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At least 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Characterisation and comparative analysis of mitochondrial genomes of false, yellow, black and blushing morels provide insights on their structure and evolution

Morchella species have considerable significance in terrestrial ecosystems, exhibiting a range of ecological lifestyles along the saprotrophism-to-symbiosis continuum. However, the mitochondrial genomes of these ascomycetous fungi have not been thoroughly studied, thereby impeding a comprehensive understanding of their genetic makeup and ecological role. In this study, we analysed the mitogenomes of 30 Morchellaceae species, including yellow, black, blushing and false morels. These mitogenomes are either circular or linear DNA molecules with lengths ranging from 217 to 565 kbp and GC content ranging from 38% to 48%. Fifteen core protein-coding genes, 28–37 tRNA genes and 3–8 rRNA genes were identified in these Morchellaceae mitogenomes. The gene order demonstrated a high level of conservation, with the cox1 gene consistently positioned adjacent to the rnS gene and cob gene flanked by apt genes. Some exceptions were observed, such as the rearrangement of atp6 and rps3 in Morchella importuna and the reversed order of atp6 and atp8 in certain morel mitogenomes. However, the arrangement of the tRNA genes remains conserved. We additionally investigated the distribution and phylogeny of homing endonuclease genes (HEGs) of the LAGLIDADG (LAGs) and GIY-YIG (GIYs) families. A total of 925 LAG and GIY sequences were detected, with individual species containing 19–48HEGs. These HEGs were primarily located in the cox1, cob, cox2 and nad5 introns and their presence and distribution displayed significant diversity amongst morel species. These elements significantly contribute to shaping their mitogenome diversity. Overall, this study provides novel insights into the phylogeny and evolution of the Morchellaceae.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Integrating Viral Metagenomics into an Ecological Framework

Viral metagenomics has expanded our knowledge of the ecology of uncultured viruses, within both environmental (e.g., terrestrial and aquatic) and host-associated (e.g., plants and animals, including humans) contexts. Here, we emphasize the implementation of an ecological framework in viral metagenomic studies to address questions in virology rarely considered ecological, which can change our perception of viruses and how they interact with their surroundings. Additionally, an ecological framework explicitly considers diverse variants of viruses in populations that make up communities of interacting viruses, with ecosystem-level effects. It provides a structure for the study of the diversity, distributions, dynamics, and interactions of viruses with one another, hosts, and the ecosystem, including interactions with abiotic factors. An ecological framework in viral metagenomics stands poised to broadly expand our knowledge in basic and applied virology. We highlight specific fundamental research needs to capitalize on its potential and advance the field.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Climate change alters slug abundance but not herbivory in a temperate grassland

Climate change will significantly impact the world’s ecosystems, in part by altering species interactions and ecological processes, such as herbivory and plant community dynamics, which may impact forage quality and ecosystem production. Yet relatively few field experimental manipulations assessing all of these parameters have been performed to date. To help fill this knowledge gap, we evaluated the effects of increased temperature (+3°C day and night, year-round) and precipitation (+30% of mean annual rainfall) on slug herbivory and abundance and plant community dynamics biweekly in a pasture located in central Kentucky, U.S.A. Warming increased slug abundance once during the winter, likely due to improving conditions for foraging, whereas warming reduced slug abundance at times in late spring, mid-summer, and early fall (from 62–95% reduction depending on month). We found that warming and increased precipitation did not significantly modify slug herbivory at our site, despite altering slug abundance and affecting plant community composition and forage quality. Climate change will alter seasonal patterns of slug abundance through both direct effects on slug biology and indirect effects mediated by changes in the plant community, suggesting that pasture management practices may have to adapt.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

AmeriFlux FLUXNET-1F US-xKZ NEON Konza Prairie Biological Station (KONZ)

This is the AmeriFlux Management Project (AMP) created FLUXNET-1F version of the carbon flux data for the site US-xKZ NEON Konza Prairie Biological Station (KONZ). This is the FLUXNET version of the carbon flux data for the site US-xKZ NEON Konza Prairie Biological Station (KONZ) produced by applying the standard ONEFlux (1F) software. Site Description - Konza Prairie Biological Station (KPBS) was established to provide a "natural laboratory" to conduct ecological research and is located on a 3,487 hectare native tallgrass prairie preserve. KPBS is a field research station dedicated to conservation, education and long-term ecological research. Over 1,580 scientific papers have been published by scientists conducting studies at KPBS. The study of ecological patterns and processes in native tallgrass prairie ecosystems is the primary subject of research.

Network), NEON (National Ecological Observatory↗
DOE OSTI2025

Fine root and soil carbon stocks are positively related in grasslands but not in forests

Increasing fine root carbon (FRC) inputs into soils has been proposed as a solution to increasing soil organic carbon (SOC). However, FRC inputs can also enhance SOC loss through priming. Here, we tested the broad-scale relationships between SOC and FRC at 43 sites across the US National Ecological Observatory Network. We found that SOC and FRC stocks were positively related with an across-ecosystem slope of 7 ± 3 kg SOC m −2 per kg FRC m −2 , but this relationship was driven by grasslands. Grasslands had double the across-ecosystem slope while forest FRC and SOC were unrelated. Furthermore, deep grassland soils primarily showed net SOC accrual relative to FRC input. Conversely, forests had high variability in whether FRC inputs were related to net SOC priming or accrual. We conclude that while FRC increases could lead to increased SOC in grasslands, especially at depth, the FRC-SOC relationship remains difficult to characterize in forests.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Root traits as drivers of plant and ecosystem functioning: current understanding, pitfalls and future research needs

The effects of plants on the biosphere, atmosphere and geosphere are key determinants of terrestrial ecosystem functioning. However, despite substantial progress made regarding plant belowground components, we are still only beginning to explore the complex relationships between root traits and functions. Drawing on the literature in plant physiology, ecophysiology, ecology, agronomy and soil science, we reviewed 24 aspects of plant and ecosystem functioning and their relationships with a number of root system traits, including aspects of architecture, physiology, morphology, anatomy, chemistry, biomechanics and biotic interactions. Based on this assessment, we critically evaluated the current strengths and gaps in our knowledge, and identify future research challenges in the field of root ecology. Most importantly, we found that belowground traits with the broadest importance in plant and ecosystem functioning are not those most commonly measured. Also, the estimation of trait relative importance for functioning requires us to consider a more comprehensive range of functionally relevant traits from a diverse range of species, across environments and over time series. Finally, we also advocate that establishing causal hierarchical links among root traits will provide a hypothesis-based framework to identify the most parsimonious sets of traits with the strongest links on functions, and to link genotypes to plant and ecosystem functioning.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

VirION2: a short- and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature

Microbes play fundamental roles in shaping natural ecosystem properties and functions, but do so under constraints imposed by their viral predators. However, studying viruses in nature can be challenging due to low biomass and the lack of universal gene markers. Though metagenomic short-read sequencing has greatly improved our virus ecology toolkit—and revealed many critical ecosystem roles for viruses—microdiverse populations and fine-scale genomic traits are missed. Some of these microdiverse populations are abundant and the missed regions may be of interest for identifying selection pressures that underpin evolutionary constraints associated with hosts and environments. Though long-read sequencing promises complete virus genomes on single reads, it currently suffers from high DNA requirements and sequencing errors that limit accurate gene prediction. Here we introduce VirION2, an integrated short- and long-read metagenomic wet-lab and informatics pipeline that updates our previous method (VirION) to further enhance the utility of long-read viral metagenomics. Using a viral mock community, we first optimized laboratory protocols (polymerase choice, DNA shearing size, PCR cycling) to enable 76% longer reads (now median length of 6,965 bp) from 100-fold less input DNA (now 1 nanogram). Using a virome from a natural seawater sample, we compared viromes generated with VirION2 against other library preparation options (unamplified, original VirION, and short-read), and optimized downstream informatics for improved long-read error correction and assembly. VirION2 assemblies combined with short-read based data (‘enhanced’ viromes), provided significant improvements over VirION libraries in the recovery of longer and more complete viral genomes, and our optimized error-correction strategy using long- and short-read data achieved 99.97% accuracy. In the seawater virome, VirION2 assemblies captured 5,161 viral populations (including all of the virus populations observed in the other assemblies), 30% of which were uniquely assembled through inclusion of long-reads, and 22% of the top 10% most abundant virus populations derived from assembly of long-reads. Viral populations unique to VirION2 assemblies had significantly higher microdiversity means, which may explain why short-read virome approaches failed to capture them. These findings suggest the VirION2 sample prep and workflow can help researchers better investigate the virosphere, even from challenging low-biomass samples. Our new protocols are available to the research community on protocols.io as a ‘living document’ to facilitate dissemination of updates to keep pace with the rapid evolution of long-read sequencing technology.

Long-reads↗
DOE OSTI2026

Viromics approaches for the study of viral diversity and ecology in microbiomes

Viruses are found across all ecosystems and infect every type of organism on Earth. Traditional culture-based methods have proven insufficient to explore this viral diversity at scale, driving the development of viromics, the sequence-based analysis of uncultivated viruses. Viromics approaches have been particularly useful for studying viruses of microorganisms, which can act as crucial regulators of microbiomes across ecosystems. They have already revealed the broad geographic distribution of viral communities and are progressively uncovering the expansive genetic and functional diversity of the global virome. Moving forward, large-scale viral ecogenomics studies combined with new experimental and computational approaches to identify virus activity and host interactions will enable a more complete characterization of global viral diversity and its effects.

Ecology↗
DOE OSTI2021

Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater

While oligotrophic deep groundwaters host active microbes attuned to the low-end of the bioenergetics spectrum, the ecological constraints on microbial niches in these ecosystems and their consequences for microbiome convergence are unknown. Here, we provide a genome-resolved, integrated omics analysis comparing archaeal and bacterial communities in disconnected fracture fluids of the Fennoscandian Shield in Europe. Leveraging a dataset that combines metagenomes, single cell genomes, and metatranscriptomes, we show that groundwaters flowing in similar lithologies offer fixed niches that are occupied by a common core microbiome. Functional expression analysis highlights that these deep groundwater ecosystems foster diverse, yet cooperative communities adapted to this setting. We suggest that these communities stimulate cooperation by expression of functions related to ecological traits, such as aggregate or biofilm formation, while alleviating the burden on microorganisms producing compounds or functions that provide a collective benefit by facilitating reciprocal promiscuous metabolic partnerships with other members of the community. We hypothesize that an episodic lifestyle enabled by reversible bacteriostatic functions ensures the subsistence of the oligotrophic deep groundwater microbiome.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

SCCOUT: Surveying for Categorization and Control of Organism in Unwelcome Territory

Advancements in the fields of science, technology, and medicine have contributed largely to the growth of society over the last century. Thanks to these discoveries, all corners of the planet are connected both digitally and physically. Progress in the field of medicine has led to people living longer, fuller lives and a general increase in global population. Awareness of our world’s changing climate and the effects that has on local and global ecosystems has spurred great efforts to protect the environment. These discoveries along with many others have helped our world grow in a myriad of ways; however, certain efforts in agriculture, natural resource management, and ecosystem management have not scaled to accommodate this growth. Increasing prevalence and ease of dissemination of invasive plants and animals, diseases, and changing ecological conditions pose significant challenges to biodiversity, ecosystem health, and agricultural productivity. Moreover, as the world population grows, there are more people to feed and less viable farmland to produce food for them. Despite the increasing prevalence of these issues, methods for addressing and tracking them have stayed relatively the same for at least the last several decades.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

The Zooplankton International Geospatial (ZIG) dataset: A global repository of spatiotemporal freshwater zooplankton community composition data to support ecological research

Zooplankton play critical roles in aquatic ecosystem function and food webs. Nevertheless, global syntheses of their abundance and community dynamics are challenging due to methodological differences across monitoring programs, taxonomic inconsistencies, and a lack of standardized metadata. To reconcile these challenges, we assembled, curated, validated, and harmonized the Zooplankton International Geospatial (ZIG) dataset, which includes co-located and contemporaneous zooplankton, water chemistry, and limnological data from 307 lakes and reservoirs. ZIG includes waterbodies from each major lake thermal region and range in size from 0.8-2,805,8600 hectares. Temporal coverage for individual waterbodies ranges between 1-60 years of data (median = 4 years) with sampling from once annually to weekly. ZIG is publicly available and can be used to understand freshwater biodiversity change and its drivers at unprecedented scales, and we consider it to be a cornerstone for future investigations of freshwater biology, chemistry, and ecology.

Figary, Stephanie [Cornell University, Ithaca, NY]↗
DOE OSTI2021

Comparative Genomic Analysis of Three Pseudomonas Species Isolated from the Eastern Oyster (Crassostrea virginica) Tissues, Mantle Fluid, and the Overlying Estuarine Water Column

The eastern oysters serve as important keystone species in the United States, especially in the Gulf of Mexico estuarine waters, and at the same time, provide unparalleled economic, ecological, environmental, and cultural services. One ecosystem service that has garnered recent attention is the ability of oysters to sequester impurities and nutrients, such as nitrogen (N), from the estuarine water that feeds them, via their exceptional filtration mechanism coupled with microbially-mediated denitrification processes. It is the oyster-associated microbiomes that essentially provide these myriads of ecological functions, yet not much is known on these microbiota at the genomic scale, especially from warm temperate and tropical water habitats. Among the suite of bacterial genera that appear to interplay with the oyster host species, pseudomonads deserve further assessment because of their immense metabolic and ecological potential. To obtain a comprehensive understanding on this aspect, we previously reported on the isolation and preliminary genomic characterization of three Pseudomonas species isolated from minced oyster tissue (P. alcaligenes strain OT69); oyster mantle fluid (P. stutzeri strain MF28) and the water collected from top of the oyster reef (P. aeruginosa strain WC55), respectively. In this comparative genomic analysis study conducted on these three targeted pseudomonads, native to the eastern oyster and its surrounding environment, provided further insights into their unique functional traits, conserved gene pools between the selected pseudomonads, as well as genes that render unique characteristics in context to metabolic traits recruited during their evolutionary history via horizontal gene transfer events as well as phage-mediated incorporation of genes. Moreover, the strains also supported extensively developed resistomes, which suggests that environmental microorganisms native to relatively pristine environments, such as Apalachicola Bay, Florida, have also recruited an arsenal of antibiotic resistant gene determinants, thus posing an emerging public health concern.

Pathak, Ashish↗
DOE OSTI2022

Editorial: Exogenous carbon-based materials in soil ecosystems

Various exogenous carbon-based materials (ECMs) such as crop straw, biochar, carbon-based nano-fertilizer, and microplastics have accumulated in soil ecosystems. These ECMs may cause direct and indirect impacts on soil properties, processes, productivity, and health, thus potentially changing the function and stability of soil ecosystems. However, large knowledge gaps still exist on ECMs in soil ecosystems, including their accumulation, interactions with soil components, and potential ecological impacts and risks. Therefore, more efforts are needed to further understand the impacts especially the long-term effects of ECMs in soil ecosystems. By generating new knowledge, this Research Topic aims to improve the understanding of the effects of ECMs on soil ecosystems, including soil quality, nutrient cycling, microbial ecology, crop growth, environmental health and ecological risk.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Roadmap for the future of extreme wildfire events

Background Extreme wildfire events (EWEs) represent a growing threat globally, posing substantial risks to ecosystems, human communities, and infrastructure. Despite increased recognition of their ecological, social, and economic significance, current definitions of EWEs vary widely, reflecting disciplinary biases and regional contexts. This article emerges from an interdisciplinary workshop convened to reassess and refine the definition of EWEs, examine their impacts across ecological and social dimensions, and identify critical knowledge gaps impeding our understanding of these infrequent but important events. Results Our synthesis highlights significant limitations with existing definitions, particularly their reliance on subjective thresholds and their emphasis on extreme fire behavior alone. EWEs encompass a spectrum of complex, multi-dimensional phenomena that extend beyond immediate biophysical characteristics to include cumulative social, economic, and ecological impacts. These impacts often manifest over extended timeframes and include hazardous environmental contamination, severe geomorphic disturbances, ecosystem transformations, and unintended consequences of post-fire management actions. Current wildfire modeling frameworks inadequately capture these compounding factors, particularly the interactions among social systems, ecological conditions, and extreme fire behavior. To overcome these issues, we advocate for an interdisciplinary and context-sensitive approach to defining and studying EWEs. This revised definition emphasizes wildfires exhibiting anomalies in fire behavior, ecological outcomes, or social impacts relative to historically observed baselines, accommodating variability across different geographic regions and ecological settings. Conclusions Adopting an interdisciplinary framework that integrates biophysical and social sciences will enhance the predictive capability of wildfire models and improve resilience planning and response strategies. Filling identified knowledge gaps—such as limited high-quality empirical fire behavior data and insufficient integration of social dynamics into modeling—will better prepare communities and ecosystems to cope with and adapt to EWEs. This inclusive approach underscores the necessity for collaboration across disciplines and sectors, essential to managing extreme wildfires in an era of increasing climatic and ecological uncertainty.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Assessing impacts of selective logging on water, energy, and carbon budgets and ecosystem dynamics in Amazon forests using the Functionally Assembled Terrestrial Ecosystem Simulator

Abstract. Tropical forest degradation from logging, fire, and fragmentation not only alters carbon stocks and carbon fluxes, but also impacts physical land surface properties such as albedo and roughness length. Such impacts are poorly quantified to date due to difficulties in accessing and maintaining observational infrastructures, as well as the lack of proper modeling tools for capturing the interactions among biophysical properties, ecosystem demography, canopy structure, and biogeochemical cycling in tropical forests. As a first step to address these limitations, we implemented a selective logging module into the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) by mimicking the ecological, biophysical, and biogeochemical processes following a logging event. The model can specify the timing and aerial extent of logging events, splitting the logged forest patch into disturbed and intact patches; determine the survivorship of cohorts in the disturbed patch; and modifying the biomass and necromass (total mass of coarse woody debris and litter) pools following logging. We parameterized the logging module to reproduce a selective logging experiment at the Tapajós National Forest in Brazil and benchmarked model outputs against available field measurements. Our results suggest that the model permits the coexistence of early and late successional functional types and realistically characterizes the seasonality of water and carbon fluxes and stocks, the forest structure and composition, and the ecosystem succession following disturbance. However, the current version of FATES overestimates water stress in the dry season and therefore fails to capture seasonal variation in latent and sensible heat fluxes. Moreover, we observed a bias towards low stem density and leaf area when compared to observations, suggesting that improvements are needed in both carbon allocation and establishment of trees. The effects of logging were assessed by different logging scenarios to represent reduced impact and conventional logging practices, both with high and low logging intensities. The model simulations suggest that in comparison to old-growth forests the logged forests rapidly recover water and energy fluxes in 1 to 3 years. In contrast, the recovery times for carbon stocks, forest structure, and composition are more than 30 years depending on logging practices and intensity. This study lays the foundation to simulate land use change and forest degradation in FATES, which will be an effective tool to directly represent forest management practices and regeneration in the context of Earth system models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Large ecosystem-scale effects of restoration fail to mitigate impacts of land-use legacies in longleaf pine savannas

Ecological restoration is a global priority, with potential to reverse biodiversity declines and promote ecosystem functioning. Yet, successful restoration is challenged by lingering legacies of past land-use activities, which are pervasive on lands available for restoration. Although legacies can persist for centuries following cessation of human land uses such as agriculture, we currently lack understanding of how land-use legacies affect entire ecosystems, how they influence restoration outcomes, or whether restoration can mitigate legacy effects. Using a large-scale experiment, we evaluated how restoration by tree thinning and land-use legacies from prior cultivation and subsequent conversion to pine plantations affect fire-suppressed longleaf pine savannas. In this work, we evaluated 45 ecological properties across four categories: 1) abiotic attributes, 2) organism abundances, 3) species diversity, and 4) species interactions. The effects of restoration and land-use legacies were pervasive, shaping all categories of properties, with restoration effects roughly twice the magnitude of legacy effects. Restoration effects were of comparable magnitude in savannas with and without a history of intensive human land use; however, restoration did not mitigate numerous legacy effects present prior to restoration. As a result, savannas with a history of intensive human land use supported altered properties, especially related to soils, even after restoration. The signature of past human land-use activities can be remarkably persistent in the face of intensive restoration, influencing the outcome of restoration across diverse ecological properties. Understanding and mitigating land-use legacies will maximize the potential to restore degraded ecosystems.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

DVMDOSTEM v0.8.3: a terrestrial ecosystem model designed to represent arctic, boreal and permafrost ecosystem dynamics

The impacts of climate change on natural ecosystems are the result of complex physical and ecological processes operating and interacting at a variety of spatio-temporal scales, that can be represented in process-based ecosystem models. DVMDOSTEM is an advanced process-based terrestrial ecosystem model (TEM) designed to study ecosystem responses to climate changes and disturbances. It has a particular focus on permafrost regions (i.e. regions characterized by soils that stay partially frozen all year round for at least two consecutive years), encompassing boreal, arctic, and alpine landscapes. The model couples two previous versions of the Terrestrial Ecosystem Model (TEM) (McGuire et al., 1992): DVMTEM that includes a dynamic vegetation module (DVM) (E. S. Euskirchen et al., 2009), and DOSTEM that includes a dynamic organic soil module (DOS) (H. Genet et al., 2013; Yi et al., 2010). DVMDOSTEM simulates processes at yearly and monthly scales, with some physical processes operating at an even finer temporal resolution. Its versatility allows for site-specific to regional simulations, making it valuable for predicting shifts in permafrost, vegetation, and carbon (C) and nitrogen (N) dynamics. While DVMDOSTEM has been described in the methods sections of many manuscripts, this paper is the first stand alone description of DVMDOSTEM, independent of a particular scientific investigation.

Carman, Tobey B. [Univ. of Alaska, Fairbanks, AK (↗