Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “ecological modeling”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 325 records · Page 18
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Disentangling natural and anthropogenic effects on benthic macroinvertebrate assemblages in western US streams

Abstract Stream macroinvertebrate assemblages are shaped by natural and human‐related factors that operate through complex hierarchical pathways. Quantifying these relationships can provide additional insights into stream ecological assessment. We applied a structural equation modeling framework to evaluate hypothesized pathways by which watershed, riparian, and in‐stream factors affect benthic macroinvertebrate condition in the Western Mountains (WMT) and Xeric (XER) ecoregions in the United States. We developed a conceptual model grounded in theory, empirical evidence, and expert opinion to evaluate the following hypotheses: (1) macroinvertebrate assemblages are primarily driven by proximal, in‐stream factors (e.g., water quality and physical habitat); (2) anthropogenic land uses affect macroinvertebrates indirectly by altering in‐stream characteristics; and (3) riparian vegetation cover attenuates land use effects. We tested our model separately on three measures of benthic macroinvertebrate assemblage condition: ratio of observed‐to‐expected taxonomic richness (O/E); a multimetric index (MMI); and richness of Ephemeroptera, Plecoptera, and Trichoptera taxa (EPT). In the WMT, site‐level riparian cover, in‐stream physical habitat (relative bed stability), and water chemistry (total nitrogen) were the top three predictors of macroinvertebrate assemblages, each having over two times the magnitude of effect on macroinvertebrates compared with watershed‐level predictors. In the arid XER, annual precipitation and stream flow characteristics were top predictors of macroinvertebrate assemblages and had similar magnitudes of effect as in‐stream water chemistry. Path analyses revealed that land use activities in the watershed and at the stream site degraded macroinvertebrate assemblages indirectly by altering relative bed stability, water quality, and riparian cover/complexity. Increased riparian cover was associated with greater macroinvertebrate condition by reducing land use impacts on stream flow, streambed substrate, and water quality, but the pathways differed among ecoregions. In the WMT, site‐level riparian cover affected macroinvertebrate assemblages partly through indirect pathways associated with greater streambed stability and reduced total nitrogen concentrations. In contrast, in the XER, watershed‐level riparian cover affected macroinvertebrate assemblages through greater specific stream power. Identifying the relative effects of and pathways by which natural and anthropogenic factors affect macroinvertebrates can serve as a framework for prioritizing management and conservation efforts.

Environmental Sciences & Ecology↗
DOE OSTI2021

Tribal Revegetation Project Final Project Report: 92-Acre Area, Area 5 Radioactive Waste Management Complex, Nevada National Security Site, Nevada

Nuwu (Southern Paiute), Newe (Western Shoshone), and Nuumu (Owens Valley Paiute) are linguistically related, Numic-speaking peoples who are part of the broader Uto-Aztecan language group. Numic peoples view the land as a holistic, living, sentient being with feelings and purpose. The land is personified with human characteristics and it needs to be experienced to be understood through “learning by doing.” Numic peoples do not support ground disturbing activities within their ancestral lands, including activities tied to the storage of low-level radioactive waste or classified materials on the NNSS, which they view as culturally inappropriate. These deep-rooted ancestral connections are the impetus for reinforcing Numic responsibility for healing disturbed areas by integrating respect and patience with consistent Tribal interaction. Tribal Ecological Knowledge (TEK) is the science of describing Tribal approaches for understanding natural resources. Numic TEK is embedded in traditional teachings learned incrementally over time though experience and it evolves through lessons learned and responses to environmental changes over millennia. Therefore, TEK can broaden and enhance Western scientific knowledge associated with revegetation, especially in highly disturbed areas. The project blended TEK with Western scientific ecological methods to create a vegetative cover within test plots on the 92-Acre Area located at the Radioactive Waste Management Complex (RWMC) located in Area 5 on the Nevada National Security Site (NNSS). The vegetated test plots were systematically created for the Department of Energy (DOE) in tandem with the existing Federal Facilities Agreement and Consent Order (FFACO) with the Nevada Department of Environmental Protection (NDEP). Three previous contractor-lead attempts at revegetation, one targeting full cover revegetation and two targeting test plot revegetation, did not achieve the anticipated results at this location. When presented to the 16 American Indian Tribal nations and affiliated groups with cultural and historical ties to the NNSS, the group appointed a Tribal Revegetation Committee (TRC) that included six expert Tribal knowledge holders to collaborate with an ethnoecologist/cultural anthropologist and two biologists. Project design, planning, seed and outplant selection, spiritual land preparation, and methodology were guided by the TRC and an ethnoecologist/cultural anthropologist from Portland State University (PSU) and biologists from Desert Research Institute (DRI). Using TEK, the TRC recommended a specific seed mixture that contained nine native plant species and three species of outplants. The revegetation effort included preparing and planting thirty 10 m × 10 m (32.8 ft × 32.8 ft) seeded plots, twelve of which also included outplants; and eight 10 m × 100 m (32.8 ft × 328 ft) plots that only received outplants, all atop a waste cell cover. The TRC and the project team creatively adapted TEK with Western scientific methods so that the planned revegetation efforts could occur within the safety and security parameters of the RWMC. Test plots were subjected to one of five soil treatments with varying combinations of straw or mulch applications, soil amendment, and/or outplant planting and one of two watering treatments (watered or unwatered). Planting was divided into two events: one in the fall season and another during the subsequent spring season based on TEK and a corresponding recommendation from the TRC. Monitoring and spiritual management was conducted by the TRC to evaluate plant progress on a monthly basis (in conjunction with the biologist and anthropologist) during each respective growing season for a period of three years after planting. This approach allowed Tribal members the opportunity to conduct traditional blessings and other culturally appropriate activities to restore balance to the land in accordance with Tribal protocols. Following TEK-guided methods, successful plant establishment from seed stock and outplants was observed in many plots. Overall, plots planted in the spring, as recommended by the TRC, showed higher rates of outplant survival and native seedling emergence than those planted in the fall. This finding is significant because it is contrary to the original guidance and previous approaches provided for planting in this region. The TRC believes the frequent co-occurrence of native seedlings near surviving outplants indicates an important symbiotic relationship understood by Tribal communities and overlooked by others. Watered outplants displayed much higher survivability than unwatered plants, even after watering was reduced after the plants were established. Soil amendments and mulch created higher densities of native plants from seed. Many native seedlings showed significant delays in germination, which is considered a normal adaptation to desert climates. Some native plants did not germinate until the third growing year, whereas others germinated during the first growing year, which demonstrates the complexity of the desert environment. Evidence of native insects, reptiles, mammals, and birds, as well as native plants that were not part of the planted species, were noted and considered culturally significant. Despite the presence of non-native plants, native outplants continued to thrive and the incidence of native plant germination from seed increased over time. These successful revegetation results where previous efforts were unsuccessful reinforce the importance of integrating regionally appropriate, TEK-guided methodology with Western science to achieve positive results and the necessity of integrating Tribal involvement in all stages of the revegetation effort. Expanded approaches coupled with Tribal knowledge and tools from Western science addressed a complex problem tied to revegetating atop a low-level radioactive waste cell. The level of Tribal participation serves as a progressive model for building collaborative relationships and addressing ecological challenges on the NNSS.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Delayed fire mortality has long‐term ecological effects across the Southern Appalachian landscape

Abstract Fire is a critical ecological process to the forests of the Southern Appalachians. Where fire was excluded from forest types that historically burned frequently, unanticipated changes can occur when fire is reintroduced. For example, the development of new fuel characteristics can change the patterns of fire mortality and associated ecological responses. To test the fire effects of delayed fire mortality (mortality initiated by fire that occurs subsequent to the fire year) in the Southern Appalachians, USA, we developed a fire‐effects model using both field studies and remote sensing. We then simulated these effects at a landscape scale to estimate broader ecological effects. Fire‐effects models that accounted for delayed mortality increased landscape biomass removed annually (~23%) and increased the number of sites with high light conditions (leaf area index < 4) when compared to simulations that only account for immediate mortality. While delayed mortality occurred across species and age classes, it was especially prevalent among older trees (>100 years old) and fire‐resistant species ( Quercus spp.). Overall, regeneration (trees <20 years old) changed very little, even with the inclusion of delayed mortality. This evidence suggests that, even when accounting for delayed mortality, individual fires are unlikely to shift the landscape composition toward the conditions of forests prior to fire exclusion and may even increase mesophication long term due to the loss of overstory dominant xeric trees.

Robbins, Zachary J.↗
DOE OSTI2020

A Comparison of RESRAD and GoldSim Models for Assessing Radiological Dose for a RCRA Landfill - 20418

US Ecology Idaho (USEI) operates a Resource Conservation and Recovery Act (RCRA) Subtitle C, Hazardous Waste Treatment, Storage, and Disposal (TSD) Facility on a 640-acre property in Owyhee County, Idaho. USEI accepts a wide variety of RCRA-exempt low activity radioactive wastes, including naturally occurring radioactive material (NORM) and technologically enhanced NORM (TENORM) (USEI 2009). The performance of the landfill with regard to radiological operating permit requirements was previously assessed using a model constructed with the residual radioactivity (RESRAD) computer program, developed by Argonne National Laboratory for the U.S. Department of Energy (DOE). RESRAD supports the evaluation of several environmental transport pathways related to a radionuclide-contaminated soil source term, but it was not conceived as a model for the evaluation of landfill radiological performance. A more comprehensive and realistic model is desired in order to better support submissions to both the State of Idaho's Department of Environmental Quality as well as the U.S. Nuclear Regulatory Commission. A Performance Assessment (PA) computer model was developed using GoldSim software for the USEI RCRA Subtitle C landfill. The RESRAD computer model was specifically developed for calculating soil cleanup criteria and radiological dose and cancer risk from residual radioactive material in soil. To evaluate site-specific conditions, users may select from among a number of available environmental transport and exposure pathways and modify 'default' parameter values. In GoldSim, a user must construct the model 'from scratch.' However, this modeling is facilitated by a number of specialized elements available in GoldSim to support a radiological mass transport model. These include elements for defining radiological decay and ingrowth, container failure and radiological release, advective and diffusive transport, and other processes. Advantages afforded by the use of RESRAD for modeling radiological dose for a RCRA Subtitle C landfill include ease of use and reasonable flexibility in specifying site-specific conditions. GoldSim allows for considerably more flexibility and site-specificity than RESRAD, including evaluation of potentially relevant environmental transport processes not supported in RESRAD. The probabilistic modeling capabilities of GoldSim also far exceed those of RESRAD. The pros and cons of RESRAD and GoldSim for this modeling problem are explored with a focus on identifying approaches and critical factors in identifying the appropriate platform. The capabilities of RESRAD and GoldSim for mathematically modeling the disposal system will be contrasted and compared. For example, the existing RESRAD radiological safety assessment evaluated potentially complete exposure pathways related to infiltration to groundwater and upwards diffusion of radon. Additional transport pathways identified in the USEI Idaho facility Conceptual Site Model include deposition of radon decay products in cover material, root uptake of radionuclides in disposed wastes by native plants, and mixing of cover material by burrowing animals. Results of the two models and how the different transport and dose pathways affect results will be discussed. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2026

Evaluation of daily gridded climate products using in situ FLUXNET data and tree growth modeling

Gridded climate data products have facilitated research in climate and ecology by providing meteorological data continuously across large spatial scales. However, the sensitivity of scientific outcomes to dataset choice remains poorly understood, and evaluation using station-based records can favor datasets built heavily on weather stations. Here, we evaluate seven high-resolution daily gridded datasets covering the contiguous United States using independent meteorology from the FLUXNET2015 dataset, with a focus on the implications of dataset choice for process-based tree growth modeling. We find that gridded products tend to capture temperature accurately while consistently overestimating the magnitude and frequency of precipitation and its extremes. Moreover, datasets vary in how they define a ‘day,’ which significantly affects temporal alignment with FLUXNET2015 observations. Despite differences among the datasets, the interannual variability in tree ring simulations is insensitive to dataset choice, likely because daily-scale biases are averaged out through accumulated growth across several months. However, inaccuracies in temperature and precipitation can significantly bias modeled xylem cell production, with systematically higher annual precipitation in the gridded datasets leading to greater xylem production compared to simulations using in situ data. Our results suggest that model applications, especially those that integrate to time scales longer than one day, are likely insensitive to climate dataset choice, but applications that are sensitive to daily climate variations or to absolute climate values need to carefully consider biases in gridded climate products.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Stressors Reveal Ecosystems' Hidden Characteristics

Abstract Vegetation responds dynamically to local microclimates at both short and long time scales via mechanisms ranging from physiological behaviors, such as stomatal closure, to acclimation and adaptation. These responses influence the carbon, water, and energy cycles directly and are therefore crucial to understanding and predicting Earth system responses to a changing climate. Several recent studies have demonstrated that differences in microclimate can induce structural and functional acclimations, and potentially adaptations, within the same ecosystem. Such microclimate divergence can be caused by variability in slopes, disturbance history, or even localized resource availability. Ecosystem stressors such as low soil water availability, limited photoperiod, or high vapor pressure deficit have been shown to reveal the large impact of the subtle differences within these systems such as the number of sun versus shade leaves or differences in whole‐plant water acquisition and use. These findings highlight the linkages between plant canopy structure and ecosystem function, alongside the need for comprehensive analyses of vegetation within the broader context of its environment. This commentary addresses some of the key implications of ecosystem stress responses and accompanying acclimations across three ecosystem types for ecosystem ecology, plant physiology, ecohydrology and trait‐based modeling of vegetation‐climate dynamics.

Matheny, Ashley M.↗
DOE OSTI2021

Non-additive microbial community responses to environmental complexity

Environmental composition is a major, though poorly understood, determinant of microbiome dynamics. Here we ask whether general principles govern how microbial community growth yield and diversity scale with an increasing number of environmental molecules. By assembling hundreds of synthetic consortia in vitro, we find that growth yield can remain constant or increase in a non-additive manner with environmental complexity. Conversely, taxonomic diversity is often much lower than expected. To better understand these deviations, we formulate metrics for epistatic interactions between environments and use them to compare our results to communities simulated with experimentally-parametrized consumer resource models. We find that key metabolic and ecological factors, including species similarity, degree of specialization, and metabolic interactions, modulate the observed non-additivity and govern the response of communities to combinations of resource pools. Our results demonstrate that environmental complexity alone is not sufficient for maintaining community diversity, and provide practical guidance for designing and controlling microbial ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Organizing principles for vegetation dynamics

Understanding vegetation dynamics is very challenging because of the multitude of contributing processes at 64widely different spatial and temporal scales. In this Perspective we propose that understanding of vegetation dynamics can be improved, permitting better predictions, based on organizing principles that constrain plant and ecosystem be haviour: natural selection, self-organization, and entropy maximization. Although these ideas are increasingly used,a limited common understanding of their theoretical basis has prevented their full potential to be realized. We explain the power of natural selection-based optimality to predict photosynthesis and carbon allocation responses to multiple environmental drivers, and how individual plasticity leads to the predictable self-organization of forest canopies. We show how models of natural selection acting on a few key traits can generate realistic plant communities, and how entropy maximization can distinguish between stochastic and deterministic drivers of vegetation patterns. In combination with empirical exploration of patterns in plant functional variation, these principles can accelerate the development of dynamic vegetation models as well as trait-based ecology resting on strengthened theoretical and empirical foundations.

Geosciences↗
DOE OSTI2025

Intraspecific Reaction Norm Variation Controls the Eco-Evolutionary Consequences of Environmental Change

As environmental change accelerates globally, understanding concurrent organismal, species, and community responses is increasingly vital. Here, we examine these collective responses by incorporating genotype-specific thermal reaction norms into an eco-evolutionary predator-prey model, allowing us to track simultaneous phenotypic, ecological, and evolutionary responses to environmental change within ecological communities. We show that the reaction norms expressed by genotypes within a population determine how a community switches between different eco-evolutionary outcomes with changes in temperature. We identify how different components of phenotypic variation in thermal reaction norms—environmental (E), additive environmental and genetic (E + G), and gene-by-environment interactions (G × E)—influence eco-evolutionary dynamics and outcomes as temperature changes. Furthermore, our findings underscore how complex eco-evolutionary responses to environmental change ultimately emerge from variation in reaction norms among genotypes, offering new mechanistic insights into environmental impacts on adaptation, the maintenance of phenotypic and genetic variation, and ecological stability, which is crucial for understanding and predicting eco-evolutionary effects of rapid environmental change in the future.

Eco-evolutionary↗
DOE OSTI2021

Coordinated resource allocation to plant growth–defense tradeoffs

Summary Plant resource allocation patterns often reveal tradeoffs that favor growth (G) over defense (D), or vice versa. Ecologists most often explain G–D tradeoffs through principles of economic optimality, in which negative trait correlations are attributed to the reconciliation of fitness costs. Recently, researchers in molecular biology have developed ‘big data’ resources including multi‐omic (e.g. transcriptomic, proteomic and metabolomic) studies that describe the cellular processes controlling gene expression in model species. In this synthesis, we bridge ecological theory with discoveries in multi‐omics biology to better understand how selection has shaped the mechanisms of G–D tradeoffs. Multi‐omic studies reveal strategically coordinated patterns in resource allocation that are enabled by phytohormone crosstalk and transcriptional signal cascades. Coordinated resource allocation justifies the framework of optimality theory, while providing mechanistic insight into the feedbacks and control hubs that calibrate G–D tradeoff commitments. We use the existing literature to describe the coordinated resource allocation hypothesis (CoRAH) that accounts for balanced cellular controls during the expression of G–D tradeoffs, while sustaining stored resource pools to buffer the impacts of future stresses. The integrative mechanisms of the CoRAH unify the supply‐ and demand‐side perspectives of previous G–D tradeoff theories.

Monson, Russell K.↗
DOE OSTI2025

The architecture of resilience: a genome assembly of Myrothamnus flabellifolia sheds light on desiccation tolerance and sex determination

Myrothamnus flabellifolia is a dioecious resurrection plant endemic to southern Africa that has become an important model for understanding desiccation tolerance. Despite its ecological and medicinal significance, genomic and transcriptomic resources for the species are limited. We generated a chromosome-level, haplotype-resolved reference genome assembly and annotation for M. flabellifolia and conducted transcriptomic profiling across a natural dehydration–rehydration time course in the field. Genome architecture and sex determination were characterized, and co-expression network and cis-regulatory element (CRE) enrichment analyses were used to investigate dynamic responses to desiccation. The 1.28-Gb genome exhibits unusually consistent chromatin architecture with unique chromosome organization across highly divergent haplotypes. We identified an XY sexual system with a small sex-determining region on Chromosome 8. Transcriptomic responses varied with dehydration severity, pointing to early suppression of growth, progressive activation of protective mechanisms, and subsequent return to homeostasis upon rehydration. Late embryogenesis abundant and early light-induced protein transcripts were dynamically regulated and showed enrichment of abscisic acid and stress-responsive CREs pointing toward conserved responses. Together, this study provides foundational resources for understanding the genomic architecture and reproductive biology of M. flabellifolia and offers new insights into the mechanisms of desiccation tolerance.

chromosome structure↗
DOE OSTI2025

Infection and Genomic Properties of Single- and Double-Stranded DNA Cellulophaga Phages

Bacterial viruses (phages) are abundant and ecologically impactful, but laboratory-based experimental model systems vastly under-represent known phage diversity, particularly for ssDNA phages. Here, we characterize the genomes and infection properties of two unrelated marine flavophages—ssDNA generalist phage phi18:4 (6.5 Kbp) and dsDNA specialist phage phi18:1 (39.2 Kbp)—when infecting the same Cellulophaga baltica strain #18 (Cba18), of the class Flavobacteriia. Phage phi18:4 belongs to a new family of ssDNA phages, has an internal lipid membrane, and its genome encodes primarily structural proteins, as well as a DNA replication protein common to ssDNA phages and a unique lysis protein. Phage phi18:1 is a siphovirus that encodes several virulence genes, despite not having a known temperate lifestyle, a CAZy enzyme likely for regulatory purposes, and four DNA methyltransferases dispersed throughout the genome that suggest both host modulation and phage DNA protection against host restriction. Physiologically, ssDNA phage phi18:4 has a shorter latent period and smaller burst size than dsDNA phage phi18:1, and both phages efficiently infect this host. These results help augment the diversity of characterized environmental phage–host model systems by studying infections of genomically diverse phages (ssDNA vs. dsDNA) on the same host.

Howard-Varona, Cristina (ORCID:0000000241495818)↗
DOE OSTI2025

Discrete global grid system-based flow routing datasets in the Amazon and Yukon basins

Abstract. Discrete global grid systems (DGGS) are emerging spatial data structures widely used to organize geospatial datasets across scales. While DGGS have found applications in various scientific disciplines, including atmospheric science and ecology, their integration into physically based hydrological models and Earth system models (ESMs) has been hindered by the lack of flow routing datasets based on DGGS. In response to this gap, this study pioneers the development of new flow routing datasets using icosahedral Snyder equal-area (ISEA) DGGS and a novel mesh-independent flow direction model. We present flow routing datasets for two large basins, the tropical Amazon River basin and the Arctic Yukon River basin. These datasets (1) facilitate the adoption of DGGS for hydrological models and (2) provide flow routing inputs for evaluation of DGGS-based flow routing in the Amazon and Yukon river basins. The data are available at https://doi.org/10.5281/zenodo.8377765 (Liao, 2023).

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1986

Support for global science - Remote sensing's challenge

Advances in remote sensing techniques are discussed. The benefits possible to remote sensing with the new Earth Observing System, which is composed of the Space Station and coorbiting and polar satellite platforms, are examined. Current changes in the remote sensing field, which involve a change from an industrial society to an informational society, force technology to high technology with high touch, short term to long term, centralized to decentralized, hierarchies to networks, and either/or to multiple option systems are studied. The explanatory and objective types of analyses for investigating biophysical, geochemical, and socioeconomic processes are described; the procedures include: morphometric, cause and effect, temporal and functional and ecological system analyses, inventory, mapping, monitoring, and modeling.

Estes, J. E.↗
NASA NTRS1998

A natural view of microbial biodiversity within hot spring cyanobacterial mat communities

This review summarizes a decade of research in which we have used molecular methods, in conjunction with more traditional approaches, to study hot spring cyanobacterial mats as models for understanding principles of microbial community ecology. Molecular methods reveal that the composition of these communities is grossly oversimplified by microscopic and cultivation methods. For example, none of 31 unique 16S rRNA sequences detected in the Octopus Spring mat, Yellowstone National Park, matches that of any prokaryote previously cultivated from geothermal systems; 11 are contributed by genetically diverse cyanobacteria, even though a single cyanobacterial species was suspected based on morphologic and culture analysis. By studying the basis for the incongruity between culture and molecular samplings of community composition, we are beginning to cultivate isolates whose 16S rRNA sequences are readily detected. By placing the genetic diversity detected in context with the well-defined natural environmental gradients typical of hot spring mat systems, the relationship between gene and species diversity is clarified and ecological patterns of species occurrence emerge. By combining these ecological patterns with the evolutionary patterns inherently revealed by phylogenetic analysis of gene sequence data, we find that it may be possible to understand microbial biodiversity within these systems by using principles similar to those developed by evolutionary ecologists to understand biodiversity of larger species. We hope that such an approach guides microbial ecologists to a more realistic and predictive understanding of microbial species occurrence and responsiveness in both natural and disturbed habitats.

Review↗
NASA NTRS2021

TLSLEAF: Automatic Leaf Angle Estimates From Single-Scan Terrestrial Laser Scanning

Leaf angle distribution (LAD) in forest canopies affects estimates of leaf area, light interception, and global-scale photosynthesis, but is often simplified to a single theoretical value. Here, we present TLSLeAF (Terrestrial Laser Scanning Leaf Angle Function), an automated open-source method of deriving LADs from terrestrial laser scanning. TLSLeAF produces canopy-scale leaf angle and LADs by relying on gridded laser scanning data. The approach increases processing speed, improves angle estimates, and requires minimal user input. Key features are automation, leaf–wood classification, beta parameter output, and implementation in R to increase accessibility for the ecology community. TLSLeAF precisely estimates leaf angle with minimal distance effects on angular estimates while rapidly producing LADs on a consumer-grade machine. We challenge the popular spherical LAD assumption, showing sensitivity to ecosystem type in plant area index and foliage profile estimates that translate to c. 25% and c. 11% increases in canopy net photosynthesis (c. 25%) and solar-induced chlorophyll fluorescence (c. 11%). TLSLeAF can now be applied to the vast catalog of laser scanning data already available from ecosystems around the globe. The ease of use will enable widespread adoption of the method outside of remote-sensing experts, allowing greater accessibility for addressing ecological hypotheses and large-scale ecosystem modeling efforts.

3D↗
DOE OSTI2021

Predicting measures of soil health using the microbiome and supervised machine learning

Soil health encompasses a range of biological, chemical, and physical soil properties that sustain the commercial and ecological value of agroecosystems. Monitoring soil health requires a comprehensive set of diagnostics that can be cost-prohibitive for routine analyses. The soil microbiome provides a rich source of information about soil properties, which can be assayed in a high-throughput, cost-effective way. We evaluated the accuracy of random forest (RF) and support vector machine (SVM) regression and classification models in predicting 12 measures of soil health, tillage status, and soil texture from 16S rRNA gene amplicon data with an operationally relevant sample set. We validated the efficacy of the best performing models against independent datasets and also tested best practices for processing microbiome data for use in machine learning. Soil health metrics could be predicted from microbiome data with the best models achieving a Kappa value of ~0.65, for categorical assessments, and a R2 value of ~0.8, for numerical scores. Biological health ratings were better predicted than chemical or physical ratings. Validation with independent datasets revealed that models had general predictive value for soil properties, including yield. The ecological profiles of several taxa important for model accuracy matched the observed relationships with soil health, including Pyrinomonadaceae, Nitrososphaeraceae, and Candidatus Udeaobacter. Models trained at the highest taxonomic resolution proved most accurate, with losses in accuracy resulting from rarefying, sparsity filtering, and aggregating at higher taxonomic ranks. Furthermore, our study provides the groundwork for developing scalable technology to use microbiome-based diagnostics for the assessment of soil health.

16S rRNA gene↗