Abstract
The microbial community in anaerobic digestion has been analysed through microbial fingerprinting techniques, such as terminal restriction fragment length polymorphism (TRFLP), for decades. In the last decade, high-throughput 16S rRNA gene amplicon sequencing has replaced these techniques, but the time-consuming and complex nature of high-throughput techniques is a potential bottleneck for full-scale anaerobic digestion application, when monitoring community dynamics. Here, the bacterial and archaeal TRFLP profiles were compared with 16S rRNA gene amplicon profiles (Illumina platform) of 25 full-scale anaerobic digestion plants. The α-diversity analysis revealed a higher richness based on Illumina data, compared with the TRFLP data. This coincided with a clear difference in community organisation, Pareto distribution, and co-occurrence network statistics, i.e., betweenness centrality and normalised degree. The β-diversity analysis showed a similar clustering profile for the Illumina, bacterial TRFLP and archaeal TRFLP data, based on different distance measures and independent of phylogenetic identification, with pH and temperature as the two key operational parameters determining microbial community composition. The combined knowledge of temporal dynamics and projected clustering in the β-diversity profile, based on the TRFLP data, distinctly showed that TRFLP is a reliable technique for swift microbial community dynamics screening in full-scale anaerobic digestion plants.
Highlights
Anaerobic digestion (AD) can be considered the first microbial technologies for organic waste treatment to reach full-scale application, and it has been implemented extensively treating various waste streams since the 1980s1–3
The combination of generation amplicon sequencing and terminal restriction fragment length polymorphism (TRFLP) analysis in AD ecosystems, far, remained restricted to lab-scale experiments[52,53] or only a limited number of full-scale plants[54]. Even though these studies yielded interesting results, the observed differences between the TRFLP and generation amplicon sequencing microbial community profile in AD requires further investigation. This will allow to determine the different levels of community profiling for which TRFLP can serve as a proxy of generation amplicon sequencing in AD
The objective of this research was to investigate the microbial community in various full-scale AD plants using both TRFLP analysis and amplicon sequencing (Illumina platform) of the 16S rRNA gene to determine the potential of TRFLP for a reliable capture of a useful ecological picture of the AD microbiome
Summary
Anaerobic digestion (AD) can be considered the first microbial technologies for organic waste treatment to reach full-scale application, and it has been implemented extensively treating various waste streams since the 1980s1–3. The combination of generation amplicon sequencing and TRFLP analysis in AD ecosystems, far, remained restricted to lab-scale experiments[52,53] or only a limited number of full-scale plants[54]. Even though these studies yielded interesting results, the observed differences between the TRFLP and generation amplicon sequencing microbial community profile in AD requires further investigation. The objective of this research was to investigate the microbial community in various full-scale AD plants using both TRFLP analysis and amplicon sequencing (Illumina platform) of the 16S rRNA gene to determine the potential of TRFLP for a reliable capture of a useful ecological picture of the AD microbiome. A comparison was made based on (1) alpha-diversity, (2) beta-diversity, (3) community organization, (4) the impact of operational parameters on the community profile, and (5) co-occurrence network formation to estimate the potential of TRFLP analysis on different levels
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