Multi -omics reveal lifestyle of acidophile, mineral-oxidizing model species Leptospirillum ferriphilumT

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
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This stores:
Processed data files
Links to raw data files
Links to repositories containing applied workflows

Collection for experimental SOPs

Genomics data, for L.ferriphilum
Sequencing of the genome and functional annotation

Proteomics data for L.ferriphilum samples (continuous and with mineral)

RNAseq data for L.ferriphilum samples

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

Filtering of data in Perseus and t-test between conditions
Perseus save file

Link to the repository for functional annotation

Genbank file for the L.ferriphilum chromosome, annotated with prokka 1.12beta

Raw data and assembly for pacbio sequencing of L.ferriphilum.

Comparison for LFQs with t-test in Perseus

LFQ intensities from maxquant from combined search (mineral and continuous samples), log-transformed

LFQ intensities from maxquant from combined search (mineral and continuous samples), filtered (at least 3 values in each condition), log-transformed

Comparison between axenic and planktonic readcounts with deseq2

Table combining data for L.ferriphilum.
RNAseq data, Proteomics LFQs, Functional annotation

Repository for omics data analysis

Normalized counts (tpm) for L.ferriphilum samples from continuous culture.

Normalized counts (tpm) for LF samples with mineral

Raw read files for samples

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.

steps conducted to pellet cells for RNA and protein extraction

Initial configuration and parameters of the Bioleaching