What are microorganisms?
Technically a microorganism or microbe is an organism that is microscopic. The study of microorganisms is called microbiology. Microorganisms can be bacteria, fungi, archaea or protists. The term microorganisms does not include viruses and prions, which are generally classified as non-living.
There is currently a great deal of discussion about the organisation and classification of life, particularly in the study of microorganisms. The basic distinction divides living organisms into two groups: prokaryotes (cells without internal membrane bound organelles - the monera, including most microorganisms) and eukaryotes (cells containing membrane bound organelles - protists, fungi, plants and animals).
Before the advent of the microscope, living organisms were conveniently divided into two kingdoms: plant or animal. This division was unsatisfactory, however - what about fungi? Today kingdom taxonomists have defined systems based on five or six kingdoms (Archaea - the sixth, Monera, Protoctista, Fungi, Plantae, and Animalia), neither of which include viruses (or prions). Viruses are considered to be on the line between living and non-living.
It has been argued extensively whether viruses are living organisms. Most virologists consider them non-living, as they do not meet all the criteria of the generally accepted definition of life. For instance, most viruses do not respond to changes in the environment, which is a definitive trait for living organisms. In addition, viruses can replicate themselves only by infecting a host cell. They therefore cannot reproduce on their own.
Prions are a recently discovered infectious agent. They are proteins that are folded abnormally (folding is a property of proteins enabling them to take on a shape that is critical for their function), and which can convert normally folded proteins to abnormally folded ones.
The advent of genome analysis has both simplified and complicated the question. DNA sequence analysis led Dr. Carl Woese in the 70s to propose a three domain division: bacteria, archaea and eukaryota. The grounds for this division can be seen in the tree of life he produced from the sequence data. This tree of life clearly shows that microorganisms account by far for the majority of life on earth. Scientists estimate that 99% of the microorganisms on earth have not yet been identified!
Research into deep sea hydrothermal vent microorganisms may help to clarify some of these classification issues.