Abundance and composition data of microbiomes in agricultural biogas plants of Lower Saxony, Germany, with variation in organic substrates, process parameters and nutrients

This article presents high-throughput DNA sequencing, quantitative PCR data of microbial communities, and process parameters as recovered from eight biogas plants (BPs) located in Lower Saxony, Germany. Samples were collected from both the main (MD) and secondary digesters (SD). Additionally, for 4 BPs, samples were also obtained from the residue digester storage (RDS). Different BPs employed various types of substrates originating from cattle manure, chicken manure, pig manure, or renewable resources. Information on physico-chemical process parameters and concentrations of macro- and micro-nutrients in the BPs is provided. Total DNA from all samples were extracted using a phenol-chloroform-based method. To determine the abundance of bacteria and archaea, their 16S rRNA genes were quantified by real-time PCR (qPCR), and to characterize their community composition, paired-end DNA sequence reads were generated from PCR amplicons with Illumina MiSeq. All statistical analyses were performed in R to explore the microbial diversity, abundance, and community structure among different BPs and digesters (MD, SD, RDS). The presence and distribution of the major bacterial and archaeal phyla indicated for each BP unique and diverse microbial communities with typically higher bacterial than archaeal abundances.