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174 results for “soil microbial community”
Soil and litter chemistry, soil microbial communities and litter decomposition from tropical forest and oil palm
<b>Description: </b><p>A study examining the interactions between soil chemistry, litter chemistry and soil microbial decomposers as controls on rates of litter decomposition across a tropical land use disturbance gradient. Co-located soil and litter samples were collected from old growth forest, moderately logged forest, heavily logged forest and oil palm plantations. Soil and litter were chemically characterised and soil bacterial and fungal community composition and abundance were measured. These were then combined in fully factorial ex-situ microcosms and measured litter decomposition rates at 3 time points during different stages of decomposition.</p><p><b>Project: </b>This dataset was collected as part of the following SAFE research project: <a href="https://www.safeproject.net/projects/project_view/124"><b>Biodiversity and land-use impacts on tropical ecosystem function (BALI): Quantifying biogeochemistry across forest disturbance gradients in Sabah</b></a></p><p><b>Funding: </b>These data were collected as part of research funded by: </p><ul><li>UK NERC-funded Biodiversity And Land-use Impacts on Tropical Ecosystem Function (BALI) consortium (Standard grant, NE/K016377/1)</li></ul><p>This dataset is released under the CC-BY 4.0 licence, requiring that you cite the dataset in any outputs, but has the additional condition that you acknowledge the contribution of these funders in any outputs.</p><p></p><p><b>Permits: </b>These data were collected under permit from the following authorities:</p><ul><li>Sabah Biodiversity Centre (Research licence JKM/MBS.1000-2/2 JLD.5 (20))</li><li>Sabah Biodiversity Centre (Export licence JKM/MBS.1000-2/3 JLD.2 (70))</li></ul><p></p><p><b>XML metadata: </b>GEMINI compliant metadata for this dataset is available <a href="https://www.safeproject.net/datasets/xml_metadata?id=3929632">here</a></p><p><b>Files: </b>This consists of 1 file: SAFE_Dataset.xlsx</p><p><b>SAFE_Dataset.xlsx</b></p><p>This file contains dataset metadata and 5 data tables:</p><ol><li><p><b>Soil_Properties</b> (described in worksheet Soil_Properties)</p><p>Description: Basic measured soil properties</p><p>Number of fields: 9</p><p>Number of data rows: 20</p><p>Fields: </p><ul><li><b>Plot</b>: Plot name corresponding to the GEM Carbon plot where soils were sampled (Field type: id)</li><li><b>Plot_ID</b>: Plot ID indicating land use as referenced in the Frontiers in forests and global change publication "Soil microbial community and litter quality controls on decomposition across a tropical forest disturbance gradient" (Field type: categorical)</li><li><b>location_name</b>: Name of subplot where soils were collected (Field type: location)</li><li><b>gravimetric moisture content</b>: Soil moisture content at the time of sample collection (Field type: numeric)</li><li><b>soil_pH</b>: Soil pH measured on fresh soils (Field type: numeric)</li><li><b>soil_N</b>: Total soil Nitrogen (Field type: numeric)</li><li><b>soil_C</b>: Total soil Carbon (Field type: numeric)</li><li><b>soil_C.N</b>: Soil carbon to nitrogen ratio (Field type: numeric)</li><li><b>soil_P</b>: soil inorganic phosphorus (Field type: numeric)</li></ul></li><li><p><b>Litter_Chemistry</b> (described in worksheet Litter_Chemistry)</p><p>Description: Litter chemistry data of mixed forest floor litter, collected, sorted to remove humified material, woody debris and dried</p><p>Number of fields: 20</p><p>Number of data rows: 40</p><p>Fields: </p><ul><li><b>Plot</b>: Plot name corresponding to the GEM Carbon plot where soils were sampled (Field type: id)</li><li><b>Plot_ID</b>: Plot ID indicating land use as referenced in the Frontiers in forests and global change publication "Soil microbial community and litter quality controls on decomposition across a tropical forest disturbance gradient" (Field type: categorical)</li><li><b>location_name</b>: Name of subplot where soils were collected (Field type: location)</li><li><b>Pretreatment</b>: Whether the litter sample was sterilised by autoclaving or not (Field type: categorical)</li><li><b>leaf_K</b>: leaf potassium concentration (Field type: numeric)</li><li><b>leaf_Ca</b>: leaf Calcium concentration (Field type: numeric)</li><li><b>leaf_Mg</b>: leaf Magnesium concentration (Field type: numeric)</li><li><b>leaf_Al</b>: leaf aluminium concentration (Field type: numeric)</li><li><b>leaf_P</b>: leaf phosphorus concentrations (Field type: numeric)</li><li><b>solubles</b>: leaf soluble cell content (Field type: numeric)</li><li><b>hem_pro_cel_lig_rec</b>: leaf hemicellulose, proteins, cellulose, lignin and recalcitrant fibres (Field type: numeric)</li><li><b>hem_pro</b>: leaf hemicellulose and proteins (Field type: numeric)</li><li><b>cel_lig_rec</b>: leaf cellulose, lignin and recalcitrant fibres (Field type: numeric)</li><li><b>cel</b>: leaf cellulose (Field type: numeric)</li><li><b>lig_rec</b>: leaf lignin and recalcitrants (Field type: numeric)</li><li><b>leaf_N</b>: leaf nitrogen concentration (Field type: numeric)</li><li><b>leaf_C</b>: leaf carbon concentration (Field type: numeric)</li><li><b>c.n</b>: leaf carbon to nitrogen ration (Field type: numeric)</li><li><b>d13c</b>: leaf carbon stable isotope ratio (Field type: numeric)</li><li><b>d15n</b>: leaf nitrogen stable isotope ratio (Field type: numeric)</li></ul></li><li><p><b>PLFA_Concentrations</b> (described in worksheet PLFA_Concentrations)</p><p>Description: Phospolipid Fatty Acid (PLFA) concentrations as biomarkers of soil bacteria and fungi. Extracted from freeze dried soils prior to the microcosm experiment</p><p>Number of fields: 10</p><p>Number of data rows: 20</p><p>Fields: </p><ul><li><b>Plot</b>: Plot name corresponding to the GEM Carbon plot where soils were sampled (Field type: id)</li><li><b>Plot_ID</b>: Plot ID indicating land use as referenced in the Frontiers in forests and global change publication "Soil microbial community and litter quality controls on decomposition across a tropical forest disturbance gradient" (Field type: categorical)</li><li><b>location_name</b>: Name of subplot where soils were collected (Field type: location)</li><li><b>Total_PLFA</b>: Total PLFA concentrations extracted from soil samples (Field type: numeric)</li><li><b>Fungal_PLFA</b>: Fungal PLFA biomarker concentrations extracted from soils (Field type: numeric)</li><li><b>Bacteria_PLFA</b>: Bacteria PLFA biomarkers extracted from soils (Field type: numeric)</li><li><b>Fungal:Bacteria</b>: Ratio of fungal to bacteria PLFAs (Field type: numeric)</li><li><b>Gram_Pos_PLFA</b>: Gram Positive PLFA Biomarker concentrations extracted from soil (Field type: numeric)</li><li><b>Gram_Neg_PLFA</b>: Gram Negative PLFA Biomarker concentrations extracted from soil (Field type: numeric)</li><li><b>GramPos:GramNeg</b>: Gram positive to Gram negative PLFA ratios (Field type: numeric)</li></ul></li><li><p><b>Soil_Microbial_Communities</b> (described in worksheet Soil_Microbial_Communities)</p><p>Description: Summary diversity statistics from bacterial 16S and fungal ITS biomarker microbial sequencing. DNA extracted from soils prior to microcosm experiment</p><p>Number of fields: 9</p><p>Number of data rows: 20</p><p>Fields: </p><ul><li><b>Plot</b>: Plot name corresponding to the GEM Carbon plot where soils were sampled (Field type: id)</li><li><b>Plot_ID</b>: Plot ID indicating land use as referenced in the Frontiers in forests and global change publication "Soil microbial community and litter quality controls on decomposition across a tropical forest disturbance gradient" (Field type: categorical)</li><li><b>location_name</b>: Name of subplot where soils were collected (Field type: location)</li><li><b>Bacteria_Richness</b>: Number of observed bacterial taxa from sequencing of 16S marker genes from soil samples (Field type: numeric)</li><li><b>Bacteria_Shannon</b>: Bacterial Shannon diversity from 16S Marker gene sequencing (Field type: numeric)</li><li><b>Fungal_Richness</b>: Number of observed fungal taxa from sequencing of 16S marker genes from soil samples (Field type: numeric)</li><li><b>Fungal_Shannon</b>: Fungal Shannon diversity from 16S Marker gene sequencing (Field type: numeric)</li><li><b>Saprotrophic_Fungal_Richness</b>: Number of observed saprotrophic fungal taxa from sequencing of 16S marker genes from soil samples (Field type: numeric)</li><li><b>Saprotrophic_Fungal_Shannon</b>: Saprotrophic Fungal Shannon diversity from 16S Marker gene sequencing (Field type: numeric)</li></ul></li><li><p><b>Ex_Situ_Litter_Decomposition</b> (described in worksheet Ex_Situ_Litter_Decomposition)</p><p>Description: Fully factorial litter decomposition experiment. 16 unique soil and litter combinations (4x4) were incubated in petri dishes at constant temperature and moisture and mass loss measured after 31, 105 and 398 days.</p><p>Number of fields: 8</p><p>Number of data rows: 240</p><p>Fields: </p><ul><li><b>location_name</b>: Name of subplot where soils were collected (Field type: location)</li><li><b>Soil_ID</b>: Soil ID indicating which land use soil was collected from (Field type: categorical)</li><li><b>Litter_Location</b>: Location of which GEM carbon plot the litter was collected from. Litter was collected from the 5 carbon subplots as per soil collection and homogenised into one composite sample per carbon plot (Field type: location)</li><li><b>Litter_ID</b>: Litter ID indicating which land use litter was collected from (Field type: categorical)</li><li><b>Experimental_Block</b>: Which experimental block the microcosm was assigned to. N= 5 (Field type: replicate)</li><li><b>Timepoint</b>: At what timepoint the litter was harvested from each microcosm (Field type: categorical)</li><li><b>Mass_Loss</b>: The mass loss of litter relative to the starting mass of 1g (Field type: numeric)</li><li><b>home_away</b>: Descriptor for whether the soil and litter combination in microcosm (Field type: categorical)</li></ul></li></ol><p><b>Date range: </b>2014-10-01 to 2018-09-01</p><p><b>Latitudinal extent: </b>4.6402 to 4.9539</p><p><b>Longitudinal extent: </b>117.4518 to 117.7942</p>
Data from: Spatial patterning of soil microbial communities created by fungus-farming termites
<p><span><span><span><span><span><span><span><span><span><span><span>Spatially overdispersed mounds of fungus-farming termites (Macrotermitinae) are hotspots of nutrient availability and primary productivity in tropical savannas, creating spatial heterogeneity in communities and ecosystem functions. These termites influence the local availability of nutrients in part by redistributing nutrients across the landscape, but the links between termite ecosystem engineering and the soil microbes that are the metabolic agents of nutrient cycling are little understood. We used DNA metabarcoding of soils from <i>Odontotermes montanus</i> mounds to examine the influence of termites on soil microbial communities in a semi-arid Kenyan savanna. We found that bacterial and fungal communities were compositionally distinct in termite-mound topsoils relative to the surrounding savanna, and that bacterial communities were more diverse on mounds. The higher microbial alpha and beta diversity associated with mounds created striking spatial patterning in microbial community composition, and boosted landscape-scale microbial richness and diversity. Selected enzyme assays revealed consistent differences in potential enzymatic activity, suggesting links between termite-induced heterogeneity in microbial community composition and the spatial distribution of ecosystem functions. We conducted a large-scale field experiment in which we attempted to simulate termites' effects on microbes by fertilizing mound-sized patches; this altered both bacterial and fungal communities, but in a different way than natural mounds. Elevated levels of inorganic nitrogen, phosphorus, and potassium may help to explain the distinctive fungal communities in termite-mound soils, but cannot account for the distinctive bacterial communities associated with mounds.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Plant selection initiates alternative successional trajectories in the soil microbial community after disturbance
Because interactions between plants and microbial organisms can influence species diversity and rates of nutrient cycling, how plants shape microbial communities is fundamental to understanding the structure of ecosystems. Despite this, the spatial and temporal scales over which plants influence microbial communities is poorly understood, particularly whether past abiotic or biotic legacies strongly constrain microbial community development. We examined biogeochemical cycling and microbial community structure in a coastal landscape where historical patterns of vegetation transition after a large fire in 1995 are well known, allowing us to account for past abiotic and biotic conditions. We found that alternative states in microbial community structure and ecosystem processes emerged under different plant species, regardless of past conditions. Greenhouse studies further demonstrated that these differences arise from direct plant selection of microbes, with selection stronger in roots compared with soils, especially for bacteria. Correlation of microbial community structure with seedling growth rates was also stronger for fungi compared to bacteria. Despite these effects, minimal overlap between seedling and field microbial communities indicates that the effects of initial plant selection are not stable, rather plant selection initiated alternative successional trajectories after the fire. Using data from a guild where we have abundant natural history information - ectomycorrhizal fungi - we show that greenhouse communities are dominated by ruderal taxa that are also common in the field after the fire, and that these ruderal fungi strongly alter spatial patterns in plant-soil feedback, enabling invasion and transformation of soils previously occupied by heterospecific plants, thus potentially acting as keystone mutualists.
Data from: Do temperate tree species diversity and identity influence soil microbial community function and composition?
Studies of biodiversity-ecosystem function in treed ecosystems have generally focused on aboveground functions. The present study investigates inter-trophic links between tree diversity and soil microbial community function and composition.We examined how microbial communities in surface mineral soil responded to experimental gradients of tree species richness (SR), functional diversity (FD), community-weighted mean trait value (CWM) and tree identity. The site was a 4-yr-old common garden experiment near Montreal, Canada, consisting of deciduous and evergreen tree species mixtures. Microbial community composition, community-level physiological profiles (CLPP) and respiration were evaluated using phospholipid fatty acid (PLFA) analysis and the MicroRespTM system, respectively. The relationship between tree species richness and glucose induced respiration (GIR), basal respiration (BR), metabolic quotient (qCO2) followed a positive but saturating shape. Microbial communities associated with species mixtures were more active (basal respiration (BR)), with higher biomass (glucose induced respiration (GIR)), and used a greater number of carbon sources than monocultures. Communities associated with deciduous tree species used a greater number of carbon sources than those associated with evergreen species, suggesting a greater soil carbon storage capacity. There were no differences in microbial composition (PLFA) between monocultures and SR mixtures. The FD and the CWM of several functional traits affected both BR and GIR. In general, the CWM of traits had stronger effects than did FD, suggesting that certain traits of dominant species have more effect on ecosystem processes than does FD. Both the functions of GIR and BR were positively related to aboveground tree community productivity. Both tree diversity (SR) and identity (species and functional identity – leaf habit) affected soil microbial community respiration, biomass and composition. For the first time, we identified functional traits related to life history strategy, as well as root traits that influence another trophic level, soil microbial community function, via effects on BR and GIR.
Fertilization can accelerate the pace of soil microbial community response to rest-grazing duration in the Three-river Source Region of China
<div> <div> <p><strong><span>Objectives</span></strong> </p> <p><span>Overgrazing leads to grassland degradation and productivity decline. Rest-grazing during the regreen-up period can quickly restore grassland and fertilization is a common restoration measure. Meanwhile, soil microorganisms are more sensitive indicators. Therefore, the experiment of rest-grazing time and fertilization was carried out to explore the response of soil microorganisms to rest-grazing time and fertilization measures. </span></p> <p><span><strong>Methods</strong> </span></p> <p><span>A field control experiment with rest-grazing time and fertilization as factors was conducted from the time when grass returned to green till the livestock moved to the summer pasture in Dawu Town of Maqin County.</span> <span>The primary treatment we established was the five</span> <span>rest-grazing times, including rest-grazing times of 20 days, 30 days, 40 days, 50 days, and traditional grazing was used as a check group. At the same time, the secondary treatment was nitrogen addition of 300 kg·hm<sup>-2</sup> in each primary treatment. </span></p> <p><span><strong>Results</strong> </span></p> <p><span>The results showed that: the total phospholipid fatty acid (total PLFA), actinomyces (Act) and arbuscular </span><span>mycorrhizal fungi (AMF) showed an ever-increasing biomass with the increase of rest-grazing time and the highest was at 50 days of rest-grazing, and they were all significantly higher than CK. In addition, soil microbial biomass carbon-nitrogen ratio (MBC/MBN)</span> <span>had a great influence on the change of microbial community. Applying nitrogen fertilizer can increase the maximum value of biomass of all PLFA groups and the biomass of all PLFA groups changed in an "inverted V" shape with the increase of rest-grazing time. Besides, </span><span>instead of MBC/MBN, NO<sub>3</sub><sup>-</sup>-N</span><span> was positively affected by the biomass of</span> <span>all PLFA groups, which actively regulated the trend of microbial functions. </span></p> <p><span><strong>Conclusions</strong> </span></p> <p><span>The longer rest-grazing time is more conducive to the biomass of all PLFA groups. However, applying nitrogen fertilizer could break this pattern, namely, the 30d rest-grazing would</span> <span>be beneficial to the biomass of all PLFA groups. These findings provide key information that rest-grazing during the regreen-up period is beneficial to all PLFA groups and </span><span>fertilization could change the response of microorganisms to rest-grazing</span><span>, which provides reference measures for the restoration of degraded alpine meadows.</span></p> </div> </div>
Data from: Uniqueness of tree stand composition and soil microbial communities are related across urban spruce-dominated forests
<p>The dataset contains data obtained from urban spruce-dominated forests in southern Finland where we have measured tree stand composition, forest management history, soil chemical properties, and soil microbial communities. Data files include (1) microbial OTU tables describing microbial community composition (sequence read counts of Operational Taxonomic Units) across the study plots, (2) taxonomic assignments and other metadata related to OTUs, and (3) measured and calculated variables describing the characteristics of sites and their microbial assemblages (site metadata).</p>
Data for: Male, female and mixed-sex poplar plantations support divergent soil microbial communities
<p>Mixed-species forests are often more productive than monocultures because of a lower niche overlap and higher taxonomic and functional diversity of soil microbial communities. Males and females of dioecious plants have sex-specific adaptations to diverse habitats. The potential of using sexual differences in establishing more diverse poplar plantations has not been explored in degraded areas. We conducted a series of greenhouse and field experiments to investigate how belowground competition, soil microbial communities and seasonal variation nitrogen content differ among female, male and mixed-sex <em>Populus cathayana</em> plantations. In the greenhouse experiment, female neighbors suppressed the growth of males under optimal nitrogen conditions. However, male neighbors enhanced δ<sup>15</sup>N of females under inter-sexual competition. In the field, the root length density, root area density and biomass of fine roots were lower in female plantations than in male or mixed-sex plantations. Bacterial networks of female, male and mixed-sex plantations were characterized by different composition of hub nodes, including connectors, module and network hubs. The sex composition of plantations altered bacterial and fungal community structures according to Bray-Curtis distances, with 44% and 65% of variance explained by the root biomass, respectively. The total soil nitrogen content of mixed-sex plantation was higher than that in female plantation in spring and summer. The mixed-sex plantation also had a higher β-1,4-N-acetyl-glucosaminidase activity in summer and a higher nitrification rate in autumn than the other two plantations. The seasonal soil N content, nitrification rate and root distribution traits demonstrated spatiotemporal niche separation in the mixed-sex plantation. We argue that a strong female-female competition and limited nitrogen content could strongly impede plant growth and reduce the resistance of monosex plantations to climate change and the mixed-sex plantations constitutes a promising way to restore degraded land.</p>
Data from: Relationships between rhizosphere microbial communities, soil abiotic properties and root trait variation within a pine species
<p>Rhizosphere microbes play important roles in plant performance and ecosystem functioning. It is becoming increasingly clear that rhizosphere communities vary with soil properties and variation in root traits among plant species. However, less is known about whether and how variation in root traits within plant species influences the rhizosphere microbial communities.</p> <p>We evaluated the intraspecific root traits variation and explored their associations with bacterial and fungal communities in rhizosphere by focusing on an ectomycorrhizal tree<em> </em>species, i.e., <em>Pinus massoniana</em>, in 22 sites in subtropical China.</p> <p>The first dimension of the principal component analysis on root traits revealed evidence for the 'conservation' gradient of the root economics space. Overall, root traits explained more variation in fungal communities than in bacterial communities in the rhizosphere. Functional composition of rhizosphere microbial communities changed significantly along the 'conservation' gradient, with fast-growing copiotrophic bacteria and symbiotic ectomycorrhizal fungi were significantly enriched on the 'acquisition' side, while slow-growing oligotrophic bacteria were significantly enriched on the 'conservation' side of the gradient.</p> <p><strong><em>Synthesis</em></strong>: Our study demonstrates that intraspecific variation in plant roots significantly influence rhizosphere microbial communities, which in turn can influence plant nutrition and therefore plant performance within the community.</p>
Data for A first-year melon/cowpea intercropping system improves soil nutrients and changes the soil microbial community
<p>A first-year melon/cowpea intercropping system improves soil nutrients and changes the soil microbial community data</p>
Plastic mulch film residues in agriculture: impact on soil suppressiveness, plant growth, and microbial communities
<p>Plastic mulch film residues have been accumulating in agricultural soils for decades, but so far, little is known about its consequences on soil microbial communities and functions. Here, we tested the effects of plastic residues of low-density polyethylene and biodegradable mulch films on soil suppressiveness and microbial community composition. We investigated how plastic residues in a Fusarium culmorum suppressive soil affect the level of disease suppressiveness, plant biomass, nutrient status, and microbial communities in rhizosphere using a controlled pot experiment. The addition of 1% plastic residues to the suppressive soil did not affect the level of suppression and the disease symptoms index. However, we did find that plant biomasses decreased, and that plant nutrient status changed in the presence of plastic residues. No significant changes in bacterial and fungal rhizosphere communities were observed. Nonetheless, bacterial and fungal communities closely attached to the plastisphere were very different from the rhizosphere communities with overrepresentation of potential plant pathogens. The plastisphere revealed a high abundance of specific bacterial phyla (Actinobacteria, Bacteroidetes, and Proteobacteria) and fungal genera (Rhizoctonia and Arthrobotrys). Our work revealed new insights and raises emerging questions for further studies on the impact of microplastics on the agroecosystems.</p>
Soil microbial diversity and community composition during conversion from conventional to organic agriculture
<p>It is generally assumed that the dependence of conventional agriculture on artificial fertilizers and pesticides strongly impacts the environment, while organic agriculture relying more on microbial functioning may mitigate these impacts. However, it is not well known how microbial diversity and community composition change in conventionally managed farmers' fields that are converted to organic management. Here, we sequenced bacterial and fungal communities of 34 organic fields on sand and marine clay soils in a time series (chronosequence) covering 25 years of conversion. Nearby conventional fields were used as references. We found that community composition of bacteria and fungi differed between organic and conventionally managed fields. In the organic fields, fungal diversity increased with time since conversion. However, this effect disappeared when the conventional paired fields were included. There was a relationship between pH and soil organic matter content and the diversity and community composition of bacteria and fungi. In marine clay soils, when time since organic management increased, fungal communities in organic fields became more dissimilar to those in conventional fields. We conclude that conversion to organic management in these Dutch farmers' fields did not increase microbial community diversity. Instead, we observed that in organic fields in marine clay when time since conversion increased soil fungal community composition became progressively dissimilar from that in conventional fields. Our results also showed that the paired sampling approach of organic and conventional fields was essential in order to control for environmental variation that was otherwise unaccounted for.</p>
Data and metadata of soil microbial community structure, enzyme activities, functional genes and earthworms derived from H2020 Diverfarming project
<p>Soil data and metadata of soil microbial community structure, enzyme activities (dehydrogenase, β-glucosidase, leucine-aminopeptidase, alkaline phosphatase and arylsusfatase activities), N functional genes and earthworms from the different cases studies and long terms from WP4 "Impact of crop diversification on biodiversity", derived from H2020 Diverfarming project. The main objective of workpackage is to provide a scientific understanding of the link between diversified cropping systems, above- and belowground biodiversity, and the resulting ecosystem services provided by soil microorganisms, soil invertebrates and vegetation in agro-ecosystems. Soil organisms contribute to all biogeochemical cycles, Soil organic matter mineralization and stabilization, shape soil structure and have associations with plant species promoting growth and development. http://www.diverfarming.eu.</p>
Biochar and nitrogen fertilizer promote rice yield by altering soil enzyme activity and microbial community structure
<p><span>Biochar can significantly change soil properties and improve soil quality.</span> <span>However, the effects of long-term combined application of biochar (B) and nitrogen (N) fertilizer on relationships between soil enzyme activity, microbial community structure and crop yield are still obscure. We characterized these relationships in a long-term (8 years) field experiment with rice, two biochar rates of 0 and 13.5 t ha<sup>-1</sup> year<sup>-1</sup> (B0 and B) and two N fertilizer rates of 0 and 300 kg N ha<sup>-1</sup> year<sup>-1</sup> (N0 and N).</span><span> The repeated, long-term combined applications of biochar and N fertilizer significantly increased microbial biomass carbon and nitrogen (MBC and MBN), but biochar decreased the abundance of total bacteria, fungi, actinomycetes, Gram-positive and Gram-negative bacteria as well as the amount of total phospholipid fatty acids. </span><span>The activity of leucine aminopeptidase (LAP) </span><span>decreased significantly in the biochar-amended and N fertilized treatment, but</span><span> the LAP activity either remained unchanged or increased with biochar amendment at N0. The relative abundance of bacterial phylum <em>Chloroflexi</em> was increased in the combined biochar and N fertilizer treatment. The changes in soil organic matter and the activity of α-1,4-xylosidase were the major properties influencing soil bacterial community composition, whereas the structure of fungal community was governed by MBC, MBN and LAP activity. In addition, long-term biochar and N fertilizer applied together significantly increased rice yield (more than biochar and nitrogen fertilizer applied alone). Yield</span> <span>was significantly positively correlated with LAP activity, but significantly negatively correlated with the relative abundance of Chloroflexi. In conclusion, long-term biochar and nitrogen fertilizer applications increased rice yield, which was associated with altered soil microbial community and enhanced activity of some enzymes.</span></p>
Data from: Earthworms promote crop growth by enhancing the connections among soil microbial communities
<p>Earthworms benefit plant growth and play a vital role in shaping soil microbial communities. However, how earthworms modify the soil microorganisms and thus affect plant growth is still unclear. Although fertilizers alter the assembly of microbial communities, further investigations are required to test the effect of fertilizer type on the relationship between earthworms, soil microbial communities, and plants. We evaluated the role of earthworms in soil microorganisms and maize plant growth characteristics under organic or chemical fertilizers in field and greenhouse experiments. We explored the relationships between earthworms, soil microbial community, and plant growth under different fertilizer types. We found that the presence of earthworms promoted plant growth, increased the amount of plant root exudates, and enhanced the connections between rhizosphere bacterial, fungal, and protist communities. Both earthworms and fertilizer application significantly changed the structure of soil bacterial, fungal, and protist communities. The complexity of the soil microbial community network increased under organic, compared to chemical fertilizer application. The greenhouse experiment showed that the effect of earthworms on plant growth was weakened when maize plants were grown in sterilized soil under organic or chemical fertilizers.</p> <p><em>Synthesis and applications:</em> Our study provides solid evidence that earthworms largely depend on soil microorganisms for their effects on plants under the application of different fertilizer conditions. This may provide new insights into reducing the amounts of fertilizer used by enhancing the role of earthworms and soil microorganisms.</p>
Slope position affects growth and allometry of the endangered conifer Calocedrus macrolepis by mediating soil properties and microbial communities
<p><strong>Premise:</strong><em> </em>The allometric relationships among growth traits are highly relevant for a tree's fitness, however, the mechanism of how the slope position affects the plant growth and allometry remains poorly understood, hindering our understanding of the variation in allometry of trees along slope position in mountainous areas.</p> <p><strong>Methods:</strong> A typical slope of <em>Calocedrus macrolepis</em> plantation in southwest China was chosen to measure growth traits and their allometric relationships. In addition, spatial variations in soil properties and microbial communities were also investigated.</p> <p><strong>Results:</strong><em> </em>Slope position altered the allometric growth pattern with the larger allometric exponents of the tree height, diameter and wood volume relative to the crown size and height under the branch for the downslope. Additionally, most of soil nutrients, microbial diversity and abundances were greater at mesoslope and downslope, especially at the surface soil layer. The relative abundance both in Chloroflexi and Actinobacteria differed significantly among slope positions, while fungal dominant phyla abundances varied little across slope positions, indicating that bacterial community was more sensitive to slope position than fungal community. The growth traits and allometry were affected by the slope position, which is mainly caused by the variations of soil properties and microbial communities, and bacteria were more important than fungi in their relationships to growth traits and allometry.</p> <p><strong>Conclusions:</strong> Together, results emphasized that slope position indirectly influences the growth traits and allometry of <em>C. macrolepis</em> by regulating soil nutrients and microbial communities, which will provide important theoretical basis for the plantation management of <em>C. macrolepis</em>.</p>
Tundra soil viruses mediate the responses of microbial communities to climate warming
<p>The dataset of this study contains the information of metagenomic data, environmental factors, GeoChip data, vOTUs table, mOTUs tables, and the viral and microbial sequences.</p> <p>If this study dataset is useful, please cite: Ji M, et al. Tundra Soil Viruses Mediate Responses of Microbial Communities to Climate Warming[J]. Mbio, 2023: e03009-22.</p> <p>For any other dataset/analysis inquiries, please contact me: jimengzhi@mail.sdu.edu.cn.</p>
Soil microbial community shifts explain habitat heterogeneity in two Haloxylon species from a nutrient perspective
<p><span><em>Haloxylon</em> <em>ammodendron</em> and <em>Haloxylon</em> <em>persicum</em> (as sister taxa) are dominant shrubs in the Gurbantunggut Desert. The former grows in inter-dune lowlands while the latter in sand dunes. However, little information is available regarding the possible role of soil microorganisms in their habitat heterogeneity from a nutrient perspective in deserts</span><span>. </span><span>Rhizosphere is the interface of plant-microbe-soil interactions and f</span><span>ertile islands usually occur around the roots of desert shrubs. </span><span>Given this, </span><span>we applied quantitative real-time PCR combined with MiSeq amplicon sequencing to compare their rhizosphere effects on microbial abundance and community structures at three soil depths (0–20, 20</span><span>–</span><span>40, and 40</span><span>–</span><span>60 cm). The rhizosphere effects on microbial activity (respiration) and soil properties had also been estimated. The rhizospheres of both shrubs exerted significant positive effects on microbial activity and abundance (e.g. eukarya, bacteria and </span><span>nitrogen-fixing microbes</span><span>). The rhizosphere effect of <em>H</em>. <em>ammodendron</em> on microbial activity and abundance of bacteria and </span><span>nitrogen-fixing microbes</span><span> was greater than that of <em>H</em>. <em>persicum</em>. However, </span><span>the fertile island effect of </span><span><em>H</em>. <em>ammodendron</em></span><span> was weaker than that of </span><span><em>H</em>. <em>persicum</em></span><span>.</span><span> Moreover, t</span><span>here existed distinct differences in microbial community structure between the two rhizosphere soils. </span><span>Soil-available nitrogen, especially nitrate nitrogen was shown to be a</span><span> driver</span> <span>of microbial community </span><span>differentiation </span><span>among rhizosphere and non-rhizosphere soils in the desert.</span><span> In general, the rhizosphere of <em>H</em>. <em>ammodendron</em> recruited more </span><span>copiotrophs (e.g. </span><span>Firmicutes, Bacteroidetes and Proteobacteria), </span><span>nitrogen-fixing microbes and </span><span>ammonia-oxidizing bacteria, and with stronger microbial activities. This helps it maintain a competitive advantage in relatively nutrient-rich lowlands. <em>H</em>. <em>persicum</em> relied more on </span><span>fungi, actinomycetes, archaea</span><span> (including </span><span>ammonia-oxidizing archaea</span><span>) </span><span>and</span><span> eukarya, with higher nutrient use efficiency, which help it adapt to the harsher dune crests. This study provides insights into the microbial mechanisms of habitat heterogeneity in two <em>Haloxylon</em> species in the poor desert soil. </span></p>
Data for: Local conditions matter: Minimal and variable effects of soil disturbance on microbial communities and functions in European vineyards
<p>Soil tillage or herbicide applications are commonly us<span>ed in agriculture for weed control. These measures may also represent a disturbance for soil microbial communities and their functions. However, the generality of response patterns of microbial communities and functions to disturbance have rarely been studied at large geographical scales. We investigated how a soil disturbance gradient (low, intermediate, high), realized by either tillage or herbicide application, affects diversity and composition of soil bacterial and fungal communities as well as soil functions in vineyards across five European countries. Microbial alpha-diversity metrics responded to soil disturbance sporadically, but inconsistently across countries. Increasing soil disturbance changed soil microbial community composition at the European level. However, the effects of soil disturbance on the variation of microbial communities were smaller compared to the effects of location and soil covariates. Microbial respiration was consistently impaired by soil disturbance, while effects on decomposition of organic substrates were inconsistent and showed positive and negative responses depending on the respective country. </span><span>Therefore, we conclude that it is difficult to extrapolate results from one locality to others because microbial communities and environmental conditions vary strongly over larger geographical scales.</span><span> </span></p>
Data set for the article "One-time freeze-thawing or carbon input events have long-term legacies in soil microbial communities"
<p>The following are data and code used for statistical analysis and figure plotting in the manuscript</p> <p>Gorka et al. (2023) "One-time freeze-thawing or carbon input events have long-term legacies in soil microbial communities", Geoderma, <a href="https://doi.org/10.1016/j.geoderma.2023.116399">https://doi.org/10.1016/j.geoderma.2023.116399</a></p> <p>It contains the following files:</p> <ol> <li>Microbial PLFA and NLFA analysis files (contained in <em>Fatty_acid_analysis.zip</em>) <ul> <li>PLFA and NLFA abundance data, in nmol C g<sup>-1</sup> dw (in <em>fatty_acid_data.csv</em>)</li> <li>Taxonomic specificities of fatty acids, needed for R-script to run (in <em>phylum.csv</em>)</li> <li>An R Script reproducing the statistical analysis, figure plotting and output for tables, as used in the manuscript (<em>Fatty_acid_analysis.R</em>)</li> </ul> </li> <li>Soil C and N stoichiometry analysis files (contained in <em>TOC_TN_analysis.zip</em>) <ul> <li>Dissolved organic C (DOC), total dissolved N (TN), and C and N in microbial biomass (Cmic, Nmic) abundance data, in mg g<sup>-1</sup> dw (in <em>toc_tn_data.csv</em>)</li> <li>An R Script reproducing the statistical analysis, figure plotting and output for tables, as used in the manuscript (<em>TOC_TN_analysis.R</em>)</li> </ul> </li> </ol>
The contribution of Fe(III) reduction to soil carbon mineralization in montane meadows depends on soil chemistry, not parent material or microbial community
<p>The long-term stability of soil carbon (C) is strongly influenced by organo-mineral interactions. Iron (Fe)-oxides can both inhibit microbial decomposition by providing physicochemical protection for organic molecules and enhance rates of C mineralization by serving as a terminal electron acceptor, depending on redox conditions. Restoration of floodplain hydrology in montane meadows has been proposed as a method of sequestering C for climate change mitigation. However, dissimilatory microbial reduction of Fe(III) could lead to C losses under increased reducing conditions. In this study, we explored variations in Fe-C interactions over a range of redox conditions and in soils derived from two distinct parent materials to elucidate biochemical and microbial controls on soil C cycling in Sierra Nevada montane meadows. Differences in parent material were associated with different rates of Fe(III) reduction at increasing soil moisture levels, but not with differences in soil C mineralization. Known Fe(III)-reducing taxa were present in all samples but neither the relative abundance nor richness of Fe(III) reducers corresponded with measured rates of Fe(III) reduction. Under reducing conditions, our results suggest that Fe(III) reduction contributes to C mineralization only when Fe-bound C is present. However, Fe-bound C was not present in all of our soils and was below theoretical limits for C sorption onto Fe-oxides where it was found. Overall, our results suggest that meadow-specific soil chemistry drives Fe-C interactions and that the impact of Fe on C cycling in montane meadows may be smaller than in other ecosystems.</p>
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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.