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47 results for “Soil mechanics”
The temporal dimension of plant-soil microbe interactions: mechanisms promoting feedback between generations
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Data from: Unraveling the mechanisms underlying pulse dynamics of soil respiration in tropical dry forests
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Data from: Beyond plant-soil feedbacks: mechanisms driving plant community shifts due to land-use legacies in post-agricultural forests
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Island biogeography of soil bacteria and fungi: similar patterns, but different mechanisms
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Data from: Aboveground mammal and invertebrate exclusions cause consistent changes in soil food webs of two subalpine grassland types, but mechanisms are system-specific
Ungulates, smaller mammals, and invertebrates can each affect soil biota through their influence on vegetation and soil characteristics. However, direct and indirect effects of the aboveground biota on soil food webs remain to be unraveled. We assessed effects of progressively excluding aboveground large-, medium- and small-sized mammals as well as invertebrates on soil nematode diversity and feeding type abundances in two subalpine grassland types: short- and tall-grass vegetation. We explored pathways that link exclusions of aboveground biota to nematode feeding type abundances via changes in plants, soil environment, soil microbial biomass, and soil nutrients. In both vegetation types, exclusions caused a similar shift toward higher abundance of all nematode feeding types, except plant feeders, lower Shannon diversity, and lower evenness. These effects were strongest when small mammals, or both small mammals and invertebrates were excluded in addition to excluding larger mammals. Exclusions resulted in a changed abiotic soil environment that only affected nematodes in the short-grass vegetation. In each vegetation type, exclusion effects on nematode abundances were mediated by different drivers related to plant quantity and quality. In the short-grass vegetation, not all exclusion effects on omni–carnivorous nematodes were mediated by the abundance of lower trophic level nematodes, suggesting that omni–carnivores also depended on other prey than nematodes. We conclude that small aboveground herbivores have major impacts on the soil food web of subalpine short- and tall-grass ecosystems. Excluding aboveground animals caused similar shifts in soil nematode assemblages in both subalpine vegetation types, however, mechanisms turned out to be system-specific.
Hydro-mechanical Responses of Microbial Mineralization Improved Clayey Soil Subjected to Climatic Wetting-Drying Cycles
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Premelting theory-based mechanism for water freezing in saline soil
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Study on the influence mechanism of different grassland utilization on soil preferential flow in semi-arid grassland in northern China
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Data from: Contrasting effects of ectomycorrhizal and arbuscular mycorrhizal tropical tree species on soil nitrogen cycling: the potential mechanisms and corresponding adaptive strategies
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Data from: Aboveground mammal and invertebrate exclusions cause consistent changes in soil food webs of two subalpine grassland types, but mechanisms are system-specific
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Mechanisms driving the soil organic matter decomposition response to nutrient enrichment:Nutrient Network. A cross-site investigation of bottom-up control over herbaceous plant community dynamics and ecosystem function.
This experiment is one implementation of a globally distributed experiment, known as the Nutrient Network. At Cedar Creek, as in over 70 other sites in grasslands around the world, the experiment aims to describe impacts of increased nutrients (nitrogen, phosphorus, potassium, sulfur and other metals) and decreased herbivory (removal of mammals by fencing). Two overarching questions are being explored with these manipulations: 1. To what extent are plant production and diversity co-limited by multiple nutrients in herbaceous-dominated communities? 2. Under what conditions do grazers or fertilization control plant biomass, diversity, and composition? By utilizing identical protocols at diverse grassland sites around the world, NutNet aims to uncover both the generalities in ecosystem functioning, and the contingencies or differences which can obscure those common mechanisms. In addition to the standard NutNet protocol, e247 includes an additional low Nitrogen gradient (1 gram Nitrogen per meter squared per year and 5 grams Nitrogen per meter squared per year in addition to the standard 10 grams Nitrogen per meter squared per year).
High-throughput gene expression in soil invertebrate embryos – mechanisms of Cd toxicity in Enchytraeus crypticus
GEO Series GSE108133. Enchytraeus crypticus. 9 samples. Type: Expression profiling by array.
3-D micro-architecture and mechanical response of soil cemented via microbial-induced calcite precipitation
<p>The datasets generated and analysed during the current study related to the microstructural and mechanical characterization become available prior to publication date. Data series obtained and analysed for the kinetics study are available from the corresponding author on reasonable request.</p>
Resistance and resilience of the soil microbiome to mechanical compaction under different agricultural management systems
<p>The growing demand for food production over the past decades has led to an increase in agricultural land intensity that requires intensive management and use of highly mechanized equipment. The increasing weight of such equipment and the continuation of mechanized operations for tillage, seeding, fertilizing, spraying, and harvesting even at low frequency can lead to soil compaction. In Europe for example, soil compaction is estimated to affect about 32-36% of the agricultural areas and this percentage is constantly rising.</p> <p>Soil compaction affects soil physical properties by increasing soil bulk density, changing aggregate size distribution and altering pore connectivity. As a result, macropore functions such as facilitating water infiltration, hydraulic conductivity, air permeability and diffusion are reduced. The decreased pore size and connectivity lead to a decrease in oxygen availability that further increases the number of anaerobic niches within soil. The impact of all these changes in soil physics and chemistry does ultimately affect the soil microbial community and shifts bacterial, archaeal and fungal diversity and function.</p> <p>Although researchers, farmers and stakeholders have a relatively good understanding of the impact of soil compaction on physical and chemical soil properties, much less is known about what soil compaction does to microbes. However, microbes are the ultimate operators of all enzymatic transformations in every soil’s biogeochemical cycle, making their understanding crucial under soil compaction. Moreover, there is a lack of standard measurements to investigate compaction effects on soil microorganisms and their associated ecosystem functions. This often leads to inaccurate assessments of soil compaction effects on the entire ecosystem and, as a consequence, poor regulations and managerial decisions.</p> <p>This thesis aims to improve the scientific understanding of the effects of soil compaction on microbial community diversity and function, as well as their resistance (impact) and resilience (recovery) under different agricultural management systems. The objectives of this study were (i) to assess the resistance and the resilience of the soil microbial community structure to compaction under different agricultural management systems, (ii) to assess if the previously observed shifts in microbial diversity under compaction translated into shifts in function potential and (iii) to provide more mechanistic insights into the nitrogen cycle in agricultural systems under different levels of soil compaction.</p> <p>In the first chapter of this thesis, we assessed for the first time the resistance and the resilience of the soil microbial diversity to compaction under different agricultural management systems. For the purpose of this chapter, permanent ley and two crop rotations with and without tillage were used after a single compaction event in a long-term field experiment with a microbial DNA metabarcoding approach. The DNA metabarcoding approach highlighted a shift in microbial diversity under compaction, specific for each agricultural management system. A relative increase in potential anaerobically metabolizing prokaryotes and saprotrophic fungi and bacteria under soil compaction was found. Additionally, microorganisms with aerobic or plant-host-associated lifestyles were generally negatively affected. Those observations appear to be a unifying concept that agrees with previous studies carried out in forest soils. Whereas crop yield recovered after two growing seasons, for the microbial community four growing seasons were not sufficient to recover although soil properties were similar between compaction treatments and control at the end of the experiment.</p> <p>Building on the first chapter, we assessed in the second chapter, if shifts in microbial diversity under compaction translated as well into shifts in its function potential because of functional redundancy among microbial species. For the purpose, shotgun metagenomics approach was used. For instance, shotgun metagenomics results confirmed the increase in metabolic potential of anaerobic functions and the decrease in the aerobic ones. This observation supported our previous findings on the microbial diversity and our inference on their potential lifestyle. However, in contrary to the microbial diversity, the shift in microbial metabolic potential under compaction was independent of agricultural management systems.</p> <p>In the third and last chapter of this thesis, we tested the effect of different moisture contents on compaction severity and used a more closed system to better understand nitrogen partitioning in soil. For this purpose, we have set up pea and wheat cropping systems in microcosms and used the qPCR method to target key nitrogen function groups and further measured concentrations of different nitrogen forms (ammonium, nitrate and nitrous oxide). Our findings confirmed that the severity and effects of soil compaction are linked to the initial soil water content. This chapter highlighted that soil compaction favored denitrifying bacteria. As a result, soil nitrate concentration decreased and soil nitrous oxide concentration increased. Less clear observations were made regarding the nitrification process; whereas there was an accumulation of soil ammonium concentration, the abundance of nitrifying bacteria and archaea showed no notable change. Additionally, like for the previous chapters, those changes in functions involved in the nitrogen cycle were independent of the cropping system and not necessarily aligned with plant growth.</p> <p>Overall, the results based on the hypotheses tested and methods used within this PhD thesis, either taken individually or combined, help to better understand the resistance and resilience of soil microbial community under different agricultural management systems affected by compaction. The combined use of molecular tools, such as metabarcoding and metagenomic approaches, was considered as a suitable approach to have an overview of the microbial diversity and metabolic potential. Those first observations can be the basis to formulate more precise hypothesis to be tested with qPCR as it has been done for this PhD thesis. Nevertheless, in order to make tangible inference on the potential lifestyle of each microbe and their potential metabolic function, these molecular tools -metabarcoding, metagenomics and qPCR - need to be upheld by physico-chemical soil analysis and metabolic process measurements. Only by using this combined approach, studies can finally interpret the increase or decrease in relative abundance of taxa or function under compaction. Finally, the interdisciplinary, long-term and mechanistic approaches involved in this thesis demonstrated that the studied biological actors (e.g., plant and microbes) as well as the soil physical properties were not necessarily aligned in their resistance and recovery. All those findings bring new and unique knowledges on the compaction impact on microbial diversity and function and highlight the need of assessing many components of the agricultural system in order to make policy recommendations towards a more sustainable agriculture.</p>
The mechanisms underlying soil fungal α and β diversity patterns during forest secondary succession
<p>This repository contains key data related to the study.</p>
Antifungal mechanism of volatile compounds emitted by Actinomycetota Paenarthrobacter ureafaciens from a disease-suppressive soil on Saccharomyces cerevisiae.
GEO Series GSE240052. Saccharomyces cerevisiae. 6 samples. Type: Expression profiling by high throughput sequencing.
Transcriptome assembly and microarray construction for Enchytraeus crypticus, a model oligochaete to assess stress response mechanisms derived from soil conditions
GEO Series GSE51838. Enchytraeus crypticus. 8 samples. Type: Expression profiling by array.
The soil organic matter decomposition mechanisms in ectomycorrhizal fungi are tuned for liberating soil organic nitrogen
GEO Series GSE110485. Paxillus involutus; Laccaria bicolor. 24 samples. Type: Expression profiling by high throughput sequencing.
APOLLO 15 LSRP SOIL MECHANICS DATA V1.0
This dataset contains tables of raw readings and reduced data from all six runs on 01 August 1971 of the Lunar Self-Recording Penetrometer (LSRP) on the surface of the Moon for the Apollo 15 Soil Mechanics experiment. Supporting documentation includes digitized scans in JPEG and PDF format of the original LSRP soil mechanics dataset on microfilm, videos and transcripts of the LSRP as it was operated on the Moon, diagrams and maps of the experiment areas, and photography of the Apollo 15 Station 8 where the experiment was performed.
APOLLO 16 LSRP SOIL MECHANICS DATA V1.0
This dataset contains tables of raw readings and reduced data from ten runs on 22 April 1972 of the Lunar Self-Recording Penetrometer (LSRP) on the surface of the Moon for the Apollo 16 Soil Mechanics experiment. Supporting documentation includes digitized scans in JPEG and PDF format of the original LSRP soil mechanics dataset on microfilm, videos and transcripts of the LSRP as it was operated on the Moon, diagrams and maps of the experiment areas, and photography of the Apollo 16 Stations 4 and 10 where the experiment was performed.
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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.