Metagenomics is the culture-independent
genomic analysis of microbial communities. The term is derived from
the statistical concept of meta-analysis (the process of statistically
combining separate analyses) and genomics (the comprehensive analysis
of an organism’s genetic material). Metagenomics can be used to address
the challenge of studying prokaryotes in the environment that are,
as yet, unculturable and which represent more than 99% of the organisms
in some environments. This approach builds on recent advances in microbial
genomics and in the polymerase chain reaction (PCR)
amplification and cloning of genes that share sequence similarity
(e.g. 16S rRNA, nif, recA) directly from environmental samples. Such
samples can then be analyzed by techniques such as DGGE andRFLP gel electrophoresis providing
information as to the species diversity in a sample. Alternatively,
the sequences can be labeled with a fluorescent marker and used to
locate and, in some cases quantitate, the distribution of species
in an environmental sample by FISH (fluorescent in situ hybridization)
Microorganisms that inhabit pristine and anthropogenic acidic environments,
such as Iron Mountain, California, the Rio Tinto, Spain, industrial
bioleaching operations and coal refuse piles, play major roles in
the solubilization of metals in the environment. They can also reduce
metals under anaerobic conditions and their oxido-reductive capabilities
contribute significantly to the geomicrobiological cycling of iron,
copper and toxic metals (Johnson, 1998) [Abstract] .
A metagenomics project conducted at Iron Mountain revealed the presence
of a very restricted microbial population composed principally of
Leptospirillum ferrooxidans Group II, Leptospirillum
ferrodiazotrophum Group III and Ferroplasma acidarmanus
(Tyson et al., 2004, [Abstract] Ram,
2005 [Abstract]).
This project was not only important for its pioneering description
of a microbial consortia in an extremely acidic environmental (<pH1)
but also for highlighting that species diversity counts – for example,
it was discovered that L. ferriphilum, although only a minor
constituent of the total biomass, supplied all the fixed nitrogen
to the community. A limited amount of bacterial diversity was also
found in extremely acidic conditions in an abandoned copper mine in
North Wales (Hallberg et al., 2006 [Abstract] ).
In contrast to Iron Mountain, a very diverse community of acidophiles
has been described in the Rio Tinto, developed over thousands of years
of natural selection, and including the presence of abundant phototrophs
that can supply the majority of fixed carbon (Gonzalez-Toril et al.,
2003 [Abstract] [Full text] ).
The extensive cellular diversity in this ecosystem, including a significant
contribution to genome complexity by eukaryotes, means that a major
metagenomics effort would have to be mounted in order to begin to
describe the ecophysiology of the Rio Tinto.
The third major group of extremely acidic environments is anthropogenic
in origin and is constituted by industrial bioleaching heaps used
for the recovery of copper and by abandoned coal refuse piles. It
appears that they are substantially more restricted in species diversity
compared to the Rio Tinto but somewhat more complex than Iron Mountain.
From a practical standpoint, this is important because the fairly
restricted diversity of microorganisms in this niche suggests that
a meaningful interpretation of community structure, evolution and
function can be derived.
Preliminary examinations of microbial community structure and dynamics
of bioleaching heaps (Johnson, 1998; [Abstract] ;
Demergasso et al., 2005 [Abstract] ;
Coram-Uliana et al., 2005 [Abstract] )
has shown that there is a recognizable ecological succession that
proceeds in three stages, driven by temperature increases due to exothermic
biological oxidation of iron and sulfur: an early stage favoring mesophilic
bacteria (30-400C) such as Acidithiobacillus ferrooxidans
and A. thiooxidans; a second stage, when the temperature
begins to rise (40-550C) when A. caldus, Leptospirillum
and Ferroplasma groups become dominant and a final stage
(55-650C) where the bacteria Sulfobacillus and Metallosphaera
and the archaea Ferroplasma became dominant. This means that
the development and interaction of each of these microbial communities
must be described in order to increase our comprehension of microbial
metal solubilization (and precipitation) processes.
The microbial dynamics and interactions that occur in space and time
during heap bioleaching remain poorly comprehended and we propose
to initiate a
metagenomics project
in collaboration with the Punta de Cobre
copper mining company of Copiapo, Chile in order to address this deficiency. It is anticipated that a metagenomics project will advance our understanding of the microbial community structure of a bioleaching heap and how this community integrates biological signals to grow and develop. Such information is needed in order to be able to suggest strategies to optimize heap bioleaching.
