Identification of excised PCR-DGGE bands.

a<p>Source of the closest rice associated bacteria: PF – Paddy Field <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030438#pone.0030438-Cuong1" target="_blank">[65]</a>; PS – Paddy Soil <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030438#pone.0030438-Shrestha1" target="_blank">[28]</a>; R - Rhizosphere <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030438#pone.0030438-Steindler1" target="_blank">[25]</a>; RE1 - Root Endosphere <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030438#pone.0030438-Hardoim2" target="_blank">[20]</a> and RE2 - Root Endosphere <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030438#pone.0030438-Sun1" target="_blank">[64]</a>.</p

Dynamics of rice endophytes as revealed by PCR-DGGE profiles of seed, three- and five-week-old rice plants.

<p>Rice endophyte PCR-DGGE patterns of surface-sterilized dehulled seeds and five-day-old shoot, root and remainder of the seeds from two consecutive generations are shown (panel A). PCR-DGGE patterns of root and shoot endosphere community of three- B) and five- C) week-old rice plants cultivated in two soil types. Six replicates per treatments are shown. Arrow heads indicate identified communities from excised PCR-DGGE bands (only numbers) and strains with identical motility (preceded by letter R; see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030438#pone-0030438-t001" target="_blank">Table 1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030438#pone-0030438-t002" target="_blank">2</a>), M – marker with a selection of 15 endophyte ribotypes (panel A).</p

PCR-DGGE fingerprints and canonical analyses.

<p>PCR-DGGE 16S rRNA gene fingerprints of <i>S. spinosulus</i>, <i>I. variabilis</i> and seawater DNA samples generated with “total-community” bacterial primers (A) and specific primer systems for <i>Actinobacteria</i> (C) and <i>Alphaproteobacteria</i> (E). The arrows indicate bands that were excised from DG-gels and sequenced. Corresponding ordination biplots of PCR-DGGE fingerprints and qualitative environmental variables are shown in panels B, D, F. Symbols: ▴ <i>S. spinosulus</i>, ▪ <i>I. variabilis</i> and • Seawater. Labels displayed on the diagram axes refer to the percentage variations of PCR-DGGE ribotypes - environment correlation accounted for the respective axis. The “star” symbols represent the centroid positions of the environmental variables in the diagram. Variables that significantly (<i>p</i><0.05) influence the bacterial community composition are indicated by an asterisk.</p

Closest 16S rRNA gene relatives of seawater-derived and “cosmopolitan” PCR-DGGE bands.

1<p>Closest 16S rRNA gene relative using the “sequence match” tool of the Ribosomal Database Project (RDP).</p>2<p>Closest 16S rRNA gene relatives as determined by the blast-n search in the National Center for Biotechnology Information (NCBI) database.</p