PCAT Exam: Biological Processes - Microorganisms

Microorganisms are tiny single-celled or multicellular organism that can only be seen through a microscope. They include all bacteria and archaea (prokaryotes that live in extreme environmental conditions), and almost all protozoa, fungi, algae, and some rotifers (round microorganisms that reside in freshwater and have three-layered body cavities). Microorganisms have an important role in the environment, as they’re found all over and help to recycle nutrients and energy.

Biodiversity
Biodiversity refers to the variety of life and species on Earth. There are many types of microorganisms on our planet. Four main classes of microorganisms are viruses, bacteria, protozoa, and fungi.

Although viruses are acellular, they use a host species to replicate themselves, allowing for the cycling of nutrients, bacteria, and algae. They can also be pathogens and spread diseases.

Bacteria are unicellular and obtain energy through photosynthesis, chemosynthesis (the synthesis of organic material from inorganic material for use as energy particularly in the absence of sunlight), and heterotropism (the ability to only produce organic material from carbon derived from animal or plant biosynthesis).

Protozoa are a diverse group of unicellular organisms that carry out complex metabolic activities. They’re also non-photosynthetic, so they cannot use light as an energy source. Amoebae, flagellates, and ciliates are all protozoa.

Fungi can be unicellular or multicellular and they convert organic matter into nutrients. They are the primary decomposers of an ecological system.

Microbial Systematics 
Microbial systematics is the scientific study of the types of microorganisms and the relationships between them. It can be divided into three areas: classification, nomenclature, and identification. This area of discipline allows microbiologists to further study genomic similarities between different species or microorganisms.



Domain Bacteria 
The domain Bacteria includes many of the prokaryotic species that people encounter daily. Most are heterotrophic, which means they acquire their food from organic matter. Some are parasitic, which means they live within a host and cause disease. Some are autotrophic and synthesize their own food, such as by photosynthesis or chemosynthesis. They can be aerobic or anaerobic. Bacteria can also be beneficial to the environment by turning nitrogen from the air into organic compounds available to plants. They also help with the decay of landfill materials and other environmental debris. Bacteria swap genetic material through horizontal gene transfer, which can happen by transformation, transduction, or conjugation. Transformation involves the naturally-transforming bacteria taking up short fragments of naked DNA. Transduction involves the uptake of DNA by bacteriophages. Conjugation requires cell-to-cell contact and DNA is transferred by sexual pilus.

Domain Archaea 
The domain Archaea is comprised of single-cell prokaryotes, which means that they don’t have a cell nucleus or any membrane-bound organelles within them. Although they are similar in size and shape to bacteria, they contain genes on a single circular chromosome and have several metabolic pathways including transcription and translation. There are three types of archaeal species that use different sources of energy: Phototrophs use sunlight for energy, lithotrophs use inorganic compounds for energy, and organotrophs use organic compounds for energy.

Protists 
Protists are a diverse group of unicellular eukaryotic organisms. They are often grouped by convenience and because they are not an animal, plant, or fungus. As eukaryotes, they have a nucleus and organelles. Photosynthetic protists contain plastids, which are organelles responsible for converting light to energy. Protists that use oxygen for energy contain mitochondria. Those that live in hypoxic environments, which lack oxygen, have hydrogenosomes, which appear to be like modified mitochondria. Protists can gain nutrition in many ways, such as photosynthesis or heterotrophism. A few common protists are euglena, amoeba, paramecium, and volvox.

Fungi 
Fungi are a group of microorganisms that includes yeasts, molds, and mushrooms. They have the distinct characteristic of having chitin in their cell walls. Chitin is a long carbohydrate chain that adds rigidity to the walls of the fungi cells. Fungi are also solely heterotrophic; they break down dead organic material and use the released nutrients. They play an important role in cycling nutrients throughout an ecosystem. Many vascular plants only grow because of the symbiotic fungi that inhabit their roots and supply them with essential nutrition. Some fungi are responsible for the production of antibiotics, such as penicillin. Contrastingly, fungi can also cause many diseases in plants and animals, such as rusts and stem rot in plants and ringworm and athlete’s foot in humans.

Helminths 
Helminths are large multicellular organisms generally known as parasitic worms. Many worms classified as helminths are the cause of intestinal infections. They live in and feed off their living hosts. They disrupt their host’s nutrient absorption, causing them to feel weak and be ridden with disease. Although they share a similar form, many species classified as helminths are not actually evolutionarily related.

Viruses and Virus-Like Agents 
Viruses are acellular units comprised of a nucleic acid core surrounded by a layer of protein. As they are acellular and therefore non-living, they cannot reproduce or metabolize on their own—they must use a host organism to do both. Viruses can have a variety of effects on their host. Many viruses disable their hosts and cause cell death. Other viruses are latent and don’t show signs of infection within their host.

Microbial Growth, Nutrition, and Metabolism 
Most microorganisms reproduce by binary fission, a process where a cell grows to twice its normal size and then divides in half to produce two equally-sized daughter cells. These two cells can eventually divide again and become four cells, and the four cells can grow and divide to become eight total cells, and so on, to make the microorganism population larger. The growth of the microorganisms depends on intake and metabolism of appropriate nutrients. The most important nutrients are carbon, oxygen, nitrogen, and hydrogen. Different microorganisms can metabolize these elements for use as both food and energy. The flagella of protozoa are like those of human sperm and can aid in the study of human reproduction.

Microbial Genetics 
Microbial genetics looks at the genotype and phenotypic expression of microorganisms. Because microorganisms have a rapid growth rate and a short generation time, they have been used for centuries to study different processes and pathways. The distinct traits of microorganisms allow for a variety of things to be studied. Bacteria have been used to study gene transfer systems. Archaea can withstand harsh environments and are used to study extreme environmental conditions in vitro. Fungi are used to study cell cycle regulation, chromatin structure, and gene regulation. Although their gene function isn’t well understood, it is thought that both archaea and fungi have horizontal gene transfer functions like bacteria. Viruses are important for the study of genetics, as well as the study of viral pathogenic properties. Molecular biologists often use viral vectors to insert genetic material into cells.

Physical and Chemical Methods of Controlling Microorganisms 
It is important to be able to control microorganisms to prevent the transmission and spread of diseases, and to stop decomposition of organisms and food spoilage. They can be controlled by both physical and chemical methods. Physical control can occur through changes in temperature, humidity, osmotic pressure, and by filtration. These changes can inhibit microorganism growth and make the environment less ideal for their survival. Filtration includes the physical removal of microorganisms by preventing their passage through a porous material. Chemical control occurs using disinfectants, antibiotics, antiseptics, and antimicrobial chemicals, which all work by selective toxicity. These agents seek out and kill the microorganisms without harming anything else.

Tools for Studying Microorganisms 
Microorganisms cannot be seen by the naked eye and can only be visualized using a microscope. Certain types of microscopy, such as bright field, phase-contrast, and dark field, allow the cells to be seen without staining. Cells can also be stained and then viewed under a microscope so that different characteristics of the cell can be illuminated.

Electron microscopy uses a beam of electrons to magnify specimens so that their details can be seen more clearly.