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

Volpiano, Camila Gazolla; Sant’Anna, Fernando Hayashi; Ambrosini, Adriana; José, Jackson Freitas Brilhante de São; Beneduzi, Anelise; Whitman, William B.; Souza, Emanuel Maltempi de; Lisboa, Bruno Brito; Vargas, Luciano Kayser; Passaglia, Luciane Maria Pereira

doi:10.3389/fmicb.2021.614957

Cited by 42 publications

(21 citation statements)

References 117 publications

(166 reference statements)

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“…Through the use of dDDH and ANI to delineate species boundaries, several synonyms have been found within the genus Methylobacterium ( Hördt et al, 2020 ) and the family Rhizobiales ( Volpiano et al, 2021 ). Our results support the consideration of Mb.…”

Section: Discussionmentioning

confidence: 99%

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Comprehensive Comparative Genomics and Phenotyping of Methylobacterium Species

et al. 2021

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The pink-pigmented facultative methylotrophs (PPFMs), a major bacterial group found in the plant phyllosphere, comprise two genera: Methylobacterium and Methylorubrum. They have been separated into three major clades: A, B (Methylorubrum), and C. Within these genera, however, some species lack either pigmentation or methylotrophy, which raises the question of what actually defines the PPFMs. The present study employed a comprehensive comparative genomics approach to reveal the phylogenetic relationship among the PPFMs and to explain the genotypic differences that confer their different phenotypes. We newly sequenced the genomes of 29 relevant-type strains to complete a dataset for almost all validly published species in the genera. Through comparative analysis, we revealed that methylotrophy, nitrate utilization, and anoxygenic photosynthesis are hallmarks differentiating the PPFMs from the other Methylobacteriaceae. The Methylobacterium species in clade A, including the type species Methylobacterium organophilum, were phylogenetically classified into six subclades, each possessing relatively high genomic homology and shared phenotypic characteristics. One of these subclades is phylogenetically close to Methylorubrum species; this finding led us to reunite the two genera into a single genus Methylobacterium. Clade C, meanwhile, is composed of phylogenetically distinct species that share relatively higher percent G+C content and larger genome sizes, including larger numbers of secondary metabolite clusters. Most species of clade C and some of clade A have the glutathione-dependent pathway for formaldehyde oxidation in addition to the H4MPT pathway. Some species cannot utilize methanol due to their lack of MxaF-type methanol dehydrogenase (MDH), but most harbor an XoxF-type MDH that enables growth on methanol in the presence of lanthanum. The genomes of PPFMs encode between two and seven (average 3.7) genes for pyrroloquinoline quinone-dependent alcohol dehydrogenases, and their phylogeny is distinctly correlated with their genomic phylogeny. All PPFMs were capable of synthesizing auxin and did not induce any immune response in rice cells. Other phenotypes including sugar utilization, antibiotic resistance, and antifungal activity correlated with their phylogenetic relationship. This study provides the first inclusive genotypic insight into the phylogeny and phenotypes of PPFMs.

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Section: Discussionmentioning

confidence: 99%

“…The quality of the available assembly of Mb. organophilum T (GCA_003096615.1) was sufficiently high, but the source strain DSM 760 T is believed to have been contaminated such that the available assembly did not accurately represent its taxonomic status ( Kato et al, 2005 ; Volpiano et al, 2021 ). Therefore, the strain Mb.…”

Section: Methodsmentioning

confidence: 99%

Comprehensive Comparative Genomics and Phenotyping of Methylobacterium Species

et al. 2021

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“…nov., for this strain. Note that the order Hyphomicrobiales of the class Alphaproteobacteria was recently proposed as a replacement for Rhizobiales [10] and is herein tentatively described as Hyphomicrobiales (Rhizobiales) in reference to previous research [11].…”

Section: Introductionmentioning

confidence: 89%

Characterization of Terrihabitans soli gen. nov., sp. nov., a Novel 0.2 μm-Filterable Soil Bacterium Belonging to a Widely Distributed Lineage of Hyphomicrobiales (Rhizobiales)

et al. 2021

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We previously showed that novel filterable bacteria remain in “sterile” (<0.2 μm filtered) terrestrial environmental samples from Japan, China, and Arctic Norway. Here, we characterized the novel filterable strain IZ6T, a representative strain of a widely distributed lineage. Phylogenetic analysis showed that this strain was affiliated with the Rhizobiales (now proposed as Hyphomicrobiales) of Alphaproteobacteria, but distinct from any other type strains. Strain IZ6T shared the following chemotaxonomic features with the closest (but distantly) related type strain, Flaviflagellibacter deserti SYSU D60017T: ubiquinone-10 as the major quinone; phosphatidylethanolamine, phosphatidylcholine, and phosphatidylglycerol as major polar lipids; and slightly high G+C content of 62.2 mol%. However, the cellular fatty acid composition differed between them, and the unsaturated fatty acid (C18:1ω7c/C18:1ω6c) was predominantly found in our strain. Moreover, unlike methyrotrophs and nitrogen-fixers of the neighboring genera of Hyphomicrobiales (Rhizobiales), strain IZ6T cannot utilize a one-carbon compound (e.g., methanol) and fix atmospheric nitrogen gas. These findings were consistent with the genome-inferred physiological potential. Based on the phylogenetic, physiological, and chemotaxonomic traits, we propose that strain IZ6T represents a novel genus and species with the name Terrihabitans soli gen. nov., sp. nov. (=NBRC 106741T = NCIMB 15058T). The findings will provide deeper insight into the eco-physiology of filterable microorganisms.

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“…Currently, bacterial species are defined as including strains that have 95.00-96.00% of average nucleotide identity (ANI) and 70.00% of digital DDH (dDDH) [61]. Analysis between Microtetraspora sp.…”

Section: Microtetraspora Sp Ac03309 Taxonomic Delineationmentioning

confidence: 99%

“…AC04546 had a 99.85% identity to Dactylosporangium sucinum strain RY35-23 (NR_145935.1) and genome-based phylogeny also shows that they are closely related (Figure 5) (TYGS, https://tygs.dsmz.de, accessed on 25 June 2021). Bacterial species are defined as including strains that present 95.00-96.00% of average nucleotide identity (ANI) and 70.00% of digital DDH (dDDH) [61]. Due to the low dDDH value of 44.40%, Average Amino Acid identity (AAI) was carried out [73].…”

Section: Dactylosporangium Sp Ac04546 Taxonomic Delineationmentioning

confidence: 99%

Rubber Degrading Strains: Microtetraspora and Dactylosporangium

et al. 2021

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Rubber composed of highly unsaturated hydrocarbons, modified through addition of chemicals and vulcanization are widely used to date. However, the usage of rubber, faces many obstacles. These elastomeric materials are difficult to be re-used and recovered, leading to high post-consumer waste and vast environmental problems. Tyres, the major rubber waste source can take up to 80 years to naturally degrade. Experiments show that the latex clearing proteins (Lcp) found in Actinobacteria were reportedly critical for the initial oxidative cleavage of poly(cis-1,4-isoprene), the major polymeric unit of rubber. Although, more than 100 rubber degrading strains have been reported, only 8 Lcp proteins isolated from Nocardia (3), Gordonia (2), Streptomyces (1), Rhodococcus (1), and Solimonas (1) have been purified and biochemically characterized. Previous studies on rubber degrading strains and Lcp enzymes, implied that they are distinct. Following this, we aim to discover additional rubber degrading strains by randomly screening 940 Actinobacterial strains isolated from various locations in Sarawak on natural rubber (NR) latex agar. A total of 18 strains from 5 genera produced clearing zones on NR latex agar, and genes encoding Lcp were identified. We report here lcp genes from Microtetraspora sp. AC03309 (lcp1 and lcp2) and Dactylosporangium sp. AC04546 (lcp1, lcp2, lcp3), together with the predicted genes related to rubber degradation. In silico analysis suggested that Microtetraspora sp. AC03309 is a distinct species closely related to Microtetraspora glauca while Dactylosporangium sp. AC04546 is a species closely related to Dactylosporangium sucinum. Genome-based characterization allowed the establishment of the strains taxonomic position and provided insights into their metabolic potential especially in biodegradation of rubber. Morphological changes and the spectrophotometric detection of aldehyde and keto groups indicated the degradation of the original material in rubber samples incubated with the strains. This confirms the strains’ ability to utilize different rubber materials (fresh latex, NR product and vulcanized rubber) as the sole carbon source. Both strains exhibited different levels of biodegradation ability. Findings on tyre utilization capability by Dactylosporangium sp. AC04546 is of interest. The final aim is to find sustainable rubber treatment methods to treat rubber wastes.

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

Cited by 42 publications

References 117 publications

Comprehensive Comparative Genomics and Phenotyping of Methylobacterium Species

Comprehensive Comparative Genomics and Phenotyping of Methylobacterium Species

Characterization of Terrihabitans soli gen. nov., sp. nov., a Novel 0.2 μm-Filterable Soil Bacterium Belonging to a Widely Distributed Lineage of Hyphomicrobiales (Rhizobiales)

Rubber Degrading Strains: Microtetraspora and Dactylosporangium

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