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At least 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

The nitrogen gap in soil health concepts and fertility measurements

Soil nitrogen (N) often limits productivity in agroecosystems, prompting fertilizer applications that increase crop yields but can degrade the environment. Nitrogen's dual role in both productivity and environmental quality should center it in soil health frameworks. We use recent evidence to argue that N availability is an emergent property of the integrated soil biogeochemical system and is strongly influenced by plant traits and their interactions with microbes and minerals. Building upon this, we theorize that the sources of plant and microbial N shift across soil health gradients, from inorganic N dependence in ecologically simple systems with poor soil health to a highly networked supply of organic N in healthy soils; ergo, investments in soil health should increase ecological complexity and the pathways by which plants can access N, leading to more resilient nutrient supplies and yields in a variable climate. However, current N assessment methods derive from a historical emphasis on inorganic N pool sizes and are unable to capture the shifting drivers of N availability across soil health gradients. We highlight the need to better understand the plant-microbial-mineral interactions that regulate bioavailable N as a first step to improving our ability to measure it. We conclude it will be necessary to harness agroecosystem complexity, account for plant and microbial drivers, and carefully integrate external N inputs into soils' internal N network to expand the routes by which N from organic pools can be made bioavailable. Finally, by emphasizing N in soil health concepts, we argue that researchers can accelerate advances in N use efficiency and resiliency.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

N-induced soil acidification triggers metal stimulation of soil methane oxidation in a temperate steppe ecosystem

Methane (CH 4 ) is a potent greenhouse gas, and it is well established that low nitrogen (N) stimulates- and high N suppresses CH 4 oxidation in grassland ecosystems. Here, in this study, we examined the response of CH 4 uptake to long-term (>10 years) multi-level N additions in a temperate steppe of northern China. The N impacts on CH 4 uptake transitioned from positive to negative at the N addition rate of 4 g N m -2 y -1 . However, the high-N suppression on CH 4 uptake was partially relieved when the continuous (>10 years) high N inputs (16 g N m -2 y -1 to 64 g N m -2 y -1 ) caused soil pH drop to < 5.7. Further experiments revealed that continuous high-N inputs acidified soil to pH < 5.7 that released metal ions to stimulate monooxygenase enzyme activity; therefore, the CH 4 oxidation suppression was partially relieved under continuous N loading. Structural equation model results confirmed that metal ions, such as Iron (Fe 3+ ), Manganese (Mn 4+ ), and Copper (Cu) desorbed by soil particles, were negatively correlated with soil pH while positively correlated with CH 4 oxidation under high N inputs. These analyses suggested that continuous high N inputs-induced soil acidification can release previously bounded metal elements that partially alleviated the N suppression on CH 4 uptake. The N-induced soil acidification impacts on CH 4 uptake might play a critical role in global CH 4 cycling and deserve further investigation as external N inputs continue climbing.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

MPK6-mediated phosphorylation destabilizes MYC2 and attenuates its transcriptional activity in jasmonate signaling

Given the role of MYC2 as a pivotal regulator in the jasmonate (JA) signaling pathway, influencing the expression of a multitude of downstream genes (Zander et al., 2020), understanding the regulatory dynamics of MYC2 is essential for unraveling plant responses to stress conditions and hormonal signals. Previous studies on the regulation of MYC2 by MPK6 have reported conflicting findings. Takahashi et al. (2007) reported that MPK6 acts as a negative regulator of MYC2, whereas Sethi et al. (2014) proposed a positive regulatory role. Despite these findings, the precise genetic and biochemical mechanisms underlying the MPK6–MYC2 interaction remain poorly understood, highlighting the need for further investigation.

Im, Jong Hee [Michigan State University, East Lans↗
DOE OSTI2021

Food–Energy–Water Crises in the United States and China: Commonalities and Asynchronous Experiences Support Integration of Global Efforts

Food, energy, and water (FEW) systems have been recognized as an issue of critical global importance. Understanding the mechanisms that govern the FEW nexus is essential to develop solutions and avoid humanitarian crises of displacement, famine, and disease. The U.S. and China are the world’s leading economies. Although the two nations are shaped by fundamentally different political and economic systems, they share FEW trajectories in several complementary ways. These realities place the U.S. and China in unique positions to engage in problem definition, dialogue, actions, and transdisciplinary convergence of research to achieve productive solutions addressing FEW challenges. By comparing the nexus and functions of the FEW systems in the two nations, this perspective aims to facilitate collaborative innovations that reduce disciplinary silos, mitigate FEW challenges, and enhance environmental sustainability. Finally, the review of experiences and challenges facing the U.S. and China also offers valuable insights for other nations seeking to achieve sustainable development goals.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

The tepary bean genome provides insight into evolution and domestication under heat stress

Tepary bean (Phaseolus acutifolis A. Gray), native to the Sonoran Desert, is highly adapted to heat and drought. It is a sister species of common bean (Phaseolus vulgaris L.), the most important legume protein source for direct human consumption, and whose production is threatened by climate change. Here, we report on the tepary genome including exploration of possible mechanisms for resilience to moderate heat stress and a reduced disease resistance gene repertoire, consistent with adaptation to arid and hot environments. Extensive collinearity and shared gene content among these Phaseolus species will facilitate engineering climate adaptation in common bean, a key food security crop, and accelerate tepary bean improvement.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Diversification of mandarin citrus by hybrid speciation and apomixis

The origin and dispersal of cultivated and wild mandarin and related citrus are poorly understood. Here, comparative genome analysis of 69 new east Asian genomes and other mainland Asian citrus reveals a previously unrecognized wild sexual species native to the Ryukyu Islands: C. ryukyuensis sp. nov. The taxonomic complexity of east Asian mandarins then collapses to a satisfying simplicity, accounting for tachibana, shiikuwasha, and other traditional Ryukyuan mandarin types as homoploid hybrid species formed by combining C. ryukyuensis with various mainland mandarins. These hybrid species reproduce clonally by apomictic seed, a trait shared with oranges, grapefruits, lemons and many cultivated mandarins. We trace the origin of apomixis alleles in citrus to mangshanyeju wild mandarins, which played a central role in citrus domestication via adaptive wild introgression. Our results provide a coherent biogeographic framework for understanding the diversity and domestication of mandarin-type citrus through speciation, admixture, and rapid diffusion of apomictic reproduction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Chromosome evolution and the genetic basis of agronomically important traits in greater yam

The nutrient-rich tubers of the greater yam, Dioscorea alata L., provide food and income security for millions of people around the world. Despite its global importance, however, greater yam remains an orphan crop. Here, we address this resource gap by presenting a highly contiguous chromosome-scale genome assembly of D. alata combined with a dense genetic map derived from African breeding populations. The genome sequence reveals an ancient allotetraploidization in the Dioscorea lineage, followed by extensive genome-wide reorganization. Using the genomic tools, we find quantitative trait loci for resistance to anthracnose, a damaging fungal pathogen of yam, and several tuber quality traits. Genomic analysis of breeding lines reveals both extensive inbreeding as well as regions of extensive heterozygosity that may represent interspecific introgression during domestication. These tools and insights will enable yam breeders to unlock the potential of this staple crop and take full advantage of its adaptability to varied environments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Genome analyses reveal population structure and a purple stigma color gene candidate in finger millet

Finger millet is a key food security crop widely grown in eastern Africa, India and Nepal. Long considered a ‘poor man’s crop’, finger millet has regained attention over the past decade for its climate resilience and the nutritional qualities of its grain. To bring finger millet breeding into the 21 st century, here we present the assembly and annotation of a chromosome-scale reference genome. We show that this ~1.3 million years old allotetraploid has a high level of homoeologous gene retention and lacks subgenome dominance. Population structure is mainly driven by the differential presence of large wild segments in the pericentromeric regions of several chromosomes. Trait mapping, followed by variant analysis of gene candidates, reveals that loss of purple coloration of anthers and stigma is associated with loss-of-function mutations in the finger millet orthologs of the maize R1/B1 and Arabidopsis GL3/EGL3 anthocyanin regulatory genes. Proanthocyanidin production in seed is not affected by these gene knockouts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Fertilizer management for global ammonia emission reduction

Crop production is a large source of atmospheric ammonia (NH 3 ), which poses risks to air quality, human health and ecosystems. However, estimating global NH 3 emissions from croplands is subject to uncertainties because of data limitations, thereby limiting the accurate identification of mitigation options and efficacy. In this report we develop a machine learning model for generating crop-specific and spatially explicit NH 3 emission factors globally (5-arcmin resolution) based on a compiled dataset of field observations. We show that global NH 3 emissions from rice, wheat and maize fields in 2018 were 4.3 ± 1.0 Tg N yr -1 , lower than previous estimates that did not fully consider fertilizer management practices. Furthermore, spatially optimizing fertilizer management, as guided by the machine learning model, has the potential to reduce the NH3 emissions by about 38% (1.6 ± 0.4 Tg N yr -1 ) without altering total fertilizer nitrogen inputs. Specifically, we estimate potential NH3 emissions reductions of 47% (44–56%) for rice, 27% (24–28%) for maize and 26% (20–28%) for wheat cultivation, respectively. Under future climate change scenarios, we estimate that NH3 emissions could increase by 4.0 ± 2.7% under SSP1–2.6 and 5.5 ± 5.7% under SSP5–8.5 by 2030–2060. However, targeted fertilizer management has the potential to mitigate these increases.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

The complex polyploid genome architecture of sugarcane

Sugarcane, the world’s most harvested crop by tonnage, has shaped global history, trade and geopolitics, and is currently responsible for 80% of sugar production worldwide. While traditional sugarcane breeding methods have effectively generated cultivars adapted to new environments and pathogens, sugar yield improvements have recently plateaued. The cessation of yield gains may be due to limited genetic diversity within breeding populations, long breeding cycles and the complexity of its genome, the latter preventing breeders from taking advantage of the recent explosion of whole-genome sequencing that has benefited many other crops. Thus, modern sugarcane hybrids are the last remaining major crop without a reference-quality genome. Here we take a major step towards advancing sugarcane biotechnology by generating a polyploid reference genome for R570, a typical modern cultivar derived from interspecific hybridization between the domesticated species (Saccharum officinarum) and the wild species (Saccharum spontaneum). In contrast to the existing single haplotype (‘monoploid’) representation of R570, our 8.7 billion base assembly contains a complete representation of unique DNA sequences across the approximately 12 chromosome copies in this polyploid genome. Using this highly contiguous genome assembly, we filled a previously unsized gap within an R570 physical genetic map to describe the likely causal genes underlying the single-copy Bru1 brown rust resistance locus. This polyploid genome assembly with fine-grain descriptions of genome architecture and molecular targets for biotechnology will help accelerate molecular and transgenic breeding and adaptation of sugarcane to future environmental conditions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Global nitrogen deposition inputs to cropland at national scale from 1961 to 2020

Nitrogen (N) deposition is a significant nutrient input to cropland and consequently important for the evaluation of N budgets and N use efficiency (NUE) at different scales and over time. However, the spatiotemporal coverage of N deposition measurements is limited globally, whereas modeled N deposition values carry uncertainties. Here, we reviewed existing methods and related data sources for quantifying N deposition inputs to crop production on a national scale. We utilized different data sources to estimate N deposition input to crop production at national scale and compared our estimates with 14 N budget datasets, as well as measured N deposition data from observation networks in 9 countries. We created four datasets of N deposition inputs on cropland during 1961–2020 for 236 countries. These products showed good agreement for the majority of countries and can be used in the modeling and assessment of NUE at national and global scales. One of the datasets is recommended for general use in regional to global N budget and NUE estimates.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Metagenome-assembled-genomes recovered from the Arctic drift expedition MOSAiC

The Multidisciplinary Observatory for Study of the Arctic Climate (MOSAiC) expedition consisted of a year-long drifting survey of the Central Arctic Ocean. The ecosystems component of MOSAiC included the sampling of molecular data, with metagenomes collected from a diverse range of environments. The generation of metagenome-assembled-genomes (MAGs) from metagenomes are a starting point for genome-resolved analyses. This dataset presents a catalogue of MAGs recovered from a set of 73 samples from MOSAiC, including 2407 prokaryotic and 56 eukaryotic MAGs, as well as annotations of a near complete eukaryotic MAG using the Joint Genome Institute (JGI) annotation pipeline. The metagenomic samples are from the surface ocean, chlorophyll maximum, mesopelagic and bathypelagic, within leads and under-ice ocean, as well as melt ponds, ice ridges, and first- and second-year sea ice. This set of MAGs can be used to benchmark microbial biodiversity in the Central Arctic Ocean, compare individual strains across space and time, and to study changes in Arctic microbial communities from the winter to summer, at a genomic level.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

A coupled human–natural system analysis of freshwater security under climate and population change

Limited water availability, population growth, and climate change have resulted in freshwater crises in many countries. Jordan’s situation is emblematic, compounded by conflict-induced population shocks. Integrating knowledge across hydrology, climatology, agriculture, political science, geography, and economics, we present the Jordan Water Model, a nationwide coupled human–natural-engineered systems model that is used to evaluate Jordan’s freshwater security under climate and socioeconomic changes. The complex systems model simulates the trajectory of Jordan’s water system, representing dynamic interactions between a hierarchy of actors and the natural and engineered water environment. A multiagent modeling approach enables the quantification of impacts at the level of thousands of representative agents across sectors, allowing for the evaluation of both systemwide and distributional outcomes translated into a suite of water-security metrics (vulnerability, equity, shortage duration, and economic well-being). Model results indicate severe, potentially destabilizing, declines in freshwater security. Per capita water availability decreases by approximately 50% by the end of the century. Without intervening measures, >90% of the low-income household population experiences critical insecurity by the end of the century, receiving <40 L per capita per day. Widening disparity in freshwater use, lengthening shortage durations, and declining economic welfare are prevalent across narratives. To gain a foothold on its freshwater future, Jordan must enact a sweeping portfolio of ambitious interventions that include large-scale desalinization and comprehensive water sector reform, with model results revealing exponential improvements in water security through the coordination of supply- and demand-side measures.

42 ENGINEERING↗
DOE OSTI2021

Integrate health into decision-making to foster climate action

The COVID-19 pandemic reveals that societies place a high value on healthy lives. Leveraging this momentum to establish a more central role for human health in the policy process will provide further impetus to a sustainable transformation of energy and food systems.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2025

Field-scale mapping of California crop water productivity to inform water management in critically overdrafted groundwater basins

Crop water productivity (CWP) metrics can reveal how the dynamics of crop production and water use change across space and time. We use field-scale satellite inputs from 2016–2021 to estimate potential water savings for four crops (almonds, grapes, walnuts, and citrus—which collectively account for approximately one-third of California’s cropland area), within critically overdrafted groundwater sub-basins of California’s San Joaquin Valley. These annual estimates of field-level water savings potential are based on locally achievable CWP values for each crop type. Our findings show considerable spatial variation in CWP and potential water savings within each sub-basin. We find that increasing CWP to peak efficiency (defined as improving fields to the 95th percentile of observed CWP) for four crops could meet up to 36% of the estimated annual overdraft in San Joaquin Valley. For comparison, fallowing 5% of the four crop type fields in the same study area could potentially reduce annual overdraft by 11%. By delivering results at the field scale, our work can inform targeted interventions by irrigation district managers and more efficient allocation of state incentives for improved water management. For example, we estimate that state grant funding for water efficiency upgrades could have amplified potential water savings threefold by targeting investments to the least efficient fields.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

A Chromosome-Scale Genome Assembly of a Helicoverpa zea Strain Resistant to Bacillus thuringiensis Cry1Ac Insecticidal Protein

Helicoverpa zea (Lepidoptera: Noctuidae) is an insect pest of major cultivated crops in North and South America. The species has adapted to different host plants and developed resistance to several insecticidal agents, including Bacillus thuringiensis (Bt) insecticidal proteins in transgenic cotton and maize. Helicoverpa zea populations persist year-round in tropical and subtropical regions, but seasonal migrations into temperate zones increase the geographic range of associated crop damage. To better understand the genetic basis of these physiological and ecological characteristics, we generated a high-quality chromosome-level assembly for a single H. zea male from Bt-resistant strain, HzStark_Cry1AcR. Hi-C data were used to scaffold an initial 375.2 Mb contig assembly into 30 autosomes and the Z sex chromosome (scaffold N50 = 12.8 Mb and L50 = 14). The scaffolded assembly was error-corrected with a novel pipeline, polishCLR. The mitochondrial genome was assembled through an improved pipeline and annotated. Assessment of this genome assembly indicated 98.8% of the Lepidopteran Benchmark Universal Single-Copy Ortholog set were complete (98.5% as complete single copy). Repetitive elements comprised approximately 29.5% of the assembly with the plurality (11.2%) classified as retroelements. This chromosome-scale reference assembly for H. zea, ilHelZeax1.1, will facilitate future research to evaluate and enhance sustainable crop production practices.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Optimizing genomic prediction for complex traits via investigating multiple factors in switchgrass

Genomic prediction has accelerated breeding processes and provided mechanistic insights into the genetic bases of complex traits. To further optimize genomic prediction, we assess the impact of genome assemblies, genotyping approaches, variant types, allelic complexities, polyploidy levels, and population structures on the prediction of 20 complex traits in switchgrass (Panicum virgatum L.), a perennial biofuel feedstock. Surprisingly, short read-based genome assembly performs comparably to or even better than long read-based assembly. Due to higher gene coverage, exome capture and multi-allelic variants outperform genotyping-by-sequencing and bi-allelic variants, respectively. Tetraploid models show higher prediction accuracy than octoploid models for most traits, likely due to the greater genetic distances among tetraploids. Depending on the trait in question, different types of variants need to be integrated for optimal predictions. Furthermore, our study provides insights into the factors influencing genomic prediction outcomes, guiding best practices for future studies and for improving agronomic traits in switchgrass and other species through selective breeding.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Novel and Emerging Capabilities that Can Provide a Holistic Understanding of the Plant Root Microbiome

In recent years, the root microbiome (i.e., microorganisms growing inside, on, or in close proximity to plant roots) has been shown to play an important role in plant health and productivity. Despite its importance, the root microbiome is challenging to study because of its complexity, heterogeneity, and subterranean location. Fortunately, root microbiome research has seen a tremendous influx of novel technologies (e.g., imaging tools, robotics, and molecular analyses), experimental platforms (e.g., micro- and mesocosms), and data integration, modeling, and prediction tools in the past decade that have greatly increased our ability to dissect the complex network of interactions between above- and belowground environmental parameters, plants, bacteria, and fungi that dictate soil and broader ecosystem health. Herein, we discuss methods that are currently used in root microbiome research and that can be expanded to phytobiome research in general ranging from laboratory studies to mesocosm-scale studies and, finally, to field studies; evaluate their relevance to ecosystem studies; and discuss future root microbiome research directions.

59 BASIC BIOLOGICAL SCIENCES↗