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United States Department of Agriculture

Agricultural Research Service

Research Project: Molecular Identification and Phylogenetic Analyses of Unique Microorganisms from Swine Feces and Manure Storage Pits

Location: Bioenergy Research Unit

2012 Annual Report


1a.Objectives (from AD-416):
To isolate and identify bacterial isolates from swine feces and manure storage pits that may be involved in production of gaseous emissions and/or malodorous compounds during long-term storage of swine manure. Identifying such bacteria would be beneficial for developing potential intervention strategies for reducing emissions from large-scale swine facilities.


1b.Approach (from AD-416):
The predominant bacterial populations from swine feces and stored manure from swine facilities will be isolated under anaerobic conditions with various media. These isolates will be purified and initially characterized for production of various compounds involved in gaseous emissions such as ammonia, volatile fatty acids, and phenolics. The isolates will then be analyzed using molecular methods to determine their potential identity. Molecular studies will be centered primarily on the 16S rDNA gene sequence determination. Large fragments of the 16S rDNA gene will be amplified by PCR, and generated sequences will be screened against rDNAs in reference libraries. Those sequences representing potential novel organisms will then be subjected to phylogenetic analyses using a variety of treeing methods (e.g., Neighbor-Joining, bootstrap resampling) to determine their taxonomic associations. Based on the results of these investigations, isolates belonging to the new genera/species will be delineated and named as appropriate. Generated novel sequences will be deposited in GenBank to facilitate future comparative studies, and reference strains of novel taxa will be deposited in International Public Culture Collections (U.S. and Europe).


3.Progress Report:

The objective of this study is to isolate and identify bacterial isolates from swine feces and manure storage pits that may be involved in production of gaseous emissions and/or malodorous compounds during long-term storage of swine manure or display antibiotic resistance. Identifying such bacteria would be beneficial for developing potential intervention strategies for reducing emissions from large-scale swine facilities and overall levels of antibiotic resistance. Researchers had earlier developed methods for identifying and naming new bacterial genera and species based primarily on the 16S rDNA gene sequence database, as well as biochemical characteristics. This approach allows identification of new and novel bacteria isolated from the swine gastrointestinal tract and stored swine manure. This year researchers identified, characterized, and named two new bacterial species. In addition, a microorganism (Robinsoniella peoriensis) previously discovered as part of this research was reported by doctors in China to be involved in blood infection in a cancer patient. Other information generated from this project was communicated to the scientific community via presentations at domestic/international meetings and scientific publications.


Last Modified: 7/24/2014
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