Abstract
BackgroundRumen ciliates play important roles in rumen function by digesting and fermenting feed and shaping the rumen microbiome. However, they remain poorly understood due to the lack of definitive direct evidence without influence by prokaryotes (including symbionts) in co-cultures or the rumen. In this study, we used RNA-Seq to characterize the transcriptome of Entodinium caudatum, the most predominant and representative rumen ciliate species.ResultsOf a large number of transcripts, > 12,000 were annotated to the curated genes in the NR, UniProt, and GO databases. Numerous CAZymes (including lysozyme and chitinase) and peptidases were represented in the transcriptome. This study revealed the ability of E. caudatum to depolymerize starch, hemicellulose, pectin, and the polysaccharides of the bacterial and fungal cell wall, and to degrade proteins. Many signaling pathways, including the ones that have been shown to function in E. caudatum, were represented by many transcripts. The transcriptome also revealed the expression of the genes involved in symbiosis, detoxification of reactive oxygen species, and the electron-transport chain. Overall, the transcriptomic evidence is consistent with some of the previous premises about E. caudatum. However, the identification of specific genes, such as those encoding lysozyme, peptidases, and other enzymes unique to rumen ciliates might be targeted to develop specific and effective inhibitors to improve nitrogen utilization efficiency by controlling the activity and growth of rumen ciliates. The transcriptomic data will also help the assembly and annotation in future genomic sequencing of E. caudatum.ConclusionAs the first transcriptome of a single species of rumen ciliates ever sequenced, it provides direct evidence for the substrate spectrum, fermentation pathways, ability to respond to various biotic and abiotic stimuli, and other physiological and ecological features of E. caudatum. The presence and expression of the genes involved in the lysis and degradation of microbial cells highlight the dependence of E. caudatum on engulfment of other rumen microbes for its survival and growth. These genes may be explored in future research to develop targeted control of Entodinium species in the rumen. The transcriptome can also facilitate future genomic studies of E. caudatum and other related rumen ciliates.
Highlights
Rumen ciliates play important roles in rumen function by digesting and fermenting feed and shaping the rumen microbiome
Overview of the Entodinium caudatum transcriptome From nearly 60 million raw sequencing reads, approximately 21.6 million sequences resulted after filtering with a Q score ≥ 30 and joining of the paired reads (Additional file 1: Table S1)
The transcripts at the highest abundance were annotated to coding for proteins involved in cellular structures and processes that are essential to eukaryotic cells (Additional file 2: Table S2)
Summary
Rumen ciliates play important roles in rumen function by digesting and fermenting feed and shaping the rumen microbiome. Because of the unknown confounding factors, such as variations of rumen microbiome in the absence or presence of protozoa and potential prokaryotic contamination, the fundamental biological characteristics of rumen protozoa remain to be definitively determined Their substrate spectrum, fermentation products, metabolic pathways, recruitment of symbionts, and prey selection all remain to be fully elucidated. As another example, rumen ciliates are thought to scavenge O2 that enters the rumen (together with the ingested feed, drinking water, saliva, and perfusion from the rumen wall), thereby protecting strictly anaerobic archaea and bacteria, cellulolytic bacteria [10]. It remains to be determined if and how rumen ciliates utilize O2
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