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12 results for “core microbiome”
SUPPLEMENTARY TABLES: Defining the Sphagnum core microbiome across the North American continent reveals a central role for diazotrophic-methanotrophs in the nitrogen and carbon cycles of boreal peatland ecosystems
<p>Peat mosses of the genus <em>Sphagnum</em> are ecosystem engineers that frequently predominate over photosynthetic production in boreal peatlands. <em>Sphagnum</em> spp. host diverse microbial communities capable of nitrogen-fixation (diazotrophy) and methane oxidation (methanotrophy), thereby potentially supporting plant growth under severely nutrient-limited conditions. Moreover, diazotrophic-methanotrophs represent a possible "missing link" between the carbon and nitrogen cycles, but the functional contributions of the <em>Sphagnum</em>-associated microbiome remain in question<em>.</em> A combination of metagenomics, metatranscriptomics, and dual-isotope incorporation assays was applied to investigate <em>Sphagnum</em> microbiome community composition across the North American continent and provide empirical evidence for diazotrophic-methanotrophy in <em>Sphagnum</em>-dominated ecosystems. Remarkably consistent prokaryotic communities were detected in over 250 <em>Sphagnum</em> SSU rRNA libraries from peatlands across the US (5 states, 17 bog/fen sites, 18 <em>Sphagnum</em> species), with twelve genera of the core microbiome comprising 60% of the relative microbial abundance. Additionally, nitrogenase (<em>nifH</em>) and SSU rRNA gene amplicon analysis revealed that nitrogen-fixing populations made up nearly 15% of the prokaryotic communities, predominated by <em>Nostocales</em> cyanobacteria and <em>Rhizobiales</em> methanotrophs. While cyanobacteria comprised the vast majority (>95%) of diazotrophs detected in amplicon and metagenome analyses, obligate methanotrophs of the genus <em>Methyloferula</em> (order <em>Rhizobiales</em>) accounted for one-quarter of transcribed <em>nifH</em> genes. Furthermore, in dual-isotope tracer experiments, members of the <em>Rhizobiales</em> showed substantial incorporation of <sup>13</sup>C-CH<sub>4</sub> and <sup>15</sup>N-N<sub>2</sub> isotopes into their rRNA. Our study characterizes the core <em>Sphagnum</em> microbiome across large spatial scales and indicates that diazotrophic methanotrophs, here defined as obligate methanotrophs of the rare biosphere (<em>Methyloferula</em> spp. of the <em>Rhizobiales</em>) that also carry out diazotrophy, play a keystone role in coupling of the carbon and nitrogen cycles in nutrient-poor peatlands.</p>
Data from: A first draft of the core fungal microbiome of Schedonorus arundinaceus with and without its fungal mutualist Epichloë coenophiala
<p>Tall fescue (<em>Schedonorus arundinaceus</em>) is a cool-season grass that is commonly infected with the fungal endophyte <em>Epichloë</em> <em>coenophiala</em>. Although the relationship between tall fescue and <em>E</em>. <em>coenophiala</em> is well-studied, less is known about its broader fungal communities. We used next-generation sequencing of the ITS2 region to describe the complete foliar fungal microbiomes in a set of field-grown tall fescue plants over two years, and whether these fungal communities were affected by the presence of <em>Epichloë</em>. We used the Georgia 5 cultivar of tall fescue, grown in the field for six years prior to sampling. Plants were either uninfected with <em>E</em>. <em>coenophiala</em>, or they were infected with one of two <em>E</em>. <em>coenophiala</em> strains: the common toxic strain or the AR542 strain (sold commercially as MaxQ). We observed 3,487 amplicon sequence variants (ASVs) across all plants and identified 43 ASVs that may make up a potential core microbiome. Fungal communities did not differ strongly between <em>Epichloë</em> treatments but did show a great deal of variation between the two years. Plant fitness also changed over time but was not influenced by <em>E</em>. <em>coenophiala</em> infection.</p>
Epiphytic common core bacteria in the microbiomes of co-located green (Ulva), brown (Saccharina, Gelidium) and red (Grateloupia) macroalgae
<p>We collected specimens of <em>Ulva </em>sp. (green algae), <em>Saccharina </em>sp. (brown algae), <em>Grateloupia </em>sp., and <em>Gelidium </em>sp. (both red algae) during all four seasons from a coastal reef in Weihai, China, and analyzed their surface-colonizing bacteria in comparison to surrounding seawater and sediment controls. 16S rRNA amplicon sequencing, extensive plate cultivation, sequencing of selected strains, and sequencing of 23 metagenomes were performed in this study. Besides composition, we analyzed the potential of phycosphere bacteria to degrade algal polysaccharides and to produce bioactive secondary metabolites. This comprehensive dataset represents a significant stepping stone towards a better understanding of macroalgal phycosphere bacteria and paves the way to functional studies on representative strains.</p>
Data from: A first draft of the core fungal microbiome of Schedonorus arundinaceus with and without its fungal mutualist Epichloë coenophiala
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Data from: Group living and male dispersal predict the core gut microbiome in wild baboons
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Data from: A 454 survey reveals the community composition and core microbiome of the common bed bug (Cimex lectularius) across an urban landscape
Elucidating the spatial dynamic and core constituents of the microbial communities found in association with arthropod hosts is of crucial importance for insects that may vector human or agricultural pathogens. The hematophagous Cimex lectularius (Hemiptera: Cimicidae), known as the human bed bug, has made a recent resurgence in North America, as well as worldwide, potentially owing to increased travel, climate change and resistance to insecticides. A comprehensive survey of the bed bug microbiome has not been performed to date, nor has an assessment of the spatial dynamics of its microbiome. Here we present a survey of internal and external bed bug microbial communities by amplifying the V4–V6 hypervariable region of the 16S rDNA gene region followed by 454 Titanium sequencing using 31 individuals from eight distinct collection locations obtained from residences in Cincinnati, OH. Across all samples, 97% of the microbial community is made up of two dominant OTUs, previously identified as the α-proteobacterium Wolbachia and an unnamed γ-proteobacterium from the Enterobacteriaceae. Microbial communities varied among host locations for measures of community diversity and exhibited structure according to collection location. This broad survey represents the most in-depth assessment, to date, of the microbes that associate with bed bugs.
Data from: Diet breadth and exploitation of exotic plants shift the core microbiome of Cephaloleia, a group of tropical herbivorous beetles
The beetle genus Cephaloleia has evolved in association with tropical ginger plants and for many species their specific host plant associations are known. Here we show that the core microbiome of six closely related Costa Rican Cephaloleia species comprises only eight bacterial groups, including members of the Acinetobacter, Enterobacteriacea, Pseudomonas, Lactococcus, and Comamonas. The Acinetobacter and Enterobacteriacea together accounted for 35% of the total average 16S rRNA ribotypes recovered from all specimens. Further, microbiome diversity and community structure was significantly linked to beetle diet breadth, between those foraging on less than two plant types (specialists) versus over nine plant types (generalists). Moraxellaceae, Enterobacteriaceae, and Pseudomonadaceae were highly prevalent in specialist species, and also present in eggs, while Rickettsiaceae associated exclusively with generalist beetles. Bacteria isolated from Cephaloleia digestive systems had distinct capabilities and suggested a possible beneficial role in both digestion of plant-based compounds, including xylose, mannitol, and pectin, and possible detoxification, via lipases. Cephaloleia species are currently expanding their diets to include exotic invasive plants, yet it is unknown whether their microbial community plays a role in this transition. In this study, colonization of invasive plants was correlated with a dysbiosis of the microbiome, suggesting a possible relationship between gut bacteria and niche adaptation.
Data from: Diet breadth and exploitation of exotic plants shift the core microbiome of Cephaloleia, a group of tropical herbivorous beetles
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Data from: The core microbiome bonds the Alpine bog vegetation to a transkingdom metacommunity
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Data from: A 454 survey reveals the community composition and core microbiome of the common bed bug (Cimex lectularius) across an urban landscape
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Data from: Burying beetles regulate the microbiome of carcasses and use it to transmit a core microbiota to their offspring
Necrophagous beetles utilize carrion, a highly nutritious resource that is susceptible to intense microbial competition, by treating it with antimicrobial anal and oral secretions. However, how this regulates the carcass microbiota remains unclear. Here, we show that carcasses prepared by the burying beetle Nicrophorus vespilloides undergo significant changes in their microbial communities subsequent to their burial and 'preparation'. Prepared carcasses hosted a microbial community that was more similar to that of beetles' anal and oral secretions than to the native carcass community or the surrounding soil, indicating that the beetles regulated the carcass microbiota. A core microbial community (Xanthomonadaceae, Enterococcaceae, Enterobacteriaceae, and Yarrowia yeasts) was transmitted by the beetles to the larvae via the anal and oral secretions and the carcass surface. These core taxa proliferated on the carcass, indicating a growth conducive environment for these microbes when associated with beetles. However, total bacterial loads were higher on decomposing carcasses without beetles than on beetle-prepared carcasses, indicating that the beetles and/or their associated symbionts suppress the growth of competing microbes. Thus, apart from being a nutritional resource, the carcass provides a medium for vertical transmission of a tightly regulated symbiotic microbiota, whose activity on the carcass and in the larval gut may involve carcass preservation as well as digestion.
Data from: Burying beetles regulate the microbiome of carcasses and use it to transmit a core microbiota to their offspring
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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.