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At least 55 records · Page 3

Thermal adaptation of soil microbial growth traits in response to chronic warming

ABSTRACT Adaptation of soil microbes due to warming from climate change has been observed, but it remains unknown what microbial growth traits are adaptive to warming. We studied bacterial isolates from the Harvard Forest Long-Term Ecological Research site, where field soils have been experimentally heated to 5°C above ambient temperature with unheated controls for 30 years. We hypothesized that Alphaproteobacteria from warmed plots have (i) less temperature-sensitive growth rates; (ii) higher optimum growth temperatures; and (iii) higher maximum growth temperatures compared to isolates from control plots. We made high-throughput measurements of bacterial growth in liquid cultures over time and across temperatures from 22°C to 37°C in 2–3°C increments. We estimated growth rates by fitting Gompertz models to the growth data. Temperature sensitivity of growth rate, optimum growth temperature, and maximum growth temperature were estimated by the Ratkowsky 1983 model and a modified Macromolecular Rate Theory (MMRT) model. To determine evidence of adaptation, we ran phylogenetic generalized least squares tests on isolates from warmed and control soils. Our results showed evidence of adaptation of higher optimum growth temperature of bacterial isolates from heated soils. However, we observed no evidence of adaptation of temperature sensitivity of growth and maximum growth temperature. Our project begins to capture the shape of the temperature response curves, but illustrates that the relationship between growth and temperature is complex and cannot be limited to a single point in the biokinetic range. IMPORTANCE Soils are the largest terrestrial carbon sink and the foundation of our food, fiber, and fuel systems. Healthy soils are carbon sinks, storing more carbon than they release. This reduces the amount of carbon dioxide released into the atmosphere and buffers against climate change. Soil microbes drive biogeochemical cycling and contribute to soil health through organic matter breakdown, plant growth promotion, and nutrient distribution. In this study, we determined how soil microbial growth traits respond to long-term soil warming. We found that bacterial isolates from warmed plots showed evidence of adaptation of optimum growth temperature. This suggests that increased microbial biomass and growth in a warming world could result in greater carbon storage. As temperatures increase, greater microbial activity may help reduce the soil carbon feedback loop. Our results provide insight on how atmospheric carbon cycling and soil health may respond in a warming world.

59 BASIC BIOLOGICAL SCIENCES↗

Controlling matric potential in microfluidics to examine microbial dynamics in unsaturated porous media

The use of microfluidics for the study of soil microbial ecology is an emerging field. Most microfluidic studies of biological systems, however, have been performed under fully saturated conditions that are not representative of natural soil. Therefore, while microfluidics offer many unique capabilities that other methodologies cannot, they are not currently suited to address the effects of matric potential, an important variable defining the microbial moisture niche. Here, a methodology is presented that allows the user to control the aqueous conditions within microfluidic networks by manipulating matric potential using a hanging water column. The method relies on hydrophilic surface treatment of the microfluidic device using polyvinyl alcohol (PVA) and incorporating a bed of small pores at the network boundaries, which serve as a porous ceramic plate analogue (PPA). The method was validated on a simple capillary bundle and then on a more complex pore network. A water retention curve, exhibiting hysteresis, was generated for the pore network over a narrow matric potential range of 0 to – 5 kPa. Both the drainage and wetting curves were reproducible, as were the spatial configuration and the number of fragmented moisture niches in the pore network, particularly on the drainage curve. In contrast, the wetting curve exhibited greater variability in spatial configuration due to the “ink bottle effect,” where capillarity was interrupted by wider pore bodies. Ultimately, the methodology provides realistic pore-scale moisture conditions that can be easily manipulated and maintained, enabling new opportunities to explore soil biophysics and microbial biogeography in unsaturated porous media. As a brief example, images showing the localization of fluorescently tagged Pantoea sp. YR343 at −4.3 kPa are presented, highlighting bacterial distributions in water films and air-water interfaces.

59 BASIC BIOLOGICAL SCIENCES↗

Postfire Biogeochemical Processes: Implications to Source Water Quality in Fire-Influenced Watersheds

Forested watersheds are instrumental in providing purified and reliable water to millions of people worldwide. The changing climate has increased the frequency and severity of global fire events. Forested watersheds and their ecosystem functions are greatly disrupted during fire activity. Postfire concerns in forested watersheds include unpredictable and potentially simultaneous alterations in source water quality and hydro-biogeochemical processes. Here, the degree of fire severity can complexly modify water quality through the production of fire-transformed constituents on the burned forest floor (i.e., nutrients, metal(loid)s, dissolved organic matter, and the formation of disinfection byproducts). Correspondingly, fire severity and postfire rainfall patterns can refine hydro-biogeochemical processes that influence the transport of the fire-transformed constituents (i.e., vegetation function, soil structure, hydrological pathways, and microbial communities). Postfire alterations to water quality and hydro-biogeochemical processes introduce further complexity with varying temporal influence, which ranges from months to decades. As postfire water quality and watershed response research progresses, it is essential to homogenize interdisciplinary expertise to bridge knowledge gaps between fields ranging from forest ecology, hydrology, microbiology, and geochemistry. A multidisciplinary approach in wildfire research will facilitate a comprehensive perception of the diverse water quality risks associated with fire activity and mitigate fire concerns on a global level.

Disinfection Byproducts↗

Optimal reference genes for RNA tissue analysis in small animal models of hemorrhagic fever viruses

Abstract Reverse-transcription quantitative polymerase chain reaction assays are frequently used to evaluate gene expression in animal model studies. Data analyses depend on normalization using a suitable reference gene (RG) to minimize effects of variation due to sample collection, sample processing, or experimental set-up. Here, we investigated the suitability of nine potential RGs in laboratory animals commonly used to study viral hemorrhagic fever infection. Using tissues (liver, spleen, gonad [ovary or testis], kidney, heart, lung, eye, brain, and blood) collected from naïve animals and those infected with Crimean–Congo hemorrhagic fever (mice), Nipah (hamsters), or Lassa (guinea pigs) viruses, optimal species-specific RGs were identified based on five web-based algorithms to assess RG stability. Notably, the Ppia RG demonstrated stability across all rodent tissues tested. Optimal RG pairs that include Ppia were determined for each rodent species ( Ppia and Gusb for mice; Ppia and Hrpt for hamsters; and Ppia and Gapdh for guinea pigs). These RG pair assays were multiplexed with viral targets to improve assay turnaround time and economize sample usage. Finally, a pan-rodent Ppia assay capable of detecting Ppia across multiple rodent species was developed and successfully used in ecological investigations of field-caught rodents, further supporting its pan-species utility.

Davies, Katherine A.↗

Hanford Site Roadside Bird Surveys Report for Calendar Years 2021-2023

The U.S. Department of Energy, Hanford Field Office (HFO) conducts ecological monitoring on the Hanford Site to collect and track data needed to ensure compliance with an array of environmental laws, regulations, and policies governing HFO activities. Ecological monitoring data provide baseline information about the plants, animals, and habitats under HFO stewardship at Hanford which is required for decision-making under the National Environmental Policy Act (NEPA) and Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA). The Hanford Site Comprehensive Land Use Plan (CLUP, DOE/EIS-0222-F), which is the Environmental Impact Statement for Hanford Site activities, helps ensure that HFO, its contractors, and other entities conducting activities on the Hanford Site are in compliance with NEPA.

54 ENVIRONMENTAL SCIENCES↗

Hanford Reach Fall Chinook Salmon Redd Monitoring Report for Calendar Year 2024

The U.S. Department of Energy, Hanford Field Office (HFO) conducts ecological monitoring on the Hanford Site to collect and track data needed to ensure compliance with an array of environmental laws, regulations, and policies governing HFO activities. Ecological monitoring data provide baseline information about the plants, animals, and habitats under HFO stewardship at the Hanford Site required for decision making under the National Environmental Policy Act (NEPA) and Comprehensive Environmental Response, Compensation, and Liability Act. DOE/EIS-0222, Final Hanford Comprehensive Land-Use Plan Environmental Impact Statement, (CLUP) evaluates the potential environmental impacts associated with implementing a comprehensive land-use plan for the Hanford Site for at least the next 50 years, and ensures that HFO, its contractors, and other entities conduct activities on the Hanford Site in compliance with NEPA.

54 ENVIRONMENTAL SCIENCES↗

Hanford Reach Fall Chinook Salmon Redd Monitoring Report for Calendar Year 2023

The U.S. Department of Energy, Hanford Field Office (HFO) conducts ecological monitoring on the Hanford Site to collect and track data needed to ensure compliance with an array of environmental laws, regulations, and policies governing HFO activities. Ecological monitoring data provide baseline information about the plants, animals, and habitats under HFO stewardship at the Hanford Site required for decision making under the National Environmental Policy Act (NEPA) and Comprehensive Environmental Response, Compensation, and Liability Act. DOE/EIS-0222, Final Hanford Comprehensive Land-Use Plan Environmental Impact Statement, (CLUP) evaluates the potential environmental impacts associated with implementing a comprehensive land-use plan for the Hanford Site for at least the next 50 years, and ensures that HFO, its contractors, and other entities conduct activities on the Hanford Site in compliance with NEPA.

54 ENVIRONMENTAL SCIENCES↗

Hanford Site Freshwater Mussel Monitoring Report for Calendar Year 2024

The U.S. Department of Energy, Hanford Field Office (HFO) conducts ecological monitoring at the Hanford Site to collect and maintain data to ensure compliance with an array of environmental laws, regulations, and policies governing HFO activities. Ecological monitoring data provides baseline information about the plants, animals, and habitats under HFO stewardship at the Hanford Site that is required for decision making under the National Environmental Policy Act of 1969 and the Comprehensive Environmental Response, Compensation, and Liability Act of 1980. In addition, ecological monitoring helps ensure that HFO, its contractors, and other entities conducting activities at the Hanford Site are in compliance with DOE/EIS-0222-F, Final Hanford Comprehensive Land-Use Plan Environmental Impact Statement. HFO places priority on monitoring those plant and animal species or habitats with specific regulatory protections or requirements that are rare and/or declining (i.e., federal or state listed endangered, threatened, or sensitive species) or are of significant interest to federal, state, or tribal governments or the public.

54 ENVIRONMENTAL SCIENCES↗

Townsend's Ground Squirrel Conservation on the Hanford Site for Calendar Year 2025

The U.S. Department of Energy (DOE), Hanford Field Office (HFO) conducts ecological monitoring on the DOE-managed portion of Hanford Site (hereby referred to as Central Hanford) to collect and track data needed to ensure compliance with an array of environmental laws, regulations, and policies governing HFO activities. Ecological monitoring data provides baseline information about the plants, animals, and habitat under HFO stewardship on the Hanford Site, which is required for accurate ecological impact assessment decision making under the National Environmental Policy Act and the Comprehensive Environmental Response, Compensation, and Liability Act. In addition, ecological monitoring helps ensure that HFO, its contractors, and other entities conducting activities on the Hanford Site are in compliance with DOE/EIS-0222-F, Final Hanford Comprehensive Land Use Plan Environmental Impact Statement. HFO places priority on monitoring plant and animal species or habitats that have specific regulatory protections or requirements; that are rare and/or declining (federal or state listed endangered, threatened, or sensitive species); or are of significant interest to federal, state, or tribal governments or to the public.

54 ENVIRONMENTAL SCIENCES↗

Hanford Site Mule Deer Monitoring Report for Fiscal Years 2024 and 2026

The U.S. Department of Energy, Hanford Field Office (HFO) conducts ecological monitoring on the Hanford Site to collect and track data needed to ensure compliance with environmental laws, regulations, and policies governing Department of Energy activities. The vision for the HFOmanaged portion of the Hanford Site, hereby referred to as Central Hanford, focuses not only on the cleanup of nuclear facilities and waste sites but on the protection and restoration of the Hanford Site lands. As the HFO moves toward accomplishing this vision, understanding of the ecological resources present and the need for conservation and/or protection of those resources will be critical for making informed decisions for responsible site stewardship. Ecological monitoring data provides baseline information about the plants, animals, and habitats under HFO stewardship at Central Hanford required for decision-making under the National Environmental Policy Act of 1969 (NEPA) and Comprehensive Environmental Response, Compensation, and Liability Act of 1980.

54 ENVIRONMENTAL SCIENCES↗

Hanford Reach Fall Chinook Salmon Redd Monitoring Report for Calendar Year 2025

The U.S. Department of Energy, Hanford Field Office (HFO) conducts ecological monitoring on the Hanford Site to collect and track data needed to ensure compliance with an array of environmental laws, regulations, and policies governing HFO activities. Ecological monitoring data provide baseline information about the plants, animals, and habitats under HFO stewardship at the Hanford Site required for decision making. Fall Chinook salmon redds have been monitored at the Hanford Site annually since 1948, including aerial counts, to provide an index of relative abundance among spawning areas and years

54 ENVIRONMENTAL SCIENCES↗

New Orthophoto Generation Strategies from UAV and Ground Remote Sensing Platforms for High-Throughput Phenotyping

Remote sensing platforms have become an effective data acquisition tool for digital agriculture. Imaging sensors onboard unmanned aerial vehicles (UAVs) and tractors are providing unprecedented high-geometric-resolution data for several crop phenotyping activities (e.g., canopy cover estimation, plant localization, and flowering date identification). Among potential products, orthophotos play an important role in agricultural management. Traditional orthophoto generation strategies suffer from several artifacts (e.g., double mapping, excessive pixilation, and seamline distortions). The above problems are more pronounced when dealing with mid- to late-season imagery, which is often used for establishing flowering date (e.g., tassel and panicle detection for maize and sorghum crops, respectively). In response to these challenges, this paper introduces new strategies for generating orthophotos that are conducive to the straightforward detection of tassels and panicles. The orthophoto generation strategies are valid for both frame and push-broom imaging systems. The target function of these strategies is striking a balance between the improved visual appearance of tassels/panicles and their geolocation accuracy. The new strategies are based on generating a smooth digital surface model (DSM) that maintains the geolocation quality along the plant rows while reducing double mapping and pixilation artifacts. Moreover, seamline control strategies are applied to avoid having seamline distortions at locations where the tassels and panicles are expected. The quality of generated orthophotos is evaluated through visual inspection as well as quantitative assessment of the degree of similarity between the generated orthophotos and original images. Several experimental results from both UAV and ground platforms show that the proposed strategies do improve the visual quality of derived orthophotos while maintaining the geolocation accuracy at tassel/panicle locations.

54 ENVIRONMENTAL SCIENCES↗

Do We Need a New Sustainability Assessment Method for the Circular Economy? A Critical Literature Review

The goal of the circular economy (CE) is to transition from today's take-make-waste linear pattern of production and consumption to a circular system in which the societal value of products, materials, and resources is maximized over time. Yet circularity in and of itself does not ensure social, economic, and environmental performance (i.e., sustainability). Sustainability of CE strategies needs to be measured against their linear counterparts to identify and avoid strategies that increase circularity yet lead to unintended externalities. The state of the practice in quantitatively comparing sustainability impacts of circular to linear systems is one of experimentation with various extant methods developed in other fields and now applied here. While the proliferation of circularity metrics has received considerable attention, to-date, there is no critical review of the methods and combinations of methods that underlie those metrics and that specifically quantify sustainability impacts of circular strategies. Our critical review herein analyzes identified methods according to six criteria: temporal resolution, scope, data requirements, data granularity, capacity for measuring material efficiency potentials, and sustainability completeness. Results suggest that the industrial ecology and complex systems science fields could prove complementary when assessing the sustainability of the transition to a CE. Both fields include quantitative methods differing primarily with regard to their inclusion of temporal aspects and material efficiency potentials. Moreover, operations research methods such as multiple-criteria decision-making (MCDM) may alleviate the common contradictions which often exist between circularity metrics. This review concludes by suggesting guidelines for selecting quantitative methods most appropriate to a particular research question and making the argument that while there are a variety of existing methods, additional research is needed to combine existing methods and develop a more holistic approach for assessing sustainability impacts of CE strategies.

36 MATERIALS SCIENCE↗

Meeting report: The first soil viral workshop 2022

Soil viral ecology is a growing research field; however, the state of knowledge still lags behind that of aquatic systems. Therefore, to facilitate progress, the first Soil Viral Workshop was held to encourage international scientific discussion and collaboration, suggest guidelines for future research, and establish soil viral research as a concrete research area. The workshop took place at Søminestationen, Denmark, between 15 and 17th of June 2022. The meeting was primarily held in person, but the sessions were also streamed online. The workshop was attended by 23 researchers from ten different countries and from a wide range of subfields and career stages. Eleven talks were presented, followed by discussions revolving around three major topics: viral genomics, virus-host interactions, and viruses in the soil food web. The main take-home messages and suggestions from the discussions are summarized in this report.

09 BIOMASS FUELS↗

Clarifying Terminology in Microbial Ecology: A Call for Precision in Scientific Communication

The rapid evolution of microbiology as a field of research has led to the introduction of new terminology and the adaptation of existing terms. However, inconsistencies in the use of these terms, including variations across different scientific disciplines, can lead to confusion and miscommunication within the scientific community. This article discusses the importance of precise terminology in microbiome research, highlighting examples where terms have been misused or redefined without clear justification. We also present a list of frequently used terms in microbial ecology along with their specific definitions. We argue that the misuse of terminology can hinder scientific progress by creating ambiguity and misunderstanding. To address this, we propose a set of guidelines for the consistent use of key terms and provide clear definitions for some of the most commonly misused or newly introduced terms in the field. The definitions provided herein will also function as a guide for young researchers new to the field of microbial ecology. Accurate and consistent use of terminology is crucial for effective communication and collaboration in microbiology research. By adhering to standardised definitions, researchers can ensure that their work is clearly communicated and contributes meaningfully to the progress of science.

definitions↗

CHESS 2025: Field-collected vegetation attributes and site photos

This dataset represents field observations of vegetation samples collected as part of the Colorado Headwaters Ecological Spectroscopy Study (CHESS) during June and July of 2025. Samples were collected in the field using tablet computers and digital forms, with target data differing by sample type (individual trees, individual shrubs, or 1-meter square plots of meadow and subshrub vegetation). Field samples were collected within 72 hours of airborne data collection using the National Ecological Observatory Network’s Aerial Observation Platform (NEON AOP). The NEON AOP collected waveform LiDAR (Light Detection and Ranging) and imaging spectrometer data in 426 spectral bands from the visible to shortwave infrared. Remote sensing data for the project is available on ESS-DIVE (DOI and citation to be added upon publication). Field data collected included canopy height and per-species horizontal proportional cover for meadow plots, species identity and height information for shrubs, as well as species identity, height, diameter at breast height, and health assessment information for trees. Photos of the focal site and surrounding landscape were taken for all sampling sites and are included in this archive. Green leaves or needles were collected for plant trait and foliar chemistry analysis. This data is archived separately (DOI and citation to be added upon publication). High-precision geospatial data for each sample (crown perimeter polygons for trees and shrubs, plot boundaries for meadow plots) is available here (Henderson et al., 2026). Field and remote sensing protocols largely followed those of a previous field and airborne imaging campaign performed in 2018 (described in Chadwick et al. 2020). Field data from the 2018 campaign can be found here (Chadwick et al., 2020 doi:10.15485/1618130). Because different field measurements were taken for meadow, shrub, and tree sites, data from these three sample types are archived as separate tables (chess_meadow_site_cleaned.csv, chess_shrub_site_cleaned.csv, chess_tree_site_cleaned.csv). Meadow proportional cover data is stored in a separate table (chess_meadow_cover_cleaned.csv). Taxonomy was treated identically between sample types, and the dataset shares a common set of voucher specimens (chess_voucher_IDs_cleaned.csv), as well as a single species list (chess_species_list_cleaned.csv). All taxonomic determinations were performed to the species level, and adhere to the Global Biodiversity Information Facility (GBIF) backbone taxonomy as of January 10th, 2026 (GBIF Secretariat 2023). CHESS Project Description: The Colorado Headwaters Ecological Spectroscopy Study (CHESS) comprised a multi-week airborne remote sensing and field observation campaign in the Upper Gunnison Basin, Colorado, conducted in June and July of 2025. Airborne remote sensing was conducted by the National Ecological Observatory Network Airborne Observation Platform (NEON AOP), concurrent with a field campaign run by the Rocky Mountain Biological Laboratory (RMBL), the Lawrence Berkeley National Laboratory (LBNL) and SLAC National Accelerator Laboratory Watershed Function Science Focus Area (SFA), and NASA-JPL (Jet Propulsion Laboratory) Earth Surface Mineral Dust Source Investigation (EMIT) program. Between June 10 and July 18, 2025, the NEON AOP flight team collected high-resolution aerial imaging spectroscopy and Light Detection and Ranging (LiDAR) data over three domains: the Upper East River (CRBU), Almont Triangle (ALMO), and the Upper Taylor Basin (UPTA). In coordination with the flights, a field campaign acquired ground-truth observations, including observations of vegetation composition, foliar traits, forest demography, and subsurface properties in 18 core sampling areas within the domains. Additional surface water observations were taken at over 380 point locations. All CHESS campaign datasets can be found within the CHESS ESS-DIVE data portal: https://data.ess-dive.lbl.gov/portals/chess. Funding Acknowledgment: Field and remote-sensing data acquisition was performed under a grant from the National Aeronautics and Space Administration (80NSSC24K1005). This work was also supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231.

2018 NEON and 2025 CHESS Campaigns↗

CHESS 2025: Location data for field observations and sampling

This dataset represents geolocation data associated with field observations and sampling from the Colorado Headwaters Ecological Spectroscopy Study (CHESS) during June and July of 2025. Location data were collected using Trimble DA2 Global Navigation Satellite System (GNSS) receivers with Trimble Catalyst 2 centimeter (cm) positioning service and the Environmental Systems Research Institute (Esri) Field Maps mobile app. Files in this data package include meadow site polygons, shrub site polygons, tree site polygons and stem point locations, and Leaf Area Index (LAI) plot polygons (.geojson). The geojson files can be opened with open-source GIS software (e.g, QGIS). A csv file is also provided with point coordinates for all locations. CHESS Project Description: The Colorado Headwaters Ecological Spectroscopy Study (CHESS) comprised a multi-week airborne remote sensing and field observation campaign in the Upper Gunnison Basin, Colorado, conducted in June and July of 2025. Airborne remote sensing was conducted by the National Ecological Observatory Network Airborne Observation Platform (NEON AOP), concurrent with a field campaign run by the Rocky Mountain Biological Laboratory (RMBL), the Lawrence Berkeley National Laboratory (LBNL) and SLAC National Accelerator Laboratory Watershed Function Science Focus Area (SFA), and NASA-JPL (Jet Propulsion Laboratory) Earth Surface Mineral Dust Source Investigation (EMIT) program. Between June 10 and July 18, 2025, the NEON AOP flight team collected high-resolution aerial imaging spectroscopy and Light Detection and Ranging (LiDAR) data over three domains: the Upper East River (CRBU), Almont Triangle (ALMO), and the Upper Taylor Basin (UPTA). In coordination with the flights, a field campaign acquired ground-truth observations, including observations of vegetation composition, foliar traits, forest demography, and subsurface properties in 18 core sampling areas within the domains. Additional surface water observations were taken at over 380 point locations. All CHESS campaign datasets can be found within the CHESS ESS-DIVE data portal: https://data.ess-dive.lbl.gov/portals/chess. Funding Acknowledgment: Field and remote-sensing data acquisition was performed under a grant from the National Aeronautics and Space Administration (80NSSC24K1005). This work was also supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231.

2018 NEON and 2025 CHESS Campaigns↗

AmeriFlux FLUXNET-1F US-xJE NEON Jones Ecological Research Center (JERC)

This is the AmeriFlux Management Project (AMP) created FLUXNET-1F version of the carbon flux data for the site US-xJE NEON Jones Ecological Research Center (JERC). This is the FLUXNET version of the carbon flux data for the site US-xJE NEON Jones Ecological Research Center (JERC) produced by applying the standard ONEFlux (1F) software. Site Description - This terrestrial relocatable field site is located in the Joseph Jones Ecological Research Center is an 11,000-hectare reserve located within the Lower Coastal Plains and Flatwoods areas in southern Georgia. The Jones site has been managed with low intensity, dormant-season prescribed fires for the past 75 years at a frequency of every 3-4 years.

Network), NEON (National Ecological Observatory↗