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At least 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Deconstructing the root system of grasses through an exploration of development, anatomy and function

Abstract Well‐adapted root systems allow plants to grow under resource‐limiting environmental conditions and are important determinants of yield in agricultural systems. Important staple crops such as rice and maize belong to the family of grasses, which develop a complex root system that consists of an embryonic root system that emerges from the seed, and a postembryonic nodal root system that emerges from basal regions of the shoot after germination. While early seedling establishment is dependent on the embryonic root system, the nodal root system, and its associated branches, gains in importance as the plant matures and will ultimately constitute the bulk of below‐ground growth. In this review, we aim to give an overview of the different root types that develop in cereal grass root systems, explore the different physiological roles they play by defining their anatomical features, and outline the genetic networks that control their development. Through this deconstructed view of grass root system function, we provide a parts‐list of elements that function together in an integrated root system to promote survival and crop productivity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

VA EDH Data Curation Documentation FY23-Q4

The health and well-being of the Nation’s men and women who have served in uniform is the highest priority for the U.S. Department of Veterans Affairs (VA). VA is committed to providing timely access to high-quality, recovery-oriented, evidence-based mental health care that anticipates and responds to Veterans’ needs and supports the reintegration of returning service members into their communities. Since its creation, the VA has been working to eliminate suicide among all veterans by developing and implementing innovative suicide prevention approaches and resources. Health outcomes, such as suicide, are typically modeled as a function of genetics and environment, where environment refers to factors beyond medical, e.g., air quality, access to transportation and food, homelessness status, etc. Mental health outcomes for each individual are considered to be associated with multiple stressors that fall under a variety of categories, including socioeconomic, economic, and physical environments. Understanding the relationships between these stressors, covariates, and health outcomes requires curated, standardized data that can be input into the VA’s Recovery Engagement and Coordination for Health, Veterans Enhanced Treatment (REACH VET) or other health outcomes model. Environmental Determinants of Health (EDH), as defined by the World Health Organization (WHO), refer to clean air, stable climate, adequate water, sanitation and hygiene, safe use of chemicals, protection from radiation, healthy and safe workplaces, sound agricultural practices, health-supportive cities and built environments, and a preserved nature, which are all prerequisites for good health.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Identifying biomass yield potential of tetra, hexa, and octoploid prairie cordgrass populations grown on marginal lands

As the demand for renewable energy sources with reduced carbon emissions to the atmosphere increases, bioenergy crops remain an attractive alternative to fossil fuels. Another appeal of bioenergy crops is the potential utilization of marginal lands not suitable for food crops. Prairie cordgrass is a perennial warm season polyploid grass species being considered as a bioenergy crop that also exhibits a high tolerance for salinity and flooding. The ploidy level of prairie cordgrass has previously been suggested to correlate with agronomic traits. However, little is known about the agricultural performance of prairie cordgrass on marginal lands and if a correlation of ploidy level to stress tolerance exists. In this experiment, the productivity of tetraploids, hexaploids, and octoploids was investigated when grown on three different marginal sites including waterlogged, saline, and low-nutrient gravelly soils. Here we found that prairie cordgrass populations annually produced dry biomass on a wet marginal site comparable to normal cropland. However, the productivity was remarkedly decreased at both a salt-affected site and a limestone mine reclamation site. We were unable to conclude that different ploidy levels affected the biomass yield of prairie cordgrass grown under abiotic stress. However, there was a differential response of populations to various types of marginal sites. Finally, these results indicate potential genetic resources for developing breeding targets and identifying mechanisms of abiotic stress tolerance. Moreover, we highlight the need to generate diverse ploidy levels of prairie cordgrass in the same genetic backgrounds for future testing.

09 BIOMASS FUELS↗
DOE OSTI2024

Intraspecific variability in plant and soil chemical properties in a common garden plantation of the energy crop Populus

Optimizing crops for synergistic soil carbon (C) sequestration can enhance CO 2 removal in food and bioenergy production systems. Yet, in bioenergy systems, we lack an understanding of how intraspecies variation in plant traits correlates with variation in soil biogeochemistry. This knowledge gap is exacerbated by both the heterogeneity and difficulty of measuring belowground traits. Here, we provide initial observations of C and nutrients in soil and root and stem tissues from a common garden field site of diverse, natural variant, Populus trichocarpa genotypes—established for aboveground biomass-to-biofuels research. Our goal was to explore the value of such field sites for evaluating genotype-specific effects on soil C, which ultimately informs the potential for optimizing bioenergy systems for both aboveground productivity and belowground C storage. To do this, we investigated variation in chemical traits at the scale of individual trees and genotypes and we explored correlations among stem, root, and soil samples. We observed substantial variation in soil chemical properties at the scale of individual trees and specific genotypes. While correlations among elements were observed both within and among sample types (soil, stem, root), above-belowground correlations were generally poor. We did not observe genotype-specific patterns in soil C in the top 10 cm, but we did observe genotype associations with soil acid-base chemistry (soil pH and base cations) and bulk density. Finally, a specific phenotype of interest (high vs low lignin) was unrelated to soil biogeochemistry. Our pilot study supports the usefulness of decade-old, genetically-variable, Populus bioenergy field test plots for understanding plant genotype effects on soil properties. Finally, this study contributes to the advancement of sampling methods and baseline data for Populus systems in the Pacific Northwest, USA. Further species- and region-specific efforts will enhance C predictability across scales in bioenergy systems and, ultimately, accelerate the identification of genotypes that optimize yield and carbon storage.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2002

Analysis of Salinity Intrusion in the San Francisco Bay-Delta using a GA- Optimized Neural Net, and Application of the Model to Prediction in the Elkhorn Slough Habitat

The San Francisco Bay Delta is a large hydrodynamic complex that incorporates the Sacramento and San Joaquin Estuaries, the Burman Marsh, and the San Francisco Bay proper. Competition exists for the use of this extensive water system both from the fisheries industry, the agricultural industry, and from the marine and estuarine animal species within the Delta. As tidal fluctuations occur, more saline water pushes upstream allowing fish to migrate beyond the Burman Marsh for breeding and habitat occupation. However, the agriculture industry does not want extensive salinity intrusion to impact water quality for human and plant consumption. The balance is regulated by pumping stations located alone the estuaries and reservoirs whereby flushing of fresh water keeps the saline intrusion at bay. The pumping schedule is driven by data collected at various locations within the Bay Delta and by numerical models that predict the salinity intrusion as part of a larger model of the system. The Interagency Ecological Program (IEP) for the San Francisco Bay/Sacramento-San Joaquin Estuary collects, monitors, and archives the data, and the Department of Water Resources provides a numerical model simulation (DSM2) from which predictions are made that drive the pumping schedule. A problem with this procedure is that the numerical simulation takes roughly 16 hours to complete a C:~ prediction. We have created a neural net, optimized with a genetic algorithm, that takes as input the archived data from multiple stations and predicts stage, salinity, and flow at the Carquinez Straits (at the downstream end of the Burman Marsh). This model seems to be robust in its predictions and operates much faster than the current numerical DSM2 model. Because the system is strongly tidal driven, we used both Principal Component Analysis and Fast Fourier Transforms to discover dominant features within the IEP data. We then filtered out the dominant tidal forcing to discover non-primary tidal effects, and used this to enhance the neural network by mapping input-output relationships in a more efficient manner. Furthermore, the neural network implicitly incorporates both the hydrodynamic and water quality models into a single predictive system. Although our model has not yet been enhanced to demonstrate improve pumping schedules, it has the possibility to support better decision-making procedures that may then be implemented by State agencies if desired. Our intention is now to use this model in the smaller Elkhorn Slough complex near Monterey Bay where no such hydrodynamic model currently exists. At the Elkhorn Slough, we are fusing the neural net model of tidally-driven flow with in situ flow data and airborne and satellite remote sensation data. These further constrain the behavior of the model in predicting the longer-term health and future of this vital estuary.

Thompson, David E.↗
DOE OSTI2022

Leaf endophytic microbiomes of different almond cultivars grafted to the same rootstock

Abstract Aims We compared the bacterial endophytic communities of three genetically different almond cultivars that were all grafted on the same type of rootstock, growing side by side within a commercial orchard. Methods and Results We examined the diversity of leaf bacterial endophytes using cultivation-independent techniques and assessed the relative abundance of bacterial families. Two of these three cultivars were dominated by Pseudomonadaceae, while the bacterial composition of the third cultivar consisted mainly of Streptococcaceae. Conclusions The experimental set up allowed us to analyse the impact of the shoot cultivar on endophytes, minimizing the influence of rootstock, biogeography, and cultivation status. Our data suggest that the shoot cultivar can shape the leaf endophytic community composition of almond trees. Significance and Impact of the Study Our results suggest that the shoot cultivar controls the composition of the foliar bacterial endophytic community of almonds. Overall, our results could provide a first step to develop strategies for a more sustainable almond agriculture.

Saldierna Guzmán, J. Paola (ORCID:0000000317288154↗
NASA NTRS2009

The Crop Evaluation Research for Environmental Strategies (CERES) Remote Sensing 2008 Project Activities

In recent years, the use of Plant Incorporated Protectant (PIP) corn by American producers has been increasing dramatically. PIP corn contains genetically inserted traits that produce toxins in the plant that provide narrowly targeted protection against specific insect pests. The plant producing t oxms can offer significant reductions in the application of broad -spectrum pesticides that have ecological and human health consequences. PIP corn as a percentage of total corn acreage planted in the US is expected to continue to increase as these protective traits are "stacked" with other desirable traits by seed companies, and producers are seeing considerable increases in corn yield as a result. The introduction of corn as a bio-fuel source for ethanol has increased production by over 6 million hectares in 2007. The United States Environmental Protection Agency (USEPA), which is responsible for the registration of PIP crops under the Federal Insecticide, Fungicide and Rodenticide Act, views the use of PIP corn as positive. Broad spectrum pesticide use has declined since the PIP traits have been introduced. As the agricultural landscape sees a higher percentage of corn acres using the PIP technology, the risk of the targeted insect pest populations developing resistance to the toxins, thereby rendering the in will increase as well. This result would negate the effectiveness of the PIP corn traits and could reduce production of a US field corn crop valued at $33 billion dollars in 2006 and place US food and now energy security at risk. Concerns over insect pest resistance development to PIP traits have led the USEPA to team with NASA and the Institute for Technology Development (ITD) to develop geo-spatial technologies designed to proactively monitor the corn production landscape for insect pest infestation and possible resistance development. USEPA resistance management simulation models are combined with NASA remote sensi ng products to monitor the corn landscape for resistance development. The two agencies have entered into an agreement which could potentially lead to the development of next generation NASA sensors that will more specifically address the requirements of the USEPA's resistance development strategy and offer opportunities to study the ever changing ecosystem complexities. The USEPA/NASA/ITD team has developed a broad research project entitled CERES (Crop Evaluation Research for Environmental Strategies). CERES is a research effort leading to decision support system tools that are designed to integrate multi-resolution NASA remote sensing data products and USEPA geo -spatial models to monitor the potential for insect pest resistance development from the regional to the landscape and then to the field level.

Casas, Joseph C.↗
DOE OSTI2025

Status on Genetic Resistance to Rice Blast Disease in the Post-Genomic Era

Rice blast, caused by Magnaporthe oryzae, is a major threat to global rice production, necessitating the development of resistant cultivars through genetic improvement. Breakthroughs in rice genomics, including the complete genome sequencing of japonica and indica subspecies and the availability of various sequence-based molecular markers, have greatly advanced the genetic analysis of blast resistance. To date, approximately 122 blast-resistance genes have been identified, with 39 of these genes cloned and molecularly characterized. The application of these findings in marker-assisted selection (MAS) has significantly improved rice breeding, allowing for the efficient integration of multiple resistance genes into elite cultivars, enhancing both the durability and spectrum of resistance. Pangenomic studies, along with AI-driven tools like AlphaFold2, RoseTTAFold, and AlphaFold3, have further accelerated the identification and functional characterization of resistance genes, expediting the breeding process. Future rice blast disease management will depend on leveraging these advanced genomic and computational technologies. Emphasis should be placed on enhancing computational tools for the large-scale screening of resistance genes and utilizing gene editing technologies such as CRISPR-Cas9 for functional validation and targeted resistance enhancement and deployment. These approaches will be crucial for advancing rice blast resistance, ensuring food security, and promoting agricultural sustainability.

Pedrozo, Rodrigo↗
DOE OSTI2020

The genetic architecture of biomechanical traits in sorghum

Sorghum bicolor (L.) Moench is the fifth most commonly grown cereal crop worldwide with unrivaled drought tolerance compared with other cereal crops. Drought and heat tolerance and high biomass yield potential make sorghum a promising bioenergy crop. However, stem lodging is a significant problem that results in substantial yield losses. Stem biomechanical traits influence the mechanical stability of crops and breeding for desirable biomechanical traits may result in improved lodging resistance. In this study, we report the identification of quantitative trait loci (QTL) for stem mechanical and morphological traits in three recombinant inbred line (RIL; populations from Tx623/Rio, Tx623/Della, and Tx631/Della) crosses between elite grain and sweet sorghum parents. The genetic architecture of stem biomechanical traits in the three RIL populations is multigenic and pleiotropic. Additionally, eight QTL affecting mechanical and morphological traits were detected; two main effects of these QTL were consistently found in all populations and colocated with previously identified dwarfing genes Dw1 and Dw3. These results indicate that dwarfing genes affect the mechanical properties of sorghum stems and their lodging resistance, while also having demonstrable effects on stem morphology. The identification of these QTL provides new opportunities for improving stem lodging resistance via genomics-assisted breeding.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Engineering Anti-Microbial Peptide Production in Fungi and Bioprocess Development (CRADA 502)

Crop Protection, specifically controlling agricultural diseases and pests, is essential for crop production at every agricultural scale. Biologics hold enormous potential in this equation to decrease use of more toxic pesticides. Currently, the widespread use of biologics in crop protection is severely hampered by the lack of available tools for their mass production. To ensure biologics are regulated under EPA Biopesticide regulations, the following must be true: The biopesticide is a naturally occurring substance or structurally similar and functionally identical to a naturally occurring substance with a history of exposure to humans and the environment demonstrating minimal toxicity. Since this pertains to the marketed product it is also essential that fermentation hosts have a history of exposure and safe use by humans This research focuses on developing a novel platform for the production and delivery of the cghSAMP peptide using the filamentous fungus Aspergillus niger. A. niger is a well-established industrial microorganism, widely recognized for its strong protein secretion capabilities, high-yield production of enzymes, and classification as a generally recognized as safe (GRAS) organism. By genetically modifying A. niger to express the cghSAMP peptide transgene, we aim to leverage the fungus's robust fermentation system to produce a high volume of the antimicrobial agent. This engineered system represents a potential breakthrough in sustainable disease management, offering an environmentally friendly method for localized application or large-scale production of a biopesticide designed to mitigate the effects of citrus greening disease. The main objectives of this project were: 1. Developing a high-yield and cost-efficient bioprocess to produce an AMP in a current ABF host or readily onboarded hosts. 2. Scale up the process in stirred tank reactors and produce at least 100 grams of AMP at 1- 5g/L

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Understanding and Harnessing the Robustness of Undomesticated Yarrowia lipolytica Strains for Biosynthesis of Designer Bioesters (Final Report)

This project seeks to elucidate and harness the exceptional robustness of novel and undomesticated Y. lipolytica isolates, which were identified from a genetic diversity screening for compatibility with bioenergy development. Bioenergy-relevant isolates were further developed as microbial platforms for efficient conversion of undetoxified biomass hydrolysates into designer bio-esters continuously recovered by solvent extraction. The project has three major goals. Goal 1. Elucidate and enhance the endogenous metabolism of Y. lipolytica for superior growth, sugar utilization, and lipid accumulation in undetoxified biomass hydrolysates under hypoxic conditions. Goal 2. Understand and enhance the underlying mechanism of exceptional tolerance of Y. lipolytica to organic solvents. Goal 3. Elucidate and rewire endogenous metabolism of the most robust Y. lipolytica strains for effective conversion of accumulating lipids to designer bio-esters. Significant progress has been made toward completing all research goals. We elucidated and optimized the robustness of Y. lipolytica by utilizing mixed C5 and C6 sugars in switchgrass hydrolysates (SGH) for lipid production (Aim 1). We conducted extensive omics analysis to investigate how genetic diversity among Yarrowia strains, derived from natural isolates or developed through adaptive laboratory evolution, influences lipid production when utilizing SGH. In Aim 2, novel mechanisms and underlying genetics were discovered that enabled Yarrowia strains to thrive in cultures containing high ionic liquid (IL) concentrations. Amongst other novel findings, it was found that sterols strengthened cell membranes to confer IL toxicity resistance, specifically via increased ergosterol content upon exposure to IL. In Aim 3, mechanistic studies elucidated how Y. lipolytica utilized intracellular lipids and alkanes/alkenes, leading to our discovery of novel enzymes and pathways for making short-chain esters. Most notably, thermostable chloramphenicol transferases were repurposed to function as alcohol acetyltransferases in Y. lipolytica, as well as the Gram-negative and Gram-positive bacteria Escherichia coli and thermophile Clostridium thermocellum, respectively.

09 BIOMASS FUELS↗
DOE OSTI2020

Isolation, Characterization, and Pathogenicity of Two Pseudomonas syringae Pathovars from Populus trichocarpa Seeds

Pseudomonas syringae is a ubiquitous plant pathogen, infecting both woody and herbaceous plants and resulting in devastating agricultural crop losses. Characterized by a remarkable specificity for plant hosts, P. syringae pathovars utilize a number of virulence factors including the type III secretion system and effector proteins to elicit disease in a particular host species. Here, two Pseudomonas syringae strains were isolated from diseased Populustrichocarpa seeds. The pathovars were capable of inhibiting poplar seed germination and were selective for the Populus genus. Sequencing of the newly described organisms revealed similarity to phylogroup II pathogens and genomic regions associated with woody host-associated plant pathogens, as well as genes for specific virulence factors. The host response to infection, as revealed through metabolomics, is the induction of the stress response through the accumulation of higher-order salicylates. Combined with necrosis on leaf surfaces, the plant appears to quickly respond by isolating infected tissues and mounting an anti-inflammatory defense. This study improves our understanding of the initial host response to epiphytic pathogens in Populus and provides a new model system for studying the effects of a bacterial pathogen on a woody host plant in which both organisms are fully genetically sequenced.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Are scenario projections overly optimistic about future yield progress?

Historical increases in agricultural production were achieved predominantly by large increases in agricultural productivity. Intensification of crop and livestock production also plays a key role in future projections of agricultural land use. Here, we assess and discuss projections of crop yields by global agricultural land-use and integrated assessment models. To evaluate these crop yield projections, we compare them to empirical data on attainable yields by employing a linear and plateauing continuation of observed attainable yield trends. While keeping in mind the uncertainties of attainable yields projections and future climate change impacts, we find that, on average for all cereals on the global level, global projected yields by 2050 remain below the attainable yields. Additionally, this is also true for future pathways with high technological progress and mitigation efforts, indicating that projected yield increases are not overly optimistic, even under systemic transformations. Furthermore, on a regional scale, we find that for developing regions, specifically for sub-Saharan Africa, projected yields stay well below attainable yields, indicating that the large yield gaps which could be closed through improved crop management, may also persist in the future. In OECD countries, in contrast, current yields are already close to attainable yields, and the projections approach or, for some models, even exceed attainable yields by 2050. This observation parallels research suggesting that future progress in attainable yields in developed regions will mainly have to be achieved through new crop varieties or genetic improvements. The models included in this study vary widely in their implementation of yield progress, which are often split into endogenous (crop management) improvements and exogenous (technological) trends. More detail and transparency are needed in these important elements of global yields and land use projections, and this paper discusses possibilities of better aligning agronomic understanding of yield gaps and yield potentials with modelling approaches.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Turbo‐charging crop improvement: harnessing multiplex editing for polygenic trait engineering and beyond

Multiplex CRISPR editing has emerged as a transformative platform for plant genome engineering, enabling the simultaneous targeting of multiple genes, regulatory elements, or chromosomal regions. This approach is effective for dissecting gene family functions, addressing genetic redundancy, engineering polygenic traits, and accelerating trait stacking and de novo domestication. Its applications now extend beyond standard gene knockouts to include epigenetic and transcriptional regulation, chromosomal engineering, and transgene‐free editing. These capabilities are advancing crop improvement not only in annual species but also in more complex systems such as polyploids, undomesticated wild relatives, and species with long generation times. At the same time, multiplex editing presents technical challenges, including complex construct design and the need for robust, scalable mutation detection. We discuss current toolkits and recent innovations in vector architecture, such as promoter and scaffold engineering, that streamline workflows and enhance editing efficiency. High‐throughput sequencing technologies, including long‐read platforms, are improving the resolution of complex editing outcomes such as structural rearrangements—often missed by standard genotyping—when targeting repetitive or tandemly spaced loci. To fully realize the potential of multiplex genome engineering, there is growing demand for user‐friendly, synthetic biology‐compatible, and scalable computational workflows for gRNA design, construct assembly, and mutation analysis. Experimentally validated inducible or tissue‐specific promoters are also highly desirable for achieving spatiotemporal control. As these tools continue to evolve, multiplex CRISPR editing is poised to become a foundational technology of next‐generation crop improvement to address challenges in agriculture, sustainability, and climate resilience.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Metabolic Model of the Nitrogen-Fixing Obligate Aerobe Azotobacter vinelandii Predicts Its Adaptation to Oxygen Concentration and Metal Availability

There is considerable interest in promoting biological nitrogen fixation (BNF) as a mechanism to reduce the inputs of nitrogenous fertilizers in agriculture, but considerable fundamental knowledge gaps still need to be addressed. BNF is catalyzed by nitrogenase, which requires a large input of energy in the form of ATP and low potential electrons. Diazotrophs that respire aerobically have an advantage in meeting the ATP demands of BNF but face challenges in protecting nitrogenase from inactivation by oxygen. Here, we constructed a genome-scale metabolic model of the nitrogen-fixing bacterium Azotobacter vinelandii, which uses a complex respiratory protection mechanism to consume oxygen at a high rate to keep intracellular conditions microaerobic. Our model accurately predicts growth rate under high oxygen and substrate concentrations, consistent with a large electron flux directed to the respiratory protection mechanism. While a partially decoupled electron transport chain compensates for some of the energy imbalance under high-oxygen conditions, it does not account for all substrate intake, leading to increased maintenance rates. Interestingly, the respiratory protection mechanism is required for accurate predictions even when ammonia is supplemented during growth, suggesting that the respiratory protection mechanism might be a core principle of metabolism and not just used for nitrogenase protection. We have also shown that rearrangement of flux through the electron transport system allows A. vinelandii to adapt to different oxygen concentrations, metal availability, and genetic disruption, which cause an ammonia excretion phenotype. Accurately determining the energy balance in an aerobic nitrogen-fixing metabolic model is required for future engineering approaches.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

The future of fungi: threats and opportunities

The fungal kingdom represents an extraordinary diversity of organisms with profound impacts across animal, plant, and ecosystem health. Fungi simultaneously support life, by forming beneficial symbioses with plants and producing life-saving medicines, and bring death, by causing devastating diseases in humans, plants, and animals. With climate change, increased antimicrobial resistance, global trade, environmental degradation, and novel viruses altering the impact of fungi on health and disease, developing new approaches is now more crucial than ever to combat the threats posed by fungi and to harness their extraordinary potential for applications in human health, food supply, and environmental remediation. To address this aim, the Canadian Institute for Advanced Research (CIFAR) and the Burroughs Wellcome Fund convened a workshop to unite leading experts on fungal biology from academia and industry to strategize innovative solutions to global challenges and fungal threats. This report provides recommendations to accelerate fungal research and highlights the major research advances and ideas discussed at the meeting pertaining to 5 major topics: (1) Connections between fungi and climate change and ways to avert climate catastrophe; (2) Fungal threats to humans and ways to mitigate them; (3) Fungal threats to agriculture and food security and approaches to ensure a robust global food supply; (4) Fungal threats to animals and approaches to avoid species collapse and extinction; and (5) Opportunities presented by the fungal kingdom, including novel medicines and enzymes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Continuous culture of anaerobic fungi enables growth and metabolic flux tuning without use of genetic tools

Anaerobic gut fungi (AGF) have potential to valorize lignocellulosic biomass owing to their diverse repertoire of carbohydrate-active enzymes (CAZymes). However, AGF metabolism is poorly understood, and no stable genetic tools are available to manipulate growth and metabolic flux to enhance production of specific targets, e.g., cells, CAZymes, or metabolites. Herein, a cost-effective, Arduino-based, continuous-flow anaerobic bioreactor with online optical density control is presented to probe metabolism and predictably tune fluxes in Caecomyces churrovis. Varying the C. churrovis turbidostat setpoint titer reliably controlled growth rate (from 0.04 to 0.20 h −1 ), metabolic flux, and production rates of acetate, formate, lactate, and ethanol. Bioreactor setpoints to maximize production of each product were identified, and all continuous production rates significantly exceed batch rates. Formate spike-ins increased lactate flux and decreased acetate, ethanol, and formate fluxes. The bioreactor and turbidostat culture schemes demonstrated here offer tools to tailor AGF fermentations to application-specific hydrolysate product profiles.

Agriculture↗
DOE OSTI2025

Synthetic communities as a model for determining interactions between a biofertilizer chassis organism and native microbial consortia

Biofertilizers are critical for sustainable agriculture because they can replace ecologically disruptive chemical fertilizers while improving the trajectory of soil and plant health. However, for improving deployment, the persistence of biofertilizers within native soil consortia must be elucidated and enhanced. In this study we characterized a high-throughput, modular, and automation-friendly in vitro approach to screen for biofertilizer persistence within soil-derived consortia after co-cultivation with stable synthetic soil microbial communities (SynComs) obtained through a top-down cultivation process. Here, we profiled ~1200 SynComs isolated from various soil sources and cultivated in divergent media types, and we detected significant phylogenetic diversity (e.g. Shannon index >4) and richness (observed richness >400) across these communities. We observed high reproducibility in SynCom community structure from common soil and media types, which provided a testbed for assessing biofertilizer persistence within representative native consortia. Furthermore, we demonstrated that the screening method described herein can be coupled with microbial engineering to efficiently identify soil-derived SynComs in which an engineered biofertilizer organism (i.e. Bacillus subtilis) persists. Accordingly, we discovered that B. subtilis persisted in ~10% of SynComs that generally followed the diversity–invasion principle. Additionally, our approach enabled analysis of the ecological impact of B. subtilis inoculation on SynCom structure and profile alterations in community diversity and richness associated with the presence of a genetically modified model bacterium. Ultimately, this work has established a modular pipeline that could be integrated into a variety of microbiology/microbiome-relevant workflows or related applications that would benefit from assessment of the persistence of a specific organism of interest and its interaction with native consortia.

biofertilizers↗