In nature’s ecosystems, energy is flowing and the matter is circulating. Microorganisms are the essential link in maintaining balance in returning the substances into circulation. They are capable of degrading the biomasses. Modern sustainable bio-industries should be based on the biomass and waste utilization by the microbial strains and their enzymes, which carry out the energetically favorable biocatalysis. The ordinary methods for researching the microorganisms include their propagation in

laboratory conditions using:

• solid media, • liquid media, or • semisolid media. The chosen medium has to contain the carbon (C) source, energy source, nitrogen (N) source,

other minerals, trace elements and vitamins, according to the requirements of the cultivated organism(s). Any microbe has its optimum and limits regarding such parameters as pH, dissolved oxygen, or production temperature. The optimal conditions may be different for the microbial growth and for the product formation. In this chapter, we concentrate on the production of fuels and bulk chemicals by microbe cultures. In some sense, this also has been the original meaning of the concept “biotechnology”. It also provides the humanity vast potential for rearranging the economies to be based on sustainable industrial microbiology. The processes could then be based on the degradation and circulation chains in nature. In many recent considerations, the word “biorefinery” has been designating technologies,

which could use biomass raw materials instead of oil and other fossil deposits for the foundation of the energy maintenance and the chemical industries. Those applications, where the microbes liberate the chemically bonded energies in and from various organic raw materials could give a positive overall energetic balance, for example for waste treatment processes. These natural reactionsmake possible the flexible use of alternative biomass sources aswell asmultiple use of the bioreactor plants and installations.Wewish to open up a view into these potentials, and challenges, of the old and at the same time extremely modern discipline of industrial biotechnology. In the research purposes, we have been using aminiaturized cultivator system, PMEU (Portable

Microbe Enrichment Unit) for the experimentation. In this device, it is possible to use various gas flows in selected temperatures for themicrobial bio-reactions. The resulting activities and changes are measurable optically, or by following up the gas and volatiles emissions from the minireactor system. By using the PMEU, it has been possible to investigate the interactions of severalmicrobes in mixed cultures, as well as optimize the physicochemical conditions for different processes. In practice, the implementation of microbial bioengineering requires research on biocatalysis.

This enzymatic powerhouse of cell systems is offering a basis for industries on a large scale. In order to facilitate the change into more sustainable biomass-based industries we need to improve the efficiencies of the pretreatments, and productivity of the bioprocesses, togetherwith improving the integration of the downstream processing with the production itself. As a result, we learn to