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United States Department of Agriculture

Agricultural Research Service

2009 Annual Report

1a.Objectives (from AD-416)
Develop fundamental knowledge concerning the microbial populations of swine manure and the swine intestinal tract. Apply this knowledge to understand the relationship between microbial populations and the production of odorous compounds. Develop improved methods to quantitate changes in bacterial populations in feces and stored manure and correlate these with emissions/odorous compounds produced.

1b.Approach (from AD-416)
Determine the identity, relative concentration, and metabolic activities of microorganisms present in stored manure. Carry out physiological, biochemical, and genetic characterization of isolated bacterial cultures; determining which organisms and processes are responsible for production of odor causing chemicals. An extension of this work will be to examine the intestinal flora of the pig and its potential impact on the properties of the manure and the concentrations of potential odor precursors. This research will be conducted using samples from representative swine farms. Evaluate potential compounds for control of specific microorganisms or the metabolic processes responsible for odors.

3.Progress Report
For FY 2009, researchers developed new techniques for quantifying the levels of methanogenic bacteria in swine manure samples, which are responsible for production of the greenhouse gas methane. These techniques involve the use of quantitative real-time polymerase chain reaction (qRT-PCR) and allow the researchers to assay the effects of potential additives to stored manure on the levels of these bacterial populations. The qRT-PCR approach was also used to determine levels of sulfate-reducing bacteria in stored swine manure treated with condensed tannins and borax in a joint study with Michigan State University. In collaboration with the University of Leeds and the Institute of Food Research, Norwich, United Kingdom, research was also carried out targeting expression of therapeutic proteins in the human gastrointestinal tract by genetically modified bacteria. These results were communicated to the scientific community via presentations at domestic/international meetings and scientific publications.

1. DEVELOPMENT OF QUANTITATIVE REAL-TIME POLYMERASE CHAIN REACTION (qRT-PCR) ASSAYS FOR METHANE-PRODUCING BACTERIA. Quantifying the levels of bacteria responsible for producing methane (methanogens) is important for evaluating the effects of management practices on these microbes in stored swine manure. qRT-PCR methods have been shown to be a robust approach towards monitoring and quantifying populations of a variety of bacteria in manure. In this research, qRT-PCR techniques were developed to quantitate the levels of methanogens which produce methane. These techniques can now be used to assess the effects of abatement strategies such as the addition of condensed tannins (patent applied for) to manure on the populations of methanogens.

6.Technology Transfer

Number of New Patent Applications Filed1

Review Publications
Spence, C., Whitehead, T.R., Cotta, M.A. 2008. Development and Comparison of SYBR Green Quantitative Real-time PCR Assays for Detection and Enumeration of Sulfate-reducing Bacteria in Stored Swine Manure. Journal of Applied Microbiology. 105(6):2143-2152.

Hamady, Z.Z.R., Farrar, M.D., Whitehead, T.R., Holland, K.T., Lodge, J.P.A., Carding, S.R. 2008. Identification and Use of the Putative Bacteroides ovatus Xylanase Promoter for the Inducible Production of Recombinant Human Proteins. Microbiology. 154(10):3165-3174.

Sela, D.A., Chapman, J., Adeuya, A., Kim, J.H., Chen, F., Whitehead, T.R., Lapidus, A., Rokhsar, D.S., Lebrilla, C.B., German, J.B., Price, N.P., Richardson, P.M., Mills, D.A. 2008. The Genome Sequence of Bifidobacterium longum subsp. infantis Reveals Adaptations for Milk Utilization Within the Infant Microbiome. Proceedings of the National Academy of Sciences. 105(48):18964-18969.

Cotta, M.A., Whitehead, T.R., Falsen, E., Moore, E., Lawson, P.A. 2009. Robinsoniella peoriensis Gen. Nov., Sp. Nov., Isolated from a Swine-manure Storage Pit and a Human Clinical Source. International Journal of Systematic and Evolutionary Microbiology. 59(1):150-155.

Last Modified: 5/27/2015
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