Automatic selection of representative proteins for bacterial phylogeny

The utilization of an unconventional approach to introduce basic bacteriology in a medical school bridge program

Bacteria form an intense portion of reading and learning for students enrolled in microbiology education. As a part of the foundational course outline of bacteriology, bacterial classification is a significant topic of discussion. The purpose of our study was to analyze whether bacterial classification can be taught with a phylogenetic tree approach that might be more engaging and beneficial to student learners of microbiology. This methodology is unique compared to the conventional approach applied in introductory lectures of bacteriology that relies on morphology and Gram-staining to classify bacteria. The participants of this study were students enrolled in a two-semester medical school bridge program that offers a Master's degree in Pre-clinical Sciences. We presented bacterial origin and classification in the light of evolution and used a phylogenetic tree to signify clinically relevant groups of bacteria. Students were also taught the traditional bacterial classification using Gram stains and morphology. Both methods of classification were delivered in a didactic classroom session considering equal time spent and utilizing the same format. An online survey was distributed to the students after the session to collect their feedback. The results from the survey showed that 74% of participants would prefer learning bacterial classification using a combined approach that includes both Gram-staining and morphology as well as the phylogenetic tree. When asked if the study of bacterial classification through an evolutionary tree diagram is a clear and concise way of understanding bacteria, 79% of the students either agreed or strongly agreed with this statement. Interestingly, the alternative phylogenetic tree approach was considered more engaging and regarded as a means to expand the clinical knowledge of bacteria by 78% and 71% of the students, respectively. Overall, our study strongly supports the use of tree-based classification as an additional method to improve the learning of medically important groups of bacteria at varying levels of education.

Transcription termination and antitermination of bacterial CRISPR arrays

A hallmark of CRISPR-Cas immunity systems is the CRISPR array, a genomic locus consisting of short, repeated sequences ('repeats') interspersed with short, variable sequences ('spacers'). CRISPR arrays are transcribed and processed into individual CRISPR RNAs that each include a single spacer, and direct Cas proteins to complementary sequences in invading nucleic acid. Most bacterial CRISPR array transcripts are unusually long for untranslated RNA, suggesting the existence of mechanisms to prevent premature transcription termination by Rho, a conserved bacterial transcription termination factor that rapidly terminates untranslated RNA. We show that Rho can prematurely terminate transcription of bacterial CRISPR arrays, and we identify a widespread antitermination mechanism that antagonizes Rho to facilitate complete transcription of CRISPR arrays. Thus, our data highlight the importance of transcription termination and antitermination in the evolution of bacterial CRISPR-Cas systems.

Distribution of RecBCD and AddAB recombination-associated genes among bacteria in 33 phyla

Homologous recombination plays key roles in fundamental processes such as recovery from DNA damage and in bacterial horizontal gene transfer, yet there are still open questions about the distribution of recognized components of recombination machinery among bacteria and archaea. RecBCD helicase-nuclease plays a central role in recombination among Gammaproteobacteria like Escherichia coli; while bacteria in other phyla, like the Firmicute Bacillus subtilis, use the related AddAB complex. The activity of at least some of these complexes is controlled by short DNA sequences called crossover hotspot instigator (Chi) sites. When RecBCD or AddAB complexes encounter an autologous Chi site during unwinding, they introduce a nick such that ssDNA with a free end is available to invade another duplex. If homologous DNA is present, RecA-dependent homologous recombination is promoted; if not (or if no autologous Chi site is present) the RecBCD/AddAB complex eventually degrades the DNA. We examined the distribution of recBCD and addAB genes among bacteria, and sought ways to distinguish them unambiguously. We examined bacterial species among 33 phyla, finding some unexpected distribution patterns. RecBCD and addAB are less conserved than recA, with the orthologous recB and addA genes more conserved than the recC or addB genes. We were able to classify RecB vs. AddA and RecC vs. AddB in some bacteria where this had not previously been done. We used logo analysis to identify sequence segments that are conserved, but differ between the RecBC and AddAB proteins, to help future differentiation between members of these two families.

Role of microbial diversity for sustainable pyrite oxidation control in acid and metalliferous drainage prevention

Acid and metalliferous drainage (AMD) remains a challenging issue for the mining sector. AMD management strategies have attempted to shift from treatment of acid leachates post-generation to more sustainable at-source prevention. Here, the efficacy of microbial-geochemical at-source control approach was investigated over a period of 84 weeks. Diverse microbial communities were stimulated using organic carbon amendment in a simulated silicate-containing sulfidic mine waste rock environment. Mineral waste in the unamended leach system generated AMD quickly and throughout the study, with known lithotrophic iron- and sulfur-oxidising microbes dominating column communities. The organic-amended mineral waste column showed suppressed metal dissolution and AMD generation. Molecular DNA-based next generation sequencing confirmed a less diverse lithotrophic community in the acid-producing control, with a more diverse microbial community under organic amendment comprising organotrophic iron/sulfur-reducers, autotrophs, hydrogenotrophs and heterotrophs. Time-series multivariate statistical analyses displayed distinct ecological patterns in microbial diversity between AMD- and non-AMD-environments. Focused ion beam-TEM micrographs and elemental mapping showed that silicate-stabilised passivation layers were successfully established across pyrite surfaces in organic-amended treatments, with these layers absent in unamended controls. Organic amendment and resulting increases in microbial abundance and diversity played an important role in sustaining these passivating layers in the long-term.

Persistent Core Populations Shape the Microbiome Throughout the Water Column in the North Pacific Subtropical Gyre

Marine microbial communities are responsible for many important ecosystem processes in the oceans. Their variability across time and depths is well recognized, but mostly at a coarse-grained taxonomic resolution. To gain a deeper perspective on ecological patterns of bacterioplankton diversity in the North Pacific Subtropical Gyre, we characterized bacterioplankton communities throughout the water column at a fine-grained taxonomic level with a focus on temporally persistent (core) populations. Considerable intra-clade microdiversity was evident in virtually every microbial clade examined. While some of the most abundant populations comprised only a small fraction of the intra-clade microdiversity, they formed a temporally persistent core within a more diverse array of less abundant ephemeral populations. The depth-stratified population structure within many phylogenetically disparate clades suggested that ecotypic variation was the rule among most planktonic bacterial and archaeal lineages. Our results suggested that the abundant, persistent core populations comprised the bulk of the biomass within any given clade. As such, we postulate that these core populations are largely responsible for microbially driven ecosystem processes, and so represent ideal targets for elucidating key microbial processes in the open-ocean water column.

Geological and Geochemical Constraints on the Origin and Evolution of Life

The traditional tree of life from molecular biology with last universal common ancestor (LUCA) branching into bacteria and archaea (though fuzzy) is likely formally valid enough to be a basis for discussion of geological processes on the early Earth. Biologists infer likely properties of nodal organisms within the tree and, hence, the environment they inhabited. Geologists both vet tenuous trees and putative origin of life scenarios for geological and ecological reasonability and conversely infer geological information from trees. The latter approach is valuable as geologists have only weakly constrained the time when the Earth became habitable and the later time when life actually existed to the long interval between ∼4.5 and ∼3.85 Ga where no intact surface rocks are known. With regard to vetting, origin and early evolution hypotheses from molecular biology have recently centered on serpentinite settings in marine and alternatively land settings that are exposed to ultraviolet sunlight. The existence of these niches on the Hadean Earth is virtually certain. With regard to inferring geological environment from genomics, nodes on the tree of life can arise from true bottlenecks implied by the marine serpentinite origin scenario and by asteroid impact. Innovation of a very useful trait through a threshold allows the successful organism to quickly become very abundant and later root a large clade. The origin of life itself, that is, the initial Darwinian ancestor, the bacterial and archaeal roots as free-living cellular organisms that independently escaped hydrothermal chimneys above marine serpentinite or alternatively from shallow pore-water environments on land, the Selabacteria root with anoxygenic photosynthesis, and the Terrabacteria root colonizing land are attractive examples that predate the geological record. Conversely, geological reasoning presents likely events for appraisal by biologists. Asteroid impacts may have produced bottlenecks by decimating life. Thermophile roots of bacteria and archaea as well as a thermophile LUCA are attractive.

WXG100 protein superfamily consists of three subfamilies and exhibits an α-helical C-terminal conserved residue pattern

Members of the WXG100 protein superfamily form homo- or heterodimeric complexes. The most studied proteins among them are the secreted T-cell antigens CFP-10 (10 kDa culture filtrate protein, EsxB) and ESAT-6 (6 kDa early secreted antigen target, EsxA) from Mycobacterium tuberculosis. They are encoded on an operon within a gene cluster, named as ESX-1, that encodes for the Type VII secretion system (T7SS). WXG100 proteins are secreted in a full-length form and it is known that they adopt a four-helix bundle structure. In the current work we discuss the evolutionary relationship between the homo- and heterodimeric WXG100 proteins, the basis of the oligomeric state and the key structural features of the conserved sequence pattern of WXG100 proteins. We performed an iterative bioinformatics analysis of the WXG100 protein superfamily and correlated this with the atomic structures of the representative WXG100 proteins. We find, firstly, that the WXG100 protein superfamily consists of three subfamilies: CFP-10-, ESAT-6- and sagEsxA-like proteins (EsxA proteins similar to that of Streptococcus agalactiae). Secondly, that the heterodimeric complexes probably evolved from a homodimeric precursor. Thirdly, that the genes of hetero-dimeric WXG100 proteins are always encoded in bi-cistronic operons and finally, by combining the sequence alignments with the X-ray data we identify a conserved C-terminal sequence pattern. The side chains of these conserved residues decorate the same side of the C-terminal α-helix and therefore form a distinct surface. Our results lead to a putatively extended T7SS secretion signal which combines two reported T7SS recognition characteristics: Firstly that the T7SS secretion signal is localized at the C-terminus of T7SS substrates and secondly that the conserved residues YxxxD/E are essential for T7SS activity. Furthermore, we propose that the specific α-helical surface formed by the conserved sequence pattern including YxxxD/E motif is a key component of T7SS-substrate recognition.

Serpentinite and the dawn of life

Submarine hydrothermal vents above serpentinite produce chemical potential gradients of aqueous and ionic hydrogen, thus providing a very attractive venue for the origin of life. This environment was most favourable before Earth's massive CO(2) atmosphere was subducted into the mantle, which occurred tens to approximately 100 Myr after the moon-forming impact; thermophile to clement conditions persisted for several million years while atmospheric pCO(2) dropped from approximately 25 bar to below 1 bar. The ocean was weakly acid (pH ∼ 6), and a large pH gradient existed for nascent life with pH 9-11 fluids venting from serpentinite on the seafloor. Total CO(2) in water was significant so the vent environment was not carbon limited. Biologically important phosphate and Fe(II) were somewhat soluble during this period, which occurred well before the earliest record of preserved surface rocks approximately 3.8 billion years ago (Ga) when photosynthetic life teemed on the Earth and the oceanic pH was the modern value of approximately 8. Serpentinite existed by 3.9 Ga, but older rocks that might retain evidence of its presence have not been found. Earth's sequesters extensive evidence of Archaean and younger subducted biological material, but has yet to be exploited for the Hadean record.

The nucleotide addition cycle of RNA polymerase is controlled by two molecular hinges in the Bridge Helix domain

Background

Cellular RNA polymerases (RNAPs) are complex molecular machines that combine catalysis with concerted conformational changes in the active center. Previous work showed that kinking of a hinge region near the C-terminus of the Bridge Helix (BH-H_C) plays a critical role in controlling the catalytic rate.

Results

Here, new evidence for the existence of an additional hinge region in the amino-terminal portion of the Bridge Helix domain (BH-H_N) is presented. The nanomechanical properties of BH-H_N emerge as a direct consequence of the highly conserved primary amino acid sequence. Mutations that are predicted to influence its flexibility cause corresponding changes in the rate of the nucleotide addition cycle (NAC). BH-H_N displays functional properties that are distinct from BH-H_C, suggesting that conformational changes in the Bridge Helix control the NAC via two independent mechanisms.

Conclusions

The properties of two distinct molecular hinges in the Bridge Helix of RNAP determine the functional contribution of this domain to key stages of the NAC by coordinating conformational changes in surrounding domains.

Evidence of selection upon genomic GC-content in bacteria

The genomic GC-content of bacteria varies dramatically, from less than 20% to more than 70%. This variation is generally ascribed to differences in the pattern of mutation between bacteria. Here we test this hypothesis by examining patterns of synonymous polymorphism using datasets from 149 bacterial species. We find a large excess of synonymous GC→AT mutations over AT→GC mutations segregating in all but the most AT-rich bacteria, across a broad range of phylogenetically diverse species. We show that the excess of GC→AT mutations is inconsistent with mutation bias, since it would imply that most GC-rich bacteria are declining in GC-content; such a pattern would be unsustainable. We also show that the patterns are probably not due to translational selection or biased gene conversion, because optimal codons tend to be AT-rich, and the excess of GC→AT SNPs is observed in datasets with no evidence of recombination. We therefore conclude that there is selection to increase synonymous GC-content in many species. Since synonymous GC-content is highly correlated to genomic GC-content, we further conclude that there is selection on genomic base composition in many bacteria.

Trade-offs between efficiency and robustness in bacterial metabolic networks are associated with niche breadth

The relation between structure and function in biologic networks is a central point of systems biology research. Key functional features--notably, efficiency and robustness--are linked to the topologic structure of a network, and there appears to be a degree of trade-off between these features, i.e., simulation studies indicate that more efficient networks tend to be less robust. Here, we investigate this issue in metabolic networks from 105 lineages of bacteria having a wide range of ecologies. We take quantitative measurements on each network and integrate this network data with ecologic data using a phylogenetic comparative model. In this setting, we find that biologic conclusions obtained with classical phylogenetic comparative methods are sensitive to correlations between model covariates and phylogenetic branch length. To avoid this problem, we propose a revised statistical framework--hierarchical mixed-effect regression--to accommodate phylogenetic nonindependence. Using this approach, we show that the cartography of metabolic networks does indeed reflect a trade-off between efficiency and robustness. Furthermore, ecologic characteristics related to niche breadth are strong predictors of network shape. Given the broad variation in niche breadth seen among species, we predict that there is no universally optimal balance between efficiency and robustness in bacterial metabolic networks and, thus, no universally optimal network structure. These results highlight the biologic relevance of variation in network structure and the potential role of niche breadth in shaping metabolic strategies of efficiency and robustness.

Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria

Background

Despite a large agreement between ribosomal RNA and concatenated protein phylogenies, the phylogenetic tree of the bacterial domain remains uncertain in its deepest nodes. For instance, the position of the hyperthermophilic Aquificales is debated, as their commonly observed position close to Thermotogales may proceed from horizontal gene transfers, long branch attraction or compositional biases, and may not represent vertical descent. Indeed, another view, based on the analysis of rare genomic changes, places Aquificales close to epsilon-Proteobacteria.

Results

To get a whole genome view of Aquifex relationships, all trees containing sequences from Aquifex in the HOGENOM database were surveyed. This study revealed that Aquifex is most often found as a neighbour to Thermotogales. Moreover, informational genes, which appeared to be less often transferred to the Aquifex lineage than non-informational genes, most often placed Aquificales close to Thermotogales. To ensure these results did not come from long branch attraction or compositional artefacts, a subset of carefully chosen proteins from a wide range of bacterial species was selected for further scrutiny. Among these genes, two phylogenetic hypotheses were found to be significantly more likely than the others: the most likely hypothesis placed Aquificales as a neighbour to Thermotogales, and the second one with epsilon-Proteobacteria. We characterized the genes that supported each of these two hypotheses, and found that differences in rates of evolution or in amino-acid compositions could not explain the presence of two incongruent phylogenetic signals in the alignment. Instead, evidence for a large Horizontal Gene Transfer between Aquificales and epsilon-Proteobacteria was found.

Conclusion

Methods based on concatenated informational proteins and methods based on character cladistics led to different conclusions regarding the position of Aquificales because this lineage has undergone many horizontal gene transfers. However, if a tree of vertical descent can be reconstructed for Bacteria, our results suggest Aquificales should be placed close to Thermotogales.

Evolutionary ecology during the rise of dioxygen in the Earth's atmosphere

Pre-photosynthetic niches were meagre with a productivity of much less than 10(-4) of modern photosynthesis. Serpentinization, arc volcanism and ridge-axis volcanism reliably provided H(2). Methanogens and acetogens reacted CO(2) with H(2) to obtain energy and make organic matter. These skills pre-adapted a bacterium for anoxygenic photosynthesis, probably starting with H(2) in lieu of an oxygen 'acceptor'. Use of ferrous iron and sulphide followed as abundant oxygen acceptors, allowing productivity to approach modern levels. The 'photobacterium' proliferated rooting much of the bacterial tree. Land photosynthetic microbes faced a dearth of oxygen acceptors and nutrients. A consortium of photosynthetic and soil bacteria aided weathering and access to ferrous iron. Biologically enhanced weathering led to the formation of shales and, ultimately, to granitic rocks. Already oxidized iron-poor sedimentary rocks and low-iron granites provided scant oxygen acceptors, as did freshwater in their drainages. Cyanobacteria evolved dioxygen production that relieved them of these vicissitudes. They did not immediately dominate the planet. Eventually, anoxygenic and oxygenic photosynthesis oxidized much of the Earth's crust and supplied sulphate to the ocean. Anoxygenic photosynthesis remained important until there was enough O(2) in downwelling seawater to quantitatively oxidize massive sulphides at mid-ocean ridge axes.

The Biological Big Bang model for the major transitions in evolution

BACKGROUND

Major transitions in biological evolution show the same pattern of sudden emergence of diverse forms at a new level of complexity. The relationships between major groups within an emergent new class of biological entities are hard to decipher and do not seem to fit the tree pattern that, following Darwin's original proposal, remains the dominant description of biological evolution. The cases in point include the origin of complex RNA molecules and protein folds; major groups of viruses; archaea and bacteria, and the principal lineages within each of these prokaryotic domains; eukaryotic supergroups; and animal phyla. In each of these pivotal nexuses in life's history, the principal "types" seem to appear rapidly and fully equipped with the signature features of the respective new level of biological organization. No intermediate "grades" or intermediate forms between different types are detectable. Usually, this pattern is attributed to cladogenesis compressed in time, combined with the inevitable erosion of the phylogenetic signal.

HYPOTHESIS

I propose that most or all major evolutionary transitions that show the "explosive" pattern of emergence of new types of biological entities correspond to a boundary between two qualitatively distinct evolutionary phases. The first, inflationary phase is characterized by extremely rapid evolution driven by various processes of genetic information exchange, such as horizontal gene transfer, recombination, fusion, fission, and spread of mobile elements. These processes give rise to a vast diversity of forms from which the main classes of entities at the new level of complexity emerge independently, through a sampling process. In the second phase, evolution dramatically slows down, the respective process of genetic information exchange tapers off, and multiple lineages of the new type of entities emerge, each of them evolving in a tree-like fashion from that point on. This biphasic model of evolution incorporates the previously developed concepts of the emergence of protein folds by recombination of small structural units and origin of viruses and cells from a pre-cellular compartmentalized pool of recombining genetic elements. The model is extended to encompass other major transitions. It is proposed that bacterial and archaeal phyla emerged independently from two distinct populations of primordial cells that, originally, possessed leaky membranes, which made the cells prone to rampant gene exchange; and that the eukaryotic supergroups emerged through distinct, secondary endosymbiotic events (as opposed to the primary, mitochondrial endosymbiosis). This biphasic model of evolution is substantially analogous to the scenario of the origin of universes in the eternal inflation version of modern cosmology. Under this model, universes like ours emerge in the infinite multiverse when the eternal process of exponential expansion, known as inflation, ceases in a particular region as a result of false vacuum decay, a first order phase transition process. The result is the nucleation of a new universe, which is traditionally denoted Big Bang, although this scenario is radically different from the Big Bang of the traditional model of an expanding universe. Hence I denote the phase transitions at the end of each inflationary epoch in the history of life Biological Big Bangs (BBB).

CONCLUSION

A Biological Big Bang (BBB) model is proposed for the major transitions in life's evolution. According to this model, each transition is a BBB such that new classes of biological entities emerge at the end of a rapid phase of evolution (inflation) that is characterized by extensive exchange of genetic information which takes distinct forms for different BBBs. The major types of new forms emerge independently, via a sampling process, from the pool of recombining entities of the preceding generation. This process is envisaged as being qualitatively different from tree-pattern cladogenesis.

A prototype taxonomic microarray targeting the rpsA housekeeping gene permits species identification within the rhizobial genus Ensifer

To develop a reliable tool for the identification and classification of the different Ensifer species, without the need for sequencing, a prototype DNA microarray that targets the rpsA housekeeping gene was designed and tested. Internal segments of the rpsA gene from 34 reference strains, representing the different Ensifer species, were sequenced and the sequences were used to select 44 diagnostic oligonucleotides that served as probes for the identification microarray. Both, genomic DNA and specific rpsA PCR-products were tested as a target in hybridisation experiments. Experimental conditions were optimised and the diagnostic oligonucleotides were validated. Hybridisation results with the rpsA PCR-products showed reliable identification of the reference strains to species and genomovar level. Our data indicate that a microarray targeting housekeeping genes is a promising, accurate and relatively simple genotyping technique that would also be applicable for the identification and characterization of other bacterial groups of interest.

The evolutionary origin of Xanthomonadales genomes and the nature of the horizontal gene transfer process

Determining the influence of horizontal gene transfer (HGT) on phylogenomic analyses and the retrieval of a tree of life is relevant for our understanding of microbial genome evolution. It is particularly difficult to differentiate between phylogenetic incongruence due to noise and that resulting from HGT. We have performed a large-scale, detailed evolutionary analysis of the different phylogenetic signals present in the genomes of Xanthomonadales, a group of Proteobacteria. We show that the presence of phylogenetic noise is not an obstacle to infer past and present HGTs during their evolution. The scenario derived from this analysis and other recently published reports reflect the confounding effects on bacterial phylogenomics of past and present HGT. Although transfers between closely related species are difficult to detect in genome-scale phylogenetic analyses, past transfers to the ancestor of extant groups appear as conflicting signals that occasionally might make impossible to determine the evolutionary origin of the whole genome.

Data mining for proteins characteristic of clades

A synapomorphy is a phylogenetic character that provides evidence of shared descent. Ideally a synapomorphy is ubiquitous within the clade of related organisms and nonexistent outside the clade, implying that it arose after divergence from other extant species and before the last common ancestor of the clade. With the recent proliferation of genetic sequence data, molecular synapomorphies have assumed great importance, yet there is no convenient means to search for them over entire genomes. We have developed a new program called Conserv, which can rapidly assemble orthologous sequences and rank them by various metrics, such as degree of conservation or divergence from out-group orthologs. We have used Conserv to conduct a largescale search for molecular synapomorphies for bacterial clades. The search discovered sequences unique to clades, such as Actinobacteria, Firmicutes and gamma-Proteobacteria, and shed light on several open questions, such as whether Symbiobacterium thermophilum belongs with Actinobacteria or Firmicutes. We conclude that Conserv can quickly marshall evidence relevant to evolutionary questions that would be much harder to assemble with other tools.

The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance

In the rRNA-based tree of life four bacterial phyla, comprising the Planctomycetes, Verrucomicrobia, Chlamydiae and Lentisphaerae, form together with the candidate phyla Poribacteria and OP3 a monophyletic group referred to as the PVC superphylum. This assemblage contains organisms that possess dramatically different lifestyles and which colonize sharply contrasting habitats. Some members of this group are among the most successful human pathogens, others are abundant soil microbes, and others still are of major importance for the marine nitrogen cycle and hold much promise for sustainable wastewater treatment. Recent comparative genomic and metagenomic analyses of a few representatives of this group revealed many unusual features and generated unexpected hypotheses regarding their physiology, some of which have already been confirmed experimentally. Furthermore, the availability of these genome sequences offered new insights into the evolutionary history of this peculiar group of microbes with major medical, ecological and biotechnological relevance.

The first lines of divergence in the Bacteria domain were the hyperthermophilic organisms, the Thermotogales and the Aquificales, and not the mesophilic Planctomycetales

In order to establish whether the first lines of divergence in the Bacteria domain were the mesophilic or the hyperthermophilic organisms, we have performed a phylogenetic analysis on a concatenamer obtained from the fusion of 20 different proteins. The phylogenetic analysis carried out using five different methods has shown that, contrary to what is reported in the literature [Brochier, C., Philippe, H., 2002. A non-hyperthermophilic ancestor for Bacteria. Nature 417, 244], it was probably the hyperthermophilic organisms, the Thermotogales and the Aquificales, which were the first lines of divergence in the Bacteria domain, and not the mesophilic Planctomycetales. This strengthens the hypothesis that the last universal common ancestor might have been a hyperthermophilic 'organism' and that, more generally, life might have originated at high temperature.