Microbial community analysis in the roots of aquatic plants and isolation of novel microbes including an organism of the candidate phylum OP10

Abstract

A number of molecular ecological studies have revealed complex and unique microbial communities in various terrestrial plant roots; however, little is known about the microbial communities of aquatic plant roots in spite of their potential use for water quality improvement in aquatic environments (e.g. floating treatment wetland system). Here, we report the microbial communities inhabiting the roots of emerged plants, reed (Phragmites australis) and Japanese loosestrife (Lythrum anceps), collected from a floating treatment wetland in a pond by both culture-independent and culture-dependent approaches. Culture-independent analysis based on 16S rRNA gene sequences revealed that the microbial compositions between the two aquatic plant roots were clearly different (e.g. the predominant microbe was Betaproteobacteria for reed and Alphaproteobacteria for Japanese loosestrife). In comparisons of microbial communities between the plant roots and pond water taken from near the plants, the microbial diversity in the plant roots (e.g. 4.40-4.26 Shannon-Weiner index) were higher than that of pond water (e.g. 3.15 Shannon-Weiner index). Furthermore, the plant roots harbored 2.5-3.5 times more phylogenetically novel clone phylotypes than pond water. The culture-dependent approach also revealed differences in the microbial composition and diversity among the two plant roots and pond water. More importantly, compared to pond water, we succeeded in isolating approximately two times more novel isolate phylotypes, including a bacterium of candidate phylum OP10 (recently named Armatimonadetes) from the plant roots. These findings suggest that aquatic plants roots are significant sources for a variety of novel organisms.

Fig. 1

Phylogenetic distribution of the 16S rRNA gene clones (A) and isolates (B) belonging to different bacterial taxa in the roots of reed and Japanese loosestrife, and pond water.

Fig. 2

Novel clonal 16S rRNA gene sequences (A) and isolates (B) recovered from the roots of reed and Japanese loosestrife, and pond water. The similarity percentages between the clones (A) or isolates (B) and their closest species in the GenBank database are shown.

Fig. 3

Phylogenetic tree showing the relationship between strain YO-36 and related sequences of the candidate phylum OP10. The tree was constructed using the neighbor-joining (NJ) method on the basis of the 16S rRNA gene sequences. Node with bootstrap values of >90% and >80%, estimated using the NJ method and maximum likelihood (ML) methods, are shown as a closed circle and an open circle, respectively. The tree was rooted against a group of 26 sequences belonging to different phyla in the domains Bacteria and Archaea. Scale bar indicates 0.05 substitutions per nucleotide position.