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At least 73 records · Page 4

Systems-Level Modeling for CRISPR-Based Metabolic Engineering

The CRISPR-Cas system has enabled the development of sophisticated, multigene metabolic engineering programs through the use of guide RNA-directed activation or repression of target genes. To optimize biosynthetic pathways in microbial systems, we need improved models to inform design and implementation of transcriptional programs. Recent progress has resulted in new modeling approaches for identifying gene targets and predicting the efficacy of guide RNA targeting. Genome-scale and flux balance models have successfully been applied to identify targets for improving biosynthetic production yields using combinatorial CRISPR-interference (CRISPRi) programs. Here, the advent of new approaches for tunable and dynamic CRISPR activation (CRISPRa) promises to further advance these engineering capabilities. Once appropriate targets are identified, guide RNA prediction models can lead to increased efficacy in gene targeting. Developing improved models and incorporating approaches from machine learning may be able to overcome current limitations and greatly expand the capabilities of CRISPR-Cas9 tools for metabolic engineering.

59 BASIC BIOLOGICAL SCIENCES↗

Disturbance–diversity relationships of microbial communities change based on growth substrate

Disturbance events can impact ecological community dynamics. Understanding how communities respond to disturbances and how those responses can vary is a challenge in microbial ecology. In this study, we grew a previously enriched specialized microbial community on either cellulose or glucose as a sole carbon source and subjected them to one of five different disturbance regimes of varying frequencies ranging from low to high. Using 16S rRNA gene amplicon sequencing, we show that the community structure is largely driven by substrate, but disturbance frequency affects community composition and successional dynamics. When grown on cellulose, bacteria in the genera Cellvibrio, Lacunisphaera, and Asticcacaulis are the most abundant microbes. However, Lacunisphaera is only abundant in the lower disturbance frequency treatments, while Asticcacaulis is more abundant in the highest disturbance frequency treatment. When grown on glucose, the most abundant microbes are two Pseudomonas sequence variants and a Cohnella sequence variant that is only abundant in the highest disturbance frequency treatment. Communities grown on cellulose exhibited a greater range of diversity (1.95–7.33 Hill 1 diversity) that peaks at the intermediate disturbance frequency treatment or one disturbance every 3 days. Communities grown on glucose, however, ranged from 1.63 to 5.19 Hill 1 diversity with peak diversity at the greatest disturbance frequency treatment. These results demonstrate that the dynamics of a microbial community can vary depending on substrate and the disturbance frequency and may potentially explain the variety of diversity–disturbance relationships observed in microbial systems.

59 BASIC BIOLOGICAL SCIENCES↗

Remodeling BioSentinel’s Microbial Metabolism Measurement System

BioSentinel, the first biological CubeSat beyond low Earth orbit, will investigate how Saccharomyces cerevisiae responds to ionizing radiation using optical measurements of a colorimetric metabolic indicator dye (alamarBlue). To map optical data to more detailed metabolic measurements, a microbial culture system for ground testing was designed consisting of a 400 mL beaker and a rubber stopper with pass-through holes for its five sensor probes (electrical conductivity, pH, oxidation-reduction potential, dissolved oxygen, optical density). The initial design had several drawbacks. It was only partially reusable due to its one-time sealants: Teflon tape and parafilm. A steady increase in oxygen levels within the sensor’s testingdata indicated the design was not sufficiently airtight. Degradation of the rubber stopper’s elasticity due to sterilization and reinsertion of the probes led to poor robustness and eventual replacement. The vessel’s large headspace didn’t reproduce flight conditions and a large culture volume required more reagents. The system has been redesigned to contain a rigid, biocompatible polycarbonate disc lid that allows for threaded inserts. The culture vessel’s height will be reduced from 110 mm to 65 mm to decrease overhead space and material costs. A more reliable seal will be achieved with a gasket and clamps. The optical probe records absorbance at four wavelengths to characterize cell density and alamarBlue dye ratios. A pneumatically operated plunger draws media through the hollow interior of the probe. Currently, deformation of the silicone on the plunger causes asymmetrical movement and a drift from its initial state. Designs are being developed to limit the plunger’s travel for a more accurate measurement cycle. The remodeled system is under construction and will be tested for leaks and accuracy. The measurements collected will be used to provide additional insight into the optical data returned from the BioSentinel mission.

Astrobiology↗

Cyanobacterial mats: Microanalysis of community metabolism

The microbial communities in two sites were studied using several approaches: (1) light microscopy; (2) the measurement of microprofiles of oxygen and sulfide at the surface of the microbial mat; (3) the study of diurnal variation of oxygen and sulfides; (4) in situ measurement of photosynthesis and sulfate reduction and study of the coupling of these two processes; (5) measurement of glutathione in the upper layers of the microbial mat as a possible oxygen quencher; (6) measurement of reduced iron as a possible intermediate electron donor along the established redoxcline in the mats; (7) measurement of dissolved phosphate as an indicator of processes of break down of organic matter in these systems; and (8) measurement of carbon dioxide in the interstitial water and its delta C-13 in an attempt to understand the flow of CO2 through the systems. Microbial processes of primary production and initial degradation at the most active zone of the microbial mat were analyzed.

Cohen, Y.↗

Site Selection for Mars Exopaleontology in 2001

The microbial fossil record encompasses a wide range of information, including cellular remains, stromatolites, biofabrics, trace fossils, biominerals and chemofossils. The preservation of fossils is strongly influenced by the physical, chemical and biological factors of the environment which, acting together, ultimately determine the types of information that will be captured and retained in the rock record. The critical factor in assessing the suitability of a site for a microbial fossil record is the paleoenvironment. The reconstruction of ancient sedimentary environments usually requires the integration of a wide variety of geological information, including the shape, geometry and internal structure of sedimentary deposits, their mineralogy, and geochemistry. For Mars, much of our knowledge about past environments is based on orbital imaging of geomorphic features. This evidence provides an important context and starting point for site selection. However, our knowledge of the martian surface is quite limited, and a major goal of the upcoming exploration effort is to reconstruct the history of Martian volatiles, climate, and hydrology as a context for the exploration for past or present life. Mineralogical mapping from orbit will be an important key in this effort. In exploring for evidence of past life, terrestrial experience suggests that the long-term preservation of biological information as fossils occurs under a fairly narrow range of geological conditions that are well known to paleontologists (1). In detrital sedimentary systems, microbial fossilization is favored by rapid burial in fine-grained, clay-rich sediments. In chemical sedimentary systems, preservation is enhanced by rapid entombment in fine-grained chemical precipitates. For long term preservation, host rocks must be composed of stable minerals that resist chemical weathering, and which form an impermeable matrix and closed chemical system that can protect biosignatures from alteration during subsequent diagenetic change or metamorphism. In this context, host rocks composed of highly ordered, chemically-stable mineral phases, like silica (forming cherts) or phosphate (forming phosphorites), are especially favored. Such lithologies tend to have very long crustal residence times and (along with carbonates and shales), are the most common host rocks for the Precambrian microfossil record on Earth. If we assume that a subsurface hydrosphere has been present throughout martian history, then life could have originated there at any time, perhaps emerging at the surface periodically when climate changes, induced by external forcing or endogenous processes (e.g. volcanism), allowed liquid water to exist at the surface. The recent discovery of subsurface chemolithoautotrophic organisms which are capable of synthesizing organic substrates from C02 and H2 liberated from the aqueous weathering of basalt, is especially. relevant as a model for martian life. While a subsurface habitable zone may yet exist on Mars, access to such environments will likely require drilling to depths of several kilometers. Given the technological challenge of deep drilling, this is unlikely to occur prior to human missions. So, even if there is extant life on Mars today in subsurface habitats, it may be much easier to find its fossil counterparts in ancient deposits exposed at the surface. In exploring for a fossil record in subsurface environments on Mars there are several geological situations that may provide access to the appropriate materials. These include 1) ejecta from impact craters, 2) talus slopes, debris flows or alluvial fans developed below the walls of deep canyons, and 3) the deposits of outflood channels. Examples of aqueous mineral deposits of formed in subsurface environments that could harbor a microbial fossil record include such things as cements in detrital sedimentary rocks, low temperature diagenetic minerals deposited in veins, or filling vesicles in volcanic rocks, and hydrothermal deposits formed below the upper temperature limit for life (about 160 degrees C). There are many sites within the present latitudinal constraints for the 2001 mission (15 deg S to 30 deg N) that meet these requirements. But the practical problem with these kinds of deposits is that they tend to be disseminated, making up only a small percentage of a host rock. Even with mineralogical information provided by the Thermal Emission Spectrometer (TES) presently in orbit around Mars, predicting their occurrence ahead of time may be quite difficult. The deposits of surficial aqueous sedimentary systems are likely to provide the largest targets for site selection in 2001. Of these, the deposits of hydrothermal systems (subaerial and subaqueous thermal springs) have been discussed previously. It is likely that hydrothermal systems were widespread on Mars early in its history and a number of common geo-tectonic settings on Mars are likely to have hosted hydrothermal activity. Most of these are represented within the latitudinal constraints presently identified for 2001. However, the deposits of surface spring systems are likely to be difficult to find as well. On Earth, exposure areas for hydrothermal spring mounds are typically a few square kms, less than a single TES pixel. But such deposits may be quite abundant within some volcanic terrains, It is estimated, for example, that between 15-20% of the floor of Yellowstone caldera is covered by thermal spring deposits. In such abundances, subaerial sinters could well be detected by TES. Where exposed, the shallow subsurface portions of these systems may be quite a lot larger (perhaps tens of square kms), although (as noted above) mineralization may be finely disseminated in the basement rock, making remote detection more difficult. Paleolake Basins. There are a large number of potential paleolake basins on Mars (inclusive of impact craters and volcanic calderas) that have been previously identified using Viking images. Most of these lie in the southern highlands beyond the l5 deg S constraint for 2001. However, deposits of paleolakes may offer the largest and most easily identified exopaleontological targets from orbit. Based on a variety of arguments, some workers have suggested that there was once an ancient ocean on the northern plains, and some sites of interest (potential shoreline terraces) fall within the 30 deg N constraint. From a paleontological standpoint the most interesting places of this type are terminal paleolake basins which are likely to have been both saline and alkaline. Models by Schaefer suggest such environments could be widespread on Mars. The conditions in terminal lake basin settings favor widespread chemical sedimentation, an important condition for microbial fossilization. Important lithological targets for a microbial fossil record in terminal lake basins include spring-deposited carbonates, shoreline cements, a wide variety of evaporite minerals and fine-grained detrital sediments including shales, marls, and water-lain volcanic ash deposits. In developing a strategy to explore for ancient hydrothermal deposits on Mars, we can learn from the methods that have been developed by explorationists to explore for economic mineral deposits on Earth. Due to their simple mineralogy, hydrothermal deposits can often be detected using remote sensing methods. Common thermal spring mineral assemblages include silica, carbonate, and various metallic oxides and sulfides. But there are also a number of diagnostic silicate minerals, including clays, formed by the hydrothermal alteration of country rocks. These hydrothermal minerals have characteristic spectral signatures that could be detected from Mars orbit using high resolution infrared remote sensing methods. In playa lake settings, evaporite deposits often form a predictable "bull's eye" pattern with carbonates being deposited in marginal basin areas, and sulfates and halides occurring progressively more basinward. The floors of some impact craters on Mars, such as "White Rock" and Bequeral Crater (see Oxia Palus NE, Site 148), have floor deposits that could be evaporites, inclusive of carbonates. Evaporite minerals possess characteristic spectral signatures in the infrared and could similarly be identified from Mars orbit using high resolution remote sensing methods. Clearly, utilization of TES data will be important for optimizing site selection for Exopaleontology, and every effort should be made to benefit from that data before a final decision is made.

Farmer, Jack↗

Ecosystems and Networks Integrated with Genes and Molecular Assemblies (ENIGMA): Integrating Metabolomics into Environmental Systems Biology

Our research endeavors entail ambitious objectives to explore the communities of microorganisms and quantify their chemical input and output to determine specific biochemical activity. To achieve these scientific aims, we are creating advanced algorithms to scrutinize extensive experimental data produced through high-throughput technologies, enabling us to elucidate how biological functions are influenced by environmental factors on various scales, and how microbial systems alter their surroundings. By studying the metabolic interdependence of bacterial communities for their survival and reproductive prosperity, we can gain insights into their biochemical capabilities. To accomplish this, we employed cutting-edge mass spectrometry-based techniques and metabolic fingerprinting methods, which offer high chemical specificity and sensitivity. As our efforts progressed, the project evolved into ENIGMA, encompassing a broader range of technology development, including untargeted metabolomics and its implementation for system-level organism analysis.

54 ENVIRONMENTAL SCIENCES↗

Capturing the microbial volatilome: an oft overlooked 'ome'

Among the diverse metabolites produced by microbial communities, some are volatile. Volatile organic compounds (VOCs) are vigorously cycled by microbes as metabolic substrates and products and as signaling molecules. Yet, current microbial metabolomic studies predominantly focus on nonvolatile metabolites and overlook VOCs, which therefore represent a missing component of the metabolome. Advances in VOC detection now allow simultaneous observation of the numerous VOCs constituting the ‘volatilome’ of microbial systems. Here, we present a roadmap for integrating and advancing VOC and other ‘omics approaches and highlight the potential for realtime VOC measurements to help overcome limitations in discrete ‘omics sampling. Including volatile metabolites in metabolomics, both conceptually and in practice, will build a more comprehensive understanding of microbial processes across ecological communities.

59 BASIC BIOLOGICAL SCIENCES↗

Biomanufacturing and Scale-Up: Pathways to Biochemicals, Biofuels, and Biomaterials

Advancing the bioeconomy requires the development of large-scale microbial bioprocesses capable of converting waste carbon streams into biofuels, biochemicals, and biomaterials at industrially relevant scales. While biomanufacturing has been successfully demonstrated at the laboratory scale for a wide range of chemicals, only a few have reached industrial-scale production. This is partly due to the inherent complexity of microbial systems, which rely on living cells with intricate metabolic pathways that are highly sensitive to environmental changes, making large-scale production difficult to optimize and predict. As a result, scaling-up bioprocesses remains a high-stakes challenge that requires deeper exploration. This involves integrating feedstock and microbial selection, upstream and downstream processes, and computational modelling, among other research efforts. Bulk and specialty chemicals derived from biological processes also face competition from fossil-based production routes, which have been refined through decades of technological advancements. While biologically derived molecules may offer more environmentally friendly production pathways than traditional chemical manufacturing, their widespread adoption depends on achieving cost parity-or superiority-relative to fossil-based methods. This emphasizes the importance of holistic research, including techno-economic analyses and life cycle assessments, to ensure both economic viability and environmental sustainability. This editorial and special issue explores state-of-the-art strategies for converting waste carbon sources into valuable products. It discusses how enzymes, single microbes (e.g., extremophiles), and microbiomes (e.g., through division of labor) can be integrated with upstream and downstream process innovations-such as consolidated bioprocessing and in situ product recovery-to improve the efficiency and scalability of biomanufacturing. The editorial further highlights the role of computational modelling in understanding, predicting, and controlling bioprocess performance across scales, and concludes by emphasizing the importance of techno-economic modelling to identify technologies that can move to market.

09 BIOMASS FUELS↗

Biological Carbon Sequestration for Climate and Soil Health

The United States recently launched the Net Zero World Initiative on decarbonization. As temperatures and sea levels rise, strong action is needed to mitigate high atmospheric CO 2 levels. In response to this need, a joint workshop between the US Department of Energy’s Oak Ridge National Laboratory (ORNL) and Lawrence Berkeley National Laboratory (LBNL) was convened to assess the challenges and opportunities within biological carbon (C) capture. The virtual workshop on Biological Carbon Sequestration for Climate and Soil Health focused on three aspects of biological C capture research: natural systems, engineered systems, and modeling. For this workshop, the scope of natural systems included unmanaged (e.g., grasslands, wetlands, natural forests) and managed (e.g., agricultural lands, commercial forests, forest biofuels) ecosystems. The engineered systems group covered topics in genetically modified plants and microbes, synthetic microbiomes, and altered plant–microbe interactions for enhancing C capture, storage, and utilization. The modeling group focused on computational tools and data collection to predict and assess the effectiveness of new biocarbon sequestration advances. Participant expertise included plant and microbial systems biology, synthetic biology, soil biogeochemistry, and techno-economic analysis. Together, participants outlined key scientific advances in support of biological C capture and storage. Among the major findings of the meeting were the need to better measure C flux within natural, agricultural, and fabricated ecosystems for experimentation; better understand the role of soil composition, plant roots, and the rhizosphere (i.e., the soil surrounding the plant root) in the underground storage of organic C; and design plant–microbe systems for maximal C storage.

54 ENVIRONMENTAL SCIENCES↗

Advances in systems metabolic engineering of autotrophic carbon oxide-fixing biocatalysts towards a circular economy

High levels of anthropogenic CO 2 emissions are driving the warming of global climate. If this pattern of increasing emissions does not change, it will cause further climate change with severe consequences for the human population. On top of this, the increasing accumulation of solid waste within the linear economy model is threatening global biosustainability. The magnitude of these challenges requires several approaches to capture and utilize waste carbon and establish a circular economy. Microbial gas fermentation presents an exciting opportunity to capture carbon oxides from gaseous and solid waste streams with high feedstock flexibility and selectivity. Here we discuss available microbial systems and review in detail the metabolism of both anaerobic acetogens and aerobic hydrogenotrophs and their ability to utilize C1 waste feedstocks. More specifically, we provide an overview of the systems-level understanding of metabolism, key metabolic pathways, scale-up opportunities and commercial successes, and the most recent technological advances in strain and process engineering. Finally, we also discuss in detail the gaps and opportunities to advance the understanding of these autotrophic biocatalysts for the efficient and economically viable production of bioproducts from recycled carbon.

59 BASIC BIOLOGICAL SCIENCES↗

Space Biophysics: Accomplishments, Trends, Challenges

Physics and biology are inextricably linked. All the chemical and biological processes of life are dutifully bound to follow the rules and laws of physics. In space, these physical laws seem to turn on their head and biological systems, from microbes to humans, adapt and evolve in myriad ways to cope with the changed physical influences of the space environment. Gravity is the most prominent change in space that influences biology. In microgravity, the physical processes of sedimentation, density-driven convective flow, influence of surface tension and fluid pressure profoundly influence biology at the molecular and cellular level as well as at the whole-body level. Gravity sensing mechanisms are altered, structural and functional components of biology (such as bone and muscle) are reduced and changes in the way fluids and gasses behave also drive the way microbial systems and biofilms grow as well as the way plants and animals adapt. The radiation environment also effects life in space. Solar particle events and high energy cosmic radiation can cause serious damage to DNA and other biomolecules. The results can cause mutation, cellular damage or death, leading to health consequences of acute radiation damage or long-term health consequences such as increased cancer risk. Space Biophysics is the study and utilization of physical changes in space that cause changes in biological systems. The unique physical environment in space has been used successfully to grow high-quality protein crystals and 3D tissue cultures that could not be grown in the presence of unidirectional gravitational acceleration here on Earth. All biological processes that change in space have their root in a biophysical alteration due to microgravity and/or the radiation environment of space. In order to fully-understand the risks to human health in space and to fully-understand how humans, plants, animals and microbes can safely and effectively travel and eventually live for long periods beyond the protective environment of Earth, the biophysical properties underlying these changes must be studied, characterized and understood. This lecture reviews the current state of NASA biophysics research accomplishments and identifies future trends and challenges for biophysics research on the International Space Station and beyond.

Space Biophysics: Accomplishments↗

Metaoptics Enabled Multifunctional Imaging

Despite the fact that most microorganisms occupy two- and three-dimensional space in heterogeneous arrangements and in proximity to other microorganisms of different species, much of our current knowledge about their metabolic processes is derived from homogenizing, then analyzing, the chemical content of cultures containing a single microbial species. This project addressed this fundamental dichotomy by developing a set of optical imaging principles combining multiple new technologies. The imaging strategies developed in this project combine metaoptics structures with active in situ nanoscale control of the chemical environment and applied them to a microbial system, Myxococcus xanthus, with particular relevance to the DoE mission. The combination of metaoptical architectures and nanoscale control over the molecular environment enables: (a) precise control over the electromagnetic (EM) field at length scales smaller than the wavelength of light; (b) control of the interaction of the EM field with critical molecular systems in DOE relevant microbes; (c) control over the chemical environment – especially the presence and quantity of reactive oxygen species (ROS) that can affect redox homeostasis; and (d) the ability to ask new kinds of questions not accessible to ‘omics’ approaches or standard methods of biological imaging. These capabilities are applicable to detailed studies of metabolic pathways in microbes and to lignocellulosic biomass deconstruction. To accomplish these objectives, we pursued two over-arching technical goals: (1) the development of new metaoptics-enabled approaches to imaging and spectroscopic characterization; and (2) the development of tools to control the chemical environment of a microbial sample with nanometer-scale precision. Goal 1 was addressed through the design, fabrication, and characterization of new metasurfaces capable of super-resolution imaging through extreme confinement of the optical field. Goal 2 was addressed by controlling the redox potential on the nanoscale in microbial communities and characterizing their effect on intrinsic bacterial fluorophores which act as molecular sentinels and through characterization of soluble factors secreted by Myxococcus xanthus by confocal Raman imaging. The optical imaging/sensing approaches developed here make it possible to use these powerful new imaging and sensing modalities in metabolic studies by making it possible to visualize and track the spatial and temporal expression patterns of natural or engineered pathways in microorganisms.

09 BIOMASS FUELS↗

Gaia: An AI-enabled genomic context–aware platform for protein sequence annotation

Protein sequence similarity search is fundamental to biology research, but current methods are typically not able to consider crucial genomic context information indicative of protein function, especially in microbial systems. Here, we present Gaia (Genomic AI Annotator), a sequence annotation platform that enables rapid, context-aware protein sequence search across genomic datasets. Gaia leverages gLM2, a mixed-modality genomic language model trained on both amino acid sequences and their genomic neighborhoods to generate embeddings that integrate sequence-structure-context information. This approach allows for the identification of functionally and/or evolutionarily related genes that are found in conserved genomic contexts, which may be missed by traditional sequence- or structure-based search alone. Gaia enables real-time search of a curated database comprising more than 85 million protein clusters from 131,744 microbial genomes. We compare the homolog retrieval performance of Gaia search against other embedding and alignment-based approaches. We provide Gaia as a web-based, freely available tool.

Jha, Nishant↗

Predictive CRISPR-mediated gene downregulation for enhanced production of sustainable aviation fuel precursor in Pseudomonas putida

CRISPR interference (CRISPRi) has emerged as a valuable tool for redirecting metabolic flux to enhance bioproduction. However, its application is often constrained by two challenges: (i) rationally identifying effective gene targets for downregulation and (ii) efficiently constructing multiplexed CRISPRi systems. In this study, we address both challenges by integrating a computational prioritization tool with a versatile assembly method for building multiplexed CRISPRi systems. FluxRETAP (Flux-Reaction Target Prioritization) accurately identified gene targets whose knockdown led to substantial increase of isoprenol titers in Pseudomonas putida KT2440, outperforming a conventional non-computational, pathway-guided target selection. The highest isoprenol titer of nearly 1.5 g/L was achieved by knocking down PP_4118 (a gene encoding α-ketoglutarate dehydrogenase). The use of VAMMPIRE (Versatile Assembly Method for MultiPlexing CRISPRi-mediated downREgulation) enabled accurate assembly of CRISPRi constructs containing up to five sgRNA arrays, reducing context dependency and achieving uniform, position-independent gene downregulation. The integration of FluxRETAP and VAMMPIRE has the potential to advance metabolic engineering by rapidly identifying CRISPRi-mediated knockdowns and knockdown combinations that enhance bioproduction titers, with potential applicability to other microbial systems.

CRISPR interference↗

A distinct subpopulation of membrane vesicles in Pseudomonas putida is enriched in enzymes for lignin catabolism

Bacterial membrane vesicles (MVs) mediate diverse microbial processes and are emerging as powerful biomedical tools, but MV population heterogeneity remains an open question. Here, we separate, enumerate, and characterize two MV populations from the soil bacterium Pseudomonas putida during growth with or without lignin-derived carbon, a major carbon source from plant cells in the rhizosphere. Small MVs (MV-S, diameter ~100 nm) were produced from all cultures, whereas large MVs (MV-L, diameter ~300 nm) were observed during the late stationary phase of lignin cultivations. MV-S contained selectively packaged proteins with diverse physiological functions, whereas the MV-L proteome was smaller and largely enriched in outer membrane proteins. Interestingly, enzymes known to mediate the catabolism of lignin-derived aromatic compounds were enriched in MV-S. Overall, this study highlights the need for careful consideration of MV populations in microbial systems.

59 BASIC BIOLOGICAL SCIENCES↗

Chapter 14: Dynamic Flux Analysis: An Experimental Approach of Fluxomics

Metabolic flux analysis represents an essential perspective to understand cellular physiology and offers quantitative information to guide pathway engineering. A valuable approach for experimental elucidation of metabolic flux is dynamic flux analysis, which estimates the relative or absolute flow rates through a series of metabolic intermediates in a given pathway. It is based on kinetic isotope labeling experiments, liquid chromatography-mass spectrometry (LC-MS), and computational analysis that relate kinetic isotope trajectories of metabolites to pathway activity. Herein, we illustrate the mathematic principles underlying the dynamic flux analysis and mainly focus on describing the experimental procedures for data generation. This protocol is exemplified using cyanobacterial metabolism as an example, for which reliable labeling data for central carbon metabolites can be acquired quantitatively. This protocol is applicable to other microbial systems as well and can be readily adapted to address different metabolic processes.

BASIC BIOLOGICAL SCIENCES↗

Biotechnological advances in algae-based foods: applications in nutrition and microbiome health

Algae are a sustainable, nutrient-rich resource with growing potential in food biotechnology. Their ability to thrive in diverse environments makes them a promising alternative to conventional crops. Rich in proteins, essential fatty acids, and bioactive compounds, algae support the development of functional foods, including plant-based meat and seafood alternatives. Advances in synthetic biology and fermentation have enhanced algal nutrient profiles and enabled novel applications. Algae-derived polysaccharides, such as alginate, fucoidan, laminarin, and porphyran, exhibit prebiotic effects by modulating the gut microbiota and promoting SCFA production. Enzymatic hydrolysis efficiently produces bioactive oligosaccharides, while engineered microbial systems support scalable production. Algae also enable synbiotic food development by serving as both prebiotic substrates and probiotic carriers.

Yu, Sora↗

RB-TnSeq identifies genetic targets for improved tolerance of Pseudomonas putida towards compounds relevant to lignin conversion

We report lignin-derived mixtures intended for bioconversion commonly contain high concentrations of aromatic acids, aliphatic acids, and salts. The inherent toxicity of these chemicals places a significant bottleneck upon the effective use of microbial systems for the valorization of these mixtures. Pseudomonas putida KT2440 can tolerate stressful quantities of several lignin-related compounds, making this bacterium a promising host for converting these chemicals to valuable bioproducts. Nonetheless, further increasing P. putida tolerance to chemicals in lignin-rich substrates has the potential to improve bioprocess performance. Accordingly, we employed random barcoded transposon insertion sequencing (RB-TnSeq) to reveal genetic determinants in P. putida KT2440 that influence stress outcomes during exposure to representative constituents found in lignin-rich process streams. The fitness information obtained from the RB-TnSeq experiments informed engineering of strains via deletion or constitutive expression of several genes. Namely, ΔgacAS, ΔfleQ, ΔlapAB, ΔttgR::P tac :ttgABC, Ptac:PP_1150:PP_1152, ..delta..relA, and ΔPP_1430 mutants showed growth improvement in the presence of single compounds, and some also exhibited greater tolerance when grown using a complex chemical mixture representative of a lignin-rich chemical stream. Overall, this work demonstrates the successful implementation of a genome-scale screening tool for the identification of genes influencing stress tolerance against notable compounds within lignin-enriched chemical streams, and the genetic targets identified herein offer promising engineering targets for improving feedstock tolerance in lignin valorization strains of P. putida KT2440.

09 BIOMASS FUELS↗