Bacterial community ecology and fate in integrated livestock production systems
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The application of animal manure as a fertilizer source is a common practice in Western Canada. Manure acts as an organic amendment, while providing an economic means of restoring soil nutrients imperative to plant growth. This being said, manure is also microbiologically active, capable of introducing new bacteria into the soil and groundwater environments. The development of high-throughput molecular techniques has provided a means of characterizing the bacterial communities of animal manures, and ecosystems affected by their presence. This study examined the impact of pig slurry amendments on the bacterial communities of soil, groundwater, and the hindgut of grazing cattle over the growing season using three common molecular methods (Terminal-restriction fragment length polymorphism (T-RFLP), Sanger sequencing, and pyrosequencing). T-RFLP results show that sample occasion had more of an impact on the bacterial communities in cattle, soil and groundwater than slurry application. T-RFLP, Sanger sequencing and pyrosequencing characterized the pig slurry as being dominated by Firmicutes, specifically Clostridium spp. Sanger sequencing confirmed that very few classified genera present in the pig slurry were common to the three other environments. Pyrosequencing provided a more in-depth characterization of soil and groundwater over the growing season following the application of slurry. Firmicutes were again dominant in the pig slurry, and were comprised mainly of Clostridium spp. Slurry treated soils had greater relative abundance of Firmicutes, specifically Clostridium spp., compared to unamended soil. Pyrosequencing identified only one groundwater sequence out of 13,578 sequences that was common to the pig slurry, which indicates very little transfer from slurry to groundwater. Pyrosequencing was then performed on an annual cropping system to compare the impact of manures (solid dairy, and solid pig), and synthetic N on the bacterial community of soil in the short- (within a growing season) and medium-term (after three successive years). Solid pig manure treatments revealed greater diversity compared to synthetic and control treatments and diversity was also higher at post-harvest than post-planting. Bacterial communities between treatments were distinct in the short-term but returned to their original structure by the end of the growing season indicating a resilient soil bacterial community.