Introduction

Much of microbiology is focused on prokaryotic organisms (bacteria and archaea). However, there is also a great deal of research concerning eukaryotic organisms, both micro and macroscopic, as well as viruses. Microscopic eukaryotes include fungi, protozoas, algae, lichens (which are mutualistic combinations of a fungus and an alga or cyanobacterium) and slime molds. Macroscopic eukaryotes include the parasitic helminths (flat worms of the phylum Platyhelminthes and round worms of the phylum Nematoda).

Viruses are acellular entities (neither prokaryotic nor eukaryotic) that require a host cell in order to replicate. Viruses contain either DNA or RNA (prokaryotes and eukaryotes have both) but lack the enzymes necessary to multiply on their own. Viruses are approximately 100 times smaller than typical bacteria and can only be seen with an electron microscope.

Fungi

The Fungi kingdom contains more than 100,000 species. Similar to bacteria, many fungi are quite beneficial to humans, other animals, and plants, while others are pathogenic. Fungi structure includes cell walls composed of glucans (also found in plant cell walls) and chitin (also found in the exoskeletons of arthropods). One of the most common fungi is Saccharomyces cerevisiae. This eukaryotic microorganism is classified as a fungus, and is more commonly referred to simply as baker's or brewer's yeast. S. cerevisiae is used in bread, beer, and wine production. Another common fungi is Rhizopus stolonifer, which is the fungus responsible for the dark green or black mold that sometimes forms on old bread. Mushrooms are also well known and are the fruiting bodies of a variety of fungi.

Figure 1: Pure culture of baker's yeast (Saccharomyces cerevisiae) growing on an agar plate.

Fungi are commonly grouped into two categories: yeasts and molds (filamentous). Yeast cells are unicellular, spherical or oval in shape, and can grow as a colony on the appropriate media. They can perform either aerobic respiration or fermentation.

Mold structures (including mushrooms) consist of individual filaments, called hyphae, that grow together to form a mycelium. Hyphae grow through elongation. The hyphae may be separated (septate) by cell walls or continuous (non-septate or coenocytic) without cell walls.

Some fungi can grow as either yeasts or molds, depending on environmental conditions. These types of fungi are called dimorphic fungi since they display two growth patterns. Many pathogenic fungi fall into the dimorphic category.

Figure 2: Diversity of the Kingdom Fungi. The fruiting body that contains spores for asexual reproduction in mushrooms (multicellular) are shown in A and B. Image A is the edible white, or button, mushroom. Image B is the highly poisonous Amanita phalloides, otherwise known as death cap.

Figure 3: Photomicrograph of Candida albicans on a slide. This yeast can cause fungal infections on the skin, mucous membranes, or systemically. It is a normal component of human flora and its growth is typically restricted by the immune system and the presence of bacteria residing in the same location.

Fungi can reproduce by both asexual and sexual means, and many of their life cycles can be rather complex. Divisions of the kingdom Fungi are based on two primary features: sexual spores and whether the hyphae is septate or coenocytic. Some of the divisions are Glomeromycota (formerly class Zygomycetes), Ascomycota (formerly class Ascomycetes), and Basidiomycota (formerly class Basidiomycetes). Members of the division Glomeromycota include Rhizopus species (the black bread mold, Rhizopus stolonifer, is one), some of which produce a fungal infection, zygomycosis, in diabetics and immunocompromised individuals. The division Ascomycota includes both baker's yeast (Saccharomyces cerevisiae), and Candida albicans.

Many yeast species are found living within humans without causing concern. However, they can potentially cause serious infections in immunocompromised individuals. Ascomycota also includes molds of the genus Penicillium, which is the source of the antibiotic penicillin. Some Penicillium species are pathogenic, while others are used to give certain cheeses distinctive flavors (Penicillium roquefortii for blue cheese; Penicillium camembertiii for some soft cheeses). Mushrooms belong to the Basidiomycota division; Amantia phalloides (the death cap mushroom) is a member, as is Cryptococcus neoformans which causes cryptococcosis (lung infection and fungal meningitis) in immunocompromised individuals.

Protozoa

Protozoas are unicellular chemoheterotrophic microorganisms that reside in water and soil. Protozoa typically have two life cycle stages, a vegetative stage and a resting stage. The vegetative stage occurs when the organism is feeding and growing. This period of gorging is also known as the trophozoite. In the trophozoite stage, the protozoa eats bacteria and other available particulates for nutrients. The resting stage is characterized by the formation of cysts. Cysts form under suboptimal environmental conditions and are an important stage for parasitic (those that require a host to survive) protozoa. Most protozoa reproduce asexually, although some do reproduce sexually (e.g., Paramecium species).

Protozoas include amoebas, sporozoas, ciliates, and flagellates. There are a number of protozoans that are pathogenic to humans. Amoebozoas that infect humans include Acanthamoeba, Entamoeba, and Balamuthia; these are typically ingested from contaminated drinking water. Balantidium coli is the only known ciliate protozoan to cause disease in humans. It can result in dysentery and is found in contaminated water. Giardia lamblia, Trichomonas vaginalis, and Trypanosoma brucei are protozoan flagellates that cause giardiasis, trichomoniasis, and African sleeping sickness, respectively, in humans. T. brucei is transmitted to humans through the bite of the tsetse fly.

Sporozoan protists are non-motile organisms. They are obligate intracellular parasites. This group includes the Plasmodium species. This species uses mosquitos as a vehicle for transmitting malaria and is the primary reason for its spread to humans. Toxoplasmosis is also caused by another sporozoan protist called Toxoplasma gondii and can be transmitted via infected cat litter. Finally, cryptosporidiosis (caused by the Cryptosporidium species) is another infection found within sporozoan protists and is the most common cause of waterborne disease in the US.

Parasitic Helminths

Microbiologists study parasitic helminths because their life cycles include microscopic stages. Parasitic worms are of the phyla Platyhelminthes (or flatworms) and Nematoda (or roundworms). Flukes (trematodes) and tapeworms (cestodes) are Platyhelminthes. Flukes are dorso-ventrally flattened with ventral and oral suckers that are used to attach to a host. Flukes absorb nutrients through their cuticle (outer coverig) and are named for the organ in which they live (e.g., liver, lung, blood, etc.). Flukes cause disease in these organs as a result of their reproduction in those sites. Tapeworms infect the intestines, where they attach by means of suckers and/or hooks and absorb nutrients through their cuticle. Examples of parasitic tapeworms include Taenia species (beef and pork tapeworms) and Hymenolepis nana (or dwarf tapeworm), which is the most common cause of cestodes infections in human.

Nematodes are cylindrical in shape, tapered at each end, and have a complete digestive system, unlike the flatworms. Some nematodes can be found in soil and water samples while others are found only in their host organism. In humans, either nematode eggs or larva are infectious. Pinworms (Enterobius vermicularis) complete their life cycle in humans. The eggs are the infective agents and can be passed to humans by exposure to contaminated clothes or bedding. Hookworms (including Necator americanus), another parasitic nematode, also live in human intestines and have eggs that are passed via feces, contaminated soil, or contaminated water. The larva hatch in the soil or water and feed on bacteria, then enter humans through the skin. Children often get hookworms in the summer when play outdoors without shoes. Poorly cooked pork (worldwide) or wild game (U.S.) is the source of Trichinella spiralis, the causative agent of trichinosis. Strict guidelines for pork production and processing have virtually eliminated pork as source of Trichinella in the U.S.

Viruses

Viruses are obligate intracellular parasites that must hijack a host cell's enzymes in order to replicate. Viruses have been found to infect all organisms on earth, from bacteria and plants to humans. They can occasionally jump from one species to another after mutations or recombinations with other viruses. Viral genetic material is stored either DNA or RNA, and can be single or double stranded. In contrast, prokaryotes and eukaryotes always have double stranded DNA as genetic material.

The viral genome is surrounded by a protein coat called a capsid. This is used to protect the DNA or RNA. In some viruses the capsid is enveloped, or surrounded by part of the host cell's membrane after the virus is released from the cell. Viruses which do not have an envelope are called nonenveloped viruses.

In a typical viral infection, the virus must first attach to a host cell. Then, the capsid fuses to the host cell membrane. The host cell takes up the viral particle and the genetic material of the virus is released to the cell. The host cells synthetic machinery (polymerase, etc.) replicates the viral DNA or RNA and produces the viral proteins in the hosts local environment. This includes structural and protective proteins (such as the capsid). New viral particles (virions) are then assembled and released from the host cell.

RNA containing viruses of the family Retroviridae encode an enzyme called reverse transcriptase that makes double stranded DNA from the viral RNA, rather than using the cellular machinery. The double stranded DNA is then stably integrated into the host cell genome and can produce a long-term infection. An example of this type of virus is Lentivirus (subspecies HIV-1 and HIV-2) that cause acquired immunodeficiency syndrome (AIDS) in humans.

Viruses known as oncoviruses can also cause cancer in humans through host oncogene activation. Oncoviral DNA integrates with the host cell's DNA and is therefore reproduced as the host cell divides. Oncoviruses can be either DNA or RNA-containing viruses. DNA oncoviruses are found in several different viral families and include human papillomavirus (HPV; cervical cancer). Epstein-Barr virus (lymphoma), and hepatitis B virus (HBV; liver cancer). RNA oncoviruses all come from the family Retroviridae and include human T-cell leukemia viruses (HTVL-1 and -2; T-cell leukemias).