Bacterial community dynamics in liquid swine manure during storage: molecular analysis using DGGE/PCR of 16S rDNA

Abstract

Denaturant gradient gel electrophoresis (DGGE) analysis of polymerase chain reaction-amplified DNA fragments prepared from extracted DNA using universal 16S rDNA primers was used to compare the composition of bacterial communities in liquid swine manure (LSM) during incubation in aerated and in non-aerated laboratory reactors. The LSM was initially dominated by 13 phylotypes whose identities were established by excising and cloning DGGE bands, and comparing the 16S rDNA sequences with those available in GenBank. With varying degrees of similarity, Clostridium butyricum, Clostridium disporicum, a Pedobacter sp., two Rhodanobacter sp., a spirochete, and seven uncultured eubacterial sequences were identified. The chemical composition, total microbial populations determined by direct microscopic count, and DGGE profiles of the LSM were stable during anaerobic storage for 7 weeks. However, the community composition of the LSM changed substantially with aeration, the DGGE bands in the original sample receding in intensity as the manure community became dominated by phylotypes most closely related to the aerobes Bacillus thuringiensis, Sphingobacterium mizutae, a ‘Sphingobacterium-like’ bacterium, and a Paenibacillus sp. When continuously aerated, the pH rose from 8 to 9.5, the ammonium-N content decreased, populations of culturable aerobes increased 150-fold, and total bacterial populations remained stable. DGGE analysis of manure fractionated into planktonic and biofilm (flocs and aggregates) communities suggested that Clostridium populations were stable in biofilms during aeration, whereas the aerobes that ultimately dominated the LSM community were primarily in the planktonic phase.