Dissolved organic matter, calcium ion and extracellular polymeric substances on living associated bacteria of Microcystis colony are crucial for unicellular Microcystis to efficiently form colonies

Microcystis typically forms colonies under natural conditions, which contributes to occurrence and prevalence of algal blooms. The colonies consist of Microcystis and associated bacteria (AB), embedded in extracellular polymeric substances (EPS). Previous studies indicate that AB can induce Microcystis to form colonies, however the efficiency is generally low and results in a uniform morphotype. In this study, by using filtrated natural water, several AB strains induced unicellular M. aeruginosa to form colonies resembling several Microcystis morphotypes. The mechanisms were investigated with Methylobacterium sp. Z5. Ca2+ was necessary for Z5 to induce Microcystis to form colonies, while dissolved organic matters (DOM) facilitated AB to agglomerate Microcystis to form large colonies. EPS of living Z5, mainly the aromatic protein components, played a key role in colony induction. Z5 initially aggregated Microcystis via the bridging effects of Ca2+ and DOM, followed by the induction of EPS synthesis and secretion in Microcystis. In this process, the colony forming mode shifted from cell adhesion to a combination of cell adhesion and cell division. Intriguingly, Z5 drove the genomic rearrangement of Microcystis by upregulating some transposase genes. This study unveiled a novel mechanism about Microcystis colony formation and identified a new driver of Microcystis genomic evolution.

Engineering photo-methylotrophic Methylobacterium for enhanced 3-hydroxypropionic acid production during non-growth stage fermentation

This study explored the potential of methanol as a sustainable feedstock for biomanufacturing, focusing on Methylobacterium extorquens, a well-established representative of methylotrophic cell factories. Despite this bacterium's long history, its untapped photosynthetic capabilities for production enhancement have remained unreported. Using genome-scale flux balance analysis, it was hypothesized that introducing photon fluxes could boost the yield of 3-hydroxypropionic acid (3-HP), an energy- and reducing equivalent-consuming chemicals. To realize this, M. extorquens was genetically modified by eliminating the negative regulator of photosynthesis, leading to improved ATP levels and metabolic activity in non-growth cells during a two-stage fermentation process. This modification resulted in a remarkable 3.0-fold increase in 3-HP titer and a 2.1-fold increase in its yield during stage (II). Transcriptomics revealed that enhanced light-driven methanol oxidation, NADH transhydrogenation, ATP generation, and fatty acid degradation were key factors. This development of photo-methylotrophy as a platform technology introduced novel opportunities for future production enhancements.

Application and effectiveness of Methylobacterium symbioticum as a biological inoculant in maize and strawberry crops

The effectiveness of Methylobacterium symbioticum in maize and strawberry plants was measured under different doses of nitrogen fertilisation. The biostimulant effect of the bacteria was observed in maize and strawberry plants treated with the biological inoculant under different doses of nitrogen fertiliser compared to untreated plants (control). It was found that bacteria allowed a 50 and 25% decrease in the amount of nitrogen applied in maize and strawberry crops, respectively, and the photosynthetic capacity increased compared with the control plant under all nutritional conditions. A decrease in nitrate reductase activity in inoculated maize plants indicated that the bacteria affects the metabolism of the plant. In addition, inoculated strawberry plants grown with a 25% reduction in nitrogen had a higher concentration of nitrogen in leaves than control plants under optimal nutritional conditions. Again, this indicates that Methylobacterium symbioticum provide an additional supply of nitrogen.

Impact of Phyllosphere Methylobacterium on Host Rice Landraces

The genus Methylobacterium includes widespread plant-associated bacteria that are abundant in the plant phyllosphere (leaf surfaces), consume plant-secreted methanol, and can produce plant growth-promoting metabolites. However, despite the potential to increase agricultural productivity, their impact on host fitness in the natural environment is relatively poorly understood. Here, we conducted field experiments with three traditionally cultivated rice landraces from northeastern India. We inoculated seedlings with native versus nonnative phyllosphere Methylobacterium strains and found significant impacts on plant growth and grain yield. However, these effects were variable. Whereas some Methylobacterium isolates were beneficial for their host, others had no impact or were no more beneficial than the bacterial growth medium on its own. Host plant benefits were not consistently associated with Methylobacterium colonization and did not have altered phyllosphere microbiome composition, changes in the early expression of plant stress response pathways, or bacterial auxin production. We provide the first demonstration of the benefits of phyllosphere Methylobacterium for rice yield under field conditions and highlight the need for further analysis to understand the mechanisms underlying these benefits. Given that the host landrace-Methylobacterium relationship was not generalizable, future agricultural applications will require careful testing to identify coevolved host-bacterium pairs that may enhance the productivity of high-value rice varieties. IMPORTANCE Plants are associated with diverse microbes in nature. Do the microbes increase host plant health, and can they be used for agricultural applications? This is an important question that must be answered in the field rather than in the laboratory or greenhouse. We tested the effects of native, leaf-inhabiting bacteria (genus Methylobacterium) on traditionally cultivated rice varieties in a crop field. We found that inoculation with some bacteria increased rice grain production substantially while a nonnative bacterium reduced plant health. Overall, the effect of bacterial inoculation varied across pairs of rice varieties and their native bacteria. Thus, knowledge of evolved associations between specific bacteria hosted by specific rice varieties is necessary to develop ways to increase the yield of traditional rice landraces and preserve these important sources of cultural and genetic diversity.

EfgA is a conserved formaldehyde sensor that leads to bacterial growth arrest in response to elevated formaldehyde

Normal cellular processes give rise to toxic metabolites that cells must mitigate. Formaldehyde is a universal stressor and potent metabolic toxin that is generated in organisms from bacteria to humans. Methylotrophic bacteria such as Methylorubrum extorquens face an acute challenge due to their production of formaldehyde as an obligate central intermediate of single-carbon metabolism. Mechanisms to sense and respond to formaldehyde were speculated to exist in methylotrophs for decades but had never been discovered. Here, we identify a member of the DUF336 domain family, named efgA for enhanced formaldehyde growth, that plays an important role in endogenous formaldehyde stress response in M. extorquens PA1 and is found almost exclusively in methylotrophic taxa. Our experimental analyses reveal that EfgA is a formaldehyde sensor that rapidly arrests growth in response to elevated levels of formaldehyde. Heterologous expression of EfgA in Escherichia coli increases formaldehyde resistance, indicating that its interaction partners are widespread and conserved. EfgA represents the first example of a formaldehyde stress response system that does not involve enzymatic detoxification. Thus, EfgA comprises a unique stress response mechanism in bacteria, whereby a single protein directly senses elevated levels of a toxic intracellular metabolite and safeguards cells from potential damage.

Impact of plants on the diversity and activity of methylotrophs in soil

BACKGROUND

Methanol is the second most abundant volatile organic compound in the atmosphere, with the majority produced as a metabolic by-product during plant growth. There is a large disparity between the estimated amount of methanol produced by plants and the amount which escapes to the atmosphere. This may be due to utilisation of methanol by plant-associated methanol-consuming bacteria (methylotrophs). The use of molecular probes has previously been effective in characterising the diversity of methylotrophs within the environment. Here, we developed and applied molecular probes in combination with stable isotope probing to identify the diversity, abundance and activity of methylotrophs in bulk and in plant-associated soils.

RESULTS

Application of probes for methanol dehydrogenase genes (mxaF, xoxF, mdh2) in bulk and plant-associated soils revealed high levels of diversity of methylotrophic bacteria within the bulk soil, including Hyphomicrobium, Methylobacterium and members of the Comamonadaceae. The community of methylotrophic bacteria captured by this sequencing approach changed following plant growth. This shift in methylotrophic diversity was corroborated by identification of the active methylotrophs present in the soils by DNA stable isotope probing using ¹³C-labelled methanol. Sequencing of the 16S rRNA genes and construction of metagenomes from the ¹³C-labelled DNA revealed members of the Methylophilaceae as highly abundant and active in all soils examined. There was greater diversity of active members of the Methylophilaceae and Comamonadaceae and of the genus Methylobacterium in plant-associated soils compared to the bulk soil. Incubating growing pea plants in a ¹³CO₂ atmosphere revealed that several genera of methylotrophs, as well as heterotrophic genera within the Actinomycetales, assimilated plant exudates in the pea rhizosphere.

CONCLUSION

In this study, we show that plant growth has a major impact on both the diversity and the activity of methanol-utilising methylotrophs in the soil environment, and thus, the study contributes significantly to efforts to balance the terrestrial methanol and carbon cycle. Video abstract.

Phyllosphere-associated Methylobacterium: a potential biostimulant for ginger (Zingiber officinale Rosc.) cultivation

Methanol, a by-product associated with plant metabolism, is a substrate for pink pigmented facultative methylotrophs (PPFMs) of phyllosphere. The symbiotic interaction of PPFMs has many desirable effects on plant growth and disease resistance. The present study investigated the potential of native PPFMs for mitigating biotic stress and plant growth promotion in ginger. PPFMs were isolated from ginger phyllosphere by leaf imprint technique and screened against major fungal phytopathogens of ginger viz. Macrophomina phaseolina, Sclerotium rolfsii, Pythium myriotylum, Colletotrichum gloeosporioides and Fusarium oxysporum. Among the 60 PPFMs, IISRGPPFM13 was selected for its highly inhibitory activity against the target pathogens. The isolate was useful for mineral solubility, production of IAA, siderophores and hydrolytic enzymes like cellulase, pectinase, lipase, amylase and chitinase. On in planta experiments revealed that IISRGPPFM13 considerably increased plant growth parameters when the bacterium was applied as soil drenching cum foliar spraying. Methanol utilization potential of the isolate was confirmed by mxaF gene analysis where the sequence showing 95.51% identity towards Methylobacterium platani and M. iners. Further, 16S rRNA gene sequence showing 98.73% identity with M. komagatae 002-079 T (AB252201). This is the first report of its kind that a genus of Methylobacterium with biostimulant potential isolated from the phyllosphere of ginger.

Gaseous Formaldehyde Degrading by Methylobacterium sp. XJLW

Formaldehyde is harmful to human beings. It is widely used in chemical industry, medicine, and agriculture and is frequently discharged into the sewage. Microbial metabolism of formaldehyde has attracted increasing attention for its potential application in formaldehyde removal, especially for indoor gaseous formaldehyde degradation. Methylobacterium sp. XJLW capable of degrading formaldehyde was isolated and exhibited a strong activity for liquid formaldehyde degradation. In the present study, the survival rate of XJLW was evaluated under drought, 30 °C, 4 °C, 15 °C, 35 °C, and 40 °C. After 4 days, the average survival rate under 30°C is the greatest (83.97%) among the five temperatures. Whether the temperature was above or below 30°C, the average survival rate decreased significantly. However, the resistance of XJLW to reduced temperatures seemed better than that to increased temperatures. The average survival rate under 15°C and 4°C was 71.1% and 58.67%, while that under 35 °C and 40 °C was 49.47% and 0.1%. Two batches of gaseous formaldehyde treatments were carried out in an analog device with super absorbent polymer (SAP) as the carrier materials of XJLW. The results showed that XJLW could effectively degrade gaseous formaldehyde in the analog device for a long period.

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.

Genes related to antioxidant metabolism are involved in Methylobacterium mesophilicum-soybean interaction

The genus Methylobacterium is composed of pink-pigmented methylotrophic bacterial species that are widespread in natural environments, such as soils, stream water and plants. When in association with plants, this genus colonizes the host plant epiphytically and/or endophytically. This association is known to promote plant growth, induce plant systemic resistance and inhibit plant infection by phytopathogens. In the present study, we focused on evaluating the colonization of soybean seedling-roots by Methylobacterium mesophilicum strain SR1.6/6. We focused on the identification of the key genes involved in the initial step of soybean colonization by methylotrophic bacteria, which includes the plant exudate recognition and adaptation by planktonic bacteria. Visualization by scanning electron microscopy revealed that M. mesophilicum SR1.6/6 colonizes soybean roots surface effectively at 48 h after inoculation, suggesting a mechanism for root recognition and adaptation before this period. The colonization proceeds by the development of a mature biofilm on roots at 96 h after inoculation. Transcriptomic analysis of the planktonic bacteria (with plant) revealed the expression of several genes involved in membrane transport, thus confirming an initial metabolic activation of bacterial responses when in the presence of plant root exudates. Moreover, antioxidant genes were mostly expressed during the interaction with the plant exudates. Further evaluation of stress- and methylotrophic-related genes expression by qPCR showed that glutathione peroxidase and glutathione synthetase genes were up-regulated during the Methylobacterium-soybean interaction. These findings support that glutathione (GSH) is potentially a key molecule involved in cellular detoxification during plant root colonization. In addition to methylotrophic metabolism, antioxidant genes, mainly glutathione-related genes, play a key role during soybean exudate recognition and adaptation, the first step in bacterial colonization.

Biotechnological and agronomic potential of endophytic pink-pigmented methylotrophic Methylobacterium spp

The genus Methylobacterium is composed of pink-pigmented facultative methylotrophic (PPFM) bacteria, which are able to synthesize carotenoids and grow on reduced organic compounds containing one carbon (C1), such as methanol and methylamine. Due to their high phenotypic plasticity, these bacteria are able to colonize different habitats, such as soil, water, and sediment, and different host plants as both endophytes and epiphytes. In plant colonization, the frequency and distribution may be influenced by plant genotype or by interactions with other associated microorganisms, which may result in increasing plant fitness. In this review, different aspects of interactions with the host plant are discussed, including their capacity to fix nitrogen, nodule the host plant, produce cytokinins, auxin and enzymes involved in the induction of systemic resistance, such as pectinase and cellulase, and therefore plant growth promotion. In addition, bacteria belonging to this group can be used to reduce environmental contamination because they are able to degrade toxic compounds, tolerate high heavy metal concentrations, and increase plant tolerance to these compounds. Moreover, genome sequencing and omics approaches have revealed genes related to plant-bacteria interactions that may be important for developing strains able to promote plant growth and protection against phytopathogens.

[Aerobic methylobacteria as promising objects of modern biotechnology]

The experimental data of the past decade concerning the metabolic peculiarities of aerobic meth ylobacteria and the prospects for their use in different fields of modern biotechnology, including genetic engineering techniques, have been summarized.

[Advenella kashmirensis subsp. methylica PK1, a facultative methylotroph from carex rhizosphere]

A strain (PK1) of facultative methylobacteria growing on methanol as a carbon and energy source was isolated from carex rhizosphere (Pamukkale National Park, Turkey). The cells were nonmotile gram-negative rods propagating by binary fission. The organism was a strict anaerobe, oxidase- and catalase-positive. Optimal growth occurred at 29°C, pH 8.0-8.5, and 0.5% NaCl; no growth occurred at 2% NaCl. The organism used the ribulose bisphosphate pathway of C1 assimilation. Predominant fatty acids were 11-octodecenoic (18:1ω7) and cis-hexadecenoic (16:1ω7c). Phosphatidylethanolamine and diphosphatidylglycerol were the dominant phospholipids. Q8 was the main ubiquinone. DNA G+C content was 55.4 mol % (mp). Sequencing of the 16S rRNA gene revealed that strain PK1 belonged to the genus Advenella with 98.8 and 99.2% similarity to the type strains A. incenata CCUG 45225T and A. kashmirensis WT001T, respectively. DNA-DNA homology of strain PK1 and A. kashmirensis WT001T was 70%. While MALDI analysis confirmed their close clusterization, RAPD analysis revealed the differences between strain PKI and other Advenella strains. Based on its geno- and phenotypic properties, the isolate PK1 was classified as A. kashmirensis subsp. methylica PK1 (VKM-B 2850 = DSM 27514), the first known methylotroph of the genus Advenella.

Effective use of a horizontally-transferred pathway for dichloromethane catabolism requires post-transfer refinement

When microbes acquire new abilities through horizontal gene transfer, the genes and pathways must function under conditions with which they did not coevolve. If newly-acquired genes burden the host, their utility will depend on further evolutionary refinement of the recombinant strain. We used laboratory evolution to recapitulate this process of transfer and refinement, demonstrating that effective use of an introduced dichloromethane degradation pathway required one of several mutations to the bacterial host that are predicted to increase chloride efflux. We then used this knowledge to identify parallel, beneficial mutations that independently evolved in two natural dichloromethane-degrading strains. Finally, we constructed a synthetic mobile genetic element carrying both the degradation pathway and a chloride exporter, which preempted the adaptive process and directly enabled effective dichloromethane degradation across diverse Methylobacterium environmental isolates. Our results demonstrate the importance of post-transfer refinement in horizontal gene transfer, with potential applications in bioremediation and synthetic biology.

Bacterial acquisition of hexachlorobenzene-derived carbon in contaminated soil

Pesticides are a class of xenobiotics intentionally released into the environment. Hexachlorobenzene (HCB) was used as a fungicide from 1945, leaving behind many contaminated sites. Very few studies have examined the biodegradation of HCB or the fate of HCB-derived carbon. Here we report that certain bacterial populations are capable of deriving carbon from HCB in contaminated soil under aerobic conditions. These populations are primarily Proteobacteria, including Methylobacterium and Pseudomonas, which predominated as detected by stable isotope probing (SIP) and 16S rRNA gene amplicon pyrosequencing. Due to the nature of SIP, which can be used as a functional method solely for assimilatory processes, it is not possible to elucidate whether these populations metabolized directly HCB or intermediates of its metabolism produced by different populations. The possibility exists that HCB is degraded via the formation of pentachlorophenol (PCP), which is further mineralized. With this in mind, we designed primers to amplify PCP 4-monooxygenase-coding sequences based on the available pcpB gene sequence from Methylobacterium radiotolerans JCM 2831. Based on 16S rRNA gene analysis, organisms closely related to this strain were detected in (13)C-labeled DNA. Using the designed primers, we were able to amplify pcpB genes in both total community DNA and (13)C-DNA. This indicates that HCB might be transformed into PCP before it gets assimilated. In summary, this study is the first report on which bacterial populations benefit from carbon originating in the pesticide HCB in a contaminated soil.

[Functional activity of the modA, gene in Methylobacterium dichloromethanicum DM4]

The putative METDI2644 (modA2) gene of Methylobacterium dichloromethanicum DM4, present in the 126-kbp chromosomal fragment associated with dichloromethane (DCM) degradation was investigated. While this gene is presumed to encode the periplasmic substrate-binding subunit of the molybdate ABC transporter, its conceptual translation also exhibits similarity to the proteins containing the ostA conservative domain and responsible for resistance of gram-negative bacteria to organic solvents. Reverse transcription polymerase chain reaction (RT-PCR) revealed the RNA transcripts of this gene in the cells grown on either DCM or methanol. The mobilizable suicide vector pK18mob was used to obtain a knockout mutant with the METDI2644 gene inactivated by insertion of the gentamycin cassette. The mutant pregrown on methanol exhibited lower growth rate on DCM than the wild-type strain DM4. The difference was not alleviated by addition of sodium molybdate. Our results suggest that the METDI2644 gene product plays a role in cell adaptation to DCM degradation.

Effective utilization of dichloromethane by a newly isolated strain Methylobacterium rhodesianum H13

An effective dichloromethane (DCM) utilizer Methylobacterium rhodesianum H13 was isolated from activated sludge. A response surface methodology was conducted, and the optimal conditions were found to be 4.5 g/L Na2HPO4·12H2O, 0.5 g/L (NH4)2SO4, an initial pH of 7.55, and a temperature of 33.7 °C. The specific growth rate of 0.25 h(-1) on 10 mM DCM was achieved, demonstrating that M. rhodesianum H13 was superior to the other microorganisms in previous investigations of DCM utilization. DCM mineralization paralleled the production of cells, CO2, and water-soluble metabolites, as well as the release of Cl(-), whereas the carbon distribution and Cl(-) yield varied with DCM concentrations. The facts that complete degradation only occurred with DCM concentrations below 15 mM and repetitive degradation of 5 mM DCM could proceed for only three cycles were ascribed to pH decrease (from 7.55 to 3.02) though a buffer system was employed.

[Phosphate-solubilizing activity of aerobic methylobacteria]

Phosphate-solubilizing activity was found in 14 strains of plant-associated aerobic methylobacteria belonging to the genera Methylophilus, Methylobacillus, Methylovorus, Methylopila, Methylobacterium, Delftia, and Ancyclobacter. The growth of methylobacteria on medium with methanol as the carbon and energy source and insoluble tricalcium phosphate as the phosphorus source was accompanied by a decrease in pH due to the accumulation of up to 7 mM formic acid as a methanol oxidation intermediate and by release of 120-280 μM phosphate ions, which can be used by both bacteria and plants. Phosphate-solubilizing activity is a newly revealed role of methylobacteria in phytosymbiosis.

[Isolation and degradation characteristics of dichloromethane-degradation bacterial strain by Methylobacterium rhodesianum H13]

A dichloromethane-degrading bacterium Methylobacterium rhodesianum H13 which utilized the DCM as the sole carbon and energy source was isolated. According to the research, M. rhodesianum H13 could completely degrade 5 mmol x L(-1) DCM in 23 h with the initial cell concentration of 0.82 mg x L(-1), pH 7.0, 30 degrees C, and the cell yield rate was about 0.136 g x g(-1) DCM. With the degradation of DCM, Cl- concentration gradually raised (the release of Cl- concentration was about 2 times higher as the DCM), pH value dropped to 6.75, and the solution was weakly acidic. Temperature, pH, DCM concentration, Cl- concentration and other factors were investigated through the shake flask experiments, and the optimal conditions for DCM degradation were: temperature 30 degrees C, pH 7.0. The study also indicated that 5 mmol x L(-1) of DCM was the optimum concentration for M. rhodesianum H13 and high levels of DCM could inhibit the degradation. The research has an important application value for the DCM environmental pollution.

[Isolation of a methanol-utilizing strain and its application for determining methanol]

OBJECTIVE

To isolate and characterize bacteria that can be used todevelop microbial biosensor for methanol (MeOH) determination.

METHODS

We used selective medium and streak plate to isolate bacteria. Morphological, physiological characteristics and 16S rDNA sequence analysis were used to identify the strain. An MeOH biosensor was then developed by immobilizing M211 along with dissolved oxygen (O2) sensor.

RESULT

An MeOH utilizing bacterium was isolated from biogas-producing tank using methanol as the sole carbon source, and identified as Methylobacteriumorganophilium. Decrease of O2 concentration is linearly related to the MeOH concentration in the range from 0.02% to 1%, with the MeOH detection limit of 0.27 mg/L. The response time of the biosensor is within 20 min. Furthermore, the result of interference test and the detection of methanol sample are both satisfactory.

CONCLUSION

Good results are obtained in interference test and the detection of methanol sample. The proposed method seems very attractive in monitoring methanol.

[Aerobic methylobacteria as the basis for a biosensor for dichloromethane detection]

Cells of dichloromethane (DChM) bacteria-destructors were immobilized by sorption on different types of membranes, which were fixed on the measuring surface of a pH-sensitive field transistor. The presence of DChM in the medium (0.6-8.8 mM) led to a change in the transistor's output signal, which was determined by the appearance of H+ ions in the medium due to DChM utilization by methylobateria. Among four strains of methylobacteria--Methylobacterium dichloromethanicum DM4, Methylobacterium extorquens DM 17, Methylopila helvetica DM6, and Ancylobacter dichloromethanicus DM 16--the highest and most stable activity toward DChM degradation was observed in the strain M. dichloromethanicum DM4. Among 11 types of membranes for cell immobilization, Millipore nitrocellulose membranes and chromatographic fiber paper GF/A, which allow one to obtain stable biosensor signals for 2 weeks without a bioreceptor change, were chosen as optimal carriers.

[Diversity of endophytic bacteria in rice seeds and their secretion of indole acetic acid]

OBJECTIVE

This study aimed to investigate the diversity of endophytic bacteria isolated from rice seeds, and screen indole acetic acid secrecting srtains.

METHOD

Conventional culture-dependent methods were used to isolate the endopytic bacteria from rice seeds. Phylogenetic analysis was done based on partial 16s rRNA gene sequences. The ability to indole acetic acid secretion of tested strains was analyzed qualitatively and quantitatively by colorimetry.

RESULT

In total 66 isolates were identified as belonging to 26 species of 15 genera of 5 phyla. Of them 26 strains were chosen to test indole acetic acid secretion. Four isolates had more ability of indole acetic acid secretion; they belonged to the genera of Staphylococcus, Rhizobium, Microbacterium and Methylobacterium.

CONCLUSION

The endophytic bacteria in rice seeds are diverse. Some of them could produce indole acetic acid.

Polyhydroxyalkanoates accumulation by Methylobacterium organophilum CZ-2 during methane degradation using citrate or propionate as cosubstrates

Methylobacterium organophilum CZ-2 synthesized polyhydroxyalkanoates (PHAs) under nitrogen limitation with CH4 as carbon source and when either citrate or propionate was added as cosubstrates. The highest PHAs content (yPHA) in closed flasks was obtained in the CH4-citrate and CH4-propionate experiments attaining values of 0.82 and 0.68, respectively. M. organophilum CZ-2 cultivated in bioreactors with citrate and continuous CH4 addition yielded a final PHAs concentration of 143 gm(-3) containing hydroxybutyrate (HB), hydroxyvalerate (HV) and hydroxyoctanoate (HO), in a 55:35:10 ratio, with, yPHA of 0.88 and a CH4 elimination capacity (EC) of 20 gm(-3) h(-1). With propionate, the yPHA was 0.3 and the EC around 8 gm(-3) h(-1). From 1H and 13C NMR experiments it was found that the polymer produced with CH4-citrate contained six different monomers: 3HB, 3HV, 4HV, 4-hydroxyheptanoate (4HH), 3HO and 4HO, showing the great versatility of this PHAs producing bacterium.

Salt stress tolerance of methylotrophic bacteria Methylophilus sp. and Methylobacterium sp. isolated from coal mine spoils

Two methylotrophic strains of Bina coalmine spoil BNV7b and BRV25 were identified based on physiological traits and 16S rDNA sequence as Methylophilus and Methylobacterium species.' The strains exhibited similar carbon utilization but differed in N utilization and their response to the metabolic inhibitors. Methylophilus sp. was less tolerant to salt stress and it viability declined to one tenth within 4 h of incubation in 2M NaCI due to membrane damage and leakage of the intracellular electrolytes as evident from malondiaaldehyde (MDA) assay. In 200 mM NaCI, they exhibited increased superoxide dismutase (SOD), catalase (CAT) and ascorbate peroxidase (APX) activity while in 500 mM NaCI, enzyme activities declined in Methylophilus sp. and increased in Methylobacterium sp. Among exogenously applied osmoprotectants proline was most efficient; however, polyols (mannitol, sorbitol and glycerol) also supported growth under lethal NaCI concentration.

[Functional analysis of the genome fragment involved in aerobic dichloromethane degradation by methylobacterium dichloromethanicum DM4]

The hypothetical genes of Methylobacterium dichloromethanicum DM4, METDI 2671 (bioD2), and METDI 2680 located within the chromosomal fragment (126 kb) associated with dichloromethane (DCM) degradation have been studied. The reverse transcription polymerase chain reaction method (RT-PCR) showed the presence of transcripts of both genes in cells grown on DCM and methanol. The mobilized suicidal vector pK18mob was used to obtain knockout mutants in these genes. The BIO mutant (with an insertion in the bioD2 gene) after cultivation on methanol was characterized by a lower growth rate on DCM compared to the wild-type DM4 strain, while the MT mutant (with an insertion in the METDI 2680 gene) did not differ from the initial strain in respect of these characteristics. The results demonstrate the involvement of the bioD2 gene in biotin biosynthesis coupled with DCM degradation.

Practical application of methanol-mediated mutualistic symbiosis between Methylobacterium species and a roof greening moss, Racomitrium japonicum

Bryophytes, or mosses, are considered the most maintenance-free materials for roof greening. Racomitrium species are most often used due to their high tolerance to desiccation. Because they grow slowly, a technology for forcing their growth is desired. We succeeded in the efficient production of R. japonicum in liquid culture. The structure of the microbial community is crucial to stabilize the culture. A culture-independent technique revealed that the cultures contain methylotrophic bacteria. Using yeast cells that fluoresce in the presence of methanol, methanol emission from the moss was confirmed, suggesting that it is an important carbon and energy source for the bacteria. We isolated Methylobacterium species from the liquid culture and studied their characteristics. The isolates were able to strongly promote the growth of some mosses including R. japonicum and seed plants, but the plant-microbe combination was important, since growth promotion was not uniform across species. One of the isolates, strain 22A, was cultivated with R. japonicum in liquid culture and in a field experiment, resulting in strong growth promotion. Mutualistic symbiosis can thus be utilized for industrial moss production.

The abundance of pink-pigmented facultative methylotrophs in the root zone of plant species in invaded coastal sage scrub habitat

Pink-pigmented facultative methylotrophic bacteria (PPFMs) are associated with the roots, leaves and seeds of most terrestrial plants and utilize volatile C(1) compounds such as methanol generated by growing plants during cell division. PPFMs have been well studied in agricultural systems due to their importance in crop seed germination, yield, pathogen resistance and drought stress tolerance. In contrast, little is known about the PPFM abundance and diversity in natural ecosystems, let alone their interactions with non-crop species. Here we surveyed PPFM abundance in the root zone soil of 5 native and 5 invasive plant species along ten invasion gradients in Southern California coastal sage scrub habitat. PPFMs were present in every soil sample and ranged in abundance from 10(2) to 10(5) CFU/g dry soil. This abundance varied significantly among plant species. PPFM abundance was 50% higher in the root zones of annual or biennial species (many invasives) than perennial species (all natives). Further, PPFM abundance appears to be influenced by the plant community beyond the root zone; pure stands of either native or invasive species had 50% more PPFMs than mixed species stands. In sum, PPFM abundance in the root zone of coastal sage scrub plants is influenced by both the immediate and surrounding plant communities. The results also suggest that PPFMs are a good target for future work on plant-microorganism feedbacks in natural ecosystems.

Production of poly-β-hydroxybutyrate (PHB) by Methylobacterium organophilum isolated from a methanotrophic consortium in a two-phase partition bioreactor

The biodegradation of methane, a greenhouse gas, and the accumulation of poly-β-hydroxybutyrate (PHB) were studied using a methanotrophic consortium and an isolated strain thereof. The specific rates for methane consumption were 100 and [Formula: see text] for the isolate and the consortium, respectively. Also the effect of including 10% (vv(-1)) of silicone oil in a two-phase partitioning bioreactor (TPPB) was assayed for the elimination of 1% methane in air stream. TPPB allowed a 33-45% increase of methane elimination under growing conditions. Nitrogen limitation was assayed in bioreactors to promote PHB production. Under this condition, the specific methane degradation rate remained unchanged for the consortium and decreased to [Formula: see text] for the isolated strain. The accumulated PHB in the reactor was 34% and 38% (ww(-1)) for the consortium and the isolate, respectively. The highest productivity was obtained in the TPPB and was 1.61 mg(PHB)g(x)(-1) h(-1). The CZ-2 isolate was identified as Methylobacterium organophilum, this is the first study that reports this species as being able to grow on methane and accumulate up to 57% (ww(-1)) of PHB under nitrogen limitation in microcosm experiments.

Isolation and genetic characterization of Aurantimonas and Methylobacterium strains from stems of hypernodulated soybeans

The aims of this study were to isolate Aurantimonas and Methylobacterium strains that responded to soybean nodulation phenotypes and nitrogen fertilization rates in a previous culture-independent analysis (Ikeda et al. ISME J. 4:315-326, 2010). Two strategies were adopted for isolation from enriched bacterial cells prepared from stems of field-grown, hypernodulated soybeans: PCR-assisted isolation for Aurantimonas and selective cultivation for Methylobacterium. Thirteen of 768 isolates cultivated on Nutrient Agar medium were identified as Aurantimonas by colony PCR specific for Aurantimonas and 16S rRNA gene sequencing. Meanwhile, among 187 isolates on methanol-containing agar media, 126 were identified by 16S rRNA gene sequences as Methylobacterium. A clustering analysis (>99% identity) of the 16S rRNA gene sequences for the combined datasets of the present and previous studies revealed 4 and 8 operational taxonomic units (OTUs) for Aurantimonas and Methylobacterium, respectively, and showed the successful isolation of target bacteria for these two groups. ERIC- and BOX-PCR showed the genomic uniformity of the target isolates. In addition, phylogenetic analyses of Aurantimonas revealed a phyllosphere-specific cluster in the genus. The isolates obtained in the present study will be useful for revealing unknown legume-microbe interactions in relation to the autoregulation of nodulation.

Autoregulation of nodulation interferes with impacts of nitrogen fertilization levels on the leaf-associated bacterial community in soybeans

The diversities leaf-associated bacteria on nonnodulated (Nod(-)), wild-type nodulated (Nod(+)), and hypernodulated (Nod(++)) soybeans were evaluated by clone library analyses of the 16S rRNA gene. To analyze the impact of nitrogen fertilization on the bacterial leaf community, soybeans were treated with standard nitrogen (SN) (15 kg N ha(-1)) or heavy nitrogen (HN) (615 kg N ha(-1)) fertilization. Under SN fertilization, the relative abundance of Alphaproteobacteria was significantly higher in Nod(-) and Nod(++) soybeans (82% to 96%) than in Nod(+) soybeans (54%). The community structure of leaf-associated bacteria in Nod(+) soybeans was almost unaffected by the levels of nitrogen fertilization. However, differences were visible in Nod(-) and Nod(++) soybeans. HN fertilization drastically decreased the relative abundance of Alphaproteobacteria in Nod(-) and Nod(++) soybeans (46% to 76%) and, conversely, increased those of Gammaproteobacteria and Firmicutes in these mutant soybeans. In the Alphaproteobacteria, cluster analyses identified two operational taxonomic units (OTUs) (Aurantimonas sp. and Methylobacterium sp.) that were especially sensitive to nodulation phenotypes under SN fertilization and to nitrogen fertilization levels. Arbuscular mycorrhizal infection was not observed on the root tissues examined, presumably due to the rotation of paddy and upland fields. These results suggest that a subpopulation of leaf-associated bacteria in wild-type Nod(+) soybeans is controlled in similar ways through the systemic regulation of autoregulation of nodulation, which interferes with the impacts of N levels on the bacterial community of soybean leaves.

Production of the chiral compound (R)-3-hydroxybutyrate by a genetically engineered methylotrophic bacterium

In this study, a methylotrophic bacterium, Methylobacterium rhodesianum MB 126, was used for the production of the chiral compound (R)-3-hydroxybutyrate (R-3HB) from methanol. R-3HB is formed during intracellular degradation of the storage polymer (R)-3-polyhydroxybutyrate (PHB). Since the monomer R-3HB does not accumulate under natural conditions, M. rhodesianum was genetically modified. The gene (hbd) encoding the R-3HB-degrading enzyme, R-3HB dehydrogenase, was inactivated in M. rhodesianum. The resulting hbd mutant still exhibited low growth rates on R-3HB as the sole source of carbon and energy, indicating the presence of alternative pathways for R-3HB utilization. Therefore, transposon mutagenesis was carried out with the hbd mutant, and a double mutant unable to grow on R-3HB was obtained. This mutant was shown to be defective in lipoic acid synthase (LipA), resulting in an incomplete citric acid cycle. Using the hbd lipA mutant, we produced 3.2 to 3.5 mM R-3HB in batch and 27 mM (2,800 mg liter(-1)) in fed-batch cultures. This was achieved by sequences of cultivation conditions initially favoring growth, then PHB accumulation, and finally PHB degradation.

Metabolite profiling uncovers plasmid-induced cobalt limitation under methylotrophic growth conditions

BACKGROUND

The introduction and maintenance of plasmids in cells is often associated with a reduction of growth rate. The reason for this growth reduction is unclear in many cases.

METHODOLOGY/PRINCIPAL FINDINGS

We observed a surprisingly large reduction in growth rate of about 50% of Methylobacterium extorquens AM1 during methylotrophic growth in the presence of a plasmid, pCM80 expressing the tetA gene, relative to the wild-type. A less pronounced growth delay during growth under non-methylotrophic growth conditions was observed; this suggested an inhibition of one-carbon metabolism rather than a general growth inhibition or metabolic burden. Metabolome analyses revealed an increase in pool sizes of ethylmalonyl-CoA and methylmalonyl-CoA of more than 6- and 35-fold, respectively, relative to wild type, suggesting a strongly reduced conversion of these central intermediates, which are essential for glyoxylate regeneration in this model methylotroph. Similar results were found for M. extorquens AM1 pCM160 which confers kanamycin resistance. These intermediates of the ethylmalonyl-CoA pathway have in common their conversion by coenzyme B(12)-dependent mutases, which have cobalt as a central ligand. The one-carbon metabolism-related growth delay was restored by providing higher cobalt concentrations, by heterologous expression of isocitrate lyase as an alternative path for glyoxylate regeneration, or by identification and overproduction of proteins involved in cobalt import.

CONCLUSIONS/SIGNIFICANCE

This study demonstrates that the introduction of the plasmids leads to an apparent inhibition of the cobalt-dependent enzymes of the ethylmalonyl-CoA pathway. Possible explanations are presented and point to a limited cobalt concentration in the cell as a consequence of the antibiotic stress.

Increasing the accuracy of mass isotopomer analysis through calibration curves constructed using biologically synthesized compounds

Mass isotopomer analysis is an important technique to measure the production and flow of metabolites in living cells, tissues, and organisms. This technique depends on accurate quantifications of different mass isotopomers using mass spectrometry. Constructing calibration curves using standard samples is the most universal approach to convert raw mass spectrometry measurements into quantitative distributions of mass isotopomers. Calibration curve approach has been, however, of very limited use in comprehensive analyses of biological systems, mainly suffering from the lack of extensive range of standard samples with accurately known isotopic enrichment. Here, we present a biological method capable of synthesizing specifically labeled amino acids. These amino acids have well-determined and estimable mass isotopomer distributions and thus can serve as standard samples. In this method, the bacterium strain Methylobacterium salsuginis sp. nov. was cultivated with partially 13C-labeled methanol as the only carbon source to produce 13C-enriched compounds. We show that the mass isotopomer distributions of the various biosynthesized amino acids are well determined and can be reasonably estimated based on proposed binomial approximation if the labeling state of the biomass reached an isotopic steady state. The interference of intramolecular inhomogeneity of 13C isotope abundances caused by biological isotope fractionation was eliminated by estimating average 13C isotope abundance. Further, the predictions are tested experimentally by mass spectrometry (MS) spectra of the labeled glycine, alanine, and aspartic acid. Most of the error in mass spectrometry measurements was less than 0.74 mol% in the test case, significantly reduced as compared with uncalibrated results, and this error is expected to be less than 0.4 mol% in real experiment as revealed by theoretical analysis.

Statistical media optimization for growth and PHB production from methanol by a methylotrophic bacterium

Media components were optimized by statistical design for cell growth and PHB production of Methylobacterium extorquens DSMZ 1340. Four important components of growth media were optimized by central composite design. The growth increased from an OD=1.35 for Choi medium as control to an OD=2.15 for optimal medium. Then media components for PHB production were optimized. Optimization of five important factors was conducted by response surface method. The optimal composition of PHB production medium was found to be at 7.8 (g/L) Na2HPO4 x 12H2O, and surprisingly at zero concentration of (NH4)2SO4, KH2PO4, MgSO4 and MnSO4. The PHB production was found to be 2.95 (g/L) at this medium. RSM results indicated that a deficiency of nitrogen and magnesium is crucial for PHB accumulation in this microorganism. Also, PHB production was carried out in a 5 L fermentor at the optimum condition which resulted in 9.5 g/L PHB and 15.4 g/L cell dry weight with 62.3% polymer content.

Thiosulfate Oxidation and mixotrophic growth of Methylobacterium goesingense and Methylobacterium fujisawaense

The mixotrophic growth with methanol plus thiosulfate was examined in nutrient-limited mixotrophic condition for Methylobacterium goesingense CBMB5 and Methylobacterium fujisawaense CBMB37. Thiosulfate oxidation increased the growth and protein yield in mixotrophic medium that contained 150 mM methanol and 20 mM sodium thiosulfate, at 144 h. Respirometric study revealed that thiosulfate was the most preferable reduced inorganic sulfur source, followed by sulfite and sulfur. M. goesingense CBMB5 and M. fujisawaense CBMB37 oxidized thiosulfate directly to sulfate, and intermediate products of thiosulfate oxidation such as polythionates, sulfite, and sulfur were not detected in spent medium and they did not yield positive amplification for tested soxB primers. Enzymes of thiosulfate oxidation such as rhodanese and sulfite oxidase activities were detected in cell-free extracts of M. goesingense CBMB5, and M. fujisawaense CBMB37, and thiosulfate oxidase (tetrathionate synthase) activity was not observed. It indicated that both the organisms use the "non-S4 intermediate" sulfur oxidation pathway for thiosulfate oxidation. It is concluded from this study that M. goesingense CBMB5, and M. fujisawaense CBMB37 exhibited mixotrophic metabolism in medium containing methanol plus thiosulfate and that thiosulfate oxidation and the presence of a "Paracoccus sulfur oxidation" (PSO) pathway in methylotrophic bacteria are species dependant.

[Effect of operational modes on community structure of type I methanotroph in the cover soil of municipal solid waste landfill]

Type I methanotroph is crucial for methane oxidization and it responses fast to the changes in environment. In this study, 16S rDNA-based denaturing gradient gel electrophoresis (DGGE) gene fingerprint technology was applied to investigate the effect of operational modes, i. e. high-density polyethylene liner (HDPE) isolation or subsurface irrigation of landfill leachate and vegetation, on community structure and diversity of type I methanotroph in soils covering municipal solid waste landfill. 16S rDNA based phylogenetic analysis reveals type I methanotroph in all tested soils belongs to Methylobacter. According to Shannon-Wiener diversity index and principal component analysis, landfill leachate subsurface irrigation and vegetation have more impact on type I methanotroph community structure and diversity than HDPE liner isolation does, and they reduce type I methanotroph diversity. Leachate irrigation is supposed to inhibit the growth of Methylobacter population. Community structure of type I methanotroph in landfill cover soil isolated by HDPE, i.e. invaded by landfill gas, shifts during long-term gas interference. When cover age is 1.5 years old, Shannon-Wiener diversity index of type I methanotroph reaches its maximum.

Enhanced PHB production and scale up studies using cheese whey in fed batch culture of Methylobacterium sp. ZP24

Methylobacterium sp. ZP24 produced polyhydroxybutyrate (PHB) from disaccharides like lactose and sucrose. As Methylobacterium sp. ZP24 showed growth associated PHB production, an intermittent feeding strategy having lactose and ammonium sulfate at varying concentration was used towards reaching higher yield of the polymer. About 1.5-fold increase in PHB production was obtained by this intermittent feeding strategy. Further increase in PHB production by 0.8-fold could be achieved by limiting the dissolved oxygen (DO) levels in the fermenter. The decreased DO is thought to increase flux of acetyl CO-A towards PHB accumulation over TCA cycle. Cheese whey, a dairy waste product and being a rich source of utilizable sugar and other nutrients, when used in the bioreactor as a main substrate replacing the lactose, led to further increase in the PHB production by 2.5-fold. A total of 4.58-fold increase in the PHB production was obtained using limiting DO conditions with processed cheese whey supplemented with ammonium sulfate in fed batch culture of Methylobacterium sp. ZP24. The present investigation therefore reflects on the possibility of developing a cheap biological route for production of green thermoplastics.

Reuse of low concentrated electronic wastewater using selected microbe immobilised cell system

This work describes a novel technology for the reuse of low concentrated electronic wastewater using selected microbe immobilisation cell (SMIC) system. The SMIC system is an innovative technology to maximise the activity of specific microorganisms capable of decomposing tetramethyl ammonium hydroxide (TMAH) as a major organic compound in the low concentrated electronic wastewater. The versatility of the SMIC system has been studied by using continuous-flow reactors. The TOC in a SMIC system was removed completely, indicating that SMIC is a useful technology to remove TOC biologically in low concentrated wastewater. The most important advantages of this system are highly effective and stable in view of TMAH removal. These characteristics make well suited to various applications depending on targeted compounds and microorganisms and, especially, in the wastewater of electronic facilities.

[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.

Metal tolerating methylotrophic bacteria reduces nickel and cadmium toxicity and promotes plant growth of tomato (Lycopersicon esculentum L)

Inoculation of plants with microorganisms may reduce the toxicity of heavy metals to plants in contaminated soils. In this study, we have shown that the plant growth promoting bacteria Methylobacterium oryzae strain CBMB20 and Burkholderia sp. strain CBMB40 from rice reduce the toxicity of Ni and Cd in tomato and promote plant growth under gnotobiotic and pot culture experiments. The bacterial strains bound considerable amounts of Ni(II) and Cd(II) in their growing and resting cells and showed growth in the presence of NiCl2 and CdCl2. In gnotobiotic assay, inoculation with the bacterial strains reduced the ethylene emission and increased the tolerance index of the seedlings against different concentrations of NiCl2/CdCl2. In pot experiments carried out with non-polluted, Ni and Cd supplemented Wonjo-Mix bed soil, the results clearly demonstrated reduction in the accumulations of Ni(II) and Cd(II) in roots and shoots, with significant increase in the plant growth attributes with bacterial inoculations compared to untreated control. Strain CBMB20 performed better than CBMB40 in reducing the heavy metal accumulations in plants. Our results suggest conclusively, that protection against the heavy metals toxicity is rendered by these bacterial strains by reducing their uptake and further translocation to shoots in plants and promote the plant growth by other PGP characteristics.

Over-expression of a hydroxypyruvate reductase in Methylobacterium sp. MB200 enhances glyoxylate accumulation

Methylobacterium sp. MB200 capable of producing glyoxylate from methanol was obtained by enrichment culture using a medium containing methanol as the sole carbon source. A hpr gene that encodes a hydroxypyruvate reductase (HPR) was cloned from this strain and was ligated into the vector pLAFR3 to obtain the recombinant plasmid pLAFRh, which was transferred into M. sp. MB200 to generate an recombinant strain MB201. Homologous expression of hpr under the control of the lacZ promoter led to the enhanced glyoxylate accumulation in cultures of Methylobacterium sp MB201. The yield of glyoxylate reached 14.38 mg/mL, representing nearly a twofold increase when compared with the wild-type strain.

Complete degradation of dimethyl isophthalate requires the biochemical cooperation between Klebsiella oxytoca Sc and Methylobacterium mesophilicum Sr Isolated from Wetland sediment

Two bacterial strains Klebsiella oxytoca Sc and Methylobacterium mesophilicum Sr were isolated and identified from enrichment cultures using dimethyl isophthalate (DMI) as the sole source of carbon and energy, and mangrove sediment as an inoculum. DMI was rapidly transformed by K. oxytoca Sc in the culture with formation of monomethyl isophthalate (MMI), which accumulated in the culture medium. M. mesophilicum Sr, incapable of utilizing DMI, showed high capability of degrading MMI to a transitory intermediate isophthalic acid (IPA), which was further mineralized by this strain. The biochemical pathway of DMI degradation by these two bacteria in a consortium was proposed: DMI to MMI by K. oxytoca Sc, MMI to IPA by M. mesophilicum Sr, and IPA by both K. oxytoca Sc and M. mesophilicum Sr based on the identified degradation intermediates. The consortium comprising K. oxytoca Sc and M. mesophilicum Sr was effective in mineralization of DMI. The results suggest that complete degradation of environmental pollutant DMI requires the biochemical cooperation between different microorganisms of the mangrove environment.

Thiosulfate oxidation and mixotrophic growth of Methylobacterium oryzae

Thiosulfate oxidation and mixotrophic growth with succinate or methanol plus thiosulfate was examined in nutrient-limited mixotrophic condition for Methylobacterium oryzae CBMB20, which was recently characterized and reported as a novel species isolated from rice. Methylobacterium oryzae was able to utilize thiosulfate in the presence of sulfate. Thiosulfate oxidation increased the protein yield by 25% in mixotrophic medium containing 18.5 mmol·L–1of sodium succinate and 20 mmol·L–1of sodium thiosulfate on day 5. The respirometric study revealed that thiosulfate was the most preferable reduced inorganic sulfur source, followed by sulfur and sulfite. Thiosulfate was predominantly oxidized to sulfate and intermediate products of thiosulfate oxidation, such as tetrathionate, trithionate, polythionate, and sulfur, were not detected in spent medium. It indicated that bacterium use the non-S4intermediate sulfur oxidation pathway for thiosulfate oxidation. Thiosulfate oxidation enzymes, such as rhodanese and sulfite oxidase activities appeared to be constitutively expressed, but activity increased during growth on thiosulfate. No thiosulfate oxidase (tetrathionate synthase) activity was detected.

Intercellular colonization and growth promoting effects of Methylobacterium sp. with plant-growth regulators on rice (Oryza sativa L. Cv CO-43)

The Methylobacterium sp. strain NPFM-SB3, isolated from Sesbania rostrata stem nodules possessed nitrogenase activity and nodA genes. Pure culture of NPFM-SB3 strain produced indole-3-acetic acid, cytokinins and on inoculation to rice plants resulted in numerous lateral roots. Inoculation of synthetic auxins 2,4-dichlorophenoxy acetic acid, naphthalene acetic acid or flavonoids naringenin and dihydroxy-4-methoxyisoflavone individually or to bacterial inoculated rice seedlings improved the plant growth and lateral root formation under hydroponic condition. The formation of nodule-like structure and nitrogenase activity which is purely auxin dependent was observed in 2,4-dichlorophenoxy acetic acid treatments to Methylobacterium sp. NPFM-SB3 inoculated rice plants. The rhizobia entered through fissures formed due to lateral root emergence and spread intercellularly in the nodular structures concluded that the effect of 2,4-dichlorophenoxy acetic acid treatment for rice seedlings grown under gnotobiotic conditions is to create a niche in which these bacteria can grow.

Capillary electrophoresis-mass spectrometry of citrus endophytic bacteria siderophores

CE-ESI-MS with a liquid sheath interface and IT mass analyzer was used for analysis of siderophores from different strains of Methylobacterium spp. citrus endophyte extracts. Three Methylobacterium strains were investigated according to positive bioassay tests. Bacteria cultures were grown under Fe(III) absence (siderophore producing cultures) and under Fe(III) presence (control cultures). Siderophores were extracted from culture supernatant with polystyrene resins. BGE and sheath-liquid composition were optimized, respectively, in order to assure both, best peak resolution and ESI-MS sensitivity. The best analysis conditions were obtained with 100 mmol/L ammonium bicarbonate at pH 8 as BGE and methanol:H(2)O 25:75 + 0.05% formic acid as sheath liquid. CZE-ESI-MS analysis revealed two possible siderophores, according to bacterium species, presenting M(r) of 1004.3 and 798.3 Da.

Production of polyhydroxyalkanoates from methanol by a new methylotrophic bacterium Methylobacterium sp. GW2

A new bacterial strain, isolated from groundwater contaminated with explosives, was characterized as a pink-pigmented facultative methylotroph, affiliated to the genus Methylobacterium. The bacterial isolate designated as strain GW2 was found capable of producing the homopolymer poly-3-hydroxybutyrate (PHB) from various carbon sources such as methanol, ethanol, and succinate. Methanol acted as the best substrate for the production of PHB reaching 40 % w/w dry biomass. PHB accumulation was observed to be a growth-associated process, so that there was no need for two-step fermentation. Optimal growth occurred at 0.5 % (v/v) methanol concentration, and growth was strongly inhibited at alpha concentration above 2 % (v/v). Methylobacterium sp. strain GW2 was also able to accumulate the copolyester poly-3-hydroxybutyrate-poly-3-hydroxyvalerate (PHB/HV) when valeric acid was supplied as an auxiliary carbon source to methanol. After 66 h, a copolymer content of 30 % (w/w) was achieved with a PHB to PHV ratio of 1:2. Biopolymers produced by strain GW2 had an average molecular weight ranging from 229,350 to 233,050 Da for homopolymer PHB and from 362,430 to 411,300 Da for the copolymer PHB/HV.

Characterization of Ni-tolerant methylobacteria associated with the hyperaccumulating plant Thlaspi goesingense and description of Methylobacterium goesingense sp. nov

Various pink-pigmented facultative methylotrophic (PPFM) bacteria (strains iEII3, iEIV1, iEI6, iEII1, iEIII3 iEIII4, iEIII5, iRII1, iRII2, iRIII1, iRIV1 and iRIV2) were obtained from the rhizosphere and endosphere of hyperaccumulating plant Thlaspi goesingense grown in Redschlag, Austria [R. Idris, R. Trifonova, M. Puschenreiter, W.W. Wenzel, A. Sessitsch, Bacterial communities associated with flowering plants of the Ni hyperaccumulator Thlaspi goesingense, Appl. Environ. Microbiol. 70 (2004) 2667-2677]. Due to their unexpected diversity, abundance and nickel tolerance they were further characterized by detailed 16S rRNA gene analysis, DNA-DNA hybridization, fatty acid analysis, heavy metal tolerance, screening for known Ni resistance genes and phenotypic analysis. These strains were found to exhibit different multiple heavy metal resistance characteristics to Ni, Cd, Co, Zn and Cr. On the basis of their physiological and genotypic properties, strains could be grouped with Methylobacterium extorquens and M. mesophilicum. One endophyte, strain iEII3, was found to belong to a novel species for which the name M. goesingense is proposed.

Reclassification of Methylobacterium chloromethanicum and Methylobacterium dichloromethanicum as later subjective synonyms of Methylobacterium extorquens and of Methylobacterium lusitanum as a later subjective synonym of Methylobacterium rhodesianum

Phylogenetic analysis based on 16S rDNA sequences was performed on all type strains of the 14 validly described Methylobacterium species to ascertain the genealogic relationships among these species. The results showed that type strains of Methylobacterium were divided into two monophyletic groups whose members were distinct species with sequence similarity values greater than 97.0% between any two of the members in the same group. Only M. organophilum JCM 2833(T) and ATCC 27886(T) were not divided into those two groups. In particular, strains of M. dichloromethanicum and M. chloromethanicum exhibited extremely high similarity values (99.9 and 100%, respectively) with the type strain of M. extorquens. To clarify the relationships among Methylobacterium species in more detail, phylogenetic analysis based on the 5' end hyper-variable region of 16S rDNA (HV region), ribotyping analysis, fatty acid analysis, G+C content analysis and DNA-DNA hybridization experiments was performed on 58 strains of Methylobacterium species. Results of the ribotyping analysis and the phylogenetic analysis based on HV region sequences indicated that many Methylobacterium strains, including M. 'organophilum' DSM 760(T), have been erroneously identified. The DNA G+C content of Methylobacterium strains were between 68.1 and 71.3%. Results of whole-cell fatty-acid profiles showed that all strains contained 18 : 1omega7c as the primary fatty acid component (82.8-90.1%), with 16 : 0 and 18 : 0 as minor components. M. dichloromethanicum DSM 6343(T), M. chloromethanicum NCIMB 13688(T), and M. extorquens IAM 12631(T) exhibited high DNA-DNA relatedness values between each other (69-80%). M. lusitanum NCIMB 13779(T) also showed a close relationship with M. rhodesianum DSM 5687(T) at DNA-DNA relatedness levels of 89-92%. According to these results, many Methylobacterium strains should be reclassified, with M. dichloromethanicum and M. chloromethanicum regarded as a synonym of M. extorquens, and M. lusitanum a synonym for M. rhodesianum.