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Phylogenomics reveals the basis of adaptation of Pseudorhizobium species to extreme environments and supports a taxonomic revision of the genus
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Lassalle, Florent, Dastgheib, Seyed M. M., Zhao, Fang-Jie, Zhang, Jun, Verbarg, Susanne, Frühling, Anja, Brinkmann, Henner, Osborne, Thomas H., Sikorski, Johannes, Balloux, Francois, Didelot, Xavier, Santini, Joanne M. and Petersen, Jörn (2021) Phylogenomics reveals the basis of adaptation of Pseudorhizobium species to extreme environments and supports a taxonomic revision of the genus. Systematic and Applied Microbiology, 44 (1). 126165. doi:10.1016/j.syapm.2020.126165
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Official URL: https://doi.org/10.1016/j.syapm.2020.126165
Abstract
The family Rhizobiaceae includes many genera of soil bacteria, often isolated for their association with plants. Herein, we investigate the genomic diversity of a group of Rhizobium species and unclassified strains isolated from atypical environments, including seawater, rock matrix or polluted soil. Based on whole-genome similarity and core genome phylogeny, we show that this group corresponds to the genus Pseudorhizobium. We thus reclassify Rhizobium halotolerans, R. marinum, R. flavum and R. endolithicum as P. halotolerans sp. nov., P. marinum comb. nov., P. flavum comb. nov. and P. endolithicum comb. nov., respectively, and show that P. pelagicum is a synonym of P. marinum. We also delineate a new chemolithoautotroph species, P. banfieldiae sp. nov., whose type strain is NT-26 (=DSM 106348 =CFBP 8663 ). This genome-based classification was supported by a chemotaxonomic comparison, with increasing taxonomic resolution provided by fatty acid, protein and metabolic profiles. In addition, we used a phylogenetic approach to infer scenarios of duplication, horizontal transfer and loss for all genes in the Pseudorhizobium pangenome. We thus identify the key functions associated with the diversification of each species and higher clades, shedding light on the mechanisms of adaptation to their respective ecological niches. Respiratory proteins acquired at the origin of Pseudorhizobium were combined with clade-specific genes to enable different strategies for detoxification and nutrition in harsh, nutrient-poor environments. [Abstract copyright: Copyright © 2020 The Author(s). Published by Elsevier GmbH.. All rights reserved.]
| Item Type: | Journal Article | ||||||||||||
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| Subjects: | Q Science > QH Natural history Q Science > QR Microbiology |
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| Divisions: | Faculty of Science > Life Sciences (2010- ) | ||||||||||||
| SWORD Depositor: | Library Publications Router | ||||||||||||
| Library of Congress Subject Headings (LCSH): | Rhizobium, Genomes , Phylogeny | ||||||||||||
| Journal or Publication Title: | Systematic and Applied Microbiology | ||||||||||||
| Publisher: | Urban und Fischer Verlag | ||||||||||||
| ISSN: | 0723-2020 | ||||||||||||
| Official Date: | January 2021 | ||||||||||||
| Dates: |
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| Date of first compliant deposit: | 12 January 2021 | ||||||||||||
| Volume: | 44 | ||||||||||||
| Number: | 1 | ||||||||||||
| Article Number: | 126165 | ||||||||||||
| DOI: | 10.1016/j.syapm.2020.126165 | ||||||||||||
| Status: | Peer Reviewed | ||||||||||||
| Publication Status: | Published | ||||||||||||
| Access rights to Published version: | Open Access | ||||||||||||
| RIOXX Funder/Project Grant: |
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