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At least 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Synthetic microbial communities: Bridging research and application in second-generation bioenergy feedstock microbiomes

The sustainable production of purpose-grown bioenergy feedstocks is essential in transitioning away from fossil fuels. Synthetic communities (SynComs) are consortia of microorganisms that can be used as biological interventions to support objectives like plant growth and stress tolerance. This review examines the state of knowledge regarding microbiomes and SynComs of second-generation bioenergy feedstocks, focusing on the rhizosphere. We first provide an overview of second-generation feedstocks, including switchgrass (Panicum virgatum), miscanthus (Miscanthus × giganteus), sorghum (Sorghum spp.), sugarcane (Saccharum spp.), and poplar (Populus spp.), and summarize our current understanding of their plant-soil-microbiome ecology. We next discuss considerations in the objectives, design, and evaluation of SynComs to enhance feedstock production, and then critically review the literature around their use. Our literature analysis revealed that SynCom performance varied substantially between controlled pilot experiments and field trials, possibly due to system complexity that could not be fully considered in their design and pilot evaluation. We identified a gap in the use of SynComs to support the unique sustainability objectives of biofuel feedstock agriculture, presenting an opportunity to leverage these additional microbial traits in SynCom designs. Finally, we emphasize the importance of targeted research to identify the ecological principles that govern the assembly, activation, and persistence of microbes in the feedstock rhizosphere, thereby enhancing our capacity to manage microbiomes under diverse environmental conditions and ensure their functionality. Beyond biofuels, SynComs are a promising microbiome management strategy for crop production; however, an ecologically informed design and evaluation of SynComs are advised.

SynCom↗
DOE OSTI2021

The Utility of Macroecological Rules for Microbial Biogeography

Macroecological rules have been developed for plants and animals that describe large-scale distributional patterns and attempt to explain the underlying physiological and ecological processes behind them. Similarly, microorganisms exhibit patterns in relative abundance, distribution, diversity, and traits across space and time, yet it remains unclear the extent to which microorganisms follow macroecological rules initially developed for macroorganisms. Additionally, the usefulness of these rules as a null hypothesis when surveying microorganisms has yet to be fully evaluated. With rapid advancements in sequencing technology, we have seen a recent increase in microbial studies that utilize macroecological frameworks. Here, we review and synthesize these macroecological microbial studies with two main objectives: (1) to determine to what extent macroecological rules explain the distribution of host-associated and free-living microorganisms, and (2) to understand which environmental factors and stochastic processes may explain these patterns among microbial clades (archaea, bacteria, fungi, and protists) and habitats (host-associated and free living; terrestrial and aquatic). Overall, 78% of microbial macroecology studies focused on free living, aquatic organisms. In addition, most studies examined macroecological rules at the community level with only 35% of studies surveying organismal patterns across space. At the community level microorganisms often tracked patterns of macroorganisms for island biogeography (74% confirm) but rarely followed Latitudinal Diversity Gradients (LDGs) of macroorganisms (only 32% confirm). However, when microorganisms and macroorganisms shared the same macroecological patterns, underlying environmental drivers (e.g., temperature) were the same. Because we found a lack of studies for many microbial groups and habitats, we conclude our review by outlining several outstanding questions and creating recommendations for future studies in microbial ecology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

The Global Spectra-Trait Initiative: A database of paired leaf spectroscopy and functional traits associated with leaf photosynthetic capacity

Accurate assessment of leaf functional traits is crucial for a diverse range of applications from crop phenotyping to parameterizing global climate models. Leaf reflectance spectroscopy offers a promising avenue to advance ecological and agricultural research by complementing traditional, time-consuming gas exchange measurements. However, the development of robust hyperspectral models for predicting leaf photosynthetic capacity and associated traits from reflectance data has been hindered by limited data availability across species and environments. Here we introduce the Global Spectra-Trait Initiative (GSTI), a collaborative repository of paired leaf hyperspectral and gas exchange measurements from diverse ecosystems. The GSTI repository currently encompasses over 7500 observations from 397 species and 41 sites gathered from 36 published and unpublished studies, thereby offering a key resource for developing and validating hyperspectral models of leaf photosynthetic capacity. The GSTI database is developed on GitHub (https://github.com/plantphys/gsti, last access: 4 January 2026) and published to ESS-DIVE https://doi.org/10.15485/2530733, Lamour et al., 2025). It includes gas exchange data, derived photosynthetic parameters, and key leaf traits often associated with traditional gas exchange measurements such as leaf mass per area and leaf elemental composition. By providing a standardized repository for data sharing and analysis, we present a critical step towards creating hyperspectral models for predicting photosynthetic traits and associated leaf traits for terrestrial plants.

Lamour, Julien [Université of Toulouse (France); U↗
DOE OSTI2022

Increasing Functional Diversity in a Global Land Surface Model Illustrates Uncertainties Related to Parameter Simplification

Abstract Simulations of the land surface carbon cycle typically compress functional diversity into a small set of plant functional types (PFT), with parameters defined by the average value of measurements of functional traits. In most earth system models, all wild plant life is represented by between five and 14 PFTs and a typical grid cell (≈100 × 100 km) may contain a single PFT. Model logic applied to this coarse representation of ecological functional diversity provides a reasonable proxy for the carbon cycle, but does not capture the non‐linear influence of functional traits on productivity. Here we show through simulations using the Energy Exascale Land Surface Model in 15 diverse terrestrial landscapes, that better accounting for functional diversity markedly alters predicted total carbon uptake. The shift in carbon uptake is as great as 30% and 10% in boreal and tropical regions, respectively, when compared to a single PFT parameterized with the trait means. The traits that best predict gross primary production vary based on vegetation phenology, which broadly determines where traits fall within the global distribution. Carbon uptake is more closely associated with specific leaf area for evergreen PFTs and the leaf carbon to nitrogen ratio in deciduous PFTs.

58 GEOSCIENCES↗
DOE OSTI2024

Genetic and Functional Diversity Help Explain Pathogenic, Weakly Pathogenic, and Commensal Lifestyles in the Genus Xanthomonas

The genus Xanthomonas has been primarily studied for pathogenic interactions with plants. However, besides host and tissue-specific pathogenic strains, this genus also comprises nonpathogenic strains isolated from a broad range of hosts, sometimes in association with pathogenic strains, and other environments, including rainwater. Based on their incapacity or limited capacity to cause symptoms on the host of isolation, nonpathogenic xanthomonads can be further characterized as commensal and weakly pathogenic. This study aimed to understand the diversity and evolution of nonpathogenic xanthomonads compared to their pathogenic counterparts based on their cooccurrence and phylogenetic relationship and to identify genomic traits that form the basis of a life history framework that groups xanthomonads by ecological strategies. We sequenced genomes of 83 strains spanning the genus phylogeny and identified eight novel species, indicating unexplored diversity. While some nonpathogenic species have experienced a recent loss of a type III secretion system, specifically the hrp2 cluster, we observed an apparent lack of association of the hrp2 cluster with lifestyles of diverse species. We performed association analysis on a large data set of 337 Xanthomonas strains to explain how xanthomonads may have established association with the plants across the continuum of lifestyles from commensals to weak pathogens to pathogens. Presence of distinct transcriptional regulators, distinct nutrient utilization and assimilation genes, transcriptional regulators, and chemotaxis genes may explain lifestyle-specific adaptations of xanthomonads.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Linkage mapping evidence for a syntenic QTL associated with flowering time in perennial C 4 rhizomatous grasses Miscanthus and switchgrass

Flowering in perennial species is directed via complex signalling pathways that adjust to developmental regulations and environmental cues. Synchronized flowering in certain environments is a prerequisite to commercial seed production, and so the elucidation of the genetic architecture of flowering time in Miscanthus and switchgrass could aid breeding in these underdeveloped species. In this context, we assessed a mapping population in Miscanthus and two ecologically diverse switchgrass mapping populations over 3 years from planting. Multiple flowering time quantitative trait loci (QTL) were identified in both species. Remarkably, the most significant Miscanthus and switchgrass QTL proved to be syntenic, located on linkage groups 4 and 2, with logarithm of odds scores of 17.05 and 21.8 respectively. These QTL regions contained three flowering time transcription factors: Squamosa Promoter-binding protein-Like, MADS-box SEPELLATA2 and gibberellin-responsive bHLH137. The former is emerging as a key component of the age-related flowering time pathway.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRSDate not supplied

Linking Individual Variation in Movement Behavior to Infection Dynamics in Highly Mobile Species

Animal movements are linked to infectious disease dynamics in wildlife through multiple mechanisms across various spatial and temporal scales. For example, infections can impede the movement of infected individuals, but infected hosts can also disperse infectious agents as they move. Individuals inevitably vary in their responses to infections and their roles in determining infection dynamics, which means that considering variation among individuals – whether across species, across time, or within populations – is important for understanding movement-disease relationships and their implications for epidemiology. Here, I draw on studies from multiple systems to examine how variation in movement behavior links to infectious disease epidemiology. For example, a comparative study of habitat selection across multiple waterfowl species highlights that diel behavioral patterns, rather than individual or seasonal variation, is the most important driver of the risk of overlap between waterfowl and poultry farms, and therefore for the risk of avian influenza spillover. Together, these studies show that individual traits interact with the environment to influence the roles of individuals for infectious disease ecology.

Claire Stewart Teitelbaum↗
DOE OSTI2023

Identifying ecological and evolutionary research targets and risks in climate change studies to break barriers to broad inference

Understanding the responses of plants, microbes, and their interactions to long-term climate change is essential to identifying the traits, genes, and functions of organisms that maintain ecosystem stability and function of the biosphere. However, many studies investigating organismal responses to climate change are limited in their scope along several key ecological, evolutionary, and environmental axes, creating barriers to broader inference. Broad inference, or the ability to apply and validate findings across these axes, is a vital component of achieving climate preparedness in the future. Breaking barriers to broad inference requires accurate cross-ecosystem interpretability and the identification of reliable frameworks for how these responses will manifest. Current approaches have generated a valuable, yet sometimes contradictory or context dependent, understanding of responses to climate change factors from the organismal- to ecosystem-level. In this synthesis, we use plants, soil microbial communities, and their interactions as examples to identify five major barriers to broad inference and resultant target research areas. We also explain risks associated with disregarding these barriers to broad inference and potential approaches to overcoming them. Developing and funding experimental frameworks that integrate basic ecological and evolutionary principles and are designed to capture broad inference across levels of organization is necessary to further our understanding of climate change on large scales.

Love, Sarah J. (ORCID:0000000180787373)↗
DOE OSTI2023

Thermal adaptation of soil microbial growth traits in response to chronic warming

ABSTRACT Adaptation of soil microbes due to warming from climate change has been observed, but it remains unknown what microbial growth traits are adaptive to warming. We studied bacterial isolates from the Harvard Forest Long-Term Ecological Research site, where field soils have been experimentally heated to 5°C above ambient temperature with unheated controls for 30 years. We hypothesized that Alphaproteobacteria from warmed plots have (i) less temperature-sensitive growth rates; (ii) higher optimum growth temperatures; and (iii) higher maximum growth temperatures compared to isolates from control plots. We made high-throughput measurements of bacterial growth in liquid cultures over time and across temperatures from 22°C to 37°C in 2–3°C increments. We estimated growth rates by fitting Gompertz models to the growth data. Temperature sensitivity of growth rate, optimum growth temperature, and maximum growth temperature were estimated by the Ratkowsky 1983 model and a modified Macromolecular Rate Theory (MMRT) model. To determine evidence of adaptation, we ran phylogenetic generalized least squares tests on isolates from warmed and control soils. Our results showed evidence of adaptation of higher optimum growth temperature of bacterial isolates from heated soils. However, we observed no evidence of adaptation of temperature sensitivity of growth and maximum growth temperature. Our project begins to capture the shape of the temperature response curves, but illustrates that the relationship between growth and temperature is complex and cannot be limited to a single point in the biokinetic range. IMPORTANCE Soils are the largest terrestrial carbon sink and the foundation of our food, fiber, and fuel systems. Healthy soils are carbon sinks, storing more carbon than they release. This reduces the amount of carbon dioxide released into the atmosphere and buffers against climate change. Soil microbes drive biogeochemical cycling and contribute to soil health through organic matter breakdown, plant growth promotion, and nutrient distribution. In this study, we determined how soil microbial growth traits respond to long-term soil warming. We found that bacterial isolates from warmed plots showed evidence of adaptation of optimum growth temperature. This suggests that increased microbial biomass and growth in a warming world could result in greater carbon storage. As temperatures increase, greater microbial activity may help reduce the soil carbon feedback loop. Our results provide insight on how atmospheric carbon cycling and soil health may respond in a warming world.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Ecological trade-offs drive phenotypic and genetic differentiation of Arabidopsis thaliana in Europe

Plant diversity is shaped by trade-offs between traits related to competitive ability, propagule dispersal, and stress resistance. However, we still lack a clear understanding of how these trade-offs influence species distribution and population dynamics. In Arabidopsis thaliana , recent genetic analyses revealed a group of cosmopolitan genotypes that successfully recolonized Europe from its center after the last glaciation, excluding older (relict) lineages from the distribution except for their north and south margins. Here, we tested the hypothesis that cosmopolitans expanded due to higher colonization ability, while relicts persisted at the margins due to higher tolerance to competition and/or stress. We compared the phenotypic and genetic differentiation between 71 European genotypes originating from the center, and the south and north margins. We showed that a trade-off between plant fecundity and seed mass shapes the differentiation of A. thaliana in Europe, suggesting that the success of the cosmopolitan groups could be explained by their high dispersal ability. However, at both north and south margins, we found evidence of selection for alleles conferring low dispersal but highly competitive and stress-resistance abilities. This study sheds light on the role of ecological trade-offs as evolutionary drivers of the distribution and dynamics of plant populations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Microbial and Environmental Processes Shape the Link between Organic Matter Functional Traits and Composition

Dissolved organic matter (DOM) is a large and complex mixture of molecules that fuels biogeochemical reaction in virtually all ecosystems on Earth. However, the relative importance of deterministic and stochastic processes in structuring DOM composition remains poorly characterized. Here we develop a framework for partitioning molecular composition based on key molecular traits, including lability vs. recalcitrance and activity vs. inactivity. Within this framework, we examine the ecological processes governing the assembly of DOM fractions by deploying aquatic microcosms on mountainsides that span gradients of temperature and nutrient loading in subtropical and subarctic ecosystems. Across study regions, deterministic and stochastic processes primarily structure active and inactive fractions, respectively. However, recalcitrant molecules are more deterministically assembled than labile molecules in the inactive fraction. Deterministic processes leading to variable selection generally exhibit more variation across the energy supply gradient for inactive fractions, and their importance increases with energy supply for recalcitrant molecules in both active and inactive fractions. Together, our results indicate that active and inactive fractions of DOM assemblages are structured by contrasting ecological processes, and their recalcitrant components are sensitive to global change. In conclusion, our framework opens new avenues to understand the assembly and turnover of DOM in a changing world, which can be used to predict carbon cycling at local to global scales.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Eco-evolutionary strategies for relieving carbon limitation under salt stress differ across microbial clades

With the continuous expansion of saline soils under climate change, understanding the eco-evolutionary tradeoff between the microbial mitigation of carbon limitation and the maintenance of functional traits in saline soils represents a significant knowledge gap in predicting future soil health and ecological function. Through shotgun metagenomic sequencing of coastal soils along a salinity gradient, we show contrasting eco-evolutionary directions of soil bacteria and archaea that manifest in changes to genome size and the functional potential of the soil microbiome. In salt environments with high carbon requirements, bacteria exhibit reduced genome sizes associated with a depletion of metabolic genes, while archaea display larger genomes and enrichment of salt-resistance, metabolic, and carbon-acquisition genes. This suggests that bacteria conserve energy through genome streamlining when facing salt stress, while archaea invest in carbon-acquisition pathways to broaden their resource usage. These findings suggest divergent directions in eco-evolutionary adaptations to soil saline stress amongst microbial clades and serve as a foundation for understanding the response of soil microbiomes to escalating climate change.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2009

The Crop Evaluation Research for Environmental Strategies (CERES) Remote Sensing 2008 Project Activities

In recent years, the use of Plant Incorporated Protectant (PIP) corn by American producers has been increasing dramatically. PIP corn contains genetically inserted traits that produce toxins in the plant that provide narrowly targeted protection against specific insect pests. The plant producing t oxms can offer significant reductions in the application of broad -spectrum pesticides that have ecological and human health consequences. PIP corn as a percentage of total corn acreage planted in the US is expected to continue to increase as these protective traits are "stacked" with other desirable traits by seed companies, and producers are seeing considerable increases in corn yield as a result. The introduction of corn as a bio-fuel source for ethanol has increased production by over 6 million hectares in 2007. The United States Environmental Protection Agency (USEPA), which is responsible for the registration of PIP crops under the Federal Insecticide, Fungicide and Rodenticide Act, views the use of PIP corn as positive. Broad spectrum pesticide use has declined since the PIP traits have been introduced. As the agricultural landscape sees a higher percentage of corn acres using the PIP technology, the risk of the targeted insect pest populations developing resistance to the toxins, thereby rendering the in will increase as well. This result would negate the effectiveness of the PIP corn traits and could reduce production of a US field corn crop valued at $33 billion dollars in 2006 and place US food and now energy security at risk. Concerns over insect pest resistance development to PIP traits have led the USEPA to team with NASA and the Institute for Technology Development (ITD) to develop geo-spatial technologies designed to proactively monitor the corn production landscape for insect pest infestation and possible resistance development. USEPA resistance management simulation models are combined with NASA remote sensi ng products to monitor the corn landscape for resistance development. The two agencies have entered into an agreement which could potentially lead to the development of next generation NASA sensors that will more specifically address the requirements of the USEPA's resistance development strategy and offer opportunities to study the ever changing ecosystem complexities. The USEPA/NASA/ITD team has developed a broad research project entitled CERES (Crop Evaluation Research for Environmental Strategies). CERES is a research effort leading to decision support system tools that are designed to integrate multi-resolution NASA remote sensing data products and USEPA geo -spatial models to monitor the potential for insect pest resistance development from the regional to the landscape and then to the field level.

Casas, Joseph C.↗
NASA NTRS2023

Approaching a Thermal Tipping Point in the Eurasian Boreal Forest at its Southern Margin

Climate change is increasing the intensity and frequency of extreme heat events. Ecological responses to extreme heat will depend on vegetation physiology and thermal tolerance. Here we report that Larix sibirica, a foundation species across boreal Eurasia, is vulnerable to extreme heat at its southern range margin due to its low thermal tolerance (T crit of photosynthesis: ~ 37–48 °C). Projections from CMIP6 Earth System Models (ESMs) suggest that leaf temperatures might exceed the 25 th percentile of Larix sibirica’s T crit by two to three days per year within the next two to three decades (by 2050) under high emission scenarios (SSP3-7.0 and SSP5-8.5). This degree of warming will threaten the biome’s continued ability to assimilate and sequester carbon. This work highlights that under high emission trajectories we may approach an abrupt ecological tipping point in southern boreal Eurasian forests substantially sooner than ESM estimates that do not consider plant thermal tolerance traits.

Boreal ecology↗
DOE OSTI2025

Enrichment of root-associated Streptomyces strains in response to drought is driven by diverse functional traits and does not predict beneficial effects on plant growth

The genus Streptomyces has consistently been found enriched in drought-stressed plant root microbiomes, yet the ecological basis and functional variation underlying this enrichment at the strain and isolate level remain unclear. Using two 16S rRNA sequencing methods with different levels of taxonomic resolution, we confirmed drought-associated enrichment (DE) of Streptomyces in field-grown sorghum roots and identified five closely related but distinct amplicon sequence variants (ASVs) belonging to the genus with variable drought enrichment patterns. From a culture collection of sorghum root endophytes, we selected 12 Streptomyces isolates representing these ASVs for phenotypic and genomic characterization. Whole-genome sequencing revealed substantial variation in gene content, even among closely related isolates, and exometabolomic profiling showed distinct metabolic responses to media supplemented with drought- versus well-watered root tissue. Traits linked to drought survival, including osmotic stress tolerance, siderophore production, and carbon utilization, varied widely among isolates and were not phylogenetically conserved. Using a broader panel of 48 Streptomyces, we demonstrate that DE scores, determined through mono-association experiments in gnotobiotic sorghum systems, showed high variability and lacked correlation with plant growth promotion. Pangenome-wide association identified orthogroups involved in osmolyte transport (e.g., proP) and membrane biosynthesis (e.g., fabG) as positively associated with DE, though most associations lacked phylogenetic signal. Collectively, these results demonstrate that Streptomyces DE is not a conserved genus-level trait but is instead strain-specific and functionally heterogeneous. Furthermore, DE in the root microbiome was shown not to predict beneficial effects on plant growth. This work underscores the need to resolve functional traits at the strain level and highlights the complexity of microbe-host-environment interactions under abiotic stress.

Fonseca-Garcia, Citlali↗
DOE OSTI2023

Microdiverse bacterial clades prevail across Antarctic wetlands

Antarctica's extreme environmental conditions impose selection pressures on microbial communities. Indeed, a previous study revealed that bacterial assemblages at the Cierva Point Wetland Complex (CPWC) are shaped by strong homogeneous selection. Yet which bacterial phylogenetic clades are shaped by selection processes and their ecological strategies to thrive in such extreme conditions remain unknown. Here, we applied the phyloscore and feature-level βNTI indexes coupled with phylofactorization to successfully detect bacterial monophyletic clades subjected to homogeneous (HoS) and heterogenous (HeS) selection. Remarkably, only the HoS clades showed high relative abundance across all samples and signs of putative microdiversity. The majority of the amplicon sequence variants (ASVs) within each HoS clade clustered into a unique 97% sequence similarity operational taxonomic unit (OTU) and inhabited a specific environment (lotic, lentic or terrestrial). Our findings suggest the existence of microdiversification leading to sub-taxa niche differentiation, with putative distinct ecotypes (consisting of groups of ASVs) adapted to a specific environment. We hypothesize that HoS clades thriving in the CPWC have phylogenetically conserved traits that accelerate their rate of evolution, enabling them to adapt to strong spatio-temporally variable selection pressures. Variable selection appears to operate within clades to cause very rapid microdiversification without losing key traits that lead to high abundance. Variable and homogeneous selection, therefore, operate simultaneously but on different aspects of organismal ecology. The result is an overall signal of homogeneous selection due to rapid within-clade microdiversification caused by variable selection. It is unknown whether other systems experience this dynamic, and we encourage future work evaluating the transferability of our results.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Warming of alpine tundra enhances belowground production and shifts community towards resource acquisition traits

Abstract Climate warming is expected to stimulate plant growth in high‐elevation and high‐latitude ecosystems, significantly increasing aboveground net primary production (ANPP). However, the effects of simultaneous changes in temperature, snowmelt timing, and summer water availability on total net primary production (NPP)—and elucidation of both above‐ and belowground responses—remain an important area in need of further study. In particular, measures of belowground net primary productivity (BNPP) are required to understand whether ANPP changes reflect changes in allocation or are indicative of a whole plant NPP response. Further, plant functional traits provide a key way to scale from the individual plant to the community level and provide insight into drivers of NPP responses to environmental change. We used infrared heaters to warm an alpine plant community at Niwot Ridge, Colorado, and applied supplemental water to compensate for soil water loss induced by warming. We measured ANPP, BNPP, and leaf and root functional traits across treatments after 5 yr of continuous warming. Community‐level ANPP and total NPP (ANPP + BNPP) did not respond to heating or watering, but BNPP increased in response to heating. Heating decreased community‐level leaf dry matter content and increased total root length, indicating a shift in strategy from resource conservation to acquisition in response to warming. Water use efficiency (WUE) decreased with heating, suggesting alleviation of moisture constraints that may have enabled the plant community to increase productivity. Heating may have decreased WUE by melting snow earlier and creating more days early in the growing season with adequate soil moisture, but stimulated dry mass investment in roots as soils dried down later in the growing season. Overall, this study highlights how ANPP and BNPP responses to climate change can diverge, and encourages a closer examination of belowground processes, especially in alpine systems, where the majority of NPP occurs belowground.

54 ENVIRONMENTAL SCIENCES↗