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66 results for “soil microbiome”
Data from: Resistance and resilience of soil microbiomes under climate change
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Soil microbiome dataset from the University of Wisconsin Arlington and Lancaster agricultural research stations and cheese maker and vegetable processor wastewater land application sites
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Data from: Chemical structure predicts the effect of plant-derived low-molecular weight compounds on soil microbiome structure and pathogen suppression
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Steering the soil microbiome by repeated litter addition
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Data from: Microbiomes of a specialist caterpillar are consistent across different habitats but also resemble the local soil microbial communities
<p><b>Background</b>: Insect-associated microorganisms can provide a wide range of benefits to their host, but insect dependency on these microbes varies greatly. The origin and functionality of insect microbiomes is not well understood. Many caterpillars can harbor symbionts in their gut that impact host metabolism, nutrient uptake and pathogen protection. Despite our lack of knowledge on the ecological factors driving microbiome assemblages of wild caterpillars, they seem to be highly variable and influenced by diet and environment. Several recent studies have shown that shoot-feeding caterpillars acquire part of their microbiome from the soil. Here, we examine microbiomes of a monophagous caterpillar (<i>Tyria jacobaeae</i>) collected from its natural host plant (<i>Jacobaeae vulgaris</i>) growing in three different environments: coastal dunes, natural inland grasslands and riverine grasslands, and compare the bacterial communities of the wild caterpillars to those of soil samples collected from underneath each of the host plants from which the caterpillars were collected.</p> <p><b>Results</b>: The microbiomes of the caterpillars were dominated by Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes. Only 5% of the total bacterial diversity represented 86.2% of the total caterpillar's microbiome. Interestingly, we found a high consistency of dominant bacteria within the family Burkholderiaceae in all caterpillar samples across the three habitats. There was one amplicon sequence variant belonging to the genus <i>Ralstonia</i> that represented on average 53% of total community composition across all caterpillars. On average, one quarter of the caterpillar microbiome was shared with the soil.</p> <p><b>Conclusions</b>: We found that the monophagous caterpillars collected from fields located more than 100 kilometers apart were all dominated by a single <i>Ralstonia</i>. The remainder of the bacterial communities that were present resembled the local microbial communities in the soil in which the host plant was growing. Our findings provide an example of a caterpillar that has just a few key associated bacteria, but that also contains a community of low abundant bacteria characteristic of soil communities.</p>
Data from: Soil microbiome responses to the short-term effects of Amazonian deforestation
Slash-and-burn clearing of forest typically results in increase in soil nutrient availability. However, the impact of these nutrients on the soil microbiome is not known. Using next generation sequencing of 16S rRNA gene and shotgun metagenomic DNA, we compared the structure and the potential functions of bacterial community in forest soils to deforested soils in the Amazon region and related the differences to soil chemical factors. Deforestation decreased soil organic matter content and factors linked to soil acidity and raised soil pH, base saturation and exchangeable bases. Concomitant to expected changes in soil chemical factors, we observed an increase in the alpha diversity of the bacterial microbiota and relative abundances of putative copiotrophic bacteria such as Actinomycetales and a decrease in the relative abundances of bacterial taxa such as Chlamydiae, Planctomycetes and Verrucomicrobia in the deforested soils. We did not observe an increase in genes related to microbial nutrient metabolism in deforested soils. However, we did observe changes in community functions such as increases in DNA repair, protein processing, modification, degradation and folding functions, and these functions might reflect adaptation to changes in soil characteristics due to forest clear-cutting and burning. In addition, there were changes in the composition of the bacterial groups associated with metabolism-related functions. Co-occurrence microbial network analysis identified distinct phylogenetic patterns for forest and deforested soils and suggested relationships between Planctomycetes and aluminium content, and Actinobacteria and nitrogen sources in Amazon soils. The results support taxonomic and functional adaptations in the soil bacterial community following deforestation. We hypothesize that these microbial adaptations may serve as a buffer to drastic changes in soil fertility after slash-and-burning deforestation in the Amazon region.
Data from: Diffuse symbioses: roles of plant–plant, plant–microbe and microbe–microbe interactions in structuring the soil microbiome
A conceptual model emphasizing direct host–microbe interactions has dominated work on host-associated microbiomes. To understand plant–microbiome associations, however, broader influences on microbiome composition and functioning must be incorporated, such as those arising from plant–plant and microbe–microbe interactions. We sampled soil microbiomes associated with target plant species (Andropogon gerardii, Schizachyrium scoparium, Lespedeza capitata, Lupinus perennis) grown in communities varying in plant richness (1-, 4-, 8- or 16-species). We assessed Streptomyces antagonistic activity and analysed bacterial and Streptomyces populations via 454 pyrosequencing. Host plant species and plant richness treatments altered networks of coassociation among bacterial taxa, suggesting the potential for host plant effects on the soil microbiome to include changes in microbial interaction dynamics and, consequently, co-evolution. Taxa that were coassociated in the rhizosphere of a given host plant species often showed consistent correlations between operational taxonomic unit (OTU) relative abundance and Streptomyces antagonistic activity, in the rhizosphere of that host. However, in the rhizosphere of a different host plant species, the same OTUs showed no consistency, or a different pattern of responsiveness to such biotic habitat characteristics. The diversity and richness of bacterial and Streptomyces communities exhibited distinct relationships with biotic and abiotic soil characteristics. The rhizosphere soil microbiome is influenced by a complex and nested array of factors at varying spatial scales, including plant community, plant host, soil edaphics and microbial taxon and community characteristics.
Data from: Temporal turnover of the soil microbiome composition is guild-specific
<p>Although spatial and temporal variation are both important components structuring microbial communities, the exact quantification of temporal turnover rates of fungi and bacteria has not been performed to date. In this study, we utilized repeated resampling of bacterial and fungal communities at specific locations across multiple years to describe their patterns and rates of temporal turnover. Our results show that microbial communities undergo temporal change at a rate of 0.010-0.025 per year (in units of Sorensen similarity), and the change in soil is slightly faster in fungi than in bacteria, with bacterial communities changing more rapidly in litter than soil. Importantly, temporal development differs across fungal guilds and bacterial phyla with different ecologies. While some microbial guilds show consistent responses across regional locations, others show site-specific development with weak general patterns. These results indicate that guild-level resolution is important for understanding microbial community assembly, dynamics and responses to environmental factors.</p>
Steering microbiomes by organic amendments towards climate-smart agricultural soils
<p>We steered the soil microbiome via applications of organic residues (mix of cover crop residues, sewage sludge + compost, and digestate + compost) to enhance multiple ecosystem services in line with climate-smart agriculture. Our result highlights the potential to reduce greenhouse gases (GHG) emissions from agricultural soils by the application of specific organic amendments (especially digestate + compost). Unexpectedly, also the addition of mineral fertilizer in our mesocosms led to similar combined GHG emissions than one of the specific organic amendments. However, the application of organic amendments has the potential to increase soil C, which is not the case when using mineral fertilizer. While GHG emissions from cover crop residues were significantly higher compared to mineral fertilizer and the other organic amendments, crop growth was promoted. Furthermore, all organic amendments induced a shift in the diversity and abundances of key microbial groups. We show that organic amendments have the potential to not only lower GHG emissions by modifying the microbial community abundance and composition, but also favour crop growth-promoting microorganisms. This modulation of the microbial community by organic amendments bears the potential to turn soils into more climate-smart soils in comparison to the more conventional use of mineral fertilizers.</p>
Scale dependence in functional equivalence and difference in the soil microbiome
<p>Climatic history can shape the functioning of soil microbial communities and thus rates of ecosystem processes such as organic matter decomposition. For example, broad spatial scale differences in climatic history, such as contrasting precipitation regimes, have been shown to generate unique microbial functional responses to contemporary moisture conditions. Yet it is an open question as to whether local differences in soil microclimate similarly influence the functional potential of decomposer communities. Here, we use a multi-scale approach within and among two temperate forest field sites to investigate this question. Soils from fifty-four microsites, that vary in their soil moisture climate-regimes, were used as inocula for a common leaf litter (<em>Quercus rubra</em>) in a controlled, laboratory microcosm study. Microcosms were placed under dry, mesic and wet lab-moisture conditions and the rate of carbon (C) mineralization of the litter was measured over 202 days. Our results reveal differences in decomposition rates under controlled conditions that highlight broad-scale functional differences between the soil communities at each site. Specifically, we found that C mineralization differed by as much as two-fold for soil communities when compared between the sites. Our results also show that functional differences of soil communities are observable within one site but not the other. In the site where local-scale functional legacies were apparent, the historical soil moisture microclimate-regimes generated as much as an 89% change in C mineralization rates of the leaf litter under the same contemporary, lab-imposed moisture conditions. A similar pattern was not observable in the other site; instead, laboratory moisture conditions explained almost all variation in C mineralization. Our findings confirm those from prior studies where regional-scale moisture-regime differences shape microbial function, and extends this prior work by providing evidence that pronounced local-scale differences in soil moisture microclimate-regimes can generate microbial functional legacies.</p>
Watershed and fire severity are stronger determinants of soil chemistry and microbiomes than within-watershed woody encroachment in a tallgrass prairie system
<p>Fire can impact terrestrial ecosystems by changing abiotic and biotic conditions. Short fire intervals maintain grasslands and communities adapted to frequent, low-severity fires. Shrub encroachment that follows longer fire intervals accumulates fuel and can increase fire severity. This patchily distributed biomass creates mosaics of burn severities in the landscape—pyrodiversity. Afforded by a scheduled burn of a watershed protected from fires for 27 years, we investigated effects of woody encroachment and burn severity on soil chemistry and soil-inhabiting bacteria and fungi. We compared soils before and after fire within the fire-protected, shrub-encroached watershed and soils in an adjacent, annually burned and non-encroached watershed. Organic matter and nutrients accumulated in the fire-protected watershed but responded less to woody encroachment within the encroached watershed. Bioavailable nitrogen and phosphorus and fungal and bacterial communities responded to high-severity burn regardless of encroachment. Low-severity fire effects on soil nutrients differed, increased bacterial but decreased fungal diversity and effects of woody encroachment within the encroached watershed were minimal. High-severity burns in the fire-protected watershed led to a novel soil system state distinct from non-encroached and encroached soil systems. We conclude that severe fires may open grassland restoration opportunities to manipulate soil chemistry and microbial communities in shrub-encroached habitats.</p>
DRAM raw annotations for "Cover Crop Root Exudates Impact Soil Microbiome Functional Trajectories in Agricultural Soils" Seitz et al 2024
<p>Additional File 5: <span>Raw DRAM MAG annotations. </span></p>
Impact of Rhizosphere Quantitative Microbiome and Soil Properties on Alkaloid Dynamics in Lycoris aurea
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FTICR-MS Dataset for 'Playing with FiRE: A genome resolved view of the soil microbiome responses to high severity forest wildfire'
<p>This dataset is the raw data for FTICR-MS used in Nelson et al.: 'Playing with FiRE: A genome resolved view of the soil microbiome responses to high severity forest wildfire'. The files correspond to the raw spectral files for each sample and can be opened with Bruker data analysis software. The numbers correspond to sample number (See Supplementary Data 1 in publication for sample metadata) and the r1 and r2 identifiers indicate if there were replicates of that sample.</p>
Effects of Hedysarum leguminous plants on soil bacterial microbiome in the Mu Us desert, northwest China
<p><span>By assessing the influence of rhizocompartment types (i.e. root, rhizosphere soil, root zone soil, and inter-shrub bulk soil) on the diversity of soil microbial communities under desert leguminous plant shrubs, and the influence of, and variations in, soil physicochemical factors in interactions among leguminous plants, soil, and microbes. Both 16S rRNA high-throughput genome sequencing and conventional soil physicochemical index determination were used to characterise the bacterial diversity and soil physicochemical properties in the rhizocompartments of two <i>Hedysarum</i> spp. (<i>Hedysarum mongolicum</i> and <i>Hedysarum scoparium</i>) in the Mu Us Desert. We found that all the nutrient indices (except TP and AP), values in rhizosphere soil were uniformly higher than those in root zone soil and inter-shrub bulk soil (<i>P</i> < 0.05). The bacterial community diversity in the root, under-shrub (rhizosphere, root zone) and inter-shrub bulk soil also have significant differences (<i>P</i> < 0.05). Desert leguminous plants had significant effects on hierarchical filtration and enrichment of specific soil bacterial microbiomes (<i>P</i> < 0.05). Root endophyte and rhizosphere soil microbiomes were mainly influenced by soil nutrients, while the bacterial communities in root zones soil and inter-shrub bulk soil were mainly influenced by soil pH and NH<sub>4</sub><sup>+</sup>-N. The rhizocompartment types of desert leguminous plants have a significant influence on the diversity of soil microbial communities. According to our findings, nitrogen-fixing rhizobia can co-exist with non-symbiotic endophytes in the roots of desert leguminous plants, and plants have a hierarchical filtering and enriching effect on beneficial microbes in soil via rhizocompartments. Soil physicochemical factors have a significant influence on the structure and composition of microbial communities in various rhizocompartments, and this influence is derived from the interactions among leguminous plants, soil, and microbes.</span></p>
The soil microbiome increases plant survival and modifies interactions with root endosymbionts in the field
<p>Evidence is accumulating that the soil microbiome—the community of microorganisms living in soils—has a major effect on plant traits and fitness. However, most work to date has taken place under controlled laboratory conditions and has not experimentally disentangled the effect of the soil microbiome on plant performance from the effects of key endosymbiotic constituents. As a result, it is difficult to extrapolate from existing data to understand the role of the soil microbiome in natural plant populations. To address this gap, we performed a field experiment using the black medick Medicago lupulina to test how the soil microbiome influences plant performance and colonization by two root endosymbionts (the mutualistic nitrogen-fixing bacteria Ensifer spp. and the parasitic root-knot nematode Meloidogyne hapla) under natural conditions. We inoculated all plants with nitrogen-fixing bacteria and factorially manipulated the soil microbiome and nematode infection. We found that plants grown in microbe-depleted soil exhibit greater mortality, but that among the survivors there was no effect of the soil microbiome on plant performance (shoot biomass, root biomass, or shoot-to-root ratio). The soil microbiome also impacted parasitic nematode infection and affected colonization by mutualistic nitrogen-fixing bacteria in a plant genotype-dependent manner, increasing colonization in some plant genotypes and decreasing it in others. Our results demonstrate the soil microbiome has complex effects on plant-endosymbiont interactions and may be critical for survival under natural conditions.</p>
Data from: Soil microbiome responses to the short-term effects of Amazonian deforestation
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Data from: Diffuse symbioses: roles of plant–plant, plant–microbe and microbe–microbe interactions in structuring the soil microbiome
Open the record for dataset details and reuse information.
Steering microbiomes by organic amendments towards climate-smart agricultural soils
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Scale dependence in functional equivalence and difference in the soil microbiome
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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.