Exploring the Diversity of Active Ureolytic Bacteria in the Rumen by Comparison of cDNA and gDNA

SIMPLE SUMMARY: Ureolytic bacteria produce urease that hydrolyzes dietary or recycled urea to ammonia, which can then be converted into microbial proteins. The diversity of ruminal ureolytic bacteria benefits N utilization efficiency in ruminants. However, there is no information at the complementary DNA (cDNA) level to reflect the active status of ureolytic bacteria. To reveal the diversity of active ureolytic bacteria in the rumen, we compared ureC amplicons between genomic DNA (gDNA) and cDNA. These results revealed distinct ureolytic bacterial community profiles based on gDNA and cDNA. The dominant ureolytic bacterial had high transcriptional activity, and the differential were mainly distributed in the genus of low abundance. ABSTRACT: In this study we revealed the diversity of active ureolytic bacteria in the rumen by compared ureC amplicons between gDNA and cDNA. Rumen fluid was collected from four Holstein dairy cows with rumen fistulas at 0, 2, and 6 h after morning feeding. Total microbial gDNA and RNA were isolated, and the RNA was reverse-transcribed into cDNA. The ureC gene amplicons of gDNA and cDNA were produced and sequenced by MiSeq. These results revealed that the sampling time had no significant difference on the alphssa and beta diversity indices of the ureolytic bacteria. The Shannon diversity of the ureC gene for cDNA was greater than that for gDNA (p < 0.05). There were significant difference in the beta diversity of ureolytic bacteria between gDNA and cDNA (p < 0.01), which indicates a shift in the community of active ureolytic bacteria. Approximately 67% of ureC sequences from cDNA could not be confidently classified at the genus level. The active ureolytic bacteria were mainly from Helicobacter, Herbaspirillum, Clostridium, Paenibacillus, Synechococcus, and Sphingobacterium sp. Changes in the operational taxonomic units revealed that the top abundant ureC genes were mostly consistent between gDNA and cDNA, and most differences occurred in the ureC genes with lower abundances. These results revealed distinct ureolytic bacteria community profiles based on gDNA and cDNA. The dominant ureolytic bacteria had high transcriptional activity, and the differential were mainly distributed in the genus of low abundance.