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At least 307 records · Page 17

Experimental testing of hypotheses for temperature‐ and pH ‐based niche specialization of ammonia oxidizing archaea and bacteria

Summary Investigation of niche specialization in microbial communities is important in assessing consequences of environmental change for ecosystem processes. Ammonia oxidizing bacteria (AOB) and archaea (AOA) present a convenient model for studying niche specialization. They coexist in most soils and effects of soil characteristics on their relative abundances have been studied extensively. This study integrated published information on the influence of temperature and pH on AOB and AOA into several hypotheses, generating predictions that were tested in soil microcosms. The influence of perturbations in temperature was determined in pH 4.5, 6 and 7.5 soils and perturbations in pH were investigated at 15°C, 25°C and 35°C. AO activities were determined by analysing changes in amoA gene and transcript abundances, stable isotope probing and nitrate production. Experimental data supported major predictions of the effects of temperature and pH, but with several significant discrepancies, some of which may have resulted from experimental limitations. The study also provided evidence for unpredicted activity of AOB in pH 4.5 soil. Other discrepancies highlighted important deficiencies in current knowledge, particularly lack of consideration of niche overlap and the need to consider combinations of factors when assessing the influence of environmental change on microbial communities and their activities.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Soils' dirty little secret: Depth–based comparisons can be inadequate for quantifying changes in soil organic carbon and other mineral soil properties

Quantifying changes in soil organic carbon (SOC) stocks and other soil properties is essential for understanding how soils will respond to land management practices and global change. Although they are widely used, comparisons of SOC stocks at fixed depth (FD) intervals are subject to errors when changes in bulk density or soil organic matter occur. The equivalent soil mass (ESM) method has been recommended in lieu of FD for assessing changes in SOC stocks in mineral soils, but ESM remains underutilized for SOC stocks and has rarely been used for other soil properties. In this paper, we draw attention to the limitations of the FD method and demonstrate the advantages of the ESM approach. We provide illustrations to show that the FD approach is susceptible to errors not only for quantifying SOC stocks but also for soil mass-based properties such as SOC mass percent, C:N mass ratio, and δ 13 C. Here we describe the ESM approach and show how it mitigates the FD method limitations. Using bulk density change simulations applied to an empirical dataset from bioenergy cropping systems, we show that the ESM method provides consistently lower errors than FD when quantifying changes in SOC stocks and other soil properties. To simplify the use of ESM, we detail how the method can be integrated into sampling schemes, and we provide an example R computer script that can perform ESM calculations on large datasets. We encourage future studies, whether temporal or comparative, to utilize sampling methods that are amenable to the ESM approach. Overall, we agree with previous recommendations that ESM should be the standard method for evaluating SOC stock changes in mineral soils, but we further suggest that ESM may also be preferred for comparisons of other soil properties including mass percentages, elemental mass ratios, and stable isotope composition.

59 BASIC BIOLOGICAL SCIENCES↗

Shifts in bacterial traits under chronic nitrogen deposition align with soil processes in arbuscular, but not ectomycorrhizal-associated trees

Nitrogen (N) deposition increases soil carbon (C) storage by reducing microbial activity. These effects vary in soil beneath trees that associate with arbuscular (AM) and ectomycorrhizal (ECM) fungi. Variation in carbon C and N uptake traits among microbes may explain differences in soil nutrient cycling between mycorrhizal associations in response to high N loads, a mechanism not previously examined due to methodological limitations. Here, we used quantitative Stable Isotope Probing (qSIP) to measure bacterial C and N assimilation rates from an added organic compound, which we conceptualize as functional traits. As such, we applied a trait-based approach to explore whether variation in assimilation rates of bacterial taxa can inform shifts in soil function under chronic N deposition. We show taxon-specific and community-wide declines of bacterial C and N uptake under chronic N deposition in both AM and ECM soils. N deposition-induced reductions in microbial activity were mirrored by declines in soil organic matter mineralization rates in AM but not ECM soils. Our findings suggest C and N uptake traits of bacterial communities can predict C cycling feedbacks to N deposition in AM soils, but additional data, for instance on the traits of fungi, may be needed to connect microbial traits with soil C and N cycling in ECM systems. In conclusion, our study also highlights the potential of employing qSIP in conjunction with trait-based analytical approaches to inform how ecological processes of microbial communities influence soil functioning.

59 BASIC BIOLOGICAL SCIENCES↗

Comparative nutrient drawdown capacities of farmed kelps and implications of metabolic strategy and nutrient source

Abstract Seaweed aquaculture, particularly kelp farming, is a popular topic as a potential solution for mitigating anthropogenic pollutants and enhancing coastal drawdown of carbon and nitrogen. Using a common garden approach, this study evaluated nutrient drawdown capacities of Alaria marginata (ribbon kelp) and Saccharina latissima (sugar kelp) across four commercial kelp farms in Southeast and Southcentral Alaska. Our findings show that A. marginata exhibited ~30% more carbon and 21% more nitrogen content compared to S. latissima . These results demonstrate the potential for A. marginata to serve as a more efficient species for nutrient drawdown into farmed kelp tissues (per unit biomass) for consideration of potential mitigative actions. The efficacy of this drawdown is likely to be driven by the careful pairing of kelp species with farming environment. Temporally, there was a noted increase in carbon content and a decline in nitrogen content from March to May for both species, consistent with known seasonal nutrient dynamics in coastal waters. Notably, differences in the carbon stable isotope signatures (δ 13 C) between the kelps may hint at variations in metabolic pathways and nutrient sourcing, particularly concerning the preferential assimilation of CO 2 versus , and highlight the need for further work on this topic for applied macroalgal research.

Stephens, Tiffany↗

Plants and mycorrhizal symbionts acquire substantial soil nitrogen from gaseous ammonia transport

Nitrogen (N) is an essential nutrient that limits plant growth in many ecosystems. Here we investigate an overlooked component of the terrestrial N cycle – subsurface ammonia (NH 3 ) gas transport and its contribution to plant and mycorrhizal N acquisition. In this work, we used controlled mesocosms, soil incubations, stable isotopes, and imaging to investigate edaphic drivers of NH 3 gas efflux, track lateral subsurface N transport originating from 15 NH 3 gas or 15 N-enriched organic matter, and assess plant and mycorrhizal N assimilation from this gaseous transport pathway. NH3 is released from soil organic matter, travels belowground, and contributes to root and fungal N content. Abiotic soil properties (pH and texture) influence the quantity of NH 3 available for subsurface transport. Mutualisms with arbuscular mycorrhizal (AM) fungi can substantially increase plant NH 3 -N uptake. The grass Brachypodium distachyon acquired 6–9% of total plant N from organic matter-N that traveled as a gas belowground. Colonization by the AM fungus Rhizophagus irregularis was associated with a two-fold increase in total plant N acquisition from subsurface NH 3 gas. NH 3 gas transport and uptake pathways may be fundamentally different from those of more commonly studied soil N species and warrant further research.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Hydrazinoacetic acid is a biosynthetic precursor of the bacterially produced nitramine, N -nitroglycine

Nitramines [R(R′)N–NO 2 ; R,R′=H or alkyl] are valuable synthetic products, but knowledge of the biosynthetic processes that generate these compounds is limited. This work sought to elucidate the biosynthesis of a nitramine natural product, N-nitroglycine (NNG) by Streptomyces noursei . Stable isotope studies showed that S. noursei cells supplemented with L-(ε- 15 N)lysine, ( 15 N)glycine, or ( 13 C)hydrazinoacetic acid (HAA) incorporated 67%, 88%, and 67% of the isotope label into NNG, respectively, indicating that these compounds are biosynthetic precursors of NNG. Liquid chromatography coupled tandem mass spectrometry (LC-MS/MS) of 15 N-Lys-labeled NNG confirmed that the nitro nitrogen of NNG originates from Lys. Bioinformatics analysis of the S. noursei genome showed evidence for a biosynthetic gene cluster (BGC) that contained machinery for HAA biosynthesis ( nngKLM ), consistent with the results of the isotope labeling. In vitro reconstitution of the gene products produced HAA. The borders of this BGC were defined by cross-referencing the predicted BGC with previously published differential proteomics data. Furthermore, we show that azaserine is produced alongside NNG in S. noursei cultures, linking the two biosynthetic pathways via a proposed nitrosamine biosynthetic intermediate. Finally, the oxygen balance for NNG is −20.2% for the formation of carbon dioxide (CO 2 ), which is comparable to that of hexahydro-1,3,5- trinitro-1,3,5-triazene (common name: RDX; −21.6%). Crystal structure data of NNG indicate that the unit crystalizes as a pure material, not a hydrate, suggesting a favorable energetic crystallization phase. The combined results suggest a route that, with further development, could lead to sustainable production of energetic nitramines via synthetic biology or biocatalytic approaches.

biosynthesis↗

Interpretation of hydrothermal conditions, production-injection induced effects, and evidence for enhanced geothermal system-type heat exchange in response to >30 years of production at Roosevelt Hot Springs, Utah, USA

The Roosevelt Hot Springs hydrothermal system is located at the base of the Mineral Mountains in southwestern Utah on the eastern side of the Basin and Range. Hydrothermal activity is related to relatively recent bimodal magmatism, and the system is hosted in coarsely crystalline rock made of Oligocene–Miocene granitoids and Precambrian gneiss. The hydrothermal plume covers ~5 km 2 , with a maximum temperature of 268 °C at ~750 m depth, and a vertically extensive fault-fracture mesh east of the Opal Mound fault controls the upflow of hydrothermal fluids. Power generation (currently 38 MWe gross) began in 1984, and up through 2016, four wells were used for fluid production, and three wells were used for edge-field injection. Chemical analyses of produced fluids show that modern reservoir fluid compositions are similar to but more concentrated than those at the start of production, having near-neutral pH, total dissolved solids of 7000–10,000 mg/kg, and ionic ratios of Cl/HCO 3 ~50–100, Cl/SO4 ~50–100, and Na/K ~4–5. Chemical geothermometers indicate equilibration temperatures that mainly range between 240° and 300 °C. Early production induced a steep drop in pressure (~3.0–3.5 MPa), which was accompanied by a 250–300 m lowering of piezometric levels in wells and development of a shallow steam zone across the system. Hydrothermal fluid compositions evolved continuously in response to production-related steam-loss and injection breakthrough, which is reflected by gradual increases in chloride of up to 35% and stable isotope ratios of up to ~2‰δ 18 O and ~10‰δD. Simple mixing model calculations suggest that there has been a significant amount, ~10–20 MW th , of sustained multi-decadal heat mining and enhanced geothermal system (EGS)–type heat transfer by the injectate as it returns to the production zone. Overall, the two factors that have sustained long-term power production (currently 38 MWe gross) are the increased upflow of deep chloride water and, to a lesser extent, the mining of heat at <1 km depth.

58 GEOSCIENCES↗

Has primary production declined in the Salish Sea?

Declining primary production has been proposed as an explanation for the declines in coho (Oncorhynchus kisutch) and Chinook (Oncorhynchus tshawytscha) salmon in the Salish Sea since the 1970s. Marine sediments maintain a continuous record of conditions in the overlying water. We used stable isotopes of organic carbon and nitrogen measured in 21 sediment cores to determine the contributions and fluxes of marine-derived and terrigenous organic matter over time. The flux of marine-derived organic matter shows no trend for at least the last 100 years. An apparent increase in the marine flux in recent years is due to remineralization of organic matter as it passes through surface sediments. In contrast, the flux of terrigenous organic matter has increased over the last century in the Strait of Georgia, while in Puget Sound, terrigenous flux peaked in the mid-20th century. Total primary production has neither increased nor decreased in the Salish Sea over the last century. Consequently, a decline in primary production cannot explain recent declines in fish populations.

58 GEOSCIENCES↗

Metal Organic Complexation in Seawater: Historical Background and Future Directions

The speciation of most biologically active trace metals in seawater is dominated by complexation by organic ligands. This review traces the history of work in this area, from the early observations that showed surprisingly poor recoveries using metal preconcentration protocols to the present day, where advances in mass spectroscopy and stable isotope geochemistry are providing new insights into the structure, origin, fate, and biogeochemical impact of organic ligands. Many long-standing hypotheses about the specific biological origin of ligands such as siderophores in seawater are finally being validated. This work has revealed the complexity of organic complexation, with multiple ligands and, in some cases, timescales of ligand exchange that are much slower than originally thought. The influence of organic complexation on scavenging is now a key parameter in biogeochemical models of biologically essential metals, especially iron. New insights about the sources and sinks of ligands are required to enhance the usefulness of these models.

Geochemistry & Geophysics↗

LANL contributions to isoWater R package

The ratio of heavy-to-light stable isotope abundance in water vapor is a tracer of atmospheric processes including evapotranspiration, condensation, mixing, and transport. Measurements of these isotope ratios at the surface, in the atmospheric column, or from satellites provide insights into atmospheric processes that cannot be gained from measurements of water vapor mixing ratios alone. A number of theoretical models for how water vapor isotope ratios should vary in response to atmospheric processes have been developed, and LANL contributions to the isoWater R package provides a simplified interface for calculating expected vapor isotope ratios based on these models and adding them to plots of water vapor isotope ratios.

Fiorella, Richard↗

Winter warming in Alaska accelerates lignin decomposition contributed by Proteobacteria

Background: In a warmer world, microbial decomposition of previously frozen organic carbon (C) is one of the most likely positive climate feedbacks of permafrost regions to the atmosphere. However, mechanistic understanding of microbial mediation on chemically recalcitrant C instability is limited; thus, it is crucial to identify and evaluate active decomposers of chemically recalcitrant C, which is essential for predicting C-cycle feedbacks and their relative strength of influence on climate change. Using stable isotope probing of the active layer of Arctic tundra soils after depleting soil labile C through a 975-day laboratory incubation, the identity of microbial decomposers of lignin and, their responses to warming were revealed. Results: The β - Proteobacteria genus Burkholderia accounted for 95.1% of total abundance of potential lignin decomposers. Consistently, Burkholderia isolated from our tundra soils could grow with lignin as the sole C source. A 2.2 °C increase of warming considerably increased total abundance and functional capacities of all potential lignin decomposers. In addition to Burkholderia , α - Proteobacteria capable of lignin decomposition (e.g. Bradyrhizobium and Methylobacterium genera) were stimulated by warming by 82-fold. Those community changes collectively doubled the priming effect, i.e., decomposition of existing C after fresh C input to soil. Consequently, warming aggravates soil C instability, as verified by microbially enabled climate-C modeling. Conclusions: Our findings are alarming, which demonstrate that accelerated C decomposition under warming conditions will make tundra soils a larger biospheric C source than anticipated.

54 ENVIRONMENTAL SCIENCES↗

Data for "A 13-year record indicates differences in the duration and depth of soil carbon accrual among potential bioenergy crops"

Data sets for material included in "A 13-year record indicates differences in the duration and depth of soil carbon accrual among potential bioenergy crops" by Kantola et al., 2025, in Global Change Biology Bioenergy. Data include soil organic carbon (SOC), carbon stable isotope ratios, annual belowground biomass, and annual post-harvest litter for four crops, maize/soybean, miscanthus, switchgrass, and prairie, between 2008 and 2021.

bioenergy crops↗

Multicellular magnetotactic bacteria are genetically heterogeneous consortia with metabolically differentiated cells

Consortia of multicellular magnetotactic bacteria (MMB) are currently the only known example of bacteria without a unicellular stage in their life cycle. Because of their recalcitrance to cultivation, most previous studies of MMB have been limited to microscopic observations. To study the biology of these unique organisms in more detail, we use multiple culture-independent approaches to analyze the genomics and physiology of MMB consortia at single-cell resolution. We separately sequenced the metagenomes of 22 individual MMB consortia, representing 8 new species, and quantified the genetic diversity within each MMB consortium. This revealed that, counter to conventional views, cells within MMB consortia are not clonal. Single consortia metagenomes were then used to reconstruct the species-specific metabolic potential and infer the physiological capabilities of MMB. To validate genomic predictions, we performed stable isotope probing (SIP) experiments and interrogated MMB consortia using fluorescence in situ hybridization (FISH) combined with nanoscale secondary ion mass spectrometry (NanoSIMS). By coupling FISH with bioorthogonal noncanonical amino acid tagging (BONCAT), we explored their in situ activity as well as variation of protein synthesis within cells. We demonstrate that MMB consortia are mixotrophic sulfate reducers and that they exhibit metabolic differentiation between individual cells, suggesting that MMB consortia are more complex than previously thought. These findings expand our understanding of MMB diversity, ecology, genomics, and physiology, as well as offer insights into the mechanisms underpinning the multicellular nature of their unique lifestyle.

59 BASIC BIOLOGICAL SCIENCES↗

Microbial ecology and biogeochemistry of hypersaline sediments in Orca Basin

In deep ocean hypersaline basins, the combination of high salinity, unusual ionic composition and anoxic conditions represents significant challenges for microbial life. We used geochemical porewater characterization and DNA sequencing based taxonomic surveys to enable environmental and microbial characterization of anoxic hypersaline sediments and brines in the Orca Basin, the largest brine basin in the Gulf of Mexico. Full-length bacterial 16S rRNA gene clone libraries from hypersaline sediments and the overlying brine were dominated by the uncultured halophilic KB1 lineage, Deltaproteobacteria related to cultured sulfate-reducing halophilic genera, and specific lineages of heterotrophic Bacteroidetes. Archaeal clones were dominated by members of the halophilic methanogen genus Methanohalophilus, and the ammonia-oxidizing Marine Group I (MG-I) within the Thaumarchaeota. Illumina sequencing revealed higher phylum- and subphylum-level complexity, especially in lower-salinity sediments from the Orca Basin slope. Illumina and clone library surveys consistently detected MG-I Thaumarchaeota and halotolerant Deltaproteobacteria in the hypersaline anoxic sediments, but relative abundances of the KB1 lineage differed between the two sequencing methods. The stable isotopic composition of dissolved inorganic carbon and methane in porewater, and sulfate concentrations decreasing downcore indicated methanogenesis and sulfate reduction in the anoxic sediments. While anaerobic microbial processes likely occur at low rates near their maximal salinity thresholds in Orca Basin, long-term accumulation of reaction products leads to high methane concentrations and reducing conditions within the Orca Basin brine and sediments.

54 ENVIRONMENTAL SCIENCES↗

Hawaii Play Fairway Analysis: Noble Gas Raw Data for Hawaii, Maui, Oahu, Kauai, and Lanai islands

Noble gas raw data for the Hawaiian islands of Big Island, Maui, Oahu, Lanai, and Kauai. Based on results from prior phases of the Hawaii Play Fairway Analysis, this project targeted 66 wells on the islands of Hawaii, Maui, Lanai, Oahu, and Kauai for sampling of dissolved noble gases, trace metals, common ions, and the stable isotopes 2H and 18O. Ultimately, 23 of the 66 well targets were sampled. Noble gas data from this study is supplemented with data shared by the United States Geologic Survey for the summit of Kilauea, and by the geothermal energy company Ormat Technologies Inc. for their geothermal power plant Puna Geothermal Venture on the Lower East Rift of Kilauea, and for their exploration of Kona and Hualalai on Hawaii, as well as the Southwest Rift of Haleakala on Maui. The noble gas helium is used as an indicator of geothermal heat when excess 3He and/or 4He is present when compared to the atmospheric ratio of those isotopes (R/Ra). R/Ra is minimally affected by dilution and transport, allowing even those wells not perfectly situated over a geothermal system to indicate a geothermal anomaly. R/Ra anomalies are present on every island in this study. There is a strong correlation between R/Ra anomalies and proximity to rift zones and calderas. The Hawaii Play Fairway project was funded by the U.S. Department of Energy Geothermal Technologies Office (award DE-EE0006729). For more information, see Colin Ferguson's Master of Science thesis "Exploration for Blind Geothermal Resources in the State of Hawaii Utilizing Dissolved Noble Gasses in Well Waters."

15 GEOTHERMAL ENERGY↗

Exploration for Blind Geothermal Resources in the State of Hawaii Utilizing Dissolved Noble Gasses in Well Waters

This study is an extension of the Hawaii Play Fairway Analysis (PFA), a statewide geothermal exploration project funded by the United States Department of Energy. Based on results from prior phases of the PFA, this project targeted 66 wells on the islands of Hawaii, Maui, Lanai, Oahu, and Kauai for sampling of dissolved noble gases, trace metals, common ions, and the stable isotopes 2H and 18O. Ultimately, 23 of the 66 well targets were sampled. The noble gas helium is used as an indicator of geothermal heat when excess 3He and/or 4He is present when compared to the atmospheric ratio of those isotopes (R/Ra). R/Ra is minimally affected by dilution and transport, allowing even those wells not perfectly situated over a geothermal system to indicate a geothermal anomaly. R/Ra anomalies are present on every island in this study. There is a strong correlation between R/Ra anomalies and proximity to rift zones and calderas. Across the islands R/Ra ranged from 15-16 on Kilauea's lower east rift zone, which is a mantle plume value, to 0.37 on Lanai, which is a crustal value. The majority of anomalous well samples had R/Ra values consistent with an upper mantle source. Mixing between upper mantle and crustal helium is evident on all islands. Geographically, R/Ra decreases from the high at Kilauea to upper mantle values at Mauna Loa, and remains at upper mantle values for all wells across the other volcanoes, with the exception of two of four sampled wells on Lanai.

15 GEOTHERMAL ENERGY↗

Waterlevel, geochemical, and borehole data from Rifle, Colorado from 2006-2016

The files included in this data package provide site wide water level data, geochemical data, and borehole information associated with the Rifle site in Colorado during the Lawrence Berkeley National Lab (LBNL) led Integrated Field Research Challenge (IFRC) and Scientific Focus Area (SFA) research projects. The data informs hydrogeochemical interactions occurring in the watershed. The readme file contains detailed metadata for the files, including naming conventions, column headers, and data validation.The borehole information is provided in the file called rifle_boreholes.csv. It provides names and location for boreholes/wells at the Rifle. The waterlevel data is provided in the folder rifle_waterlevels. The geochemical data is provided in two folders: the rifle_floodplain_geochemistry folder has data which was collected from wells across the floodplain and a variety of offsite locations that contribute solutes to the floodplain given their upgradient locations. The rifle_plotC_geochemistry folder has data which was collected primarily in plot C, which was a focused study area in which a large number of groundwater manipulation / biostimulation experiments were conducted. While not all geochemical constituents are included for each well location and sampling date, they include anions, cations, trace metals, dissolved organic and inorganic carbon, stable isotopes of water and sulfur (as sulfate), and water quality parameters including pH, groundwater electrical conductivity (EC) and dissolved oxygen (DO). All files are in csv or txt format.

54 ENVIRONMENTAL SCIENCES↗

Intra-canopy leaf trait variation facilitates high LAI and compensatory growth in a clonal woody encroaching shrub in the tallgrass prairie

This data package contains the data for Tooley et al. (2022) Intra-canopy leaf trait variation facilitates high leaf area index and compensatory growth in a clonal woody encroaching shrub. The purpose of this project was to evaluate the leaf ecophysiological traits of Cornus drummondii C.A. Mey to better understand how C. drummondii maximizes photosynthetic rates across large gradients of light availability in its short, dense canopies. We also evaluate how C. drummondii modifies its allocation of leaf traits in response to grassland disturbance. High LAI canopies and a compensatory growth response to disturbance are two key factors contributing to the success of C. drummondii and other woody species responsible for the encroachment of grasslands.The data package contains ecophysiological measurements, including leaf morphological, physiological, and chemical traits; photosynthetic measurements, leaf carbon and nitrogen stable isotopes, leaf area index, and photosynthetically active radiation. All measurements were taken vertically across canopies of the clonal woody-encroaching shrub Cornus drummondii under browsed, grazed, and control (unbrowsed and ungrazed) conditions.Files:SeasonalMeasurements_Archive.csv - Data for all seasonal measurements used in the study.LeafPhotoSeasonalRaw_Archive.zip - zip file containing raw data from an li-6400 for each sampling period in the study.LAI_Archive.xlsx - Data for LAI Measurements.ACiandLightCurveResults_Archive.xlsx - Contains parameters extracted from A-ci and Light Response curves along with the morphological and chemical traits for each leaf.ACiRaw Archive.xlsx - Raw data from Li-6400 for A-ci response curvesLightCurves_Raw.zip - zip file containing raw data for Li-6400 light response curves. Excel file format: "IslandID"-"Depth"-lc.xlsx (or .csv)DataCollectionMethods.docx - file containing the methods of data collection, processing, and QA/QC for all data files. File also contains a list of excel file headers, abbreviations, and their units.

54 ENVIRONMENTAL SCIENCES↗