Genetic diversity and ecological evaluation of fluorescent pseudomonads isolated from the leaves and roots of potato plants

Abstract

A total of 828 isolates of fluorescent pseudomonads (FPs) were obtained from the leaves (305 isolates) and roots (523 isolates) of potato plants grown in different geographical locations in Japan, and 16S rRNA gene sequences of 776 isolates were successfully determined by direct PCR sequencing. Clustering analysis (≥99% identity) identified 13 and 26 operational taxonomic units (OTUs) for leaf- and root-associated FPs, respectively, and 29 OTUs were identified in the phytosphere of potato plants. Among them, 7 and 9 OTUs showed a significantly biased distribution to the leaves and roots, respectively. Phylogenetic analysis revealed that 3 dominant OTUs for leaf-associated FPs were grouped in a cluster of leaf-associated pathogens, such as Pseudomonas cichorii and Pseudomonas viridiflava. In contrast, 4 OTUs were located in a cluster of saprophytic pseudomonads. Among them, 3 OTUs showed high similarity to Pseudomonas koreensis and Pseudomonas vancouverensis, both of which have been reported to be beneficial for biological control or plant growth promotion. These data provide key information for efficient surveying and utilization of beneficial FPs in agricultural practices.

Fig. 1

Phylogenetic distribution of operational taxonomic units (OTUs) of fluorescent pseudomonads (FPs) isolated from the phyllosphere and rhizosphere of potato plants cultivated in various locations across Japan. The dendrogram indicates the phylogenetic relationships among the representative sequences of OTUs (defined by ≥99% identity). The table indicates the relative abundance (%) of clones belonging to each OTU in each column and the results of a pair-wise BLAST between a representative sequence and its closest type strain. The sampling sites (prefecture) were as follows: FUK, Fukuoka; HOK, Hokkaido; IBA, Ibaraki; KAG, Kagoshima; KAN, Kanagawa; NAG, Nagasaki. The percentages of isolates analyzed are shown for each column of libraries. “*” and “**” mean statistical significance at 0.05 and 0.01 levels, respectively.

Fig. 2

Phylogenetic tree of 16S rRNA genes based on the representative sequences of operational taxonomic units (OTUs) for potato-associated fluorescent pseudomonads (FPs). The tree was constructed using the neighbor-joining method. Scale represents 0.1 substitutions per site. Numbers at the nodes are the proportions of 1,000 bootstrap resamplings, and values <500 are not shown. Dominant OTUs showing a significantly biased distribution in terms of the numbers of isolates in the leaf compared with the root are indicated as L and R, respectively. LR indicates dominant OTUs with no significantly biased distribution to the leaf or root.