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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.

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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Analysis of digitized herbarium records and community science observations provides a glimpse of downy mildew species diversity of North America, reveals potentially undescribed species, and documents the need for continued digitization and collecting

Downy mildew diseases caused by Peronosporaceae cause significant crop losses globally, with several emerging and resurgent threats in recent decades. Biodiversity data from digitized herbarium specimens provide an opportunity to develop a baseline census of species diversity, however, these resources may represent aggregations of nonrandom and opportunistic collecting efforts, which could lead to spurious results. Here, the MyCoPortal census of digitized herbarium records for downy mildew species collected from North America 1800 to present were analyzed. From 9838 unique records, 196 species were identified, reflecting ~28% of known species diversity. Temporal and geographic collecting biases were observed, with 90% of the collections made prior to 1960 and the efforts of six “super-collectors” accounting for 25% of the collections. The presence of 50–100 undescribed species in North America was inferred from the records. Together, these results highlight the need for continued downy mildew collections, taxonomic research and digitization efforts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Characterizing Boreal Peatland Plant Composition and Species Diversity with Hyperspectral Remote Sensing

Peatlands, which account for approximately 15% of land surface across the arctic and boreal regions of the globe, are experiencing a range of ecological impacts as a result of climate change. Factors that include altered hydrology resulting from drought and permafrost thaw, rising temperatures, and elevated levels of atmospheric carbon dioxide have been shown to cause plant community compositional changes. Shifts in plant composition affect the productivity, species diversity, and carbon cycling of peatlands. We used hyperspectral remote sensing to characterize the response of boreal peatland plant composition and species diversity to warming, hydrologic change, and elevated CO2. Hyperspectral remote sensing techniques offer the ability to complete landscape-scale analyses of ecological responses to climate disturbance when paired with plot-level measurements that link ecosystem biophysical properties with spectral reflectance signatures. Working within two large ecosystem manipulation experiments, we examined climate controls on composition and diversity in two types of common boreal peatlands: a nutrient rich fen located at the Alaska Peatland Experiment (APEX) in central Alaska, and an ombrotrophic bog located in northern Minnesota at the Spruce and Peatland Responses Under Changing Environments (SPRUCE) experiment. We found a strong effect of plant functional cover on spectral reflectance characteristics. We also found a positive relationship between species diversity and spectral variation at the APEX field site, which is consistent with other recently published findings. Based on the results of our field study, we performed a supervised land cover classification analysis on an aerial hyperspectral dataset to map peatland plant functional types (PFTs) across an area encompassing a range of different plant communities. Our results underscore recent advances in the application of remote sensing measurements to ecological research, particularly in far northern ecosystems.

McPartland, Mara (ORCID:0000000212420438)↗
DOE OSTI2022

MIDAS2: Metagenomic Intra-species Diversity Analysis System

The Metagenomic Intra-Species Diversity Analysis System (MIDAS) is a scalable metagenomic pipeline that identifies single nucleotide variants (SNVs) and gene copy number variants in microbial populations. Here, we present MIDAS2, which addresses the computational challenges presented by increasingly large reference genome databases, while adding functionality for building custom databases and leveraging paired-end reads to improve SNV accuracy. This fast and scalable reengineering of the MIDAS pipeline enables thousands of metagenomic samples to be efficiently genotyped.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Drought responses by individual tree species are not often correlated with tree species diversity in European forests

Drought frequency and intensity are predicted to increase in many parts of the Northern Hemisphere and the effects of such changes on forest growth and tree mortality are already evident in many regions around the world. Mixed-species forests and increasing tree species diversity have been put forward as important risk reduction and adaptation strategies in the face of climate change. But, little is known about whether the species interactions that occur in diverse forests will reduce drought susceptibility or water stress. In this study, we focused on the effect of drought on individual tree species (n = 16) within six regions of Europe and assessed whether this response was related to tree species diversity and stand density, and whether community-level responses resulted from many similar or contrasting species-level responses. For each species in each plot, we calculated the increase in carbon isotope composition of latewood from a wet to a dry year (Δδ13C) as an estimate of its drought stress level. Furthermore, when significant community-level relationships occurred (three of six regions), there was only one species within the given community that showed a significant relationship (three of 25 species–region combinations), showing that information about a single species can be a poor indicator of the response of other species or the whole community. There were many two-species mixtures in which both species were less water-stressed compared with their monocultures, but also many mixtures where both species were more stressed compared with their monocultures. Furthermore, a given species combination responded differently in different regions. Synthesis and applications. Our study shows that drought stress may sometimes be reduced in mixed-species forests, but this is not a general pattern, and even varies between sites for a given combination. The management or prediction of drought stress requires consideration of the physiological characteristics of the mixed species, and how this complements the water-related climatic and edaphic features of the site, rather than species richness.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2016

Species diversity driven by morphological and ecological disparity: a case study of comparative seed morphology and anatomy across a large monocot order

Phenotypic variation can be attributed to genetic heritability as well as biotic and abiotic factors. Across Zingiberales, there is a high variation in the number of species per clade and in phenotypic diversity. Factors contributing to this phenotypic variation have never been studied in a phylogenetic or ecological context. Seeds of 166 species from all eight families in Zingiberales were analyzed for 51 characters using synchrotron based 3D X-ray tomographic microscopy to determine phylogenetically informative characters and to understand the distribution of morphological disparity within the order. All families are distinguishable based on seed characters. Non-metric multidimensional scaling analyses show Zingiberaceae occupy the largest seed morphospace relative to the other families, and environmental analyses demonstrate that Zingiberaceae inhabit both temperate and tropical regions, while other Zingiberales are almost exclusively tropical. Temperate species do not cluster in morphospace nor do they share a common suite of character states. This suggests that the diversity seen is not driven by adaptation to temperate niches; rather, the morphological disparity seen likely reflects an underlying genetic plasticity that allowed Zingiberaceae to repeatedly colonize temperate environments. The notable morphoanatomical variety in Zingiberaceae seeds may account for their extraordinary ecological success and high species diversity as compared to other Zingiberales.

Cannaceae↗
DOE OSTI2025

Tree-level carbon stock estimations across diverse species using multi-source remote sensing integration

Forests are critical carbon sinks, and remote sensing has been increasingly widely used for forest monitoring and biomass estimations. However, species-specific tree-level studies remain limited. In this study, we demonstrated the feasibility of integrating UAV-based LiDAR with high-resolution optical satellite imagery (0.5 m) to estimate biomass for individual trees across different species. The proposed method accurately estimated biomass for 53 trees (R² = 0.82, rRMSE = 0.44), with species-specific datasets, showing an average 25.2% increase in R² and a 14.8% reduction in rRMSE. A novel vegetation index combining forest structure parameters with vegetation indices (VIs) was developed using high-resolution multispectral satellite data (3 m) to explore its relationship with individual tree biomass. Combining forest structural parameters with VIs further improved estimation accuracy, achieving an R²of 0.89 and an rRMSE of 0.34. Species-specific datasets show an 11.6% increase in R²compared to methods without VIs, and a 22.2% improvement over methods using only VIs. SHapley Additive exPlanations (SHAP) analysis shows that the volume feature played a key role in model performance and remained stable throughout the training process. Altogether, the proposed approach enhances individual tree biomass and carbon sink estimations, showing great potential for large-scale precise forest carbon monitoring using multi-source remote sensing data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Frequency-based modulation of diverse species in a nucleic acid library

A method of processing a collection of nucleic acid sequences is provided including connecting an adaptor to one or more or each nucleic acid sequence in the collection to create a processed nucleic acid template library, wherein the adaptor includes a first DNA sequence encoding a PAM sequence and at least a tracr mate.

Kalhor, Reza↗
DOE OSTI2017

Primary and heterotrophic productivity relate to multikingdom diversity in a hypersaline mat

Benthic microbial ecosystems are widespread yet knowledge gaps still remain on the relationships between the diversity of species across kingdoms and productivity. Here, we ask two fundamental questions: (i) How does species diversity relate to the rates of primary and heterotrophic productivity? (ii) How do diel variations in light-energy inputs influence productivity and microbiome diversity? To answer these questions, microbial mats from a magnesium sulfate hypersaline lake were used to establish microcosms. Both the number and relatedness between bacterial and eukaryotic taxa in the microbiome were assayed via amplicon-based sequencing of 16S and 18S rRNA genes over two diel cycles. These results correlated with biomass productivity obtained from substrate-specific 13 C stable isotope tracers that enabled comparisons between primary and heterotrophic productivity. Both bacterial and eukaryotic species richness and evenness were related only to the rates of 13 C-labeled glucose and acetate biomass incorporation. Interestingly, measures of these heterotrophic relationships changed from positive and negative correlations depending on carbon derived from glucose or acetate, respectively. The bacterial and eukaryotic diversity of this ecosystem is also controlled, in part, from energy constraints imposed by changing irradiance over a diel cycle.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2018

Co-occurring woody species have diverse hydraulic strategies and mortality rates during an extreme drought: Belowground hydraulic failure during drought

From 2011 to 2013, Texas experienced its worst drought in recorded history. This event provided a unique natural experiment to assess species-specific responses to extreme drought and mortality of four co-occurring woody species: Quercus fusiformis, Diospyros texana, Prosopis glandulosa and Juniperus ashei. We examined hypothesized mechanisms that could promote these species’ diverse mortality patterns using post-drought measurements on surviving trees coupled to retrospective process modeling. The species exhibited a wide range of gas exchange responses, hydraulic strategies, and mortality rates. Multiple proposed indices of mortality mechanisms were not consistent with the observed mortality patterns across species, including measures of iso/anisohydry, photosynthesis, carbohydrate depletion, and hydraulic safety margins. Large losses of growing season whole-tree conductance (driven by belowground losses of conductance), and shallower rooting depths, were associated with species that exhibited greater mortality. Based on this retrospective analysis, we suggest that species more vulnerable to drought were more likely to have succumbed to hydraulic failure belowground.

carbon gain↗
DOE OSTI2016

Informing models through empirical relationships between foliar phosphorus, nitrogen and photosynthesis across diverse woody species in tropical forests of Panama

Here, our objective was to analyze and summarize data describing photosynthetic parameters and foliar nutrient concentrations from tropical forests in Panama to inform model representation of phosphorus (P) limitation of tropical forest productivity. Gas exchange and nutrient content data were collected from 144 observations of upper canopy leaves from at least 65 species at two forest sites in Panama, differing in species composition, rainfall and soil fertility. Photosynthetic parameters were derived from analysis of assimilation rate vs internal CO 2 concentration curves ( A/C i ), and relationships with foliar nitrogen (N) and P content were developed. The relationships between area-based photosynthetic parameters and nutrients were of similar strength for N and P and robust across diverse species and site conditions. The strongest relationship expressed maximum electron transport rate (J max ) as a multivariate function of both N and P, and this relationship was improved with the inclusion of independent data on wood density. Models that estimate photosynthesis from foliar N would be improved only modestly by including additional data on foliar P, but doing so may increase the capability of models to predict future conditions in P-limited tropical forests, especially when combined with data on edaphic conditions and other environmental drivers.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Phylometagenomics of cycad coralloid roots reveals shared symbiotic signals

Cycads are known to host symbiotic cyanobacteria, includingNostocalesspecies, as well as other sympatric bacterial taxa within their specialized coralloid roots. Yet, it is unknown if these bacteria share a phylogenetic origin and/or common genomic functions that allow them to engage in facultative symbiosis with cycad roots. To address this, we obtained metagenomic sequences from 39 coralloid roots sampled from diverse cycad species and origins in Australia and Mexico. Culture-independent shotgun metagenomic sequencing was used to validate sub-community co-cultures as an efficient approach for functional and taxonomic analysis. Our metanalysis shows a host-independent microbiome core consisting of seven bacterial orders with high species diversity within the identified taxa. Moreover, we recovered 43 cyanobacterial metagenome-assembled genomes, and in addition toNostocspp., symbiotic cyanobacteria of the genusAulosirawere identified for the first time. Using this robust dataset, we used phylometagenomic analysis to reveal three monophyletic cyanobiont clades, two host-generalist and one cycad-specific that includesAulosiraspp. Although the symbiotic clades have independently arisen, they are enriched in certain functional genes, such as those related to secondary metabolism. Furthermore, the taxonomic composition of associated sympatric bacterial taxa remained constant. Our research quadruples the number of cycad cyanobiont genomes and provides a robust framework to decipher cyanobacterial symbioses, with the potential of improving our understanding of symbiotic communities. This study lays a solid foundation to harness cyanobionts for agriculture and bioprospection, and assist in conservation of critically endangered cycads.

Genetics & Heredity↗
DOE OSTI2016

Vertical Structure of Phyllosphere Fungal Communities in a Tropical Forest in Thailand Uncovered by High-Throughput Sequencing

Phyllosphere fungi harbor a tremendous species diversity and play important ecological roles. However, little is known about their distribution patterns within forest ecosystems. We examined how species diversity and community composition of phyllosphere fungi change along a vertical structure in a tropical forest in Thailand. Fungal communities in 144 leaf samples from 19 vertical layers (1.28–34.4 m above ground) of 73 plant individuals (27 species) were investigated by metabarcoding analysis using Ion Torrent sequencing. In total, 1,524 fungal operational taxonomic units (OTUs) were detected among 890,710 reads obtained from the 144 leaf samples. Taxonomically diverse fungi belonging to as many as 24 orders of Ascomycota and 21 orders of Basidiomycota were detected, most of which inhabited limited parts of the lowest layers closest to the forest floor. Species diversity of phyllosphere fungi was the highest in the lowest layers closest to the forest floor, decreased with increasing height, and lowest in the canopy; 742 and 55 fungal OTUs were detected at the lowest and highest layer, respectively. On the layers close to the forest floor, phyllosphere fungal communities were mainly composed of low frequency OTUs and largely differentiated among plant individuals. Conversely, in the canopy, fungal communities consisted of similar OTUs across plant individuals, and as many as 86.1%–92.7% of the OTUs found in the canopy (≥22 m above ground) were also distributed in the lower layers. Overall, our study showed the variability of phyllosphere fungal communities along the vertical gradient of plant vegetation and environmental conditions, suggesting the significance of biotic and abiotic variation for the species diversity of phyllosphere fungi.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Effects of industrial disturbances on biodiversity of carrion-associated beetles

Energy production systems such as nuclear reactors and coal-burning power plants produce a multitude of waste contaminants including radionuclides, trace elements, and heavy metals. Among invertebrates, much of the effort to understand the impact of these contaminants has focused in aquatic environments, while relatively less attention has been on terrestrial communities. In this work, we investigated the effects of trace element and radionuclide contamination on assemblages of beetles that are drawn to vertebrate carrion. Samples were collected from riparian sites at the Savannah River Site in South Carolina to compare trap catches (i.e., measure of relative abundance) of beetles and species diversity along a habitat gradient (0–300 m) away from an aquatic habitat and between uncontaminated and contaminated sites. We collected 17,800 carrion-associated beetles representing 112 species in nine families, which were classified as either scavenger or predatory beetles. Beetle catches and species diversity were generally higher at contaminated than uncontaminated sites. These trends were likely driven by scavenger species, which showed similar patterns between sites, whereas patterns of catches and species diversity were variable between sites for predatory beetles. Species compositions of contaminated and uncontaminated sites were generally distinct, however habitat edges appeared to substantially affect beetle assemblages. Overall, our study suggests carrion beetle assemblages are sensitive to edge effects and may exhibit variable responses to the presence of anthropogenic contaminants or disturbances associated with energy production systems. Such results reflect the inherent variability among individual beetle species, populations, and communities to local environmental conditions, and underscores the need for multi-taxa approach in environmental impact assessments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Passive Acoustic Monitoring Provides Insights into Avian Use of Energycane Cropping Systems in Southern Florida

Birds are important indicators of ecosystem health and provide a range of benefits to society. It is important, therefore, to understand the impacts of agricultural land use changes on bird populations. The cultivation of energycane (EC)—a sugarcane hybrid—for biofuel production represents one form of agricultural land use change in southern Florida. We used passive acoustic monitoring (PAM) to examine bird community use of experimental EC fields and other agricultural land uses at two study sites in southern Florida. We deployed 16 acoustic recorders in different study plots and used the automatic species identifier BirdNET to identify 40 focal bird species. We found seasonal differences in daily avian species diversity and richness between EC experimental plots and reference agricultural fields (corn fields, orchards, pastureland), and between time periods (pre-planting, post-planting). Daily avian species diversity and richness were lower in the EC experimental plots during Fall and Winter months when plants reached maximum height (>400 cm in some areas). Despite seasonal differences in daily measures of species diversity and richness, we found no differences in cumulative species richness, suggesting that there may be little overall (season-long) effects of EC production. These findings could provide insight to avian seasonal habitat preferences and underscore the potential limitations of PAM in areas experiencing dynamic vegetation changes. More research is needed to better understand if utilization of EC cropping systems results in positive or negative effects on avian populations (e.g., foraging habitat quality, predator–prey dynamics, nest success).

BirdNET↗
DOE OSTI2023

Targeted rRNA depletion enables efficient mRNA sequencing in diverse bacterial species and complex co-cultures

Bacterial mRNA sequencing is inefficient due to the abundance of ribosomal RNA that is challenging to deplete. While commercial kits target rRNA from common bacterial species, they are frequently inefficient when applied to divergent species, including those from environmental isolates. Similarly, other methods typically employ large probe sets that tile the entire length of rRNAs; however, such approaches are infeasible when applied to many species. Therefore, we present EMBR-seq+, which requires fewer than 10 oligonucleotides per rRNA by combining rRNA blocking primers with RNase H-mediated depletion to achieve rRNA removal efficiencies of up to 99% in diverse bacterial species. Furthermore, in more complex microbial co-cultures between Fibrobacter succinogenes strain UWB7 and anaerobic fungi, EMBR-seq+ depleted both bacterial and fungal rRNA, with a fourfold improvement in bacterial rRNA depletion compared with a commercial kit, thereby demonstrating that the method can be applied to non-model microbial mixtures. Notably, for microbes with unknown rRNA sequences, EMBR-seq+ enables rapid iterations in probe design without requiring to start experiments from total RNA. Finally, efficient depletion of rRNA enabled systematic quantification of the reprogramming of the bacterial transcriptome when cultured in the presence of the anaerobic fungi Anaeromyces robustus or Caecomyces churrovis. We observed that F. succinogenes strain UWB7 downregulated several lignocellulose-degrading carbohydrate-active enzymes in the presence of anaerobic gut fungi, suggesting close interactions between two cellulolytic species that specialize in different aspects of biomass breakdown. Thus, EMBR-seq+ enables efficient, cost-effective, and rapid quantification of the transcriptome to gain insights into non-model microbial systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Prairies Thrive Where Row Crops Drown: A Comparison of Yields in Upland and Lowland Topographies in the Upper Midwest US

Cellulosic biofuel production is expected to increase in the US, and the targeted establishment of biofuel agriculture in marginal lands would reduce competition between biofuels and food crops. While poorly drained, seasonally saturated lowland landscape positions are marginal for production of row crops and switchgrass (Panicum virgatum L.), it is unclear whether species-diverse tallgrass prairie yield would suffer similarly in saturated lowlands. Prairie yields typically increase as graminoids become more dominant, but it is uncertain whether this trend is due to greater aboveground net primary productivity (ANPP) or higher harvest efficiency in graminoids compared to forbs. Belowground biomass, a factor that is important to ecosystem service provisioning, is reduced when switchgrass is grown in saturated lowlands, but it is not known whether the same is true in species-diverse prairie. Our objectives were to assess the effect of topography on yields and live belowground biomass in row crops and prairie, and to determine the mechanisms by which relative graminoid abundance influences tallgrass prairie yield. We measured yield, harvest efficiency, and live belowground biomass in upland and lowland landscape positions within maize silage (Zea mays L.), winter wheat (Triticum aestivum L.), and restored tallgrass prairie. Maize and winter wheat yields were reduced by more than 60% in poorly drained lowlands relative to well-drained uplands, but diverse prairie yields were equivalent in both topographic settings. Prairie yields increased by approximately 45% as the relative abundance of graminoids increased from 5% to 95%. However, this trend was due to higher harvest efficiency of graminoids rather than greater ANPP compared to forbs. In both row crops and prairie, live belowground biomass was similar between upland and lowland locations, indicating consistent biomass nutrient sequestration potential and soil organic matter inputs between topographic positions. While poorly drained, lowland landscape positions are marginal lands for row crops, they appear prime for the cultivation of species-diverse tallgrass prairie for cellulosic biofuel.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Aggregation of Leslie matrix models with application to ten diverse animal species

Some grouping is necessary when constructing a Leslie matrix model because it involves discretizing a continuous process of births and deaths. Here, the level of grouping is determined by the number of age classes and frequency of sampling. It is largely unknown what is lost or gained by using fewer age classes, and I address this question using aggregation theory. I derive an aggregator for a Leslie matrix model using weighted least squares, determine what properties an aggregated matrix inherits from the original matrix, evaluate aggregation error, and measure the influence of aggregation on asymptotic and transient behaviors. To gauge transient dynamics, I employ reactivity of the standardized Leslie matrix. I apply the aggregator to 10 Leslie models developed for animal populations drawn from a diverse set of species. Several properties are inherited by the aggregated matrix: (a) it is a Leslie matrix; (b) it is irreducible whenever the original matrix is irreducible; (c) it is primitive whenever the original matrix is primitive; and (d) its stable population growth rate and stable age distribution are consistent with those of the original matrix if the least squares weights are equal to the original stable age distribution. In the application, depending on the population modeled, when the least squares weights do not follow the stable age distribution, the stable population growth rate of the aggregated matrix may or may not be approximately consistent with that of the original matrix. Transient behavior is lost with high aggregation.

54 ENVIRONMENTAL SCIENCES↗