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At least 541 records · Page 30

Plant Cell Wall Loosening by Expansins

Expansins comprise an ancient group of cell wall proteins ubiquitous in land plants and their algal ancestors. During cell growth, they facilitate passive yielding of the wall's cellulose networks to turgor-generated tensile stresses, without evidence of enzymatic activity. Expansins are also implicated in fruit softening and other developmental processes and in adaptive responses to environmental stresses and pathogens. The major expansin families in plants include α-expansins (EXPAs), which act on cellulose-cellulose junctions, and β-expansins, which can act on xylans. EXPAs mediate acid growth, which contributes to wall enlargement by auxin and other growth agents. The genomes of diverse microbes, including many plant pathogens, also encode expansins designated expansin-like X. Expansins are proposed to disrupt noncovalent bonding between laterally aligned polysaccharides (notably cellulose), facilitating wall loosening for a variety of biological roles.

Cell Biology↗

ATCCfinder - Download and Search the ATCC Genome Portal

Much strain-specific sequence data exists in research conducted before the deployment of large sequencing repositories, making it challenging to identify and validate the identity of strains used in these studies through bioinformatics and phenotyping. The American Type Culture Collection (ATCC) is an organization that sells a wide variety of microbes with strain-level taxonomy classification and associated sequenced reference genomes. Currently, ATCC does not provide a method for searching for sequence similarity between a query sequence and their database of reference genomes. Here I propose the software ATCCfinder, which utilizes ATCC application interface software (API) to generate query-able databases from ATCC Genome resources.

Koehler, Samuel↗

Multi-tube-OD-reader [SWR-24-126]

This software accompanies an NREL-designed machine for observing changes in optical density of 16 biological samples growing in Hungate tubes. It involves hardware & app for Multi-Tube OD Reader. Our Multi-Tube-OD-Reader device is based on the TubeOD reader (linked below), but with a housing to maximize throughput. This repository contains the schematics for 3D printing an enclosure, a parts list for constructing, and the code for controlling the 16-tube, in-line optical density monitoring device. This device and software are particularly useful for researchers studying microbes that grow well in Hungate tubes, but are not amenable to growth in microplate readers. Related publication: https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.790576/full

Hebdon, Skyler↗

Host Onboarding Tool (HObT) v1.0.0

The Host OnBoarding Tool (Hobt) is a publicly accessible, web-based software designed to organize and share information about microbial hosts under development at the Agile BioFoundry (ABF). It streamlines the assessment, tracking, and sharing of information related to microbial host development and provides a centralized platform where users can rapidly evaluate hosts' readiness for various bio processes. HObT leverages the Tier System, a standardized host development framework that organizes and assesses microbial hosts based on their readiness for biomanufacturing. Each tier outlines key targets—including genetic tools, growth conditions, omics data, and predictive models—needed to transform new or emerging microbes into established production platforms. By applying clear criteria for advancement, the Tier System helps users quickly evaluate each organism's current development status, identify gaps in available knowledge or tools, and prioritize future strain improvement efforts. Through its user-friendly interface, HObT encourages contributions of new data and insights from researchers, fostering collaboration and accelerating host development. By providing structured guidance for microbial strain advancement, HObT and the Tier System support more systematic, rapid, and cost-effective development of non-traditional microbial hosts, ultimately enhancing the efficiency and impact of biomanufacturing research and applications.

Plahar, Hector [Lawrence Berkeley National Laborat↗

Identification of carbohydrate gene clusters obtained from in vitro fermentations as predictive biomarkers of prebiotic responses

Prebiotic fibers are non-digestible substrates that modulate the gut microbiome by promoting expansion of microbes having the genetic and physiological potential to utilize those molecules. Although several prebiotic substrates have been consistently shown to provide health benefits in human clinical trials, responder and non-responder phenotypes are often reported. These observations had led to interest in identifying, a priori, prebiotic responders and non-responders as a basis for personalized nutrition. In this study, we conducted in vitro fecal enrichments and applied shotgun metagenomics and machine learning tools to identify microbial gene signatures from adult subjects that could be used to predict prebiotic responders and non-responders. Using short chain fatty acids as a targeted response, we identified genetic features, consisting of carbohydrate active enzymes, transcription factors and sugar transporters, from metagenomic sequencing of in vitro fermentations for three prebiotic substrates: xylooligosacharides, fructooligosacharides, and inulin. A machine learning approach was then used to select substrate-specific gene signatures as predictive features. These features were found to be predictive for XOS responders with respect to SCFA production in an in vivo trial. Our results confirm the bifidogenic effect of commonly used prebiotic substrates along with inter-individual microbial responses towards these substrates. We successfully trained classifiers for the prediction of prebiotic responders towards XOS and inulin with robust accuracy (≥ AUC 0.9) and demonstrated its utility in a human feeding trial. Overall, the findings from this study highlight the practical implementation of pre-intervention targeted profiling of individual microbiomes to stratify responders and non-responders.

59 BASIC BIOLOGICAL SCIENCES↗

RhizoMAP: a comprehensive, nondestructive, and sensitive platform for metabolic imaging of the rhizosphere

Elucidating the intricate structural organization and spatial gradients of biomolecular composition within the rhizosphere is critical to understanding important biogeochemical processes, which include the mechanisms of root-microbe interactions for maintaining sustainable plant ecosystem services. While various analytical methods have been developed to assess the spatial heterogeneity within the rhizosphere, a comprehensive view of the fine distribution of metabolites within the root-soil interface has remained a significant challenge. This is primarily due to the difficulty of maintaining the original spatial organization during sample preparation without compromising its molecular content.

59 BASIC BIOLOGICAL SCIENCES↗

Time-series metagenomics reveals changing protistan ecology of a temperate dimictic lake

Abstract Background Protists, single-celled eukaryotic organisms, are critical to food web ecology, contributing to primary productivity and connecting small bacteria and archaea to higher trophic levels. Lake Mendota is a large, eutrophic natural lake that is a Long-Term Ecological Research site and among the world’s best-studied freshwater systems. Metagenomic samples have been collected and shotgun sequenced from Lake Mendota for the last 20 years. Here, we analyze this comprehensive time series to infer changes to the structure and function of the protistan community and to hypothesize about their interactions with bacteria. Results Based on small subunit rRNA genes extracted from the metagenomes and metagenome-assembled genomes of microeukaryotes, we identify shifts in the eukaryotic phytoplankton community over time, which we predict to be a consequence of reduced zooplankton grazing pressures after the invasion of a invasive predator (the spiny water flea) to the lake. The metagenomic data also reveal the presence of the spiny water flea and the zebra mussel, a second invasive species to Lake Mendota, prior to their visual identification during routine monitoring. Furthermore, we use species co-occurrence and co-abundance analysis to connect the protistan community with bacterial taxa. Correlation analysis suggests that protists and bacteria may interact or respond similarly to environmental conditions. Cryptophytes declined in the second decade of the timeseries, while many alveolate groups (e.g., ciliates and dinoflagellates) and diatoms increased in abundance, changes that have implications for food web efficiency in Lake Mendota. Conclusions We demonstrate that metagenomic sequence-based community analysis can complement existing efforts to monitor protists in Lake Mendota based on microscopy-based count surveys. We observed patterns of seasonal abundance in microeukaryotes in Lake Mendota that corroborated expectations from other systems, including high abundance of cryptophytes in winter and diatoms in fall and spring, but with much higher resolution than previous surveys. Our study identified long-term changes in the abundance of eukaryotic microbes and provided context for the known establishment of an invasive species that catalyzes a trophic cascade involving protists. Our findings are important for decoding potential long-term consequences of human interventions, including invasive species introduction.

59 BASIC BIOLOGICAL SCIENCES↗

Dataset for "A Microfluidic Spore Chamber for Long-Term Imaging of Single-Spore Hyphal Development"

Understanding the life cycle of fungal spores is essential for elucidating their roles in pathogenesis, dispersal, and survival. However, studying spore development under controlled, spatially defined conditions remains challenging. Here, we present the Spore Chamber, a custom-built microfluidic platform engineered for parallel trapping and long-term imaging of individual spores under defined media conditions, enabling real-time visualization of hyphal development. Using Aspergillus fumigatus as a model organism, we demonstrate that sparse trapping of individual spores within size-matched trap geometries enables long-term time-lapse imaging of key developmental stages, including germination, polarized hyphal elongation, branching, and conidiophore formation. To assess the device’s capacity to resolve morphogenetic responses to exogenous signals, we introduced lipochitooligosaccharides (LCOs) and short-chain chitooligosaccharides (COs). Rhizobium-derived, non-sulfated LCO (nsLCO) mixtures induced enhanced secondary branching (hyperbranching), a response not previously reported in A. fumigatus under these signal conditions, to our knowledge, whereas sulfated LCOs and CO4 did not significantly alter branching patterns. In addition, long-term confinement and imaging revealed rare developmental morphologies previously described primarily in mutant strains, including split conidiophore formation, elongated phialides, microcyclic conidiation, and chlamydospore development. Together, these results establish the Spore Chamber as a targeted microfluidic platform for single-spore phenotyping and long-term developmental analysis, with applications in fungal biology, chemical signaling studies, and host–microbe interaction research. Videos of the observed phenomena are included in this data set.

59 BASIC BIOLOGICAL SCIENCES↗

Sub-daily virus sampling at the Bermuda Atlantic Time Series reveals diel and depth-structured population dynamics without community-level shifts

Ocean microbes contribute to biogeochemical cycles and ecosystem function, but they do so under top-down pressure imposed by viruses. While viruses are increasingly understood spatially and beginning to be incorporated into predictive modeling, high-frequency ocean virus dynamics remain understudied due to methodological challenges. Here we sampled stratified Bermuda Atlantic Time Series (BATS) waters for 112 hours at sub-daily 4- (surface) or 12- (deep chlorophyll maximum) hour intervals, purified viral particles from these samples, sequenced their metagenomes, and used the resulting data to characterize high-frequency virus community dynamics. Aggregated community diversity metrics changed with depth, but were not statistically significant temporally at a fixed location. However, finer-scale population-level analyses revealed both depth and temporal change, including physicochemical depth-driven differences and, in surface waters, thousands of viral populations that exhibited statistically significant diel rhythms. Statistical analyses revealed three main archetypes of temporal dynamics that themselves differed in abundance patterns, host predictions, viral taxonomy, and gene functions. Among these, highlights include viruses resembling an archetype with a night peaking pattern in activity that include an over-representation of viruses that putatively infect Prochlorococcus, a phototrophic cyanobacteria. Together, these efforts provide baseline community- and population-scale short-time-frame observations relevant to future climate state modeling.

Carrillo, Alfonso [The Ohio State University, Colu↗

Enrichment of root-associated Streptomyces strains in response to drought is driven by diverse functional traits and does not predict beneficial effects on plant growth

The genus Streptomyces has consistently been found enriched in drought-stressed plant root microbiomes, yet the ecological basis and functional variation underlying this enrichment at the strain and isolate level remain unclear. Using two 16S rRNA sequencing methods with different levels of taxonomic resolution, we confirmed drought-associated enrichment (DE) of Streptomyces in field-grown sorghum roots and identified five closely related but distinct amplicon sequence variants (ASVs) belonging to the genus with variable drought enrichment patterns. From a culture collection of sorghum root endophytes, we selected 12 Streptomyces isolates representing these ASVs for phenotypic and genomic characterization. Whole-genome sequencing revealed substantial variation in gene content, even among closely related isolates, and exometabolomic profiling showed distinct metabolic responses to media supplemented with drought- versus well-watered root tissue. Traits linked to drought survival, including osmotic stress tolerance, siderophore production, and carbon utilization, varied widely among isolates and were not phylogenetically conserved. Using a broader panel of 48 Streptomyces, we demonstrate that DE scores, determined through mono-association experiments in gnotobiotic sorghum systems, showed high variability and lacked correlation with plant growth promotion. Pangenome-wide association identified orthogroups involved in osmolyte transport (e.g., proP) and membrane biosynthesis (e.g., fabG) as positively associated with DE, though most associations lacked phylogenetic signal. Collectively, these results demonstrate that Streptomyces DE is not a conserved genus-level trait but is instead strain-specific and functionally heterogeneous. Furthermore, DE in the root microbiome was shown not to predict beneficial effects on plant growth. This work underscores the need to resolve functional traits at the strain level and highlights the complexity of microbe-host-environment interactions under abiotic stress.

Fonseca-Garcia, Citlali↗

Competition and cooperation: The plasticity of bacterial interactions across environments

Bacteria live in diverse communities, forming complex networks of interacting species. A central question in bacterial ecology is whether species engage in cooperative or competitive interactions. But this question often neglects the role of the environment. Here, we use genome-scale metabolic networks from two different open-access collections (AGORA and CarveMe) to assess pairwise interactions of different microbes in varying environmental conditions (provision of different environmental compounds). By computationally simulating thousands of environments for 10,000 pairs of bacteria from each collection, we found that most pairs were able to both compete and cooperate depending on the availability of environmental resources. This modeling approach allowed us to determine commonalities between environments that could facilitate the potential for cooperation or competition between a pair of species. Namely, cooperative interactions, especially obligate, were most common in less diverse environments. Further, as compounds were removed from the environment, we found interactions tended to degrade towards obligacy. However, we also found that on average at least one compound could be removed from an environment to switch the interaction from competition to facultative cooperation or vice versa. Together our approach indicates a high degree of plasticity in microbial interactions in response to the availability of environmental resources.

Biochemistry & Molecular Biology↗

A miniaturized feedstocks-to-fuels pipeline for screening the efficiency of deconstruction and microbial conversion of lignocellulosic biomass

Sustainably grown biomass is a promising alternative to produce fuels and chemicals and reduce the dependency on fossil energy sources. However, the efficient conversion of lignocellulosic biomass into biofuels and bioproducts often requires extensive testing of components and reaction conditions used in the pretreatment, saccharification, and bioconversion steps. This restriction can result in a significant and unwieldy number of combinations of biomass types, solvents, microbial strains, and operational parameters that need to be characterized, turning these efforts into a daunting and time-consuming task. Here we developed a high-throughput feedstocks-to-fuels screening platform to address these challenges. The result is a miniaturized semi-automated platform that leverages the capabilities of a solid handling robot, a liquid handling robot, analytical instruments, and a centralized data repository, adapted to operate as an ionic-liquid-based biomass conversion pipeline. The pipeline was tested by using sorghum as feedstock, the biocompatible ionic liquid cholinium phosphate as pretreatment solvent, a “one-pot” process configuration that does not require ionic liquid removal after pretreatment, and an engineered strain of the yeast Rhodosporidium toruloides that produces the jet-fuel precursor bisabolene as a conversion microbe. By the simultaneous processing of 48 samples, we show that this configuration and reaction conditions result in sugar yields (~70%) and bisabolene titers (~1500 mg/L) that are comparable to the efficiencies observed at larger scales but require only a fraction of the time. We expect that this Feedstocks-to-Fuels pipeline will become an effective tool to screen thousands of bioenergy crop and feedstock samples and assist process optimization efforts and the development of predictive deconstruction approaches.

09 BIOMASS FUELS↗

Bacteria isolated from the grape phyllosphere capable of degrading guaiacol, a main volatile phenol associated with smoke taint in wine

Recent wildfires near vineyards in the Pacific United States have caused devastating financial losses due to smoke taint in wine. When wine grapes (Vitis vinifera) are exposed to wildfire smoke, their berries absorb volatile phenols derived from the lignin of burning plant material. Volatile phenols are released during the winemaking process giving the finished wine an unpleasant, smokey, and ashy taste known as smoke taint. Bacteria are capable of undergoing a wide variety of metabolic processes and therefore present great potential for bioremediation applications in many industries. In this study, we identify two strains of the same species that colonize the grape phyllosphere and are able to degrade guaiacol, a main volatile phenol responsible for smoke taint in wine. We identify the suite of genes that enable guaiacol degradation in Gordonia alkanivorans via RNAseq of cells growing on guaiacol as a sole carbon source. Additionally, we knockout guaA, a cytochrome P450 gene involved in the conversion of guaiacol to catechol; ΔguaA cells cannot catabolize guaiacol in vitro, providing evidence that GuaA is necessary for this process. Furthermore, we analyze the microbiome of berries and leaves exposed to smoke in the vineyard to investigate the impact of smoke on the grape microbial community. We found smoke has a significant but small effect on the microbial community, leading to an enrichment of several genera belonging to the Bacilli class. Collectively, this research shows that studying microbes and their enzymes has the potential to identify novel tools for alleviating smoke taint.

Castro, Claudia [United States Department of Agric↗

Biochar-compost-based controlled-release nitrogen fertilizer intended for an active microbial community

Nitrogen (N) fertilizers in agriculture suffer losses by volatilization of N to the air, surface runoff and leaching into the soil, resulting in low N use efficiency (NUE) (< 50%) and raising severe environmental pollutions. Controlled- release nitrogen fertilizers (CRNFs) can control the release of N nutrients to NUE in crop production. Different methods were used to develop new CRNFs. However, different CRNF technologies are still underdeveloped due to inadequate controlling on N releasing time and/or unsustainable diffusion. The study on the influences of CRNF processing parameters on microbial conditions are lacking when the CRNFs composed of various bio-ingredients such as biochar, composts, and biowaste. The complexity of processing methods, material biodegradability, and other physical properties make current CRNFs of questionable value in agricultural production. This research aims to develop a novel biochar-compost-based controlled-release urea fertilizer (BCRUF) to preserve microbial properties carried by the compost. The BCRUF was synthesized by pelletizing the 50:50 (dry, wt/wt) mixture of biochar and compost. BCRUF was loaded with urea and then spray-coated with polylactic acid (PLA). The releasing time of two types of BCRUFs, coated and uncoated with PLA, for 80% of N release in water was up to 6 h at three different temperatures (4, 23, and 40 °C), compared to conventional urea fertilizer and commercial environmentally smart N (ESN) fertilizer. The releasing time of coated BCRUF for 80% N release in soil was up to 192 h (8 days). Fourier-transform infrared spectroscopy (FTIR) analysis revealed that no new functional groups were found in the release solution, indicating no new chemical hazards generated. The differential scanning calorimetry (DSC) tests also verified that its thermal stability could be up to 160 °C. The microbe populations in the BCRUF pellets were reduced after the pelleting and drying processes in BCRUF fabrication, but a few bacteria can endure in the air-drying process. BCRUF pellets soaked in water for 4 days retained some bacteria. The BCRUF showed very promising characteristics to improve NUE and sustainability in agricultural production.

58 GEOSCIENCES↗

EXCHANGE Campaign 2 - Microbial Biomass Collapse (EC2-MBC): Carbon Availability Under Prolonged Flooding in Mid-Atlantic and Great Lakes Coastal Ecosystems

Our collective research focus is on investigating the interaction between carbon availability and microbial demands during prolonged flooding. Through laboratory experiments utilizing freshly collected soil samples from diverse transition zone environments, we aim to simulate flooding and understand the mechanisms governing carbon cycling under anoxic conditions. Our primary objective is to elucidate how carbon becomes available to microbes and how they utilize it, discerning between maintenance and investment processes. By examining soils from regions with differing native redox conditions, our aim is to gain comprehensive insights into carbon dynamics across various soil types. Future data types will be added to the ESS-DIVE data package as they are completed and will be version-controlled in the Change History section of EC2_MBC_README.pdf. This data package includes: EC2_MBC_README.pdf flmd.csv dd.csv EC2_SampleIdentificationKey.csv EC2_SoilMoistureKey.csv Processed_GHGFlux_Entisols.csv Processed_GHGFlux_Inceptisols.csv Processed_GHGFlux_Ultisols.csv Processed_Porewater_Iron_II.csv Processed_Porewater_Nutrients.csv Processed_Porewater_Sulfate.csv Processed_Probe_Measurements.csv Processed_Soil_HydrolyticEnzymes.csv Processed_Soil_MicrobialCN.csv Processed_Soil_NPOC_TN_SaltExtracted.csv Processed_Soil_NPOC_TN_WaterExtracted.csv Processed_Soil_Nutrients_OlsenPExtracted.csv Processed_Soil_Nutrients_SaltExtracted.csv Processed_Soil_Nutrients_WaterExtracted.csv Processed_DO_Probe.zip Processed_Temperature_Probe.zip

Carbon Cycling↗

Microbial community data from throughfall exclusion experiment: Metadata, SI, community composition, LefSe, and FunGuilR data tables from PARCHED Panama tropical forest soils, 2024-2025

Soil contains more carbon (C) than terrestrial vegetation and the atmosphere combined, with some of the largest terrestrial C stocks in tropical rainforests. Soil microbes decompose organic matter, playing a vital role in the storage or loss of soil C. With climate change, drought conditions are predicted to increase in many tropical regions, including both chronic drying and extended drought, potentially influencing these processes. This project explored the effects of chronic and seasonal drying on soil microbial communities across four distinct tropical forests in a long-term drying experiment. We investigated the effects of a chronic drying manipulation on soil microbial community abundance and variation across different forests and seasons. We also compared findings with previously published data from these forests after short-term drying. This project used soils from a long-term drying experiment established in 2018 across four seasonal lowland forests in Panama. Soils were collected from 0 – 10 cm depths during three seasonal periods in control and drying plots in 2024 and 2025 from a total of 32 plots (n = 4 per forest per treatment). The forests varied in baseline rainfall and soil fertility. We calculated alpha and beta diversity indices and compared taxonomic community composition. We found significant biogeographic variation in microbial diversity and taxonomy, with significant differences across the forests and significant effects of the drying treatment. Metadata and sample IDs are within Metadata_16S.csv and Metadata_ITS.csv. Relative abundance tables of every sample at every season are shown in the Excel workbooks 16S Relative Abundance.xlsx and ITS Relative Abundance.xlsx. They are then also shown in CSV files by each taxonomic level. Linear discriminant analysis effect size (LefSe) tables are shown for the full 16S and ITS datasets (n = 96), subsets for every site at every season (n = 8), and then for the forests with each plot merged by season (n = 8). FunGuildR data table of ITS data is uploaded.

Bacteria↗

Effects of hurricane disturbance and increased temperature on carbon cycling and storage of a Puerto Rican forest: a mechanistic investigation of above- and belowground processes (Final Technical Report)

The overall goal of the Tropical Responses for Altered Climate Experiment (TRACE) is to assess the effects of increasing temperature on tropical plant and soil carbon fluxes and storage as the forest recovers from major hurricane disturbance that occurred in September 2017. Ultimately, we aimed to reduce uncertainty and increase confidence with which tropical forests are represented in Earth System models to make more accurate global forecasts of future climate. We focused on both above- and belowground processes and explored temperature controls over critical aspects of carbon and nutrient cycling for tropical plants, soil, and microbes. TRACE is located in a wet tropical forest in the Luquillo Experimental Forest close to the USDA Forest Service Sabana Field Research Station in Luquillo, Puerto Rico. The warming treatment consists of six 4.7 m diameter plots. Three of the plots receive infrared warming and three have the same infrastructure but are not warmed (using ‘dummy’ heaters). Each plot was monitored from 2018-2023 to investigate two major questions: 1) Are there legacy effects of prior warming on forest recovery following hurricane disturbance? 2) Will the trajectory of forest recovery following disturbance be affected by warmer temperatures? Concurrent soil incubation experiments were conducted to enable more controlled mechanistic investigations of temperature response on microbial function. In sum, our goal was to use this novel climate manipulation experiment (the only of its kind in any tropical forest) and once-in-a-lifetime chance to assess how temperature and hurricane disturbance interact to affect coupled biogeochemical cycling in a tropical forest.

54 ENVIRONMENTAL SCIENCES↗

Investigation of encapsulin nanocompartment systems as a scaffold for biomaterials synthesis in Rhodococcus species

Engineered protein compartmentalization systems hold significant promise to enhance reaction efficiencies through co-localization, concentration, and sequestration of biosynthetic pathways. As such, they have the potential to enable the bioproduction of next generation bioproducts and biomaterials in genetically engineered microbes in support of DOE’s mission to build a strong bioeconomy. Among systems of particular interest are protein nanocompartment systems called encapsulins that are natively produced by a variety of bacteria including those with a high potential for bioproduction. This ECRP project is focused on understanding how encapsulins can be used to enhance the biosynthesis of next-generation biomaterials in Rhodococcusspecies. Specifically, we seek: (1) to probe the mechanistic basis for how these compartments are regulated, biosynthesized, and maintained, and (2) to engineer these systems to achieve new biosynthetic functions (e.g., CdS nanoparticle biosynthesis). We anticipate that this work will establish encapsulin compartmentalization systems as a means of improving yields and enabling biosynthetic routes toward new biomaterials, thus advancing the U.S. bioeconomy.

59 BASIC BIOLOGICAL SCIENCES↗