Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
553
datasets available to search
ShareScore release 0.9.0
Dataset results
553 results for “soil communities”
A comprehensive study to understand the effects of climate warming, simulated by soil transplant, on soil microbial community and its feedback responses
GEO Series GSE51592. Bacteria; uncultured bacterium. 54 samples. Type: Genome variation profiling by array.
Data from: Effect of coupled reduced irrigation and nitrogen fertilizer on soil mite community composition in a wheat field
Overuse of groundwater and nitrogen fertilizer constitute a severe threat to crop production, thus, low inputs of irrigation and nitrogen fertilizer were required in current ecological agriculture. The effects of combined reduced irrigation and nitrogen fertilizer addition on soil organism (e.g., mite) community and biodiversity remain poorly understood. We analyzed soil mite community composition, wheat grain yields, and soil characteristics in a ten-year manipulation experiment with two levels of irrigation (reduced irrigation and conventional irrigation) and five levels of nitrogen fertilizer (0, 70, 140, 210, 280 kg N ha-1). The study showed that reduced irrigation (20% reduction, from 280 to 220 mm) and nitrogen fertilizer (25% reduction, from 280 to 210 kg N ha-1) addition did not significantly influence soil mite community and wheat yields. The relative abundances of fungivore and predator showed negative quadratic relationships with wheat yields, while that of plant parasite was positive. The relationships between soil mite trophic groups and wheat yields revealed that we can elevated the impacts of reduced irrigation and nitrogen fertilizer addition from the perspective of soil fauna. The soil mite community composition was altered by soil abiotic factors prior to reduced irrigation and nitrogen fertilizer addition. On the whole, moderate reductions of irrigation and nitrogen fertilizer may not threaten to soil mite community and diversity or decrease crop production, on the contrary, it will benefit to the development of mite community and the sustainable agriculture.
Data from: Contrasting effects of ammonium and nitrate additions on the biomass of soil microbial communities and enzyme activities in subtropical China
The nitrate to ammonium ratios in nitrogen (N) compounds in wet atmospheric deposits have increased over the recent past, which is a cause for some concern as the individual effects of nitrate and ammonium deposition on the biomass of different soil microbial communities and enzyme activities are still poorly defined. We established a field experiment and applied ammonium (NH4Cl) and nitrate (NaNO3) at monthly intervals over a period of 4 years. We collected soil samples from the ammonium and nitrate treatments and control plots in three different seasons, namely spring, summer, and fall, to evaluate the how the biomass of different soil microbial communities and enzyme activities responded to the ammonium (NH4Cl) and nitrate (NaNO3) applications. Our results showed that the total contents of phospholipid fatty acids (PLFAs) decreased by 24 and 11 % in the ammonium and nitrate treatments, respectively. The inhibitory effects of ammonium on Gram-positive bacteria (G+) and bacteria, fungi, actinomycetes, and arbuscular mycorrhizal fungi (AMF) PLFA contents ranged from 14 to 40 % across the three seasons. We also observed that the absolute activities of C, N, and P hydrolyses and oxidases were inhibited by ammonium and nitrate, but that nitrate had stronger inhibitory effects on the activities of acid phosphatase (AP) than ammonium. The activities of N-acquisition specific enzymes (enzyme activities normalized by total PLFA contents) were about 21 and 43 % lower in the ammonium and nitrate treatments than in the control, respectively. However, the activities of P-acquisition specific enzymes were about 19 % higher in the ammonium treatment than in the control. Using redundancy analysis (RDA), we found that the measured C, N, and P hydrolysis and polyphenol oxidase (PPO) activities were positively correlated with the soil pH and ammonium contents, but were negatively correlated with the nitrate contents. The PLFA biomarker contents were positively correlated with soil pH, soil organic carbon (SOC), and total N contents, but were negatively correlated with the ammonium contents. The soil enzyme activities varied seasonally, and were highest in March and lowest in October. In contrast, the contents of the microbial PLFA biomarkers were higher in October than in March and June. Ammonium may inhibit the contents of PLFA biomarkers more strongly than nitrate because of acidification. This study has provided useful information about the effects of ammonium and nitrate on soil microbial communities and enzyme activities.
Data from: Secondary successional trajectories of structural and catabolic bacterial communities in oil polluted soil planted with hybrid poplar
Poplars have widely been used for rhizoremediation of a broad range of organic contaminants for the past two decades. Still, there is a knowledge gap regarding the rhizosphere associated bacterial communities of poplars and their dynamics during the remediation process. It is envisaged that a detailed understanding of rhizosphere associated microbial populations will greatly contribute to a better design and implementation of rhizoremediation. In order to investigate the long-term succession of structural and catabolic bacterial communities in oil polluted soil planted with hybrid poplar, we carried out a 2-year field study. Hybrid aspen (Populus tremula x tremuloides) seedlings were planted in polluted soil excavated from an accidental oil-spill site. Vegetated and un-vegetated soil samples were collected for microbial community analyses at 7 different time-points during the course of 2 years and sampling time-points were chosen to cover the seasonal variation in the boreal climate zone. Bacterial community structure was accessed by means of 16S rRNA gene amplicon pyrosequencing whereas catabolic diversity was monitored by pyrosequencing of alkane hydroxylase and extradiol dioxygenase genes. We observed a clear succession of bacterial communities on both structural and functional levels from early to late phase communities. Sphingomonas type extradiol dioxygenases and alkane hydroxylase homologs of Rhodococcus clearly dominated the early phase communities. The high dominance-low diversity functional gene communities underwent a transition to low-dominance-high diversity communities in the late phase. These results pointed towards increased catabolic capacities and a change from specialist to generalist strategy of bacterial communities during the course of secondary succession.
Data from: Differences in the soil microbial community and carbon use efficiency following development of Vochysia guatemalensis tree plantations in unproductive pastures in Costa Rica
This study shows that Vochysia guatemalensis tree plantations were associated with enhanced soil biotic and abiotic characteristics in previously cleared forests in the Northern Zone of Costa Rica, suggesting the possible use of this practice as a restoration strategy for local land owners. Soil samples from a primary forest (PF), secondary forest (SF), and a 13-year-old (OV) plantation of V. guatemalensis had greater relative abundances of DNA sequences of microbial genera critical for C-use efficiency (i.e., the saprobe, complex C and wood rot/lignin decomposer fungi, and bacterial lignin and other complex C degraders), and greater levels of total organic C, C-biomass, and Microbial Quotients as indicators of enhanced C-use efficiency, than found in soils of adjacent 5-year-old (NV) V. guatemalensis plantations and abandoned non-productive pasture/grasslands (GR). The major research conclusions were that: 1) conversion of forested land into abandoned pasture/grasslands decreased the C-use efficiency in the soils and the microbial groups associated with C-use efficiency; 2) soils in plantations of V. guatemalensis were associated with increased abundances of the DNA of these same microbial groups and enhanced C-use efficiency; 3) DNA-based taxonomic analysis of microbes and analysis of the Microbial Quotient values can be used to monitor soil ecosystems for assessment of the efficacy of restoration activities. Thus, planting V. guatemalensis on damaged lands in the Maquenque National Wildlife Refuge (MNWR) should be encouraged to provide a sustainable forestry crop that can be harvested rotationally, while improving soil ecosystem health and reducing the pressure to harvest other forest sites.
Temperate forest elevational gradient: spatial variation and deterministic processes in soil oribatid mite community assembly
<p>The data sets were analyzed during the current study. Data from: Temperate forest elevational gradient: spatial variation and deterministic processes in soil oribatid mite community assembly.</p>
Figure 1 in Effect of land cover on biodiversity and composition of a soil macrofauna community in a reclaimed coastal area at Yancheng, China
Figure 1. The distribution of sample sites on the reclaimed coast.
Data from: Contrasting effects of ammonium and nitrate additions on the biomass of soil microbial communities and enzyme activities in subtropical China
Open the record for dataset details and reuse information.
Data from: Effect of coupled reduced irrigation and nitrogen fertilizer on soil mite community composition in a wheat field
Open the record for dataset details and reuse information.
Data from: Differences in the soil microbial community and carbon use efficiency following development of Vochysia guatemalensis tree plantations in unproductive pastures in Costa Rica
Open the record for dataset details and reuse information.
Data from: Secondary successional trajectories of structural and catabolic bacterial communities in oil polluted soil planted with hybrid poplar
Open the record for dataset details and reuse information.
Effect of land use and soil organic matter quality on the structure and function of microbial communities in pastoral soils: implications for disease suppression
GEO Series GSE112489. Archaea; uncultured soil bacterium; Bacteria; Eukaryota. 50 samples. Type: Other.
GeoChip data from fungal community in Alaskan tundra soil
GEO Series GSE127899. soil metagenome; Fungi. 12 samples. Type: Genome variation profiling by array.
Comparison of hexachlorocyclohexane (HCH) contaminated soils from Spain with a community-specific microarray
GEO Series GSE1985. Bacteria. 19 samples. Type: Other.
Microbial community analyses of two 1,4-dioxane degrading consortia enriched from uncontaminated soils [16s rRNA]
GEO Series GSE97756. 1,4-dioxane-degrading enrichment culture. 4 samples. Type: Other.
Local adaptation of a fungal pathogen introduced into a soil community
GEO Series GSE30175. Metarhizium anisopliae; Metarhizium robertsii. 20 samples. Type: Expression profiling by array.
Contrasting biogeography of fungal communities associated with roots versus soils and the role of root morphology in mycobiome assembly in coast redwood, Sequoia sempervirens
Open the record for dataset details and reuse information.
Functional gene abundance of tundra soil microbial communities sampled at the EML Thaw Gradient site, AK in May 2004
GEO Series GSE97107. Eukaryota; Viruses; synthetic construct; Bacteria; Archaea. 107 samples. Type: Genome variation profiling by array.
Microbial community structure and functions are resilient to metal pollution along two forest soil gradients
GEO Series GSE59620. uncultured bacterium; Bacteria. 12 samples. Type: Genome variation profiling by array.
A study to investigate the effects of long-term organic and integrated fertilization on soil microbial community
GEO Series GSE104014. soil metagenome; uncultured soil microorganism. 18 samples. Type: Other.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.