Engineering topics

Cronin, Dylan

Publications and source records attributed to Cronin, Dylan.

8 records

DOE OSTI2026

Mobile genetic elements shape microbial diversity and functions in thawing permafrost soils

Ecosystems are shaped by communities of microorganisms whose niches and impacts depend on functional profiles influenced by gene gains and losses. Culture-based experiments demonstrate that mobile genetic elements (MGEs) can mediate gene flux, but quantitative understanding of these dynamics in natural systems remains limited. Here we develop and apply a systematic, meta-omic framework to investigate MGEs in a complex natural system using an 8-year soil time series collected at Stordalen Mire, in Sweden’s thawing permafrost margin. In this climate-critical peatland, we identify ~2.1 million MGE recombinases across 89 microbial phyla and assess ecological distributions, affected functions, past mobility and current activity. This revealed an active mobilome that shapes natural genetic diversity via differential impacts on major phyla and affects a wide range of functions, including metabolic genes involved in carbon flux and nutrient cycling. These findings and this analytic framework suggest avenues towards a better understanding of MGE diversity, activity, mobility and impacts across ecosystems.

Biological and medical sciences↗

DOE OSTI2024

Virus ecology and 7‐year temporal dynamics across a permafrost thaw gradient

Abstract Soil microorganisms are pivotal in the global carbon cycle, but the viruses that affect them and their impact on ecosystems are less understood. In this study, we explored the diversity, dynamics, and ecology of soil viruses through 379 metagenomes collected annually from 2010 to 2017. These samples spanned the seasonally thawed active layer of a permafrost thaw gradient, which included palsa, bog, and fen habitats. We identified 5051 virus operational taxonomic units (vOTUs), doubling the known viruses for this site. These vOTUs were largely ephemeral within habitats, suggesting a turnover at the vOTU level from year to year. While the diversity varied by thaw stage and depth‐related patterns were specific to each habitat, the virus communities did not significantly change over time. The abundance ratios of virus to host at the phylum level did not show consistent trends across the thaw gradient, depth, or time. To assess potential ecosystem impacts, we predicted hosts in silico and found viruses linked to microbial lineages involved in the carbon cycle, such as methanotrophy and methanogenesis. This included the identification of viruses of Candidatus Methanoflorens, a significant global methane contributor. We also detected a variety of potential auxiliary metabolic genes, including 24 carbon‐degrading glycoside hydrolases, six of which are uniquely terrestrial. In conclusion, these long‐term observations enhance our understanding of soil viruses in the context of climate‐relevant processes and provide opportunities to explore their role in terrestrial carbon cycling.

Microbiology↗

DOE OSTI2024

Impact of storage and extraction methods on peat soil microbiomes

Recovered microbial community structure is known to be influenced by sample storage conditions and nucleic acid extraction methods, and the impact varies by sample type. Peat soils store a large portion of soil carbon and their microbiomes mediate climate feedbacks. Here, we tested three storage conditions and five extraction protocols on peat soils from three physicochemically distinct habitats in Stordalen Mire, Sweden, revealing significant methodological impacts on microbial (here, meaning bacteria and archaea) community structure. Initial preservation method impacted alpha but not beta diversity, with in-field storage in LifeGuard buffer yielding roughly two-thirds the richness of in-field flash-freezing or transport from the field on ice (all samples were stored at −80 °C after return from the field). Nucleic acid extraction method impacted both alpha and beta diversity; one method (the PowerSoil Total RNA Isolation kit with DNA Elution Accessory kit) diverged from the others (PowerMax Soil DNA Isolation kit-High Humic Acid Protocol, and three variations of a modifiedPowerMax Soil DNA/RNA isolation kit), capturing more diverse microbial taxa, with divergent community structures. Although habitat and sample depth still consistently dominated community variation, method-based biases in microbiome recovery for these climatologically-relevant soils are significant, and underscore the importance of methodological consistency for accurate inter-study comparisons, long-term monitoring, and consistent ecological interpretations.

Science & Technology - Other Topics↗

DOE OSTI2023

Quantitation of olefins in sustainable aviation fuel intermediates using principal component analysis coupled with vacuum ultraviolet spectroscopy

Olefins, a common intermediate from biomass conversion processes, are undesirable in jet fuel because of their poor thermal stability. This paper presents an approach for olefin quantitation using 2D gas chromatography coupled with vacuum ultraviolet spectroscopy. Principal component analysis was used to reduce the dimensionality of the spectroscopic data from a highly olefinic fuel intermediate. A principal component template was created that enabled olefin quantitation, which was compared to the existing GCxGC-VUV approach from the literature. The principal component method was able to identify and quantify trace amounts of cyclodienes, which were present at only 0.01 wt% in the fuel sample. The principal component approach also identifies species that fall outside of the GCxGC template. For instance, quantitation with the literature method resulted in an olefin concentration of 0.95 times that of the principal component method due to olefins falling outside of the expected GCxGC regions. The principal component results were compared with 13 C and 1 H NMR data, which confirmed that the fuel had a high concentration of olefins and alkanes with little aromatic content.

Kosir, Shane↗

DOE OSTI2023

Unrealized Critical Lanthanide Extraction from Sea Algae Mining (UNCLE SAM): Domestic production of critical minerals from seawater

The UNCLE-SAM project, under the Biotechnologies to Ensure a Robust Supply of Critical Materials for Clean Energy program, examined the biomining applications of seaweeds for sustainable, domestic production of critical mineral feedstocks. The ocean is a vast reserve of mineralogical wealth including rare earth elements (REEs) and platinum group metal (PGMs). These elements, categorized as “critical minerals”, are used in telecommunication devices, lasers, LED lighting, turbine generators, electric car motors, jet engine alloys, and many other applications. These critical elements are increasingly vital to a thriving, efficient and sustainable society. However, only a few countries in the global market currently produce and export REEs, leading to potential geopolitical supply disruptions. Marine macroalgae, often referred to as seaweeds, bioconcentrate critical minerals from seawater, including REEs and PGMs. Marine algae cultivation can generate a significant amount of biomass with minimal freshwater, fertilizer, and land requirements. In summary, the UNCLE-SAM project successfully evaluated the technological feasibility for marine macroalgal cultivation as a feedstock for critical minerals, explored the biological capacity of different seaweeds to provide economically relevant domestic mineral production, assessed processing techniques for thermal co-conversion of seaweeds into renewable fuel and mineral feedstocks, and executed techno-economic and lifecycle assessments for identifying the most critical gaps in our current understanding to move the technology into commercially relevant deployment. Further development of this technology could transform the bioproduct and REE mining industries and catalyze the development of a more sustainable future.

58 GEOSCIENCES↗

DOE OSTI2022

Production and Catalytic Upgrading of 2,3-Butanediol Fermentation Broth into Sustainable Aviation Fuel Blendstock and Fuel Properties Measurement

With the increasing demand for sustainable supplies of aviation fuel and need to address climate change, new conversion technologies are needed to efficiently process biomass, produce high quality jet fuel blendstock, and meet carbon emission targets. This study demonstrates the synthesis, conditioning, and catalytic upgrading of 2,3-butanediol (BDO) fermentation broth into a jet fuel blendstock candidate. A high-titer 2,3-BDO fermentation broth (i.e., ~90 g/L) was produced at a 100-L scale and pretreated via nanofiltration to decrease the impurities level in the broth from 4.6 to 0.6 wt%. A novel process for catalytic upgrading of aqueous 2,3-BDO into a jet fuel blendstock candidate was developed, and each step was efficiently demonstrated. The catalytic steps include 1) 2,3-BDO dehydration into methyl ethyl ketone (MEK) over AlPO4, 2) MEK conversion into olefins over Zn1Zr10Ox, 3) oligomerization of olefins over a zeolite beta, and 4) hydrogenation over platinum/carbon. Both the model feed and real 2,3-BDO fermentation broth were tested for upgrading 2,3-BDO to MEK. With the real feed, a continuous loss of conversion (i.e., >50% loss over ~140 h time-on-stream [TOS]) was partly attributed to reversible deactivation from coking species. However, the conversion remained stable with the model feed, which demonstrates the efficiency of the first step for converting aqueous 2,3-BDO (10 wt% in water). For upgrading MEK to olefins, high selectivity to olefins (i.e., 82.5%) was obtained at high conversion levels (i.e., 93-98%) with stable conditions being achieved for > 70-hours TOS. Oligomerization of light olefins, which was demonstrated for > 270 h TOS, mainly led to the formation of dimers (C8-10) and trimers (C13-14). The oligomerized product was hydrogenated and distilled to recover the jet fraction (35 mass% or 40.9% carbon based yield), which consists mostly of desired isoalkanes (31.7 wt%), n-alkanes (24.5 wt%), and cycloalkanes (29.6 wt%). While some improvement is still needed to meet ASTM D7566 specifications for viscosity and final boiling point temperature, freezing point, density, aromatics content, and sulfur content of the jet blendstock candidate were within acceptable ranges, thus highlighting the potential of this process for production of jet fuel blendstock.

ADVANCED PROPULSION SYSTEMS,BIOMASS FUELS↗

DOE OSTI2022

Wet Waste Hydrothermal Liquefaction and Biocrude Upgrading to Hydrocarbon Fuels: 2021 State of Technology

Each year the U.S. Department of Energy Bioenergy Technologies Office (BETO) assesses progress in their research and development efforts toward sustainable production of renewable fuels (DOE 2016) through the annual state of technology (SOT) assessment. The SOT assessment evaluates the impact of the year’s research progress on the modeled minimum fuel selling price (MFSP) for selected biofuel conversion pathways and measures the current state of the technology relative to defined goal case projections. Supply chain sustainability analysis to track and guide research toward improved greenhouse gas (GHG) emissions, energy usage, water usage and other environmental metrics for the pathway is performed by Argonne National Laboratory (Cai et al. 2018, 2020). Technical and cost targets for a projected goal case set for the year 2022 were previously established for the wet waste hydrothermal liquefaction (HTL) and biocrude upgrading pathway and summarized in a design report (Snowden-Swan et al. 2017). Process performance advancements made for HTL and biocrude hydrotreating have resulted yearly reductions in the modeled MFSP relative to the initial SOT (2018) (Snowden-Swan et al. 2020, 2021). This report summarizes the research and associated techno-economic analysis (TEA) for the pathway 2021 SOT. Methods and economic assumptions for the nth plant analysis used for the TEA are consistent with the design report (Snowden-Swan et al. 2017), with the exception of updates in the modeled cost year (2016) and income tax rate (21%).

09 BIOMASS FUELS↗

DOE OSTI2021

efam: an e xpanded, metaproteome-supported HMM profile database of viral protein fam ilies

Viruses infect, reprogram and kill microbes, leading to profound ecosystem consequences, from elemental cycling in oceans and soils to microbiome-modulated diseases in plants and animals. Although metagenomic datasets are increasingly available, identifying viruses in them is challenging due to poor representation and annotation of viral sequences in databases. Here, we establish efam, an expanded collection of Hidden Markov Model (HMM) profiles that represent viral protein families conservatively identified from the Global Ocean Virome 2.0 dataset. This resulted in 240 311 HMM profiles, each with at least 2 protein sequences, making efam >7-fold larger than the next largest, pan-ecosystem viral HMM profile database. Adjusting the criteria for viral contig confidence from ‘conservative’ to ‘eXtremely Conservative’ resulted in 37 841 HMM profiles in our efam-XC database. To assess the value of this resource, we integrated efam-XC into VirSorter viral discovery software to discover viruses from less-studied, ecologically distinct oxygen minimum zone (OMZ) marine habitats. This expanded database led to an increase in viruses recovered from every tested OMZ virome by ~24% on average (up to ~42%) and especially improved the recovery of often-missed shorter contigs (<5 kb). Additionally, to help elucidate lesser-known viral protein functions, we annotated the profiles using multiple databases from the DRAM pipeline and virion-associated metaproteomic data, which doubled the number of annotations obtainable by standard, single-database annotation approaches. Together, these marine resources (efam and efam-XC) are provided as searchable, compressed HMM databases that will be updated bi-annually to help maximize viral sequence discovery and study from any ecosystem.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗