Methylobacterium frigidaeris sp. nov., isolated from an air conditioning system

Lee, Yunho; Jeon, Che Ok

doi:10.1099/ijsem.0.002500

Cited by 14 publications

(7 citation statements)

References 35 publications

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“…Similarly, Methylobacterium frigidaeris IER25-16 T presented only one 16S rRNA sequence, and it was assigned to Bacillus (Table 2). The WGS accession provided from its description corresponded to the genome employed here (Lee and Jeon, 2018), and despite that, it presented only 86.2% of identity with the reference (KY864396). In the core-proteome dendrogram (Supplementary Figure 2), M. frigidaeris IER25-16 T was also found along with other Methylobacterium instead of Bacillus strains.…”

Section: Quality Analysis Of the Genome Collectionmentioning

confidence: 97%

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

et al. 2021

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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.

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Section: Quality Analysis Of the Genome Collectionmentioning

confidence: 97%

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

et al. 2021

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“…Strains: 1: Methylobacterium sp. nov. (n = 3, where n: IF7SW-B2 T , IIF1SW-B5 and IIF4SW-B5) (this study); 2: M. currus PR1016A T (Park et al, 2018); 3: M. aquaticum DSM 16371 T (Gallego et al, 2005a;Park et al, 2018); 4: M. variable DSM 16961 T (Gallego et al, 2005b;Park et al, 2018); 5: M. platani JCM 14648 T (Kang et al, 2007;Park et al, 2018); 6: M. tarhaniae DSM 25844 T (Veyisoglu et al, 2013;Kim et al, 2019); 7: M. terrae KCTC 52904 T (Kim et al, 2019); 8: M. indicum SE2.11 T (Chaudhry et al, 2016); 9: M. frigidaeris IER25-16 T (Lee and Jeon, 2018). w, weakly positive; +, Positive; -, Negative; N.D., not determined.…”

Section: Functional Characteristics Of the Novel Iss Strainmentioning

confidence: 88%

“…The product of the miaA gene was reported to be responsible for isopentenylation of a specific adenine in some tRNAs and confirmed the secretion of zeatin originated from tRNA in M. extorquens (Koenig et al, 2002). Furthermore, multiple components of the cobalamin synthesis pathway, such as cobalamin biosynthesis protein BluB, L-threonine 3-O-phosphate decarboxylase (EC 4.1.1.81), adenosylcobinamide-phosphate guanylyltransferase (EC 2.7.7.62), cobyric acid synthase (EC 6.3.5.10), nicotinatenucleotide-dimethylbenzimidazole phosphoribosyltransferase (EC 2.4.2.21), adenosylcobinamide-phosphate synthase (EC Strains: 1: IF7SW-B2 T (this study), 2: IIF1SW-B5 (this study); 3: IIF4SW-B5 (this study); 4: M. currus PR1016A T (Park et al, 2018); 5: M. aquaticum DSM 16371 T (Kim et al, 2019); 6: M. variable DSM 16961 T (Park et al, 2018); 7: M. platani JCM 14648 T (Kang et al, 2007); 8: M. tarhaniae DSM 25844 T (Kim et al, 2019); 9: M. terrae KCTC 52904 T (Kim et al, 2019); 10: M. indicum SE2.11 T (Chaudhry et al, 2016); 11: M. frigidaeris IER25-16 T (Lee and Jeon, 2018). -: Not detected, tr: trace amount (<1%).…”

Section: Genes Essential For Interaction With Plants In the Iss Strainmentioning

confidence: 99%

Methylobacterium ajmalii sp. nov., Isolated From the International Space Station

et al. 2021

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Four strains belonging to the family of Methylobacteriaceae were isolated from different locations on the International Space Station (ISS) across two consecutive flights. Of these, three were identified as Gram-negative, rod-shaped, catalase-positive, oxidase-positive, motile bacteria, designated as IF7SW-B2T, IIF1SW-B5, and IIF4SW-B5, whereas the fourth was identified as Methylorubrum rhodesianum. The sequence similarity of these three ISS strains, designated as IF7SW-B2T, IIF1SW-B5, and IIF4SW-B5, was <99.4% for 16S rRNA genes and <97.3% for gyrB gene, with the closest being Methylobacterium indicum SE2.11T. Furthermore, the multi-locus sequence analysis placed these three ISS strains in the same clade of M. indicum. The average nucleotide identity (ANI) values of these three ISS strains were <93% and digital DNA-DNA hybridization (dDDH) values were <46.4% with any described Methylobacterium species. Based on the ANI and dDDH analyses, these three ISS strains were considered as novel species belonging to the genus Methylobacterium. The three ISS strains showed 100% ANI similarity and dDDH values with each other, indicating that these three ISS strains, isolated during various flights and from different locations, belong to the same species. These three ISS strains were found to grow optimally at temperatures from 25 to 30°C, pH 6.0 to 8.0, and NaCl 0 to 1%. Phenotypically, these three ISS strains resemble M. aquaticum and M. terrae since they assimilate similar sugars as sole carbon substrate when compared to other Methylobacterium species. Fatty acid analysis showed that the major fatty acid produced by the ISS strains are C18:1−ω7c and C18:1−ω6c. The predominant quinone was ubiquinone 10, and the major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, and an unidentified lipid. Therefore, based on genomic, phylogenetic, biochemical, and fatty acid analyses, strains IF7SW-B2T, IIF1SW-B5, and IIF4SW-B5, are assigned to a novel species within the genus Methylobacterium, and the name Methylobacterium ajmalii sp. nov. is proposed. The type strain is IF7SW-B2T (NRRL B-65601T and LMG 32165T).

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“…Members of the genus Methylobacterium are typically strictly aerobic methylotrophic bacteria and grow well on single-carbon compounds as the sole sources of carbon and energy, as well as on a wide range of multicarbon growth substrates (28). Recently, novel Methylobacterium species have been isolated from ACS (29,30), and 12 species of Methylobacterium were identified in the ECs of automobile ACS in this study, implying that Methylobacterium members might have the ability to metabolize VOCs as the nutrient or carbon source to grow in the ECs of automobile ACS.…”

Section: Discussionmentioning

confidence: 99%

Dominance of Gas-Eating, Biofilm-Forming Methylobacterium Species in the Evaporator Cores of Automobile Air-Conditioning Systems

Park

Jung

Park

et al. 2020

mSphere

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Microbial communities in the evaporator core (EC) of automobile air-conditioning systems have a large impact on indoor air quality, such as malodor and allergenicity. DNA-based microbial population analysis of the ECs collected from South Korea, China, the United States, India, and the United Arab Emirates revealed the extraordinary dominance of Methylobacterium species in EC biofilms. Mixed-volatile organic compound (VOC) utilization and biofilm-forming capabilities were evaluated to explain the dominance of Methylobacterium species in the ECs. The superior growth of all Methylobacterium species could be possible under mixed-VOC conditions. Interestingly, two lifestyle groups of Methylobacterium species could be categorized as the aggregator group, which sticks together but forms a small amount of biofilm, and the biofilm-forming group, which forms a large amount of biofilm, and their genomes along with phenotypic assays were analyzed. Pili are some of the major contributors to the aggregator lifestyle, and succinoglycan exopolysaccharide production may be responsible for the biofilm formation. However, the coexistence of these two lifestyle Methylobacterium groups enhanced their biofilm formation compared to that with each single culture. IMPORTANCE Air-conditioning systems (ACS) are indispensable for human daily life; however, microbial community analysis in automobile ACS has yet to be comprehensively investigated. A bacterial community analysis of 24 heat exchanger fins from five countries (South Korea, China, the United States, India, and the United Arab Emirates [UAE]) revealed that Methylobacterium species are some of the dominant bacteria in automobile ACS. Furthermore, we suggested that the predominance of Methylobacterium species in automobile ACS is due to the utilization of mixed volatile organic compounds and their great ability for aggregation and biofilm formation.

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Methylobacterium frigidaeris sp. nov., isolated from an air conditioning system

Cited by 14 publications

References 35 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

Methylobacterium ajmalii sp. nov., Isolated From the International Space Station

Dominance of Gas-Eating, Biofilm-Forming Methylobacterium Species in the Evaporator Cores of Automobile Air-Conditioning Systems

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