Isolation and characterization of a copper-resistant methanogen from a copper-mining soil sample

A copper-resistant methanogen for which the CuSO4 MICs were approximately 2- to 36-fold higher than those for other methanogens tested was isolated from a copper-mining area in the upper peninsula of Michigan. The rod-shaped methanogen used H2-CO2 or formate, but not acetate or methanol, as a growth substrate. Standing incubation with H2-CO2 medium resulted in a mat-like surface growth, dependent on the presence of hydrogen. The presence of 1 mM cupric salt resulted in longer filamentous and intertwined cells. Antigenic fingerprinting, 16S rRNA gene analysis, morphology, and substrate use suggest that the new isolate is a novel strain of Methanobacterium bryantii that is able to use formate.

Conservation and variability in Archaea: protein antigens with tandem repeats encoded by a cluster of genes with common motifs in Methanosarcina mazei S-6

Three open reading frames, orf492, orf375 and orf783, were identified in a 5.9-kb DNA fragment from the genome of Methanosarcina mazei S-6 that code for proteins recognized by antibodies against cell-surface antigens. The deduced amino-acid (aa) sequences of orfs492 and 375, i.e., ORF492 and ORF375, contain seven and four copies of an approx. 42-aa repeat, respectively. The aa sequence of ORF783 contains nine copies of an approx. 85-aa repeat, one of which is also present once in each of the first two ORFs. The organization of the repeats is similar to that of some Gram+ cell-wall-associated proteins. Comparative analyses of aa sequences, compositions and hydropathy profiles of the archaeal ORFs showed similarity with surface (S-) layer and outer-membrane proteins of Bacteria and Archaea.

An archaeal gene upstream of grpE different from eubacterial counterparts

In some eubacteria with a dnaK locus in which grpE is close upstream of dnaK, grpE is preceded by an open reading frame (orf) believed to be a heat-shock gene. We also found an orf, orf16, upstream of grpE in the archaeon Methanosarcina mazei S-6, but this gene differs from the eubacterial counterpart: it is shorter, does not respond to a temperature upshift as heat-shock genes do, and the deduced protein Orf16, does not resemble the proteins coded by the eubacterial equivalents. orf16 is expressed monocistronically, with a transcription initiation site 24 bases upstream of the translation start codon, 22 bases downstream of a putative promoter identical to the consensus promoter for genes in methanogens. This initiation site is used by heat-shocked and non-heat-shocked cells in the two morphologic stages of M. mazei S-6 tested, i.e., packets and single cells. Three transcription termination sites were identified, one of which is detectable only in non-heat-shocked cells. Data from comparative analyses of the Orf16 deduced amino acid sequence and those of other known proteins, as well as the apparent biochemical characteristics of Orf16, suggest that the latter is a membrane molecule.

Transcription of the archaeal trkA homolog in Methanosarcina mazei S-6

Transcription of the archaeal trkA gene homolog in Methanosarcina mazei S-6 was studied at the optimal growth temperature of 37 degrees C and after heat shock at 45 degrees C. Northern (RNA) blotting results (transcript size) and data from primer extension experiments to map the transcription initiation site indicate that trkA is cotranscribed with another gene. The latter, orf11, encodes a protein of 94 amino acids (10,611 Da) and is located upstream of trkA, with which it overlaps: the translation stop codon of orf11, TGA, shares the bases T and G with the translation start codon of trkA, ATG. These genes' transcription was decreased by heat shock to the point of making the transcript undetectable by Northern or dot blotting procedures. orf11 and trkA differ in codon usage patterns, and the proteins coded by them, i.e., Orf11 and TrkA, are dissimilar in amino acid sequence and composition.

The archaeal dnaK-dnaJ gene cluster: organization and expression in the methanogen Methanosarcina mazei

The organization and expression of the first archeael dnaK-dnaJ gene cluster cloned and sequenced have been elucidated. The work focused on the methanogen Methanosarcina mazei strain S-6, but a survey of two other strains (JC3 and LYC) and species (Methanosarcina sp. JCV and Methanosarcina acetivorans) showed that the findings are pertinent to other mesophilic methanosarcinas as well. The organization and some expression features of the archaeal genes resemble eubacterial equivalents for which comparable sequence information is available. However, the archaeal genes also display characteristics that are distinct from those of eubacterial and eucaryotic homologs. dnaK and dnaJ are transcribed into monocistronic messages. The initiation site is the same for transcription under optimal cell-growth conditions, and under stress due to a temperature upshift. The two genes are expressed constitutively at lower levels than those observed after heat shock. The constitutive and post-heat-shock expression levels are higher for dnaK than for dnaJ. Both genes withstand heat shocks of at least one and a half hours without a decline in transcript levels. While the transcription termination signals are to some extent reminiscent of those of eubacteria, the initiation signals are not. These have archaeal characteristics, which resemble those of eukaryotes. The intergenic dnaK-dnaJ region contains inverted repeats. These have the potential to build firm stem-loops in the transcript and in single-stranded DNA.

Heat-shock response in Archaea

The Archaea are one of the three phylogenetic domains into which all organisms have been classified, and include extreme halophiles, extreme thermophiles and methanogens. Some of these organisms inhabit inhospitable environments on Earth, and thus have evolved stress responses to cope with the extremes of heat, pH and salinity that they encounter. Although the archaeal stress or heat-shock response bears some similarity to the heat-shock responses of other organisms, it possesses some unique features. A better understanding of this response would facilitate its exploitation in the biotechnological industries; for example, in engineering cells that exhibit an improved ability to withstand, or recover from, stress.

An archaeal S-layer gene homolog with repetitive subunits

An S-layer protein gene homolog of the slgA gene of two Methanothermus species was found in the genome of another methanogenic archaeon of a different family, Methanosarcina mazei S-6. The new gene (slgB) encodes a molecule (SlpB) with the characteristics of S-layer proteins. The N-terminal half of SlpB is 44% identical to that encoded by SlgA, but the other half shows distinctive features: four 56 amino acid long tandem repeats, and Trp-Xaa-Trp clusters located six amino acids from the N-terminus of each repeat.

Identification of a grpE heat-shock gene homolog in the archaeon Methanosarcina mazei

A grpE heat-shock gene was found by sequencing in the genome of the methanogenic archaeon Methanosarcina mazei S-6. It is the first example of grpE from the phylogenetic domain Archaea. Since the other seven sequenced homologs are from the domain Bacteria, it may be concluded that grpE appeared early in evolution, before the two domains separated. The archaeal grpE is located in the dnaK locus, 431 base-pairs upstream of dnaK, which is followed downstream by the dnaJ gene. The organization of these three genes is known for Bacillus subtilis, Clostridium acetobutylicum, Borrelia burgdorferi and Mycobacterium tuberculosis. The archaeal locus organization, grpE-dnaK-dnaJ, is similar to that of the former three bacteria, but different from that of M. tuberculosis. This, and sequence homologies, suggest that the M. tuberculosis GrpE belongs, together with the Streptomyces coelicolor homolog, to a subgroup of the GrpE proteins. The M. mazei grpE gene encodes a protein of 209 amino acid residues. The deduced amino acid sequence shows 28.2 to 34.6% identities, and 50.3 to 58.9 similarities (identities plus conservative substitutions) with the other six complete GrpE sequences available. These percentages fall within the range observed for the other GrpEs. Two regions in the second and fourth quarters of the GrpE molecule show higher homology, particularly in three stretches of nine, six and nine amino acid residues, respectively. The archaeal gene uses all codons but three, whereas the bacterial homologs lack higher numbers of codons. The M. mazei grpE responded to heat-shock by increasing transcription, in a manner similar to that of the nearby heat-shock gene dnaK.

An archaeal trkA homolog near dnaK and dnaJ

The first trkA gene homolog in the phylogenetic domain Archaea is reported. The gene is located near the dnaK-dnaJ gene cluster in the genome of Methanosarcina mazei S-6, and encodes a protein homologous to the only other TrkA known, i.e., that of the bacterium Escherichia coli, involved in K+ transport. This finding supports an essential, evolutionarily early, and conserved role for this gene in cell survival and adaptation.

Effect of medium composition and sludge removal on the production, composition, and architecture of thermophilic (55 degrees C) acetate-utilizing granules from an upflow anaerobic sludge blanket reactor

A thermophilic upflow anaerobic sludge blanket (UASB) reactor degrading acetate was started by applying published methods (W. M. Wiegant and A. W. A. de Man, Biotechnol. Bioeng. 28:718-77, 1986) for production of granules dominated by Methanothrix spp. The reactor was inoculated with thermophilic digested sludge. No granules were observed during the first 7 months of start-up of the UASB reactor. However, after the concentrations of potassium, phosphate, ammonium, and magnesium in the medium were gradually increased, granules developed, indicating that there was a critical concentration of one or more of the ions required for production of granules from the starting material. After several years of stable operation, the effect of removing 60% of the granular sludge was investigated. Immunologic qualitative and quantitative studies showed that removal of the granular sludge resulted in an increase in the number of the predominant methanogens, antigenically related to Methanosarcina thermophila TM-1 and Methanosarcina mazeii S-6, and Methanobacterium thermoautotrophicum delta H and GC1. These changes were accompanied by modifications of the microanatomy of the granules, as demonstrated histochemically and immunohistochemically. The results indicated that different catabolic pathways dominated in different regions of the granules, i.e., acetate oxidation in the middle of the granules, where there is a low acetate concentration, and an aceticlastic reaction in the outer surfaces, with a high acetate concentration. The results also showed that removal of granules from a UASB reactor which has been under steady-state operation for a long period can improve the reactor's performance via formation of denser and larger granules with improved microbial activities.

Immunochemistry and localization of the enzyme disaggregatase in Methanosarcina mazei

The enzyme disaggregatase (Dag) from Methanosarcina mazei was studied immunochemically. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of purified Dag under reducing and nonreducing conditions revealed a single band with a 94-kDa molecular mass. Dag was found to be immunogenic in rabbits; a polyclonal antibody probe was prepared and used to detect the enzyme by slide immunoenzymatic assay, immunofluorescence, and immunoblotting in various species of Methanosarcina known to convert from packets to single cells, including M. mazei. The enzyme could not be detected in other members of the family Methanosarcinaceae that do not convert. By immunogold electron microscopy, Dag was mapped to the cell wall of packets and to the cell membrane of single cells of two M. mazei strains.

Introduction of a de novo bioremediation ability, aryl reductive dechlorination, into anaerobic granular sludge by inoculation of sludge with Desulfomonile tiedjei

Methanogenic upflow anaerobic granular-sludge blanket (UASB) reactors treat wastewaters at a high rate while simultaneously producing a useful product, methane; however, recalcitrant environmental pollutants may not be degraded. To impart 3-chlorobenzoate (3-CB)-dechlorinating ability to UASB reactors, we inoculated granular sludge in UASB reactors with either a pure culture of Desulfomonile tiedjei (a 3-CB-dechlorinating anaerobe) or a three-member consortium consisting of D. tiejei, a benzoate degrader, and an H2-utilizing methanogen. No degradation occurred in an uninoculated control reactor which was started with the same granular sludge, but inoculated reactors and granules from the inoculated UASB systems rapidly transformed 3-CB (54 mumol/day/g of granule biomass). After several months at a hydraulic retention time of 0.5 day, much shorter than the generation time of D. tiedjei, the reactors still dechlorinated 3-CB. This indicated that the bacteria were immobilized in the reactor granules, and by using an antibody probe for D. tiedjei, we demonstrated that this microorganism had colonized the sludge granules. These results represent the first addition of a pure culture or a defined microbial mixture to a viable waste treatment process to introduce a specific de novo degradative pathway into a granular-sludge consortium.

Immunochemical differences among Methanosarcina mazei S-6 morphologic forms

Methanosarcinae are the only archaeobacteria known to undergo major morphologic changes during growth involving unicellular and multicellular forms, and Methanosarcina mazei S-6 is the only strain for which three distinct forms, packets, single cells, and lamina, have so far been observed. It is reported that two pairs of these forms, either packets and single cells or single cells and lamina, grew and interconverted in medium with the same composition, Ca2+ and Mg2+ concentrations, and growth substrate, and that the two forms in each pair displayed distinctive differences revealed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and immunoblotting, the same growth medium-substrate notwithstanding.

DNA relatedness among some thermophilic members of the genus Methanobacterium: emendation of the species Methanobacterium thermoautotrophicum and rejection of Methanobacterium thermoformicicum as a synonym of Methanobacterium thermoautotrophicum

DNA reassociation was used to determine levels of relatedness among four thermophilic Methanobacterium strains that are able to use formate and between these organisms and two representative strains of Methanobacterium thermoautotrophicum, strain delta HT (= DSM 1053T = ATCC 29096T) (T = type strain) and strain Marburg (= DSM 2133). Three homology groups were delineated, and these groups coincided with the clusters identified by antigenic fingerprinting. The first group, which had levels of cross hybridization that ranged from 73 to 99%, included M. thermoautotrophicum delta HT, Methanobacterium thermoformicicum Z-245, Methanobacterium sp. strain THF, and Methanobacterium sp. strain FTF. The second and third groups were each represented by only one strain, Methanobacterium sp. strain CB-12 and M. thermoautotrophicum Marburg, respectively (cross-hybridization levels, 13 to 30 and 29 to 33%, respectively). Our results indicate that the name M. thermoformicicum should be rejected as it is a synonym of M. thermoautotrophicum. The taxonomic positions of strains Marburg and CB-12 need further investigation.

Effect of magnesium on methanogenic subpopulations in a thermophilic acetate-degrading granular consortium

The effects of Mg2+ on thermophilic (55 degrees C) granules grown on acetate in 0.2-liter upflow anaerobic sludge blanket reactors were studied. The methanogens in the granules were identified and counted by using antibody probes and the antigenic fingerprinting method. Packets of large coccoidal cells antigenically related to Methanosarcina thermophila TM-1 were scarce in the absence of Mg2+ but increased with increasing Mg2+ concentrations up to 30 mM; Methanosarcina packets immunologically related to Methanosarcina barkeri R1M3 showed a similar trend, and their numbers increased up to 100 mM Mg2+. The number of single cells antigenically related to TM-1, R1M3, and Methanosarcina mazei S-6 were scarce at low Mg2+ concentrations but increased drastically at 30 and 100 mM Mg2+. The number of rod-shaped bacteria antigenically related to Methanobacterium thermoautotrophicum GC1 and delta H was highest with no Mg2+ present, and their numbers decreased with increasing concentrations of the cation. These quantitative data, obtained by counting cells in suspensions made from disrupted granules, were confirmed by microscopic observation of the methanogenic subpopulations in thin histologic sections of the granules.

Lamina, a novel multicellular form of Methanosarcina mazei S-6

A novel multicellular form of Methanosarcina mazei S-6 is described. It was termed lamina, and it formed during the exponential growth phase when packets or single cells were grown in 40 mM trimethylamine and a total concentration of 8.3 to 15.6 mM Ca2+ and/or Mg2+, in cultures that were not shaken. A distinct molecular event represented by the increment in expression and a spatial redistribution of an antigen during lamina formation is documented.

A dnaK homolog in the archaebacterium Methanosarcina mazei S6

A fragment of genomic DNA cloned from the methanogenic archaebacterium, Methanosarcina mazei strain S6, was found to contain an 1857-bp open reading frame (ORF). A sequence matching the consensus ribosome-binding sequence determined for other methanogens was found upstream from the ORF. The amino acid (aa) sequence encoded by the ORF was compared with reference sequences and was found to be related to six DnaK sequences determined for five species of eubacteria (none exist for archaebacteria). The M. mazei S6 aa sequence was over 61% identical and over 77% similar (identities plus conservative substitutions) to the closest four reference sequences, which were all DnaKs. The gene described here is therefore proposed to be the first member of the dnaK family sequenced from the archaebacterial kingdom (Archaea). This finding confirms that DnaK proteins are highly conserved, occurring not only in eubacteria (Bacteria) and eukaryotes (Eucaria), but also in archaebacteria (Archaea).

Diversity and Population Dynamics of Methanogenic Bacteria in a Granular Consortium

Upflow anaerobic sludge blanket bioreactor granules were used as an experimental model microbial consortium to study the dynamics and distribution of methanogens. Immunologic methods revealed a considerable diversity of methanogens that was greater in mesophilic granules than in the same granules 4 months after a temperature shift from 38 to 55°C. During this period, the sizes of the methanogenic subpopulations changed with distinctive profiles after the initial reduction caused by the shift. Methanogens antigenically related to Methanobrevibacter smithii PS and ALI, Methanobacterium hungatei JF1, and Methanosarcina thermophila TM1 increased rapidly, reached a short plateau, and then fell to lower concentrations that persisted for the duration of the experiment. A methanogen related to Methanogenium cariaci JR1 followed a similar profile at the beginning, but it soon diminished below detection levels. Methanothrix rods weakly related to the strain Opfikon increased rapidly, reaching a high-level, long-lasting plateau. Two methanogens related to Methanobrevibacter arboriphilus AZ and Methanobacterium thermoautotrophicum ΔH emerged from very low levels before the temperature shift and multiplied to attain their highest numbers 4 months after the shift. Histochemistry and immunohistochemistry revealed thick layers, globular clusters, and lawns of variable density which were distinctive of the methanogens related to M. thermoautotrophicum ΔH, M. thermophila TM1, and M. arboriphilus AZ and M. soehngenii Opfikon, respectively, in thin sections of granules grown at 55°C for 4 months. Mesophilic granules showed a different pattern of methanogenic subpopulations.

Quantitative Microbiological Analysis of Bacterial Community Shifts in a High-Rate Anaerobic Bioreactor Treating Sulfite Evaporator Condensate

The bacterial population of a high-rate, anaerobic, fixed-bed loop reactor treating sulfite evaporator condensate from the pulp industry was studied over a 14-month period. This period was divided into seven cycles that included a startup at the beginning of each cycle. Some 82% of the total biomass was immobilized on and between the porous glass rings filling the reactor. The range of the total number of microorganisms in these biofilms was 2 × 10 9 to 7 × 10 9 cells per ml. Enumeration and characterization by microbiological methods and by phase-contrast, epifluorescence, and electron microscopy showed that the samples consisted mainly of the following methanogens: a Methanobacterium sp., a Methanosarcina sp., a Methanobrevibacter sp., and a Methanothrix sp., as well as furfural-degrading sulfate-reducing bacteria resembling Desulfovibrio furfuralis. Viable counts of hydrogenotrophic methanogens were relatively stable (mostly within the range of 3.2 × 10 8 to 7.5 × 10 8 cells per ml), but Methanobrevibacter cells increased from <5 to 30% of the total hydrogenotrophic count after transfer of the fixed bed into a second reactor vessel. Acetotrophic methanogens reached their highest numbers of 1.3 × 10 8 to 2.6 × 10 8 cells per ml in the last fermentation cycles. They showed a morphological shift from sarcinalike packets in early samples to single coccoid forms in later phases of the fermentation. Furfural-degrading sulfate reducers reached counts of 1 × 10 7 to 5.8 × 10 7 cells per ml. The distribution of the chief metabolic groups between free fluid and biofilms was analyzed in the fifth fermentation cycle: 4.5 times more furfural degraders were found in the free fluid than in the biofilms. In contrast, 5.8 times more acetotrophic and 16.6 times more hydrogenotrophic methanogens were found in the biofilms than in the free liquid. The data concerning time shifts of morphotypes among the trophic groups of methanogens corroborated the trends observed by using immunological assays on the same samples.

Methanogenic bacteria in human vaginal samples

Twelve vaginal samples were collected from separate patients, processed anaerobically, and added to methanogenic enrichment medium. Methanogenic activity was detected in two samples, both of which were from patients with bacterial vaginosis. None of the samples from healthy patients yielded positive methanogen cultures. One sample from a patient with bacterial vaginosis did not show any detectable methanogenic activity. Two methanogen isolates were obtained from one of the methanogen-positive samples, and both were identified as Methanobrevibacter smithii on the basis of morphological, cultural, and immunological features.

Adaptation of the slide immunoenzymatic assay for quantification of DNA hybridization: SIA-DNA

A quantitative, non-radioisotopic microsystem has been developed for measuring nucleic acid hybridization using microliter volumes of test sample and reagents. This new method, Slide Immunoenzymatic Assay-DNA, is a modification of the Slide Immunoenzymatic Assay technology originally designed for quantifying antigens and antibodies. It features small, circular solid phases (circles) of transparent material for nucleic acid immobilization. This allows the use of enzyme-labelled gene probes and substrates that generate color which, due to the distribution pattern of the circles on their support, can be measured by automated microtitration plate readers. Slide Immunoenzymatic Assay-DNA has been standardized to measure hybridization of probe to purified DNA or to DNA in cells lysed directly on the circles. Owing to its simplicity, relative low cost and expeditiousness, i.e., providing results in four hours. Slide Immunoenzymatic Assay-DNA is also suitable for use in simple laboratories and field studies.