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26 results for “soil metagenome”
Noccaea root and soil metagenomes
<p>Datasets comprise metagenomic data of hyperaccumulating <em>Noccaea praecox</em> and <em>N. caerulescens</em> from bulk soil, rhizosphere, and root compartments.</p>
New Soil Metagenome-Assembled Genomes Catalogue Boosts Genetic Resources
<p><strong>Soil harbors a vast expanse of unidentified microbes, termed as microbial dark matter, presenting an untapped reservoir of microbial biodiversity and genetic resources, but has yet to be fully explored. In this study, we conducted the first large-scale excavation of soil microbial dark matter by reconstructing 40,039 metagenome-assembled genome bins (the SMAG catalog) from 3,304 soil metagenomes. We identified 16,530 of 21,077 species-level genome bins (SGBs) as unknown SGBs (uSGBs), which greatly expand archaeal and bacterial diversity across the tree of life. We also illustrate the pivotal role of uSGBs in augmenting soil microbiome's functional landscape and intra-species genome diversity, providing large proportions of the 43,169 biosynthetic gene clusters and 8,545 CRISPR-Cas genes. Additionally, we determined that uSGBs contributed 84.6% of novel viral-host associations identified from the SMAG catalog. Our results propose the SMAG catalog, a novel and expansive genomic resource that brings the soil microbial biodiversity and novel genetic resources to light.</strong></p>
Figure 6 in Bacterial diversity in high Andean grassland soils disturbed with Lepidium meyenii crops evaluated by metagenomics
Figure 6. Analysis of principal coordinates of sampling sectors according to the distribution of bacterial families reported at 40% contribution according to SIMPER analysis.
Figure 2 in Bacterial diversity in high Andean grassland soils disturbed with Lepidium meyenii crops evaluated by metagenomics
Figure 2. Good quality DNA samples from bacterial populations divided by sampling time factor in soils with pre-sowing levels (A), Lepidium meyenii hypocotyl development (B) and post-harvest (C).
Figure 7 in Bacterial diversity in high Andean grassland soils disturbed with Lepidium meyenii crops evaluated by metagenomics
Figure 7. Dendogram of bacterial families at 40% contribution according to SIMPER analysis in fields disturbed by Lepidium meyenii culture under the effect of the two factors under study (use pressure and sampling period).
Figure 8 in Bacterial diversity in high Andean grassland soils disturbed with Lepidium meyenii crops evaluated by metagenomics
Figure 8. Analysis of the behavior of the clusters of bacterial families significantly differentiated (p<0.05) according to the SIMPROF analysis at a 40% contribution of the total of families registered in soils under the factors use pressure and sampling period.
Figure 3 in Bacterial diversity in high Andean grassland soils disturbed with Lepidium meyenii crops evaluated by metagenomics
Figure 3. Band migration in bacterial populations according to the V3 - V4 region of the 16S bacterial rRNA genes, for the 12 samples divided by the sampling time factor in soils with pre-sowing levels (A),Lepidium meyenii hypocotyl development (B) and post-harvest (C).
Figure 5 in Bacterial diversity in high Andean grassland soils disturbed with Lepidium meyenii crops evaluated by metagenomics
Figure 5. Non-metric MSD and cluster analysis of sampling sectors divided by use pressure and sampling period factors.
Data from: Mitochondrial metagenomics reveals the ancient origin and phylodiversity of soil mites and provides a phylogeny of the Acari
<p>High-throughput DNA methods hold great promise for phylogenetic analysis of lineages that are difficult to study with conventional molecular and morphological approaches. The mites (Acari), and in particular the highly diverse soil-dwelling lineages, are among the least known branches of the metazoan Tree-of-Life. We extracted numerous minute mites from soils in an area of mixed forest and grassland in southern Iberia. Selected specimens representing the full morphological diversity were shotgun sequenced in bulk, followed by genome assembly of short reads from the mixture, which produced >100 mitochondrial genomes representing diverse acarine lineages. Phylogenetic analyses in combination with taxonomically limited mitogenomes available publicly resulted in plausible trees defining basal relationships of the Acari. Several critical nodes were supported by ancestral-state reconstructions of mitochondrial gene rearrangements. Molecular calibration placed the minimum age for the common ancestor of the superorder Acariformes, which includes most soil-dwelling mites, to the Cambrian-Ordovician (likely within 455–552 Mya), while the origin of the superorder Parasitiformes was placed later in the Carboniferous-Permian. Most family-level taxa within the Acariformes were dated to the Jurassic and Triassic. The ancient origin of Acariformes and the early diversification of major extant lineages linked to the soil are consistent with a pioneering role for mites in building the earliest terrestrial ecosystems.</p>
Metagenome-assembled genomes(MAGs) generated from soil dataset.
<p>MAGs generated from soil dataset with Maxbin2, VAMB, Metabat2, SemiBin(single-sample binning) and VAMB, SemiBin(multi-sample binning).</p> <p>Single-sample binning: Maxbin2.tar.gz, Metabat2.tar.gz, VAMB.tar.gz and SemiBin(pretrain).tar.gz. </p> <p>Multi-sample binning: VAMB_multi.tar.gz and SemiBin_multi.tar.gz.</p>
16S counts of soil metagenomes
<p>Count of 16S matches in soil microbiomes, a subset of the 214K metagenomic collection https://zenodo.org/record/6919377#.Y5hhQnbMJD8</p>
Data from: Mitochondrial metagenomics reveals the ancient origin and phylodiversity of soil mites and provides a phylogeny of the Acari
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Data from: Metabarcoding and mitochondrial metagenomics of endogean arthropods to unveil the mesofauna of the soil
Biological communities inhabiting the soil are among the most diversified, complex and yet most poorly studied terrestrial ecosystems. The greatest knowledge gaps apply to the arthropod mesofauna (0·1–2 mm body size) because conventional morphological and molecular approaches are in many cases insufficient for the characterisation of these complex communities. The development of high-throughput sequencing (HTS) methodologies is required to solve current impediments and to further advance our understanding of below-ground biodiversity. We propose a flotation–Berlese–flotation (FBF) protocol for sampling and specimen processing to obtain 'clean' DNA extractions of arthropod mesofauna from the soil. In addition, we developed and tested HTS protocols for the characterisation of arthropod communities from these bulk DNA extractions using cox1 metabarcoding and shotgun metagenomic sequencing on the MiSeq Illumina platform. The FBF protocol provided DNA of soil arthropods from sufficiently large volumes of soil and free from contaminating bacteria and inhibitors. Metabarcoding and metagenomic sequencing on two deep soil samples from Iberian grasslands revealed >100 species of Acari and Collembola from 28 families. Genome assembly straight from shotgun sequencing of bulk specimens produced partial and full mitogenomes for 54 species with average length of >6000 bp. Metabarcoding and metagenomic sequencing resulted in closely congruent OTUs, but species numbers were highest with metabarcoding, while ∼73% of species were confirmed by matching shotgun sequence reads and ∼48% by contig assembly from those shotgun reads. In combination, the FBF protocol together with the PCR-based and shotgun sequencing pipelines addressed most of the challenges of studying soil arthropod mesofauna on the MiSeq Illumina platform. They are powerful, cost-efficient tools for characterising soil diversity in a phylogenetic and community ecology context. These methodological developments of HTS approaches for the study of mesofauna will accelerate ecological and evolutionary studies, biomonitoring of soil arthropods, and progress in both theoretical and applied soil science.
Data from: Phylogenetic community ecology of soil biodiversity using mitochondrial metagenomics
High-throughput DNA methods hold great promise for the study of taxonomically intractable mesofauna of the soil. Here, we assess species diversity and community structure in a phylogenetic framework, by sequencing total DNA from bulk specimen samples and assembly of mitochondrial genomes. The combination of mitochondrial metagenomics and DNA barcode sequencing of 1494 specimens in 69 soil samples from three geographic regions in southern Iberia revealed >300 species of soil Coleoptera (beetles) from a broad spectrum of phylogenetic lineages. A set of 214 mitochondrial sequences longer than 3000 bp was generated and used to estimate a well-supported phylogenetic tree of the order Coleoptera. Shorter sequences, including cox1 barcodes, were placed on this mitogenomic tree. Raw Illumina reads were mapped against all available sequences to test for species present in local samples. This approach simultaneously established the species richness, phylogenetic composition and community turnover at species and phylogenetic levels. We find a strong signature of vertical structuring in soil fauna that shows high local community differentiation between deep soil and superficial horizons at phylogenetic levels. Within the two vertical layers, turnover among regions was primarily at the tip (species) level and was stronger in the deep soil than leaf litter communities, pointing to layer-mediated drivers determining species diversification, spatial structure and evolutionary assembly of soil communities. This integrated phylogenetic framework opens the application of phylogenetic community ecology to the mesofauna of the soil, among the most diverse and least well-understood ecosystems, and will propel both theoretical and applied soil science.
Viral metagenomic sequences from Mediterranean grassland soils
<p>Database of 6088 de-replicated viral contigs identified in viral-fraction metagenomes (viromes) generated from Mediterranean grassland soils.</p>
Data from: Metabarcoding and mitochondrial metagenomics of endogean arthropods to unveil the mesofauna of the soil
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Data from: Phylogenetic community ecology of soil biodiversity using mitochondrial metagenomics
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NGS amplicon metagenomic 16S seq of soybean rhizosphere under contrasting nutrient-deficient and acidic-stress soils
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Supplementary material 1 from: Clasen LA, Detheridge AP, Scullion J, Griffith GW (2020) Soil stabilisation for DNA metabarcoding of plants and fungi. Implications for sampling at remote locations or via third-parties. Metabarcoding and Metagenomics 4: e58365. https://doi.org/10.3897/mbmg.4.58365
Combined Supplemntary Data Files 1–8
Figure 4 in Bacterial diversity in high Andean grassland soils disturbed with Lepidium meyenii crops evaluated by metagenomics
Figure 4. Diagram of the processes for the metagenomic analysis of soils I. DNA metagenomic extraction, II. Polymerase chain reaction, III. Genomic sequencing of bacterial DNA (Modified from Hernández et al., 2010; Yang et al., 2018).
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.