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DOE OSTI2020

High-throughput mapping of the phage resistance landscape in E. coli

Bacteriophages (phages) are critical players in the dynamics and function of microbial communities and drive processes as diverse as global biogeochemical cycles and human health. Phages tend to be predators finely tuned to attack specific hosts, even down to the strain level, which in turn defend themselves using an array of mechanisms. However, to date, efforts to rapidly and comprehensively identify bacterial host factors important in phage infection and resistance have yet to be fully realized. Here, we globally map the host genetic determinants involved in resistance to 14 phylogenetically diverse double-stranded DNA phages using two model Escherichia coli strains (K-12 and BL21) with known sequence divergence to demonstrate strain-specific differences. Using genome-wide loss-of-function and gain-of-function genetic technologies, we are able to confirm previously described phage receptors as well as uncover a number of previously unknown host factors that confer resistance to one or more of these phages. We uncover differences in resistance factors that strongly align with the susceptibility of K-12 and BL21 to specific phage. We also identify both phage specific mechanisms, such as the unexpected role of cyclic-di-GMP in host sensitivity to phage N4, and more generic defenses, such as the overproduction of colanic acid capsular polysaccharide that defends against a wide array of phages. Our results indicate that host responses to phages can occur via diverse cellular mechanisms. Our systematic and high-throughput genetic workflow to characterize phage-host interaction determinants can be extended to diverse bacteria to generate datasets that allow predictive models of how phage-mediated selection will shape bacterial phenotype and evolution. The results of this study and future efforts to map the phage resistance landscape will lead to new insights into the coevolution of hosts and their phage, which can ultimately be used to design better phage therapeutic treatments and tools for precision microbiome engineering.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Chemical and isotopic evolution of flowback fluids from the Utica Gas Shale Play, Eastern Ohio USA

For this work, hydraulic fracturing flowback fluids were collected from two Utica/Point Pleasant well pads in eastern Ohio. One site was in the wet gas zone (UPPW), while the site ~50 km south consisted of four wells on the same pad in the dry gas zone (UPPS). Samples of input fluids also were collected before and during hydraulic fracturing. Flowback fluids are Na-Ca-Cl brines with total dissolved salt (TDS) concentrations that increase over several months from ~100 to 200 g/L. The slightly higher TDS of the dry gas fluids are in part due to recycled flowback used as input fluids, and in part due to lower volume of water used in hydraulic fracturing. Concentrations of most major ions (Ca 2+ , Mg 2+ , Na + , Sr2 + , Fe, Mn, Cl – , Br – ) are similar for the five wells sampled, although small but systematic changes occur in the major element ratios over time. Most notably, an increase in the Sr/Cl ratio corresponds to an increase in the 87 Sr/ 86 Sr ratio in the fluids, suggesting interactions with a more radiogenic Sr source in the subsurface. Dissolved Ba concentrations and Ra activities were different between the two sites, reflecting a high SO 4 2– fluid used at the UPPW site, and water-rock reactions occurring during hydraulic fracturing at the UPPS site. Water oxygen (δ 18 O) and hydrogen (δD) isotopes for input fluids used in the UPPW4 well and fresh water used for the UPPS wells fall on the Global Meteoric waterline (GMWL). Flowback fluids from both sites are relatively enriched in δ 18 O and δD compared to the input, but do not appear to follow a simple mixing trend, suggesting reaction and isotopic exchange with carbonates and fractionation due to imbibition in the rock. Cl isotopes, δ 37 Cl in the FP fluids varied from ~ –0.43 to +0.13‰, the largest variation was observed in the earlier stages of flowback, while in the later stages δ 37 Cl exhibited a small but systematic increase over time, suggesting diffusion control of isotopic composition. Some of the trace species measured (dissolved Fe, Mn, thiosulfate and organic acids) do not follow the same trends as the major ions, suggesting contributions from input fluids, or microbially mediated reactions are exerting control on their concentrations. Input water chemistry exerts an important control on the Sr and Ba concentrations in flowback water. High SO 4 2– in the input fluids used for hydraulically fracturing the wet gas well leads to precipitation of barite-celestite in flowback fluids.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1995

Microfossils from the Neoarchean Campbell Group, Griqualand West Sequence of the Transvaal Supergroup, and their paleoenvironmental and evolutionary implications

The oldest filament- and colonial coccoid-containing microbial fossil assemblage now known is described here from drill core samples of stromatolitic cherty limestones of the Neoarchean, approximately 2600-Ma-old Campbell Group (Ghaap Plateau Dolomite, Lime Acres Member) obtained at Lime Acres, northern Cape Province, South Africa. The assemblage is biologically diverse, including entophysalidacean (Eoentophysalis sp.), probable chroococcacean (unnamed colonial coccoids), and oscillatoriacean cyanobacteria (Eomycetopsis cf. filiformis, and Siphonophycus transvaalensis), as well as filamentous fossil bacteria (Archaeotrichion sp.); filamentous possible microfossils (unnamed hematitic filaments) also occur. The Campbell Group microorganisms contributed to the formation of stratiform and domical to columnar stromatolitic reefs in shallow subtidal to intertidal environments of the Transvaal intracratonic sea. Although only moderately to poorly preserved, they provide new evidence regarding the paleoenvironmental setting of the Campbell Group sediments, extend the known time-range of entophysalidacean cyanobacteria by more than 400 million years, substantiate the antiquity and role in stromatolite formation of Archean oscillatoriacean cyanobacteria, and document the exceedingly slow (hypobradytelic) evolutionary rate characteristic of this early evolving prokaryotic lineage.

Non-NASA Center↗

DOE OSTI2026

A trait syndrome ties cell morphology to glycolysis across the yeast subphylum

Co-variation of traits provides fundamental insights into constraints governing their evolution. An inverse correlation between glucose uptake rates (GURs) and cell surface area-to-volume (SA:V) ratios across 11 yeast species was recently reported. Here, we expand the analysis to 282 species to assess the generalizability of this correlation across Saccharomycotina yeasts and the contribution of shared evolutionary history to the co-variation of these traits. Using phylogenetic regression models, we found extracellular acidification rates (ECARs, used as a proxy for GURs) were weakly, but significantly, correlated with SA:V across Saccharomycotina. ECARs were also correlated with genome sizes and growth rates. Our findings support the reported correlation between GURs and SA:V ratios, but suggest other associated traits, including genome sizes. Specifically, yeasts that consume glucose faster tend to have lower SA:V, faster growth rates, and larger genomes, suggesting a trait syndrome governing several metabolic, genomic, and morphological traits across the yeast subphylum.

biological sciences↗

DOE OSTI2023

Codon Optimization Improves the Prediction of Xylose Metabolism from Gene Content in Budding Yeasts

Xylose is the second most abundant monomeric sugar in plant biomass. Consequently, xylose catabolism is an ecologically important trait for saprotrophic organisms, as well as a fundamentally important trait for industries that hope to convert plant mass to renewable fuels and other bioproducts using microbial metabolism. Although common across fungi, xylose catabolism is rare within Saccharomycotina, the subphylum that contains most industrially relevant fermentative yeast species. The genomes of several yeasts unable to consume xylose have been previously reported to contain the full set of genes in the XYL pathway, suggesting the absence of a gene–trait correlation for xylose metabolism. Here, we measured growth on xylose and systematically identified XYL pathway orthologs across the genomes of 332 budding yeast species. Although the XYL pathway coevolved with xylose metabolism, we found that pathway presence only predicted xylose catabolism about half of the time, demonstrating that a complete XYL pathway is necessary, but not sufficient, for xylose catabolism. We also found that XYL1 copy number was positively correlated, after phylogenetic correction, with xylose utilization. We then quantified codon usage bias of XYL genes and found that XYL3 codon optimization was significantly higher, after phylogenetic correction, in species able to consume xylose. Finally, we showed that codon optimization of XYL2 was positively correlated, after phylogenetic correction, with growth rates in xylose medium. We conclude that gene content alone is a weak predictor of xylose metabolism and that using codon optimization enhances the prediction of xylose metabolism from yeast genome sequence data.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1997

Searching for Biogeochemical Cycles on Mars

The search for life on Mars clearly benefits from a rigorous, yet broad, definition of life that compels us to consider all possible lines of evidence for a martian biosphere. Recent studies in microbial ecology illustrate that the classic definition of life should be expanded beyond the traditional definition of a living cell. The traditional defining characteristics of life are threefold. First, life is capable of metabolism, that is, it performs chemical reactions that utilize energy and also synthesize its cellular constituents. Second, life is capable of self-replication. Third, life can evolve in order to adapt to environmental changes. An expanded, ecological definition of life also recognizes that life is a community of organisms that must interact with their nonliving environment through processes called biogeochemical cycles. This regenerative processing maintains, in an aqueous conditions, a dependable supply of nutrients and energy for growth. In turn, life can significantly affect those processes that control the exchange of materials between the atmosphere, ocean, and upper crust. Because metabolic processes interact directly with the environment, they can alter their surroundings and thus leave behind evidence of life. For example, organic matter is produced from single-carbon-atom precursors for the biosynthesis of cellular constituents. This leads to a reservoir of reduced carbon in sediments that, in turn, can affect the oxidation state of the atmosphere. The harvesting of chemical energy for metabolism often employs oxidation-reduction reactions that can alter the chemistry and oxidation state of the redox-sensitive elements carbon, sulfur, nitrogen, iron, and manganese. Have there ever been biogeochemical cycles on Mars? Certain key planetary processes can offer clues. Active volcanism provides reduced chemical species that biota can use for organic synthesis. Volcanic carbon dioxide and methane can serve as greenhouse gases. Thus the persistence of volcanism on Mars may well have influenced the persistence of a martian biosphere. The geologic processing of the crust can affect the availability of nutrients and also control the deposition of minerals that could have served as a medium for the preservation of fossil information. Finally, the activity of liquid water is crucial to life. Was there ever an Earth-like hydrologic cycle with rainfall? Has aqueous activity instead been restricted principally to hydrothermal activity below the surface? To what extent did the inorganic chemistry driven by sunlight and hydrothermal activity influence organic chemistry (prebiotic chemical evolution)? This paper addresses these and other key questions.

DesMarais, David J.↗

DOE OSTI2017

Genomic Comparison of Two Family-Level Groups of the Uncultivated NAG1 Archaeal Lineage from Chemically and Geographically Disparate Hot Springs

Recent progress based on single-cell genomics and metagenomic investigations of archaea in a variety of extreme environments has led to significant advances in our understanding of the diversity, evolution, and metabolic potential of archaea, yet the vast majority of archaeal diversity remains undersampled. In this work, we coordinated single-cell genomics with metagenomics in order to construct a near-complete genome from a deeply branching uncultivated archaeal lineage sampled from Great Boiling Spring (GBS) in the U.S. Great Basin, Nevada. This taxon is distantly related (distinct families) to an archaeal genome, designated “Novel Archaeal Group 1” (NAG1), which was extracted from a metagenome recovered from an acidic iron spring in Yellowstone National Park (YNP). We compared the metabolic predictions of the NAG1 lineage to better understand how these archaea could inhabit such chemically distinct environments. Similar to the NAG1 population previously studied in YNP, the NAG1 population from GBS is predicted to utilize proteins as a primary carbon source, ferment simple carbon sources, and use oxygen as a terminal electron acceptor under oxic conditions. However, GBS NAG1 populations contained distinct genes involved in central carbon metabolism and electron transfer, including nitrite reductase, which could confer the ability to reduce nitrite under anaerobic conditions. Despite inhabiting chemically distinct environments with large variations in pH, GBS NAG1 populations shared many core genomic and metabolic features with the archaeon identified from YNP, yet were able to carve out a distinct niche at GBS.

59 BASIC BIOLOGICAL SCIENCES↗