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DOE OSTI2023

Mycorrhiza Better Predict Soil Fungal Community Composition and Function than Aboveground Traits in Temperate Forest Ecosystems

Forests in the northeastern US are experiencing shifts in community composition due to the northward migration of warm-adapted tree species and certain species’ declines (for example, white ash and eastern hemlock) due to invasive insects. Changes in belowground fungal communities and associated functions will inevitably follow. Therefore, we sought to investigate the relative importance of two important tree characteristics—mycorrhizal type [ectomycorrhizal (EcM) or arbuscular mycorrhizal (AM)] and leaf habit (deciduous or evergreen) on soil fungal community composition and organic matter cycling. We sampled soil in the organic and mineral horizons beneath two AM-associated (Fraxinus americana and Thuja occidentalis) and two ECM-associated tree species (Betula alleghaniensis and Tsuga canadensis), with an evergreen and deciduous species in each mycorrhizal group. To characterize fungal communities and organic matter decomposition beneath each tree species, we sequenced the ITS1 region of fungal DNA and measured the potential activity of carbon- and nitrogen-targeting extracellular enzymes. Each tree species harbored distinct fungal communities, supporting the need to consider both mycorrhizal type and leaf habit. However, between tree characteristics, mycorrhizal type better predicted fungal communities. Across fungal guilds, saprotrophic fungi were the most important group in shaping fungal community differences in soils beneath all tree species. The effect of leaf habit on carbon- and nitrogen-targeting hydrolytic enzymes depended on tree mycorrhizal association in the organic horizon, while oxidative enzyme activities were higher beneath EcM-associated trees across both soil horizons and leaf habits.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Variability in soil redox response to seasonal flooding in a vernal pond

Vernal ponds are ephemeral landscape features that experience intermittent flooding and drying, leading to variable saturation in underlying soils. Redox potential (E h ) is an important indicator of biogeochemical processes that changes in response to these hydrological shifts; however, high-resolution measurements of E h in variably inundated environments remain sparse. In this study, the responses of soil E h to ponding, drying, and rewetting of a vernal pond were investigated over a 5-month period from late spring through early autumn. Soil E h was measured at 10-min frequencies and at multiple soil depths (2–48 cm below the soil surface) in shallow and deep sections within the seasonally ponded lowland and in unsaturated soils of the surrounding upland. Over the study period, average E h in surface soils (0–8 cm) was oxidizing in the upland (753 ± 79 mV) but relatively reducing in the shallow lowland (369 ± 49 mV) and deep lowland (198 ± 37 mV). Reducing conditions (E h <300 mV) in surface soils prevailed for up to 6 days in the shallow lowland and up to 24 days in the deep lowland after surface water dried out. Intermittent reflooding resulted in multiple shifts between reducing and oxidizing conditions in the shallow lowland while the deep lowland remained reducing following reflooding. Soil E h in the uplands was consistently oxidizing over the study period with transient increases in response to rain events. Reducing conditions in the lowland resulted in greater Fe-oxide dissolution and release of dissolved Fe and P into porewater than in the surrounding uplands. We determined that change in water depth alone was not a good indicator of soil E h , and additional factors such as soil saturation and clay composition should be considered when predicting how E h responds to surface flooding and drying. These findings highlight the spatial and temporal variability of E h within ponds and have implications for how soil processes and ecosystem function are impacted by shifts in hydrology at terrestrial-aquatic interfaces.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Novel and Emerging Capabilities that Can Provide a Holistic Understanding of the Plant Root Microbiome

In recent years, the root microbiome (i.e., microorganisms growing inside, on, or in close proximity to plant roots) has been shown to play an important role in plant health and productivity. Despite its importance, the root microbiome is challenging to study because of its complexity, heterogeneity, and subterranean location. Fortunately, root microbiome research has seen a tremendous influx of novel technologies (e.g., imaging tools, robotics, and molecular analyses), experimental platforms (e.g., micro- and mesocosms), and data integration, modeling, and prediction tools in the past decade that have greatly increased our ability to dissect the complex network of interactions between above- and belowground environmental parameters, plants, bacteria, and fungi that dictate soil and broader ecosystem health. Herein, we discuss methods that are currently used in root microbiome research and that can be expanded to phytobiome research in general ranging from laboratory studies to mesocosm-scale studies and, finally, to field studies; evaluate their relevance to ecosystem studies; and discuss future root microbiome research directions.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2024

Assessment of landscape-scale fluxes of carbon dioxide and methane in subtropical coastal wetlands of South Florida

Coastal wetlands play a significant role in the storage of “blue carbon,” indicating their importance in the carbon biogeochemistry in the coastal zone and in global climate change mitigation strategies. We present airborne eddy covariance observations of CO 2 and CH 2 fluxes collected in southern Florida as part of the NASA BlueFlux mission during April 2022, October 2022, February 2023, and April 2023. The flux data generated from this mission consists of over 100 flight hours and more than 6,000 km of horizontal distance over coastal saline and freshwater wetlands. We find that the spatial and temporal heterogeneity in CO 2 and CH 2 exchange is primarily influenced by season, vegetation type, ecosystem productivity, and soil inundation. The largest CO 2 uptake fluxes of more than 20 μmol m -2 s -1 were observed over mangroves during all deployments and over swamp forests during flights in April. The greatest CH 4 effluxes of more than 250 nmol m -2 s -1 were measured at the end of the wet season in October 2022 over freshwater marshes and swamp shrublands. Although the combined Everglades National Park and Big Cypress National Preserve region was a net sink for carbon, CH 4 emissions reduced the ecosystem carbon uptake capacity (net CO 2 exchange rates) by 11%–91%. Average total net carbon exchange rates during the flight periods were −4 to −0.2 g CO 2 -eq m -2 d -1 . Our results highlight the importance of preserving mangrove forests and point to potential avenues of further research for greenhouse gas mitigation strategies.

atmosphere↗

DOE OSTI2020

Active layer depth and soil properties impact specific leaf area variation and ecosystem productivity in a boreal forest

Specific leaf area (SLA, leaf area per unit dry mass) is a key canopy structural characteristic, a measure of photosynthetic capacity, and an important input into many terrestrial process models. Although many studies have examined SLA variation, relatively few data exist from high latitude, climate-sensitive permafrost regions. We measured SLA and soil and topographic properties across a boreal forest permafrost transition, in which dominant tree species changed as permafrost deepened from 54 to >150 cm over 75 m hillslope transects in Caribou-Poker Creeks Research Watershed, Alaska. We characterized both linear and threshold relationships between topographic and edaphic variables and SLA and developed a conceptual model of these relationships. We found that the depth of the soil active layer above permafrost was significantly and positively correlated with SLA for both coniferous and deciduous boreal tree species. Intraspecific SLA variation was associated with a fivefold increase in net primary production, suggesting that changes in active layer depth due to permafrost thaw could strongly influence ecosystem productivity. While this is an exploratory study to begin understanding SLA variation in a non-contiguous permafrost system, our results indicate the need for more extensive evaluation across larger spatial domains. These empirical relationships and associated uncertainty can be incorporated into ecosystem models that use dynamic traits, improving our ability to predict ecosystem-level carbon cycling responses to ongoing climate change.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Transition Zones at the Changing Coastal Terrestrial‐Aquatic Interface

Coastal soils are a significant but highly uncertain component of global biogeochemical cycles. These systems experience spatial and temporal variability in biogeochemical processes, driven by marsh‐to‐upland gradients and hydrological fluctuations. These fluctuations make it difficult to understand and predict biogeochemical processes in these highly dynamic systems. We studied coastal soil biogeochemistry and its variability (a) at regional scales and (b) across transects from upland forest to marsh, in two contrasting regions—Lake Erie, a freshwater lacustrine system, and Chesapeake Bay, a saltwater estuarine system. Salinity‐related analytes were a key source of variability in soil biogeochemistry, not just in the saltwater system, but surprisingly, also in the freshwater system. We had hypothesized linear trends in biogeochemical parameters along the TAI—however, contrary to expectations, transition soils were not consistently intermediate between upland and marsh endmembers; the non‐monotonic trends of C, P, Fe along our transects suggest that these do not behave as expected and may be difficult to model and predict—thus these are key analytes to study in our regions. Rapidly changing soil factors across coastal gradients (e.g., Ca, K, CEC, and TS) may act as precursors to ecosystem shifts. Our comprehensive soil characterization represents a snapshot of a single timepoint of surface soils and provides essential data for mechanistic modeling of ecosystem dynamics across coastal transects.

Patel, Kaizad F. [Pacific Northwest National Labor↗

DOE OSTI2021

Beyond denitrification: The role of microbial diversity in controlling nitrous oxide reduction and soil nitrous oxide emissions

Many biotic and abiotic processes contribute to nitrous oxide (N 2 O) production in the biosphere, but N 2 O consumption in the environment has heretofore been attributed primarily to canonical denitrifying microorganisms. The nosZ genes encoding the N 2 O reductase enzyme, NosZ, responsible for N 2 O reduction to dinitrogen are now known to include two distinct groups: the well-studied Clade I which denitrifiers typically possess, and the novel Clade II possessed by diverse groups of microorganisms, most of which are non-denitrifiers. Clade II N 2 O reducers could play an important, previously unrecognized role in controlling N 2 O emissions for several reasons, including: (1) the consumption of N 2 O produced by processes other than denitrification, (2) hypothesized non-respiratory functions of NosZ as an electron sink or for N 2 O detoxification, (3) possible differing enzyme kinetics of Clade II NosZ compared to Clade I NosZ, and (4) greater nosZ gene abundance for Clade II compared to Clade I in soils of many ecosystems. Despite the potential ecological significance of Clade II NosZ, a census of 800 peer-reviewed original research articles discussing nosZ and published from 2013 to 2019 showed that the percentage of articles evaluating or mentioning Clade II nosZ increased from 5% in 2013 to only 22% in 2019. The census revealed that the slowly spreading awareness of Clade II nosZ may result in part from disciplinary silos, with the percentage of nosZ articles mentioning Clade II nosZ ranging from 0% in Agriculture and Agronomy journals to 32% in Multidisciplinary Sciences journals. In addition, inconsistent nomenclature for Clade I nosZ and Clade II nosZ, with 17 different terminologies used in the literature, may have created confusion about the two distinct groups of N 2 O reducers. Furthermore, we provide recommendations to accelerate advances in understanding the role of the diversity of N 2 O reducers in regulating soil N 2 O emissions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Soil-related developments of the Biome-BGCMuSo v6.2 terrestrial ecosystem model

Terrestrial biogeochemical models are essential tools to quantify climate–carbon cycle feedback and plant–soil relations from local to global scale. In this study, a theoretical basis is provided for the latest version of the Biome-BGCMuSo biogeochemical model (version 6.2). Biome-BGCMuSo is a branch of the original Biome-BGC model with a large number of developments and structural changes. Earlier model versions performed poorly in terms of soil water content (SWC) dynamics in different environments. Moreover, lack of detailed nitrogen cycle representation was a major limitation of the model. Since problems associated with these internal drivers might influence the final results and parameter estimation, additional structural improvements were necessary. In this paper the improved soil hydrology as well as the soil carbon and nitrogen cycle calculation methods are described in detail. Capabilities of the Biome-BGCMuSo v6.2 model are demonstrated via case studies focusing on soil hydrology, soil nitrogen cycle, and soil organic carbon content estimation. Soil-hydrology-related results are compared to observation data from an experimental lysimeter station. The results indicate improved performance for Biome-BGCMuSo v6.2 compared to v4.0 (explained variance increased from 0.121 to 0.8 for SWC and from 0.084 to 0.46 for soil evaporation; bias changed from -0.047 to -0.007 m 3 m -3 for SWC and from -0.68 to -0.2 mm d -1 for soil evaporation). Simulations related to nitrogen balance and soil CO 2 efflux were evaluated based on observations made in a long-term field experiment under crop rotation. The results indicated that the model is able to provide realistic nitrate content estimation for the topsoil. Soil nitrous oxide (N 2 O) efflux and soil respiration simulations were also realistic, with overall correspondence with the observations (for the N 2 O efflux simulation bias was between -0.13 and -0.1 mgNm -2 d -1 , and normalized root mean squared error (NRMSE) was 32.4 %–37.6 %; for CO 2 efflux simulations bias was 0.04–0.17 gCm -2 d -1 , while NRMSE was 34.1 %–40.1 %). Sensitivity analysis and optimization of the decomposition scheme are presented to support practical application of the model. The improved version of Biome-BGCMuSo has the ability to provide more realistic soil hydrology representation as well as nitrification and denitrification process estimation, which represents a major milestone.

58 GEOSCIENCES↗

NASA NTRS2016

The SMAP Level 4 Carbon PRODUCT for Monitoring Terrestrial Ecosystem-Atmosphere CO2 Exchange

The NASA Soil Moisture Active Passive (SMAP) mission Level 4 Carbon (L4_C) product provides model estimates of Net Ecosystem CO2 exchange (NEE) incorporating SMAP soil moisture information as a primary driver. The L4_C product provides NEE, computed as total respiration less gross photosynthesis, at a daily time step and approximate 14-day latency posted to a 9-km global grid summarized by plant functional type. The L4_C product includes component carbon fluxes, surface soil organic carbon stocks, underlying environmental constraints, and detailed uncertainty metrics. The L4_C model is driven by the SMAP Level 4 Soil Moisture (L4_SM) data assimilation product, with additional inputs from the Goddard Earth Observing System, Version 5 (GEOS-5) weather analysis and Moderate Resolution Imaging Spectroradiometer (MODIS) satellite data. The L4_C data record extends from March 2015 to present with ongoing production. Initial comparisons against global CO2 eddy flux tower measurements, satellite Solar Induced Canopy Florescence (SIF) and other independent observation benchmarks show favorable L4_C performance and accuracy, capturing the dynamic biosphere response to recent weather anomalies and demonstrating the value of SMAP observations for monitoring of global terrestrial water and carbon cycle linkages.

SMAP↗

DOE OSTI2024

Bacterial community dynamics as a result of growth-yield trade-off and multispecies metabolic interactions toward understanding the gut biofilm niche

Abstract Bacterial communities are ubiquitous, found in natural ecosystems, such as soil, and within living organisms, like the human microbiome. The dynamics of these communities in diverse environments depend on factors such as spatial features of the microbial niche, biochemical kinetics, and interactions among bacteria. Moreover, in many systems, bacterial communities are influenced by multiple physical mechanisms, such as mass transport and detachment forces. One example is gut mucosal communities, where dense, closely packed communities develop under the concurrent influence of nutrient transport from the lumen and fluid-mediated detachment of bacteria. In this study, we model a mucosal niche through a coupled agent-based and finite-volume modeling approach. This methodology enables us to model bacterial interactions affected by nutrient release from various sources while adjusting individual bacterial kinetics. We explored how the dispersion and abundance of bacteria are influenced by biochemical kinetics in different types of metabolic interactions, with a particular focus on the trade-off between growth rate and yield. Our findings demonstrate that in competitive scenarios, higher growth rates result in a larger share of the niche space. In contrast, growth yield plays a critical role in neutralism, commensalism, and mutualism interactions. When bacteria are introduced sequentially, they cause distinct spatiotemporal effects, such as deeper niche colonization in commensalism and mutualism scenarios driven by species intermixing effects, which are enhanced by high growth yields. Moreover, sub-ecosystem interactions dictate the dynamics of three-species communities, sometimes yielding unexpected outcomes. Competitive, fast-growing bacteria demonstrate robust colonization abilities, yet they face challenges in displacing established mutualistic systems. Bacteria that develop a cooperative relationship with existing species typically obtain niche residence, regardless of their growth rates, although higher growth yields significantly enhance their abundance. Our results underscore the importance of bacterial niche dynamics in shaping community properties and succession, highlighting a new approach to manipulating microbial systems.

Microbiology↗

DOE OSTI2021

Merging Fungal and Bacterial Community Profiles via an Internal Control

Integrated measurements of fungi and bacteria are critical to understand how interactions between these taxa drive key processes in ecosystems ranging from soils to animal guts. High-throughput amplicon sequencing is commonly used to census microbiomes, but the genetic markers targeted for fungi and bacteria (typically ribosomal regions) are domain-specific so profiling must be performed separately, obscuring relationships between these groups. To solve this problem, we developed a spike-in method with an internal control (IC) construct containing primer sites commonly used for bacterial and fungal taxonomic profiling. The internal control offers several advantages: estimation of absolute abundances, estimation of fungal to bacterial ratios (F:B), integration of bacterial and fungal profiles for holistic community analysis, and lower costs compared to other quantitation methods. To validate the IC as a scaling method, we compared IC-derived measures of F:B to measures from quantitative PCR (qPCR) using a commercial mock community (the ZymoBiomic Microbial Community DNA Standard II, containing two fungi and eight bacteria) and complex environmental samples. For both the mock community and the environmental samples, the IC produced F:B values that were statistically consistent with qPCR. Merging the environmental fungal and bacterial profiles based on the IC-derived F:B values revealed new relationships among samples in terms of community similarity. As a result, this IC method is the first spike-in method to employ a single construct for cross-domain amplicon sequencing, offering more reliable measurements.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Risk to ecological resources following remediation can be due mainly to increased resource value of successful restoration: A case study from the Department of Energy's Hanford Site

Several nations are faced with the need to remediate large contaminated sites following World War II, the Cold War, and abandoned industrial sites, and to return them to productive land uses. In the United States, the Department of Energy (DOE) has the largest cleanup challenge, and its Hanford Site in the state of Washington has the most extensive and most expensive cleanup task. Ideally, the risk to ecological resources on remediation sites is evaluated before, during, and after remediation, and the risk from, or damage to, ecological resources from contaminants should be lower following remediation. In this paper, we report the risk to ecological resources before, during, and as a consequence of remediation on contaminated units requiring cleanup, and then examine the causes for changes in risk by evaluating 56 cleanup evaluation units (EUs) at the Hanford Site. In this case, remediation includes a restoration phase. In general, the risk to ecological and eco-cultural resources is currently not discernible or low at most contaminated units, increases during remediation, and decreases thereafter. Remediation often causes physical disruption to ecosystems as it reduces the risk from exposure to contaminants. Most new remediation projects at the Hanford Site include ecological restoration. Ecological restoration results in the potential for the presence of higher quality resources after remediation than currently exists on these contaminated lands and facilities. Although counter-intuitive, our evaluation of the risk to ecological resources following remediation indicated that a significant percentage of units (61%) will be at increased risk in the post-remediation period. This increased risk is due to DOE's successful remediation and restoration that results in a higher percent of native vegetation and higher ecological value on the sites in the post-remediation period than before. These newly-created resources can then be at risk from post-remediation activities. Risks to these new higher quality resources include the potential for spread of invasive species and of noxious grasses used in previous cleanup actions, disruption of ecosystems (including those with state or federally listed species and unique ecosystems), compaction of soil, use of pesticides to control invasive species, and the eventual need for continued monitoring activities. Thus, by greatly improving the existing habitat and health of eco-receptors, and maintaining habitat corridors between high quality habitats, the ecological resources in the post-remediated units are at risk unless care is taken to protect them. Many of the negative effects of both remediation and future monitoring (or other future land uses) can be avoided by planning and management early in the remediation process. We suggest DOE and other agencies convene a panel of managers, remediation scientists, regulators, environmental and ecological scientists, Native Americans, economists, and the public to develop a generic list of performance metrics for the restoration phase of remediation, including evaluation of success, which could be applied across the DOE complex.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Quantifying the influence of different biocrust community states and their responses to warming temperatures on soil biogeochemistry in field and mesocosm studies

Biocrusts influence soil biogeochemistry by fixing carbon (C) and nitrogen (N) and through leachate inputs to soils. Functional rates can vary among biocrust community states and in response to edaphic properties, heterotrophic microbial activity, and global change. Using soils and biocrusts from the Colorado Plateau, Utah, USA, we aimed to quantify the influence of early-successional (ES) and late-successional (LS) biocrust community states on soil biogeochemistry. In a field setting, we found soil was less “fertile” under ES than LS biocrust, but ES biocrust had a relative influence 1.3 times greater than LS biocrust on soil fertility. Leachate collected from LS biocrust had, on average, 6 times more organic C and 1.7 times more dissolved N than ES biocrust, but concentrations of phosphorus (P) and inorganic N did not differ among the two biocrust types. Here, to disentangle influences of biocrusts and soil properties on biogeochemical pools, we constructed mesocosms from homogenized soil and left the surface bare or covered with ES or LS biocrust, before assignment to ambient or warmed (+5 °C) temperature treatments for 3 months. Multivariate biogeochemical properties differed among cover types, yet all exhibited losses of P, N, and organic C and nearly half of the biogeochemical variables considered did not differ among cover types. Mesocosms with LS biocrust retained more dissolved N, supported 8 additional, significant correlations among biogeochemical pools of the biocrust and mineral soil layer on average, and lost fewer of these correlations under warming. Overall, while soils under LS biocrusts were more fertile (i.e., had higher nutrient concentrations) than under ES, we did not find evidence implicating leachate as the primary driver of this difference. Biocrust influences on soil fertility were greater when mineral soil nutrients were in lower concentrations, highlighting the value of even incipient biocrusts for dryland functioning.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Fungi-on-a-Chip: microfluidic platforms for single-cell studies on fungi

Abstract This review highlights new advances in the emerging field of ‘Fungi-on-a-Chip’ microfluidics for single-cell studies on fungi and discusses several future frontiers, where we envisage microfluidic technology development to be instrumental in aiding our understanding of fungal biology. Fungi, with their enormous diversity, bear essential roles both in nature and our everyday lives. They inhabit a range of ecosystems, such as soil, where they are involved in organic matter degradation and bioremediation processes. More recently, fungi have been recognized as key components of the microbiome in other eukaryotes, such as humans, where they play a fundamental role not only in human pathogenesis, but also likely as commensals. In the food sector, fungi are used either directly or as fermenting agents and are often key players in the biotechnological industry, where they are responsible for the production of both bulk chemicals and antibiotics. Although the macroscopic fruiting bodies are immediately recognizable by most observers, the structure, function, and interactions of fungi with other microbes at the microscopic scale still remain largely hidden. Herein, we shed light on new advances in the emerging field of Fungi-on-a-Chip microfluidic technologies for single-cell studies on fungi. We discuss the development and application of microfluidic tools in the fields of medicine and biotechnology, as well as in-depth biological studies having significance for ecology and general natural processes. Finally, a future perspective is provided, highlighting new frontiers in which microfluidic technology can benefit this field.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Soil resistance and recovery during neotropical forest succession

The recovery of soil conditions is crucial for successful ecosystem restoration and, hence, for achieving the goals of the UN Decade on Ecosystem Restoration. Here, we assess how soils resist forest conversion and agricultural land use, and how soils recover during subsequent tropical forest succession on abandoned agricultural fields. Our overarching question is how soil resistance and recovery depend on local conditions such as climate, soil type and land-use history. For 300 plots in 21 sites across the Neotropics, we used a chronosequence approach in which we sampled soils from two depths in old-growth forests, agricultural fields (i.e. crop fields and pastures), and secondary forests that differ in age (1–95 years) since abandonment. We measured six soil properties using a standardized sampling design and laboratory analyses. Soil resistance strongly depended on local conditions. Croplands and sites on high-activity clay (i.e. high fertility) show strong increases in bulk density and decreases in pH, carbon (C) and nitrogen (N) during deforestation and subsequent agricultural use. Resistance is lower in such sites probably because of a sharp decline in fine root biomass in croplands in the upper soil layers, and a decline in litter input from formerly productive old-growth forest (on high-activity clays). Soil recovery also strongly depended on local conditions. During forest succession, high-activity clays and croplands decreased most strongly in bulk density and increased in C and N, possibly because of strongly compacted soils with low C and N after cropland abandonment, and because of rapid vegetation recovery in high-activity clays leading to greater fine root growth and litter input. Furthermore, sites at low precipitation decreased in pH, whereas sites at high precipitation increased in N and decreased in C : N ratio. Extractable phosphorus (P) did not recover during succession, suggesting increased P limitation as forests age. These results indicate that no single solution exists for effective soil restoration and that local site conditions should determine the restoration strategies.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2026

Comparative physiological and genomic characterization of a novel Nitrobacter vulgaris strain from a nitrate-contaminated subsurface

Nitrite-oxidizing bacteria (NOB) represent a crucial node in the global nitrogen cycle. By catalyzing the second step of nitrification—the oxidation of nitrite to nitrate to generate energy for growth—NOB activity controls the fate of nitrite (NO 2 - ) in aerobic environments. Despite thriving in diverse environments, including soils, freshwater, marine ecosystems, subsurface habitats, and water treatment systems, organisms capable of nitrite oxidation are confined to Nitrobacter, Nitrospira, Nitrospina, Nitrotoga, and a few other specific lineages. The genus Nitrobacter, recognized for its facultative heterotrophic metabolism, is often associated with high-nitrogen environments. Here, we report the physiological characterization of a novel strain, Nitrobacter vulgaris strain MLSD-S22, isolated from a nitrate- and heavy-metal-contaminated subsurface. Growth inhibition experiments revealed that strain MLSD-S22 and the N. vulgaris type strain Z exhibited similar sensitivities to nitrite and nitrate, with nitrite being the most inhibitory. Microrespirometry demonstrated that the two N. vulgaris strains and Nitrobacter winogradskyi Nb-255 possessed higher affinities for nitrite and oxygen than previously reported for Nitrobacter, suggesting potential to compete in low-substrate environments. Long-read DNA sequencing provided a complete genome for strain MLSD-S22, revealing two plasmids and an intact nitrous oxide (N 2 O) reduction operon—an unexpected feature for Nitrobacter. While N 2 O reduction activity was not observed under the tested conditions, this discovery raises questions about the contribution of Nitrobacter NOB to the N 2 O sink. These findings broaden the physiological and genomic diversity of Nitrobacter, offering new insights into their adaptation strategies and providing a framework for future evaluation of their potential roles in nitrogen loss.

Nitrobacter↗

DOE OSTI2021

Investigating the Chemolithoautotrophic and Formate Metabolism of Nitrospira moscoviensis by Constraint-Based Metabolic Modeling and 13 C-Tracer Analysis

Nitrospira spp. are globally abundant nitrifying bacteria in soil and aquatic ecosystems and in wastewater treatment plants, where they control the oxidation of nitrite to nitrate. Despite their critical contribution to nitrogen cycling across diverse environments, detailed understanding of their metabolic network and prediction of their function under different environmental conditions remains a major challenge.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Annual Site Environmental Report (2019)

Los Alamos National Laboratory’s (the Laboratory’s) annual site environmental reports are prepared by the Laboratory’s environmental organizations, as required by U.S. Department of Energy Order 231.1B, Administrative Change 1, Environment, Safety, and Health Reporting, and Order 458.1, Administrative Change 3, Radiation Protection of the Public and the Environment. The following chapters in this report discuss our success in complying with environmental laws, regulations, and orders (Chapter 2, Compliance Summary); how we manage the Laboratory’s environmental performance (Chapter 3, Environmental Programs); how we monitor for air emissions of radioactive materials and climate conditions (Chapter 4, Air Quality); how we monitor for effects of Laboratory operations on groundwater quality (Chapter 5, Groundwater Protection); how we monitor the movement of chemicals and radionuclides by storm water runoff and the levels of chemicals and radionuclides in deposited sediment (Chapter 6, Watershed Quality); how we monitor for the presence, levels, and effects of chemicals and radionuclides in plants, animals, and soil (Chapter 7, Ecosystem Health); and finally, what radionuclide dose or risk from chemical exposure members of the public may experience as a result of Laboratory operations (Chapter 8, Public Dose and Risk Assessment).

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗