Separation of the diastereomers of phosphorothioated siRNAs by anion-exchange chromatography under non-denaturing conditions.

In recent years, several small interfering RNA (siRNA) therapeutics have been approved, and most of them are phosphorothioate (PS)-modified for improving nuclease resistance. This chemical modification induces chirality in the phosphorus atom, leading to the formation of diastereomers. Recent studies have revealed that Sp and Rp configurations of PS modifications of siRNAs have different biological properties, such as nuclease resistance and RNA-induced silencing complex (RISC) loading. These results highlight the importance of determining diastereomeric distribution in quality control. Although various analytical approaches have been used to separate diastereomers (mainly single-stranded oligonucleotides), it becomes more difficult to separate all of them as the number of PS modifications increases. Despite siRNA exhibits efficacy in the double-stranded form, few reports have examined the separation of diastereomers in the double-stranded form. In this study, we investigated the applicability of non-denaturing anion-exchange chromatography (AEX) for the separation of PS-modified siRNA diastereomers. Separation of the four isomers of the two PS bonds tended to improve in the double-stranded form compared to the single-stranded form. In addition, the effects of the analytical conditions and PS-modified position on the separation were evaluated. Moreover, the elution order of the Sp and Rp configurations was confirmed, and the steric difference between them, i.e., the direction of the anionic sulfur atom, appeared to be important for the separation mechanism in non-denaturing AEX. Consequently, all 16 peak tops of the four PS modifications were detected in one sequence, and approximately 30 peak tops were detected out of 64 isomers of six PS bonds, indicating that non-denaturing AEX is a useful technique for the quality control of PS-modified siRNA therapeutics.

A copper(I) thiocyanate-based photoresponsive semiconducting 2D coordination polymer.

A coordination polymer, [Cu(SCN)(iqi)]n (iqi = isoquinoline), containing copper(I) thiocyanate and a nitrogen-containing π-conjugated ligand, iqi, has been synthesized and its physical properties were evaluated. This coordination polymer has a two-dimensional (2D) sheet structure consisting of copper(I) thiocyanate and shows photoluminescence derived from 3MLCT and photoconductive properties.

Structural diversity of copper(I)-ethylene complexes with 2,4-bis(2-pyridyl)pyrimidine directed by anions.

The 3 : 1 reaction of [Cu(C2H4)n]ClO4 with 2,4-bis(2-pyridyl)pyrimidine (bpprd) in Me2CO under C2H4 afforded yellow prism crystals of the dinuclear Cu(I)-C2H4 complex [Cu2(bpprd)(η2-C2H4)2(ClO4)2] (1). The 3 : 1 reaction of [Cu(C2H4)n]NO3 with bpprd in Me2CO under C2H4 afforded yellow plate crystals of the tetranuclear Cu(I)-C2H4 complex [Cu4(bpprd)2(η2-C2H4)4(µ-NO3)2](NO3)2 (2). The 10 : 1 reaction of [Cu(C2H4)n]BF4 with bpprd in Me2CO under C2H4 afforded yellow plate crystals of the dinuclear Cu(I)-C2H4 complex [Cu2(bpprd)(η2-C2H4)2(BF4)]BF4 (3). The 3 : 1 reaction of [Cu(C2H4)n]BF4 with bpprd in Me2CO under C2H4 afforded red prism crystals of the polymeric Cu(I)-C2H4 complex {[Cu6(bpprd)4(η2-C2H4)2(µ-η2:η2-C2H4)(µ-BF4)2](BF4)4}n (4). The X-ray crystal structures of complexes 1-4 have been determined. The structural diversity of Cu(I)-C2H4 complexes bridged by bpprd with different anions was demonstrated. The 1D Cu(I)-bpprd/C2H4 coordination polymer 4 bridged by unusual µ-η2:η2-C2H4 and the µ-BF4- anion is of particular significance. Complex 1 exhibited relatively well-resolved 1H NMR signals of bpprd and C2H4 (δ = 4.97 ppm) in (CD3)2CO at 23 °C.

High cytotoxicity of a degraded TBBPA, dibromobisphenol A, through apoptotic and necrosis pathways.

Halogenated flame retardants comprising bisphenol A (BPA) derivatives, such as tetrabromobisphenol A (TBBPA), have been studied their adverse effects on human health. However, despite the fact that these halogenated BPAs are easily degraded in the environment, the risks to living organisms due to these degraded products have mostly been overlooked. To evaluate the potential toxicity of degraded TBBPAs and related compounds, we examined the cytotoxicity of halogenated bisphenol A derivatives possessing one to four halogen atoms in vitro. The results indicated that the degraded TBBPA derivatives exhibited strong cytotoxicity against HeLa cells than TBBPA. Interestingly, the di-halogenated BPA derivatives possessing two halogen atoms exhibited the strongest cytotoxicity among tested compounds. In addition, a lactate dehydrogenase release assay, fluorescence spectroscopy and flow cytometry results indicated that dibromo-BPA and diiodo-BPA induced both apoptotic and necrotic cell death by damaging the cell membranes of HeLa cells. Moreover, Escherichia coli growth was inhibited in the presence of dehalogenated TBBPA and related compounds. These findings suggest that halogenated BPA derivatives that leak from various flame-retardant-containing products require strict monitoring, as not only TBBPA but also its degraded products in environment can exert adverse effects to human health.

Retention behavior of short double-stranded oligonucleotide and its potential impurities by anion-exchange chromatography under non-denaturing conditions.

Small interfering RNA (siRNA), consisting of two complementary single-stranded RNAs with overhanging bases, is being adopted as a potent and specific inhibitor of target gene expression. However, non-duplexed single strands and undesired double strands composed of impurities (e.g., n-1 mer) could be produced in addition to the target double strand in the siRNA manufacturing process. Compared to the liquid chromatography analysis of single strands, the analysis of the duplexes under non-denaturing conditions is challenging, since restricted chromatographic conditions are required to maintain the Watson-Crick hydrogen bonds. This study reports the analysis of double-stranded oligomers having approximately 20 base pairs with some overhanging bases as non-denatured forms by anion-exchange chromatography (AEX). Optimization of the chromatographic conditions could potentially achieve the adequate separation of excess single strands from the double strand. Non-optimal duplexes, such as duplexes with long overhangs or bulge structures, were prepared by intentionally deleting terminal or middle nucleotide(s) of either the sense or the antisense strand, and these non-optimal duplexes were eluted at different retention times in most of the cases. Interestingly, under alkaline chromatographic conditions (pH 9.0), non-optimal duplexes containing a shortmer tended to exhibit a stronger retention than their parent duplexes, although they possessed a less negative charge. This study demonstrated some retention behavior of double strands with overhangs by AEX under non-denaturing conditions.

Metabolic potential of the imperfect denitrifier Candidatus Desulfobacillus denitrificans in an anammox bioreactor.

The imperfect denitrifier, Candidatus (Ca.) Desulfobacillus denitrificans, which lacks nitric oxide (NO) reductase, frequently appears in anammox bioreactors depending on the operating conditions. We used genomic and metatranscriptomic analyses to evaluate the metabolic potential of Ca. D. denitrificans and deduce its functional relationships to anammox bacteria (i.e., Ca. Brocadia pituitae). Although Ca. D. denitrificans is hypothesized to supply NO to Ca. B. pituitae as a byproduct of imperfect denitrification, this microbe also possesses hydroxylamine oxidoreductase, which catalyzes the oxidation of hydroxylamine to NO and potentially the reverse reaction. Ca. D. denitrificans can use a range of electron donors for denitrification, including aromatic compounds, glucose, sulfur compounds, and hydrogen, but metatranscriptomic analysis suggested that the major electron donors are aromatic compounds, which inhibit anammox activity. The interrelationship between Ca. D. denitirificans and Ca. B. pituitae via the metabolism of aromatic compounds may govern the population balance of both species. Ca. D. denitrificans also has the potential to fix CO2 via an irregular Calvin cycle and couple denitrification to the oxidation of hydrogen and sulfur compounds under chemolithoautotrophic conditions. This metabolic versatility, which suggests a mixotrophic lifestyle, would facilitate the growth of Ca. D. denitrificans in the anammox bioreactor.

Correction: Dinuclear cobalt complexes with a redox active biphenyl bridging ligand [Co2(BP)(tqa)2](PF6)2 (H4BP = 4,4'-bis(3-tert-butyl-1,2-catechol), tqa = tris(2-quinolylmethyl)amine): structure and magnetic properties.

Correction for 'Dinuclear cobalt complexes with a redox active biphenyl bridging ligand [Co2(BP)(tqa)2](PF6)2 (H4BP = 4,4'-bis(3-tert-butyl-1,2-catechol), tqa = tris(2-quinolylmethyl)amine): structure and magnetic properties' by Yusaku Suenaga et al., Dalton Trans., 2021, DOI: .

Community structure and metabolic potentials of the traditional rice beer starter 'emao'.

The emao, a traditional beer starter used in the North-East regions of India produces a high quality of beer from rice substrates; however, its microbial community structure and functional metabolic modules remain unknown. To address this gap, we have used shot-gun whole-metagenome sequencing technology; accordingly, we have detected several enzymes that are known to catalyze saccharification, lignocellulose degradation, and biofuel production indicating the presence of metabolic functionome in the emao. The abundance of eukaryotic microorganisms, specifically the members of Mucoromycota and Ascomycota, dominated over the prokaryotes in the emao compared to previous metagenomic studies on such traditional starters where the relative abundance of prokaryotes occurred higher than the eukaryotes. The family Rhizopodaceae (64.5%) and its genus Rhizopus (64%) were the most dominant ones, followed by Phaffomycetaceae (11.14%) and its genus Wickerhamomyces (10.03%). The family Leuconostocaceae (6.09%) represented by two genera (Leuconostoc and Weissella) was dominant over the other bacteria, and it was the third-highest in overall relative abundance in the emao. The comprehensive microbial species diversity, community structure, and metabolic modules found in the emao are of practical value in the formulation of mixed-microbial cultures for biofuel production from plant-based feedstocks.

Dinuclear cobalt complexes with a redox active biphenyl bridging ligand [Co2(BP)(tqa)2](PF6)2 (H4BP = 4,4'-bis(3-tert-butyl-1,2-catechol), tqa = tris(2-quinolylmethyl)amine): structure and magnetic properties.

The biscatechol, H4BP (4,4'-bis(3-tert-butyl-1,2-catechol)) that can directly connect two redox active catechol moieties was synthesized. Also, tris(2-pyridylmethyl)amine (tpa), bis(2-pyridylmethyl)(2-quinolylmethyl)amine (bpqa), (2-pyridylmethyl)bis(2-quinolyl methyl)amine (pbqa), and tris (2-quinolylmethyl)amine (tqa) were synthesized as terminal ligands of the tetracoordinated tripod. In total, five different dinuclear Co complexes were synthesized from H4BP with various terminal ligands as follows, [Co2(BP)(tpa)2](PF6)2 (1), [Co2(BP)(tpa)2](PF6)3 (2), [Co2(BP)(bpqa)2](PF6)2 (3), [Co2(BP)(pbqa)2](PF6)2 (4), and [Co2(BP)(tqa)2](PF6)2 (5). After a one-electron oxidation reaction of complex (1), complex (2), was isolated as a mixed valence state lsCoIII-[SQ-Cat]-lsCoIII, with an absorption intensity of about 1370 nm (intervalence charge transfer (IVCT) bands) in CH3CN solution. In addition, an investigation of the magnetic properties of the dinuclear Co complex (3) with SQUID showed that the χMT value gradually increased as the temperature increased from 280 to 380 K. Studies in the solid and solution states using electronic spectra, cyclic voltammetry and SQUID for the above complexes provide clear evidence for three different charge distributions: complexes (1) and (3) are CoIII-[Cat-Cat]-CoIII, complex (2) is CoIII-[Sq-Cat]-CoIII, complexes (4) and (5) are CoII-[Sq-Sq]-CoII. Of the five cobalt dinuclear complexes, only complex (3) shows evidence of the temperature dependence of the charge distribution, displaying a thermally induced valence tautomeric transition from the lsCoIII-[Cat-Cat]-lsCoIII to hsCoII-[Sq-Sq]-hsCoII in both solid and solution states. However, this valence tautomeric step is incomplete at 380 K, with the χMT value of hsCoII-[Sq-Sq]-hsCoII. This suggests that the steric hindrance of the quinolyl rings around the Co ion produces a coordination atmosphere that is weaker than that observed with pyridyl rings, which facilitates a change in the CoIII ions to CoII.

Community Analysis-based Screening of Plant Growth-promoting Bacteria for Sugar Beet.

Clone libraries of bacterial 16S rRNA genes (a total of 1,980 clones) were constructed from the leaf blades, petioles, taproots, and lateral roots of sugar beet (Beta vulgaris L.) grown under different fertilization conditions. A principal coordinate analysis revealed that the structures of bacterial communities in above- and underground tissues were largely separated by PC1 (44.5%). The bacterial communities of above-ground tissues (leaf blades and petioles) were more tightly clustered regardless of differences in the tissue types and fertilization conditions than those of below-ground tissues (taproots and lateral roots). The bacterial communities of below-ground tissues were largely separated by PC2 (26.0%). To survey plant growth-promoting bacteria (PGPBs), isolate collections (a total of 665 isolates) were constructed from the lateral roots. As candidate PGPBs, 44 isolates were selected via clustering analyses with the combined 16S rRNA gene sequence data of clone libraries and isolate collections. The results of inoculation tests using sugar beet seedlings showed that eight isolates exhibited growth-promoting effects on the seedlings. Among them, seven isolates belonging to seven genera (Asticcacaulis, Mesorhizobium, Nocardioides, Sphingobium, Sphingomonas, Sphingopyxis, and Polaromonas) were newly identified as PGPBs for sugar beet at the genus level, and two isolates belonging to two genera (Asticcacaulis and Polaromonas) were revealed to exert growth-promoting effects on the plant at the genus level for the first time. These results suggest that a community analysis-based selection strategy will facilitate the isolation of novel PGPBs and extend the potential for the development of novel biofertilizers.

The physiological potential of anammox bacteria as revealed by their core genome structure.

We present here the second complete genome of anaerobic ammonium oxidation (anammox) bacterium, Candidatus (Ca.) Brocadia pituitae, along with those of a nitrite oxidizer and two incomplete denitrifiers from the anammox bacterial community (ABC) metagenome. Although NO2- reduction to NO is considered to be the first step in anammox, Ca. B. pituitae lacks nitrite reductase genes (nirK and nirS) responsible for this reaction. Comparative genomics of Ca. B. pituitae with Ca. Kuenenia stuttgartiensis and six other anammox bacteria with nearly complete genomes revealed that their core genome structure contains 1,152 syntenic orthologues. But nitrite reductase genes were absent from the core, whereas two other Brocadia species possess nirK and these genes were horizontally acquired from multiple lineages. In contrast, at least five paralogous hydroxylamine oxidoreductase genes containing candidate ones (hao2 and hao3) encoding another nitrite reductase were observed in the core. Indeed, these two genes were also significantly expressed in Ca. B. pituitae as in other anammox bacteria. Because many nirS and nirK genes have been detected in the ABC metagenome, Ca. B. pituitae presumably utilises not only NO supplied by the ABC members but also NO and/or NH2OH by self-production for anammox metabolism.

Evaluation of the Influence of Halogenation on the Binding of Bisphenol A to the Estrogen-Related Receptor γ.

Halogenation of organic compounds is one the most important transformations in chemical synthesis and is used for the production of various industrial products. A variety of halogenated bisphenol analogs have recently been developed and are used as alternatives to bisphenol A (BPA), which is a raw material of polycarbonate that has adverse effects in animals. However, limited information is available on the potential toxicity of the halogenated BPA analogs. In the present study, to assess the latent toxicity of halogenated BPA analogs, we evaluated the binding and transcriptional activities of halogenated BPA analogs to the estrogen-related receptor γ (ERRγ), a nuclear receptor that contributes to the growth of nerves and sexual glands. Fluorinated BPA analogs demonstrated strong ERRγ binding potency, and inverse antagonistic activity, similar to BPA. X-ray crystallography and fragment molecular orbital (FMO) calculation revealed that a fluorine-substituted BPA analog could interact with several amino acid residues of ERRγ-LBD, strengthening the binding affinity of the analogs. The ERRγ binding affinity and transcriptional activity of the halogenated BPAs decreased with the increase in the size and number of halogen atom(s). The IC50 values, determined by the competitive binding assay, correlated well with the binding energy obtained from the docking calculation, suggesting that the docking calculation could correctly estimate the ERRγ binding potency of the BPA analogs. These results confirmed that ERRγ has a ligand binding pocket that fits very well to BPA. Furthermore, this study showed that the binding affinity of the BPA analogs can be predicted by the docking calculation, indicating the importance of the calculation method in the risk assessment of halogenated compounds.

Crystal structure of a new mixed-metal coordin-ation polymer consisting of NiII piperidine-di-thio-carbamate and penta-nuclear CuI-I cluster units.

A new heterometallic CuI-NiII coordination polymer, poly[[tetra-µ3-iodido-µ2-iodido-bis-(µ3-piperidine-1-di-thio-carbamato)propio-nitrilepenta-copper(I)nickel(II)] chloro-form monosolvate], {[CuI5NiIII5(C6H10NS2)2(C3H5N)]·CHCl3} n , has been synthesized and structurally characterized. This coordination polymer consists of an NiII mononuclear unit of NiII(Pip-dtc)2 (Pip-dtc- is piperidine-1-di-thio-carbamate) and a penta-nuclear copper(I) cluster unit of Cu5I5(CH3CH2CN). The NiII ion, which lies on an inversion centre, is surrounded by four S atoms in a square-planar coordination geometry while all CuI ions have distorted tetra-hedral coordination geometries. In the penta-nuclear copper(I) cluster unit, a mirror plane passes through one CuI ion and three I ions. All the S atoms in NiII(Pip-dtc) are also coordinated by the CuI ions, forming an infinite zigzag chain structure along the b-axis direction. The chains are weakly connected by solvent CHCl3 mol-ecules via Cl⋯I [3.653 (1) Å] and Cl⋯S [3.4370 (1) Å] short-contact inter-actions.

Crystal Structure and Band-Gap Engineering of a Semiconducting Coordination Polymer Consisting of Copper(I) Bromide and a Bridging Acceptor Ligand.

A new semiconducting 3D coordination polymer, [Cu2Br2(ttz)] n (1), with an acceptor bridging ligand, 1,2,4,5-tetrazine (ttz), was synthesized. The complex shows large absorption bands extending to the near-IR region, indicating a small band gap in the coordination polymer. This complex shows higher conductivity than those of [CuBr(pyz)] n (2), including pyrazine (pyz) with a higher lowest unoccupied molecular orbital level. We performed density functional theory band calculations using the VASP program to understand the electronic states and conducting paths of the coordination polymer.

Nitrate Supply-Dependent Shifts in Communities of Root-Associated Bacteria in Arabidopsis.

Root-associated bacterial communities are necessary for healthy plant growth. Nitrate is a signal molecule as well as a major nitrogen source for plant growth. In this study, nitrate-dependent alterations in root-associated bacterial communities and the relationship between nitrate signaling and root-associated bacteria in Arabidopsis were examined. The bacterial community was analyzed by a ribosomal RNA intergenic spacer analysis (RISA) and 16S rRNA amplicon sequencing. The Arabidopsis root-associated bacterial community shifted depending on the nitrate amount and timing of nitrate application. The relative abundance of operational taxonomic units of 25.8% was significantly changed by the amount of nitrate supplied. Moreover, at the family level, the relative abundance of several major root-associated bacteria including Burkholderiaceae, Paenibacillaceae, Bradyrhizobiaceae, and Rhizobiaceae markedly fluctuated with the application of nitrate. These results suggest that the application of nitrate strongly affects root-associated bacterial ecosystems in Arabidopsis. Bulk soil bacterial communities were also affected by the application of nitrate; however, these changes were markedly different from those in root-associated bacteria. These results also suggest that nitrate-dependent alterations in root-associated bacterial communities are mainly affected by plant-derived factors in Arabidopsis. T-DNA insertion plant lines of the genes for two transcription factors involved in nitrate signaling in Arabidopsis roots, NLP7 and TCP20, showed similar nitrate-dependent shifts in root-associated bacterial communities from the wild-type, whereas minor differences were observed in root-associated bacteria. Thus, these results indicate that NLP7 and TCP20 are not major regulators of nitrate-dependent bacterial communities in Arabidopsis roots.

Rapid Removal and Mineralization of Bisphenol A by Heterosupramolecular Plasmonic Photocatalyst Consisting of Gold Nanoparticle-Loaded Titanium(IV) Oxide and Surfactant Admicelle.

The establishment of technology for rapid and complete removal and mineralization of harmful phenolic compounds from water is of great importance for environmental conservation. Visible-light irradiation (λ > 430 nm, light intensity integrated from 420 to 485 nm = 6.0 mW cm-2) of Au nanoparticle (NP)-loaded TiO2 (Au/TiO2) in dilute aqueous solutions of bisphenol A (BPA) and p-cresol (PC) causes degradation of the phenols. The addition of trimethylstearylammonium chloride (C18TAC) enhances the adsorption of BPA on Au/TiO2 to greatly increase the rate of reaction. Consequently, 10 µM phenols are completely removed from the solutions within 2.5 h irradiation, and prolonging irradiation time to 24 h quantitatively oxidizes BPA to CO2. Dynamic light scattering ζ-potential measurements indicate that a C18TAC bilayer or admicelle is formed on the Au/TiO2 particle surface at C18TAC concentration >50 µM. The action spectrum for reaction shows that this reaction is driven by the Au NP localized surface plasmon resonance excitation-induced interfacial electron transfer from Au to TiO2. We propose a possible reaction scheme on the basis of the experimental results including intermediate analysis.

An acid-tolerant ammonia-oxidizing γ-proteobacterium from soil.

Nitrification, the microbial oxidation of ammonia to nitrate via nitrite, occurs in a wide range of acidic soils. However, the ammonia-oxidizing bacteria (AOB) that have been isolated from soil to date are acid-sensitive. Here we report the isolation and characterization of an acid-adapted AOB from an acidic agricultural soil. The isolated AOB, strain TAO100, is classified within the Gammaproteobacteria based on phylogenetic characteristics. TAO100 can grow in the pH range of 5-7.5 and survive in highly acidic conditions until pH 2 by forming cell aggregates. Whereas all known gammaproteobacterial AOB (γ-AOB) species, which have been isolated from marine and saline aquatic environments, are halophiles, TAO100 is not phenotypically halophilic. Thus, TAO100 represents the first soil-originated and non-halophilic γ-AOB. The TAO100 genome is considerably smaller than those of other γ-AOB and lacks several genes associated with salt tolerance which are unnecessary for survival in soil. The ammonia monooxygenase subunit A gene of TAO100 and its transcript are higher in abundance than those of ammonia-oxidizing archaea and betaproteobacterial AOB in the strongly acidic soil. These results indicate that TAO100 plays an important role in the nitrification of acidic soils. Based on these results, we propose TAO100 as a novel species of a new genus, Candidatus Nitrosoglobus terrae.

Origin and Evolution of Nitrogen Fixation Genes on Symbiosis Islands and Plasmid in Bradyrhizobium.

The nitrogen fixation (nif) genes of nodule-forming Bradyrhizobium strains are generally located on symbiosis islands or symbiosis plasmids, suggesting that these genes have been transferred laterally. The nif genes of rhizobial and non-rhizobial Bradyrhizobium strains were compared in order to infer the evolutionary histories of nif genes. Based on all codon positions, the phylogenetic tree of concatenated nifD and nifK sequences showed that nifDK on symbiosis islands formed a different clade from nifDK on non-symbiotic loci (located outside of symbiosis islands and plasmids) with elongated branches; however, these genes were located in close proximity, when only the 1st and 2nd codon positions were analyzed. The guanine (G) and cytosine (C) content of the 3rd codon position of nifDK on symbiosis islands was lower than that on non-symbiotic loci. These results suggest that nif genes on symbiosis islands were derived from the non-symbiotic loci of Bradyrhizobium or closely related strains and have evolved toward a lower GC content with a higher substitution rate than the ancestral state. Meanwhile, nifDK on symbiosis plasmids clustered with nifDK on non-symbiotic loci in the tree representing all codon positions, and the GC content of symbiotic and non-symbiotic loci were similar. These results suggest that nif genes on symbiosis plasmids were derived from the non-symbiotic loci of Bradyrhizobium and have evolved with a similar evolutionary pattern and rate as the ancestral state.

Metagenomic Analysis Revealed Methylamine and Ureide Utilization of Soybean-Associated Methylobacterium.

Methylobacterium inhabits the phyllosphere of a large number of plants. We herein report the results of comparative metagenome analyses on methylobacterial communities of soybean plants grown in an experimental field in Tohoku University (Kashimadai, Miyagi, Japan). Methylobacterium was identified as the most dominant genus (33%) among bacteria inhabiting soybean stems. We classified plant-derived Methylobacterium species into Groups I, II, and III based on 16S rRNA gene sequences, and found that Group I members (phylogenetically close to M. extorquens) were dominant in soybean-associated Methylobacterium. By comparing 29 genomes, we found that all Group I members possessed a complete set of genes for the N-methylglutamate pathway for methylamine utilization, and genes for urea degradation (urea carboxylase, urea amidolyase, and conventional urease). Only Group I members and soybean methylobacterial isolates grew in a culture supplemented with methylamine as the sole carbon source. They utilized urea or allantoin (a urea-related compound in legumes) as the sole nitrogen source; however, group III also utilized these compounds. The utilization of allantoin may be crucial in soybean-bacterial interactions because allantoin is a transported form of fixed nitrogen in legume plants. Soybean-derived Group I strain AMS5 colonized the model legume Lotus japonicus well. A comparison among the 29 genomes of plant-derived and other strains suggested that several candidate genes are involved in plant colonization such as csgG (curli fimbriae). Genes for the N-methylglutamate pathway and curli fimbriae were more abundant in soybean microbiomes than in rice microbiomes in the field. Based on these results, we discuss the lifestyle of Methylobacterium in the legume phyllosphere.