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At least 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Ectomycorrhizal fungi alter soil food webs and the functional potential of bacterial communities

Most of Earth’s trees rely on critical soil nutrients that ectomycorrhizal fungi (EcMF) liberate and provide, and all of Earth’s land plants associate with bacteria that help them survive in nature. Yet, our understanding of how the presence of EcMF modifies soil bacterial communities, soil food webs, and root chemistry requires direct experimental evidence to comprehend the effects that EcMF may generate in the belowground plant microbiome. To this end, we grew Pinus muricata plants in soils that were either inoculated with EcMF and native forest bacterial communities or only native bacterial communities. We then profiled the soil bacterial communities, applied metabolomics and lipidomics, and linked omics data sets to understand how the presence of EcMF modifies belowground biogeochemistry, bacterial community structure, and their functional potential. We found that the presence of EcMF (i) enriches soil bacteria linked to enhanced plant growth in nature, (ii) alters the quantity and composition of lipid and non-lipid soil metabolites, and (iii) modifies plant root chemistry toward pathogen suppression, enzymatic conservation, and reactive oxygen species scavenging. Using this multi-omic approach, we therefore show that this widespread fungal symbiosis may be a common factor for structuring soil food webs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Biostimulation of Salicornia europaea L. crops with plant growth-promoting bacteria in laboratory and field conditions: effects on growth and metabolite profile

Abstract Aim The objective of the work was to assess the effect of biostimulation with selected plant growth-promoting bacteria on growth and metabolite profile of Salicornia europaea. Methods and results Salicornia europaea seeds were inoculated with different combinations of plant growth-promoting bacteria Brevibacterium casei EB3, Pseudomonas oryzihabitans RL18, and Bacillus aryabhattai SP20. Plants germinated from inoculated seeds were grown either in laboratory conditions or in a saline crop field. Fresh and dry weight were determined at the end of the experiment, for biomass quantification. The microbiological quality of fresh shoots for human consumption as salad greens was assessed, and the persistence of the inoculated strains in the plant rhizosphere was confirmed by next-generation sequencing (Illumina) of the 16S rDNA gene. The primary metabolite profile of biostimulated plants was characterized by GC–TOF-MS. In laboratory conditions, inoculation with the two strains Br. casei EB3 and Ps. oryzihabitans RL18 caused the most significant increase in biomass production (fresh and dry weight), and caused a shift in the central metabolic pathways of inoculated plants toward amino acid biosynthesis. In the field experiment, no significant biostimulation effect was detected with any of the tested inoculants. Seed inoculation had no significant effect on the microbiological quality of the edible parts. The persistence of inoculants was confirmed in both experiments. Conclusions Manipulation of the plant microbiome can trigger primary metabolic reconfiguration and modulate the plant metabolism while promoting plant growth.

Ferreira, Maria J.↗
DOE OSTI2021

Lettuce ( Lactuca sativa ) productivity influenced by microbial inocula under nitrogen-limited conditions in aquaponics

The demand for food will outpace productivity of conventional agriculture due to projected growth of the human population, concomitant with shrinkage of arable land, increasing scarcity of freshwater, and a rapidly changing climate. While aquaponics has potential to sustainably supplement food production with minimal environmental impact, there is a need to better characterize the complex interplay between the various components (fish, plant, microbiome) of these systems to optimize scale up and productivity. Here, we investigated how the commonly-implemented practice of continued microbial community transfer from pre-existing systems might promote or impede productivity of aquaponics. Specifically, we monitored plant growth phenotypes, water chemistry, and microbiome composition of rhizospheres, biofilters, and fish feces over 61-days of lettuce (Lactuca sativa var. crispa) growth in nitrogen-limited aquaponic systems inoculated with bacteria that were either commercially sourced or originating from a pre-existing aquaponic system. Lettuce above- and below-ground growth were significantly reduced across replicates treated with a pre-existing aquaponic system inoculum when compared to replicates treated with a commercial inoculum. Reduced productivity was associated with enrichment in specific bacterial genera in plant roots, including Pseudomonas, following inoculum transfer from pre-existing systems. Increased productivity was associated with enrichment of nitrogen-fixing Rahnella in roots of plants treated with the commercial inoculum. Thus, we show that inoculation from a pre-existing system, rather than from a commercial inoculum, is associated with lower yields. Further work will be necessary to test the putative mechanisms involved.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Root-associated bacterial communities and root metabolite composition are linked to nitrogen use efficiency in sorghum

ABSTRACT The development of cereal crops with high nitrogen use efficiency (NUE) is a priority for worldwide agriculture. In addition to conventional plant breeding and genetic engineering, the use of the plant microbiome offers another approach to improving crop NUE. To gain insight into the bacterial communities associated with sorghum lines that differ in NUE, a field experiment was designed comparing 24 diverse Sorghum bicolor lines under sufficient and deficient nitrogen (N). Amplicon sequencing and untargeted gas chromatography–mass spectrometry were used to characterize the bacterial communities and the root metabolome associated with sorghum genotypes varying in sensitivity to low N. We demonstrated that N stress and sorghum type (energy, sweet, and grain sorghum) significantly impacted the root-associated bacterial communities and root metabolite composition of sorghum. We found a positive correlation between sorghum NUE and bacterial richness and diversity in the rhizosphere. The greater alpha diversity in high NUE lines was associated with the decreased abundance of a dominant bacterial taxon, Pseudomonas . Multiple strong correlations were detected between root metabolites and rhizosphere bacterial communities in response to low N stress. This indicates that the shift in the sorghum microbiome due to low N is associated with the root metabolites of the host plant. Taken together, our findings suggest that host genetic regulation of root metabolites plays a role in defining the root-associated microbiome of sorghum genotypes differing in NUE and tolerance to low N stress. IMPORTANCE The development of crops that are more nitrogen use-efficient (NUE) is critical for the future of the enhanced sustainability of agriculture worldwide. This objective has been pursued mainly through plant breeding and plant molecular engineering, but these approaches have had only limited success. Therefore, a different strategy that leverages soil microbes needs to be fully explored because it is known that soil microbes improve plant growth through multiple mechanisms. To design approaches that use the soil microbiome to increase NUE, it will first be essential to understand the relationship among soil microbes, root metabolites, and crop productivity. Using this approach, we demonstrated that certain key metabolites and specific microbes are associated with high and low sorghum NUE in a field study. This important information provides a new path forward for developing crop genotypes that have increased NUE through the positive contribution of soil microbes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Genetic determinants of switchgrass-root-associated microbiota in field sites spanning its natural range

A fundamental goal in plant microbiome research is to determine the relative impacts of host and environmental effects on root microbiota composition, particularly how host genotype impacts bacterial community composition. Most studies characterizing the effect of plant genotype on root microbiota undersample host genetic diversity and grow plants outside of their native ranges, making the associations between host and microbes difficult to interpret. Here, we characterized the root microbiota of a large diversity panel of switchgrass, a North American native C4 bioenergy crop, in three field locations spanning its native range. Our data, composed of 1,961 samples, suggest that field location is the primary determinant of microbiome composition; however, substantial heritable variation is widespread across bacterial taxa, especially those in the Sphingomonadaceae family. Despite diverse compositions, relatively few highly prevalent taxa make up the majority of the switchgrass root microbiota, a large fraction of which is shared across sites. Local genotypes preferentially recruit/filter for local microbes, supporting the idea of affinity between local plants and their microbiota. Using genome-wide association, we identified loci impacting the abundance of >400 microbial strains and found an enrichment of genes involved in immune responses, signaling pathways, and secondary metabolism. We found loci associated with over half of the core microbiota (i.e., microbes in >80% of samples), regardless of field location. Finally, we show a genetic relationship between a basal plant immunity pathway and relative abundances of root microbiota. Furthermore, this study brings us closer to harnessing and manipulating beneficial microbial associations via host genetics.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

In Situ Non-Destructive Temporal Measurements of the Rhizosphere Microbiome ‘Hot-Spots’ Using Metaproteomics

Rhizosphere arguably embodies the most diverse microbial ecosystem on the planet, yet it is largely a functional ‘black box’ of belowground plant-microbiome interactions. The rhizosphere is the primary site of entry for subsurface injection of fixed carbon (C) into soil with impacts on local to global scale C biogeochemistry and ultimately Earth’s climate. While spatial organization of rhizosphere is central to its function, small scale and steep microbial and geochemical gradients within this dynamic region make it easily disrupted by sampling. The significant challenge presented by sampling blocks elucidation of discreet functions, drivers, and interactions within rhizosphere ecosystems. Here, we describe a non-destructive sampling method linked to metaproteomic analysis in order to measure temporal shifts in the microbial composition and function of rhizosphere. A robust, non-destructive method of sampling microbial hotspots within rhizosphere provides an unperturbed window into the elusive functional interactome of this system over time and space.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Symbiosis Under Stress: How Arbuscular Mycorrhizal Fungi and Sorghum Metabolism Shift Under Drought

As drought becomes more prevalent across the globe, causing billions of dollars in agricultural loss, the need to maintain crop health and productivity grows increasingly important. Out of the most important cereal crops, sorghum shows the greatest drought tolerance, and plant-microbiome interactions at the root region play a crucial role in this. A key microbial player is arbuscular mycorrhizal fungi (AMF), which deliver water and nutrients to plants in exchange for nutrients they cannot produce. Using sorghum as a model plant, we combine mass-spectrometry based proteomics and metabolomics to examine metabolic interactions between sorghum roots and AMF under drought stress. With AMF, sorghum downregulated lipid-related biological processes involving fatty acid biosynthesis and metabolism. Similarly, amino acid biosynthesis pathways were also suppressed; however, metabolite analysis revealed increased amino acid abundance related to the phenylpropanoid pathway. AMF also enhanced the upregulation of drought-protective osmolytes, such as mannitol and sorbitol, suggesting their key role in mediating sorghum’s response to drought stress. AMF hyphal biomass also had an increased abundance of key osmoprotectant amino acids, indicating similar mechanisms of drought tolerance between sorghum and AMF. Metabolomic evidence also suggested that carbohydrate exchange between sorghum and AMF shifted under stress, indicating an altered exudation pattern likely driven by drought response. Our results demonstrate the molecular mechanisms through which AMF modulate sorghum metabolism under drought conditions, highlighting their promising role in improving crop resilience. By identifying the molecular targets that can improve drought tolerance, we can begin engineering drought resistant agricultural biosystems.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Specificity in plant-mycorrhizal fungal relationships: prevalence, parameterization, and prospects

Species interactions exhibit varying degrees of specialization, ranging from generalist to specialist interactions. For many interactions (e.g., plant-microbiome) we lack standardized metrics of specialization, hindering our ability to apply comparative frameworks of specificity across niche axes and organismal groups. Here, we discuss the concept of plant host specificity of arbuscular mycorrhizal (AM) fungi and ectomycorrhizal (EM) fungi, including the predominant theories for their interactions: Passenger, Driver, and Habitat Hypotheses. We focus on five major areas of interest in advancing the field of plant-mycorrhizal fungal host specificity: phylogenetic specificity, host physiology specificity, functional specificity, habitat specificity, and mycorrhizal fungal-mediated plant rarity. Considering the need to elucidate foundational concepts of specificity in this globally important symbiosis, we propose standardized metrics and comparative studies to enhance our understanding. We also emphasize the importance of analyzing global mycorrhizal data holistically to draw meaningful conclusions and suggest a shift toward single-species analyses to unravel the complexities underlying these associations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Improved Biofuel Production through Discovery and Engineering of Terpene Metabolism in Switchgrass

Project Objectives - Of the myriad specialized metabolites that plants deploy to adapt to environmental challenges, terpenes form the largest group. In many major crops, unique terpene blends serve as key stress defenses that directly impact plant fitness and yield. In addition, terpenes, such as bisabolene and pinene, are used for producing renewable biofuels. Essential to advancing a broader use of terpenes for biofuel feedstock engineering is a system-wide knowledge of the diverse biosynthetic machinery and defensive potential of often species-specific terpene blends. The proposed project would merge genome-wide enzyme discovery with comparative –omics, protein structural and plant microbiome studies to define the biosynthesis and stress-defensive functions of the switchgrass (Panicum virgatum) terpene network. These insights would be combined with developing and applying non-transgenic genome editing tools to design plants with desirable terpene blends for higher productivity and biofuel production on marginal lands. As a dedicated lignocellulosic feedstock for U.S. biofuel production with high net energy yield, stress tolerance, and available genome resources, switchgrass is well-suited for devising new avenues for biofuel production. Project Description – The diversity of plant terpene defenses is governed by species-specific families of terpene synthase (TPS) and cytochrome P450 monooxygenase (P450) enzymes. Mining of the switchgrass genome (genotype Alamo) identified ~100 TPS and P450 candidate genes, and combinatorial biochemical analysis of synthesized TPSs and P450s revealed more than a dozen enzymes with common and novel activities. In addition, several identified terpene metabolites and the corresponding transcripts were up-regulated in response to abiotic stressors. These findings demonstrate a unique switchgrass terpene network with probable importance to abiotic stress tolerance, thus providing a large chemical portfolio for optimizing crop resistance, yield, and biofuel composition. Leveraging these preliminary data, we propose to generate a genome-wide map of the switchgrass terpene metabolic network through multi-gene co-expression analyses that allow the efficient cross-validation of TPS and P450 functions. Key enzymes would further be applied to structure-function studies via X-ray protein crystallography, homology modeling and site-directed mutagenesis to gain mechanistic insight into the catalytic specificity of switchgrass terpene metabolism and provide gene and amino acid targets for genome editing. In tandem with terpene pathway discovery, system-wide metabolomics, transcriptomics and proteomics studies in switchgrass accessions of contrasting drought tolerance would define the role of switchgrass terpene metabolism in conferring abiotic stress resilience. Metabolic changes would be assessed in a combined approach of targeted (terpenes) and untargeted metabolite profiling using a high-resolution LC-MS/MS approach, differential gene expression analyses through multiplexed Illumina RNA sequencing, and quantitative analysis of high-priority pathway enzymes using multiple reaction monitoring (MRM). Drawing on these insights, knock-down/out mutants of stress-associated pathway nodes would be generated by optimizing transient virus-induced gene silencing (VIGS) and CRISPR/Cas9 systems under control of the Tobacco Rattle Virus (TRV). The resulting mutant lines would then be analyzed for stress susceptibility and the impact on the root microbiome to define gene functions in planta. Knowledge of terpene pathways, enzyme mechanisms and bioactivities would be applied to enhance switchgrass stress resilience and to tailor-make terpene blends for biofuel production. Here, TRV-enabled CRISPR/Cas9 genome editing, including allele-specific knock-out of redundant genes, engineering of enzyme specificity via structure-guided point mutations, and overexpression of terpene genes relevant to stress-protection or biofuel production, would be used to increase metabolic flux toward desired pathways. Broader Impacts - Integrating the system-wide discovery, mechanistic analysis and non-transgenic genome engineering of the switchgrass terpene network aligns the required steps to unlock the chemical potential of this important metabolite class to generate crops that are more resistant to stress and provide advanced biofuel production in light of rising climate pressures as foreseeable challenges for bioenergy crop cultivation. The proposed project would further offer interdisciplinary student training through active involvement in the project and integration of research concepts and outcomes into newly-developed graduate and undergraduate courses on Plant Biotechnology.

09 BIOMASS FUELS↗
NASA NTRSDate not supplied

Seed surface sanitization and persistence of E.coli through different tissues of ‘Red Robin’ Tomato (Solanum lycopersicum cv. Red Robin)

Seed surface sanitization via chemical processes removes/reduces microbes from the external surfaces of the seed and thereby could have an impact on the plants’ health or productivity. To determine the impact of seed surface sanitization on the plants’ microbiome, sanitized and unsanitized seeds from ‘Red Robin’ Tomato (Solanumlycopersicum cv. Red Robin) were exposed to Escherichia coli (E. coli) and grown in a controlled environment growth chamber simulating environmental conditions aboard the International Space Station (ISS). Plants were harvested at four intervals, days 11, 33,42 and 76 post-germination. Changes in the microbial communities of leaf, stem, root, and fruit because of E. coli exposure and the persistence of E. coli itself were investigated using aerobic plate count (APC), qPCR and 16S rRNA sequencing. It was determined that E. coli persisted for longer periods of time in plants from sanitized versus unsanitized seeds and was identified in root tissue more frequently than in leaf or stem tissue. E. coli was not detected in fruits raised from either sanitized or unsanitized seeds. The 16S rRNA sequencing showed dynamic changes in the abundance of members of the phylum Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes in all tissue types studied. We observed minimal or no changes in the alpha diversity of leaf stem and fruit tissue with time, or between sanitized and unsanitized seeds. Roots showed significant differences in alpha diversity with time and seed sanitization status. Beta-diversity showed that time had more of an influence on all samples versus the E. coli treatment. Members of phyla Proteobacteria and Bacteroidetes were found to be differentially abundant across leaf, stem and root tissue. Our results indicated that the seed surface sanitization, although a requirement for sending seeds to space, might influence the developing microbiome. This research was funded by NASA’s Space Life and Physical Sciences Research and Applications.

Anirudha R Dixit↗
DOE OSTI2022

Increased signal-to-noise ratios within experimental field trials by regressing spatially distributed soil properties as principal components

Environmental variability poses a major challenge to any field study. Researchers attempt to mitigate this challenge through replication. Thus, the ability to detect experimental signals is determined by the degree of replication and the amount of environmental variation, noise, within the experimental system. A major source of noise in field studies comes from the natural heterogeneity of soil properties which create microtreatments throughout the field. In addition, the variation within different soil properties is often nonrandomly distributed across a field. We explore this challenge through a sorghum field trial dataset with accompanying plant, microbiome, and soil property data. Diverse sorghum genotypes and two watering regimes were applied in a split-plot design. We describe a process of identifying, estimating, and controlling for the effects of spatially distributed soil properties on plant traits and microbial communities using minimal degrees of freedom. Importantly, this process provides a method with which sources of environmental variation in field data can be identified and adjusted, improving our ability to resolve effects of interest and to quantify subtle phenotypes.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Plant myo -inositol transport influences bacterial colonization phenotypes

Plant microbiomes are assembled and modified through a complex milieu of biotic and abiotic factors. Despite dynamic and fluctuating contributing variables, specific host metabolites are consistently identified as important mediators of microbial interactions. We combine information from a large-scale metatranscriptomic dataset from natural poplar trees and experimental genetic manipulation assays in seedlings of the model plant Arabidopsis thaliana to converge on a conserved role for transport of the plant metabolite myo-inositol in mediating host-microbe interactions. While microbial catabolism of this compound has been linked to increased host colonization, we identify bacterial phenotypes that occur in both catabolism-dependent and -independent manners, suggesting that myo-inositol may additionally serve as a eukaryotic-derived signaling molecule to modulate microbial activities. Our data suggest host control of this compound and resulting microbial behavior are important mechanisms at play surrounding the host metabolite myo-inositol.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Predictions of rhizosphere microbiome dynamics with a genome-informed and trait-based energy budget model

Abstract Soil microbiomes are highly diverse, and to improve their representation in biogeochemical models, microbial genome data can be leveraged to infer key functional traits. By integrating genome-inferred traits into a theory-based hierarchical framework, emergent behaviour arising from interactions of individual traits can be predicted. Here we combine theory-driven predictions of substrate uptake kinetics with a genome-informed trait-based dynamic energy budget model to predict emergent life-history traits and trade-offs in soil bacteria. When applied to a plant microbiome system, the model accurately predicted distinct substrate-acquisition strategies that aligned with observations, uncovering resource-dependent trade-offs between microbial growth rate and efficiency. For instance, inherently slower-growing microorganisms, favoured by organic acid exudation at later plant growth stages, exhibited enhanced carbon use efficiency (yield) without sacrificing growth rate (power). This insight has implications for retaining plant root-derived carbon in soils and highlights the power of data-driven, trait-based approaches for improving microbial representation in biogeochemical models.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Heterospecific Neighbor Plants Impact Root Microbiome Diversity and Molecular Function of Root Fungi

Within the forest community, competition and facilitation between adjacent-growing conspecific and heterospecific plants are mediated by interactions involving common mycorrhizal networks. The ability of plants to alter their neighbor’s microbiome is well documented, but the molecular biology of plant-fungal interactions during competition and facilitation has not been previously examined. We used a common soil-plant bioassay experiment to study molecular plant-microbial interactions among rhizosphere communities associated with Pinus taeda (native host) and Populus trichocarpa (non-native host). Gene expression of interacting fungal and bacterial rhizosphere communities was compared among three plant-pairs: Populus growing with Populus , Populus with Pinus , and Pinus with Pinus . Our results demonstrate that heterospecific plant partners affect the assembly of root microbiomes, including the changes in the structure of host specific community. Comparative metatranscriptomics reveals that several species of ectomycorrhizal fungi (EMF) and saprotrophic fungi exhibit different patterns of functional and regulatory gene expression with these two plant hosts. Heterospecific plants affect the transcriptional expression pattern of EMF host-specialists (e.g., Pinus -associated Suillus spp.) on both plant species, mainly including the genes involved in the transportation of amino acids, carbohydrates, and inorganic ions. Alteration of root microbiome by neighboring plants may help regulate basic plant physiological processes via modulation of molecular functions in the root microbiome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Switchgrass-associated soil microbes have subtle but distinct effects on germination vs. growth under drought

Soil microbial communities can play a large role in plant fitness, including plants’ response to drought. How microbes mediate drought response may also differ across the plants’ life stage, but studies rarely study causal effects of microbes on plant fitness at multiple stages. We conducted a greenhouse experiment on switchgrass (Panicum virgatum L.) to investigate how microbial presence (sterile bulk vs. live bulk soils) and microbial source (communities from bulk vs. rhizosphere soil) affect germination and seedling growth (life-stage) during drought. We also investigated how drought and life-stage alter the assembly of the inoculated communities. Both drought conditions and the absence of microbes reduced germination (49% and 50% fewer seedlings, respectively, p < 0.05), but there were few effects of microbial presence on older seedlings. In addition, microbial source had no effect on the evaluated plant traits, but interestingly, the initially similar bulk and rhizosphere communities became compositionally distinct after 34 days with germinating seeds, but not with seedlings. Therefore, it may be that the plants did respond to microbial source through changes in seed or root exudates, and calls for further study. Finally, while sometimes microbes did benefit plants under drought, we did not find evidence that they are especially beneficial in this condition. We suggest that microbes’ effects differ across plant life stage, and may be both positive and negative. Further research should advance understanding of plant stress tolerance within a framework of plant-microbiome co-development.

drought↗
DOE OSTI2026

Genomic signatures in Variovorax enabling colonization of the Populus endosphere

Microbial colonization of plant roots involves strong selective pressures that shape the structure and function of root-associated communities. In particular, the endosphere represents a highly selective environment requiring host entry and in planta persistence. However, strain-specific microbial traits that enable endosphere colonization remain poorly understood. Here, we use a defined, genome-resolved community of 28 Variovorax strains isolated from the roots of Populus deltoides and Populus trichocarpa (poplar trees) to determine which strains partition between rhizosphere and endosphere compartments and to identify the genomic traits associated with endosphere specialization. By combining strain-resolved metagenomic profiling, comparative genomics, and functional assays, we demonstrate that dominant endosphere colonizers are enriched in genes related to nutrient metabolism, redox balance, transcriptional regulation, and a conserved L-fucose utilization pathway experimentally shown to enhance root colonization. Not all strains succeed through the same strategy. Community-wide functional profiling revealed a distinct and reduced set of traits in the endosphere, including orthogroups associated with low-abundance strains that were overlooked in strain-level analyses. These findings reveal that multiple ecological strategies, such as metabolic competition, regulatory adaptation, and niche specialization, can support endosphere colonization. Our results advance the understanding of how bacterial colonization traits are distributed and deployed within a plant microbiome and suggest that host filtering selects for distinct, and sometimes complementary, microbial strategies. This work supports a shift toward mechanistic, genome-resolved models of microbiome assembly and offers a framework for linking microbial function to host colonization success.

comparative genomics↗
DOE OSTI2024

Rapid Design and Engineering of Smart and Secure Microbiological Systems (Final Report)

The design and application of successfully engineered biosystems requires an understanding of how engineered microbes will interact with other organisms – either as one-on-one competitors or in the context of microbial consortia. Engineering microorganisms from first principles for non-laboratory, environmental applications is inherently challenging because: (1) engineered systems tend to quickly revert back to their wild-type behaviors; and (2) these systems typically pay a price in reduced fitness, making them uncompetitive against invasive contaminating species (i.e., metabolic burden). For this project, we used a synthetic biology-based strategy to investigate the organization, control, stabilization, and destabilization of natural and engineered microbes. This approach enabled development of (1) single-strain systems capable of detecting and responding to target organisms in the environment; (2) a pipeline for refining and engineering biological constructs in new, non-model host organisms; and (3) improved systems for rapidly designing, engineering, and assaying new biological modules. This coupled approach to safeguard system design is predictable and portable across bacterial species and is focused on microbes that are part of the beneficial plant microbiome. A long-term goal beyond the proposed research is to enable the rational engineering of microbial communities based on first principles of biological design that mimic the smart performance of microorganisms observed in natural systems.

59 BASIC BIOLOGICAL SCIENCES↗