Symbiotic and non-symbiotic members of the genus<i>Ensifer</i>(syn.<i>Sinorhizobium</i>) are separated into two clades based on comparative genomics and high-throughput phenotyping

Fagorzi, Camilla; Ilie, Alexandru; Decorosi, Francesca; Cangioli, Lisa; Viti, Carlo; Mengoni, Alessio; diCenzo, George C.

doi:10.1101/2020.04.23.055285

Cited by 7 publications

(7 citation statements)

References 96 publications

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“…The ability of bacteria to grow in LB broth medium at 30°C was assessed using 96-well microplates as detailed by Fagorzi et al (2020). Growth was estimated (over a 48 h period) on the basis of optical density (595 nm) by taking readings at hourly intervals using a FLUOstar OPTIMA plate reader (BMG LABTECH, Germany).…”

Section: Phenotypic Characterizationmentioning

confidence: 99%

“…The genus Ensifer consists of diverse species of soil bacteria and includes bacterial predators and agriculturally important species capable of fixing nitrogen in symbiotic association with legume plants such as alfalfa (Medicago sativa). This bacterial genus is currently divided into two major clades based on phylogenetic analysis of multiple housekeeping (core) genes (Martens et al, 2008;Kumar et al, 2017;Fagorzi et al, 2020;Kuzmanović et al, 2022). One of these clades is represented by the non-symbiotic species, Ensifer morelensis (Wang et al, 2002) and the predatory species, Ensifer adhaerens (Casida, 1982), and the other clade by symbiotic nitrogen fixing species such as Ensifer meliloti (de Lajudie et al, 1994) and Ensifer medicae (Rome et al, 1996).…”

Section: Introductionmentioning

confidence: 99%

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Ensifer canadensis sp. nov. strain T173T isolated from Melilotus albus (sweet clover) in Canada possesses recombinant plasmid pT173b harbouring symbiosis and type IV secretion system genes apparently acquired from Ensifer medicae

2023

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A bacterial strain, designated T173T, was previously isolated from a root-nodule of a Melilotus albus plant growing in Canada and identified as a novel Ensifer lineage that shared a clade with the non-symbiotic species, Ensifer adhaerens. Strain T173T was also previously found to harbour a symbiosis plasmid and to elicit root-nodules on Medicago and Melilotus species but not fix nitrogen. Here we present data for the genomic and taxonomic description of strain T173T. Phylogenetic analyses including the analysis of whole genome sequences and multiple locus sequence analysis (MLSA) of 53 concatenated ribosome protein subunit (rps) gene sequences confirmed placement of strain T173T in a highly supported lineage distinct from named Ensifer species with E. morelensis Lc04T as the closest relative. The highest digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values of genome sequences of strain T173T compared with closest relatives (35.7 and 87.9%, respectively) are well below the respective threshold values of 70% and 95–96% for bacterial species circumscription. The genome of strain T173T has a size of 8,094,229 bp with a DNA G + C content of 61.0 mol%. Six replicons were detected: a chromosome (4,051,102 bp) and five plasmids harbouring plasmid replication and segregation (repABC) genes. These plasmids were also found to possess five apparent conjugation systems based on analysis of TraA (relaxase), TrbE/VirB4 (part of the Type IV secretion system (T4SS)) and TraG/VirD4 (coupling protein). Ribosomal RNA operons encoding 16S, 23S, and 5S rRNAs that are usually restricted to bacterial chromosomes were detected on plasmids pT173d and pT173e (946,878 and 1,913,930 bp, respectively) as well as on the chromosome of strain T173T. Moreover, plasmid pT173b (204,278 bp) was found to harbour T4SS and symbiosis genes, including nodulation (nod, noe, nol) and nitrogen fixation (nif, fix) genes that were apparently acquired from E. medicae by horizontal transfer. Data for morphological, physiological and symbiotic characteristics complement the sequence-based characterization of strain T173T. The data presented support the description of a new species for which the name Ensifer canadensis sp. nov. is proposed with strain T173T (= LMG 32374T = HAMBI 3766T) as the species type strain.

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Section: Phenotypic Characterizationmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Ensifer canadensis sp. nov. strain T173T isolated from Melilotus albus (sweet clover) in Canada possesses recombinant plasmid pT173b harbouring symbiosis and type IV secretion system genes apparently acquired from Ensifer medicae

2023

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“…In the most recent studies about the nonsymbiotic Ensifer and symbiotic Sinorhizobium , Fagorzi et al . (2020) suggested that the currently combined genus Ensifer should be divided back into pre‐existing of two genera, based on their distinct genomic and phenotypic properties and large segregation in two phylogenetically distinct clades.…”

Section: Alpha‐rhizobia (α‐Rhizobia)mentioning

confidence: 99%

Recent development and new insight of diversification and symbiosis specificity of legume rhizobia: mechanism and application

Chen

Wang²,

et al. 2021

J Appl Microbiol

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SummaryCurrently, symbiotic rhizobia (sl., rhizobium) refer to the soil bacteria in aand b-Proteobacteria that can induce root and/or stem nodules on some legumes and a few of nonlegumes. In the nodules, rhizobia convert the inert dinitrogen gas (N 2 ) into ammonia (NH 3 ) and supply them as nitrogen nutrient to the host plant. In general, this symbiotic association presents specificity between rhizobial and leguminous species, and most of the rhizobia use lipochitooligosaccharides, so called Nod factor (NF), for cooperating with their host plant to initiate the formation of nodule primordium and to inhibit the plant immunity. Besides NF, effectors secreted by type III secretion system (T3SS), exopolysaccharides and many microbeassociated molecular patterns in the rhizobia also play important roles in nodulation and immunity response between rhizobia and legumes. However, the promiscuous hosts like Glycine max and Sophora flavescens can nodulate with various rhizobial species harbouring diverse symbiosis genes in different soils, meaning that the nodulation specificity/efficiency might be mainly determined by the host plants and regulated by the soil conditions in a certain cases. Based on previous studies on rhizobial application, we propose a '1+nÀN' model to promote the function of symbiotic nitrogen fixation (SNF) in agricultural practice, where '1' refers to appreciate rhizobium; '+n' means the addition of multiple trace elements and PGPR bacteria; and 'ÀN' implies the reduction of chemical nitrogen fertilizer. Finally, open questions in the SNF field are raised to future think deeply and researches. Current rhizobial taxonomic outline and use of genome sequence in rhizobial systematicsCurrently, all the symbiotic nitrogen-fixing bacteria associating with legumes are found in the Phylum Proteobacteria, mainly in the Classes Alphaproteobacteria (a-rhizobia) and Betaproteobacteria (b-rhizobia), but maybe also Gammaproteobacteria (c-rhizobia) (Shiraishi et al. 2010) , with about 180 species in 20 genera at the time of writing (Fig. 1). Among them, a-rhizobia are the most common group with a very wide distribution in biogeography and host plants, and beta-rhizobia are also well established with specific legumes though less widely distributed.It is common that symbiotic rhizobia are usually intermingled with nonsymbiotic bacteria at different taxonomic levels. For example, a group of nonsymbiotic bacteria isolated from maize root endosphere, Rhizobium

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“…7.1. Based on an extensive genomic and phenotypic analysis of the genus Ensifer / Sinorhizobium , Fagorzi et al [ 10 ] concluded that it is made of two distinct clades, with inter-clade genomic similarity under 85 % average nucleotide identity (ANI) and 90 % average amino acid identity (AAI). They presented a large body of biological evidence suggesting that these clades harbour significantly different organisms, with one containing symbiotic strains and the other non-symbiotic strains.…”

Section: Minute 7 Recent Relevant Publications In Genome-based Taxonomymentioning

confidence: 99%

International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Rhizobia and Agrobacteria Minutes of the closed meeting by videoconference, 6 July 2020

Lajudie

Mousavi

Young

2021

International Journal of Systematic and Evolutionary Microbiology

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Symbiotic and non-symbiotic members of the genusEnsifer(syn.Sinorhizobium) are separated into two clades based on comparative genomics and high-throughput phenotyping

Abstract: symbiotic members of the genus Ensifer (syn. Sinorhizobium) are 1 separated into two clades based on comparative genomics and high-throughput phenotyping 2 3

Cited by 7 publications

References 96 publications

Ensifer canadensis sp. nov. strain T173T isolated from Melilotus albus (sweet clover) in Canada possesses recombinant plasmid pT173b harbouring symbiosis and type IV secretion system genes apparently acquired from Ensifer medicae

Ensifer canadensis sp. nov. strain T173T isolated from Melilotus albus (sweet clover) in Canada possesses recombinant plasmid pT173b harbouring symbiosis and type IV secretion system genes apparently acquired from Ensifer medicae

Recent development and new insight of diversification and symbiosis specificity of legume rhizobia: mechanism and application

International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Rhizobia and Agrobacteria Minutes of the closed meeting by videoconference, 6 July 2020

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