Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Microbial Interactions”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 613 records · Page 34
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

iVirus 2.0: Cyberinfrastructure-supported tools and data to power DNA virus ecology

Microbes drive myriad ecosystem processes, but under strong influence from viruses. Because studying viruses in complex systems requires different tools than those for microbes, they remain underexplored. To combat this, we previously aggregated double-stranded DNA (dsDNA) virus analysis capabilities and resources into ‘iVirus’ on the CyVerse collaborative cyberinfrastructure. Here we substantially expand iVirus’s functionality and accessibility, to iVirus 2.0, as follows. First, core iVirus apps were integrated into the Department of Energy’s Systems Biology KnowledgeBase (KBase) to provide an additional analytical platform. Second, at CyVerse, 20 software tools (apps) were upgraded or added as new tools and capabilities. Third, nearly 20-fold more sequence reads were aggregated to capture new data and environments. Finally, documentation, as “live” protocols, was updated to maximize user interaction with and contribution to infrastructure development. Together, iVirus 2.0 serves as a uniquely central and accessible analytical platform for studying how viruses, particularly dsDNA viruses, impact diverse microbial ecosystems.

Bolduc, Benjamin (ORCID:0000000324200755)↗
DOE OSTI2023

Climate drivers alter nitrogen availability in surface peat and decouple N 2 fixation from CH 4 oxidation in the Sphagnum moss microbiome

Peat mosses (Sphagnum spp.) are keystone species in boreal peatlands, where they dominate net primary productivity and facilitate the accumulation of carbon in thick peat deposits. Sphagnum mosses harbor a diverse assemblage of microbial partners, including N 2 -fixing (diazotrophic) and CH 4 -oxidizing (methanotrophic) taxa that support ecosystem function by regulating transformations of carbon and nitrogen. In this work, we investigate the response of the Sphagnum phytobiome (plant + constituent microbiome + environment) to a gradient of experimental warming (+0°C to +9°C) and elevated CO 2 (+500 ppm) in an ombrotrophic peatland in northern Minnesota (USA). By tracking changes in carbon (CH 4 , CO 2 ) and nitrogen (NH 4 -N) cycling from the belowground environment up to Sphagnum and its associated microbiome, we identified a series of cascading impacts to the Sphagnum phytobiome triggered by warming and elevated CO 2 . Under ambient CO 2 , warming increased plant-available NH 4 -N in surface peat, excess N accumulated in Sphagnum tissue, and N 2 fixation activity decreased. Elevated CO 2 offset the effects of warming, disrupting the accumulation of N in peat and Sphagnum tissue. Methane concentrations in porewater increased with warming irrespective of CO 2 treatment, resulting in a ~10× rise in methanotrophic activity within Sphagnum from the +9°C enclosures. Warming's divergent impacts on diazotrophy and methanotrophy caused these processes to become decoupled at warmer temperatures, as evidenced by declining rates of methane-induced N 2 fixation and significant losses of keystone microbial taxa. In addition to changes in the Sphagnum microbiome, we observed ~94% mortality of Sphagnum between the +0°C and +9°C treatments, possibly due to the interactive effects of warming on N-availability and competition from vascular plant species. Collectively, these results highlight the vulnerability of the Sphagnum phytobiome to rising temperatures and atmospheric CO 2 concentrations, with significant implications for carbon and nitrogen cycling in boreal peatlands.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Colonization of Naive Roots from Populus tremula × alba Involves Successive Waves of Fungi and Bacteria with Different Trophic Abilities

ABSTRACT Through their roots, trees interact with a highly complex community of microorganisms belonging to various trophic guilds and contributing to tree nutrition, development, and protection against stresses. Tree roots select for specific microbial species from the bulk soil communities. The root microbiome formation is a dynamic process, but little is known on how the different microorganisms colonize the roots and how the selection occurs. To decipher whether the final composition of the root microbiome is the product of several waves of colonization by different guilds of microorganisms, we planted sterile rooted cuttings of gray poplar obtained from plantlets propagated in axenic conditions in natural poplar stand soil. We analyzed the root microbiome at different time points between 2 and 50 days of culture by combining high-throughput Illumina MiSeq sequencing of the fungal ribosomal DNA internal transcribed spacer and bacterial 16S rRNA amplicons with confocal laser scanning microscopy observations. The microbial colonization of poplar roots took place in three stages, but bacteria and fungi had different dynamics. Root bacterial communities were clearly different from those in the soil after 2 days of culture. In contrast, if fungi were also already colonizing roots after 2 days, the initial communities were very close to that in the soil and were dominated by saprotrophs. They were slowly replaced by endophytes and ectomycorhizal fungi. The replacement of the most abundant fungal and bacterial community members observed in poplar roots over time suggest potential competition effect between microorganisms and/or a selection by the host. IMPORTANCE The tree root microbiome is composed of a very diverse set of bacterial and fungal communities. These microorganisms have a profound impact on tree growth, development, and protection against different types of stress. They mainly originate from the bulk soil and colonize the root system, which provides a unique nutrient-rich environment for a diverse assemblage of microbial communities. In order to better understand how the tree root microbiome is shaped over time, we observed the composition of root-associated microbial communities of naive plantlets of poplar transferred in natural soil. The composition of the final root microbiome relies on a series of colonization stages characterized by the dominance of different fungal guilds and bacterial community members over time. Our observations suggest an early stabilization of bacterial communities, whereas fungal communities are established following a more gradual pattern.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Soil Origin and Plant Genotype Modulate Switchgrass Aboveground Productivity and Root Microbiome Assembly

Switchgrass (Panicum virgatum) is a model perennial grass for bioenergy production that can be productive in agricultural lands that are not suitable for food production. There is growing interest in whether its associated microbiome may be adaptive in low- or no-input cultivation systems. However, the relative impact of plant genotype and soil factors on plant microbiome and biomass are a challenge to decouple. To address this, a common garden greenhouse experiment was carried out using six common switchgrass genotypes, which were each grown in four different marginal soils collected from long-term bioenergy research sites in Michigan and Wisconsin. We characterized the fungal and bacterial root communities with high-throughput amplicon sequencing of the ITS and 16S rDNA markers, and collected phenological plant traits during plant growth, as well as soil chemical traits. At harvest, we measured the total plant aerial dry biomass. Significant differences in richness and Shannon diversity across soils but not between plant genotypes were found. Generalized linear models showed an interaction between soil and genotype for fungal richness but not for bacterial richness. Community structure was also strongly shaped by soil origin and soil origin × plant genotype interactions. Overall, plant genotype effects were significant but low. Random Forest models indicate that important factors impacting switchgrass biomass included NO 3 – , Ca 2+ , PO 4 3– , and microbial biodiversity. We identified 54 fungal and 52 bacterial predictors of plant aerial biomass, which included several operational taxonomic units belonging to Glomeraceae and Rhizobiaceae, fungal and bacterial lineages that are involved in provisioning nutrients to plants.

plant biomass↗
NASA NTRS1989

Distribution of inorganic species in two Antarctic cryptoendolithic microbial communities

Chemical differences were noted between two Antarctic cryptoendolithic (hidden within rock) microenvironments colonized by different microbial communities. Microenvironments dominated by cyanobacteria (BPC) had a higher pH (pH 7-8) than those dominated by lichen (LTL) (pH 4.5-5.5). In order to understand the interactions between the microbiota and the inorganic environment, the inorganic environment was characterized. Water-soluble, carbonate-bound, metal-oxide, organically bound, and residual inorganic species were sequentially extracted from rock samples by chemical means. Each fraction was then quantified using inductively coupled plasma atomic emission spectrometry. BPC contained much more water-soluble and carbonate-bound Ca and Mg than LTL. Metal-oxide species of Al, Fe, and Mn were more abundant in LTL than BPC. Metal oxides appeared to be mobilized (in the order Mn > Fe > Al) from the LTL lichen zone but remained immobile in BPC sandstone. The distribution of K and P bound to metal oxide reflected the distribution of iron oxide in LTL, an indication of the importance of iron in controlling the availability of nutrients in this ecosystem. Metal oxides in turn were likely controlled or influenced by organic matter associated with the lichen community. Despite overall depletion of Fe, Al, and K in the lichen zone, SEM X-ray analysis showed that they were enriched in fungal hyphae. Water-soluble P was present despite the presence of metal oxides, which sequester phosphate. This has biological relevance since P is an essential nutrient.

NASA Program Exobiology↗
NASA NTRSDate not supplied

Microbial Mutualism in (Modeled) Microgravity: Measuring the Effects of A Spaceflight-Like Fluid Environment on Cross-Feeding Communities

Microorganisms grow differently in spaceflight than they do on Earth. While numerous factors likely contribute, one ubiquitous feature of the space environment is altered gravity - but because microbes are generally considered too small to detect gravity directly, they likely experience the effects of gravity via changes in their fluid environment, primarily a reduction in convective mixing. This theory is supported by evidence that individual microbial strains experience starvation and acid stress in microgravity. If it is true, then microgravity would also have measurable effects on microbes in mixed communities, because many interspecies interactions involve the exchange of soluble metabolites through their medium (cross-feeding). Specifically, cooperative cross-feeding communities would grow more slowly in microgravity, and this effect should be reproducible in ground-based rotational culture systems (rotating wall vessels, RWVs) designed to simulate the quiescent environment of microgravity. Here we present preliminary results of our efforts to test this hypothesis using using a model system of Eschericia coli and Salmonella enterica that grow only when they can exchange methionine and acetate through the medium. We report on the development of a novel laboratory system that allows us measure growth rates and species ratios in real-time using fluorescence spectrometry as the organisms grow in RWVs. We are able to track growth rates of individual species and the co-culture continuously with high temporal resolution for several hours, a substantial improvement over prior RWV systems that require destructive sampling. We vary the fidelity of the microgravity simulation by varying the rotation rate, and find that rotation rate affects growth rates of the community more than that of individual strains, consistent with the claim that RWVs can simulate a microgravity-like quiescent environment. While more work needs to be done to probe the mechanisms of this effect, we hope that our system will ultimately allow us to generate quantitative predictions about the effects of spaceflight on organisms that are tiny but essential to sustaining long-term human space exploration.

microgravity↗
DOE OSTI2023

Changing Microbiomes: A Symposium Hosted by the Microbiome Center at the Pennsylvania State University

The first “Changing Microbiomes” conference was successfully held at the Pennsylvania State University from May 31st – June 3rd, 2022. The overall goal of the symposium was to provide space for researchers to connect, exchange knowledge, and partner to advance our understanding of the mechanisms and applications of ecological and evolutionary changes in microbiomes across systems. The symposium spanned terrestrial and aquatic contexts and host-associated and free-living microbial communities. As such, the symposium will enable cross-disciplinary knowledge and idea exchange to promote future interdisciplinary collaborations. In addition, the program allowed formal and informal interactions between and among students, postdocs, PIs, and industry scientists.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2010

Mutualism in a Reduced Gravity Environment (MuRGE)

Mutualism in a Reduced Gravity Environment (MuRGE) is a ground research study to determine the feasibility of assessing fungi-plant (Piriformospora indica-Arabidopsis thaliana) interactions in microgravity. Seeds from the plant Arabiddospsis thaliana (At) will be grown in the presence of Piriformospora indica (Pi) an endophytic Sebacinacae family fungus. Pi is capable of colonizing the roots of a wide variety of plant species, including non-mycorrhizal hosts like At, and promoting plant growth similarly to AMF (arbusuclar mychorrizal fungi) unlike most AMF, Pi is not an obligate plant symbiont and can be grown in the absence of a host. In the presence of a suitable plant host, Pi can attach to and colonize root tips. Interaction visualization is accomplished with strong autofluorescence in the roots, followed by root colonization via fungal hyphae, and chlamydospore production. Increased root growth can be observed even before root colonization is detectable. In addition, Pi chlamydospores generated from axenic culture in microgravity will be used to inoculate roots of At grown in 1g to determine the effect of microgravity upon the inherent virulence or beneficial effects. Based on recent reports of increased virulence of S. typhimurium, P. aeruginosa, and S. Pneumoniae in reduced gravity, differences in microbial pathogenic responses and host plant systemic acquired resistance are expected. The focus of this project within MuRGE involved the development P. indica culture media evaluation and microscopy protocol development. High, clean spore harvest yields for the detection of fungi-plant interactions microscopically was the immediate goal of this experiment.

Haire, Timothy C.↗
DOE OSTI2026

Quantifying Membrane Structure and Dynamics during Bioproduct Production in Zymomonas mobilis by Molecular Simulation

The conversion of lignocellulosic biomass into biofuels and bioproducts by microbial biorefineries is central to a sustainable chemical industry. Zymomonas mobilis is one such biorefinery chassis and is resistant to ethanol stress, leading to its use in biomass conversion to biofuels and bioproducts. However, Z. mobilis growth is often inhibited by organic acids, aldehydes, alcohols, ketones, and amides found in biomass hydrolysate. The resulting slow growth inhibits production and as a result drives up the price for the resulting products. One hypothesis is that these molecules interact with or disrupt the bacterial membrane, triggering stress responses and hindering growth. To test this hypothesis at the molecular level, we employ all-atom molecular dynamics (MD) simulations to investigate lignocellulose-derived small molecules and their impact on a biologically relevant Z. mobilis membrane model. Simulations were conducted across a range of inhibitor concentrations from 0 to 2.5 mol %, analyzing key membrane properties such as area per lipid (APL), membrane thickness, lipid-order parameter (−S CH ), lateral diffusion coefficient (D xy ), and permeability coefficient (Pm). From simulation, we observed altered membrane structure and dynamics at these modest small molecule concentrations commonly found in hydrolysates. Generally, the membranes become thinner, with a higher area per lipid and lower-order parameter as the small molecule concentration increases. These trends are stronger for more hydrophobic molecules with greater hydrophobic bulk, as isobutanol, propanol, and propanoic acid showed greater membrane perturbations as the concentration increased compared to other small molecules. Tracking small molecule distributions directly in our equilibrium simulations allows us to determine concentration-dependent free energy profiles for these molecules. While the trends are noisy, generally the barriers to crossing the membrane decrease as the concentration increases, indicating that the membranes become leakier as small molecule concentrations rise. Comparing between native Z. mobilis membranes with hopanoids and membranes sharing the same phospholipid composition but without hopanoids, hopanoids stabilize and order the membrane for smaller molecules to maintain membrane structure but appear insufficient for larger hydrophobic molecules like isobutanol. These findings provide a mechanistic understanding of how small molecules found in biomass degradation streams interact with the Z. mobilis membrane, offering valuable insights for future strain engineering efforts to optimize biofuel and bioproduct synthesis from biomass feedstocks by highlighting limits to small molecule tolerance. This knowledge can guide the modification of membrane composition to develop more robust microbes, thereby improving microbial survival and yields in industrial contexts.

Singh, Nitin Kumar [Michigan State Univ., East Lan↗
DOE OSTI2026

Sampling Microbial Dynamics in the Salish Sea Estuary: Evaluating Methods to Capture Cyanobacteria and Cyanophage

Introduction: Picocyanobacteria from the genera Prochlorococcus and Synechococcus thrive across the globe in aquatic environments, have relatively small genomes, and have growth dynamics regulated by both viral interactions and abiotic conditions, making them excellent model organisms for exploring host-pathogencoevolution. Methods: We developed and refined methods to sample and sequence cyanobacteria, cyanophages, and measured features of their abiotic environment. Results: The protocol described herein can successfully discriminate large-cell eukaryotic organisms, but size fractionation of picocyanobacteria appears to be affected by the presence of free DNA, multicellular structures, and abundant tycheposons. Our preferred final protocol from this exploratory effort included a combination of in-line and single vacuum flask filtrations, which reduced filtration processing time by over threefold in some cases compared to other tested methods, such as a fully in-line sequence or in-site filtrations. We successfully extracted an average of approximately 400–1200 ng for all filter fractions, with some variations between kits. Discussion: The protocol described herein can successfully discriminate large-cell eukaryotic organisms, but size fractionation of picocyanobacteria appears to be affected by the presence of free DNA, multicellular structures, and abundant tycheposons.

Salish Sea↗
DOE OSTI2023

Throughfall exclusion and fertilization effects on tropical dry forest tree plantations, a large-scale experiment

Abstract. Across tropical ecosystems, global environmental change is causing drier climatic conditions and increased nutrient deposition. Such changes represent large uncertainties due to unknown interactions between drought and nutrient availability in controlling ecosystem net primary productivity (NPP). Using a large-scale manipulative experiment, we studied for 4 years whether nutrient availability affects the individual and integrated responses of aboveground and belowground ecosystem processes to throughfall exclusion in 30-year-old mixed plantations of tropical dry forest tree species in Guanacaste, Costa Rica. We used a factorial design with four treatments: control, fertilization (F), drought (D), and drought + fertilization (D + F). While we found that a 13 %–15 % reduction in soil moisture only led to weak effects in the studied ecosystem processes, NPP increased as a function of F and D + F. The relative contribution of each biomass flux to NPP varied depending on the treatment, with woody biomass being more important for F and root biomass for D + F and D. Moreover, the F treatment showed modest increases in maximum canopy cover. Plant functional type (i.e., N fixation or deciduousness) and not the experimental manipulations was the main source of variation in tree growth. Belowground processes also responded to experimental treatments, as we found a decrease in nodulation for F plots and an increase in microbial carbon use efficiency for F and D plots. Our results emphasize that nutrient availability, more so than modest reductions in soil moisture, limits ecosystem processes in tropical dry forests and that soil fertility interactions with other aspects of drought intensity (e.g., vapor pressure deficit) are yet to be explored.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Iron as a driver of organic carbon fate in permafrost regions

Iron (Fe) and its biogeochemical interactions with organic carbon (OC) exert critical controls over carbon storage and water quality across Arctic and sub-Arctic landscapes. Permafrost thaw affects Fe–organic carbon interactions by exposing thawed material and driving shifts in hydrologic regimes. Here we propose a conceptual framework describing how Fe–OC interactions respond to permafrost thaw and the implications for global carbon cycling. The framework builds on current understanding of hydrologically driven processes that are altered by permafrost thaw, including microbial Fe reduction that influences OC decomposition and carbon emissions; Fe cycling through redox transformations and sulfide oxidation; dissolution and reprecipitation of Fe–OC assemblages; and Fe export to river networks. We put forward four testable hypotheses—on topics from Fe supply to its role in soil OC storage and transfer to rivers—to advance understanding of the coupled environmental controls on pore-scale reactions (that is, microscale reactions at mineral–water–microorganism interfaces) that are central to global Fe–OC cycling. Our framework highlights how soil-profile- and landscape-scale processes, such as hydrologic connectivity and redox dynamics, regulate pore-scale Fe–OC reactions.

Herndon, Elizabeth [ORNL] (ORCID:0000000291945493)↗
DOE OSTI2024

Engineering Methanogenic Microbiomes to Redirect Flux to Biomass

In this study, we present a method for acquiring and characterizing novel microbial consortia that regulates methanogens and methanotrophs through selective cultivation and metagenomic analysis of indigenous microorganisms in the environment. In addition, we present the work performed as part of this project to model the pathways that act as limiting factors in microbial methane metabolism based on a carbon cycle model. In this report, we describe the methods for selective cultivation of methane-metabolism-related microorganisms from environmental samples, the method for monitoring their methane consumption performance, and the method and results for verifying their functions using quantitative PCR and metagenomics techniques. The microbial consortia containing methanotrophs were obtained through selective cultivation and molecular biological verification, and their methane consumption performance was evaluated. In addition, the potential of the existence of bacteriophages interacting with methane metabolism-related microorganisms was identified through metagenomic sequencing.

09 BIOMASS FUELS↗
NASA NTRS2012

Low Biotoxicity of Mars Analog Soils Suggests that the Surface of Mars May be Habitable for Terrestrial Microorganisms

Recent studies on the interactive effects of hypobaria, low temperatures, and CO2-enriched anoxic atmospheres on the growth of 37 species of mesophilic bacteria identified 14 potential biocidal agents that might affect microbial survival and growth on the martian surface. Biocidal or inhibitory factors include (not in priority): (1) solar UV irradiation, (2) low pressure, (3) extreme desiccating conditions, (4) extreme diurnal temperature fluctuations, (5) solar particle events, (6) galactic cosmic rays, (7) UV-glow discharge from blowing dust, (8) solar UV-induced volatile oxidants [e.g., O2(-), O(-), H2O2, O3], (9) globally distributed oxidizing soils, (10) extremely high salts levels [e.g., MgCl2, NaCl, FeSO4, and MgSO4] in surficial soils at some sites on Mars, (11) high concentrations of heavy metals in martian soils, (12) likely acidic conditions in martian fines, (13) high CO2 concentrations in the global atmosphere, and (14) perchlorate-rich soils. Despite these extreme conditions several studies have demonstrated that dormant spores or vegetative cells of terrestrial microorganisms can survive simulated martian conditions as long as they are protected from UV irradiation. What has not been explored in depth are the effects of potential biotoxic geochemical components of the martian regolith on the survival and growth of microorganisms. The primary objectives of the research included: (1) prepare and characterize Mars analog soils amended with potential biotoxic levels of sulfates, salts, acidifying minerals, etc.; and (2) use the simulants to conduct biotoxicity assays to determine if terrestrial microorganisms from spacecraft can survive direct exposure to the analog soils.

Schuerger, A. C.↗
NASA NTRSDate not supplied

Microbial Communities in Microgravity: Simulation in Lab and on the Computer

Microorganisms grow differently in spaceflight than they do on Earth. While much remains unexplained about how microgravity affects microbial growth, one dominant hypothesis is that the lack of density-driven convection in the liquid growth environment makes mixing diffusion-limited, and therefore slower. This is supported by evidence that individual microbial strains experience starvation and acid stress in microgravity. However, if it is true, then microgravity would also have measurable effects on microbes in mixed communities, because many interspecies interactions involve the exchange of soluble metabolites through the medium (cross-feeding). Specifically, cooperative cross-feeding communities would grow more slowly in microgravity, and cooperation would be less stable on evolutionary timescales. Here we describe our efforts to test this hypothesis by simulating microgravity in silico and in the lab, using a model system of Eschericia coli and Salmonella enterica that grow only when they can exchange methionine and acetate. We created CAMDLES (CFD-DEM Artificial Microgravity Developments for Living Ecosystem Simulation) as an extension of CFDEM®coupling software, to carry out computational modeling of biological flows, growth, and mass transfer in microgravity and also in laboratory artificial microgravity devices (rotating wall vessels, RWV). Using CAMDLES, we found distinct differences in growth rates between RWV and true microgravity, and we were able to identify several features, such as spatial distribution, biofilm formation, and product yield parameters, that influence the degree to which RWV growth recapitulates microgravity growth. In addition, we report on the development of a laboratory system for monitoring growth rates and species ratios of the community in RWVs, using fluorescent strains. Pairing CAMDLES with the laboratory model system allows us to generate quantitative predictions about the effects of spaceflight on organisms that will be essential to sustaining human space exploration in the long term.

microbiology↗
DOE OSTI2023

Microbial growth under drought is confined to distinct taxa and modified by potential future climate conditions

Climate change increases the frequency and intensity of drought events, affecting soil functions including carbon sequestration and nutrient cycling, which are driven by growing microorganisms. Yet we know little about microbial responses to drought due to methodological limitations. Here, we estimate microbial growth rates in montane grassland soils exposed to ambient conditions, drought, and potential future climate conditions (i.e., soils exposed to 6 years of elevated temperatures and elevated CO 2 levels). For this purpose, we combined 18 O-water vapor equilibration with quantitative stable isotope probing (termed ‘vapor-qSIP’) to measure taxon-specific microbial growth in dry soils. In our experiments, drought caused >90% of bacterial and archaeal taxa to stop dividing and reduced the growth rates of persisting ones. Under drought, growing taxa accounted for only 4% of the total community as compared to 35% in the controls. Drought-tolerant communities were dominated by specialized members of the Actinobacteriota, particularly the genus Streptomyces. Six years of pre-exposure to future climate conditions (3 °C warming and + 300 ppm atmospheric CO 2 ) alleviated drought effects on microbial growth, through more drought-tolerant taxa across major phyla, accounting for 9% of the total community. Our results provide insights into the response of active microbes to drought today and in a future climate, and highlight the importance of studying drought in combination with future climate conditions to capture interactive effects and improve predictions of future soil-climate feedbacks.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

A genomic view of Earth’s biomes

Microorganisms are essential to all life on Earth through critical roles in key biological processes and diverse interactions with other organisms that shape ecosystems, drive biogeochemical cycles and influence both human health and environmental health. High-throughput sequencing from environmental samples has revolutionized the understanding of microbial diversity and functions. With vast amounts of genomes now available across Earth’s biomes, these data provide a blueprint of microbial life that can be harnessed for a more holistic understanding of microbiome structure and function across the various ecosystems on Earth. Here we review the application of genome-centric approaches, including recent advances in single-cell sequencing and functional profiling, to survey microbial and viral diversity. Furthermore, we highlight some of the most impactful evolutionary and functional discoveries, explore the spatial diversity and temporal dynamics of microorganisms across diverse environments, and discuss genome-enabled insights into host-associated microorganisms.

Ecology↗
DOE OSTI2023

Temperature and nutrients drive eco-phenotypic dynamics in a microbial food web

Anthropogenic increases in temperature and nutrient loads will likely impact food web structure and stability. Although their independent effects have been reasonably well studied, their joint effects—particularly on coupled ecological and phenotypic dynamics—remain poorly understood. Here we experimentally manipulated temperature and nutrient levels in microbial food webs and used time-series analysis to quantify the strength of reciprocal effects between ecological and phenotypic dynamics across trophic levels. We found that (1) joint—often interactive—effects of temperature and nutrients on ecological dynamics are more common at higher trophic levels, (2) temperature and nutrients interact to shift the relative strength of top-down versus bottom-up control, and (3) rapid phenotypic change mediates observed ecological responses to changes in temperature and nutrients. Our results uncover how feedback between ecological and phenotypic dynamics mediate food web responses to environmental change. As a result, this suggests important but previously unknown ways that temperature and nutrients might jointly control the rapid eco-phenotypic feedback that determine food web dynamics in a changing world.

59 BASIC BIOLOGICAL SCIENCES↗