Bacterial scum can be discovered in unlikely places.   Under the digital binocular microscope, a pink, bacterial scum on the floor of an abandoned mine is actually a microbial mat. It is an unlikely place to study but researchers want to probe and study this microbial mat.
Bacteria in a slime, or biofilm, are responsible for acidic drainage from the mine. Scientists can pluck out genomes of five dominant bacteria in a biofilm or bacteria in slime. They have likewise identified the proteins that go with these five organisms, their so-called proteomes.
The Importance of Genome
The technique used is the first successful leveraging of a community genome to obtain the complete complement of proteins produced by that community of organisms.  It also allows for the possible identification of protein in each bacterium as well as how much of each protein is produced.  This is an important factor in understanding the role each bacteria species plays in the biofilm community.
Genomes tell about the genetic capability of organisms present in the environment. Banfield and   colleagues have been extensively studying the microbial biofilm community for nine years with the use of the digital binocular microscope.  They aim to understand how the organism live and interact with minerals to produce  the hot, heavy-metal rich and highly acidic water that drains from the mine and contaminates surrounding streams. The film, which can form a tough sheet that is millimeters thick, sits atop green, 108 degree Fahrenheit runoff containing zinc, iron, copper and arsenic. This system is a very tightly coupled biogeochemical system.
Microbial Community
What was noted was that the microbial community is thriving at the extreme edge.  A pH level of 0.8 is like swimming in sulfuric acid.  Scientists would like to know how this community can survive and how to use this information to better understand microbial systems in real-world conditions.
As studied with the use of the digital binocular microscope, bacteria, along with ancient microbes called Archaea, in the biofilm can capture carbon and nitrogen from the atmosphere.  They have the capacity to get the energy from iron that has been leached out of the iron sulfide rock otherwise known as pyrite or fool’s gold.  They also produce sulfuric acid that leaches more iron from the pyrite and releases other heavy metals.
The complete genomes of the five major bacteria in the biofilm are nearly complete, four of them new to science. The current study provides almost half the proteins predicted to be produced by the dominant bacteria, a Leptospirillum group II bacterium.  A smaller fraction comes from other bacteria. The lesser coverage of the minor bacteria in the community is   because their genomes are more fragmented and in part because these bacteria are in lower concentrations. Thus their proteins are at correspondingly lower concentrations.
What are Proteomes?
Proteomes are proteins that go with the genomes of five dominant bacteria in a biofilm.
Statistics indicate that of the 2,033 proteins detected, 572 were unique to the biofilm bacteria. A new protein produced by the Leptospirillum group II bacterium seems to be an important protein in the production of acid mine drainage. The protein known as cytochrome, oxidizes iron, as well as controls the rate of production of acid mine drainage. This is its way of getting   energy from the environment and possibly the initial step in the electron transport chain associated with the metabolism of the organism.
Majority of the proteins produced by the biofilm bacteria are responsible for maintaining correctly folded proteins and protecting them against free radicals.  This implies that these are significant challenges in the hot, acid environment.  Another interesting thing is that   there are a number of proteins that do not resemble any other proteins.   Many are enzymes whose job is to maintain the correct structure of other proteins   exposed to the unusually harsh acidic environment.
The Proteogenomic Technique
The proteogenomic technique is utilized to extract the proteome from the biofilm which involve the dicing up all the proteins in a melange of the organisms.  The masses of these short proteins, called peptides are determined with shotgun mass spectrometry. Genomes were utilized to identify the peptides from their masses.  The genomes    paved the way in the prediction of proteins in each member of the biofilm community.  From this protein fragments can be predicted.  Correlation permits the reconstruction of the complete protein and its association with a particular organism.
This method shows the power of the genome sequencing.  Scientists can now study not only the community genome, but likewise the resulting community proteome for enzymes and pathways which can help clean up some of the worst environmental sites in the nation.More on this topic