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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Collective motion conceals fitness differences in crowded cellular populations

Many cellular populations are tightly packed, such as microbial colonies and biofilms, or tissues and tumours in multicellular organisms. The movement of one cell in these crowded assemblages requires motion of others, so that cell displacements are correlated over many cell diameters. Whenever movement is important for survival or growth, these correlated rearrangements could couple the evolutionary fate of different lineages. However, little is known about the interplay between mechanical forces and evolution in dense cellular populations. Here, by tracking slower-growing clones at the expanding edge of yeast colonies, we show that the collective motion of cells prevents costly mutations from being weeded out rapidly. Joint pushing by neighbouring cells generates correlated movements that suppress the differential displacements required for selection to act. This mechanical screening of fitness differences allows slower-growing mutants to leave more descendants than expected under non-mechanical models, thereby increasing their chance for evolutionary rescue. Our work suggests that, in crowded populations, cells cooperate with surrounding neighbours through inevitable mechanical interactions. This effect has to be considered when predicting evolutionary outcomes, such as the emergence of drug resistance or cancer evolution.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2020

Exploring Carbon Mineral Systems: Recent Advances in C Mineral Evolution, Mineral Ecology, and Network Analysis

Large and growing data resources on the spatial and temporal diversity and distribution of the more than 400 carbon-bearing mineral species reveal patterns of mineral evolution and ecology. Recent advances in analytical and visualization techniques leverage these data and are propelling mineralogy from a largely descriptive field into one of prediction within complex, integrated, multidimensional systems. These discoveries include: (1) systematic changes in the character of carbon minerals and their networks of coexisting species through deep time; (2) improved statistical predictions of the number and types of carbon minerals that occur on Earth but are yet to be discovered and described; and (3) a range of proposed and ongoing studies related to the quantification of network structures and trends, relation of mineral “natural kinds” to their genetic environments, prediction of the location of mineral species across the globe, examination of the tectonic drivers of mineralization through deep time, quantification of preservational and sampling bias in the mineralogical record, and characterization of feedback relationships between minerals and geochemical environments with microbial populations. These aspects of Earth’s carbon mineralogy underscore the complex coevolution of the geosphere and biosphere and highlight the possibility for scientific discovery in Earth and planetary systems.

Carbon↗
DOE OSTI2023

Astrovirology: how viruses enhance our understanding of life in the Universe

Abstract Viruses are the most numerically abundant biological entities on Earth. As ubiquitous replicators of molecular information and agents of community change, viruses have potent effects on the life on Earth, and may play a critical role in human spaceflight, for life-detection missions to other planetary bodies and planetary protection. However, major knowledge gaps constrain our understanding of the Earth's virosphere: (1) the role viruses play in biogeochemical cycles, (2) the origin(s) of viruses and (3) the involvement of viruses in the evolution, distribution and persistence of life. As viruses are the only replicators that span all known types of nucleic acids, an expanded experimental and theoretical toolbox built for Earth's viruses will be pivotal for detecting and understanding life on Earth and beyond. Only by filling in these knowledge and technical gaps we will obtain an inclusive assessment of how to distinguish and detect life on other planetary surfaces. Meanwhile, space exploration requires life-support systems for the needs of humans, plants and their microbial inhabitants. Viral effects on microbes and plants are essential for Earth's biosphere and human health, but virus–host interactions in spaceflight are poorly understood. Viral relationships with their hosts respond to environmental changes in complex ways which are difficult to predict by extrapolating from Earth-based proxies. These relationships should be studied in space to fully understand how spaceflight will modulate viral impacts on human health and life-support systems, including microbiomes. In this review, we address key questions that must be examined to incorporate viruses into Earth system models, life-support systems and life detection. Tackling these questions will benefit our efforts to develop planetary protection protocols and further our understanding of viruses in astrobiology.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Differential Exudation Creates Biogeochemically Distinct Microenvironments during Rhizosphere Evolution

Plant roots and associated microbes release a diverse range of functionally distinct exudates into the surrounding rhizosphere with direct impacts on soil carbon storage, nutrient availability, and contaminant dynamics. Yet mechanistic linkages between root exudation and emergent biogeochemical processes remain challenging to measure nondestructively, in real soil, over time. Here we used a novel combination of in situ microsensors with high-resolution mass spectrometry to measure, nondestructively, changing exudation and associated biogeochemical dynamics along single growing plant roots (Avena sativa). We found that metabolite and dissolved organic carbon (DOC) concentrations as well as microbial growth, redox potential (EH), and pH dynamics vary significantly among bulk soil, root tip, and more mature root zones. Surprisingly, the significant spike of rhizosphere DOC upon root tip emergence did not significantly correlate with any biogeochemical parameters. However, the presence of sugars significantly correlated with declines in EH following the arrival of the root tip, likely due to enhanced microbial oxygen demand. Similarly, the presence of organic acids significantly correlated to declines in pH upon root tip emergence. Altogether, our in situ measurements highlight how different exudates released along growing roots create functionally distinct soil microenvironments that evolve over time.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Comparative genomics reveals a dynamic genome evolution in the ectomycorrhizal milk-cap ( Lactarius ) mushrooms

Ectomycorrhizal fungi play a key role in forests by establishing mutualistic symbioses with woody plants. Genome analyses have identified conserved symbiosis-related traits among ectomycorrhizal fungal species, but the molecular mechanisms underlying host specificity remain poorly known. We sequenced and compared the genomes of seven species of milk-cap fungi (Lactarius, Russulales) with contrasting host specificity. We also compared these genomes with those of symbiotic and saprotrophic Russulales species, aiming to identify genes involved in their ecology and host specificity. The size of Lactarius genomes is significantly larger than other Russulales species, owing to a massive accumulation of transposable elements and duplication of dispensable genes. As expected, their repertoire of genes coding for plant cell wall-degrading enzymes is restricted, but they retained a substantial set of genes involved in microbial cell wall degradation. Notably, Lactarius species showed a striking expansion of genes encoding proteases, such as secreted ectomycorrhiza-induced sedolisins. A high copy number of genes coding for small secreted LysM proteins and Lactarius-specific lectins were detected, which may be linked to host specificity. This study revealed a large diversity in the genome landscapes and gene repertoires within Russulaceae. The known host specificity of Lactarius symbionts may be related to mycorrhiza-induced species-specific genes, including secreted sedolisins.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1989

Viking and Mars Rover exobiology

Other than Earth, Mars is the planet generating the greatest interest among those researching and contemplating the origin and distribution of life throughout the universe. The similarity of the early environments of Earth and Mars, and the biological evolution on early Earth provides the motivation to seriously consider the possibility of a primordial Martian biosphere. In 1975 the Viking project launched two unmanned spacecraft to Mars with the intent of finding evidence of the existence of present or past life on this planet. Three Viking Biology experiments were employed: the Labeled Release experiment, the Gas Exchange Experiment, and the Pyrolytic Release experiment. Each of these three experiments tested for microbial existence and utilization of a substrate by examining the gases evolved from specific chemical reactions. Although the results of these experiments were inconclusive, they inferred that there are no traces of extant life on Mars. However, the experiments did not specifically look for indication of extinct life. Therefore, most of the exobiologic strategies and experiments suggested for the Mars Rover Sample Return Mission involve searching for signature of extinct life. The most significant biological signatures and chemical traces to detect include: isotopic and chemical signatures of metabolic activity, anomalous concentrations of certain metals, trace and microfossils, organically preserved materials, carbonates, nitrates, and evaporites.

Schwartz, D. E.↗
NASA NTRS1991

Microbial mats, stromatolites and the rise of oxygen in the Precambrian atmosphere

Microbial mats are stratified communities that develop within the environmental microgradients established at the interfaces of water and solid substrates (Cohen, 1989). Stromatolites, the lithified remains of layered accumulations of microbial mats, occur in rocks as old as 3.5 Ga (Lowe, 1980; Walter et al., 1980). These lithified microbial communities represent the most ancient, widespread ecosystems known, and it is useful to explore their role in the accumulation of free oxygen in the ancient atmosphere.

NASA Program Exobiology↗
DOE OSTI2021

Patterns of Gene Content and Co-occurrence Constrain the Evolutionary Path toward Animal Association in Candidate Phyla Radiation Bacteria

Studying the genetic differences between related microorganisms from different environment types can indicate factors associated with their movement among habitats. This is particularly interesting for bacteria from the Candidate Phyla Radiation because their minimal metabolic capabilities require associations with microbial hosts.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1999

Rapid direct methods for enumeration of specific, active bacteria in water and biofilms

Conventional methods for detecting indicator and pathogenic bacteria in water may underestimate the actual population due to sublethal environmental injury, inability of the target bacteria to take up nutrients and other physiological factors which reduce bacterial culturability. Rapid and direct methods are needed to more accurately detect and enumerate active bacteria. Such a methodological advance would provide greater sensitivity in assessing the microbiological safety of water and food. The principle goal of this presentation is to describe novel approaches we have formulated for the rapid and simultaneous detection of bacteria plus the determination of their physiological activity in water and other environmental samples. The present version of our method involves the concentration of organisms by membrane filtration or immunomagnetic separation and combines an intracellular fluorochrome (CTC) for assessment of respiratory activity plus fluorescent-labelled antibody detection of specific bacteria. This approach has also been successfully used to demonstrate spatial and temporal heterogeneities of physiological activities in biofilms when coupled with cryosectioning. Candidate physiological stains include those capable of determining respiratory activity, membrane potential, membrane integrity, growth rate and cellular enzymatic activities. Results obtained thus far indicate that immunomagnetic separation can provide a high degree of sensitivity in the recovery of seeded target bacteria (Escherichia coli O157:H7) in water and hamburger. The captured and stained target bacteria are then enumerated by either conventional fluorescence microscopy or ChemScan(R), a new instrument that is very sensitive and rapid. The ChemScan(R) laser scanning instrument (Chemunex, Paris, France) provides the detection of individual fluorescently labelled bacterial cells using three emission channels in less than 5 min. A high degree of correlation has been demonstrated between results obtained with the ChemScan and traditional plate counts of mixed natural bacterial populations in water. The continuing evolution of these methods will be valuable in the rapid and accurate analysis of environmental samples.

Review, Tutorial↗
DOE OSTI2025

Community‐Level Metabolic Shifts Following Land Use Change in the Amazon Rainforest Identified by a Supervised Machine Leaning Approach

ABSTRACT The Amazon rainforest has been subjected to high rates of deforestation, mostly for pasturelands, over the last few decades. This change in plant cover is known to alter the soil microbiome and the functions it mediates, but the genomic changes underlying this response are still unresolved. In this study, we used a combination of deep shotgun metagenomics complemented by a supervised machine learning approach to compare the metabolic strategies of tropical soil microbial communities in pristine forests and long‐term established pastures in the Amazon. Machine learning‐derived metagenome analysis indicated that microbial community structures (bacteria, archaea and viruses) and the composition of protein‐coding genes were distinct in each plant cover type environment. Forest and pasture soils had different genomic diversities for the above three taxonomic groups, characterised by their protein‐coding genes. These differences in metagenome profiles in soils under forests and pastures suggest that metabolic strategies related to carbohydrate and energy metabolisms were altered at community level. Changes were also consistent with known modifications to the C and N cycles caused by long‐term shifts in aboveground vegetation and were also associated with several soil physicochemical properties known to change with land use, such as the C/N ratio, soil temperature and exchangeable acidity. In addition, our analysis reveals that these alterations in land use can also result in changes to the composition and diversity of the soil DNA virome. Collectively, our study indicates that soil microbial communities shift their overall metabolic strategies, driven by genomic alterations observed in pristine forests and long‐term established pastures with implications for the C and N cycles.

carbon and nitrogen cycles↗
NASA NTRS1998

Deep Basalt Aquifers in Orcus Patera, Elysium Basin Mars: Perspectives for Exobiology Exploration

Direct indicators of shorelines, spillways, and terraces allowed to determine the extent of the Elysium Paleolake between the contour-lines 1000 and 500 m below the Martian datum. The Elysium Paleolake is bordered north by Orcus Patera (14N/181W), which lies west of the Tartarus Montes and Tartarus Colles. The Orcus Patera displays an ellipse-shaped collapsed caldera of 360-km long and 100-km wide. Viking topographic data show that the bottom of the caldera is located at 2500 below the Martian datum, and surrounded by a steep-walled ram art which crest is located at about 0 m elevation. Considering the localization of Orcus Patera in the Elysium paleolake, its altimetry, and the magmatic origin of this caldera, we propose the existence of a paleolake in Orcus Patera generated (a) by juvenile water from magma during the Noachian period, and (b) by intermittent influx of the Elysium Basin from Hesperian to Amazonian. Results are encouraging to consider this site as a potential high-energy source environment for microbial communities. are circumscribed by a 50-km wide lava field mapped as Noachian material. The structure of Orcus Patera represents the record of material erupted from a magmatic reservoir. The caldera is enclosed by steep inner walls (25% measured from topographic data), values which could be in agreement with the presence of a deep magmatic reservoir, as suggested by the typology of Crumpler et.al. The depth of the caldera might be due to the collapse of the magma reservoir, and the release of gases accompanying the magma thermal evolution. Origins of water for the paleolake(s): The water that generated a paleolake in Orcus Patera may have come from two origins: (1) Juvenile water: Plescia and Crips estimated a magma H20 content by weight between 0.5% and 1.5% using for the first value a comparison with terrestrial basalt, and for the second values from a Martian meteorite. The amount of H20 can be estimated by the volume of erupted lava, and the lava content of the caldera. In this study, we adopt a water content of 1%. The total volume of magma that has been contained in the caldera, and the volume of lava contained in the observed lava field is about 110 x 10(exp 6) cubic km, that gives a total volume of 1.10 x 10(exp 6) cubic km of water. The juvenile water expelled by the overpressure within the magma chamber charged with desolved water-vapor may have moved into the crust. The decrease in overburden pressure led to bubble formation. The ascent of these bubbles generated a pressurization of the magma, which was sufficient to fracture the overlaying magma layer, (2) Water from Elysium paleolake. During the Amazonian, the rise of the Elysium paleolake level generated an overspilling that supplied the caldera with water. The southern portion of the crest shows a deep gap 12-km wide at -1500 m elevation, locating the gap between 500 to 1000 in below the assumed water of Elysium paleolake, thus facilitating the influx of Elysium paleolake water into Orcus Patera. Bathymetric calculations give a floor area of 25,500 sq km at -2000 m elevation, and a water volume of 42,000 cubic km, with a lake-level at -1500 m. A substantial amount of water may have percolated through the fractured lava, and part of the volume may have overspilled the northern crest of Orcus Patera to debouch in the Tartarus Montes region. We envision the formation of a subsurface aqueous environment in basaltic rocks at the contact of the two water-source origins, possibly the percolating surface lake water, and more likely the juvenile water. Similarly to terrestrial calderas, Orcus Patera might be surrounded by ring-fractures caused by the collapse of the magma chamber that followed the release of gases. These ring-fractures may have been covered later by sedimentation in the caldera (lacustrine, aeolian, and volcanic), and by mass wasting. The detumescence of the magma in the caldera, and the vesiculation of the juvenile water may have operated simultaneously. Comparatively to terrestrial melts, Martian iron-rich melts are denser. This greater density implies greater effusion rates (eight-times terrestrial values), and larger fissuration widths (two-times terrestrial ones). With increasing vesiculation of magma, the bubbles interact with one-another because there are of similar pressure. They make a magma froth at the contact with the caldera surface, and on the walls of the fractures. In the saturated magma, froth, where the volume ratio of gases-to-liquid is about 4:1, the bubbles form a huge surface area of interconnected spaces. Bubbles near the caldera surface disrupt the magma, and fragmentation takes place, which moves downward through the magma column. On Earth, the bubbles are likely to grow between 1 and 50 mm in diameter due to the difference between the magma surface tension, and the bubble supersaturation pressure. The Martian low-pressure at surface level is likely to accelerate the expansion of the bubbles, and increase their final diameter and number, creating more voids in the magma. The strong magma froth with enclosed juvenile water bubbles interconnected with exsolved gas bubbles constitute a potential geothermal environment for geochemical energy production from basalt and water that does not require excessive temperatures. This process can start at +20C. Similar types of environments have been shown on Earth as potential energy sources for microbial metabolism, and could have provided deep aqueous basaltic niches for possible Martian microorganisms, even geologically recently. During the Amazonian, combination of volcanism and water activity still existed on Mars. Moreover, this type of potential niches open ways for investigation of possible oases of extinct or extant life, not only on paleolakes, and surface hydrothermalism spring areas, but also all large systems of fossae, which combine hydrologic and volcanic activities, and which provide an energy source, and an underground shelter to prevent surface UV bombardment. Additional information contained in the original.

Grin, E. A.↗
NASA NTRS1998

Biomarkers in Carbonate Thermal Springs: Implications for Mars

Evidence of possible relict biogenic activity has been reported in carbonate inclusions within martian meteorite ALH 84001. The initial evidence included ovoid and elongated forms 50 - 500 nanometers in length, morphologically similar to but significantly smaller than many terrestrial microbes. More recently, thin structures resembling the remains of organic biofilms have been reported in the same meteorite. Carbonates have also been discussed in the context of Mars sample return missions. Thermal spring deposits have often been cited as prime locations for exobiological exploration. By analogy to Earth, specialized microbes may have existed in the heated, mineralized waters, and precipitates of carbonate and/or silica from these waters may have trapped and preserved evidence of life. Since the geological interactions that produce thermal springs can be recognized in orbital imagery, directed searches for microfossils in such deposits are deemed possible. We are engaged in a study of the signatures produced by contemporary biogenic activity (biomarkers) in carbonate thermal springs. We are examining the microbes that live in such environments and the preservation of microbial forms, biofilms, and petrographic fabrics indicative of life in thermal spring mineral deposits. This work is part of a much more extensive study to refine the appropriate tools, techniques, and approaches to seek evidence of life in a range of planetary samples. A deeper understanding of biological signatures will prepare us for the detailed search for life on Mars and eventually on other planets. Overall. the study of biomarkers in rocks and soils will provide insight into the evolution of life because such signatures are a record of how life interacts with its environment, how it adapts to changing conditions, and how life can influence geology and climate.

Allen, C. C.↗
DOE OSTI2023

Lower viral evolutionary pressure under stable versus fluctuating conditions in subzero Arctic brines

Climate change threatens Earth’s ice-based ecosystems which currently offer archives and eco-evolutionary experiments in the extreme. Arctic cryopeg brine (marine-derived, within permafrost) and sea ice brine, similar in subzero temperature and high salinity but different in temporal stability, are inhabited by microbes adapted to these extreme conditions. However, little is known about their viruses (community composition, diversity, interaction with hosts, or evolution) or how they might respond to geologically stable cryopeg versus fluctuating sea ice conditions. We used long- and short-read viromics and metatranscriptomics to study viruses in Arctic cryopeg brine, sea ice brine, and underlying seawater, recovering 11,088 vOTUs (~species-level taxonomic unit), a 4.4-fold increase of known viruses in these brines. More specifically, the long-read-powered viromes doubled the number of longer (≥25 kb) vOTUs generated and recovered more hypervariable regions by >5-fold compared to short-read viromes. Distribution assessment, by comparing to known viruses in public databases, supported that cryopeg brine viruses were of marine origin yet distinct from either sea ice brine or seawater viruses, while 94% of sea ice brine viruses were also present in seawater. A virus-encoded, ecologically important exopolysaccharide biosynthesis gene was identified, and many viruses (~half of metatranscriptome-inferred “active” vOTUs) were predicted as actively infecting the dominant microbial genera Marinobacter and Polaribacter in cryopeg and sea ice brines, respectively. Evolutionarily, microdiversity (intra-species genetic variations) analyses suggested that viruses within the stable cryopeg brine were under significantly lower evolutionary pressures than those in the fluctuating sea ice environment, while many sea ice brine virus-tail genes were under positive selection, indicating virus-host co-evolutionary arms races. Our results confirmed the benefits of long-read-powered viromics in understanding the environmental virosphere through significantly improved genomic recovery, expanding viral discovery and the potential for biological inference. Evidence of viruses actively infecting the dominant microbes in subzero brines and modulating host metabolism underscored the potential impact of viruses on these remote and underexplored extreme ecosystems. Microdiversity results shed light on different strategies viruses use to evolve and adapt when extreme conditions are stable versus fluctuating. Together, these findings verify the value of long-read-powered viromics and provide foundational data on viral evolution and virus-microbe interactions in Earth’s destabilized and rapidly disappearing cryosphere.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Changes in pore structure of coal caused by coal-to-gas bioconversion

Microbial enhanced coalbed methane (ME-CBM) recovery is critically examined as a viable technology for natural gas recovery from coalbed methane (CBM) reservoirs. Since the majority of gas-in-place (GIP) is stored as an adsorbed phase in fine pores of coal matrix, the nano-pore structure directly influences gas storage and transport properties. Only limited studies have quantified the alteration of the nano-pore structure due to ME-CBM treatment. This study examines the evolution of the pore structure using a combination of small angle X-ray scattering (SAXS), low-pressure N 2 and CO 2 adsorption (LPGA) and high-pressure methane adsorption methods. The results show that the surface fractal dimension decreases for the two bioconverted coals compared to the untreated coal. After bio-treatment, the mesopore surface area and pore volume decrease with the average pore diameter increases, while the micropore surface area increases with pore volume decreases. Both inaccessible meso-/micropore size distributions decrease after bioconversion, while the accessible micropore size distribution increases, making a portion of closed micropore network accessible. In addition, the methane adsorption capacities increase after bio-treatment, which is confirmed by the increase of micropore surface area. A conceptual physical model of methanogenesis is proposed based on the evolution of the pore structure.

01 COAL, LIGNITE, AND PEAT↗
DOE OSTI2026

High-quality Acinetobacter genomes recovered from combat wounds via metagenomic sequencing resemble cultured isolate genomes

The ability to accurately characterize wound pathogens is critical to informing clinical decisions for wound infections with complex treatment requirements. Acinetobacter baumannii is an impactful nosocomial pathogen in combat wounds and civilian hospital-acquired infections. An informed understanding of the phylogenetics and epidemiology of A. baumannii infections in military and civilian environments could guide approaches that improve antibiotic treatment regimens for both military and civilian patients. Whole-genome data for bacterial strains can be difficult to obtain due to challenges in culturing isolates from preserved military specimens. Metagenomic sequencing and assembly create opportunities for genomic analysis of pathogens directly from clinical specimens. The ability to perform comparative analyses between metagenome-derived genomes and culture-derived genomes would support a range of comparative bacterial genomic studies. Wound tissue biopsy and effluent samples from combat injuries were subjected to metagenomic sequencing and assembly. In total, 42 microbial metagenome-assembled genomes (MAGs) were obtained directly from metagenomic sequence data, 36 of which were designated “high” quality. Thirty of these genomes corresponded to Acinetobacter, with 29 mapping specifically to A. baumannii. Other observed genera included Bordetella, Citrobacter, Escherichia, and Pseudomonas. Single-copy and multi-copy orthologs were identified across Acinetobacter MAGs and publicly available isolate genomes derived from military and civilian sources. Both MAG and military isolate genomes were annotated with antimicrobial resistance data, and MAG genomes were statistically comparable to genomes obtained from isolates. Our results highlight the potential of de novo metagenome assembly for enabling high-resolution characterization directly from clinical specimens, thereby improving diagnostic precision, guiding antimicrobial stewardship, and enhancing understanding of pathogen evolution across diverse healthcare and battlefield environments.

Acinetobacter baumannii↗
DOE OSTI2026

Shrub and sedge rhizosphere communities display distinct affinities toward exudates and soil organic matter degradation: a quantitative stable isotope probing analysis

Warming temperatures are accelerating permafrost thaw and changing tundra vegetation, where woody shrubs are displacing sedges. Shrubs, such as Betula nana, and sedges, such as Eriophorum vaginatum, exhibit distinct life strategies including unique root-associated, or rhizosphere microbial communities. As permafrost thaws it unlocks previously unavailable carbon and nutrient sources resulting in deeper roots and a translocation of rhizosphere communities. Because permafrost microbial communities contain lower diversity and biomass than rhizosphere communities, the coalescence of rhizosphere and permafrost microbial communities could alter soil organic matter (SOM) degradation rates and increase greenhouse gas emissions. To identify metabolic strategies across distinct rhizosphere and permafrost microbial communities we conducted an isotope tracing incubation experiment. We inoculated thawed permafrost with shrub and sedge rhizosphere communities while adding exudates or water daily and compared this to an uninoculated control. After 46 days, we spiked samples with 18O enriched water or 13C enriched exudates and measured isotope incorporation into microbial DNA with quantitative stable isotope probing (qSIP). Our results indicate that exudate additions had little effect on uninoculated permafrost communities but the addition of exudates and rhizosphere inoculants had a compounding effect on respiration rates. We found that soils inoculated with shrub rhizosphere communities contained a mixture of exudate and SOM degraders while soils inoculated with sedge rhizosphere communities contained mainly SOM degraders. Finally, we found that individual microbial taxa exhibited maximum growth rates under specific combinations of microbial inoculant communities and exudate addition treatments. Our results reveal that microbial niches are strongly influenced by substrate preferences and community context, and suggest that a reduction in sedges and an expansion of shrubs may provide a mechanism by which permafrost carbon losses are mitigated through corresponding shifts in microbial communities and their substrate preferences.

Schaefer, Sean R [Natural Resources and Earth Syst↗
DOE OSTI2020

Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome

Abstract Introduction Microbial residents of the human oral cavity have long been a major focus of microbiology due to their influence on host health and intriguing patterns of site specificity amidst the lack of dispersal limitation. However, the determinants of niche partitioning in this habitat are yet to be fully understood, especially among taxa that belong to recently discovered branches of microbial life. Results Here, we assemble metagenomes from tongue and dental plaque samples from multiple individuals and reconstruct 790 non-redundant genomes, 43 of which resolve to TM7, a member of the Candidate Phyla Radiation, forming six monophyletic clades that distinctly associate with either plaque or tongue. Both pangenomic and phylogenomic analyses group tongue-specific clades with other host-associated TM7 genomes. In contrast, plaque-specific TM7 group with environmental TM7 genomes. Besides offering deeper insights into the ecology, evolution, and mobilome of cryptic members of the oral microbiome, our study reveals an intriguing resemblance between dental plaque and non-host environments indicated by the TM7 evolution, suggesting that plaque may have served as a stepping stone for environmental microbes to adapt to host environments for some clades of microbes. Additionally, we report that prophages are widespread among oral-associated TM7, while absent from environmental TM7, suggesting that prophages may have played a role in adaptation of TM7 to the host environment. Conclusions Our data illuminate niche partitioning of enigmatic members of the oral cavity, including TM7, SR1, and GN02, and provide genomes for poorly characterized yet prevalent members of this biome, such as uncultivated Flavobacteriaceae.

60 APPLIED LIFE SCIENCES↗
NASA NTRS1985

Aerobic sulfur-oxidizing bacteria: Environmental selection and diversification

Sulfur-oxidizing bacteria oxidize reduced inorganic compounds to sulfuric acid. Lithotrophic sulfur oxidizer use the energy obtained from oxidation for microbial growth. Heterotrophic sulfur oxidizers obtain energy from the oxidation of organic compounds. In sulfur-oxidizing mixotrophs energy are derived either from the oxidation of inorganic or organic compounds. Sulfur-oxidizing bacteria are usually located within the sulfide/oxygen interfaces of springs, sediments, soil microenvironments, and the hypolimnion. Colonization of the interface is necessary since sulfide auto-oxidizes and because both oxygen and sulfide are needed for growth. The environmental stresses associated with the colonization of these interfaces resulted in the evolution of morphologically diverse and unique aerobic sulfur oxidizers.

Caldwell, D.↗