Halite metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA484015 | ENA |
REPOSITORIES: ENA
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Project description:Regulatory small RNAs (sRNAs) represent a major class of regulatory molecules that play large-scale and essential roles in many cellular processes across all domains of life. Microbial sRNAs have been primarily investigated in a few model organisms and little is known about the dynamics of sRNA synthesis in natural environments, and the roles of these short transcripts at the community level. Analyzing the metatranscriptome of a model extremophilic community inhabiting halite nodules (salt rocks) from the Atacama Desert, sampled over two years with different weather conditions, with SnapT – a new sRNA annotation pipeline – we discovered hundreds of intergenic (itsRNAs) and antisense (asRNAs) sRNAs expressed.
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Project description:SG1-2017 halite metagenome and metatranscriptome
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Project description:Drivers of Diversity for Microbial Communities Inhabiting Halites from the Hyper-arid Zone of the Atacama Desert
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Project description:Halophilic microorganisms have long been known to survive within the brine inclusions of salt crystals, as evidenced by their pigmentation. However, the molecular mechanisms allowing this survival has remained an open question for decades. While protocols for the surface sterilization of halite (NaCl) have enabled isolation of cells and DNA from within halite brine inclusions, “-omics” based approaches have faced two main technical challenges: (1) removal of all contaminating organic biomolecules (including proteins) from halite surfaces, and (2) performing selective biomolecule extractions directly from cells contained within halite brine inclusions with sufficient speed to avoid modifications in gene expression during extraction. In this study, we present methods to resolve these two technical challenges. In addition, we apply these methods to perform the first examination of the early acclimation of a model haloarchaeon (Halobacterium salinarum NRC-1) to halite brine inclusions. Examinations of the proteome of Halobacterium cells two months post-evaporation revealed a high degree of similarity with stationary phase liquid cultures, but with a sharp down-regulation of ribosomal proteins. Low quantities of RNA from halite brine inclusions corroborate the hypothesis of low transcriptional and translational activities. While proteins for central metabolism were part of the shared proteome between liquid cultures and halite brine inclusions, proteins involved in cell mobility (archaellum, gas vesicles) were either absent or less abundant in halite samples. Proteins unique to cells within brine inclusions included transporters, suggesting modified interactions between cells and the surrounding brine inclusions microenvironment. The methods and hypotheses presented here enable future studies of the survival of halophiles in both culture model and natural halite systems.
2023-03-10 | PXD037167 | Pride
Project description:Kidney proteomes of Rufous-collared sparrows from two different areas of the Atacama desert (Chile) were identified and compared by bottom-up proteomics utilizing nanoUPLC coupled online to tandem mass spectrometry. All experiments and sample collections were performed by the team of Dr. Paulina Gonzalez-Gomez. Proteomics sample preparation and biological mass spectrometry were performed in the laboratory of Prof. Dietmar Kueltz at UC Davis.
2018-04-26 | MSV000082314 | MassIVE
Project description:Functional analysis of the archaea, bacteria, and viruses from a halite endolithic microbial community
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