211 Analysis of microbial communities from a commercial-size swine manure pit and their association with production of volatile organic compounds

Abstract

Abstract Global pollution and emission concerns have been linked to concentrated animal feeding operations (CAFOs). Indeed, the U.S Environmental Protection Agency (US EPA) warns that there is a significant danger to human health, soil, and water quality from CAFOs. Volatile organic compounds (VOCs), which are amongst air contaminants that pose a serious risk, are abundantly produced in swine manure pits. While VOC emissions from swine manure have been well studied, the microbial species responsible for their production remain mostly uncharacterized. Thus, a deeper comprehension of the microorganisms responsible for VOC production in swine manure pits may help in the development of management approaches that target the microbiome in these environments. In this context, this study aimed to identify the major bacterial species populating the manure pit of a commercial-size swine wean-to-finish research facility. Manure collected from two sampling locations at different time points were analyzed using the 16S rRNA gene through PCR-amplification of the V1-V3 regions from microbial genomic DNA, followed by Illumina MiSeq 2X300 sequencing. An analysis of the most highly represented microorganisms identified 24 bacterial Operational Taxonomic Units (OTUs), with only four showing a species-level nucleotide sequence identity to currently known or valid species. As these results indicated that the majority of bacterial species from this manure pit were unknown, a metagenomics approach was used to assemble partial to full length genomes from the two most abundant OTUs: Pit_9-00239 [5.09% - 19.44%; Clostridium saccharoperbutylacetonicum (96.60%)] and Pit_ 7-00035 [5.58% - 17.30%; Bacteroides eggerthii (87.66%)]. From genome assembly analysis, 979 contigs were generated for a combined length of 12,367,510 bp, which together included 21,776 coding sequences. Predicted metabolic functions from these contig sets included pathways involved in carbohydrate utilization (glycolysis), vitamin synthesis (riboflavin), and butyrate production (volatile fatty acids). Notably, an enzyme responsible for the production of indole, a common VOC produced from swine manure pits, was also identified. Together, the results from this analysis provide insights on metabolic capabilities of abundant bacterial species from manure pits. These can in turn be used for the future development of management strategies or products that can reduce VOC emissions that result from swine CAFO manure storage.