Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria

Hördt, Anton; López, Marina García; Meier‐Kolthoff, Jan P.; Schleuning, Marcel; Weinhold, Lisa-Maria; Tindall, Brian J.; Gronow, Sabine; Kyrpides, Nikos C.; Woyke, Tanja; Göker, Markus

doi:10.3389/fmicb.2020.00468

Cited by 1,575 publications

(444 citation statements)

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“…While a recent large-scale analysis of Alphaproteobacteria type strain genomes suggested that the genus Pseudorhizobium should be merged into Rhizobium [16], we bring extensive evidence that Pseudorhizobium is well differentiated genomically and phenotypically and forms a bona fide bacterial genus. Through the phylogeny-aware comparison of genomes, we explored the functional specificities of lineages within this genus (Figure 3).…”

Section: Discussionmentioning

confidence: 84%

“…The strains NT-25 and NT-26 can withstand very high levels of arsenic (greater than 20 mM arsenite and 0.5 M arsenate), thanks to functions encoded notably by the arsenic-resistance ( ars ) genes [49]. In addition, they can gain energy from the oxidation of arsenite, with the mechanism in NT-26 studied in detail [5,6,16,49,50,52,70]. Analysis of the NT-26 genome sequence revealed other key genes involved in the resistance to arsenic, including the phn / pst genes, which encode phosphate-specific transporters with high affinity for phosphate but not for its structural analogue arsenate.…”

Section: Introductionmentioning

confidence: 99%

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Phylogenomic analysis reveals the basis of adaptation of Pseudorhizobium species to extreme environments

Lassalle

Smm²,

Zhao

et al. 2019

Preprint

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AbstractThe 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 comb. nov., P. marinum comb. nov., P. flavum comb. nov. and R. 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-26T (= DSM 106348T = CFBP 8663T). This genome-based classification was supported by a chemotaxonomic comparison, with gradual 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 are combined with clade-specific genes to encode different strategies for detoxification and nutrition in harsh, nutrient-poor environments. Finally, we predict diagnostic phenotypes for the distinction of P. banfieldiae from other Pseudorhizobium species, including autotrophy and sensitivity to the azo dye Congo Red, which we experimentally validated.

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Section: Discussionmentioning

confidence: 84%

Section: Introductionmentioning

confidence: 99%

Phylogenomic analysis reveals the basis of adaptation of Pseudorhizobium species to extreme environments

Lassalle

Smm²,

Zhao

et al. 2019

Preprint

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“…The effects of temperature (10-45 °C), initial pH (5.0-9.5) and NaCl concentration (0-9%, w/v) on growth were determined by monitoring OD 660 in MPM medium with sucrose (2 g l −1 ) and yeast extract (0.2 g l −1 ). Growth at different salt concentrations (0, 0.1, 0.3 and 0.5-9.0% at intervals of 0.5% NaCl (w/v)) and temperatures (10,15,18,20,25,30,35,40,42 and 45 °C) was tested at pH 6.5. The pH ranges for growth were confirmed in MPM medium at pH 5.0-9.5 with increments of ~0.5 pH unit, using the appropriate biological buffers, namely citrate/phosphate (pH 5.0-7.5), Tris/HCl (pH 7.5-8.5) and carbonate/bicarbonate (pH 9.0-9.5) at optimal temperature (30 °C) and NaCl concentration (1.5% (w/v) NaCl).…”

Section: Introductionmentioning

confidence: 99%

“…The phylogenetic tree had high branch support, which provides for reliable determination of the phylogenetic position of the genus Sphaerochaeta. Recently, it was suggested that Sphaerochaeta with the phylogenetically most closely related genus Pleomorphochaeta belong to the same family [35]. This proposal was based only on topology of the tree based on the 16S rRNA gene sequences and on the fact that representatives of both genera have spherical cells.…”

Section: Introductionmentioning

confidence: 99%

Sphaerochaeta halotolerans sp. nov., a novel spherical halotolerant spirochete from a Russian heavy oil reservoir, emended description of the genus Sphaerochaeta, reclassification of Sphaerochaeta coccoides to a new genus Parasphaerochaeta gen. nov. as Parasphaerochaeta coccoides comb. nov. and proposal of Sphaerochaetaceae fam. nov.

Bidzhieva

Соколова

Grouzdev

et al. 2020

International Journal of Systematic and Evolutionary Microbiology

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Anaerobic, fermentative, halotolerant bacteria, strains 4-11T and 585, were isolated from production water of two low-temperature petroleum reservoirs (Russia) and were characterized by using a polyphasic approach. Cells of the strains were spherical, non-motile and 0.30–2.5 µm in diameter. Strain 4-11T grew optimally at 35 °C, pH 6.0 and 1.0–2.0% (w/v) NaCl. Both strains grew chemoorganotrophically with mono-, di- and trisaccharides. The major cellular fatty acids of both strains were C14:0, C16:0, C16:1 ω9 and C18:0 3-OH. Major polar lipids were glycolipids and phospholipids. The 16S rRNA gene sequences of the strains 4-11T and 585 had 99.9% similarity and were most closely related to the sequence of Sphaerochaeta associata GLS2T (96.9, and 97.0% similarity, respectively). The G+C content of the genomic DNA of strains 4-11T and 585 were 46.8 and 46.9%, respectively. The average nucleotide identity and digital DNA–DNA hybridization values between the genomes of strain 4-11T and S. associata GLS2T were 73.0 and 16.9%, respectively. Results of phylogenomic metrics analysis of the genomes and 120 core proteins of strains 4-11T and 585 and their physiological and biochemical characteristics confirmed that the strains represented a novel species of the genus Sphaerochaeta , for which the name Sphaerochaeta halotolerans sp. nov. is proposed, with the type strain 4-11T (=VKM B-3269T=KCTC 15833T). Based on the results of phylogenetic analysis, Sphaerochaeta coccoides was reclassified as member of a new genus Parasphaerochaeta gen. nov., Parasphaerochaeta coccoides comb. nov. The genera Sphaerochaeta and Parasphaerochaeta form a separate clade, for which a novel family, Sphaerochaetaceae fam. nov., is proposed.

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“…Recently, Hördt et al (2) analyzed more 1000 α-Proteobacteria type-strain genome composites, and suggested major emendation's for many species according to phylogenetic features, resting on genomic data. One of the changes suggested by these authors includes the genus…”

Section: Introductionmentioning

confidence: 99%

Reclassification of Brucella ciceri as later heterotypic synonyms of Brucella intermedia

Sánchez-Reyes

2020

Preprint

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Recently Hordt et al. 2020 proposed to merge Ochrobactrum and Brucella genera based on up to date phylogenomic evidence and overall genomic divergence among Brucella-Ochrobactrum clade. This led to the description of the new combinations Brucella ciceri comb. nov., basonym: Ochrobactrum ciceri Imran et al. 2010 and Brucella intermedia comb. nov., basonym: Ochrobactrum intermedium Velasco et al. 1998. However, the type species for Brucella ciceri DSM 22292T and Brucella intermedia LMG 3301T show whole-genome coherence at the species level (ANI = 98.21 %, Mash D = 0.0154006, dDDH relatedness >70%), suggesting that may belong to the same genomospecies. Also, both taxa formed a single clade in the phylogenomic tree based on single-copy gene sequences. Previously reported phenotypic data offer a context where both taxa are highly related supporting this synonymy. Therefore, Brucella ciceri should be reclassified as later heterotypic synonyms of Brucella intermedia, which has priority. The species description is consequently amended.

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Analysis of 1,000+ Type-Strain Genomes Substantially Improves Taxonomic Classification of Alphaproteobacteria

Cited by 1,575 publications

References 898 publications

Phylogenomic analysis reveals the basis of adaptation of Pseudorhizobium species to extreme environments

Phylogenomic analysis reveals the basis of adaptation of Pseudorhizobium species to extreme environments

Reclassification of Brucella ciceri as later heterotypic synonyms of Brucella intermedia

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