Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “microbial systems”

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 1,711 records · Page 95
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Interplay of microbial communities with mineral environments in coralline algae

Coralline algae are worldwide carbonate builders, considered to be foundational species and biodiversity hotspots. Coralline habitats face increasing pressure from human activities and effects related to Global Change, yet their ecological properties and adaptive responses remain poorly understood. The relationships of the algal microbiota with the mineral bioconstructions, as well as plasticity and resilience of coralline holobionts in a changing environment, are of particular interest. In the Gulf of California, Neogoniolithon trichotomum (Rhodophyta) is the main carbonate builder in tidal pools. We performed a multi-disciplinary assessment of the N. trichotomum microstructure using XRD, SEM microscopy and SR-FTIR spectromicroscopy. In the algal perithallus, magnesium-calcite and aragonite were spatially segregated and embedded in a polysaccharide matrix (rich in sulfated polysaccharides). Mg-calcites (18-19 mol% Mg) were the main mineral components of the thallus overall, followed by iron carbonates related to dolomite (ankerite) and siderite. Minerals of late evaporitic sequences (sylvite and bischofite) were also present, suggesting potential halophilic microenvironments within the algal thalli. The diverse set of abundant halophilic, halotolerant and oligotrophic taxa, whose abundance increase in the summer, further suggests this condition. We created an integrated model, based on environmental parameters and the microbiota distribution, that identified temperature and nutrient availability (particularly nitrate and silicate) as the main parameters related to specific taxa patterns. Among these, Hahella, Granulossicoccus, Ferrimonas, Spongiibacteraceae and cyanobacterial Xenococcaceae and Nostocaceae change significantly between seasons. These bacterial components might play relevant roles in algal plasticity and adaptive responses to a changing environment. This study contributes to the understanding of the interplay of the prokaryotic microbiota with the mineral microenvironments of coralline algae. Because of their carbonates with potential resistance to dissolution in a higher pCO 2 world and their seasonally dynamic bacteria, coralline algae are relevant targets to study coastal resilience and carbonated systems responses to changing environments.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

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

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

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Bleach Rescues Nannochloropsis from an Obligate Parasite and Alters Microbial and Metabolite Signatures of Outdoor Cultures

Chemical agents are commonly used to protect algal crops. Yet, few studies have characterized the effects of these agents on associated microbial communities to understand effects on microbial functions relevant to algal crop production and protection. Here, we used shotgun metagenomic sequencing and untargeted exometabolite profiling to link the application of bleach, a -cidal agent used to protect algae from pests, to changes in community composition, metabolic pathways, and exometabolies - at a whole community level. Bleach protected the algal crop from crashing but altered bacterial diversity. Analysis of metagenome-assembled genomes (MAGs) revealed a classic predator-prey cycle between Oligoflexus and our target alga Nannochloropsis. Olifoflexus genomes from our study were notably similar to a previously identified BALO (Bdellovibrio and like organism), FD111, known to kill Nannochloropsis cultures, providing strong evidence that an FD111-like organism was responsible for the crash. Metabolic pathway composition differed between bleached and unbleached ponds, with abundance of twelve pathways related to stress tolerance, including the superpathway of methylglyoxal degradation, lipid IVA biosynthesis, and ectoine biosynthesis, greater in bleached ponds compared to unbleached ponds. Virulence factors related to adherence, biofilm formation, motility, and pathogenicity increased dramatically in bleached ponds with time, although this increase was not coupled with an increase in pathogens - algal or otherwise - or a decline in algal health. Our study highlights the importance of coupling 16S rRNA gene sequencing with whole genome data and other -omics tools to sketch a larger picture of community structure and function in crop systems. Moreover, our results highlight that continued long-term bleaching may lead to negative effects to crop health or downstream adverse health effects to humans or animals, depending on the algal product (i.e. human supplements or animal feedstocks). Future work on alternative treatment methods that would reduce resistance is necessary in the field.

09 BIOMASS FUELS↗
NASA NTRS1996

Survival of Potentially Pathogenic Human-Associated Bacteria in the Rhizosphere of Hydroponically Grown Wheat

Plants may serve as reservoirs for human-associated bacteria (H-AB) in long-term space missions containing bioregenerative life support systems. The current study examined the abilities of five human-associated potential pathogens, Pseudomonas aeruginosa, Pseudomonas cepacia, Staphylococcus aureus, Streptococcus pyogenes, and Escherichia coli, to colonize and grow in the rhizosphere of hydroponically grown wheat, a candidate crop for life support. All of these bacteria have been recovered from past NASA missions and present potential problems for future missions. The abilities of these organisms to adhere to the roots of axenic five-day-old wheat (Triticum aestivum L. cv. Yecora rojo) were evaluated by enumeration of the attached organisms after a one hour incubation of roots in a suspension (approximately 10(exp 8 cu/ml)) of the H-AB. Results showed that a greater percentage of P. aeruginosa cells adhered to the wheat roots than the other four H-AB. Similarly incubated seedlings were also grown under attempted axenic conditions for seven days to examine the potential of each organism to proliferate in the rhizosphere (root colonization capacity). P. cepacia and P. aeruginosa showed considerable growth. E. coli and S. aureus showed no significant growth, and S. pyogenes died off in the wheat rhizosphere. Studies examining the effects of competition on the survival of these microorganisms indicated that P. aeruginosa was the only organism that survived in the rhizosphere of hydroponically grown wheat in the presence of different levels of microbial competition.

Morales, Anabelle↗
DOE OSTI2024

Characterizing suburban soil and microbial properties along a soil age chronosequence

Abstract Rapid urbanization is drastically altering ecosystem processes in landscapes around the world. In particular, suburban residential neighborhoods comprise novel ecosystems with water and nutrient inputs that differ greatly from the surrounding land area. These impacts generate concern over the sustainability of urban ecosystems, especially whether they will be characterized by net carbon gain or loss over time. To address this knowledge gap, we established a chronosequence of residential yards in Southern California to test how urban soils change after development. We predicted that urbanized soils would experience shifts in physical characteristics and microbial function over time consistent with ecological succession theory, but residential soils would maintain novel moisture and nutrient regimes compared to undeveloped soils, never “recovering” to a pre‐developed state. We compared different vegetation types to quantify impacts of homeowner landscaping choices and characterized yard soils and their microbial communities. We found that yard soils were nutrient‐ and moisture‐enriched compared to an adjacent undeveloped ecosystem, and turfgrass was associated with higher levels of water and nitrogen. Despite high respiration rates, yard soils accumulated carbon and nitrogen over time. We conclude that suburban residential soils comprise dynamic and heterogeneous ecosystems that are highly influenced by landscaping choices and management practices, and warrant closer study at small management‐relevant scales.

Suratt, Andie [Department of Ecology and Evolution↗
NASA NTRS1985

Precision and sensitivity of the measurement of 15N enrichment in D-alanine from bacterial cell walls using positive/negative ion mass spectrometry

Sensitive detection of cellular components from specific groups of microbes can be utilized as 'signatures' in the examination of microbial consortia from soils, sediments or biofilms. Utilizing capillary gas chromatography/mass spectrometry and stereospecific derivatizing agents, D-alanine, a component localized in the prokaryotic (bacterial) cell wall, can be detected reproducibly. Enrichments of D-[15N]alanine determined in E. coli grown with [15N]ammonia can be determined with precision at 1.0 atom%. Chemical ionization with methane gas and the detection of negative ions (M - HF)- and (M - F or M + H - HF)- formed from the heptafluorobutyryl D-2 butanol ester of D-alanine allowed as little as 8 pg (90 fmol) to be detected reproducibly. This method can be utilized to define the metabolic activity in terms of 15N incorporation at the level of 10(3)-10(4) cells, as a function of the 15N-14N ratio.

Non-NASA Center↗
DOE OSTI2021

Soil organic matter is principally root derived in an Ultisol under oak forest

To a large degree, the sources and stability of soil organic carbon remain poorly constrained. A clear understanding of links among the components of the soil C cycle is hampered by the complexity of the system as well as challenges associated with partitioning bulk soil C into meaningful fractions. A large accidental 14 CO 2 release at the Oak Ridge Reservation in Tennessee, USA provided a strong label pulse into adjacent, well-studied oak forests, resulting in highly elevated Δ 14 C values in leaf litter (~1000‰) and roots (~260–450‰). A four-year manipulative study was conducted to determine the relative contribution of litter versus roots to the bulk mineral soil C pool, as well as to free light, occluded light and heavy fractions. The heavy fraction was further split into fractions with densities of 1.7–2.4 g cm –3 and >2.4 g cm –3 to test the homogeneity of the mineral-associated fraction of C. Substantial concentrations of label were detected in all soil fractions within a year of the 14 CO 2 release, indicating rapid incorporation of newly fixed photosynthates in all fractions of soil organic C, regardless of differences in stability inferred by previous work. This rapid incorporation of label occurred only in treatments where roots were labeled, indicating that roots are the major source of inputs to mineral soil C stocks at these sites. Separation of the heavy fraction into subfractions of intermediate (1.7–2.4 g cm –3 ) and high (>2.4 g cm –3 ) density indicated that both subfractions incorporated label at similar rates, despite significant differences in degree of microbial processing. In general, the rate of label incorporation suggested a much faster turnover for all fractions than indicated by natural radiocarbon abundance values. This study suggests that within each soil fraction there are portions of slow-cycling and fast-cycling materials, and the determination of an average turnover time or mean age is dependent on experimental approach. The rapid incorporation of label into all fractions within a year regardless of inferred stability implies a high degree of heterogeneity in all fractions regardless of how finely the soils are partitioned. Further refinement of the nature and drivers of this heterogeneity could yield important insights into the soil C cycle.

58 GEOSCIENCES↗
NASA NTRS1993

Planetary protection implementation on future Mars lander missions

A workshop was convened to discuss the subject of planetary protection implementation for Mars lander missions. It was sponsored and organized by the Exobiology Implementation Team of the U.S./Russian Joint Working Group on Space Biomedical and Life Support Systems. The objective of the workshop was to discuss planetary protection issues for the Russian Mars '94 mission, which is currently under development, as well as for additional future Mars lander missions including the planned Mars '96 and U.S. MESUR Pathfinder and Network missions. A series of invited presentations was made to ensure that workshop participants had access to information relevant to the planned discussions. The topics summarized in this report include exobiology science objectives for Mars exploration, current international policy on planetary protection, planetary protection requirements developed for earlier missions, mission plans and designs for future U.S. and Russian Mars landers, biological contamination of spacecraft components, and techniques for spacecraft bioload reduction. In addition, the recent recommendations of the U.S. Space Studies Board (SSB) on this subject were also summarized. Much of the discussion focused on the recommendations of the SSB. The SSB proposed relaxing the planetary protection requirements for those Mars lander missions that do not contain life detection experiments, but maintaining Viking-like requirements for those missions that do contain life detection experiments. The SSB recommendations were found to be acceptable as a guide for future missions, although many questions and concerns about interpretation were raised and are summarized. Significant among the concerns was the need for more quantitative guidelines to prevent misinterpretation by project offices and better access to and use of the Viking data base of bioassays to specify microbial burden targets. Among the questions raised were how will the SSB recommendations be integrated with existing Committee on Space Research (COSPAR) policy and how will they apply to and affect Mars '94, Mars '96, MESUR Pathfinder, and MESUR Network missions? One additional topic briefly considered at the workshop was the identification of some issues related to planetary protection considerations for Mars sample return missions. These issues will form the basis for a follow-on joint U.S./Russian workshop on that subject.

Howell, Robert↗
NASA NTRS2015

Coordination of International Risk-Reduction Investigations by the Multilateral Human Research Panel for Exploration

Effective use of the unique capabilities of the International Space Station (ISS) for risk reduction on future deep space missions involves preliminary work in analog environments to identify and evaluate the most promising techniques, interventions and treatments. This entails a consolidated multinational approach to biomedical research both on ISS and in ground analogs. The Multilateral Human Research Panel for Exploration (MHRPE) was chartered by the five ISS partners to recommend the best combination of partner investigations on ISS for risk reduction in the relatively short time available for ISS utilization. MHRPE will also make recommendations to funding agencies for appropriate preparatory analog work. In 2011, NASA's Human Research Program (HRP) and the Institute of Biomedical Problems (IBMP) of the Russian Academy of Science, acting for MHRPE, developed a joint US-Russian biomedical program for the 2015 one-year ISS mission (1YM) of American and Russian crewmembers. This was to evaluate the possibilities for multilateral research on ISS. An overlapping list of 16 HRP, 9 IBMP, 3 Japanese, 3 European and 1 Canadian investigations were selected to address risk-reduction goals in 7 categories: Functional Performance, Behavioral Health, Visual Impairment, Metabolism, Physical Capacity, Microbial and Human Factors. MHRPE intends to build on this bilateral foundation to recommend more fully-integrated multilateral investigations on future ISS missions commencing after the 1YM. MHRPE has also endorsed an on-going program of coordinated research on 6-month, one-year and 6-week missions ISS expeditions that is now under consideration by ISS managers. Preparatory work for these missions will require coordinated and collaborative campaigns especially in the psychological and psychosocial areas using analog isolation facilities in Houston, Köln and Moscow, and possibly elsewhere. The multilateral Human Analogs research working group (HANA) is the focal point of those planning discussions, with MHRPE coordinating between the national programs and then supporting implementation on ISS. Experience gained during preparations for the 1YM has identified improvements in both American and Russian processes to enable well-integrated investigations on all subsequent ISS expeditions. Among those is that the greatest efficiency is to be gained with investigations that are fully integrated from their conception, with co-principal investigators, a consolidated proposal and integrated plans for crewmember time and other flight-related resources. Analog investigations preceding future ISS expeditions will employ these lessons in efficiency to evaluate the techniques and tools to be validated aboard ISS. In this way, the resources and capabilities of ISS can be applied most efficiently to solving the problems facing astronauts of all nations in missions deep into the solar system.

Charles, John B.↗
DOE OSTI2024

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

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

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2023

Virus Infection of Phytoplankton Increases Average Molar Mass and Reduces Hygroscopicity of Aerosolized Organic Matter

Viral infection of phytoplankton is a pervasive mechanism of cell death and bloom termination, which leads to the production of dissolved and colloidal organic matter that can be aerosolized into the atmosphere. Earth-observing satellites can track the growth and death of phytoplankton blooms on weekly time scales but the impact of viral infection on the cloud forming potential of associated aerosols is largely unknown. Here, we determine the influence of viral-derived organic matter, purified viruses, and marine hydrogels on the cloud condensation nuclei activity of their aerosolized solutions, compared to organic exudates from healthy phytoplankton. Dissolved organic material derived from exponentially growing and infected cells of well-characterized eukaryotic phytoplankton host-virus systems, including viruses from diatoms, coccolithophores and chlorophytes, was concentrated, desalted, and nebulized to form aerosol particles composed of primarily of organic matter. Aerosols from infected phytoplankton cultures resulted in an increase in critical activation diameter and average molar mass in three out of five combinations evaluated, along with a decrease in organic kappa (hygroscopicity) compared to healthy cultures and seawater controls. The infected samples also displayed evidence of increased surface tension depression at realistic cloud water vapor supersaturations. Amending the samples with xanthan gum to simulate marine hydrogels increased variability in organic kappa and surface tension in aerosols with high organic to salt ratios. Our findings suggest that the pulses of increased dissolved organic matter associated with viral infection in surface waters may increase the molar mass of dissolved organic compounds relative to surface waters occupied by healthy phytoplankton or low phytoplankton biomass.

Atmospheric science↗
DOE OSTI2025

Diurnal Trends and Meteorological Factors Influencing the Variability of Fluorescent Bioaerosol in Mt. Crested Butte, Colorado During SAIL

Abstract Despite the crucial role of bioaerosol particles (BAP) in our climate system, local ecosystems, and human health, our grasp on their atmospheric interactions is hampered by a lack of high‐resolution and long‐term data, which is essential for understanding their abundance and variability in response to meteorological conditions. To discern these relationships in a high‐altitude mountainous terrain is even less well‐studied. Therefore, we deployed a Wideband Integrated Bioaerosol Sensor (WIBS‐Neo) for three months during the first biologically active season of the Surface Atmosphere Integrated Field Laboratory (SAIL) campaign in summer 2022 on Mt. Crested Butte in Colorado (elevation 3,140 m ASL). Here, we report real‐time fluorescent BAP (FBAP) data collected from 15 June to 13 September 2022, sampled from within the ARM Aerosol Observing System (AOS). To our knowledge, these are the first high altitude (>3,000 m ASL) continuous measurements of FBAP made in North America. During this deployment, we observed on average 21% and as many as 48% (hourly maximum) of particles within the detection size range ( to ) of the WIBS as FBAP. Our analysis presents the diurnal cycles for seven distinct types of FBAP, showing unique patterns and, in some cases, correlations with temperature and solar radiation cycles. Abundance and composition of FBAP varied with relative humidity and precipitation. Precipitation events appeared to both cause emission and removal of FBAP, whereas dust and smoke events had no significant effect, highlighting the critical role of meteorology on FBAP at high altitudes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Interactive effects of salinity, redox, and colloids on greenhouse gas production and carbon mobility in coastal wetland soils

Coastal wetlands, including freshwater systems near large lakes, rapidly bury carbon, but less is known about how they transport carbon either to marine and lake environments or to the atmosphere as greenhouse gases (GHGs) such as carbon dioxide and methane. This study examines how GHG production and organic matter (OM) mobility in coastal wetland soils vary with the availability of oxygen and other terminal electron acceptors. We also evaluated how OM and redox-sensitive species varied across different size fractions: particulates (0.45–1μm), fine colloids (0.1–0.45μm), and nano particulates plus truly soluble (<0.1μm; NP+S) during 21-day aerobic and anaerobic slurry incubations. Soils were collected from the center of a freshwater coastal wetland (FW-C) in Lake Erie, the upland-wetland edge of the same wetland (FW-E), and the center of a saline coastal wetland (SW-C) in the Pacific Northwest, USA. Anaerobic methane production for FW-E soils were 47 and 27,537 times greater than FW-C and SW-C soils, respectively. High Fe 2+ and dissolved sulfate concentrations in FW-C and SW-C soils suggest that iron and/or sulfate reduction inhibited methanogenesis. Aerobic CO 2 production was highest for both freshwater soils, which had a higher proportion of OM in the NP+S fraction (64±28% and 70±10% for FW-C and FW-E, respectively) and organic C:N ratios reflective of microbial detritus (5.3±5.3 and 5.3±7.0 for FW-E and FW-C, respectively) compared to SW-C, which had a higher fraction of particulate (58±9%) and fine colloidal (19±7%) OM and organic C:N ratios reflective of vegetation detritus (11.4 ± 1.7). The variability in GHG production and shifts in OM size fractionation and composition observed across freshwater and saline soils collected within individual and across different sites reinforce the high spatial variability in the processes controlling OM stability, mobility, and bioavailability in coastal wetland soils.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Microdiverse bacterial clades prevail across Antarctic wetlands

Antarctica's extreme environmental conditions impose selection pressures on microbial communities. Indeed, a previous study revealed that bacterial assemblages at the Cierva Point Wetland Complex (CPWC) are shaped by strong homogeneous selection. Yet which bacterial phylogenetic clades are shaped by selection processes and their ecological strategies to thrive in such extreme conditions remain unknown. Here, we applied the phyloscore and feature-level βNTI indexes coupled with phylofactorization to successfully detect bacterial monophyletic clades subjected to homogeneous (HoS) and heterogenous (HeS) selection. Remarkably, only the HoS clades showed high relative abundance across all samples and signs of putative microdiversity. The majority of the amplicon sequence variants (ASVs) within each HoS clade clustered into a unique 97% sequence similarity operational taxonomic unit (OTU) and inhabited a specific environment (lotic, lentic or terrestrial). Our findings suggest the existence of microdiversification leading to sub-taxa niche differentiation, with putative distinct ecotypes (consisting of groups of ASVs) adapted to a specific environment. We hypothesize that HoS clades thriving in the CPWC have phylogenetically conserved traits that accelerate their rate of evolution, enabling them to adapt to strong spatio-temporally variable selection pressures. Variable selection appears to operate within clades to cause very rapid microdiversification without losing key traits that lead to high abundance. Variable and homogeneous selection, therefore, operate simultaneously but on different aspects of organismal ecology. The result is an overall signal of homogeneous selection due to rapid within-clade microdiversification caused by variable selection. It is unknown whether other systems experience this dynamic, and we encourage future work evaluating the transferability of our results.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

The Role of Quantum Science Concepts in Enhancing Sensing and Imaging Technologies: Applications for Biology: Proceedings of a Workshop

Quantum concepts hold the potential to enable significant advances in sensing and imaging technologies that could be vital to the study of biological systems. The workshop Quantum Science Concepts in Enhancing Sensing and Imaging Technologies: Applications for Biology, held online March 8–10, 2021, was organized to examine the research and development needs to advance biological applications of quantum technology. Hosted by the National Academies of Sciences, Engineering, and Medicine, the event brought together experts working on state-of-the-art, quantum-enabled technologies and scientists who are interested in applying these technologies to biological systems. Through talks, panels, and discussions, the workshop facilitated a better understanding of the current and future biological applications of quantum-enabled technologies in fields such as microbiology, molecular biology, cell biology, plant science, mycology, and many others. The workshop was organized around three main themes. The first, quantum in biology, examined quantum concepts that are hypothesized to be important for life processes and that researchers are working to observe through biological imaging and sensing. The second, quantum for biology, addressed ways to use quantum concepts to enhance technologies for biological imaging and sensing. The third, biology for quantum, offered a wider discussion of how the frontiers of biological imaging and sensing could enable future study using quantum concepts, tools, or technologies. Throughout the workshop, participants identified a wide range of emerging approaches and opportunities at the intersection of quantum physics and biological sensing and imaging. During the workshop, there were some differences in how each speaker defined the term quantum. During one of the panels, Prem Kumar offered thoughts on what phenomena are classical versus quantum, explaining that techniques get progressively more quantum as you move from just having superposition to having superposition with measurement and entanglement. Another explanation from Clarice Aiello delineates the definition into several levels. This includes a base level of “quantum-ness,” which reflects that all matter is made of atoms, and when these particles are isolated they behave based on quantum mechanical principles. A second level is related to quantum coherence, where a single quantum object might be found in a coherent superposition state. A final level, which she described as the quantum-entangled level, involves multiple quantum systems which are entangled among themselves. Overall, the workshop touched on concepts such as superposition, entanglement, and squeezing and their potential implications for communication, computing, and simulation, in addition to the workshop’s main focal area, biological sensing and imaging. At the opening of the workshop, Thorsten Ritz of the University of California, Irvine, identified two questions at the heart of quantum biology: Is the machinery of life quantum mechanical, and can quantum mechanics be used to study the machinery of life in new ways? Participants highlighted systems in which researchers have explored these questions, from the vast array of molecular interactions involved in biological processes such as photosynthesis, to the mechanics involved in cellular functions such as differentiation and aggregation, to the role of oscillating magnetic fields in flight orientation among birds. Sensing and imaging technologies are crucial to biological research; these technologies could both enhance the study of quantum effects and be enhanced by quantum concepts. A critical challenge in biological research is to develop imaging and sensing tools that do not damage or interfere with the often fragile and fleeting systems being studied. Attendees discussed a variety of established and emerging technologies that could enhance noninvasive biological imaging, including single- and two-photon spectroscopy, single-molecule spectroscopy, quantum illumination, ghost imaging, and cryo-electron microscopy. One example came from Marlan Scully who gave a keynote address on the first day of the workshop. Scully emphasized the use of different laser technologies, which exhibit coherence and other quantum properties, in moving toward real-world biological applications, such as the detection of SARS-CoV-2. Both tools and theory will play an important role in advancing quantum biology research and applications. Several participants suggested theorists and experimentalists should work in tandem to understand and model biological processes. While physics often reduces systems to their simplest forms for fundamental insights, participants also noted the value of observing and understanding biological systems in all their “messiness,” capturing both the inner workings of biological systems and the complex interactions that occur within and between organisms. In discussions among participants, several attendees stressed the need to match emerging tools with the right scientific questions. Rather than developing quantum technologies as “a hammer looking for a nail,” participants emphasized a focus on exploring the problems these technologies are best suited to address. For example, it is important to consider the size of the phenomenon being studied, the timescales that are important in answering the scientific question, and other relevant considerations. Every tool along the spectrum from classical to quantum involves its own set of trade-offs. For example, Ted Laurence of the Lawrence Livermore National Laboratory said that quantum measurements, such as single photon counting, fluorescence transitions, and lasers, can take longer to produce the same results as classical measurements. These quantum measurements, however, do not require calibration and can enable new research questions to be answered. Prem Kumar, Northwestern University, noted that, despite their promise, quantum approaches should not be used simply for the sake of using quantum, especially in situations where classical approaches better meet the needs of the researcher. Understanding and applying quantum concepts could enable advances in a wide range of application areas including energy, synthetic biology, medicine, and sustainability. For example, Michelle O’Malley, University of California, Santa Barbara, described how improved noninvasive imaging approaches could help capture the complex interactions and functions involved in the breakdown of organic matter by microbial communities and lead to new technologies for capturing valuable products from plant waste. Several other participants discussed needs in tracking the movement of metabolites and molecules in microbial communities for insights into nutrient cycling in environments such as soil. Margaret Ahmad, Sorbonne University, discussed potential opportunities to leverage the magnetic properties of cryptochromes to advance new treatment approaches for diseases such as COVID-19 and cancer. Looking toward the future development of the field, participants discussed challenges to advancing quantum biology that arise from disciplinary disconnects between physicists and biologists. The siloing of academic research disciplines represents a significant barrier to progress. Disconnects in terminology, motivations and priorities, and structural barriers to collaborative work underscore the need for concerted efforts to bridge these divides. Attendees and speakers offered suggestions for resolving these divergences, establishing a shared language, moving the field forward, and fostering meaningful feedback between disciplines. Overall, participants stressed a need for balance, open communication, collaboration, unity, and clear dialogue on trade-offs between quantum and classical approaches. Keiko Torii, The University of Texas at Austin, said that the best collaborations happen when the project provides mutual advantages that can show off everyone’s talents, each team finds the work interesting, and partners develop a camaraderie to pursue new knowledge. To enable near- and long-term opportunities in this space, participants suggested that exploratory, high-risk funding could improve existing instrumentation to explore quantum enhancement collaboratively. They also emphasized the need for collaboration between quantum physicists and sensing/imaging scientists, which could be advanced through a dedicated quantum biology investigator program. People, even more than technology, will be crucial to the future of quantum biology. Participants explored training, education, and workforce needs to further develop this burgeoning field and cultivate the next generation of scientists. While many programs are still in their nascent stages, participants highlighted examples of approaches and programs being developed at various types of institutions to engage students and professional scientists in quantum biology research. Several participants stressed the need for an inclusive approach, spanning disciplines as well as communities to foster a diverse field fueled by the intellectual contributions of a wide range of people, including historically under-resourced schools and students. To increase awareness and excitement about quantum physics and related areas of biology, attendees suggested capitalizing on the “buzz” around quantum. Several participants emphasized the need to start early, introducing students to quantum concepts and their appealing “weirdness” in K–12 education. Engaging students early—before they become entrenched in traditional disciplinary siloes as typically happens in graduate school—could help to galvanize interest in the area and foster a generation of scientists with the interdisciplinary mindset and skills needed to advance this interdisciplinary field. While these efforts could be advanced at many levels and across multiple sectors, several participants suggested a national quantum biology center could be a valuable hub to coordinate and support quantum biology education and workforce development across academia, industry, and government.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Geochemistry and metagenomics analyses of bacterial community structure in selected waste dumpsites in Lagos Metropolis, Nigeria

Dumpsites are reservoirs of persistent organic pollutants (POPs) and heavy metals (HMs), constituting environmental hazards to humanity. Autochthonous microorganisms in dumpsites exhibit various degrees of responses to contaminants. Unfortunately, there is a dearth of information on the types and concentration of pollutants and the array of microorganisms in these dumpsites which may play important roles in the metabolism of such pollutants or other community processes. Therefore, determining the microbial community structure in such contaminated sites across a municipality is essential for profiling the taxa that would serve as consensus degraders of the pollutants. In this study, soil samples from three dumpsites (Cele, CS; Solous, SS; and Computer Village, CVS) were characterized for geochemical properties using GC-MS, MP-AES, and other analytical protocols, while the dynamics of bacterial communities were evaluated based on their 16S rRNA gene barcodes. A significant difference in the bacterial communities was observed among the dumpsites in relation to the extent of pollution caused by POPs and HMs. CVS, with the highest HM contamination, was rich in Actinobacteria (41.7%) and Acidobacteria (10.2%), in contrast to CS and SS. Proteobacteria (34.1%) and Firmicutes (20%) were the dominant phyla in CS (highest POP contamination), while Bacteroidetes (45.5%) and Proteobacteria (39.9%) were dominant in SS soil.Bacilluswas the dominant genus in the most polluted dumpsite. Canonical correspondence analysis revealed that polycyclic aromatic hydrocarbons (PAHs) and HMs shaped the structure of the bacterial operational taxonomic units (OTUs) in the most polluted dumpsite. Out of a total of 706 OTUs, 628 OTUs exhibited a significant correlation (>50%) with benzo(b)fluoranthene, azobenzene, dibenzofurans, pyrene, dibenzo(a,l)pyrene, Cu, and Zn. In particular, Proteobacteria (Achromobactersp. andSerratiasp.), Bacteroidetes (Zhouiasp.), and Firmicutes (Bacillussp.) were suggested to be pivotal to the ecophysiology of dumpsite soils contaminated with POPs and HMs. The results generally underscored the importance of metagenomic and physicochemical analyses of polluted systems in enabling correlations for useful prediction of drivers of such ecosystems. This will further improve our understanding of the metabolic potential and adaptation of organisms in such systems.

Environmental Sciences & Ecology↗
DOE OSTI2022

Understanding the structure and composition of recalcitrant oligosaccharides in hydrolysate using high-throughput biotin-based glycome profiling and mass spectrometry

Novel Immunological and Mass Spectrometry Methods for Comprehensive Analysis of Recalcitrant Oligosaccharides in AFEX Pretreated Corn Stover. Lignocellulosic biomass is a sustainable alternative to fossil fuel and is extensively used for developing bio-based technologies to produce products such as food, feed, fuel, and chemicals. The key to these technologies is to develop cost competitive processes to convert complex carbohydrates present in plant cell wall to simple sugars such as glucose, xylose, and arabinose. Since lignocellulosic biomass is highly recalcitrant, it must undergo a combination of thermochemical treatment such as Ammonia Fiber Expansion (AFEX), dilute acid (DA), Ionic Liquid (IL) and biological treatment such as enzyme hydrolysis and microbial fermentation to produce desired products. However, when using commercial fungal enzymes during hydrolysis, only 75–85% of the soluble sugars generated are monomeric sugars, while the remaining 15–25% are soluble recalcitrant oligosaccharides that cannot be easily utilized by microorganisms. Previously, we successfully separated and purified the soluble recalcitrant oligosaccharides using a combination of charcoal and celite-based separation followed by size exclusion chromatography and studies their inhibitory properties on enzymes. We discovered that the oligosaccharides with higher degree of polymerization (DP) containing methylated uronic acid substitutions were more recalcitrant towards commercial enzyme mixtures than lower DP and neutral oligosaccharides. Here, we report the use of several complementary techniques that include glycome profiling using plant biomass glycan specific monoclonal antibodies (mAbs) to characterize sugar linkages in plant cell walls and enzymatic hydrolysate, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) using structurally-informative diagnostic peaks offered by negative ion post-secondary decay spectra, gas chromatography followed by mass spectrometry (GC–MS) to characterize oligosaccharide sugar linkages with and without derivatization. Since oligosaccharides (DP 4–20) are small, it is challenging to mobilize these molecules for mAbs binding and characterization. To overcome this problem, we have applied a new biotin-coupling based oligosaccharide immobilization method that successfully tagged most of the low DP soluble oligosaccharides on to a micro-plate surface followed by specific linkage analysis using mAbs in a high-throughput system. This new approach will help develop more advanced versions of future high throughput glycome profiling methods that can be used to separate and characterize oligosaccharides present in biomarkers for diagnostic applications.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRSDate not supplied

A Science-Focused Artificial Intelligence (AI) Responding in Real-Time to New Information: Capability Demonstration for Ocean World Missions

Introduction: Artificial intelligence (AI) has long been considered a potential mechanism to explore increasingly challenging environments, including those with extreme temperatures and pressures, limited communication capabilities, or those with demanding terrain. We posit that missions in extreme environments could deploy an onboard AI focused on science observations and goals in order to augment a traditional concept(s) of operations (ConOps). An onboard AI capability could perform functions such as data analysis in order to make high-level decisions, including prioritized data transmission for analysis by ground-based teams or autonomously-guided follow-on analyses that maximize science return. Such a capability would empower missions to respond to scientific data of interest in real-time; a mission could make observations and perform a preliminary analysis to alert ground-based scientists to an observation of interest, enabling an informed, rapid response from Earth-based teams. Enceladus Case Study for Onboard AI: We are developing an onboard AI capability for real-time telemetry response that formulates and carries-out informed decisions in service to established mission goals, enabling increased science return of a mission. We focus our AI development for use on a constellation of SmallSats orbiting Enceladus. Our Enceladus case study tests autonomous decision-making capabilities in scenarios with complex orbital dynamics, plume ejecta, extreme cold environments, power restrictions, and a requirement to maximize science return for a potential positive detection of life, while critically evaluating the potential for false positives. Telemetry includes simulated scientific data, spacecraft onboard operational data (e.g., position, velocity, and rotation), and engineering hardware performance data. Enceladus SmallSat Constellation. Our constellation includes eight SmallSat spacecraft in an 8:35 resonant orbit-based formation, leveraging Saturn’s gravitational forces to maintain stable orbits with global coverage around Enceladus. To our knowledge, we simulate the first stable configuration of multiple spacecraft in closed orbits around Enceladus, using a full ephemeris force model (Russell and Lara, 2009). Each spacecraft’s orbit will precess, causing an eastward ground track shift (from an orbiter’s perspective) of each spacecraft for each orbit. However, all spacecraft return to their original positions relative to Enceladus after eight Enceladus revolutions around Saturn. We model communication pathways between SmallSats to understand how information would need to be transmitted across the constellation to enable AI-driven decision-making and resource allocation across the fleet. Capability Demonstration. Our simulated capability demonstration inputs position, velocity, and rotation telemetry from our Enceladus-focused constellation simulations, and mass spectrometry data collected from abiotic and biotic laboratory-analog ocean world experiments (Theiling et al., 2018; Theiling, 2021; Da Poian et al., 2023). Data from these experiments are used to simulate MS measurements and different scenarios of science observations for onboard analysis performed on each of the eight spacecraft. For these demonstrations, we integrate 24 machine learning (ML) algorithms into an onboard intelligence as a ‘knowledge base’, including algorithms evaluating data quality and those predicting (with % confidence) gas composition, ocean aqueous chemistry, and whether the sample was influenced by microbial life. The onboard AI capability is designed to use the knowledge base to come to a consensus-based decision in the interpretation of the observed data in order to request additional action outside of a pre-defined ConOps. Requested actions could include e.g., prioritized downlink to Earth (for analysis by ground-based teams) or follow-on analyses performed across the constellation. The spacecraft’s intelligent onboard planner must then determine whether sufficient resources (e.g., time, power, etc.) are available and weigh the request with mission priorities. In our simulation, the constellation is able to identify potential biosignatures using onboard ML algorithms, evaluate the confidence of that prediction, and perform follow-on analyses across the fleet to confirm the detection, in order to best prepare a transmission of these data to Earth-based teams.

astrobiology↗