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. 2019 Aug 13;10:1896. doi: 10.3389/fmicb.2019.01896

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Copyright © 2019 Gan, Szegedi, Fersi, Chebil, Kovács, Kawaguchi, Hudson, Burr and Savka.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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A maximum-likelihood tree constructed based on the alignment of Agrobacterium and Allorhizobium ASVs to the V3–V4 16S rRNA gene region of Agrobacterium, Allorhizobium, Pararhizobium, and Rhizobium strains. The tree was rooted with members from the genus Ochrobactrum as the outgroup. Tips representing ASVs included in the tree construction were colored based on the percentage nucleotide identity (values after the tilde symbols) of an ASV to its best matching OTU, with blue and red indicating perfect match (100% identity) and near-perfect (98% < x < 100% identity) match, respectively. Numbers at nodes indicate Shimodaira–Hasegawa (SH)-like local support values and branch lengths indicate the number of nucleotide substitutions per site. Codes preceding the genus name of each type strain are their NCBI accession numbers. The GS# labels present at the end of some Agrobacterium tip labels correspond their genospecies and the red box indicates an Agrobacterium clade consisting of multiple Agrobacterium genospecies with zero branch length or identical 16S rRNA V3–V4 gene sequence. Each ASV tip label associated with an abundance profile (right) that displays the average percentage relative abundance of the ASV in the major sampling sites.