title: Culture-dependent and independent analyses of the microbial communities inhabiting the giant duckweed (Spirodela polyrrhiza) rhizoplane and isolation of a variety of rarely cultivated organisms within the phylum Verrucomicrobia.
abstract: The microbial communities of the rhizoplane, the surface part of roots, in aquatic plants are not understood at all. In this study, we analyzed microbial communities in the rhizoplane of a floating aquatic plant, giant duckweed (Spirodela polyrrhiza), based on cultivation-dependent and independent analyses. The cultivation-based analysis using agar and gellan gum plates revealed that the rhizoplane isolates were affiliated with four bacterial lineages; the Alphaproteobacteria, Betaproteobacteria, Bacteroidetes and Verrucomicrobia. Interestingly, microbes belonging to the phylum Verrucomicrobia accounted for 24% of all the isolates, suggesting that the rhizoplane of S. polyrrhiza forms a specific habitat for the organisms within this phylum. Culture-independent 16S rRNA gene cloning showed that the clonal sequences were affiliated with eight bacterial classes and phyla: the classes Alphaproteobacteria (14% total clones), Betaproteobacteria (45%), Gammaproteobacteria (2%) and Deltaproteobacteria (2%), and the phyla Bacteroidetes (11%), Verrucomicrobia (2%), Planctomycetes (2%) and Cyanobacteria (22%). Comparative analysis of the microbial communities in the rhizoplane between culture-dependent and independent methods revealed that 33% of the taxonomic groups of bacterial species detected in the molecular analysis were cultivable. Our findings suggest that the microbes in the rhizoplane of giant duckweed are comprised of a diverse array of readily cultured organisms including a variety of strains within the Verrucomicrobia, a well-known phylum that contains a number of yet-to-be cultivated organisms.
authors.affiliation: Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 4–3–11 Takeda, Kofu, Yamanashi 400–8511, Japan.
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Matsuzawa
authors.forename: Yasuhiro
authors.initials: Y
authors.lastname: Tanaka
authors.forename: Hideyuki
authors.initials: H
authors.lastname: Tamaki
authors.forename: Yoichi
authors.initials: Y
authors.lastname: Kamagata
authors.forename: Kazuhiro
authors.initials: K
authors.lastname: Mori
mesh_terms: D029064:Araceae / Q000382:microbiology*; D001419:Bacteria / Q000145:classification* / Q000235:genetics / Q000254:growth & development / Q000302:isolation & purification*; D015169:Colony Count, Microbial; D008969:Molecular Sequence Data; D010802:Phylogeny; D018517:Plant Roots / Q000382:microbiology; D058441:Rhizosphere; D012988:Soil Microbiology