Mesorhizobium composti sp. nov., isolated from compost

Lin, Shih-Yao; Hameed, Asif; Hsieh, Yu‐Ting; Young, Chiu-Chung

doi:10.1007/s10482-019-01270-y

Cited by 12 publications

(7 citation statements)

References 39 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…"Mesorhizobium composti" was proposed by Lin et al (2019), although the name is not validly published. The assembly employed here was based upon the WGS accession given for the type strain CC-YTH430 T , and the 16S rRNA sequence extracted from the genome and the reference KX988315 presented 100% identity.…”

Section: Quality Analysis Of the Genome Collectionmentioning

confidence: 99%

“…The assembly employed here was based upon the WGS accession given for the type strain CC-YTH430 T , and the 16S rRNA sequence extracted from the genome and the reference KX988315 presented 100% identity. In a 16S rRNA gene tree, "M. composti" CC-YTH430 T was reported to form a cluster with Mesorhizobium and Pseudaminobacter species (Lin et al, 2019), which could explain its wrong assignment to Pseudaminobacter in SILVA SSU r138 (Table 2). Besides, several Mesorhizobium species have been described as intermixed with Pseudaminobacter in 16S rRNA gene (Lin et al, 2019) and GBDP d5 phylogenies Hördt et al (2020).…”

Section: Quality Analysis Of the Genome Collectionmentioning

confidence: 99%

“…In a 16S rRNA gene tree, "M. composti" CC-YTH430 T was reported to form a cluster with Mesorhizobium and Pseudaminobacter species (Lin et al, 2019), which could explain its wrong assignment to Pseudaminobacter in SILVA SSU r138 (Table 2). Besides, several Mesorhizobium species have been described as intermixed with Pseudaminobacter in 16S rRNA gene (Lin et al, 2019) and GBDP d5 phylogenies Hördt et al (2020). Taken into consideration, the genome available for "M. composti" CC-YTH430 T seems to be authentic.…”

Section: Quality Analysis Of the Genome Collectionmentioning

confidence: 99%

See 2 more Smart Citations

Genomic Metrics Applied to Rhizobiales (Hyphomicrobiales): Species Reclassification, Identification of Unauthentic Genomes and False Type Strains

et al. 2021

View full text Add to dashboard Cite

Taxonomic decisions within the order Rhizobiales have relied heavily on the interpretations of highly conserved 16S rRNA sequences and DNA–DNA hybridizations (DDH). Currently, bacterial species are defined as including strains that present 95–96% of average nucleotide identity (ANI) and 70% of digital DDH (dDDH). Thus, ANI values from 520 genome sequences of type strains from species of Rhizobiales order were computed. From the resulting 270,400 comparisons, a ≥95% cut-off was used to extract high identity genome clusters through enumerating maximal cliques. Coupling this graph-based approach with dDDH from clusters of interest, it was found that: (i) there are synonymy between Aminobacter lissarensis and Aminobacter carboxidus, Aurantimonas manganoxydans and Aurantimonas coralicida, “Bartonella mastomydis,” and Bartonella elizabethae, Chelativorans oligotrophicus, and Chelativorans multitrophicus, Rhizobium azibense, and Rhizobium gallicum, Rhizobium fabae, and Rhizobium pisi, and Rhodoplanes piscinae and Rhodoplanes serenus; (ii) Chelatobacter heintzii is not a synonym of Aminobacter aminovorans; (iii) “Bartonella vinsonii” subsp. arupensis and “B. vinsonii” subsp. berkhoffii represent members of different species; (iv) the genome accessions GCF_003024615.1 (“Mesorhizobium loti LMG 6,125T”), GCF_003024595.1 (“Mesorhizobium plurifarium LMG 11,892T”), GCF_003096615.1 (“Methylobacterium organophilum DSM 760T”), and GCF_000373025.1 (“R. gallicum R-602 spT”) are not from the genuine type strains used for the respective species descriptions; and v) “Xanthobacter autotrophicus” Py2 and “Aminobacter aminovorans” KCTC 2,477T represent cases of misuse of the term “type strain”. Aminobacter heintzii comb. nov. and the reclassification of Aminobacter ciceronei as A. heintzii is also proposed. To facilitate the downstream analysis of large ANI matrices, we introduce here ProKlust (“Prokaryotic Clusters”), an R package that uses a graph-based approach to obtain, filter, and visualize clusters on identity/similarity matrices, with settable cut-off points and the possibility of multiple matrices entries.

show abstract

Section: Quality Analysis Of the Genome Collectionmentioning

confidence: 99%

Section: Quality Analysis Of the Genome Collectionmentioning

confidence: 99%

Section: Quality Analysis Of the Genome Collectionmentioning

confidence: 99%

See 1 more Smart Citation

Genomic Metrics Applied to Rhizobiales (Hyphomicrobiales): Species Reclassification, Identification of Unauthentic Genomes and False Type Strains

et al. 2021

View full text Add to dashboard Cite

show abstract

“…The above results indicate that strains from the clusters I, III and VI possess the potential of symbiotic nitrogen fixation with the corresponding legume hosts. In this study, all the Mesorhizobium type strains in Cluster II, IV, V and VII lacked nod and nif genes, and they were isolated from compost ( M. composti CC-YTH430 T ) [ 16 ], soil ( M. terrae NIBRBAC000500504 T ) [ 14 ], root endosphere ( M. ephedrae 6GN30 T ) [ 17 ], rhizosphere ( Mesorhizobium soli JCM 19897 T ) [ 15 ], and aquatic environments ( M. sediminum KCTC 42205 T and M. microcysteis MaA-C15 T ) [ 18 , 19 ].…”

Section: Resultsmentioning

confidence: 99%

“…Nevertheless, type strains of nine of the other Mesorhizobium species were not isolated from legume nodules and they did not present nodulation abilities, i.e. M. comanense 3P27G6 T from groundwater [ 12 ], M. hankyongi Gsoil 531 T , M. soli JCM 19897 T , M. terrae NIBRBAC000500504 T and M. thiogangeticum SJ T from soil [ 13 – 15 ], M. composti CC-YTH430 T from compost [ 16 ], M. ephedrae 6GN30 T from root of Ephedra przewalskii [ 17 ], M. sediminum KCTC 42205 T from deep-sea sediment [ 18 ], and M. microcysteis MaA-C15 T from xenic culture of Microcystis aeruginosa [ 19 ]. Over the years, extensive work has been carried out on classification of Mesorhizobium based on polyphasic taxonomy, leading to the description of 71 (63 validly named) species in this genus, making it the largest genus in the family Phyllobacteriaceae ( https://www.bacterio.net/genus/mesorhizobium/ ).…”

Section: Introductionmentioning

confidence: 99%

Phylogenomic analyses and reclassification of the Mesorhizobium complex: proposal for 9 novel genera and reclassification of 15 species

Li,

Guo,

Sun

et al. 2024

BMC Genomics

View full text Add to dashboard Cite

Backgroud The genus Mesorhizobium is shown by phylogenomics to be paraphyletic and forms part of a complex that includes the genera Aminobacter, Aquamicrobium, Pseudaminobacter and Tianweitania. The relationships for type strains belong to these genera need to be carefully re-evaluated. Results The relationships of Mesorhizobium complex are evaluated based on phylogenomic analyses and overall genome relatedness indices (OGRIs) of 61 type strains. According to the maximum likelihood phylogenetic tree based on concatenated sequences of 539 core proteins and the tree constructed using the bac120 bacterial marker set from Genome Taxonomy Database, 65 type strains were grouped into 9 clusters. Moreover, 10 subclusters were identified based on the OGRIs including average nucleotide identity (ANI), average amino acid identity (AAI) and core-proteome average amino acid identity (cAAI), with AAI and cAAI showing a clear intra- and inter-(sub)cluster gaps of 77.40–80.91% and 83.98–86.16%, respectively. Combined with the phylogenetic trees and OGRIs, the type strains were reclassified into 15 genera. This list includes five defined genera Mesorhizobium, Aquamicrobium, Pseudaminobacter, Aminobacterand Tianweitania, among which 40/41 Mesorhizobium species and one Aminobacter species are canonical legume microsymbionts. The other nine (sub)clusters are classified as novel genera. Cluster III, comprising symbiotic M. alhagi and M. camelthorni, is classified as Allomesorhizobium gen. nov. Cluster VI harbored a single symbiotic species M. albiziae and is classified as Neomesorhizobium gen. nov. The remaining seven non-symbiotic members were proposed as: Neoaquamicrobium gen. nov., Manganibacter gen. nov., Ollibium gen. nov., Terribium gen. nov., Kumtagia gen. nov., Borborobacter gen. nov., Aerobium gen. nov.. Furthermore, the genus Corticibacterium is restored and two species in Subcluster IX-1 are reclassified as the member of this genus. Conclusion The Mesorhizobium complex are classified into 15 genera based on phylogenomic analyses and OGRIs of 65 type strains. This study resolved previously non-monophyletic genera in the Mesorhizobium complex.

show abstract

Mesorhizobium alexandrii sp. nov., isolated from phycosphere microbiota of PSTs-producing marine dinoflagellate Alexandrium minutum amtk4

Yang

Jiang

Zhang

et al. 2020

Antonie van Leeuwenhoek

View full text Add to dashboard Cite

Mesorhizobium composti sp. nov., isolated from compost

Cited by 12 publications

References 39 publications

Genomic Metrics Applied to Rhizobiales (Hyphomicrobiales): Species Reclassification, Identification of Unauthentic Genomes and False Type Strains

Genomic Metrics Applied to Rhizobiales (Hyphomicrobiales): Species Reclassification, Identification of Unauthentic Genomes and False Type Strains

Phylogenomic analyses and reclassification of the Mesorhizobium complex: proposal for 9 novel genera and reclassification of 15 species

Mesorhizobium alexandrii sp. nov., isolated from phycosphere microbiota of PSTs-producing marine dinoflagellate Alexandrium minutum amtk4

Contact Info

Product

Resources

About