The 2012 ASHS Annual Conference

Composted dairy manure has good potential for use as a potting mix amendment. However, some prospective consumers have concerns that harmful fecal microorganisms might survive the composting process. The changing bacterial communities in dairy manure over nine months of composting were analyzed using 454 pyrosequencing. DNA was extracted from 10 day, 3, 6, and 9 month old compost and the V1 through V3 region amplified by PCR using mixture of the 27F primer composed of equal concentrations of seven degenerative primers and unique tagged reverse primers targeting the 534 region. The DNA analysis technique resulted in 83,555 quality sequence reads that could be classified. Representatives of 18 different bacterial phyla were identified. The dominant phyla were the Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, Deinococcus-Thermus and Chloroflexi. The relative abundances of the different phyla changed over time, with microbial composition changing the most between the 10 day and 3 month old compost. In the 10 day old compost, the Firmicutes were the dominant phyla, comprising 68% of the bacterial community. The relative abundance of this group decreased significantly during the other months, but it remained the dominant phyla averaging around 30% of the population.  The second or third most prevalent groups were either the Actinobacteria or the Proteobacteria depending on the compost’s age. Analysis of the sequencing results at the genus level revealed that bacterial diversity was high, comprising of 472 different genera, although the relative abundance of the majority of genera was low (comprising less than 1%). Sixty-two genera were present at more than 0.5% of the population, and were considered the dominant genera. Sequences with strong homology to E. coli or other enteric bacteria were absent, whereas halotolerant or halophilic bacteria were prevalent. These findings indicated that composting reduced the levels of fecal coliforms to below the 454 pyrosequencing detection limit (~10⁴ cfu/ml), and that temperature and salt concentration were the primary factors impacting the microbial community in the aging compost.