Transcriptomic and Metabolomic Responses to Carbon and Nitrogen Sources in Methylomicrobium album BG8.

Methanotrophs use methane as their sole carbon and energy source and represent an attractive platform for converting single-carbon feedstocks into value-added compounds. Optimizing these species for biotechnological applications involves choosing an optimal growth substrate based on an understanding of cellular responses to different nutrients. Although many studies of methanotrophs have examined growth rate, yield, and central carbon flux in cultures grown with different carbon and nitrogen sources, few studies have examined more global cellular responses to different media. Here, we evaluated global transcriptomic and metabolomic profiles of Methylomicrobium album BG8 when grown with methane or methanol as the carbon source and nitrate or ammonium as the nitrogen source. We identified five key physiological changes during growth on methanol: M. album BG8 cultures upregulated transcripts for the Entner-Doudoroff and pentose phosphate pathways for sugar catabolism, produced more ribosomes, remodeled the phospholipid membrane, activated various stress response systems, and upregulated glutathione-dependent formaldehyde detoxification. When using ammonium, M. album BG8 upregulated hydroxylamine dehydrogenase (haoAB) and overall central metabolic activity, whereas when using nitrate, cultures upregulated genes for nitrate assimilation and conversion. Overall, we identified several nutrient source-specific responses that could provide a valuable basis for future research on the biotechnological optimization of these species. IMPORTANCE Methanotrophs are gaining increasing interest for their biotechnological potential to convert single-carbon compounds into value-added products such as industrial chemicals, fuels, and bioplastics. Optimizing these species for biotechnological applications requires a detailed understanding of how cellular activity and metabolism vary across different growth substrates. Although each of the two most commonly used carbon sources (methane or methanol) and nitrogen sources (ammonium or nitrate) in methanotroph growth media have well-described advantages and disadvantages in an industrial context, their effects on global cellular activity remain poorly characterized. Here, we comprehensively describe the transcriptomic and metabolomic changes that characterize the growth of an industrially promising methanotroph strain on multiple combinations of carbon and nitrogen sources. Our results represent a more holistic evaluation of cellular activity than previous studies of core metabolic pathways and provide a valuable basis for the future biotechnological optimization of these species.

Halotolerance mechanisms of the methanotroph Methylomicrobium alcaliphilum.

Methylomicrobium alcaliphilum is an alkaliphilic and halotolerant methanotroph. The physiological responses of M. alcaliphilum to high NaCl concentrations, were studied using RNA sequencing and metabolic modeling. This study revealed that M. alcaliphilum possesses an unusual respiratory chain, in which complex I is replaced by a Na+ extruding NQR complex (highly upregulated under high salinity conditions) and a Na+ driven adenosine triphosphate (ATP) synthase coexists with a conventional H+ driven ATP synthase. A thermodynamic and metabolic model showing the interplay between these different components is presented. Ectoine is the main osmoprotector used by the cells. Ectoine synthesis is activated by the transcription of an ect operon that contains five genes, including the ectoine hydroxylase coding ectD gene. Enzymatic tests revealed that the product of ectD does not have catalytic activity. A new Genome Scale Metabolic Model for M. alcaliphilum revealed a higher flux in the oxidative branch of the pentose phosphate pathway leading to NADPH production and contributing to resistance to oxidative stress.

XoxF Acts as the Predominant Methanol Dehydrogenase in the Type I Methanotroph Methylomicrobium buryatense.

UNLABELLED: Many methylotrophic taxa harbor two distinct methanol dehydrogenase (MDH) systems for oxidizing methanol to formaldehyde: the well-studied calcium-dependent MxaFI type and the more recently discovered lanthanide-containing XoxF type. MxaFI has traditionally been accepted as the major functional MDH in bacteria that contain both enzymes. However, in this study, we present evidence that, in a type I methanotroph, Methylomicrobium buryatense, XoxF is likely the primary functional MDH in the environment. The addition of lanthanides increases xoxF expression and greatly reduces mxa expression, even under conditions in which calcium concentrations are almost 100-fold higher than lanthanide concentrations. Mutations in genes encoding the MDH enzymes validate our finding that XoxF is the major functional MDH, as XoxF mutants grow more poorly than MxaFI mutants under unfavorable culturing conditions. In addition, mutant and transcriptional analyses demonstrate that the lanthanide-dependent MDH switch operating in methanotrophs is mediated in part by the orphan response regulator MxaB, whose gene transcription is itself lanthanide responsive. IMPORTANCE: Aerobic methanotrophs, bacteria that oxidize methane for carbon and energy, require a methanol dehydrogenase enzyme to convert methanol into formaldehyde. The calcium-dependent enzyme MxaFI has been thought to primarily carry out methanol oxidation in methanotrophs. Recently, it was discovered that XoxF, a lanthanide-containing enzyme present in most methanotrophs, can also oxidize methanol. In a methanotroph with both MxaFI and XoxF, we demonstrate that lanthanides transcriptionally control genes encoding the two methanol dehydrogenases, in part by controlling expression of the response regulator MxaB. Lanthanides are abundant in the Earth's crust, and we demonstrate that micromolar amounts of lanthanides are sufficient to suppress MxaFI expression. Thus, we present evidence that XoxF acts as the predominant methanol dehydrogenase in a methanotroph.

Genome Characteristics of Two Novel Type I Methanotrophs Enriched from North Sea Sediments Containing Exclusively a Lanthanide-Dependent XoxF5-Type Methanol Dehydrogenase.

Microbial methane oxidizers play a crucial role in the oxidation of methane in marine ecosystems, as such preventing the escape of excessive methane to the atmosphere. Despite the important role of methanotrophs in marine ecosystems, only a limited number of isolates are described, with only four genomes available. Here, we report on two genomes of gammaproteobacterial methanotroph cultures, affiliated with the deep-sea cluster 2, obtained from North Sea sediment. Initial enrichments using methane as sole source of carbon and energy and mimicking the in situ conditions followed by serial subcultivations and multiple extinction culturing events over a period of 3 years resulted in a highly enriched culture. The draft genomes of the methane oxidizer in both cultures showed the presence of genes typically found in type I methanotrophs, including genes encoding particulate methane monooxygenase (pmoCAB), genes for tetrahydromethanopterin (H4MPT)- and tetrahydrofolate (H4F)-dependent C1-transfer pathways, and genes of the ribulose monophosphate (RuMP) pathway. The most distinctive feature, when compared to other available gammaproteobacterial genomes, is the absence of a calcium-dependent methanol dehydrogenase. Both genomes reported here only have a xoxF gene encoding a lanthanide-dependent XoxF5-type methanol dehydrogenase. Thus, these genomes offer novel insight in the genomic landscape of uncultured diversity of marine methanotrophs.

Detoxification of mercury by methanobactin from Methylosinus trichosporium OB3b.

Many methanotrophs have been shown to synthesize methanobactin, a novel biogenic copper-chelating agent or chalkophore. Methanobactin binds copper via two heterocyclic rings with associated enethiol groups. The structure of methanobactin suggests that it can bind other metals, including mercury. Here we report that methanobactin from Methylosinus trichosporium OB3b does indeed bind mercury when added as HgCl2 and, in doing so, reduced toxicity associated with Hg(II) for both Alphaproteobacteria methanotrophs, including M. trichosporium OB3b, M. trichosporium OB3b ΔmbnA (a mutant defective in methanobactin production), and Methylocystis sp. strain SB2, and a Gammaproteobacteria methanotroph, Methylomicrobium album BG8. Mercury binding by methanobactin was evident in both the presence and absence of copper, despite the fact that methanobactin had a much higher affinity for copper due to the rapid and irreversible binding of mercury by methanobactin. The formation of a gray precipitate suggested that Hg(II), after being bound by methanobactin, was reduced to Hg(0) but was not volatilized. Rather, mercury remained associated with methanobactin and was also found associated with methanotrophic biomass. It thus appears that although the mercury-methanobactin complex was cell associated, mercury was not removed from methanobactin. The amount of biomass-associated mercury in the presence of methanobactin from M. trichosporium OB3b was greatest for M. trichosporium wild-type strain OB3b and the ΔmbnA mutant and least for M. album BG8, suggesting that methanotrophs may have selective methanobactin uptake systems that may be based on TonB-dependent transporters but that such uptake systems exhibit a degree of infidelity.

Conversion of biogas to bioproducts by algae and methane oxidizing bacteria.

Biogas produced by anaerobic digestion is typically converted into electricity and low value heat. In this study, biogas is microbially transformed into valuable bioproducts. As proof of principle, the production of feed additives, i.e. lipids and polyhydroxybutyrate, out of biogas was evaluated. In a first stage, the CO2 in a synthetic biogas was photosynthetically fixed by an algae Scenedesmus sp. culture at an average rate of 192 ± 9 mg CO2 L⁻¹ liquid d⁻¹, resulting in concomitant O2 production. After N-depletion, more than 30% of the 220 ± 7 mg lipids g⁻¹ total organic carbon were unsaturated. In a second stage, the theoretical resulting gas mixture of 60% CH4 and 40% O2 was treated by a methane oxidizing Methylocystis parvus culture, with oxidation rates up to 452 ± 7 mg⁻¹ CH4-C L⁻¹ liquid d⁻¹. By repeated N-limitation, concentrations of 295 ± 50 mg intracellular polyhydroxybutyrate g⁻¹ cell dry weight were achieved. Finally, a one-stage approach with controlled coculturing of both microbial groups resulted in harvestable bioflocs. This is the first time that a total microbial conversion of both greenhouse gases into biomass was achieved without external O2 provision. Based on these results, a biotechnological approach is discussed whereby all kinds of biogas can be transformed into valuable bioproducts.

Stimulation of cell growth by addition of tungsten in batch culture of a methanotrophic bacterium, Methylomicrobium alcaliphilum 20Z on methane and methanol.

It is carried out for researches to convert methane, the second most potent greenhouse gas, to high-value chemicals and fuels by using methanotrophs. In this study, we observed that cell growth of Methylomicrobium alcaliphilum 20Z in the batch cultures on methane or methanol was stimulated by the addition of tungsten (W) without formate accumulation. Not only biomass yield but also the total products yield (biomass and formate) on carbon basis increased up to 11.50-fold and 1.28-fold respectively in W-added medium. Furthermore, a significant decrease in CO2 yield from formate was observed in the W-added cells, which indicates that W might have affected the activity of certain enzymes involved in carbon assimilation as well as formate dehydrogenase (FDH). The results of this study suggest that M. alcaliphilum 20Z is a promising model system for studying the physiology of the aerobic methanotroph and for enabling its industrial use for methane conversion through high cell density cultivation.

The short- and long-term effects of nitrite on denitrifying anaerobic methane oxidation (DAMO) organisms.

The denitrifying anaerobic methane oxidation (DAMO) process can achieve methane oxidation and denitrification at the same time by using nitrate or nitrite as an electron acceptor. The short- and long-term effects of nitrite on DAMO organisms were studied from macro (such as denitrification) to micro (such as microbial structure and community) based on two types of DAMO microbial systems. The results showed that the inhibitory effects of nitrite on the two DAMO microbial systems increased with rising concentration and prolonged time. In the short-term inhibitory phase, nitrite with concentrations below 100 mg N L-1 did not inhibit the two distinct DAMO enrichments. When nitrite concentration was increased to 950 mg N L-1, the nitrogen removal performance was completely inhibited. However, in the long-term inhibition experiment, when nitrite concentration was increased to 650 mg N L-1, the nitrogen removal performance was completely inhibited. In addition, in acidic conditions, the real inhibitor of nitrite is FNA (free nitrous acid), while in alkaline conditions, the real inhibitor is the ionized form of nitrite. By using high-throughput sequencing technology, the species abundance and diversity of the two DAMO microbial systems showed an apparent decrease after long-term inhibition, and the community structure also changed significantly. For the enrichment culture dominated by DAMO bacteria, the substantial drop of Methylomonas may be the internal cause of the decreased nitrogen removal rate, and for the coexistence system that hosted both DAMO bacteria and archaea, the reduction of Nitrospirae may be an internal reason for the decline of the denitrification rate.

Selective stimulation of type I methanotrophs in a rice paddy soil by urea fertilization revealed by RNA-based stable isotope probing.

Methane-oxidizing bacteria (MOB) in soil are not only controlled by their main substrates, methane and oxygen, but also by nitrogen availability. We compared an unfertilized control with a urea-fertilized treatment and applied RNA-stable-isotope-probing to follow activity changes upon fertilization as closely as possible. Nitrogen fertilization of an Italian rice field soil increased the CH4 oxidation rates sevenfold. In the fertilized treatment, isopycnic separation of 13C-enriched RNA became possible after 7 days when 300 micromol 13CH4 g(dry soil)(-1) had been consumed. Terminal-restriction fragment length polymorphism (T-RFLP) fingerprints and clone libraries documented that the type I methanotrophic genera Methylomicrobium and Methylocaldum assimilated 13CH4 nearly exclusively. Although previous studies had shown that the same soil contains a much larger diversity of MOB, including both type I and type II, nitrogen fertilization apparently activated only a small subset of the overall diversity of MOB, type I MOB in particular.

Effects of 17ß-estradiol on emissions of greenhouse gases in simulative natural water body.

Environmental estrogens are widely spread across the world and are increasingly thought of as serious contaminators. The present study looks at the influence of different concentrations of 17ß-estradiol on greenhouse gas emissions (CO2 , CH4 , and N2 O) in simulated systems to explore the relationship between environmental estrogen-pollution and greenhouse gas emissions in natural water bodies. The present study finds that 17ß-estradiol pollution in simulated systems has significant promoting effects on the emissions of CH4 and CO2 , although no significant effects on N2 O emissions. The present study indicates that 17ß-estradiol has different effects on the different elements cycles; the mechanism of microbial ecology is under review.

Chloromethane stimulates growth of Methylomicrobium album BG8 on methanol.

Studies were performed to determine if the growth of Methylomicrobium album BG8 on methanol could be enhanced through the provision of chloromethane. M. album BG8 was found to be able to oxidize chloromethane via the particulate methane monooxygenase with an apparent K(s) of 11+/-3 microM and V(max) of 15+/-0.6 nmol (min mg protein)(-1). When up to 2.6 mM chloromethane was provided with 5 mM methanol, methanotrophic growth was significantly enhanced in comparison to the absence of chloromethane, indicating that methanotrophs can utilize chloromethane to support growth, although it could not serve as a sole growth substrate. [(14)C]chloromethane was found to be oxidized to [(14)C]CO(2) as well as incorporated into biomass. These results indicate that reactions previously thought to be cometabolic may actually provide some benefit to methanotrophs and that these cells can use multiple compounds to enhance growth.

Evidence for the synthesis of the multi-positional isomers of monounsaturated fatty acid in Methylococcus capsusatus by the anaerobic pathway.

The biosynthesis of the positional isomers of the monounsaturated fatty acids of Methylococcus capsulatus (Bath) has been investigated by studying the incorporation of [2-14C]malonyl CoA into long-chain fatty acids in vitro. The major unsaturated products were delta 9 16 : 1 and delta 11 18 : 1; however, delta 8, delta 10, and delta 11, 16 : 1, as well as, delta 10, delta 12 and delta 13 18 : 1 were also synthesized. The exclusion of O2 from the reaction vessel did not affect the synthesis of unsaturated fatty acids or the double bonds positions. Cerulenin inhibited the synthesis of unsaturated fatty acid more than saturated fatty acid. The use of both [1-14C] octanoate and [1-14C] decanote as substrate resulted in the synthesis of long-chain fatty acids, however, unsaturates were only synthesized from octanoate. These results imply that the unique positional isomers of M. capsulatus are not synthesized by an aerobic mechanism.

Role of vitamin B12 and enzymes related to methylmalonyl-CoA mutase in a methanol-utilizing bacterium, Protaminobacter ruber.

A methanol-utilizing bacterium, Protaminobacter ruber, required cobalt ion or vitamin B12 as its growth factor, which could be replaced by succinate among various additions to the cobalt-deficient medium. The presence of adenosylcobalamin (adenosyl-B12)-dependent methylmalonyl-coenzyme A (CoA) mutase was demonstrated in the cell-free extracts of P. ruber. The specific activity of this mutase was not only fairly high in comparison with that reported with other organisms but also detected at a similar level throughout the cultivation period. The cell-free extracts of P. ruber grown on non-C1 compounds as a sole carbon and energy source also had methylmalonyl-CoA mutase activity. Furthermore, the extracts of this microorganism catalyzed the reactions from propionyl-CoA to succinyl-CoA and from alpha-ketoglutarate to alpha-hydroxyglutarate.

Methanol suppression of trichloroethylene degradation by Methylosinus trichosporium (OB3b) and methane-oxidizing mixed cultures.

The effect of methanol on trichloroethylene (TCE) degradation by mixed and pure methylotrophic cultures was examined in batch culture experiments. Methanol was found to relieve growth inhibition of Methylosinus trichosporium (OB3b) at high (14 mg/L) TCE concentrations. Degradation of TCE was determined by both radiolabeling and gas chromatography techniques. When cultures were grown on methanol over 10 to 14 d with 0.3 mg/L TCE, OB3b degraded 16.89 +/- 0.82% (mean +/- SD) of the TCE, and a mixed culture (DT type II) degraded 4.55 +/- 0.11%. Mixed culture (JS type I) degraded 4.34 +/- 0.06% of the TCE. When grown on methane with 0.3 mg/L TCE, 32.93 +/- 2.01% of the TCE was degraded by OB3b, whereas the JS culture degraded 24.3 +/- 1.38% of the TCE, and the DT culture degraded 34.3 +/- 2.97% of the TCE. The addition of methanol to cultures grown on methane reduced TCE degradation to 16.21 +/- 1.17% for OB3b and to 5.08 +/- 0.56% for JS. Although methanol reduces the toxicity of TCE to the cultures, biodegradation of TCE cannot be sustained in methanol-grown cultures. Since high TCE concentrations appear to inhibit methane uptake and growth, we suggest the primary toxicity of TCE is directed towards the methane monooxygenase.

[Growth of Methylomonas Z201 cells and production of epoxypropane in monophasic and biphasic fermentation systems].

The growth of Methylomonas Z201 cells and production of epoxypropane in mono- and biphasic fermentation systems were studied. In monophasic fermentation systems, the inhibitions of propene and epoxypropane on the growth of Methylomonas Z201 cells were observed and the concentration of epoxypropane reached 1.3 mmol/L. In biphasic fermentation systems, hexadecane acted as the "reservoir" of growth substrate (methane) and reactants (propene, molecular oxygen), the decrease of propene and epoxypropane in aqueous phase reduced the inhibition effect of propene and epoxypropane on the growth of cells, the concentrations of epoxypropane in both water phase and hexadecane phase reached 1.7 mmol/L and 2.6 mmol/L. In both monophasic and biphasic fermentation systems, the operational stability of cells was enhanced compared to that of resting cells.

[Stability of genetic markers in methane-oxidizing bacteria]. / Stabil'nost' geneticheskikh markerov u metanokisliaiushchikh bakterii.

A number of Methylococcus thermophilus 111p clones have been obtained which have acquired resistance to tetracycline. The stability of maintenance of marker resistance in these clones and also in already designed Methylomonas rubra 15sh mutants has been investigated. Chromosomal markers resistance to antibiotics or formaldehyde were maintained in the marked strains Methylococcus thermophilus 111p and Methylomonas rubra 15sh after storage in nonselective conditions. The markers of resistance to antibiotics, which were coded by plasmids (pAS8-121 and pULB113), were not always preserved in Methylomonas rubra and Methylococcus thermophilus. The stability of maintenance of chromosomal markers in the investigated methane oxidizing bacteria testifies to the fact that they can be used in laboratory and industrial practice for testing the marked bacteria on selective media. The collection of the marked bacteria-mutants Methylomonas rubra 15sh and Methylococcus thermophilus 111p has been created. These strains stably support the marker resistance to various antibiotics or formaldehyde in unselective conditions.

Effects of ammonium on the activity and community of methanotrophs in landfill biocover soils.

The influence of NH4(+) on microbial CH4 oxidation is still poorly understood in landfill cover soils. In this study, effects of NH4(+) addition on the activity and community structure of methanotrophs were investigated in waste biocover soil (WBS) treated by a series of NH4(+)-N contents (0, 100, 300, 600 and 1200mgkg(-1)). The results showed that the addition of NH4(+)-N ranging from 100 to 300mgkg(-1) could stimulate CH4 oxidation in the WBS samples at the first stage of activity, while the addition of an NH4(+)-N content of 600mgkg(-1) had an inhibitory effect on CH4 oxidation in the first 4 days. The decrease of CH4 oxidation rate observed in the last stage of activity could be caused by nitrogen limitation and/or exopolymeric substance accumulation. Type I methanotrophs Methylocaldum and Methylobacter, and type II methanotrophs (Methylocystis and Methylosinus) were abundant in the WBS samples. Of these, Methylocaldum was the main methanotroph in the original WBS. With incubation, a higher abundance of Methylobacter was observed in the treatments with NH4(+)-N contents greater than 300mgkg(-1), which suggested that NH4(+)-N addition might lead to the dominance of Methylobacter in the WBS samples. Compared to type I methanotrophs, the abundance of type II methanotrophs Methylocystis and/or Methylosinus was lower in the original WBS sample. An increase in the abundance of Methylocystis and/or Methylosinus occurred in the last stage of activity, and was likely due to a nitrogen limitation condition. Redundancy analysis showed that NH4(+)-N and the C/N ratio had a significant influence on the methanotrophic community in the WBS sample.

Differential effects of nitrogenous fertilizers on methane-consuming microbes in rice field and forest soils.

The impact of environmental perturbation (e.g., nitrogenous fertilizers) on the dynamics of methane fluxes from soils and wetland systems is poorly understood. Results of fertilizer studies are often contradictory, even within similar ecosystems. In the present study the hypothesis of whether these contradictory results may be explained by the composition of the methane-consuming microbial community and hence whether methanotrophic diversity affects methane fluxes was investigated. To this end, rice field and forest soils were incubated in microcosms and supplemented with different nitrogenous fertilizers and methane concentrations. By labeling the methane with 13C, diversity and function could be coupled by analyses of phospholipid-derived fatty acids (PLFA) extracted from the soils at different time points during incubation. In both rice field and forest soils, the activity as well as the growth rate of methane-consuming bacteria was affected differentially. For type I methanotrophs, fertilizer application stimulated the consumption of methane and the subsequent growth, while type II methanotrophs were generally inhibited. Terminal restriction fragment length polymorphism analyses of the pmoA gene supported the PLFA results. Multivariate analyses of stable-isotope-probing PLFA profiles indicated that in forest and rice field soils, Methylocystis (type II) species were affected by fertilization. The type I methanotrophs active in forest soils (Methylomicrobium/Methylosarcina related) differed from the active species in rice field soils (Methylobacter/Methylomonas related). Our results provide a case example showing that microbial community structure indeed matters, especially when assessing and predicting the impact of environmental change on biodiversity loss and ecosystem functioning.

[Immobilization of methane-oxidizing bacterial cells]. / Immobilizatsiia kletok metanokisliaiushchikh bakterii.

The purpose of this work was to study how the conditions for immobilizing the cells of the methane oxidizing bacterium Methylomonas rubra using chemical and physical techniques influence their functional catalytical properties. These properties were found to depend on the chemical nature of a matrix and the mode of binding the cells to the carrier. The best carriers were shown to be silochrome with introduced carboxy groups and agar gel.

Effects of toxicity, aeration, and reductant supply on trichloroethylene transformation by a mixed methanotrophic culture.

The trichloroethylene (TCE) transformation rate and capacity of a mixed methanotrophic culture at room temperature were measured to determine the effects of time without methane (resting), use of an alternative energy source (formate), aeration, and toxicity of TCE and its transformation products. The initial specific TCE transformation rate of resting cells was 0.6 mg of TCE per mg of cells per day, and they had a finite TCE transformation capacity of 0.036 mg of TCE per mg of cells. Formate addition resulted in increased initial specific TCE transformation rates (2.1 mg/mg of cells per day) and elevated transformation capacity (0.073 mg of TCE per mg of cells). Significant declines in methane conversion rates following exposure to TCE were observed for both resting and formate-fed cells, suggesting toxic effects caused by TCE or its transformation products. TCE transformation and methane consumption rates of resting cells decreased with time much more rapidly when cells were shaken and aerated than when they remained dormant, suggesting that the transformation ability of methanotrophs is best preserved by storage under anoxic conditions.