Environment microorganisms
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA648476 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12321636_1.fastq.gz | Fastqsanger.gz | |||
| SRR12321636_2.fastq.gz | Fastqsanger.gz | |||
| SRR12321637_1.fastq.gz | Fastqsanger.gz | |||
| SRR12321637_2.fastq.gz | Fastqsanger.gz | |||
| SRR12321638_1.fastq.gz | Fastqsanger.gz |
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Project description:Biofilm samples of injection wellbore
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Project description:Ultra-small microorganisms are ubiquitous in Earth's environments. Ultramicrobacteria, which are defined as having a cell volume of <0.1 μm3, are often numerically dominant in aqueous environments. Cultivated representatives among these bacteria, such as members of the marine SAR11 clade (e.g., "Candidatus Pelagibacter ubique") and freshwater Actinobacteria and Betaproteobacteria, possess highly streamlined, small genomes and unique ecophysiological traits. Many ultramicrobacteria may pass through a 0.2-μm-pore-sized filter, which is commonly used for filter sterilization in various fields and processes. Cultivation efforts focusing on filterable small microorganisms revealed that filtered fractions contained not only ultramicrocells (i.e., miniaturized cells because of external factors) and ultramicrobacteria, but also slender filamentous bacteria sometimes with pleomorphic cells, including a special reference to members of Oligoflexia, the eighth class of the phylum Proteobacteria. Furthermore, the advent of culture-independent "omics" approaches to filterable microorganisms yielded the existence of candidate phyla radiation (CPR) bacteria (also referred to as "Ca. Patescibacteria") and ultra-small members of DPANN (an acronym of the names of the first phyla included in this superphyla) archaea. Notably, certain groups in CPR and DPANN are predicted to have minimal or few biosynthetic capacities, as reflected by their extremely small genome sizes, or possess no known function. Therefore, filtered fractions contain a greater variety and complexity of microorganisms than previously expected. This review summarizes the broad diversity of overlooked filterable agents remaining in "sterile" (<0.2-μm filtered) environmental samples.
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Project description:To elucidate ecosystem functioning, it is fundamental to recognize what processes occur in which environments (where) and which microorganisms carry them out (who). Here, we present PREGO, a one-stop-shop knowledge base providing such associations. PREGO combines text mining and data integration techniques to mine such what-where-who associations from data and metadata scattered in the scientific literature and in public omics repositories. Microorganisms, biological processes, and environment types are identified and mapped to ontology terms from established community resources. Analyses of comentions in text and co-occurrences in metagenomics data/metadata are performed to extract associations and a level of confidence is assigned to each of them thanks to a scoring scheme. The PREGO knowledge base contains associations for 364,508 microbial taxa, 1090 environmental types, 15,091 biological processes, and 7971 molecular functions with a total of almost 58 million associations. These associations are available through a web portal, an Application Programming Interface (API), and bulk download. By exploring environments and/or processes associated with each other or with microbes, PREGO aims to assist researchers in design and interpretation of experiments and their results. To demonstrate PREGO's capabilities, a thorough presentation of its web interface is given along with a meta-analysis of experimental results from a lagoon-sediment study of sulfur-cycle related microbes.
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Project description:Extracted environmental biofilms grown on plastic devices (bioelements). The immersion site was in Jyllinge Harbour, Denmark (55.744920 N, 12.094893 E). Bottles were immersed in June 2021, followed by sampling at day 4, 7, 14, 28, 42, 56, 70, 84, 98, 112 and 126, for 12 sampling points in total.
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