Transconjugant range of PromA plasmids in microbial communities is predicted by sequence similarity with the bacterial host chromosome

Abstract

Nucleotide sequence similarity, including k-mer plasmid composition, has been used for prediction of plasmid evolutionary host range, representing the hosts in which a plasmid has replicated at some point during its evolutionary history. However, the relationships between the bacterial taxa of experimentally identified transconjugants and the predicted evolutionary host ranges are poorly understood. Here, four different PromA group plasmids showing different k-mer compositions were used as model plasmids. Filter mating assays were performed with a donor harbouring plasmids and recipients of bacterial communities extracted from environmental samples. A broad range of transconjugants was obtained with different bacterial taxa. A calculation of the dissimilarities in k-mer compositions as Mahalanobis distance between the plasmid and its sequenced transconjugant chromosomes revealed that each plasmid and transconjugant were significantly more similar than the plasmid and other non-transconjugant chromosomes. These results indicate that plasmids with different k-mer compositions clearly have different host ranges to which the plasmid will be transferred and replicated. The similarity of the nucleotide compositions could be used for predicting not only the plasmid evolutionary host range but also future host ranges.

Keywords: Plasmid; PromA; conjugation; host range; nucleotide compositions.

Fig. 1.

Procedures of the mating assay with four PromA plasmids and microbial communities showing the types of samples analysed using the CI method (red). These mating assays were performed using three mating conditions, Soil-LBAgar, Soil-Agar, and Lake-Sanaru-LBAgar as described in the Methods.

Fig. 2.

A clustered heatmap showing the dissimilarity of 3-mer compositions in PromA plasmids. Dissimilarities were calculated using Euclidean distance. Three-mer frequency is the observed 3-mer frequency divided by the expected 3-mer frequency. Nine plasmids carrying known accessory genes are indicated by ‘+’.

Fig. 3.

(a) Microbial communities of the isolated transconjugants by culture-independent methods from the samples of Lake-Sanaru-LBAgar. (b) Principal coordinate analysis (PCoA) plot based on weighted UniFrac distances of microbial communities in mating assays with four PromA plasmids.

Fig. 4.

Distribution of Mahalanobis distances of 3-mer compositions between plasmids and chromosomes of Alpha-, Beta-, and Gammaproteobacteria . Bold lines in each histogram indicate the median value of the Mahalanobis distance.

Fig. 5.

Box plots of Mahalanobis distances of 3-mer between each PromA plasmid and its transconjugants (coloured) and between the plasmid and 965 recipient reference genomes (grey). A median value in each data is shown by a black line in each box.