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NASA NTRS1987

The green non-sulfur bacteria: a deep branching in the eubacterial line of descent

Ribosomal RNA sequence comparisons define a phylogenetic grouping, the green non-sulfur bacteria and relatives (GNS), known to contain the genera Chloroflexus, Herpetosiphon and Thermomicrobium--organisms that have little phenotypic similarity. The unit is phylogenetically deep, but entirely distinct from any other eubacterial division (phylum). It is also relatively ancient--branching from the common eubacterial stem earlier than any other group of eubacteria reported thus far. The group phenotype is predominantly thermophilic, and its thermophilic members, especially Thermomicrobium, are more slowly evolving than Herpetosiphon, a mesophile. The GNS unit appears significantly older than either the green sulfur bacteria or the cyanobacteria--making it likely that organisms such as Chloroflexus, not the cyanobacteria, generated the oldest stromatolites, which formed over three billion years ago.

Non-NASA Center↗
NASA NTRS1987

Were the original eubacteria thermophiles?

Thermotoga maritima is one of the more unusual eubacteria: It is highly thermophilic, growing at temperatures higher than any other eubacterium; its cell wall appears to have a unique structure and its lipids a unique composition; and the organism is surrounded by a loose-fitting sheath of unknown function. Its phenotypic uniqueness is matched by its phylogenetic position; Thermotoga maritima represents the deepest known branching in the eubacterial line of descent, as measured by ribosomal RNA sequence comparisons. T. maritima also represents the most slowly evolving of eubacterial lineages. The fact that the two deepest branchings in the eubacterial line of descent (the other, the green non-sulfur bacteria and relatives, i.e. Chloroflexus, Thermomicrobium, etc.) are both basically thermophilic and slowly evolving, strongly suggests that all eubacteria have ultimately arisen from a thermophilic ancestor.

NASA Discipline Exobiology↗
NASA NTRS1986

Characteristic archaebacterial 16S rRNA oligonucleotides

A method of analyzing 16S rRNA catalog data has been developed in which groupings at various taxonomic levels can be characterized in terms of specific "signature" oligonucleotides. This approach provides an alternative means for evaluating higher order branching possibilities and can be used to assess the phylogenetic position of isolates that are poorly placed by the usual clustering procedures. This signature approach has been applied to forty archaebacterial catalogs and every oligonucleotide with significant signature value has been identified. Sets of specific oligonucleotides were identified for every major group on a dendrogram produced by cluster analysis procedures. Signatures that would establish between group relationships were also sought and found. In the case of the Methanobacteriaceae the clustering methods suggest a specific relationship to the Methanococcaceae. This inclusion is in fact supported by six strong signature oligonucleotides. However there are also significant numbers of signature oligonucleotides supporting a specific relationship of the Methanobacteriaceae to either the Halobacteriaceae or the Methanomicrobiaceae. Thus the placement of the Methanobacteriaceae is less certain than the usual dendrograms imply. The signature approach also was used to assess the phylogenetic position of Thermoplasma acidophilum which is found to be more closely related to the methanogen/halophile Division than to the sulfur dependent Division of the archaebacteria. This does not imply however that Thermoplasma acidophilum is properly regarded as being in the methanogen/halophile Division.

NASA Discipline Exobiology↗
NASA NTRS1997

Paleobiology of the Mesoproterozoic-Neoproterozoic transition: the Sukhaya Tunguska Formation, Turukhansk Uplift, Siberia

Silicified carbonates of the latest Mesoproterozoic Sukhaya Tunguska Formation, northwestern Siberia, contain abundant and diverse permineralized microfossils. Peritidal environments are dominated by microbial mats built by filamentous cyanobacteria comparable to modern species of Lyngbya and Phormidium. In subtidal to lower intertidal settings, mat-dwelling microbenthos and possible coastal microplankton are abundant. In contrast, densely woven mat populations with few associated taxa characterize more restricted parts of tidal flats; the preservation of vertically oriented sheath bundles and primary fenestrae indicates that in these mats carbonate cementation was commonly penecontemporaneous with mat growth. Eoentophysalis mats are limited to restricted environments where microlaminated carbonate precipitates formed on or just beneath the sediment surface. Most microbenthic populations are cyanobacterial, although eukaryotic microfossils may occur among the simple spheroidal cells interpreted as coastal plankton. Protists are more securely represented by large (up to 320 micrometers in diameter) but poorly preserved acritarchs in basinal facies. The Sukhaya Tunguska assemblage contains 27 species in 18 genera. By virtue of their stratigraphic longevity and their close and predictable association with specific paleoenvironmental conditions, including substrates, Proterozoic cyanobacteria support a model of bacterial evolution in which populations adapt rapidly to novel environments and, thereafter, resist competitive replacement. The resulting evolutionary pattern is one of accumulation and stasis rather than the turnover and replacement characteristic of Phanerozoic plants and animals.

NASA Discipline Exobiology↗
NASA NTRS1997

Comparative diversification dynamics among palaeocontinents during the Ordovician Radiation

The Ordovician Radiation was among the most extensive intervals of diversification in the history of life. However, a delineation of the proximal cause(s) of the Radiation remains elusive. Any such determination should involve an analysis of geographic overprints on diversification: did the Radiation occur randomly around the world or, alternatively, was it focused in particular geographic or depositional regimes? Here, I present a comparative evaluation of Ordovician diversification among several palaeocontinents to determine whether biotas associated with certain palaeocontinents exhibited different diversification patterns than others; in part, this involves a numerical "correction" to raw diversity trajectories. Clear disparities among palaeocontinents are indicated by the data, which appear to reflect differences in the extent of siliciclastic input partly in association with tectonic activity. Further testing will be required to fully substantiate the implication that siliciclastic influx was a predominant factor in the Ordovician Radiation, affecting a variety of higher taxa among all three Phanerozoic evolutionary faunas.

Non-NASA Center↗
NASA NTRS1992

A partial phylogenetic analysis of the "flavobacter-bacteroides" phylum: basis for taxonomic restructuring

On the basis of small subunit rRNA sequence analyses five major subgroups within the flavobacteria-bacteroides phylum have been defined. These are tentatively designated the cytophaga subgroup (comprising largely Cytophaga species), the flavobacter subgroup (comprising the true flavobacteria and the polyphyletic genus Weeksella), the bacteroides subgroup (comprising the bacteroides and certain cytophaga-like bacteria), the sphingobacter subgroup (which contains the known sphingolipid-producing members of the phylum), and the saprospira subgroup (comprising particular species of Flexibacter, Flavobacterium, Haliscomenobacter, and, of course, the genus Saprospira). These groupings are given not only by evolutionary distance analysis, but can be defined and distinguished on the basis of a simple small subunit rRNA signatures.

NASA Discipline Exobiology↗
NASA NTRS1994

Characterization of a new thermophilic sulfate-reducing bacterium Thermodesulfovibrio yellowstonii, gen. nov. and sp. nov.: its phylogenetic relationship to Thermodesulfobacterium commune and their origins deep within the bacterial domain

A thermophilic sulfate-reducing vibrio isolated from thermal vent water in Yellowstone Lake, Wyoming, USA is described. The gram-negative, curved rod-shaped cells averaged 0.3 micrometer wide and 1.5 micrometers long. They were motile by means of a single polar flagellum. Growth was observed between 40 degrees and 70 degrees C with optimal growth at 65 degrees C. Cultures remained viable for one year at 27 degrees C although spore-formation was not observed. Sulfate, thiosulfate and sulfite were used as electron acceptors. Sulfur, fumarate and nitrate were not reduced. In the presence of sulfate, growth was observed only with lactate, pyruvate, hydrogen plus acetate, or formate plus acetate. Pyruvate was the only compound observed to support fermentative growth. Pyruvate and lactate were oxidized to acetate. Desulfofuscidin and c-type cytochromes were present. The G + C content was 29.5 mol%. The divergence in the 16 S ribosomal RNA sequences between the new isolate and Thermodesulfobacterium commune suggests that these two thermophilic sulfate-reducing bacteria represent different genera. These two bacteria depict a lineage that branches deeply within the Bacteria domain and which is clearly distinct from previously defined phylogenetic lines of sulfate-reducing bacteria. Strain YP87 is described as the type strain of the new genus and species Thermodesulfovibrio yellowstonii.

Non-NASA Center↗
NASA NTRS1997

A new look at age and area: the geographic and environmental expansion of genera during the Ordovician Radiation

Although available paleobiological data indicate that the geographic ranges of marine species are maintained throughout their entire observable durations, other evidence suggests, by contrast, that the ranges of higher taxa expand as they age, perhaps in association with increased species richness. Here, I utilize a database of Ordovician genus occurrences collected from the literature for several paleocontinents to demonstrate that a significant aging of the global biota during the Ordovician Radiation was accompanied by a geographic and environmental expansion of genus ranges. The proportion of genera occurring in two or more paleocontinents in the database, and two or more environmental zones within a six-zone onshore-offshore framework, increased significantly in the Caradocian and Ashgillian. Moreover, widespread genera tended to be significantly older than their endemic counterparts, suggesting a direct link between their ages and their environmental and geographic extents. Expansion in association with aging was corroborated further by demonstrating this pattern directly among genera that ranged from the Tremadocian through the Ashgillian. Taken together, these results are significant not only for what they reveal about the kinetics of a major, global-scale diversification, but also for what they suggest about the interpretation of relationships between diversity trends at the alpha (within-community) and beta (between-community) levels.

NASA Discipline Exobiology↗
NASA NTRS1997

Dissecting global diversity patterns: examples from the Ordovician Radiation

Although the history of life has been characterized by intermittent episodes of radiation that can be recognized in global compilations of biodiversity, it does not necessarily follow that these episodes are caused by processes that occurred uniformly around the world. Major diversity increases could be generated by the cumulative effects of different mechanisms operating simultaneously at several geographic or environmental scales. The purpose of this review is to describe ongoing research on the manifestations, at several scales, of the Ordovician Radiation, which was among the most extensive intervals of diversification in the history of life. Through much of the period, diversity was concentrated most heavily near regions of active mountain building and volcanism; differences in diversity patterns from continent to continent, and among regions within continents, reflect this overprint. While this suggests a linkage of the Radiation and tectonic activity, this is by no means the only mediating agent. Outcrop-based research in North America has demonstrated that tectonic activity was detrimental to some biotic elements, in contrast to its effects on other organisms. Moreover, in the Great Basin of North America where the local stratigraphic record is of particularly high quality, biotic transitions characteristic of the period occurred far more rapidly than observed in global compilations of diversity, suggesting that the global rate of transition may represent the aggregate sum of transitions that occurred abruptly, but at different times, around the world. Finally, it has been demonstrated that, in concert with an increase in average age, the environmental and geographic ranges of Ordovician genera both increased significantly through the period, indicating a role for intrinsic factors in producing Ordovician biotic patterns.

Non-NASA Center↗
NASA NTRS1988

An extreme-halophile archaebacterium possesses the interlock type of prephenate dehydratase characteristic of the Gram-positive eubacteria

The focal point of phenylalanine biosynthesis is a dehydratase reaction which in different organisms may be prephenate dehydratase, arogenate dehydratase, or cyclohexadienyl dehydratase. Gram-positive, Gram-negative, and cyanobacterial divisions of the eubacterial kingdom exhibit different dehydratase patterns. A new extreme-halophile isolate, which grows on defined medium and is tentatively designated as Halobacterium vallismortis CH-1, possesses the interlock type of prephenate dehydratase present in Gram-positive bacteria. In addition to the conventional sensitivity to feedback inhibition by L-phenylalanine, the phenomenon of metabolic interlock was exemplified by the sensitivity of prephenate dehydratase to allosteric effects produced by extra-pathway (remote) effectors. Thus, L-tryptophan inhibited activity while L-tyrosine, L-methionine, L-leucine and L-isoleucine activated the enzyme. L-Isoleucine and L-phenylalanine were effective at micromolar levels; other effectors operated at mM levels. A regulatory mutant selected for resistance to growth inhibition caused by beta-2-thienylalanine possessed an altered prephenate dehydratase in which a phenomenon of disproportionately low activity at low enzyme concentration was abolished. Inhibition by L-tryptophan was also lost, and activation by allosteric activators was diminished. Not only was sensitivity to feedback inhibition by L-phenylalanine lost, but the mutant enzyme was now activated by this amino acid (a mutation type previously observed in Bacillus subtilis). It remains to be seen whether this type of prephenate dehydratase will prove to be characteristic of all archaebacteria or of some archaebacterial subgroup cluster.

NASA Discipline Number 52-30↗
NASA NTRS1992

A phylogenetic analysis of Aquifex pyrophilus

The 16S rRNA of the bacterion Aquifex pyrophilus, a microaerophilic, oxygen-reducing hyperthermophile, has been sequenced directly from the the PCR amplified gene. Phylogenetic analyses show the Aq. pyrophilus lineage to be probably the deepest (earliest) in the (eu)bacterial tree. The addition of this deep branching to the bacterial tree further supports the argument that the Bacteria are of thermophilic ancestry.

Non-NASA Center↗
NASA NTRS1991

The sequence of Methanospirillum hungatei 23S rRNA confirms the specific relationship between the extreme halophiles and the Methanomicrobiales

We have determined the sequence of the 23S rRNA from the methanogenic archaeon Methanospirillum hungatei. This is the first such sequence from a member of the Methanomicrobiales. Moreover, it brings additional evidence to bear on the possible specific relationship between this particular group of methanogens and the extreme halophiles. Such evidence is critical in that several new (and relatively untested) methods of phylogenetic inference have lead to the controversial conclusion that the extreme halophiles are either not related to the archaea, or are only peripherally so. Analysis of the Methanospirillum hungatei 23S rRNA sequence shows the Methanomicrobiales are indeed a sister group of the extreme halophiles, further strengthening the conclusions reached from analysis of 16S rRNA sequences.

Non-NASA Center↗
NASA NTRS1991

Methanopyrus kandleri: an archaeal methanogen unrelated to all other known methanogens

Analysis of its 16S rRNA sequence shows that the newly discovered hyperthermophilic methanogen, Methanopryus kandleri, is phylogenetically unrelated to any other known methanogen. The organism represents a separate lineage originating near the root of the archaeal tree. Although the 16S rRNA sequence of Mp. kandleri resembles euryarchaeal 16S rRNAs more than it does crenarchaeal, it shows more crenarchaeal signature features than any known euryarchaeal rRNA. Attempts to place it in relation to the root of the archaeal tree show that the Mp. kandleri lineage likely arises from the euryarchaeal branch of the tree. While the existence of so deeply branching a methanogenic lineage brings into question the thesis that methanogenesis evolved from an earlier metabolism similar to that seen in Thermococcus, it at the same time reinforces the notion that the aboriginal [correction of aborginal] archaeon was a thermophile.

NASA Discipline Number 52-30↗
NASA NTRS1991

A definition of the domains Archaea, Bacteria and Eucarya in terms of small subunit ribosomal RNA characteristics

The number of small subunit rRNA sequences is now great enough that the three domains Archaea, Bacteria and Eucarya (Woese et al., 1990) can be reliably defined in terms of their sequence "signatures". Approximately 50 homologous positions (or nucleotide pairs) in the small subunit rRNA characterize and distinguish among the three. In addition, the three can be recognized by a variety of nonhomologous rRNA characters, either individual positions and/or higher-order structural features. The Crenarchaeota and the Euryarchaeota, the two archaeal kingdoms, can also be defined and distinguished by their characteristic compositions at approximately fifteen positions in the small subunit rRNA molecule.

NASA Program Exobiology↗
NASA NTRS1995

Diverse Thermus species inhabit a single hot spring microbial mat

Through an effort to characterize aerobic chemoorganotrophic bacteria in the Octopus Spring cyano-bacterial mat community, we cultivated four Thermus isolates with unique 16S rRNA sequences. Isolates clustered within existing Thermus clades, including those containing Thermus ruber, Thermus aquaticus, and a subgroup closely related to T. aquaticus. One Octopus Spring isolate is nearly identical (99.9% similar) to isolates from Iceland, and two others are closely related to a T. ruber isolated from Russia. Octopus Spring isolates similar to T. aquaticus and T. ruber exhibited optimal growth rates at high (65-70 degrees C) and low (50 degrees C) temperatures, respectively, with the most abundant species best adapted to the temperature of the habitat (50-55 degrees C). Our results display a diversity of Thermus genotypes defined by 16S rRNA within one hot spring microbial community. We suggest that specialization to temperature and perhaps other local environmental features controls the abundance of Thermus populations.

Non-NASA Center↗
NASA NTRS1995

Life as a planetary phenomenon: the colonization of Mars

Life is a planet-wide phenomenon in which its components incessantly move and interact. Life imperatively recycles its parts at the surface of the Earth in a chemical transformation and physical transport that depends utterly on the energy from a recent star, the Sun. Humanity, entirely dependent on other beings, plays a recent and relatively small part in the great phenomenon of life that transports and transforms the surface of the Earth. Our species accelerates but does not dominate the metabolism of the Earth system. Ironically, during the Apollo days of the sixties, fears were rampant that Martian or other extraterrestrial "germs" might "contaminate" our planet. After Viking, such fears are seen as the manifestation of cultural paranoia. The Viking missions complemented ground-based astronomical observation and yielded definitive evidence for the lack of life on the red planet. The Gaia hypothesis states that the surface temperature, composition of the reactive gases, oxidation state, alkalinity-acidity on today's Earth are kept homeorrhetically at values set by the sum of the activities of the current biota. Life, in other words, not only produces and maintains its immediate environment, but appears on Earth only as a planetary phenomenon. Since the natural tendency of all life is to grow exponentially to fill proximal volume, the question now "can life ecopoietically expand to Mars?" is entirely equivalent to the query of "can Gaia reproduce?".

Non-NASA Center↗
NASA NTRS1993

Evolution in vitro: analysis of a lineage of ribozymes

Background: Catalytic RNAs, or ribozymes, possessing both a genotype and a phenotype, are ideal molecules for evolution experiments in vitro. A large, heterogeneous pool of RNAs can be subjected to multiple rounds of selection, amplification and mutation, leading to the development of variants that have some desired phenotype. Such experiments allow the investigator to correlate specific genetic changes with quantifiable alterations of the catalytic properties of the RNA. In addition, patterns of evolutionary change can be discerned through a detailed examination of the genotypic composition of the evolving RNA population. Results: Beginning with a pool of 10(13) variants of the Tetrahymena ribozyme, we carried out in vitro evolution experiments that led to the generation of ribozymes with the ability to cleave an RNA substrate in the presence of Ca2+ ions, an activity that does not exist for the wild-type molecule. Over the course of 12 generations, a seven-error variant emerged that has substantial Ca(2+)-dependent RNA-cleavage activity. Advantageous mutations increased in frequency in the population according to three distinct dynamics--logarithmic, linear and transient. Through a comparative analysis of 31 individual variants, we infer how certain mutations influence the catalytic properties of the ribozyme. Conclusions: In vitro evolution experiments make it possible to elucidate important aspects of both evolutionary biology and structural biochemistry on a reasonable short time scale.

Non-NASA Center↗
NASA NTRS1989

Evolution and extinction in the marine realm: some constraints imposed by phytoplankton

The organic and mineralized remains of planktonic algae provide a rich record of microplankton evolution extending over nearly half of the preserved geological record. In general, Phanerozoic patterns of phytoplankton radiation and extinction parallel those documented for skeletonized marine invertebrates, both augmenting and constraining thought about evolution in the oceans. Rapidly increasing knowledge of Proterozoic plankton is making possible the recognition of additional episodes of diversification and extinction that antedate the Ediacaran radiation of macroscopic animals. In contrast to earlier phytoplankton history, the late Mesozoic and Cainozoic record is documented in sufficient detail to constrain theories of mass extinction in more than a general way. Broad patterns of diversity change in planktonic algae show similarities across the Cretaceous-Tertiary and Eocene-Oligocene boundaries, but detailed comparisons of origination and extinction rates in calcareous nannoplankton, as well as other algae and skeletonized protozoans, suggest that the two episodes were quite distinct. Common causation appears unlikely, casting doubt on monolithic theories of mass extinction, whether periodic or not. Studies of mass extinction highlight a broader class of insights that paleontologists can contribute to evolutionary biology: the evaluation of evolutionary change in the context of evolving Earth-surface environments.

NASA Discipline Number 52-30↗