Methanosarcina mazei LYC, a New Methanogenic Isolate Which Produces a Disaggregating Enzyme

Quantitative assessment of exposure to fecal contamination in urban environment across nine cities in low-income and lower-middle-income countries and a city in the United States

BACKGROUND

During 2014 to 2019, the SaniPath Exposure Assessment Tool, a standardized set of methods to evaluate risk of exposure to fecal contamination in the urban environment through multiple exposure pathways, was deployed in 45 neighborhoods in ten cities, including Accra and Kumasi, Ghana; Vellore, India; Maputo, Mozambique; Siem Reap, Cambodia; Atlanta, United States; Dhaka, Bangladesh; Lusaka, Zambia; Kampala, Uganda; Dakar, Senegal.

OBJECTIVE

Assess and compare risk of exposure to fecal contamination via multiple pathways in ten cities.

METHODS

In total, 4053 environmental samples, 4586 household surveys, 128 community surveys, and 124 school surveys were collected. E. coli concentrations were measured in environmental samples as an indicator of fecal contamination magnitude. Bayesian methods were used to estimate the distributions of fecal contamination concentration and contact frequency. Exposure to fecal contamination was estimated by the Monte Carlo method. The contamination levels of ten environmental compartments, frequency of contact with those compartments for adults and children, and estimated exposure to fecal contamination through any of the surveyed environmental pathways were compared across cities and neighborhoods.

RESULTS

Distribution of fecal contamination in the environment and human contact behavior varied by city. Universally, food pathways were the most common dominant route of exposure to fecal contamination across cities in low-income and lower-middle-income countries. Risks of fecal exposure via water pathways, such as open drains, flood water, and municipal drinking water, were site-specific and often limited to smaller geographic areas (i.e., neighborhoods) instead of larger areas (i.e., cities).

CONCLUSIONS

Knowledge of the relative contribution to fecal exposure from multiple pathways, and the environmental contamination level and frequency of contact for those "dominant pathways" could provide guidance for Water, Sanitation, and Hygiene (WASH) programming and investments and enable local governments and municipalities to improve intervention strategies to reduce the risk of exposure to fecal contamination.

Correlation of Key Physiological Properties of Methanosarcina Isolates with Environment of Origin

It is known that the physiology of Methanosarcina species can differ significantly, but the ecological impact of these differences is unclear. We recovered two strains of Methanosarcina from two different ecosystems with a similar enrichment and isolation method. Both strains had the same ability to metabolize organic substrates and participate in direct interspecies electron transfer but also had major physiological differences. Strain DH-1, which was isolated from an anaerobic digester, used H2 as an electron donor. Genome analysis indicated that it lacks an Rnf complex and conserves energy from acetate metabolism via intracellular H2 cycling. In contrast, strain DH-2, a subsurface isolate, lacks hydrogenases required for H2 uptake and cycling and has an Rnf complex for energy conservation when growing on acetate. Further analysis of the genomes of previously described isolates, as well as phylogenetic and metagenomic data on uncultured Methanosarcina in anaerobic digesters and diverse soils and sediments, revealed a physiological dichotomy that corresponded with environment of origin. The physiology of type I Methanosarcina revolves around H2 production and consumption. In contrast, type II Methanosarcina species eschew H2 and have genes for an Rnf complex and the multiheme, membrane-bound c-type cytochrome MmcA, shown to be essential for extracellular electron transfer. The distribution of Methanosarcina species in diverse environments suggests that the type I H2-based physiology is well suited for high-energy environments, like anaerobic digesters, whereas type II Rnf/cytochrome-based physiology is an adaptation to the slower, steady-state carbon and electron fluxes common in organic-poor anaerobic soils and sediments. IMPORTANCE Biogenic methane is a significant greenhouse gas, and the conversion of organic wastes to methane is an important bioenergy process. Methanosarcina species play an important role in methane production in many methanogenic soils and sediments as well as anaerobic waste digesters. The studies reported here emphasize that the genus Methanosarcina is composed of two physiologically distinct groups. This is important to recognize when interpreting the role of Methanosarcina in methanogenic environments, especially regarding H2 metabolism. Furthermore, the finding that type I Methanosarcina species predominate in environments with high rates of carbon and electron flux and that type II Methanosarcina species predominate in lower-energy environments suggests that evaluating the relative abundance of type I and type II Methanosarcina may provide further insights into rates of carbon and electron flux in methanogenic environments.

Structural studies of geranylgeranylglyceryl phosphate synthase, a prenyltransferase found in thermophilic Euryarchaeota

Archaea are uniquely adapted to thrive in harsh environments, and one of these adaptations involves the archaeal membrane lipids, which are characterized by their isoprenoid alkyl chains connected via ether linkages to glycerol 1-phosphate. The membrane lipids of the thermophilic and acidophilic euryarchaeota Thermoplasma volcanium are exclusively glycerol dibiphytanyl glycerol tetraethers. The first committed step in the biosynthetic pathway of these archaeal lipids is the formation of the ether linkage between glycerol 1-phosphate and geranylgeranyl diphosphate, and is catalyzed by the enzyme geranylgeranylglyceryl phosphate synthase (GGGPS). The 1.72 Å resolution crystal structure of GGGPS from T. volcanium (TvGGGPS) in complex with glycerol and sulfate is reported here. The crystal structure reveals TvGGGPS to be a dimer, which is consistent with the absence of the aromatic anchor residue in helix α5a that is required for hexamerization in other GGGPS homologs; the hexameric quaternary structure in GGGPS is thought to provide thermostability. A phylogenetic analysis of the Euryarchaeota and a parallel ancestral state reconstruction investigated the relationship between optimal growth temperature and the ancestral sequences. The presence of an aromatic anchor residue is not explained by temperature as an ecological parameter. An examination of the active site of the TvGGGPS dimer revealed that it may be able to accommodate longer isoprenoid substrates, supporting an alternative pathway of isoprenoid membrane-lipid synthesis.

Methanogenic degradation of tetramethylammonium hydroxide by Methanomethylovorans and Methanosarcina

This study evaluated the methanogens responsible for methanogenic degradation of tetramethylammonium hydroxide (TMAH) in a continuous flow bioreactor. The enriched methanogens attained an estimated maximum specific TMAH degradation rate and half-saturation constant of 39.5 mg TMAH/gVSS/h and 820 mg/L, following the Monod-type kinetic expression for methanogenic TMAH degradation. Presence of sulfide more than 20 mg/L significantly extended lag period and slowed down specific TMAH degradation rates. The results of terminal restriction fragment length polymorphism (T-RFLP), cloning/sequencing, and quantitative real-time PCR analyses targeting on the methyl coenzyme M reductase alpha subunit (mcrA) genes retrieved from the bioreactor and batch experiments indicated that Methanomethylovorans species were the dominant methanogens responsible for methanogenic degradation of TMAH. The isolated TMAH-degrading methanogen from the bioreactor, however, was identified closely related to Methanosarcina mazei. It is likely that a very low TMAH environment in the bioreactor favored the growth of Methanomethylovorans hollandica, while the much higher TMAH in the isolation growth medium proliferated Methanosarcina mazei.

Pilot study of cold-rolling wastewater treatment using single-stage anaerobic fluidized membrane bioreactor

A pilot-scale single-stage anaerobic fluidized membrane bioreactor (AFMBR) was firstly used in this study to treat cold-rolling emulsion wastewater from steel industry. It was continuously operated for 302 days with influent COD concentration of 860-1120 mg/L. Under a hydraulic retention time of 1.5 d, the average effluent COD concentration of 72 mg/L achieved corresponding 90% of COD removal. The permeate flux was varied between 1.7 and 2.9 L/m²/h during operation which decreased with increased biomass concentration inside AFMBR. The trans-membrane pressure (TMP) was generally around 35-40 kPa, however, it increased up to 60 kPa when volatile suspended solid increased to above 2.5 g/L. Both flux and TMP data reveal the importance of biomass control for AFMBR operation. Results from terminal restriction fragment length polymorphism (T-RFLP) show the genus Methanosaeta was dominant on GAC and it shared dominance with the genera Methanomethylovorans and Methanosarcina in suspended sludge.

Identification of syntrophic acetate-oxidizing bacteria in anaerobic digesters by combined protein-based stable isotope probing and metagenomics

Inhibition of anaerobic digestion through accumulation of volatile fatty acids occasionally occurs as the result of unbalanced growth between acidogenic bacteria and methanogens. A fast recovery is a prerequisite for establishing an economical production of biogas. However, very little is known about the microorganisms facilitating this recovery. In this study, we investigated the organisms involved by a novel approach of mapping protein-stable isotope probing (protein-SIP) onto a binned metagenome. Under simulation of acetate accumulation conditions, formations of (13)C-labeled CO2 and CH4 were detected immediately following incubation with [U-(13)C]acetate, indicating high turnover rate of acetate. The identified (13)C-labeled peptides were mapped onto a binned metagenome for improved identification of the organisms involved. The results revealed that Methanosarcina and Methanoculleus were actively involved in acetate turnover, as were five subspecies of Clostridia. The acetate-consuming organisms affiliating with Clostridia all contained the FTFHS gene for formyltetrahydrofolate synthetase, a key enzyme for reductive acetogenesis, indicating that these organisms are possible syntrophic acetate-oxidizing (SAO) bacteria that can facilitate acetate consumption via SAO, coupled with hydrogenotrophic methanogenesis (SAO-HM). This study represents the first study applying protein-SIP for analysis of complex biogas samples, a promising method for identifying key microorganisms utilizing specific pathways.

Biotic and abiotic dynamics of a high solid-state anaerobic digestion box-type container system

A solid-state anaerobic digestion box-type container system for biomethane production was observed in 12 three-week batch fermentations. Reactor performance was monitored using physico-chemical analysis and the methanogenic community was identified using ANAEROCHIP-microarrays and quantitative PCR. A resilient community was found in all batches, despite variations in inoculum to substrate ratio, feedstock quality, and fluctuating reactor conditions. The consortia were dominated by mixotrophic Methanosarcina that were accompanied by hydrogenotrophic Methanobacterium, Methanoculleus, and Methanocorpusculum. The relationship between biotic and abiotic variables was investigated using bivariate correlation analysis and univariate analysis of variance. High amounts of biogas were produced in batches with high copy numbers of Methanosarcina. High copy numbers of Methanocorpusculum and extensive percolation, however, were found to negatively correlate with biogas production. Supporting these findings, a negative correlation was detected between Methanocorpusculum and Methanosarcina. Based on these results, this study suggests Methanosarcina as an indicator for well-functioning reactor performance.

Physiological and genetic basis for self-aggregation of a thermophilic hydrogenotrophic methanogen, Methanothermobacter strain CaT2

Several thermophilic hydrogenotrophic methanogens naturally aggregate in their habitats in association with hydrogen-producing bacteria for efficient transfer of the methane fermentation intermediates to produce methane. However, physiology of aggregation and the identity of aggregation-specific genes remain to be elucidated. Here, we isolated and characterized a hydrogen and formate-utilizing Methanothermobacter sp. CaT2 that is capable of self-aggregation and utilizing formate. CaT2 produced methane from propionate oxidation in association with a syntrophic propionate-oxidizing bacterium faster than other methanogens, including Methanothermobacter thermautotrophicus ΔH and Methanothermobacter thermautotrophicus Z-245. CaT2 also aggregated throughout the culture period and was coated with polysaccharides, which was not found on the ΔH and Z-245 cells. Sugar content (particularly of rhamnose and mannose) was also higher in the CaT2 cells than the ΔH and Z-245 cells. Comparative genomic analysis of CaT2 indicated that four candidate genes, all of which encode glycosyltransferase, were involved in aggregation of CaT2. Transcriptional analysis showed that one glycosyltransferase gene was expressed at relatively high levels under normal growth conditions. The polysaccharide layer on the CaT2 cell surface, which is probably assembled by these glycosyltransferases, may be involved in cell aggregation.

Microbial ecology of anaerobic digesters: the key players of anaerobiosis

Anaerobic digestion is the method of wastes treatment aimed at a reduction of their hazardous effects on the biosphere. The mutualistic behavior of various anaerobic microorganisms results in the decomposition of complex organic substances into simple, chemically stabilized compounds, mainly methane and CO₂. The conversions of complex organic compounds to CH₄ and CO₂ are possible due to the cooperation of four different groups of microorganisms, that is, fermentative, syntrophic, acetogenic, and methanogenic bacteria. Microbes adopt various pathways to evade from the unfavorable conditions in the anaerobic digester like competition between sulfate reducing bacteria (SRB) and methane forming bacteria for the same substrate. Methanosarcina are able to use both acetoclastic and hydrogenotrophic pathways for methane production. This review highlights the cellulosic microorganisms, structure of cellulose, inoculum to substrate ratio, and source of inoculum and its effect on methanogenesis. The molecular techniques such as DGGE (denaturing gradient gel electrophoresis) utilized for dynamic changes in microbial communities and FISH (fluorescent in situ hybridization) that deal with taxonomy and interaction and distribution of tropic groups used are also discussed.

Searching for links in the biotic characteristics and abiotic parameters of nine different biogas plants

To find links between the biotic characteristics and abiotic process parameters in anaerobic digestion systems, the microbial communities of nine full‐scale biogas plants in South Tyrol (Italy) and Vorarlberg (Austria) were investigated using molecular techniques and the physical and chemical properties were monitored. DNA from sludge samples was subjected to microarray hybridization with the ANAEROCHIP microarray and results indicated that sludge samples grouped into two main clusters, dominated either by Methanosarcina or by Methanosaeta, both aceticlastic methanogens. Hydrogenotrophic methanogens were hardly detected or if detected, gave low hybridization signals. Results obtained using denaturing gradient gel electrophoresis (DGGE) supported the findings of microarray hybridization. Real‐time PCR targeting Methanosarcina and Methanosaeta was conducted to provide quantitative data on the dominating methanogens. Correlation analysis to determine any links between the microbial communities found by microarray analysis, and the physicochemical parameters investigated was conducted. It was shown that the sludge samples dominated by the genus Methanosarcina were positively correlated with higher concentrations of acetate, whereas sludge samples dominated by representatives of the genus Methanosaeta had lower acetate concentrations. No other correlations between biotic characteristics and abiotic parameters were found. Methanogenic communities in each reactor were highly stable and resilient over the whole year.

Methanosarcina: the rediscovered methanogen for heavy duty biomethanation

Anaerobic digestion is an important technology in the framework of renewable energy production. The anaerobic digestion system is susceptible to perturbations due to the sensitivity of the methanogens towards environmental factors. Currently, technology is evolving from conventional waste treatment, i.e. the removal of pollutants, to very intensive biogas production from concentrated wastes, in the framework of bio-energy production. In the latter configuration Methanosarcina species appear to be of crucial importance. Methanosarcina sp. are, compared to other methanogens, quite robust towards different impairments. They are reported to be tolerant to total ammonium concentrations up to 7000 mg L(-1), salt concentrations up to 18,000 mg Na(+)L(-1), a pH shock of 0.8-1.0 units and acetate concentrations up to 15,000 mg CODL(-1). The possibilities of Methanosarcina sp. as key organisms in specific types of anaerobic digestion systems are demonstrated in this review.

Effects of the antimicrobial tylosin on the microbial community structure of an anaerobic sequencing batch reactor

The effects of the antimicrobial tylosin on a methanogenic microbial community were studied in a glucose-fed laboratory-scale anaerobic sequencing batch reactor (ASBR) exposed to stepwise increases of tylosin (0, 1.67, and 167 mg/L). The microbial community structure was determined using quantitative fluorescence in situ hybridization (FISH) and phylogenetic analyses of bacterial 16S ribosomal RNA (rRNA) gene clone libraries of biomass samples. During the periods without tylosin addition and with an influent tylosin concentration of 1.67 mg/L, 16S rRNA gene sequences related to Syntrophobacter were detected and the relative abundance of Methanosaeta species was high. During the highest tylosin dose of 167 mg/L, 16S rRNA gene sequences related to Syntrophobacter species were not detected and the relative abundance of Methanosaeta decreased considerably. Throughout the experimental period, Propionibacteriaceae and high GC Gram-positive bacteria were present, based on 16S rRNA gene sequences and FISH analyses, respectively. The accumulation of propionate and subsequent reactor failure after long-term exposure to tylosin are attributed to the direct inhibition of propionate-oxidizing syntrophic bacteria closely related to Syntrophobacter and the indirect inhibition of Methanosaeta by high propionate concentrations and low pH.

Disaggregation of Methanosarcina spp. and Growth as Single Cells at Elevated Osmolarity

The effect of medium osmolarity on the morphology and growth of Methanosarcina barkeri, Methanosarcina thermophila, Methanosarcina mazei, Methanosarcina vacuolata, and Methanosarcina acetivorans was examined. Each strain was adapted for growth in NaCl concentrations ranging from 0.05 to 1.0 M. Methanosarcina spp. isolated from both marine and nonmarine sources exhibited similar growth characteristics at all NaCl concentrations tested, demonstrating that these species are capable of adapting to a similar range of medium osmolarities. Concomitant with the adaptation in 0.4 to 1.0 M NaCl, all strains disaggregated and grew as single cells rather than in the characteristic multicellular aggregates. Aggregated cells had a methanochondroitin outer layer, while disaggregated single cells lacked the outer layer but retained the protein S-layer adjacent to the cell membrane. Synthesis of glucuronic acid, a major component of methanochondroitin, was reduced 20-fold in the single-cell form of M. barkeri when compared with synthesis in aggregated cells. Strains with the methanochondroitin outer cell layer exhibited enhanced stability at low (<0.2 M NaCl) osmolarity and grew at higher temperatures. Disaggregated cells could be converted back to aggregated cells by gradually readapting cultures to lower NaCl (<0.2 M) and Mg (<0.005 M) concentrations. Disaggregated Methanosarcina spp. could also be colonized and replica plated with greater than 95% recovery rates on solidified agar basal medium that contained 0.4 to 0.6 M NaCl and either trimethylamine, methanol, or acetate as the substrate. The ability to disaggregate and grow Methanosarcina spp. as viable, detergent-sensitive, single cells on agar medium makes these species amenable to mutant selection and screening for genetic studies and enables cells to be gently lysed for the isolation of intact genetic material.

Spontaneous Disaggregation of Methanosarcina mazei S-6 and Its Use in the Development of Genetic Techniques for Methanosarcina spp

When monomethylamine was the growth substrate, spontaneous disaggregation of Methanosarcina mazei S-6 commenced at the mid-exponential phase and resulted in the formation of a suspension containing 10 to 10 free cells per ml. Free cells were osmotically fragile and amenable to extraction of DNA. Hypertonic media for the manipulation and regeneration of free cells into aggregates were developed, and plating efficiencies of 100% were achieved for M. mazei S-6 and LYC. Free cells of strain S-6 required MgCl(2) (10 mM) for growth, whereas aggregates did not. Specific growth rates of strains S-6 and LYC were increased by MgCl(2). Treatment with pronase caused sphere formation and removal of the protein wall of cells of strain S-6, but protoplasts could not be regenerated. The disaggregating enzyme produced by strain S-6 facilitated the preparation of suspensions of free cells of some strains of Methanosarcina barkeri. Although this provided a means of extracting high-molecular-weight DNA from M. barkeri, less than 0.1% of free cells were viable.

Life Cycles in the Methanogenic Archaebacterium Methanosarcina mazei

Methanosarcina mazei S6 and LYC were used to study the structure and differentiation of the aggregating methanogens. Cultures harvested under various conditions are described at the ultrastructural level. Cells of strain S6 are enclosed by a layer 12 nm thick in contact with the plasma membrane. In sarcinal colonies, cells are held in close association by a fibrous matrix up to 60 nm thick. Colony maturation was examined in strain S6 over a period of 1 year. Changes occurred in the shape and staining of individual cells. Also, various inclusion bodies were observed that either persist throughout colony maturation or are only found at certain growth stages. Two types of cores that are composed of double membranes in M. mazei S6 are described. One has a 90-nm diameter and contains electron-dense granules similar to those found in the cytoplasm. The other core type does not contain granules, is more numerous, and is found in older cultures. Two life cycles are described for M. mazei based on electron microscope examinations. A complex life cycle involving the release of single cells is described with two variations for strains S6 and LYC. When released cells of strain S6 are placed in fresh medium they can repeat the cycle. In addition, a limited cycle is described for both strains of M. mazei. This limited cycle contains the only sarcinal morphotypes observed in M. barkeri. When M. mazei S6 remains in the limited cycle and does not disaggregate in stationary phase, several types of possible resting forms are found.

Halotolerance in Methanosarcina spp.: Role of N(sup(epsilon))-Acetyl-(beta)-Lysine, (alpha)-Glutamate, Glycine Betaine, and K(sup+) as Compatible Solutes for Osmotic Adaptation

The methanogenic Archaea, like the Bacteria and Eucarya, possess several osmoregulatory strategies that enable them to adapt to osmotic changes in their environment. The physiological responses of Methanosarcina species to different osmotic pressures were studied in extracellular osmolalities ranging from 0.3 to 2.0 osmol/kg. Regardless of the isolation source, the maximum rate of growth for species from freshwater, sewage, and marine sources occurred in extracellular osmolalities between 0.62 and 1.0 osmol/kg and decreased to minimal detectable growth as the solute concentration approached 2.0 osmol/kg. The steady-state water-accessible volume of Methanosarcina thermophila showed a disproportionate decrease of 30% between 0.3 and 0.6 osmol/kg and then a linear decrease of 22% as the solute concentration in the media increased from 0.6 to 2.0 osmol/kg. The total intracellular K(sup+) ion concentration in M. thermophila increased from 0.12 to 0.5 mol/kg as the medium osmolality was raised from 0.3 to 1.0 osmol/kg and then remained above 0.4 mol/kg as extracellular osmolality was increased to 2.0 osmol/kg. Concurrent with K(sup+) accumulation, M. thermophila synthesized and accumulated (alpha)-glutamate as the predominant intracellular osmoprotectant in media containing up to 1.0 osmol of solute per kg. At medium osmolalities greater than 1.0 osmol/kg, the (alpha)-glutamate concentration leveled off and the zwitterionic (beta)-amino acid N(sup(epsilon))-acetyl-(beta)-lysine was synthesized, accumulating to an intracellular concentration exceeding 1.1 osmol/kg at an osmolality of 2.0 osmol/kg. When glycine betaine was added to culture medium, it caused partial repression of de novo (alpha)-glutamate and N(sup(epsilon))-acetyl-(beta)-lysine synthesis and was accumulated by the cell as the predominant compatible solute. The distribution and concentration of compatible solutes in eight strains representing five Methanosarcina spp. were similar to those found in M. thermophila grown in extracellular osmolalities of 0.3 and 2.0 osmol/kg. Results of this study demonstrate that the mechanism of halotolerance in Methanosarcina spp. involves the regulation of K(sup+), (alpha)-glutamate, N(sup(epsilon))-acetyl-(beta)-lysine, and glycine betaine accumulation in response to the osmotic effects of extracellular solute.

Control of the Life Cycle of Methanosarcina mazei S-6 by Manipulation of Growth Conditions

The morphology of Methanosarcina mazei was controlled by magnesium, calcium, and substrate concentrations and by inoculum size; these factors allowed manipulation of the morphology and interconversions between pseudosarcinal aggregates and individual, coccoid cells. M. mazei grew as aggregates in medium with a low concentration of catabolic substrate (either 50 mM acetate, 50 mM methanol, or 10 mM trimethylamine) unless Ca and Mg concentrations were high. Growth in medium high in Ca, Mg, and substrate (i.e., 150 mM acetate, 150 mM methanol, or 40 mM trimethylamine) converted pseudosarcinal aggregates to individual cocci. In such media, aggregates separated into individual cells which continued to grow exclusively as single cells during subsequent transfers. Conversion of single cells back to aggregates was complicated, because conditions which supported the aggregated morphology (e.g., low calcium or magnesium concentration) caused lysis of coccoid inocula. We recovered aggregates from coccoid cells by inoculating serial dilutions into medium high in calcium and magnesium. Cells from very dilute inocula grew into aggregates which disaggregated on continued incubation. However, timely transfer of the aggregates to medium low in calcium, magnesium, and catabolic substrates allowed continued growth as aggregates. We demonstrated the activity of the enzyme (disaggregatase) which caused the dispersion of aggregates into individual cells; disaggregatase was produced not only during disaggregation but also in growing cultures of single cells. Uronic acids, the monomeric constituents of the Methanosarcina matrix, were also produced during disaggregation and during growth as coccoids.

Archaic chaos: intrinsically disordered proteins in Archaea

BACKGROUND

Many proteins or their regions known as intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) lack unique 3D structure in their native states under physiological conditions yet fulfill key biological functions. Earlier bioinformatics studies showed that IDPs and IDRs are highly abundant in different proteomes and carry out mostly regulatory functions related to molecular recognition and signal transduction. Archaea belong to an intriguing domain of life whose members, being microbes, are characterized by a unique mosaic-like combination of bacterial and eukaryotic properties and include inhabitants of some of the most extreme environments on the planet. With the expansion of the archaea genome data (more than fifty archaea species from five different phyla are known now), and with recent improvements in the accuracy of intrinsic disorder prediction, it is time to re-examine the abundance of IDPs and IDRs in the archaea domain.

RESULTS

The abundance of IDPs and IDRs in 53 archaea species is analyzed. The amino acid composition profiles of these species are generally quite different from each other. The disordered content is highly species-dependent. Thermoproteales proteomes have 14% of disordered residues, while in Halobacteria, this value increases to 34%. In proteomes of these two phyla, proteins containing long disordered regions account for 12% and 46%, whereas 4% and 26% their proteins are wholly disordered. These three measures of disorder content are linearly correlated with each other at the genome level. There is a weak correlation between the environmental factors (such as salinity, pH and temperature of the habitats) and the abundance of intrinsic disorder in Archaea, with various environmental factors possessing different disorder-promoting strengths. Harsh environmental conditions, especially those combining several hostile factors, clearly favor increased disorder content. Intrinsic disorder is highly abundant in functional Pfam domains of the archaea origin. The analysis based on the disordered content and phylogenetic tree indicated diverse evolution of intrinsic disorder among various classes and species of Archaea.

CONCLUSIONS

Archaea proteins are rich in intrinsic disorder. Some of these IDPs and IDRs likely evolve to help archaea to accommodate to their hostile habitats. Other archaean IDPs and IDRs possess crucial biological functions similar to those of the bacterial and eukaryotic IDPs/IDRs.

Differences in hydrogenase gene expression between Methanosarcina acetivorans and Methanosarcina barkeri

Methanosarcina acetivorans C2A encodes three putative hydrogenases, including one cofactor F(420)-linked (frh) and two methanophenazine-linked (vht) enzymes. Comparison of the amino acid sequences of these putative hydrogenases to those of Methanosarcina barkeri and Methanosarcina mazei shows that each predicted subunit contains all the known residues essential for hydrogenase function. The DNA sequences upstream of the genes in M. acetivorans were aligned with those in other Methanosarcina species to identify conserved transcription and translation signals. The M. acetivorans vht promoter region is well conserved among the sequenced Methanosarcina species, while the second vht-type homolog (here called vhx) and frh promoters have only limited similarity. To experimentally determine whether these promoters are functional in vivo, we constructed and characterized both M. acetivorans and M. barkeri strains carrying reporter gene fusions to each of the M. acetivorans and M. barkeri hydrogenase promoters. Generally, the M. acetivorans gene fusions are not expressed in either organism, suggesting that cis-acting mutations inactivated the M. acetivorans promoters. The M. barkeri hydrogenase gene fusions, on the other hand, are expressed in both organisms, indicating that M. acetivorans possesses the machinery to express hydrogenases, although it does not express its own hydrogenases. These data are consistent with specific inactivation of the M. acetivorans hydrogenase promoters and highlight the importance of testing hypotheses generated by using genomic data.

Identification of the gene for disaggregatase from Methanosarcina mazei

The gene sequences encoding disaggregatase (Dag), the enzyme responsible for dispersion of cell aggregates of Methanosarcina mazei to single cells, were determined for three strains of M. mazei (S-6(T), LYC and TMA). The dag genes of the three strains were 3234 bp in length and had almost the same sequences with 97% amino acid sequence identities. Dag was predicted to comprise 1077 amino acid residues and to have a molecular mass of 120 kDa containing three repeats of the DNRLRE domain in the C terminus, which is specific to the genus Methanosarcina and may be responsible for structural organization and cell wall function. Recombinant Dag was overexpressed in Escherichia coli and preparations of the expressed protein exhibited enzymatic activity. The RT-PCR analysis showed that dag was transcribed to mRNA in M. mazei LYC and indicated that the gene was expressed in vivo. This is the first time the gene involved in the morphological change of Methanosarcina spp. from aggregate to single cells has been identified.

Methanethiol degradation in anaerobic bioreactors at elevated pH (8): reactor performance and microbial community analysis

The degradation of methanethiol (MT) at 30 degrees C under saline-alkaline (pH 8-10, 0.5M Na(+)) conditions was studied in a lab-scale Upflow Anaerobic Sludge Blanket (UASB) reactor inoculated with estuarine sediment from the Wadden Sea (The Netherlands). At a sodium concentration of 0.5M and a pH between 8 and 9 complete MT degradation to sulfide, methane and carbon dioxide was possible at a maximum loading rate of 22mmolMTL(-1)day(-1) and a hydraulic retention time of 6h. The presence of yeast extract (100mg/L) in the medium was essential for complete MT degradation. 16S rRNA based DGGE and sequence analysis revealed that species related to the genera Methanolobus and Methanosarcina dominated the archaeal community in the reactor sludge. Their relative abundance fluctuated in time, possibly as a result of the changing operational conditions in the reactor. The most dominant MT-degrading archaeon was enriched from the reactor and obtained in pure culture. This strain WR1, which was most closely related to Methanolobus taylorii, degraded MT, dimethyl sulfide (DMS), methanol and trimethylamine. Its optimal growth conditions were 0.2M NaCl, 30 degrees C and pH 8.4. In batch and reactor experiments operated at pH 10, MT was not degraded.

Anaerobic methanethiol degradation in upflow anaerobic sludge bed reactors at high salinity (≥0.5 M Na+)

The feasibility of anaerobic methanethiol (MT) degradation at elevated sodium concentrations was investigated in a mesophilic (30 degrees C) lab-scale upflow anaerobic sludge bed (UASB) reactor, inoculated with estuarine sediment originating from the Wadden Sea (The Netherlands). MT was almost completely degraded (>95%) to sulfide, methane and carbon dioxide at volumetric loading rates up to 37 mmol MT x L(-1) x day(-1), 0.5 M sodium (NaCl or NaHCO(3)) and between pH 7.3 and 8.4. Batch experiments revealed that inhibition of MT degradation started at sodium (both NaCl and NaHCO(3)) concentrations exceeding 0.8 M. Sulfide inhibited MT degradation already around 3 mM (pH 8.3).

Use of an alternative Archaea-specific probe for methanogen detection

An alternative 16S rRNA-targeted oligonucleotide probe specific for Archaea was developed and used for detection of methanogens in anaerobic reactors. The designed probe was checked for its specificity by computer-aided comparative sequence analysis. For in situ application, optimal stringency conditions were adjusted by performing whole cell hybridization using target and nontarget organisms. Anaerobic sludge samples were examined by in situ hybridization for methanogenic populations. The relative abundance of methanogens was monitored with epifluorescence microscopy. Individual cells could be visualized with strong fluorescence signals after hybridization with the newly developed probe.

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.

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.

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.

Isolation and characterization of disaggregatase from Methanosarcina mazei LYC

At certain stages in its growth cycle, Methanosarcina mazei produces an enzyme (disaggregatase) that causes aggregates to separate into single cells. M. mazei S-6 and LYC both produce this enzymatic activity, although the specificities of activities differ. The disaggregatase of M. mazei S-6 had little effect on strain LYC cells, but the disaggregatase of M. mazei LYC disaggregated both strain LYC and strain S-6 cells. The disaggregatase of M. mazei LYC was purified by column chromatography, and it apparently consisted of two similar subunits with a combined molecular size of about 180,000 Da. Strain S-6 culture supernatants contained 14 U of activity per liter when activity was measured as uronic acids released from purified cell wall material. When the activity was quantified as the release of uronic acids from boiled M. mazei S-6 cells, the highest activity was found at pH 4.7 and at 35 degrees C.

Presence of an Unusual Methanogenic Bacterium in Coal Gasification Waste

Methanogenic bacteria growing on a pilot-scale, anaerobic filter processing coal gasification waste were enriched in a mineral salts medium containing hydrogen and acetate as potential energy sources. Transfer of the enrichments to methanol medium resulted in the initial growth of a strain of Methanosarcina barkeri, but eventually small cocci became dominant. The cocci growing on methanol produced methane and exhibited the typical fluorescence of methanogenic bacteria. They grew in the presence of the cell wall synthesis-inhibiting antibiotics d -cycloserine, fosfomycin, penicillin G, and vancomycin as well as in the presence of kanamycin, an inhibitor of protein synthesis in eubacteria. The optimal growth temperature was 37°C, and the doubling time was 7.5 h. The strain lysed after reaching stationary phase. The bacterium grew poorly with hydrogen as the energy source and failed to grow on acetate. Morphologically, the coccus shared similarities with Methanosarcina sp. Cells were 1 μm wide, exhibited the typical thick cell wall and cross-wall formation, and formed tetrads. Packets and cysts were not formed.

Adaptation for growth at various saline concentrations by the archaebacterium Methanosarcina thermophila

We report the ability of Methanosarcina thermophila TM-1 to adapt and grow in media containing NaCl concentrations of 0.005 to 1.2 M. When adapted to marine NaCl concentrations, this species ceased to produce the heteropolysaccharide outer layer typically formed by species of nonmarine origin. concomitant with this adaptation, M. thermophila ceased to grow as multicellular aggregates and existed solely in single-cell form. The sodium ion concentration was critical for the adaptation process, although magnesium ion appeared to contribute to the cell wall stability of single cells. The results suggest that these archaebacteria possess regulatory systems that enable them to adapt to environments with a wide range of saline concentrations.