ADP-Dependent Phosphofructokinases in Mesophilic and Thermophilic Methanogenic Archaea

Phosphofructokinase (PFK) is a key enzyme of the glycolytic pathway in all domains of life. Two related PFKs, ATP-dependent and PP(i)-dependent PFK, have been distinguished in bacteria and eucarya, as well as in some archaea. Hyperthermophilic archaea of the order Thermococcales, including Pyrococcus and Thermococcus spp., have recently been demonstrated to possess a unique ADP-dependent PFK (ADP-PFK) that appears to be phylogenetically distinct. Here, we report the presence of ADP-PFKs in glycogen-producing members of the orders Methanococcales and Methanosarcinales, including both mesophilic and thermophilic representatives. To verify the substrate specificities of the methanogenic kinases, the gene encoding the ADP-PFK from Methanococcus jannaschii was functionally expressed in Escherichia coli, and the produced enzyme was purified and characterized in detail. Compared to its counterparts from the two members of the order Thermococcales, the M. jannaschii ADP-PFK has an extremely low K(m) for fructose 6-phosphate (9.6 microM), and it accepts both ADP and acetyl-phosphate as phosphoryl donors. Phylogenetic analysis of the ADP-PFK reveals it to be a key enzyme of the modified Embden-Meyerhof pathway of heterotrophic and chemolithoautotrophic archaea. Interestingly, uncharacterized homologs of this unusual kinase are present in several eucarya.     

Detection and Quantification of Functional Genes of Cellulose- Degrading,Fermentative, and Sulfate-Reducing Bacteria and Methanogenic Archaea

Cellulose degradation, fermentation, sulfate reduction, and methanogenesis are microbial processes that coexist in a variety of natural and engineered anaerobic environments. Compared to the study of 16S rRNA genes, the study of the genes encoding the enzymes responsible for these phylogenetically diverse functions is advantageous because it provides direct functional information. However, no methods are available for the broad quantification of these genes from uncultured microbes characteristic of complex environments. In this study, consensus degenerate hybrid oligonucleotide primers were designed and validated to amplify both sequenced and unsequenced glycoside hydrolase genes of cellulose-degrading bacteria, hydA genes of fermentative bacteria, dsrA genes of sulfate-reducing bacteria, and mcrA genes of methanogenic archaea. Specificity was verified in silico and by cloning and sequencing of PCR products obtained from an environmental sample characterized by the target functions. The primer pairs were further adapted to quantitative PCR (Q-PCR), and the method was demonstrated on samples obtained from two sulfate-reducing bioreactors treating mine drainage, one lignocellulose based and the other ethanol fed. As expected, the Q-PCR analysis revealed that the lignocellulose-based bioreactor contained higher numbers of cellulose degraders, fermenters, and methanogens, while the ethanol-fed bioreactor was enriched in sulfate reducers. The suite of primers developed represents a significant advance over prior work, which, for the most part, has targeted only pure cultures or has suffered from low specificity. Furthermore, ensuring the suitability of the primers for Q-PCR provided broad quantitative access to genes that drive critical anaerobic catalytic processes.The gene encoding the 16S small ribosomal subunit has served as a highly suitable target for studying bacterial species. When one obtains 16S rRNA gene sequence information, it is sometimes possible to infer function from an identical match to a well-characterized pure culture. More commonly, however, the similarity to pure cultures is low, and/or the highest similarities correspond to 16S rRNA gene sequences identified without isolation or phenotypic characterization. In either case, care must be taken, because distinct phenotypes [e.g., dissimilatory Fe(III) reduction, chlorate reduction] are found in microorganisms with highly similar (e.g., 99.5%) 16S rRNA gene sequences (1). In addition, 16S rRNA gene surveys of broad phylogenetic groups can be time-, labor-, and cost-intensive. For example, it is estimated that the 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing bacteria (SRB) would require approximately 132 16S rRNA gene-targeted microarray probes (32).A more-direct approach for the study of microbes that span phylogenetic groups is to target them as a physiologically coherent guild by using specific genetic markers (functional genes) for the functions of interest. Functional genes have been successfully targeted in bioremediation studies to investigate microbial populations responsible for the degradation of various contaminants. Some examples include the use of the large alpha subunit of benzylsuccinate synthase to monitor anaerobic hydrocarbon-degrading bacteria (5), the monitoring of ars genes for the identification and quantification of arsenic-metabolizing bacteria (45), and the detection of catechol 1,2-dioxygenase in aromatic-hydrocarbon-degrading Rhodococcus spp. (48). In the field of mine drainage/metal remediation, functional genes have been used to target SRB (17, 26), but the methods have suffered both from a lack of broad specificity for SRB and from the inability to distinguish SRB from sulfur-oxidizing bacteria (SOB). A general challenge to the functional-gene approach has been the relative lack of characterization and unavailability of target sequences. As a consequence, the primer sets that are available tend to be more relevant to pure cultures than to complex environmental samples.Microbial communities in natural and engineered anaerobic environments that utilize cellulose as the primary carbon source, such as those in rumina (56), termite guts (54), decomposing wood (7), sulfate-reducing and methanogenic sediments (9, 22), wetlands (28), and sulfate-reducing bioreactors (26), are particularly challenging to characterize. 16S rRNA gene-based studies have revealed the complexity of these microbial communities and their high levels of phylogenetic and functional diversity. In such anaerobic environments, mineralization of complex organic matter occurs through the concerted action of a variety of microorganisms. Primary fermenters, such as cellulose degraders, break down the complex molecules and ferment the hydrolysis products. Secondary fermenters also ferment the hydrolysis products. When sulfate is available, SRB utilize the fermentation products as carbon and energy sources. In addition, methanogens can also utilize some of the fermentation products. In many cases, functionally important members, such as SRB, are present only as a small fraction of the community (36, 38), making them difficult to detect by use of 16S rRNA gene-targeted fingerprinting methods. Furthermore, the phylogenetic diversity of cellulose degraders, fermenters, and SRB prevents their quantification using a small number of 16S rRNA gene-targeted probes.In this study, degenerate PCR primers were developed, validated, and demonstrated for the amplification of key functional groups in anaerobic environments possessing genes encoding glycoside hydrolases of families 5 (collectively designated cel5 in this study) and 48 (collectively designated cel48 in this study) (cellulose degradation), the alpha subunit of iron hydrogenase (hydA) (fermentation), dissimilatory sulfite reductase (dsrA) (sulfate reduction), and methyl coenzyme M reductase (mcrA) (methanogenesis). This work is particularly novel considering that the vast majority of existing methods are suitable only for pure cultures, especially in the cases of cel5, cel48, and hydA (21, 44, 47). Thus, the approach provides access to uncultured and unsequenced markers, a critical feature for the study of key anaerobic processes in complex environments. Specificity was also enhanced where possible, notably in the case of dsrA, for which existing primers either do not distinguish SRB from SOB (14, 17) or have good alignment with only a narrow range of SRB (31, 52). Finally, all primers in this study were designed and validated for quantitative PCR (Q-PCR), in order to provide valuable quantitative functional information about complex anaerobic communities. The approach is demonstrated on mine drainage remediation systems and is expected to be of broad value to a variety of fields, including advancing the understanding of biohydrogen production, global carbon cycling, and other important biogeochemical processes.     

(R)-Citramalate Synthase in Methanogenic Archaea

The Methanococcus jannaschii gene MJ1392 was cloned, and its protein product was hyperexpressed in Escherichia coli. The resulting protein was purified and shown to catalyze the condensation of pyruvate and acetyl coenzyme A, with the formation of (R)-citramalate. Thus, this gene (cimA) encodes an (R)-citramalate synthase (CimA). This is the first identification of this enzyme, which is likely involved in the biosynthesis of isoleucine.     

Distance-Decay and Taxa-Area Relationships for Bacteria,Archaea and Methanogenic Archaea in a Tropical Lake Sediment

The study of of the distribution of microorganisms through space (and time) allows evaluation of biogeographic patterns, like the species-area index (z). Due to their high dispersal ability, high reproduction rates and low rates of extinction microorganisms tend to be widely distributed, and they are thought to be virtually cosmopolitan and selected primarily by environmental factors. Recent studies have shown that, despite these characteristics, microorganisms may behave like larger organisms and exhibit geographical distribution. In this study, we searched patterns of spatial diversity distribution of bacteria and archaea in a contiguous environment. We collected 26 samples of a lake sediment, distributed in a nested grid, with distances between samples ranging from 0.01 m to 1000 m. The samples were analyzed using T-RFLP (Terminal restriction fragment length polymorphism) targeting mcrA (coding for a subunit of methyl-coenzyme M reductase) and the genes of Archaeal and Bacterial 16S rRNA. From the qualitative and quantitative results (relative abundance of operational taxonomic units) we calculated the similarity index for each pair to evaluate the taxa-area and distance decay relationship slopes by linear regression. All results were significant, with mcrA genes showing the highest slope, followed by Archaeal and Bacterial 16S rRNA genes. We showed that the microorganisms of a methanogenic community, that is active in a contiguous environment, display spatial distribution and a taxa-area relationship.     

An Intertwined Evolutionary History of Methanogenic Archaea and Sulfate Reduction

Hydrogenotrophic methanogenesis and dissimilatory sulfate reduction, two of the oldest energy conserving respiratory systems on Earth, apparently could not have evolved in the same host, as sulfite, an intermediate of sulfate reduction, inhibits methanogenesis. However, certain methanogenic archaea metabolize sulfite employing a deazaflavin cofactor (F₄₂₀)-dependent sulfite reductase (Fsr) where N- and C-terminal halves (Fsr-N and Fsr-C) are homologs of F₄₂₀H₂ dehydrogenase and dissimilatory sulfite reductase (Dsr), respectively. From genome analysis we found that Fsr was likely assembled from freestanding Fsr-N homologs and Dsr-like proteins (Dsr-LP), both being abundant in methanogens. Dsr-LPs fell into two groups defined by following sequence features: Group I (simplest), carrying a coupled siroheme-[Fe₄-S₄] cluster and sulfite-binding Arg/Lys residues; Group III (most complex), with group I features, a Dsr-type peripheral [Fe₄-S₄] cluster and an additional [Fe₄-S₄] cluster. Group II Dsr-LPs with group I features and a Dsr-type peripheral [Fe₄-S₄] cluster were proposed as evolutionary intermediates. Group III is the precursor of Fsr-C. The freestanding Fsr-N homologs serve as F₄₂₀H₂ dehydrogenase unit of a putative novel glutamate synthase, previously described membrane-bound electron transport system in methanogens and of assimilatory type sulfite reductases in certain haloarchaea. Among archaea, only methanogens carried Dsr-LPs. They also possessed homologs of sulfate activation and reduction enzymes. This suggested a shared evolutionary history for methanogenesis and sulfate reduction, and Dsr-LPs could have been the source of the oldest (3.47-Gyr ago) biologically produced sulfide deposit.     

Pathways for Methanogenesis and Diversity of Methanogenic Archaea in Three Boreal Peatland Ecosystems

The main objectives of this study were to uncover the pathways used for methanogenesis in three different boreal peatland ecosystems and to describe the methanogenic populations involved. The mesotrophic fen had the lowest proportion of CH₄ produced from H₂-CO₂. The oligotrophic fen was the most hydrogenotrophic, followed by the ombrotrophic bog. Each site was characterized by a specific group of methanogenic sequences belonging to Methanosaeta spp. (mesotrophic fen), rice cluster-I (oligotrophic fen), and fen cluster (ombrotrophic bog).     

Postinoculation Protozoan Establishment and Association Patterns of Methanogenic Archaea in the Ovine Rumen

Association patterns between archaea and rumen protozoa were evaluated by analyzing archaeal 16S rRNA gene clone libraries from ovine rumen inoculated with different protozoa. Five protozoan inoculation treatments, fauna free (negative control), holotrich and cellulolytic protozoa, Isotricha and Dasytricha spp., Entodinium spp., and total fauna (type A) were tested. We used denaturing gradient gel electrophoresis, quantitative PCR, and phylogenetic analysis to evaluate the impact of the protozoan inoculants on the respective archaeal communities. Protozoan 18S ribosomal DNA clone libraries were also evaluated to monitor the protozoal population that was established by the inoculation. Phylogenetic analysis suggested that archaeal clones associated with the fauna-free, the Entodinium, and the type A inoculations clustered primarily with uncultured phylotypes. Polyplastron multivesiculatum was the predominant protozoan strain established by the holotrich and cellulolytic protozoan treatment, and this resulted predominantly in archaeal clones affiliated with uncultured and cultured methanogenic phylotypes (Methanosphaera stadtmanae, Methanobrevibacter ruminantium, and Methanobacterium bryantii). Furthermore, the Isotricha and Dasytricha inoculation treatment resulted primarily in archaeal clones affiliated with Methanobrevibacter smithii. This report provides the first assessment of the influence of protozoa on archaea within the rumen microbial community and provides evidence to suggest that different archaeal phylotypes associate with specific groups of protozoa. The observed patterns may be linked to the evolution of commensal and symbiotic relationships between archaea and protozoa in the ovine rumen environment. This report further underscores the prevalence and potential importance of a rather large group of uncultivated archaea in the ovine rumen, probably unrelated to known methanogens and undocumented in the bovine rumen.     

Evidence of Increased Diversity of Methanogenic Archaea with Plant Extract Supplementation

This study evaluated the effects of selected essential oils on archaeal communities using the ovine rumen model. Forty weaned Canadian Arcott ewes, fed with barley-based diet, were allotted to one of three essential oil supplementation treatments or a control (10 ewes per treatment) for 13 weeks. The treatments were cinnamaldehyde, garlic oil, juniper berry oil, and a control with no additive. Rumen content was sampled after slaughter and grouped by treatment by combining subsamples from each animal. DNA was extracted from the pooled samples and analyzed for methanogenic archaea using quantitative polymerase chain reaction, denaturing gradient gel electrophoresis, cloning, and sequencing. Our results suggest that the total copy number of archaeal 16S rRNA was not significantly affected by the treatments. The phylogenetic analysis indicated a trend toward an increased diversity of methanogenic archaea related to Methanosphaera stadtmanae, Methanobrevibacter smithii, and some uncultured groups with cinnamaldehyde, garlic, and juniper berry oil supplementation. The trends in the diversity of methanogenic archaea observed with the essential oil supplementation may have resulted from changes in associated protozoal species. Supplementation of ruminant diets with essential oils may alter the diversity of rumen methanogens without affecting the methanogenic capacity of the rumen.     

Correlation of Campylobacter Bacteriophage with Reduced Presence of Hosts in Broiler Chicken Ceca

Campylobacter jejuni and Campylobacter-specific bacteriophage were enumerated from broiler chicken ceca selected from 90 United Kingdom flocks (n = 205). C. jejuni counts in the presence of bacteriophage (mean log₁₀ 5.1 CFU/g) were associated with a significant (P < 0.001) reduction compared to samples with Campylobacter alone (mean log₁₀ 6.9 CFU/g).     

Methane Production and Methanogenic Archaea in the Digestive Tracts of Millipedes (Diplopoda)

Methane production by intestinal methanogenic Archaea and their community structure were compared among phylogenetic lineages of millipedes. Tropical and temperate millipedes of 35 species and 17 families were investigated. Species that emitted methane were mostly in the juliform orders Julida, Spirobolida, and Spirostreptida. The irregular phylogenetic distribution of methane production correlated with the presence of the methanogen-specific mcrA gene. The study brings the first detailed survey of methanogens’ diversity in the digestive tract of millipedes. Sequences related to Methanosarcinales, Methanobacteriales, Methanomicrobiales and some unclassified Archaea were detected using molecular profiling (DGGE). The differences in substrate preferences of the main lineages of methanogenic Archaea found in different millipede orders indicate that the composition of methanogen communities may reflect the differences in available substrates for methanogenesis or the presence of symbiotic protozoa in the digestive tract. We conclude that differences in methane production in the millipede gut reflect differences in the activity and proliferation of intestinal methanogens rather than an absolute inability of some millipede taxa to host methanogens. This inference was supported by the general presence of methanogenic activity in millipede faecal pellets and the presence of the 16S rRNA gene of methanogens in all tested taxa in the two main groups of millipedes, the Helminthophora and the Pentazonia.     

Biodiversity of Methanogenic and Other Archaea in the Permanently Frozen Lake Fryxell, Antarctica

Archaea were detected in molecular diversity studies of the permanently frozen Lake Fryxell, Antarctica. Two clusters of methanogens were detected in the sediments, and another cluster of possibly methanotrophic Euryarchaeota was detected in the anoxic water column just above the sediments. One crenarchaeote was detected in water just below the oxycline. The Archaea present in Lake Fryxell are likely involved in the major biogeochemical cycles that occur there.     

鸡粪沼气池产甲烷菌多样性

采用分子生物学方法构建16SrDNA基因文库,研究鸡粪沼气池发酵液中产甲烷菌的菌群结构。随机分析文库中50个克隆的16SrDNA基因序列,结果发现,其中46个克隆属于产甲烷菌属,与Methanogenium marinum strain AK-1菌株的相似性为99%-100%,占总数的92%;3个克隆(KD525、KD526和KD567)属于甲烷袋状菌属,与Methanoculleus sp.dm2菌株的相似性均为99%,占总数的6%;1个克隆(KD519)属于甲烷粒菌属,与Methanocorpusculum bavaricum菌株的相似性为99%,占总数的2%。另外,同样分析了样品中甲基辅酶M还原酶alpha亚基mcrA基因氨基酸序列的差异。气相色谱法分析结果显示,发酵液中甲酸含量为28.85g/L,约占总有机酸含量的81.7%;沼气的主要成分为甲烷、二氧化碳和氢气,分别约占总气体量的55.5%、41.1%和3.2%。     

Structure and Function of the A1A0-ATPases from Methanogenic Archaea

Recent molecular studies revealed nine to ten gene products involved infunction/assembly of the methanoarchaeal ATPase and unravel a closerelationship of the A₁A₀-ATPase and theV₁V₀-ATPase with respect to subunit composition and thestructure of individual subunits. Most interestingly, there is anastonishing variability in the size of the proteolipids in methanoar chaealA₁A₀-ATPases with six, four, or two transmembranehelices and a variable number of conserved protonizable groups per monomer.Despite the structural similarities the A₁A₀-ATPasediffers fundamentally from the V₁V₀-ATPase by itsability to synthesize ATP, a feature shared withF₁F₀-ATPases. The discovery of duplicated andtriplicated versions of the proteolipid in A₁A₀-ATPsynthases questions older views of the structural requirements for ATPsynthases versus ATP hydrolases and sheds new light on the evolutionof these secondary energy converters.     

Survival of Methanogenic Archaea from Siberian Permafrost under Simulated Martian Thermal Conditions

Methanogenic archaea from Siberian permafrost complementary to the already well-studied methanogens from non-permafrost habitats were exposed to simulated Martian conditions. After 22 days of exposure to thermo-physical conditions at Martian low- and mid-latitudes up to 90% of methanogenic archaea from Siberian permafrost survived in pure cultures as well as in environmental samples. In contrast, only 0.3%–5.8% of reference organisms from non-permafrost habitats survived at these conditions. This suggests that methanogens from terrestrial permafrost seem to be remarkably resistant to Martian conditions. Our data also suggest that in scenario of subsurface lithoautotrophic life on Mars, methanogenic archaea from Siberian permafrost could be used as appropriate candidates for the microbial life on Mars.     

Analysis of Cultured Methanogenic Archaea from the Tarkhankut Peninsula Coastal Methane Seeps

Microbiology - The major substrates for methanogenesis were used for investigation of cultured methanogenic archaea from coastal methane seeps near the Tarkhankut Peninsula, Black Sea. Analysis of...     

Identification of Protein-Tyrosine Phosphatases in Archaea

Protein-tyrosine dephosphorylation is a major mechanism in cellular regulation. A large number of protein-tyrosine phosphatases is known from Eukarya, and more recently bacterial homologues have also been identified. By employing conserved sequence patterns from both eukaryotic and bacterial protein-tyrosine phosphatases, we have identified three homologous sequences in two of the four complete archaeal genomes. Two hypothetical open reading frames in the genome of Methanococcus jannaschii (MJ0215 and MJECL20) and one in the genome of Pyrococcus horikoshii (PH1732) clearly bear all the conserved residues of this family. No homologues were found in the genomes of Archaeoglobus fulgidus and Methanobacterium thermoautotrophicum. This is the first report of protein-tyrosine phosphatase sequences in Archaea. Received: 29 April 1998 / Accepted: 27 November 1998     

Degradation of Methanethiol by Methylotrophic Methanogenic Archaea in a Lab-Scale Upflow Anaerobic Sludge Blanket Reactor

In a lab-scale upflow anaerobic sludge blanket reactor inoculated with granular sludge from a full-scale wastewater treatment plant treating paper mill wastewater, methanethiol (MT) was degraded at 30°C to H₂S, CO₂, and CH₄. At a hydraulic retention time of 9 h, a maximum influent concentration of 6 mM MT was applied, corresponding to a volumetric loading rate of 16.5 mmol liter⁻¹ day⁻¹. The archaeal community within the reactor was characterized by anaerobic culturing and denaturing gradient gel electrophoresis analysis, cloning, and sequencing of 16S rRNA genes and quantitative PCR. Initially, MT-fermenting methanogenic archaea related to members of the genus Methanolobus were enriched in the reactor. Later, they were outcompeted by Methanomethylovorans hollandica, which was detected in aggregates but not inside the granules that originated from the inoculum, the microbial composition of which remained fairly unchanged. Possibly other species within the Methanosarcinacaea also contributed to the fermentation of MT, but they were not enriched by serial dilution in liquid media. The archaeal community within the granules, which was dominated by Methanobacterium beijingense, did not change substantially during the reactor operation. Some of the species related to Methanomethylovorans hollandica were enriched by serial dilutions, but their growth rates were very low. Interestingly, the enrichments could be sustained only in the presence of MT and did not utilize any of the other typical substrates for methylotrophic methanogens, such as methanol, methyl amine, or dimethylsulfide.     

Characterization of Flagellum Gene Families of Methanogenic Archaea and Localization of Novel Flagellum Accessory Proteins

Archaeal flagella are unique motility structures, and the absence of bacterial structural motility genes in the complete genome sequences of flagellated archaeal species suggests that archaeal flagellar biogenesis is likely mediated by novel components. In this study, a conserved flagellar gene family from each of Methanococcus voltae, Methanococcus maripaludis, Methanococcus thermolithotrophicus, and Methanococcus jannaschii has been characterized. These species possess multiple flagellin genes followed immediately by eight known and supposed flagellar accessory genes, flaCDEFGHIJ. Sequence analyses identified a conserved Walker box A motif in the putative nucleotide binding proteins FlaH and FlaI that may be involved in energy production for flagellin secretion or assembly. Northern blotting studies demonstrated that all the species have abundant polycistronic mRNAs corresponding to some of the structural flagellin genes, and in some cases several flagellar accessory genes were shown to be cotranscribed with the flagellin genes. Cloned flagellar accessory genes of M. voltae were successfully overexpressed as His-tagged proteins in Escherichia coli. These recombinant flagellar accessory proteins were affinity purified and used as antigens to raise polyclonal antibodies for localization studies. Immunoblotting of fractionated M. voltae cells demonstrated that FlaC, FlaD, FlaE, FlaH, and FlaI are all present in the cell as membrane-associated proteins but are not major components of isolated flagellar filaments. Interestingly, flaD was found to encode two proteins, each translated from a separate ribosome binding site. These protein expression data indicate for the first time that the putative flagellar accessory genes of M. voltae, and likely those of other archaeal species, do encode proteins that can be detected in the cell.