archaea

..In many Bacteria and most Archaea, clustered regularly interspaced short palindromic repeats (CRISPR) form peculiar genetic loci, which provide ..

..evolutionary relationships, we have sequenced and analysed the genomes of 56 culturable species of Bacteria and Archaea selected to maximize phylogenetic coverage...

Globally distributed archaea comprising ammonia oxidizers of moderate terrestrial and marine environments are considered the most abundant archaeal organisms on Earth...

All cellular systems evolve ways to combat predators and genomic parasites. In bacteria and archaea, numerous resistance mechanisms have developed against phage...

..Unlike the highly diverse Bacteria, the Archaea comprised mainly members of the order Methanobacteriales, which are H(2)-oxidizing methanogens...

..nM) closely resemble kinetics of in situ nitrification in marine systems and directly link ammonia-oxidizing Archaea to oligotrophic nitrification...

..Putative chimeras were identified in 3% of environmental sequences and in 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages in the Archaea and Bacteria.

..Sulfur-chemolithotrophic metabolism in Archaea, largely restricted to Sulfolobales, is distinct from those in Bacteria...

..Many archaea live in volcanic habitats under such constraints, in high temperatures with only inorganic substances and often ..

The recent discovery of ammonia-oxidizing archaea (AOA) dramatically changed our perception of the diversity and evolutionary history of microbes involved in nitrification...

..coli, a computational analysis of gene-transfer rates across available bacterial and archaeal genomes supports that the barriers observed in our study are general across the tree of life...

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..molecular markers have provided the outlines of a universal tree of life (ToL), the three-domain pattern of archaea, bacteria, and eucarya...

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The widespread occurrence and diversity of ammonia oxidizing Archaea suggests their contribution to the nitrogen cycle is of global significance...

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..In many bacteria and most archaea, clustered, regularly interspaced short palindromic repeats (CRISPRs) are involved in a more recently discovered ..

..Here, Multi Locus Sequence Typing (MLST) datasets from a wide variety of bacteria and archaea are analyzed using the ClonalFrame method...

..Recent discoveries have expanded the known ammonia-oxidizing prokaryotes from the domain Bacteria to Archaea. However, in the complex soil environment it remains unclear whether ammonia oxidation is exclusively or ..

..we undertook a comparative genomic analysis of the machineries for cell division and vesicle formation in Archaea. Archaea possess at least three distinct membrane remodelling systems: the FtsZ-based bacterial-type system, the ..

..Mallard is freely available from our website at http://www.cardiff.ac.uk/biosi/research/biosoft/...

..For example, we place the phylum Acidobacteria as a sister group of delta-Proteobacteria, support a Gram-positive origin of Bacteria, and suggest a thermophilic last universal common ancestor...

Methane-forming archaea are strictly anaerobic, ancient microbes that are widespread in nature...

..as yet uncultivated microorganisms in natural environments, yet there are gaps in our knowledge-particularly for Archaea-that occur at relatively low abundance and in extreme environments...

..The forest site also showed far less diversity of the Archaea with only 0...

..Nevertheless, the idea that it is impossible to reconstruct the evolutionary history of prokaryotes because of horizontal gene transfer has become very popular. We review this important debate and how it can be solved...

..Recent reports have shown that the newly discovered ammonia-oxidizing archaea can be both abundant and diverse in aquatic and terrestrial ecosystems...

..Homologues of this complex exist in bacteria, archaea, in mitochondria of eukaryotes and in chloroplasts of plants...

..The results reject all but two of the current hypotheses for the origin of eukaryotes: those assuming a sulfur-dependent or hydrogen-dependent syntrophy for the origin of mitochondria...

Although of limited metabolic diversity, methanogenic archaea or methanogens possess great phylogenetic and ecological diversity...

..bulk water pH, suggesting that geography may play a role in structuring communities of putative ammonia-oxidizing archaea (AOA)...

..Recently, cultivation-independent ribosomal RNA gene surveys have indicated a potential importance for archaea in the subsurface ocean...

..Structured RNAs can be detected by comparative genomics, in which homologous sequences are identified and inspected for mutations that conserve RNA secondary structure...

Ammonia-oxidizing archaea (AOA) are thought to be among the most abundant microorganisms on Earth and may significantly impact the global nitrogen and carbon cycles...

..Therefore, a quantitative PCR approach was applied using primers targeting the domains of Bacteria and Archaea, and key functional genes for sulfate reduction (dsrA) and methanogenesis (mcrA)...

..studies and subsequent cultivation efforts have recently demonstrated that microorganisms of the domain archaea are also capable of performing this process...

..We evaluate the relationships between the abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) amoA genes; potential nitrification rates and environmental variables ..

The diversity and spatio-temporal distribution of ammonia-oxidizing Archaea (AOA) and Bacteria (AOB) were investigated along a salinity gradient in sediments of the Westerschelde estuary...

..submersed macrophyte Littorella uniflora, archaeal amoA was 500- to >8,000-fold enriched compared to bacterial amoA, suggesting that the enhanced nitrification activity observed in the rhizosphere was due to ammonia-oxidizing Archaea.

..9% of the codon tables in Archaea. Previously, the content of intron-containing tRNA genes in Archaea was estimated to be approximately 15% of the ..

..This importance reflects these genes' origin as the ancestral nuclear component of the eukaryotic genome...

..Thus, analysis of the glacial metagenome provided insights into the microbial life in frozen habitats on Earth, thereby possibly shedding light onto microbial life in analogous extraterrestrial environments...

..However, mostly in archaea, the short genes encoding tRNAs can be found disrupted, fragmented, with permutations or with non-functional ..

We investigated the diversity, spatial distribution, and abundances of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in sediment samples of different depths collected from a transect with different distances to ..

..Later on, chemotaxonomic and genotypic methods were widely used for a more satisfactory classification. Archaea were first classified as a separate group of prokaryotes in 1977...

The following unusual tRNAs have recently been discovered in the genomes of Archaea and primitive Eukaryota: multiple-intron-containing tRNAs, which have more than one intron; split tRNAs, which are produced from two pieces of RNA ..

Diversity and abundance of ammonia-oxidizing Betaproteobacteria (beta-AOB) and archaea (AOA) were investigated in a New England salt marsh at sites dominated by short or tall Spartina alterniflora (SAS and SAT sites, respectively) or ..

..The majority of the retrieved archaeal amoA sequences exhibited identities of less than 95% to those in the GenBank database. Novel ammonia-oxidizing archaea may exist in the hydrothermal vent environments.

Communities of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in freshwater sediments and those in association with the root system of the macrophyte species Littorella uniflora, Juncus bulbosus, and Myriophyllum alterniflorum were ..

The origin of eukaryotes and their evolutionary relationship with the Archaea is a major biological question and the subject of intense debate...

The ecological characteristics of the deep-sea amoA-encoding archaea (AEA) are largely unsolved...

..Our findings indicate that, although translation initiation is indispensable for all protein-coding genes in the genome of every species, its mechanisms have dynamically changed during evolution...

..This, in combination with its biochemical and genetic tractability, has made Hfx. volcanii a key model organism, not only for the study of halophilicity, but also for archaeal biology in general...

..The host's dependence upon molecular hydrogen produced by the symbiont is put forward as the selective principle that forged the common ancestor of eukaryotic cells...

..This provides evidence that the eocyte prokaryotes are the closest prokaryotic relatives of the eukaryotes...

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We describe a rapid, reproducible, and sensitive method for detection and quantification of archaea in naturally occurring microbial communities...

..in a single run, with multiple samples tagged uniquely by multiplex identifiers, using different primers for Archaea or Bacteria...

..These findings show that the marine subsurface is a distinct microbial habitat and is different from environments studied by metagenomics, especially because of the predominance of uncultivated archaeal groups...

Interspecies electron transfer is a key process in methanogenic and sulphate-reducing environments. Bacteria and archaea that live in syntrophic communities take advantage of the metabolic abilities of their syntrophic partner to ..

..We find that the majority of domain combinations were unique to Archaea, Bacteria, or Eukarya, suggesting most combinations originated after life had diversified...

..sulfate-reducing, and methane-oxidizing Bacteria as well as methanogenic and anaerobic methane-oxidizing Archaea. The presence of these metabolic groups indicates that microbial cycling of sulfur and methane may be the ..

..These observations point to a functional equivalence of the two classes of primases, which seem to have repeatedly displaced each other in various extrachromosomal replicons...

..These results provide a framework for understanding the kinds of organisms that build contemporary stromatolites, their ecology, and their relevance to stromatolites preserved in the geological record...

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..SEM results indicated a considerable loss in the integrity of the sludge granules during the operation, with risk of sludge buoyancy...

..Crenarchaeota clusters were identified in close associated with methanogenic Archaea and both were localised with acetate uptake in biofilm structure.

..open reading frames with homology to characterized P(IB)-type ATPases from the genomes of 188 bacteria and 22 archaea were investigated. Major findings were as follows...

..It contains both RNA and protein subunits and occurs in all three domains of life: namely, Archaea, Bacteria and Eukarya...

..b>Archaea were less abundant than Bacteria, their diversity was lower, and the community was less stratified...

..were affiliated to Actinobacteria, Firmicutes, Proteobacteria and the CFB group while none related to Archaea. Analysis of 16S rRNA gene libraries revealed the presence of species related to Bacteria and Archaea...

..The depth distribution of methanogenic archaea correlated with the sulfate profile and could be explained by electron donor competition with sulfate-reducing ..

..Altogether, these results are consistent with Rh proteins not being the orthologue of Amt proteins but having gained the function for CO2/HCO3- transport, with important roles in systemic pH regulation...

..Remarkably, in several extant prokaryotes both classes of the enzyme coexist, a unique phenomenon that has yet to receive its due attention...

Reverse gyrase, an enzyme of uncertain funtion, is present in all hyperthermophilic archaea and bacteria...

..Hemerythrins, are the non-heme, diiron binding respiratory proteins of brachiopods, priapulids and sipunculans; they are also found in annelids and bacteria, where their functions have not been fully elucidated...

Most methanogenic archaea can reduce CO(2) with H(2) to methane, and it is generally assumed that the reactions and mechanisms of energy conservation that are involved are largely the same in all methanogens...

16S rRNA-based stable isotope probing identified active xylose- and glucose-fermenting Bacteria and active Archaea, including methanogens, in anoxic slurries of material obtained from a moderately acidic, CH(4)-emitting fen...

..Such microbe-based methane production holds promise for producing a clean-burning and efficient form of energy from underutilized hydrocarbon-bearing resources...

..This suggested that the diagnosis of an anaerobic digestion process could be possible by monitoring bacterial community shifts...

The abundance and composition of soil ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) communities under different long-term (17 years) fertilization practices were investigated using real-time polymerase chain ..

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..Comparative genomic and phylogenetic analyses show that homologues of PAB0719 and PAB0760 occur only in a few Archaea, these genes having been acquired via a single horizontal gene transfer from a bacterial donor to the common ..

..FSF complement of the last common ancestor to the trichotomy was more like that of modern eukaryotes than that of archaea and bacteria...

..Our results indicate that there are unique microbial communities that are sustained by active chemosynthetic primary production rather than by photosynthetic production in a shallow hydrothermal system where sunlight is abundant...

..were present in the outer shell of the granule, Firmicutes were found in the middle layer, and aceticlastic Archaea were restricted to the inner layer...

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..In the communities in the lowest sediment layer sampled (22-34 cm), sulfate-reducing bacteria and archaea of the ANME-2 cluster (likely involved in anaerobic methane oxidation) were prevalent, whereas heterotrophic ..

..Full-length 16S rRNA gene sequences of 22 clones, representing the predominant bacteria and archaea, were determined. Most bacterial clones (80%) clustered within the Clostridiaceae...

..In sediments below Beggiatoa mats encircling the center of the HMMV, methanotrophic archaea of the ANME-3 clade dominated the zone of anaerobic methane oxidation...

..mainly into a mixture of methane, CO2 and H2O-a conversion that is carried out by a consortium of bacteria and archaea. Especially in the municipal plants dedicated towards waste treatment, the reactor feed may vary considerably, ..

..In this study, the composition of the Bacteria and Archaea communities was determined by 16S rRNA phylogenetic analyses of clone libraries derived from RNA and DNA ..

..support the monophyly of methanogens, and propose instead that there are two distantly related groups of extant archaea that produce methane, which we have named Class I and Class II...

..Recently, information from completely sequenced genomes of bacteria, archaea, and eukaryotes has revealed the presence of genes that encode homologues of cation/Ca(2+) exchangers in many ..

The initiation factor 5A (IF-5A) of archaea and eukaryotes undergoes an unusual post-translational modification consisting of the transformation of a specific conserved lysine residue into the amino acid hypusine...

Phylogenetic analysis of the Archaea has been mainly established by 16S rRNA sequence comparison. With the accumulation of completely sequenced genomes, it is now possible to test alternative approaches by using large sequence datasets...

..undetected, complex, partially conserved neighborhood consisting of more than 20 genes was discovered in most Archaea (with the exception of Thermoplasma acidophilum and Halobacterium NRC-1) and some bacteria, including the ..

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..proteobacteria, putative sulfide oxidizers of the gamma proteobacteria, Flavobacteria, Planctomycetales, and Archaea. rRNA hybridization analyses also indicated that these groups were present at similar levels in the top layer ..

..The archaea necessarily have higher throughput isoprenoid biosynthesis machinery; as their membrane lipids are based solely ..

..The transcription apparatus in Archaea can be described as a simplified version of its eukaryotic RNA polymerase II (Pol II) counterpart, comprising a ..

..The transcription apparatus in Archaea can be described as a simplified version of its eukaryotic RNA polymerase II (Pol II) counterpart, comprising a ..

..SRI and SRII are sensors for phototaxis in Hatobacterium salinarum and related halophilic archaea. SRI mediates attractant motility responses to green-orange wavelengths used by the ion pumps BR and HR, while ..

..g. the 16S rRNA PhyloChip that detects all known bacteria and archaea. Drs...

..M. smithii, and E. rectale/E. eligens. These studies should provide new approaches for monitoring and manipulating the functions of the microbiota to promote human health. ..

..Successful completion of this project may increase the understanding of how PP1 is regulated in cells, and do so in molecular detail. ..

..Additionally, the SR-I transducer is eubacterial in origin and this novel receptor/transducer combination may reveal a new mechanism of signal transduction. ..

..paradigm might be the ideal one for understanding these diverse mechanisms in the broad sweep of bacteria and archaea because of its inclusion of most known chemotaxis proteins and its similarity to the mechanism used in many ..

..Results from these experiments will support future microbiological studies of the role of this system in chlamydial infection and survival in the host cell. ..

..paradigm might be the ideal one for understanding these diverse mechanisms in the broad sweep of bacteria and archaea because of its inclusion of most known chemotaxis proteins and its similarity to the mechanism used in many ..

..led to general principles of substrate specificity, these are not sufficient to understand synthetases of the archaea domain, which consists of organisms that thrive in extreme environments...

..Broad long-term objectives of this AREA application are to characterize various RNA processing events in Archaea. Both Archaea and Bacteria are prokaryotes; yet Archaea exhibit several molecular features resembling Eukaryotes...

..characterization of a novel tRNA ligase(s) will lead to a better understanding of tRNA processing in humans and archaea. PUBLIC HEALTH RELEVANCE: The unexpected diversity of aminoacyl-tRNA synthesis (processes that maintain the ..

..relationship between the structure and function of archaeal initiator tRNAs and the translational machinery of archaea in general...

..interspaced, short, palindromic repeat (CRISPR) loci, present in the genomes of many eubacteria and nearly all archaea, have been shown to confer adaptive, heritable, sequence-based immunity against phages...

..protein modifiers (SAMP1 and SAMP2) that cluster to the 2-grasp fold superfamily, are highly conserved among archaea and are differentially conjugated to a large number of proteins in the halophilic archaeon Haloferax volcanii...

..Two classes of enzyme systems exist. In eubacteria, all psi are made by a set of site-specific proteins. In archaea and eukarya, psi in tRNA and some sn(o) RNAs are made by specific proteins also, but psi in rRNA and other sn(o)..

..Two classes of enzyme systems exist. In eubacteria, all psi are made by a set of site-specific proteins. In archaea and eukarya, psi in tRNA and some sn(o) RNAs are made by specific proteins also, but psi in rRNA and other sn(o)..

..study of chemotaxis during the past decade is that the well-studied enteric model may not be representative of archaea and eubacteria ("bacteria')...

The Sulfolobus islandicus rod-shaped virus (SIRV) is a fibrous virus that infects thermophilic, acidophilic Archaea found in thermal vents and hot springs around the world...

..This operon is over 26 kb and contains at least 27 genes. We will also examine the mechanism by which both hag and mot transcription and methanol formation on chemotactic stimulation depend on the morphology of the basal body. ..

..understanding of energy-dependent proteolysis in the cell, especially as it relates to the metabolically diverse Archaea which play a major role in global carbon mineralization and the production of greenhouse gases...

Iron-sulfur [Fe-S] proteins are ubiquitous occurring in all life forms from the most primitive bacteria and archaea to the most advanced eucaryotes...

Iron-sulfur [Fe-S] proteins are ubiquitous occurring in all life forms from the most primitive bacteria and archaea to the most advanced eucaryotes...

..A collection of enzymes from primitive to more advanced organisms (Archaea to Eukarya) will be created that will allow us to extract conserved or noel structures and to correlate them with ..

..separate Domains; queuosine is ubiquitous among Bacteria and Eukarya, while archaeosine is only present in the Archaea. The 7-deazapurine structure in general is widespread in biology, where it is found in a variety of natural ..

..paradigm might be the ideal one for understanding these diverse mechanisms in the broad sweep of bacteria and archaea because of its inclusion of most known chemotaxis proteins and its similarity to the mechanism used in many ..

..It is widely distributed in eubacteria and in the Archaea, suggesting that it is a very ancient class of iron transporter...

..rules' of transcription have been delineated in higher eukaryotes, extensive work in lower eukaryotes and archaea have clearly indicated many differences in the mechanics of gene expression...