Molecular phylogenies divide all living organisms into three domains – Bacteria (“true bacteria”), Archaea, and Eukarya (eukaryotes: protists, fungi, plants, animals). The place of viruses (Box 1.1) in the phylogenetic tree of life is uncertain. In this book, we focus on the contributions of Bacteria, Archaea, and Fungi to microbial biotechnology. In so doing, we include organisms from all three domains. We also devote some attention to the uses of viruses as well as to the problems they pose in certain technological contexts.

The domains of Bacteria and Archaea encompass a huge diversity of organisms that differ in their sources of energy, their sources of cell carbon or nitrogen, their metabolic pathways, the end products of their metabolism, and their ability to attack various naturally occurring organic compounds. Different bacteria and archaea have adapted to every available climate and microenvironment on Earth. Halophilic microorganisms grow in brine ponds encrusted with salt, thermophilic microorganisms grow on smoldering coal piles or in volcanic hot springs, and barophilic microorganisms live under enormous pressure in the depths of the seas. Some bacteria are symbionts of plants; other bacteria live as intracellular parasites inside mammalian cells or form stable consortia with other microorganisms. The seemingly limitless diversity of the microorganisms provides an immense pool of raw material for applied microbiology.

The morphological variety of organisms classified as fungi rivals that of the bacteria and archaea. Fungi are particularly effective in colonizing dry wood and are responsible for most of the decomposition of plant materials by secreting powerful extracellular enzymes to degrade biopolymers (proteins, polysaccharides, and lignin).