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360 results for “Microbes”
Genetic diversity of Shaw's agave and soil associated microbes in Southern California preserve
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On the spread of microbes that manipulate reproduction in marine invertebrates
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Transmission efficiency drives host-microbe associations
<p>MatLab code to accompany "Transmission efficiency drives host-microbe associations" Modelling is divided into three files - Asexual hosts, Male mate choice and Female mate choice. </p>
Fossil microbodies are melanosomes: evaluating and rejecting the 'fossilised decay-associated microbes' hypothesis
<p>Melanosomes are membrane-bound organelles of varying geometry, commonly found within a range of vertebrate tissues, that contain the pigment melanin. Melanosomes have been identified in the fossil record in many exceptionally preserved fossils allowing reconstructions of the coloration of many extinct animals. However, these microstructures have also been interpreted as "microbial cells" or melanin producing bacteria based on their geometric similarities to melanosomes. Here we test these two conflicting hypotheses experimentally. Our results demonstrate multiple lines of evidence that these fossil microbodies are indeed melanosomes: the geometry of decay-associated microbes differs significantly from fossil microbodies; fossil microbodies are very strongly localized to in vivo melanized tissues and are absent in tissues typically unmelanized in vivo, in all fossils examined regardless of lithology or age. On the basis of these results, as well as a thorough review of existing literature on melanin like pigments, we are able to rule out a bacterial origin for fossil microbodies and demonstrate that fossil microbodies associated with exceptional vertebrate fossils are in fact preserved melanosomes.</p>
Data from: Adaptation to temperature stress by Vibrio fischeri facilitates this microbe's symbiosis with the Hawaiian bobtail squid (Euprymna scolopes)
For microorganisms cycling between free-living and host-associated stages, where reproduction occurs in both of these lifestyles, an interesting inquiry is whether adaptation to stress during the free-living stage can impact microbial fitness in the host. To address this topic, the mutualism between the Hawaiian bobtail squid (Euprymna scolopes) and the marine bioluminescent bacterium Vibrio fischeri was utilized. Using microbial experimental evolution, V. fischeri was selected to low (8⁰C), high (34⁰C), and fluctuating temperature stress (8⁰C/34⁰C) for 2,000 generations. The temperatures 8⁰C and 34⁰C were the lower and upper growth limits, respectively. V. fischeri was also selected to benign temperatures (21⁰C and 28⁰C) for 2,000 generations, which served as controls. V. fischeri demonstrated significant adaptation to low, high, and fluctuating temperature stress. V. fischeri did not display significant adaptation to the benign temperatures. Adaptation to stressful temperatures facilitated V. fischeri's ability to colonize the squid host relative to the ancestral lines. Bioluminescence levels also increased. Evolution to benign temperatures did not manifest these results. In summary, microbial adaptation to stress during the free-living stage can promote coevolution between hosts and microorganisms.
Intraspecific variation in symbiont density in an insect-microbe symbiosis
<p><span><span><span><span><span><span><span><span><span><span><span>Many insects host vertically-transmitted microbes, which can confer benefits to their hosts but are costly to maintain and regulate. A key feature of these symbioses is variation: for example, symbiont density can vary among host and symbiont genotypes. However, the evolutionary forces maintaining this variation remain unclear. We studied variation in symbiont density using the pea aphid (<i>Acyrthosiphon pisum</i>) and the bacterium <i>Regiella insecticola</i>, a symbiont that can protect its host against fungal pathogens. We found that relative symbiont density varies both between two <i>Regiella</i> phylogenetic clades and among aphid 'biotypes'. Higher-density symbiont infections are correlated with stronger survival costs, but variation in density has little effect on the protection <i>Regiella</i> provides against fungi. Instead, we found that in some aphid genotypes, a dramatic decline in symbiont density precedes the loss of a symbiont infection. Together, our data suggest that the optimal density of a symbiont infection is likely different from the perspective of aphid and microbial fitness. <i>Regiella</i> might prevent loss by maintaining high within-host densities, but hosts do not appear to benefit from higher symbiont numbers and may be advantaged by losing costly symbionts in certain environments. The standing variation in symbiont density observed in natural populations could therefore be maintained by antagonistic coevolutionary interactions between hosts and their symbiotic microbes. </span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics
Background: Microbial diversity and community structures in acidic hot springs have been characterized by 16S rRNA gene-based diversity surveys. However, our understanding regarding the interactions among microbes, or between microbes and environmental factors, remains limited. Results: In the present study, a metagenomic approach, followed by bioinformatics analyses, were used to predict interactions within the microbial ecosystem in Shi-Huang-Ping (SHP), an acidic hot spring in northern Taiwan. Characterizing environmental parameters and potential metabolic pathways highlighted the importance of carbon assimilatory pathways. Four distinct carbon assimilatory pathways were identified in five dominant genera of bacteria. Of those dominant carbon fixers, Hydrogenobaculum bacteria outcompeted other carbon assimilators and dominated the SHP, presumably due to their ability to metabolize hydrogen and to withstand an anaerobic environment with fluctuating temperatures. Furthermore, most dominant microbes were capable of metabolizing inorganic sulfur-related compounds (abundant in SHP). However, Acidithiobacillus ferrooxidans was the only species among key rare microbes with the capability to fix nitrogen, suggesting a key role in nitrogen cycling. In addition to potential metabolic interactions, based on the 16S rRNAs gene sequence of Nanoarchaeum-related and its potential host Ignicoccus-related archaea, as well as sequences of viruses and CRISPR arrays, we inferred that there were complex microbe-microbe interactions. Conclusions: Our study provided evidence that there were numerous microbe-microbe and microbe-environment interactions within the microbial community in an acidic hot spring. We proposed that Hydrogenobaculum bacteria were the dominant microbial genus, as they were able to metabolize hydrogen, assimilate carbon and live in an anaerobic environment with fluctuating temperatures.
Data from: Environmental variability counteracts priority effects to facilitate species coexistence: evidence from nectar microbes
The order of species arrival during community assembly can greatly affect species coexistence, but the strength of these effects, known as priority effects, appears highly variable across species and ecosystems. Furthermore, the causes of this variation remain unclear despite their fundamental importance in understanding species coexistence. Here, we show that one potential cause is environmental variability. In laboratory experiments using nectar-inhabiting microorganisms as a model system, we manipulated spatial and temporal variability of temperature, and examined consequences for priority effects. If species arrived sequentially, multiple species coexisted under variable temperature, but not under constant temperature. Temperature variability prevented extinction of late-arriving species that would have been excluded owing to priority effects if temperature had been constant. By contrast, if species arrived simultaneously, species coexisted under both variable and constant temperatures. We propose possible mechanisms underlying these results using a mathematical model that incorporates contrasting effects of microbial species on nectar pH and amino acids. Overall, our findings suggest that understanding consequences of priority effects for species coexistence requires explicit consideration of environmental variability.
Data from: Dipteran larvae and microbes facilitate nutrient sequestration in the Nepenthes gracilis pitcher plant host
The fluid-containing traps of Nepenthes carnivorous pitcher plants (Nepenthaceae) are often inhabited by organisms known as inquilines. Dipteran larvae are key components of such communities and are thought to facilitate pitcher nitrogen sequestration by converting prey protein into inorganic nitrogen, although this has never been demonstrated in Nepenthes. Pitcher fluids are also inhabited by microbes, although the relationship(s) between these and the plant is still unclear. In this study, we examined the hypothesis of digestive mutualism between N. gracilis pitchers and both dipteran larvae and fluid microbes. Using dipteran larvae, prey and fluid volumes mimicking in situ pitcher conditions, we conducted in vitro experiments and measured changes in available fluid nitrogen in response to dipteran larvae and microbe presence. We showed that the presence of dipteran larvae resulted in significantly higher and faster releases of ammonium and soluble protein into fluids in artificial pitchers, and that the presence of fluid microbes did likewise for ammonium. We showed also that niche segregation occurs between phorid and culicid larvae, with the former fragmenting prey carcasses and the latter suppressing fluid microbe levels. These results clarify the relationships between several key pitcher-dwelling organisms, and show that pitcher communities facilitate nutrient sequestration in their host.
Data from: Experimental taphonomy of Artemia reveals the role of endogenous microbes in mediating decay and fossilization
Exceptionally preserved fossils provide major insights into the evolutionary history of life. Microbial activity is thought to play a pivotal role in both the decay of organisms and the preservation of soft tissue in the fossil record, though this has been the subject of very little experimental investigation. To remedy this, we undertook an experimental study of the decay of the brine shrimp Artemia, examining the roles of autolysis, microbial activity, oxygen diffusion and reducing conditions. Our findings indicate that endogenous gut bacteria are the main factor controlling decay. Following gut wall rupture, but prior to cuticle failure, gut-derived microbes spread into the body cavity, consuming tissues and forming biofilms capable of mediating authigenic mineralization, that pseudomorph tissues and structures such as limbs and the haemocoel. These observations explain patterns observed in exceptionally preserved fossil arthropods. For example, guts are preserved relatively frequently, while preservation of other internal anatomy is rare. They also suggest that gut-derived microbes play a key role in the preservation of internal anatomy and that differential preservation between exceptional deposits might be because of factors that control autolysis and microbial activity. The findings also suggest that the evolution of a through gut and its bacterial microflora increased the potential for exceptional fossil preservation in bilaterians, providing one explanation for the extreme rarity of internal preservation in those animals that lack a through gut.
Data from: Microbe-mediated host defence drives the evolution of reduced pathogen virulence
Microbes that protect their hosts from pathogens are widespread in nature and are attractive disease control agents. Given that pathogen adaptation to barriers against infection can drive changes in pathogen virulence, 'defensive microbes' may shape disease severity. Here we show that co-evolving a microbe with host-protective properties (Enterococcus faecalis) and a pathogen (Staphylococcus aureus) within Caenorhabditis elegans hosts drives the evolution of reduced pathogen virulence as a by-product of adaptation to the defensive microbe. Using both genomic and phenotypic analyses, we discover that the production of fewer iron-scavenging siderophores by the pathogen reduces the fitness of the defensive microbe and underpins the decline in pathogen virulence. These data show that defensive microbes can shape the evolution of pathogen virulence and that the mechanism of pathogen resistance can determine the direction of virulence evolution.
Supplemental video - Actin microbes
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Supplementary material 2 from: Jiménez Elvira N, Ushio M, Sakai S (2022) Are microbes growing on flowers evil? Effects of old flower microbes on fruit set in a wild ginger with one-day flowers, Alpinia japonica (Zingiberaceae). Metabarcoding and Metagenomics 6: e84331. https://doi.org/10.3897/mbmg.6.84331
Fruit and seed set datasets
Supplementary material 1 from: Jiménez Elvira N, Ushio M, Sakai S (2022) Are microbes growing on flowers evil? Effects of old flower microbes on fruit set in a wild ginger with one-day flowers, Alpinia japonica (Zingiberaceae). Metabarcoding and Metagenomics 6: e84331. https://doi.org/10.3897/mbmg.6.84331
Tables S1, S2 and Figures S1–S4
Gene gain/loss analysis for Bombella and related microbes
<p>Synergistic effects of multiple stressors underpinned by limited nutrition (Dolezal and Toth, 2018). Poor nutrition is most damaging in developing honey bee larvae, who mature into workers unable to meet the needs of their colony (Scofield and Mattila, 2015). It is therefore essential that we better understand the nutritional landscape experienced by honey bee larvae. In this study, we characterize the metabolic capabilities of a honey bee larvae-associated bacterium, <em>Bombella apis </em>(formerly <em>Parasaccharibacter apium</em>)<em>, </em>and its effects on the nutritional resilience of larvae. We found that <em>B. apis </em>is the only bacterium associated with larvae that can withstand the antimicrobial larval diet. Further, we found that <em>B. apis </em>can synthesize all essential amino acids and significantly alters the amino acid content of synthetic larval diet, largely by increasing the essential amino acid lysine. Analyses of gene gain/loss across the phylogeny suggest that four amino acid transporters were gained in recent <em>B. apis </em>ancestors. In addition, the transporter LysE is conserved across all sequenced strains of <em>B. apis. </em>This result<em> </em>suggests that amino acid export is a key feature conserved within the <em>Bombella </em>clade. Finally, we tested the impact of <em>B. apis </em>on developing honey bee larvae subjected to nutritional stress and found that larvae supplemented with <em>B. apis </em>are bolstered against mass reduction despite limited nutrition. Together, these data suggest an important role of <em>B. apis </em>as a nutritional mutualist of honey bee larvae.</p>
Dataset for: Cure or Curse? Simulation Indicates that Microbes Proliferate under Disinfection Measures in the Space Station
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Soil microbes explain changes in ecosystem multifunctionality
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Phosphorous starved Maize plant root exudate strigolactone and rhizosphere microbes
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Scripts and data for: Increased host diversity limits bacterial generalism but may promote microbe-microbe interactions
<p>Research Overview: In this project, we compared cloacal microbiome communities from reptiles from six localities that spanned a gradient in host taxonomic diversity. We found that diversity of the bacterial communities was relatively stable across locations, but that host-specific taxa were overrepresented in high host diversity communities. ASVs in high host diversity communities were more likely to have strong interactions with other bacterial lineages across multiple hosts. Host generalist bacteria were more likely to be from a generalist phylum.</p> <p>Methodology: We used a 16S rRNA metabarcoding approach to quantify bacterial community diversity. We processed the output fastq files using qiime2, and processed the output files using the qiime2R package. We performed our analyses in R. Processed input files and scripts are described below. </p>
plant mixtures on soil microbes
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ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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.