Methanothrix Soehngenii Research Articles

A fluoride-insensitive inorganic pyrophosphatase isolated from Methanothrix soehngenii.

An inorganic pyrophosphatase [E.C. 3.6.1.1] was isolated from Methanothrix soehngenii. In three steps the enzyme was purified 400-fold to apparent homogeneity. The molecular mass estimated by gelfiltration was 139 +/- 7 kDa. Sodium dodecyl sulfate/polyacrylamide gel electrophoresis indicated that the enzyme is composed of subunits with molecular masses of 35 and 33 kDa in an alpha 2 beta 2 oligomeric structure. The enzyme catalyzed the hydrolysis of inorganic pyrophosphate, tri- and tetrapolyphosphate, but no activity was observed with a variety of other phosphate esters. The cation Mg2+ was required for activity. The pH optimum was 8 at 1 mM PPi and 5 mM Mg2+. The enzyme was heat-stable, insensitive to molecular oxygen and not inhibited by fluoride. Analysis of the kinetic properties revealed an apparent Km for PPi of 0.1 mM in the presence of 5 mM Mg2+. The Vmax was 590 mumol of pyrophosphate hydrolyzed per min per mg protein, which corresponds to a Kcat of 1400 per second. The enzyme was found in the soluble enzyme fraction after ultracentrifugation, when cells were disrupted by French Press. Upto 5% of the pyrophosphatase was associated with the membrane fraction, when gentle lysis procedure were applied.

Comparison of acetate utilization among strains of an aceticlastic methanogen, Methanothrix soehngenii.

The kinetics of acetate utilization by concentrated suspensions of cells was examined in five strains of Methanothrix soehngenii. The rate of acetate utilization by all strains was dependent on the initial acetate concentration and followed simple Michaelis-Menten kinetics. The ability to utilize acetate differed among the various strains of M. soehngenii and was highest in the strain designated MTAS.

EPR characterization of a high‐spin system in carbon monoxide dehydrogenase from Methanothrix soehngenii

Carbon monoxide dehydrogenase and methyl-coenzyme M reductase were purified from 61Ni-enriched and natural-abundance nickel-grown cells of the methanogenic archae Methanothrix soehngenii. The nickel-EPR signal from cofactor F-430 in methyl-CoM reductase was of substoichiometric intensity and exhibited near-axial symmetry with g = 2.153, 2.221 and resolved porphinoid nitrogen superhyperfine splittings of approximately 1 mT. In the spectrum from 61Ni-enriched enzyme a well-resolved parallel I = 3/2 nickel hyperfine splitting was observed, A parallel = 4.4 mT. From a computer simulation of this spectrum the final enrichment in 61Ni was estimated to be 69%, while the original enrichment of the nickel metal was 87%. Carbon monoxide dehydrogenase isolated from the same batch exhibited four different EPR spectra. However, in none of these signals could any splitting or broadening from 61Ni be detected. Also, the characteristic g = 2.08 EPR signal found in some other carbon monoxide dehydrogenases and ascribed to a Ni-Fe-C complex, was never observed by us under any conditions of detection (4 to 100 K) and incubation in the presence of ferricyanide, dithionite, CO, coenzyme A, or acetyl-coenzyme A. Novel, high-spin EPR was found in the oxidized enzyme with effective g-values at g = 14.5, 9.6, 5.5, 4.6, 4.2, 3.8. The lines at g = 14.5 and 5.5 were tentatively ascribed to an S = 9/2 system (approximately 0.3 spins/alpha beta) with rhombicity E/D = 0.047 and D less than 0. The other signals were assigned to an S = 5/2 system (0.1 spins/alpha beta) with E/D = 0.27. Both sets of signals disappear upon reduction with Em,7.5 = - 280 mV. With a very similar reduction potential, Em,7.5 = - 261 mV, an S = 1/2 signal (0.1 spins/alpha beta) appears with the unusual g-tensor 2.005, 1.894, 1.733. Upon further lowering of the potential the putative double cubane signal also appears. At a potential E approximately - 320 mV the double cubane is only reduced by a few percent and this allows the detection of individual cubane EPR not subjected to dipolar interaction; a single spectral component is observed with g-tensor 2.048, 1.943, 1.894.

Population dynamics of biofilm development during start-up of a butyrate-degrading fluidized-bed reactor

Population dynamics during start-up of a fluidized-bed reactor with butyrate or butyrate plus acetate as sole substrates as well as biofilm development on the sand substratum were studied microbiologically, immunologically and by scanning electron microscopy. An adapted syntrophic consortium consisting of Syntrophospora sp., Methanothrix soehngenii, Methanosarcina mazei and Methanobrevibacter arboriphilus or Methanogenium sp. achieved high-rate butyrate degradation to methane and carbon dioxide. Desulfovibrio sp., Methanocorpusculum sp., and Methanobacterium sp. were also present in lower numbers. Immunological analysis demonstrated methanogens antigenically related to Methanobrevibacter ruminantium M1, Methanosarcina mazei S6, M. thermophila TM1, Methanobrevibacter arboriphilus AZ and Methanothrix soehngenii Opfikon in the biofilm. Immunological analysis also showed that the organisms isolated from the butyrate-degrading culture used as a source of inoculum were related to M. soehngenii Opfikon, Methanobacterium formicicum MF and Methanospirillum hungatei JF1.

Adenine nucleotide content and energy charge of Methanothrix soehngenii during acetate degradation

Adenine nucleotide content and energy charge of Methanothrix soehngenii during acetate degradation

Adenine nucleotide content and energy charge ofMethanothrix soehngeniiduring acetate degradation

The interconversion of adenine nucleotides during acetate fermentation was investigated with concentrated cell suspensions of Methanothrix soehngenii. Starved cells contained high levels of AMP (2.2 nmol/mg protein), but had hardly any ADP or ATP. The energy charge of these cells was 0.1. Immediately after the addition of the substrate acetate, the level of ATP increased, reaching a maximum of 1.4 nmol/mg protein, corresponding to an energy charge of 0.7 when half of the acetate was consumed. Once the acetate was depleted, the ATP concentration decreased to its original level of 0.1 nmol/mg protein. As M. soehngenii contained relatively high amounts of AMP, the luciferase system for the determination of ATP gave not always satisfactory results. Therefore a reliable method based on the separation of adenine nucleotides by anion exchange HPLC was used.

Cloning, sequence analysis, and functional expression of the acetyl coenzyme A synthetase gene from Methanothrix soehngenii in Escherichia coli

In the acetoclastic methanogen Methanothrix soehngenii, acetate is activated to acetyl coenzyme A by acetyl coenzyme A synthetase (Acs). The acs gene, coding for the single Acs subunit, was isolated from a genomic library of M. soehngenii DNA in Escherichia coli by using antiserum raised against the purified Acs. After introduction in E. coli, the acs gene was expressed, resulting in the production of an immunoreactive protein of 68 kDa, which is approximately 5 kDa smaller than the known size of purified Acs. In spite of this difference in size, the Acs enzymes are produced in similar quantities in E. coli and M. soehngenii and show comparable specific activities. Upstream from the acs gene, consensus archaeal expression signals were identified. Immediately downstream from the acs gene there was a putative transcriptional stop signal. The amino acid sequence deduced from the nucleotide sequence of the acs gene showed homology with those of functionally related proteins, i.e., proteins involved in the binding of coenzyme A, ATP, or both.

Strain GP6 Is Proposed as the Neotype Strain of Methanothrix soehngeniiVP pro synon. Methanothrix conciliiVP and Methanosaeta conciliiVP: Request for an Opinion

No axenic cultures of Methanothrix soehngenii OpfikonT (T = type strain), exist, nor is any extant contaminated culture known to be derived from strain OpfikonT. I propose strain GP6 as the neotype strain of this taxon. Strain GP6 is the type strain of Methanosaeta concilii and Methanothrix concilii, but both of these names are widely considered to be subjective synonyms of Methanothrix soehngenii.

Bacteriological composition and structure of granular sludge adapted to different substrates

The bacteriological composition and ultrastructure of mesophilic granular methanogenic sludge from a large-scale Upflow Anaerobic Sludge Blanket reactor treating wastewater from a sugar plant and of sludge granules adapted to ethanol and propionate were studied by counting different bacterial groups and by immunocytochemical methods. Propionate-grown granular sludge consisted of two types of clusters, those of a rod-shaped bacterium immunologically related to Methanothrix soehngenii and those consisting of two different types of bacteria with a specific spatial orientation. One of these bacteria reacted with antiserum against Methanobrevibacter arboriphilus AZ, whereas the other is most likely a propionate-oxidizing bacterium immunologically unrelated to Syntrophobacter wolinii. Sludge granules obtained from the large-scale Upflow Anaerobic Sludge Blanket reactor and granules cultivated on ethanol did not show the typical spatial orientation of bacteria. Examination of the bacterial composition of the three types of granules by light and electron microscopy, the most-probable-number method, and by isolations showed that M. arboriphilus and M. soehngenii were the most abundant hydrogenotrophic and acetoclastic methanogens in propionate-grown sludge. Methanospirillum hungatei and Methanosarcina barkeri predominated in ethanol-grown granules, whereas many morphotypes of methanogens were abundant in granules from the full-scale reactor.

Isolation and Characterization of a Novel Thermophilic Methanosaeta Strain

A novel thermophilic acetotrophic Methanosaeta strain was isolated from a thermophilic anaerobic digest or by using acetate enrichment and serial dilution in the presence of vancomycin and neomycin. This isolate, designated Methanosaeta sp. strain PT, resembled Methanosaeta sp. strain CALS-1 morphologically; however, it occasionally formed filaments longer than 100 μm and exhibited autofluorescence. The content of coenzyme F420 was much higher than that of Methanosaeta reference strains, and coenzyme F420 with four glutamyl residues on the side chain was the predominant component. Furthermore, a comparative analysis of the antigenic fingerprint of strain PT with the fingerprints of reference organisms showed that this isolate was not related antigenically to the reference methanogens, including Methanosaeta sp. (“Methanothrix” sp.) strain CALS-1 and Methanosaeta concilii (“Methanothrix soehngenii”) Opfikon. Strain PT formed visible colonies in a deep agar medium when high cell concentrations were present. However, transfer of a colony into liquid medium resulted in no growth. Strain PT could utilize only acetate as a sole carbon and energy source. The optimum temperature and optimum pH for methanogenesis were near 55°C and 6.7, respectively. The specific methane formation rate μCH 4 under optimum conditions was 0.47 day−1, and the doubling time was 1.49 days. The DNA base composition was 52.7 mol% guanine plus cytosine.

Activities of formylmethanofuran dehydrogenase, methylenetetrahydromethanopterin dehydrogenase, methylenetetrahydromethanopterin reductase, and heterodisulfide reductase in methanogenic bacteria

The activities of formylmethanofuran dehydrogenase, methylenetetrahydromethanopterin dehydrogenase, methylenetetrahydromethanopterin reductase, and heterodisulfide reductase were tested in cell extracts of 10 different methanogenic bacteria grown on H2/CO2 or on other methanogenic substrates. The four activities were found in all the organisms investigated: Methanobacterium thermoautotrophicum,M. wolfei, Methanobrevibacter arboriphilus, Methanosphaera stadtmanae, Methanosarcina barkeri (strains Fusaro and MS), Methanothrix soehngenii, Methanospirillum hungatei, Methanogenium organophilum, and Methanococcus voltae. Cell extracts of H2/CO2 grown M. barkeri and of methanol grown M. barkeri showed the same specific activities suggesting that the four enzymes are of equal importance in CO2 reduction to methane and in methanol disproportionation to CO2 and CH4. In contrast, cell extracts of acetate grown M. barkeri exhibited much lower activities of formylmethanofuran dehydrogenase and methylenetetrahydromethanopterin dehydrogenase suggesting that these two enzymes are not involved in methanogenesis from acetate. In M. stadtmanae, which grows on H2 and methanol, only heterodisulfide reductase was detected in activities sufficient to account for the in vivo methane formation rate. This finding is consistent with the view that the three other oxidoreductases are not required for methanol reduction to methane with H2.

Cloning, expression, and sequence analysis of the genes for carbon monoxide dehydrogenase of Methanothrix soehngenii.

The cdhA and cdhB genes that code for the large and the small subunits of carbon monoxide dehydrogenase (CDH), respectively, were isolated from a genomic library of Methanothrix soehngenii DNA in Escherichia coli, using polyclonal antibodies raised against purified CDH. After introduction in E. coli or Desulfovibrio vulgaris, the cdh genes appeared to be expressed irrespective of their orientation, yielding immunoreactive proteins of 79 and 19 kDa, corresponding in size to the known subunits of purified CDH. However, no CDH activity could be detected in these heterologous hosts. The cdh genes are preceded by consensus ribosome-binding sites and are arranged in an operon-like structure, with cdhA preceding cdhB. Upstream from this operon, sequences similar to archaeal promoters were identified. The amino acid sequence, deduced from the primary sequence of cdhA, showed homology with ferredoxins and with acyl-CoA oxidase. This is compatible with the proposed functions of CDH.

Paramagnetic centers and acetyl‐coenzyme A/CO exchange activity of carbon monoxide dehydrogenase from Methanothrix soehngenii

Carbon monoxide (CO) dehydrogenase was purified, both aerobically and anaerobically, to apparent homogeneity from Methanothrix soehngenii. The enzyme contained 18 +/- 2 (n = 6) mol Fe/mol and 2.0 +/- 0.1 (n = 6) mol Ni/mol. Electron paramagnetic resonance (EPR) spectra of the aerobically purified CO dehydrogenase showed one sharp EPR signal at g = 2.014 with several characteristics of a [3Fe-4S]1+ cluster. The integrated intensity of this signal was low, 0.03 S = 1/2 spin/alpha beta dimer. The 3Fe spectrum was not affected by incubation with CO or acetyl-coenzyme A, but could be reduced by dithionite. The spectrum of the reduced, aerobically purified enzyme showed complex EPR spectra, which had several properties typical of two [4Fe-4S]1+ clusters, whose S = 1/2 spins weakly interacted by dipolar coupling. The integrated intensity was 0.1-0.2 spin/alpha beta dimer. The anaerobically isolated enzyme showed EPR spectra different from the reduced aerobically purified enzyme. Two major signals were apparent. One with g values of 2.05, 1.93 and 1.865, and an Em7.5 of -410 mV, which quantified to 0.9 S = 1/2 spin/alpha beta dimer. The other signal with g values of 1.997, 1.886 and 1.725, and an Em7.5 of -230 mV gave 0.1 spin/alpha beta dimer. When the enzyme was incubated with its physiological substrate acetyl-coenzyme A, these two major signals disappeared. Incubation of the enzyme under CO atmosphere resulted in a partial disappearance of the spectral component with g = 1.997, 1.886, 1.725. Acetyl-coenzyme A/CO exchange activity, 35 nmol.min-1.mg-1 protein, which corresponded to 7 mol CO exchanged min-1 mol-1 enzyme, could be detected in anaerobic enzyme preparations, but was absent in aerobic preparations. Carbon dioxide also exchanged with C-1 of acetyl-coenzyme A, but at a much lower rate than CO and to a much lower extent.

The internal architecture of anaerobic sludge granules

AbstractThe structural characteristics of well‐formed anaerobic granular sludges were examined using scanning electron microscopy and light microscopy of thin sections. Transverse sections were found to consist of randomly orientated filaments of Methanothrix soehngenii. These were tightly packed with little space between the individual filament sheaths, revealing a ‘honeycomb’ appearance. Sections cut from wax‐embedded granules were stained using a number of histochemical procedures. Detailed examination of the overall structure of the granules was possible, revealing the presence of filamentous bundles of Methanothrix surrounded by a matrix found to be carbohydrate in nature. Interpretation of serial sections through the depth of the granule allowed for the construction of a diagrammatic illustration of the internal structure. A relationship between the measured diameter of these microcolonies of Methanothrix and the distance from the centre of the granule was established. Together these results enabled a proposal to be made as to the possible mechanisms involved in the growth of granules. This supports previous suggestions relating to the involvement of Methanothrix and bacterial polymers.

An immunological study of corrinoid proteins from bacteria revealed homologous antigenic determinants of a soluble corrinoid-dependent methyltransferase and corrinoid-containing membrane proteins from Methanobacterium species

The hypothesis of common epitopes in corrinoid-dependent enzymes was tested by a monospecific polyclonal antiserum against the 33 kDa corrinoid-containing membrane protein from Methanobacterium thermoautotrophicum Marburg. Cross-reaction was detected with the 33 kDa and the 31 kDa subunits of the corrinoid-containing enriched 5-methyl-H4MPT: 5-hydroxybenzimidazolyl cobamide methyltransferase from the cytoplasmic fraction and a 33 kDa protein from the membrane fraction of Methanobacterium thermoauto-trophicum ΔH. This indicates that both proteins have similar antigenic determinants and that they may have similar function as methyltransfer proteins. Also a soluble 20 kDa protein of yet unknown function from Clostridium barkeri cross-reacted with the antiserum. No cross-reactions were observed with the purified corrinoid-containing 2-methyleneglutarate mutase from C. barkeri, the corrinoid/iron-sulfur protein from C. thermoaceticum, the carbon monoxide dehydrogenases from C. thermoaceticum and Methanothrix soehngenii, and the corrinoid-binding protein intrinsic factor from porcine gastric mucosa. Also cell extracts from the corrinoid-rich bacteria Sporomusa ovata, Methanolobus tindarius, Chloroflexus aurantiacus, Propionibacterium shermanii, the membrane fraction and the cytoplasmic fraction of Methanococcus voltae or extracts from human liver, contained no antibody combining sites others than with the preimmunological serum. These findings indicate, that many corrinoid-containing proteins from bacteria have no common antigenic determinants.

Evidence for the glycoprotein nature of the cell sheath of Methanosaeta-like cells in the culture of Methanothrix soehngenii strain FE

The resilient of Methanothrix soehngenii strain FE was isolated. It contained carbohydrates (7%), mainly rhamnose, ribose, and fucose, which could be specifically liberated by alkaline hydrolysis or hydrazinolysis. Four oligosaccharide-containing fractions were separated; the two major fractions corresponded to large glycans composed of 15–30 residues. The whole sheath preparation was soluble in anhydrous hydrazine. A mild hydrazinolysis treatment led to a water-soluble glycoprotein fraction, which represented 60% of the starting material and contained 100% of the carbohydrates. These high molecular mass (> 500 kDa) glycoproteins were sensitive to pronase. Fast atom bombardment mass spectrometry analysis of the major glycopeptide fraction obtained after hydrogen fluoride treatment was in accordance with the presence of asparaginyl-rhamnose linkages on a Asn-X-Ser glycosylation site. This type of glycosidic linkage has been described previously in the surface layer of Bacillus stearothermophilus. Key words: Methanothrix soehngenii, Methanosaeta concilii, archaebacteria, bacterial glycoprotein, proteic sheath, asparaginyl-rhamnose.

Methanogens revealed immunologically in granules from five Upflow Anaerobic Sludge Blanket (UASB) bioreactors grown on different substrates

Methanogens were identified and quantified using antibody probes and the antigenic fingerprinting method in five different kinds of granular sludge taken from five Uplow Anaerobic Sludge Blanket (UASB) bioreactors maintained on different substrates. The methanogenic flora present in each bioreactor was elucidated and expressed in cells per garm dry weight. Autofluorescence, phase-contrast and bright field-microscopy of unstained and Gram-stained preparations were used in parallel with immunotechnology to characterize each methanogenic subpopulation. Ten different methanogens were prevalent in the five bioreactor systems. Methanogens antigenically related to Methanobacterium formicicum MF, Methanobrevibacter arboriphilus AZ and Methanothrix soehngenii Opfikon were found in all five granules, while other methanogens were present in only some. A trend was observed towards a wider diversity of methanogenic subpopulations parallelling an increase in the complexity of the bioreactor's substrate.

Methanogens revealed immunologically in granules from five Upflow Anaerobic Sludge Blanket (UASB) bioreactors grown on different substrates

Methanogens were identified and quantified using antibody probes and the antigenic fingerprinting method in five different kinds of granular sludge taken from five Uplow Anaerobic Sludge Blanket (UASB) bioreactors maintained on different substrates. The methanogenic flora present in each bioreactor was elucidated and expressed in cells per garm dry weight. Autofluorescence, phase-contrast and bright field-microscopy of unstained and Gram-stained preparations were used in parallel with immunotechnology to characterize each methanogenic subpopulation. Ten different methanogens were prevalent in the five bioreactor systems. Methanogens antigenically related to Methanobacterium formicicum MF, Methanobrevibacter arboriphilus AZ and Methanothrix soehngenii Opfikon were found in all five granules, while other methanogens were present in only some. A trend was observed towards a wider diversity of methanogenic subpopulations parallelling an increase in the complexity of the bioreactor's substrate.

Purification and some properties of the methyl-CoM reductase ofMethanothrix soehngenii

Abstract The methyl-CoM reductase from Methanothrix soehngenii was purified 18-fold to apparent homogeneity with 50% recovery in three steps. The native molecular mass of the enzyme estimated by gel-fitration was 280 kDa. SDS-polyacrylamide gel electrophoresis revealed three protein bands corresponding to M r 63 900, 41 700 and 30 400 Da. The methyl-coenzyme M reductase constitutes up to 10% of the soluble cell protein. The enzyme has K m apparent values of 23 μM and 2 mM for N -7-mercaptoheptanoylthreonine phosphate (HS- HTP = component B ) and methyl-coenzyme M (CH 3 CoM) respectively. At the optimum pH of 7.0 60 nmol of methane were formed per min per mg protein.

Purification and some properties of the methyl-CoM reductase of Methanothrix soehngenii

The methyl-CoM reductase from Methanothrix soehngenii was purified 18-fold to apparent homogeneity with 50% recovery in three steps. The native molecular mass of the enzyme estimated by gel-fitration was 280 kDa. SDS-polyacrylamide gel electrophoresis revealed three protein bands corresponding to M r 63 900, 41 700 and 30 400 Da. The methyl-coenzyme M reductase constitutes up to 10% of the soluble cell protein. The enzyme has K m apparent values of 23 μM and 2 mM for N-7-mercaptoheptanoylthreonine phosphate (HS- HTP = component B) and methyl-coenzyme M (CH 3CoM) respectively. At the optimum pH of 7.0 60 nmol of methane were formed per min per mg protein.