Results for “conservation biology” — Page 3

DOE OSTI2026

Protection of U.S. streams is insufficient to safeguard stream diversity and prevent habitat impairment

Despite covering a small portion of Earth’s surface, streams support a disproportionate amount of biodiversity. Here, we measure progress against the Global Biodiversity Framework 30×30 protection target for streams within the conterminous U.S., in terms of quantity, representation, and effectiveness of habitat protection under primarily land-based protection strategies. We evaluated the geophysical and biogeographical diversity of streams falling under protection measures. Additionally, we expose a paradox of streams being protected yet simultaneously impaired from human disturbances. Without considering impairment, approximately 30% of streams are currently protected through land-based conservation of their local or upstream watersheds; when considering impairment, only 9% to 28% of streams are truly protected from disturbances depending on impairment thresholds and protection criteria. Furthermore, despite protection approaching 30×30 targets, only 5% of the most prevalent physical stream habitat types are protected. We provide a targeted protection strategy, overcoming the impairment paradox and ensuring adequate representation of streams.

Biogeography↗

DOE OSTI2025

Lost and Found: Rediscovering Microbiome-Associated Phenotypes that Reshape Agricultural Sustainability

Overview Code and data repository for NIL Manuscript. Documentation includes sequence processing examples and data analysis. Supplemental sequence processing and R statistical analysis for publication, which compares the microbiome of teosinte-B73 Near Isogenic Lines. Sample Data Amplicon sequence data for 16S rRNA genes, the fungal ITS2 region, and nitrogen-cycling functional genes are available through the NCBI Sequence Read Archive (SRA) under accession number PRJNA1042643(https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1042643). Raw metabolomic data are available on Metabolomics Workbench, Project ID: PR002654. This study is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org where it has been assigned Study ID ST004211. The data can be accessed directly via its Project DOI: http://dx.doi.org/10.21228/M8KV8T.

Near Isogeneic Lines↗

DOE OSTI2022

Development of DNA methylation‐based epigenetic age predictors in loblolly pine ( Pinus taeda )

Abstract Biological ageing is connected to life history variation across ecological scales and informs a basic understanding of age‐related declines in organismal function. Altered DNA methylation dynamics are a conserved aspect of biological ageing and have recently been modelled to predict chronological age among vertebrate species. In addition to their utility in estimating individual age, differences between chronological and predicted ages arise due to acceleration or deceleration of epigenetic ageing, and these discrepancies are linked to disease risk and multiple life history traits. Although evidence suggests that patterns of DNA methylation can describe ageing in plants, predictions with epigenetic clocks have yet to be performed. Here, we resolve the DNA methylome across CpG, CHG, and CHH‐methylation contexts in the loblolly pine tree ( Pinus taeda ) and construct epigenetic clocks capable of predicting ages in this species within 6% of its maximum lifespan. Although patterns of CHH‐methylation showed little association with age, both CpG and CHG‐methylation contexts were strongly associated with ageing, largely becoming hypomethylated with age. Among age‐associated loci were those in close proximity to malate dehydrogenase, NADH dehydrogenase, and 18S and 26S ribosomal RNA genes. This study reports one of the first epigenetic clocks in plants and demonstrates the universality of age‐associated DNA methylation dynamics which can inform conservation and management practices, as well as our ecological and evolutionary understanding of biological ageing in plants.

60 APPLIED LIFE SCIENCES↗

NASA NTRS2017

The Formation of Nucleobases from the UV Irradiation of Astrophysical Ice Analogs

Nucleobases are the fundamental information bearing components of both RNA and DNA. They are central to all known terrestrial life and they are generally conserved between species. Biological nucleobases can be divided into two groups based on the N-heterocyclic molecules pyrimidine (uracil, cytosine, and thymine) and purine (adenine and guanine) respectively. Do date, no experimental conditions have been determined that could produce both pyrimidines and purines together, abiotically, in a ter-restrial environment or an early terrestrial analog. Organic materials produced in extraterrestrial envi-ronments may have been delivered to the primitive earth by comets and meteorites and may have contrib-uted to the emergence of life. To date, some, but not all nucleobases have been detected in meteorites and their isotopic signatures may be consistent with an extraterrestrial origin. Earlier work in our lab demonstrated that it is possible to produce all of the pyrimidine group nucleobases from the UV-irradiation of pyrimidine in astrophysically relevant ice analogs. Here we report our most recent work, which studied the formation of the purine group nucleobases under similar conditions.

Astrophysical Ice↗

DOE OSTI2022

Comparative and pangenomic analysis of the genus Streptomyces

Abstract Streptomycetes are highly metabolically gifted bacteria with the abilities to produce bioproducts that have profound economic and societal importance. These bioproducts are produced by metabolic pathways including those for the biosynthesis of secondary metabolites and catabolism of plant biomass constituents. Advancements in genome sequencing technologies have revealed a wealth of untapped metabolic potential from Streptomyces genomes. Here, we report the largest Streptomyces pangenome generated by using 205 complete genomes. Metabolic potentials of the pangenome and individual genomes were analyzed, revealing degrees of conservation of individual metabolic pathways and strains potentially suitable for metabolic engineering. Of them, Streptomyces bingchenggensis was identified as a potent degrader of plant biomass. Polyketide, non-ribosomal peptide, and gamma-butyrolactone biosynthetic enzymes are primarily strain specific while ectoine and some terpene biosynthetic pathways are highly conserved. A large number of transcription factors associated with secondary metabolism are strain-specific while those controlling basic biological processes are highly conserved. Although the majority of genes involved in morphological development are highly conserved, there are strain-specific varieties which may contribute to fine tuning the timing of cellular differentiation. Overall, these results provide insights into the metabolic potential, regulation and physiology of streptomycetes, which will facilitate further exploitation of these important bacteria.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Technical note: A modified formulation of dynamic energy budget theory for faster computation of biological growth

Abstract. The mass conservation equation in the presence of boundary fluxes and chemical reactions from non-equilibrium thermodynamics is used to derive a modified dynamic energy budget (mDEB) model. Compared to the standard dynamic energy budget (sDEB) model (Kooijman, 2009), this modified formulation does not place the dilution effect in the mobilization kinetics of reserve biomass, and it maintains the partition principle for reserve mobilization dynamics for both linear and non-linear kinetics. Overall, the mDEB model shares most features with the sDEB model. However, for biological growth that requires multiple nutrients, the mDEB model is computationally much more efficient by not requiring numerical iterations for obtaining the specific growth rate. In an example of modeling the growth of Thalassiosira weissflogii in a nitrogen-limiting chemostat, the mDEB model was found to have almost the same accuracy as the sDEB model while requiring almost half of the computing time of the sDEB model. Since the sDEB model has been successfully applied in numerous studies, we believe that the mDEB model can help improve the modeling of biological growth and the associated ecosystem processes in various contexts.

Tang, Jinyun↗

DOE OSTI2020

Structural conserved moiety splitting of a stoichiometric matrix

Characterising biochemical reaction network structure in mathematical terms enables the inference of functional biochemical consequences from network structure with existing mathematical techniques and spurs the development of new mathematics that exploits the peculiarities of biochemical network structure. The structure of a biochemical network may be specified by reaction stoichiometry, that is, the relative quantities of each molecule produced and consumed in each reaction of the network. A biochemical network may also be specified at a higher level of resolution in terms of the internal structure of each molecule and how molecular structures are transformed by each reaction in a network. The stoichiometry for a set of reactions can be compiled into a stoichiometric matrix N ϵ Z mxn where each row corresponds to a molecule and each column corresponds to a reaction. We demonstrate that a stoichiometric matrix may be split into the sum of m - rank(N) moiety transition matrices, each of which corresponds to a subnetwork accessible to a structurally identifiable conserved moiety. The existence of this moiety matrix splitting is a property that distinguishes a stoichiometric matrix from an arbitrary rectangular matrix.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Accelerating Biological Insight for Understudied Genes

Synopsis The rapid expansion of genome sequence data is increasing the discovery of protein-coding genes across all domains of life. Annotating these genes with reliable functional information is necessary to understand evolution, to define the full biochemical space accessed by nature, and to identify target genes for biotechnology improvements. The majority of proteins are annotated based on sequence conservation with no specific biological, biochemical, genetic, or cellular function identified. Recent technical advances throughout the biological sciences enable experimental research on these understudied protein-coding genes in a broader collection of species. However, scientists have incentives and biases to continue focusing on well documented genes within their preferred model organism. This perspective suggests a research model that seeks to break historic silos of research bias by enabling interdisciplinary teams to accelerate biological functional annotation. We propose an initiative to develop coordinated projects of collaborating evolutionary biologists, cell biologists, geneticists, and biochemists that will focus on subsets of target genes in multiple model organisms. Concurrent analysis in multiple organisms takes advantage of evolutionary divergence and selection, which causes individual species to be better suited as experimental models for specific genes. Most importantly, multisystem approaches would encourage transdisciplinary critical thinking and hypothesis testing that is inherently slow in current biological research.

Zoology↗

NASA NTRS2010

Projecting the Local Impacts of Climate Change on a Central American Montane Avian Community

Significant changes in the climates of Central America are expected over the next century. Lowland rainforests harbor high alpha diversity on local scales (<1 km2), yet montane landscapes often support higher beta diversity on 10-100 km2 scales. Climate change will likely disrupt the altitudinal zonation of montane communities that produces such landscape diversity. Projections of biotic response to climate change have often used broad-scale modelling of geographical ranges, but understanding likely impacts on population viability is also necessary for anticipating local and global extinctions. We model species abundances and estimate range shifts for birds in the Tilaran Mountains of Costa Rica, asking whether projected changes in temperature and rainfall could be sufficient to imperil high-elevation endemics and whether these variables will likely impact communities similarly. We find that nearly half of 77 forest bird species can be expected to decline in the next century. Almost half of species projected to decline are endemic to Central America, and seven of eight species projected to become locally extinct are endemic to the highlands of Costa Rica and Panam . Logistic-regression modelling of distributions and similarity in projections produced by temperature and rainfall models suggest that changes in both variables will be important. Although these projections are probably conservative because they do not explicitly incorporate biological or climate variable interactions, they provide a starting point for incorporating more realistic biological complexity into community-change models. Prudent conservation planning for tropical mountains should focus on regions with room for altitudinal reorganization of communities comprised of ecological specialists.

Gasner, Matthew R.↗

DOE OSTI2020

Forensic species identification of elasmobranchs landed in Costa Rican artisanal fisheries

Elasmobranchs represent one of the most imperiled taxa, yet few nations have developed catch limits and no international or bilateral catch limits exist. One barrier to establishing catch limits is a lack of accurate species-specific extraction rates due to many species looking similar, distinguishing characteristics (fins and head) being removed, or grouping of all elasmobranchs together in fisheries data. To better understand the species-specific impacts fisheries are having on elasmobranchs we used forensic genetic techniques to identify the types and quantities of shark species landed in Costa Rican artisanal small-scale and mid-scale fisheries. We collected elasmobranch tissue samples from fishermen in three locations along Costa Rica’s Pacific Coast: Coyote, Bejuco, and Ojochal, from April 2013 to September 2014. We used DNA barcoding techniques, utilizing a 1044 base pair region of the NADH dehydrogenase subunit 2 gene, to identify to species 275 of the 416 samples collected. Within these fisheries, seven species of shark and one ray were identified, with the scalloped hammerhead shark (Sphyrna lewini) accounting for ~750-80% of all sharks landed. Observed total lengths (TL) for the scalloped hammerhead shark (10.9–99 cm) in these fisheries suggests the sharks sampled were all either juveniles or neonates. Based on these data it is likely that the areas from which these samples were collected represent nursery grounds for the scalloped hammerhead shark. The quantity of young scalloped hammerhead sharks removed from these areas, and ones similar to them, by these artisanal fisheries could be of great importance when determining future conservation measures for this species. We conclude our findings also indicate that sharks caught in these artisanal fisheries do not appear to represent those sold in markets around San Jose.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Intrinsic and environmental drivers of pairwise cohesion in wild Canis social groups

Animals within social groups respond to costs and benefits of sociality by adjusting the proportion of time they spend in close proximity to other individuals in the group (cohesion). Variation in cohesion between individuals, in turn, shapes important group-level processes such as subgroup formation and fission–fusion dynamics. Although critical to animal sociality, a comprehensive understanding of the factors influencing cohesion remains a gap in our knowledge of cooperative behavior in animals. We tracked 574 individuals from six species within the genus Canis in 15 countries on four continents with GPS telemetry to estimate the time that pairs of individuals within social groups spent in close proximity and test hypotheses regarding drivers of cohesion. Pairs of social canids (Canis spp.) varied widely in the proportion of time they spent together (5%–100%) during seasonal monitoring periods relative to both intrinsic characteristics and environmental conditions. The majority of our data came from three species of wolves (gray wolves, eastern wolves, and red wolves) and coyotes. For these species, cohesion within social groups was greatest between breeding pairs and varied seasonally as the nature of cooperative activities changed relative to annual life history patterns. Across species, wolves were more cohesive than coyotes. For wolves, pairs were less cohesive in larger groups, and when suitable, small prey was present reflecting the constraints of food resources and intragroup competition on social associations. Pair cohesion in wolves declined with increased anthropogenic modification of the landscape and greater climatic variability, underscoring challenges for conserving social top predators in a changing world. We show that pairwise cohesion in social groups varies strongly both within and across Canis species, as individuals respond to changing ecological context defined by resources, competition, and anthropogenic disturbance. Our work highlights that cohesion is a highly plastic component of animal sociality that holds significant promise for elucidating ecological and evolutionary mechanisms underlying cooperative behavior.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Overestimated natural biological nitrogen fixation translates to an exaggerated CO 2 fertilization effect in Earth system models

CO 2 fertilization of the terrestrial biosphere is limited by nitrogen. Biological nitrogen fixation (BNF) is the dominant natural nitrogen source to the terrestrial biosphere and can alleviate nitrogen limitation but is poorly constrained in Earth system models (ESMs). Here, in this study, we compare terrestrial BNF from an ensemble of ESMs of the 6th Coupled Model Intercomparison Project to a new global synthesis of observations across natural and agricultural biomes. We find that compared to observations, ESMs underestimate agricultural BNF but overestimate natural BNF in the present day by over 50%. Natural BNF is overestimated in the most productive ecosystems that contribute most to the terrestrial carbon sink (forests and grasslands). ESMs with different BNF representations yield a range of BNF responses to CO 2 enrichment. Some ESMs with phenomenological representations of BNF predict a natural BNF increase in response to a doubling of CO 2 that aligns with a meta-analysis of CO 2 enrichment experiments (31% increase) but fail to account for the substantial carbon cost of BNF. In contrast, ESMs with mechanistic representations of BNF account for its carbon cost as well as its regulation by nitrogen limitation but overestimate the BNF response to a doubling of CO 2 (135% increase). Overall, all current BNF representations in ESMs fall short of fully capturing its response to rising atmospheric CO 2 . Finally, we find a positive correlation between modeled present-day natural BNF and the CO 2 fertilization effect across ESMs, suggesting that overestimated natural BNF translates to an exaggerated CO 2 fertilization effect of approximately 11% in ESMs.

Biological nitrogen fixation↗

DOE OSTI2020

Highly Conserved Molecular Features in IgLONs Contrast Their Distinct Structural and Biological Outcomes

Abstract not provided

Venkannagari, Harikanth↗

DOE OSTI2025

Global terrestrial nitrogen fixation and its modification by agriculture

Biological nitrogen fixation (BNF) is the largest natural source of new nitrogen (N) that supports terrestrial productivity, yet estimates of global terrestrial BNF remain highly uncertain. Here, in this study, we show that this uncertainty is partly because of sampling bias, as field BNF measurements in natural terrestrial ecosystems occur where N fixers are 17 times more prevalent than their mean abundances worldwide. To correct this bias, we develop new estimates of global terrestrial BNF by upscaling field BNF measurements using spatially explicit abundances of all major biogeochemical N-fixing niches. We find that natural biomes sustain lower BNF, 65 (52–77) Tg N yr −1 , than previous empirical bottom-up estimates, with most BNF occurring in tropical forests and drylands. We also find high agricultural BNF in croplands and cultivated pastures, 56 (54–58) Tg N yr −1 . Agricultural BNF has increased terrestrial BNF by 64% and total terrestrial N inputs from all sources by 60% over pre-industrial levels. Our results indicate that BNF may impose stronger constraints on the carbon sink in natural terrestrial biomes and represent a larger source of agricultural N than is generally considered in analyses of the global N cycle, with implications for proposed safe operating limits for N use.

Reis Ely, Carla R. [Oregon State Univ., Corvallis,↗

DOE OSTI2025

A global dataset of terrestrial biological nitrogen fixation

Biological nitrogen fixation (BNF) is the main natural source of new nitrogen inputs in terrestrial ecosystems, supporting terrestrial productivity, carbon uptake, and other Earth system processes. We assembled a comprehensive global dataset of field measurements of BNF in all major N-fixing niches across natural terrestrial biomes derived from the analysis of 376 BNF studies. The dataset comprises 32 variables, including site location, biome type, N-fixing niche, sampling year, quantification method, BNF rate (kg N ha −1 y −1 ), the percentage of nitrogen derived from the atmosphere (%N dfa ), N fixer or N-fixing substrate abundance, BNF rate per unit of N fixer abundance, and species identity. Overall, the dataset combines 1,207 BNF rates for trees, shrubs, herbs, soil, leaf litter, woody litter, dead wood, mosses, lichens, and biocrusts, 152 herb %N dfa values, 1,005 measurements of N fixer or N-fixing substrate abundance, and 762 BNF rates per unit of N fixer abundance for a total of 424 species across 66 countries. This dataset facilitates synthesis, meta-analysis, upscaling, and model benchmarking of BNF fluxes at multiple spatial scales.

Reis Ely, Carla R. [Oregon State Univ., Corvallis,↗

NASA NTRS2020

Costa Rica & Panama Ecological Forecasting II: Identifying Current and Future Areas of Environmental Concern in La Amistad International Park to Inform Resource Management

Seven percent of all scientifically known life forms lie within the 202,230 square miles of Central America, making this area ecologically unique and increasing the need for environmental management. The Mesoamerican Biological Corridor forms a conservation partnership throughout Central America to establish a forested corridor of over 600 protected areas. Although conservation programs exist, deforestation still afflicts the area, putting strain on these diverse ecosystems. La Amistad International Park in southern Costa Rica and northern Panama in particular faces conflicting land use changes. Expanding agricultural development and urbanization, combined with concern over indigenous land rights, have raised questions about the implementation of sustainability goals and communication strategies within the region. To help address these issues, the NASA DEVELOP Costa Rica & Panama Ecological Forecasting II team continued a partnership with the Ministry of Environment and Energy in Costa Rica and the National Environmental Authority in Panama. The team created a Land Use Conflict Identification Strategy (LUCIS) model based on land cover maps for 2019 and 2029 that were created in term I using imagery from Landsat 8 Operational Land Imager (OLI). With partner input, the team applied weights to different objectives and combined suitability maps to identify areas of potential biodiversity conflict. Additionally, the team created a Short-term Forest Change (SFTC) Tool using Terra Moderate Resolution Imaging Spectroradiometer, Landsat 8 OLI, and Sentinel-2 Multispectral Instrument to help the partners identify areas of immediate, major forest changes. The LUCIS model indicated higher agricultural growth when compared to the ecological category.

Ecological Forecasting↗

NASA NTRS2020

Costa Rica & Panama Ecological Forecasting II: Identifying Current and Future Areas of Environmental Concern in La Amistad International Park to Inform Resource Management

Seven percent of all scientifically known life forms lie within the 202,230 square miles of Central America, making this area ecologically unique and increasing the need for environmental management. The Mesoamerican Biological Corridor forms a conservation partnership throughout Central America to establish a forested corridor of over 600 protected areas. Although conservation programs exist, deforestation still afflicts the area, putting strain on these diverse ecosystems. La Amistad International Park in southern Costa Rica and northern Panama in particular faces conflicting land use changes. Expanding agricultural development and urbanization, combined with concern over indigenous land rights, have raised questions about the implementation of sustainability goals and communication strategies within the region. To help address these issues, the NASA DEVELOP Costa Rica & Panama Ecological Forecasting II team continued a partnership with the Ministry of Environment and Energy in Costa Rica and the National Environmental Authority in Panama. The team created a Land Use Conflict Identification Strategy (LUCIS) model based on land cover maps for 2019 and 2029 that were created in term I using imagery from Landsat 8 Operational Land Imager (OLI). With partner input, the team applied weights to different objectives and combined suitability maps to identify areas of potential biodiversity conflict. Additionally, the team created a Short-term Forest Change (SFTC) Tool using Terra Moderate Resolution Imaging Spectroradiometer, Landsat 8 OLI, and Sentinel-2 Multispectral Instrument to help the partners identify areas of immediate, major forest changes. The LUCIS model indicated higher agricultural growth when compared to the ecological category.

Ecological Forecasting↗

NASA NTRS2020

Costa Rica & Panama Ecological Forecasting II: Identifying Current and Future Areas of Environmental Concern in La Amistad International Park to Inform Resource Management

Seven percent of all scientifically known life forms lie within the 202,230 square miles of Central America, making this area ecologically unique and increasing the need for environmental management. The Mesoamerican Biological Corridor forms a conservation partnership throughout Central America to establish a forested corridor of over 600 protected areas. Although conservation programs exist, deforestation still afflicts the area, putting strain on these diverse ecosystems. La Amistad International Park in southern Costa Rica and northern Panama in particular faces conflicting land use changes. Expanding agricultural development and urbanization, combined with concern over indigenous land rights, have raised questions about the implementation of sustainability goals and communication strategies within the region. To help address these issues, the NASA DEVELOP Costa Rica & Panama Ecological Forecasting II team continued a partnership with the Ministry of Environment and Energy in Costa Rica and the National Environmental Authority in Panama. The team created a Land Use Conflict Identification Strategy (LUCIS) model based on land cover maps for 2019 and 2029 that were created in term I using imagery from Landsat 8 Operational Land Imager (OLI). With partner input, the team applied weights to different objectives and combined suitability maps to identify areas of potential biodiversity conflict. Additionally, the team created a Short-term Forest Change (SFTC) Tool using Terra Moderate Resolution Imaging Spectroradiometer, Landsat 8 OLI, and Sentinel-2 Multispectral Instrument to help the partners identify areas of immediate, major forest changes. The LUCIS model indicated higher agricultural growth when compared to the ecological category.

Ecological Forecasting↗