Ontology highlight
ABSTRACT:
PROVIDER: PRJNA815675 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The rate, timing, and mode of species dispersal is recognized as a key driver of the structure and function of communities of macroorganisms, and may be one ecological process that determines the diversity of microbiomes. Many previous studies have quantified the modes and mechanisms of bacterial motility using monocultures of a few model bacterial species. But most microbes live in multispecies microbial communities, where direct interactions between microbes may inhibit or facilitate dispersal through a number of physical (e.g., hydrodynamic) and biological (e.g., chemotaxis) mechanisms, which remain largely unexplored. Using cheese rinds as a model microbiome, we demonstrate that physical networks created by filamentous fungi can impact the extent of small-scale bacterial dispersal and can shape the composition of microbiomes. From the cheese rind of Saint Nectaire, we serendipitously observed the bacterium Serratia proteamaculans actively spreads on networks formed by the fungus Mucor. By experimentally recreating these pairwise interactions in the lab, we show that Serratia spreads on actively growing and previously established fungal networks. The extent of symbiotic dispersal is dependent on the fungal network: diffuse and fast-growing Mucor networks provide the greatest dispersal facilitation of the Serratia species, while dense and slow-growing Penicillium networks provide limited dispersal facilitation. Fungal-mediated dispersal occurs in closely related Serratia species isolated from other environments, suggesting that this bacterial-fungal interaction is widespread in nature. Both RNA-seq and transposon mutagenesis point to specific molecular mechanisms that play key roles in this bacterial-fungal interaction, including chitin utilization and flagellin biosynthesis. By manipulating the presence and type of fungal networks in multispecies communities, we provide the first evidence that fungal networks shape the composition of bacterial communities, with Mucor networks shifting experimental bacterial communities to complete dominance by motile Proteobacteria. Collectively, our work demonstrates that these strong biophysical interactions between bacterial and fungi can have community-level consequences and may be operating in many other microbiomes.
2017-08-02 | GSE85095 | GEO
Project description:Fungal communities in groundwater springs along the volcanic zone of Iceland
| PRJEB34808 | ENA
Project description:Characterization of Early Bacterial and Fungal Communities on Volcanic Deposits along a Vegetation Gradient in the Island of Miyake, Japan
| PRJDB2468 | ENA
Project description:Sargassum is one of the most diverse brown algal genus with more than 150 known species, mostly benthic and few pelagic species. They contribute significantly to global primary production and serve as important habitat for wide range of marine organisms. Sargassum vulgare is one of the dominant habitat forming species along Mediterranean coast. Despite their huge ecological importance, it is relatively unknown how they will respond under future global climate change scenario. This work used de novo transcriptome sequencing approach to understand the molecular response of S. vulgare to chronic acidification at the shallow underwater volcanic CO2 vents off Ischia Island, Italy. Keywords: brown algae, Sargassum, de novo transcriptome, ocean acidification, CO2 vents.
2017-01-16 | GSE78707 | GEO
Project description:A functional biodiversity microarray (EcoChip) prototype has been developed to facilitate the analysis of fungal communities in environmental samples with broad functional and phylogenetic coverage and to enable the incorporation of nucleic acid sequence data as they become available from large-scale (next generation) sequencing projects. A dual probe set (DPS) was designed to detect a) functional enzyme transcripts at conserved protein sites and b) phylogenetic barcoding transcripts at ITS regions present in precursor rRNA. Deviating from the concept of GeoChip-type microarrays, the presented EcoChip microarray phylogenetic information was obtained using a dedicated set of barcoding microarray probes, whereas functional gene expression was analyzed by conserved domain-specific probes. By unlinking these two target groups, the shortage of broad sequence information of functional enzyme-coding genes in environmental communities became less important. The novel EcoChip microarray could be successfully applied to identify specific degradation activities in environmental samples at considerably high phylogenetic resolution. Reproducible and unbiased microarray signals could be obtained with chemically labeled total RNA preparations, thus avoiding the use of enzymatic labeling steps. ITS precursor rRNA was detected for the first time in a microarray experiment, which confirms the applicability of the EcoChip concept to selectively quantify the transcriptionally active part of fungal communities at high phylogenetic resolution. In addition, the chosen microarray platform facilitates the conducting of experiments with high sample throughput in almost any molecular biology laboratory. In this study, two independent RNA samples from a pine forest soil were labelled and hybridised to a custom-made EcoChip microarray consisting of about 9000 probes targeting expressed fungals genes and about 5000 probes targeting the precursor-rRNA of different fungal lineages
2011-11-14 | E-GEOD-28018 | biostudies-arrayexpress
Project description:Affymetrix single nucleotide polymorphism (SNP) array data were collected to study genome-wide patterns of genomic variation across a broad geographical range of Island Southeast Asian populations. This region has experienced an extremely complex admixture history. Initially settled ~50,000 years ago, Island Southeast Asia has since been the recipient of multiple waves of population movements, most recently by Austronesian-speaking groups ultimately from Neolithic mainland Asia and later arrivals during the historic era from India and the Middle East. We have genotyped SNPs in ~500 individuals from 30 populations spanning this entire geographical region, from communities close to mainland Asia through to New Guinea. Particular attention has been paid to genomic data that are informative for population history, including the role of recent arrivals during the historic era and admixture with archaic hominins.
2017-08-02 | GSE80534 | GEO
Project description:FOGO volcanic soil microbial communities
| PRJEB30019 | ENA
Project description:Lifespan Cancer Institute serves over 50% of cancer patients in the state. Rhode Island is known for strong medical care and high rates of cancer screening with mammography and colonoscopy. However, cancer screening has plummeted during the COVID-19 pandemic, in part to closing physician offices and stopping non-urgent medical procedures. In addition, anecdotal reports suggest the public remains concerned about returning to physician’s offices and risking possible exposure to COVID-19. As in the United States as a whole, COVID-19 has disproportionately impacted ethnic and minority individuals within underserved communities; and in Rhode Island, African Americans, Hispanics and undocumented individuals living in communities such as Central Falls, Pawtucket, Providence, East Providence and North Providence have had the highest rate of COVID-19. These communities are also impacted by healthcare disparities to access and affordability of healthcare, and as such, may be among the least likely to resume cancer screening.
The Lifespan Cancer Institute will institute a project to address health disparities in cancer screening during the pandemic through the use of a targeted campaign involving social media. The goals will be to re-establish screening in the era of COVID-19 and ensure timeliness of care for those found to be at risk, or are positive for, cancer.
| 2354509 | ecrin-mdr-crc
Project description:Illumina single nucleotide polymorphism (SNP) array data were generated to study genome-wide patterns of genomic variation on Sumba and Timor, two small islands in eastern Indonesia. Both islands have a complex history from their initial settlement ~50,000 years ago, to admixture with Austronesian-speaking groups during the Neolithic farming expansion, and more recent intra-island gene flow and community interactions. As part of this detailed microgeographic study, we also collected associated cultural and linguistic information. The primary study location was Sumba, for which we genotyped SNPs in 235 individuals from eight communities that span the island, including groups that speak most of Sumba’s nine languages. Particular attention was paid to genomic data that are informative for recent aspects of population history, including reconstructions of past gene flow, socio-genetic interactions and possible signals of selection.
2016-07-14 | GSE76645 | GEO