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All sourcesNASA NTRSDOE OSTI
NASA NTRS1995

Anomalous carbonate precipitates: is the Precambrian the key to the Permian?

Late Permian reefs of the Capitan complex, west Texas; the Magnesian Limestone, England; Chuenmuping reef, south China; and elsewhere contain anomalously large volumes of aragonite and calcite marine cements and sea-floor crusts, as well as abundant microbial precipitates. These components strongly influenced reef growth and may have been responsible for the construction of rigid, open reefal frames in which bryozoans and sponges became encrusted and structurally reinforced. In some cases, such as the upper biostrome of the Magnesian Limestone, precipitated microbialites and inorganic crusts were the primary constituents of the reef core. These microbial and inorganic reefs do not have modern marine counterparts; on the contrary, their textures and genesis are best understood through comparison with the older rock record, particularly that of the early Precambrian. Early Precambrian reefal facies are interpreted to have formed in a stratified ocean with anoxic deep waters enriched in carbonate alkalinity. Upwelling mixed deep and surface waters, resulting in massive seafloor precipitation of aragonite and calcite. During Mesoproterozoic and early Neoproterozoic time, the ocean became more fully oxidized, and seafloor carbonate precipitation was significantly reduced. However, during the late Neoproterozoic, sizeable volumes of deep ocean water once again became anoxic for protracted intervals; the distinctive "cap carbonates" found above Neoproterozoic tillites attest to renewed upwelling of anoxic bottom water enriched in carbonate alkalinity and 12C. Anomalous late Permian seafloor precipitates are interpreted as the product, at least in part, of similar processes. Massive carbonate precipitation was favored by: 1) reduced shelf space for carbonate precipitation, 2) increased flux of Ca to the oceans during increased continental erosion, 3) deep basinal anoxia that generated upwelling waters with elevated alkalinities, and 4) further evolution of ocean water in the restricted Delaware, Zechstein, and other basins. Temporal coincidence of these processes resulted in surface seawater that was greatly supersaturated by Phanerozoic standards and whose only precedents occurred in Precambrian oceans.

Non-NASA Center↗
DOE OSTI2017

RNA-Dependent Cysteine Biosynthesis in Bacteria and Archaea

ABSTRACT The diversity of the genetic code systems used by microbes on earth is yet to be elucidated. It is known that certain methanogenic archaea employ an alternative system for cysteine (Cys) biosynthesis and encoding; tRNA Cys is first acylated with phosphoserine (Sep) by O -phosphoseryl-tRNA synthetase (SepRS) and then converted to Cys-tRNA Cys by Sep-tRNA:Cys-tRNA synthase (SepCysS). In this study, we searched all genomic and metagenomic protein sequence data in the Integrated Microbial Genomes (IMG) system and at the NCBI to reveal new clades of SepRS and SepCysS proteins belonging to diverse archaea in the four major groups (DPANN, Euryarchaeota , TACK, and Asgard) and two groups of bacteria (“ Candidatus Parcubacteria” and Chloroflexi ). Bacterial SepRS and SepCysS charged bacterial tRNA Cys species with cysteine in vitro . Homologs of SepCysE, a scaffold protein facilitating SepRS⋅SepCysS complex assembly in Euryarchaeota class I methanogens, are found in a few groups of TACK and Asgard archaea, whereas the C-terminally truncated homologs exist fused or genetically coupled with diverse SepCysS species. Investigation of the selenocysteine (Sec)- and pyrrolysine (Pyl)-utilizing traits in SepRS-utilizing archaea and bacteria revealed that the archaea carrying full-length SepCysE employ Sec and that SepRS is often found in Pyl-utilizing archaea and Chloroflexi bacteria. We discuss possible contributions of the SepRS-SepCysS system for sulfur assimilation, methanogenesis, and other metabolic processes requiring large amounts of iron-sulfur enzymes or Pyl-containing enzymes. IMPORTANCE Comprehensive analyses of all genomic and metagenomic protein sequence data in public databases revealed the distribution and evolution of an alternative cysteine-encoding system in diverse archaea and bacteria. The finding that the SepRS-SepCysS-SepCysE- and the selenocysteine-encoding systems are shared by the Euryarchaeota class I methanogens, the Crenarchaeota AK8/W8A-19 group, and an Asgard archaeon suggests that ancient archaea may have used both systems. In contrast, bacteria may have obtained the SepRS-SepCysS system from archaea. The SepRS-SepCysS system sometimes coexists with a pyrrolysine-encoding system in both archaea and bacteria. Our results provide additional bioinformatic evidence for the contribution of the SepRS-SepCysS system for sulfur assimilation and diverse metabolisms which require vast amounts of iron-sulfur enzymes and proteins. Among these biological activities, methanogenesis, methylamine metabolism, and organohalide respiration may have local and global effects on earth. Taken together, uncultured bacteria and archaea provide an expanded record of the evolution of the genetic code.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Persistence and plasticity in bacterial gene regulation

Organisms orchestrate cellular functions through transcription factor (TF) interactions with their target genes, although these regulatory relationships are largely unknown in most species. Here we report a high-throughput approach for characterizing TF-target gene interactions across species and its application to 354 TFs across 48 bacteria, generating 17,000 genome-wide binding maps. This dataset revealed themes of ancient conservation and rapid evolution of regulatory modules. We observed rewiring, where the TF sensing and regulatory role is maintained while the arrangement and identity of target genes diverges, in some cases encoding entirely new functions. We further integrated phenotypic information to define new functional regulatory modules and pathways. So, we identified 242 new TF DNA binding motifs, including a 70% increase of known Escherichia coli motifs and the first annotation in Pseudomonas simiae, revealing deep conservation in bacterial promoter architecture. Our method provides a versatile tool for functional characterization of genetic pathways in prokaryotes and eukaryotes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Smart Microbial Cells Couple Catalysis and Sensing to Provide High-Throughput Selection of an Organophosphate Hydrolase

Enzyme engineering for gain of function requires navigating a large combinatorial sequence space efficiently. Typically, many mutations are needed to get significant improvements, while a single “bad” mutation can inactivate the enzyme. To establish high-throughput screening and achieve enhanced resolution between two variants, genetic libraries of the organophosphate hydrolase enzyme paraoxonase 1 (PON 1 ) were rapidly screened via an engineered positive-feedback circuit: a p-nitrophenol (PNP)-specific transcription factor (TF) regulated expression of PON 1 , which catalyzed paraoxon breakdown and PNP production. Rare active mutant colonies, picked by simple visual fluorescence of a PON 1 –green fluorescent protein (GFP) fusion, were characterized. Furthermore, in a single screening round, high (library-scale) throughput enabled the discovery of enhanced paraoxon degradation activity in PON 1 , including structurally unexpected mutations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Sepsis reconsidered: Identifying novel metrics for behavioral landscape characterization with a high-performance computing implementation of an agent-based model

Objectives: Sepsis affects nearly 1 million people in the United States per year, has a mortality rate of 28–50% and requires more than $20 billion a year in hospital costs. Over a quarter century of research has not yielded a single reliable diagnostic test or a directed therapeutic agent for sepsis. Central to this insufficiency is the fact that sepsis remains a clinical/physiological diagnosis representing a multitude of molecularly heterogeneous pathological trajectories. Advances in computational capabilities offered by High Peformance Computing (HPC) platforms call for an evolution in the investigation of sepsis to attempt to define the boundaries of traditional research (bench, clinical and computational) through the use of computational proxy models. We present a novel investigatory and analytical approach, derived from how HPC resources and simulation are used in the physical sciences, to identify the epistemic boundary con- ditions of the study of clinical sepsis via the use of a proxy agent-based model of systemic inflammation. Design: Current predictive models for sepsis use correlative methods that are limited by patient heterogeneity and data sparseness. We address this issue by using an HPC version of a system-level validated agent-based model of sepsis, the Innate Immune Response ABM (IIRBM), as a proxy system in order to identify boundary conditions for the possible behavioral space for sepsis. We then apply advanced analysis derived from the study of Random Dynamical Systems (RDS) to identify novel means for characterizing system behavior and providing insight into the tractability of traditional investigatory methods. Results: The behavior space of the IIRABM was examined by simulating over 70 million sepsis patients for up to 90 days in a sweep across the following parameters: cardio-respiratory-metabolic resilience; microbial invasiveness; microbial toxigenesis; and degree of nosocomial exposure. In addition to using established methods for describing parameter space, we developed two novel methods for characterizing the behavior of a RDS: Probabilistic Basins of Attraction (PBoA) and Stochastic Trajectory Analysis (STA). Computationally generated behavioral landscapes demonstrated attractor structures around stochastic re- gions of behavior that could be described in a complementary fashion through use of PBoA and STA. The stochasticity of the boundaries of the attractors highlights the challenge for correlative attempts to characterize and classify clinical sepsis. Conclusions: HPC simulations of models like the IIRABM can be used to generate approximations of the behavior space of sepsis to both establish “boundaries of futility” with respect to existing investi- gatory approaches and apply system engineering principles to investigate the general dynamic properties of sepsis to provide a pathway for developing control strategies. Here, the issues that bedevil the study and treatment of sepsis, namely clinical data sparseness and inadequate experimental sampling of system behavior space, are fundamental to nearly all biomedical research, manifesting in the “Crisis of Reproducibility” at all levels. HPC-augmented simulation-based research offers an investigatory strategy more consistent with that seen in the physical sciences (which combine experiment, theory and simulation), and an opportunity to utilize the leading advances in HPC, namely deep machine learning and evolutionary computing, to form the basis of an iterative scientific process to meet the full promise of Precision Medicine (right drug, right patient, right time).

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2002

Long Term Manipulations of Intact Microbial Mat Communities in a Greenhouse Collaboratory: Simulating Earth's Present and Past Field Environments

Photosynthetic microbial mat communities were obtained from marine hypersaline saltern ponds, maintained in a greenhouse facility, and examined for the effects of salinity variations. Because these microbial mats are considered to be useful analogs of equivalent ancient marine communities, they offer insights about evolutionary events during the greater than 3 billion year time interval wherein mats co-evolved with Earth's geosphere and atmosphere. Although photosynthetic mats can be highly dynamic and exhibit extremely high activity, the mats in the present study have been maintained for more than one year with relatively minor changes. The major groups of microorganisms, as assayed using microscopic, genetic, and biomarker methodologies, are essentially the same as those in the original field samples. Field and greenhouse mats were similar with respect to rates of exchange of oxygen and dissolved inorganic carbon across the mat-water interface, both during the day and at night. Field and greenhouse mats exhibited similar rates of efflux of methane and hydrogen. Manipulations of salinity in the water overlying the mats produced changes in the community that strongly resemble those observed in the field. A collaboratory testbed and an array of automated features are being developed to support remote scientific experimentation with the assistance of intelligent software agents. This facility will permit teams of investigators to explore ancient environmental conditions that are rare or absent today but might have influenced the early evolution of these photosynthetic ecosystems.

Bebout, Brad↗
NASA NTRS1989

Lipophilic pigments from cyanobacterial (blue-green algal) and diatom mats in Hamelin Pool, Shark Bay, Western Australia

Lipophilic pigments were examined in microbial mat communities dominated by cyanobacteria in the intertidal zone and by diatoms in the subtidal and sublittoral zones of Hamelin Pool, Shark Bay, Western Australia. These microbial mats have evolutionary significance because of their similarity to lithfied stromatolites from the Proterozoic and Early Paleozoic eras. Fucoxanthin, diatoxanthin, diadinoxanthin, beta-carotene, and chlorophylls a and c characterized the diatom mats, whereas cyanobacterial mats contained myxoxanthophyll, zeaxanthin, echinenone, beta-carotene, chlorophyll a and, in some cases, sheath pigment. The presence of bacteriochlorophyll a within the mats suggest a close association of photosynthetic bacteria with diatoms and cyanobacteria. The high carotenoids : chlorophyll a ratios (0.84-2.44 wt/wt) in the diatom mats suggest that carotenoids served a photoprotective function in this high light environment. By contrast, cyanobacterial sheath pigment may have largely supplanted the photoprotective role of carotenoids in the intertidal mats.

NASA Discipline Exobiology↗
NASA NTRS2005

Lunar and Planetary Science XXXVI, Part 22

The Lunar and Planetary Science XXXVI, Part 22 is presented. The topics include: 1) Pressure Histories from Thin and Thick Shock-induced Melt Veins in Meteorites; 2) Nano-structured Minerals as Signature of Microbial Activity; 3) The Insoluble Carbonaceous Material of CM Chondrites as Possible Source of Discrete Organics During the Asteroidal Aqueous Phase; 4) Discovery of Abundant Presolar Silicates in Subgroups of Antarctic Micrometeorites; 5) Characteristics of a Seismometer for the LUNAR-A Penetrator; 6) Heating Experiments of the HaH 262 Eucrite and Implication for the Metamorphic History of Highly Metamorphosed Eucrites; 7) Measurements of Ejecta Velocity Distribution by a High-Speed Video Camera; 8) Petrological Comparison of Mongolian Jalanash Ureilite and Twelve Antarctic Ureilites; 9) Metallographic Cooling Rate of IVA Irons Revisited; 10) Inhomogeneous Temperature Distribution in Chondrules in Shock-Wave Heating Model; 11) Subsurface Weathering of Rocks and Soils at Gusev Crater; 12) Extinct Radioactivities in the Early Solar System and the Mean Age of the Galaxy; 13) Correlation of Rock Spectra with Quantitative Morphologic Indices: Evidence for a Single Rock Type at the Mars Pathfinder Landing Site; 14) Silicon Isotopic Ratios of Presolar Grains from Supernovae; 15) Current Status and Readiness on In-Situ Exploration of Asteroid Surface by MINERVA Rover in Hayabusa Mission; 16) Long Formation Period of Single CAI: Combination of O and Mg Isotope Distribution; 17) Supra-Canonical Initial 26Al/27Al Indicate a 105 Year Residence Time for CAIs in the Solar Proto-Planetary Disk; 18) Evolution of Mercury's Obliquity; 19) First Results from the Huygens Surface Science Package; 20) Polyhedral Serpentine Grains in CM Chondrites; 21) Mountainous Units in the Martian Gusev Highland Region: Volcanic, Tectonic, or Impact Related? 22) Petrography of Lunar Meteorite MET 01210, A New Basaltic Regolith Breccia; 23) Earth-Moon Impacts at ~300 Ma and ~500 Ma Ago; 24) Chemical and Isotopic Analyses of Apollo 16 Glasses: An Integrated Approach; 25) Measuring the Surfaces on Mars; 26) Melting in Martian Snowbanks; 27) The Effect of Ni on Fe-FeS Phase Relations: Implications for the Chemistry of the Martian Core; 28) Shorelines in the Western United States as Analogs for Hypothesized Shoreline Features on Mars; 29) Al and Ti Isotopic Ratios of Presolar SiC Grains of Type Z; 30) Physicochemical Conditions of Clinopyroxene Crystallization in the Parental Bodies of Ordinary Chondrites; 31) Metamorphosed CM and CI Carbonaceous Chondrites Could be from the Breakup of the Same Earth-crossing Asteroid; 32) Aqueous Alteration and Hydrogen Generation on Parent Bodies of Unequilibrated Ordinary Chondrites: Thermodynamic Modeling for the Semarkona Composition; and 33) Preliminary Analysis of Relative Abundances of Hydrothermal Alteration Products in the C1-N10, Y6-N19, and Yax-1_863.51 Impact Melt Samples, Chicxulub Structure, Mexico

Source record↗
DOE OSTI2026

Harnessing evolution: leveraging bacterial isoprenoid pathway diversity toward improved bioengineering strategies

Isoprenoids play vital roles in all domains of life, from beta-carotene in bacteria to heme in humans. Two distinct metabolic pathways have evolved to synthesize the critical precursor of all mature isoprenoids: the mevalonate (MEV) and the methylerythritol phosphate (MEP) pathways. Here, we quantify the extensive inter- and intra-genus heterogeneity in the usage of these two pathways with particular emphasis on rare bacteria that encode both, or neither, pathways. Furthermore, MEP intermediates themselves have non-isoprenogenic roles that may underlie evolutionary pressures driving pathway diversification. Understanding isoprenoid biosynthesis in bacteria offers new avenues toward more sustainable engineering of economically relevant molecules in microbes.

Biotechnology and Synthetic Biology↗
NASA NTRS1998

Biomarkers as tracers for life on early earth and Mars

Biomarkers in geological samples are products derived from biochemical (natural product) precursors by reductive and oxidative processes (e.g., cholestanes from cholesterol). Generally, lipids, pigments and biomembranes are preserved best over longer geological times and labile compounds such as amino acids, sugars, etc. are useful biomarkers for recent times. Thus, the detailed characterization of biomarker compositions permits the assessment of the major contributing species of extinct and/or extant life. In the case of the early Earth, work has progressed to elucidate molecular structure and carbon isotropic signals preserved in ancient sedimentary rocks. In addition, the combination of bacterial biochemistry with the organic geochemistry of contemporary and ancient hydrothermal ecosystems permits the modeling of the nature, behavior and preservation potential of primitive microbial communities. This approach uses combined molecular and isotopic analyses to characterize lipids produced by cultured bacteria (representative of ancient strains) and to test a variety of culture conditions which affect their biosynthesis. On considering Mars, the biomarkers from lipids and biopolymers would be expected to be preserved best if life flourished there during its early history (3.5-4 x 10(9) yr ago). Both oxidized and reduced products would be expected. This is based on the inferred occurrence of hydrothermal activity during that time with the concomitant preservation of biochemically-derived organic matter. Both known biomarkers (i.e., as elucidated for early terrestrial samples and for primitive terrestrial microbiota) and novel, potentially unknown compounds should be characterized.

Non-NASA Center↗
DOE OSTI2021

Distinct protein architectures mediate species-specific beta-glucan binding and metabolism in the human gut microbiota

Complex glycans that evade our digestive system are major nutrients that feed the human gut microbiota (HGM). The prevalence of Bacteroidetes in the HGM of populations worldwide is engendered by the evolution of polysaccharide utilization loci (PULs), which encode concerted protein systems to utilize the myriad complex glycans in our diets. Despite their crucial roles in glycan recognition and transport, cell-surface glycan-binding proteins (SGBPs) remained understudied cogs in the PUL machinery. Here, we report the structural and biochemical characterization of a suite of SGBP-A and SGBP-B structures from three syntenic β(1,3)-glucan utilization loci (1,3GULs) from Bacteroides thetaiotaomicron (Bt), Bacteroides uniformis (Bu), and B. fluxus (Bf), which have varying specificities for distinct β-glucans. Ligand complexes provide definitive insight into β(1,3)-glucan selectivity in the HGM, including structural features enabling dual β(1,3)-glucan/mixed-linkage β(1,3)/β(1,4)-glucan-binding capability in some orthologs. The tertiary structural conservation of SusD-like SGBPs-A is juxtaposed with the diverse architectures and binding modes of the SGBPs-B. Specifically, the structures of the trimodular BtSGBP-B and BuSGBP-B revealed a tandem repeat of carbohydrate-binding module-like domains connected by long linkers. In contrast, BfSGBP-B comprises a bimodular architecture with a distinct β-barrel domain at the C terminus that bears a shallow binding canyon. The molecular insights obtained here contribute to our fundamental understanding of HGM function, which in turn may inform tailored microbial intervention therapies.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2024

Current Status of Martian Moons eXploration (MMX) Contamination Control and Curation Activity

Martian Moons eXploration (MMX) is a sample return mission from the Martian moon Phobos. The MMX spacecraft is scheduled to launch in 2026 and return to Earth in 2031. The main science goals of MMX are “to reveal the origin of the Martian moons and make progress in the understanding of planetary system formation and material transport in the solar system, and to observe processes that impact the circumplanetary and surface environments of Mars”. MMX has two sampling systems: coring (C)-sampler and pneumatic (P)-sampler and plans to bring back >10 g of Phobos sample. The retuned sample in the sample capsule will be transferred to the curation facility in ISAS/JAXA for sample curation and subsequent sample analysis. Contamination control of the sample return mission requires special care to prevent terrestrial contamination to the spacecraft, which would ruin the scientific value of the returned sample. Retaining the pristineness of the retuned sample is an important task of the MMX Curation and Sampler Science teams. The basis of the contamination control is (1) to minimize and understand the nature and amount of contaminants, (2) to perform contamination assessment and evaluate the effect of contaminants in the spacecraft on the retuned sample, (3) to employ a contamination knowledge (CK) material coupon in the spacecraft to identify the contaminants in the returned samples. In the MMX contamination control plan, the allowable contamination level for each contaminant is carefully defined. They are mostly set to be 1/1000 of the expected amount of each material in the returned sample and are divided into two main categories: organic and inorganic. The allowable atmospheric leakage rate to the sample container is also defined. The allowable contamination level of the organic materials is based on the composition of carbonaceous chondrites. The target contaminants are amino acids, aliphatic and aromatic hydrocarbons, carboxylic acids, etc. In case of the inorganic materials, the target contaminants are important elements to permit distinguishing the origin of the Martian moon by nucleosynthetic isotope anomalies (Cr, Ti, and Mo) and to reveal the evolution of the Martian moon by chronology (Hf, W, U, Pb, Rb, Sr, Sm, and Nd). The key instrument of contamination control in the sample return mission is the sampler system. The C-sampler has been developed by JAXA and the P-sampler was provided by Honeybee/NASA. In MMX, materials used in the two samplers (C- and P- sampler) were carefully selected to avoid potential contamination from the design stage of the system. The individual parts of the C-sampler FM (Flight Model) were thoroughly cleaned at the curation facility in ISAS/JAXA by the full-course cleaning procedure, which is an ultrasonic cleaning with organic solvents and ultrapure water in several steps. The equivalent level of cleaning was also carried out on the P-Samper FM as well by Honeybee Robotics in the USA. Now, MMX is in the critical phase for contamination control called ATLO: Assembly, Test, and Launch Operations. During the ATLO phase, sampler FM is constantly purged with nitrogen gas and maintained at positive pressure to prevent environmental contamination. The surrounding environments of the sampler FM are also simultaneously monitored using the CK Monitoring Coupon Set, which consists of several witness materials such as a glass petri dish, sapphire glass disk, and carbon adhesive tape (Figure 1). The detailed environmental assessment of each clean room used for the assembly and test of the sampler FM has also been conducted. This assessment includes microbial analysis, which was performed for OSIRIS-REx. Regarding the sample recovery and sample curation, we have started the designing of Sample Container Disassembling Instrument for the sample recovery from the sample container and the MMX curation chamber for sample curation. The curation protocol for the Phobos returned sample has also been discussed by the MMX Sample Analysis Working Team (SAWT). The MMX curation protocol consists of three phases: (1) quick analysis, (2) pre-basic characterization, and (3) basic characterization. (1) is extraction of the sample gas from the sample container and analysis by mass spectrometry, (2) is observation in bulk level, and (3) is observation in grain level and allocation of the sample aliquots. In parallel with the curation protocol, the returned sample undergoes preliminary examination for scientific investigations to achieve science goals. In addition, the CK witness plates made of sapphire glass are on board the sampler system. The CK witness plates will be recovered from the sampler system and analyzed by SAWT for the assessment of in-flight contamination.

Haruna Sugahara↗
NASA NTRS2004

Impact-shocked rocks--insights into Archean and extraterrestrial microbial habitats (and sites for prebiotic chemistry?)

Impact-shocked gneiss shocked to greater than 10 GPa in the Haughton impact structure in the Canadian High Arctic has an approximately 25-times greater pore surface area than unshocked rocks. These pore spaces provide microhabitats for a diversity of heterotrophic microorganisms and in the near-surface environment of the rocks, where light levels are sufficient, cyanobacteria. Shocked rocks provide a moisture retaining, UV protected microenvironment. During the Archean, when impact fluxes were more than two orders of magnitude higher than today, the shocked-rock habitat was one of the most common terrestrial habitats and might have provided a UV-shielded refugium for primitive life. These potential habitats are in high abundance on Mars where impact crater habitats could have existed over geologic time periods of billions of years, suggesting that impact-shocked rocks are important sites to search for biomolecules in extraterrestrial life detection strategies. In addition to being favourable sites for life, during the prebiotic period of planetary history impact-shocked rocks might have acted as a site for the concentration of reactants for prebiotic syntheses. c2004 COSPAR. Published by Elsevier Ltd. All rights reserved.

Evolution, Chemical↗
DOE OSTI2022

Coupled abiotic-biotic cycling of nitrous oxide in tropical peatlands

Atmospheric nitrous oxide (N 2 O) is a potent greenhouse gas thought to be mainly derived from microbial metabolism as part of the denitrification pathway. Here we report that in unexplored peat soils of Central and South America, N 2 O production can be driven by abiotic reactions (≤98%) highly competitive to their enzymatic counterparts. Extracted soil iron positively correlated with in situ abiotic N 2 O production determined by isotopic tracers. Moreover, we found that microbial N 2 O reduction accompanied abiotic production, essentially closing a coupled abiotic-biotic N 2 O cycle. Anaerobic N 2 O consumption occurred ubiquitously (pH 6.4–3.7), with proportions of diverse clade II N 2 O reducers increasing with consumption rates. Our findings show that denitrification in tropical peat soils is not a purely biological process but rather a ‘mosaic’ of abiotic and biotic reduction reactions. Here, we predict that hydrological and temperature fluctuations differentially affect abiotic and biotic drivers and further contribute to the high N 2 O flux variation in the region.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Distinct and rich assemblages of giant viruses in Arctic and Antarctic lakes

Giant viruses (GVs) are key players in ecosystem functioning, biogeochemistry, and eukaryotic genome evolution. GV diversity and abundance in aquatic systems can exceed that of prokaryotes, but their diversity and ecology in lakes, especially polar ones, remain poorly understood. We conducted a comprehensive survey and meta-analysis of GV diversity across 20 lakes, spanning polar to temperate regions, combining our extensive lake metagenome database from the Canadian Arctic and subarctic with publicly available datasets. Leveraging a novel GV genome identification tool, we identified 3304 GV metagenome-assembled genomes, revealing lakes as untapped GV reservoirs. Phylogenomic analysis highlighted their dispersion across all Nucleocytoviricota orders. Strong GV population endemism emerged between lakes from similar regions and biomes (Antarctic and Arctic), but a polar/temperate barrier in lacustrine GV populations and differences in their gene content could be observed. Our study establishes a robust genomic reference for future investigations into lacustrine GV ecology in fast changing polar environments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Thermophilic Dehalococcoidia with unusual traits shed light on an unexpected past

Abstract Although the phylum Chloroflexota is ubiquitous, its biology and evolution are poorly understood due to limited cultivability. Here, we isolated two motile, thermophilic bacteria from hot spring sediments belonging to the genus Tepidiforma and class Dehalococcoidia within the phylum Chloroflexota. A combination of cryo-electron tomography, exometabolomics, and cultivation experiments using stable isotopes of carbon revealed three unusual traits: flagellar motility, a peptidoglycan-containing cell envelope, and heterotrophic activity on aromatics and plant-associated compounds. Outside of this genus, flagellar motility has not been observed in Chloroflexota, and peptidoglycan-containing cell envelopes have not been described in Dehalococcoidia. Although these traits are unusual among cultivated Chloroflexota and Dehalococcoidia, ancestral character state reconstructions showed flagellar motility and peptidoglycan-containing cell envelopes were ancestral within the Dehalococcoidia, and subsequently lost prior to a major adaptive radiation of Dehalococcoidia into marine environments. However, despite the predominantly vertical evolutionary histories of flagellar motility and peptidoglycan biosynthesis, the evolution of enzymes for degradation of aromatics and plant-associated compounds was predominantly horizontal and complex. Together, the presence of these unusual traits in Dehalococcoidia and their evolutionary histories raise new questions about the timing and selective forces driving their successful niche expansion into global oceans.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Common origin of sterol biosynthesis points to a feeding strategy shift in Neoproterozoic animals

Steranes preserved in sedimentary rocks serve as molecular fossils, which are thought to record the expansion of eukaryote life through the Neoproterozoic Era (~1000-541 Ma). Scientists hypothesize that ancient C 27 steranes originated from cholesterol, the major sterol produced by living red algae and animals. Similarly, C 28 and C 29 steranes are thought to be derived from the sterols of prehistoric fungi, green algae, and other microbial eukaryotes. However, recent work on annelid worms–an advanced group of eumetazoan animals–shows that they are also capable of producing C 28 and C 29 sterols. In this paper, we explore the evolutionary history of the 24-C sterol methyltransferase (smt) gene in animals, which is required to make C 28+ sterols. We find evidence that the smt gene was vertically inherited through animals, suggesting early eumetazoans were capable of C 28+ sterol synthesis. Our molecular clock of the animal smt gene demonstrates that its diversification coincides with the rise of C 28 and C 29 steranes in the Neoproterozoic. This study supports the hypothesis that early eumetazoans were capable of making C 28+ sterols and that many animal lineages independently abandoned its biosynthesis around the end-Neoproterozoic, coinciding with the rise of abundant eukaryotic prey.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2018

The Habitability of Proxima Centauri b: Environmental States and Observational Discriminants

Proxima Centauri b provides an unprecedented opportunity to understand the evolution and nature of terrestrial planets orbiting M dwarfs. Although Proxima Cen b orbits within its star’s habitable zone, multiple plausible evolutionary paths could have generated different environments that may or may not be habitable. Here, we use 1-D coupled climate-photochemical models to generate self-consistent atmospheres for several evolutionary scenarios, including high-O2, high-CO2, and more Earth-like atmospheres, with both oxic and anoxic compositions. We show that these modeled environments can be habitable or uninhabitable at Proxima Cen b's position in the habitable zone. We use radiative transfer models to generate synthetic spectra and thermal phase curves for these simulated environments, and use instrument models to explore our ability to discriminate between possible planetary states. These results are applicable not only to Proxima Cen b but to other terrestrial planets orbiting M dwarfs. Thermal phase curves may provide the first constraint on the existence of an atmosphere. We find that James Webb Space Telescope ( JWST) observations longward of 10 mm could characterize atmospheric heat transport and molecular composition. Detection of ocean glint is unlikely with JWST but may be within the reach of larger-aperture telescopes. Direct imaging spectra may detect O4 absorption, which is diagnostic of massive water loss and O2 retention, rather than a photosynthetic biosphere. Similarly, strong CO2 and CO bands at wavelengths shortward of 2.5 mm would indicate a CO2-dominated atmosphere. If the planet is habitable and volatile-rich, direct imaging will be the best means of detecting habitability. Earth-like planets with microbial biospheres may be identified by the presence of CH4-which has a longer atmospheric lifetime under Proxima Centauri's incident UV-and either photosynthetically produced O2 or a hydrocarbon haze layer.

Meadows, Victoria S.↗