共查询到20条相似文献,搜索用时 15 毫秒
1.
Aims
The aim of the present study was to design and test a method allowing the detection and quantification of methanogenic consortia in organic‐rich rocks to determine the potential of methane biotransformation.Methods and Results
Methanogen numbers in the rock are often below the detection levels of quantification methods. Biostimulation was tested as a means to specifically increase bacterial and archaeal numbers above the detection levels in microcosms. Biostimulation reveals the presence of active heterotrophic and syntrophic bacterial consortia, methane accumulation and methanogens in one of four rock samples. Syntrophs and heterotrophs were dominated by Firmicutes, whereas archaeal diversity was limited to methanogens. Methane‐producing microcosms were characterized by a higher Firmicutes diversity.Conclusions
Biostimulation is a reliable tool for detection of methanogenic consortia in organic‐rich rocks. For routine and large scale experimentation, methane accumulation monitoring after biostimulation appears as the most time, work and cost efficient approach to detect the presence of active methanogenic consortia.Significance and Impact of the Study
We report for the first time the presence of live methanogenic consortia in organic‐rich shales and their ability to mineralize the rock into methane. This approach will be instrumental to quantify the potential of these rocks to produce methane as a novel energy source. 相似文献2.
Background
As bacteria, motile archaeal species swim by means of rotating flagellum structures driven by a proton gradient force. Interestingly, experimental data have shown that the archaeal flagellum is non-homologous to the bacterial flagellum either in terms of overall structure, components and assembly. The growing number of complete archaeal genomes now permits to investigate the evolution of this unique motility system. 相似文献3.
A widespread and highly conserved family of apparently inactivated derivatives of archaeal B-family DNA polymerases is described. Phylogenetic analysis shows that the inactivated forms comprise a distinct clade among archaeal B-family polymerases and that, within this clade, Euryarchaea and Crenarchaea are clearly separated from each other and from a small group of bacterial homologs. These findings are compatible with an ancient duplication of the DNA polymerase gene followed by inactivation and parallel loss in some of the lineages although contribution of horizontal gene transfer cannot be ruled out. The inactivated derivative of the archaeal DNA polymerase could form a complex with the active paralog and play a structural role in DNA replication. 相似文献
4.
Background
SelB is the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome. In archaea, only a subset of methanogens utilizes selenocysteine and encodes archaeal SelB (aSelB). A SelB-like (aSelBL) homolog has previously been identified in an archaeon that does not encode selenosysteine, and has been proposed to be a pyrrolysyl-tRNA-specific elongation factor (EF-Pyl). However, elongation factor EF-Tu is capable of binding archaeal Pyl-tRNA in bacteria, suggesting the archaeal ortholog EF1A may also be capable of delivering Pyl-tRNA to the ribosome without the need of a specialized factor. 相似文献5.
Background and Aims
The effect of transgenic insect-resistant crops on soil microorganisms has become an issue of public concern. The goal of this study was to firstly realize the variation of in situ methane (CH4) emission flux and methanogenic and methanotrophic communities due to planting transgenic Bt rice (Bt) cultivar.Methods
CH4 emitted from paddy soil was collected by static closed chamber technique. Denaturing gradient gel electrophoresis and real-time PCR methods were employed to analyze methanogenic archaeal and methanotrophic bacterial community structure and abundance.Results
Results showed that planting Bt rice cultivar effectively reduced in situ CH4 emission flux and methanogenic archaeal and methanotrophic bacterial community abundance and diversity. Data analysis showed that in situ CH4 emission flux increased significantly with the increase of methanogenic archaeal abundance (R 2 ?=?0.839, p?<?0.001) and diversity index H′ (R 2 ?=?0.729, p?<?0.05), whereas was not obviously related to methanotrophic bacterial community.Conclusions
Our results suggested that the lower in situ CH4 emission flux from Bt soil may result from lower methanogenic archaeal community abundance and diversity, lower methanogenic activity and higher methanotrophic activity. Moreover, our results inferred that specific functional microorganisms may be a more sensitive indicator than the total archaeal, bacterial or fungal population to assess the effects of transgenic insect-resistant plants on soil microorganisms. 相似文献6.
Phylogenetic analysis of methanogens from the bovine rumen 总被引:2,自引:0,他引:2
Background
Interest in methanogens from ruminants has resulted from the role of methane in global warming and from the fact that cattle typically lose 6 % of ingested energy as methane. Several species of methanogens have been isolated from ruminants. However they are difficult to culture, few have been consistently found in high numbers, and it is likely that major species of rumen methanogens are yet to be identified. 相似文献7.
Matthias Schlesner Arthur Miller Stefan Streif Wilfried F Staudinger Judith Müller Beatrix Scheffer Frank Siedler Dieter Oesterhelt 《BMC microbiology》2009,9(1):56
Background
Archaea share with bacteria the ability to bias their movement towards more favorable locations, a process known as taxis. Two molecular systems drive this process: the motility apparatus and the chemotaxis signal transduction system. The first consists of the flagellum, the flagellar motor, and its switch, which allows cells to reverse the rotation of flagella. The second targets the flagellar motor switch in order to modulate the switching frequency in response to external stimuli. While the signal transduction system is conserved throughout archaea and bacteria, the archaeal flagellar apparatus is different from the bacterial one. The proteins constituting the flagellar motor and its switch in archaea have not yet been identified, and the connection between the bacterial-like chemotaxis signal transduction system and the archaeal motility apparatus is unknown. 相似文献8.
Background
The origin and early evolution of the active site of the ribosome can be elucidated through an analysis of the ribosomal proteins' taxonomic block structures and their RNA interactions. Comparison between the two subunits, exploiting the detailed three-dimensional structures of the bacterial and archaeal ribosomes, is especially informative. 相似文献9.
Background
Horizontal or lateral transfer of genetic material between distantly related prokaryotes has been shown to play a major role in the evolution of bacterial and archaeal genomes, but exchange of genes between prokaryotes and eukaryotes is not as well understood. In particular, gene flow from eukaryotes to prokaryotes is rarely documented with strong support, which is unusual since prokaryotic genomes appear to readily accept foreign genes. 相似文献10.
Background
Using sequence-structure threading we have conducted structural characterization of complete proteomes of 37 archaeal, bacterial and eukaryotic organisms (including worm, fly, mouse and human) totaling 167,888 genes. 相似文献11.
12.
Kira S Makarova Nick V Grishin Svetlana A Shabalina Yuri I Wolf Eugene V Koonin 《Biology direct》2006,1(1):7-26
Background
All archaeal and many bacterial genomes contain Clustered Regularly Interspaced Short Palindrome Repeats (CRISPR) and variable arrays of the CRISPR-associated (cas) genes that have been previously implicated in a novel form of DNA repair on the basis of comparative analysis of their protein product sequences. However, the proximity of CRISPR and cas genes strongly suggests that they have related functions which is hard to reconcile with the repair hypothesis. 相似文献13.
Background
As in eukaryotes, precursor transfer RNAs in Archaea often contain introns that are removed in tRNA maturation. Two unrelated archaeal species display unique pre-tRNA processing complexity in the form of split tRNA genes, in which two to three segments of tRNAs are transcribed from different loci, then trans-spliced to form a mature tRNA. Another rare type of pre-tRNA, found only in eukaryotic algae, is permuted, where the 3' half is encoded upstream of the 5' half, and must be processed to be functional. 相似文献14.
Qiangwei Xia Tiansong Wang Erik L Hendrickson Thomas J Lie Murray Hackett John A Leigh 《BMC microbiology》2009,9(1):149
Background
Methanogenic Archaea play key metabolic roles in anaerobic ecosystems, where they use H2 and other substrates to produce methane. Methanococcus maripaludis is a model for studies of the global response to nutrient limitations. 相似文献15.
Laurence R. Bird Katherine S. Dawson Grayson L. Chadwick James M. Fulton Victoria J. Orphan Katherine H. Freeman 《Geobiology》2019,17(6):611-627
Archaeal ANaerobic MEthanotrophs (ANME) facilitate the anaerobic oxidation of methane (AOM), a process that is believed to proceed via the reversal of the methanogenesis pathway. Carbon isotopic composition studies indicate that ANME are metabolically diverse and able to assimilate metabolites including methane, methanol, acetate, and dissolved inorganic carbon (DIC). Our data support the interpretation that ANME in marine sediments at methane seeps assimilate both methane and DIC, and the carbon isotopic compositions of the tetrapyrrole coenzyme F430 and the membrane lipids archaeol and hydroxy‐archaeol reflect their relative proportions of carbon from these substrates. Methane is assimilated via the methyl group of CH3‐tetrahydromethanopterin (H4MPT) and DIC from carboxylation reactions that incorporate free intracellular DIC. F430 was enriched in 13C (mean δ13C = ?27‰ for Hydrate Ridge and ?80‰ for the Santa Monica Basin) compared to the archaeal lipids (mean δ13C = ?97‰ for Hydrate Ridge and ?122‰ for the Santa Monica Basin). We propose that depending on the side of the tricarboxylic acid (TCA) cycle used to synthesize F430, its carbon was derived from 76% DIC and 24% methane via the reductive side or 57% DIC and 43% methane via the oxidative side. ANME lipids are predicted to contain 42% DIC and 58% methane, reflecting the amount of each assimilated into acetyl‐CoA. With isotope models that include variable fractionation during biosynthesis for different carbon substrates, we show the estimated amounts of DIC and methane can result in carbon isotopic compositions of ? 73‰ to ? 77‰ for F430 and ? 105‰ for archaeal lipids, values close to those for Santa Monica Basin. The F430 δ13C value for Hydrate Ridge was 13C‐enriched compared with the modeled value, suggesting there is divergence from the predicted two carbon source models. 相似文献
16.
17.
18.
The diversity of the methyl‐coenzyme reductase A (mcrA) and 16S rRNA genes was investigated in gas hydrate containing sediment from the Kazan mud volcano, eastern Mediterranean Sea. mcrA was detected only at 15 and 20 cm below seafloor (cmbsf) from a 40‐cm long push core, while based on chemical profiles of methane, sulfate, and sulfide, possible anaerobic oxidation of methane (AOM) depth was inferred at 12–15 cmbsf. The phylogenetic relationships of the obtained mcrA, archaeal and bacterial 16S rRNA genes, showed that all the found sequences were found in both depths and at similar relative abundances. mcrA diversity was low. All sequences were related to the Methanosarcinales, with the most dominant (77.2%) sequences falling in group mcrA‐e. The 16S rRNA‐based archaeal diversity also revealed low diversity and clear dominance (72.8% of all archaeal phylotypes) of the Methanosarcinales and, in particular, ANME‐2c. Bacteria showed higher diversity but 83.2% of the retrieved phylotypes from both sediment layers belonged to the δ‐Proteobacteria. These phylotypes fell in the SEEP‐SRB1 putative AOM group. In addition, the rest of the less abundant phylotypes were related to yet‐uncultivated representatives of the Actinobacteria, Spirochaetales, and candidate divisions OP11 and WS3 from gas hydrate‐bearing habitats. These phylotype patterns indicate that AOM is occurring in the 15 and 20 cmbsf sediment layers. 相似文献
19.
Sinead C. Leahy William J. Kelly Eric Altermann Ron S. Ronimus Carl J. Yeoman Diana M. Pacheco Dong Li Zhanhao Kong Sharla McTavish Carrie Sang Suzanne C. Lambie Peter H. Janssen Debjit Dey Graeme T. Attwood 《PloS one》2010,5(1)
Background
Methane (CH4) is a potent greenhouse gas (GHG), having a global warming potential 21 times that of carbon dioxide (CO2). Methane emissions from agriculture represent around 40% of the emissions produced by human-related activities, the single largest source being enteric fermentation, mainly in ruminant livestock. Technologies to reduce these emissions are lacking. Ruminant methane is formed by the action of methanogenic archaea typified by Methanobrevibacter ruminantium, which is present in ruminants fed a wide variety of diets worldwide. To gain more insight into the lifestyle of a rumen methanogen, and to identify genes and proteins that can be targeted to reduce methane production, we have sequenced the 2.93 Mb genome of M. ruminantium M1, the first rumen methanogen genome to be completed.Methodology/Principal Findings
The M1 genome was sequenced, annotated and subjected to comparative genomic and metabolic pathway analyses. Conserved and methanogen-specific gene sets suitable as targets for vaccine development or chemogenomic-based inhibition of rumen methanogens were identified. The feasibility of using a synthetic peptide-directed vaccinology approach to target epitopes of methanogen surface proteins was demonstrated. A prophage genome was described and its lytic enzyme, endoisopeptidase PeiR, was shown to lyse M1 cells in pure culture. A predicted stimulation of M1 growth by alcohols was demonstrated and microarray analyses indicated up-regulation of methanogenesis genes during co-culture with a hydrogen (H2) producing rumen bacterium. We also report the discovery of non-ribosomal peptide synthetases in M. ruminantium M1, the first reported in archaeal species.Conclusions/Significance
The M1 genome sequence provides new insights into the lifestyle and cellular processes of this important rumen methanogen. It also defines vaccine and chemogenomic targets for broad inhibition of rumen methanogens and represents a significant contribution to worldwide efforts to mitigate ruminant methane emissions and reduce production of anthropogenic greenhouse gases. 相似文献20.