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12 results for “microbial biodiversity”
Data from: Agricultural land-use history and restoration impact soil microbial biodiversity
<ol> <li>Human land uses, such as agriculture, can leave long-lasting legacies as ecosystems recover. As a consequence, active restoration may be necessary to overcome land-use legacies; however, few studies have evaluated the joint effects of agricultural history and restoration on ecological communities. Those that have studied this joint effect have largely focused on plants and ignored other communities, such as soil microbes.</li> <li>We conducted a large-scale experiment to understand how agricultural history and restoration tree thinning affect soil bacterial and fungal communities within longleaf pine savannas of the southern United States. This experiment contained 64 pairs of remnant (no history of tillage agriculture) and post-agricultural (reforested following abandonment from tillage agriculture >60 years prior) longleaf pine savanna plots. Plots were each 1-ha and arranged into 27 blocks to minimize land-use decision making biases. We experimentally restored half of the remnant and post-agricultural plots by thinning trees to reinstate open-canopy savanna conditions and collected soils from all plots five growing seasons after tree thinning. We then evaluated soil bacterial and fungal communities using metabarcoding.</li> <li>Agricultural history increased bacterial diversity but decreased fungal diversity, while restoration increased both bacterial and fungal diversity. Both bacterial and fungal richness were correlated with a range of environmental variables including aboveground variables like leaf litter and plant diversity, and belowground variables such as soil nutrients, pH, and organic matter, many of which were also impacted by agricultural history and restoration.</li> <li>Fungal and bacterial community compositions were shaped by restoration and agricultural history resulting in four distinct communities across the four treatment combinations.</li> <li>Past agricultural land use left persistent legacies on soil microbial biodiversity, even over half a century after agricultural abandonment and after intensive restoration activities. The impacts of these changes on soil microbe biodiversity could play important roles in the functioning of ecosystems following agricultural abandonment and during restoration.</li> </ol>
Data from: Plant biodiversity responds more strongly to climate warming and anthropogenic activities than microbial biodiversity in the Qinghai-Tibetan alpine grasslands
<p>Biodiversity serves as the fundamental underpinning for ecosystem functions and services. As a result of human-induced global change, there is a growing awareness of the substantial alterations in terrestrial aboveground biodiversity, particularly within alpine regions. However, it remains uncertain whether belowground biodiversity will exhibit similar responses, both in terms of magnitude and manner, to anthropogenic global changes as aboveground biodiversity.</p> <p>Here, we conducted a meta-analysis to assess the impacts of warming, nutrient addition, and grazing on plant and soil microbial biodiversity in alpine grasslands on the Qinghai-Tibetan Plateau, which are known to be climate-sensitive and vulnerable. The analysis included 819 experimental observations from 152 studies, focusing on species richness, Shannon diversity, and Pielou's evenness.</p> <p>We found that plant biodiversity exhibited greater sensitivity to climate warming and anthropogenic activities compared to soil microbial biodiversity. Specifically, plant richness and Shannon diversity were reduced by warming and nutrient addition, while plant evenness was increased by grazing. However, only microbial richness was increased by grazing and microbial evenness was increased by warming slightly.</p> <p>The responses of biodiversity to climate warming and anthropogenic activities were modulated by multiple factors. Specifically, the negative effects of warming on plant biodiversity were more pronounced in long-term experiments under warmer or drier environmental conditions. The negative effects of nitrogen addition on biodiversity were enhanced by the intensity and duration of nitrogen treatment. Appropriate intensity and frequency of grazing were beneficial to sustaining plant biodiversity. Soil microbial biodiversity was weakly regulated, where bacterial Shannon diversity was more sensitive to nutrient addition, while fungal species richness was sensitive to grazing.</p> <p><strong>Synthesis: </strong>Our findings reveal a mismatch between aboveground plant and belowground microbial biodiversity in response to climate warming and anthropogenic activities in alpine grasslands, with plant biodiversity being more sensitive. In the context of future global change, plant biodiversity may be at greater risk than soil microbial biodiversity. In addition, biodiversity responses of different experimental and environmental conditions should be distinguished, and more attention is needed on biodiversity conservation in alpine steppe, or areas with warmer and drier environmental conditions, high-intensity fertilization or heavy grazing. </p>
Data from: Connectivity loss in experimental pond networks leads to biodiversity loss in microbial metacommunities
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First atlas of soil microbial biodiversity in Mexico: a biogeographical approach
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Data from: Plant biodiversity responds more strongly to climate warming and anthropogenic activities than microbial biodiversity in the Qinghai-Tibetan alpine grasslands
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Data from: Agricultural land-use history and restoration impact soil microbial biodiversity
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Soil microbial functions and enzyme activity:BAC: Biodiversity and Climate
Climate changes forecast for our region by GCM???s and shifts in biodiversity and composition each have the potential to alter ecosystem functioning; their interactive effects are unknown. The "BAC" experiment is designed to determine the direct and interactive effects of plant species numbers, plant community composition, temperature, and precipitation on 11 productivity, C and N dynamics, stability, and plant, microbe, and insect species abundances in CDR grassland ecosystems.
Data from: Strength of species interactions determines biodiversity and stability in microbial communities
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Soil microbial respiration rate:Dimensions of Biodiversity - Genetic, Phylogenetic, Functional, and Remotely Sensed Diversity
Novel remote sensing methods for monitoring the Earth's biodiversity will be applied to experimental manipulations of plant diversity - allowing scientists to examine the linkages between plant biodiversity, soil microbe diversity and ecosystem function at multiple scales of spatial resolution. Specifically, we propose to link remotely sensed optical diversity to plant functional, phylogenetic and genotypic diversity aboveground and to net primary production (NPP), and soil properties and microbial processes belowground, as a basis for predicting ecosystem processes with remote sensing. Our central hypothesis is that i) biodiversity (genotypic, functional and phylogenetic diversity) at one trophic level (plants) drives genetic and functional diversity in other trophic levels (soil microbes) with consequences for ecosystem function and ii) that such diversity can be detected remotely at multiple scales of spatial resolution. We propose to test this hypotheses within the long-term prairie biodiversity experiment (e120 Big Bio), the newly established Forest and Biodiversity (e271 FAB 1) experiment, and the Biodiversity of Willows and Poplars (e277 BiWaP) experiment. We will measure optical properties of these plots at the leaf level, 1 m above the plant canopy and from aircraft. Leaf level sampling and percent cover estimates will be non-destructive. Biomass sampling in Big Bio will follow standard protocol for the long-term experiment. Biomass estimates in FAB and BiWaP will use non-destructive methods. Below ground sampling in BigBio will be taken within the clip strip for biomass harvest. The proposed research involves researchers at the University of Minnesota, the University of Alberta, the University of Nebraska Lincoln, the University of Wisconsin, and Appalachian State University.
Data from: Measuring the biodiversity of microbial communities by flow cytometry
1. Measuring the microbial diversity in natural and engineered environments is important for ecosystem characterization, ecosystem monitoring and hypothesis testing. Although the conventional assessment through single marker gene surveys has resulted in major advances, the complete procedure remains slow (i.e., weeks to months), labour-intensive and susceptible to multiple sources of laboratory and data processing bias. Growing interest, in highly resolved, temporal surveys of microbial diversity, necessitates rapid, inexpensive and robust analytical platforms that require limited computational effort. 2. Here, we demonstrate that sensitive single-cell measurements of phenotypic attributes, obtained via flow cytometry, can provide fast (i.e., within minutes) first-line assessments of microbial diversity dynamics, without demanding extensive sample preparation and downstream data processing. We developed a data processing pipeline that fits bivariate kernel density functions to phenotypic parameter combinations of an entire microbial community, and concatenates them to a single one-dimensional phenotypic fingerprint. By calculating established diversity metrics from such phenotypic fingerprints, we construct an alternative interpretation of the microbial diversity that incorporates distinct phenotypic traits underlying cell-to-cell heterogeneity (i.e., morphology and nucleic acid content). 3. Based on a detailed longitudinal study of a highly dynamic microbial ecosystem, our approach delivered temporal alpha diversity profiles that strongly correlated with the reference diversity, as estimated by 16S rRNA amplicon sequencing. This strongly suggests that the distribution of a limited amount of phenotypic features within a microbial community already provides sufficient resolving power for the measurement of diversity dynamics at the species level. 4. We present a fast, robust analysis method for monitoring the microbial biodiversity of natural and engineered ecosystems that correlates well with the conventional marker gene surveys. Our work has both applied and fundamental implications that stretch from ecosystem monitoring and studies on microbial community dynamics, to supervised sampling strategies. Furthermore, our approach offers perspectives for the development of on-line and in situ monitoring systems for microbial ecosystems.
Data from: Measuring the biodiversity of microbial communities by flow cytometry
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Marine microbial endoliths: biodiversity and function
<p><span>Organisms that colonize the interior of rocks, shell hash and other skeletal fragments are known as endoliths. Coastal euendoliths are ideal model systems for microbial biogeographical studies, as coasts comprise the most abundant biome on the Earth that is stable, characterized by relatively low productivity and turnover rates. Euendoliths of marine environments especially along the intertidal and supratidal ranges of carbonate coasts are significant contributors to marine bioerosion, as documented by microscopic, but hardly any molecular studies. Endoliths expand our understanding about the ability of organisms to survive and even thrive in extreme conditions. They also raise new ideas regarding the possibility of extraterrestrial life and may alter our ideas about the origin of life on Earth. </span></p> <p><span>Despite their environmental relevance, the mechanism that enables them to dissolve carbonates, even in waters supersaturated with respect to calcite and aragonite, has remained elusive. In our study we provide a comparative sequence analysis using MiSeq DNA and RNA pyrosequencing of the 16S rRNA gene combined with extensive microscopy of the endolithic community from different geographical regions, and different nutrient regimes.</span></p> <p><span>Our forte is the use of molecular tools for the first time to carbonate penetrating microorganisms, where they naturally occur, an approach that will provide a direct information link between cell´s phylogenetic and metabolic markers.</span><span> Our data provide information concerning16S rRNA RNA-seq vs. DNA pyrosequencing of heterotrophic bacteria and cyanobacteria in order to differentiate between active and dormant populations from coastal endoliths. </span></p> <p><span>We applied for the first time single cell genomics (SCG) to endolithic organisms, matching phylogeny and metabolism in the uncultured cyanobacterial endoliths that dominate marine rocks and biochemical cycles.</span></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.