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FEMS Microbiology Letters Jan 2023Methylobacterium species are abundant colonizers of the phyllosphere due to the availability of methanol, a waste product of pectin metabolism during plant cell...
Methylobacterium species are abundant colonizers of the phyllosphere due to the availability of methanol, a waste product of pectin metabolism during plant cell division. The phyllosphere is an extreme environment, with a landscape that is heterogeneous and continuously changing as the plant grows and is exposed to high levels of ultraviolet irradiation. Geographically, New Zealand (NZ) has been isolated for over a million years, has a biologically diverse flora, and is considered a biodiversity hotspot, with most native plants being endemic. We therefore hypothesize that the phyllosphere of NZ native plants harbor diverse groups of Methylobacterium species. Leaf imprinting using methanol-supplemented agar medium was used to isolate bacteria, and diversity was determined using ARDRA and 16S rRNA gene sequencing. Methylobacterium species were successfully isolated from the phyllosphere of 18 of the 20 native NZ plant species in this study, and six different species were identified: M. marchantiae, M. mesophilicum, M. adhaesivum, M. komagatae, M. extorquens, and M. phyllosphaerae. Other α, β, and γ-Proteobacteria, Actinomycetes, Bacteroidetes, and Firmicutes were also isolated, highlighting the presence of other potentially novel methanol utilizers within this ecosystem. This study identified that Methylobacterium are abundant members of the NZ phyllosphere, with species diversity and composition dependent on plant species.
Topics: Methylobacterium; Ecosystem; RNA, Ribosomal, 16S; Methanol; New Zealand; Plants; Plant Leaves
PubMed: 37985695
DOI: 10.1093/femsle/fnad124 -
The ISME Journal Nov 2018Microbes frequently rely on metabolites excreted by other bacterial species, but little is known about how this cross-feeding influences the effect of antibiotics. We...
Microbes frequently rely on metabolites excreted by other bacterial species, but little is known about how this cross-feeding influences the effect of antibiotics. We hypothesized that when species rely on each other for essential metabolites, the minimum inhibitory concentration (MIC) for all species will drop to that of the "weakest link"-the species least resistant in monoculture. We tested this hypothesis in an obligate cross-feeding system that was engineered between Escherichia coli, Salmonella enterica, and Methylobacterium extorquens. The effect of tetracycline and ampicillin were tested on both liquid and solid media. In all cases, resistant species were inhibited at significantly lower antibiotic concentrations in the cross-feeding community than in monoculture or a competitive community. However, deviation from the "weakest link" hypothesis was also observed in cross-feeding communities apparently as result of changes in the timing of growth and cross-protection. Comparable results were also observed in a clinically relevant system involving facultative cross-feeding between Pseudomonas aeruginosa and an anaerobic consortium found in the lungs of cystic fibrosis patients. P. aeruginosa was inhibited by lower concentrations of ampicillin when cross-feeding than when grown in isolation. These results suggest that cross-feeding significantly alters tolerance to antibiotics in a variety of systems.
Topics: Ampicillin; Anti-Bacterial Agents; Cystic Fibrosis; Drug Resistance, Bacterial; Escherichia coli; Humans; Methylobacterium extorquens; Pseudomonas aeruginosa; Salmonella enterica; Tetracycline
PubMed: 29991761
DOI: 10.1038/s41396-018-0212-z -
PloS One 2017Hopanoids are sterol-like membrane lipids widely used as geochemical proxies for bacteria. Currently, the physiological role of hopanoids is not well understood, and...
Hopanoids are sterol-like membrane lipids widely used as geochemical proxies for bacteria. Currently, the physiological role of hopanoids is not well understood, and this represents one of the major limitations in interpreting the significance of their presence in ancient or contemporary sediments. Previous analyses of mutants lacking hopanoids in a range of bacteria have revealed a range of phenotypes under normal growth conditions, but with most having at least an increased sensitivity to toxins and osmotic stress. We employed hopanoid-free strains of Methylobacterium extorquens DM4, uncovering severe growth defects relative to the wild-type under many tested conditions, including normal growth conditions without additional stressors. Mutants overproduce carotenoids-the other major isoprenoid product of this strain-and show an altered fatty acid profile, pronounced flocculation in liquid media, and lower growth yields than for the wild-type strain. The flocculation phenotype can be mitigated by addition of cellulase to the medium, suggesting a link between the function of hopanoids and the secretion of cellulose in M. extorquens DM4. On solid media, colonies of the hopanoid-free mutant strain were smaller than wild-type, and were more sensitive to osmotic or pH stress, as well as to a variety of toxins. The results for M. extorquens DM4 are consistent with the hypothesis that hopanoids are important for membrane fluidity and lipid packing, but also indicate that the specific physiological processes that require hopanoids vary across bacterial lineages. Our work provides further support to emerging observations that the role of hopanoids in membrane robustness and barrier function may be important across lineages, possibly mediated through an interaction with lipid A in the outer membrane.
Topics: Carotenoids; Cell Membrane; Cellulase; Culture Media; Fatty Acids; Flocculation; Hydrogen-Ion Concentration; Membrane Fluidity; Membrane Lipids; Methylobacterium extorquens; Mutation; Osmolar Concentration; Stress, Physiological
PubMed: 28319163
DOI: 10.1371/journal.pone.0173323 -
Systematic and Applied Microbiology May 2021Two Gram-negative, aerobic, rod-shaped and yellow-orange pigmented bacterial strains (LMG 31523 and LMG 31524) were isolated from roots of wild-growing Alkanna tinctoria...
Two Gram-negative, aerobic, rod-shaped and yellow-orange pigmented bacterial strains (LMG 31523 and LMG 31524) were isolated from roots of wild-growing Alkanna tinctoria plants collected near Thessaloniki, Greece. Analysis of their 16S rRNA gene sequences revealed that they form a separate cluster related to the genus Roseomonas. A comparative whole genome analysis of the two strains and the type strains of related Roseomonas species revealed average nucleotide identity values from 78.84 and 80.32%. The G + C contents of the genomic DNA of strains LMG 31523 and LMG 31524 were 69.69% and 69.74%, respectively. Combined data from phenotypic, phylogenetic and chemotaxonomic studies indicated that the strains LMG 31523 and LMG 31524 represent a novel species of the genus Roseomonas. Genome analysis of the new strains showed a number of genes involved in survival in the rhizosphere environment and in plant colonization and confirmed the endophytic characteristics of LMG 31523 and LMG 31524. Since the strains LMG 31523 and LMG 31524 were isolated from a plant collected in Greece the name Roseomonas hellenica sp. nov. is proposed. The type strain is LMG 31523 (=CECT 30032).
Topics: Bacterial Typing Techniques; Base Composition; Boraginaceae; DNA, Bacterial; Endophytes; Greece; Methylobacteriaceae; Phylogeny; Pigmentation; Plant Roots; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 33945925
DOI: 10.1016/j.syapm.2021.126206 -
Antonie Van Leeuwenhoek Oct 2010This study was performed in order to characterize the relationship between adhesion and biofilm formation abilities of drinking water-isolated bacteria (Acinetobacter...
This study was performed in order to characterize the relationship between adhesion and biofilm formation abilities of drinking water-isolated bacteria (Acinetobacter calcoaceticus, Burkholderia cepacia, Methylobacterium sp., Mycobacterium mucogenicum, Sphingomonas capsulata and Staphylococcus sp.). Adhesion was assessed by two distinct methods: thermodynamic prediction of adhesion potential by quantifying hydrophobicity and the free energy of adhesion; and by microtiter plate assays. Biofilms were developed in microtiter plates for 24, 48 and 72 h. Polystyrene (PS) was used as adhesion substratum. The tested bacteria had negative surface charge and were hydrophilic. PS had negative surface charge and was hydrophobic. The free energy of adhesion between the bacteria and PS was > 0 mJ/m(2) (thermodynamic unfavorable adhesion). The thermodynamic approach was inappropriate for modelling adhesion of the tested drinking water bacteria, underestimating adhesion to PS. Only three (B. cepacia, Sph. capsulata and Staphylococcus sp.) of the six bacteria were non-adherent to PS. A. calcoaceticus, Methylobacterium sp. and M. mucogenicum were weakly adherent. This adhesion ability was correlated with the biofilm formation ability when comparing with the results of 24 h aged biofilms. Methylobacterium sp. and M. mucogenicum formed large biofilm amounts, regardless the biofilm age. Given time, all the bacteria formed biofilms; even those non-adherents produced large amounts of matured (72 h aged) biofilms. The overall results indicate that initial adhesion did not predict the ability of the tested drinking water-isolated bacteria to form a mature biofilm, suggesting that other events such as phenotypic and genetic switching during biofilm development and the production of extracellular polymeric substances (EPS), may play a significant role on biofilm formation and differentiation. This understanding of the relationship between adhesion and biofilm formation is important for the development of control strategies efficient in the early stages of biofilm development.
Topics: Acinetobacter calcoaceticus; Bacterial Adhesion; Bacterial Physiological Phenomena; Biofilms; Burkholderia cepacia; Drinking; Food Microbiology; Fresh Water; Hydrophobic and Hydrophilic Interactions; Methylobacterium; Mycobacterium; Polystyrenes; Quorum Sensing; Sphingomonas; Staphylococcus; Water Microbiology; Water Supply
PubMed: 20405208
DOI: 10.1007/s10482-010-9444-2 -
Proceedings of the National Academy of... Oct 2018Gaseous one-carbon (C1) compounds or formic acid (FA) converted from CO can be an attractive raw material for bio-based chemicals. Here, we report the development of...
Gaseous one-carbon (C1) compounds or formic acid (FA) converted from CO can be an attractive raw material for bio-based chemicals. Here, we report the development of strains assimilating FA and CO through the reconstructed tetrahydrofolate (THF) cycle and reverse glycine cleavage (gcv) pathway. The formate-THF ligase, methenyl-THF cyclohydrolase, and methylene-THF dehydrogenase genes were expressed to allow FA assimilation. The gcv reaction was reversed by knocking out the repressor gene () and overexpressing the genes. This engineered strain synthesized 96% and 86% of proteinogenic glycine and serine, respectively, from FA and CO in a glucose-containing medium. Native serine deaminase converted serine to pyruvate, showing 4.5% of pyruvate-forming flux comes from FA and CO The pyruvate-forming flux from FA and CO could be increased to 14.9% by knocking out , , and , chromosomally expressing under , and overexpressing the reconstructed THF cycle, , and genes in one vector. To reduce glucose usage required for energy and redox generation, the formate dehydrogenase (Fdh) gene was expressed. The resulting strain showed specific glucose, FA, and CO consumption rates of 370.2, 145.6, and 14.9 mg⋅g dry cell weight (DCW)⋅h, respectively. The C1 assimilation pathway consumed 21.3 wt% of FA. Furthermore, cells sustained slight growth using only FA and CO after glucose depletion, suggesting that combined use of the C1 assimilation pathway and Fdh will be useful for eventually developing a strain capable of utilizing FA and CO without an additional carbon source such as glucose.
Topics: Bacterial Proteins; Carbon Dioxide; Escherichia coli; Formate-Tetrahydrofolate Ligase; Formates; Gene Knockdown Techniques; Methylobacterium extorquens; Microorganisms, Genetically-Modified
PubMed: 30224468
DOI: 10.1073/pnas.1810386115 -
Chembiochem : a European Journal of... Sep 2019Lanthanide (Ln)-dependent methanol dehydrogenases (MDHs) have recently been shown to be widespread in methylotrophic bacteria. Along with the core MDH protein, XoxF,...
Lanthanide (Ln)-dependent methanol dehydrogenases (MDHs) have recently been shown to be widespread in methylotrophic bacteria. Along with the core MDH protein, XoxF, these systems contain two other proteins, XoxG (a c-type cytochrome) and XoxJ (a periplasmic binding protein of unknown function), about which little is known. In this work, we have biochemically and structurally characterized these proteins from the methyltroph Methylobacterium extorquens AM1. In contrast to results obtained in an artificial assay system, assays of XoxFs metallated with La , Ce , and Nd using their physiological electron acceptor, XoxG, display Ln-independent activities, but the K for XoxG markedly increases from La to Nd. This result suggests that XoxG's redox properties are tuned specifically for lighter Lns in XoxF, an interpretation supported by the unusually low reduction potential of XoxG (+172 mV). The X-ray crystal structure of XoxG provides a structural basis for this reduction potential and insight into the XoxG-XoxF interaction. Finally, the X-ray crystal structure of XoxJ reveals a large hydrophobic cleft and suggests a role in the activation of XoxF. These studies enrich our understanding of the underlying chemical principles that enable the activity of XoxF with multiple lanthanides in vitro and in vivo.
Topics: Alcohol Oxidoreductases; Bacterial Proteins; Cytochrome c Group; Enzyme Assays; Kinetics; Lanthanoid Series Elements; Methanol; Methylobacterium extorquens; Oxidation-Reduction; Periplasmic Binding Proteins; Rhodothermus; Saccharomyces cerevisiae
PubMed: 31017712
DOI: 10.1002/cbic.201900184 -
International Journal of Molecular... Aug 2022Herein, a novel laccase gene, , was amplified from and successfully expressed in with a molecular weight of approximately 50 kDa. The purified Melac13220 had no...
Herein, a novel laccase gene, , was amplified from and successfully expressed in with a molecular weight of approximately 50 kDa. The purified Melac13220 had no absorption peak at 610 nm and remained silent within electron paramagnetic resonance spectra, suggesting that Melac13220 belongs to the non-blue laccase group. Both inductively coupled plasma spectroscopy/optical emission spectrometry (ICP-OES) and isothermal titration calorimetry (ITC) indicated that one molecule of Melac13220 can interact with two iron ions. Furthermore, the optimal temperature of Melac13220 was 65 °C. It also showed a high thermolability, and its half-life at 65 °C was 80 min. Melac13220 showed a very good acid environment tolerance; its optimal pH was 1.5. Cu and Co can slightly increase enzyme activity, whereas Fe could increase Melac13220's activity five-fold. Differential scanning calorimetry (DSC) indicated that Fe could also stabilize Melac13220. Unlike most laccases, Melac13220 can efficiently decolorize Congo Red and Indigo Carmine dyes even in the absence of a redox mediator. Thus, the non-blue laccase from shows potential application value and may be valuable for environmental protection, especially in the degradation of dyes at low pH.
Topics: Coloring Agents; Escherichia coli; Hydrogen-Ion Concentration; Indigo Carmine; Laccase; Methylobacterium extorquens; Temperature
PubMed: 36077196
DOI: 10.3390/ijms23179804 -
Applied and Environmental Microbiology Jun 2019,-Dimethylformamide (DMF) is one of the most common xenobiotic chemicals, and it can be easily emitted into the environment, where it causes harm to human beings....
,-Dimethylformamide (DMF) is one of the most common xenobiotic chemicals, and it can be easily emitted into the environment, where it causes harm to human beings. Herein, an efficient DMF-degrading strain, DM1, was isolated and identified as sp. This strain can use DMF as the sole source of carbon and nitrogen. Whole-genome sequencing of strain DM1 revealed that it has a 5.66-Mbp chromosome and a 200-kbp megaplasmid. The plasmid pLVM1 specifically harbors the genes essential for the initial steps of DMF degradation, and the chromosome carries the genes facilitating subsequent methylotrophic metabolism. Through analysis of the transcriptome sequencing data, the complete mineralization pathway and redundant gene clusters of DMF degradation were elucidated. The dimethylformamidase (DMFase) gene was heterologously expressed, and DMFase was purified and characterized. Plasmid pLVM1 is catabolically crucial for DMF utilization, as evidenced by the phenotype identification of the plasmid-free strain. This study systematically elucidates the molecular mechanisms of DMF degradation by DMF is a hazardous pollutant that has been used in the chemical industry, pharmaceutical manufacturing, and agriculture. Biodegradation as a method for removing DMF has received increasing attention. Here, we identified an efficient DMF degrader, sp. strain DM1, and characterized the complete DMF mineralization pathway and enzymatic properties of DMFase in this strain. This study provides insights into the molecular mechanisms and evolutionary advantage of DMF degradation facilitated by plasmid pLVM1 and redundant genes in strain DM1, suggesting the emergence of new ecotypes of .
Topics: Biodegradation, Environmental; Carbon; Dimethylformamide; Methylobacterium; Nitrogen; Plasmids
PubMed: 30952664
DOI: 10.1128/AEM.00275-19 -
Bioresource Technology May 2022In the context of algal wastewater bioremediation, this study has identified a novel consortium formed by the bacterium Methylobacterium oryzae and the microalga...
In the context of algal wastewater bioremediation, this study has identified a novel consortium formed by the bacterium Methylobacterium oryzae and the microalga Chlamydomonas reinhardtii that greatly increase biomass generation (1.22 g L·d), inorganic nitrogen removal (>99%), and hydrogen production (33 mL·L) when incubated in media containing ethanol and methanol. The key metabolic aspect of this relationship relied on the bacterial oxidation of ethanol to acetate, which supported heterotrophic algal growth. However, in the bacterial monocultures the acetate accumulation inhibited bacterial growth. Moreover, in the absence of methanol, ethanol was an unsuitable carbon source and its incomplete oxidation to acetaldehyde had a toxic effect on both the alga and the bacterium. In cocultures, both alcohols were used as carbon sources by the bacteria, the inhibitory effects were overcome and both microorganisms mutually benefited. Potential biotechnological applications in wastewater treatment, biomass generation and hydrogen production are discussed.
Topics: Acetates; Biomass; Carbon; Chlamydomonas; Denitrification; Ethanol; Hydrogen; Methanol; Methylobacterium; Nitrogen
PubMed: 35364237
DOI: 10.1016/j.biortech.2022.127088