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At least 217 records · Page 12

The 2025 “Hacking Limnology” Workshop Series and DSOS Virtual Summit: A Half Decade of Data‐Intensive Aquatic Science

The 5th Aquatic Ecosystem MOdeling Network—Junior (AEMON-J) “Hacking Limnology” Workshop and 6th Virtual Summit: Incorporating Data Science and Open Science in the Aquatic Sciences (DSOS) convened 21–25 July 2025. As in previous years (Fig. 1; Meyer and Zwart 2020; Meyer et al. 2021b, 2021c, 2022, 2024), the virtual workshops and summit were free of charge, the content was formatted to allow for broad engagement from a globally distributed audience, and workshop materials and recordings were made available on the AEMON-J/DSOS archive (Meyer et al. 2021a). In contrast to previous years, which primarily focused on inland aquatic ecosystems, this year's workshops and summit showcased a notable plurality of ecosystem types, with workshops spanning marine, riverine, and lacustrine environments. The weeklong event brought together researchers and practitioners interested in the nexus of data science, open science, and the aquatic sciences, hosting between 47 and 65 attendees at a single time and a higher number of registrants (n = 389), who might opt to access the material asynchronously.

Meyer, Michael F. [US Geological Survey, Portland,↗

N 2 Onet: a global collaborative network facilitating advances in measurement, modeling, and mitigation of agricultural soil nitrous oxide emissions

Nitrogen (N) fertilizer supports global food production, but its use and overuse drive emissions of nitrous oxide (N 2 O), a potent and long-lived greenhouse gas. Understanding the drivers of N 2 O fluxes remains elusive, making it difficult to predict emissions in time and space and to develop and evaluate ways to lower emissions through management. Major scientific uncertainties underlying the understanding of the drivers of N 2 O fluxes identified in a workshop of N 2 O emissions experts include poor process-based understanding of controls on soil N 2 O emissions in the field; insufficient data to reduce uncertainty in N 2 O budgets from the field to regional scales, including N 2 O emission measurements and importantly, field-scale N balances; and high uncertainty in model predictions of soil N 2 O emissions across environmental and management conditions. To reduce these uncertainties, we present the concept of N 2 Onet, a global collaborative initiative to accelerate advances in N 2 O measurement, analyses, and mitigation. N 2 Onet will serve as an observational network of supersites with multi-scale measurements; a database hub for N 2 O flux and ancillary data; and a catalyst for community building, information sharing, and training. By coalescing and coordinating the global community of researchers, N 2 Onet will provide a roadmap for reducing N 2 O emissions from agriculture worldwide.

54 ENVIRONMENTAL SCIENCES↗

PS3: The Pheno-Synthesis software suite for integration and analysis of multi-scale, multi-platform phenological data

Phenology is the study of recurring plant and animal life-cycle stages which can be observed across spatial and temporal scales that span orders of magnitude (e.g., organisms to landscapes). The variety of scales at which phenological processes operate is reflected in the range of methods for collecting phenologically relevant data, and the programs focused on these collections. Consideration of the scale at which phenological observations are made, and the platform used for observation, is critical for the interpretation of phenological data and the application of these data to both research questions and land management objectives. However, there is currently little capacity to facilitate access, integration and analysis of cross-scale, multi-platform phenological data. This paper reports on a new suite of software and analysis tools – the “Pheno-Synthesis Software Suite,” or PS3 – to facilitate integration and analysis of phenological and ancillary data, enabling investigation and interpretation of phenological processes at scales ranging from organisms to landscapes and from days to decades. We use PS3 to investigate phenological processes in a semi-aride, mixed shrub-grass ecosystem, and find that the apparent importance of seasonal precipitation to vegetation activity (i.e., “greenness”) is affected by the scale and platform of observation. We end by describing potential applications of PS3 to phenological modeling and forecasting, understanding patterns and drivers of phenological activity in real-world ecosystems, and supporting agricultural and natural resource management and decision-making.

54 ENVIRONMENTAL SCIENCES↗

Attention-based convolutional capsules for evapotranspiration estimation at scale

Evapotranspiration (ET) measures the amount of water lost from the Earth's surface to the atmosphere and is an integral metric for both agricultural and environmental sciences. Understanding and quantifying ET is critical for achieving effective management of freshwater and irrigation systems. However, current ET estimation models suffer from a trade-off between accuracy and spatial coverage. In this study, we introduce our model Quench, a neural network architecture that achieves highly-accurate ET estimates over large continuous spatial extents. Quench uses our novel Attention-Based Convolutional Capsule for its neural network layers to identify areas of focus and efficiently extract ET information from satellite imagery. Benchmarks that profile our model's performance show substantive improvements in accuracy, with up to 128% increase in accuracy compared to traditional convolutional-based and process-based models. Finally, Quench also demonstrates consistent model performance over high geospatial variability and a diverse array of regions, seasons, climates, and vegetations.

54 ENVIRONMENTAL SCIENCES↗

PAVC: The foundation for a Pan-Arctic Vegetation Cover database

Field-measured Arctic vegetation cover data is essential for creating accurate, high-quality vegetation structure and composition maps. Extrapolating field data into high-resolution cover maps provides detailed, function-specific information for use in Earth System Models, vegetation classifications, and monitoring vegetation change over time and space. However, field campaigns that collect plant cover vary substantially in scope, method, and purpose, which makes them difficult to unify across data stores, and they are often not designed to meet remote sensing needs. In this work, we synthesized and harmonized field-based fractional cover data from various data stores to create a high-quality, consistent repository schema for remote sensing-based vegetation cover mapping applications. We developed a reproducible workflow for synthesizing visual estimate and point-intercept fractional cover data. The resultant Pan-Arctic Vegetation Cover (PAVC) database contains synthesized fractional cover at both the species and plant functional type levels. The latter includes absolute foliar cover for deciduous shrubs and trees, evergreen shrubs and trees, forbs, graminoids, lichen, bryophytes, and “other” vegetation, as well as absolute cover for litter and top cover for water and bare ground.

Steckler, Morgan R. [Oak Ridge National Laboratory↗

Fine-Root Ecology Database (FRED): A Global Collection of Root Trait Data with Coincident Site, Vegetation, Edaphic, and Climatic Data, Version 4.

To address the need for a centralized root trait database, we compiled the Fine-Root Ecology Database (FRED) from published and unpublished data sources. We have continued to add to the FRED database since the release of FRED 1.0 in 2017, followed by 2.0 in 2018, and 3.0 in 2021. This new release of FRED 4.0 now has 213,941 observations of 238 root traits, for a combined total of roughly 3.4 million data fields for root traits and ancillary data together. FRED 4.0 has 39.8% more root trait observations than FRED 3.0 and a 34.4% increase in unique data sources. This release of FRED 4.0 also includes significant increases in geographic regions that have long been underrepresented in global datasets, notably in the tropical low latitudes. Ancillary data on associated site, vegetation, edaphic, and climatic conditions from across the globe have also increased concurrently with root trait observations. FRED is focused on fine roots (traditionally defined as roots less than 2 mm in diameter), as coarse roots are studied using different methodology, often at very different scales, and have different traits and trait interpretations. Despite this fine-root focus, FRED accepts data collected from roots of all sizes and contains observations of many root classes including coarse roots. Data collection will continue for the foreseeable future. The FRED4_Entire_Database_2026.csv file is the flat csv data file for FRED 4.0, and the FRED4_dd.csv file is the data dictionary of all columns available in FRED, including column IDs, column names, definitions, and unit (where applicable).

54 ENVIRONMENTAL SCIENCES↗

VLM4Bio: A Benchmark Dataset to Evaluate Pretrained Vision-Language Models for Trait Discovery from Biological Images

Images are increasingly becoming the currency for documenting biodiversity on the planet, providing novel opportunities for accelerating scientific discoveries in the field of organismal biology, especially with the advent of large vision-language models (VLMs). We ask if pre-trained VLMs can aid scientists in answering a range of biologically relevant questions without any additional fine-tuning. In this paper, we evaluate the effectiveness of 12 state-of-the-art (SOTA) VLMs in the field of organismal biology using a novel dataset, VLM4Bio, consisting of 469K question8 answer pairs involving 30K images from three groups of organisms: fishes, birds, and butterflies, covering five biologically relevant tasks. We also explore the effects of applying prompting techniques and tests for reasoning hallucination on the performance of VLMs, shedding new light on the capabilities of current SOTA VLMs in answering biologically relevant questions using images

Maruf, M [Virginia Tech, Blacksburg]↗

AmeriFlux US-xCL NEON LBJ National Grassland (CLBJ)

This is the AmeriFlux version of the carbon flux data for the site US-xCL NEON LBJ National Grassland (CLBJ). Site Description - The LBJ Grasslands is 16,800 acres of land managed by the US Forest Service under the US Department of Agriculture. There is a rich legacy of land use, ranging back to the mid-19th century. Currently, LBJ Grasslands are used for recreation and hunting, livestock grazing, and fossil fuel extraction. Ongoing ecological monitoring is performed at the site, along with prescribed burning.

Network), NEON (National Ecological Observatory↗

AmeriFlux FLUXNET-1F US-xCL NEON LBJ National Grassland (CLBJ)

This is the AmeriFlux Management Project (AMP) created FLUXNET-1F version of the carbon flux data for the site US-xCL NEON LBJ National Grassland (CLBJ). This is the FLUXNET version of the carbon flux data for the site US-xCL NEON LBJ National Grassland (CLBJ) produced by applying the standard ONEFlux (1F) software. Site Description - The LBJ Grasslands is 16,800 acres of land managed by the US Forest Service under the US Department of Agriculture. There is a rich legacy of land use, ranging back to the mid-19th century. Currently, LBJ Grasslands are used for recreation and hunting, livestock grazing, and fossil fuel extraction. Ongoing ecological monitoring is performed at the site, along with prescribed burning.

Network), NEON (National Ecological Observatory↗

Predicting lake surface water phosphorus dynamics using process-guided machine learning

Phosphorus (P) loading to lakes is degrading the quality and usability of water globally. Accurate predictions of lake P dynamics are needed to understand whole-ecosystem P budgets, as well as the consequences of changing lake P concentrations for water quality. However, complex biophysical processes within lakes, along with limited observational data, challenge our capacity to reproduce short-term lake dynamics needed for water quality predictions, as well as long-term dynamics needed to understand broad scale controls over lake P. Here we use an emerging paradigm in modeling, process-guided machine learning (PGML), to produce a phosphorus budget for Lake Mendota (Wisconsin, USA) and to accurately predict epilimnetic phosphorus over a time range of days to decades. In our implementation of PGML, which we term a Process-Guided Recurrent Neural Network (PGRNN), we combine a process-based model for lake P with a recurrent neural network, and then constrain the predictions with ecological principles. We test independently the process-based model, the recurrent neural network, and the PGRNN to evaluate the overall approach. The process-based model accounted for most of the observed pattern in lake P; however it missed the long-term trend in lake P and had the worst performance in predicting winter and summer P in surface waters. The root mean square error (RMSE) for the process-based model, the recurrent neural network, and the PGRNN was 33.0 μg P L -1 , 22.7 μg P L -1 , and 20.7 μg P L -1 , respectively. All models performed better during summer, with RMSE values for the three models (same order) equal to 14.3 μg P L -1 , 10.9 μg P L -1 , and 10.7 μg P L -1 . Although the PGRNN had only marginally better RMSE during summer, it had lower bias and reproduced long-term decreases in lake P missed by the other two models. For all seasons and all years, the recurrent neural network had better predictions than process alone, with root mean square error (RMSE) of 23.8 μg P L -1 and 28.0 μg P L -1 , respectively. The output of PGRNN indicated that new processes related to water temperature, thermal stratification, and long term changes in external loads are needed to improve the process model. By using ecological knowledge, as well as the information content of complex data, PGML shows promise as a technique for accurate prediction in messy, real-world ecological dynamics, while providing valuable information that can improve our understanding of process.

54 ENVIRONMENTAL SCIENCES↗

Integrated Land Suitability Assessment for Depots Siting in a Sustainable Biomass Supply Chain

A sustainable biomass supply chain would require not only an effective and fluid transportation system with a reduced carbon footprint and costs, but also good soil characteristics ensuring durable biomass feedstock presence. Unlike existing approaches that fail to account for ecological factors, this work integrates ecological as well as economic factors for developing sustainable supply chain development. For feedstock to be sustainably supplied, it necessitates adequate environmental conditions, which need to be captured in supply chain analysis. Using geospatial data and heuristics, we present an integrated framework that models biomass production suitability, capturing the economic aspect via transportation network analysis and the environmental aspect via ecological indicators. Production suitability is estimated using scores, considering both ecological factors and road transportation networks. These factors include land cover/crop rotation, slope, soil properties (productivity, soil texture, and erodibility factor) and water availability. This scoring determines the spatial distribution of depots with priority to fields scoring the highest. Two methods for depot selection are presented using graph theory and a clustering algorithm to benefit from contextualized insights from both and potentially gain a more comprehensive understanding of biomass supply chain designs. Graph theory, via the clustering coefficient, helps determine dense areas in the network and indicate the most appropriate location for a depot. Clustering algorithm, via K-means, helps form clusters and determine the depot location at the center of these clusters. An application of this innovative concept is performed on a case study in the US South Atlantic, in the Piedmont region, determining distance traveled and depot locations, with implications on supply chain design. The findings from this study show that a more decentralized depot-based supply chain design with 3depots, obtained using the graph theory method, can be more economical and environmentally friendly compared to a design obtained from the clustering algorithm method with 2 depots. In the former, the distance from fields to depots totals 801,031,476 miles, while in the latter, it adds up to 1,037,606,072 miles, which represents about 30% more distance covered for feedstock transportation.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

AmeriFlux FLUXNET-1F US-xKA NEON Konza Prairie Biological Station - Relocatable (KONA)

This is the AmeriFlux Management Project (AMP) created FLUXNET-1F version of the carbon flux data for the site US-xKA NEON Konza Prairie Biological Station - Relocatable (KONA). This is the FLUXNET version of the carbon flux data for the site US-xKA NEON Konza Prairie Biological Station - Relocatable (KONA) produced by applying the standard ONEFlux (1F) software. Site Description - Konza Prairie Biological Station (KPBS) was established to provide a "natural laboratory" to conduct ecological research and is located on a 3,487 hectare native tallgrass prairie preserve.

Network), NEON (National Ecological Observatory↗

AmeriFlux FLUXNET-1F US-xKZ NEON Konza Prairie Biological Station (KONZ)

This is the AmeriFlux Management Project (AMP) created FLUXNET-1F version of the carbon flux data for the site US-xKZ NEON Konza Prairie Biological Station (KONZ). This is the FLUXNET version of the carbon flux data for the site US-xKZ NEON Konza Prairie Biological Station (KONZ) produced by applying the standard ONEFlux (1F) software. Site Description - Konza Prairie Biological Station (KPBS) was established to provide a "natural laboratory" to conduct ecological research and is located on a 3,487 hectare native tallgrass prairie preserve. KPBS is a field research station dedicated to conservation, education and long-term ecological research. Over 1,580 scientific papers have been published by scientists conducting studies at KPBS. The study of ecological patterns and processes in native tallgrass prairie ecosystems is the primary subject of research.

Network), NEON (National Ecological Observatory↗

AmeriFlux US-xGR NEON Great Smoky Mountains National Park, Twin Creeks (GRSM)

This is the AmeriFlux version of the carbon flux data for the site US-xGR NEON Great Smoky Mountains National Park, Twin Creeks (GRSM). Site Description - Great Smoky Mountains National Park straddles the ridgeline of the Great Smoky Mountains, the lower section in latitude of the Blue Ridge Mountains, which divides the larger Appalachian Mountain chain. The border between Tennessee and North Carolina runs northeast to southwest through the centerline of the park. Plants and animals common in the country's Northeast have found suitable ecological niches in the park's higher elevations, while southern species find homes in the balmier lower reaches.

Network), NEON (National Ecological Observatory↗

AmeriFlux FLUXNET-1F US-xGR NEON Great Smoky Mountains National Park, Twin Creeks (GRSM)

This is the AmeriFlux Management Project (AMP) created FLUXNET-1F version of the carbon flux data for the site US-xGR NEON Great Smoky Mountains National Park, Twin Creeks (GRSM). This is the FLUXNET version of the carbon flux data for the site US-xGR NEON Great Smoky Mountains National Park, Twin Creeks (GRSM) produced by applying the standard ONEFlux (1F) software. Site Description - Great Smoky Mountains National Park straddles the ridgeline of the Great Smoky Mountains, the lower section in latitude of the Blue Ridge Mountains, which divides the larger Appalachian Mountain chain. The border between Tennessee and North Carolina runs northeast to southwest through the centerline of the park. Plants and animals common in the country's Northeast have found suitable ecological niches in the park's higher elevations, while southern species find homes in the balmier lower reaches.

Network), NEON (National Ecological Observatory↗

AmeriFlux FLUXNET-1F US-xHA NEON Harvard Forest (HARV)

This is the AmeriFlux Management Project (AMP) created FLUXNET-1F version of the carbon flux data for the site US-xHA NEON Harvard Forest (HARV). This is the FLUXNET version of the carbon flux data for the site US-xHA NEON Harvard Forest (HARV) produced by applying the standard ONEFlux (1F) software. Site Description - The Harvard Forest site is comprised of 3,750 acres of land and multiple research facilities; it is the core NEON site for the Northeast region. Harvard Forest is a department of the Faculty of Arts and Sciences of Harvard University. Representative habitats at Harvard Forest include northern, transition, and central forests; marshes, swamps, and conifer-dominated bogs; and forest plantations. Since its inception in 1907, research and education have been the focus of Harvard Forest: the original purpose was to develop a field laboratory for students, a research center in forestry and related disciplines, and a demonstration of practical sustained forestry. Since 1988, Harvard Forest has been a Long-Term Ecological Research site, funded by the National Science Foundation to conduct integrated, long-term studies of forest dynamics.

Network), NEON (National Ecological Observatory↗

Multi‐Omics Analyses Reveal Divergent Molecular Mechanisms Underlying Plant Biomass Conversion by Five Fungi

Fungal plant biomass conversion (FPBC) is of great importance to the global carbon cycle and has been increasingly applied for the production of biofuel and biochemicals from lignocellulose. However, the comprehensive understanding of relevant molecular mechanisms in different fungi remains challenging. Here, we comparatively analyzed the transcriptome, proteome and metabolome profile of four ascomycetes and one basidiomycete fungi during their growth on two common agricultural feedstocks (soybean hulls and corn stover). We revealed strong time‐, substrate‐ and species‐specific responses at multi‐omics levels for the tested fungi, highlighting species‐specific carbon utilization approaches and evolutionary adaptation to environmental niches. Notably, a remarkable expressional diversity of lignocellulose degrading enzymes, sugar transporter and metabolic genes, as well as industrially relevant metabolites were identified across different fungi and cultivation conditions. The findings improves our understanding of complex molecular networks underlying FPBC and fungal ecological roles, offering novel insights that can guide future genetic engineering of fungi for valorization of agriculture waste into value‐added bioproducts.

CAZy↗