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At least 811 records · Page 45
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Automated Bacterial Identification and Morphological Feature Analysis in Low‐Dose Cryo‐EM Using YOLOv11

Bacteria rapidly adapt to environmental cues through morphological and ultrastructural changes that correlate with physiology and behavior. Cryogenic transmission electron microscopy (cryo‐TEM) can capture these phenotypic changes in near‐native, vitrified states, but manual analysis of low‐dose micrographs is labor intensive and limits throughput. Here, we present an end‐to‐end workflow that combines low‐dose cryo‐TEM imaging with a YOLOv11‐based instance‐segmentation model to automatically identify bacteria and quantify key structural features directly from the micrographs. This workflow enables (i) robust bacterial localization and counting from low‐magnification atlas/montage images, (ii) automated measurements of cell‐envelope (outer–inner membrane) thickness and anisotropy from higher‐magnification views, and (iii) detection and quantification of bacteria–flagella interactions, including overlap length and curvature metrics for interacting versus noninteracting flagella. Using Pantoea sp. YR343 grown under distinct media conditions, we show that the automated measurements agree with manual annotations while substantially reducing analysis time. Together, these tools provide a practical framework for scalable bacterial identification and quantitative phenotyping in low‐dose cryo‐TEM datasets and establish a foundation for extending cryo‐TEM image analysis toward higher‐throughput studies of microbial heterogeneity and biointerfaces.

YOLOv11↗
DOE OSTI2021

A probabilistic economic and environmental impact assessment of a cyanobacteria-based biorefinery

Microbial based biofuels represent a potential promising solution as an environmentally favorable transportation fuel. Cyanobacteria have many of the same advantages as microalgae: ability for rapid growth in otherwise non-arable regions, suitability for genetic engineering, and simple nutritional needs. Additionally, cyanobacteria can be engineered to secrete valuable co-products that can be harvested independent from the produced biomass. However, little work has been done to identify the processes and the economic and environmental impacts associated with a large-scale cyanobacteria-to-fuels facility. The present study is a concurrent techno-economic and life cycle assessment of a facility that generates fuels and methyl laurate, an oleochemical, from the cyanobacterial species Synechocystis sp. PCC 6803. Here, the biorefinery model includes all aspects of cultivation, separation of the secreted methyl laurate, biomass harvesting and fuel processing via hydrothermal liquefaction (HTL) of the dewatered biomass. The assessments leverage Monte Carlo analysis (MCA) to address uncertainty and variability inherent in the most significant input parameters, replacing them with probabilistic functions. For the facility configuration producing both fuels and the oleochemical co-product, the MCA average minimum fuel selling price (MFSP) is $\$2.47$ per decimeter (dm 3 ) or $\$9.34$ per gallon of gasoline equivalent (gge) with the corresponding average global warming potential determined to be 118 g CO 2 -eq-MJ -1 . The case producing only fuels results in an MCA average MFSP of $\$2.01$-(dm 3 ) -1 ($\$7.60$-gge -1 ) and an average environmental impact of 100 g CO 2 -eq-MJ -1 . These results are compared to static optimistic and conservative scenario analysis estimates, illustrating the over- and under-estimation of outcomes associated with non-stochastic methods. Suggested facility improvements include increases in pond productivity of both the biomass and methyl laurate oil production, as well as improvements to carbon utilization and bio-crude yield from HTL processing.

09 BIOMASS FUELS↗
DOE OSTI2020

Mercury Methylation and Soil Organic Matter Degradation in Incubations with Added Acetate, Isotope-Labeled Mercury, and Selective Microbial Inhibitors, Teller and Council Sites, Seward Peninsula, 2018-2019

This dataset provides the results of laboratory soil microcosm incubation experiments conducted under anaerobic conditions with added acetate, isotope-labeled mercury, and selective microbial inhibitors (2-bromoethanesulfonate and sodium molybdate). The microcosms contained soil collected in August 2018 from the NGEE Arctic Teller Road Site at mile marker 27 (TL_MM27) near Intensive Site 9 (TL_IS_9) and from the Council Road Site (CN_MM71). Incubations were conducted at 8°C for 180 days (Teller incubations) or 60 days (Council incubations). The microcosm headspace was sampled at designated intervals for greenhouse gas concentrations, then destructively harvested and extracted using ultrapure water and 0.1 M KCl for analysis of the porewater geochemistry. This dataset contains one pdf, two csv data files, and one zipped file with raw data.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research.The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Impact of Variable Gas Mixtures on Bubble Size Distribution and Mass Transfer in Gas Fermentation Reactors

Gas fermentation has emerged as a promising new technology for the generation of fuels and chemicals from mixtures of greenhouse and energy rich gas streams (CO2/CH4/H2/CO) via microbial bioreaction. Example pathways include biomethanation (CO2/H2 to CH4), biogas upgrading, CO fermentation and wet-waste conversion. Effective Gas-liquid mass-transfer is an important physical phenomenon that determines the design and scale-up of these systems. There is currently a knowledge-gap regarding bubble-size distributions when using a mixture of gases with vastly different properties, which can have a significant impact on overall mass-transfer. For example, hydrogen bubbles are more buoyant compared to other relatively heavier gases (CO2/CH4/CO), resulting in a large distribution of residence times and bubble sizes. This work therefore develops a deeper understanding of bubble dynamics and interphase mass transfer in such heterogenous gas mixtures through well-resolved computational models. We use a detailed multiphase computational-fluid-dynamics (CFD) model to study the impact of gas-mixtures on overall mass-transfer in bubble column and air-lift reactors. The CFD tool previously developed by the authors (1) for simulating aerobic fermentation reactors at scale is used in this study. The Reynolds-averaged mass, momentum, energy, and species transport equations are solved for interpenetrating gas and liquid phase in this model. We use a population balance-based bubble-size-distribution model that is validated against small-scale experiments in our solver. Results pertaining to multiple simulations of gas-fermentation reactors are presented where gas mixtures with varying compositions of CO2/CH4/CO/H2 are imposed at the sparger boundaries. The spatio-temporal variations in bubble-size distribution and mass transfer coefficient is analyzed for varying superficial velocities and gas-compositions for varying sizes of bubble-column and airlift reactors.

BIOMASS FUELS,MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Distinct Fracture Mineralogy That is Out of Equilibrium With Modern Groundwaters Provides Important Context for Subsurface Life

Rock fracture surfaces in the crust are essential habitat for microorganisms. Fracture‐groundwater interfaces provide physical substrates for biofilm growth and are sources of carbon, nutrients, and electron donors and acceptors. To better understand geochemical processes impacting fracture surfaces and the subsurface microbiome, we identified fractures in archived rock cores from the Soudan formation, which is known to host saline groundwaters and isolated microbial communities dependent on rock‐water interactions. Cores with open fractures were thin sectioned and studied via electron microprobe and synchrotron X‐ray fluorescence microprobe. Most fracture surfaces had mineralogy distinct from that of the bulk rock. Chlorite minerals were abundant on fracture surfaces and had elemental compositions suggesting deposition during late‐stage hydrothermal alteration. Fracture‐lining chlorites likely limit access to iron oxide and sulfide minerals that are active in subsurface biogeochemical cycles. Calcium‐rich rinds were also observed along fracture edges. These rinds were too thin and poorly ordered to be identified via light microscopy or X‐ray diffraction; however, Ca K‐edge micro‐X‐ray absorption near‐edge structure spectroscopy identified them as carbonates, minerals not observed in the bulk rock. Thermodynamic modeling shows that carbonate precipitation is largely unfavorable in Soudan groundwaters, indicating that fracture edge conditions differed from those in modern water samples. Because of the low carbon concentrations in Soudan groundwaters, carbonate rinds likely play an important role in subsurface carbon cycling and may mark fracture surfaces that once hosted biofilms. Overall, this study suggests that fracture alteration can both play an active role in and suppress rock‐water interactions essential to subsurface life.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Pyrodictium abyssi AbpX reveals a calcium-responsive family of microbial biomatrix proteins that form thermostable hydrogels

Evolutionary pressure on microbial communities propagating under extreme environmental conditions often results in unique structural adaptations to promote cell survival. In this work, we report an investigation of AbpX, a biomatrix protein identified in cultures of the hyperthermophilic archaeon Pyrodictium abyssi. Under ex vivo and in vitro conditions, AbpX assembles into a paracrystalline lattice composed of semiflexible fibrils. CryoEM analysis of recombinant AbpX fibrils reveals that the precursor protein polymerizes through donor strand complementation (DSC), a process previously reported for chaperone-usher fimbriae in Gram-negative bacteria. Unlike the latter DSC protein polymers, AbpX undergoes chaperone-free polymerization in the presence of calcium ions, which are sequestered at the donor strand-acceptor groove interface between protomers in the fibril. Using a combination of cryoEM and crystallographic information, a structural model is proposed for the AbpX lattice that provides insight into its potential role in biofilm formation. These findings suggest that calcium ion coordination may contribute to fibril assembly and preorganize fibrils for incorporation into the protein lattice. Bioinformatic analysis indicates that AbpX exemplifies a distinct and broadly distributed clade of calcium ion responsive biomatrix proteins within the TasA superfamily that can be fabricated into hydrogel biomaterials in vitro under environmentally benign conditions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Elucidation of complex respiratory chains: a straightforward strategy to monitor electron transfer between cytochromes

Abstract Cytochromes are electron transfer (ET) proteins essential in various biological systems, playing crucial roles in the respiratory chains of bacteria. These proteins are particularly abundant in electrogenic microorganisms and are responsible for the efficient delivery of electrons to the cells’ exterior. The capability of sending electrons outside the cells open new avenues to be explored for emerging biotechnological applications in bioremediation, microbial electrosynthesis, and bioenergy fields. To develop these applications, it is critical to identify the different redox partners and to elucidate the stepwise ET along the respiratory paths. However, investigating direct ET events between proteins with identical features in nearly all spectroscopic techniques is extremely challenging. Nuclear magnetic resonance (NMR) spectroscopy offers the possibility to overcome this difficulty by analysing the alterations of the spectral signatures of each protein caused by electron exchange events. The uncrowded NMR spectral regions containing the heme resonances of the cytochromes display unique and distinct signatures in the reduced and oxidized states, which can be explored to monitor ET within the redox complex. In this study, we present a strategy for a fast and straightforward monitorization of ET between c-type cytochromes, using as model a triheme periplasmic cytochrome and a membrane-associated monoheme cytochrome from the electrogenic bacterium Geobacter sulfurreducens. The comparison between the 1D 1H NMR spectra obtained for samples containing the two cytochromes and for samples containing the individual proteins clearly demonstrated a unidirectional ET within the redox complex. This strategy provides a simple and straightforward means to elucidate complex biologic respiratory ET chains.

Morgado, Leonor (ORCID:0000000237605180)↗
DOE OSTI2023

A bacterial sensor taxonomy across earth ecosystems for machine learning applications

Microbial communities have evolved to colonize all ecosystems of the planet, from the deep sea to the human gut. Microbes survive by sensing, responding, and adapting to immediate environmental cues. This process is driven by signal transduction proteins such as histidine kinases, which use their sensing domains to bind or otherwise detect environmental cues and “transduce” signals to adjust internal processes. We hypothesized that an ecosystem’s unique stimuli leave a sensor “fingerprint,” able to identify and shed insight on ecosystem conditions. To test this, we collected 20,712 publicly available metagenomes from Host-associated, Environmental, and Engineered ecosystems across the globe. We extracted and clustered the collection’s nearly 18M unique sensory domains into 113,712 similar groupings with MMseqs2. We built gradient-boosted decision tree machine learning models and found we could classify the ecosystem type (accuracy: 87%) and predict the levels of different physical parameters (R2 score: 83%) using the sensor cluster abundance as features. Feature importance enables identification of the most predictive sensors to differentiate between ecosystems which can lead to mechanistic interpretations if the sensor domains are well annotated. To demonstrate this, a machine learning model was trained to predict patient’s disease state and used to identify domains related to oxygen sensing present in a healthy gut but missing in patients with abnormal conditions. Moreover, since 98.7% of identified sensor domains are uncharacterized, importance ranking can be used to prioritize sensors to determine what ecosystem function they may be sensing. Furthermore, these new predictive sensors can function as targets for novel sensor engineering with applications in biotechnology, ecosystem maintenance, and medicine.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Targeted Biomining and Machine Learning Approaches in Critical Minerals Revealed by a Biogeochemical Survey of a Coal Mine Drainage Remediation System

Abandoned coal mine drainage (AMD) remediation systems in Pennsylvania can concentrate critical minerals and materials (CMM) at levels comparable to mining-grade ores. Remediation systems have varying engineering features and are open to the environment, resulting in diverse microbial colonization and seasonal climate influences that may impact CMM speciation. The location of CMMs, the types of bacterial communities tolerant of these pollutant conditions, and the influence of localized climate on CMM rich remediation systems are not well characterized. Through a one-year spatiotemporal survey of biogeochemistry at a remediation system, we have initiated the process to address these questions. Rare Earth Elements (REE) ranged 180-1,200 ppm and greater than 1,500 bacterial ASVs were classified via 16S sequencing. Analyses indicate biogeochemical differences are heavily influenced by engineering features. Additionally, REE precipitants correlate strongly with the elements Al, Cu, Zn, Be, and U. Unearthing these trends has refined our line of inquiry to explore biological mining opportunities more closely with these metals. Furthermore, we created a Machine Learning Model for predicting AMD REE content, with 89% accuracy, using the data from this study and several others. Further training data is required to create a more reputable model. Recently, global research efforts have prioritized modeling work or the use of the few historical surveys to design experiments. Through our data, we challenge this approach, emphasizing the importance of expanding fundamental survey efforts prior to advanced product design and experimentation.

critical minerals↗
DOE OSTI2025

A roadmap to understanding and anticipating microbial gene transfer in soil communities

Engineered microbes are being programmed using synthetic DNA for applications in soil to overcome global challenges related to climate change, energy, food security, and pollution. However, we cannot yet predict gene transfer processes in soil to assess the frequency of unintentional transfer of engineered DNA to environmental microbes when applying synthetic biology technologies at scale. This challenge exists because of the complex and heterogeneous characteristics of soils, which contribute to the fitness and transport of cells and the exchange of genetic material within communities. Here, we describe knowledge gaps about gene transfer across soil microbiomes. Here, we propose strategies to improve our understanding of gene transfer across soil communities, highlight the need to benchmark the performance of biocontainment measures in situ, and discuss responsibly engaging community stakeholders. We highlight opportunities to address knowledge gaps, such as creating a set of soil standards for studying gene transfer across diverse soil types and measuring gene transfer host range across microbiomes using emerging technologies. By comparing gene transfer rates, host range, and persistence of engineered microbes across different soils, we posit that community-scale, environment-specific models can be built that anticipate biotechnology risks. Such studies will enable the design of safer biotechnologies that allow us to realize the benefits of synthetic biology and mitigate risks associated with the release of such technologies.

bioccontainment↗
DOE OSTI2023

The Efficacy and Safety of an Intra-articular Dual-Acting Antibacterial Agent (TNP-2092) for Implant Infection–Associated Methicillin-Resistant Staphylococcus aureus

Abstract Owing to the presence of microbial biofilm on the implant, the eradication of biofilm-associated infections poses a challenge for antibiotic therapies. The study aimed to investigate the efficacy and safety of the novel antibiotic agent TNP-2092 in the context of implant infections. In vivo, rats with periprosthetic joint infection (PJI) treated with antibiotics showed an increase in body weight and decrease in swelling, temperature, and width of knee, compared with the control group. Meanwhile, inflammatory markers in synovium and serum were decreased in the TNP-2092 group, consistent with the pathological results. Moreover, TNP-2092 was effective in eliminating bacteria and disruption biofilm formation, and further alleviated the abnormal bone absorption and reactive bone changes around the prosthesis. In conclusion, intra-articular injection of TNP-2092 is safe and effective in treating knee PJI in a rat model. The study provides a foundation for the future utilization of TNP-2092 in the management of implant-related infections.

Dai, Tianyu↗
DOE OSTI2022

Microbial Metabolite 3-Indolepropionic Acid Mediates Immunosuppression

The microbial-derived metabolite, 3-indolepropionic acid (3-IPA), has been intensely studied since its origins were discovered in 2009; however, 3-IPA’s role in immunosuppression has had limited attention. Untargeted metabolomic analyses of T-cell exhaustion and immunosuppression, represented by dysfunctional under-responsive CD8+ T cells, reveal a potential role of 3-IPA in these responses. T-cell exhaustion was examined via infection of two genetically related mouse strains, DBA/1J and DBA/2J, with lymphocytic choriomeningitis virus (LCMV) Clone 13 (Cl13). The different mouse strains produced disparate outcomes driven by their T-cell responses. Infected DBA/2J presented with exhausted T cells and persistent infection, and DBA/1J mice died one week after infection from cytotoxic T lymphocytes (CTLs)-mediated pulmonary failure. Metabolomics revealed over 70 metabolites were altered between the DBA/1J and DBA/2J models over the course of the infection, most of them in mice with a fatal outcome. Cognitive-driven prioritization combined with statistical significance and fold change were used to prioritize the metabolites. 3-IPA, a tryptophan-derived metabolite, was identified as a high-priority candidate for testing. To test its activity 3-IPA was added to the drinking water of the mouse models during LCMV Cl13 infection, with the results showing that 3-IPA allowed the mice to survive longer. This negative immune-modulation effect might be of interest for the modulation of CTL responses in events such as autoimmune diseases, type I diabetes or even COVID-19. Moreover, 3-IPA’s bacterial origin raises the possibility of targeting the microbiome to enhance CTL responses in diseases such as cancer and chronic infection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Multiple biomarkers highlight the importance of water column processes in treatment wetland organic matter cycling

A suite of biomarkers, including amino acids, pigments, and lignin phenols coupled with high resolution mass spectrometry were used to evaluate differences in the sources and fate of organic matter (OM) in Everglades treatment wetlands as a model for OM cycling in shallow water wetlands. Five components of the system (water column particulate organic matter, vertical traps, flocculent material, periphyton, and surface soil) were assessed for OM transformations down-profile (i.e. water column to soil) and between treatment cells dominated by emergent aquatic vegetation (EAV) and submerged aquatic vegetation (SAV), with comparisons to reference sites that resemble historic Everglades conditions. We found that OM cycling is fundamentally different between EAV and SAV wetlands, and that SAV wetlands have some shared characteristics with similar habitats in the Everglades. Other than locations densely populated by Typha spp., water column particulate organic C was derived from microbial/cryptomonad sources, rather than macroscopic sources (vascular plants and algal mats). Bacterial amino acid biomarkers were positively correlated with amino acid degradation indices and organic P (Po), respectively suggesting that microbial abundance is associated with "fresher" OM, and that further investigation into relationships between microbial biomass and Po is warranted. Overall, this multi-biomarker approach can evaluate the relative "freshness" of OM pools, identify sources of OM, and highlight the importance of water column processes in shallow water wetlands.

treatment wetlands, organic matter, Everglades, am↗
DOE OSTI2021

Bacterial response to spatial gradients of algal-derived nutrients in a porous microplate

Abstract Photosynthetic microalgae are responsible for 50% of the global atmospheric CO2 fixation into organic matter and hold potential as a renewable bioenergy source. Their metabolic interactions with the surrounding microbial community (the algal microbiome) play critical roles in carbon cycling, but due to methodological limitations, it has been challenging to examine how community development is influenced by spatial proximity to their algal host. Here we introduce a copolymer-based porous microplate to co-culture algae and bacteria, where metabolites are constantly exchanged between the microorganisms while maintaining physical separation. In the microplate, we found that the diatom Phaeodactylum tricornutum accumulated to cell abundances ~20 fold higher than under normal batch conditions due to constant replenishment of nutrients through the porous structure. We also demonstrate that algal-associated bacteria, both single isolates and complex communities, responded to inorganic nutrients away from their host as well as organic nutrients originating from the algae in a spatially predictable manner. These experimental findings coupled with a mathematical model suggest that host proximity and algal culture growth phase impact bacterial community development in a taxon-specific manner through organic and inorganic nutrient availability. Our novel system presents a useful tool to investigate universal metabolic interactions between microbes in aquatic ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Elucidating algal-bacterial community interactions by tracking volatile biomarkers (Final Report)

This feasibility study project aimed to lay further groundwork for studying and understanding how microorganisms interact with each other at the molecular level using model algal-bacterial co-cultures. A better understanding of such interactions is critical to optimizing and operating biotic platforms for a number of applications, including bioenergy, algal bioproducts and agriculture, and carbon capture. Here we explored the feasibility of characterizing and following these interactions by identifying and tracking volatile metabolites and biomarkers in the complex gaseous headspace of such cultures. We set up an experimental platform using a co-culture of Phaeodactylum tricornutum and Marinobacter subspecies 3-2 as a model system, used solid-phase microextraction fibers for volatile collection at various time points throughout culture growth, and employed gas chromatography mass spectrometry-based instrumentation available at LLNL for compound identification and quantification. We found that it is feasible to determine volatile profiles from the growth of Phaeodactylum tricornutum and Marinobacter subspecies 3-2 using our methodology and monitor profile changes over time. We also observed that volatiles distinguishing between cultures of the individual species and the co-cultures could be detected. We expect that results of this project will feed into the ongoing LLNL’s DOE BER funded Biofuels Scientific Focus Area (SFA) on algal-bacterial interactions and pave the way for future expanded volatile studies supported by DOE. The approach and technologies developed here would also be applicable and transferable to other microbial communities under study, such as cyanobacteria, rhizosphere communities and biofilms.

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

Reduce Revenue Versus Increase Expenditure: Fires and Plant Invasion Drive Soil Carbon Loss With Different Mechanisms in a Mediterranean Shrubland

Fires and plant invasions threaten Mediterranean ecosystems substantially, particularly in the context of changing climate. Our study utilized a data-model integration approach to assess the response of soil organic carbon (SOC) to fires and plant invasion under three Shared Socio-Economic Pathway (SSP) scenarios (SSP1-26, SSP2-45, and SSP5-85). We parameterized the CLM-Microbe model and then investigated the individual and interactive impacts of fires and plant invasion on soil C by comparing factorial simulations of initialization (fire/no wildfire in 2021), fire module on/off, and with and without plant invasion during 2023–2100 in a Mediterranean ecosystem. The simulations indicated a marked C loss due to the 2021 wildfire, projected fires, and plant invasion across all future climate scenarios. Specifically, the 2021 wildfire, projected fires, and plant invasion reduced the SOC (0–30 cm) by 0.12, 0.26, and 0.15 kg C m −2 under SSP1-26, 0.12, 0.30, and 0.12 kg C m −2 under SSP2-45, and 0.12, 0.24, and 0.13 kg C m −2 under SSP5-85, respectively. However, fires and plant invasion decreased SOC through distinct mechanisms. The effects of the 2021 wildfire occurred due to its negative legacy on soil microbial community and, thus, litter accumulation, suppressing the formation of soil carbon via decomposition. Influences of projected fires happen via consuming fuel and suppressing carbon input to soils. In contrast, the impacts of plant invasions were due to enhanced microbial respiration, leading to C loss. In conclusion, these findings emphasize the need for tailored C sequestration strategies considering the disparate effects of fires and plant invasions in the Mediterranean climate.

microbe↗
DOE OSTI2024

Nitrogen-Fixing Gamma Proteobacteria Azotobacter vinelandii—A Blueprint for Nitrogen-Fixing Plants?

The availability of fixed nitrogen limits overall agricultural crop production worldwide. The so-called modern “green revolution” catalyzed by the widespread application of nitrogenous fertilizer has propelled global population growth. It has led to imbalances in global biogeochemical nitrogen cycling, resulting in a “nitrogen problem” that is growing at a similar trajectory to the “carbon problem”. As a result of the increasing imbalances in nitrogen cycling and additional environmental problems such as soil acidification, there is renewed and increasing interest in increasing the contributions of biological nitrogen fixation to reduce the inputs of nitrogenous fertilizers in agriculture. Interestingly, biological nitrogen fixation, or life’s ability to convert atmospheric dinitrogen to ammonia, is restricted to microbial life and not associated with any known eukaryotes. It is not clear why plants never evolved the ability to fix nitrogen and rather form associations with nitrogen-fixing microorganisms. Perhaps it is because of the large energy demand of the process, the oxygen sensitivity of the enzymatic apparatus, or simply failure to encounter the appropriate selective pressure. Whatever the reason, it is clear that this ability of crop plants, especially cereals, would transform modern agriculture once again. Successfully engineering plants will require creating an oxygen-free niche that can supply ample energy in a tightly regulated manner to minimize energy waste and ensure the ammonia produced is assimilated. Nitrogen-fixing aerobic bacteria can perhaps provide a blueprint for engineering nitrogen-fixing plants. This short review discusses the key features of robust nitrogen fixation in the model nitrogen-fixing aerobe, gamma proteobacteria Azotobacter vinelandii, in the context of the basic requirements for engineering nitrogen-fixing plants.

Microbiology↗
DOE OSTI2021

Interplay of microbial communities with mineral environments in coralline algae

Coralline algae are worldwide carbonate builders, considered to be foundational species and biodiversity hotspots. Coralline habitats face increasing pressure from human activities and effects related to Global Change, yet their ecological properties and adaptive responses remain poorly understood. The relationships of the algal microbiota with the mineral bioconstructions, as well as plasticity and resilience of coralline holobionts in a changing environment, are of particular interest. In the Gulf of California, Neogoniolithon trichotomum (Rhodophyta) is the main carbonate builder in tidal pools. We performed a multi-disciplinary assessment of the N. trichotomum microstructure using XRD, SEM microscopy and SR-FTIR spectromicroscopy. In the algal perithallus, magnesium-calcite and aragonite were spatially segregated and embedded in a polysaccharide matrix (rich in sulfated polysaccharides). Mg-calcites (18-19 mol% Mg) were the main mineral components of the thallus overall, followed by iron carbonates related to dolomite (ankerite) and siderite. Minerals of late evaporitic sequences (sylvite and bischofite) were also present, suggesting potential halophilic microenvironments within the algal thalli. The diverse set of abundant halophilic, halotolerant and oligotrophic taxa, whose abundance increase in the summer, further suggests this condition. We created an integrated model, based on environmental parameters and the microbiota distribution, that identified temperature and nutrient availability (particularly nitrate and silicate) as the main parameters related to specific taxa patterns. Among these, Hahella, Granulossicoccus, Ferrimonas, Spongiibacteraceae and cyanobacterial Xenococcaceae and Nostocaceae change significantly between seasons. These bacterial components might play relevant roles in algal plasticity and adaptive responses to a changing environment. This study contributes to the understanding of the interplay of the prokaryotic microbiota with the mineral microenvironments of coralline algae. Because of their carbonates with potential resistance to dissolution in a higher pCO 2 world and their seasonally dynamic bacteria, coralline algae are relevant targets to study coastal resilience and carbonated systems responses to changing environments.

54 ENVIRONMENTAL SCIENCES↗