Complete nucleotide sequence of a cryptic plasmid from the ruminal bacterium Selenomonas ruminantium HD4 and identification of two predicted open reading frames

Insights into the bovine rumen plasmidome

Plasmids are self-replicating genetic elements capable of mobilization between different hosts. Plasmids often serve as mediators of lateral gene transfer, a process considered to be a strong and sculpting evolutionary force in microbial environments. Our aim was to characterize the overall plasmid population in the environment of the bovine rumen, which houses a complex and dense microbiota that holds enormous significance for humans. We developed a procedure for the isolation of total rumen plasmid DNA, termed rumen plasmidome, and subjected it to deep sequencing using the Illumina paired-end protocol and analysis using public and custom-made bioinformatics tools. A large number of plasmidome contigs aligned with plasmids of rumen bacteria isolated from different locations and at various time points, suggesting that not only the bacterial taxa, but also their plasmids, are defined by the ecological niche. The bacterial phylum distribution of the plasmidome was different from that of the rumen bacterial taxa. Nevertheless, both shared a dominance of the phyla Firmicutes, Bacteroidetes, and Proteobacteria. Evidently, the rumen plasmidome is of a highly mosaic nature that can cross phyla. Interestingly, when we compared the functional profile of the rumen plasmidome to two plasmid databases and two recently published rumen metagenomes, it became apparent that the rumen plasmidome codes for functions, which are enriched in the rumen ecological niche and could confer advantages to their hosts, suggesting that the functional profiles of mobile genetic elements are associated with their environment, as has been previously implied for viruses.

pSRD191, a new member of RepL replicating plasmid family from Selenomonas ruminantium

A numerous plasmid population was detected in strain 19 of Selenomonas ruminantium. The population was found to consist of six plasmids in size ranging from 1.4 to more than 20kb. The smallest 1.4kb cryptic plasmid pSRD191 was further characterized. Sequence analysis identified a single ORF encoding the 177-residue putative replication protein (Rep191) which shared significant homology with RepL family of replication protein from Firmicutes (staphylococci and bacilli). PCR analysis and Southern hybridisation showed that pSRD191 related plasmids are frequently encountered in rumen selenomonads.

Plasmids of Selenomonas ruminantium and development of host-vector system

A high frequency of plasmids was detected in the rumen bacterium Selenomonas ruminantium. Plasmids 0.9-20 kb in size were detected in more than 50% tested strains. Densitometric analysis indicated that plasmid DNA could represents more than 25% of total cellular DNA. Up to six plasmids were detected in strain S. ruminantium 18. Two smallest cryptic plasmids pSRD181 and pSRD182 from this strain were cloned into Escherichia coli vector pBluescriptSK+ and partially characterized. The plasmid pSRD181 is 1.4 kb and pSRD182 is 2.0 kb. While computer analysis of pSRD181 sequence data showed high homology with replication protein of Staphylococcus aureus plasmids, the pSRD182 sequence showed no significant homology in GenBank data. Strain S. ruminantium 28 was successfully transformed with pJW1 derived plasmid pJ1B1 using ampicillin resistance gene as marker. This is the first report on transformation of selenomonads with foreign DNA.