Table 1 - uploaded by Reinhard Rachel
Content may be subject to copyright.
Source publication
A novel genus of hyperthermophilic, strictly chemolithotrophic archaea, Ignicoccus, has been described recently, with (so far) three isolates in pure culture. Cells were prepared for ultrastructural investigation by cultivation in cellulose capillaries and processing by high-pressure freezing, freeze-substitution and embedding in Epon. Cells prepar...
Similar publications
Ignicoccus is the only archaeal genus known today whose cells possess an outer membrane. According to freeze-etch experiments, it is composed of two leaflets which become separated in the fracture process. Here we show by transmission electron microscopy that the two leaflets can also be visualized in ultrathin sections; they exhibit highly differe...
Citations
... It is thought that these MVs play a key role in the transfer of several signaling molecules between the inner and OM. Of note, ultrastructural analyses have revealed the lack of an S layer in Ignicoccus species [94]. ...
Every single cell can communicate with other cells in a paracrine manner via the production of nano-sized extracellular vesicles. This phenomenon is conserved between prokaryotic and eukaryotic cells. In eukaryotic cells, exosomes (Exos) are the main inter-cellular bioshuttles with the potential to carry different signaling molecules. Likewise, bacteria can produce and release Exo-like particles, namely microvesicles (MVs) into the extracellular matrix. Bacterial MVs function with diverse biological properties and are at the center of attention due to their inherent therapeutic properties. Here, in this review article, the comparable biological properties between the eukaryotic Exos and bacterial MVs were highlighted in terms of biomedical application.
... Some archaea are perfectly capable of generating extracellular protrusions (Rachel et al., 2002;Baker et al., 2006;Marguet et al., 2013). In addition, as we will see below, the inside-out model is perfectly compatible with the hypotheses made regarding the possible nature of the guest. ...
The authors use the mathematical tool of Maccone's lognormal distribution to further factor the Drake equation, which calculates the number of advanced civilizations in the galaxy, from the seven original levels of the Drake equation to 49 levels of overall analysis. The Maccone approach, in fact, supported by the central limit theorem, becomes more reliable the more levels are introduced. The resulting study necessarily draws upon an array of disciplines ranging from astronomy, chemistry and geology to biology, palaeontology and futurology. The final result calculates the number of planetary systems suitable for life in its various stages of development: those which have probably hosted life in the past and those which still host it at its various evolutionary levels. The final evolutionary level is the so-called galactic civilization (often called ETC, or extraterrestrial civilizations). The number of resulting galactic civilizations is divided between static civilizations, which do not move around the galaxy and whose Kardašëv rating is still low (<1.4), of which we find three examples (we ourselves plus, perhaps, two others), and potentially dynamic civilizations, which move around the galaxy and have a sufficiently high Kardašëv rating (≥1.4), of which we find 2000.
... 10 µl of cell suspension was placed on copper grids (400-mesh; Plano, Wetzlar, Germany) coated in-house with a 10 nm carbon film, and the samples were subsequently shadowed with Pt/C (15° angle; CFE 50; Cressington). Freeze-etching was performed as described previously (Rachel et al. 2002). Transmission electron micrographs were imaged using a CM12 transmission electron microscope (FEI) operated at 120 keV and fitted with a slow-scan CCD camera (TEM 0124; TVIPS). ...
A novel interdomain consortium composed of a methanogenic Archaeon and a sulfate-reducing bacterium was isolated from a microbial biofilm in an oil well in Cahuita National Park, Costa Rica. Both organisms can be grown in pure culture or as stable co-culture. The methanogenic cells were non-motile rods producing CH 4 exclusively from H 2 /CO 2. Cells of the sulfate-reducing partner were motile rods forming cell aggregates. They utilized hydrogen, lactate, formate, and pyru-vate as electron donors. Electron acceptors were sulfate, thiosulfate, and sulfite. 16S rRNA sequencing revealed 99% gene sequence similarity of strain CaP3V-M-L2A T to Methanobacterium subterraneum and 98.5% of strain CaP3V-S-L1A T to Desulfomicrobium baculatum. Both strains grew from 20 to 42 °C, pH 5.0-7.5, and 0-4% NaCl. Based on our data, type strains CaP3V-M-L2A T (= DSM 113354 T = JCM 39174 T) and CaP3V-S-L1A T (= DSM 113299 T = JCM 39179 T) represent novel species which we name Methanobacterium cahuitense sp. nov. and Desulfomicrobium aggregans sp. nov.
... In addition, members of the hyperthermophilic order Thermoproteales tend to have a thin rod shape, while others have been reported to assume branched and club-like morphologies. Among the well-studied Crenarchaeota, the members of the Ignicoccus genus are the structurally most striking, having no S-layer, pseudomurein or glycocalyx, but instead possessing a double membrane 17,18 . The DNA and cytoplasm of these species are contained within an inner compartment from which membrane "tubes" emerge that connect to the overlying membrane in a manner that remains poorly defined 19 . ...
The past decade has revealed the diversity and ubiquity of archaea in nature, with a growing number of studies highlighting their importance in ecology, biotechnology and even human health. Myriad lineages have been discovered, which expanded the phylogenetic breadth of archaea and revealed their central role in the evolutionary origins of eukaryotes. These discoveries, coupled with advances that enable the culturing and live imaging of archaeal cells under extreme environments, have underpinned a better understanding of their biology. In this Review we focus on the shape, internal organization and surface structures that are characteristic of archaeal cells as well as membrane remodelling, cell growth and division. We also highlight some of the technical challenges faced and discuss how new and improved technologies will help address many of the key unanswered questions.
... Samples on grids were then either negatively stained for 1 min with 2% uranyl acetate (w/v) or shadowed with Pt/C (15° angle; CFE 50; Cressington). Freeze etching was carried out as described previously (Rachel et al. 2002). ...
A novel methanogenic strain, CaP3V-MF-L2AT, was isolated from an exploratory oil well from Cahuita National Park, Costa Rica. The cells were irregular cocci, 0.8–1.8 μm in diameter, stained Gram-negative and were motile. The strain utilized H2/CO2, formate and the primary and secondary alcohols 1-propanol and 2-propanol for methanogenesis, but not acetate, methanol, ethanol, 1-butanol or 2-butanol. Acetate was required as carbon source. The novel isolate grew at 25–40 °C, pH 6.0–7.5 and 0–2.5% (w/v) NaCl. 16S rRNA gene sequence analysis revealed that the strain is affiliated to the genus Methanofollis. It shows 98.8% sequence similarity to its closest relative Methanofollis ethanolicus. The G + C content is 60.1 mol%. Based on the data presented here type strain CaP3V-MF-L2AT (= DSM 113321T = JCM 39176T) represents a novel species, Methanofollis propanolicus sp. nov.
... While FISH-TAMB provides the first step towards identifying rare, uncultured taxa as active players or keystone species in the deep biosphere and other ecosystems, continued development of FISH-TAMB is necessary to understand the limits of its application in other systems (e.g., temperature, salinity, and pH extremes; sensitivity to spore forming, gram-positive bacteria; double-membraned archaea [49]; the detection limit for transcript copy numbers; optimal, toxic, and lethal dosages respective to microbial lineages). Then, FISH-TAMB can truly enable us to characterize the genomes and physiologies of the labeled cells and subsequently to evaluate or perhaps even quantify their ecological importance. ...
Keystone species or ecological engineers are vital to the health of an ecosystem; however, often, their low abundance or biomass present challenges for their discovery, identification, visualization and selection. We report the development of fluorescent in situ hybridization of transcript-annealing molecular beacons (FISH-TAMB), a fixation-free protocol that is applicable to archaea and bacteria. The FISH-TAMB method differs from existing FISH methods by the absence of fixatives or surfactants in buffers, the fast hybridization time of as short as 15 min at target cells’ growth temperature, and the omission of washing steps. Polyarginine cell-penetrating peptides are employed to deliver molecular beacons (MBs) across prokaryotic cell walls and membranes, fluorescently labeling cells when MBs hybridize to target mRNA sequences. Here, the detailed protocol of the preparation and application of FISH-TAMB is presented. To demonstrate FISH-TAMB’s ability to label intracellular mRNA targets, differentiate transcriptional states, detect active and rare taxa, and keep cell viability, labeling experiments were performed that targeted the messenger RNA (mRNA) of methyl-coenzyme M reductase A (mcrA) expressed in (1) Escherichia coli containing a plasmid with a partial mcrA gene of the methanogen Methanosarcina barkeri (E. coli mcrA⁺); (2) M. barkeri; and (3) an anaerobic methanotrophic (ANME) enrichment from a deep continental borehole. Although FISH-TAMB was initially envisioned for mRNA of any functional gene of interest without a requirement of prior knowledge of 16S ribosomal RNA (rRNA)-based taxonomy, FISH-TAMB has the potential for multiplexing and going beyond mRNA and thus is a versatile addition to the molecular ecologist’s toolkit, with potentially widespread application in the field of environmental microbiology.
... 18 and 32) and encapsulates ATP conservation (14), acetyl-CoA synthesis (22), CO 2 fixation via a pathway consisting of 14 reactions (Fig. 1A), and potentially other metabolic pathways. It also contains a tubular network and a filamentous matrix presumably functioning as a cytoskeleton within this compartment (13,21,33). This is unprecedented in the microbial world and demonstrates that the I. hospitalis peripheric CC is strikingly different from other known cellular structures, including the periplasm of gram-negative bacteria. ...
... Desulfurococcales that possess only one membrane but also in the I. islandicus protein (SI Appendix, Fig. S6). As I. islandicus has the same two-membrane cellular structure as I. hospitalis (33), it seems unlikely that this putative signal peptide is essential for the enzyme trafficking. The incapability of the used signal peptide prediction tools to predict signal sequences in the proteins studied here or investigated in the past (Ihomp, ATPase) might be due to exceptional signal peptide pattern or the usage of an unknown secretion system. ...
Significance
In a typical prokaryotic cell, hundreds of metabolites are present and interconverted simultaneously, some serving as allosteric regulators for unrelated reactions or accidental substrates for promiscuous enzymes or being downright reactive and toxic. Although certain spatial separation of prokaryotic cells has long been proposed, only few examples are known. In many bacteria, the key carboxylase of the Calvin–Benson cycle is located in carboxysomes to concentrate CO 2 and deplete O 2 , while other enzymes of the cycle are in the cytoplasm. The archaeon Ignicoccus hospitalis exhibits a two-membrane structure with an energized outer membrane. Here, we show that CO 2 fixation in this organism takes place in a peripheric cytoplasmic compartment, being separated from information processing occurring in the central cytoplasmic compartment.
... Ce type de structure pariétale est retrouvé chez Ignicoccus (Crenarchaeota) et chez certains ARMAN (« Archaeal Richmond Mine acidophilic nanoorganisms »), des archées affiliées au phylum des Euryarchaeota (Rachel et al., 2002;Comolli et al., 2009). Les observations au microscope électronique à transmission de la souche Ca. 'Mp. ...
Les Methanomassiliicoccales (MX) sont des archées méthanogènes hydrogénotrophes méthyle-dépendantes (MHMD) réparties en deux clusters phylogénétiques reflétant leurs adaptations aux écosystèmes digestifs (host-associated) ou non-digestifs (free-living). Nos connaissances les concernant se limitent surtout à des études centrées sur des milieux digestifs. De nombreuses questions demeurent sur le mode de vie et les adaptations des représentants du cluster free-living dans des habitats non-digestifs. Cette thèse visait à améliorer nos connaissances sur leur biologie en étudiant leur distribution, leur diversité, leur abondance et potentiels métaboliques et physiologiques dans des habitats non-digestifs. Des analyses de diversité et d’abondance sur un panel d’échantillons de natures et d’origines variées ont permis de mettre en évidence la faible abondance et diversité taxonomique des MX dans les échantillons criblés. Des approches culturales ont permis d’obtenir un enrichissement significatif en MX à partir d'un microcosme inoculé avec des sédiments d'eau douce. Une analyse en métagénomique de cet enrichissement a permis la reconstruction d'un metagenome assembled genome (MXMAG1) de grande qualité correspondant à une nouvelle espèce candidate affiliée au cluster free-living. Son analyse a révélé la présence des gènes impliqués dans la réponse et la régulation de stress environnementaux (ex : pH, métaux lourds) et ceux impliqués dans la MHMD. Enfin, des analyses en réseaux de cooccurrence basées sur des données de diversité ont révélé la cooccurrence des MX avec des taxa bactériens inféodés aux tractus digestifs et connus pour entretenir des relations syntrophiques avec des archées méthanogènes.
... While FISH-TAMB provides the rst step towards identifying rare, uncultured taxa as active players or keystone species in the deep biosphere and other ecosystems, continued development of FISH-TAMB is necessary to understand the limits of its application in other systems (e.g. temperature, salinity, and pH extremes; sensitivity to spore forming, gram-positive bacteria; double-membraned archaea [48]; the detection limit for transcript copy numbers; optimal, toxic and lethal dosages respective to microbial lineages, etc.). Then, FISH-TAMB can truly enable us to characterize the genomes and physiologies of the labeled cells, and subsequently to evaluate or perhaps even quantify their ecological importance. ...
Keystone species or ecological engineers are vital to the health of an ecosystem, however, often their low abundance or biomass present challenges for their discovery, identification, visualization and selection. We report the development of fluorescent in situ hybridization of transcript-annealing molecular beacons (FISH-TAMB), a fixation-free protocol that is applicable to archaea and bacteria. The FISH-TAMB method differs from existing FISH methods by the absence of fixatives or surfactants in buffers, and the fast hybridization time of as short as 15 minutes at target cells’ growth temperature. Polyarginine cell-penetrating peptides are employed to deliver molecular beacons (MBs) across prokaryotic cell walls and membranes, fluorescently labeling cells when MBs hybridize to target mRNA sequences. Here, the detailed protocol of the preparation and application of FISH-TAMB is presented. To demonstrate FISH-TAMB’s ability to label intracellular mRNA targets, differentiate transcriptional states, detect active and rare taxa, and keep cell viability, labeling experiments were performed that targeted the messenger RNA (mRNA) of methyl-coenzyme M reductase A ( mcr A) expressed in 1) Escherichia coli containing a plasmid with a partial mcr A gene of the methanogen Methanosarcina barkeri ( E. coli mcr A + ); 2) M. barkeri ; and 3) an anaerobic methanotrophic (ANME) enrichment from a deep continental borehole. Although FISH-TAMB was initially envisioned for mRNA of any functional gene of interest without a requirement of prior knowledge of 16S ribosomal RNA (rRNA)-based taxonomy, FISH-TAMB has the potential for multiplexing and going beyond mRNA, thus is a versatile addition to the molecular ecologist’s toolkit, with potentially widespread application in the field of environmental microbiology.
... A 2 µL aliquot of the concentrated cell suspension was loaded onto a gold carrier and frozen rapidly in liquid nitrogen. The sample was cut with a cold knife (≤ −185 • C), etched for 4 min (−97 • C; pressure ≤ 1.3105 Pa) in a CFE-50 freeze-etch unit (Cressington, Watford, United Kingdom), shadowed (1 nm Pt/C, 45 • C; 10 nm C, 90 • C), and cleaned in fresh 70% H 2 SO 4 for 16 h [23]. Air-dried sample surface replicas were examined using a FEI Morgagni 268(D) transmission electron microscope at 80 kV. ...
Membrane proteins are targeted not only to specific membranes in the cell architecture, but also to distinct lateral microdomains within individual membranes to properly execute their biological functions. Yeast tetraspan protein Nce102 has been shown to migrate between such microdomains within the plasma membrane in response to an acute drop in sphingolipid levels. Combining microscopy and biochemistry methods, we show that upon gradual ageing of a yeast culture, when sphingolipid demand increases, Nce102 migrates from the plasma membrane to the vacuole. Instead of being targeted for degradation it localizes to V-ATPase-poor, i.e., ergosterol-enriched, domains of the vacuolar membrane, analogous to its plasma membrane localization. We discovered that, together with its homologue Fhn1, Nce102 modulates vacuolar morphology, dynamics, and physiology. Specifically, the fusing of vacuoles, accompanying a switch of fermenting yeast culture to respiration, is retarded in the strain missing both proteins. Furthermore, the absence of either causes an enlargement of ergosterol-rich vacuolar membrane domains, while the vacuoles themselves become smaller. Our results clearly show decreased stability of the V-ATPase in the absence of either Nce102 or Fhn1, a possible result of the disruption of normal microdomain morphology of the vacuolar membrane. Therefore, the functionality of the vacuole as a whole might be compromised in these cells.
