Effects of DNA-damaging Agents on Aerobic Methylobacteria Capable and Incapable of Utilizing Dichloromethane

Methylobacterium dichloromethanicum DM4, a degrader of dichloromethane (DCM), was more tolerant to the effect of H₂O₂ and UV irradiation than Methylobacterium extorquens AM1, which does not consume DCM. The addition of CH₂Cl₂ to methylobacteria with active serine, ribulose monophosphate, and ribulose bisphosphate pathways of C₁ metabolism, grown on methanol, resulted in a 1.1- to 2.5-fold increase in the incorporation of [α-³²P]dATP into DNA by the Klenow fragment (exo^?). Since DCM dehalogenase was not induced in this process, the increase in the total lengths of DNA gaps resulted from the action of DCM rather than S-chloromethylglutathione (intermediate of primary dehalogenation). The degree of DNA damage in the presence of CH₂Cl₂ was lower in DCM degraders than methylobacteria incapable of degrading this pollutant. This suggests that DCM degraders possess a more efficient mechanism of DNA repair.     

Adaptation of aerobic methylobacteria to dichloromethane degradation

A shortening of the lag phase in dichloromethane (DCM) consumption was observed in the methylobacteria Methylopila helvetica DM6 and Albibacter methylovorans DM10 after prior growth on methanol with the presence of 1.5% NaCI. Neither heat nor acid stress accelerated methylobacterium adaptation to DCM consumption. Sodium azide (1 mM) and potassium cyanide (1 mM) inhibited consumption of DCM by these degraders but not by transconjugants Methylobacterium extorquens AM1, expressing DCM dehalogenase but unable to grow on DCM. This indicates that the degrader strains possess energy-dependent systems of transport of DCM or chloride anions produced during DCM dehalogenation. Inducible proteins were found in the membrane fraction of A. methylovorans DM10 cells adapted to DCM and elevated NaCl concentration.     

Adaptation of aerobic methylobacteria to dichloromethane degradation

A shortening of the lag phase in dichloromethane (DCM) consumption was observed in the methylobacteria Methylopila helvetica DM6 and Albibacter methylovorans DM10 after prior growth on methanol with the presence of 1.5% NaCl. Neither heat nor acid stress accelerated methylobacterium adaptation to DCM consumption. Sodium azide (1 mM) and potassium cyanide (1 mM) inhibited consumption of DCM by these degraders but not by transconjugants Methylobacterium extorquens AM1, expressing DCM dehalogenase but unable to grow on DCM. This indicates that the degrader strains possess energy-dependent systems of transport of DCM or chloride anions produced during DCM dehalogenation. Inducible proteins were found in the membrane fraction of A. methylovorans DM10 cells adapted to DCM and elevated NaCl concentration.     

Changes of chlorine isotope composition characterize bacterial dehalogenation of dichloromethane

Fractionation of dichloromethane (DCM) molecules with different chlorine isotopes by aerobic methylobacteria Methylobacterium dichloromethanicum DM4 and Albibacter nethylovorans DM10; cell-free extract of strain DM4; and transconjugant Methylobacterium evtorquens Al1/pME 8220, expressing the dcmA gene for DCM dehalogenase but unable to grow on DCM, was studied. Kinetic indices of DCM isotopomers for chlorine during bacterial dehalogenation and diffusion were compared. A two-step model is proposed, which suggests diffusional DCM transport to bacterial cells.     

The fractionation of chlorine isotopes by the aerobic methylotrophic bacterium Methylobacterium dichloromethanicum grown on dichloromethane

Methylobacterium dichloromethanicum was found to be able to utilize dichloromethane (DCM) as the source of carbon and energy with the production of biomass, CO2, and HCl. A comparative analysis of abundances of the major DCM isotopomers 35Cl(2)12C1H2, 35Cl37Cl12C1H2 and 37Cl(2)12CH2 made it possible to estimate the fractionation of chlorine isotopes during the bacterial metabolism of DCM. The kinetic chlorine isotope effects for 35Cl37Cl12C1H2 (m/z 86) and 37Cl(2)12C1H2 (m/z 88) relative to 35Cl(2)12C1H2 (m/z 84) turned out to be alpha 86/84 = 1.006 +/- 0.002 and alpha 88/84 = 1.023 +/- 0.003, respectively. The inference is made that the growth of M. dichloromethanicum on DCM is accompanied by the mass-independent fractionation of the DCM isotopomers.     

Physiological and biochemical analysis of the transformants of aerobic methylobacteria expressing the dcm A gene of dichloromethane dehydrogenase

The transformants of Methylobacterium dichloromethanicum DM4 (DM4-2cr-/pME8220 and DM4-2cr-/pME8221) and of Methylobacterium extorquens AM1 (AM1/pME8220 and AM1/pME8221) that express the dcm A gene of dichloromethane dehalogenase undergo lysis when incubated in the presence of dichloromethane and are sensitive to acidic shock. The lysis of the transformants was found to be related neither to the accumulation of Cl- ions, CH2O, and HCOOH, nor to the impairment of glutathione synthesis or to the maintenance of intracellular pH. The (exo-) Klenow fragment-mediated incorporation of [alpha-32P]dATP into the DNA of the transformants DM4-2cr-/pME8220 and AM1/pME8220 was considerably greater when the transformed cells were incubated with CH2Cl2 than when they were incubated with CH3OH, indicating the occurrence of a significant increase in the total length of gaps. At the same time, the strain AM1 (which lacks dichloromethane dehalogenase) and the dichloromethane-degrading strain DM4 incubated with CH2Cl2 showed an insignificant increase in the total length of the gaps. The transformed cells are likely to lyse due to the relatively inefficient repair of DNA lesions that are induced in response to the alkylating action of S-chloromethylglutathione, an intermediate product of CH2Cl2 degradation. The data obtained suggest that the bacterial mineralization of dichloromethane requires an efficient DNA repair system.     

Functional genomics of dichloromethane utilization in Methylobacterium extorquens DM4

Dichloromethane (CH(2)Cl(2) , DCM) is a chlorinated solvent mainly produced by industry, and a common pollutant. Some aerobic methylotrophic bacteria are able to grow with this chlorinated methane as their sole carbon and energy source, using a DCM dehalogenase/glutathione S-transferase encoded by dcmA to transform DCM into two molecules of HCl and one molecule of formaldehyde, a toxic intermediate of methylotrophic metabolism. In Methylobacterium extorquens DM4 of known genome sequence, dcmA lies on a 126 kb dcm genomic island not found so far in other DCM-dechlorinating strains. An experimental search for the molecular determinants involved in specific cellular responses of strain DM4 growing with DCM was performed. Random mutagenesis with a minitransposon containing a promoterless reporter gfp gene yielded 25 dcm mutants with a specific DCM-associated phenotype. Differential proteomic analysis of cultures grown with DCM and with methanol defined 38 differentially abundant proteins. The 5.5 kb dcm islet directly involved in DCM dehalogenation is the only one of seven gene clusters specific to the DCM response to be localized within the dcm genomic island. The DCM response was shown to involve mainly the core genome of Methylobacterium extorquens, providing new insights on DCM-dependent adjustments of C1 metabolism and gene regulation, and suggesting a specific stress response of Methylobacterium during growth with DCM. Fatty acid, hopanoid and peptidoglycan metabolisms were affected, hinting at the membrane-active effects of DCM due to its solvent properties. A chloride-induced efflux transporter termed CliABC was also newly identified. Thus, DCM dechlorination driven by the dcm islet elicits a complex adaptive response encoded by the core genome common to dechlorinating as well as non-dechlorinating Methylobacterium strains.     

Changes of chlorine isotope composition characterize bacterial dehalogenation of dichloromethane

Fractionation of dichloromethane (DCM) molecules with different chlorine isotopes by aerobic methylobacteria Methylobacterium dichloromethanicum DM4 and Albibacter methylovorans DM10; cell-free extract of strain DM4; and transconjugant Iethylobacterium extorquens AI1/pME 8220, expressing the dcmA gene for DCM dehalogenase but unable to grow on DCM, was studied. Kinetic indices of DCM isotopomers for chlorine during bacterial dehalogenation and diffusion were compared. A two-step model is proposed, which suggests diffusional DCM transport to bacterial cells.     

Analysis of the key functional genes in new aerobic degraders of dichloromethane

The genes of dichloromethane (CH₂C1₂, DCM) degradation have been characterized in the aerobic degraders “Gottschalkia methylica” DM15, “Ancylobacter dichloromethanicus” DM16, and Methylobac- terium extorquens DM17, isolated from different regions of Russia. The sequencing of the structural gene dcmA of DCM dehalogenase, followed by phylogenetic analysis, showed that the new degraders possess A-type dehalogenases. The DcmAs of the strains DM15 and DM17 were identical to the known orthologous proteins of Methylorhabdus multivorans DM 13 and Methylobacterium dichloromethanicum DM4, respectively. DcmA of the degrader DM16 differed by three amino acid substitutions from DcmA of strain DM4. In agreement with the organization of the cluster of DCM degradation genes in M. dichloromethanicum DM4, the regulatory gene dcmR and the open reading frame orf353, flanking dcmA, were identified in the new degraders. The similarity of DCM degradation genes in aerobic degraders of different taxonomic position and geographical origin suggests their distribution among methylotrophic bacteria by means of horizontal transfer.     

苏北海岸带盐沼二氯甲烷和1,2-二氯乙烷通量沿高程梯度的变化特征

2004年4月到2005年1月在我国东部海岸带盐沼上沿高程梯度采用静态箱技术原位测定二氯甲烷(DCM, CH2Cl2)和1,2-二氯乙烷(1, 2-DCA, CH2CH2Cl2)气体通量.为确定高等植物对通量的贡献,进行了高等植物地上部分去除实验.也对通量与生态因子间关系进行了分析.研究结果表明:在高程梯度上,生长季(4～10月份)盐沼整体上表现为DCM和1, 2-DCA的净汇,其中,米草带和光滩对DCM和1, 2-DCA的消耗率最高.非生长季(11月到翌年3月份)表层冻结的植被带表现为DCM和1, 2-DCA的弱源,但是受非生长季采样量不足的限制,难以确定盐沼究竟是DCM和1, 2-DCA的净源还是净汇.高等植物去除实验结果表明生长季高等植物地上部分是DCM和1, 2-DCA的重要汇,而非生长季为净源,然而高等植物排放和消耗DCM和1, 2-DCA气体的基本机制还不清楚.盐沼DCM和1, 2-DCA通量正相关于光照强度、土壤可溶性盐含量、土壤有机质和全氮含量,而负相关于土壤温度、硫酸盐含量和大气中DCM和1, 2-DCA浓度.这表明盐沼对DCM和1, 2-DCA的吸收可能与相对较高的DCM和1, 2-DCA大气背景浓度和丰富的土壤有机质含量有关.     

Aerobic methylobacteria are capable of synthesizing auxins

Obligately and facultatively methylotrophic bacteria with different pathways of C1 metabolism were found to be able to produce auxins, particularly indole-3-acetic acid (IAA), in amounts of 3-100 micrograms/ml. Indole-3-pyruvic acid and indole-3-acetamide were detected only in methylobacteria with the serine pathway of C1 metabolism, Methylobacterium mesophilicum and Aminobacter aminovorans. The production of auxins by methylobacteria was stimulated by the addition of tryptophan to the growth medium and was inhibited by ammonium ions. The methylobacteria under study lacked tryptophan decarboxylase and tryptophan side-chain oxidase. At the same time, they were found to contain several aminotransferases. IAA is presumably synthesized by methylobacteria through indole-3-pyruvic acid.     

Aerobic Methylobacteria Are Capable of Synthesizing Auxins

Obligately and facultatively methylotrophic bacteria with different pathways of C1 metabolism were found to be able to produce auxins, particularly indole-3-acetic acid (IAA), in amounts of 3–100 g/ml. Indole-3-pyruvic acid and indole-3-acetamide were detected only in methylobacteria with the serine pathway of C1 metabolism (Methylobacterium mesophilicumand Aminobacter aminovorans).The production of auxins by methylobacteria was stimulated by the addition of L-tryptophan to the growth medium and was inhibited by ammonium ions. The methylobacteria under study lacked tryptophan decarboxylase and tryptophan side-chain oxidase. At the same time, they were found to contain several aminotransferases. IAA is presumably synthesized by methylobacteria through indole-3-pyruvic acid.     

Methylobacterium sp. resides in unculturable state in potato tissues in vitro and becomes culturable after induction by Pseudomonas fluorescens IMGB163

Aims:  To induce growth of endophytic bacteria residing in an unculturable state in tissues of in vitro -grown potato plantlets. To isolate and identify the induced bacteria and to localize the strains in tissues of in vitro -grown potato plantlets.
Methods and Results:  The inoculation of in vitro -grown potato plants with Pseudomonas fluorescens IMBG163 led to induction of another bacterium, a pink-pigmented facultative methylotroph that was identified as Methylobacterium sp . using phylogenetic 16S rDNA approach . Two molecular methods were used for localizing methylobacteria in potato plantlets: PCR and in situ hybridization (ISH/FISH). A PCR product specific for the Methylobacterium genus was found in DNA isolated from the surface-sterilized plantlet leaves. Presence of Methylobacterium rRNA was detected by ISH/FISH in leaves and stems of inoculated as well as axenic potato plantlets although the bacterium cannot be isolated from the axenic plants.
Conclusion:  Methylobacterium sp. resides in unculturable state within tissues of in vitro -grown potato plants and becomes culturable after inoculation with P. fluorescens IMBG163.
Significance and Impact of the Study:  In order to develop endophytic biofertilizers and biocontrol agents, a detailed knowledge of the life-style of endophytes is essential. To our knowledge, this is the first report on increase of the culturability of endophytes in response to inoculation by nonpathogenic bacteria.     

Plasmid analysis and cloning of the dichloromethane-utilization genes of Methylobacterium sp. DM4

The dichloromethane (DCM)-utilizing facultative methylotroph Methylobacterium sp. DM4 was shown to contain three plasmids with approximate size of 120 kb, 40 kb and 8 kb. Curing experiments suggested that the DCM-utilization character was correlated with the possession of an intact 120 kb plasmid. The DCM-utilization genes were cloned on the broad-host-range vector pVK100. Plasmid pME1510, a recombinant plasmid carrying a 21 kb HindIII fragment complemented DCM-utilization-negative derivatives of Methylobacterium sp. DM4 and conferred the DCM-utilization-positive phenotype to a number of Gram-negative methylotrophic bacteria. In Southern hybridization experiments with pMe1510 as a probe, chromosomal DNA from Methylobacterium sp. DM4 gave definite signals while purified plasmid DNA did not. Plasmid pME1510 did not hybridize with total DNA from a cured DCM-non-utilizing derivative of Methylobacterium sp. DM4. It is concluded that the DCM-utilization genes are located on the chromosome or on a megaplasmid. Curing procedures thus led to the formation of a chromosomal or megaplasmid deletion larger than 21 kb and covering the DCM-utilization genes or to the loss of an undetected megaplasmid.     

Biodegradation of dichloromethane and its utilization as a growth substrate under methanogenic conditions.

Biodegradation of dichloromethane (DCM) to environmentally acceptable products was demonstrated under methanogenic conditions (35 degrees C). When DCM was supplied to enrichment cultures as the sole organic compound at a low enough concentration to avoid inhibition of methanogenesis, the molar ratio of CH4 formed to DCM consumed (0.473) was very close to the amount predicted by stoichiometric conservation of electrons. DCM degradation was also demonstrated when methanogenesis was partially inhibited (with 0.5 to 1.5 mM 2-bromoethanesulfonate or approximately 2 mM DCM) or completely stopped (with 50 to 55.5 mM 2-bromoethanesulfonate). Addition of a eubacterial inhibitor (vancomycin, 100 mg/liter) greatly reduced the rate of DCM degradation. 14CO2 was the principal product of [14C]DCM degradation, followed by 14CH4 (when methanogenesis was uninhibited) or 14CH3COOH (when methanogenesis was partially or completely inhibited). Hydrogen accumulated during DCM degradation and then returned to background levels when DCM was consumed. These results suggested that nonmethanogenic organisms mediated DCM degradation, oxidizing a portion to CO2 and fermenting the remainder to acetate; acetate formation suggested involvement of an acetogen. Methanogens in the enrichment culture then converted the products of DCM degradation to CH4. Aceticlastic methanogens were more easily inhibited by 2-bromoethanesulfonate and DCM than were CO2-reducing methanogens. When DCM was the sole organic-carbon and electron donor source supplied, its use as a growth substrate was demonstrated. The highest observed yield was 0.085 g of suspended organic carbon formed per g of DCM carbon consumed. Approximately 85% of the biomass formed was attributable to the growth of nonmethanogens, and 15% was attributable to methanogens.     

Biodegradation of dichloromethane and its utilization as a growth substrate under methanogenic conditions.

Biodegradation of dichloromethane (DCM) to environmentally acceptable products was demonstrated under methanogenic conditions (35 degrees C). When DCM was supplied to enrichment cultures as the sole organic compound at a low enough concentration to avoid inhibition of methanogenesis, the molar ratio of CH4 formed to DCM consumed (0.473) was very close to the amount predicted by stoichiometric conservation of electrons. DCM degradation was also demonstrated when methanogenesis was partially inhibited (with 0.5 to 1.5 mM 2-bromoethanesulfonate or approximately 2 mM DCM) or completely stopped (with 50 to 55.5 mM 2-bromoethanesulfonate). Addition of a eubacterial inhibitor (vancomycin, 100 mg/liter) greatly reduced the rate of DCM degradation. 14CO2 was the principal product of [14C]DCM degradation, followed by 14CH4 (when methanogenesis was uninhibited) or 14CH3COOH (when methanogenesis was partially or completely inhibited). Hydrogen accumulated during DCM degradation and then returned to background levels when DCM was consumed. These results suggested that nonmethanogenic organisms mediated DCM degradation, oxidizing a portion to CO2 and fermenting the remainder to acetate; acetate formation suggested involvement of an acetogen. Methanogens in the enrichment culture then converted the products of DCM degradation to CH4. Aceticlastic methanogens were more easily inhibited by 2-bromoethanesulfonate and DCM than were CO2-reducing methanogens. When DCM was the sole organic-carbon and electron donor source supplied, its use as a growth substrate was demonstrated. The highest observed yield was 0.085 g of suspended organic carbon formed per g of DCM carbon consumed. Approximately 85% of the biomass formed was attributable to the growth of nonmethanogens, and 15% was attributable to methanogens.     

Enhanced Resistance of Pea Plants to Oxidative Stress Caused by Paraquat during Colonization by Aerobic Methylobacteria

The influence of colonization of the pea (Pisum sativum L.) by aerobic methylobacteria of five different species (Methylophilus flavus Ship, Methylobacterium extorquens G10, Methylobacillus arboreus Iva, Methylopila musalis MUSA, Methylopila turkiensis Side1) on plant resistance to paraquat-induced stresses has been studied. The normal conditions of pea colonization by methylobacteria were characterized by a decrease in the activity of antioxidant enzymes (superoxide dismutase, catalase, and peroxidases) and in the concentrations of endogenous H₂O₂, proline, and malonic dialdehyde, which is a product of lipid peroxidation and indicator of damage to plant cell membranes, and an increase in the activity of the photosynthetic apparatus (the content of chlorophylls а, b and carotenoids). In the presence of paraquat, the colonized plants had higher activities of antioxidant enzymes, stable photosynthetic indices, and a less intensive accumulation of the products of lipid peroxidation as compared to noncolonized plants. Thus, colonization by methylobacteria considerably increased the adaptive protection of pea plants to the paraquat-induced oxidative stress.