Reclassification of Paenibacillus riograndensis as a Genomovar of Paenibacillus sonchi: Genome-Based Metrics Improve Bacterial Taxonomic Classification.

Fernando H Sant’Anna,Gabriela De Carvalho Fernandes,Fábio De Oliveira Pedrosa,Volker F Wendisch,Adriana Ambrosini,Luciana F Brito,Emanuel M De Souza,Valter Baura,Luciane M P Passaglia,Eduardo Balsanelli,Rocheli De Souza,Evelise Bach

doi:10.3389/fmicb.2017.01849

Abstract

Species from the genus Paenibacillus are widely studied due to their biotechnological relevance. Dozens of novel species descriptions of this genus were published in the last couple of years, but few utilized genomic data as classification criteria. Here, we demonstrate the importance of using genome-based metrics and phylogenetic analyses to identify and classify Paenibacillus strains. For this purpose, Paenibacillus riograndensis SBR5T, Paenibacillus sonchi X19-5T, and their close relatives were compared through phenotypic, genotypic, and genomic approaches. With respect to P. sonchi X19-5T, P. riograndensis SBR5T, Paenibacillus sp. CAR114, and Paenibacillus sp. CAS34 presented ANI (average nucleotide identity) values ranging from 95.61 to 96.32%, gANI (whole-genome average nucleotide identity) values ranging from 96.78 to 97.31%, and dDDH (digital DNA–DNA hybridization) values ranging from 68.2 to 73.2%. Phylogenetic analyses of 16S rRNA, gyrB, recA, recN, and rpoB genes and concatenated proteins supported the monophyletic origin of these Paenibacillus strains. Therefore, we propose to assign Paenibacillus sp. CAR114 and Paenibacillus sp. CAS34 to P. sonchi species, and reclassify P. riograndensis SBR5T as a later heterotypic synonym of P. sonchi (type strain X19-5T), with the creation of three novel genomovars, P. sonchi genomovar Sonchi (type strain X19-5T), P. sonchi genomovar Riograndensis (type strain SBR5T), P. sonchi genomovar Oryzarum (type strain CAS34T = DSM 102041T; = BR10511T).

Highlights

The genus Paenibacillus includes nitrogen-fixing species that were isolated from roots of wheat (Beneduzi et al, 2010), maize (Berge et al, 2002), rice (Beneduzi et al, 2008; de Souza et al, 2014), and other plants (Ambrosini et al, 2015)
Average nucleotide identity values based on Blast alignments from all pairwise genome comparisons were computed at JspeciesWS1 (Richter and Rosselló-Móra, 2009). dDDH values were estimated at GGDC (Genome-to-Genome Distance Calculator)2 using GGDC 2.0 BLAST+ and recommended formula 2 (Meier-Kolthoff et al, 2013a)
Concerning the tests performed, P. sonchi X19-5T and P. riograndensis SBR5T only diverged with respect to starch degradation

Summary

Introduction

The genus Paenibacillus includes nitrogen-fixing species that were isolated from roots of wheat (Beneduzi et al, 2010), maize (Berge et al, 2002), rice (Beneduzi et al, 2008; de Souza et al, 2014), and other plants (Ambrosini et al, 2015). Many of these bacterial isolates arose from the search for strains that exert positive effects on the development of agricultural plants. The complete genome sequence of P. riograndensis SBR5T (Brito et al, 2015) and a draft genome sequence of P. sonchi X19-5T (Xie et al, 2014) were determined, and preliminary computation of their ANI (average nucleotide identity) suggested that they belong to the same species

Methods

Results

Conclusion