. We evaluated different fixation methods and tested the sample stability. Stable abundance and fluorescence intensity were recorded up to 26 days during aerobic storage in PBS at 6 °C. The discrimination of the whole microbial community from the ubiquitous particle noise was facilitated by SYBR Green I staining and enabled calculation of relative abundances of methanogenic archaea of up to 9.64 ± 0.23% in the MEC and up to 4.43 ± 0.74% in the DS. The metaprofiling of the mcrA gene reinforced the results.


The presented method allows for fast and reliable quantification of methanogenic archaea in microbial communities under authentic digester conditions and can thus be useful for process monitoring and control in biogas digesters.

Persistent UFZ Identifier
Lambrecht, J., Cichocki, N., Hübschmann, T., Koch, C., Harms, H., Müller, S. (2017):
Flow cytometric quantification, sorting and sequencing of methanogenic archaea based on F420 autofluorescence
Microb. Cell. Fact. 16 , art. 180 10.1186/s12934-017-0793-7