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553 results for “soil communities”
Data from: Metabarcoding of soil environmental DNA replicates plant community variation but not specificity
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Soil fungal community and activity under dominant plant species at the Sevilleta National Wildlife Refuge, New Mexico: October 2013
We measured fungal composition and activity in the soil under dominant plant species across a grassland to shrubland transition to determine if shrubs cultivate soil microbial communities as they encroach grasslands. The project was conducted in the northern Chihuahuan desert at the Sevilleta National Wildlife Refuge (site of the Sevilleta LTER) in New Mexico on October 20, 2013. Soils were collected under one shrub (Larrea tridentata) and three grass (Bouteloua eriopoda, Bouteloua gracilis, Pleuraphis jamesii) species in grassland, shrubland, and the ecotone region between grasslands and shrublands. Soil fungal communities were evaluated using DNA amplicon sequencing and fungal activity was quantified using several extracellular enzyme activity assays. Soil texture and soil chemistry were also measured.
Soil Microbial and N cycling data along a wetland plant community gradient
This dataset contains soil chemical and microbial data taken from surface soil cores (15cm) from the Black Spruce, Willow/Birch, Tussock, Emergent Fen, and Rich Fen plant communities along the APEX boardwalk. Data include DOC, soil C, potential nitrification, potential denitrification, soil DNA concentration, water content, ammonium concentration, nitrate concentration, archaea abundance, NirK functional gene abundance, ammonia oxidizing bacteria (AOB) abundance, ammonia oxidizing archaea (AOA) abundance, NosZ functional gene abundance, and eubacteria abundance.
Average soil nitrogen: Long-Term Nitrogen Deposition: Population, Community, and Ecosystem Consequences
The purpose of this experiment is to measure how adding nitrogen over a long time will affect the number of species, the type of species present, the amount of annual growth, and the change from year to year in the growth of each species in a plant community which is also relieved of grazing by large and small mammals. The experiment is being conducted within fields (A, B, C, and D) which were initially low in soil nutrients. There are 8 different levels of nitrogen addition with other nutrients added to ensure that nitrogen remains the limiting nutrient, and a control which receives no nutrients. There are 6 replicates of the 9 treatments in fields A, B, and C and 5 replicates in field D. The treatments were randomly assigned to the plots. In fields A, B, and C the plots are in 6 by 9 grids and are 4 by 4 meters in size with 1 meter aisles between plots. In field D the plots are 1.5 by 4 meters and are placed in a 3 by 17 grid. The plots are enclosed by a fence to keep out mammalian herbivores. Gophers are trapped and removed as they appear. Nitrogenfertilizer (NH4NO3) is applied twice per year, once in early May and once in late June. This experiment was begun in 1982 by David Tilman.
Soil ammonium: Long-Term Nitrogen Deposition: Population, Community, and Ecosystem Consequences
The purpose of this experiment is to measure how adding nitrogen over a long time will affect the number of species, the type of species present, the amount of annual growth, and the change from year to year in the growth of each species in a plant community which is also relieved of grazing by large and small mammals. The experiment is being conducted within fields (A, B, C, and D) which were initially low in soil nutrients. There are 8 different levels of nitrogen addition with other nutrients added to ensure that nitrogen remains the limiting nutrient, and a control which receives no nutrients. There are 6 replicates of the 9 treatments in fields A, B, and C and 5 replicates in field D. The treatments were randomly assigned to the plots. In fields A, B, and C the plots are in 6 by 9 grids and are 4 by 4 meters in size with 1 meter aisles between plots. In field D the plots are 1.5 by 4 meters and are placed in a 3 by 17 grid. The plots are enclosed by a fence to keep out mammalian herbivores. Gophers are trapped and removed as they appear. Nitrogenfertilizer (NH4NO3) is applied twice per year, once in early May and once in late June. This experiment was begun in 1982 by David Tilman.
Plant and soil organic matter responses to ten years of nutrient enrichment in the Nutrient Network:Nutrient Network. A cross-site investigation of bottom-up control over herbaceous plant community dynamics and ecosystem function
This experiment is one implementation of a globally distributed experiment, known as the Nutrient Network. At Cedar Creek, as in over 70 other sites in grasslands around the world, the experiment aims to describe impacts of increased nutrients (nitrogen, phosphorus, potassium, sulfur and other metals) and decreased herbivory (removal of mammals by fencing). Two overarching questions are being explored with these manipulations: 1. To what extent are plant production and diversity co-limited by multiple nutrients in herbaceous-dominated communities? 2. Under what conditions do grazers or fertilization control plant biomass, diversity, and composition? By utilizing identical protocols at diverse grassland sites around the world, NutNet aims to uncover both the generalities in ecosystem functioning, and the contingencies or differences which can obscure those common mechanisms. In addition to the standard NutNet protocol, e247 includes an additional low Nitrogen gradient (1 gram Nitrogen per meter squared per year and 5 grams Nitrogen per meter squared per year in addition to the standard 10 grams Nitrogen per meter squared per year).
Operational taxonomic unit (OTU) table characterizing water track and adjacent soil microbial communities in Taylor Valley, Antarctica during the 2012-13 austral summer
This data package includes the abundance of microbial operational taxonomic units (OTUs) for samples collected during the austral summer of 2012-2013 in the Lake Hoare and Goldman Glacier Basins of Taylor Valley, Antarctica. A total of twenty samples from on- and off-water track soils were collected and analyzed. Samples were collected from the Lake Hoare Basin on 27 December 2012 and from the Goldman Glacier Basin on 4 January 2013. The aim of the study was to identify how variation in the measured physical and chemical environment of water tracks within the two water track systems influenced soil microbial community structure and diversity. Soil bacterial biodiversity was assessed using cultivation independent 16S rRNA gene sequencing.
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: Local soil legacy effects in a multi-species grassland community are underlain by root foraging and soil nutrient availability
<p>1. Plant soil legacies consisting of species-specific microbial communities are hypothesized to play a critical, structuring role in plant species co-existence processes. Plant species are thought to perform worse on soil conditioned by the same species compared to soil of other species, which serves as a self-limitation mechanism and averts mono-dominance of strong competitors. Here we test in a multi-species community setting, whether root colonisation and resource utilisation of soil patches with distinct soil legacies, are consistent with this hypothesis. 2. We grew eight grassland species together in an outdoor mesocosm setup in unconditioned soil and created soil patches in these communities conditioned by one of four plant species, or a soil mixture of all four. During two subsequent growing seasons, we tested the effect of these conditioned soil patches on belowground root colonisation into the patches of each surrounding plant species using a novel sequencing based approach. In addition, we tested the effect of soil conditioning on local root functioning by injecting tracers into the soil patches and measuring the recovery in aboveground biomass. 3. Against expectations, plant species did not place less roots in own soil patches compared to foreign soil patches, nor did species take up less tracer from own compared to foreign soil patches. Using structural equation modelling, we found that tracer uptake of the plant species was to a varying degree explained by root densities in the various soil patches and by differing soil nutrient availability of the soil patches. We conclude that soil legacy effects are inextricably connected to soil nutrient availability, which needs to be taken into account in plant-soil feedback research to understand the processes that shape plant communities. 4. Synthesis. We found that soil legacy effects in complex, multi-species semi-field conditions did not match expectations based on theory and experiments in controlled conditions. Among the many complicating factors that may modify or even overrule soil legacy effects in semi-field settings, we identified soil nutrient availability as a critical force that may, together with soil biota, shape plant species co-existence processes.</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>
Long-term nitrogen addition alters the community and energy channel but not diversity of soil nematodes in a subtropical forest
Summary <ol> <li>Research has indicated that increases in nitrogen (N) deposition can greatly affect ecosystem processes and functions. There is limited information about the effects of long-term N addition on soil nematodes and their functional composition, although nematodes are the most abundant multicellular animals on Earth.</li> <li>We conducted a field experiment in 2004 with four levels of N addition (0, 60, 120, and 240 kg N ha<sup>-1 </sup>yr<sup>-1</sup>) in a subtropical <i>Cunninghamia lanceolata</i> forest. Soil samples with three depths (0-20, 20-40 and 40-60 cm) were collected and the community structure, diversity and trophic groups of soil nematodes were determined in 2014.</li> <li>N addition significantly increased the abundance of bacterial- and fungal-feeding nematodes, but decreased the abundance of plant-feeding nematodes at the 0-20 cm soil layer. Accordingly, the plant parasite index and enrichment index decreased but the basal index and channel index increased, which weaken the importance of the plant-based energy channel, but enhance the importance of the fungal-based energy channel. N addition had no effects on the diversity of soil nematodes in three soil depths. Structural equation modeling analysis indicated that N loading directly changed plant-feeding (total <i>r<sup>2</sup></i>=0.42) nematodes, or indirectly affected bacterial- (<i>r<sup>2</sup></i>=0.43), fungal- (<i>r<sup>2</sup></i>=0.31) and plant-feeding nematodes via change soil nutrients, soil water content and pH.</li> <li>These findings suggest that N addition can change the community structure and energy channels soil nematodes, which would affect soil processes and food web functions in forest soils under future environmental change scenarios.</li> </ol>
Data from: Environmental filtering by pH and soil nutrients drives community assembly in fungi at fine spatial scales
Whether niche processes, like environmental filtering, or neutral processes, like dispersal limitation, are the primary forces driving community assembly is a central question in ecology. Here, we use a natural experimental system of isolated tree "islands" to test whether environment or geography primarily structures fungal community composition at fine spatial scales. This system consists of isolated pairs of two distantly-related, congeneric pine trees established at varying distances from each other and the forest edge, allowing us to disentangle the effects of geographic distance versus host and edaphic environment on associated fungal communities. We identified fungal community composition with Illumina sequencing of ITS amplicons, measured all relevant environmental parameters for each tree - including tree age, size, and soil chemistry - and calculated geographic distances from each tree to all others and to the nearest forest edge. We applied generalized dissimilarity modeling to test whether total and ectomycorrhizal fungal (EMF) communities were primarily structured by geographic or environmental filtering. Our results provide strong evidence that, as in many other organisms, niche and neutral processes both contribute significantly to turnover in community composition in fungi, but environmental filtering plays the dominant role in structuring both free-living and symbiotic fungal communities at fine spatial scales. In our study system, we found pH and organic matter primarily drive environmental filtering in total soil fungal communities and that pH and cation exchange capacity – and, surprisingly, not host species - were the largest factors affecting EMF community composition. These findings support an emerging paradigm that pH may play a central role in the assembly of all soil mediated systems.
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.
Community-level interactions between plants and soil biota during range expansion
1. Plant species that expand their range in response to current climate change will encounter soil communities that may hinder, allow, or even facilitate plant performance. It has been shown repeatedly for plant species originating from other continents that these plants are less hampered by soil communities from the new than from the original range. However, information about the interactions between intra-continental range expanders and soil communities is sparse, especially at community level. 2. Here we used a plant-soil feedback experiment approach to examine if the interactions between range expanders and soil communities change during range expansion. We grew communities of range-expanding and native plant species with soil communities originating from the original and new range of range expanders. We determined the composition of fungi, bacteria and nematodes in these conditioned soils by high-throughput amplicon sequencing of the ITS region and the 16S rRNA gene and using morphological methods, respectively. Then we tested how these soil communities influence the growth of subsequent communities of range expanders and natives. 3. We found that after the conditioning phase soil bacterial, fungal and nematode communities differed by origin and by conditioning plant communities. Despite differences in bacterial, fungal and nematode communities between original and new range, soil origin did not influence the biomass production of plant communities. Both native and range expanding plant communities produced most aboveground biomass in soils that were conditioned by plant communities distantly related to them. 4. Synthesis. We conclude that communities of range-expanding plant species shape specific soil communities in both original and new range soil. Plant-soil interactions of range expanders in communities can be similar to the ones of their closely related native plant species.
Sequences, taxonomic assignments, and R script from Comparison of Lava Cave Bacterial Mat Communities to Overlying Surface Soil Bacterial Communities from Lava Beds National Monument, USA
<p>This set of files contain the 16S rDNA, taxonomic assignments from the greengenes database, and the R script for processing the data. </p> <p><strong>Abstract</strong></p> <p>Lava caves around the world often support extensive microbial mats on ceilings and walls in a range of colors. Little is known about lava cave microbial diversity and how these subsurface mats differ from microbial communities in overlying surface soils. We generated and analyzed bacterial 16S rDNA from 454 pyrosequencing from three colors of microbial mats (tan, white, and yellow) from seven lava caves in Lava Beds National Monument, CA, USA, and compared them with surface soils overlying each cave. <em>Actinobacteria</em> dominated in all samples, with 39% (caves) and 21% (surface soils). <em>Proteobacteria</em> made up 30% of phyla from caves and 36% from surface soil with <em>Gamma</em>- 20% and <em>Alpha</em>- 10% in the caves and <em>Gamma</em>- 18% with <em>Alpha</em>-17% in soil. Other major phyla in caves were <em>Nitrospirae</em> (7%) followed by Minor Phyla (7%), compared to surface soils with <em>Bacteriodetes</em> (8%) and Minor phyla (8%). A very high proportion (53.33%) of the most abundant sequences could not be identified to genus, indicating a high degree of novelty. Surface soil samples had more OTUs and greater diversity indices than cave samples. The same phyla were represented in both soils and cave microbial mats, but the overlap was only 11.2% at the operational taxonomic unit (OTU). Although surface soil microbes immigrate into underlying caves, the environment selects for microbes able to live in the cave habitats, resulting in very different cave microbial communities. In terms of species richness, diversity by mat color differed, but not significantly. Number of entrances per cave, distance from an entrance, cave length, and temperature also contributed to observed differences in diversity. With high levels of novel microbes, caves may represent excellent habitats for the isolation of new bioactive compounds. This study is the first comprehensive comparisons of bacterial communities in lava caves with the overlying soil community.</p>
Ecoregional patterns of protist communities in mineral and organic soils: assembly processes, functional traits and diversity of testate amoebae in Northern Eurasia
<p>TA_Traits.csv file includes trait data for testate amoebae. TA_Abundance.csv file includes environmental variables (soil type and region) and relative abundance data of testate amoebae.</p>
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>
Soil BON Earthworm - Community data template
<p>The Soil BON Earthworm consortium built a data template for everyone to use and format their data, so that it can be collated in a straightforward way. The template is an updated version of the one developed for the EUdaphobase COST Action <a href="https://www.zotero.org/google-docs/?ar5Q1g">(Tsiafouli et al. 2022)</a>. More information on Soil BON Earthworm initiative and the data templates created are available in the associated publication (insert DOI when available).</p><p>It is composed of different leaflets:</p><ol><li>"Readme": this leaflet contains all column names from the next leaflet and provides the necessary information to properly fill the information needed.</li><li>"Template to fill with data": this leaflet is composed of several columns where the data provider can enter the information on dataset, site, methodology and taxa sampled. This leaflet is to be filled with density data, and another file should be produced for biomass data.</li><li>"drop down list": this leaflet is non-modifiable and contains the different lists from which values are taken for certain variables, such as soil type which follow the WRB FAO classification <a href="https://www.zotero.org/google-docs/?XHAIOm">(IUSS Working Group WRB 2015)</a>.</li></ol>
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>
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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.