Horizontal gene transfer from Bacteria to rumen Ciliates indicates adaptation to their anaerobic, carbohydrates-rich environment

Abstract

Background: The horizontal transfer of expressed genes from Bacteria into Ciliates which live in close contact with each other in the rumen (the foregut of ruminants) was studied using ciliate Expressed Sequence Tags (ESTs). More than 4000 ESTs were sequenced from representatives of the two major groups of rumen Cilates: the order Entodiniomorphida (Entodinium simplex, Entodinium caudatum, Eudiplodinium maggii, Metadinium medium, Diploplastron affine, Polyplastron multivesiculatum and Epidinium ecaudatum) and the order Vestibuliferida, previously called Holotricha (Isotricha prostoma, Isotricha intestinalis and Dasytricha ruminantium).

Results: A comparison of the sequences with the completely sequenced genomes of Eukaryotes and Prokaryotes, followed by large-scale construction and analysis of phylogenies, identified 148 ciliate genes that specifically cluster with genes from the Bacteria and Archaea. The phylogenetic clustering with bacterial genes, coupled with the absence of close relatives of these genes in the Ciliate Tetrahymena thermophila, indicates that they have been acquired via Horizontal Gene Transfer (HGT) after the colonization of the gut by the rumen Ciliates.

Conclusion: Among the HGT candidates, we found an over-representation (>75%) of genes involved in metabolism, specifically in the catabolism of complex carbohydrates, a rich food source in the rumen. We propose that the acquisition of these genes has greatly facilitated the Ciliates' colonization of the rumen providing evidence for the role of HGT in the adaptation to new niches.

Figure 1

Distribution of Best Hits over the proteomes. Only proteomes with a number of Best Hits ≥ 0.2% are displayed. The 12 most represented proteomes are eukaryotic, the remaining set contains a large fraction of Firmicutes proteomes (orange).

Figure 2

Distribution of functional classes in HGT and in the complete set of sequences. There is a clear over-representation of the metabolic KOG/COGs within the HGT candidates. green – the KOG/COG corresponding to the "information storage and processing"; yellow-orange – "cellular processes and signalling"; blue – "metabolism"; grey – "poorly characterised".

Figure 3

A likely horizontally transferred gene in Entodinium. The tree contains the target sequence (AM054010) and its homologuous proteins. To determine whether the target sequence is HGT candidate, an algorithm examines the presence or absence of Bacteria, Archaea and Eukaryotes in the second smaller partition containing the target sequence. In the example, the smallest second partition containing the target sequence contains also the sequences from Bacillus halodurans, Xanthomonas axonopodis, Xanthomonas campestris and Thermotoga maritima, which are all Bacteria. AM054010 was therefore retained as a HGT candidate.