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2,078 results for “soil data”
Data from: Taxonomic and phylogenetic diversity of vascular plants at Ma'anling volcano urban park in tropical Haikou, China: Reponses to soil properties
Anthropogenic processes and socio-economic factors play important roles in shaping plant diversity in urban parks. To investigate how plant diversity of Ma' anling urban volcano park in Hainan Province, China respond to these factors, we carried out a field investigation on the taxonomic and phylogenetic diversity of vascular plants and soil properties in this area. We found 284 species of vascular plants belonging to 88 families and 241 genera, which included 194 native species, 23 invasive species, 31 naturalized species, 40 cultivars, and 4 rare / endangered plant species. Tree composition and richness significantly varied between different vegetation formations (plantation, secondary forest, and abandoned land). Plant species richness and community composition were significantly affected by elevation (El), soil water content (WC), total soil nitrogen (TN) and soil organic matter (SOM). There were significant diversity differences between plantations and abandoned lands, but not between the plantations and secondary forests. The flora in the study site was tropical in nature, characterized by pantropic distributions. Compared to adjacent areas, floristic composition in the study site was most similar to that of Guangdong, followed by that of Vietnam. Our study revealed the diversity patterns of volcanic plants and provided the basis for future planning of plant conservation, such as preserving plant species, maintaining plant habitats, and coordinating plant management in this region.
Data from: Thermal acclimation and adaptation across populations in a broadly distributed soil arthropod
The relative contributions of phenotypic plasticity and adaptive evolution to the respons-es of species to climate change are poorly understood. It has been suggested that some species or populations will have to rely on their ability to adjust their phenotype rather than on adaptation through evolutionary adaptation. 2. We test the extent of intra- and inter-population patterns of acclimation and genetic varia-tion in multiple traits directly related to environmental tolerance limits in the broadly dis-tributed soil dwelling collembolan Orchesella cincta. 3. Genetic variation in both dynamic and static assays of thermal tolerance was present across seven populations spanning 14° of latitude and both heat and cold tolerance were significantly correlated with latitude. Short term heat and cold acclimation significantly increased thermal tolerance limits across all populations and there was local adaptation for acclimation responses for some traits. Furthermore, results showed large acclimatiza-tion responses in the field within populations for cold tolerance throughout a 13-month period and smaller acclimatization responses for heat tolerance. Acclimatization respons-es were correlated with microhabitat temperature at the site of collection suggesting that plastic responses are highly dynamic and allow organisms to cope with changes in tem-perature. 4. Our findings demonstrate small differences in upper and lower thermal tolerance limits across populations, but substantial local acclimatization effects dictated by microhabitat temperatures, and also highlight the limited scope and strong trade-offs to respond to in-creasing temperatures. These findings demonstrate the need for incorporating infor-mation on species' ability to respond to environmental change using both laboratory and field approaches into climate change models.
Data from: Direct and indirect effects of nitrogen enrichment on soil organisms and carbon and nitrogen mineralization in a semi‐arid grassland
1. Semi-arid grasslands on the Mongolian Plateau are expected to experience high inputs of anthropogenic reactive nitrogen in this century. It remains unclear, however, how soil organisms and nutrient cycling are directly affected by N enrichment (i.e., without mediation by plant input to soil) vs. indirectly affected via changes in plant-related inputs to soils resulting from N enrichment. 2. To test the direct and indirect effects of N enrichment on soil organisms (bacteria, fungi, and nematodes) and their associated C and N mineralization, in 2010 we designated two subplots (with plants and without plants) in every plot of a six-level N-enrichment experiment established in 1999 in a semi-arid grassland. 3. In 2014, 4 years after subplots with and without plant were established, N enrichment had substantially altered the soil bacterial, fungal, and nematode community structures due to declines in biomass or abundance whether plants had been removed or not. N enrichment also reduced the diversity of these groups (except for fungi) and the soil C mineralization rate and induced a hump-shaped response of soil N mineralization. As expected, plant removal decreased the biomass or abundance of soil organisms and C and N mineralization rates due to declines in soil substrates or food resources. 4. Analyses of plant removal-induced changes (ratios of without- to with-plant subplots) showed that microorganisms and C and N mineralization rates were not enhanced as N enrichment increased but that nematodes were enhanced as N enrichment increased, indicating that the effects of plant removal on soil organisms and mineralization depended on trophic level and nutrient status.5. Surprisingly, there was no statistical interaction between N enrichment and plant removal for most variables, indicating that plant-related inputs did not qualitatively change the effects of N enrichment on soil organisms or mineralization. Structural equation modeling confirmed that changes in soil communities and mineralization rates were more affected by the direct effects of N enrichment (via soil acidification and increased N availability) than by plant-related indirect effects. Our results provide insight into how future changes in N-deposition and vegetation may modify below-ground communities and processes in grassland ecosystems.
Data from: Patterns of local adaptation in space and time among soil bacteria
Our understanding of microbial biogeography has been governed by the dictum "Everything is everywhere, but the environment selects." In other words, the distribution of microbes is thought to occur in a regime of extensive dispersal and strong selection, generating local adaptation. However, direct tests of these assumptions are rare. Here, we investigate the extent of local adaptation in space and time of a collection of soil-derived microbial isolates, most belonging to the genus Pseudomonas, across a growing season from a deciduous forest in western Quebec, Canada, using a reciprocal transplant design. Average performance of all clones varied substantially in both space and time, in line with the expectation of strong selection in both dimensions. The behavior of genotype-by-environment variance in fitness and its components, responsiveness and inconsistency, in space and through time suggests that the strength of divergent selection increases as sites become more distant from each other in both dimensions. However, divergent selection was not strong enough to maintain different specialized types across the environments studied, which suggests that Pseudomonas and their close relatives are not locally adapted to the prevailing conditions of growth.
Data from: Bacterial diversity amplifies nutrient-based plant-soil feedbacks
Plants foster diverse assemblages of bacteria in the rhizosphere serving important functions which may result in enhanced plant growth. Microbial diversity is increasingly recognized to shape the functionality of microbial communities. This leads to the assumption that there is a positive relationship between rhizosphere diversity and plant growth. Here we investigate how bacterial diversity affects the mineralization of organic matter and plant nutrient acquisition. We hypothesized that altered bacterial diversity will affect nitrogen mineralisation, uptake by plants and ultimately plant growth. We set up a controlled model system with Arabidopsis thaliana colonized by defined assemblages of fluorescent pseudomonads, a well-characterised plant-beneficial rhizosphere taxon. The growth substrate contained casein as sole nitrogen source, making the plant nitrogen uptake dependant on breakdown by bacterial enzymes. Bacterial diversity was associated with a higher enzyme activity which increased nitrogen mineralization and enhanced plant growth. The effect of bacterial diversity on plant growth increased with time, pointing to a positive feedback between bacteria and plants: Bigger plants associated with species-rich bacterial communities supported more bacterial growth, which further enhanced the impact of bacteria on plant growth. We demonstrate that plant-soil feedbacks establish rapidly during one single growth season and that bacterial diversity modulates this interaction. Preserving soil microbial diversity therefore may improve positive plant-soil feedbacks and thereby plant growth.
Data from: Cascading spatial and trophic impacts of oak decline on the soil food web
1. Tree defoliation and mortality have considerably increased worldwide during the last decades due to global change drivers such as increasing drought or invasive pests and pathogens. However, the effects of this tree decline on soil food webs are poorly understood. 2. In this study we evaluated the impacts of Quercus suber decline on soil food webs of Mediterranean mixed forests invaded by the exotic oomycete pathogen Phytophthora cinnamomi, using soil nematodes as bioindicator taxa. We used a spatially-explicit neighborhood approach to predict the characteristics of the nematode community (diversity, trophic structure, and several indices indicative of soil food web conditions) as a function of the characteristics of the tree and shrub community (species composition, size and health status). 3. Our results indicate that the process of defoliation and mortality of Q. suber caused significant alterations in the nematode trophic structure increasing the abundance of lower trophic levels (bacterivores, fungivores and herbivores) and decreasing the abundance of higher levels (predators and omnivores). Furthermore, Q. suber decline altered the functional composition of soil communities, producing a setback of the ecological succession in the soil food web to an earlier stage (decrease in the maturity index and increase in the plant-parasitic index), simplified soil food webs (decrease in the structure index), and shifts in the predominant decomposition channel (increase in the fungivores/bacterivores ratio). 4. We also detected contrasting characteristics of the nematode community in neighborhoods dominated by coexistent woody species, which suggests potential for long-term indirect effects on soil food webs due to the substitution of Q. suber by non-declining species. 5. Synthesis: Our study provides novel results that show the major impacts that ongoing health deterioration of dominant tree species can have on the structure and composition of soil food webs in forest systems invaded by exotic pathogens, with cascading consequences for soil biogeochemical processes in both the short- and long-term.
Data from: Testing the plant growth-defense hypothesis belowground: do faster-growing herbaceous plant species suffer more negative effects from soil biota than slower-growing ones?
According to the growth-defense hypothesis in ecology, faster-growing plant species should suffer more from herbivores and pathogens than slower-growing species. Tests of this hypothesis have focused on aboveground plant tissues, herbivores, and pathogens; however, it should also apply to root defense. To test whether faster-growing species suffer more negatively from soil biota than slower-growing species, we estimated first-season growth rates of 34 herbaceous plant species and used weighted linear regressions to assess the relationship between growth rates and responses to being grown in sterilized versus unsterilized soil (biotic soil effects) and to growing in soil previously occupied by conspecifics versus a mixture of species (conspecific soil effects). We found a negative relationship between relative growth rate and biotic soil effects, with slower-growing species tending to suffer less or even benefit from the presence of soil biota, while faster-growing species were more negatively affected. Biotic soil effects were also negatively related to size-corrected growth rates. These relationships remained negative after accounting for influential species, but a large amount of variation remained unexplained. Moreover, there was no clear relationship between growth rates and conspecific soil effects. A simple relationship between growth and defense aboveground may not be so clearly reflected belowground because of the many interacting antagonistic and mutualistic organisms likely involved.
Data from: Traits including leaf dry matter content and leaf pH dominate over forest soil pH as drivers of litter decomposition among 60 species
1. Soil pH varies by several units among ecosystems. While soil pH is known to be a key driver of plant species composition, we still have a poor understanding of how it affects carbon cycling processes. For instance, soil pH, or its associated chemistry in terms of base cations and organic acids, may affect decomposition rates of dead matter directly, by controlling decomposer composition and activity, and indirectly, by controlling the traits of the plant species and thereby the afterlife effects of those traits on litter decomposition. Leaf and litter pH may play a role in this control. Based on the very limited empirical data available, we hypothesized that variation in species traits including leaf (litter) pH, within and between ecosystems contrasting in soil pH, would have stronger effects on leaf litter decomposition rates than variation in soil chemistry would. 2. We tested this hypothesis by carrying out a 'common garden' litterbed experiment in subtropical SW China, in which leaf litters of the 30 predominant plant species from mid-successional forest on acidic sandstone (soil pH around 4.0) and calcareous soil (pH around 7.5) respectively, were incubated and their decomposition rates measured over two harvests in fourteen months, both in soil plus litter matrix from their 'home' forest and in those from the "away" forest. 3. We found that leaf (litter) trait variation among species and plant functional types, headed by species' dry matter content but also including tissue pH, was the strongest driver of variation in leaf litter decomposition rates. Surprisingly however, while these effects of interspecific trait variation were very strong among species from the same site, there was no overall difference in litter decomposability between the species from the acidic versus calcareous site. Equally surprising was that this strong difference in pH of soil substrate plus litter matrix from an acidic sandstone site versus a calcareous karst site did not directly affect leaf litter decomposition rates across a given species set. 4. This first attempt to disentangle the multiple potential direct and indirect ways in which soil and leaf (litter) acidity might be related to litter decomposition rates, has important implications for our understanding of soil-plant feedbacks. Based on our forest-based study, we predict that soil-plant feedbacks via acidity are unlikely to be strong in ecosystems with wide-ranging species in terms of their leaf functional traits, including leaf pH.
Data from: Positive selection inhibits gene mobilization and transfer in soil bacterial communities
Horizontal gene transfer (HGT) between bacterial lineages is a fundamental evolutionary process that accelerates adaptation. Sequence analyses show that conjugative plasmids are principal agents of HGT in natural communities. However, we lack understanding of how the ecology of bacterial communities and their environments affect the dynamics of plasmid-mediated gene mobilization and transfer. Here we show, in simple experimental soil bacterial communities containing a conjugative mercury resistance plasmid, the repeated, independent mobilization of transposon-borne genes from chromosome to plasmid, plasmid to chromosome and, in the absence of mercury selection, interspecific gene transfers from the chromosome of one species to the other via the plasmid. By reducing conjugation, positive selection for plasmid-encoded traits, like mercury resistance, can consequently inhibit HGT. Our results suggest that interspecific plasmid-mediated gene mobilization is most likely to occur in environments where plasmids are infectious, parasitic elements rather than those where plasmids are positively selected, beneficial elements.
Data from: Functional diversity of Collembola is reduced in soils subjected to short-term, but not long-term, geothermal warming
1. Human activities have caused global changes of atmospheric chemistry resulting in increased temperature especially in the colder regions of the northern hemisphere. Since warming of the environment can have drastic effects on terrestrial ecosystems it is important to experimentally evaluate the extent of such effects in long-term field-based experiments. In the present study we make use of both recent (short-term) and long-term geothermal warming of Icelandic soils to examine the responses of Collembola, an ecologically important group of soil invertebrates, to warming. 2. Based on metabolic scaling theory, we hypothesized that species of small size would be more successful in warmed soils than species of larger size. Further we expected that top-soil dwelling species would benefit more from warming than deep-soil dwelling species. In order to test these hypotheses we sampled Collembola along replicated gradients of increasing temperature in areas that had been heated for about six years and more than 50 years, respectively. Collembola were identified to species level, counted, and the community-weighted mean trait scores for six functional and ecological traits were calculated. 3. Results show that both short-term and long-term soil warming caused a shift towards a higher relative abundance of species with small body size. Further, abundance of top-soil dwelling Collembola tended to increase after short-term warming, but the opposite was observed after long-term warming. 4. Using trait-based diversity indices (Frich and RaoQ), we show that functional richness and diversity of Collembola communities was significantly reduced (almost halved) as a result of short-term soil warming to about 10 °C above normal, but this effect was not detected in plots equally warmed for more than 50 years. This indicates that the functional diversity of Collembola communities have high resilience towards soil warming in a long-term perspective.
Data from: Soil acidification exerts a greater control on soil respiration than soil nitrogen availability in grasslands subjected to long-term nitrogen enrichment
Terrestrial ecosystems worldwide are receiving increasing amounts of biologically reactive nitrogen (N) as a consequence of anthropogenic activities. This intended or unintended fertilization can have a wide-range of impacts on biotic communities and hence on soil respiration. Reduction in below-ground carbon (C) allocation induced by high N availability has been assumed to be a major mechanism determining the effects of N enrichment on soil respiration. In addition to increasing available N, however, N enrichment causes soil acidification, which may also affect root and microbial activities. The relative importance of increased N availability vs. soil acidification on soil respiration in natural ecosystems experiencing N enrichment is unclear. We conducted a 12-year N enrichment experiment and a 4-year complementary acid addition experiment in a semi-arid Inner Mongolian grassland. We found that N enrichment had contrasting effects on root and microbial respiration. N enrichment significantly increased root biomass, root N content and specific root respiration, thereby promoting root respiration. In contrast, N enrichment significantly suppressed microbial respiration likely by reducing total microbial biomass and changing the microbial community composition. The effect on root activities was due to both soil acidity and increased available N, while the effect on microbes primarily stemmed from soil acidity, which was further confirmed by results from the acid addition experiment. Our results indicate that soil acidification exerts a greater control than soil N availability on soil respiration in grasslands experiencing long-term N enrichment. These findings suggest that N-induced soil acidification should be included in predicting terrestrial ecosystem C balance under future N deposition scenarios.
Data from: Species-specific plant–soil feedbacks alter herbivore-induced gene expression and defense chemistry in Plantago lanceolata
Plants actively interact with antagonists and beneficial organisms occurring in the above- and belowground domains of terrestrial ecosystems. In the past decade, studies have focused on the role of plant–soil feedbacks (PSF) in a broad range of ecological processes. However, PSF and its legacy effects on plant defense traits, such as induction of defense-related genes and production of defensive secondary metabolites, have not received much attention. Here, we study soil legacy effects created by twelve common grassland plant species on the induction of four defense-related genes, involved in jasmonic acid signaling, related to chewing herbivore defense (LOX2, PPO7), and in salicylic acid signaling, related to pathogen defense (PR1 and PR2) in Plantago lanceolata in response to aboveground herbivory by Mamestra brassicae. We also assessed soil legacy and herbivory effects on the production of terpenoid defense compounds (the iridoid glycosides aucubin and catalpol) in P. lanceolata. Our results show that both soil legacy and herbivory influence phenotypes of P. lanceolata in terms of induction of Pl PPO7 and Pl LOX2, whereas the expression of Pl PR1 and Pl PR2-1 is not affected by soil legacies, nor by herbivory. We also find species-specific soil legacy effects on the production of aucubin. Moreover, P. lanceolata accumulates more catalpol when they are grown in soils conditioned by grass species. Our study highlights that PSF can influence aboveground plant–insect interactions through the impacts on plant defense traits and suggests that aboveground plant defense responses can be determined, at least partly, by plant-specific legacy effects induced by belowground organisms.
Data from: Stimulation of boreal tree seedling growth by wood-derived charcoal: effects of charcoal properties, seedling species and soil fertility
1. Fire is a major disturbance in many ecosystems worldwide including the boreal forest, and significant quantities of charcoal can be input to the soil from fire. Some recent studies have provided evidence that wood-derived charcoal produced by fire can significantly stimulate plant growth. However, the mechanisms by which charcoal affects plant growth are poorly understood, and little is known about how charcoal effects on plant growth are influenced by charcoal type, soil type and plant species. 2. Seedlings from four common boreal tree species, two evergreen gymnosperms and two deciduous angiosperms, were grown in each of two soils of contrasting nutrient availability amended with charcoal with each of nine charcoal types (each produced from wood from a different plant species) in a greenhouse experiment. We also measured several functional traits for each of the charcoal types, as well as of the wood used to prepare the charcoal. 3. Charcoal addition had either positive or neutral effects on seedling growth, with great variability among charcoal types. The charcoal types that had the strongest positive effect were those that had the greatest concentrations of phosphate and total phosphorus, and in some cases were derived from woods that had the highest total phosphorus concentration. Addition of charcoal on average had a stronger positive effect on plant growth on soil with the lowest levels of phosphate and total phosphorus. 4. Generally, charcoal derived from angiosperms stimulated seedling growth more than charcoal from gymnosperms. Further, angiosperm seedlings were on average stimulated more by charcoal addition than were gymnosperm seedlings. These results indicate that charcoal produced by fire could contribute to the initial dominance of angiosperm trees in post-fire succession, and suggests a possible feedback whereby charcoal from angiosperm tree species favors growth of angiosperm seedlings. 5. This study highlights a new means by which functional trait variation among tree species could potentially exert "after-life" effects in forested ecosystems through influencing traits (and notably phosphate concentrations) of the charcoal that they produce following wildfire, with potentially important consequences for plant growth and community and ecosystem properties during post-fire succession.
Data from: Relationships between plant traits, soil properties and carbon fluxes differ between monocultures and mixed communities in temperate grassland
1. The use of plant traits to predict ecosystem functions has been gaining growing attention. Aboveground plant traits, such as leaf nitrogen (N) content and specific leaf area (SLA), have been shown to strongly relate to ecosystem productivity, respiration, and nutrient cycling. Further, increasing plant functional trait diversity has been suggested as a possible mechanism to increase ecosystem carbon (C) storage. However, it is uncertain whether belowground plant traits can be predicted by aboveground traits, and if both above- and belowground traits can be used to predict soil properties and ecosystem-level functions. 2. Here, we used two adjacent field experiments in temperate grassland to investigate if above- and belowground plant traits are related, and whether relationships between plant traits, soil properties and ecosystem C fluxes (i.e., ecosystem respiration and net ecosystem exchange) measured in potted monocultures could be detected in mixed field communities. 3. We found that certain shoot traits (e.g., shoot N and C, and leaf dry matter content) were related to root traits (e.g., root N, root C:N, and root dry matter content) in monocultures, but such relationships were either weak or not detected in mixed communities. Some relationships between plant traits (i.e., shoot N, root N and/or shoot C:N) and soil properties (i.e., inorganic N availability and microbial community structure) were similar in monocultures and mixed communities, but they were more strongly linked to shoot traits in monocultures and root traits in mixed communities. Structural equation modelling showed that above- and belowground traits and soil properties improved predictions of ecosystem C fluxes in monocultures, but not in mixed communities on the basis of community-weighted mean traits. 4. Synthesis: Our results from a single grassland habitat detected relationships in monocultures between above- and belowground plant traits, and between plant traits, soil properties and ecosystem C fluxes. However, these relationships were generally weaker or different in mixed communities. Our results demonstrate that while plant traits can be used to predict certain soil properties and ecosystem functions in monocultures, they are less effective for predicting how changes in plant species composition influence ecosystem functions in mixed communities.
Data from: Plant functional groups regulate soil respiration responses to nitrogen addition and mowing over a decade
1. Nitrogen (N) deposition and land-use practice (e.g. mowing) could have profound effects on soil respiration. However, the changes in other ecosystem components, such as plant functional groups (PFGs), may control soil carbon (C) efflux response to long term global change. 2. A 10-year (2005-2014) field experiment was conducted with both N addition (10g N m-2 yr-1) and mowing (once a year) in a northern Chinese temperate grassland. We collected continuous data on soil respiration over 10 years accompanied with data on abiotic and biotic factors, and attempted to determine (i) the temporal variation in soil respiration and its responses to N addition and mowing, (ii) the regulation of soil respiration by PFGs and the underlying long-term mechanisms of control. 3. Soil respiration varied significantly among years. This was mainly caused by changes in precipitation pattern (e.g. frequency and distribution) during the growing-season rather than total rainfall. N addition significantly suppressed soil respiration by 10.4% whereas mowing stimulated it by 8.4% over the 10 years. The interaction of N addition with mowing had little effect on soil respiration. However, the significant effects of both N addition and mowing appeared only in the third year and thereafter, indicating the differences between long- and short-term responses. These long-term effects of N addition and mowing were mainly caused by changes in the PFGs of covers (e.g. grasses and forbs) and in soil pH rather than in soil microclimate. Forb-dominant patches had greater soil respiration than grass patches owing to their higher litter quality and photosynthetic capacity. 4. Our results highlight that shifts in aboveground plant community could play an important role in regulating soil respiration responses to N addition and mowing in the long-term. This is potentially important for improving our understanding of the link between above- and belowground ecological processes.
Data from: Fungal community reveals less dispersal limitation and potentially more connected network than that of bacteria in bamboo forest soils
A central aim of current microbial ecology research is to investigate the mechanisms shaping the assembly of soil microbial communities. Despite the importance of bacterial and fungal mediation of carbon cycling in forest ecosystems, knowledge concerning their distribution patterns and underlying mechanisms remains insufficient. Here, soils were sampled from six bamboo forests across the main planting area of Moso bamboo in southern China. The bacterial and fungal diversities were assessed by sequencing 16S rRNA and ITS gene amplicons, respectively, with an Illumina MiSeq. Based on structural equation modeling, dispersal limitation had strongest impact on bacterial beta diversity, while the mean annual precipitation had a smaller impact by directly or indirectly mediating the soil organic carbon density. However, only the mean annual temperature and precipitation played direct roles in fungal beta diversity. Moreover, the co-occurrence network analyses revealed a possibly much higher network connectivity in the fungal network than in the bacteria. With less dispersal limitation, stronger environmental selection, and a potentially more connected network, the fungal community had more important roles in the soil carbon metabolisms in bamboo forests. Fungal beta diversity and the clustering coefficient explained approximately 14.4% and 6.1% of the variation in the carbon metabolic profiles among sites, respectively, but that of bacteria only explained approximately 1.7% and 1.8%, respectively. This study explored soil microbial spatial patterns along with the underlying mechanisms of dispersal limitation, selection, and connectivity of ecological networks, thus providing novel insights into the study of the distinct functional traits of different microbial taxa.
Data from: Litter carbon and nutrient chemistry control the magnitude of soil priming effect
1. Plant litter inputs can promote the decomposition of soil organic matter (OM) through the priming effect (PE). However, whereas leaf litter chemistry has long been identified as the primary driver of litter decomposition within biomes worldwide, little is known about how litter chemical traits influence the occurrence and strength of the PE. 2. Here, we studied the effects of 15 co-occurring C3 leaf litters of contrasting chemistry on C4 soil respiration by analyzing changes in 13C natural abundance during early and later stages of litter decomposition (up to 125 days). 3. Besides an apparent PE of 16% in the first three days, soil C respiration was increased by 24% on average with leaf litter addition in the initial stage of decomposition (426 d) and by 8% at later stages (27125 d). Most interestingly, soil PE related well to initial litter chemistry and the dominant factors influencing the magnitude of the PE changed with decomposition stage. In the early stage of decomposition, litter leachate C content and litter hemicellulose concentration were positively correlated with the strength of the PE, whereas tannin concentration was negatively associated with soil PE. Together, tannin and hemicellulose explained half of the observed variation in the PE (R2 = 0.58). In the later phase of decomposition, lignin and lignin:N ratios were negatively related to the PE, whereas Ca, K and Mg concentrations were positively related to the PE; lignin alone gave the best prediction of the PE (R2 = 0.58) at later decomposition stages. 4. Our findings provide evidence that the magnitude and direction of the PE is influenced by the chemistry of organic matter inputs and suggest that, as decomposition proceeds differently among litter of contrasting chemistry, litters can also have variable effect on soil PE through time. The predictive power of litter chemical traits on soil PE opens new perspectives for improving our mechanistic understanding of soil PE and improving our abilities to model soil C dynamics at variable scales.
Data from: Biotransformation of chlorothalonil by strain Stenotrophomonas acidaminiphila BJ1 isolated from farmland soil
The chlorothalonil is a widely used fungicide while the contamination of soil and water environments by this chemical causes potential threats to the biodiversity. Given the metabolic potential of soil microorganisms, there is a need for developing microbiological approaches to degrade persistent compounds, such as chlorothalonil, in the contaminated sites. Here in this study, we isolated a bacterial strain (namely, BJ1) capable of degrading chlorothalonil from a chlorothalonil-contaminated farmland soil in the Shandong Province, China. Using 16S rDNA gene sequencing, morphological and biological characteristics, we identified the strain BJ1 as Stenotrophomonas acidaminiphila. The strain BJ1 utilizes chlorothalonil as a sole carbon source. At initial concentrations of 50, 100, 200, 300 mg l-1, it degraded 91.5%, 89.4%, 86.5 and 83.5% of chlorothalonil after 96 h of inoculation under optimum conditions (30 °C and pH 7.0), respectively. Two metabolites, methyl-2, 5, 6-trichloro-3-cyano-4-methoxy-benzoate and methyl-3- cyano-2, 4, 5, 6-tetrachlorobenzoate, were detected and identified based on HPLC-MS analysis, which suggests that the strain BJ1 metabolized chlorothalonil through the hydroxylation of chloro-group and hydration of cyano-group. The results of this study highlight the great potential for this bacterium to be used in chlorothalonil pollution remediation.
Data from: Integrating quantitative morphological and qualitative molecular methods to analyze soil nematode community responses to plant range expansion
1. Belowground nematodes are important for soil functioning, as they are ubiquitous and operate at various trophic levels in the soil food web. However, morphological nematode community analysis is time consuming and requires ample training. qPCR-based nematode identification techniques are well available, but high throughput sequencing (HTS) might be more suitable for non-targeted nematode community analysis. 2. We compared effectiveness of qPCR and HTS-based approaches with morphological nematode identification while examining how climate warming-induced plant range expansion may influence belowground nematode assemblages. We extracted nematodes from soil of Centaurea stoebe and C. jacea populations in Slovenia, where both plant species are native, and Germany, where C. stoebe is range expander and C. jacea is native. Half of each nematode sample was identified morphologically and the other half was analysed using targeted qPCR and a novel HTS approach. 3. HTS produced the highest taxonomic resolution of the nematode community. Nematode taxa abundances correlated between the methods. Therefore, especially relative HTS and relative morphological data revealed nearly identical ecological patterns. All methods showed lower numbers of plant feeding nematodes in rhizosphere soils of C. stoebe compared to C. jacea. However, a profound difference was observed between absolute and relative abundance data; both sampling origin and plant species affected relative abundances of bacterivorous nematodes, whereas there was no effect on absolute abundances. 4. Taken together, as HTS correlates with relative analyses of soil nematode communities, while providing highest taxonomic resolution and sample throughput, we propose a combination of HTS with microscopic counting to supplement important quantitative data on soil nematode communities. This provides the most cost-effective, in-depths methodology to study soil nematode community responses to changes in the environment. This methodology will also be applicable to nematode analyses in aquatic systems.
Data from: A replicated climate change field experiment reveals rapid evolutionary response in an ecologically important soil invertebrate
Whether species can respond evolutionarily to current climate change is crucial for the persistence of many species. Yet, very few studies have examined genetic responses to climate change in manipulated experiments carried out in natural field conditions. We examined the evolutionary response to climate change in a common annelid worm using a controlled replicated experiment where climatic conditions were manipulated in a natural setting. Analyzing the transcribed genome of 15 local populations, we found that about 12% of the genetic polymorphisms exhibit differences in allele frequencies associated to changes in soil temperature and soil moisture. This shows an evolutionary response to realistic climate change happening over short-time scale, and calls for incorporating evolution into models predicting future response of species to climate change. It also shows that designed climate change experiments coupled with genome sequencing offer great potential to test for the occurrence (or lack) of an evolutionary response.
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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.