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DOE OSTI2020

BioGeoChemistry of Actinides (LLNL SFA OBER - SBR FY20 Program Management and Performance Report)

The focus of the BioGeoChemistry of Actinides SFA is to identify and quantify the biogeochemical processes and the underlying mechanisms that control actinide mobility in an effort to reliably predict and control the cycling and migration of actinides in the environment. The research approach includes: (1) Field Studies (Research Thrust 1) that capture actinide behavior on the timescale of decades and (2) Fundamental Laboratory Studies (Research Thrust 2) that isolate specific biogeochemical processes observed in the field. These research thrusts are underpinned by the unique capabilities and staff expertise at Lawrence Livermore National Laboratory (LLNL), allowing the BioGeoChemistry of Actinides SFA to advance our understanding of actinide migration behavior in the environment, and serve as an international resource for environmental radiochemistry research (Figure 1). Research Thrusts 1 and 2 are guided by broad central hypotheses: Thrust 1 Hypothesis: Biogeochemical processes occurring on the timescale of years to decades lead to greater actinide recalcitrance in sediments and limit their migration in surface and groundwater. Thrust 2 Hypothesis: Long-term biogeochemical processes include mineral and surface alteration, which leads to stabilization of actinide surface associations or incorporation into mineral precipitates. Our strategic goal is to use the knowledge gained from our Science Plan to advance our understanding of the behavior of actinides, providing DOE with the scientific basis for remediation and long-term stewardship of DOE’s legacy sites and, more broadly, increasing our understanding of transport phenomena in environmental systems sciences with a particular emphasis on environmentally relevant (long-term) timescales. Although our focus is on actinide biogeochemistry, the increased focus on biogeochemistry at unique Test Bed locations associated with this SFA is providing fundamental information on redox processes and associated microbiological processes that control the cycling of redox sensitive metals under dynamic and transient biogeochemical conditions.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

DOE OSTI2020

Hanford Double Shell Waste Tank Corrosion Studies (Final Report FY2019)

During fiscal year (FY) 2019, the Savannah River National Laboratory (SRNL) focused on four primary tasks for Hanford Double Shell Tanks (DSTs) corrosion studies. The first task, New Limits, was a continuation from the electrochemical work started in FY16, to expand electrochemical testing to elevated temperatures and elevated hydroxide concentrations and evaluate how these factors will influence pitting corrosion. Using the pitting factor (PF) equation, these new conditions were validated to provide a conservative estimate for the susceptibility of pitting corrosion on legacy carbon steel. The second task, Secondary Liner Corrosion, focused on Vapor Space Corrosion (VSC) and immersion testing studies using two commercially available vapor corrosion inhibitors (VCIs). For this FY, the VCI strategy was applied mid-experiment to determine performance on weathered coupons. The third task, Long-Term Open Circuit Potential (OCP) Drift, was performed using simplified simulated chemistries to evaluate change in pitting corrosion risk due to evolution of corrosion potential for mill-scale and freshly polished 600-grit surfaces. Finally, the fourth task, Microbiologically-Influenced Corrosion (MIC) studies, was focused on the study of leak detection pit (LDP) water sent from the Hanford tank farm for determination of bacteria that can be conducive to corrosion using commercially available kits: BART TM and MICkit® 5. In addition, this FY, a secondary task was added which was a continuation of the study of the Quartz-enhanced Photoacoustic Spectroscopy (QEPAS) system. Work was started but was ultimately not pursued. A summary of each task performed is presented below.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2020

Mechanistic and predictive understanding of needle litter decay in semi-arid mountain ecosystems experiencing unprecedented vegetation mortality. Final report

This research compared needle litter decay rates and underlying mechanisms between litter released from insect-killed trees to that of naturally senesced litter from healthy trees across climate variables with elevation and snowmelt rates as variables. Our research was designed to address questions of whether there is a significant impact to C and N cycling at the terrestrial-atmospheric interface in association with pine needle decomposition and the role of changes in soil moisture and temperature as a function of these processes. Field activities were primarily conducted within the Rocky Mountain Biological Laboratory’s (RMBL) East River watershed across a spectrum of ecoregions that spanned approximately 700 vertical meters. Forested catchments at these elevations in southwestern Colorado are threatened by heat-induced drought, altered snowmelt patterns, and invasive insect infestation that have all been associated with climate change. Needle litter from two members of the Pinaceae family experiencing large-scale insect infestations (spruce and lodgepole pine) were collected, redeployed and then sampled over the course of three years. We experimentally tested three tractable parameters that are known to impact litter decay and biogeochemical cycling and are relevant to bark beetle-induced tree mortality: (1) moisture content, (2) temperature by using elevation as a surrogate, and (3) changes to litter compositional chemistry that result from beetle infestation. We examined decay processes and monitored the migration of soluble and gaseous nitrogen and carbon species as well as microbiological signatures of decay such as biodegradable fractions, metal availability and the temporal succession of associated microorganisms at the terrestrial interface.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Evaluation of the Lawrence Livermore Microbal Detection Array at the Statens Serum Institut

This was a collaborative effort between Lawrence Livermore National Security, LLC as manager and operator of Lawrence Livermore National Laboratory (LLNL) and Statens Serum Institut to evaluate and transition the Lawrence Livermore Microarray Detection Array (LLMDA) analysis software package, the Composite Likelihood Maximization method (CLiMax) to the SSI. The SSI is a public enterprise under the Danish Ministry of Health that operates a microbiology reference laboratory for the Danish population and analyzes tens to thousands of human clinical samples annually. SSI has been collaborating with the LLNL team for several years to use the LLMDA to analyze viral and bacterial infections from human clinical samples. The collaboration has resulted in two joint publications thus far, describing improvements to LLMDA sample preparation, and the utility of the LLMDA for detecting emerging viruses in clinical samples.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Exploring the Interaction of Amphiphilic Mycobacterial Lipoarabinomannan with Lipoproteins: Implications for Blood Based Diagnosis

Currently, over one-third of the global population is infected with tuberculosis (TB), one of the world’s most deadly infectious diseases. The current gold standard for TB diagnosis is microbiological culture, which can take up to 6-8 weeks, which is not conducive to timely treatment. There are no reliable diagnostics for TB. Disease manifestation and outcome of diagnostic tests for TB is influenced by co-morbidities such as HIV co-infection, further complicating diagnostics development. Thus, there is a need for reliable diagnostics for TB. This is especially true in pediatric populations where the differential disease presentation further complicates outcomes. This dissertation describes the development and evaluation of new tailored methods-lipoprotein capture and membrane insertion- for the discriminative detection of an amphiphilic mycobacterial biomarker, lipoarabinomannan (LAM), for diagnosis of TB in adult and pediatric populations. LAM is released by Mycobacterium tuberculosis during active infection and associates with serum lipoproteins such as high and low density lipoproteins (HDL/LDL) in the human host. The guiding hypothesis of this work is that the vi sequestration of LAM in immune complexes and by lipoprotein carriers in the host contributes to difficulty in detection of the amphiphilic antigen in blood. To this end, we have evaluated the use of tailored amphiphile detection assays to process and measure sequestered LAM in host blood, and examined the application of this methodology in adults and children with TB disease. In addition, we have developed and studied an in vitro cell model to further extrapolate the impact of association of LAM with host carriers on its ability to induce innate immune processes, in order to better refine and design strategies for its direct detection. Overall, our conclusions indicate that the amphiphilic biochemistry of LAM and its interaction with lipoproteins is a feature which should be taken into account for the effective development of diagnostics.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Functionalized Cellular Magmatics

We are pioneering the development of fundamental and applied research related to engineered cellular magmatics (ECM) technology. Over the course of our first year, we developed the methodology and measured the effects of various additives on ECM properties. We demonstrated the ability to control the phase and morphology of post-process secondary minerals on ECMs based on starting conditions and compositions. Both achievements are critical to advancing the use of ECMs for applications such as water filtration and runoff remediation. We established the ability to grow various microbiologic consortia on ECM surfaces as well as a process that allows industrial scaling of the technology for rapid field deployment in applications such as the cleanup of fossil fuel contamination. Furthermore, this biotechnology also has potential application in the nascent fields of biomining of precious metals and bioremediation of toxic heavy metals.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Analysis of Microbial Communities as Indicators of Microbially Induced Corrosion Potential in Stainless Steel Piping

The 200 West Area Pump-and-Treat (200W P&T) facility is part of the final remedy decision for the 200 ZP-1 Operable Unit (OU) and is the interim remedial action for 200-UP-1 OU at the Hanford Site. The facility also treats water from other sources across the site, including 200-DV-1 OU perched water, groundwater from the 200-BP-5 OU, and leachate from the Environmental Restoration Disposal Facility. The facility originally operated a biological treatment process for nitrate that resulted in systemic biofouling and loss of injection well capacity, requiring frequent and costly well rehabilitation. Biofouling has also contributed to corrosion of welds and pitting of stainless-steel piping at the facility. The biological treatment for nitrate was suspended at the end of 2019 calendar year to eliminate negative impacts from biological treatments which improve facility operations and treatment of carbon tetrachloride. Evaluation of the 200W P&T facility’s response to operational improvements, specifically the suspension of the biological treatment, provides information on the potential for continued microbially induced corrosion (MIC). To this end, historical data sets (2015-2017) were compared with molecular biological analyses of 200W P&T water samples from 2018-2020 to quantify trends in total microbial biomass and specific microbial indicator species (iron, sulfate, nitrate, and manganese reducing bacteria) known to cause and enhance metal corrosion. Results showed unequivocal reductions (in excess of 90%) in all microbiological indicators measured following the suspension of the biological treatment. Although abundance measurements for all corrosive MIC populations initially declined after removal of the treatment system, nitrate-reducing bacteria (nirK) and sulfate-reducing bacteria remain highly abundant in the system, an order of magnitude higher than the number of cells present prior to the removal of the biological treatment system [5.14e (1.4) cells/L, vs. 1.14e (0.07) cells/L, reported as average (±SD) for n=3]. In addition, there was an unexpected inflection point in 2019 where all microbial indicators increased unexpectedly in abundance in 2020 by as much as two orders of magnitude compared to 2019 samples. Given the limited number of water samples available for this analysis, the cause of the increase in microbial indicators post-biological treatment has not yet been determined. Systematic sampling of the facility for continued monitoring is recommended so that the responses of MIC populations can be evaluated to ensure that further corrosion is avoided, allowing the 200W P&T facility to operate safely and efficiently at design capacity.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2022

Bioreactors: Design, Background, and Applications

A bioreactor is any reaction vessel designed to contain a biological reaction with the aims of either growing an organism, producing a biological product, bioremediating waste, or investigating the workings of a biological process within a controlled environment. Bioreactors compose a broad category of useful and ubiquitous technologies present throughout the bioeconomy, which are inherently “dualuse” technologies: holding both immense potential for both benefit and harm to society. Due to this duality, national security professionals must bridge technological understanding and policy acumen to understand how bioreactors are integrated into both, many peaceful applications throughout the global bioeconomy such as in developing or manufacturing life-saving pharmaceuticals, as well as potentially harmful and/or illicit uses, such as producing biowarfare agent. The following document gives a surface-level introduction into this broad category of technology. The first two sections of this document describe the historical origins, then typical contemporary uses of bioreactors as a critical component of the modern bioeconomy providing examples for each use case. The following two sections begin to give a technical description of bioreactor technology introducing the features commonly found in simple bioreactors and providing a non-exhaustive framework for categorizing bioreactors commonly found in wet-microbiology applications. The last two sections present two short discussions on the challenges facing modern bioreactor technology, firstly from a technical standpoint, and then from the non-technical standpoint with special attention to the dual-use dilemma and issue of responsible technological development inherent in most biotechnology.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Investigation of Technologies to Improve Condenser Heat Transfer and Performance in a Relevant Coal-Fired Power Plant

Improvements in thermal power-generating plant performance is correlated directly to societal benefits including lower cost of reduced fuel consumption, resulting in lower cost of electricity for the consumer and reduced carbon emissions to the atmosphere. Warm steam exhausted from low-pressure steam turbines is condensed to liquid water on the exterior of thin-walled metal condenser tubes with cooling water passing through the tube interior. The condensation of steam creates a vacuum that supports turbine rotation and the concurrent generation of electricity. This vacuum is optimized when heat transfer across the wall of condenser tube is maximized. Common hindrances to heat transfer include foulants in cooling water that may form and adhere to the interior of condenser tubes, including mineral scale, microbiological films, and particulate deposition. Flowing cooling water may also include a laminar layer at the interior metal surfaces that travels more slowly than bulk water flow, serving to impede heat transfer. On the tube exterior, condensing steam forms an insulating layer of water that flows down the tube and reduces the effectiveness of cooling. Both the interior and exterior barriers to optimal heat transfer may be alleviated to some extent by surface treatments. On the tube interior, hydrophobic coatings may be applied that can reduced the adherence of foulants and of the laminar flow layer to the tube surface. On the tube exterior, hydrophobic coatings or mechanical treatments can be applied that may result in the termination of droplet growth and the departure of droplets from the surface rather than coalescence into a continuous layer of flowing water. Fourteen surface treatments were applied to condenser tubes in this study, including eight interior coatings and six exterior treatments, five of which were coatings and one a microstructural texture. Heat transfer measurement equipment simulating conditions in the condenser of an operating power plant was used to determine heat transfer coefficients by measuring sufficient flow, temperature, water chemistry and other data. Several of the tubes with interior surface treatments showed improvement in heat transfer coefficients compared with a plain (uncoated) tube, and several of the tubes with exterior surface treatments also showed enhanced heat transfer coefficients.

01 COAL, LIGNITE, AND PEAT↗

DOE OSTI2020

Biogeochemical Processes Across Aquatic Interfaces

The aquatic interfaces exposing terrestrial soils to oxic-anoxic regime shifts represent biogeochemical “hotspots” that are extremely sensitive to climate and environmental change. However, processes and interaction across theses aquatic interfaces are poorly understood and underrepresented in current Earth system models. In this project, we aim to develop predictive understanding of the feedbacks between microbial systems and geochemical environments that determine emergent ecosystem behaviors and resilience in response to disturbances. We use experimental, mechanistic modeling and meta-analysis tools to elucidate interactions among soil, water, geomorphology and microbiology that regulate the molecular transformations and fluxes of carbon, nutrients, and redox-sensitive compounds across aquatic interfaces.

58 GEOSCIENCES↗

DOE OSTI2023

Reservoir Thermal Energy Storage Benchmarking (Rev. 3)

A benchmarking analysis of RTES research funded by GTO through the Beyond Batteries projects was conducted against the ESGC to see where they fit within the identified ESGC Use Cases. The projects were found to advance knowledge in multiple ESGC use cases, either directly or in some cases, indirectly as enabling technologies. This analysis is helpful to understand where RTES and associated research fits into the larger discussion around energy storage technologies. Also, a retrospective analysis of the Beyond Batteries projects was conducted to evaluate what the projects learned and how the results can be applied to advance the value of RTES. Major results of each of the studies are summarized in Table 2. Additionally, a comparative metrics analysis for RTES was completed to understand where RTES lies within the energy storage industry. Metrics for evaluation of RTES and its comparison to other storage technologies were selected and ranges of their values compiled. The selected metrics – LCOE (levelized cost of energy), capital costs, roundtrip efficiency, energy storage capacity, and storage time – were chosen based on data availability and have a particularly strong influence on the potential deployment of a storage technology. Charts which compare the metrics are presented in section 4.3 and show ranges for each of the 10 selected technologies. However, due to a lack of domestic operational facilities, values for RTES and for portions of the remaining technologies are based on theoretical modeling and studies of best-case scenarios. LCOE estimates for RTES fall within the lower reaches of Figure 15, but nevertheless amount to 2 – 5 times the ESGC Roadmap goal for LCOE, for example in the Facilitating and Evolving Grid Use Case. Capital costs for RTES sit on the higher end (Figure 16) but are expected to decrease as new projects are developed and the technology is refined. The theoretical roundtrip efficiency reported for RTES varies from mid to high percentages (Figure 17) with efficiencies upwards of 93% in modeled scenarios in the Portland Basin (Bershaw et al.,2020). RTES is also expected to have the largest energy storage capacities and longest storage times, likely matched only by lower efficiency hydrogen storage. To better assess the role that RTES could play in energy storage we examined it’s potential in the U.S. The potential depends on many factors. Recently, many researchers have started looking at deep sedimentary basins, depleted oil and gas fields, and basalt formations as potential targets for RTES development. The United States Geological Survey (USGS) has analyzed various cities and shown substantial RTES potential in the cooling sector (Pepin et al., 2021). By modeling RTES in low-quality groundwater (e.g., brackish), it is shown to be favorable across the U.S. with particular suitability in the Illinois Basin, Coastal Plains, and Basin and Range regions. Seasonal RTES operations have also been modeled in the Portland Basin by those at the USGS and Portland State University to simulate an RTES system supplying heating loads needed for the Oregon Health and Science University. Simulations suggest that high conductive heat loss in the initial years exists but tends to decrease with increasing time and development of the resource due to self-insulating nature of the basalts (Burns et al., 2020). Other national laboratory efforts are taking a close look at many of the technical issues involved with RTES (McLing et al., 2019, McLing et al., 2022). These include difficulties in understanding geochemical, hydrogeological, mechanical, and microbiological changes at such elevated temperatures and operational scenarios. Major gaps in research are identified and suggested for future work. With this increased focus to understand how to make RTES successful in the U.S., this technology could be a potential solution to many of the nation’s energy storage problems. For the energy independence of this country, the DOE should prioritize de-risking this technology by making future investments in pilot-scale demonstrations to attract potential investors.

15 GEOTHERMAL ENERGY↗

DOE OSTI2023

Multiphysics Computational Fluid Dynamics for Design and Scale-Up of CO 2 /Syngas Bioreactors [Poster]

What are we trying to do? Develop validated, high fidelity computational models for gas fermentation using CO 2 , CO and H 2 . How is it done today? Microbiological advances are made at the lab scale in well mixed reactors. Process scale-up remains an open question when considering novel microorganisms/reaction systems. Why is this important? Lab-to-production scale transition is required to achieve CO 2 conversion at Mton/Gton scale and computational models can de-risk/accelerate this transition.

09 BIOMASS FUELS↗

DOE OSTI2024

Corrinoids as model nutrients to probe microbial interactions in a soil ecosystem

Earth’s soils are habitats for microbial communities that drive biogeochemical cycling, plant growth, and carbon storage and persistence. The thousands of microbial species living in soil form an intricate web of interactions involving the exchange of molecules produced by different microbes. Understanding in detail how these molecular exchanges occur and how they shape microbial communities may lead to new methods to improve soil health, bioremediation efforts, and better understanding of biogeochemical processes. The overall goal of this research is to gain a deeper knowledge of the microbial interactions that drive soil community structure. However, the high functional and genomic diversity in soil microbiomes has posed a challenge for current microbiology methods to achieve this goal. This research leverages a model group of key metabolites related to cobalamin (vitamin B 12 ), known as corrinoids, to investigate microbial interactions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Genomes to ecosystem function: Targeting critical knowledge gaps in methanogenesis and translation to updated global biogeochemical models

Natural freshwater temperate wetland systems currently represent the largest natural source of atmospheric methane, but are relatively understudied using systems biology tools (e.g. meta-omics) compared to other high producing methane systems (e.g. peat, tropical, or reconstructed wetlands). Using field investigations at the NOAA operated sentinel site on Lake Erie, methane producing activities and responses to geochemical conditions will be determined along seasonal and spatial gradients (Objective 1). Here, a combination of high-throughput activity and gas measurements, combined with high-resolution systems biology and analytical methods, will provide in depth knowledge of the microbiological, chemical, and physical constraints on methane production in wetlands. Using laboratory microcosms, the formation of anoxic microsites and their capacity to facilitate methane production in wetland soils will be simulated (Objective 2). This objective will validate the findings from the field investigations, offering a more controlled environment for teasing out the role of different yet interrelated variables. Lastly, these field and laboratory data will be used for multi-scale, process-level evaluation of an ecosystem biogeochemical model that accommodates these newly identified processes and parameterizes representation of these processes along relevant environmental gradients (Objective 3).This research will identify multiple interacting geochemical, ecological, and metabolic constraints that are poorly understood, oversimplified, or missing in global biogeochemical methane models. This proposal targets the role of oxygen limitation on methane processes in soil domains, to improve reactive transport models of microbial carbon cycling across terrestrial-aquatic soils and generate data on nutrient cycling activities in Great Lake wetlands. This information could provide new insights into the microbial controllers of Lake Erie eutrophication.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Brochure for the DOE Office of Science Workshop on Envisioning Frontiers in AI and Computing for Biological Research

In February of 2025 a joint ASCR/BER workshop was held to identify key transformational research directions for understanding biology using artificial intelligence (AI), digital twins and high-performance (HPC) computational methods to facilitate scientific discovery and innovation in support of the Department of Energy mission. AI technologies offer exciting new groundbreaking methods to analyze large volumes of complex biological data, thereby greatly accelerating the ability to understand, predict, and design biological processes for beneficial purposes. In the laboratory, the bridging of AI-enabled automated experimental technologies, HPC and digital twins will provide potent tools for researchers to explore the fundamental nature of biology and harness its inherent metabolic potential for a variety of beneficial purposes. The focus of this workshop was on how high-performance computational methods can impact this objective by exploring digital twins, foundational models, and data-driven approaches with applications to advance automated laboratory experiments, modeling of complex living systems and engineering new functions into plants and microbial systems relevant to DOE mission. Workshop attendees with expertise in plant science, microbiology, mathematics, computer science, and AI assessed the current state of the science, trends, and AI challenges at the interface of plant and microbial systems biology and computational science to identify opportunities for high-impact research. This collaborative effort capitalized on ASCR's advancements in applied mathematics, computer science, and Exascale systems, and BER's expertise in basic genomics-enabled research on DOE relevant plant and microbial systems. The workshop culminated in four key priority research directions to guide future research and development within DOE Office of Science programs.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Fitness For Service Assessment of a Corroded Heat Exchanger

Within the Fermi National Accelerator complex, there exist various water systems that support accelerator operations. One of these systems is extremely vital to the operation of the machine; that is the cooling system. The cooling system consists of nine relatively large heat exchangers that take untreated pond water and use it to cool the process fluid that further cools machine components. Over the 30 years these heat exchangers have been in operation, they have undergone significant material loss on the channels. This material loss, due to various forms of corrosion such as galvanic and microbiologically influenced corrosion (MIC) and possibly others, has deteriorated more than 80% of the nominal wall thickness of some of the exchangers and placed them in a questionable state. ASME FFS-1 (API 579) has been applied to address the condition of the heat exchangers due to their noncompliance with the governing code, BPVC Sec. VIII Div. 1. The assessments encompassed ASME FFS-1 parts 4: General Metal Loss and 9: Crack Like Flaw using level 1, 2, and 3 analysis techniques based on inspection data obtained by API 510 inspections. Level 1 and 2 assessments were deemed unfit for the corroded regions due to their location relative to a major structural discontinuity (channel to tube-sheet joint), so a level 3 analysis was conducted according to ASME Sec. VIII Div. 2 (design by analysis) rules for pressure vessels. Supplemental information included pond water tests to determine an accurate future corrosion allowance due to lacking inspection history. A leak before break (LBB) route was chosen to evaluate the possibility of leaking prior to the onset of failure. The analysis of one heat exchanger shows that the possibility the channel will develop a pinhole leak over 2.5 more years of operation should not be overlooked, but burst was unlikely from operation. The use of fracture mechanics show, that if a through-wall crack were to develop, it would not propagate further than the channel geometry and cause a leak not greater than 35 GPM. Using ASME Section XI Code Case N-705-1, allowing us to operate with a leak until the next outage given certain operating conditions and developing a leak mitigation procedure, this heat exchanger is deemed fit-for-service.

Humenik, Alex [Fermilab]↗

DOE OSTI2025

Expedition UT-GOM2-2 Methods

Methods used during the University of Texas (UT) Deepwater Hydrate Coring Expedition (UT-GOM2-2) include work done onboard the Helix Q4000 in the offshore Gulf of America (Gulf of Mexico), herein “the Gulf”, “dockside” in Salt Lake City, Utah, and some shore-based work in individual laboratories. The goal of this report is two-fold: to provide enough detail on the methods so they can be repeated by others; and to provide a reference document for the team to enhance cross-disciplinary understanding and knowledge. Methods include drilling operations, depth references and depth modification, downhole tool deployment, coring tool performance assessment, core processing, lithostratigraphy, biostratigraphy, as well as physical properties, including core logging and imaging, rock magnetism, dissolved methane concentration, hydrate saturation, microbiology, and geochemistry. An extensive amount of operational work and planning was required before mobilization of the expedition to permit, build mobile labs, and test downhole tools for deepwater drilling.

03 NATURAL GAS↗

DOE OSTI2025

Evaluation of DNA Extraction Efficiency in Diverse Algae Strains Using Commercial Kits and Lysis Approaches

Efficient DNA extraction is essential for accurately monitoring microalgae communities in large-scale cultivation systems such as raceway ponds and wastewater ponds. Traditional phenol chloroform extracts are a staple in microbiology but are obsolete for routine sampling due to its high toxicity reagents and time intensive setups. Commercial DNA extraction kits are more favorable for the microbes found in these ponds, but lack specific kits made for these communities. Little is known about which kits perform the best, leading researchers to use a variety of different kits with inconsistent results. This project compared one precipitation based commercial kit (Lucigen Masterpure) and five wash based kits (Monarch, Zymo Quick-DNA, and three Qiagen DNeasy kits) using four brackish algae strains to determine which methods yield the greatest quantity and quality of genomic DNA. Extractions were evaluated using the manufacturers protocol, and additional pretreatment options were administered before a single kit to compare its potential in being added routinely before extractions. Pretreatment options included both cryogenic freeze-thawing and heat incubation using enzymes. DNA was quantified using Qubit fluorometry and NanoDrop purity ratios. Overall, the Qiagen PowerWater kit provided the highest DNA yield and purity, but at a significantly higher cost then the precipitation-based kit (MasterPure). It was also noted that while the precipitation-based kit was significantly cheaper, provided similar results, it took significantly more time to complete a single run. Cryogenic pretreatment (6x cycles) increased average DNA yields by up to 80%, whereas enzymatic pretreatment most improved purity ratios without substantially improving quantity. The results suggest that it may be more cost and time efficient to use Qiagen kits with the addition of lysis pretreatments to procure better results. Future works includes developing a better system to efficiently collect multi variable data, and to upscale to artificial polycultures using similar methodologies alongside sequencing to confirm kit results.

59 BASIC BIOLOGICAL SCIENCES↗