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177 results for “soil dynamics”
Carbon Cycle Dynamics in Soil Warming Experiments at Harvard Forest 2019
Microbes are responsible for cycling carbon (C) through soils, and predicted changes in soil C stocks under climate change are highly sensitive to shifts in the mechanisms assumed to control the microbial physiological response to warming. Two mechanisms have been suggested to explain the long-term warming impact on microbial physiology: microbial thermal acclimation and changes in the quantity and quality of substrates available for microbial metabolism. Yet studies disentangling these two mechanisms are lacking. To resolve the drivers of changes in microbial physiology in response to long-term warming, we sampled soils from 13- and 28-year-old soil warming experiments in different seasons. We performed short-term laboratory incubations across a range of temperatures to measure the relationships between temperature sensitivity of physiology (growth, respiration, carbon use efficiency, and extracellular enzyme activity) and the chemical composition of soil organic matter. We observed apparent thermal acclimation of microbial respiration, but only in summer, when warming had exacerbated the seasonally-induced, already small dissolved organic matter pools. Irrespective of warming, greater quantity and quality of soil carbon increased the extracellular enzymatic pool and its temperature sensitivity. We propose that fresh litter input into the system seasonally cancels apparent thermal acclimation of C-cycling processes to decadal warming. Our findings reveal that long-term warming has indirectly affected microbial physiology via reduced C availability in this system, implying that earth system models including these negative feedbacks may be best suited to describe long-term warming effects on these soils.
Trace Gas Fluxes and Soil N Dynamics in Simulated Hurricane Experiment at Harvard Forest 1989-1991
This study examined the fluxes of greenhouse gases between soils and the atmosphere in the Simulated Hurricane Experiment. The abstract from the published paper (see Methods) is reproduced below. "Fluxes of nitrous oxide (N2O), carbon dioxide (CO2), and methane (CH4) between soils and the atmosphere were measured monthly for one year in a 77-year-old temperate hardwood forest following a simulated hurricane blowdown. Emissions of CO2 and uptake of CH4 for the control plot were 4.92 MT C ha-1 y-1 and 3.87 kg C ha-1 y-1, respectively, and were not significantly different from the blowdown plot. Annual N2O emissions in the control plot (0.23 kg N ha-1 y-1) were low and were reduced 78% by the blowdown. Net N mineralization was not affected by the blowdown. Net nitrification was greater in the blowdown than in the control, however, the absolute rate of net nitrification, as well as the proportion of mineralized N that was nitrified, remained low. Fluxes of CO2 and CH4 were correlated positively to soil temperature, and CH4 uptake showed a negative relationship to soil moisture. Substantial resprouting and leafing out of downed or damaged trees, and increased growth of understory vegetation following the blowdown, were probably responsible for the relatively small differences in soil temperature, moisture, N availability, and net N mineralization and net nitrification between the control and blowdown plots, thus resulting in no change in CO2 or CH4 fluxes, and no increase in N2O emission."
Assessing the role of soil microbes in the dynamics of P release from poorly soluble P forms
<p>Dataset and script used for the publication <em>Assessing the role of soil microbes in the dynamics of P release from poorly soluble P forms, </em>doi (to be determined).</p>
Soil organic carbon and nutrient dynamics in response to anaerobic digestate application to farm fields, Eastern Iowa, 2011-2023
This dataset documents a long-term, field-scale study of anaerobic digestate application on commercial croplands in eastern Iowa, USA. It includes detailed records of digestate composition, application rates, and timing, as well as soil test results collected over a 12-year period (2011–2023) from 14 agricultural fields. The dataset supports analysis of soil organic carbon (SOC), nutrient dynamics, and isotopic composition in response to digestate inputs. It contains 421 georeferenced soil samples, digestate nutrient profiles, field management histories, and spatial boundaries. The data were collected as part of a collaborative effort between researchers at Iowa State University and Sievers Family Farms to evaluate the agronomic and environmental implications of integrating anaerobic digestion into row crop and livestock systems.
Live cribwall + slope grating + fascines drainage system - soil-water dynamics
<p>Dataset containing raw time series (August 2022) for soil-water dynamics -i.e., volumetric soil moisture, matric suction, soil-pore water pressure, and soil temperature - retrieved from a live, vegetated cribwall+slope grating+fascines drainage system built in Catterline, Scotland. NBS intervention built to restore a landslide taking place in February 2021. </p>
Soil organic matter dynamics in the tabonuco forest, a plantation and a secondary forest in Guzman
In this project we try to find out the relationship between the primary production and the soil organic carbon fractions. Support for this work was provided by grants BSR-8811902, DEB-9411973, DEB-9705814 , DEB-0080538, DEB-0218039 , DEB-0620910 , DEB-1239764, DEB-1546686, and DEB-1831952 from the National Science Foundation to the University of Puerto Rico as part of the Luquillo Long-Term Ecological Research Program. Additional support provided by the University of Puerto Rico and the International Institute of Tropical Forestry, USDA Forest Service.
Long-term dynamics of soil organic matter and aboveground net primary production in a Chihuahuan Desert Grassland at the Sevilleta National Wildlife Refuge, New Mexico (1989-2014)
Drylands contain a third of the organic carbon stored in global soils; however, the long-term dynamics of soil organic carbon and soil organic matter (SOM) in drylands remain poorly understood relative to dynamics of the vegetation carbon pool. We examined long-term patterns in SOM against both climate and prescribed fire in a Chihuahuan Desert grassland in central New Mexico, USA. SOM was measured each spring and fall for 25 years (1989–2014) in unburned desert grassland and from 2003 to 2014 following a prescribed fire. SOM concentration from 0-20 cm depth did not show a clear long-term trend but fluctuated seasonally at both burned and unburned sites, ranging from a minimum of 0.9% to a maximum of 3.3%. SOM concentration declined nonlinearly in wet seasons and peaked in dry seasons. These results not only contrast with the positive relationships between aboveground net primary production and precipitation for this region, but also with previous reports of greater SOM in wetter sites across drylands globally, suggesting that space is not a good substitute for time in predicting the dynamics of dryland SOM. We suggest that declines in SOM in wet periods are caused by increased soil respiration, runoff, leaching, and soil erosion. In addition to tracking natural variability in climate, SOM concentration also decreased by 14% following prescribed fire, a response that magnified over time and has persisted for nearly a decade due to the slow recovery of primary production. Our results document the surprisingly dynamic nature of soil organic matter and its high sensitivity to climate and fire in this dryland ecosystem.
Soil Carbon Dynamics in Soybean Cropland and Forests in Mato Grosso, Brazil
<p>These files contain the carbon content, radiocarbon, and stable isotope data for soils collected to 2 m deep in forest and soybean cropland in Mato Grosso, Brazil. </p>
Soil nitrogen: Successional Dynamics on a Resampled Chronosequence
The purpose of this observational study is to describe the dynamics of ecosystem succession. The change in the number, type, and amount of plant and grazing animal species is monitored in more than 20 fields. These fields were previously cultivated, but then abandoned from agriculture at various times in the past. The fields were left undisturbed for plants to develop from seeds within the soil or brought into the fields by wind or animals. Permanent transects have been established in these abandoned fields for purposes of sampling in a consistent location from year to year. Permanent plots along these transects have been used to sample soil nutrients, (in particular, nitrogen) abundance of vegetation, species composition and herbivore populations. The sampling occurs approximately every 6 years. In the initial survey, 100 quadrats of size 1 by 0.5 m were sampled per field in 23 different fields. Abandoned fields included in E014 are 4, 5, 10, 21, 24, 26, 27, 28, 32, 35, 39, 40, 41, 44, 45, 47, 53, 70, 72, 76, 77. Fields 22(B), 29(A), and 69(C) were originally included in E014 but used for other purposes shortly after the start of the study. This experiment was established in 1983 and 1989 by principal investigators Johannes Knops and David Tilman. Past work at CDR and elsewhere has demonstrated an overriding influence of fire frequency in maintaining prairie openings and oak savanna at the prairie-forest border. Fire regimes harm some types of species while favoring others and drive light and nutrient dynamics, which in turn drive community functional attributes and diversity levels. Ultimately, fire frequency interacts with climate, N deposition, land use, and biotic invasion to determine the outcomes of tree-grass interactions and the dynamics of vegetation at ecotones such as the prairie-forest border in Minnesota. In 2006 each field was divided in half, and one half randomly chosen for periodic prescribed burning (a fire every other year). We anticipate that th
Soil carbon: Successional Dynamics on a Resampled Chronosequence
The purpose of this observational study is to describe the dynamics of ecosystem succession. The change in the number, type, and amount of plant and grazing animal species is monitored in more than 20 fields. These fields were previously cultivated, but then abandoned from agriculture at various times in the past. The fields were left undisturbed for plants to develop from seeds within the soil or brought into the fields by wind or animals. Permanent transects have been established in these abandoned fields for purposes of sampling in a consistent location from year to year. Permanent plots along these transects have been used to sample soil nutrients, (in particular, nitrogen) abundance of vegetation, species composition and herbivore populations. The sampling occurs approximately every 6 years. In the initial survey, 100 quadrats of size 1 by 0.5 m were sampled per field in 23 different fields. Abandoned fields included in E014 are 4, 5, 10, 21, 24, 26, 27, 28, 32, 35, 39, 40, 41, 44, 45, 47, 53, 70, 72, 76, 77. Fields 22(B), 29(A), and 69(C) were originally included in E014 but used for other purposes shortly after the start of the study. This experiment was established in 1983 and 1989 by principal investigators Johannes Knops and David Tilman. Past work at CDR and elsewhere has demonstrated an overriding influence of fire frequency in maintaining prairie openings and oak savanna at the prairie-forest border. Fire regimes harm some types of species while favoring others and drive light and nutrient dynamics, which in turn drive community functional attributes and diversity levels. Ultimately, fire frequency interacts with climate, N deposition, land use, and biotic invasion to determine the outcomes of tree-grass interactions and the dynamics of vegetation at ecotones such as the prairie-forest border in Minnesota. In 2006 each field was divided in half, and one half randomly chosen for periodic prescribed burning (a fire every other year). We anticipate that th
Riparian zone seedling establishment, growth, dynamics, and the influence of Rhododendron maximum soil moisture: forest floor data at the Coweeta Hydrologic Laboratory from 1997 to 2000
The effect of Rhododendron maximum, a dominate species in the riparian zones of the Southern Appalachians, on carbon, water, and nutrients en route to the streams is an ongoing study in the LTER research program at Coweeta Hydrologic Laboratory. To study seedling establishment, growth, and dynamics in riparian zones one m2 quadrats have been established. There are four sites which include one treatment site, where the rhododendron has been removed from the riparian zone, one hurricane site, where there is extensive disturbance from Hurricane Opal, and two control sites, one upslope from the treatment site and one upstream from the hurricane site. Each of these fours sites have ten randomly located natural regeneration one m2 quadrats as well as four randomly located replicates of three adjacent one m2 quadrats. In each of the three adjacent quadrats, the litter was removed from the lower half to determine the effect of litter on the germination and growth of seedlings. Two of the adjacent quadrats have been broadcast seeded with Acer rubrum, Liriodendron tulipifera, and Quercus rubra. In one of the two quadrats that have been broadcast seeded, a predator exclusion mesh screen, 1m x 1/2m with " openings, has been installed in the quadrat to determine the effect of small mammal predation on regeneration. Quadrats were installed on 24 April 1997 and an initial vegetation survey was conducted in May 1997. All seedlings were permanently tagged at this time and quadrat physical characteristics such as slope, aspect, and distance from stream were recorded. Broadcast seeding was done on 21 May 1997. Each year censuses will be conducted in spring and fall on each quadrat and seedling species, density, age, and annual height growth will be recorded. This project will help to document the effect of Rhododendron maximum on regeneration in the riparian areas as well as the effect of hurricane disturbance on regeneration.
Eco-evolutionary dynamics of anthelmintic resistance in soil-transmitted helminths
<p>Anthelmintic resistance (AR) of helminth parasites against the most widely available drugs is an ongoing concern for both human and livestock-infecting species. Indeed, there has been substantial evidence of AR in livestock but less in humans, which may be due to a variety of reasons. In this paper, we develop an eco-evolutionary model that couples the life cycle of these parasites with their underlying evolution in a single biallelic genetic locus that confers resistance to treatment drugs. We determine the critical treatment frequency needed to effectively eliminate the population, for a fixed drug efficacy (without evolution) and use this to classify three qualitative distinct behaviors of the eco-evolutionary model. Then, we describe how aspects of the life cycle influence which qualitative outcome is achieved and the spread of the resistance allele, comparing across human- and livestock- infecting species. For all but one species, we find that lower fecundity rates and lower contact rates speed the spread of resistance, while lower larval death slows it down. The life cycle parameters of <em>Ancylostoma duodenale</em> and <em>Ostertagia circumcincta</em> are associated with the fastest and slowest spread of resistance, respectively. We discuss the mechanistic reason for these results.</p>
Fire promotes functional plant diversity and modifies soil carbon dynamics in tropical savanna
<p>The dataset associated with the manuscript "Fire promotes functional plant diversity and modifies soil carbon dynamics in tropical savanna" (Teixeira et al.) includes 6 different datasets, for which we provided one metadata.<br> </p> <p><strong>Version 2</strong> includes an update of the biomass data set, including the correct transformation to g/m2 on fine roots biomass data.<br><br><strong>Version 3 </strong>includes an update of the belowground traits data set based on correcting formatting errors in the belowground traits data. <br><br><strong>Version 4 </strong>Sorry for the inconvenience. This version includes the correct updated belowground traits data file based on the correct formatting errors in the belowground trait data. <br><br>fluxes: it includes data related to net ecosystem C and water exchange. NEE and ET from each plot were measured using the LiCOR 7500 infrared gas analyzer (Li-Cor Inc.). See the method section in the manuscript for full details.</p> <p>soil_carbon: it includes carbon soil data.<br><br>biomass_v2: it includes data related to aboveground and belowground biomass. Aboveground data were collected in 0.5m2 subplot and belowground at 0.25m2 at 20cm depth both within 1m2 sampling plot. See the method section in the manuscript for full details.</p> <p>aboveground_traits: all aboveground functional traits from plant species. See the method section in the manuscript for full details.</p> <p>belowground_traitsv3: all roots functional traits from plant species. See the method section in the manuscript for full details.</p> <p>species_composition: plant community composition. See the method section in the manuscript for full details.</p> <p><br><strong>Abstract</strong><br>Fire is an evolutionary environmental filter in tropical savanna ecosystems altering functional diversity and associated C pools in the biosphere and fluxes between the atmosphere and biosphere. Therefore, alterations in fire regimes (e.g. fire exclusion) will strongly influence ecosystem processes and associated dynamics. In those ecosystems, C dynamics and functions are underestimated by the fire-induced offset between C output and input. To determine how fire shapes ecosystem C pools and fluxes in an open savanna across recently burned and fire excluded areas, we measured the following metrics: (I) plant diversity including taxonomic (i.e. richness, evenness) and plant functional diversity (i.e. functional diversity, functional richness, functional dispersion and community weighted means); (II) structure (i.e. above- and below-ground biomass, litter accumulation); and (III) functions related to C balance (i.e. net ecosystem carbon dioxide (CO<sub>2</sub>)<sub> </sub>exchange (NEE), ecosystem transpiration (ET), soil respiration (soil CO<sub>2</sub> efflux), ecosystem water use efficiency (eWUE) and total soil organic C (SOC). We found that fire promoted aboveground live and belowground biomass, including belowground organs, and coarse and fine root biomass, and contributed to higher biomass allocation belowground. Fire also increased both functional diversity and dispersion. NEE and total SOC were higher in burned plots compared to fire-excluded plots whereas soil respiration recorded lower values in burned areas. Both ET and eWUE were not affected by fire. Fire strongly favored functional diversity, fine root, and belowground organ biomass in piecewise SEM models but the role of both functional diversity and ecosystem structure to mediate the effect of fire on ecosystem functions remain unclear. Fire regime will impact C balance, and fire exclusion may lead to lower C input in open savanna ecosystems.</p>
Reproducing nonlinear seismic response from in-situ soil dynamic parameters: application to the Delaney Park Downhole Array, Alaska
<p>The zip file named 'seismic data at DPDA.zip' contains all the seismic data used in our study.</p> <p>The DEEPSOIL file named 'ground response analysis at DPDA.dp' contains the numerical models used in our study.</p>
Figure 3 in Dynamics of arbuscular mycorrhizal fungi in relation to root colonization, spore density, and soil properties among different spreading stages of the exotic plant threeflower beggarweed (Desmodium triflorum) in a ZoysiO tenuifoliO lawn
Figure 3. Dynamics of the soil arbuscular mycorrhizal fungal spore density within Desmodium triflorum coverage levels and seasons.
Figure 6 in Dynamics of arbuscular mycorrhizal fungi in relation to root colonization, spore density, and soil properties among different spreading stages of the exotic plant threeflower beggarweed (Desmodium triflorum) in a ZoysiO tenuifoliO lawn
Figure 6. Conceptual framework demonstrating possible mechanisms of soil arbuscular mycorrhizal fungi (AMF) during the spreading process of Desmodium triflorum in the Zoysia tenuifolia lawn. Numbers 1, 2, 3, and 4 indicate different spreading stages of the invasive plant D. triflorum. Corresponding mycorrhizal structures were shown as the four microscopic views. Light-green and medium-yellow circles indicate AM fungal spores predominantly produced by the root mycorrhizal structures of Z. tenuifolia and D. triflorum, respectively. Medium-green and dark-yellow lines indicate the life cycle of spores in Z. tenuifolia plants and in D. triflorum plants, respectively. The AM fungi might influence the spread of D. triflorum by the following steps: (1) the early stage of the lawn's development with only Z. tenuifolia growing but without D. triflorum present. This occurs at the very beginning of the lawn establishment, and the AM fungal spores that previously existed in the lawn soil first infected the fine roots of Z. tenuifolia and completed the life cycle on their own. (2) The early spreading stage of D. triflorum (level 1). The roots of the two plants come into contact with each other, inducing the external hyphae that originally grow closely on the Z. tenuifolia roots to infect the roots of D. triflorum. The difference between the mycorrhizal infections of the two host plants contributes to higher root mycorrhizal colonizations of D. triflorum compared with Z.tenuifolia. However, at this stage,D. triflorum is not as competitive as Z. tenuifolia in the lawn, although it has advantages in terms of mycorrhizal infections. Therefore, the soil AM fungal spores are still predominantly produced by the mycorrhizal structures of the AMF-infected Z. tenuifolia roots. (3) The intermediate spreading stage of D. triflorum (levels 2 and 3). Desmodium triflorum continues to spread in the lawn. The contact of the two plants becomes more frequent and further induces a much closer relationship between the AM infections of the two plants. The increased D. triflorum plants in the lawn and the advantage of D. triflorum in root mycorrhizal infections facilitate the contribution of the mycorrhizal structures of the D. triflorum roots to sporulation. Thus, in this stage, the soil AM fungal spores were produced by the mycorrhizal structures of both plants, thereby inducing insignificant correlations between the spore densities and the root colonizations of either Z. tenuifolia or D. triflorum. (4) The late spreading stage of D. triflorum (levels 4 and 5). Desmodium triflorum is dominant in the lawn.The large numbers of D. triflorum plants and the AM infection advantage of D. triflorum facilitate AMF sporulation in the soil, thereby inducing significant correlations between the spore densities and the root colonizations of D. triflorum. At the different spreading stages of D. triflorum, the soil AM fungal communities also change as a result of the changed contributions of the AMF-infected host plants to the sporulation.
Figure 5 in Dynamics of arbuscular mycorrhizal fungi in relation to root colonization, spore density, and soil properties among different spreading stages of the exotic plant threeflower beggarweed (Desmodium triflorum) in a ZoysiO tenuifoliO lawn
Figure 5. The relative abundance and community composition at the family (A) and species levels (B) of arbuscular mycorrhizal fungi (AMF) in soils of different Desmodium triflorum coverage levels.
Figure 2 in Dynamics of arbuscular mycorrhizal fungi in relation to root colonization, spore density, and soil properties among different spreading stages of the exotic plant threeflower beggarweed (Desmodium triflorum) in a ZoysiO tenuifoliO lawn
Figure 2. Dynamics of the total, hyphal, and vesicular colonizations of Zoysia tenuifolia and Desmodium triflorum among different D. triflorum coverage levels and seasons. "Season," "Coverage," and "Species" indicate ANOVA results of each indicator among seasons and D. triflorum coverage levels and between the two plants, respectively.
Figure 4 in Dynamics of arbuscular mycorrhizal fungi in relation to root colonization, spore density, and soil properties among different spreading stages of the exotic plant threeflower beggarweed (Desmodium triflorum) in a ZoysiO tenuifoliO lawn
Figure 4. Correlations among the root mycorrhizal colonizations, arbuscular mycorrhizal fungal spore densities ("AMF spore density"), and soil properties in different coverage levels of Desmodium triflorum. ZTC, ZHC, and ZVC in light-green circles indicate the total colonization (TC), hyphal colonization (HC), and vesicular colonization (VC) of Zoysia tenuifolia, respectively. DTC, DHC, and DVC in light-red circles indicate the TC, HC, and VC of D. triflorum, respectively. Green lines and green-colored numbers indicate significant correlations between the colonization indicators of Z. tenuifolia and corresponding correlation coefficients, respectively. Red lines and red-colored numbers indicate significant correlations between the colonization indicators of Z. tenuifolia and corresponding correlation coefficients, respectively. Dark-green double arrows and dark-green numbers indicate the correlations between the colonizations of Z. tenuifolia and those of D. triflorum and corresponding correlation coefficients, respectively. Light-blue double arrows and light-blue numbers indicate the correlations between the spore densities and soil properties/root colonizations and corresponding correlation coefficients,respectively. Darkyellow double arrows and dark-yellow numbers indicate the correlations between the soil properties and root colonizations and corresponding correlation coefficients, respectively. Correlation is significant at: *P <0.05; **P <0.01; ***P <0.001. The minus sign indicates a negative correlation. Insignificant correlations are not shown.
Figure 1 in Dynamics of arbuscular mycorrhizal fungi in relation to root colonization, spore density, and soil properties among different spreading stages of the exotic plant threeflower beggarweed (Desmodium triflorum) in a ZoysiO tenuifoliO lawn
Figure 1. Dynamics of the soil physiochemical properties (average ± SE, n = 5) within different Desmodium triflorum coverage levels and seasons. "Season" and "Coverage" indicate ANOVA results of each indicator among seasons and D. triflorum coverage levels, respectively. Level 1, level 2, level 3, level 4, and level 5 indicate the coverage levels of D. triflorum in the Zoysia tenuifolia lawn, respectively, in this and all following figures.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.