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At least 19 records

Comparative Activity and Functional Ecology of Permafrost Soils and Lithic Niches in a Hyper-Arid Polar Desert

This study represents the first metagenomic interrogation of Antarctic permafrost and polar cryptoendolithic microbial communities. The results underlie two different habitability conditions in the same location under extreme cold and dryness: the permafrost habitat where viable microbial life and activity is questionable, and the cryptoendolithic habitat which contains organisms capable of growth under the extreme conditions of the Antarctic Dry Valleys.

Antarctic permafrost↗

A global soil plasmidome resource unveils functional and ecological roles of plasmids in soil microbiomes

Plasmids play significant roles in microbial adaptation to ecosystems, yet their dynamics remain poorly understood due to identification challenges. We present the Global Soil Plasmidome Resource (GSPR), a comprehensive dataset of 98,728 plasmid sequences amassed from 6860 terrestrial microbial communities and isolates. We explore this resource through various computational approaches, including phylogenetic diversity analysis, host prediction, and extensive functional annotation, to understand the contribution of plasmids to the genetic and functional diversity in soil, correlating these findings with sample type, as well as the soil habitat they were retrieved from. Our analysis reveals insights into plasmid-encoded functions such as effector modules, quorum sensing, and stress resistance, which may contribute to their persistence and microbial adaptation in soil. Furthermore, CRISPR analysis suggests a prevalent role of these elements related to intra-plasmid competition. By contrasting plasmids from cultivated and uncultivated organisms, we identify important functions that expand existing knowledge of plasmid roles in these habitats. This study represents a notable step forward in elucidating plasmid diversity and function within soil microbiomes and establishes a foundational framework for exploring their roles in natural environments.

Fiamenghi, Mateus B↗

A Conceptual Framework to Integrate Biodiversity, Ecosystem Function, and Ecosystem Service Models

Global biodiversity and ecosystem service models typically operate independently. Ecosystem service projections may therefore be overly optimistic because they do not always account for the role of biodiversity in maintaining ecological functions. We review models used in recent global model intercomparison projects and develop a novel model integration framework to more fully account for the role of biodiversity in ecosystem function, a key gap for linking biodiversity changes to ecosystem services. We propose two integration pathways. The first uses empirical data on biodiversity–ecosystem function relationships to bridge biodiversity and ecosystem function models and could currently be implemented globally for systems and taxa with sufficient data. We also propose a trait-based approach involving greater incorporation of biodiversity into ecosystem function models. Pursuing both approaches will provide greater insight into biodiversity and ecosystem services projections. Integrating biodiversity, ecosystem function, and ecosystem service modeling will enhance policy development to meet global sustainability goals.

biodiversity models↗

NASA’s NextGen Remote Sensing Instruments Have Arrived: Data Products For Studying Disease Vectors

Remote sensing can be used to measure, evaluate or estimate both the environment (state functions) and interfaces (processfunctions) defining vector habitats. The products of remote sensing can be integrated directly into the epidemiological equationsto significantly enhance our understanding of disease vector’s life cycles and habitats. The next generation of NASA’s remotesensing instruments which have become recently operational will provide a significant enhancement in our ability to studydisease vector’s life cycles and habitats. These instruments are on the International Space Station (ISS) and includeECOSTRESS, DESIS, and GEDI. ECOSTRESS is a 5 channel, thermal IR instrument with 70 m resolution and approximately1-5 day repeat cycle of day/night pairs. DESIS jointly developed by German Aerospace Center and Teledyne Brown Engineeringis a hyperspectral sensor system of 235 channels and 30 m resolution. DESIS data is only being acquired on demand. GEDI is ahigh-resolution laser ranger used for observing Earth’s forests and topography. NASA’s current ISS instrument configuration provides measurements of the critical environmental measures of environmentalstate functions important to vector & disease life cycles. Remote sensing data provide a spatial context and time series oflandscape scale process functions represented by land use mapping and measurements of ecological functions. Global publichealth is entering a new information age through the use of spatial models of disease vector/host ecologies driven by the use ofremotely sensed data to measure environmental and structural factors critical in determining disease vector habitats. In 2018, NASA initiated a new study for the Surface Biology and Geology (SBG) Designated Observable, identified in the 2018National Academies’ Decadal Survey entitled, “Thriving on Our Changing Planet: A Decadal Strategy for Earth Observationfrom Space.” (https://www.nap.edu/catalog/24938/thriving-on-our-changing-planet-a-decadal-strategy-for-earth) . The SBG isplanned to collect global remote sensing measurements using a hyperspectral spectrometer and multispectral thermal data. Thesedata sets will provide a significant enhancement in our ability to study disease vector’s life cycles and habitats globally. The 3sensors on the ISS provide precursor data to prepare the community for the application of future SBG data toward diseasestudies.

Disease Vectors↗

Collateral benefits: River flow normalization for endangered fish enabled riparian rejuvenation

Abstract Like most rivers worldwide, the transboundary North American Kootenay/i River has experienced multiple impacts including watershed developments, river channelization, and floodplain clearing, draining, and diking. Construction of Libby Dam was authorized by the 1964 Columbia River Treaty (CRT) between the United States and Canada, and in 1975 began regulating downstream flows for flood risk management and hydropower generation. Following cumulative impacts, the endemic Kootenai River White Sturgeon population collapsed and was designated as endangered in 1994 (U.S. Endangered Species Act). Subsequent Biological Opinions from the U.S. Fish and Wildlife Service prescribed Libby Dam operations to provide springtime flow pulses for sturgeon spawning. These provided the unanticipated benefit of substantial seedling recruitment of native and introduced riparian cottonwoods and willows. The regulated flow regime was further adaptively managed to provide a more normative (natural) regime, to balance ecological functions with flood risk management and hydropower generation. The broadened ecological considerations would be consistent with the proposed priorities for the modernization of the international CRT. The observed responses revealed that (1) diverse aquatic and riparian organisms are dependent on common river flow characteristics; (2) a normalized flow regime provided substantial ecological benefits; and (3) due to multiple influences, hybrid ecosystems develop along regulated rivers, with a blending of natural and altered processes and communities. For other regulated rivers, we recommend that (1) high springtime flows be allowed, as feasible; (2) followed by the gradual post‐peak recession; and (3) the maintenance of sufficient flows through the warm and dry interval of mid to late summer.

Rood, Stewart B.↗

Gila Water Resources II: Using Earth Observations to Identify Wildfire Impacts on Hydrologic Functions and Recovery in the Gila National Forest

Wildfires have the potential to cause devastating and long-lasting impacts on ecological systems. In the Gila NF, wildfire events have occurred with increasing frequency and severity over recent years. These disturbances such as the historic Whitewater-Baldy Complex Fire (2012) and Silver Fire (2013) have raised concerns over post-fire soil erosion, flooding, debris flows, and vegetation recovery. Understanding the connection between burn events and ecological functions is crucial for developing effective land management practices within the Gila NF that ensure the conservation of the watershed. Our Gila Water Resources II team worked in partnership with the US Department of Agriculture (USDA) US Forest Service’s (USFS) Gila National Forest and Region 3. This project was designed to provide insight into the influence of wildfires on increased flooding events and to determine if restoration efforts in the Gila NF are having a beneficial and noticeable impact on recovery. The goals of this project included generating data-supported end products to inform land management decisions, including the prioritization of specific regions and time scales for post-fire restoration efforts. To understand recovery trends and hydrologic impact in the Gila NF between 2000 and 2020, this project used NASA EO and ancillary data, including, but not limited to, Landsat 5 Thematic Mapper (TM), Landsat 7 Enhanced Thematic Mapper Plus (ETM+), Landsat 8 Operational Land Imager (OLI), USGS stream gauge data, and data provided by USDA USFS’s Gila National Forest and Region 3.

Water Resources↗

Gila Water Resources II: Using Earth Observations to Identify Wildfire Impacts on Hydrologic Functions and Recovery in the Gila National Forest

Wildfires have the potential to cause devastating and long-lasting impacts on ecological systems. In the Gila National Forest (Gila NF), wildfire events have occurred with increasing frequency and severity over recent years. These disturbances, such as the historic Whitewater Baldy Complex Fire (2012) and Silver Fire (2013), have raised concerns over post-fire flooding, debris flows, and vegetation recovery. Understanding connections between burn events and ecological functions is crucial for developing effective land management practices within the Gila NF that ensure conservation of the watershed. The Gila Water Resources II team worked in partnership with the US Department of Agriculture (USDA) US Forest Service’s (USFS) Gila National Forest and Region 3. This project provided insight into the influence of wildfires on increased flooding events and determined if restoration efforts in the Gila NF are having a beneficial impact on vegetation regeneration. To understand recovery trends and hydrologic impact in the Gila NF between 2000-2019, this project used Landsat 5 Thematic Mapper, Landsat 7 Enhanced Thematic Mapper Plus, Landsat 8 Operational Land Imager, Global Precipitation Measurement Integrated Multi-satellite Retrievals for GPM precipitation, along with ancillary data from USGS stream gauges and data provided by USDA USFS’s Gila National Forest and Region 3. Based on these data, the team identified burn areas that received restorative treatments and compared Normalized Burn Ratio for different land cover types to better inform land management decisions. Additionally, the team analyzed the relationship between precipitation and streamflow from stream gauges to investigate the impact wildfires have on hydrology within the watershed.

Water Resources↗

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↗

Rethinking the soil core microbiome

The concept of a core microbiome emerged from host-associated research to describe microbial members or functions conserved across clearly defined spatial, temporal, and biological boundaries. In soil- and plant-associated microbiome research, however, the term has increasingly shifted toward analytically defined subsets selected using study-specific thresholds or criteria. Synthesizing recent literature and cross-site analyses of bioenergy crop field soils, we show that the original biological meaning of the core microbiome has been blurred by dataset-specific analytical criteria. Taxa designated as ‘core’ were highly sensitive to methodological choices and often reflected explanatory value rather than conserved biological membership. Moreover, many studies that identify taxonomic ‘core’ members interpret their significance in functional terms, suggesting that functional conservation may be the biological interest. Taxonomic conservation may not be the most biologically meaningful target in highly heterogeneous soil and rhizosphere systems, where functional conservation may persist despite taxonomic turnover. Accordingly, ‘core microbiome’ should be reserved for microbial components explicitly demonstrated to be conserved across defined spatial, temporal, and environmental dimensions and linked to conserved ecological functions, while taxa selected for explanatory value are better described as ‘explanatory subsets of taxa’. Greater terminological precision will improve cross-study comparability and strengthen ecological inference in plant–soil microbiome research.

bioenergy crops↗

Antarctic lake viromes reveal potential virus associated influences on nutrient cycling in ice-covered lakes

The McMurdo Dry Valleys (MDVs) of Antarctica are a mosaic of extreme habitats which are dominated by microbial life. The MDVs include glacial melt holes, streams, lakes, and soils, which are interconnected through the transfer of energy and flux of inorganic and organic material via wind and hydrology. For the first time, we provide new data on the viral community structure and function in the MDVs through metagenomics of the planktonic and benthic mat communities of Lakes Bonney and Fryxell. Viral taxonomic diversity was compared across lakes and ecological function was investigated by characterizing auxiliary metabolic genes (AMGs) and predicting viral hosts. Our data suggest that viral communities differed between the lakes and among sites: these differences were connected to microbial host communities. AMGs were associated with the potential augmentation of multiple biogeochemical processes in host, most notably with phosphorus acquisition, organic nitrogen acquisition, sulfur oxidation, and photosynthesis. Viral genome abundances containing AMGs differed between the lakes and microbial mats, indicating site specialization. Using procrustes analysis, we also identified significant coupling between viral and bacterial communities (p = 0.001). Finally, host predictions indicate viral host preference among the assembled viromes. Collectively, our data show that: (i) viruses are uniquely distributed through the McMurdo Dry Valley lakes, (ii) their AMGs can contribute to overcoming host nutrient limitation and, (iii) viral and bacterial MDV communities are tightly coupled.

Microbiology↗

Hydrological Control on Soil Redox Condition and Carbon Loss of Coastal Wetland Under Sea-Level Rise

Coastal wetlands are critical carbon sinks with their biogeochemical and ecological functioning shaped by dynamic hydrological conditions that are increasingly influenced by climate change. A key unresolved question is how hydrologic flow, vegetation response, and rising sea levels interact to regulate soil redox condition and carbon loss in coastal wetlands. Using a field-tested hydrological–biogeochemical–ecological modeling framework, we reveal how the interplay between terrestrial groundwater discharge and tidal fluctuations generates complex groundwater flow patterns at the terrestrial–aquatic interface, and how these patterns modulate soil redox conditions, in turn influencing soil organic matter decomposition and carbon loss. Notably, rising sea levels suppress soil CO2 emissions while reducing lateral dissolved carbon losses, thereby enhancing litter carbon sequestration under anoxic conditions. As vegetation responds to sea-level rise and carbon inputs diminish, litter carbon subsequently declines. These findings underscore a critical hydrological control on carbon cycling, advancing our understanding of coastal ecosystem resilience in a warming world.

Chen, Kewei [ORNL] (ORCID:000000032580514X)↗

Cross-Disciplinarity in the Advance of Antarctic Ecosystem Research

The biodiversity, ecosystem services and climate variability of the Antarctic continent, and the Southern Ocean are major components of the whole Earth system. Antarctic ecosystems are driven more strongly by the physical environment than many other marine and terrestrial ecosystems. As a consequence, to understand ecological functioning, cross-disciplinary studies are especially important in Antarctic research. The conceptual study presented here is based on a workshop initiated by the Research Programme Antarctic Thresholds - Ecosystem Resilience and Adaption of the Scientific Committee on Antarctic Research, which focused on challenges in identifying and applying cross-disciplinary approaches in the Antarctic. Novel ideas, and first steps in their implementation, were clustered into eight themes, ranging from scale problems, risk maps, organism and ecosystem responses to multiple environmental changes, to evolutionary processes. Scaling models and data across different spatial and temporal scales were identified as an overarching challenge. Approaches to bridge gaps in the research programmes included multi-disciplinary monitoring, linking biomolecular findings and simulated physical environments, as well as integrative ecological modelling. New strategies in academic education are proposed. The results of advanced cross-disciplinary approaches can contribute significantly to our knowledge of ecosystem functioning, the consequences of climate change, and to global assessments that ultimately benefit humankind.

Scaling↗

Multifactorial genetic control and magnesium levels govern the production of a Streptomyces antibiotic with unusual cell density dependence

Streptomyces bacteria are renowned both for their antibiotic production capabilities and for their cryptic metabolic potential. Their metabolic repertoire is subject to stringent genetic control, with many of the associated biosynthetic gene clusters being repressed by the conserved nucleoid-associated protein Lsr2. In an effort to stimulate new antibiotic production in wild Streptomyces isolates, we leveraged the activity of an Lsr2 knockdown construct and successfully enhanced antibiotic production in the wild Streptomyces isolate WAC07094. We determined that this new activity stemmed from increased levels of the angucycline-like family member saquayamycin. Saquayamycin has both antibiotic and anti-cancer activities, and intriguingly, beyond Lsr2-mediated repression, we found saquayamycin production was also suppressed at high density on solid or in liquid growth media; its levels were greatest in low-density cultures. This density-dependent control was exerted at the level of the cluster-situated regulatory gene sqnR and was mediated in part through the activity of the PhoRP two-component regulatory system, where deleting phoRP led to both constitutive antibiotic production and sqnR expression. This suggests that PhoP functions to repress the expression of sqnR at high cell density. We further discovered that magnesium supplementation could alleviate this density dependence, although its action was independent of PhoP. Finally, we revealed that the nitrogen-responsive regulators GlnR and AfsQ1 could relieve the repression exerted by Lsr2 and PhoP. Intriguingly, we found that this low density-dependent production of saquayamycin was not unique to WAC07094; saquayamycin production by another wild isolate also exhibited low-density activation, suggesting that this spatial control may serve an important ecological function in their native environments.

59 BASIC BIOLOGICAL SCIENCES↗

Quantifying Post-fire Vegetation Recovery on the Colorado Front Range

Forest composition and structure in the Colorado Front Range has been altered by changing wildfire regimes, particularly in response to increased fire severity. Subsequent reductions in post-fire tree regeneration can result in chronic impacts to ecological function and water quality. This project partnered with the U.S. Forest Service to estimate tree canopy recovery from 15 to 21 years after four Colorado Front Range fires that burned between 1996 and 2002— the Bobcat, Buffalo Creek, Hayman, and High Meadows fires—using Landsat 5 Thematic Mapper (TM), Landsat 7 Enhanced Thematic Mapper (ETM+), and Landsat 8 Operational Land Imager (OLI). First, we evaluated relationships between recovery metrics derived from spectral vegetation indices (i.e. post-fire vegetation, normalized burn ratio, percent unrecovered vegetation) and field-collected counts of post-fire tree seedling regeneration. Then, we used high-resolution imagery paired with Landsat timeseries spectral and geomorphometric data to map forest canopy cover 15-21 years post-fire. Finally, we assessed ecological drivers of recovery including topography, climate, soils, and fire severity using Random Forest. While we found that basic vegetation index metrics failed to distinguish field-measured tree regeneration, our data showed that both aspect and burn severity were important drivers of vegetation recovery. North-facing aspects tended to have higher pre-fire Normalized Difference Vegetation Index (NDVI) and thus higher burn severities. However, areas that burned at high severity experienced slower vegetation recovery, regardless of aspect suggesting that high severity fire can mute favorable site conditions on north-facing aspects (i.e. moister, more developed soils). While this work propels our understanding of variables that influence vegetative recovery, vegetation type, forest conversion, and watershed function, more work should focus on what vegetation indices identifying areas of recovery indicate across different forest types and burn severities.

NASA DEVELOP↗

Rocky Mountain Disasters - Using NASA Earth Observations to Monitor Post-Fire Vegetation Recovery in the Colorado Front Range

Forest composition and structure in the Colorado Front Range has been altered by changing wildfire regimes. In particular, increased moderate- and high-severity fire significantly reduces forest cover following fire and often results in reduced seedling regeneration. Reduced tree canopy regrowth has chronic effects on upland ecological function and downstream water quality. This project partnered with the US Forest Service to estimate long-term vegetation recovery following four Colorado Front Range fires between 1996 and 2002—the Bobcat, Buffalo Creek, Hayman, and High Meadows fires—using Landsat 5 Thematic Mapper (TM),Landsat 7 Enhanced Thematic Mapper (ETM+), and Landsat 8 Operational Land Imager (OLI). The random forest algorithm was applied to produce maps of percent forest canopy cover for coniferous trees, deciduous trees, and all trees using time-series variables for pre- and post-fire as inputs. Similarly, maps of post-fire seedling regeneration were produced using random forest for coniferous trees,deciduous trees, and all trees using ecological drivers (soil, climate, fire, and topography) and pre-fire remote sensing predictors. Relationships between ecological drivers of post-fire vegetation trajectories were also evaluated. Additional analyses were conducted to (1) assess whether seedlings could be detected by Landsat or synthetic aperture radar (SAR) time-series analysis (2) assess pre-fire and post-fire Landsat variables against pre-fire and post-fire tree cover estimates to evaluate whether magnitude of forest change can be detected. Understanding variables that influence vegetative recovery, vegetation type conversion, and watershed characteristics will aid forest restoration efforts and water quality management.

Eric Jensen↗

TropiRoot 1.0: Database of tropical root characteristics across environments

Tropical ecosystems contain the world's largest biodiversity of vascular plants. Yet, our understanding of tropical functional diversity and its contribution to global diversity patterns is constrained by data availability. This discrepancy underscores an urgent need to bridge data gaps by incorporating comprehensive tropical root data into global datasets. Here, we provide a database of tropical root characteristics. This new database, TropiRoot 1.0, will be instrumental in evaluating an array of hypotheses pertaining to root functional ecology and plant biogeography, both within the tropics and relative to other global biomes. The data compilation was conducted by the TropiRoot Initiative, in partnership with the Fine-Root Ecology Database (FRED) and the Global Root Trait (GRooT) database, Colorado State University (CSU) and the Smithsonian Tropical Research Institute (STRI). Literature search and data extraction were conducted between 2020 and 2024. Literature was identified using Web of Science, Scopus, and complemented using the expert knowledge of members of TropiRoot. To provide broad environmental and geographical distributions, literature searches included root characteristics (traits) across global change drivers, natural gradients, and from different continents. We adopted FRED standardized data columns and streamlined the format to enhance accessibility for data extraction across various user groups. This optimized framework resulted in a smaller, yet comprehensive datasheet. To make the database compatible with other global root trait initiatives, column identification was standardized following the codes provided by FRED. These efforts culminated in data extracted from 104 new sources, resulting in more than 8000 rows of data (either species or community data). Most of the data in TropiRoot 1.0 include root characteristics such as root biomass, morphology, root dynamics, mass fraction, architecture, anatomy, physiology, and root chemistry. This initiative represents a 30% increase in the currently available data for tropical roots in FRED. TropiRoot 1.0 contains root characteristics from 25 different countries, where seven are located in Asia, six in South America, five in Central America and the Caribbean, four in Africa, two in North America, and 1 in Oceania. Due to the volume of data, when ancillary data were available, including soil data, these data were either extracted and included in the database or its availability was recorded in an additional column. Multiple contributors checked the entries for outliers during the collation process to ensure data quality. For text-based observations, we examined all cells to ensure that their content relates to their specific categories. For numerical observations, we ordered each numerical value from least to greatest and plotted the values, checking apparent outliers against the data in their respective sources and correcting or removing incorrect or impossible values. Some data (soil and aboveground) have different columns for the same variable presented in different units, including originally published units, but root characteristics data had units converted to match those reported in FRED. By filling a gap from global databases, TropiRoot 1.0 expands our knowledge of otherwise so far underrepresented regions and our ability to assess global trends. This advancement can be used to improve tropical forest representation in vegetation models. The data are freely available and should be cited when used.

FRED↗

Next generation Arctic vegetation maps: Aboveground plant biomass and woody dominance mapped at 30 m resolution across the tundra biome

The Arctic is warming faster than anywhere else on Earth, placing tundra ecosystems at the forefront of global climate change. Plant biomass is a fundamental ecosystem attribute that is sensitive to changes in climate, closely tied to ecological function, and crucial for constraining ecosystem carbon dynamics. However, the amount, functional composition, and distribution of plant biomass are only coarsely quantified across the Arctic. Therefore, we developed the first moderate resolution (30 m) maps of live aboveground plant biomass (g m −2 ) and woody plant dominance (%) for the Arctic tundra biome, including the mountainous Oro Arctic. We modeled biomass for the year 2020 using a new synthesis dataset of field biomass harvest measurements, Landsat satellite seasonal synthetic composites, ancillary geospatial data, and machine learning models. Additionally, we quantified pixel-wise uncertainty in biomass predictions using Monte Carlo simulations and validated the models using a robust, spatially blocked and nested cross-validation procedure. Observed plant and woody plant biomass values ranged from 0 to ∼6000 g m −2 (mean ≈ 350 g m −2 ), while predicted values ranged from 0 to ∼4000 g m −2 (mean ≈ 275 g m −2 ), resulting in model validation root-mean-squared-error (RMSE) ≈ 400 g m −2 and R 2 ≈ 0.6. Our maps not only capture large-scale patterns of plant biomass and woody plant dominance across the Arctic that are linked to climatic variation (e.g., thawing degree days), but also illustrate how fine-scale patterns are shaped by local surface hydrology, topography, and past disturbance. By providing data on plant biomass across Arctic tundra ecosystems at the highest resolution to date, our maps can significantly advance research and inform decision-making on topics ranging from Arctic vegetation monitoring and wildlife conservation to carbon accounting and land surface modeling.

Climate change↗