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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.

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At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Ecological strategies of microbes: Thinking outside the triangle

Abstract I asked whether Grime's triangle of competitive, stress tolerance and ruderal ecological strategies—which was originally developed for plants—applies to microbes. I conducted a synthesis of empirical studies that tested relationships among microbial traits presumed to define the competitive, stress tolerance and ruderal, and other ecological strategies. There was broad support for Grime's triangle. However, the ecological strategies were inconsistently linked to shifts in microbial communities under environmental changes like nitrogen and phosphorus addition, warming, drought, etc. We may be missing important ecological strategies that more closely influence microbial community composition under shifting environmental conditions. We may need to start by documenting changes in microbial communities in response to environmental conditions at fine spatiotemporal scales relevant for microbes. We can then develop empirically based ecological strategies, rather than modifying those based on plant ecology. Synthesis . Microbes appear to sort into similar ecological strategies as plants. However, these microbial ecological strategies do not consistently predict how community composition will shift under environmental change. By starting ‘from the ground up’, we may be able to delineate ecological strategies more relevant for microbes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Mycorrhizal nutrient acquisition strategies shape tree competition and coexistence dynamics

Mycorrhizal fungi with different nutrient acquisition strategies influence plant species performance and physiology, thereby defining their trophic niche. This might drive resource competition dynamics that cumulatively impact tree species coexistence, but few manipulative experiments have directly tested this. Combining surveys and experiments in a modern coexistence theory framework, we tested how variation in mycorrhizal strategies and nutrient conditions affects plant competitive outcomes. We focused on two genera of co-occurring tree species with different mycorrhizal states: Acer (arbuscular mycorrhizal, AM) and Populus (dual mycorrhizal, but often considered predominantly ectomycorrhizal, EM). The EM and AM fungal responsiveness in Populus species varied with latitude and nitrogen (N) limitation. Host-specific soil microbiome conditioning and inorganic N fertilization combined to qualitatively affect coexistence outcomes. Lower N conditions favoured Populus over Acer trees, and N fertilization reversed this outcome for southern species, aligning with regional-scale forest mycorrhizal transitions. Results from the coexistence experiment also predict competitive exclusion between the tree species pairs, which could arise, in part, from their mycorrhizal differences and is consistent with alternative stable states in dominant forest mycorrhizal strategies. Such bistability appears in natural systems as a bimodal distribution of Populus vs. Acer tree species dominance using long-term forest inventory data. Synthesis: The magnitude and outcome of microbially mediated competition between Populus and Acer depends on soil nutrient availability, which likely relates to their mycorrhizal differentiation. These findings support the importance of mycorrhizal symbioses for contributing to large-scale biogeographical patterns of tree species trophic niche separation across soil resource gradients and bistability in forest mycorrhizal structure.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

The relationship between gene traits and transcription in soil microbial communities varies by environmental stimulus

Codon and nucleotide frequencies are known to relate to the rate of gene transcription, yet how these traits shape transcriptional profiles of soil microbial communities remains unclear. Here we test the prediction that functional genes with high codon optimization and energetically lower cost nucleotides (i.e., nucleotides requiring less adenosine triphosphate (ATP) for synthesis) have higher transcriptional expression in a soil microbial community. In laboratory incubations, we subjected an agricultural soil to two separate short-term environmental changes: labile carbon (glucose) addition or a sudden 30-min increase in temperature from 20 °C to 60 °C. Using the total genomic codon frequencies to predict preferred codon usage for each taxon, we then estimated codon optimization for each transcript. On the community level, we found a higher average level of codon optimization after the addition of glucose. Synonymous nucleotide composition in the transcript pool also shifted towards energetically cheaper nucleotides, favoring uracil (U) over adenine (A) and cytosine (C) over guanine (G). Similarly, we found that encoded amino acid usage shifted towards energetically cheaper amino acids in response to labile carbon. In contrast, in communities responding to heat shock, there were no significant differences in the averaged gene traits of expressed transcripts. We used metagenome-assembled-genomes to further examine the ability of gene traits to predict transcriptional responses within and between taxa. We found that traits of individual genes could not reliably predict the level of transcription of a gene within or between taxa—highlighting the limits of this approach. However, we did find that when traits were averaged across several related genes, codon optimization was able to predict levels of transcription in metabolic pathways associated with growth and nutrient uptake in response to glucose. Similar relationships were not observed in response to heat, or for functions associated with stress—such as genes associated with sporulation or heat shock. These results demonstrate that gene traits, such as codon usage, nucleotide selection, and amino acid selection, relate to the transcriptional expression of genes in soil microbial communities and suggests that these relationships may be dependent on both gene function and the specific type of environmental stimuli.

Biological and medical sciences↗
DOE OSTI2025

From bench to biofactory: high-throughput technologies and automated workflows to accelerate biomanufacturing

Microbial production of target molecules has advanced significantly in recent years driven by innovations in enzyme engineering, DNA synthesis, and genomic editing. However, to access the massive potential of microbial production, a vast parametric space remains to be investigated to optimize these biobased processes for a robust bioeconomy. Here, we review the current state of the art, some key challenges and possible solutions. We see a critical role of automation, high-throughput technologies, self-driving and cloud labs, and data management to enable Artificial Intelligence/Machine Learning and mechanistic models to overcome the design space challenges and accelerate the development of novel bio-based solutions. Accurate models will expedite the development and scale-up of engineered microbes for a range of final products from many starting materials.

Petzold, Christopher J↗
DOE OSTI2023

Microbial Competition for Copper: Impacts on Carbon and Nitrogen Cycling

Activities from this DOE sponsored project focused on two general questions: (1) how does competition between microbes for copper affect emissions of greenhouse gasses, especially methane and nitrous oxide? and (2) how does a novel copper-binding compound (methanobactin) made by some methane-oxidizing bacteria bind and reduce metals, as well as what are the regulatory elements involved in controlling methanobactin synthesis? From these efforts, we have conclusively shown that microbial competition for copper does indeed exert significant control on microbial community composition, as well as affects how microbes produce and consume nitrous oxide. We have also developed much better insights into the basis for methanobactin activity, as well as how methanotrophs control its production.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Defining the Minimal Set of Microbial Genes Required for Valorization of Lignin Biomass (Final Report)

Project Goals: Lignin is the second most abundant biopolymer on earth and represents a critically underutilized biomass resource for hydrocarbon feedstocks. Despite substantial effort, there is still no efficient process to convert lignin to useable carbon-based platform chemicals and materials. The goal of this project is identify a minimal set of microbial enzymes necessary for lignin breakdown and sufficient for the synthesis of valuable chemical intermediates from lignin isolated as a byproduct of lignocellulosic ethanol production. These genes will be then used to engineer functional whole cell biocatalysts for tunable lignin metabolism. To date, although a number of enzymes have been associated with lignin degradation, most have been tested in isolation (as individual enzymes) and on drastically different substrates -- often dyes that are not related to lignin. In contrast, lignin utilization in nature likely occurs by microbial consortia with multiple enzymes acting synergistically. We propose to examine two separate stages of lignin breakdown carried out by the microbes that do it best: (1) early breakdown of native polymeric lignin into soluble fragments by a set of sequenced wood-rotting fungal species, and (2) downstream metabolism of these soluble lignin fragments to useful chemical intermediates by a panel of sequenced soil saprophytes. Our approach involves testing sets of genes that will be assayed combinatorially in the context of a heterologous expression host. The resulting engineered strains will be systematically assayed using soluble lignin fragments, synthetic defined polymeric lignin, and finally lignin directly sourced from lignocellulosic processing streams. In addition to resulting in a functional whole cell biocatalyst for lignin utilization, we anticipate that this approach will allow us to address key unanswered questions about lignin metabolism in nature, including: (1) Why does the Trametes versicolor genome contain 25 different class II peroxidases? (2) What is the role of laccases in lignin metabolism? Why do some aggressive lignin degraders have many laccases (e.g. >7 in T. versicolor) while others have none (e.g. P. chrysosporium)? (3) How is peroxide provided in a controlled manner to drive peroxidase activity without causing the enzyme inhibition that is so often observed in vitro? (4) What strategies do microbial lignin degraders use to avoid the problem of repolymerization during active lignin degradation? and (5) Can microbial lignin metabolism be diverted for high level production of defined aromatics? A final critical question is whether combining key minimal sets of enzymes from a wide range of organisms will result in engineered strains capable of highly efficient, streamlined pathways for lignin utilization that can be tuned for a specific carbon output. This effort will leverage DOE investments in microbial genome sequencing, and secure a critical channel for lignin biomass utilization that will also help to render lignocellulosic a viable feedstock for the production of renewable liquid biofuels.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A framework for soil microbial ecology in urban ecosystems

Nearly all ecosystems host diverse microbiomes that support vital ecosystem processes. At the same time, these ecosystems and their microbiomes are increasingly altered by human activities, particularly in highly managed urban environments. While microbial ecologists are beginning to understand the drivers of microbial assembly and the link between community structure and function in many ecosystems, few of these advances have been applied to urban ecosystems. In this synthesis, we review research on the urban soil microbiome and develop a framework to integrate soil microbial communities with urban ecosystem function. We identify disturbance, altered resources, and heterogeneity as key drivers through which human activities including urban development affect soils and their resident microorganisms. Steep environmental gradients in many urban systems present a unique opportunity to address fundamental questions in microbial ecology, such as how microbes respond to stress and how biogeochemical rates relate to microbial diversity and composition. Soil microbiomes in cities also provide ecosystem services and harms, making it crucial to understand how human activity drives those functions and the consequences for environmental and human health. We argue that much-needed integration across disturbance ecology, urban ecology, and microbial ecology will help generate practical and equitable strategies for managing ecosystem benefits in cities where most humans now live.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Parsed synthesis of pyocyanin via co-culture enables context-dependent intercellular redox communication

Abstract Background Microbial co-cultures and consortia are of interest in cell-based molecular production and even as “smart” therapeutics in that one can take advantage of division of labor and specialization to expand both the range of available functions and mechanisms for control. The development of tools that enable coordination and modulation of consortia will be crucial for future application of multi-population cultures. In particular, these systems would benefit from an expanded toolset that enables orthogonal inter-strain communication. Results We created a co-culture for the synthesis of a redox-active phenazine signaling molecule, pyocyanin (PYO), by dividing its synthesis into the generation of its intermediate, phenazine carboxylic acid (PCA) from the first strain, followed by consumption of PCA and generation of PYO in a second strain. Interestingly, both PCA and PYO can be used to actuate gene expression in cells engineered with the soxRS oxidative stress regulon, although importantly this signaling activity was found to depend on growth media. That is, like other signaling motifs in bacterial systems, the signaling activity is context dependent. We then used this co-culture’s phenazine signals in a tri-culture to modulate gene expression and production of three model products: quorum sensing molecule autoinducer-1 and two fluorescent marker proteins, eGFP and DsRed. We also showed how these redox-based signals could be intermingled with other quorum-sensing (QS) signals which are more commonly used in synthetic biology, to control complex behaviors. To provide control over product synthesis in the tri-cultures, we also showed how a QS-induced growth control module could guide metabolic flux in one population and at the same time guide overall tri-culture function. Specifically, we showed that phenazine signal recognition, enabled through the oxidative stress response regulon soxRS, was dependent on media composition such that signal propagation within our parsed synthetic system could guide different desired outcomes based on the prevailing environment. In doing so, we expanded the range of signaling molecules available for coordination and the modes by which they can be utilized to influence overall function of a multi-population culture. Conclusions Our results show that redox-based signaling can be intermingled with other quorum sensing signaling in ways that enable user-defined control of microbial consortia yielding various outcomes defined by culture medium. Further, we demonstrated the utility of our previously designed growth control module in influencing signal propagation and metabolic activity is unimpeded by orthogonal redox-based signaling. By exploring novel multi-modal strategies for guiding communication and consortia outcome, the concepts introduced here may prove to be useful for coordination of multiple populations within complex microbial systems.

Chun, Kayla↗
DOE OSTI2022

A soil-inspired dynamically responsive chemical system for microbial modulation

Interactions between the microbiota and their colonized environments mediate critical pathways from biogeochemical cycles to homeostasis in human health. Here, in this study, we report a soil-inspired chemical system that consists of nanostructured minerals, starch granules and liquid metals. Fabricated via a bottom-up synthesis, the soil-inspired chemical system can enable chemical redistribution and modulation of microbial communities. We characterize the composite, confirming its structural similarity to the soil, with three-dimensional X-ray fluorescence and ptychographic tomography and electron microscopy imaging. We also demonstrate that post-synthetic modifications formed by laser irradiation led to chemical heterogeneities from the atomic to the macroscopic level. The soil-inspired material possesses chemical, optical and mechanical responsiveness to yield write-erase functions in electrical performance. The composite can also enhance microbial culture/biofilm growth and biofuel production in vitro. Finally, we show that the soil-inspired system enriches gut bacteria diversity, rectifies tetracycline-induced gut microbiome dysbiosis and ameliorates dextran sulfate sodium-induced rodent colitis symptoms within in vivo rodent models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Identification and Mitigation of Inhibitory Substances Contained in High-Salinity Crude Glycerol Generated from Biodiesel Production for Polyhydroxyalkanoate Synthesis by Haloferax mediterranei

High-salinity crude glycerol generated from biodiesel production poses significant challenges to microbial valorization due to inhibitory ingredients that severely limit microbial growth. This study identified and mitigated inhibitory substances contained in high-salinity glycerol sludge to enable its conversion to polyhydroxyalkanoates (PHAs) by the extreme halophilic archaeon Haloferax mediterranei. The long-chain fatty acids (LCFAs) were consistently identified as the primary inhibitors by liquid chromatography−mass spectrometry, Fourier transform infrared spectroscopy, and ultraviolet−visible spectroscopy. Acid precipitation at pH 2 efficiently removed these LCFAs, substantially reducing the required feedstock dilution from 23 to 3 times, improving PHA titer by 40%. Furthermore, this dilution reduction also increased the feedstock salinity utilization, achieving a 46% reduction in external salt supplementation for H. mediterranei growth. In contrast, overliming and arrested anaerobic digestion were confirmed to be ineffective in inhibitor removal. This study provides deep insights into inhibitor chemistry and presents acid precipitation as an effective pretreatment strategy for waste valorization of highsalinity crude glycerol.

LC-MS↗
DOE OSTI2023

Post-fire soil emissions of nitric oxide (NO) and nitrous oxide (N 2 O) across global ecosystems: a review

Wildfires may increase soil emissions of trace nitrogen (N) gases like nitric oxide (NO) and nitrous oxide (N 2 O) by changing soil physicochemical conditions and altering microbial processes like nitrification and denitrification. When 34 studies were synthesized, we found a significant increase in both NO and N 2 O emissions up to 1 year post-fire across studies spanning ecosystems globally. However, when fluxes were separated by ecosystem type, we found that individual ecosystem types responded uniquely to fire. Forest soils tended to emit more N 2 O after fire, but there was no significant effect on NO. Shrubland soils showed significant increases in both NO and N 2 O emissions after fires; often with extremely large but short-lived NO pulses occurring immediately after fire. Grassland NO emissions increased after fire, but the size of this effect was small relative to shrublands. N 2 O emissions from burned grasslands were highly variable with no significant effect. To better understand the variation in responses to fire across global ecosystems, more consistent measurements of variables recognized as important controls on soil fluxes of NO and N 2 O (e.g., N cycling rates, soil water content, pH, and substrate availability) are needed across studies. We also suggest that fire-specific elements like burn severity, microbial community succession, and the presence of char be considered by future studies. Our synthesis suggests that fires can exacerbate ecosystem N loss long after they burn, increasing soil emissions of NO and N 2 O with implications for ecosystem N loss, climate, and regional air quality as wildfires increase globally.

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

An algal-bacterial symbiotic system of carbon fixation using formate as a carbon source

The commercial implementation of algal cultures for efficient capture of CO 2 from fossil-derived flue gases is not a reality yet due to several major challenges, particularly low gas-liquid mass transport efficiency along with loss of productivity due to pests. This study has explored an algal-bacterial symbiotic system to utilize formate as a carbon source. The algal-bacterial assemblage, after a 400-day adaptive evolution using the formate medium, has demonstrated a new capability to assimilate both formate and CO 2 to promote biomass production. The formate tolerant culture system also addresses CO 2 mass transfer limitation under high light conditions. Continuous cultivation of the assemblage on formate led to a carbon capture efficiency of 90 % with a biomass concentration of 0.92 g L -1 and biomass productivity of 0.31 g L -1 day -1 , and the system did not require CO 2 aeration. In addition, 13 C isotope tracing, proteomics, and microbial community analysis reveal a uniquely evolved community for formate utilizations and robust biomass synthesis, in which Chlorella sorokiniana is a dominant phototroph companying with highly diverse bacterial subpopulations. In the presence of formate, evidence has shown that Chlorella is able to form mutualism with formate utilizing bacteria in semi-continuous cultures, leading to a highly effective photomixotrophic metabolism. Furthermore, this study demonstrates a new route of using electrochemical-derived formate to support mutualistic algae-bacteria biorefinery while the formate as an alternative carbon source could repel pests for outdoor algal cultivations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Trends in Microbial Community Composition and Function by Soil Depth

Microbial communities play important roles in soil health, contributing to processes such as the turnover of organic matter and nutrient cycling. As soil edaphic properties such as chemical composition and physical structure change from surface layers to deeper ones, the soil microbiome similarly exhibits substantial variability with depth, with respect to both community composition and functional profiles. However, soil microbiome studies often neglect deeper soils, instead focusing on the top layer of soil. Here, we provide a synthesis on how the soil and its resident microbiome change with depth. We touch upon soil physicochemical properties, microbial diversity, composition, and functional profiles, with a special emphasis on carbon cycling. In doing so, we seek to highlight the importance of incorporating analyses of deeper soils in soil studies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Microbial inoculum effects on the rumen epithelial transcriptome and rumen epimural metatranscriptome in calves

Manipulation of the rumen microbial ecosystem in early life may affect ruminal fermentation and enhance the productive performance of dairy cows. The objective of this experiment was to evaluate the effects of dosing three different types of microbial inoculum on the rumen epithelium tissue (RE) transcriptome and the rumen epimural metatranscriptome (REM) in dairy calves. For this objective, 15 Holstein bull calves were enrolled in the study at birth and assigned to three different intraruminal inoculum treatments dosed orally once weekly from three to six weeks of age. The inoculum treatments were prepared from rumen contents collected from rumen fistulated lactating cows and were either autoclaved (control; ARF), processed by differential centrifugation to create the bacterial-enriched inoculum (BE), or through gravimetric separation to create the protozoal-enriched inoculum (PE). Calves were fed 2.5 L/d pasteurized waste milk 3x/d from 0 to 7 weeks of age and texturized starter until euthanasia at 9 weeks of age, when the RE tissues were collected for transcriptome and microbial metatranscriptome analyses, from four randomly selected calves from each treatment. The different types of inoculum altered the RE transcriptome and REM. Compared to ARF, 9 genes were upregulated in the RE of BE and 92 in PE, whereas between BE and PE there were 13 genes upregulated in BE and 114 in PE. Gene ontology analysis identified enriched GO terms in biological process category between PE and ARF, with no enrichment between BE and ARF. The RE functional signature showed different KEGG pathways related to BE and ARF, and no specific KEGG pathway for PE. We observed a lower alpha diversity index for RE microbiome in ARF (observed genera and Chao1 (p < 0.05)). Five microbial genera showed a significant correlation with the changes in host gene expression: Roseburia (25 genes), Entamoeba (two genes); Anaerosinus, Lachnospira, and Succiniclasticum were each related to one gene. sPLS-DA analysis showed that RE microbial communities differ among the treatments, although the taxonomic and functional microbial profiles show different distributions. Co-expression Differential Network Analysis indicated that both BE and PE had an impact on the abundance of KEGG modules related to acyl-CoA synthesis, type VI secretion, and methanogenesis, while PE had a significant impact on KEGGs related to ectoine biosynthesis and D-xylose transport. Our study indicated that artificial dosing with different microbial inocula in early life alters not only the RE transcriptome, but also affects the REM and its functions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Engineering Terpene Production Pathways in Methylobacterium extorquens AM1

Terpenes are diverse specialized metabolites naturally found within plants and have important roles in inter-species communication, adaptation and interaction with the environment. Their industrial applications span a broad range, including fragrances, flavors, cosmetics, natural colorants to agrochemicals and therapeutics, yet formal chemical synthesis is economically challenging due to structural complexities. Engineering terpene biosynthesis could represent an alternative in microbial biotechnological workhorses, such as Saccharomyces cerevisiae or Escherichi coli, utilizing sugars or complex media as feedstocks. Host species that metabolize renewable and affordable carbon sources may offer unique sustainable biotechnological alternatives. Methylotrophs are bacteria with the capacity to utilize one-carbon feedstocks, such as methanol or formate. They colonize the phyllosphere (above-ground area) of plants, and many accumulate abundant carotenoid pigments. Methylotrophs have the capacity to take up and use a subset of the rare earth elements known as lanthanides. These metals can enhance one-carbon (methylotrophic) metabolism. Here, we investigated whether manipulating the metabolism enables and enhances terpene production. A carotenoid-deficient mutant potentially liberates carbon, which may contribute to bioproduct accumulation. To test this hypothesis, terpene-producing bacterial strains regulated by two distinct promoters were generated. Wildtype Methylobacterium extorquens, ∆Meta1_3665, a methylotrophic mutant lacking the carotenoid pathway, and an E. coli strain were transformed with an exogenous terpene pathway and grown both in the presence and absence of lanthanides. The extraction, and the comparison of analytical profiles, provided evidence that engineered cultured M. extorquens under control of a native, inducible methylotrophic promoter can yield the sesquiterpene patchoulol when supplemented with lanthanide. In contrast, using a moderate-strength constitutive promoter failed to give production. We demonstrated colonization of the phyllosphere with the engineered strains, supporting the future engineering of selected species of the plant microbiome and with promising implications for the synthetic biology of small molecules.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Characterization of lignin-degrading enzyme PmdC, which catalyzes a key step in the synthesis of polymer precursor 2-pyrone-4,6-dicarboxylic acid

Pyrone-2,4-dicarboxylic acid (PDC) is a valuable polymer precursor that can be derived from the microbial degradation of lignin. The key enzyme in the microbial production of PDC is 4-carboxy-2-hydroxymuconate-6-semialdehyde (CHMS) dehydrogenase, which acts on the substrate CHMS. We present the crystal structure of CHMS dehydrogenase (PmdC from Comamonas testosteroni) bound to the cofactor NADP, shedding light on its three-dimensional architecture, and revealing residues responsible for binding NADP. Using a combination of structural homology, molecular docking, and quantum chemistry calculations, we have predicted the binding site of CHMS. Key histidine residues in a conserved sequence are identified as crucial for binding the hydroxyl group of CHMS and facilitating dehydrogenation with NADP. Mutating these histidine residues results in a loss of enzyme activity, leading to a proposed model for the enzyme's mechanism. These findings are expected to help guide efforts in protein and metabolic engineering to enhance PDC yields in biological routes to polymer feedstock synthesis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Biochemical approaches for synthesis of performance-advantaged polymers from lignocellulosic biomass

Lignocellulose is an abundant renewable feedstock for production of sustainable fuels, chemicals, and materials. The structural complexity of lignocellulose provides key material properties and inspires the design of advanced materials. However, this same complexity also presents challenges for conversion of lignocellulosic biomass into new materials with consistent properties. Conventional physical and chemical strategies for valorization of biomass to new materials are often limited by the technical challenges of precisely manipulating complex feedstocks, sensitivity to feedstock variability, and associated costs. In contrast, biological approaches are capable of selectively manipulating complex architectures under mild conditions. Recent advances demonstrate the potential of biological and hybrid biochemical methods to tailor biomass-derived polymers and generate new materials. This review provides an overview of biological strategies to valorize lignocellulosic biomass into novel materials, highlighting approaches for in planta engineering, biochemical modification of natural biomass polymers, microbial funneling of deconstructed biomass, and direct biosynthesis of novel polymers. In combination, these approaches open new avenues for the synthesis of performance-advantaged materials from lignocellulosic biomass.

Qian, Liangyu [ORNL] (ORCID:0009000212029938)↗
DOE OSTI2022

microTrait: A Toolset for a Trait-Based Representation of Microbial Genomes

Remote sensing approaches have revolutionized the study of macroorganisms, allowing theories of population and community ecology to be tested across increasingly larger scales without much compromise in resolution of biological complexity. In microbial ecology, our remote window into the ecology of microorganisms is through the lens of genome sequencing. For microbial organisms, recent evidence from genomes recovered from metagenomic samples corroborate a highly complex view of their metabolic diversity and other associated traits which map into high physiological complexity. Regardless, during the first decades of this omics era, microbial ecological research has primarily focused on taxa and functional genes as ecological units, favoring breadth of coverage over resolution of biological complexity manifested as physiological diversity. Recently, the rate at which provisional draft genomes are generated has increased substantially, giving new insights into ecological processes and interactions. From a genotype perspective, the wide availability of genome-centric data requires new data synthesis approaches that place organismal genomes center stage in the study of environmental roles and functional performance. Extraction of ecologically relevant traits from microbial genomes will be essential to the future of microbial ecological research. Here, we present microTrait , a computational pipeline that infers and distills ecologically relevant traits from microbial genome sequences. microTrait maps a genome sequence into a trait space, including discrete and continuous traits, as well as simple and composite. Traits are inferred from genes and pathways representing energetic, resource acquisition, and stress tolerance mechanisms, while genome-wide signatures are used to infer composite, or life history, traits of microorganisms. This approach is extensible to any microbial habitat, although we provide initial examples of this approach with reference to soil microbiomes.

Karaoz, Ulas↗