Do Ruminal Ciliates Select Their Preys and Prokaryotic Symbionts?

Tansol Park,Zhongtang Yu

doi:10.3389/fmicb.2018.01710

Abstract

Ruminal ciliates both preys on and form symbiotic relationships with other members of the ruminal microbiota for their survival. However, it remains elusive if they have selectivity over their preys or symbionts. In the present study, we investigated the above selectivity by identifying and comparing the free-living prokaryotes (FLP) and the ciliate-associated prokaryotes (CAP) using Illumina MiSeq sequencing of 16S rRNA gene amplicons. We used single ciliates cells of both monocultures of Entodinium caudatum and Epidinium caudatum and eight different ciliate genera isolated from fresh rumen fluid of dairy cows. Irrespective of the source (laboratory monocultures vs. fresh isolates) of the single ciliate cells, the CAP significantly differed from the FLP in microbiota community profiles. Many bacterial taxa were either enriched or almost exclusively found in the CAP across most of the ciliate genera. A number of bacteria were also found for the first time as ruminal bacteria in the CAP. However, no clear difference was found in methanogens between the CAP and the FLP, which was confirmed using methanogen-specific qPCR. These results suggest that ruminal ciliates probably select their preys and symbionts, the latter of which has rarely been found among the free-living ruminal prokaryotes. The bacteria enriched or exclusively found in the CAP can be target bacteria to detect and localize using specific probes designed from their 16S rRNA sequences, to characterize using single-cell genomics, or to isolate using new media designed based on genomic information.

Highlights

Rumen protozoa, exclusively ciliates, rank second only to bacteria in cellular biomass of the ruminal microbiota
On the Principal coordinates analysis (PCoA) plot, the ciliate-associated prokaryotes (CAP) and the free-living prokaryotes (FLP) of each ciliate monoculture were separated along PC1, while the CAP and the FLP of both ciliate monocultures were separated along PC2 (Figure 1A)
Technical limitations make it extremely difficult to identify true symbionts, to distinguish true endosymbionts from engulfed preys, or to determine the selectivity of symbionts and preys. Using both monocultures maintained in laboratory and fresh rumen fluid, we identified bacteria, not methanogens, enriched or exclusively found in extensively washed single cells of ruminal ciliates

Summary

Introduction

Exclusively ciliates, rank second only to bacteria in cellular biomass of the ruminal microbiota. They are only found in the rumen and similar habitats (Dehority, 1986, 2005) where they play important roles in feed digestion and homeostasis of the rumen ecosystem (Firkins et al, 2007; Newbold et al, 2015). They are blamed for promoting methane (CH4) emission due to their mutualistic relationship with methanogens by producing hydrogen (Newbold et al, 1995). The predator-prey relationship and the symbiotic relationship between ruminal ciliates and prokaryotes have attracted much research interest because both relationships are of biological interest and potential implication in improving ruminant production

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Discussion

Conclusion