Scientists consider the charismatic macrofauna as he prima donnas of organismal biology.  Little is known about this macrofauna.  The scientists are doubling their efforts to extensively study these microorganisms with the use of modern technology like the digital binocular microscope. The macrofauna is significant in the study of microbial genomics. Funding for the study of the macrofauna are scarce since the lion’s share of research and conservation funds mostly go to tigers, dolphins, pandas, and their kind.
What is Prokaryotic Fauna

In the study of Biology, the mysterious prokaryotic fauna are microorganisms that live on acidic hazardous waste in heavily polluted iron mines. The microbiologists have a hard time examining the fauna since these microbial subjects cannot be seen with the naked eye.  Likewise they cannot be photographed without a microscope. They can only be observed closely with the use of the microscope especially the digital binocular microscope.  Another characteristic of these microorganisms is that they cannot even be isolated in vitro. Many bacteria from such chemically extreme environments will not grow even in specially designed acidic media.
Prerequisites in the Study of Bacteria
In the laboratory, cultures have long been considered as a prerequisite in the study of the bacteria which leads to the taxonomic bias like that in the study of animals.  It should be noted that the pet microbes that can be isolated and cultured in the laboratory represents approximately 99% of known bacteria.  Some scientists refer to them as weeds.

The untamable microbes like the acid-mine dwellers, though often times ignored may be 100 times more numerous.  They are considered as the dark matter of life in terms of both biomass and species diversity.

The Production Sequencing Facility
In laboratory, cultures offer a glimpse into the lives of these interesting organisms.  The   Production Sequencing Facility sequences genes and genome fragments so efficiently.  Scientists can extract an entire genome from the relatively small number of microbes in a sample taken from the field.  Scientists may be able to simultaneously sequence the genomes of the different organisms found in such a sample and giving a genetic cross-section of an environment.  The Production Sequencing Facility was known to export human gene sequences at the rate of 10 million base pairs per day.

How Sequencing is Done
The shotgun approach is utilized to sequence random DNA fragments.  This   method uses search algorithms to reconnect these fragments into complete genomes.   It should be noted that there are only four different letters in the genetic code.  A microbial genome can exceed seven million base pairs in length. As the human genome is already studied, scientists are now undertaking sequencing genomes for various samples ranging from mitochondria to pufferfish.  Genetic information can be taken straight from field samples which can shed light on the mysterious lifestyles of unculturable, invisible, acid-dwelling, iron-eating organisms. With the use of the genome sequence, scientists can study a microbial sample with the aid of the digital binocular microscope which will enable them to hypothesize about the organism’s survival strategies in relation to the kinds of genes it possesses.

New discovery
A new discovered organism referred to as Ferroplasma sp. Type II, is a member of   the single-celled Archaea. Initially   grouped with the Bacteria, this Ferroplasma sp. Type II is discovered to have a diversity equaling or even surpassing that of Eukarya which includes humans, nematodes, and everything in between. The new organism is known   by its entire DNA sequence. As the new species have been identified efforts to determine its genome for genetic clues on how it survives in inconceivably harsh conditions are being taken into consideration.

Other challenges
Another challenging area of research is how to tackle all the genomes in an ecosystem. This can be done by making an inventory of the genomes present in a particular community to better understand the ecological and evolutionary relationships between community members. Extremely acidic pH, high temperatures, and heavy metal contamination can turn the acid-mine environments into an excellent starting place for environmental genomics.  Under these harsh conditions organismal diversity will be limited to fewer than ten hardy species.

The   whole-ecosystem genomics will eventually fulfill a wide range of functions, from clarifying the evolutionary relationships between organisms to profiling pollution sites.Original Article