Slurry samples from 13 industrial biogas plants using swine manure as raw substrate were collected from different regions in China. The prokaryotic community compositions were investigated using 16S rRNA amplicon high-throughput sequencing technique. The results showed that Firmicutes was the most abundant phylum in these biogas plants

followed by Bacteroidetes

Proteobacteria and Chloroflexi. The ratio of ammonium to phosphate was the main factor affecting prokaryotic community structure and diversity for similar temperatures and substrates. A high ratio of ammonium to phosphate enriched Firmicutes

especially the genus Clostridium sensu stricto

while Bacteroidetes and Proteobacteria preferred a low ratio. Ammonium influenced the compositions of methanogens since their tolerance degrees to ammonium were different (hydrogenotrophic methanoges > Methanosarcina > Methanosaeta). Community compositions of methanogens and syntrophs were the most important biotic factors affecting biogas production rate. Biogas production rate could be increased by increasing the abundances of hydrogenotrophic methanoges and syntrophic propionate-oxidizing bacteria.