|Giarrizzo, Gabriel Juan - Oregon State University|
|Wu, Sitao - University Of San Diego|
|Li, Weizhong - University Of San Diego|
|Duringer, Jenny - Oregon State University|
|Craig, Morrie - Oregon State University|
Submitted to: PLoS One
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/15/2014
Publication Date: 11/10/2014
Citation: Li, R.W., Giarrizzo, G., Wu, S., Li, W., Duringer, J.M., Craig, M.A. 2014. Metagenomic insights into RDX-degrading potential of the ovine rumen microbiome. PLoS One. 9(11):e110505. DOI:10.1371/journal.pone.0110505.
Interpretive Summary: The rumen microbiome is critical to animal nutrition, the development of host immunity and degradation of xenobiotic and toxic compounds. The rumen harbors numerous microbes that are capable of degrading explosives, such as TNT and royal demolition explosive (RDX). RDX is a potential carcinogen and can cause a broad range of harmful effects to humans and animals, such as convulsions, loss of consciousness, vomiting, and skin lesions. Moreover, RDX in contaminated soil is mobile and leads to its seepage into surface and ground water. In this study, we conducted a comprehensive study to identify dominant biological pathways responsible for rapid degradation of RDX in the rumen. Our results facilitate the development of a novel bioremediation strategy involving the use of forage plants to uptake and concentrate RDX from contaminated soil followed by grazing and subsequent degradation of RDX-containing forages by sheep. The genes and pathways identified in the ovine rumen from this study will directly contribute to the success of novel RDX bioremediation approaches.
Technical Abstract: The ovine rumen is capable of rapid degradation of nitroaromatic compounds, such as hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). While ruminal RDX-degrading bacteria have been identified, genes and biological pathways responsible for the biochemical processes in the rumen have yet to be characterized. In this study, we monitored RDX degradation kinetics and then characterized the metabolic potential of the ovine rumen using metagenomic approaches. Sequences homologous to six RDX-degrading genes cloned from environmental samples appeared to be present in the ovine rumen microbiome. Among them, diaA was the most abundant, likely reflective of predominance of the genus Clostridum in the ovine rumen. At least ten genera known to harbor RDX-degrading microorganisms were detectable. Metagenomic sequences were also annotated using public databases, such as Pfam, COG and KEGG. Five of the six Pfam protein families known to be responsible for RDX degradation in environmental samples were present in the ovine rumen. Furthermore, Gene Ontology (GO) terms associated with RDX metabolism, such as oxidoreductase activity and oxidation-reduction process, were among the most dominant. However, elevated substrate availability did not enhance the proliferation of RDX-degrading bacteria and a 4-h incubation with RDX did not appear to induce any shifts in the microbial composition structure or the metabolic pathways in the ovine rumen microbiome. The RDX-degrading capacity of the ovine rumen microbiome is likely regulated at the transcription level. Our results provided metagenomic insights into the RDX-degrading potential of the ovine rumen and will facilitate to the development of novel and economic bioremediation strategies.