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Biomining is a biotechnological process carried out in many parts of the world that exploits acid loving microorganisms to extract metals from sulphide minerals. One industrial biomining method is called ‘heap bioleaching’ where typically copper containing minerals are piled into very large heaps, acid and microorganisms are added to the top and the soluble metal is collected at the heap base.
The role of the different types of microbes in the process is to speed up metal solubilisation by oxidising ferrous iron to ferric and removing sulphur compounds that can accumulate on the mineral surface. Metals are most efficiently released from sulphide ores if the microorganisms form a thin layer, termed a ‘biofilm’, on the mineral surface and a crucial stage in bioleaching is how efficiently the microbes attach to the mineral.
This project will test how rapidly a biofilm is formed and copper is released from the mineral by different combinations of microorganisms and the order that they are added. Data on the biological processes the microorganisms carry out will be used in computer modelling to suggest the best combination and order in which to add the different types of microbes. This in turn will increase the efficiency of industrial bioleaching by reducing the time between when a heap is built and when the first metals are collected.
Programme: ERASysAPP
FAIRDOMHub ID: https://fairdomhub.org/projects/22
Public web page: http://sysmetex.eu/index.html
Organisms: Acidithiobacillus caldus, Sulfobacillus thermosulfidooxidans, Leptospirillum ferriphilum
FAIRDOM PALs: Malte Herold, Mario Vera, Antoine Buetti-Dinh
Related items
- People (15)
- Institutions (7)
- Investigations (2+3)
- Studies (1+4)
- Assays (4+15)
- Strains (1+3)
- Data files (18+74)
- Models (0+2)
- SOPs (3+14)
- Presentations (7+62)
- Events (0+5)
- Samples (0+21)
Projects: SysMetEx, Kinetics on the move - Workshop 2016
Institutions: Università della Svizzera Italiana
Disciplines: Modeller
Roles: Not specified
Expertise: ODE modelling of biological interaction network, Bioinformatics
Tools: Python, c++, Java, bash, standard bioinformatic tools
Projects: SysMetEx
Institutions: University of Luxembourg
Disciplines: Not specified
Roles: Not specified
Expertise: Not specified
Tools: Not specified
Projects: SysMetEx
Institutions: Linnaeus University
Disciplines: Not specified
Roles: Not specified
Expertise: Not specified
Tools: Not specified
Projects: SysMetEx
Institutions: University Duisburg-Essen
Projects: SysMetEx
Institutions: Ruhr University Bochum
Disciplines: Not specified
Roles: Not specified
Expertise: Molecular microbiology, Biochemistry, Bioleaching
Tools: Fluorescence and confocal microscopy, cultivation, microbiology techniques
Projects: SysMetEx
Institutions: TATAA BioCenter
Disciplines: Not specified
Roles: Not specified
Expertise: Not specified
Tools: Not specified
Projects: SysMetEx
Institutions: Università della Svizzera Italiana
Disciplines: Not specified
Roles: Not specified
Expertise: Not specified
Tools: Not specified
Experimental data and all related material for the publication "Multi -omics reveal lifestyle of acidophile, mineral-oxidizing model species Leptospirillum ferriphilumT".
Snapshots: Snapshot 1
Studies: Omics_data_analysis
Assays: Experimental methods, Genomics, Proteomics, RNAseq
This stores:
Processed data files
Links to raw data files
Links to repositories containing applied workflows
Person responsible: Malte Herold
Snapshots: No snapshots
Investigation: Multi -omics reveal lifestyle of acidophile, mi...
Assays: Experimental methods, Genomics, Proteomics, RNAseq
RNAseq data for L.ferriphilum samples
Contributor: Malte Herold
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Multi -omics reveal lifestyle of acidophile, mi...
Study: Omics_data_analysis
Organisms: No organisms
SOPs: No SOPs
Data files: LF_RNAseq_TPM_continuous, LF_RNAseq_TPM_mineral, LF_RNAseq_rawdata, LF_deseq_comparison, LF_omics_analysis, LF_omics_combined_Table
Proteomics data for L.ferriphilum samples (continuous and with mineral)
Contributor: Malte Herold
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Multi -omics reveal lifestyle of acidophile, mi...
Study: Omics_data_analysis
Organisms: No organisms
SOPs: No SOPs
Data files: LF_LFQ_comparison_ttest, LF_omics_analysis, LF_omics_combined_Table, LF_proteomics_LFQs_continuous, LF_proteomics_LFQs_mineral, LF_proteomics_LFQs_mineral_scaled, LF_proteomics_continuous_scaled, LF_proteomics_maxquant_perseus_filtered, LF_proteomics_maxquant_perseus_unfiltered, Perseus workflow t-test, Proteomics data comparing LXX cultures cultivat...
Genomics data, for L.ferriphilum
Sequencing of the genome and functional annotation
Contributor: Malte Herold
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Multi -omics reveal lifestyle of acidophile, mi...
Study: Omics_data_analysis
Organisms: No organisms
SOPs: No SOPs
Data files: Functional_annotation_repository, LF_functional_annotation_gbk, LF_omics_combined_Table, LF_sequencing_data
Collection for experimental SOPs
Contributor: Malte Herold
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Investigation: Multi -omics reveal lifestyle of acidophile, mi...
Study: Omics_data_analysis
Organisms: No organisms
SOPs: 003 Biomolecular Extractions from LAO (Qiagen A..., SOP - Bioleaching in flasks (LNU), SOP - RNA/Protein sampling for continuous culture
Data files: No Data files
Contributor: Malte Herold
Provider Name: Not specified
Provider's strain ID: Not specified
Organism: Sulfobacillus thermosulfidooxidans
Genotypes: wild-type
Phenotypes: wild-type
Comment: Created again as "Sulfobacillus thermosulfidooxidans DSM 9293" seemed to be broken
Filtering of data in Perseus and t-test between conditions
Perseus save file
Creator: Malte Herold
Contributor: Malte Herold
Investigations: Multi -omics reveal lifestyle of acidophile, mi...
Studies: Omics_data_analysis
Assays: Proteomics
Maxquant output.
Proteomics data comparing LXX cultures cultivated on mineral and in continuous culture:
mineral samples:
LNU-LXX9-Si00-14B-P-B-Pr
LNU-LXX9-Si00-14B-P-C-Pr
LNU-LXX9-Si00-14B-P-D-Pr
conitnuous culture samples:
LNU-LXX9-Si00-CnA-P-B2-Pr
LNU-LXX9-Si00-CnA-P-B3-Pr
LNU-LXX9-Si00-CnA-P-B4-Pr
LNU-LXX9-Si00-CnA-P-B5-Pr
LNU-LXX9-Si00-CnA-P-B6-Pr
LNU-LXX9-Si00-CnA-P-B7-Pr
Creator: Mohamed El Hajjami
Contributor: Mohamed El Hajjami
Investigations: Multi -omics reveal lifestyle of acidophile, mi...
Studies: Omics_data_analysis
Assays: Proteomics
Creator: Malte Herold
Contributor: Malte Herold
Investigations: Multi -omics reveal lifestyle of acidophile, mi...
Studies: Omics_data_analysis
Assays: Proteomics
Creator: Malte Herold
Contributor: Malte Herold
Investigations: Multi -omics reveal lifestyle of acidophile, mi...
Studies: Omics_data_analysis
Assays: Proteomics
Creator: Malte Herold
Contributor: Malte Herold
Investigations: Multi -omics reveal lifestyle of acidophile, mi...
Studies: Omics_data_analysis
Assays: Proteomics
Creator: Malte Herold
Contributor: Malte Herold
Investigations: Multi -omics reveal lifestyle of acidophile, mi...
Studies: Omics_data_analysis
Assays: Proteomics
LFQ intensities from maxquant from combined search (mineral and continuous samples), filtered (at least 3 values in each condition), log-transformed
Creators: Malte Herold, Ansgar Poetsch, Mohamed El Hajjami, Ansgar
Contributor: Malte Herold
Investigations: Multi -omics reveal lifestyle of acidophile, mi...
Studies: Omics_data_analysis
Assays: Proteomics
Protocol for the extraction of biomolecules (DNA,RNA,protein,metabolties) from the same sample. Originally intended for lipid accumulating organisms (LAO) from wastewater treatment plant samples.
So far succesfully used for pelleted cells from planktonic cultures.
Creator: Malte Herold
Contributor: Malte Herold
Investigations: Multi -omics reveal lifestyle of acidophile, mi... and 1 hidden item
Studies: Omics_data_analysis and 1 hidden item
Assays: Experimental methods and 5 hidden items
steps conducted to pellet cells for RNA and protein extraction
Creator: Stephan Christel
Contributor: Stephan Christel
Investigations: Multi -omics reveal lifestyle of acidophile, mi...
Studies: Omics_data_analysis
Assays: Experimental methods
Initial configuration and parameters of the Bioleaching
Creator: Stephan Christel
Contributor: Stephan Christel
Investigations: Multi -omics reveal lifestyle of acidophile, mi...
Studies: Omics_data_analysis
Assays: Experimental methods
Workshop by the fairdomhub team on reproducible and citable data and models
Creator: Antoine Buetti-Dinh
Contributor: Antoine Buetti-Dinh
Stephan's poster for presentation at IBS 2015
Creator: Stephan Christel
Contributor: Stephan Christel