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NASA NTRS1986

Microbial contributions to the Precambrian Earth

Life has existed on Earth for approximately 3.5 billion years. For most of this time, prokaryotic communities provided the major biological forces changing the Earth. Many changes in atmospheric gas composition occurred during the Archean and Proterozoic eons as a result of microbial activity. Extant microbial communities were used to help understand the dynamics which contributed to these atmospheric changes. The microbial mat communities were characterized according to the organismic constituents. Symbiosis in microbial communities is recognized as a major force in cell evolution. Among the evolutinary enigmas investigated is the problem of the origin of the undulipodia. Undulipodial microtubules are still deployed for major cellular processes such as mitosis and meiosis. Several prokaryotes were tested for the presence of the S1-type protein, so far only spirochetes were found to possess it. The S1-type protein is being sought in cyanobacteria reported to contain microtubules.

Margulis, L.↗

NASA NTRS1985

Are interpretations of ancient marine temperatures constrained by the presence of ancient marine organisms?

The relationship between marine temperature and marine organisms is investigated. The adaptation of organisms to extreme temperatures is studied; it is observed that chemautotrophic and chemoheterotrophic prokaryotes adapt to 100 C, photoautotrophic prokaryotes to 73 C, and fungi to 60 C. The physiological and molecular factors related to thermal limits in organisms such as enzymes, lipids, or plasma membranes, are examined. Two types of thermal adaptations, resistance and capacity, are detected in organisms. Reasons for species distributions according to temperature barriers are proposed by Read (1967) and Bullock (1955) and are related to enzyme limits. The effects of an organism's composition on thermal stability is analyzed.

Valentine, J. W.↗

NASA NTRS1989

Snow as a habitat for microorganisms

There are three major habitats involving ice and snow, and the microorganisms studied from these habitats are most eukaryotic. Sea ice is inhabited by algae called diatoms, glacial ice has sparse populations of green algai cal desmids, and the temporary and permanent snows in mountainous regions and high latitudes are inhabited mostly by green algal flagellates. The life cycle of green algal flagellates is summarized by discussing the effects of light, temperature, nutrients, and snow melts. Specific examples of optimal conditions and environmental effects for various snow algae are given. It is not likely that the eukaryotic snow algae presented are candidated for life on the planet Mars. Evolutionally, eukaryotic cells as know on Earth may not have had the opportunity to develop on Mars (if life evolved at all on Mars) since eukaryotes did not appear on Earth until almost two billion years after the first prokaryotic organisms. However, the snow/ice ecosystems on Earth present themselves as extreme habitats were there is evidence of prokaryotic life (eubacteria and cyanbacteria) of which literally nothing is known. Any future surveillances of extant and/or extinct life on Mars should include probes (if not landing sites) to investigate sites of concentrations of ice water. The possibility of signs of life in Martian polar regions should not be overlooked.

Hoham, Ronald W.↗

NASA NTRS1999

An ESA Robotic Package to Search for Life on Mars

Similarities in the early histories of Mars and Earth suggest that life may have arisen on Mars as it did on Earth. The early life forms on Mars were probably simple organisms, similar to terrestrial prokaryotes. In fact, given the early deterioration of the Martian climate, it is unlikely that life on Mars could ever have reached more sophisticated evolution. Based on the present knowledge of Mars, the possibility of extant life at the surface is small. However, given the adaptability of terrestrial prokaryotes under adverse conditions, it is not excluded. Any extant life is hypothesized to reside in the permafrost in a dormant state until "reanimated" by impact-caused hydrothermal activity. Using this rationale, a group of European scientists worked together to conceive a hypothetical strategy to search for life on Mars. A possible configuration for a lander/rover is outlined.

Westall, F.↗

NASA NTRS2000

Martian Magmatic-Driven Hydrothermal Sites: Potential Sources of Energy, Water, and Life

Magmatic-driven processes and impact events dominate the geologic record of Mars. Such recorded geologic activity coupled with significant evidence of past and present-day water/ice, above and below the martian surface, indicate that hydrothermal environments certainly existed in the past and may exist today. The identification of such environments, especially long-lived magmatic-driven hydrothermal environments, provides NASA with significant target sites for future sample return missions, since they (1) could favor the development and sustenance of life, (2) may comprise a large variety of exotic mineral assemblages, and (3) could potentially contain water/ice reservoirs for future Mars-related human activities. If life developed on Mars, the fossil record would presumably be at its greatest concentration and diversity in environments where long-term energy sources and water coexisted such as at sites where long-lived, magmatic-driven hydrothermal activity occurred. These assertions are supported by terrestrial analogs. Small, single-celled creatures (prokaryotes) are vitally important in the evolution of the Earth; these prokaryotes are environmentally tough and tolerant of environmental extremes of pH, temperature, salinity, and anoxic conditions found around hydrothermal vents. In addition, there is a great ability for bacteria to survive long periods of geologic time in extreme conditions, including high temperature hydrogen sulfide and sulfur erupted from Mount St. Helens volcano. Our team of investigators is conducting a geological investigation using multiple mission-derived datasets (e.g., existing geologic map data, MOC imagery, MOLA, TES image data, geophysical data, etc.) to identify prime target sites of hydrothermal activity for future hydrological, mineralogical, and biological investigations. The identification of these sites will enhance the probability of success for future missions to Mars.

Anderson, R. C.↗

NASA NTRS2003

Bacterial Actins? An Evolutionary Perspective

According to the conventional wisdom, the existence of a cytoskeleton in eukaryotes and its absence in prokaryotes constitute a fundamental divide between the two domains of life. An integral part of the dogma is that a cytoskeleton enabled an early eukaryote to feed upon prokaryotes, a consequence of which was the occasional endosymbiosis and the eventual evolution of organelles. Two recent papers present compelling evidence that actin, one of the principal components of a cytoskeleton, has a homolog in Bacteria that behaves in many ways like eukaryotic actin. Sequence comparisons reveml that eukaryotic actin and the bacterial homolog (mreB protein), unlike many other proteins common to eukaryotes and Bacteria, have very different and more highly extended evolutionary histories.

Doolittle, Russell F.↗

NASA NTRS2003

Gene Transfers Between Distantly Related Organisms

With the completion of numerous microbial genome sequences, reports of individual gene transfers between distantly related prokaryotes have become commonplace. On the other hand, transfers between prokaryotes and eukaryotes still excite the imagination. Many of these claims may be premature, but some are certainly valid. In this chapter, the kinds of supporting data needed to propose transfers between distantly related organisms and cite some interesting examples are considered.

Doolittle, Russell F.↗

NASA NTRS2002

Microarray analysis identifies Salmonella genes belonging to the low-shear modeled microgravity regulon

The low-shear environment of optimized rotation suspension culture allows both eukaryotic and prokaryotic cells to assume physiologically relevant phenotypes that have led to significant advances in fundamental investigations of medical and biological importance. This culture environment has also been used to model microgravity for ground-based studies regarding the impact of space flight on eukaryotic and prokaryotic physiology. We have previously demonstrated that low-shear modeled microgravity (LSMMG) under optimized rotation suspension culture is a novel environmental signal that regulates the virulence, stress resistance, and protein expression levels of Salmonella enterica serovar Typhimurium. However, the mechanisms used by the cells of any species, including Salmonella, to sense and respond to LSMMG and identities of the genes involved are unknown. In this study, we used DNA microarrays to elucidate the global transcriptional response of Salmonella to LSMMG. When compared with identical growth conditions under normal gravity (1 x g), LSMMG differentially regulated the expression of 163 genes distributed throughout the chromosome, representing functionally diverse groups including transcriptional regulators, virulence factors, lipopolysaccharide biosynthetic enzymes, iron-utilization enzymes, and proteins of unknown function. Many of the LSMMG-regulated genes were organized in clusters or operons. The microarray results were further validated by RT-PCR and phenotypic analyses, and they indicate that the ferric uptake regulator is involved in the LSMMG response. The results provide important insight about the Salmonella LSMMG response and could provide clues for the functioning of known Salmonella virulence systems or the identification of uncharacterized bacterial virulence strategies.

Non-NASA Center↗

NASA NTRS1995

Paleobiology of the Mesoproterozoic Billyakh Group, Anabar Uplift, northern Siberia

Silicified peritidal carbonates of the Mesoproterozoic Kotuikan and Yusmastakh Formations, Anabar Uplift, northeastern Siberia, contain exceptionally well-preserved microfossils. The assemblage is dominated by ellipsoidal akinetes of nostocalean cyanobacteria (Archaeoellipsoides) and problematic spheroidal unicells (Myxococcoides); both are allochthonous and presumably planktonic. The assemblage also includes distinctive mat-forming scytonematacean and entophysalidacean cyanobacteria, diverse short trichomes interpreted as cyanobacterial hormogonia or germinated akinetes, rare longer trichomes, and several types of colonial unicells. Although many taxa in the Kotuikan-Yusmastakh assemblage are long-ranging prokaryotes, the overall character of the assemblage is distinctly Mesoproterozoic, with its major features shared by broadly coeval floras from Canada, China, India, and elsewhere in Siberia. Microfossils also occur in middle to inner shelf shales of the Ust'-Il'ya and lower Kotuikan Formations. Leiosphaerid acritarchs (up to several hundred microns in diameter) characterize this facies. As in other Mesoproterozoic acritarch assemblages, acanthomorphic and other complex forms that typify Neoproterozoic assemblages are absent. The combination in Billyakh assemblages of exceptional preservation and low eukaryotic diversity supports the hypothesis that nucleated organisms diversified markedly near the Mesoproterozoic-Neoproterozoic boundary. The assemblages also demonstrate the antiquity of cyanobacteria capable of cell differentiation and suggest the importance of both changing peritidal substrates and evolving eukaryotes in determining stratigraphic patterns of Proterozoic prokaryotes. The permineralized assemblage contains 33 species belonging to 17 genera. Ten new species or new combinations are proposed: Archaeoellipsoides costatus n. sp., A. elongatus n. comb., A. dolichos n. comb., A. minor n. nom., A. crassus n. comb., A. major n. comb., A. bactroformis n. sp., Veteronostocale medium n. sp., Filiconstrictosus cephalon n. sp., and Partitiofilum yakschinii n. sp.

Non-NASA Center↗

NASA NTRS1994

How long did it take for life to begin and evolve to cyanobacteria?

There is convincing paleontological evidence showing that stromatolite-building phototactic prokaryotes were already in existence 3.5 x 10(9) years ago. Late accretion impacts may have killed off life on our planet as late as 3.8 x 10(9) years ago. This leaves only 300 million years to go from the prebiotic soup to the RNA world and to cyanobacteria. However, 300 million years should be more than sufficient time. All known prebiotic reactions take place in geologically rapid time scales, and very slow prebiotic reactions are not feasible because the intermediate compounds would have been destroyed due to the passage of the entire ocean through deep-sea vents every 10(7) years or in even less time. Therefore, it is likely that self-replicating systems capable of undergoing Darwinian evolution emerged in a period shorter than the destruction rates of its components (<5 million years). The time for evolution from the first DNA/protein organisms to cyanobacteria is usually thought to be very long. However, the similarities of many enzymatic reactions, together with the analysis of the available sequence data, suggest that a significant number of the components involved in basic biological processes are the result of ancient gene duplication events. Assuming that the rate of gene duplication of ancient prokaryotes was comparable to today's present values, the development of a filamentous cyanobacterial-like genome would require approximately 7 x 10(6) years--or perhaps much less. Thus, in spite of the many uncertainties involved in the estimates of time for life to arise and evolve to cyanobacteria, we see no compelling reason to assume that this process, from the beginning of the primitive soup to cyanobacteria, took more than 10 million years.

Non-NASA Center↗

NASA NTRS2007

Microfossils of Cyanobacteria in Carbonaceous Meteorites

During the past decade, Environmental and Field Emission Scanning Electron Microscopes have been used at the NASA/Marshall Space Flight Center to investigate freshly fractured interior surfaces of a large number of different types of meteorites. Large, complex, microfossils with clearly recognizable biological affinities have been found embedded in several carbonaceous meteorites. Similar forms were notably absent in all stony and nickel-iron meteorites investigated. The forms encountered are consistent in size and morphology with morphotypes of known genera of Cyanobacteria and microorganisms that are typically encountered in associated benthic prokaryotic mats. Even though many coccoidal and isodiametric filamentous cyanobacteria have a strong morphological convergence with some other spherical and filamentous bacteria and algae, many genera of heteropolar cyanobacteria have distinctive apical and basal regions and cellular differentiation that makes it possible to unambiguously recognize the forms based entirely upon cellular dimensions, filament size and distinctive morphological characteristics. For almost two centuries, these morphological characteristics have historically provided the basis for the systematics and taxonomy of cyanobacteria. This paper presents ESEM and FESEM images of embedded filaments and thick mats found in-situ in the Murchison CM2 and Orgueil cn carbonaceous meteorites. Comparative images are also provided for known genera and species of cyanobacteria and other microbial extremophiles. Energy Dispersive X-ray Spectroscopy (EDS) studies indicate that the meteorite filaments typically exhibit dramatic chemical differentiation with distinctive difference between the possible microfossil and the meteorite matrix in the immediate proximity. Chemical differentiation is also observed within these microstructures with many of the permineralized filaments enveloped within electron transparent carbonaceous sheaths. Elemental distributions of these embedded filaments are not consistent with recent cyanobacteria or other living or preserved microbial extremophiles that have been investigated during this research. The meteorite filaments often have nitrogen content below the sensitivity level of the EDS detector. Carbon, Sulphur, Iron or Silicon are often highly enriched and hence anomalous C/N and CIS ratios when compared with modem cyanobacteria. The meteorite forms that are unambiguously recognizable as biological filaments are interpreted as indigenous microfossils analogous to several known genera of modem cyanobacteria and associated trichomic filamentous prokaryotes.

Hoover, Richard B.↗

NASA NTRS2010

Inferring Properties of Ancient Cyanobacteria from Biogeochemical Activity and Genomes of Siderophilic Cyanobacteria

Interrelationships between life and the planetary system could have simultaneously left landmarks in genomes of microbes and physicochemical signatures in the lithosphere. Verifying the links between genomic features in living organisms and the mineralized signatures generated by these organisms will help to reveal traces of life on Earth and beyond. Among contemporary environments, iron-depositing hot springs (IDHS) may represent one of the most appropriate natural models [1] for insights into ancient life since organisms may have originated on Earth and probably Mars in association with hydrothermal activity [2,3]. IDHS also seem to be appropriate models for studying certain biogeochemical processes that could have taken place in the late Archean and,-or early Paleoproterozoic eras [4, 5]. It has been suggested that inorganic polyphosphate (PPi), in chains of tens to hundreds of phosphate residues linked by high-energy bonds, is environmentally ubiquitous and abundant [6]. Cyanobacteria (CB) react to increased heavy metal concentrations and UV by enhanced generation of PPi bodies (PPB) [7], which are believed to be signatures of life [8]. However, the role of PPi in oxygenic prokaryotes for the suppression of oxidative stress induced by high Fe is poorly studied. Here we present preliminary results of a new mechanism of Fe mineralization in oxygenic prokaryotes, the effect of Fe on the generation of PPi bodies in CB, as well as preliminary analysis of the diversity and phylogeny of proteins involved in the prevention of oxidative stress in phototrophs inhabiting IDHS.

McKay, David S.↗

NASA NTRS2010

Biogeochemical Activity of Siderophilic Cyanobacteria and Insights from their Genomes Implications for the Development of New Biosignatures

Verifying the links between genomie features in living organisms and their mineralization/demineralization activity will help to reveal traces of life on Earth and beyond. Among contemporary environments, iron-depositing hot springs (IDHS) may represent one of the most appropriate natural models for insights into ancient life since organisms may have originated on Earth and possibly Mars in association with hydrothennal activity and high [Fe(2+)]. Siderophilic or "iron-loving" cyanobacteria (CB) inhabiting IDHS may have genomic features and properties similar to those of ancient organisms because abundant Fe(2+) in IDHS has a strong potential to increase the magnitude of oxidative stress. That is why specific and/or additional proteins involved in Fe mineralization by siderophilic CB are expected. Inorganic polyphosphates (PPi) are known to increase the viability of prokaryotes Linder heavy metal concentrations and UV stress conditions. PPi have also been proposed as biosignatures. Ancient CB could have also been stressed by occasional migrations from the Fe(2+) rich Ocean to the basaltic land which was almost devoid of dissolved Fe(2+). Thus, the study of the adaptation reactions of siderophilic CB to fluctuation of dissolved Fe level may shed light on the paleophysiology of ancient oxygenic prokaryotes. Moreover, bioweathered Fe, Al, P, Cu, Ti and rare earth elements can be thought of as candidate organomarkers that document the effects of or ganic molecules in weathered rocks. However, the molecular mechanisms of the maintenance of Fe homeostasis in siderophilic CB, the role of PPi for this process and bioweathering activities are poorly understood. Here we present preliminary results describing a new mechanism of Fe mineralization in siderophilic CB, the effect of Fe on the generation of PPi bodies in siderophilic CB, their bioweathering activity and preliminary analysis of the diversity of proteins involved in the prevention of oxidative stress in phototrophs inhabiting IDHS.

Brown, I. I.↗

NASA NTRSDate not supplied

The membrane bioreactor (MBR): A hybrid technology for bioregenerative wastewater treatment and resource recovery in space

Extraplanetary surface habitat life support systems (LSS) on the Moon and Mars, as well as long-duration space travel, will require novel capabilities to withstand anticipated unique, harsh conditions. In order to provide safe, habitable environments for the crew, water purification and waste processing systems will be required to treat all sources of water (condensate, Sabatier, urine, hygiene, fecal, food waste) in order to achieve the necessary levels of recovery needed to sustain life over the long-duration missions. The ability to recycle organic wastes creates an opportunity to recover critical elements (e.g., C, H, O, N, P) for subsequent food production, water purification, and atmospheric regeneration. Bioregenerative systems mimic functions of nature in engineered systems, or bioreactors, utilizing combination of prokaryotes, eukaryotes and archaea. While these systems are commonly used on Earth for wastewater treatment, bioreactors for space travel face additional challenges. Terrestrial bioreactors often rely on gravitational settling of dense flocs and granules for cell retention. For micro- or partial-gravity environments, density differential alone will not be adequate for cell retention; a gravity-independent means for cell retention is crucial. The membrane bioreactor represents the state of the art in wastewater treatment. This hybrid system combines biological processes with membrane filtration to achieve performance beyond what each can accomplish individually. The complete cell retention in an MBR allows for the decoupling of hydraulic retention time (HRT) and solids retention time (SRT), which result in a high-thruput, compact, treatment system. The Bioregenerative Water Technology Team at NASA Kennedy Space Center and the University of South Florida has developed a bioregenerative platform based on the hybrid MBR technology. The overall architecture is compact, modular, flexible, and adaptable to mission evolutions. The main subsystems of the bioregenerative architecture include: 1) Anaerobic membrane bioreactor (AnMBR): Also termed the Organic processor assembly (OPA), the function of the AnMBR is to treat organic wastes such as fecal and food wastes. These wastes are characterized by a concentration of suspended solids comprised of carbohydrates, proteins and lipids. The assigned function of the AnMBR is to break down and covert suspended solids to biogas (methane, hydrogen and carbon dioxide), reduce effluent chemical oxygen demand (COD), liberate organically-bound nutrients, and remove pathogenic organisms. 2) Phototrophic membrane bioreactor (PMBR): The PMBR is comprised of a co-culture of microalgae and bacteria. The assigned function of the PMBR is to polish the permeate of the AnMBR to further remove dissolved organic carbon, manage nutrients (nitrogen transformation, load dampening), and perform air revitalization. 3) Food processor assembly (FPA): The FPA is a food production platform (prokaryotic or eukaryotic), fueled by outputs from the AnMBR, or PMBR. For the presentation, we will describe each step of the bioregenerative architecture, and present performance data from extended trials treating analog and real metabolic wastes.

Bioreactor↗

DOE OSTI2022

Soil pH influences the structure of virus communities at local and global scales

The influence of biotic and abiotic factors on viral communities across environmental gradients in soil is relatively unknown. While soil pH strongly influences microbial community structure, it is unclear whether there is a similar influence on soil viruses. In this study, prokaryotic and viral communities were characterized in soils from a long-term pH-manipulated soil gradient (pH 4.5 and 7.5), and viral populations also compared to those of other soils ranging in pH (4.0–7.5). Viral communities were significantly influenced by pH at the local scale with 99% of viral operational taxonomic units restricted to pH 4.5 or 7.5 soil only. Analysis of viromes from six other European and North American soil systems demonstrated that a selection of viral clusters from acidic and neutral pH soils were more associated with those from the local gradient pH 4.5 or 7.5 soils, respectively. While direct pH effects on virion integrity and indirect selection via host composition were not distinguished, the results reveal that soil pH is a factor in structuring viral communities at local and global scales.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

OperonSEQer: A set of machine-learning algorithms with threshold voting for detection of operon pairs using short-read RNA-sequencing data

Operon prediction in prokaryotes is critical not only for understanding the regulation of endogenous gene expression, but also for exogenous targeting of genes using newly developed tools such as CRISPR-based gene modulation. A number of methods have used transcriptomics data to predict operons, based on the premise that contiguous genes in an operon will be expressed at similar levels. While promising results have been observed using these methods, most of them do not address uncertainty caused by technical variability between experiments, which is especially relevant when the amount of data available is small. In addition, many existing methods do not provide the flexibility to determine the stringency with which genes should be evaluated for being in an operon pair. We present OperonSEQer, a set of machine learning algorithms that uses the statistic and p-value from a non-parametric analysis of variance test (Kruskal-Wallis) to determine the likelihood that two adjacent genes are expressed from the same RNA molecule. We implement a voting system to allow users to choose the stringency of operon calls depending on whether your priority is high recall or high specificity. In addition, we provide the code so that users can retrain the algorithm and re-establish hyperparameters based on any data they choose, allowing for this method to be expanded as additional data is generated. We show that our approach detects operon pairs that are missed by current methods by comparing our predictions to publicly available long-read sequencing data. OperonSEQer therefore improves on existing methods in terms of accuracy, flexibility, and adaptability.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Joint Conference Support (ISPP and ICMP)

Funds are requested to support the attendance of junior scientists at two international conferences: the International Symposium on Phototrophic Prokaryotes (ISPP) and the International Conference on Microbial Photosynthesis (ICMP). Both will be held on the campus of the University of British Colombia in Vancouver in August of 2018. The primary goal of the ISPP is to provide a forum for students and senior investigators to gather in an informal setting to share new scientific findings on all aspects of bacterial phototrophs (both anoxygenic and oxygenic). The ICMP will appeal to those working on photosynthetic processes in these organisms as well as in eukaryotic phototrophs for other reasons (e.g. as major producers in the oceans, as models for marine phytoplankton, as biofuel-producing systems, etc.). The ICMP was designed to follow the ISPP such that students and postdocs could attend two conferences for the travel costs of one. The funds will be used to defray the registration costs of graduate student and postdoctoral attendees to make it even more affordable for junior scientists.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1997

The limits of life on Earth and searching for life on Mars

Considerations of basic properties of bacteria such as size, structure, and metabolic versatility allow one to understand how these remarkable life-forms are so adaptable to environments previously thought to be uninhabitable. It is now appreciated that bacteria on Earth can utilize almost any redox couple that yields energy, taking advantage of this energy, while transforming the elements during metabolism. The ability to grow at the expense of inorganic redox couples allows the microbes to occupy niches not available to the more metabolically constrained eukaryotes. Furthermore, the simplicity of the bacterial structure allows them considerably more resistance to environmental variables (pH, salinity, temperature) that are toxic or lethal to more complex organisms. This information can be used to explain the predominance of prokaryotes in extreme environments on Earth, and to speculate as to simple types of metabolism and biogeochemical cycles that may exist on this planet, Mars, and perhaps other non-Earth environments.

Non-NASA Center↗