Indicative Marker Microbiome Structures Deduced from the Taxonomic Inventory of 67 Full-Scale Anaerobic Digesters of 49 Agricultural Biogas Plants

Abstract

There are almost 9500 biogas plants in Germany, which are predominantly operated with energy crops and residues from livestock husbandry over the last two decades. In the future, biogas plants must be enabled to use a much broader range of input materials in a flexible and demand-oriented manner. Hence, the microbial communities will be exposed to frequently varying process conditions, while an overall stable process must be ensured. To accompany this transition, there is the need to better understand how biogas microbiomes respond to management measures and how these responses affect the process efficiency. Therefore, 67 microbiomes originating from 49 agricultural, full-scale biogas plants were taxonomically investigated by 16S rRNA gene amplicon sequencing. These microbiomes were separated into three distinct clusters and one group of outliers, which are characterized by a specific distribution of 253 indicative taxa and their relative abundances. These indicative taxa seem to be adapted to specific process conditions which result from a different biogas plant operation. Based on these results, it seems to be possible to deduce/assess the general process condition of a biogas digester based solely on the microbiome structure, in particular on the distribution of specific indicative taxa, and without knowing the corresponding operational and chemical process parameters. Perspectively, this could allow the development of detection systems and advanced process models considering the microbial diversity.

Convergent Microbial Community Formation in Replicate Anaerobic Reactors Inoculated from Different Sources and Treating Ersatz Crew Waste

“…Thirteen phyla were present in all the samples, including Euryarchaeota, Firmicutes, Bacteroidetes, Cloacimonetes, Proteobacteria, Tenericutes, Spirochaetes, Aminicenantes, Chloroflexi, and Parcubacteria. Hassa et al examined the microbiomes of 67 CSTRs at 49 different biogas plants differing in operational temperature, retention time, and feedstocks [14]. A few dominant phyla (e.g., Euryarchaeota, Firmicutes, Bacteroidetes, Cloacimonetes, and Tenericutes) were similar to those reported by Calusinska et al [13].…”

“…It is not known if these differences would eventually disappear over longer operational periods as there is generally some stochasticity in community structure during initial reactor operating periods [16,18]. As previously discussed, reactors with somewhat different methanogenic communities can demonstrate a similar performance due to functional redundancy, and different sequencing efforts have resulted in different "core" microbiomes of anaerobic digesters [13][14][15]. Given the resolution of the current sequencing methods, it is possible that some of the differences detected in methanogenic communities are insignificant in terms of actual reactor performance, whether due to functional redundancy, normal temporal fluctuations in community membership, or the limitations of reactor sampling for sequencing.…”

“…The major phyla detected in inoculated small reactors included Halobacterota (12.5-39.6%) and Thermoplasmatota (0.3-1.5%) within the Archaea, and Bacteroidota (23.7-39.5%), Firmicutes (11.2-26%), Synergistota (1.5-24.2%), Proteobacteria (3.8-22.8%), Verrucomicrobiota (1.2-14.4%), Spirochaetota (2.7-11.5%), Armatimonadota (0.1-2.7%), Actinobacteriota (0.1-2%), and Desulfobacterota (0.2-1.3%) within the Bacteria (Figure 2). Most bacterial sequences were assigned to the classes Clostridia, Bacilli, and Bacteroidia, which are common, and often abundant, members of anaerobic digesters [13][14][15]. Members of these classes are metabolically diverse and participate in the hydrolysis and fermentation steps of anaerobic digestion, degrading all the major macromolecules [39,40].…”

“…However, Chloroflexi, Spirochaetes, Aminicenantes, Parcubacteria, and Proteobacteria were not detected in all the reactors. Additionally, the researchers detected the predominance of different phyla, specifically Actinobacteria and Atribacteria [14], suggesting that these phyla could be considered part of the anaerobic digestion core microbiome. Sundberg et al determined the microbial communities of 21 full-scale CSTRs, operated at mesophilic or thermophilic conditions, and fed either municipal wastewater sludge, or mixtures of co-digested substrates including slaughterhouse waste, household and restaurant food waste, agricultural residues, and manure [15].…”

“…Deterministic processes include the operational control of parameters, such as inoculum, temperature, substrate, organic loading rate, retention time, and reactor configuration. The aforementioned surveys of full-scale CSTRs determined that digester microbiomes are clustered by both temperature [14,15] and substrate [13,15], suggesting performance and microbial communities can be predicted by operational parameters. However, in these studies, reactors were receiving unsterilized waste and so there could be some contribution from the substrate to the microbiome.…”