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360 results for “microbe”
Data for: Drivers of wood decay in tropical ecosystems: Termites vs. microbes along spatial, temporal and experimental precipitation gradients
<ol> <li>Models estimating decomposition rates of dead wood across space and time are mainly based on studies carried out in temperate zones where microbes are dominant drivers of decomposition. However, most dead wood biomass is found in tropical ecosystems, where termites are also important wood consumers. Given the dependence of microbial decomposition on moisture with termite decomposition thought to be more resilient to dry conditions, the relative importance of these decomposition agents is expected to shift along gradients in precipitation that affect wood moisture.</li> <li>Here, we investigated the relative roles of microbes and termites in wood decomposition across precipitation gradients in space, time and with a simulated drought experiment in tropical Australia. We deployed mesh bags with non-native pine wood blocks, allowing termite access to half the bags. Bags were collected every six months (end of wet and dry seasons) over a four-year period across 5 sites along a rainfall gradient (ranging from savanna to wet sclerophyll to rainforest) and within a simulated drought experiment at the wettest site. We expected microbial decomposition to proceed faster in wet conditions with greater relative influence of termites in dry conditions.</li> <li>Consistent with expectations, microbial-mediated wood decomposition was slowest in dry savanna sites, dry seasons, and simulated drought conditions. Wood blocks discovered by termites decomposed 16% to 36% faster than blocks undiscovered by termites regardless of precipitation levels. Concurrently, termites were 10 times more likely to discover wood in dry savanna compared with wet rainforest sites, compensating for slow microbial decomposition in savannas. For wood discovered by termites, seasonality and drought did not significantly affect decomposition rates.</li> <li>Taken together, we found that spatial and seasonal variation in precipitation are important in shaping wood decomposition rates as driven by termites and microbes, although these different gradients do not equally impact decomposition agents. As we better understand how climate change will affect precipitation regimes across the tropics, our results can improve predictions of how wood decomposition agents will shift with potential for altering carbon fluxes.</li> </ol>
The Alteromonas Digital Microbe without Singletons
<p>This describes an <em>Alteromonas</em> digital microbe that contains a pangenome (without singleton genes) as well as corresponding item and layer data. This digital microbe is authored by Michelle DeMers (MIT) and Rogier Braakman (MIT) with help from the Meren Group and Moran Lab. The following files are included:</p> <p>Alteromonas_2_1_1_dbs.tar.gz: A compressed directory of all genomes dbs and the genome storage db used to make the pangenome.</p> <p>Alteromonas_Pangenome_2_1ns-PAN.db.tar.gz: The compressed pangenome without singletons.</p> <p>nsPangneomeFile*.tar.gz: A compressed directory of files produced while making the pangenome.</p> <p>external-genomes-v2.txt: The external genomes file that contains the name of each genome with the genome ID.</p> <p>layer_orders.txt: Phylogeny file from v 2.1.1 of this digital microbe.</p> <p>ANI2_1ns.tar.gz: Compressed directory produced when calculating ANI.</p>
Data for: Microbe-induced plant resistance alters aphid inter-genotypic competition leading to rapid evolution with consequences for plant growth and aphid abundance
<p>Plants and insect herbivores are two of the most diverse multicellular groups in the world, and both are strongly influenced by interactions with the belowground soil microbiome. Effects of reciprocal rapid evolution on ecological interactions between herbivores and plants have been repeatedly demonstrated, but it is unknown if (and how) the soil microbiome could mediate these eco-evolutionary processes on a shared host plant. We tested the role of a plant-beneficial soil bacterium (<em>Acidovorax radicis</em>) in altering eco-evolutionary interactions between different aphid genotypes (Sitobion avenae; genotypes Sickte and Fescue) feeding on barley (<em>Hordeum vulgare</em>). We measured fecundity, longevity and population growth of two aphid genotypes reared separately or together (population mixture) on three different barley varieties that were inoculated with or without <em>A. radicis</em>. Results showed that across all plant varieties <em>A. radicis</em> increased plant growth and suppressed aphid populations via reduced longevity and fecundity. The strength of effect was dependent on aphid genotype and barley variety, while the direction of effect was altered by aphid population mixture. Using Lotka-Volterra modelling, we demonstrated that while <em>A. radicis</em> inoculation decreased growth rates for both aphid genotypes it increased the competitiveness of one genotype against the other. In general, in the presence of <em>A. radicis</em>, the Fescue aphid genotype became more inhibitory of Sickte aphids, while Sickte aphids facilitated the growth of Fescue aphids. Our work demonstrates that plant rhizosphere microbiomes exert community-level influences by mediating eco-evolutionary interactions between herbivores and host plants. By altering competitive interaction outcomes among aphids and thus impacting processes such as rapid evolution, soil microbes contribute to the short- and long-term structure and functioning of terrestrial habitats.</p>
263 MAG annotations for three nested metagenomic studies describe crop-shrub-microbe interactions in an agroecology system in the Sahel
<p>The Sahel region of West Africa is a vulnerable eco-region, where climate change induced drought and a rapidly growing population pose serious threats to food security and contribute to soil degradation. Local and biologically based systems are necessary to maintain crop yields and soil health, and intercropping with native woody shrubs Guiera senegalensis has been discovered as a solution. We have previously shown that soil microbial communities are significantly altered by the presence of shrubs, and that these organisms may have plant growth promoting properties. Here, we augment those data with metagenomic and metatranscriptomic data across three nested experiments: a landscape scale experiment across a rainfall and soil type gradient, a long-term experimental site, and a growth chamber simulated drought experiment. We recovered 263 95% ANI dereplicated metagenome-assembled genomes (MAGs) of medium and high quality to evaluate their relative enrichment and what their encoded metabolisms reveal about mechanisms of microbiome millet support. These data contribute to our understanding of the role of the microbial community crop drought resilience in the Sahel and in semi-arid cropping systems globally. Here we present the DRAM annotations of each MAG, all associated metadata, viral genes and vOTUs from the Optimized Shrub Intercropping Study (OSS), and eukaryotic contigs from the OSS</p>
scmcclelland/joint-mediation-study: Data, Analysis, and Figure Scripts for "Soil organic carbon sequestration jointly-mediated by plants and microbes after compost application"
<p>This repository contains data, analysis, and figure scripts to create findings from the manuscript "Soil organic carbon sequestration jointly-mediated by plants and microbes after compost application" currently under minor revisions.</p> <p>This release includes updated code, primarily improvements to figures, and a new script for a supplementary map figure.</p>
Do flower-colonizing microbes influence floral evolution? A test with fast-cycling Brassica
<p>Pollinators are thought to be the main drivers of floral evolution. Flowers are also colonized by abundant communities of microbes that can affect the interaction between plants and their pollinators. Very little is known, however, about how flower-colonizing microbes influence floral evolution. Here we performed a six-generation experimental evolution study using fast-cycling <em>Brassica rapa</em>, in which we factorially manipulated the presence of pollinators and flower microbes to determine how pollinators and microbes interact in driving floral evolution. We measured the evolution of six morphological traits, as well as plant mating system and flower attractiveness. Only one of the six traits (flower number) evolved in response to pollinators, while microbes did not drive the evolution of any trait, nor did they interact with pollinators in driving evolution of morphological traits. Moreover, we did not find evidence that pollinators or microbes affected the evolution of flower attractiveness to pollinators. However, we found an interactive effect of pollinators and microbes on the evolution of autonomous selfing, a trait that is expected to evolve in response to pollinator limitation. Overall, we found only weak evidence that microbes mediate floral evolution. However, our ability to detect an interactive effect of pollinators and microbes might have been limited by weak pollinator-mediated selection in our experimental setting. Our results contrast with previous (similar) experimental evolution studies, highlighting the susceptibility of such experiments to drift and to experimental artefacts.</p>
Figure 2. Interaction between nitrogen x phosphorus for seeds pod-1 in Role of beneficial microbes with nitrogen and phosphorous levels on canola productivity
Figure 2. Interaction between nitrogen x phosphorus for seeds pod-1 (a), phosphorous x beneficial microbes for seeds pod-1 (b), nitrogen x beneficial microbes for grains weight (c), and nitrogen x beneficial microbes for seed yield (kg ha-1) of canola (d).
Figure 1 in Role of beneficial microbes with nitrogen and phosphorous levels on canola productivity
Figure 1. Mean monthly maximum & minimum temperature (°C), solar radiation (), relative humidity (%) and rainfall (mm) of the growing season of canola crop (2,016-2,017).
Data from: Microbe-dependent heterosis in maize
<p>Data and statistical code associated with the manuscript "<strong>Microbe-dependent heterosis in maize" </strong>Wagner, Maggie R.; Tang, Clara; Salvato, Fernanda; Clouse, Kayla M.; Bartlett, Alexandria; Vintila, Simina; Phillips, Laura; Sermons, Shannon; Hoffmann, Mark; Balint-Kurti, Peter J.; Kleiner, Manuel (2021) PNAS July 27, 2021 118 (30) e2021965118; https://doi.org/10.1073/pnas.2021965118</p> <p><strong>19 October 2020: </strong>new version posted to add <strong>fum_16S_ITS.zip</strong></p> <ul> <li>Archive containing processed 16S and ITS amplicon data (i.e., ASV tables) from the soil fumigation experiment. In addition, it contains all code and accessory files used to process and analyze the sequence data. The archive contains its own readme.txt with details on the files and their usage.</li> </ul> <p><strong>27 July 2021: </strong>new version 3 posted to add <strong>Expt4_data.xlsx</strong> and <strong>SynCom_colonization_data.xlsx</strong> . New version 4 posted to include the updated README and analytical code (mdh_analysis_revised.R)</p> <ul> <li><strong>Expt4_data.xlsx </strong>= Raw data from Experiment 4 (Kansas field experiment, summer 2020)</li> <li><strong>SynCom_colonization_data.xlsx</strong> = Raw measurements of colonization rates of SynCom bacterial strains in 4 maize genotypes</li> </ul> <p>Funding: National Science Foundation, IOS-2033621</p>
Data from: Soil microbes influence the ecology and evolution of plant plasticity
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Microbes as manipulators of egg size and developmental evolution
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Data for: Drivers of wood decay in tropical ecosystems: Termites vs. microbes along spatial, temporal and experimental precipitation gradients
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Do flower-colonizing microbes influence floral evolution? A test with fast-cycling Brassica
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Environment-mediated interactions cause an externalized and collective memory in microbes
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Is there a latitudinal diversity gradient for symbiotic microbes? A case study with sensitive partridge peas
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Data for: Microbe-induced plant resistance alters aphid inter-genotypic competition leading to rapid evolution with consequences for plant growth and aphid abundance
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Data for Lynn et al. “Soil microbes that may accompany climate warming increase alpine plant production”; accepted at Oecologia
Climate change is causing species with non-overlapping ranges to come in contact, and a key challenge is to predict the consequences of such species re-shuffling. Experiments on plants have focused largely on novel competitive interactions; other species interactions, such as plant-microbe symbioses, while less studied, may also influence plant responses to climate change. In this greenhouse study, we evaluated interactions between soil microbes and alpine-restricted plant species, simulating a warming scenario in which low elevation microbes migrate upslope into the distribution of alpine plants. We examined three alpine grasses from the Rocky Mountains, CO, USA (Poa alpina, Festuca brachyphylla, Elymus scribneri). We used soil inocula from within (resident) or below (novel) the plants' current elevation range and examined responses in plant biomass, plant traits, and fungal colonization of roots. Resident soil inocula from the species' home range decreased biomass to a greater extent than novel soil inocula. The depressed growth in resident soils suggested these soils harbor more carbon-demanding microbes, as plant biomass generally declined with greater fungal colonization of roots, especially in resident soil inocula. Although plant traits did not respond to the provenance of soil inocula, specific leaf area declined and root:shoot ratio increased when soil inocula were sterilized, indicating microbial mediation of plant trait expression. Contrary to current predictions, our findings suggest that if upwardly migrating microbes were to displace current soil microbes, alpine plants may benefit from this warming-induced microbial re-shuffling.
Temporal and spatial dynamics of Synechococcus clade II and other microbes in the eutrophic subtropical San Diego Bay
This data set comprises amplicon sequence variants (ASVs) from the nutrient-replete waters of San Diego Bay (SDB). Using 16S and 18S rRNA gene and internal transcribed spacer (ITS) region sequencing for Synechococcus, we analyzed multiple locations in San Diego Bay monthly for over a year (2021-2022) with additional samples dating back to 2015. San Diego Bay ITS region sequences were compared to nearby coastal samples collected from the Scripps Pier at Scripps Institution of Oceanography.
Data from: The effect of root-associated microbes on plant growth and chemical defence traits across two contrasted elevations,
<p>1. Ecotypic differences in plant growth and anti-herbivore defence phenotypes are determined by the complex interactions between the abiotic and the biotic environment.</p> <p>2. Root-associated microbes (RAMs) are pervasive in nature, vary over climatic gradients, and have been shown to influence the expression of multiple plant functional traits related to biomass accumulation and biotic interactions. We addressed how variation in climatic conditions between lowland and sub-alpine habitats in the Alps and RAMs can independently or interactively affect plant growth and anti-herbivore defence trait expression.</p> <p>3. To address the contribution of climate and RAMs on growth and chemical defences of high- and low-elevation Plantago major ecotypes, we performed a full-factorial reciprocal transplant field experiment at two elevations. We coupled it with plant functional trait measurements and metabolomics analyses.</p> <p>4. We found that local growing climatic conditions mostly influenced how the ecotypes grew, but we also found that the high- and low-elevation ecotypes improved biomass accumulation if in the presence of their own-elevation RAMs. Second, we found that while chemical defence expression was affected by climate, they were also more highly expressed when plants were inoculated with low elevation RAMs.</p> <p>5. Synthesis – Our research demonstrated that RAMs from contrasted elevations impact how plants grow or synthesize toxic secondary metabolites. At low elevation, where biotic interactions are stronger, RAMs enhance plant biomass accumulation and the production of toxic secondary metabolites.</p>
Data from: Effect of pH regulation by microbes on corrosion behaviour of duplex stainless steel 2205 in acidic artificial seawater environment
Sulphate reducing bacteria (SRB) can regulate environmental pH because of their metabolism. Since local acidification results in pitting corrosion, the potential capacity of pH regulation by SRB would have important consequences for electrochemical aspects of the bio-corrosion process. This study focussed on identifying the effect of pH on the corrosion of duplex stainless steel (DSS) 2205 in a nutrient rich artificial seawater medium containing SRB species, Desulfovibrio vulgaris. DSS samples were exposed to the medium for 13 days at 37 0C at pH ranging from 4.0 to 7.4. The open circuit potential value (OCP), sulphide level, pH and number of bacteria in the medium were recorded daily. Electrochemical impedance spectroscopy (EIS) and potential dynamic polarization were used to study the properties of the films and corrosion behaviour of the material. Inductively coupled plasma mass spectrometry (ICPMS) was used to measure the concentration of cations Cr, Fe, Ni, Mo, Mn in the experimental solution after 13 days. Scanning electron microscopy (SEM) and Energy Dispersive X-Ray Spectroscopy (EDX) were used for surface analysis. The results showed the pH changed from acidic values set at the beginning of the experiment to approximately pH 7.5 after 5 days due to bacterial metabolism. After 13 days, the highest iron concentration was in the solution that was initially at pH 4 accompanied by pitting on the stainless steel. Sulphide was present on all specimens but with more sulphide corrosion products at pH 4. The results of this study suggest that the corrosion process for the first few days exposure at low pH was driven by pH in solution rather than by bacteria. The increasing pH during the course of the experiment slowed down the corrosion process of materials originally at low pH. The nature and mechanism of SRB attack on duplex stainless steel at different acidic environments are discussed.
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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)
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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.