Lecture 6: Case Study Iron Mountain Flashcards
Iron Mountain:
California, acid mine
___ acid fumes from the mine is killing vegetation
sulphuric
- generated from biological activity underground (microbes)
within the mine conditions =
- dissolution (dissolving) of iron pyrite (FeS2) leafs to EXTREME acidification
- – of effluent = 2-4 pH
- – within mine -2.5 to -3.6 pH
- this drops off the ceiling into pools
dissolution of iron pyrites & microbes
- 1 atom of iron pyrite (FeS2) gives 16 H+
- Fe3+ (oxidised iron) normally limits reaction
- microbial activity accelerates as microbes oxidise Fe2+ —> Fe3+
iron pyrite common name
fools gold
sampling within the mine
- samples of a biofilm taken at the Richmond 5 way
- pH 0.83
- 42DC (warm)
- 0.3 molar Fe (hypersaline)
- toxic heavy metals
drift mine
go in from the side, not vertically down
what organisms are present in the mine
- both bacteria & Archaea
- some eukaryotes
- most of the major microbes are culturable
- relatively simple microbial community
16S rRNA sequencing of biofilm
- -> 384 separate clones were sequenced
- 3 major Bacterial lineages identified
- 3 major Archaeal lineages
what sequencing technique was used to study biofilm of the mine
16S rRNA
____ ____ can be used to detect different organisms
FISH probe
- fluorescently label
- DAPI stains DNS blue
- FISH probe stains target organism red
- –> tells you where organisms are, proportion, quantify organisms
- layer probes to identify diff organisms diff colours
biofilm often arrangement
one organism extremely sticky, others then stick to that
- FISH probes can aid see arrangements
- popular in medical, cleaning, dentistry field
metabolite flow within the biofilm:
- temperature dependent (30-50DC)
- FeS2 dissolves
- bacteria = fixes CO2 & N2 and oxidises Sulphur releasing organic compounds
- eukaryotes use organic compounds produce CO2
- Archaea use organic compounds
- bacteria & Archaea oxidise Fe2+ to Fe3+ for more of the reaction
metagenomics vs metataxonomics =
- metagenomics = sequence the whole DNA (undertsand more geens in environment, less prone to bias’)
- metataxonomics = just a section of DNA
metagenomic vs genomics
metagenomics genomes of more than one organism
= population
– genomics just one organism
metagenomics
- obtain DNA from the environment (from more than one organism)
- sequence DNA fragments
- re-assemble genome for individual organisms
- study genome to determine function
shotgun genome sequencing
- DNA is randomly sheared into small fragments
- sequence is read from thousand of fragments
- overlapping regions are identified and used to assemble the whole genome
shotgun genome sequencing: advantages
- quick
- cheap
- works well with small genomes
- no need to culture organisms
shotgun genome sequencing: disadvantages
- cannot cope with repeats in sequence
- organisms with similar genomes may be mixed up
- genome organisation may be incorrect
- inefficient for genome which are not abundant in the sample (hairless in lecture)
- v difficult to ‘finish’ the genome sequences
shotgun sequencing: how do we know which assembled sequence belongs to which organism?
- G + C content provides a useful guide
- some DNA sequences will contain known genes (e.g. 16S rRNA genes)
- gene sequences & the order of genes on the genome can be obtained from related organisms as a guide
the mine is rich in __ environments
micro
ARMAN organisms
- archaeal Richmond Mine acidophilic nanoorganisms
- missed by previos 16S rRNA screens
- as they’re so small
- attach to thermoplasma
- ectoparasites
challenges in analysing whole communities
- significant computational challenges
- presence of a gene doesn’t tell us if its expressed or functional
- non-abundant community members may play a vital role
