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68 results for “Soil ecology”
Data from: Evidence for ecological divergence across a mosaic of soil types in an Amazonian tropical tree: Protium subserratum (Burseraceae)
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Soil microbial legacy drives crop diversity advantage: linking ecological plant-soil feedback with agricultural intercropping
<ol> <li>Although the importance of the soil microbiome in mediating plant community structures and functions has been increasingly emphasized in ecological studies, the biological processes driving crop diversity overyielding remain unexplained in agriculture. Based on the plant-soil feedback (PSF) theory and method, we quantified how much soil microbes contributed to intercropping overyielding and detected which microbial groups mediated this effect.</li> <li>Soils were collected as inocula and sequenced from a unique 10-year field experiment, consisting of monoculture, intercropping and rotation planted with wheat (<i>Triticum aestivum</i>), maize (<i>Zea mays</i>) or faba bean (<i>Vicia faba</i>). A PSF study was conducted to test microbial effects on three crops' growth in monoculture or intercropping.</li> <li>In wheat & faba bean (W&F) and maize & faba bean (M&F) systems, soil microbes drove intercropping overyielding compared to monoculture, with 28-51% of the overyielding contributed by microbial legacies. The overyielding effects resulted from negative PSFs in both systems, as crops, in particular faba bean grew better in soils conditioned by other crops than itself. Moreover, faba bean grew better in soils from intercropping or rotation than from the average of monocultures, indicating a strong positive legacy effect of multispecies cropping systems. However, with positive PSF and negative legacy benefit effect of intercropping/rotation, we did not observe significant overyielding in the W&M system.</li> <li>With more bacterial and fungal dissimilarities by metabarcoding in heterospecific than its own soil, the better it improved faba bean growth. More detailed analysis showed faba bean monoculture soil accumulated more putative pathogens with higher <i>Fusarium</i> relative abundance and more <i>Fusarium oxysporum</i> gene copies by qPCR, while in heterspecific soils, there was less pathogenetic effects when cereals were engaged. Further analysis in maize/faba bean intercropping also showed an increase of rhizobia relative abundance.</li> <li> <i>Synthesis and applications</i>. Our results demonstrate a soil microbiome-mediated advantage in intercropping through suppression of the negative PSF of pathogens and increasing beneficial microbes. As microbial mediation of overyielding is context-dependent, we conclude that the dynamics of both beneficial and pathogenic microbes should be considered in designing cropping systems for sustainable agriculture, particularly including combinations of legumes and cereals.</li> </ol>
Data from: Ecological and evolutionary responses of an arctic plant to variation in microclimate and soil
<p>The arctic and alpine regions are predicted to experience some of the highest rates of climate change, and the arctic vegetation is expected to be especially sensitive to such changes. Understanding the ecological and evolutionary responses of arctic plant species to changes in climate is therefore a key objective. Geothermal areas, where natural temperature gradients occur over small spatial scales, and without many of the confounding environmental factors present in latitudinal and other gradient studies, provide a natural experimental setting in which to examine the response of arctic-alpine plants to increasing temperatures. To test the ecological and evolutionary response of the circumpolar alpine bistort (Persicaria vivipara) to temperature, we collected plant material and soil from areas with low, intermediate, and high soil temperatures and grew them at three different temperatures in a threefactorial growth chamber experiment. At higher experimental soil temperatures, sprouting was earlier, and plants had more leaves. Sprouting was earlier in soil originating from intermediate temperature and plants had more leaves when grown in soil originating from low temperatures. We did not find evidence of local adaptation or genetic variation in reaction norms among plants originating from areas with low, intermediate, and high soil temperature. Our findings suggest that the alpine bistort has a strong plastic response to warming, but that differences in soil temperature have not resulted in genetic differentiation. The lack of an observed evolutionary response may, for example, be due to the absence of temperature-mediated selection on P. vivipara, the low rate of sexual recombination, or high levels of gene flow balancing differences in selection. When placed within the context of other studies, we conclude that arctic-alpine plant species often show strong plastic responses to spring warming, while evidence of evolutionary responses varies among species.</p>
Data from: A replicated climate change field experiment reveals rapid evolutionary response in an ecologically important soil invertebrate
Whether species can respond evolutionarily to current climate change is crucial for the persistence of many species. Yet, very few studies have examined genetic responses to climate change in manipulated experiments carried out in natural field conditions. We examined the evolutionary response to climate change in a common annelid worm using a controlled replicated experiment where climatic conditions were manipulated in a natural setting. Analyzing the transcribed genome of 15 local populations, we found that about 12% of the genetic polymorphisms exhibit differences in allele frequencies associated to changes in soil temperature and soil moisture. This shows an evolutionary response to realistic climate change happening over short-time scale, and calls for incorporating evolution into models predicting future response of species to climate change. It also shows that designed climate change experiments coupled with genome sequencing offer great potential to test for the occurrence (or lack) of an evolutionary response.
Dataset and Code Accompanying the Study by Medina-Vega et al. in Nature Ecology & Evolution: Tropical Tree Ectomycorrhiza Are Distributed Independently of Soil Nutrients
<p>This Zenodo repository contains the code and the processed dataset used in the research paper titled "Tropical tree ectomycorrhiza are distributed independently of soil nutrients" published in Nature Ecology & Evolution. In this study, we investigate the distribution and abundance of ectomycorrhizal (EcM) trees in lowland tropical forests and their relationship with soil quality.</p><p><strong>Key Finding</strong>: EcM-associated trees' distribution and abundance in lowland tropical forests are independent of soil quality.</p><p><strong>Contents</strong>:</p><ol><li><strong>Code (</strong>CODE_COARSE_SCALE.R and CODE_FINE_SCALE.R<strong>)</strong>: Contains the R scripts used for data analysis.</li><li><strong>Processed Dataset</strong> (PCs_prop_EcM.csv): Includes the processed data for the fine-scale analysis.</li><li><strong>README</strong>: Provides detailed information on how to use the code, interpret the dataset, and access additional required information.</li></ol><p><strong>Data Access Information</strong>:</p><ul><li>To perform the full analyses, please request additional data from the Principal Investigators (PIs) of the plots.</li><li>ForestGEO plot data can be obtained upon request through the ForestGEO portal at http://ctfs.si.edu/datarequest/.</li><li>Refer to Extended Data Table 1 in the manuscript for a comprehensive list of data sources.</li></ul>
Ecological resilience of physical plant–soil feedback to chronic deer herbivory: slow, partial but functional recovery
<p>Ecological resilience to ungulate overbrowsing is an important issue in forest ecosystem. After chronic herbivory, the recovery rate of understory vegetation and its related functions can be slow even with decreasing grazing intensity; thus, detecting elasticity during alternative successional trajectories is fundamental to understanding state perturbations. In this context, we focused on physical plant–soil feedback (functional interactions between plant growths and soil physical conditions), and evaluated elasticity and recovery processes according to deer density. The effects of 40-year chronic herbivory by sika deer (average density 14.7 individuals km<sup>-2</sup>) on the recovery of understory plant communities and associated improvements in soil physical properties in headwater catchments were assessed. Using 8 years of catchment-wide exclusion (fenced) and reduction (only culled; average 4.3 individuals km<sup>-2</sup>) treatments, plot sampling was conducted in 2010 (before treatment) and 2018 (after treatment). The recovery of vegetation and soil physical properties were evaluated, and functional plant–soil relationships and spatial variability were assessed to detect recovery processes during alternative successional trajectory. Woody species increased only under the exclusion treatment and the average soil bulk density was lower than that under reduction treatments. Soil bulk density was negatively correlated with root biomass in the fenced catchment, and root biomass was positively associated with woody species richness. Reduced soil bulk density (~0.5 g cm<sup>-3</sup>) was observed with greater root biomass and woody species richness on upper hillslopes in the deer-excluded catchment where plant coverage was minimal. Successional failure under the reduction treatment suggested slow recovery with a depressed threshold according to deer density, indicating a clockwise hysteretic response to deer density. Unlike plant coverage during the earlier period of overbrowsing, woody species root development led the recovery of functional physical plant–soil feedback; however, this was probably limited by the higher soil erosion rate in riparian areas and an underdeveloped herb layer. Our results highlight an alternative recovery trajectory of physical plant–soil feedback driven by an alternative plant element (woody roots) to degradation trajectory with decreasing plant cover. However, riparian erosion and herb layer would still suppress recovery. Therefore, recovery might be slower at landscape scale.</p>
Supplementary material 5 from: Hristozova M, Lazarova R (2022) Radiation status of soils from the region of the Eastern Rhodopes (Southern Bulgaria). In: Chankova S, Peneva V, Metcheva R, Beltcheva M, Vassilev K, Radeva G, Danova K (Eds) Current trends of ecology. BioRisk 17: 45-57. https://doi.org/10.3897/biorisk.17.77432
Figure S5
Supplementary material 4 from: Hristozova M, Lazarova R (2022) Radiation status of soils from the region of the Eastern Rhodopes (Southern Bulgaria). In: Chankova S, Peneva V, Metcheva R, Beltcheva M, Vassilev K, Radeva G, Danova K (Eds) Current trends of ecology. BioRisk 17: 45-57. https://doi.org/10.3897/biorisk.17.77432
Figure S4
Supplementary material 3 from: Hristozova M, Lazarova R (2022) Radiation status of soils from the region of the Eastern Rhodopes (Southern Bulgaria). In: Chankova S, Peneva V, Metcheva R, Beltcheva M, Vassilev K, Radeva G, Danova K (Eds) Current trends of ecology. BioRisk 17: 45-57. https://doi.org/10.3897/biorisk.17.77432
Figure S3
Supplementary material 2 from: Hristozova M, Lazarova R (2022) Radiation status of soils from the region of the Eastern Rhodopes (Southern Bulgaria). In: Chankova S, Peneva V, Metcheva R, Beltcheva M, Vassilev K, Radeva G, Danova K (Eds) Current trends of ecology. BioRisk 17: 45-57. https://doi.org/10.3897/biorisk.17.77432
Figure S2
Supplementary material 1 from: Hristozova M, Lazarova R (2022) Radiation status of soils from the region of the Eastern Rhodopes (Southern Bulgaria). In: Chankova S, Peneva V, Metcheva R, Beltcheva M, Vassilev K, Radeva G, Danova K (Eds) Current trends of ecology. BioRisk 17: 45-57. https://doi.org/10.3897/biorisk.17.77432
Figure S1
TRACE-Soils LTER (long-term ecological research) metadata
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Fig. 2 in Introduction to special issue The Past, Present and Future of Soil Protist Ecology
Fig. 2. The Broadbalk experiment at Rothamstaed. Wheat has been grown continually here since 1843 with different fertilizer regimes used in different parts of the field. From 1910 onwards a greater attention was given to the microbiology of the soil following the demonstration that protozoa were important in the soil ecology and hence the plant production on the field (Stevenson 1989). For example, it was shown that amoebae were more common on plots receiving farmyard manure (Russell 1967).
Fig. 3 in Introduction to special issue The Past, Present and Future of Soil Protist Ecology
Fig. 3. Examples of protist diversity in a range of soil habitats. Top Left: The summit of Green Mountain (845 m a. s. l.), Ascension Island in the tropical South Atlantic. A single soil sample from under the bamboo produced three species of flagellates, two non-testate amoebae (gymnamoeba), one ciliate and three testate amoebae species (Wilkinson and Smith 2006). In addition Landolt et al. (2005) isolated eight species of protostelid slime moulds from leaf litter samples collected near the pond shown in the photograph. All the vegetation seen in the photograph is comprised of introduced plant species (Wilkinson 2004).Top Right: Summit of Mot Sper Chamana Sevenna (2424 m a. s. l.) in the European Alps, on the Swiss/Italian boarder. Two moss samples from the summit gave a total of 17 testate amoebae species (Wilkinson and Mitchell, unpublished). Bottom Left: Island in a small lake at Mere Sands Wood nature reserve in North West England. The island is heavily used by roosting and breeding water birds, so the soils probably have a high nutrient status. Seventeen species of testate amoebae and 29 species of diatoms were found in the litter and upper soil horizons taken from within the quadrat shown in the photograph (Creevy et al., unpublished). Bottom Right: Holcroft Moss – a peat bog in Cheshire, England. Twenty four species of testate amoebae were found in the surface vegetation and underlying soil of a single sample (Valentine et al., unpublished).
Fig. 2 in Ecology of Soil Eumycetozoans Review paper
Fig. 2. Fruiting bodies of Dictyostelium sphaerocephalum (Oudem.) Sacc. and Marchal (photo by Andy Swanson). Scale bar: 0.3 mm.
Fig. 1 in Ecology of Soil Eumycetozoans Review paper
Fig. 1. Fruiting bodies of Protostelium mycophaga L. S. Olive and Stoian (photo by John Shadwick). Scale bar: 50 μm.
Supplementary material 1 from: Balestrini R, Delconte C, Buffagni A, Fumagalli A, Freppaz M, Calvo E, Buzzetti I (2019) Dynamic of nitrogen and dissolved organic carbon in an alpine forested catchment: atmospheric deposition and soil solution trends. In: Mazzocchi MG, Capotondi L, Freppaz M, Lugliè A, Campanaro A (Eds) Italian Long-Term Ecological Research for understanding ecosystem diversity and functioning. Case studies from aquatic, terrestrial and transitional domains. Nature Conservation 34: 41-66. https://doi.org/10.3897/natureconservation.34.30738
: Data type: statistical data
Data from: A replicated climate change field experiment reveals rapid evolutionary response in an ecologically important soil invertebrate
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Ecological resilience of physical plant–soil feedback to chronic deer herbivory: slow, partial but functional recovery
Open the record for dataset details and reuse information.
Data from: Ecological and evolutionary responses of an arctic plant to variation in microclimate and soil
Open the record for dataset details and reuse information.
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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)
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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.