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PubMed2005

Phylogenetic diversity and ecology of environmental Archaea.

On the basis of culture studies, Archaea were thought to be synonymous with extreme environments. However, the large numbers of environmental rRNA gene sequences currently flooding into databases such as GenBank show that these organisms are present in almost all environments examined to date. Large sequence databases and new fast phylogenetic software allow more precise determination of the archaeal phylogenetic tree, but also indicate that our knowledge of archaeal diversity is incomplete. Although it is apparent that Archaea can be found in all environments, the chemistry of their ecological context is mostly unknown.

Archaea↗
PubMed2005

Protein transport in Archaea: Sec and twin arginine translocation pathways.

The transport of proteins into and across hydrophobic membranes is an essential cellular process. The majority of proteins that are translocated in an unfolded conformation traverse the membrane by way of the universally conserved Sec pathway, whereas the twin arginine translocation pathway is responsible for the transport of folded proteins across the membrane. Structural, biochemical and genetic analyses of these processes in Archaea have revealed unique archaeal features, and have also provided a better understanding of these pathways in organisms of all domains. Further study of these pathways in Archaea might elucidate fundamental principles involved in each type of transport and could help determine their relative costs and benefits as well as evolutionary adaptations in protein secretion strategies.

Amino Acid Sequence↗
PubMed2005

An update and optimisation of oligonucleotide probes targeting methanogenic Archaea for use in fluorescence in situ hybridisation (FISH).

Fluorescence in situ hybridisation (FISH) is a common and popular method used to investigate microbial populations in natural and engineered environments. DNA oligonucleotide probes require accurate determination of the optimal experimental conditions for their use in FISH. Oligonucleotides targeting the rRNA of methanogenic Archaea at various taxonomic levels have previously been published, although when applied in FISH, no optimisation data has been presented. In this study, 3000 Euryarchaeota 16S rRNA gene sequences were phylogenetically analysed and previously published oligonucleotides were evaluated for target group accuracy. Where necessary, modifications were introduced or new probes were designed. The updated set of probes was optimised for use in FISH for a more accurate detection of methanogenic Archaea.

Archaea↗
PubMed2006

Community structure of Archaea and Bacteria in a profundal lake sediment Lake Kinneret (Israel).

The microbial community structure of an anoxic profundal lake sediment, i.e., subtropical Lake Kinneret, was analysed with respect to its composition by culture-independent molecular methods including terminal restriction fragment length polymorphism (T-RFLP) analysis, comparative sequence analysis, and quantitative real-time PCR. In particular we were interested in the structure, species composition, and relative abundance of the overall microbial community in the methanogenic sediment layer (0-10 cm depth). Pairwise comparison of archaeal and bacterial 16S rRNA gene T-RFLP profiles obtained from three independent samplings indicated stability of the microbial community. The numbers of Archaea and Bacteria, quantified by real-time PCR, amounted to about 10(8) and 10(10) 16S rRNA gene copies cm(-3) sediment, respectively, suggesting that Archaea may account for only a minor fraction (approximately 1%) of the total prokaryotic community. Hydrogenotrophic Methanomicrobiales and acetoclastic Methanosaeta spp. dominated T-RFLP profiles of the archaeal community. T-RFLP profiles of the bacterial community were dominated by Deltaproteobacteria, sulphate reducers and syntrophs in particular. The second most abundant group was assigned to the Bacteroidetes-Chlorobi-group. Only one bacterial group, which was affiliated with halorespiring bacteria of subphylum II of the Chloroflexi, showed variation in abundance within the sediment samples investigated. Our study gives a comprehensive insight into the structure of the bacterial and archaeal community of a profundal lake sediment, indicating that sulphate reducers, syntrophs, bacteroidetes, halorespirers and methanogens are of particular importance in Lake Kinneret sediment.

Archaea↗
PubMed2005

Archaea with square cells.

Two groups of microbiologists have independently isolated 'Walsby's square bacterium' from salt crystallizer ponds; its growth depends on pyruvate. Genetic analysis shows that the squares, discovered 25 years ago on the Sinai Peninsula, are archaea rather than bacteria. These transparent tile-like cells might have been dismissed as surface artefacts of salt crystals but for their gas vesicles--structures peculiar to prokaryotic organisms. Paradoxically, the square archaea are the dominant microorganisms in some hypersaline environments and might be globally important.

Archaea↗
PubMed2005

Taxonomic utility of a phylogenetic analysis of phosphoglycerate kinase proteins of Archaea, Bacteria, and Eukaryota: insights by Bayesian analyses.

We studied 131 protein sequences of the essentially ubiquitous glycolytic enzyme 3-phosphoglycerate kinase (3-PGK) by Bayesian analyses in three Domains: 15 Archaea, 83 Bacteria, and 33 Eukaryota. The posterior distribution of phylogenetic trees developed were based on a uniform prior, the WAG model of protein evolution, Metropolis-Hastings sampling in a Markov chain Monte Carlo analysis, and a package of diagnostics to critically evaluate the validity of the analyses. The 15 Archaea separated with high posterior probability. The archaean Phyla Euryarchaeota and the apparently Euryarchaeota derived Crenarchaeota were monophyletic. The 33 Eukaryota separated into two main groups: the non-chlorophyllous forms with coherent sub-groupings of Euglenozoa, Alveolata, Fungi, and Metazoa and all the chlorophyllous species studied: the Plantae (Viridaeplantae), chlorophyllous Stramenopiles, and the chlorophyllous Bacteria. This association supports other opinions concerning the related lineage of cyanobacteria and the Plantae. The 3-PGK sequences from 83 Bacteria in almost every instance associated by their recognized taxal group: alpha-, beta-, gamma-, epsilon-proteobacteria, Chlamydia, Actinobacteridae, and Firmicutes. Firmicutes sequences were subdivided into three apparently monophyletic groups: the anaerobic Clostridia, the spore-forming Bacillales and a group containing the Mollicutes, Lactobacillales and non-spore-forming Bacillales. The 3-PGK-gene tree assemblage was notable both for its pervasive clustering in three Domains according to recognized taxonomic groupings of Class, Order, Family, and Genus. The 3-PGK enzyme or 3-PGK-like activity may have played a central role in the metabolism of the Universal Ancestor.

Archaea↗
PubMed2007

Respiratory transformation of nitrous oxide (N2O) to dinitrogen by Bacteria and Archaea.

N2O is a potent greenhouse gas and stratospheric reactant that has been steadily on the rise since the beginning of industrialization. It is an obligatory inorganic metabolite of denitrifying bacteria, and some production of N2O is also found in nitrifying and methanotrophic bacteria. We focus this review on the respiratory aspect of N2O transformation catalysed by the multicopper enzyme nitrous oxide reductase (N2OR) that provides the bacterial cell with an electron sink for anaerobic growth. Two types of Cu centres discovered in N2OR were both novel structures among the Cu proteins: the mixed-valent dinuclear Cu(A) species at the electron entry site of the enzyme, and the tetranuclear Cu(Z) centre as the first catalytically active Cu-sulfur complex known. Several accessory proteins function as Cu chaperone and ABC transporter systems for the biogenesis of the catalytic centre. We describe here the paradigm of Z-type N2OR, whose characteristics have been studied in most detail in the genera Pseudomonas and Paracoccus. Sequenced bacterial genomes now provide an invaluable additional source of information. New strains harbouring nos genes and capability of N2O utilization are being uncovered. This reveals previously unknown relationships and allows pattern recognition and predictions. The core nos genes, nosZDFYL, share a common phylogeny. Most principal taxonomic lineages follow the same biochemical and genetic pattern and share the Z-type enzyme. A modified N2OR is found in Wolinella succinogenes, and circumstantial evidence also indicates for certain Archaea another type of N2OR. The current picture supports the view of evolution of N2O respiration prior to the separation of the domains Bacteria and Archaea. Lateral nos gene transfer from an epsilon-proteobacterium as donor is suggested for Magnetospirillum magnetotacticum and Dechloromonas aromatica. In a few cases, nos gene clusters are plasmid borne. Inorganic N2O metabolism is associated with a diversity of physiological traits and biochemically challenging metabolic modes or habitats, including halorespiration, diazotrophy, symbiosis, pathogenicity, psychrophily, thermophily, extreme halophily and the marine habitat down to the greatest depth. Components for N2O respiration cover topologically the periplasm and the inner and outer membranes. The Sec and Tat translocons share the task of exporting Nos components to their functional sites. Electron donation to N2OR follows pathways with modifications depending on the host organism. A short chronology of the field is also presented.

Amino Acid Sequence↗
PubMed2005

Methyl-coenzyme M reductase genes: unique functional markers for methanogenic and anaerobic methane-oxidizing Archaea.

In many anoxic environments, methanogenesis is the predominant terminal electron accepting process involved in the mineralization of organic matter, which is catalyzed by methanogenic Archaea. These organisms represent a unique but phylogenetically diverse guild of prokaryotes, which can be conveniently tracked in the environment by targeting the mcrA gene as a functional marker. This gene encodes the alpha subunit of the methyl-coenzyme M reductase (MCR), which catalyzes the last step in methanogenesis and is present in all methanogens. Cultivation-independent analysis of methanogenic communities involves the polymerase chain reaction (PCR) amplification of the mcrA gene from extracted community DNA, comparative analysis of mcrA clone libraries, or PCR-based fingerprinting analysis by terminal restriction fragment polymorphism analysis (T-RFLP). It has also been suggested that anaerobic methane-oxidizing Archaea possess MCR, which facilitates detection of this novel group of "reverse methanogens" as well using the mcrA gene as a functional marker.

Archaea↗
PubMed1999

Occurrence of D-amino acids in a few archaea and dehydrogenase activities in hyperthermophile Pyrobaculum islandicum.

The contents of D-enantiomers of serine, alanine, proline, glutamate (glutamine) and aspartate (asparagine) were examined in the membrane fractions, soluble proteins and free amino acids from some species of archaea, Pyrobaculum islandicum, Methanosarcina barkeri and Halobacterium salinarium. Around 2% (D/D+L) of D-aspartate was found in the membrane fractions. In the soluble proteins, the D-amino acid content was higher in P. islandicum than that in the other archaeal cells: the concentrations in P. islandicum were 3 and 4% for D-serine and D-aspartate, respectively. High concentrations of free D-amino acids were found in P. islandicum and H. salinarium; the concentrations of D-serine (12-13%), D-aspartate (4-7%) and D-proline (3-4%) were higher than those of D-alanine and D-glutamate. This result showed a resemblance between these archaea and not bacterial, but eukaryotic cells. The presence of D-amino acids was confirmed by their digestion with D-amino acid oxidase and D-aspartate oxidase. The occurrence of D-amino acids was also confirmed by the presence of activities catalyzing catabolism of D-amino acids in the P. islandicum homogenate, as measured by 2-oxo acid formation. The catalytic activities oxidizing D-alanine, D-aspartate and D-serine at 90 degrees C were considerably high. Under anaerobic conditions, dehydrogenase activities of the homogenate were 69, 84 and 30% of the above oxidase activities toward D-alanine, D-aspartate and D-serine, respectively. Comparable or higher dehydrogenase activities were also detected with these D-amino acids as substrate by the reduction of 2, 6-dichlorophenolindophenol. No D-amino acid oxidase activity was detected in the homogenates of M. barkeri and H. salinarium.

Amino Acids↗
PubMed2001

Development of respirometry methods to assess the microbial activity of thermophilic bioleaching archaea.

Respirometry methods have been used for many years to assess the microbial activity of mainly heterotrophic bacteria. Using this technique, the consumption of oxygen and evolution of carbon dioxide for heterotrophic carbon catabolism can be used to assess microbial activity. In the case of autotrophic bioleaching bacteria, carbon dioxide is used as a carbon source resulting in the consumption of both oxygen and carbon dioxide. The use of such respirometry techniques at high temperatures (up to 80 degrees C) for the investigation of bioleaching Archaea, however, poses particular difficulties. At these elevated temperatures, the solubility of oxygen into the liquid phase is particularly poor. This work details specific methods by which high temperature constraints are overcome while monitoring the activity of thermophilic Archaea using a Micro-Oxymax respirometer (Columbus Instruments). The use of elevated headspace oxygen concentrations, in order to overcome low oxygen solubility, is demonstrated as well as the effect of such elevated oxygen concentrations on microbial oxygen consumption rates. The relative rates of oxygen and carbon dioxide consumption are also illustrated during the oxidation of a chalcopyrite concentrate. In addition, this paper details generic methods by which respirometry data can be used to quantify inhibitory effects of a compound such as Na(2)SO(4). The further use of such data in predicting minimum hydraulic reactor retention times for continuous culture bioleaching reactors, as a function of concentration of potentially inhibitory compounds, is also demonstrated.

Archaea↗
PubMed1995

Transcription: new insights from studies on Archaea.

Molecular-genetic analyses have revealed that the Archaea (archaebacteria) are phylogenetically distinct from both eukaryotes and eubacteria. Archaea lack nuclei and resemble eubacteria in morphology and genomic organization, but their molecular design shares many features with eukaryotes. Here, we review recent work that indicates that the archaeal transcriptional machinery is strikingly similar to the RNA polymerase I, II, and III systems of eukaryotic cell nuclei. These findings provide important insights into the evolution of the transcriptional apparatus.

Archaea↗
PubMed2003

Evolutionary insights from studies on viruses of hyperthermophilic archaea.

The morphological diversity of viruses which parasitize hyperthermophilic archaea thriving at temperatures > or = 80 degrees C appears to exceed that of viruses of prokaryotes living at lower temperatures. Based on assumptions of the existence of viruses in the prebiotic phase of evolution and hot origins of cellular life, we suggest that this remarkable diversity could have its source in ancestral diversity of viral morphotypes in hot environments. Attempts are made to trace evolutionary relationships of viruses of hyperthermophilic archaea with other viruses.

Archaea↗
PubMed2003

Viruses of hyperthermophilic Archaea.

The viruses of Archaea are likely to be useful tools for studying host evolution, host biochemical pathways, and as tools for the biotechnology industry. Many of the viruses isolated from Archaea show distinct morphologies and genes. The euryarchaeal viruses show morphologies similar to the head-and-tail phage isolated from Bacteria; however, sequence analysis of viral genomes from Crenarchaea shows little or no similarity to previously isolated viruses. Because viruses adapt to host organism characteristics, viruses may lead to important discoveries in archaeal biochemistry, genetics, and evolution.

Archaea↗
PubMed1994

Evolution. Archaea and eukaryotes versus bacteria?

The recent discovery of homologs of the eukaryotic transcription factor TATA-binding protein in archaea has been taken as support for the view that archaea and eukaryotes have a close phylogenetic relationship.

Archaea↗
PubMed2001

The signal recognition particle of Archaea.

It is becoming increasingly clear that similarities exist in the manner in which extracytoplasmic proteins are targeted to complexes responsible for translocating these proteins across membranes in each of the three domains of life. In Eukarya and Bacteria, the signal recognition particle (SRP) directs nascent polypeptides to membrane-embedded translocation sites. In Archaea, the SRP protein targeting pathway apparently represents an intermediate between the bacterial and eukaryal systems. Understanding the archaeal SRP pathway could therefore reveal universal aspects of targeting not detected in current comparisons of the eukaryal and bacterial systems while possibly identifying aspects of the process either not previously reported or unique to Archaea.

Amino Acid Sequence↗
PubMed1999

Gene transfer systems for the Archaea.

The recent focus on exobiology and the potential for life in extreme environments has generated a great deal of interest in the Archaea because of their adaptation to extremes of temperature, salinity and anaerobicity. Recent advances in the development of genetic transfer systems for the Archaea provide the first glimpse of their genetic mechanisms and have the potential to serve as powerful tools for studying their unique adaptive strategies.

Adaptation, Physiological↗
PubMed2006

Archaea predominate among ammonia-oxidizing prokaryotes in soils.

Ammonia oxidation is the first step in nitrification, a key process in the global nitrogen cycle that results in the formation of nitrate through microbial activity. The increase in nitrate availability in soils is important for plant nutrition, but it also has considerable impact on groundwater pollution owing to leaching. Here we show that archaeal ammonia oxidizers are more abundant in soils than their well-known bacterial counterparts. We investigated the abundance of the gene encoding a subunit of the key enzyme ammonia monooxygenase (amoA) in 12 pristine and agricultural soils of three climatic zones. amoA gene copies of Crenarchaeota (Archaea) were up to 3,000-fold more abundant than bacterial amoA genes. High amounts of crenarchaeota-specific lipids, including crenarchaeol, correlated with the abundance of archaeal amoA gene copies. Furthermore, reverse transcription quantitative PCR studies and complementary DNA analysis using novel cloning-independent pyrosequencing technology demonstrated the activity of the archaea in situ and supported the numerical dominance of archaeal over bacterial ammonia oxidizers. Our results indicate that crenarchaeota may be the most abundant ammonia-oxidizing organisms in soil ecosystems on Earth.

Ammonia↗
PubMed2005

Genomic studies of uncultivated archaea.

Archaea represent a considerable fraction of the prokaryotic world in marine and terrestrial ecosystems, indicating that organisms from this domain might have a large impact on global energy cycles. However, many novel archaeal lineages that have been detected by molecular phylogenetic approaches have remained elusive because no laboratory-cultivated strains are available. Environmental genomic analyses have recently provided clues about the potential metabolic strategies of several of the uncultivated and abundant archaeal species, including non-thermophilic terrestrial and marine crenarchaeota and methanotrophic euryarchaeota. These initial studies of natural archaeal populations also revealed an unexpected degree of genomic variation that indicates considerable heterogeneity among archaeal strains. Here, we review genomic studies of uncultivated archaea within a framework of the phylogenetic diversity and ecological distribution of this domain.

Animals↗