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APS 325: Life in Extremes > Lecture 6: Case Study Iron Mountain > Flashcards

Lecture 6: Case Study Iron Mountain Flashcards

1
Q

Iron Mountain:

A

California, acid mine

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2
Q

___ acid fumes from the mine is killing vegetation

A

sulphuric

- generated from biological activity underground (microbes)

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3
Q

within the mine conditions =

A
  • 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
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4
Q

dissolution of iron pyrites & microbes

A
  • 1 atom of iron pyrite (FeS2) gives 16 H+
  • Fe3+ (oxidised iron) normally limits reaction
  • microbial activity accelerates as microbes oxidise Fe2+ —> Fe3+
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5
Q

iron pyrite common name

A

fools gold

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6
Q

sampling within the mine

A
  • samples of a biofilm taken at the Richmond 5 way
  • pH 0.83
  • 42DC (warm)
  • 0.3 molar Fe (hypersaline)
  • toxic heavy metals
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7
Q

drift mine

A

go in from the side, not vertically down

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8
Q

what organisms are present in the mine

A
  • both bacteria & Archaea
  • some eukaryotes
  • most of the major microbes are culturable
  • relatively simple microbial community
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9
Q

16S rRNA sequencing of biofilm

A
  • -> 384 separate clones were sequenced
  • 3 major Bacterial lineages identified
  • 3 major Archaeal lineages
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10
Q

what sequencing technique was used to study biofilm of the mine

A

16S rRNA

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11
Q

____ ____ can be used to detect different organisms

A

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
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12
Q

biofilm often arrangement

A

one organism extremely sticky, others then stick to that

  • FISH probes can aid see arrangements
  • popular in medical, cleaning, dentistry field
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13
Q

metabolite flow within the biofilm:

A
  • 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
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14
Q

metagenomics vs metataxonomics =

A
  • metagenomics = sequence the whole DNA (undertsand more geens in environment, less prone to bias’)
  • metataxonomics = just a section of DNA
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15
Q

metagenomic vs genomics

A

metagenomics genomes of more than one organism
= population
– genomics just one organism

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16
Q

metagenomics

A
  • obtain DNA from the environment (from more than one organism)
  • sequence DNA fragments
  • re-assemble genome for individual organisms
  • study genome to determine function
17
Q

shotgun genome sequencing

A
  • 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
18
Q

shotgun genome sequencing: advantages

A
  • quick
  • cheap
  • works well with small genomes
  • no need to culture organisms
19
Q

shotgun genome sequencing: disadvantages

A
  • 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
20
Q

shotgun sequencing: how do we know which assembled sequence belongs to which organism?

A
  • 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
21
Q

the mine is rich in __ environments

A

micro

22
Q

ARMAN organisms

A
  • archaeal Richmond Mine acidophilic nanoorganisms
  • missed by previos 16S rRNA screens
  • as they’re so small
  • attach to thermoplasma
  • ectoparasites
23
Q

challenges in analysing whole communities

A
  • 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

APS 325: Life in Extremes (15 decks)

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