Pu•biome

Notes

The evolutionary relationships among species of the family <a class="namesforlife" title="Pseudomonadaceae - Click to open Names for Life widget" href="https://doi.org/10.1601/nm.2551" target="xrefwindow" rel="namesforlife-name">Pseudomonadaceae</a> were examined based on 255 available genomes representing &gt;85 % of the species from this family. In a phylogenetic tree based on concatenated sequences of 118 core proteins, most species of the genus <a class="namesforlife" title="Pseudomonas - Click to open Names for Life widget" href="https://doi.org/10.1601/nm.2552" target="xrefwindow" rel="namesforlife-name">Pseudomonas</a> grouped within one large cluster which also included members of the genera <a class="namesforlife" title="Azotobacter - Click to open Names for Life widget" href="https://doi.org/10.1601/nm.2713" target="xrefwindow" rel="namesforlife-name">Azotobacter</a> and <a class="namesforlife" title="Azomonas - Click to open Names for Life widget" href="https://doi.org/10.1601/nm.2709" target="xrefwindow" rel="namesforlife-name">Azomonas</a> . Within this large cluster 18&ndash;30 clades/subclades of species of the genus <a class="namesforlife" title="Pseudomonas - Click to open Names for Life widget" href="https://doi.org/10.1601/nm.2552" target="xrefwindow" rel="namesforlife-name">Pseudomonas</a> consisting of between 1 and 36 species, were observed. However, a number of species of the genus <a class="namesforlife" title="Pseudomonas - Click to open Names for Life widget" href="https://doi.org/10.1601/nm.2552" target="xrefwindow" rel="namesforlife-name">Pseudomonas</a> branched outside of this main cluster and were interspersed among other genera of the family <a class="namesforlife" title="Pseudomonadaceae - Click to open Names for Life widget" href="https://doi.org/10.1601/nm.2551" target="xrefwindow" rel="namesforlife-name">Pseudomonadaceae</a> . This included a strongly supported clade (Pertucinogena clade) consisting of 19 mainly halotolerant species. The distinctness of this clade from all other members of the family <a class="namesforlife" title="Pseudomonadaceae - Click to open Names for Life widget" href="https://doi.org/10.1601/nm.2551" target="xrefwindow" rel="namesforlife-name">Pseudomonadaceae</a> is strongly supported by 24 conserved signature indels (CSIs) in diverse proteins that are exclusively found in all members of this clade. Nine uncharacterized members of the genus <a class="namesforlife" title="Pseudomonas - Click to open Names for Life widget" href="https://doi.org/10.1601/nm.2552" target="xrefwindow" rel="namesforlife-name">Pseudomonas</a> also shared these CSIs and they branched within the Pertucinogena clade, indicating their affiliation to this clade. On the basis of the strong evidence supporting the distinctness of the Pertucinogena clade, we are proposing transfer of species from this clade into a novel genus Halopseudomonas gen. nov. <a class="namesforlife" title="Pseudomonas caeni - Click to open Names for Life widget" href="https://doi.org/10.1601/nm.14769" target="xrefwindow" rel="namesforlife-name">Pseudomonas caeni</a> also branches outside of the main cluster and groups reliably with <a class="namesforlife" title="Oblitimonas alkaliphila - Click to open Names for Life widget" href="https://doi.org/10.1601/nm.28865" target="xrefwindow" rel="namesforlife-name">Oblitimonas alkaliphila</a> and <a class="namesforlife" title="Thiopseudomonas denitrificans - Click to open Names for Life widget" href="https://doi.org/10.1601/nm.26238" target="xrefwindow" rel="namesforlife-name">Thiopseudomonas denitrificans</a> . Six identified CSIs are uniquely shared by these three species and we are proposing their integration into the emended genus <a class="namesforlife" title="Thiopseudomonas - Click to open Names for Life widget" href="https://doi.org/10.1601/nm.26237" target="xrefwindow" rel="namesforlife-name">Thiopseudomonas</a> , which has priority over the name <a class="namesforlife" title="Oblitimonas - Click to open Names for Life widget" href="https://doi.org/10.1601/nm.28864" target="xrefwindow" rel="namesforlife-name">Oblitimonas</a> . We are also proposing transfer of the deep-branching <a class="namesforlife" title="Pseudomonas hussainii - Click to open Names for Life widget" href="https://doi.org/10.1601/nm.25637" target="xrefwindow" rel="namesforlife-name">Pseudomonas hussainii</a> , for which 22 exclusive CSIs have been identified, into the genus Atopomonas gen. nov. Lastly, we present strong evidence that the species <a class="namesforlife" title="Pseudomonas cissicola - Click to open Names for Life widget" href="https://doi.org/10.1601/nm.2588" target="xrefwindow" rel="namesforlife-name">Pseudomonas cissicola</a> and <a class="namesforlife" title="Pseudomonas geniculata - Click to open Names for Life widget" href="https://doi.org/10.1601/nm.2612" target="xrefwindow" rel="namesforlife-name">Pseudomonas geniculata</a> are misclassified into the genus <a class="namesforlife" title="Pseudomonas - Click to open Names for Life widget" href="https://doi.org/10.1601/nm.2552" target="xrefwindow" rel="namesforlife-name">Pseudomonas</a> and that they are specifically related to the genera <a class="namesforlife" title="Xanthomonas - Click to open Names for Life widget" href="https://doi.org/10.1601/nm.2208" target="xrefwindow" rel="namesforlife-name">Xanthomonas</a> and <a class="namesforlife" title="Stenotrophomonas - Click to open Names for Life widget" href="https://doi.org/10.1601/nm.2255" target="xrefwindow" rel="namesforlife-name">Stenotrophomonas</a> , respectively. In addition, we are also reclassifying &lsquo;Pseudomonas acidophila&rsquo; as Paraburkholderia acidicola sp. nov. (Type strain: G-6302=ATCC 31363=BCRC 13035).

Update: Rudra2021