Mixed plug-flow loop reactor (MPFLR) has been
widely adopted by the US dairy farms to convert cattle
manure to biogas. However, the microbiome in
MPFLR digesters remains unexplored. In this study,
the microbiome in a MPFLR digester operated on a
mega-dairy farm was examined thrice over a 2 month
period. Within 23 days of retention time, 55–70% of
total manure solid was digested. Except for a few
minor volatile fatty acids (VFAs), total VFA concentration and pH remained similar along the course of
the digester and over time. Metagenomic analysis
showed that although with some temporal variations,
the bacterial community was rather stable spatially
in the digester. The methanogenic community was
also stable both spatially and temporally in the
digester. Among methanogens, genus Methanosaeta
dominated in the digester. Quantitative polymerase
chain reaction (qPCR) analysis and metagenomic
analysis yielded different relative abundance of
individual genera of methanogens, especially for
Methanobacterium, which was predominant based on
qPCR analysis but undetectable by metagenomics.
Collectively, the results showed that only small microbial and chemical gradients existed within the
digester, and the digestion process occurred similarly
throughout the MPFLR digester. The findings of this
study may help improve the operation and design of
this type of manure digesters