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At least 289 records · Page 16
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Population assignment of migratory Westslope Cutthroat Trout (WCT) in the Clark Fork–Pend Oreille River basin

Abstract Objective The Clark Fork–Pend Oreille River basin of northeastern Washington and the Idaho Panhandle historically supported a robust metapopulation of the Westslope Cutthroat Trout (WCT) Oncorhynchus lewisi, a western native salmonid of high cultural and economic value. The construction of impassible hydroelectric dams and smaller instream barriers has prevented the return of migratory WCT to spawning tributaries, leading to the fragmentation of this metapopulation over the past 100 years. One such impassible barrier is Albeni Falls Dam (AFD) near Newport, Washington, which was completed without fish passage capabilities in 1955. We sought to examine large-scale genetic patterns in the study area and determine the most likely spawning tributary of origin for migratory WCT captured below AFD. Methods We created a genetic baseline representative of populations within the Clark Fork–Pend Oreille River basin from upstream and downstream of the dam using 191 biallelic single-nucleotide polymorphism genetic markers. Our data set included 124 collections, which allowed for an examination of population structure and hatchery influence across the study area and provided a robust tool for population assignment. Population assignment tests were conducted using the program RUBIAS. Result Population assignment tests were successful for all pure WCT of unknown origin despite potential influence from hatchery lineages across the study area. Of 83 migratory WCT captured below AFD, approximately 80% were assigned to tributaries upstream of AFD with a posterior assignment probability of at least 90%. Only one fish was assigned to a tributary downstream of AFD. Conclusion Our results indicate that AFD disrupts the natural metapopulation dynamics of WCT populations in the basin. Passage for WCT at this barrier would reestablish metapopulation connectivity within the basin by allowing migratory individuals to make genetic contributions to populations upstream of the dam.

Wells, Craig D. (ORCID:0000000258513250)↗
DOE OSTI2020

Coral loss alters guarding and farming behavior of a Caribbean damselfish

Coral loss is a major element of global ecological change in the oceans that may shape the behavior of keystone species such as habitat-attached animals. Farming damselfishes cultivate and aggressively protect algal garden within their territory, thereby shaping local fish assemblages and macro-algae diversity. Following the widespread loss of live branching coral throughout Florida and the Caribbean Sea, dusky damselfish (Stegastes adustus) have modified their territorial behavior. We compared antagonistic behavior, and size and algal species composition of territories of dusky damselfish on dead branching coral rubble and live boulder coral in the Dry Tortugas National Park, USA. Even though similar numbers of “intruders” entered each habitat type, dusky damselfish on rubble territories chased out significantly more fishes, had larger territories and more species of algae were present in their gardens. This study shows that dusky damselfish successfully occupy living and dead coral areas; however, there are potential trade-offs between defending a larger territory and cultivating fewer algal species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Assessment of potential impact of magnetic fields from a subsea high-voltage DC power cable on migrating green sturgeon, Acipenser medirostris

Abstract Empirical evidence suggests that marine animals perceive and orient to local distortions in the earth’s natural magnetic field. Magnetic fields (MFs) generated by electrified underwater cables may produce similar local distortions in the earth’s main field. Concern exists that these distortions may impact migration movements of MF-sensitive animals. The Trans Bay Cable (TBC) is a ± 200-kV, 400-megawatt, 85-km high-voltage direct current transmission line buried through San Francisco Bay (37° 56′ 8.81″ N, 122° 27′ 0.19″ W). Detections of adult green sturgeon implanted with acoustic transmitters were used from six cross-bay receiver arrays from 2006 to 2015 to investigate how inbound and outbound migration movements through lower portions of their route to/from upstream breeding grounds are related to the TBC’s energization status (off/on) and other local environmental variables. Here, we assess how these variables impacted transit success, misdirection from the migration route, transit times, and migration path locations within stretches between the Bay’s mouth and the start of the Sacramento River. Overall, there was varied evidence for any effect on migration behavior associated with cable status (off/on). A higher percentage of inbound fish successfully transited after the cable was energized, but this effect was nonsignificant in models including temperature. Outbound fish took longer to transit after cable energization. Inbound and outbound migration path locations were not significantly influenced by cable energization, but results suggest a potential subtle relationship between energization and both inbound and outbound paths. Overall, additional migration-based studies are needed to investigate the impact of anthropogenic cables on marine species.

Wyman, Megan T. (ORCID:0000000256844603)↗
DOE OSTI2022

Growth and survival rates of dispersing free embryos and settled larvae of pallid sturgeon ( Scaphirhynchus albus ) in the Missouri River, Montana and North Dakota

We released nearly 1.0 million 1-day post-hatch (dph) and 5-dph pallid sturgeon (Scaphirhynchus albus) free embryos in the Missouri River on 1 July 2019 and sequentially captured survivors at multiple sites through a 240-km river reach to quantify daily growth and survival rates during the early life stages. Genetic analysis was used to assign captured fish to released family lots and known ages. Growth rate was similar (0.74–0.75 mm day –1 ) between the 1- and 5-dph age groups during the 3–4-day dispersal period when water temperature averaged 16.8 °C. Daily survival rate was 0.64 during 1–4 dph for the original 1-dph age group and 0.80 during 5–7 dph for the original 5-dph age group. Total survival during free embryo dispersal (hatch to 9 dph) was estimated as 0.0437. The transition from dispersing as free embryos to settling as benthic larvae was verified for fish originally released as 5 dph. Growth of settled larvae was quantified with a Gompertz model through 75 dph (9 September; 112 mm) when water temperature was 18.8–21.0 °C in the rearing areas. Settled larvae had an estimated daily survival rate of 0.96, and estimated total survival during 9–75 dph was 0.0714. This study provides the first empirical survival estimates for pallid sturgeon early life stages in natural settings and is one of few studies reporting similar information for other sturgeon species. Applications of this work extend to pallid sturgeon restoration programs where population models are being developed to predict recruitment potential and population responses to river management alternatives.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Manganese: The overlooked contaminant in the world largest mine tailings dam collapse

Manganese (Mn) is an abundant element in terrestrial and coastal ecosystems and an essential micronutrient in the metabolic processes of plants and animals. Mn is generally not considered a potentially toxic element due to its low content in both soil and water. However, in coastal ecosystems, the Mn dynamic (commonly associated with the Fe cycle) is mostly controlled by redox processes. Here, we assessed the potential contamination of the Rio Doce estuary (SE Brazil) by Mn after the world’s largest mine tailings dam collapse, potentially resulting in chronic exposure to local wildlife and humans. Estuarine soils, water, and fish were collected and analyzed seven days after the arrival of the tailings in 2015 and again two years after the dam collapse in 2017. Using a suite of solid-phase analyses including X-ray absorption spectroscopy and sequential extractions, our results indicated that a large quantity of Mn II arrived in the estuary in 2015 bound to Fe oxyhydroxides. Over time, dissolved Mn and Fe were released from soils when Fe III oxyhydroxides underwent reductive dissolution. Due to seasonal redox oscillations, both Fe and Mn were then re-oxidized to Fe III , Mn III , and Mn IV and re-precipitated as poorly crystalline Fe oxyhydroxides and poorly crystalline Mn oxides. In 2017, redox conditions (Eh: -47 ± 83 mV; pH: 6.7 ± 0.5) favorable to both Fe and Mn reduction led to an increase (~880%) of dissolved Mn (average for 2015: 66 ± 130 μg L -1 ; 2017: 582 ± 626 μg L -1 ) in water and a decrease (~75%, 2015: 547 ± 498 mg kg -1 ; 2017: 135 ± 80 mg kg -1 ) in the total Mn content in soils. The crystalline Fe oxyhydroxides content significantly decreased while the fraction of poorly ordered Fe oxides increased in the soils limiting the role of Fe in Mn retention. The high concentration of dissolved Mn found within the estuary two years after the arrival of mine tailings indicates a possible chronic contamination scenario, which is supported by the high levels of Mn in two species of fish living in the estuary. Our work suggests a high risk to estuarine biota and human health due to the rapid Fe and Mn biogeochemical dynamic within the impacted estuary.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Quantifying the Influence of Size, Shape, and Density of Microplastics on Their Transport Modes: A Modeling Approach

Microplastics (MPs) pose significant risks to marine ecosystems and human health, necessitating accurate predictions of their distributions in aquatic environments for effective risk mitigation. However, understanding MP transport dynamics is challenging because of the inadequate representation of MP characteristics such as size, shape, and density in numerical models. Further, the accuracy of the MP vertical profiles in existing models has not been thoroughly validated. Thus, we developed an MP transport model within the Finite Volume Community Ocean Model framework (FVCOM-MP) by integrating MP characteristics. We validated FVCOM-MP against experimental and analytical data, focusing on various MP transport modes and transitions. FVCOM-MP successfully replicates MP profiles in different transport modes, including the bedload, surface-load, suspended-load, and mixed-load modes. Additionally, we introduce phase diagrams for classifying MP transport modes based on particle characteristics, enhancing our understanding of MP dynamics in aquatic systems. The transport modes for a number of real-world MP particles, including fishing line, plastic bag/bottle fragments, synthetic fibers, tire wear particles, polyvinyl chloride and expanded polystyrene pellets, were analyzed with these phase diagrams.

Microplastic transport, Settling velocity, Rising ↗
DOE OSTI2025

Valued peaks: Sustainable water allocation for small hydropower plants in an era of explicit ecological needs

Optimizing hydropower operations to balance economic profitability and support functioning ecosystem services is integral to river management policy. In this article, we propose a dynamic, constrained optimization framework for small hydropower plants (SHPs) to evaluate trade-offs between economic profitability and socio-ecological requirements. Specifically, we examine the balance between short-term losses in hydropower generation and the potential for compensatory benefits in the form of revenue from recreational ecosystem services, irrespective of the direct beneficiary. Our framework integrates a fish habitat model, a hydropower optimization model, and a recreational ecosystem service estimate to evaluate different environmental flow scenarios. The optimization process gives three outflow release scenarios, informed by previous streamflow realisations (dam inflow), and designed environmental flow constraints. The framework is applied and tested for the river Kuusinkijoki in North-eastern Finland, which is a habitat for migratory brown trout and grayling populations. We show that the revenue loss due to the environmental flow constraints arises through a reduction in revenue per generated energy unit and through a reduction in turbine efficiency. Additionally, the simulation results reveal that all the designed environmental flow constraints cannot be met simultaneously. Under the environmental flow scenario with both minimum flow and flow ramping rate constraints, the annual hydropower revenue decreases by 16.5 %. An annual increase of 8 % in recreational fishing visits offsets the revenue loss. In conclusion, the developed framework provides knowledge of the costs and benefits of hydropower environmental flow constraints and guides the prioritizing process of environmental measures.

13 HYDRO ENERGY↗
DOE OSTI2022

How Does Flow Alteration Propagate Across a Large, Highly Regulated Basin? Dam Attributes, Network Context, and Implications for Biodiversity

Abstract Large dams are a leading cause of river ecosystem degradation. Although dams have cumulative effects as water flows downstream in a river network, most flow alteration research has focused on local impacts of single dams. Here we examined the highly regulated Colorado River Basin (CRB) to understand how flow alteration propagates in river networks, as influenced by the location and characteristics of dams as well as the structure of the river network—including the presence of tributaries. We used a spatial Markov network model informed by 117 upstream‐downstream pairs of monthly flow series (2003–2017) to estimate flow alteration from 84 intermediate‐to‐large dams representing >83% of the total storage in the CRB. Using Least Absolute Shrinkage and Selection Operator regression, we then investigated how flow alteration was influenced by local dam properties (e.g., purpose, storage capacity) and network‐level attributes (e.g., position, upstream cumulative storage). Flow alteration was highly variable across the network, but tended to accumulate downstream and remained high in the main stem. Dam impacts were explained by network‐level attributes (63%) more than by local dam properties (37%), underscoring the need to consider network context when assessing dam impacts. High‐impact dams were often located in sub‐watersheds with high levels of native fish biodiversity, fish imperilment, or species requiring seasonal flows that are no longer present. These three biodiversity dimensions, as well as the amount of dam‐free downstream habitat, indicate potential to restore river ecosystems via controlled flow releases. Our methods are transferrable and could guide screening for dam reoperation in other highly regulated basins.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Carbon monoxide oxidation expands the known metabolic capacity in anaerobic methanotrophic consortia

Consortia of anaerobic methane-oxidizing archaea (ANME-2) and sulphate-reducing bacteria (SRB) represent globally relevant syntrophic associations capable of growing with minimal amounts of free energy and can persist when methane becomes limiting. Carbon monoxide (CO) has been reported in seep environments and represents a thermodynamically favourable alternative electron donor due to its low reduction potential. Here, we show that environmental ANME-SRB consortia can oxidize CO in the absence of methane, in anoxic microcosm experiments using a combination of stable isotope geochemical tracers, metatranscriptomics, and single cell activity measurements (FISH–nanoSIMS). The oxidation of CO was coupled with sulphate-reduction by syntrophic consortia, and, in the absence of sulphate, through CO 2 reduction to methane by ANME-2. Under these conditions, the production of methane was one ninth the rate of methanotrophy coupled to sulphate-reduction. Paired single cell FISH-nanoSIMS analysis of anabolic activity indicates that CO respiration appears to support cell maintenance rather than active growth, consistent with the observed down-regulation of energy generating complexes in ANME (e.g., mtr, rnf, etc.). The versatile capability of CO oxidation by anaerobic methanotrophic consortia broadens our understanding of carbon cycling in methane seeps and highlights potential mechanisms of resilience by methanotrophic archaea under changing geochemical regimes.

03 NATURAL GAS↗
DOE OSTI2021

Simulations of wavelength-multiplexed holography for single-shot spatiotemporal characterization of NIF’s advanced radiographic capability (ARC) laser

We simulate the use of a newly developed single-shot wavelength-multiplexed holography-based diagnostic, STRIPED FISH, to fully characterize the as-delivered laser pulses of the National Ignition Facility’s Advanced Radiographic Capability (NIF-ARC) laser. To that end, we have performed simulations of the NIF-ARC pulse incorporating (a) a time-integrated spatial-profile measurement and a complete temporal-intensity-and-phase measurement using a frequency resolved optical gating, but without any spatiotemporal pulse characterizations, and (b) simulated first-order spatiotemporal distortions, which could be measured on a single shot if a STRIPED FISH device were deployed.

47 OTHER INSTRUMENTATION↗
DOE OSTI2025

Longitudinal seroprevalence of Crimean-Congo hemorrhagic fever virus in Southern Uganda

Crimean-Congo hemorrhagic fever (CCHF) is a tick-borne disease endemic to many regions of Africa, the Middle East, Southeast Asia and the Balkans. Caused by the CCHF virus (CCHFV), CCHF has been a recognized cause of illness in Uganda since the 1950s and recently, more intensive surveillance suggests CCHFV is widely endemic within the country. Most surveillance has been focused on the Ugandan cattle corridor due to the risk of CCHFV exposure associated with livestock practices. Here we evaluated the seroprevalence of CCHFV in several Southern Ugandan communities outside the cattle corridor combined with longitudinal sample sets to measure the immune response to CCHFV for up to a decade. Interestingly, across three community types, agrarian, trading and fishing, we detected CCHFV seroprevalence in all three but found the highest seroprevalence in fishing communities. We also measured consistent CCHFV-specific antibody responses for up to a decade. Our findings support the conclusion that CCHFV is widely endemic in Uganda and highlight that additional communities may be at risk for CCHFV exposure.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Rapid retrieval of first-order spatiotemporal distortions for ultrashort laser pulses

High-intensity, ultrashort laser sources are a foundational pillar for High-Energy-Density (HED) physics, and as the repetition-rates of these systems increase, diagnostics must be developed to match their data collection speed. Characterization of any spatiotemporal distortions in the laser pulse is necessary in order to standardize results across facilities. Here, we have previously developed a laser diagnostic called Spatially and Temporally Resolved Intensity and Phase Evaluation Device: Full Information from a Single Hologram, or STRIPED FISH, to measure the full spatiotemporal laser electric field on a single shot. In order to provide rapid feedback, we here adapt the STRIPED FISH retrieval algorithm, which typically has computation times of up to 30 minutes due to the high spatial resolution of the device and its retrieval of the complete four-dimensional pulse field, to distill the key electric field quantities into a handful of scalars for rapid assessment of the pulse's first order distortions. Here, our new, rapid non-iterative retrieval algorithm is validated with simulated and experimental data, and it provides, within seconds, the same first-order information as given by the full analysis. This algorithm is suitable for on-shot assessment of spatiotemporal distortions and can be adapted to assess high repetition-rate laser quality in HED experiments.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Enantioselective ecotoxicity of promethazine in two freshwater organisms: daphnia (Daphnia magna) and zebrafish ( Danio rerio )

Abstract Chiral pharmaceuticals, racemic or enantiomerically pure forms and their metabolites, can reach aquatic ecosystems via wastewater effluents (inefficient treatment operations) or by direct human disposal. They may negatively affect nontarget organisms even at low environmental concentrations. To make an accurate risk evaluation, the (eco)toxicity of both enantiomers needs to be assessed. Promethazine (PMZ) is a chiral antihistamine that has been detected in aquatic ecosystems owing to its high consumption. Promethazine undergoes metabolism in the liver, producing chiral metabolites such as promethazine sulfoxide (PMZSO) and N-desmethylpromethazine (DMPMZ) that reach water bodies. However, knowledge regarding the enantioselective toxicity of PMZ and its metabolites on aquatic organisms is missing. This study aimed to explore the potential enantioselective toxicity of PMZ and its metabolites on two relevant freshwater organisms, daphniid and fish, representing different trophic levels. The half maximal effect concentrations (EC50s) in Daphnia magna of PMZ, DMPMZ, and PMZSO were 2.33, 2.31, > 4 mg L−1, respectively, > 4 and 2.50 mg L−1 for (R) and (S)-PMZ, respectively, and > 4 mg L−1 for the enantiomers of DMPMZ and PMZSO. In studies involving zebrafish, Danio rerio, (R, S)-PMZ showed a median lethal concentration (LC50) of .72 mg L−1, and specific assays revealed that (R)-PMZ exhibited more pronounced adverse effects on larvae at the embryonic, morphological, and biochemical level than the racemate and (S)-PMZ. Toxicity and potential bioaccumulation of these compounds in daphniids and fish were also conducted using in silico tests through proprietary software. The results revealed a concordance between the experimental and predicted EC50 and LC50 values in both species.

Coelho, Maria Miguel↗
DOE OSTI2025

Metallothionein expression in Eastern mosquitofish ( Gambusia holbrooki ) exposed to 137 Cs and lead: implications for using metallothionein as a metal exposure biomarker

Given the range of threats facing aquatic ecosystems, it is critical we have monitoring tools to quickly and efficiently identify stressors within ecosystems. Metallothionein’s (MTs) are a group of proteins widely used as biomarkers of metal exposure; however, their suitability has been questioned due to their influenceable nature and ability to be induced by various stressors. Through our study, we sought to (1) evaluate induction of MT in eastern mosquitofish (Gambusia holbrooki) exposed to a radionuclide ( 137 Cs) and metal (Pb), (2) assess the influence of in situ 137 Cs pre-exposure on Pb-induced MT expression, and (3) quantify changes in MT concentrations during Pb depuration. We conducted our experiment in three phases using mosquitofish as a model species: Phase I—pre-exposure to 137 Cs in the field, Phase II—exposure to Pb in the lab immediately following 137 Cs exposure, and Phase III—depuration in the laboratory. We quantified MT concentrations over time and assessed differences among treatments. We did not find in situ exposure of mosquitofish to 137 Cs to induce MT, nor did pre-exposure to 137 Cs appear to influence induction of MT following Pb exposure. Metallothionein was rapidly induced in mosquitofish following Pb exposure; however, MT induction was also observed in control fish. Additionally, there was no apparent relationship between MT and Pb body burdens. During depuration, we found MT concentrations to be highly variable among fish demonstrating no clear response. Furthermore, our study demonstrates the high variability exhibited by MT, the need for further validation of MT as a metal exposure biomarker, and the value in additional research on these proteins under varying exposure scenarios, particularly environmentally realistic concentrations.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Novel fisheries investigations by Harald Dannevig: some parallels with Johan Hjort on the other side of the world

Abstract Harald Dannevig was Australia’s first Director of fisheries research and Director of Australia’s first ocean-going research vessel. Dannevig’s initial contributions concerned hatchery technology, freshwater fisheries, and impacts of estuarine prawn trawling. Later, he revealed the growth and migration of sea mullet, the spawning of pelagic eggs in the coastal ocean, and he was the first to demonstrate the effect of onshore winds on recruitment to estuarine fisheries. Using plans of the first Norwegian research trawler Michael Sars, he advised on the construction and commissioning of Endeavour. He organized 99 research voyages over 6 years to determine suitable trawling grounds over ∼7000 km, discovering 263 new species, including 96 new fish species and ∼5000 catalogued specimens. Harald Dannevig’s significant achievements in Australia were soon forgotten after his death with the loss of Endeavour in the Southern Ocean at the beginning of World War I. Both Johan Hjort and Dannevig were numerate, loved natural history, and were keenly observant on the deck. As these two scientists did not correspond, their innovative and parallel thinking stems from the shared university environment with G.O. Sars, and the rapport between Sars and Harald’s father Gunder Dannevig, concerning the fish hatchery and stocking of larval cod.

Suthers, Iain M.↗
DOE OSTI2021

Seabird distribution is better predicted by abundance of prey than oceanography. A case study in the Gulf of Cadiz (SW, Iberian Peninsula)

Abstract Quantifying factors that influence marine predator distributions is essential to understanding the current and future change in marine biodiversity. Here, we test whether marine predator distribution relates to prey, or is better predicted by other specific habitat features. We examine the correlation between spatial distribution of three seabird species and their prey, as well as environmental proxies (oceanographic characteristics) in the Gulf of Cadiz, NE Atlantic. We modeled the at-sea distribution of Cory's shearwater, Balearic shearwater and Northern gannet, based on: (i) pelagic fish abundance according to acoustic surveys, and (ii) a forecast-model of remotely sensed environmental variables (productivity, sea surface temperature, and salinity). In general, seabird distributions were better predicted by abundance of fish than by environmental variables at the habitat scale. We obtained consistent correlations between seabird presence and the abundance of medium-sized (10–20 cm) sardines, anchovies and Mediterranean horse mackerel, providing information on their preferred prey. Additionally, oceanographic productivity variables moderately contributed to seabird distribution models, with better predictive value for the critically endangered Balearic shearwater and Northern gannet in the summer, whilst the model for Cory's shearwater's produced poorer predictions. Predator–prey combined studies may represent essential tools for an efficient ecosystem-based management of marine environments.

de la Cruz, Andrés (ORCID:0000000203632498)↗
DOE OSTI2024

Quantifying the Variability of “Fixed-Width” Buffers on Harvested Lands in Western Oregon and Washington

In contemporary forest management, buffers of unharvested trees are left along streams to protect riparian and aquatic ecosystems. Buffer regulations often focus on specific minimum width requirements, which aid in straightforward regulation and application, but minimum widths also suggest buffered edges are uniform and contain little variability. Conceptual papers suggest that alternative buffer configurations may offer greater flexibility in landscape-level protection, increase forest complexity, and enhance aquatic and riparian biodiversity. However, before considering alternatives to fixed-width buffers, it is necessary to quantify the inherent variability in current buffer practices present on the landscape. In this study, we used aerial imagery to quantify variability of buffer widths in two hundred randomly selected recently harvested units on managed land in Oregon and Washington with both fish-bearing and non-fish-bearing sections of stream. Wider buffers on larger streams had a greater magnitude of variability, but when normalized by stream size, variation was greater in smaller streams, and overall, variation ranged from 25% to 50% of the mean width. Despite local variability, buffer widths rarely fell below 9.14 m (30 ft). The variation quantified here provides an initial measure of variability to inform future management, given emerging interest in variable retention buffers.

58 GEOSCIENCES↗
DOE OSTI2025

Clear as mud redefined: Tunable transparent mineral scaffolds for visualizing microbial processes below ground

Microbes inhabiting complex porous microenvironments in sediments and aquifers catalyze reactions that are critical to global biogeochemical cycles and ecosystem health. However, the opacity and complexity of porous sediment and rock matrices have considerably hindered the study of microbial processes occurring within these habitats. Here, we generated microbially compatible, optically transparent mineral scaffolds to visualize and investigate microbial colonization and activities occurring in these environments, in laboratory settings and in situ. Using inexpensive synthetic cryolite mineral, we produced optically transparent scaffolds mimicking the complex 3D structure of sediments and rocks by adapting a suspension-based, freeze-casting technique commonly used in materials science. Fine-tuning of parameters, such as freezing rate and choice of solvent, provided full control of pore size and architecture. The combined effects of scaffold porosity and structure on the movement of microbe-sized particles, tested using velocity tracking of fluorescent beads, showed diverse yet reproducible behaviors. The scaffolds we produced are compatible with epifluorescence microscopy, allowing the fluorescence-based identification of colonizing microbes by DNA-based staining and fluorescence in situ hybridization (FISH) to depths of 100 µm. Additionally, Raman spectroscopy analysis indicates minimal background signal in regions used for measuring deuterium and 13 C enrichment in microorganisms, highlighting the potential to directly couple D 2 O or 13 C stable isotope probing and Raman-FISH for quantifying microbial activity at the single-cell level. To demonstrate the relevance of cryolite scaffolds for environmental field studies, we visualized their colonization by diverse microorganisms within rhizosphere sediments of a coastal seagrass plant using epifluorescence microscopy. The tool presented here enables highly resolved, spatially explicit, and multimodal investigations into the distribution, activities, and interactions of underground microbes typically obscured within opaque geological materials until now.

36 MATERIALS SCIENCE↗