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2,078 results for “soil data”
Data from: Nutrient scarcity strengthens soil fauna control over leaf litter decomposition in tropical rainforests
Soil fauna is a key control of the decomposition rate of leaf litter, yet its interactions with litter quality and the soil environment remain elusive. We conducted a litter decomposition experiment across different topographic levels within the landscape replicated in two rainforest sites providing natural gradients in soil fertility to test the hypothesis that low nutrient availability in litter and soil increases the strength of fauna control over litter decomposition. We crossed these data with a large dataset of 44 variables characterizing the biotic and abiotic microenvironment of each sampling point and found that microbe-driven Carbon (C) and Nitrogen (N) losses from leaf litter were 10.1 and 17.9 % lower, respectively, in the nutrient-poorest site but this among-site difference was equalized when meso- and macrofauna had access to the litterbags. Further, on average soil fauna enhanced the rate of litter decomposition by 22.6%, and this contribution consistently increased as nutrient availability in the microenvironment declined. Our results indicate that nutrient scarcity increases the importance of soil fauna on C and N cycling in tropical rainforests. Further, soil fauna is able to equalize differences in microbial decomposition potential thus buffering to a remarkable extent nutrient shortages at an ecosystem level.
Data from: Plant neighbours rather than soil biota determine impact of an alien plant invader
1. Various factors have been shown contributing to the ecosystem impact of invasive alien plants, but their relative importance remains unclear. We focused on the effects of neighbouring plant community and soil biota as these biotic factors have been repeatedly put forward to explain invasion success (e.g. as components of the novel weapons and of the biotic release hypothesis). 2. To assess their relative importance in explaining the high impact of Centaurea stoebe during the invasion of new sites in the introduced range, we conducted a greenhouse experiment with both European (EU) and North American (NA) tetraploid C. stoebe competing with/without EU vs. NA neighbouring community and with the two neighbouring communities growing without C. stoebe. Plants were grown in sterilized commercial soil inoculated with naïve soil (from rhizosphere of plants other than C. stoebe) originating either from the home EU or the introduced NA range and half of which was sterilized to remove soil biota. 3. In the competition pots, relative competitive ability (difference between the relative growth rates of C. stoebe and neighbouring community) and impact level (biomass of the neighbouring community relative to that in non-competition pots) of C. stoebe was significantly higher when grown with the NA than with the EU neighbouring community, although growth rates of EU and NA neighbouring communities did not differ in the non-competition pots. Both soil origin and C. stoebe origin had no effect on these processes. Soil sterilization increased growth of both C. stoebe and neighbouring communities, but had only a moderate effect on impact level and type, and no effect on the relative competitive ability of C. stoebe. 4. These results suggest that during the colonization of new sites in North American grasslands, the impact of C. stoebe is strongly driven by reduced competitive ability of NA neighbours compared with EU neighbours, while altered biotic soil conditions in the introduced range and post-introduction evolutionary changes in the invader are of less importance. This differential impact appears to be due to inherently different mechanisms underlying the competitive interactions between EU and NA neighbouring communities when grown with C. stoebe.
Data from: Intensive forest harvesting increases susceptibility of northern forest soils to carbon, nitrogen and phosphorus loss
1. Understanding the impact of forest harvesting is critical to sustainable forest management, yet there remains much uncertainty regarding how harvesting affects soil carbon (C), nitrogen (N) and phosphorus (P) dynamics. 2. Here we conducted a global meta-analysis of 808 observations from 49 studies to test the effects of harvesting on the stocks and concentrations of soil C, N, and P and C:N:P ratios relative to uncut control stands. 3. With all harvesting intensities combined, C stock was unaffected by harvesting in either the forest floor or mineral soil, while harvesting reduced forest floor [C], [N], and [P] and C:N ratio, increased the mineral soil [C] and C:N ratio, but reduced mineral soil N stock,. The impacts of harvesting on forest floor C and N stocks, C:P and N:P and mineral soil [C] and [N] changed from no effects by partial, stem-only and whole-tree harvesting to significantly negative effects by the harvesting coupled with fire. Stem-only and whole-tree harvesting similarly reduced forest floor [P]. The negative effects of harvesting were most pronounced in conifer stands. Soil [C], [N] and C:N decreased with time since harvesting, but soil [P] did not, resulting in an increase in forest floor N:P. 4. Synthesis and applications. Our findings highlight the importance of harvest intensity and rotation length on long-term soil nutrient availability when managing forests. Furthermore, the lag in [P] recovery following harvesting may indicate a decoupling of the P cycle from that of C and N and a potential concern in managed forests.
Data from: Soil microbial communities alter leaf chemistry and influence allelopathic potential among coexisting plant species
While both plant–soil feedbacks and allelochemical interactions are key drivers of plant community dynamics, the potential for these two drivers to interact with each other remains largely unexplored. If soil microbes influence allelochemical production, this would represent a novel dimension of heterogeneity in plant–soil feedbacks. To explore the linkage between soil microbial communities and plant chemistry, we experimentally generated soil microbial communities and evaluated their impact on leaf chemical composition and allelopathic potential. Four native perennial old-field species (two each of Aster and Solidago) were grown in pairwise combination with each species' soil microbial community as well as a sterilized inoculum. We demonstrated unequivocally that variation in soil microbial communities altered leaf chemical fingerprints for all focal plant species and also changed their allelopathic potential. Soil microbes reduced allelopathic potential in bioassays by increasing germination 25–54% relative to sterile control soils in all four species. Plants grown with their own microbial communities had the lowest allelopathic potential, suggesting that allelochemical production may be lessened when growing with microbes from conspecifics. The allelopathic potential of plants grown in congener and confamilial soils was indistinguishable from each other, indicating an equivalent response to all non-conspecific microbial communities within these closely related genera. Our results clearly demonstrated that soil microbial communities cause changes in leaf tissue chemistry that altered their allelopathic properties. These findings represent a new mechanism of plant–soil feedbacks that may structure perennial plant communities over very small spatial scales that must be explored in much more detail.
Data from: Teasing apart plant community responses to N enrichment: the roles of resource limitation, competition and soil microbes
Although ecologists have documented the effects of nitrogen enrichment on productivity, diversity and species composition, we know little about the relative importance of the mechanisms driving these effects. We propose that distinct aspects of environmental change associated with N enrichment (resource limitation, asymmetric competition, and interactions with soil microbes) drive different aspects of plant response. We test this in greenhouse mesocosms, experimentally manipulating each factor across three ecosystems: tallgrass prairie, alpine tundra and desert grassland. We found that resource limitation controlled productivity responses to N enrichment in all systems. Asymmetric competition was responsible for diversity declines in two systems. Plant community composition was impacted by both asymmetric competition and altered soil microbes, with some contributions from resource limitation. Results suggest there may be generality in the mechanisms of plant community change with N enrichment. Understanding these links can help us better predict N response across a wide range of ecosystems.
Data from: Making soil particle size analysis by laser diffraction compatible with standard soil texture determination methods
The standard sieving, pipette and hydrometer methods for soil particle size analysis (PSA) have three main drawbacks: procedures are tedious, time-consuming, and the results are protocol-dependent. Laser diffraction PSA delivers rapid results using standardized procedures, but so far it has been difficult to reconcile results with those from standard sedimentation methods. The objective of this study was to develop a protocol that would permit direct usage of laser diffraction PSA and render results compatible with current methods. The protocol was developed using standard soil samples from different textural classes. Regression of the laser diffraction PSA against the hydrometer/pipette method yielded coefficients of determination of 0.92/0.9, 0.92/0.94 and 0.99/0.99, and root mean square errors of 0.04/0.05, 0.07/0.06 and 0.05/0.03 for clay, silt and sand, respectively. These statistics are comparable to those obtained by regressing results of the hydrometer against the sieve and pipette methods. A key factor in securing accurate and precise results was limiting the particle size range of the samples by wet sieving the sand fraction. This created representative samples and stable soil dispersed suspensions, allowing accurate estimations of particle size distribution for clay and silt fractions without empirical transformations. Results obtained with the proposed protocol matched those of standard sedimentation analyses for a wide range of soils, encouraging further adoption of laser diffraction for soil PSA.
Data from: Feedbacks between nitrogen fixation and soil organic matter increase ecosystem functions in diversified agroecosystems
Nitrogen (N) losses from intensified agriculture are a major cause of global change, due to nitrate (NO3-) export and the eutrophication of aquatic systems as well as emissions of nitrous oxide (N2O) into the atmosphere. Diversified agroecosystems with legume cover crops couple N and carbon (C) inputs to soil and reduce N pollution, but there is a need to identify controls on legume N2 fixation across ecosystems with variable soil conditions. Here, I tested the hypothesis that N mineralization from turnover of soil organic matter (SOM) regulates legume N2 fixation across 10 farms that spanned a gradient of SOM levels. I separated soil samples into two SOM fractions, based on size and density, which are indicators of soil nutrient cycling and N availability (free particulate organic matter and intra-aggregate particulate organic matter (POM)). This study indicates downregulation of legume N2 fixation in diversified agroecosystems with increasing N availability in intra-aggregate POM and increasing N mineralization. Intercropping the legume with a grass weakened the relationship between N in POM and N2 fixation due to N assimilation by the grass. Further, mean rates of N and C mineralization across sites increased with two seasons of a legume-grass cover crop mixture, which could enhance this stabilizing feedback between soil N availability and N2 fixation over time. These results suggest a potential mechanism for the diversity-ecosystem function relationships measured in long-term studies of agroecosystems, in which regular use of legume cover crops increases total soil organic C and N and reduces the environmental costs of crop production.
Data from: Does soil moisture availability explain liana seedling distribution across a tropical rainfall gradient?
Liana density tends to increase with decreasing rainfall and increasing seasonality. However, the pattern of liana distribution may be due to differences in soil water retention capacity, not rainfall and seasonality per se. We tested the effect of rainfall and soil substrate with respect to the distribution of liana seedlings in six sites across a rainfall gradient from the wet Atlantic to the dry Pacific in central Panama. Soils were either limestone, with low water-holding capacity, or laterite, with higher water-holding capacity. We sampled liana seedlings at each site using three 1 × 100 m transect. We found that relative liana seedling density was higher on limestone soils compared to laterite soils regardless of the amount of rainfall. Furthermore, liana community composition on limestone soils was more similar to dry forest sites than to adjacent wet and moist forest sites. Liana seedling species diversity relative to trees was significantly higher in a low-fertility dry forest site compared to a high-fertility forest, but did not differ from the other sites. Thus, liana seedling density and community structure may be driven more by soil type and thus by soil moisture availability than strictly by mean annual rainfall and the seasonality of rainfall.
Data from: Impacts of landscape composition, marginality of distribution, soil fertility, and climatic stability on the patterns of woody plant endemism in the Cerrado
Aim: Although various theories have been proposed to explain the outstanding endemism of plants in the Cerrado, four hypotheses about the mechanisms of diversification and distribution are most supported: (1) plateau/valley, (2) stable/unstable climate, (3) core/peripheral distribution, and (4) soil fertility. The first argues that plateaus harbor more ancient lineages than valleys and therefore presents higher endemism. The second theory suggests that climatic stable environments maintained more paleoendemic species. The third scenario attributes the distribution of endemism to gradients of conditions available to locally adapted species and predicts higher endemism in nuclear than in marginal areas. The last theory suggests that lower fertility soils account for higher endemism due to the habitat specialization of its species. We compared endemism patterns with the predictions of each theory to discuss their importance. Location: Brazil. Time period: Quaternary. Major taxa studied: Angiosperms. Methods: We mapped the endemism using records of 311 plant species of the Cerrado and applied spatial analysis and distribution models to summarize the importance of each predictor of endemism. Results: We identified 28 areas in which the higher endemism of Cerrado plants were concentrated and presented a map of its distribution. We found correlations among endemism, climate stability, elevation, and marginality, which supported the plateau/valley, core/peripheral, and stable/unstable hypotheses. No association between soil fertility and endemism was detected. We propose that plateaus are more stable climatic environments, and this characteristic along with their elevation and centrality are predictive of endemism. Main conclusions: We concluded that most of the endemism is concentrated in overlapping areas of stability of species, which are concentrated in higher elevation central regions. Soil fertility was not linked to endemism. We recommend that central plateaus in the Cerrado require special attention in conservation to optimize the protection of endemic species in the biome.
Data from: Using greenhouse gas fluxes to define soil functional types
Aim: Soils provide key ecosystem services and directly control ecosystem functions; thus, there is a need to define the reference state of soil functionality. Most common functional classifications are vegetation-centered, such as plant functional types (PFTs), and neglect soil characteristics and processes. We propose Soil Functional Types (SFTs) as a conceptual approach to represent and describe the functionality of soils based on characteristics of their greenhouse gas (GHG) flux dynamics. Methods: We used automated measurements of CO2, CH4 and N2O soil fluxes in a forested area to define SFTs as surface areas with similar GHG dynamics. We performed mixed effects models, and independent cluster analyses of our environmental variables and SFT classifications. Results Unique groupings based on SFTs, but not environmental variables, supported the hypothesis that SFTs provide additional insights on the spatial variability of soil functionality beyond information represented by commonly measured soil parameters (e.g., soil moisture, soil temperature, litter biomass). Conclusions: This approach could complement vegetation-based functional classifications to better represent the broad range of ecosystem functions. A global application of the proposed SFT framework will only be possible if there is a community-wide effort to share data and create a global database of GHG emissions from soils.
Data from: Environmental drivers of soil phosphorus composition in natural ecosystems
Abstract. Soil organic and inorganic phosphorus (P) compounds can be influenced by distinctive environmental properties. This study aims to analyze soil P composition in natural ecosystems, relating organic (inositol hexakisphosphate, DNA and phosphonates) and inorganic (orthophosphate, polyphosphate and pyrophosphate) compounds with major temporal (weathering), edaphic and climatic characteristics. A dataset including 88 sites was assembled from published papers that determined soil P composition using one-dimensional liquid state 31P nuclear magnetic resonance spectroscopy of NaOH-EDTA extracts of soils. Bivariate and multivariate regression models were used to better understand the environmental properties influencing soil P. In bivariate relationships, trends for soil P compounds were similar for mineral and organic layers but with different slopes. Independent and combined effects of weathering, edaphic and climatic properties of ecosystems explained up to 78% (inositol hexakisphosphates) and 89% (orthophosphate) of variations in organic and inorganic P compounds across the ecosystems, likely deriving from parent material differences. Soil properties, particularly pH, total carbon, and carbon-to-phosphorus ratios, over climate and weathering mainly explained the P variation. We conclude that edaphic and climatic drivers regulate key ecological processes that determine the soil P composition in natural ecosystems. These processes are related to the source of P inputs, primarily determined by the parent material and soil forming factors, plant and microbe P cycling, the bio-physico-chemical properties governing soil phosphatase activity, soil solid surface specific reactivity, and P losses through leaching, and finally the P persistence induced by the increasing complexity of organic and inorganic P compounds as the pedogenesis evolves. Soil organic and inorganic P compounds respond differently to combinations of environmental drivers, which likely indicates that each P compound has specific factors governing its presence in natural ecosystems.
Data from: Soil carbon, nitrogen and phosphorus stoichiometry (C:N:P) in relation to conifer species productivity and nutrition across British Columbia perhumid rainforests
<p>Temperate rainforest soils of the Pacific Northwest are often carbon (C) rich and encompass a wide range in fertility reflecting varying nitrogen (N) and phosphorus (P) availability. Soil resource stoichiometry (C:N:P) may provide an effective measure of site nutrient status and help refine species-dependent patterns in forest productivity across edaphic gradients. We described the nature of soil organic matter for mineral soil and forest floor substrates across very wet (perhumid) rainforest sites of southwestern Vancouver Island (Canada), and employed soil element ratios as covariates in a long-term planting density trial to test their utility in defining basal area growth response of four conifer species. There were strong positive correlations in mineral soil C, N and organic P (P<sub>o</sub>) concentrations, and close alignment in C:N and C:P<sub>o</sub> both among and between substrates. Stand basal area after five decades was best reflected by soil C:N but included a significant species-soil interaction. The conifers with ectomycorrhizal fungi had diverging growth responses displaying either competitive (<i>Picea sitchensis</i>) or stress-tolerant (<i>Tsuga heterophylla</i>, <i>Pseudotsuga menziesii</i>) attributes, in contrast to a more generalist response by an arbuscular mycorrhizal tree (<i>Thuja plicata</i>). Despite the consistent patterns in organic matter quality we found no evidence via foliar nutrition for increased P availability with declining element ratios as we did for N. The often high C:P<sub>o</sub> ratios (as much as 3000) of these soils may reflect a stronger immobilization sink for P than N, which, along with ongoing sorption of PO<sub>4</sub><sup>-</sup>, could limit the utility of C:P<sub>o</sub> or N:P<sub>o</sub> to adequately reflect P supply. The dynamics and availability of soil P to trees, particularly as P<sub>o</sub>, deserves greater attention as many perhumid rainforests were co-limited by N and P, or, in some stands, possibly P alone. </p>
Data from: Elevated CO2 and temperature increase soil C losses from a soybean-maize ecosystem
Warming temperatures and increasing CO2 are likely to have large effects on the amount of carbon stored in soil, but predictions of these effects are poorly constrained. We elevated temperature (canopy: +2.8 °C; soil growing season: +1.8 °C; soil fallow: +2.3 °C) for 3 years within the 9th–11th years of an elevated CO2 (+200 ppm) experiment on a maize–soybean agroecosystem, measured respiration by roots and soil microbes, and then used a process-based ecosystem model (DayCent) to simulate the decadal effects of warming and CO2 enrichment on soil C. Both heating and elevated CO2 increased respiration from soil microbes by ~20%, but heating reduced respiration from roots and rhizosphere by ~25%. The effects were additive, with no heat × CO2 interactions. Particulate organic matter and total soil C declined over time in all treatments and were lower in elevated CO2 plots than in ambient plots, but did not differ between heat treatments. We speculate that these declines indicate a priming effect, with increased C inputs under elevated CO2 fueling a loss of old soil carbon. Model simulations of heated plots agreed with our observations and predicted loss of ~15% of soil organic C after 100 years of heating, but simulations of elevated CO2 failed to predict the observed C losses and instead predicted a ~4% gain in soil organic C under any heating conditions. Despite model uncertainty, our empirical results suggest that combined, elevated CO2 and temperature will lead to long-term declines in the amount of carbon stored in agricultural soils.
Data from: A native parasitic plant and soil microorganisms facilitate a native plant co-occurrence with an invasive plant
Invasive plants often interact with antagonists that include native parasitic plants and pathogenic soil microbes, which may reduce fitness of the invaders. However, to date, most of the studies on the ecological consequences of antagonistic interactions between invasive plants and the resident biota focused only on pairwise interactions. A full understanding of invasion dynamics requires studies that test the effects of multiple antagonists on fitness of invasive plants and co-occurring native plants. Here, we used an invasive plant Mikania micrantha, a co-occurring native plant Coix lacryma-jobi, and a native holoparasitic plant Cuscuta campestris to test whether parasitism on M. micrantha interacts with soil fungi and bacteria to reduce fitness of the invader and promote growth of the co-occurring native plant. In a factorial set up, M. micrantha and C. lacryma-jobi were grown together in pots in the presence versus absence of parasitism on M. micrantha by C. campestris, and in the presence versus absence of full complements of soil bacteria and fungi. Fungicide and bactericide were used to suppress soil fungi and bacteria, respectively. Findings show that heavy parasitism by C. campestris caused the greatest reduction in M. micrantha biomass when soil fungi and bacteria were suppressed. In contrast, the co-occurring native plant C. lacryma-jobi experienced the greatest increase in biomass when grown with heavily parasitized M. micrantha and in the presence of a full complement of soil fungi and bacteria. Taken together, our results suggest that selective parasitism on susceptible invasive plants by native parasitic plants and soil microorganisms may diminish competitive ability of invasive plants and facilitate native plant co-existence with invasive plants.
Data from: Low abundant soil bacteria can be metabolically versatile and fast growing
The abundance of species is assumed to depend on their life history traits, such as growth rate and resource specialization. However, this assumption has not been tested for bacteria. Here we investigate how abundance of soil bacteria relates to slow growth and substrate specialization (oligotrophy) versus fast growth and substrate generalization (copiotrophy). We collected 47 saprotrophic soil bacterial isolates of differing abundances and measured their growth rate and the ability to use a variety of single carbon sources. Opposite to our expectation, there was no relationship between abundance in soil and the measured growth rate or substrate utilization profile (SUP). However, isolates with lower growth rates used fewer substrates than faster growing ones supporting the assumption that growth rate may relate to substrate specialization. Interestingly, growth rate and SUP were correlated with phylogeny, rather than with abundance in soil. Most markedly, Gammaproteobacteria on average grew significantly faster and were able to use more substrates than other bacterial classes, whereas Alphaproteobacteria were growing relatively slowly and used fewer substrates. This finding suggests that growth and substrate utilization are phylogenetically deeply conserved. We conclude that growth rate and substrate utilization of soil bacteria are not general determinants of their abundance. Future studies on explaining bacterial abundance need to determine how other factors, such as competition, predation and abiotic factors may contribute to rarity or abundance in soil bacteria.
Data from: Soil abiotic variables are more important than Salicaceae phylogeny or habitat specialization in determining soil microbial community structure
Predicting the outcome of interspecific interactions is a central goal in ecology. The diverse soil microbes that interact with plants are shaped by different aspects of plant identity, such as phylogenetic history and functional group. Species interactions may also be strongly shaped by abiotic environment, but there is mixed evidence on the relative importance of environment, plant identity, and their interactions in shaping soil microbial communities. Using a multi-factor, split-plot field experiment, we tested how hydrologic context, and three facets of Salicaceae plant identity - habitat specialization, phylogenetic distance, and species identity - influence soil microbial community structure. Analysis of microbial community sequencing data with generalized dissimilarity models showed that abiotic environment explained up to 25% of variation in community composition of soil bacteria, fungi, and archaea, while Salicaceae identity influenced less than 1% of the variation in community composition of soil microbial taxa. Multivariate linear models indicated that the influence of Salicaceae identity was small, but did contribute to differentiation of soil microbes within treatments. Moreover, results from a microbial niche breadth analysis show that soil microbes in wetlands have more specialized host associations than soil microbes in drier environments - showing that abiotic environment changed how plant identity correlated with soil microbial communities. This study demonstrates the predominance of major abiotic factors in shaping soil microbial community structure; the significance of abiotic context to biotic influence on soil microbes; and the utility of field experiments to disentangling the abiotic and biotic factors that are thought to be most essential for soil microbial communities.
Data from: Tracking earthworm communities from soil DNA
Earthworms are known for their important role within the functioning of an ecosystem, and their diversity can be used as an indicator of ecosystem health. To date, earthworm diversity has been investigated through conventional extraction methods such as handsorting, soil washing or the application of a mustard solution. Such techniques are time-consuming and often difficult to apply. We showed that combining DNA metabarcoding and next generation sequencing facilitates the identification of earthworm species from soil samples. The first step of our experiments was to create a reference database of mitochondrial DNA (mtDNA) 16S gene for 14 earthworm species found in the French Alps. Using this database, we designed two new primer pairs targeting very short and informative DNA sequences (about 30 bp and 70 bp) that allow unambiguous species identification. Finally, we analyzed extracellular DNA taken from soil samples in two localities (two plots per locality, eight samples per plot). The two short metabarcode regions led to the identification of a total of eight earthworm species. The earthworm communities identified by the DNA-based approach appeared to be well-differentiated between the two localities, and are consistent with results derived from inventories collected using the handsorting method. The possibility of assessing earthworm communities from hundreds or even thousands of localities through the use of extracellular soil DNA will undoubtedly stimulate further ecological research on these organisms. Using the same DNA extracts, our study also illustrates the potential of environmental DNA as a tool to assess the diversity of other soil-dwelling animal taxa.
Data from: Larger plants promote a greater diversity of symbiotic nitrogen-fixing soil bacteria associated with an Australian endemic legume
A major goal in microbial ecology is to understand the factors that structure bacterial communities across space and time. For microbes that are plant symbionts, community assembly processes can lead to either a positive or negative relationship between plant size or age and soil microbe diversity. Here, we evaluated the extent to which such relationships exist within a single legume species (Acacia acuminata) and their naturally occurring symbiotic nitrogen-fixing bacteria (rhizobia). 2. We quantified the diversity of rhizobia that associate with A. acuminata trees of variable size spanning a large environmental gradient in southwest Australia (72 trees in 24 sites spread across ~300,000 km2), using metabarcoding. We modelled rhizobia diversity using 16S exact genetic variants, in a binomial multivariate statistical framework that controlled for climate and local soil characteristics. 3. We identified two major phylogenetic clades of rhizobia that associate with A. acuminata. Soil sampled at the base of larger Acacia trees contained a higher richness of rhizobia genetic variants. Each major clade responds differently to environmental factors (climate and soil characteristics), but the positive association between tree size and rhizobia genetic diversity was mainly driven by responses from one of the two clades. Overall tree size explained more variation than any other factor, resulting in a ~3-fold increase in total richness and clade diversity from the smallest to the largest trees. 4. Synthesis. Previous studies have shown that plant host species is important in structuring microbial soil communities in the rhizosphere. Our results show that host size or age within a single plant species can also structure diversity of at least one group of soil microbes. A positive relationship between plant host size and rhizobia diversity suggests that hosts may modify the niche space of their surrounding soil (niche construction hypothesis) enabling a higher richness of microbial taxa. That different rhizobial groups responded differently to host size and other ecological factors suggests that rhizobia is not an ecologically uniform group, and that entirely neutral explanations for our results are unlikely. Host plants may be analogous to 'islands', where larger plant hosts may accumulate diversity over time, through migration opportunities.
Data from: A survey of invasive plants on grassland soil microbial communities and ecosystem services
<p>Invasive plants can cause changes in structure and function of the ecosystem undergoing invasion. Any changes in ecosystem diversity and community composition will likely alter ecosystem services provided by that ecosystem. However, how these ecosystem services may change is poorly understood. To elucidate how these ecosystem services will change with invasion, we sampled 561 plots undergoing invasion by smooth brome (<i>Bromus inermis</i>) and four other invasive species at a native Rough Fescue prairie located near Saskatoon, Saskatchewan, Canada. Soil and plant surveys were undertaken weekly for 26 weeks beginning in May in 2014 until November 2014, or the growing season. We measured a suite of ecosystem services, including greenhouse gasses, extracellular enzyme function, forage production, glyphosate degradation and decomposition. Furthermore, soil physical and chemical properties were measured, and soil bacterial and fungal communities were sequenced. This is a large and multifaceted dataset with complex temporal and spatial attributes that can be used to answer numerous questions regarding the functioning of prairie ecosystems and how invasive species will impact that functioning. </p>
Data from: DNA from soil mirrors plant taxonomic and growth form diversity
Ecosystems across the globe are threatened by climate change and human activities. New rapid survey approaches for monitoring biodiversity would greatly advance assessment and understanding of these threats. Taking advantage of next-generation DNA sequencing, we tested an approach we call metabarcoding: high-throughput and simultaneous taxa identification based on a very short (usually less than 100 base pairs) but informative DNA fragment. Short DNA fragments allow the use of degraded DNA from environmental samples. All analyses included amplification using plant-specific versatile primers, sequencing and estimation of taxonomic diversity. We tested in three steps whether degraded DNA from dead material in soil has the potential of efficiently assessing biodiversity in different biomes. First, soil DNA from eight boreal plant communities located in two different vegetation types (meadow and heath) was amplified. Plant diversity detected from boreal soil was highly consistent with plant functional and structural diversity estimated from conventional above-ground surveys. Second, we assessed DNA persistence using samples from formerly cultivated soils in temperate environments. We found that number of crop DNA sequences retrieved strongly varied with years since last cultivation, and crop sequences were absent from nearby, uncultivated plots. Third, we assessed the universal applicability of DNA metabarcoding using soil samples from tropical environments: a large proportion of species and families from the study site was efficiently recovered. The results open unprecedented opportunities for large-scale DNA-based biodiversity studies across a range of taxonomic groups using standardized metabarcoding approaches.
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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.