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188 results for “Microbial diversity”
Data from: Microbial functional diversity: from concepts to applications
Functional diversity is increasingly recognized by microbial ecologists as the essential link between biodiversity patterns and ecosystem functioning, determining the trophic relationships and interactions between microorganisms, their participation in biogeochemical cycles and their responses to environmental changes. Consequently, its definition and quantification have practical and theoretical implications. In this opinion paper, we present a synthesis on the concept of microbial functional diversity from its definition to its application. Initially, we revisit to the original definition of functional diversity, highlighting two fundamental aspects, the ecological unit under study and the functional traits used to characterize it. Then, we discuss how the particularities of the microbial world disallow the direct application of the concepts and tools developed for macroorganisms. Next, we provide a synthesis of the literature on the types of ecological units and functional traits available in microbial functional ecology. We also provide a list of more than 400 traits covering a wide array of environmentally relevant functions. Lastly, we provide examples of the use of functional diversity in microbial systems based on the different units and traits discussed herein. It is our hope that this paper will stimulate discussions and help the growing field of microbial functional ecology to realize a potential that thus far has only been attained in macrobial ecology.
Data from: Linking diversity, synchrony and stability in soil microbial communities
1. It is becoming well established that plant diversity is instrumental in stabilizing the temporal functioning of ecosystems through population dynamics and the so-called insurance or portfolio effect. However, it is unclear whether diversity-stability relationships and the role of population dynamics in soil microbial communities parallel those in plant communities. 2. Our study took place in a long-term land management experiment with and without perturbation to the soil ecosystem by tilling. We assessed the impacts of the soil perturbation on the diversity, synchrony and stability relationships in soil fungal and bacterial communities. 3. We found that the perturbation to the soil ecosystem not only reduced the abundance and richness of the fungal community, but it also reduced the temporal stability in both bacterial and fungal abundance. The fungal community abundance was destabilized by soil tilling due to reduced richness and increased temporal variation of individual taxa. In contrast, soil tilling destabilized the bacterial community abundance by reducing the temporal variation of individual taxa. Both bacterial and fungal community abundances were more temporally variable when taxa fluctuated more synchronously through time. 4. Our results show that land management practices, such as tilling, can destabilize soil microbial abundance by reducing the richness and disrupting the temporal dynamics belowground. However, the differences in the mechanisms that underlie the temporal variations in fungal and bacterial net abundances suggests that the mechanisms that drive the stability can differ among guilds of organisms within the same system. The different temporal responses between the fungal and bacterial communities are likely linked to changes in edaphic properties resulting from the physical alteration of the soil structure.
Plant responses to diversity-driven selection and associated rhizosphere microbial communities
<p><b>1.</b> Plant diversity loss can alter plant interactions and rhizosphere microbial communities. These altered interactions in turn exert diversity-driven selection pressures to which plants may respond with phenotypic changes. Diverse plant communities may favour the survival and fitness of individuals with traits that avoid competition. Conversely monocultures may accumulate species-specific pests favouring greater investment in defence traits. Yet it is unknown how altered plant rhizosphere interactions influence the plant diversity-driven selection for altered plant phenotypes. <b>2.</b> We tested for plant diversity-driven selection on plant aboveground traits and how these traits are modified by their rhizosphere microbial communities after 11 years in experimental plant monocultures and mixtures. Plants propagated from monocultures or mixtures were grown in combination with their 'home' vs. 'away' arbuscular mycorrhizal fungi (AMF) or non-AMF microbes in two separate experiments using five and eight plant species respectively. We hypothesized plants in monocultures may be selected for better defence and better performance in association with rhizosphere microbial communities compared with plants in mixtures. <b>3.</b> Monoculture and mixture plants significantly differed in their aboveground phenotypes. As predicted, plant traits related to defence (greater leaf mass per area and leaf dry matter content, reduced leaf damage) were more pronounced in monoculture plants in both experiments. Effects of the rhizosphere microbial communities, which generally enhanced plant growth, tended to be species-specific. Significant three-way interactions between diversity-driven selection, AMF treatment and plant species showed that home vs. away effects could be positive or negative, depending on plant species. <b>4.</b> We conclude that long-term differences in plant diversity lead to selection for altered plant phenotypes. Such differences may be further modified in association with the AMF microbial communities derived from the different plant diversity treatments, but often outcomes are species-specific. This suggests that plant species differ in their capacity to respond to diversity loss and associated changes in rhizosphere microbial communities, making it complicated to predict community-level responses to such loss.</p>
Data from: Leaf litter diversity and structure of microbial decomposer communities modulate litter decomposition in aquatic systems
1. Leaf litter decomposition is a major ecosystem process that can link aquatic to terrestrial ecosystems by flows of nutrients. Biodiversity and ecosystem functioning research hypothesizes that the global loss of species leads to impaired decomposition rates and thus to slower recycling of nutrients. Especially in aquatic systems an understanding of diversity effects on litter decomposition is still incomplete. 2. Here we conducted an experiment to test two main factors associated with global species loss that might influence leaf litter decomposition. Firstly, we tested whether mixing different leaf species alters litter decomposition rates compared to decomposition of these species in monoculture. Secondly, we tested the effect of the size structure of a lotic decomposer community on decomposition rates. 3. Overall, leaf litter identity strongly affected decomposition rates, and the observed decomposition rates matched measures of metabolic activity and microbial abundances. While we found some evidence of a positive leaf litter diversity effect on decomposition, this effect was not coherent across all litter combinations and the effect was generally additive and not synergistic. 4. Microbial communities, with a reduced functional and trophic complexity, showed a small but significant overall reduction in decomposition rates compared to communities with the naturally complete functional and trophic complexity, highlighting the importance of a complete microbial community on ecosystem functioning. 5. Our results suggest that top-down diversity effects of the decomposer community on litter decomposition in aquatic systems are of comparable importance as bottom-up diversity effects of primary producers.
Data from: Competition drives the response of soil microbial diversity to increased grazing by vertebrate herbivores
Scientists have largely neglected the effects of grazing on soil microbial communities despite their importance as drivers of ecosystem functions and services. We hypothesised that changes in soil properties resulting from grazing regulate the diversity of soil microbes by releasing/suppressing subordinate microbial taxa via competition. To test this, we examined intensity of vertebrate herbivores influences the diversity and composition of soil bacteria and fungi at 216 soil samples from 54 sites and four microsites. Increasing grazing intensity reduced soil carbon, suppressing the dominant bacterial phylum Actinobacteria (indirectly promoting bacterial diversity) and increasing the dominant fungal phylum Ascomycetes (indirectly reducing fungal diversity). Our data provide novel evidence that grazing modulates the diversity and composition of soil microbes via increases or reductions in competition by dominant taxa. Our results suggest that grazing can potentially alter soil function by altering microbial community composition, providing a clear link between grazing management, carbon availability and ecosystem functions.
Data from: A phylogenetic perspective on species diversity, β-diversity, and biogeography for the microbial world
There is an increasing interest to combine phylogenetic data with distributional and ecological records to assess how natural communities arrange under an evolutionary perspective. In the microbial world there is also a need to go beyond the problematic species definition to deeply explore ecological patterns using genetic data. We explored links between evolution/phylogeny and community ecology using bacterial 16S rRNA gene information from a high altitude lakes district dataset to describe phylogenetic community composition, spatial distribution, and β-diversity and biogeographical patterns applying evolutionary relatedness without relying on any particular operational taxonomic unit definition. High altitude lakes districts usually contain a large mosaic of highly diverse small water bodies and conform a fine biogeographical model of spatially close but environmentally heterogeneous ecosystems. We sampled eighteen lakes in the Pyrenees with a selection criteria focused on capturing the maximum environmental variation within a small geographical area. The results showed highly diverse communities non-randomly distributed with phylogenetic β-diversity patterns mainly shaped by the environment and not by the spatial distance. Community similarity based on both bacterial taxonomic composition and phylogenetic β-diversity approach shared similar patterns and were primarily structured by similar environmental drivers. We observed a positive relationship between lake area and phylogenetic diversity with a slope consistent with highly dispersive planktonic organisms. The phylogenetic approach incorporated patterns of common ancestry into bacterial community analysis and emerged as a very convenient analytical tool for direct inter- and intrabiome biodiversity comparisons and sorting out microbial habitats with potential application in conservation studies for microorganisms.
Spatial patterns and effects of invasive plants on soil microbial activity and diversity along river corridors - dataset
<p>environmental data, plant community data, CLPP profiles, microbial activity data</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>
Proteomics data for "Gut Microbial Beta-Glucuronidases Influence Endobiotic Homeostasis and Are Modulated by Diverse Therapeutics"
<p>Proteomics data used to generate results in "Gut Microbial Beta-Glucuronidases Influence Endobiotic Homeostasis and Are Modulated by Diverse Therapeutics" as published in <em>Cell Host and Microbe</em>. <a href="https://www.cell.com/cell-host-microbe/fulltext/S1931-3128(24)00138-0">Manuscript Link</a></p>
Data from: Crop health is predicted by soil microbial diversity across phylogenetic scales
<p>Soils contain diverse living communities that provide key ecosystem functions in agroecosystems. In many systems, ecosystems functions are positively related to the taxonomic, phylogenetic, and functional diversity of the community. Despite calls to incorporate microbial diversity in measures of soil health, whether increased microbial diversity <em>per se</em> can predict increased crop health and productivity has rarely been documented. Here we used microbial communities from commercial potato fields varying in diversity and composition, and experimentally assessed their ability to promote crop yield under low or high nutrient conditions and to suppress a soil-borne pathogen. Across two independent sets of communities, we found that yields under low nutrient conditions were predicted by high initial microbial diversity measured at broad phylogenetic levels, consistent with greater niche complementarity among unrelated taxa leading to greater total resource use. However, disease suppression was inconsistently linked to diversity and explained as well or better by microbial composition rather than diversity <em>per se</em>. Ecosystem multifunctionality was predicted by high diversity at broad to intermediate phylogenetic scales. These results indicate that the diversity of microbial taxa may influence multiple soil functions; however, the mechanisms underlying the diversity-function relationships may vary.</p>
Multiple diversity facets of crucial microbial groups in biological soil crusts promote soil multifunctionality
<p>Aim: Microbial diversity is one of the most important factors for maintaining the performance of multiple functions in soils (multifunctionality). However, existing studies typically consider taxonomic richness or Shannon diversity of the entire community. We know little about the connection network of taxonomic and phylogenetic diversity facets and their collective impact on multifunctionality. In this study, the linkages of diversity effects within functional groups were disentangled in drylands.</p> <p>Location: The central Tibetan Plateau.</p> <p>Time period: Present.</p> <p>Major taxa studied: Phototrophs and diazotrophs (mainly cyanobacteria).</p> <p>Methods: Given the carbon- and nitrogen-limited nature of drylands, we conducted a high throughput sequencing of C/N-fixing functional groups from biocrusts and evaluated multiple diversity facets (i.e., richness, evenness, and phylogeny-related trait dissimilarity), together with seven crucial variables of soil functioning to calculate multifunctionality. The relations between multifaceted diversity and abundance with individual functions and multifunctionality were validated by a set of solid statistical analyses.</p> <p>Results: We found that the integrated biodiversity index was a stronger predictor of multifunctionality than richness. The divergent performance of different diversity facets determined the idiosyncratic effect of each functional group on soil multifunctionality. Moreover, the evaluation of functional significance at the species level gave important clues on the trade-offs and redundancy in each functional group, explaining the distinct patterns of diversity effects. Namely, richness was the dominant factor for diazotrophs to maximize multifunctionality, whereas phylogenetic dissimilarity was the essential one for phototrophs.</p> <p>Main conclusions: our study demonstrated that multiple diversity facets should be considered when grasping the biodiversity effects. In contrast with the community level, within-functional group measures may adequately capture the features of diversity that are most correlated with soil multifunctionality. Our results provided a perspective to bridge the gap between taxonomic and trait-based approaches for elucidating the biodiversity-ecosystem function relationship.</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>
Afforestation can lower microbial diversity and functionality in deep soil layers in a semiarid region
<p>Afforestation is an effective approach to rehabilitate degraded ecosystems, but often depletes deep soil moisture. Presently, it is not known how an afforestation-induced decrease in moisture affects soil microbial community and functionality, hindering our ability to understand the sustainability of the rehabilitated ecosystems. To address this issue, we examined the impacts of 20 years of afforestation on soil bacterial community, co-occurrence pattern and functionalities along vertical profile (0-500 cm depth) in a semiarid region of China's Loess Plateau. We showed that the effects of afforestation with a deep-rooted legume tree on cropland were greater in deep than that of in top layers, resulting in decreased bacterial beta diversity, more responsive bacterial taxa and functional groups, increased homogeneous selection, and decreased network robustness in deep soils (120-500 cm). Organic carbon and nitrogen decomposition rates and multifunctionality also significantly decreased by afforestation, and microbial carbon limitation significantly increased in deep soils. Moreover, changes in microbial community and functionality in deep layer was largely related to changes in soil moisture. Such negative impacts on deep soils should be fully considered for assessing afforestation's eco-environment effects and for the sustainability of ecosystems because deep soils have important influence on forest ecosystems in semiarid and arid climates. </p>
Seasonal Variations of Microbial Communities and Viral Diversity in Fishery-Enhanced Marine Ranching Sediments: Insights into Metabolic Potentials and Ecological Interactions
<p>Sediment samples were collected in four seasons from May 2022 to January 2023 from the Tian coastal marine ranching (36°91′ N and 122°15′ E) located along Jinghai Bay in Weihai City, Shandong Province, China. We employed amplicon (16S and 18S) and metagenomic approaches aiming to reveal the seasonal patterns of microbial communities, bacterial-eukaryotic interactions, whole metabolic potential, and their coupling mechanisms with carbon (C), nitrogen (N), and sulfur (S) cycling in marine ranching sediments. Additionally, the characterization and diversity of viral communities in different seasons were explored in marine ranching sediments. This dataset mainly includes amplicon sequencing (16S and 18S) generated ASV tables (after rarefied), corresponding taxonomic classification tables, metagenome assembly (Single assembly and Co-assembly), <span>metagenome-assembled genomes (MAGs)</span> sequences, and <span>viral operational taxonomic units (vOTUs)</span> sequences.</p>
Dataset and R code for phyllosphere microbial diversity during rubber tree leaf senescence
Open the record for dataset details and reuse information.
Soil and environmental data for "Interacting management effects on soil microbial alpha and beta diversity in Swiss agricultural grassland"
<p>This data shows the soil, environmental, and management data of 86 grassland sites that were sampled within the Canton of Solothurn, Switzerland. This data was used in the manuscript by F.J. Richter, R. Feola Conz, A. Lüscher, N. Buchmann, K.H. Valentin and M. Hartmann (2024): Interacting management effects on soil microbial alpha and beta diversity in Swiss agricultural grassland, which is published in the Journal of Applied Soil Ecology. </p>
Data from: Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States
Native tallgrass prairie once dominated much of the midwestern United States, but this biome and the soil microbial diversity that once sustained this highly productive system have been almost completely eradicated by decades of agricultural practices. We reconstructed the soil microbial diversity that once existed in this biome by analyzing relict prairie soils and found that the biogeographical patterns were largely driven by changes in the relative abundance of Verrucomicrobia, a poorly studied bacterial phylum that appears to dominate many prairie soils. Shotgun metagenomic data suggested that these spatial patterns were associated with strong shifts in carbon dynamics. We show that metagenomic approaches can be used to reconstruct below-ground biogeochemical and diversity gradients in endangered ecosystems; such information could be used to improve restoration efforts, given that even small changes in below-ground microbial diversity can have important impacts on ecosystem processes.
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>
Reconstructing the landscape of gut microbial species across 29,000 diverse individuals
<p>The human gut microbiome has been linked to health and disease. Investigation of the human microbiome has largely employed 16S amplicon sequencing, with limited ability to distinguish microbes at the species level. Herein, we describe the development of Reference-based Exact Mapping (RExMap) of microbial amplicon variants that enables mapping of microbial species from standard 16S sequencing data. RExMap analysis of 16S data captures ~75% of microbial species identified by whole-genome shotgun sequencing, despite hundreds-fold less sequencing depth. RExMap re-analysis of existing 16S data from 29,349 individuals across sixteen regions from around the world reveals a detailed landscape of gut microbial species across populations and geography. Moreover, RExMap identifies a core set of fifteen gut microbes shared by humans. Core microbes are established soon after birth and closely associate with BMI across multiple independent studies. RExMap and the human microbiome dataset are presented as resources with which to explore the role of the human microbiome.</p>
Soil acidification reduces soil fungal diversity, alters microbial carbon metabolism and enhances soil C persistence in an alkaline grassland
<p>This dataset was used to make tables and figures for the study entitled "Soil acidification reduces soil fungal diversity, alters microbial carbon metabolism and enhances soil C persistence in an alkaline grassland", which will be recently submitted to Global Change Biology in October 2023. It contains data of soil properties, plant and microbial communities under soil acidification in an alkaline grassland on the Loess Plateau. </p>
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.