Eubacteria and archaea communities in seven mesophile anaerobic digester plants in Germany

Abstract

Background: Only a fraction of the microbial species used for anaerobic digestion in biogas production plants are methanogenic archaea. We have analyzed the taxonomic profiles of eubacteria and archaea, a set of chemical key parameters, and biogas production in samples from nine production plants in seven facilities in Thuringia, Germany, including co-digesters, leach-bed, and sewage sludge treatment plants. Reactors were sampled twice, at a 1-week interval, and three biological replicates were taken in each case.

Results: A complex taxonomic composition was found for both eubacteria and archaea, both of which strongly correlated with digester type. Plant-degrading Firmicutes as well as Bacteroidetes dominated eubacteria profiles in high biogas-producing co-digesters; whereas Bacteroidetes and Spirochaetes were the major phyla in leach-bed and sewage sludge digesters. Methanoculleus was the dominant archaea genus in co-digesters, whereas Methanosarcina and Methanosaeta were the most abundant methanogens in leachate from leach-bed and sewage sludge digesters, respectively.

Conclusions: This is one of the most comprehensive characterizations of the microbial communities of biogas-producing facilities. Bacterial profiles exhibited very low variation within replicates, including those of semi-solid samples; and, in general, low variation in time. However, facility type correlated closely with the bacterial profile: each of the three reactor types exhibited a characteristic eubacteria and archaea profile. Digesters operated with solid feedstock, and high biogas production correlated with abundance of plant degraders (Firmicutes) and biofilm-forming methanogens (Methanoculleus spp.). By contrast, low biogas-producing sewage sludge treatment digesters correlated with high titers of volatile fatty acid-adapted Methanosaeta spp.

Keywords: Anaerobic digesters; Archaea; Biogas; Eubacteria; Methanogens.

Fig. 1

Sampling of anaerobic digesters in Thuringia (Germany). Seven different facilities with a total of nine reactors were sampled in Schlossvippach, Weimar, Jena (two plants, one of them with three reactors), Schmölln, Rudolstadt, and Saalfeld. Sampling was repeated twice at a 1-week interval, and three replicates were processed (54 samples in total). CD three-stage plant, SS sewage plants, LB leach-bed reactors, S1 plug flow reactor, S2 continuous stirred tank reactor, S3 storage tank for digestion remnants

Fig. 2

3D plots of chemical parameters. COD, TOC, total nitrogen contents (N), conductivity, TVFA, TS, VS, pH, and produced volume of biogas are plotted in a 3D representation in which the permutation of all determined parameters define axis X, Y, and Z. The underlying biogas facilities are highlighted correspondingly (a). Plotting the parameters without the biogas yield and colorizing the dots according to their biogas production rate gives the second plot (b)

Fig. 3

Bacterial profiles of the anaerobic digester plants analyzed. Taxonomic (phylum) composition of eubacteria populations in the reactors as deduced by 16S amplicons isolated and sequenced as described in “Material and methods” section. a Three-stage co-digester (CD) plant in Jena, (b) leach-bed reactors, and (c) sewage plants. The grey scale (top right) corresponds to biogas yield ranges as shown at the right

Fig. 4

Taxonomic (genus) composition of archaea in the anaerobic digester plants. Taxonomic composition based on 16S archaea-specific amplicon sequences is shown. a The three-stage plant (CD) in Jena, (b) leach-bed reactors, and (c) sewage plants. The grey scale (top right) corresponds to biogas production values as in Fig. 2. Samples corresponding to the storage tank of the digestion remnants reactor (CD-Jena S3) are not shown as they failed to produce any amplicon with the selected oligonucleotides. Methanogenesis pathways are shown in (d) three stage plant, (e) leach-bed reactors, and (f) sewage plants