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174 results for “soil microbial communities”
Data from: A survey of invasive plants on grassland soil microbial communities and ecosystem services
<p>Invasive plants can cause changes in structure and function of the ecosystem undergoing invasion. Any changes in ecosystem diversity and community composition will likely alter ecosystem services provided by that ecosystem. However, how these ecosystem services may change is poorly understood. To elucidate how these ecosystem services will change with invasion, we sampled 561 plots undergoing invasion by smooth brome (<i>Bromus inermis</i>) and four other invasive species at a native Rough Fescue prairie located near Saskatoon, Saskatchewan, Canada. Soil and plant surveys were undertaken weekly for 26 weeks beginning in May in 2014 until November 2014, or the growing season. We measured a suite of ecosystem services, including greenhouse gasses, extracellular enzyme function, forage production, glyphosate degradation and decomposition. Furthermore, soil physical and chemical properties were measured, and soil bacterial and fungal communities were sequenced. This is a large and multifaceted dataset with complex temporal and spatial attributes that can be used to answer numerous questions regarding the functioning of prairie ecosystems and how invasive species will impact that functioning. </p>
Effects of tree species identity on soil microbial communities in Juglans nigra and Quercus rubra plantations.
<p>Black walnut (<i>Juglans nigra </i>L.) forestry within the Central Hardwoods Region (CHR) has progressed primarily based on studies of trial and error among plantations. Although <i>J. nigra</i> wood has been used for everything from gunstocks in the Revolutionary War to the artfully crafted furniture of today, gaps exist in our knowledge base regarding the impact of this hardwood species on the soil. We aim to evaluate and analyze how <i>J. nigra</i> modified soil bacterial and fungal structure in conjunction with soil properties after 10 years of establishment. Additionally, we used another hardwood tree Northern red oak (<i>Quercus rubra </i>L.) for contrast. Our results showed soil microbial structure is influenced primarily by plant species; then by season, and lastly depth. The alpha-diversity index was increased in <i>J. nigra</i> compared to bulk soil values, whereas <i>Q. rubra</i> decreased the index. The most significant disparities in microbiomes were observed between plant species with <i>J. nigra</i> displaying greater enrichment in <i>Nitrospira</i>, <i>Geobacter</i>, <i>Steroidobacter</i>, <i>Bacillus</i>, and <i>Perlucidibaca</i> while<i> Q. rubra </i>more enriched in <i>Acidobacteria</i> (<i>GP1</i>, <i>GP2</i>, and <i>GP3</i>) and ectomycorrhizal fungi (<i>Tuber</i>, <i>Inocybe</i>, <i>Amanita</i>, and <i>Russula</i>). Finally, the co-occurrence networks showed that <i>J. nigra</i> increased node numbers while <i>Q. rubra</i> increased connection (edge) numbers. Additionally, the<i> Q. rubra </i>network displayed the highest mean degree, density, and clustering coefficient while <i>J. nigra</i> exhibited the highest modularity and average connectivity. In conclusion, our findings highlight the intricate interplay between CHR tree species and soil microbiota.</p>
Data from: Interactive effects of soil moisture, air temperature and litter nutrient diversity on soil microbial communities and Folsomia candida population
<p>Soil organisms play a key role in carbon and nutrient cycling in forest ecosystems. While soil organisms are strongly influenced by litter chemistry and are highly sensitive to abiotic conditions, little is known about how the interactive effects of these two factors. To address this gap in knowledge, we conducted a 10-week microcosm experiment in which we simulated the effects of climate change on soil ecology. More specifically, we studied relationships among litter nutrient concentration, microbial biomass, Collembola demographic parameters, and litter decomposition, exploring the potential impacts of increasing air temperature and decreasing soil moisture. To develop a gradient of nutrient concentrations, we created six tree litter mixtures with materials gathered from <em>Quercus pubescens</em> and its companion species. In contrast to microbes, we observed that Collembola abundance and litter decomposition were interactively affected by soil moisture and air temperature: the negative effect of increasing air temperature on Collembola abundance was amplified by reduced soil moisture, whereas the positive effect of increasing air temperature on litter decomposition disappeared under reduced soil moisture conditions. In contrast to fungi, the response of bacterial biomass and Collembola abundance to litter nutrient concentration was dependent on abiotic conditions. More specifically, the relationships between nutrients, especially calcium and magnesium, and bacterial biomass and Collembola abundance were less robust or disappeared under drier or warmer conditions. In conclusion, our findings underscore that ongoing climate change could affect soil organisms directly as well as indirectly, by altering their responses to litter nutrient concentrations. In addition, we found that nutrient-rich habitats might be more affected than nutrient-poor habitats by altered climatic conditions.</p>
Dataset of the paper: A first-year melon/cowpea intercropping system improves soil nutrients and changes the soil microbial community
<p>Dataset and raw data</p>
Data from: No evidence of foliar disease impact on crop root functional strategies and soil microbial communities: What does this mean for organic coffee?
<p><span>Global climate change is increasing pest and pathogen pressures on plant communities, deteriorating optimal plant functioning. In plant communities, root functional trait expression and microbial communities are important indicators of plant functioning belowground, and, when confronted with pathogens aboveground, can simultaneously reflect plant defence strategies. Yet, while research is continuing to emerge on the response of root functional traits and microbial processes to pathogens aboveground, little work has investigated these interactions in tree-crops, or the role organic amendments play in moderating these relationships. The main objective of this study is to disentangle the dynamic effects of pathogens and amendments on root functional traits (i.e., specific root length and area, root diameter, root length density, root nitrogen, and root carbon to nitrogen ratio) and root endophytic fungal communities. As a model, we use <em>Coffea arabica </em>(coffee) variety Caturra along a gradient of Coffee Leaf Rust – a foliar disease prominent in coffee systems – under contrasting but widespread amendment regimes in biodiverse agroforestry systems. We found that root trait expression varies along established conservation and collaboration gradients, where fungal endophyte community composition varies significantly as a function of root traits. Belowground resource acquisition strategies do not change with foliar disease incidence, suggesting they may be decoupled. Rather, amendment regimes </span>differentially shape root trait expression and microbial communities<span>, where coffee plants under organic amendments, regardless of foliar disease incidence, expressed greater acquisitive traits and enhanced collaboration with symbiotic fungi. </span>This is an important first step in disentangling the dynamic inter-relationships between plant traits, endophytes, and pathogens, generating new questions on the role of amendments in sustainable pathogen management in biodiverse agroecosystems.</p> <p> </p>
Data from: Plant diversity improves resistance of plant biomass and soil microbial communities to drought
<p>1. Biodiversity is known to affect ecosystem resistance and have implications for the maintenance of ecosystem functions and services under climate change. Compared to numbers of studies focusing on aboveground vegetation, the response of belowground communities to abiotic stresses along plant diversity gradients is often ignored and is considered an important knowledge gap in ecosystem ecology. Here we conducted an integrative research to evaluate the resistance of plant biomass, and soil microbial communities and associated functional profiles to drought under varying plant diversity.</p> <p>2. We carried out a three-year manipulation experiment by factorially controlling plant diversity gradient (1, 2, 4, and 8 species richness) and soil moisture treatment (drought and non-drought), and investigated the responses of plant biomass, soil bacterial and fungal diversity and community composition, soil glomalin, and five key soil enzymes.</p> <p>3. We found that plant diversity significantly improved the resistance of soil fungal communities and microbial functional profiles characterized by soil glomalin and five key enzymes, which was partly driven by the availability and accessibility of soil resources (e.g., soil moisture and organic matter) mediated by plant diversity. Further, our results indicated that the enhanced resistance of fungal communities was consistent with ecological insurance theory that diverse fungal communities at high plant diversity had a higher probability of containing taxa that adapt to drought.</p> <p>4. <em>Synthesis</em>. Our study provides novel empirical insights into the mechanism underlying the regulatory effect of plant diversity on resistance of aboveground vegetation and belowground biota to drought, with implications for understanding ecosystem response to climate change and improving biodiversity conservation practices.</p>
Microbial community dynamics during decomposition of insect exuviae and frass in soil
<p><span>As the mass-rearing industry of insects for food and feed is expected to grow, </span><span>residual streams associated with this activity will become increasingly available. Before these residues can be used as organic amendments, more knowledge on the decomposition and dynamics of the involved microbial communities is needed. </span><span>This study investigated decomposition, N-mineralization, and fungal/bacterial community composition during 16 weeks of incubation of exuviae and frass of </span><span>black soldier fly, mealworm, and house cricket in arable soil</span><span>. Decomposition of insect residues in litterbags was rapid, with more than 50% weight loss in 2 weeks. Accumulation of mineral-N from insect materials distributed in the soil was also highest during the first 2 weeks, but</span><span> it was more profound for exuviae than their frass counterparts. </span><span>Soil amendment with insect residues enriched soil microbial inhabitants belonging to Gammaproteobacteria, Bacilli, Actinobacteria, and Mortierellomycetes. Comparison of microbial community composition in soil amended with sterilized and nonsterilized mealworm exuviae indicated that the presence of </span><span>microbial propagules in the exuviae had no significant influence on the composition of bacterial decomposers and a minor, but significant impact on fungal community composition. Overall, our results reveal a good prospect of using insect residual streams as soil amendment.</span></p>
Jeanbille_et_al_2024_Exclusion_experiment_ANALYSIS: code and data for "Size exclusion experiment in a grassland field unravels top-down control of the soil fauna on microbial community assembly"
<p>Release of code and data associated with the publication "Size exclusion experiment in a grassland field unravels top-down control of the soil fauna on microbial community assembly".</p>
Jeanbille_et_al_2024_Exclusion_experiment_ANALYSIS: code and data for "Size exclusion experiment in a grassland field unravels top-down control of the soil fauna on microbial community assembly"
<p>Release of code and data associated with the publication "Size exclusion experiment in a grassland field unravels top-down control of the soil fauna on microbial community assembly".</p>
Jeanbille_et_al_2024_Exclusion_experiment_ANALYSIS: code and data for "Size exclusion experiment in a grassland field unravels top-down control of the soil fauna on microbial community assembly"
<p>Release of code and data associated with the publication "Size exclusion experiment in a grassland field unravels top-down control of the soil fauna on microbial community assembly".</p>
Jeanbille_et_al_2024_Exclusion_experiment_ANALYSIS: code and data for "Size exclusion experiment in a grassland field unravels top-down control of the soil fauna on microbial community assembly"
<p>Release of code and data associated with the publication "Size exclusion experiment in a grassland field unravels top-down control of the soil fauna on microbial community assembly".</p>
From soil to sediment: Bedform migration shapes microbial communities from eroding bank soil during terrestrial-aquatic regime shift [dataset]
<p>This dataset contains raw data of metabolism measurements, microbial abundance, and nutrients that were assessed for the research paper entitled "From soil to sediment: Bedform migration shapes microbial communities from eroding bank soil during terrestrial-aquatic regime shift," which has been submitted to the Journal of Geophysics: Biogeosciences on October 19, 2024. Please note that raw sequencing data were already submitted to the NCBI library and are accessible via https://www.ncbi.nlm.nih.gov./sra/PRJNA1154565.</p> <p>The excel sheet (.xlsx) contains all relevant parameters that were used to detect the influence of environmental parameters on the microbial community structure, e.g. bacterial, fungal and algal abundance, nutrient concentrations, and final NCP and CR rates. The .zip archive contains all raw metabolism measurements during our experimental duration.</p>
Plant community composition and traits modulate the impacts of drought intensity on soil microbial community composition and function
<p>Terrestrial ecosystems are increasingly threatened by extreme drought events. Soil microbial communities are central to terrestrial ecosystem function via their role in regulating biogeochemical cycling. Consequently, the impact of increasingly intense drought events on soil microbial communities will have knock-on effects for how ecosystems cope with climate change. In an outdoor grassland mesocosm experiment, we determined how increasing drought intensity affects bacterial and fungal community composition, and functioning, during and after drought. We also tested whether plant community resource acquisition strategy (fast- versus slow-strategy plant communities), plant community composition, and plant functional traits mediate soil microbial responses to increasing drought intensity. We found that increasing drought intensity markedly shifted bacterial and fungal community composition, and these effects persisted until the end of the experiment (two months after re-wetting). Bacterial and fungal communities that experienced severe droughts did not return to baseline composition, while those that experienced a mild drought did. Microbial community functioning (potential extracellular enzyme activity) was reduced at peak drought and shortly after re-wetting. While drought intensity effects on bacterial or fungal communities were insensitive to plant community resource acquisition strategy, functional group abundance (aboveground biomass of grass or forb plant species) composition (grass:forb ratio) and leaf traits (leaf dry matter content and leaf nitrogen concentration) explained significant variation in bacterial and fungal community composition during and after drought. Notably, plant community leaf dry matter content and soil nitrogen were the key factors mediating the effect of increasing drought intensity on microbial indicator taxa (ASVs). We conclude that increasing drought intensity affects grassland soil microbial communities during and after drought, and this impact is influenced by plant community composition and functional traits.</p>
Drivers of soil microbial community assembly during recovery from selective logging and clear cutting
<p>Despite important progress in understanding the impacts of forest clearing and logging on aboveground communities, how these disturbances affect soil microbial β-diversity and the ecological processes driving microbial assemblages are poorly understood. Further, whether and how the microbial shifts affect vegetation composition and diversity during recovery of post-logged forests remain elusive. 2. Using a spatial grid experiment design in a primary tropical forest intermixed with post-logged patches naturally recovered for half century in Hainan Island, China, we characterized and explained the distance-decay relationships of soil microbial similarities in primary, selectively logged and clear cut forests. 3. Selectively logged sites showed a lower spatial turnover rate of bacterial assemblages based on phylogenetic and taxonomic β-diversity, but a higher spatial turnover rate of fungal assemblages based on phylogenetic β-diversity, suggesting a higher level of phylogenetic variability in fungal composition. Clear cut sites showed lower spatial turnover for both bacterial and fungal assemblages based on the two β-diversity, indicating community homogenization. Main drivers of microbial assemblages shifted from soil properties in primary forest to tree composition in selectively logged sites, whereas microbial-tree associations declined in clear cut sites, leading to stochastically organized microbial assemblages. 4. Synthesis and applications. The increased fungal phylogenetic turnover with tree turnover following selective logging promotes unassisted recovery of plant diversity. In contrast, the decoupling of tree and microbial turnover following clear-cutting suggests restoration approaches based on tree planting, and tree species that have strong associations with bulk soil microbial community should be considered. Our findings advance the understanding of spatial patterns, processes, and drivers of soil microbial assemblages in parallel with tree community recovery during regeneration of post-logged tropical forests, and highlight the importance of coupling assemblage patterns between tree and soil fungal communities for conserving tropical forest biodiversity.12-Jul-2021 --</p>
Unaltered soil microbial community composition, but decreased metabolic activity in a semi-arid grassland after two years of passive experimental warming
<p>Soil microbial communities regulate soil carbon feedbacks to climate warming through microbial respiration (i.e. metabolic rate). A thorough understanding of the responses of composition, biomass and metabolic rate of soil microbial community to warming is crucial to predict soil carbon stocks in a future warmer climate. Therefore, we conducted a field manipulative experiment in a semi-arid grassland on the Loess Plateau of China to evaluate the responses of the soil microbial community to increased temperature from April 2015 to December 2017. Soil temperature was 2.0 <sup>o</sup>C higher relative to the ambient when open-top chambers (OTCs) were used. Warming did not affect microbial biomass or the composition of microbial functional groups. However, warming significantly decreased microbial respiration, directly resulting from soil pH decrease driven by the co-mediation of aboveground biomass increase, inorganic nitrogen increase and moisture decrease. These findings highlight that the soil microbial community structure of semi-arid grasslands resisted the short-term warming by 2 <sup>o</sup>C, although its metabolic rate declined.</p>
Changes in microbial community structure and functioning with elevation are linked to local soil characteristics as well as climatic variables
<p>Mountain forests are important carbon stocks but are threatened by increased insect outbreaks and climate driven forest conversion. Soil microorganisms play an eminent role in nutrient cycling in forests and form the basis of soil food webs. Uncovering the driving factors shaping microbial communities and functioning at mountainsides worldwide is of importance to better understand their dynamics at local and global scales. We investigated microbial communities and their drivers along an elevational gradient of primary forests at Changbai Mountain, China. We analysed substrate-induced respiration and phospholipid fatty acids (PLFA) in litter and two soil layers at seven sites. In the litter layer the increase in microbial biomass (Cmic) as well as in stress indicator ratios with elevation were negatively correlated with Ca concentrations indicating increased nutritional stress in high microbial biomass communities at sites with lower Ca availability. PLFA profiles in litter separated low and high elevations, this was less pronounced in soil, suggesting that leaflitter functions as buffer for soil microbial communities. Annual variations in temperature correlated with PLFA profiles in all layers, while annual variations in precipitation correlated with PLFA profiles in upper soil only. Furthermore, the availability of resources, soil moisture, Ca concentrations and pH structured the microbial communities. Pronounced changes in Cmic and stress indicator ratios in the litter layer between pine dominated (800 – 1100 m) and spruce dominated (1250 – 1700 m) forests indicated a shift in the structure and functioning of microbial communities between forest types. The study highlights strong changes in microbial community structure and functioning along elevational gradients, but also shows that these changes and their driving factors vary between layers. Besides annual variations in temperature and precipitation, carbon accumulation and nitrogen acquisition shape changes in microbial communities with elevation at Changbai Mountain.</p>
Tea seed meal application promoted microbial community diversity in the soil of peach orchard
<p><span>Soil microbes are indispensable in agricultural production, and they respond differently to different fertilization regimes. However, there is limited understating of microbial composition and function responses to an organic fertilizer tea seed meal (TSM) and conventional fertilizer. Here we first reported the change rules and functions of soil microbial community in peach orchard soil after application of compound fertilizer plus urea (CFU) and different amounts (1.25, 2.50, 3.75 and 5.00 kg) of TSM. Compared to CFU, the application of 1.25, 2.50 and 3.75 kg TSM significantly decreased the Chao1 index of bacterial community in peach orchard soil. The Shannon index of bacterial and fungal communities in 2.50 kg TSM treatment was significantly higher than that in CFU. Beta diversity analysis of bacteria and fungi (based on Bray-Curtis matrix and OTUs level) revealed significant structural differences among all five experimental groups (ANOSIM, bacteria: R= 0.665, p = 0.001; fungi: R= 0.996, p = 0.001). The TSM treatments significantly decreased the relative abundances of potentially unfriendly bacteria (<em>Acidothermus</em>, <em>Acidicaldus</em>, </span><span><em>Sphingomonas</em>,</span><span> <em>Candidatus</em> <em>Koribacter</em> and <em>Candidatus</em> <em>Solibacter</em>) and fungi (<em>Fusarium</em>), and significantly increased the relative abundances of potentially beneficial fungi (<em>Trechispora</em>, <em>Sagenomella</em>, <em>Penicillium</em>, <em>Acaulium</em> <em>caviariforme</em>, <em>Leucoagaricus</em> and <em>Chlorophyllum</em>) compared with CFU. These changes were more obvious when the application amount of TSM was 2.50 kg. This study provides insights into the potential of application of TSM as an organic fertilizer in agricultural production.</span></p>
Climate warming alters the relative importance of plant root and microbial community in regulating the accumulation of soil microbial necromass carbon in a Tibetan alpine meadow
<p><span>Climate warming is predicted to considerably affect variations in soil organic carbon (SOC), especially in alpine ecosystems. Microbial necromass carbon (MNC) is an important contributor to stable soil organic carbon pools. However, accumulation and persistence of soil MNC across a gradient of warming are still poorly understood. An eight-year field experiment with four levels of warming was conducted in a Tibetan meadow</span><span>.</span> <span>We found that low-level (+0</span><span>-</span><span>1.5 ℃) warming mostly enhanced bacterial necromass carbon (BNC), fungal necromass carbon (FNC), and total MNC compared with control treatment across soil layers, while no significant effect was caused between high-level (+1.5</span><span>-</span><span>2.5 ℃) treatments and control treatments. The contributions of both MNC and BNC to soil organic carbon were not significantly affected by warming treatments across depths. Structural equation modeling analysis demonstrated that the effect of plant root traits on MNC persistence strengthened with warming intensity, while the influence of microbial community characteristics waned along with strengthened warming. Overall, our study provides novel evidence that the major determinants of MNC production and stabilization may vary with warming magnitude in alpine meadows. This finding is critical for updating our knowledge of soil carbon storage in response to climate warming.</span></p>
Plant litter chemistry drives long-lasting changes in the catabolic capacities of soil microbial communities
<p><span>Although </span><span>microbial communities play an important role in explaining plant litter decomposition rates, whether and how litter chemistry may alter catabolic capacities of soil microbial communities remains poorly studied.</span></p> <p><span>During a one-year litter decomposition experiment of twelve herbaceous species with contrasting litter chemistry, we examined the effect of plant litter type (roots vs leaves) and litter chemical traits on the resulting capacity of soil microbial communities to degrade a wide range of carbon substrates of variable complexity (MicroRespTM method).</span></p> <p><span>Litter chemistry impacted both the total catabolic activity as well as specific catabolic capacities of microbial communities. In early stages of litter decomposition total catabolic activity was mainly influenced by the amount of C and N in litter leachates, and litter N, P and Mg, then, later, by lignin concentrations. Some specific catabolic capacities could also be related to litter initial chemistry. Overall, litter trait effects on soil microbial communities decreased over time and the relative importance of traits shifted during the decomposition process.</span></p> <p><span>Our results highlight that litter chemistry is a strong driver of catabolic capacities of microbial decomposers and, whilst its effect fades with time, it remains substantial throughout the litter decomposition process. These long-lasting effects of litter chemistry suggest a persistent control on microbial catabolic capacities in ecosystems with recurrent litter production. Soil microbial catabolic activities were driven by broadly the same chemical traits across leaf and root litters. </span></p> <p><span>Synthesis.</span><span> Such long-lasting effects of litter chemistry on catabolic capacities of microbial communities may represent a substantial indirect driver of the decomposition process. Disentangling the relative importance of this overlooked effect of litter chemistry on decomposition represents the next challenge. We argue that such research line should open ground-breaking perspectives for reconsidering our current understanding of the mechanistic links between litter traits and decomposition rate. </span></p>
Soil fauna-microbial interactions complexity triggers shifts in both fungal and bacterial communities under a contamination disturbance
<p>meta.otu.june2020.txt : Willow morphological data, data related to qPCR of PAH-RHD genes and phenanthrene amounts found by GC-MS in soil, associated to the paper entitled: Soil fauna-microbial interactions complexity triggers shifts in both fungal and bacterial communities under a contamination disturbance.</p> <p>Files starting by 16s, its, gn and gp are data tables of bioinformatically processed amplicon sequencing data containing filtered and rarefied counts corresponding to 4 set of genes (16S rRNA gene, fungal ITS, PAH-RHD Gram Negative and Gram Positive bacteria) and corresponding taxonomy. </p>
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
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