SysMetEx
OverviewBiomining 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
SEEK 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
Project created: 10th Nov 2014
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https://orcid.org/0000-0003-0021-2452 
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My research is intended to contribute to the elucidation of the physiological and molecular processes involved in the biofilm formation of acidophilic leaching bacteria with emphasis in their cell-cell communication mechanisms.
In SysMetEx, our role is to understand biofilm formation at a microscopical and OMICS levels, in order to optimize it.
Projects: SysMetEx
Institutions: University of Luxembourg
Supplementary files for the submission:
Reverse Engineering Directed Gene Regulatory Networks from
Transcriptomics and Proteomics Data of Biomining Bacterial
Communities with Approximate Bayesian Computation and
Steady-State Signalling Simulations
Snapshots: Snapshot 1
Supplementary files for the publication:
Deep Neural Networks Outperform Human Expert’s Capacity in Characterizing Bioleaching Bacterial Biofilm Composition
Snapshots: Snapshot 1
Publication data made available for Biotechnology Reports, supplementary data
Snapshots: No snapshots
Experimental data and all related material for the publication "Multi -omics reveal lifestyle of acidophile, mineral-oxidizing model species Leptospirillum ferriphilumT".
changed ID
Snapshots: No snapshots
Experimental data and all related material for the publication "Multi -omics reveal lifestyle of acidophile, mineral-oxidizing model species Leptospirillum ferriphilumT".
Snapshots: Snapshot 1
Proteomics and transcriptomics data tables, sample IDs and description, source code
Person responsible: Malte Herold
Snapshots: No snapshots
Publication data made available for Biotechnology Reports, supplementary data
Person responsible: Antoine Buetti-Dinh
Snapshots: No snapshots
This stores:
Processed data files
Links to raw data files
Links to repositories containing applied workflows
Person responsible: Malte Herold
Snapshots: No snapshots
Scripts for running network simulations
Contributor: Malte Herold
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Data derived from protein samples
Contributor: Malte Herold
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
Data derived from RNAseq
Contributor: Malte Herold
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
tbd
tbd
Contributor: Malte Herold
Assay type: Experimental Assay Type
Technology type: Confocal Laser Scanning Microscopy (CLSM)
Snapshots: No snapshots
Collection for experimental SOPs
Contributor: Malte Herold
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
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
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
RNAseq data for L.ferriphilum samples
Contributor: Malte Herold
Assay type: Experimental Assay Type
Technology type: Technology Type
Snapshots: No snapshots
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
Information for RNA and protein samples and cultures they were derived from.
Creator: Malte Herold
Contributor: Malte Herold
Download
LFQ intensities derived from proteomics measurements
Creator: Malte Herold
Contributor: Malte Herold
TPM counts for protein coding genes, alongside functional annotations
Creator: Malte Herold
Contributor: Malte Herold
Images used for training and validation of deep learning algorithm to determine biofilm composition of mixed species biofilms on mineral grains
Creators: Malte Herold, Soeren Bellenberg, Antoine Buetti-Dinh
Contributor: Malte Herold
Archive contains python scripts for image analysis
Creators: Malte Herold, Antoine Buetti-Dinh
Contributor: Malte Herold
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
Filtering of data in Perseus and t-test between conditions
Perseus save file
Creator: Malte Herold
Contributor: Malte Herold
Comparison between axenic and planktonic readcounts with deseq2
Creator: Malte Herold
Contributor: Malte Herold
Table combining data for L.ferriphilum.
RNAseq data, Proteomics LFQs, Functional annotation
Genbank file for the L.ferriphilum chromosome, annotated with prokka 1.12beta
Creator: Malte Herold
Contributor: Malte Herold
External LinkRaw data and assembly for pacbio sequencing of L.ferriphilum.
Creator: Malte Herold
Contributor: Malte Herold
LFQ intensities from maxquant from combined search (mineral and continuous samples), log-transformed
Creators: Malte Herold, Ansgar Poetsch, Mohamed El Hajjami
Contributor: Malte Herold
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
SOP for extracting DNA, RNA and Proteins from the mineral pellet of a bioleaching culture using hot acidic phenol.
Current draft.
Creators: Malte Herold, Mario Vera, Soeren Bellenberg
Contributor: Malte Herold
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
steps conducted to pellet cells for RNA and protein extraction
Creator: Stephan Christel
Contributor: Stephan Christel
Initial configuration and parameters of the Bioleaching
Creator: Stephan Christel
Contributor: Stephan Christel
Abstract (Expand)
Authors: Stephan Christel, Malte Herold, Soeren Bellenberg, Mohamed El Hajjami, Antoine Buetti-Dinh, Igor Pivkin, Wolfgang Sand, Paul Wilmes, Ansgar Poetsch, Mark Dopson
Date Published: 1st Feb 2018
Journal: Appl Environ Microbiol
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
