Mycorrhizal roots slow the decay of belowground litters in a temperate hardwood forest
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Environmental Sciences & Ecology↗
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Selection and development of aptamers for pyoverdine
The rhizosphere is a small region surrounding plant roots that is enriched in biochemicals from root exudates and populated with fungi, nematode, and bacteria. Interaction of rhizosphere organisms with plants is mainly promoted by exudates from the roots. Root exudates contain biochemicals that come from primary and secondary metabolisms of plants. These biochemicals attract microbes, which influence plant nutrition. The rhizosphere bacteria (microbiome) are vital to plant nutrient uptake and influence biotic and abiotic stress and pathogenesis. Pseudomonas is a genus of gammaproteobacteria known for its ubiquitous presence in natural habitats and its striking ecological, metabolic, and biochemical diversity. Within the genus, members of the Pseudomonas fluorescens group are common inhabitants of soil and plant surfaces, and certain strains function in the biological control of plant disease, protecting plants from infection by soilborne and aerial plant pathogens. The soil bacterium Pseudomonas protegens Pf-5 (also known as Pseudomonas fluorescensPf-5) is a well-characterized biological strain, which is distinguished by its prolific production of the secondary metabolite, pyoverdine. Knowledge of the distribution of P. fluorescens secretory activity around plant roots is very important for understanding the interaction between P. fluorescens and plants and can be achieved by real time tracking of pyoverdine. To achieve the capability of real-time tracking in soil, we have used a structure-switching SELEX strategy to select high affinity ssDNA and 2’ F-Y-RNA aptamers with specificity for pyoverdine over other siderophores. Pyoverdines from various strains possess a conserved chromophore along with strain-specific peptide chain. Some of the isolated aptamers bind to chromophore of pyoverdine. These will identify pyoverdines from a variety of pseudomonads. Identification of aptamers that selectively bind the peptide portion of pyoverdine Pf-5 is underway. The identified aptamers that are broadly and narrowly specific for pyoverdines or Pf-5 will be optimized for integration into an electrochemical biosensor to track, in real time, P fluorescens activity and other pseudomonads in and around the rhizosphere.
59 BASIC BIOLOGICAL SCIENCES↗
Sedimentary Parameters Controlling Occurrence and Preservation of Microbial Mats in Siliciclastic Depositional Systems
Shallow-marine, siliciclastic depositional systems are governed by physical sedimentary processes. Mineral precipitation or penecontemporaneous cementation play minor roles. Today, coastal siliciclastic environments may be colonized by a variety of epibenthic, mat-forming cyanobacteria. Studies on microbial mats showed that they are not randomly distributed in modern tidal environments. Distribution and abundancy is mainly function of a particular sedimentary facies. Fine-grained sands composed of "clear" (translucent) quartz particles constitute preferred substrates for cyanobacteria. Mat-builders also favor sites characterized by moderate hydrodynamic flow regimes, which permit biomass enrichment and construction of mat fabrics without lethal burial of mat populations by fine sediments. A comparable facies relationship can be observed in ancient siliciclastic shelf successions from the terminal Neoproterozoic Nama Group, Namibia. Wrinkle structures that record microbial mats are present but sparsely distributed in mid- to inner shelf sandstones of the Nudaus Formation. The sporadic distribution of these structures reflects both the narrow ecological window that governs mat development and the distinctive taphonomic conditions needed to preserve the structures. These observations caution that statements about changing mat abundance across the Proterozoic-Cambrian boundary must be firmly rooted in paleoenvironmental and taphonomic analysis. Understanding the factors that influence the formation and preservation of microbial structures in siliciclastic regimes can facilitate exploration for biological signatures in Earth's oldest rocks. Moreover, insofar as these structures can be preserved on bedding surfaces and are not easily mimicked by physical processes, they constitute a set of biological markers that can be searched for on Mars by remotely controlled rovers.
Noffke, Nora↗
Ecosystem device for determining plant-microbe interactions
This disclosure provides systems, methods, and devices related to the study of ecological processes. In one aspect, a device includes a base, a substrate, and an enclosure. The substrate is in contact with a first surface of the base. The substrate and the base define a root chamber. The enclosure is in contact with a second surface of the base. The base and the enclosure define a growth chamber. The base defines a stem port connecting the root chamber and the growth chamber. The base further defines a first port in fluid communication with the root chamber and a second port in fluid communication with the root chamber. The device is operable to contain a plant, roots of the plant being in the root chamber, a stem of the plant passing through the stem port, and leaves of the plant being in the growth chamber.
Andeer, Peter↗
Causal relationships of vegetation productivity with root zone water availability and atmospheric dryness at the catchment scale
Abstract. This study explores the causal relationships between catchment water availability, vapor pressure deficit, and gross primary productivity (GPP) across 341 catchments in the contiguous US. Seasonal climatic, hydrological, and vegetation characteristics were represented using the Horton index, ecological aridity index, evaporative fraction index, and carbon uptake efficiency. Statistical methods, including circularity statistics, correlation analysis, and causality tests, were employed to determine the complex interactions between catchment wetness, atmospheric dryness, and vegetation carbon uptake. The results revealed a maximum lag of 2 months in the intra-annual variability of catchment water supply–productivity and atmospheric water demand–productivity relationships, with hysteresis patterns varying with the catchment's hydrological characteristics. In catchments not permanently under water-limited or energy-limited conditions, vegetation experiences hydrological stress during the peak growing period, coinciding with the highest gross primary productivity and carbon uptake efficiency being out of phase with the Horton index and in phase with the evaporative fraction index. Causality analysis highlights strong temporal continuity in GPP seasonal characteristics, with a cause–effect relationship between catchment water supply, atmospheric demand, and vegetation productivity spanning a maximum of 2 months. These findings underscore the need for a comprehensive functional framework that integrates catchment water supply, atmospheric demand, and vegetation productivity to enhance our understanding and predictive capabilities with regard to ecosystem responses to climate change.
54 ENVIRONMENTAL SCIENCES↗
Slope-Aspect Induced Climate Differences Influence How Water Is Exchanged Between the Land and Atmosphere
Cross-slope climate differences in the midlatitudes are ecologically important, and impact vegetation-mediated water balance between the earth surface and the atmosphere. We made high-resolution in situ observations of air temperature, relative humidity, soil moisture, insolation, and sap velocity observations on 14 Pacific madrone trees (Arbutus menziesii) spanning adjacent north and south slopes at the University of California's Angelo Coast Range Reserve. To understand the cross-slope response of sap velocity, a proxy for transpiration, to microclimate, we modeled the sap velocity on each slope using a transpiration model driven by ambient environment and parameterized with a Markov Chain Monte Carlo parameter estimation process. The results show that trees on opposing slopes do not follow a shared pattern of physiological response to transpiration drivers. This means that the observed sap velocity differences are not due entirely to observed microclimate differences, but also due to population-level physiological differences, which indicates acclimation to inhabited microclimate. While our present data set and analytical tools do not identify mechanisms of acclimation, we speculate that differing proportions of sun-adapted and shade-adapted leaves, differences in stomatal regulation, and cross-slope root zone moisture differences could explain some of the observed and modeled differences.
54 ENVIRONMENTAL SCIENCES↗
Predictive links between microbial communities and biological oxygen utilization in the Arctic Ocean
Microbial metabolism influences rates of net community production (NCP), exerting a direct biological control on marine oxygen and carbon fluxes. In the Arctic, it is increasingly important to understand and quantify this process, as ecological and oceanographic conditions shift due to changing climate. Here, we describe potential ecological links between pelagic microbial diversity and an NCP precursor, biological oxygen utilization, using machine learning and paired observations of community structure and metabolic activity from a seasonally and spatially variable transect of the Arctic Ocean (2019–2020 MOSAiC Expedition). Community structure was determined using 16S (prokaryotic) and 18S (eukaryotic) rRNA gene amplicon sequencing, and metabolic activity was derived from ΔO 2 /Ar. Using self-organizing maps, we identified clear successional patterns in observed microbial community structure that were seasonally driven in the upper ocean and vertically stratified with depth. Metabolic activity was also stratified, with a primarily net heterotrophic water column (median −1.5% biological oxygen saturation), excepting periodic oxygen supersaturation (maximum: 13.6%) within the mixed layer. Using DNA sequences as predictor variables, we then constructed a random forest regression model that reliably reconstructed biological oxygen concentrations (root mean squared error = 4.14 μmol kg −1 ). Top predictors from this model were from heterotrophic (bacteria) or potentially mixotrophic (dinoflagellate) taxa. These analyses highlight biologically driven diagnostic tools that can be used to expand biogeochemical datasets and improve the microbial perspectives and metabolisms represented in ecological models of net productivity and carbon flux in a changing Arctic Ocean.
Chamberlain, Emelia J. [Univ. of San Diego, San Di↗
Crops for Carbon Farming
Agricultural cropping systems and pasture comprise one third of the world’s arable land and have the potential to draw down a considerable amount of atmospheric CO 2 for storage as soil organic carbon (SOC) and improving the soil carbon budget. An improved soil carbon budget serves the dual purpose of promoting soil health, which supports crop productivity, and constituting a pool from which carbon can be converted to recalcitrant forms for long-term storage as a mitigation measure for global warming. In this perspective, we propose the design of crop ideotypes with the dual functionality of being highly productive for the purposes of food, feed, and fuel, while at the same time being able to facilitate higher contribution to soil carbon and improve the below ground ecology. We advocate a holistic approach of the integrated plant-microbe-soil system and suggest that significant improvements in soil carbon storage can be achieved by a three-pronged approach: (1) design plants with an increased root strength to further allocation of carbon belowground; (2) balance the increase in belowground carbon allocation with increased source strength for enhanced photosynthesis and biomass accumulation; and (3) design soil microbial consortia for increased rhizosphere sink strength and plant growth-promoting (PGP) properties.
54 ENVIRONMENTAL SCIENCES↗
Arctic shrub and Eriophorum leaf and root decomposition, northern Alaska, 2017-2018
This data package contains litter decomposition data collected from 170 plots of rapidly expanding shrub genera (Alnus, Betula, and Salix) and a widespread sedge (Eriophorum vaginatum) along a latitudinal and temperature gradient in northern Alaska. These data were produced from a litter bag experiment that took place from July 2017 to July 2018 and include mass loss and nitrogen loss decomposition metrics for both leaf and root litters. These raw data support a submitted manuscript that examines the variability in decomposition between shrub and graminoid leaf and root litters across a 1-year experiment across the graminoid-dominated Arctic tundra and reveals how deciduous shrub expansion affects litter decomposition in tundra ecosystems. Data are presented by site (n=5) and patch (shrub or sedge plot) in csv files. The site and plot location data and environmental measurement data are provided in Fraterrigo and Chen (2020). Additional methods regarding plot distribution and environmental measurements are in Chen et al. (2020) and Fraterrigo et al. (2024).
54 ENVIRONMENTAL SCIENCES↗
Global relationships in tree functional traits
Due to massive energetic investments in woody support structures, trees are subject to unique physiological, mechanical, and ecological pressures not experienced by herbaceous plants. Despite a wealth of studies exploring trait relationships across the entire plant kingdom, the dominant traits underpinning these unique aspects of tree form and function remain unclear. Here, by considering 18 functional traits, encompassing leaf, seed, bark, wood, crown, and root characteristics, we quantify the multidimensional relationships in tree trait expression. We find that nearly half of trait variation is captured by two axes: one reflecting leaf economics, the other reflecting tree size and competition for light. Yet these orthogonal axes reveal strong environmental convergence, exhibiting correlated responses to temperature, moisture, and elevation. By subsequently exploring multidimensional trait relationships, we show that the full dimensionality of trait space is captured by eight distinct clusters, each reflecting a unique aspect of tree form and function. Collectively, this work identifies a core set of traits needed to quantify global patterns in functional biodiversity, and it contributes to our fundamental understanding of the functioning of forests worldwide.
54 ENVIRONMENTAL SCIENCES↗
Tropical dry forest response to nutrient fertilization: a model validation and sensitivity analysis
Abstract. Soil nutrients, especially nitrogen (N) and phosphorus (P), regulate plant growth and hence influence carbon fluxes between the land surface and atmosphere. However, how forests adjust biomass partitioning to leaves, wood, and fine roots in response to N and/or P fertilization remains puzzling. Recent work in tropical forests suggests that trees increase fine root production under P fertilization, but it is unclear whether mechanistic models can reproduce this dynamic. In order to better understand mechanisms governing nutrient effects on plant allocation and improve models, we used the nutrient-enabled ED2 model to simulate a fertilization experiment being conducted in a secondary tropical dry forest in Costa Rica. We evaluated how different allocation parameterizations affected model performance. These parameterizations prescribed a linear relationship between relative allocation to fine roots and soil P concentrations. The slope of the linear relationship was allowed to be positive, negative, or zero. Some parameterizations realistically simulated leaf, wood, and fine root production, and these parameterizations all assumed a positive relationship between relative allocation to fine roots and soil P concentration. Model simulations of a 30-year timeframe indicated strong sensitivity to parameterization and fertilization treatment. Without P fertilization, the simulated aboveground biomass (AGB) accumulation was insensitive to the parameterization. With P fertilization, the model was highly sensitive to the parameterization and the greatest AGB accumulation occurred when relative allocation to fine roots was independent of soil P. Our study demonstrates the need for simultaneous measurements of leaf, wood, and fine root production in nutrient fertilization experiments and for longer-term experiments. Models that do not accurately represent allocation to fine roots may be highly biased in their simulations of AGB, especially on multi-decadal timescales.
Environmental Sciences & Ecology↗
A method of variable spacing for controlled plant growth systems in spaceflight and terrestrial agriculture applications
A higher plant growth system for Controlled Ecological Life Support System (CELSS) applications is described. The system permits independent movement of individual plants during growth. Enclosed within variable geometry growth chambers, the system allocates only the volume required by the growing plants. This variable spacing system maintains isolation between root and shoot environments, providing individual control for optimal growth. The advantages of the system for hydroponic and aeroponic growth chambers are discussed. Two applications are presented: (1) the growth of soybeans in a space station common module, and (2) in a terrestrial city greenhouse.
Knox, J.↗
A hybrid Penman-Monteith and machine learning model for simulating evapotranspiration and its components
Integrating physical processes with machine learning has advanced evapotranspiration (ET) simulation, yet most hybrid models fail to partition total ET into its components: soil evaporation (E) and vegetation transpiration (T). This study introduces Residual Neural Network–Penman–Monteith (RNN-PM), a novel hybrid dual-source ET model designed to overcome this limitation. The model synergizes the physically-based Penman–Monteith framework with three specialized residual neural networks trained to estimate key conductance parameters (canopy conductance, soil surface conductance, and aerodynamic conductance). Furthermore this explicit parameterization allows for the direct partitioning of total ET. Validation at National Ecological Observatory Network (NEON) flux sites using high-frequency partitioned E and T shows that RNN-PM reliably reproduces ET and the transpiration fraction (T/ET). For ET, the model achieves an average Kling–Gupta efficiency (KGE) of 0.89 and a root-mean-square error (RMSE) of 0.55 mm/day; for T/ET, the KGE is 0.87 with an RMSE of 0.06. Furthermore, RNN-PM demonstrates robust generalization, accurately simulating ET and its components well beyond the initial training dataset, even under extreme climatic conditions. This study extended the analysis by comparing the RNN-PM model with seven established dual-source ET models. The results indicate that RNN-PM outperforms both conventional machine learning models and purely physical process-based models in simulating ET components in most cases. Among the purely physical process-based dual-source models, those based on surface temperature decomposition showed improved performance as the leaf area index (LAI) decreased when evaluated against high-frequency ET component datasets. In contrast, the performance of conductance-based dual-source models declined with decreasing LAI. Although purely machine learning-based models can produce relatively accurate simulations of ET components, they often exhibit limited generalization capability, an issue that the RNN-PM model effectively overcomes. Ultimately, the RNN-PM model represents a significant advance in simulating ET components, offering a novel and scalable approach for improving the representation of land–atmosphere interactions in Earth system models.
54 ENVIRONMENTAL SCIENCES↗
Warming of the lower Columbia River , 1853 to 2018
Abstract Water temperature is a critical ecological indicator; however, few studies have statistically modeled century‐scale trends in riverine or estuarine water temperature, or their cause. Here, we recover, digitize, and analyze archival temperature measurements from the 1850s onward to investigate how and why water temperatures in the lower Columbia River are changing. To infill data gaps and explore changes, we develop regression models of daily historical Columbia River water temperature using time‐lagged river flow and air temperature as the independent variables. Models were developed for three time periods (mid‐19th, mid‐20th, and early 21st century), using archival and modern measurements (1854–1876; 1938–present). Daily and monthly averaged root‐mean‐square errors overall are 0.89°C and 0.77°C, respectively for the 1938–2018 period. Results suggest that annual averaged water temperature increased by 2.2°C ± 0.2°C since the 1850s, a rate of 1.3°C ± 0.1°C/century. Increased water temperatures are seasonally dependent. An increase of approximately 2.0°C ± 0.2°C/century occurs in the July–Dec time‐frame, while springtime trends are statistically insignificant. Rising temperatures change the probability of exceeding ecologically important thresholds; since the 1850s, the number of days with water temperatures over 20°C increased from ~5 to 60 per year, while the number below 2°C decreased from ~10 to 0 days/per year. Overall, the modern system is warmer, but exhibits less temperature variability. The reservoir system reduces sensitivity to short‐term atmospheric forcing. Statistical experiments within our modeling framework suggest that increased water temperature is driven by warming air temperatures (~29%), altered river flow (~14%), and water resources management (~57%).
54 ENVIRONMENTAL SCIENCES↗
Data from: "Lab and Field Warming Similarly Advance Germination Date and Limit Germination Rate for High and Low Elevation Provenances of Two Widespread Subalpine Conifers"
This archive contains data used to draw conclusions in “Lab and Field Warming Similarly Advance Germination Date and Limit Germination Rate for High and Low Elevation Provenances of Two Widespread Subalpine Conifers”, by Kueppers et al. 2017. Cone collection and field experiments were conducted on Niwot Ridge, Colorado, with the latter completed within the Alpine Treeline Warming Experiment (ATWE). Laboratory germination experiments were conducted at the University of California Merced. Geospatial files are also provided for additional geographical context.There are four data file formats in this package: comma-separated values (.csv), Microsoft Excel (.xlsx), keyhole markup language (.kml), and ESRI shapefile (.shp). The latter two are geospatial file formats. .csv files can be opened using any simple text editor program such as TextEdit (Mac) and Notepad (Windows), and .xlsx files can be opened using Microsoft Excel or Google Sheets. The .kml file contains coordinate data, and is compatible with Google Earth and Google Maps. ESRI shapefiles (.shp) are compatible with any geospatial software able to read the file type, such as QGIS and ESRI’s ArcGIS Suite. This data user’s guide is available in as a .pdf, and can be opened using software such as Adobe Acrobat Reader.-----------------------------------------------------------------------------------------------------------------------------------Accurately predicting upslope shifts in subalpine tree ranges with warming requires understanding how future forest populations will be affected by climate change, as these are the seed sources for new tree line and alpine populations. Early life history stages are particularly sensitive to climate and are also influenced by genetic variation among populations. We tested the climate sensitivity of germination and initial development for two widely distributed subalpine conifers, using controlled-environment growth chambers with one temperature regime from subalpine forest in the Colorado Rocky Mountains and one 5 °C warmer, and two soil moisture levels. We tracked germination rate and timing, rate of seedling development, and seedling morphology for two seed provenances separated by ~300 m elevation. Warming advanced germination timing and initial seedling development by a total of ~2 weeks, advances comparable to mean differences between provenances. Advances were similar for both provenances and species; however, warming reduced the overall germination rate, as did low soil moisture, only for Picea engelmannii. A three-year field warming and watering experiment planted with the same species and provenances yielded responses qualitatively consistent with the lab trials. Together these experiments indicate that in a warmer, drier climate, P. engelmannii germination, and thus regeneration, could decline, which could lead to declining subalpine forest populations, while Pinus flexilis forest populations could remain robust as a seed source for upslope range shifts.
54 ENVIRONMENTAL SCIENCES↗
Sub-Continental-Scale Carbon Stocks of Individual Trees in African Drylands
The distribution of dryland trees and their density, cover, size, mass and carbon content are not well known at sub-continental to continental scales. This information is important for ecological protection, carbon accounting, climate mitigation and restoration efforts of dryland ecosystems. We assessed more than 9.9 billion trees derived from more than 300,000 satellite images, covering semi-arid sub-Saharan Africa north of the Equator. We attributed wood, foliage and root carbon to every tree in the 0–1,000 mm year −1 rainfall zone by coupling field data, machine learning, satellite data and high-performance computing. Average carbon stocks of individual trees ranged from 0.54 Mg C ha −1 and 63 kg C tree −1 in the arid zone to 3.7 Mg C ha −1 and 98 kg tree −1 in the sub-humid zone. Overall, we estimated the total carbon for our study area to be 0.84 (±19.8%) Pg C. Comparisons with 14 previous TRENDY numerical simulation studies23 for our area found that the density and carbon stocks of scattered trees have been underestimated by three models and overestimated by 11 models, respectively. This benchmarking can help understand the carbon cycle and address concerns about land degradation. We make available a linked database of wood mass, foliage mass, root mass and carbon stock of each tree for scientists, policymakers, dryland-restoration practitioners and farmers, who can use it to estimate farmland tree carbon stocks from tablets or laptops.
Compton Tucker↗
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↗
Genomic signatures in Variovorax enabling colonization of the Populus endosphere
Microbial colonization of plant roots involves strong selective pressures that shape the structure and function of root-associated communities. In particular, the endosphere represents a highly selective environment requiring host entry and in planta persistence. However, strain-specific microbial traits that enable endosphere colonization remain poorly understood. Here, we use a defined, genome-resolved community of 28 Variovorax strains isolated from the roots of Populus deltoides and Populus trichocarpa (poplar trees) to determine which strains partition between rhizosphere and endosphere compartments and to identify the genomic traits associated with endosphere specialization. By combining strain-resolved metagenomic profiling, comparative genomics, and functional assays, we demonstrate that dominant endosphere colonizers are enriched in genes related to nutrient metabolism, redox balance, transcriptional regulation, and a conserved L-fucose utilization pathway experimentally shown to enhance root colonization. Not all strains succeed through the same strategy. Community-wide functional profiling revealed a distinct and reduced set of traits in the endosphere, including orthogroups associated with low-abundance strains that were overlooked in strain-level analyses. These findings reveal that multiple ecological strategies, such as metabolic competition, regulatory adaptation, and niche specialization, can support endosphere colonization. Our results advance the understanding of how bacterial colonization traits are distributed and deployed within a plant microbiome and suggest that host filtering selects for distinct, and sometimes complementary, microbial strategies. This work supports a shift toward mechanistic, genome-resolved models of microbiome assembly and offers a framework for linking microbial function to host colonization success.
comparative genomics↗