Do Ruminal Ciliates Select Their Preys and Prokaryotic Symbionts?

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.

Ferric citrate, nitrate, saponin and their combinations affect in vitro ruminal fermentation, production of sulphide and methane and abundance of select microbial populations

“…Saponins have shown the ability to inhibit CH 4 production by directly affecting the composition and activity of some rumen protozoa, bacteria, fungi and Archaea (Patra and Saxena ). Many methanogens are found in both ecto‐ and endosymbiotic associations with protozoa (Park and Yu ), which are responsible for up to 37% of the rumen CH 4 production (Finlay et al . ).…”

Extending Burk Dehority’s Perspectives on the Role of Ciliate Protozoa in the Rumen

“…When considering fresh ruminal isolates or longer term monocultures of protozoa, the co-cultured bacteria in protozoal monocultures do not necessarily have a community structure that would be typical of the rumen (Park and Yu, 2018b). These prokaryotes probably have been naturally selected over time for an ability to survive predation while also withstanding typical feeding intervals of 24 h. Protozoal formation (the main storage form of reserve carbohydrate) is much more extensive than bacterial reserve carbohydrate (Teixeira et al, 2017).…”

“…Protozoal communities fall into distinctive categories probably because of antagonism among species (Kittelmann et al, 2016). Protozoal community structure is important also for bacterial community composition because of the potential for selective predation of bacteria by different protozoal genera (Park and Yu, 2018b). Even so, researchers need to consider the difference between direct predation (i.e., assuming bacteria are the target) and indirect 'grazing' (i.e., bacteria that adhere to engulfed particulate matter).…”

“…Selective predation of rumen bacteria by rumen protozoa, at least En. caudatum, is likely (Park and Yu, 2018b); however, more research is needed to determine the prey selections by individual species of rumen protozoa and how prey selectivity is achieved.…”

“…For example, were increased protozoal numbers in monocultures a direct stimulation by the treatment imposed or a result of indirect inhibition of the uncharacterized prokaryotes in co-culture? Hence, there are some important similarities in prokaryotic diversity in ciliate monocultures compared with in vivo, but there also are major differences (Park and Yu, 2018b). Dehority (2003) contextualized the difference between protozoal counts (cells per milliliter) and protozoal pool size (total cells) in the rumen, their ruminal passage or lack thereof (sequestration), and their adaptation to host and diet based on function and taxonomy from the bottom up.…”