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At least 991 records · Page 55
All sourcesNASA NTRSDOE OSTI
DOE OSTI2013

Use of comparative genomics approaches to characterize interspecies differences in response to environmental chemicals: Challenges, opportunities, and research needs

A critical challenge for environmental chemical risk assessment is the characterization and reduction of uncertainties introduced when extrapolating inferences from one species to another. The purpose of this article is to explore the challenges, opportunities, and research needs surrounding the issue of how genomics data and computational and systems level approaches can be applied to inform differences in response to environmental chemical exposure across species. We propose that the data, tools, and evolutionary framework of comparative genomics be adapted to inform interspecies differences in chemical mechanisms of action. We compare and contrast existing approaches, from disciplines as varied as evolutionary biology, systems biology, mathematics, and computer science, that can be used, modified, and combined in new ways to discover and characterize interspecies differences in chemical mechanism of action which, in turn, can be explored for application to risk assessment. We consider how genetic, protein, pathway, and network information can be interrogated from an evolutionary biology perspective to effectively characterize variations in biological processes of toxicological relevance among organisms. We conclude that comparative genomics approaches show promise for characterizing interspecies differences in mechanisms of action, and further, for improving our understanding of the uncertainties inherent in extrapolating inferences across species in both ecological and human health risk assessment. To achieve long-term relevance and consistent use in environmental chemical risk assessment, improved bioinformatics tools, computational methods robust to data gaps, and quantitative approaches for conducting extrapolations across species are critically needed. Specific areas ripe for research to address these needs are recommended.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

Interaction of environmental contaminants with zebrafish organic anion transporting polypeptide, Oatp1d1 (Slco1d1)

Polyspecific transporters from the organic anion transporting polypeptide (OATP/Oatp) superfamily mediate the uptake of a wide range of compounds. In zebrafish, Oatp1d1 transports conjugated steroid hormones and cortisol. It is predominantly expressed in the liver, brain and testes. In this study we have characterized the transport of xenobiotics by the zebrafish Oatp1d1 transporter. We developed a novel assay for assessing Oatp1d1 interactors using the fluorescent probe Lucifer yellow and transient transfection in HEK293 cells. Our data showed that numerous environmental contaminants interact with zebrafish Oatp1d1. Oatp1d1 mediated the transport of diclofenac with very high affinity, followed by high affinity towards perfluorooctanesulfonic acid (PFOS), nonylphenol, gemfibrozil and 17α-ethinylestradiol; moderate affinity towards carbaryl, diazinon and caffeine; and low affinity towards metolachlor. Importantly, many environmental chemicals acted as strong inhibitors of Oatp1d1. A strong inhibition of Oatp1d1 transport activity was found by perfluorooctanoic acid (PFOA), chlorpyrifos-methyl, estrone (E1) and 17β-estradiol (E2), followed by moderate to low inhibition by diethyl phthalate, bisphenol A, 7-acetyl-1,1,3,4,4,6-hexamethyl-1,2,3,4 tetrahydronapthalene and clofibrate. In this study we identified Oatp1d1 as a first Solute Carrier (SLC) transporter involved in the transport of a wide range of xenobiotics in fish. Considering that Oatps in zebrafish have not been characterized before, our work on zebrafish Oatp1d1 offers important new insights on the understanding of uptake processes of environmental contaminants, and contributes to the better characterization of zebrafish as a model species. - Highlights: • We optimized a novel assay for determination of Oatp1d1 interactors • Oatp1d1 is the first SLC characterized fish xenobiotic transporter • PFOS, nonylphenol, diclofenac, EE2, caffeine are high affinity Oatp1d1substrates • PFOA, chlorpyrifos-methyl, E1, E2 are strong inhibitors of Oatp1d1 • PFOA and diclofenac can block Oatp1d1 binding of DHEAS, E3S and E17ß-glucuronide.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2019

Optimization of uranium and plutonium separations using TEVA and UTEVA cartridges for MC-ICP-MS analysis of environmental swipe samples

We report that the analysis of environmental swipe samples for ultra-trace uranium (U) and plutonium (Pu) determinations is essential in the nuclear safeguards community. While mass spectrometry techniques for U and Pu detection continually improve, established separation methods are seldom reevaluated. Currently, actinide separations within the forensics community predominantly employ either Eichrom TEVA® or UTEVA® resins. The direct optimization of U and Pu separations utilizing both resins has not been widely reported. Here, several methods were explored with goals of increasing analyte recovery, acquiring cleaner blanks, and improving the separation efficiency of ultra-trace levels of U and Pu from environmental swipe samples. Finally, the optimized separation methodology of U and Pu was examined using certified reference materials and archived environmental swipe samples.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗
DOE OSTI2024

Proof-of-concept chemometric approach for environmental forensic sourcing of crude oil samples using SPME-GC-MS

Environmental exposure to crude oil through seepage and spillage poses risks to the immediate environment and the broader ecosystem as areas along the oil distribution path are affected by the influx of crude petroleum as well as the environmental, economic, and civil unrest that accompanies it. There is a large financial burden associated with the lost resources, including the cost of rehabilitation, and the affected sources of revenue for communities affected by oil spills. As such, it is crucial to determine the responsible parties. This work outlines an environmental forensics approach to determining the source of an un-weathered crude oil sample. The researchers employed solid phase microextraction coupled with gas chromatography mass spectrometry (SPME-GC-MS) to capture and analyze the gaseous components emitted by crude oil samples sourced from five locations. Samples were analyzed using Spearman's rank correlation and 3D covariance analysis. Both chemometric approaches yielded optimal performance results with no misclassifications, true positive rate (TPR) = 100 % and false positive rate (FPR) = 0 %. The similarity metrics calculated by each test noted clear delineations between the values of same-source and differently sourced samples. The Spearman's rank correlation test and 3D covariance calculations both demonstrated the ability to correctly identify sample source origin in this dataset. Finally, the authors outline an approach to the future application of these tests and suggest their joint use in future crude oil sourcing endeavors.

3D covariance mapping↗
DOE OSTI2013

Environmental and technical assessments of the potential utilization of sewage sludge ashes (SSAs) as secondary raw materials in construction

Highlights: ► We used sewage sludge ashes in ready-mix concrete recipe. ► SSAs were used as a substitution of cement. ► Compressive strength of ready-mix concrete incorporating SSAs were similar as blank one. ► Contaminants leaching from concrete monoliths were above threshold limits. - Abstract: Ashes produced by thermal treatments of sewage sludge exhibit common properties with cement. For example, major elements present in SSA are the same of major elements of cement. Hydraulic properties of SSA are quite the same of cement ones. They may therefore be used to substitute part of cement in concrete or other cementitious materials, provided that technical prescriptions are satisfied and that environmental risks are not significantly increased. The objective of the present study was to determine the appropriate substitution ratios to satisfy both technical and environmental criteria. In a first step, the elemental composition and particle size distribution of the ashes were measured. Then the ashes were used along with Portland cement and sand at different ratios of substitution to produce mortar and concrete which were cured for up to 90 days into parallelepipedic or cylindrical monoliths. The mechanical properties of the monoliths were measured using standard procedures for flexural and compressive strengths, and compared to blanks containing no ashes. The environmental criteria were assessed using leaching tests conducted according to standard protocols both on the ashes and the monoliths, and compared to the blanks. Results showed that the characteristics of the ashes ranged between those of cement and sand because of their larger particle size and higher content in SiO{sub 2} as compared to cement. The monoliths made with the highest substitution ratios exhibited a significant decrease in flexural and compressive strengths. However, when the ashes were used in partial substitution of cement at appropriate ratios, the concrete monoliths exhibited similar compressive strengths as the blank samples. The most appropriate ratios were found to be 10% substitution of cement and 2% substitution of sand. The leaching tests conducted on the ashes in their powdery form revealed that amongst the potential contaminants analyzed only Mo and Se were leached at concentrations above the threshold limits considered. The leaching tests conducted on concrete monoliths showed however that none of the contaminants monitored, including Mo and Se, were leached above the limits. In addition, whether concrete recipe incorporated ashes or not, similar concentrations were measured for each potential contaminant in the leachates. This result indicated that mixing ash with cement and sand to produce mortar or concrete induced a stabilization of Mo and Se and thereby constituted in itself a good treatment of the ashes.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2017

Effect of a food waste disposer policy on solid waste and wastewater management with economic implications of environmental externalities

Highlights: • Integrating food waste disposers in waste management systems. • Emissions reduction can reach ∼42% depending on tested scenarios. • Economic gains can reach ∼28% including environmental externalities. • Variation in cost of sludge management exhibit a significant impact on savings. - Abstract: In this study, the carbon footprint of introducing a food waste disposer (FWD) policy was examined in the context of its implications on solid waste and wastewater management with economic assessment of environmental externalities emphasizing potential carbon credit and increased sludge generation. For this purpose, a model adopting a life cycle inventory approach was developed to integrate solid waste and wastewater management processes under a single framework and test scenarios for a waste with high organic food content typical of developing economies. For such a waste composition, the results show that a FWD policy can reduce emissions by nearly ∼42% depending on market penetration, fraction of food waste ground, as well as solid waste and wastewater management schemes, including potential energy recovery. In comparison to baseline, equivalent economic gains can reach ∼28% when environmental externalities including sludge management and emissions variations are considered. The sensitivity analyses on processes with a wide range in costs showed an equivalent economic impact thus emphasizing the viability of a FWD policy although the variation in the cost of sludge management exhibited a significant impact on savings.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2019

Exploring New Science Domains with Atom Probe Tomography Enabled by an Environmental Transfer Hub

The liquid/solid and gas/solid interface represents a rich scientific and technological frontier for discovery and innovation in many areas of science. However, the direct nano- to atomic-scale characterization of these interfaces is technically challenging within broad range of analytical tools that require high to ultrahigh vacuum conditions. This challenge has been largely addressed within the electron microscopy (EM) community through the development of unique specimen holders and differentially-pumped vacuum systems that allow researchers to probe, in situ, liquid/solid and gas/solid interfaces using electron probes [1]. However, the direct application of APT to liquid/solid and gas/solid interfaces is not possible and requires the development of unique specimen preparation and handling of cryogenically-frozen specimens and/or work with specimens under environmentally-protected conditions. At PNNL, we have developed unique suite of hardware and experimental protocols for the preparation and handling of environmentally-sensitive materials centered around the combination of a unique environmental transfer hub, specimen suitcase device, and modified cryo FIB/SEM capabilities (Fig. 1a) [2-3]. The ability to prepare, manipulate, and transfer specimens under either cryogenic or vacuum conditions thus provides a means to uniquely apply APT analysis to a wide variety of material systems that would not be possible otherwise. Here we describe some specific examples, shown in Figure 1b, of APT analysis applied to temperature sensitive material systems requiring cryo specimen preparation and transfer, as well as air sensitive materials systems requiring vacuum or inert vacuum transfer.

Cryo atom probe tomography, Atom Probe, cryogenic ↗
DOE OSTI2018

Screening and Characterization of Novel Polyesterases from Environmental Metagenomes with High Hydrolytic Activity against Synthetic Polyesters

The continuous growth of global plastics production, including polyesters, has resulted in increasing plastic pollution and subsequent negative environmental impacts. Therefore, enzyme-catalyzed depolymerization of synthetic polyesters as a plastics recycling approach has become a focus of research. In this study, we screened over 200 purified uncharacterized hydrolases from environmental metagenomes and sequenced microbial genomes and identified at least 10 proteins with high hydrolytic activity against synthetic polyesters. These include the metagenomic esterases MGS0156 and GEN0105, which hydrolyzed polylactic acid (PLA), polycaprolactone, as well as bis-(benzoyloxyethyl)-terephthalate. With solid PLA as a substrate, both enzymes produced a mixture of lactic acid monomers, dimers, and higher oligomers as products. The crystal structure of MGS0156 was determined at 1.95 angstrom resolution and revealed a modified alpha/beta hydrolase fold, with a lid domain and highly hydrophobic active site. Mutational studies of MGS0156 identified the residues critical for hydrolytic activity against both polyester and monoester substrates, with two-times higher polyesterase activity in the MGS0156 L169A mutant protein. Thus, our work identified novel, highly active polyesterases in environmental metagenomes and provided molecular insights into their activity, thereby augmenting our understanding of enzymatic polyester hydrolysis.

Hajighasemi, Mahbod↗
DOE OSTI2025

PubChemLite Plus Collision Cross Section (CCS) Values for Enhanced Interpretation of Nontarget Environmental Data

Finding relevant chemicals in the vast (known) chemical space is a major challenge for environmental and exposomics studies leveraging nontarget high resolution mass spectrometry (NT-HRMS) methods. Chemical databases now contain hundreds of millions of chemicals, yet many are not relevant. This article details an extensive collaborative, open science effort to provide a dynamic collection of chemicals for environmental, metabolomics, and exposomics research, along with supporting information about their relevance to assist researchers in the interpretation of candidate hits. The PubChemLite for Exposomics collection is compiled from ten annotation categories within PubChem, enhanced with patent, literature and annotation counts, predicted partition coefficient (logP) values, as well as predicted collision cross section (CCS) values using CCSbase. Monthly versions are archived on Zenodo under a CC-BY license, supporting reproducible research, and a new interface has been developed, including historical trends of patent and literature data, for researchers to browse the collection. This article details how PubChemLite can support researchers in environmental and exposomics studies, describes efforts to increase the availability of experimental CCS values, and explores known limitations and potential for future developments. The data and code behind these efforts are openly available.

PubChem↗
DOE OSTI2015

Where Are We Heading in Nanotechnology Environmental Health and Safety and Materials Characterization?

Every chemist, material scientist, physicist, engineer, or commercial enterprise involved in the synthesis and/or production of engineered nanomaterials (ENM) or nano-enabled products aspires to develop safe materials. Nanotechnology environmental health and safety (nanoEHS) is a research discipline that involves the study of the possible adverse health and biological effects that nanomaterials may have on humans and environmental organisms and ecosystems. NanoEHS research has provided a body of experimental evidence indicating the possibility of hazardous outcomes as a result of the interactions of unique ENM physicochemical properties with similar scale processes occurring at a wide range of nano/bio interfaces, including at biomolecular, cellular, subcellular, organ, systemic, whole organism, or ecosystems levels. This projected hazard and risk potential warrants rigorous attention to safety assessment, safe use, safe implementation, benign design, regulatory oversight, governance, and public awareness to address the possibility and prevention of nanotoxicity, now or at any time in the future.1 Thus, we should understand the properties of the ENMs that are responsible for the toxicological response, so that we can re-engineer their physicochemical characteristics for risk prevention and safer ENM design.2 However, in spite of widespread use, no human toxicological disease or major environmental impact has been reported for ENMs. Thus, while “Nanotoxicology” is a thriving sub-discipline of Nano-EHS, the use of the “root” word toxicology may elicit a feeling that nanomaterials are inherently toxic despite the fact that toxicity has not been established in real-life use so far. As a community, we may want to rename this sub-discipline as “Nanosafety,” since the objective is to use toxicology information to guide the design of safer nanomaterials for use in medicine, biology, electronics, lighting systems, etc. At ACS Nano, we are interested in publishing articles and forward-looking Perspectives and Reviews that determine and establish ENM physicochemical properties, structure-activity relationships, catalytic effects at the nano/bio interface, mechanistic injury responses, in vitro to in vivo prediction making, safer-by design strategies, actionable screening and detection methods, hazard and risk ranking, fate and transport, ENM categorization, theory and modeling, societal implications, and regulatory/governance decisions.3 Context is important in the immediate and longer-range impact of this research, as we are interested in realistic nanoEHS exposure scenarios conducted with systematic variation of ENM physicochemical properties rather than investigations of a single or a limited number of materials in isolated in vitro studies that only address cytotoxicity at unrealistic doses. In order to make these data useful for researchers, government and regulatory agencies, and other interested parties, these studies, where possible, should include either appropriate positive and negative controls or benchmark materials to answer the important question, “as compared to what?” Dosimetry should be explained in terms of appropriate dose metrics relative to the type of materials, their mechanisms of injury, and exposure conditions, using in vitro to in vivo extrapolations where possible. Another important component of these studies includes appropriate physicochemical characterization of the nanomaterials.

Nel, Andre↗
DOE OSTI2021

Sustainable Recycling of Rare-Earth Elements from NdFeB Magnet Swarf: Techno-Economic and Environmental Perspectives

Rare-earth elements (REEs) are increasingly susceptible to supply risks due to their limited geographical availability and growing demand in clean energy applications such as neodymium-iron-boron (NdFeB) magnets used in electric vehicles and wind turbines. When NdFeB magnets are produced, 6–73% of swarf is generated during the manufacturing steps. This paper presents an innovative technology that utilizes copper nitrate to dissolve REEs in NdFeB magnet swarf and subsequently recovers ~97% of them as mixed rare-earth oxides (REOs) of purity higher than 99.5%. Techno-economic analysis (TEA) and life cycle assessment (LCA) quantified the economic and environmental impacts of adopting the proposed acid-free dissolution technology, projecting a net profit margin of 12–43% and a global warming impact reduction by up to 73% compared to the prevailing REO production routes in China. As copper nitrate is the single largest contributor to the cost and environmental footprint, recycling of copper nitrate was investigated as well as using alternative copper salts (e.g., copper acetate), revealing significant improvements in TEA and LCA results. Dysprosium was a major revenue source, highlighting the importance of targeting electric vehicle magnets that are rich in dysprosium. As the REO market is volatile, sensitivity analysis was employed to evaluate the profitability of the proposed technology under different REO prices over the last 11 years. Overall, our results confirmed the economic and environmental viability of the proposed technology for sustainable recycling of REEs from the NdFeB magnet swarf.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Cellulose Nanocrystals’ Role in Critical Mineral Beneficiation: Dual Aggregate-Dispersant Behavior Supports Environmentally Benign Nickel Processing

Environmentally unsustainable and toxic chemical flocculants and dispersants from nickel (Ni) processing contribute to industrial effluents that greatly impact biodiversity and aquatic life. Despite the industry’s efforts to reduce its ecological footprint—primarily due to the lack of commercially available biodegradable, environmentally benign, and non-toxic reagents—these reagents continue to harm natural ecosystems. Chemicals used during the processing operations often target a specific unit operation that negatively affects downstream operations. In this study, we discover the concentration-dependent behavior of cellulose nanocrystals (CNCs) as a dispersant and flocculant, avoiding the use of various harmful chemicals in the nickel processing stages. Electrophoretic, optical brightfield microscopy, and quartz crystal microbalance-dissipation studies detected charge neutralization behavior by renewable and biodegradable CNCs, which can greatly benefit Ni processing operations. Microflotation experiments demonstrated that CNCs enhanced Ni recovery from 62 to 77 wt.% and concentrate grade from 15 to 20 wt.%. Settling and turbidity studies demonstrated the dual flocculant-dispersant behavior of CNCs resulting from the alignment of CNC fibers along the octahedral brucite basal and amphoteric edge plane of serpentine. CNCs can be used as dispersants during froth flotation to improve Ni beneficiation and as post-processing flocculants for tailings management and dewatering, which is one of the major environmental and social concerns facing the mining and mineral processing industry. This study paves the way for CNCs to be used as flocculants and dispersants in a range of industries from healthcare to pharmaceuticals to semiconductor devices.

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

A Pathway Analysis Framework for Evaluating the Economic and Environmental Viability of Biomass-Based Plastic Production

Plastic production from fossil feedstocks (e.g., naphtha, coal, and natural gas) is not sustainable and causes known environmental impacts such as global warming. A possible solution is to shift production pathways to use biomass, which is a sustainable feedstock that can sequester atmospheric carbon dioxide. This study presents an optimization-based pathway analysis framework for evaluating the carbon footprints of the production of mainstream plastics from biomass and fossil feedstocks. We use the modeling framework to quickly navigate complex interdependencies that exist between the production pathways of different plastics and to determine pathways of minimum production cost under a range of carbon pricing scenarios. The framework interprets carbon prices as an exogenous taxation scheme or an endogenous negative value perceived by producers. The proposed approach reveals the biomass feedstock quantities needed to displace fossil counterparts and the plastics and technologies that should be prioritized. The framework can also be used for evaluating system-wide trade-offs between production costs and carbon footprints that arise from pathway interdependencies. We also evaluate hidden environmental impacts associated with the large-scale use of biomass as a feedstock, such as land use and water eutrophication that results from a significant increase in fertilizer use. Therefore, it is important to highlight that there are trade-offs between decarbonization and other environmental issues. Here, the proposed framework provides an integrative platform for basic techno-economic and life-cycle data that can be used for analyzing diverse scenarios and determining necessary technology targets (e.g., yields, footprints, and costs) to achieve required levels of decarbonization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Take a Closer Look:Biofuels Can Support Environmental, Economic and Social Goals

The US Congress passed the Renewable Fuels Standard (RFS) seven years ago. Since then, biofuels have gone from darling to scapegoat for many environmentalists, policy makers, and the general public. The reasons for this shift are complex and include concerns about environmental degradation, uncertainties about impact on food security, new access to fossil fuels, and overly optimistic timetables. As a result, many people have written off biofuels. However, numerous studies indicate that biofuels, if managed sustainably, can help solve pressing environmental, social and economic problems (Figure 1). The scientific and policy communities should take a closer look by reviewing the key assumptions underlying opposition to biofuels and carefully consider the probable alternatives. Liquid fuels based on fossil raw materials are likely to come at increasing environmental cost. Sustainable futures require energy conservation, increased efficiency, and alternatives to fossil fuels, including biofuels.

Dale, Bruce E.↗
DOE OSTI2026

Developing Scenario‐Based Strategies for Health, Climate, and Environmental Preparedness: The One Health, One Earth Approach

Climate change amplifies many threats to human health. Despite advances in understanding climate change dynamics and impacts, there remains a critical gap in translating scientific knowledge into equitable, and community-driven health interventions. The inaugural One Earth, One Health workshop sought to explore this gap through human-centered design exercises involving interdisciplinary researchers from climate and Earth sciences, engineering, epidemiology, microbiology, and environmental health. Although participants did not co-develop solutions with affected communities, they used stakeholder role-playing to guide ideation and lay groundwork for actionable plans. Through these methods, participants identified community needs and proposed prototype solutions to alleviate health threats exacerbated by global environmental change. Prototypes were organized around infectious diseases, extreme weather, and air quality, as illustrative themes rather than an exhaustive set of risks. Key solutions included strategies for anticipatory systems and early warning (e.g., integrating environmental signals with health data), inclusive communication and infrastructure needs for responding to extreme weather events, and integrated platforms visualizing air quality trends to support tailored, context-aware guidance beyond one-size-fits-all alerts. The workshop highlighted opportunities such as leveraging machine learning, Earth observation, and real-time surveillance to protect communities, but also noted barriers including data quality, technological redundancy, privacy, and governance challenges. Additionally, participants emphasized the need for interdisciplinary teams capable of collaborating across sectors, breaking down silos and addressing gaps in training and education. Overall, the workshop illustrates how process-driven, human-centered approaches can help surface user needs and generate testable prototype concepts, while underscoring the importance of direct community partnership for implementation.

Abadi, Azar M. [University of Alabama, Birmingham,↗
DOE OSTI2017

Vulnerability of US thermoelectric power generation to climate change when incorporating state-level environmental regulations

This study explores the interactions between climate and thermoelectric generation in the U.S. by coupling an Earth System Model with a thermoelectric power generation model. We validated model simulations of power production for selected power plants (~44% of existing thermoelectric capacity) against reported values. In addition, we projected future usable capacity for existing power plants under two different climate change scenarios. Results indicate that climate change alone may reduce average thermoelectric generating capacity by 2%-3% by the 2060s. Reductions up to 12% are expected if environmental requirements are enforced without waivers for thermal variation. This study concludes that the impact of climate change on the U.S. thermoelectric power system is less than previous estimates due to an inclusion of a spatially-disaggregated representation of environmental regulations and provisional variances that temporarily relieve power plants from permit requirements. This work highlights the significance of accounting for legal constructs in which the operation of power plants are managed, and underscores the effects of provisional variances in addition to environmental requirements.

climate change↗
DOE OSTI2019

Environmental pH and peptide signaling control virulence of Streptococcus pyogenes via a quorum-sensing pathway

Bacteria control gene expression in concert with their population density by a process called quorum sensing, which is modulated by bacterial chemical signals and environmental factors. In the human pathogen Streptococcus pyogenes , production of secreted virulence factor SpeB is controlled by a quorum-sensing pathway and environmental pH. The quorum-sensing pathway consists of a secreted leaderless peptide signal (SIP), and its cognate receptor RopB. Here, we report that the SIP quorum-sensing pathway has a pH-sensing mechanism operative through a pH-sensitive histidine switch located at the base of the SIP-binding pocket of RopB. Environmental acidification induces protonation of His144 and reorganization of hydrogen bonding networks in RopB, which facilitates SIP recognition. The convergence of two disparate signals in the SIP signaling pathway results in induction of SpeB production and increased bacterial virulence. Our findings provide a model for investigating analogous crosstalk in other microorganisms.

Science & Technology - Other Topics↗
DOE OSTI2021

Pangenomics reveals alternative environmental lifestyles among chlamydiae

Chlamydiae are highly successful strictly intracellular bacteria associated with diverse eukaryotic hosts. Here we analyzed metagenome-assembled genomes of the “Genomes from Earth’s Microbiomes” initiative from diverse environmental samples, which almost double the known phylogenetic diversity of the phylum and facilitate a highly resolved view at the chlamydial pangenome. Chlamydiae are defined by a relatively large core genome indicative of an intracellular lifestyle, and a highly dynamic accessory genome of environmental lineages. We observe chlamydial lineages that encode enzymes of the reductive tricarboxylic acid cycle and for light-driven ATP synthesis. We show a widespread potential for anaerobic energy generation through pyruvate fermentation or the arginine deiminase pathway, and we add lineages capable of molecular hydrogen production. Genome-informed analysis of environmental distribution revealed lineage-specific niches and a high abundance of chlamydiae in some habitats. Together, our data provide an extended perspective of the variability of chlamydial biology and the ecology of this phylum of intracellular microbes.

59 BASIC BIOLOGICAL SCIENCES↗