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At least 973 records · Page 54
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Microbial Co-Culture Control Proteomics (MC-DP1)

Co-cultured S. elongatus PCC 7942 CscB/SPS and R. toruloides IFO0880 presented as an effective photosynthesis-driven biofuel production platform. The goal of this experiment was to understand the molecular mechanism of this co-culture system at redox post-translational modification level. The redox proteome of the co-cultured strains was compared to a mono-cultured S. elongatus in light or dark conditions. Samples were processed using a resin-assisted capture (RAC) workflow with TMT labeling to enrich and quantify modified cysteines at proteome level. The datasets were generated by a Q Exactive Plus Orbitrap Mass Spectrometer coupled with a Waters nanoAcquity UPLC, then searched by MSGF+ for downstream redox PTM analysis.

Source record↗
DOE OSTI2026

Genome-resolved insights into microbial diversity and elemental cycling in Winogradsky columns

We retained 18 MAGs with ≥50% completion and <10% contamination (i.e., at least medium quality). Of these, 10 had >90% completion and <5% contamination; however, only one (Paceibacteria Bin.003_MG) can be described as high-quality, as the others lacked a full suite of 5S, 16S, and 23S rRNA genes. To maximize the diversity of our recovered MAGs, we also retained one MAG (Chromatiaceae Bin.008_AM) with >40% (but less than 50%) completion and <5% contamination, as well as one (Rhodopseudomonas Bin.015_MK) with >90% completion and <20% (but>10%) contamination. Interestingly, significant chimerism was not detected in this MAG (40) , suggesting that the elevated contamination (20%) may instead reflect two closely related strains collapsing into a single bin. Consistent with this, contig coverage was bimodal, with roughly 17% of the assembly at ~115x and the remaining 83% at ~282x, while GC content remained uniform across both groups (~64%), arguing against contamination from a taxonomically distinct source.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Translating advances in microbial bioproduction to sustainable biotechnology

Advances in synthetic biology have radically changed our ability to rewire microorganisms and significantly improved the scalable production of a vast array of drop-in biopolymers and biofuels. The success of a drop-in bioproduct is contingent on market competition with petrochemical analogues and weighted upon relative economic and environmental metrics. While the quantification of comparative trade-offs is critical for accurate process-level decision making, the translation of industrial ecology to synthetic biology is often ambiguous and assessment accuracy has proven challenging. In this review, we explore strategies for evaluating industrial biotechnology through life cycle and techno-economic assessment, then contextualize how recent developments in synthetic biology have improved process viability by expanding feedstock availability and the productivity of microbes. By juxtaposing biological and industrial constraints, we highlight major obstacles between the disparate disciplines that hinder accurate process evaluation. The convergence of these disciplines is crucial in shifting towards carbon neutrality and a circular bioeconomy.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Prospective Study Reveals Host Microbial Determinants of Clinical Response to Fecal Microbiota Transplant Therapy in Type 2 Diabetes Patients

Increasing evidence shows that alterations in gut microbiome (GM) contribute to the development of type 2 diabetes mellitus (T2DM), and fecal microbiota transplantation (FMT) successfully treats various human diseases. However, the benefits of FMT therapy to T2DM patients remain unknown. We enrolled 17 patients with T2DM for nonblinded, one-armed intervention trial of FMT. A total of 20 healthy individuals were recruited as the baseline control. HbA1c% and metabolic parameter change were evaluated in 17 T2DM patients 12 weeks after they received FMT from healthy donors. The GM composition was characterized by 16S rRNA gene amplicon sequencing from fecal samples prior to and 12 weeks after FMT treatment. We found that the GM of T2DM patients was reconstituted by FMT. We observed a statistically significant decrease in HbA1c% (from 7.565 ± 0.148 to 7.190 ± 0.210, p<0.01), blood glucose (from 8.483 ± 0.497 to 7.286 ± 0.454 mmol/L, p<0.01), and uric acid (from 309.4 ± 21.5 to 259.1 ± 15.8 µmol/L, p<0.01) while a significant increase in postprandial C-peptide (from 4.503 ± 0.600 to 5.471 ± 0.728 ng/ml, p<0.01) at 12 weeks after FMT. Closely evaluating the changes in these assays, we found individual variability in response to FMT treatment. Out of 17 T2DM patients, 11 were found to significantly improve T2DM symptoms. The FMT responders have significantly higher levels of the family Rikenellaceae and the genus Anaerotruncus (family Ruminococcaceae) in their pretreated fecal in comparison to nonresponders, which could predict the clinical response with an area under the curve of 0.83. Our findings suggest that certain T2DM patients can potentially benefit from FMT, and the pretreated abundance of Rikenellaceae and Anaerotruncus in the fecal of patients may serve as potential biomarkers for selecting T2DM patients to receive FMT.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Harnessing selenocysteine to enhance microbial cell factories for hydrogen production

Hydrogen is a clean, renewable energy source, that when combined with oxygen, produces heat and electricity with only water vapor as a biproduct. Furthermore, it has the highest energy content by weight of all known fuels. As a result, various strategies have engineered methods to produce hydrogen efficiently and in quantities that are of interest to the economy. To approach the notion of producing hydrogen from a biological perspective, we take our attention to hydrogenases which are naturally produced in microbes. These organisms have the machinery to produce hydrogen, which when cleverly engineered, could be useful in cell factories resulting in large production of hydrogen. Not all hydrogenases are efficient at hydrogen production, and those that are, tend to be oxygen sensitive. Therefore, we provide a new perspective on introducing selenocysteine, a highly reactive proteinogenic amino acid, as a strategy towards engineering hydrogenases with enhanced hydrogen production, or increased oxygen tolerance.

08 HYDROGEN↗
DOE OSTI2026

Sampling Microbial Dynamics in the Salish Sea Estuary: Evaluating Methods to Capture Cyanobacteria and Cyanophage

Introduction: Picocyanobacteria from the genera Prochlorococcus and Synechococcus thrive across the globe in aquatic environments, have relatively small genomes, and have growth dynamics regulated by both viral interactions and abiotic conditions, making them excellent model organisms for exploring host-pathogencoevolution. Methods: We developed and refined methods to sample and sequence cyanobacteria, cyanophages, and measured features of their abiotic environment. Results: The protocol described herein can successfully discriminate large-cell eukaryotic organisms, but size fractionation of picocyanobacteria appears to be affected by the presence of free DNA, multicellular structures, and abundant tycheposons. Our preferred final protocol from this exploratory effort included a combination of in-line and single vacuum flask filtrations, which reduced filtration processing time by over threefold in some cases compared to other tested methods, such as a fully in-line sequence or in-site filtrations. We successfully extracted an average of approximately 400–1200 ng for all filter fractions, with some variations between kits. Discussion: The protocol described herein can successfully discriminate large-cell eukaryotic organisms, but size fractionation of picocyanobacteria appears to be affected by the presence of free DNA, multicellular structures, and abundant tycheposons.

Salish Sea↗
DOE OSTI2023

Effects of submerged macrophytes (Elodea nuttallii) on water quality and microbial communities of largemouth bass (Micropterus salmoides) ponds

Traditional aquaculture ponds are one of the most vulnerable ecosystems; thus, ecological aquaculture is increasingly valued for its beneficial ecological properties and ecosystem services. However, little is known about ecological aquaculture of largemouth bass with submerged vegetation. Here, we designed three ecological ponds of cultured largemouth bass with submerged macrophytes (the EM group) and three ponds with traditional aquaculture (the M group) to reveal the response of water quality, and phytoplankton and bacterial communities, to submerged macrophyte bioremediation during a 90-day culture period. We observed that Cyanobacterial outbreak occurred in the M group ponds from day 7 to the end of the experiment; however, there were no Cyanobacterial blooms in the EM group ponds throughout the culture period. Compared with the M group ponds, the EM group ponds, which had submerged hydrophytes, had significantly decreased concentrations of TP, TN, and COD Mn , but significantly increased DO concentrations throughout the experimental period. Moreover, ecological aquaculture with submerged macrophytes showed strong effects on the phytoplankton and bacterial community compositions. In particular, the M group ponds had higher phytoplankton density and mainly included Cyanobacteria, whereas the EM group had lower phytoplankton density and mainly included Chlorophyta. Moreover, higher alpha diversity, as determined by Ace and Simpson index values, was detected for bacterial communities in the EM group ponds. Furthermore, PCoA clearly grouped the bacterial communities according to the two culture modes throughout the culture period. These results indicate that ecological aquaculture with submerged macrophytes can improve water quality, control Cyanobacterial blooms, and affect the diversity and composition of bacterial communities. These valuable effects seem to be beneficial and consistent to maintaining aquaculture ecosystem stability.

Nie, Zhijuan↗
DOE OSTI2022

Lactiplantibacillus plantarum 0111 Protects Against Influenza Virus by Modulating Intestinal Microbial-Mediated Immune Responses

There are some limitations of traditional influenza vaccines concerning novel mutant strains. Therefore, it is particularly important to develop preventive means for antigen-unrelated types of influenza viruses. Recent studies have shown that probiotics can modulate the immune system and reduce the severity of viral infections. In this study, we investigated the potential of Lactiplantibacillus plantarum 0111 against influenza virus H9N2. Challenge experiments showed that L. plantarum 0111 pretreatments could effectively improve mice’s survival rate and weight loss and reduce the inflammatory cytokines IL-6 and TNF-α in the lungs and bronchoalveolar lavage fluid (BALF) along with the degree of lung and intestinal injury. FMT experiment demonstrates that the protective effect produced by L. plantarum 0111 is associated with gut microorganisms. In addition, 16S high-throughput sequencing of the mouse intestinal microbiota showed that L. plantarum 0111 remodeled the intestinal microbiota after H9N2 infection and maintained the gut microbiota balance. In a mouse model, the oral administration of L. plantarum 0111 increased IFN-β expression in the serum and BALF. At the same time, the transcript levels of IFN-β and related ISGs in the intestine and lungs of mice were also increased. In addition, the activation and polarization of T cells in mesenteric lymph nodes (MLNs) and the spleen were detected by flow cytometry, and the results showed that L. plantarum 0111 modulated cytokines in T cells and increased IgA expression in B cells in the MLNs and spleen. Thus, L. plantarum 0111 may improve gut microbiota-mediated immune responses and thus, resist infection by the influenza virus, and it could be used as an effective preventive measure against the influenza virus.

Xing, Jun-Hong↗
DOE OSTI2024

Control of hydrogen concentrations by microbial sulfate reduction in two contrasting anoxic coastal sediments

Introduction Molecular hydrogen is produced by the fermentation of organic matter and consumed by organisms including hydrogenotrophic methanogens and sulfate reducers in anoxic marine sediment. The thermodynamic feasibility of these metabolisms depends strongly on organic matter reactivity and hydrogen concentrations; low organic matter reactivity and high hydrogen concentrations can inhibit fermentation so when organic matter is poor, fermenters might form syntrophies with methanogens and/or sulfate reducers who alleviate thermodynamic stress by keeping hydrogen concentrations low and tightly controlled. However, it is unclear how these metabolisms effect porewater hydrogen concentrations in natural marine sediments of different organic matter reactivities. Methods We measured aqueous concentrations of hydrogen, sulfate, methane, dissolved inorganic carbon, and sulfide with high-depth-resolution and 16S rRNA gene assays in sediment cores with low carbon reactivity in White Oak River (WOR) estuary, North Carolina, and those with high carbon reactivity in Cape Lookout Bight (CLB), North Carolina. We calculated the Gibbs energies of sulfate reduction and hydrogenotrophic methanogenesis. Results Hydrogen concentrations were significantly higher in the sulfate reduction zone at CLB than WOR (mean: 0.716 vs. 0.437 nM H 2 ) with highly contrasting hydrogen profiles. At WOR, hydrogen was extremely low and invariant (range: 0.41–0.52 nM H 2 ) in the upper 15 cm. Deeper than 15 cm, hydrogen became more variable (range: 0.312–2.56 nM H 2 ) and increased until methane production began at ~30 cm. At CLB, hydrogen was highly variable in the upper 15 cm (range: 0.08–2.18 nM H 2 ). Ratios of inorganic carbon production to sulfate consumption show AOM drives sulfate reduction in WOR while degradation of organics drive sulfate reduction in CLB. Discussion We conclude more reactive organic matter increases hydrogen concentrations and their variability in anoxic marine sediments. In our AOM-dominated site, WOR, sulfate reducers have tight control on hydrogen via consortia with fermenters which leads to the lower observed variance due to interspecies hydrogen transfer. After sulfate depletion, hydrogen accumulates and becomes variable, supporting methanogenesis. This suggests that CLB’s more reactive organic matter allows fermentation to occur without tight metabolic coupling of fermenters to sulfate reducers, resulting in high and variable porewater hydrogen concentrations that prevent AOM from occurring through reverse hydrogenotrophic methanogenesis.

Microbiology↗
DOE OSTI2026

Beyond microbial abundance: metadata integration enhances disease prediction in human microbiome studies

Multiple studies have highlighted the interaction of the human microbiome with physiological systems such as the gut, immune, liver, and skin, via key axes. Advances in sequencing technologies and high-performance computing have enabled the analysis of large-scale metagenomic data, facilitating the use of machine learning to predict disease likelihood from microbiome profiles. However, challenges such as compositionality, high dimensionality, sparsity, and limited sample sizes have hindered the development of actionable models. One strategy to improve these models is by incorporating key metadata from both the human host and sample collection/processing protocols. This remains challenging due to sparsity and inconsistency in metadata annotation and availability. In this paper, we introduce a machine learning-based pipeline for predicting human disease states by integrating host and protocol metadata with microbiome abundance profiles from 68 different studies, processed through a consistent pipeline. Our findings indicate that metadata can enhance machine learning predictions, particularly at higher taxonomic ranks like Kingdom and Phylum, though this effect diminishes at lower ranks. Our study leverages a large collection of microbiome datasets comprising 11,208 samples, therefore enhancing the robustness and statistical confidence of our findings. This work is a critical step toward utilizing microbiome and metadata for predicting diseases such as gastrointestinal infections, diabetes, cancer, and neurological disorders.

Mathematics and Computing↗
DOE OSTI2020

Functional Imaging of Microbial Interactions With Tree Roots Using a Microfluidics Setup

Coupling microfluidics with microscopy has emerged as a powerful approach to study at cellular resolution the dynamics in plant physiology and root-microbe interactions (RMIs). Most devices have been designed to study the model plant Arabidopsis thaliana at higher throughput than conventional methods. However, there is a need for microfluidic devices which enable in vivo studies of root development and RMIs in woody plants. Here, we developed the RMI-chip, a simple microfluidic setup in which Populus tremuloides (aspen tree) seedlings can grow for over a month, allowing continuous microscopic observation of interactions between live roots and rhizobacteria. We find that the colonization of growing aspen roots by Pseudomonas fluorescens in the RMI-chip involves dynamic biofilm formation and dispersal, in keeping with previous observations in a different experimental set-up. Also, we find that whole-cell biosensors based on the rhizobacterium Bacillus subtilis can be used to monitor compositional changes in the rhizosphere but that the application of these biosensors is limited by their efficiency at colonizing aspen roots and persisting. These results indicate that functional imaging of dynamic root-bacteria interactions in the RMI-chip requires careful matching between the host plant and the bacterial root colonizer.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Microbial Communities in Model Seawater-Compensated Fuel Ballast Tanks: Biodegradation and Biocorrosion Stimulated by Marine Sediments

Some naval vessels add seawater to carbon steel fuel ballast tanks to maintain stability during fuel consumption. Marine sediments often contaminate ballast tank fluids and have been implicated in stimulating fuel biodegradation and enhancing biocorrosion. The impact of the marine sediment was evaluated in model ballast tank reactors containing seawater, fuel (petroleum-F76, Fischer–Tropsch F76, or a 1:1 mixture), and carbon steel coupons. Control reactors did not receive fuel. The marine sediment was added to the reactors after 400 days and incubated for another year. Sediment addition produced higher estimated bacterial numbers and enhanced sulfate reduction. Ferrous sulfides were detected on all coupons, but pitting corrosion was only identified on coupons exposed to FT-F76. Aerobic hydrocarbon-degrading bacteria increased, and the level of dissolved iron decreased, consistent with the stimulation of aerobic hydrocarbon degradation by iron. We propose that sediments provide an inoculum of hydrocarbon-degrading microbes that are stimulated by dissolved iron released during steel corrosion. Hydrocarbon degradation provides intermediates for use by sulfate-reducing bacteria and reduces the level of fuel components inhibitory to anaerobic bacteria. The synergistic effect of dissolved iron produced by corrosion, biodegradable fuels, and iron-stimulated hydrocarbon-degrading microbes is a poorly recognized but potentially significant biocorrosion mechanism.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Unveiling the Occupational Exposure to Microbial Contamination in Conservation–Restoration Settings

Assuring a proper environment for the fulfillment of professional activities is one of the Sustainable Development Goals and is contemplated in the One Health approach assumed by the World Health Organization. This particular study is applied to an often neglected sector of our society—the conservators/restorers—despite the many health issues reported by these professionals. Three different specialties (textiles, paintings and wood sculpture) and locations were selected for evaluation by placement of electrostatic dust cloths. After treatment of the samples, bacterial and fungal contamination were assessed, as well as mycotoxin determination, the presence of azole-resistant strains and cytotoxicity of the microorganisms encountered. Bacteria were only present in one of medias used and showed relatively low numbers. The highest level of contamination by fungi was identified in one of the textiles settings. The textile area also showed the highest variability for fungi. Aspergillus sp. are one indicator of possible environmental issues, and A. sections Fumigati and Circumdati were particularly relevant in two of the settings and identified in all of them. No mycotoxins were detected and the large majority of the fungi identified were non-cytotoxic. Overall, these can be considered low-contaminated environments but attention should be given to the Aspergillus sp. contamination. Additional studies are needed not only to make these results more robust, but also to test if the environmental sampling alone is the best approach in a setting where there is very little movement and dust displacement and where professionals are in very close proximity to the artefacts being treated, which may suggest the existence of a micro-atmosphere worth evaluating and comparing to the obtained results.

Viegas, Carla (ORCID:0000000215456479)↗
DOE OSTI2022

Soil Metabolomics Predict Microbial Taxa as Biomarkers of Moisture Status in Soils from a Tidal Wetland

We present observations from a laboratory-controlled study on the impacts of extreme wetting and drying on a wetland soil microbiome. Our approach was to experimentally challenge the soil microbiome to understand impacts on anaerobic carbon cycling processes as the system transitions from dryness to saturation and vice-versa. Specifically, we tested for impacts on stress responses related to shifts from wet to drought conditions. We used a combination of high-resolution data for small organic chemical compounds (metabolites) and biological (community structure based on 16S rRNA gene sequencing) features. Using a robust correlation-independent data approach, we further tested the predictive power of soil metabolites for the presence or absence of taxa. Here, we demonstrate that taking an untargeted, multidimensional data approach to the interpretation of metabolomics has the potential to indicate the causative pathways selecting for the observed bacterial community structure in soils.

16S rRNA gene↗
DOE OSTI2022

Elucidating the Role of Biofilm-Forming Microbial Communities in Fermentative Biohydrogen Process: An Overview

Amongst the biofuels described in the literature, biohydrogen has gained heightened attention over the past decade due to its remarkable properties. Biohydrogen is a renewable form of H 2 that can be produced under ambient conditions and at a low cost from biomass residues. Innovative approaches are continuously being applied to overcome the low process yields and pave the way for its scalability. Since the process primarily depends on the biohydrogen-producing bacteria, there is a need to acquire in-depth knowledge about the ecology of the various assemblages participating in the process, establishing effective bioaugmentation methods. This work provides an overview of the biofilm-forming communities during H 2 production by mixed cultures and the synergistic associations established by certain species during H 2 production. The strategies that enhance the growth of biofilms within the H 2 reactors are also discussed. A short section is also included, explaining techniques used for examining and studying these biofilm structures. The work concludes with some suggestions that could lead to breakthroughs in this area of research.

59 BASIC BIOLOGICAL SCIENCES↗