Microbe Mission

From Wiki - Scioly.org
Jump to navigation Jump to search

Microbe Mission is a life science event being run in the 2023-2024 season for Division B and Division C. It was first run as a trial event in 2008-2009 before being made an official event for the 2010-2011 and 2011-2012 seasons. Microbe Mission returned for the 2016-2017 and 2017-2018 seasons. After 6 long years, it is back again for the 2023-2024 season! Presumably, Microbe Mission will be held in 2024-2025 season as well.

If you are interested in contributing to the Microbe Mission page, please see Microbe Mission page improvement coordination.

Event Overview

Microbe Mission is a hybrid event that tests teams' core knowledge of microbiology and hands-on laboratory skills. In this event, teams answer questions, solve problems, and analyze data related to microbes.

Topics for 2023-2024

Refer to the 2023-2024 rules manual for Division B and 2023-2024 rules manual for Division C for comprehensive lists of the topics that may be tested at regional, state, and national competitions for each division. Some topics may be tested include.

  • the parts and advantages/disadvantages of different types of microscopes
  • use of microscopes for making measurements or estimations
  • the principles of microscopy (e.g., reflection, magnification) and relevant calculations (e.g., field of view, and object size)
  • the structure, function, metabolism (where applicable), and life/replication cycles of different types of microbes, including: archaea, bacteria, eukaryotic algae, fungi, parasitic worms, prions, prion-like particles, protozoa, viruses, and viroids
  • microbial interactions (e.g., competition, mutualism, parasitism)
  • microbial evolution, including horizontal gene transfer and the theory symbiogenesis
  • bacteriostatic vs. bacteriocidal antibiotics, methods for assessing antibiotic susceptibility, and mechanisms of antibiotic resistance and resistance transfer
  • roles of microbes and microbial population explosions in the environment and in microbiomes
  • the significance of microbes in agriculture, food production, and other industries (biofuels, bioremediation, phage therapy, pharmaceuticals, wastewater treatment)
  • modern methods for culturing and measuring the growth of microbes
  • modern methods for studying microbial communities and measuring microbial activity
  • the use of dichotomous keys to identify microbes
  • data collection, interpretation, and analysis

Stations format

If there are stations, there will usually be anywhere from 5 to 20 of them, numbered with Roman (I, II, III...) or Arabic (1, 2, 3...) numerals. Sections of the test will correspond to each station, though the format of the questions at each station is decided by the test creator and may vary widely from test-to-test. Teams typically have a time limit of anywhere between 2.5 and 10 minutes per station before they must rotate to the next station. Depending on the number of stations and the number of teams, multiple teams may be at the same station simultaneously or event coordinators may provide duplicates of the stations.

Test format

If there are stations, then the test packet will likely be an answer sheet that is divided into pages or sections corresponding to each station. In many cases, there will be no questions or diagrams in the packet, which means all work must be done at the corresponding station. At some competitions, the questions may also be included in your test packet. All answers must be recorded in the packet. As teams record their answers, they should ensure at each station that they are recording on the right section, page, and question. Rarely, but occasionally, there are additional sections of the test that do not correspond to any station. These sections must be completed while teams work through the stations. In these cases, it can be smart to have one team member work on the problems at the station while the other team member works on the remainder of the test.

If there are not stations, then the test may be given as a normal test packet. Many, but not all event coordinators allow your team to disassemble to test packet for the ease of working on different pages of the test simultaneously. Make sure you ask the event coordinators if you are allowed to do this before doing so. If you choose to disassemble the test, event coordinators will almost always require you to staple the test together in the correct order to avoid any penalties. If the pages are disordered or if any pages are missing, you may be deducted points.

Sometimes, correct spelling is considered in grading, especially if the word is spelled correctly for you somewhere else on the test. That said, some test creators are less particular than others, and there may be exceptions for minor spelling errors. Points may also be taken away if answers are not neat or legible. Some tests may have lines for team name, team number, and/or participants' names on each page. Teams should ensure this information is on every page, as points may be deducted if it is missing.

Potential question formats may include: labeling, matching, multiple choice, fill-in-the-blank, short answer, specimen identification, data collection including the use of lab instruments such as microscopes, and calculations.

Materials

Each participant must bring Z87 chemical splash goggles and a writing implement. Teams may bring two non-programmable, non-graphing calculators and one 2-sided 8.5" x 11" page of notes which can contain any information in any form, including diagrams, from any source. No other resources will be allowed.

Preparing for Microbe Mission

An AP Biology textbook or college-level microbiology textbook will help with learning important terms and concepts. It is also helpful to review all of the resources linked on the official Microbe Mission page on soinc.org. Additionally, making a binder can be a helpful step in preparing for this event. Although binders are not permitting during testing, it can be an efficient way to keep notes and practice tests in the same place.

Completing practice tests is extremely helpful when preparing for Microbe Mission and other core knowledge events. Practice tests allow teams to familiarize themselves with a variety of topics and questions types, which is important because the content covered and question formats may vary widely from test-to-test. One specific exercise that often helps team members to fill in their respective knowledge gaps is to study independently, create practice tests based on what they studied, and give those practice tests to their event partner at Science Olympiad practices/meetings. By writing practice tests, team members may be inspired to delve into more challenging topics so that they can challenge their partner with a difficult practice test. Team members also must ensure that they are confident in the answers to the questions they write, which can lead to a more thorough understanding of material. Additionally, frequent testing ensures that team members perform active recall of the information they have studied, which is a proven technique for enhancing memory.

Tips for Making the Note Sheet

  • Note sheet layout: Knowing the layout of your note sheet and how to quickly locate information is the most important part of the note sheet. Especially when using small font size, it can be good to practice locating certain information on the sheet with your partner prior to the competition. If only one partner in the team helps to create the note sheet, the other partner may be unsure where to find certain pieces of information.
  • Communication between partners: Effective communication between event partners also important. Often, teams will be allowed to disassemble tests and work on separate sections simultaneously. If this happens, there will often be moments in which team members both want to look at the note sheet (sometimes different sides of the sheet) at the same time. Also, if one team member forgets whether a piece of information was included or left off the note sheet, it is helpful to ask their event partner instead of wasting time searching through the note sheet.
  • Color coding. Consider using different, readable colors for different topics in order to make locating information during the test easier and faster. Keeping the color coding consistent will allow you to automatically associate colors with different topics by the end of the season (e.g., pink = archaea, light blue = bacteria, green = viruses, orange = fungi, gold = microscopes etc.). Also, color-coded diagrams may increase efficiency and ease of in interpretation compared to diagrams only in black/white.
  • Font size, spacing, and margins: Use as small of a font as possible in order to fit more information, but keep your notes readable. There's no point in having volumes of information if it is impossible to interpret. Recommended fonts for Microbe Mission notes (or any other note-based event) are BenchNine, Calibri Light/Narrow, and Times New Roman with a size of 4-7 depending on what is legible to your team. Teams often use single or 0.9x spacing as well as 0" margins to reduce white space on the page.
  • Diagrams: It can be helpful to create your own diagrams, either by hand or with an image manipulation program (e.g., paint, inkscape). It's also acceptable to include diagrams from the web, though making ones yourself can enrich your understanding.
  • Charts: In addition to diagrams, teams can create custom charts that include specific information and help to maximize space. By personally making charts, teams also gain a better understanding of the material.
  • Handwritten notes: While the note sheet is most legible when printed, additional notes can be handwritten in the margins or between lines where the printer might not be able to print. This is time-consuming but well worth the time spent, especially if you want to add something on the competition day after you've already printed your note sheet.
  • Fact checking: Source-check before putting anything on the note sheet to avoid using incorrect information during tests. It can be good to have your event partner review any changes you have made to your note sheet to help with this.
  • Prioritize topics: Use space efficiently by prioritizing which material to include and which material to leave off. It is generally best to include the material that is most challenging to understand or recall for your team specifically, as different teams with have different background and strengths. Extra information can be added later if there is additional space. Also, as you learn more throughout the season, it can be smart to remove any pieces of information from your note sheet that you have since memorized.
  • Printing: Laser printers are recommended for smaller font sizes (size 6 or less). If you do not have a laser printer, some community and school libraries may have one that is free to use. Also, UPS and FedEx stores have laser printers that you can use at a small cost. Font sizes can technically be reduced manually if you treat text like a picture (by typing it into an image manipulation program and then shrinking the image), though this often reduces the readability of the notes.

Microscopy

Types of Microscopes

  • Optical Microscope: Optical microscopes use visible light (or UV light in the case of fluorescence microscopy) to sharply magnify the samples. The light rays refract with optical lenses. The first microscopes that were invented were found to belong in this category. Optical microscopes can be further subdivided into several categories:
    • Compound Microscope: The compound microscope is built of two systems of lenses for greater magnification (an objective and an ocular: eyepiece). The utmost useful magnification of a compound microscope is about 1000x.
    • Stereo Microscope (dissecting microscope): The stereo microscope is an optical microscope which magnifies up to about maximum 100x and provides a 3-dimensional view of the specimen. Stereo microscopes are highly useful for observing opaque objects.
  • Confocal Laser scanning microscope: Unlike compound and stereo microscopes, Confocal Laser scanning microscopes are reserved for research organizations. Such microscopes are able to scan a sample in depth, and a computer can then assemble the data to create a 3D image.
  • Electron Microscope: Electron microscopes are the most advanced microscopes used in modern science. Modern electron microscopes use accelerated electrons that strike any objects in path, to magnify them up to 2 million times due to the very small wavelength of high energy electrons. Electron microscopes are designed specifically for studying cells and small particles of matter, as well as large objects. The high energy electrons are quite tough on the sample being observed. Because of the much shorter wavelength, the electron microscope has a higher resolving power than a light microscope. To reveal the structure of objects, it may initially require a long time to completely dehydrate and prepare the specimen; a sleek layer of a metal can be used to coat some of the biological specimens for easy observation.
    • Scanning Electron Microscope: Scanning Electron Microscopes are characterized by lower magnifying power, but can provide 3-dimensional viewing of objects. The Scanning Electron Microscope captures the image of the object in black and white after being stained with gold and palladium.
    • Reflection Electron Microscope: Reflection electron microscopes are also designed on the principle of electron beams, but they are characteristically different from transmission and scanning electron microscopes being that it is built to detect electrons that have been scattered elastically.
  • X-ray Microscope: An X-ray microscope uses a beam of x-rays to create an unparalleled high-resolution 3D image. Due to the small wavelength, the image resolution is higher as compared to optical microscopes. The greatest useful magnification is therefore also higher and it lies between the optical microscopes and electron microscopes. X-ray microscopes hold significant importance in science and research and have one special advantage over electron microscopes: it allows observing the structure of the living cells. It is adept at slicing together thousands of images to generate a single 3D X-ray image.
  • Scanning Helium Ion Microscope (SHIM or HeIM): Scanning Helium Ion Microscopes are a new imaging technology which uses a beam of Helium ions to generate an image. This technology has several advantages over the traditional electron microscopes; one advantage lies in the fact that the sample is left mostly intact (due to the low energy requirements) and that it provides a high resolution. The first commercial systems were released in 2007.
  • Scanning acoustic microscope (SAM): Scanning acoustic microscopes use focused sound waves to generate an image. An acoustic microscope has a wide range of applications in materials science to detect small cracks or tensions in materials. The scanning acoustic microscope is a powerful tool which can also be used in biology to study the physical properties of the biological structure and help uncover tensions, stress and elasticity inside the biological structure.
  • Neutron Microscope: Still under an experimental stage, Neutron microscopes generate a high-resolution image and may offer better contrast than other forms of microscopy. The new technology would use neutrons instead of beams of light or electrons to generate high-resolution images.
  • Scanning Probe Microscopes: Scanning Probe Microscope helps visualize individual atoms. The image of the atom is computer-generated, however. It provides the researchers with an imaging tool for the future where a small tip measures the surface structure of the sample. These specialized microscopes provide high image magnification to observe three-dimensional specimens. If an atom projects out of the surface, then a higher electrical current flows through the tip. The amount of current that flows is proportional to the height of the structure. A computer then assembles the position data of the tip. An enhanced 3D image is generated.

Microscope Parts

Compound light microscopes

  • Ocular: This part of a microscope magnifies the image formed by the objectives. It is the part where the viewer looks through to see the image.
  • Nosepiece: Holds the objectives and is located below the arm and the body tube.
  • Base: Supports the microscope and acts as a foundation.
  • Objectives: Lenses that form the first image (before the ocular) by receiving light from the field of view.
  • Arm: Connects to the base and holds up the ocular, body tube, objectives, and nosepiece.
  • Body Tube: The tube between the ocular and the nosepiece/objectives.
  • Coarse adjustment: Used to adjust the microscope in lower power.
  • Fine adjustment: Used to adjust the microscope in high power or for fine tuning.
  • Stage: Supports the slide and specimen when being viewed.
  • Stage clips: Clips on the stage that hold the slide in place.
  • Illuminator: A source of light, usually located below the stage. A lumarod (rod that collects light) is sometimes used as a source of light in microscopes that do not use electric power.
  • Diaphragm: Controls the amount of light reaching the specimen.

Principles of Microscopy

Appearance and movement of objects

In a microscope, objects appear upside-down and backwards. If a specimen were to move forward and right, it would appear to move backward and left when viewed through a microscope.

Magnification and changing objectives

The total magnification is found by multiplying the magnification of the ocular and the objectives. For example, if the ocular of a microscope is 10x and the objectives are on 12x, the total magnification would be 10 times 12, which is 120x total magnification. On a normal microscope, the ocular is usually 10x or 12x, while the objectives are about 5x for scanning, 10x or 12x for low power, and 40x-45x for high power.

When changing objectives to a higher power/magnification (scanning to low to high), the size of the field of view decreases and the field of view gets darker. The resolution (sharpness of image) and size of the image increase. The working distance decreases and the depth of focus is reduced.

Lenses and refraction

Many, but not all, microscopes depend on lenses to refract light and produce a clear image. Refraction is the bending or redirection of light waves as the phase velocity of the wave changes due to passes through a different medium. Refraction is frequently measured in terms of the angle of incidence, which is the angle between a ray of light and the normal line at the point at which the ray entered a new medium. Every medium through which light can travel has a property called the index of refraction, which in part controls the extent to which light is redirected. That is, light entering a medium with a 3x higher index of refraction than that of air will undergo a larger change in the angle of incidence than light entering a medium with a 2x higher index of refraction than that of air. The index of refraction is an inherent property of a medium, but in some cases depends on temperature. For example, hot air has a lower index of refraction than cool air, which sometimes results in the appearance of mirages on especially hot days as the air close to the ground redirects light; this is the reason some observers may mistakenly think they see distant puddles of water on especially hot days.

In addition to the index of refraction of the glass that comprises microscope lenses, the curvature of a lens controls how the light refracts. For instance, biconvex lenses causing light rays to converge and biconcave lenses causing light rays to diverge. Further, biconvex lenses with more dramatic curvature (i.e., a shorter radius of curvature) will converge light rays more powerfully than biconvex lenses with less dramatic curvature. Optical microscopes contain biconvex lenses to converge light. For additional information on the physics of lenses and refraction, see the optics page.

Since electrons do not readily pass through glass as light does, electron microscopes are one type of microscope that do not use lenses but instead rely on electromagnetic coils to focus the beam of electrons.

Mirrors and reflection

For additional information on the physics of mirrors and reflection, see the optics page.

Measurements

The smallest measurement on a metric ruler is usually a millimeter (mm), or 10-3 meters. There are 1000 micrometers (mcm or μm) in one millimeter, meaning 1 µm = 10-6 meters. Similarly, there are 1000 nanometers (nm) in one micrometer, meaning 1 nm = 10-9 meters. These important metric prefixes and abbreviations are listed below for relevant powers of 10.

Power of 10 Metric Prefix Metric Abbreviation Example
1018 exa E Exameter (Em)
1015 peta P Petafarad (PF)
1012 terra T Terrajoule (TJ)
109 giga G Gigahertz (GHz)
106 mega M Megasecond (Ms)
103 kilo k Kilowatt (kW)
102 hecto h Hectogram (hg)
101 deka da Dekapascal (daPa)
100 none none Meter (m)
10-1 deci d Decibel (dB)
10-2 centi c Centivolt (cV)
10-3 milli m Milliampere (mA)
10-6 micro µ or mc Micromolar (µM or mcM)
10-9 nano n Nanoliter (nL)
10-12 pico p Piconewton (pN)
10-15 femto f Femtomole (fmol)
10-18 atto a Attometer (am)

Acellular Microbes and Agents

Prions

Prions are pathogenic, misfolded versions of normal cell proteins. Specifically, in humans major prion protein (PrP) is encoded by the gene PRNP (also called CD230) located on the p arm (shorter arm) of chromosome 20. PrP is highly conserved in mammals, suggesting that it provides an evolutionary benefit despite being the precursor for prion diseases. In terms of protein evolution, mammalian PrP is highly homologous to the N-terminus of a class of proteins called ZIP metal ion transporters and exhibits a pH-dependent ability to bind metal cations with the strongest affinity for copper; for these reasons, PrP is thought to be descended from ZIP proteins. In humans, PrP is 253 amino acids long after translation, but post-translational cleavage of the signal sequence results in mature PrP having a length of 208 amino acids. The secondary structure of the correctly folded version of PrP includes 3 alpha helices, 2 antiparallel beta sheets, and a globular domain. Mature PrP is found on the cell-surface and, at the C-terminus, is covalently bound to a glycophosphatidylinositol moiety (a type of glycolipid) that anchors it to the plasma membrane. PrP can exist in the normally folded cellular isoform (PrPC) or as a misfolded, disease-causing form (PrPSc, named for its associated with the disease Scrapie) that is highly resistant to degradation by proteases. Some scientists have created protease-resistant isoforms of PrP in vitro that have not necessarily been shown to cause disease (PrPRes).

Exposure to small number of prions can facilitate the conversion of the normal isoform PrPC to the pathogenic isoform PrPSc, resulting in disease. In nervous tissue, PrPSc forms insoluble, compact aggregates called amyloid fibrils (also called amyloid filaments, or simply amyloids), which were named for the resemblance between the structure of β-sheet rich aggregates and the molecular structure of starch (specifically, amylose). Extracellular deposits of these amyloid fibrils called amyloid plaques accumulate within the central nervous system, disrupting the normal structure and function of nervous tissues. Additionally, prions cause nervous tissue to undergo vacuolation, in which neurons attempt to compartmentalize PrPSc inside vacuoles. This leads to enlarged vacuoles that appear like "holes" when analyzing tissue, and are what confer the characteristic spongiform, or sponge-like, histologic manifestation of prion diseases. Prion diseases can affect a wide range of nervous system functioning, are rapidly progressive, and are always fatal.

Prion diseases may be acquired (i.e., arising from exposure to prions via medical procedure or via ingestion of prion-containing material including biofluids, animal tissue, or contaminated soil), familial (i.e., arising from a genetic mutation), or sporadic (i.e., arising from spontaneous mutation). Prions diseases are also called transmissible spongiform encephalopathies (TSEs), which are neurodegenerative diseases that affect a wide range of vertebrate hosts. TSEs include: Bovine spongiform encephalopathy (BSE, aka mad cow disease), Camel spongiform encephalopathy (CSE), Chronic wasting disease (CWD), Creuzfeldt-Jakob (CJD; types: familial/genetic, iatrogenic, sporadic, and variant), Exotic ungulate encephalopathy (EUE), Fatal familial insomnia (FFI), Feline spongiform encephalopathy (FSE), Gerstmann-Straussler-Scheinker Syndrome (GSS), Kuru, Transmissible mink encephalopathy (TME), Scrapie, and Variably protease-sensitive prionopathy (VPSPr).

Prions were first discovered in 1982 by Stanley B. Prusiner, who coined the word "prion" as shorthand for "proteinaceous infectious particle." Indeed, prions are a unique type of microbe in that they are composed solely of protein and contain no nucleic acid component. Like viruses, prions cannot replicate on their own and rely on exploiting the cellular machinery of their hosts. In the 1970s, before prions were discovered, a team of scientists postulated that diseases like scrapie, CJD, and mad cow disease were caused by an infectious agent composed of nucleic acids and coated in a protective layer of proteins derived from host cells. They called this hypothetical particle a "virino."

Prion-like Proteins

Prion-like proteins include other misfolded versions of proteins that form amyloid aggregates associated with degenerative diseases. Unlike prions, however, these proteins do not complete a full infectious cycle. That is, prion-like proteins do not have several (*marked with an asterisk) of the 6 components involved in the chain of infection: an infectious agent* (these proteins may cause or be associated with disease, but are not necessarily infectious as they do not enter new hosts), reservoir, portal of exit*, mode of transmission*, portal of entry*, and susceptible host. Infectious transmission of prion-like proteins from one host to a new susceptible host has never been recorded, though deliberate transmission has been performed in mice for at least one prion-like protein, tau (Gibbons et al. 2019).

Referred to as "prionoids" by some scientists, one example of a prion-like proteins is amyloid-β, which is associated with Alzheimer's disease. Another example is tau proteins, which are associated with Alzheimer's disease, frontotemporal dementia, and other degenerative diseases that are collectively called tauopathies. In addition, α-Synuclein amyloids are associated with Parkinson's disease and some types of dementia. α-Synuclein amyloid fibrils aggregate inside neurons (primarily in areas of the brain called the substantia nigra and the locus coeruleus), forming intracellular deposits called Lewy bodies, a histological sign characteristic of late-stage Parkinson's disease. Proteins with expanded polyglutamine (polyQ) tracts can also form prion-like aggregates associated with disease, as in the case of polyQ-expanded huntingtin and Huntington's disease. There is ongoing research into whether protein aggregation is causal for these diseases or a manifestation of pathology.

Viroids

Viroids are small single-stranded, circular RNA molecules without a protein coat that infect flowering plants, or angiosperms. This RNA molecule often possesses a highly compact, intricate secondary structure. Viroids replicate within host cells by a process called rolling circle amplification using the host's RNA polymerase II. The accumulation of viroids inside cells can lead to plant diseases by disrupting normal cellular processes and gene regulation.

Some of the most famous viroids include Potato spindle tuber viroid (PSTVd), Coconut cadang-cadang viroid (CCCVd), Tomato apical stunt viroid (TASVd), Apple scar skin viroid (ASSVd), Chrysanthemum stunt viroid (CSVd) and the Chrysanthemum chlorotic mottle viroid (CChMVd).

Viruses

Viruses are obligate intracellular pathogens that possess DNA or RNA as their genetic material. They are much smaller than bacterial cells, usually on the order of 10s to 100s of nanometers in length. Since viruses are acellular, they are dependent on invading other cells and using host cell machinery to replicate. The genetic material contains instructions for creating viral particles called virions, which consist of the genetic material encapsulated by a protein coating called a capsid and sometimes also covered in a lipid layer called a viral envelope. The viral capsid is made up of subunits called capsomeres, which in turn are made up of protein subunits called protomers.

Viruses infect organisms from all branches of life, including archaea, bacteria, plants, animals, fungi, eukaryotic algae, and protozoa. Viruses that infect bacteria are known as bacteriophages and are sometimes simply called phages. Typically, bacteriophage genomes are composed of DNA rather than RNA.

Viruses are responsible for a variety of diseases that affect humans, such as AIDS, chicken pox, chikungunya, the common cold, cowpox, Ebola, hepatitis A-E, influenza, mononucleosis, measles, mumps, rabies, rubella, West Nile fever, yellow fever, Dengue fever, poliomyelitis, shingles, smallpox, and Zika.

The origin of viruses is unclear; some may have come from plasmids (pieces of DNA that can travel between cells) or transposons (pieces of DNA that can move themselves to different places in a cell's genome) while others may have evolved from bacteria. Since viruses depend on other cells for replication, viruses must have evolved after cellular life.

In Latin, the word virus means "poison" or "venom."

Viral capsid shapes

Viral capsids shapes vary widely across different viruses. Some viruses have helical capsids, including tobacco mosaic virus and ebola virus, and appear to be rod-shaped or filamentous when viewed with a microscope. Many viruses have polyhedral capsids that specifically take the shape of a regular, convex icosahedron, which is a 20-sided 3D shape composed of equilateral triangles. Some examples of icosahedral viruses are adenoviruses and picornaviruses, including hepatitis A virus and poliovirus.

Bacteriophages have a complex capsid shape consisting of an elongated icosahedral head (this shape is called prolate) attached to a helical sheath that terminates in a basal plate, which is connected to several leg-like tail fibers. Some viruses besides bacteriophages also assume more complex shapes, including the rabies virus (Lyssavirus) which is bullet-shaped and the brick-shaped poxviruses (e.g., cowpox, smallpox, mpox). HIV-1 and HIV-2 have cone-shaped capsids, but are enveloped viruses so appear spherical under the microscope.

Some viruses are often referred to as having a spherical shape (e.g., HIV-1, HIV-2, influenza A-D viruses, herpesviruses), but the capsids of these viruses are not actually spherical. Instead, virions appear spherical under the microscope due to the presence of a viral envelope. For instance, herpesviruses are enveloped viruses with an icosahedral capsid, HIV-1 and HIV-2 are enveloped viruses with a conical capsid, and influenza viruses have helical capsids enclosed in a viral envelope.

Baltimore classification

The Baltimore classification system divides viruses into seven different groups on the basis of their genetic material. Created in 1971 by the virologist David Baltimore, this system is often used alongside and has now been partially incorporated into standard viral taxonomy.

  • Class I viruses are double-stranded DNA viruses
  • Class II viruses are single-stranded DNA viruses
  • Class III viruses are double-stranded RNA viruses
  • Class IV viruses are positive-sense single-stranded RNA viruses
  • Class V viruses are negative-sense single-stranded RNA viruses
  • Class VI viruses are RNA retroviruses
  • Class VII viruses are DNA retroviruses

Lytic and lysogenic cycles

Viruses can be caused by either lytic or lysogenic infections. In a lytic infection, the virus injects its genome into the host cell, which cannot differentiate between viral DNA and its own DNA. The cell begins to make mRNA from the viral DNA, which is then made into viral proteins that destroy the cell's DNA. When the cell eventually shuts down, the virus continues to use the cell to replicate. Enough viruses are made to cause the cell to burst, or lyse. Hundreds or thousands of released viruses then go on to infect other cells.

In a lysogenic infection, a virus integrates its DNA into the host cell's DNA. This viral DNA is known as a prophage. The prophage remains dormant in the cell's DNA for several generations before becoming active, leaving the cell's DNA, and directing the synthesis of new viral proteins. Remaining dormant while the host cell undergoes mitosis allows the virus to enter a greater number of cells without decreasing its host population. HIV, which causes AIDS, is a lysogenic virus.

Satellite viruses and nucleic acids

Satellites are subviral particles that cannot complete the cycle of infection independently. Instead, satellites are dependent on both host machinery and the presence of a helper virus for proper viral replication. Like viruses, satellites may have single-stranded RNA, single-stranded DNA, or double-stranded DNA genomes (although not double-stranded RNA), and their genomes may be linear or circular. Satellite genomes are much shorter than viral genomes on average. While viral genomes may be 10 kilobases to well over 1 megabase in length, satellites are usually <1.5 kilobases in length. The difference between satellite viruses and satellite nucleic acids is whether or not the genome encodes proteins that form the capsid that encloses the genetic material. The genomes of satellite viruses encode a capsid, while satellite nucleic acids rely on helper viruses for encapsidation. One example of a satellite virus is hepatitis D, which is a satellite of hepatitis B virus.

Virophages

Virophages are another type of subviral particle similar to satellite viruses in that they require the help of a co-infecting virus and in that their genome encodes capsid proteins. There is ongoing debate about whether virophages should be considered a type of satellite, as they are very similar but display some key differences. Most notably, while satellite viruses and nucleic acids are thought to begin their replication cycle in the nucleus of host cells and can independently hijack host cell machinery for DNA replication, virophages are thought to remain in the cytoplasm of infected host cells and hijack the cytoplasmic virus factories (see below) established by their co-infecting viruses, a parasitic relationship. In hijacking the virus factory of another virus, virophages reduce the replication efficiency (and, therefore, also the infectivity) of co-infecting viruses, which may aid in host cell survival.

Some other defining characteristics of virophages are that they always have circular or linear double-stranded DNA genomes (never RNA and never single-stranded), are usually 16-18 kilobases in length, and display a parasitic relationship with the co-infecting virus almost always a giant virus. While scientific literature does not provide a consistent definition for giant viruses, all giant viruses have large genomes (often >1 megabase, and usually at least 300 kilobases) and large capsids (200-400+ nm) and belong to phylum Nucleocytoviricota (note: not all members of Nucleocytoviricota are giant viruses). Members of this phylum are also called  nucleocytoplasmic large DNA viruses, in part because they can perform viral replication in either the nucleus or cytoplasm of host cells. Nucleocytoplasmic large DNA viruses are unique in that they encode enzymes involved in DNA repair, replication, and transcription, which allows them to establish cytoplasmic virus factories that facilitate genome replication in addition to protein synthesis and virion assembly (note: many viruses form virus factories in the cytoplasm, but most must replicate their genomes in the host cell nucleus).

Two famous examples of virophages are called Sputnik (the Russian word for "satellite)"and Zamilon, which both belong to the family Lavidaviridae and depend on giant viruses belonging to the genus Mimivirus.

Virusoids

Virusoids are also considered to be a type of satellite. In essence, virusoids are viroids that have been enclosed in the protein capsid of another virus. Virusoids depend on both the helper virus and host cell RNA polymerase II for replication. Like viroids, virusoids have circular, single-stranded RNA genomes.

Prokaryotic Microbes

A diagram of a prokaryotic cell.

A prokaryote is a type of cell that does not have any nucleus or membrane-bound organelles. Prokaryotes include two of the three domains of life: Eubacteria (often just called bacteria) and Archaeabacteria (often just called archaea). Archaea, as their name suggests, are thought to be more ancient of the two groups. Archaea have also not yet been found to be pathogenic - that is, able to cause disease - in any other organism. The other group, bacteria, are more familiar to most people and include human pathogens as well as many bacteria that are beneficial to humans and/or important in environmental processes. Some archaea and bacteria reside in the human gut microbiome and are important for proper digestion, vitamin synthesis, and other processes.

Prokaryotic cells divide by a process called binary fission. It is similar to eukaryotic division, with the exception that DNA replication leads directly to cytokinesis (splitting of cell membrane), with no agglomeration into chromosomes first.

Prokaryotes are the most primitive forms of life, so they are immensely important in evolution. While they are far less complex than eukaryotic organisms like eukaryotic algae, protozoa, fungi, plants, and animals, they are still some of the most common life forms. They are continuing to evolve now, developing resistance to antibiotic drugs and rendering them useless.

Bacteria

Bacteria are single-celled, prokaryotic microorganisms. Some bacteria are beneficial to humans while others are pathogenic, but a majority of bacteria are harmless to humans. Pathogenic bacteria are responsible for a variety of diseases including strep throat and tetanus. Bacteria originate from the single-celled organisms that were the first to inhabit the Earth.

Bacteria, despite their small size and simple nature, have an immense impact on human society. Negatively, they have caused epidemics and pandemics, like cholera outbreaks seen in Europe up until the early 20th century, and in less developed countries in modern times. In more recent years, humans have helped to make drug-resistant strains of bacteria. Humans have brought about these stronger bacteria by using only a small amount of antibiotics, for related or unrelated purposes. This small exposure enables the bacteria to develop resistance or even immunity to larger amounts of the drug.

However, bacteria have also impacted society in a positive way. The first artificial life created was a bacterium. Also, bacteria are being studied to determine what may have been the origin of life on Earth, as well as for extraterrestrial life - they are the most likely candidates for this. Outside of science, bacteria are used in industry to create many familiar products, and some plants have nitrogen-fixing bacteria.

A diagram showing different cell shapes and arrangements of bacteria, including different arrangements of cocci, bacilli, spiral bacteria, and others.
Across different species, bacteria display variety of different cell shapes and arrangements.NOTE: This diagram is useful for depicting many possible cell shapes, but some labels in this diagram are incorrect. For example, Borellia bacteria are spirochetes, not spirilla (or corkscrew-shaped) bacteria.

Motile bacteria may utilize rotating flagella to move, or they may secrete slime to slide around like a slug. Bacteria may also be non-motile.

Bacterial cell shapes

Bacteria may assume many different shapes. Some of the most common morphologies include spherical, rod-shaped, and spiral. Spherical bacteria are called cocci (singular:coccus) and include bacterial genera such as Staphylococcus, Streptococcus, and Pneumococcus. Rod-shaped bacteria are called bacilli (singular: bacillus), and include bacterial genera such as Bacillus (confusingly, Bacillus also refers to a genus of bacteria), Escherichia (including the famous E. coli), Lactobacillus, Rhizobium, Streptobacillus, and many more. Spiral bacteria include the rigid, corkscrew- or helix-shaped spirilla (singular: spirillum) such as Campylobacter, Helicobacter, and Spirllium (again, the shape is the same name as the genus) as well as the longer, thinner, and more flexible spirochetes (e.g., Borellia, Leptospira, andTreponema). Other bacteria have more complex cell shapes, such as club-shaped (e.g., Cornyebacterium; sometimes, this shape is described as cornyeform after the genus) or comma-shaped (e.g., Vibrio, Bdellovibrio; sometimes, this shape is called a vibrio after the genus). In addition, some bacteria are pleomorphic, meaning they do not have a fixed cell shape but instead alter their morphology in response to environmental conditions.

Beyond possessing different cell shapes, bacterial cells may display various different arrangements. For example, Streptococcus bacteria form linear arrangements of cocci, and Streptobacillus bacteria form linear arrangements of rods. Staphylococcus bacteria are cocci form clustered arrangements. Diplococci are arranged as pairs of cocci, tetrads form a 2 x 2 square arrangement of cocci, and the genus Sarcina assumes a 2 x 2 x 2 cuboidal arrangement of cocci.

Bacterial processes (Division C only)

Transcription

[This section has no information yet]

Translation

[This section has no information yet]

DNA replication

[This section has no information yet]

Gene regulation via operons

[This section has no information yet]

Gram staining

Gram staining is a common microbiological technique used to classify bacteria on the basis of their cell wall structure. The method was developed by the Danish bacteriologist Hans Christian Gram in 1884. Because Gram staining yields different results for two different groups of bacteria (Gram-positive and Gram-negative bacteria), it is a type of differential stain (as opposed to a simple stain). The procedure for Gram staining involves first heat-fixing bacteria (so that the bacteria are able to hold the primary stain and keep the bacteria in place) before sequentially treating them with four different reagents:

1) A cationic (i.e., positively charged) primary stain (often crystal violet, which stains cells purple, or methylene blue) that is taken up by both Gram-positive and Gram-negative bacteria. Cells are usually incubated with the dye for at least 1 minute. In an aqueous solution, crystal violet disassociates into CV+ and Cl- ions. These ions penetrate through the cell wall and CV+ associates with negatively charged functional groups in bacterial cell walls.

2) A mordant (usually Gram's iodine solution) containing anions that complex with the positively charged primary stain inside of Gram-positive cell walls, preventing easy removal of the primary stain when cells are washed with a decolorizer. The mordant essentially acts as a trapping agent for the primary dye, and cells are usually incubated for at least one minute before rinsing off any excess mordant.

3) A decolorizer (often ethanol or acetone) used to wash the primary stain off the surface of Gram-negative bacteria, which cannot remove any primary stain molecules that were fixed inside Gram-positive cell walls by the mordant. Alcohol dissolves the outer membrane of Gram-negative bacteria, effectively removing any primary stain on Gram-negative cells, while the primary stain remains trapped in the thick cell walls of Gram-positive cells.

4) A counterstain (often safranin, basic fuchsin, or carbol fuchsin; all of which stain cells red/ pink). The counterstain stains both Gram-positive and Gram-negative cells, but is not visible on Gram-positive cells due to the darker color of the primary stain. This procedure results in Gram-positive bacteria being stained purple, while Gram-negative bacteria stain red/ pink color.

Gram-positive vs. Gram-negative bacteria

Typically, Gram-positive bacteria produce exotoxins and are susceptible to phenol disinfectants. They retain the blue-purple color of crystal violet in Gram staining because of their thicker walls of peptidoglycan. Unlike Gram-negative bacteria, they lack the periplasmic space between the cytoplasmic and outer membranes because Gram-positive bacteria lack an outer membrane. Certain types of Gram-positive bacilli, most importantly Lactobacilli (used in milk and dairy products), cannot form spores.

Gram-negative bacteria have thinner walls of peptidoglycan and two membranes and periplasmic space between them. Because of the safranin counterstain, they become red-pink after Gram staining. There are many Gram-negative aerobic (oxygen-using) bacteria.

Generally, it is more difficult to kill Gram-negative bacteria with antibiotics due to their more complex cell membrane structure.

Limitations of Gram staining

Gram staining is not always an effective technique for classifying some types of bacteria, namely acid-fast bacteria. Acid-fast bacteria usually stain weakly Gram-negative or Gram-variable. They are similar to Gram-negative bacteria in that they both have thinner layers of peptidoglycan comprising the cell wall as well as an outer lipid membrane coating the cell wall (Note: this outer membrane is in addition to the bilayer beneath the cell wall that constitutes the cytoplasmic membrane, which all types of bacteria have). While Gram-negative bacteria contain an outer phospholipid bilayer rich in lipopolysaccharide, acid-fast bacteria have a much more complex layer beyond their cell walls. Directly above the peptidoglycan cell wall is an arabinogalactan (a type of structural polysaccharide) layer, which is covalently bound to a layer of mycolic acids that comprise the inner leaflet of the outermost lipid bilayer. The outer leaflet of the outermost acid-fast lipid bilayer contains free mycolic acids, phospholipids, and glycolipids. This outer layer also contains surface proteins and porin proteins that span the outer membrane, allowing transport of specific small molecules in and out of the cell.

Some bacteria can assume growth forms in which they lack cell walls. Bacteria that lack cell walls are called L-form or L-phase bacteria and always stain Gram-negative due to the absence of a cell wall, although L-form bacteria may arise from either Gram-negative or Gram-positive bacteria.

Additionally Gram staining yields widely varying results when performed on Archaea. Many Archaea stain Gram-negative while others stain Gram-positive, and Gram staining results do not meaningfully align with phylogenetic relationships across different Archaea.

Horizontal Gene Transfer

Mechanisms of Horizontal Gene Transfer

Conjugation: A bacterium can transfer some of it's own DNA into other bacteria via pilus. This is seen with penicillin binding proteins, where a bacterium with the protein can give it to another bacterium.

Transduction: A bacteriophage infects a bacterium, and takes some of its DNA after replication. The replicated bacteriophages infect other bacteria, inserting the previous bacteria's DNA into another bacteria.

Transformation: After the process of lysis or death, a bacterium can take some of the of DNA fragments that were left behind of the other dead bacteria.

Bacterial motility

Motility structures and composition

[This section is not complete yet]

  • Bacterial flagella are made of helical filaments made of a protein called flagellin. Bacterial flagella are rotary motors that can rotate clockwise or counter-clockwise.
  • There are differences in flagella structure between gram-positive and gram-negative bacteria. Gram-positive bacteria have 2 protein rings present in the peptidoglycan cell wall and plasma membrane that act as bearings for the shaft of the flagellum. Gram-negative bacteria have 4 of these basal protein rings instead: the L ring in the outer lipopolysaccharide layer, the P ring in the peptidoglycan cell wall, the M ring in the plasma membrane, and the S ring which is directly attached to the cytoplasm.
  • Most bacterial flagella are driven by chemiosmosis (protons) rather than ATP hydrolysis. Some species have flagella that are driven by a sodium-pump (e.g., some Vibrio species)
Flagellar Arrangements

Monotrichous: Only one flagellum, on one pole of the cell. Ex: Vibrio cholera

Amphitrichous: A single flagellum on each pole of the cell. Ex: Alcaligenes faecalis

Cephalotrichous: More than one flagella on each pole of the cell. Sometimes no distinction is made between this an "amphitrichous" flagellar arrangements.

A: Monotrichous B: Amphitrichous C: Lophotrichous D: Peritrichous

Lophotrichous: More than one flagella on one pole of the cell. Ex: Helicobacter pylori

Peritrichous: Many flagella are distributed across the surface of the cell and are not necessarily localized to the poles of the cells. Ex: Escherichia Coli

Atrichous: Lacking flagella entirely. Ex: Lactobacillus delbrueckii

Archaea

Archaea (Domain Archaea) are a group of single-celled, prokaryotic microorganisms that were once thought to be bacteria due to their similar size and appearance under the microscope. Archaea were first identified as a separate domain of life The evolutionary origin of archaea (singular: archaeon) remains to be fully deciphered; however, archaea and eukaryotes are thought to share a common ancestors because of their many similarities. Phylogenetic analyses suggest that early eukaryotes arose from an ancestor that was a part of a group of archaea called the Asgard archaea, specifically the lineage Heimdallarchaeota. Evidence for the archaeal origin of eukaryotes include the presence of several key proteins involved in eukaryotic processes called eukaryotic signature proteins in the Heimdallarchaeota. Some of these eukaryotic signature proteins are involved in complex processes such as the cytoskeleton and membrane remodeling. Unlike bacteria, no species of archaea are known to form spores.

Many archaea are extremophiles, meaning they live in extreme environments that would pose major challenges for many other organisms (e.g., very hot, cold, acidic, salty, etc.). The first archaea to be discovered were extremophiles, and because few other organisms are able to withstand the harsh conditions, there is a relative abundance of these organisms in extreme environments While there are also many archaea that are mesophiles, which prefer moderate environmental conditions, the prevalence of archaea in extreme environments some extent, this

Archaea are involved in the carbon and nitrogen cycles, assist in digestion, and can be used in sewage treatment.

Archaea, especially methanogens like Methanobrevibacter smithii, play important roles in the human gut microbiome. For instance, methanogen metabolism regulates the concentration of H2 gas in the intestines, which promotes the production of short-chain fatty acids (SCFAs) by bacteria. In turn, SCFAs are involved in different metabolic pathways that are relevant to cardio-metabolic diseases like obesity, insulin resistance, and type 2 diabetes.

Interestingly, archaea are not known to cause any diseases in humans or in any other organisms. It remains to be discovered if the archaea constitute an entirely non-pathogenic Domain of organisms.

A diagram of a eukaryotic plant cell.

Eukaryotic Microbes

A eukaryote (Domain Eukarya) is a type of cell that has a nucleus and membrane-bound organelles. Examples of eukaryotes are algae, protozoa and fungi. Humans and plants are also part of the Domain Eukarya.

A diagram of a eukaryotic animal cell.

Common parts of Eukaryotic Cells:

  • Cell Wall – commonly found in plant and fungal cells; protection and support, consists of cellulose in plants and chitin in fungi.
  • Plasma Membrane – semi-permeable barrier, controls the substances exiting and entering the cell
  • Cilia - small, beating extrusions that sweep materials across the cell surface
  • Flagellum - enables a cell to propel and move in different directions. Eukaryotic cells may have zero, one, two, or many flagella.
  • Cytoplasm – intracellular fluid, contains organelles and dissolved nutrients.
  • Endoplasmic reticulum (ER) - the passageway for transport of materials within the cell; synthesis of lipids – modification of newly formed polypeptide chains (includes rough ER and smooth ER; rough ER is mostly differentiated by the ribosomes on it, hence the term "rough")
  • Ribosomes - consist of various RNAs and proteins, are the site of protein synthesis
  • Golgi apparatus - final modification of proteins and lipids; packing of materials into vacuoles for secretion out of the cell
  • Mitochondria - the site of aerobic cell respiration and ATP production, takes in oxygen and glucose and produces metabolic water and carbon dioxide
  • Hydrogenosomes - sites of anaerobic cell respiration in certain protozoa. (Trichomonas, etc.)
  • Lysosomes - contain enzymes to digest ingested material or damaged tissue
  • Chloroplasts – store chlorophyll pigments; site of light reactions of photosynthesis, produces glucose
  • Vacuoles – enclosed membrane globules, used for storage or to increase cell surface area
  • Centrioles - organize the spindle fibers during cell division
  • Cytoskeleton – cell shape, internal organization, cell movement, and locomotion

Fungi

Fungi are a group of heterotrophic eukaryotes that can be single-celled or multi-celled. Fungi may morphologically seem more similar to plants than animals, but they are more closely related to animals than they are to plants. Like animals, fungi are opisthokonts, meaning they are derived from a common ancestor that possessed a single posterior flagellum. While many types of animals and fungi have lost flagellate cells since the branching off of opisthokonts from other eukaryotes, the spores of some fungi such as Chytrids (phylum Chytridiomycota) still possess flagella, as do the sperm cells of animals. Previously, fungi were divided into only 5 phyla: Ascomycota, Basidiomycota, Chytridiomycota, Glomeromycota, and Zygomycota. Many more fungal phyla have been recognized more recently including, Basidiobolomycota, Blastocladiomycota, Entomophthoromycota, Entorrhizomycota, Kickxellomycota, Mortierellomycota, Mucoromycota, and Neocallimastigomycota. These 13 phyla are all part of the larger clade Eumycota, also called "true fungi" or Fungi sensu stricto. However, there have been several other phyla identified as sister clades to the Eumycota that are now also considered to be fungi (i.e., Fungi sensu lato). These sister clades include the Aphelidiomycota, Rozellomycota, and Microsporidia.

Fungi are distinct from plants and animals in several ways. While animals lack cell walls entirely, fungi have cell walls composed of chitin, a polysaccharide made from monomers of N-acetylglucosamine (GlcNAc). Plants also have cell walls, although they are instead made of cellulose, a polysaccharide made from monomers of beta-glucose. Also, while plants contain chloroplasts and are photoautotrophic, fungi and animals are both chemoheterotrophic and lack chloroplasts. Like some animals, fungi obtain nutrients by secreting enzymes into the environment for extracellular digestion of large molecules and absorbing the resulting smaller molecules. Specifically, fungi hydrolyze ATP to ADP+P in order to power the active transport (against concentration gradient) of protons (H+) across the plasma membrane and cell wall, establishing a chemiosmotic gradient that drives nutrient absorption through H+/glucose and H+/amino acid symporters. Perhaps for this reason, many fungi grow best in slightly acidic environments. Many fungi also thrive in moist environments, though some can also grow in areas of low moisture.

Fungi, plants, and animals all contain polycyclic lipid molecules in their plasma membranes called sterols, which help to maintain membrane fluidity and integrity despite temperature variation and, depending on the organism, may play roles in cell cycle regulation, stress responses, and other cellular functions. Different types of sterols are present in fungi, plants, and animals, with the most abundant sterol in fungal membranes being ergosterol. Plant membrane sterols usually include campesterol, stigmasterol, and beta-sitosterol, while the major sterol in animal membranes is cholesterol. Due to the biochemical differences in the final steps of sterol biosynthesis across fungi and animals, many antifungal medications target a fungal enzyme involved in ergosterol biosynthesis (e.g., fluconazole, itraconazole, ketoconazole).

Fungi are responsible for a variety of diseases that affect animals and plants. A disease caused by any fungus is called a mycosis. Some examples of mycoses are athlete's foot, ringworm, dutch elm disease, early potato blight, ergotism, histoplasmosis, oral thrush, oak wilt, white-nose bat syndrome, chytridiomycosis (in amphibians), and fungal pneumonia (caused by Pneumocystis). In addition, rusts (Pucciniomycotina) and smuts (Ustilaginomycotina) are two common types of fungal pathogens that belong to the phylum Basidiomycota and commonly infect plants, including many commercial crops like maize and other grains. Rusts are named for the reddish, rusty appearance on infected plants, while smuts are named for the black, sooty coloration of infected plants. At least one species of smut, Malassezia globosa, is a naturally occurring member of the human skin fungal community and metabolizes the lipid molecules present in our skin oil (sebum); when there is an overgrowth of this fungus, excessive depletion of sebum due to fungal metabolism causes dry skin and dandruff.

Fungi play many important roles in agriculture and food production, industry, and the environment. Baker’s yeast (Saccharomyces cerevisiae) is used for making bread and brewing alcoholic beverages. Other fungi are used in the production of certain cheeses to impart distinct flavors, namely in blue cheeses (Gorgonzola, Stilton blue cheese, and Roquefort), Brie, and Camembert cheese. The fungi Penicillium roqueforti and Penicillium glaucum are involved in the production of such cheeses. Some fungi are also used for antibiotics, with one famous example being the production of the antibiotic penicillin by Penicillium chrysogenum. Additionally, many fungi are important decomposers in the ecosystem, form symbiotic associations called mycorrhizae with plants, and play important roles in the phosphate cycle.

Lichens

Lichens are symbiotic associations of multiple eukaryotic and sometimes prokaryotic organisms. Specifically, lichens always include at least one filamentous fungal species called a mycobiont and one photosynthetic species (such as a eukaryotic alga or a Cyanobacterium) that is called a photobiont or phycobiont. Lichens are complex microbial communities that may contain more than one photobiont, additional filamentous fungal species, non-photosynthetic bacteria, and/or non-filamentous fungi such as yeasts.

Different types of lichens possess many different morphologies. Five common lichen morphologies are crustose, foliose, fruticose, leprose, and squamulose lichens.

Protists

Protists are a diverse, paraphyletic group of non-fungal, non-animal, and non-plant microbial eukaryotes. Protists are often divided into two groups: animal-like (i.e., heterotrophic) protists called protozoa and plant-like (i.e., photosynthetic) protists called eukaryotic algae. However, the terms protozoa and eukaryotic algae both refer to polyphyletic groups of organisms and, in some cases, are loosely defined or overlapping. Additionally, some groups of protists are fungus-like and were previously thought to be part of the Fungi. Now dubbed "pseudofungi," these fungus-like groups of protists include the hypochytrids and oomycetes. While many protists are unicellular eukaryotes, there are also many multicellular organisms that are considered protists, including: brown algae, diplomonads, green algae, oomycetes, plasmodial slime molds, and others. Multicellular protists do not have specialized tissues like some fungi, animals, and plants have.

In several cases, the definitions alga and protozoa begin to break down. For instance, some euglenids (those of the genus Euglena) have been considered both algae and protozoa by different microbiologists, as they contain chloroplasts and are capable of autotrophy by photosynthesis but feed heterotrophically in some stages of their life cycle. On the other hand, dinoflagellates are considered algae by most microbiologists, yet only about half of described dinoflagellates are autotrophs that posses chloroplasts; the other half are heterotrophs that cannot perform photosynthesis.

Eukaryotic Algae

Alone, the term "algae" generally refers to all photoautotrophic (or, if we consider Euglena algae, photosynthetic but heterotrophic) organisms that are not plants, namely Cyanobacteria (which are prokaryotes) and eukaryotic algae.

Eukaryotic algae include many different types of non-plant, photosynthetic eukaryotes such as coccolithophores (Prymnesiophyceae), diatoms (Bacillariophyceae or Bacillariophyta), dinoflagellates (sometimes also called Dinophyceae or Pyrrophyta), red algae (Rhodophyta), green algae (a broad clade containing Prasinodermata, Chlorophyta, and Charophyta), brown algae (Phaeophyceae), golden algae (Chrysophyceae), yellow-green algae (Xanthophyceae), and glaucophytes (Glaucophyta).

Algae are similar to plants in that they perform photosynthesis, but different in many other ways. Unlike plants, eukaryotic algae may be either unicellular or multicellular, may contain different types of pigments and plastids (e.g., rhodoplasts in red algae), and do not have cuticles that prevent water loss. While many algae live in aquatic habitats, there are also algae that live in terrestrial environments such as soil, hot springs, snow banks, animal fur, and tree trunks.

Protozoa

Protozoa are non-animal, non-fungal, heterotrophic eukaryotes such as apicomplexans, ciliates, diplomonads, euglenids, forams, jakobids, kinetoplasids (including trypanosomes), oomycetes, parabasalids, radiolarians, and more. Being heterotrophic means that these protists consume other protists and bacteria for food. Besides being heterotrophs, the cell biology and life cycles of protozoa can be complex and can vary widely across different groups of organisms. Some protozoa, namely ciliates (phylum Ciliophora), have two nuclei: the macronucleus and the micronucleus. Many move with cilia, flagella, or pseudopodia (in the case of amoebae). They also have complex life cycles. For example, some protozoa may exist in a trophozoite, or feeding form, but can also assume a dormant form known as a cyst for part of their life cycle. The cyst stage is marked by a thick wall that confers protection against adverse environmental conditions, helping the protozoan survive until it enters a susceptible host.

Parasitic Worms (Helminths)

Parasitic worms, or helminths, are multicellular heterotrophs that span several different groups of animals: Flatworms (phylum Platyhelminthes, including cestodes, trematodes, and monogeneans), Roundworms (phylum Nematoda), and Thorny-headed worms (Acanthocephalans, part of the phylum Rotifera).

Flatworms

Flatworms constitute the animal phylum Platyhelminthes (platy- = flat, -helminthes = worms). Flatworms display bilateral symmetry (symmetrical along the middle) and have no body cavity, meaning they are acoelomates (i.e., lack a coelom, a body cavity). All flatworms also lack respiratory and circulatory systems, so they absorb and excrete gases and nutrients by passive diffusion. Flatworms do, however, have nervous systems, with most nervous tissue being located at the apical ends (i.e., near the head) of worms. In many textbooks, flatworms are divided into two groups: the Turbellaria, which include all of the non-exclusively parasitic groups of worms (e.g., planarians), and the Neodermata, which contains three completely parasitic groups called Cestodes, Trematodes, and Monogeneans.

Cestodes

The class Cestoda includes the orders Cestodaria and Eucestoda (which are more commonly called tapeworms), though "cestodes" is frequently used in a manner that refers solely to the Eucestoda. Cestodaria mainly parasitize fish and, compared to Eucestodes, have been weakly studied and are poorly understood.

Eucestodes are the organisms that we commonly refer to as tapeworms. Eucestodes have segmented bodies made up of subunits called proglottids, and a chain of proglottids called a strobilia forms the body of tapeworms. The strobilia is attached to the neck, where stem cells divide by mitosis to generate new proglottids. This means the youngest proglottids are closest to the scolex, the head of the tapeworm, while the proglottids at the end of the chain are larger and more mature. Each proglottid contains several different tissues and is hermaphroditic, meaning it possesses both male and female sex organs.

The "head" of tapeworms is called the scolex and has a muscular protrusion at the apical end called a rostellum that functions in attachment. In many species, there are hooks present on the rostellum that further aid worms in attaching to the intestinal walls of their hosts. The rest of the scolex is usually decorated with pit-like or slit-like structures that form a suction to the host - these are called bothridia ("true suckers"; shaped like a round crater) and bothria ("false suckers"; more of a narrow groove), respectively. The exterior coating of Eucestodes is called the tegument. The tegument is a dynamic, multi-nucleate structure that plays critical roles in absorption and secretion.

Eucestodes infect nearly every species of vertebrate and can cause multiple different diseases in humans, including: taeniasis (T. solium, T. saginata, T. asciatica, and many more species), cysticercosis (caused by Taenia larvae), hymenolepiasis, diphyllobothriasis, alveolar echinococcosis, cystic echinococcosis (also called Hydatid disease), sparganosis, and dipylidiasis.

Trematodes

Trematodes are a class of flatworms that are also sometimes called flukes. Trematodes are further classified as blood, liver, lung, and intestinal flukes. One example of a disease caused by trematodes is schistosomiasis. There are 4 foodborne trematodiases: clonorchiasis, fasciolosis, opisthorchiasis, and paragonimiasis.

Monogeneans

Monogeneans are ectoparasites of fish and do not infect humans. Like Cestodes, mature Monogeneans are hermaphroditic (i.e., have both male and female reproductive structures).

Turbellaria

Since the classification of all non-exclusively parasitic groups of worms as turbellarians was established, this has been discovered to be a paraphyletic clade. That is, phylogenetic analysis revealed that while the parasitic Neodermata are still a monophyletic group, they actually cluster between different groups of non-parasitic flatworms. Accordingly, Turbellaria is now an obsolete and paraphyletic classification of flatworms.

Roundworms

Roundworms constitute the animal phylum Nematoda. Like flatworms, roundworms have bilateral symmetry. Unlike flatworms, however, roundworms have a complete digestive tract with 2 openings: the stoma, which functions as a mouth, and an excretory pore. In male nematodes, the excretory pore also functions as a reproductive pore and is called a cloaca. In female nematodes, there is a separate reproductive pore that is not associated with the digestive tract. Another difference between flatworms and roundworms are that while flatworms lack a body cavity, roundworms are pseudocoelomates, meaning they have a "false body cavity" present between the endoderm and mesoderm. Note that a true body cavity, or coelom, would be lined by mesodermal cells on all sides, whereas the pseudocoelom is only lined with mesoderm on one side. Roundworms have a hydrostatic skeleton, and a tough outer layer called a cuticle that is rich in collagen and keeps their body from expanding as hydrostatic pressure builds inside the pseudocoelom.

Roundworms are responsible for many different diseases in humans, other animals, and plants. Some roundworms that parasitize plants possess a rigid, spear-like structure called a stylet that can protrude from the worm's stoma to pierce cell walls. Often, the stylet is hollow to facilitate "drinking" the cell contents for nutrients and secreting substances that aid in parasitization.

Some examples of diseases caused by roundworms that affect humans are: hookworm, pinworm, dog heartworm, whipworm, guinea worm disease, lymphatic filariasis, ascariasis, dioctophymosis, strongyloidiasis, and river blindness (also called onchocerciasis). Hookworm can be caused by many different species of roundworms, with two of the most common species in humans being Ancylostoma duodenale and Necator americanus. Some examples of plant diseases caused by nematodes are: pine wilt disease, soybean cyst disease, potato cyst disease, and onion bloat.

Thorny-headed worms

Also called spiny-headed worms or Acanthocephalans, these are a group of highly modified Rotifers (phylum Rotifera) that rarely but occasionally infect the human intestinal tract.

Types of Extremophiles

Some types of microbes are extremophiles, meaning they thrive in extreme conditions that would quickly kill many other organisms. Some examples of extreme environments where microbes have been found are hot springs, saline lakes, the ocean floor, deep-sea hydrothermal vents, acid mine drainage sites, cold deserts, and subglacial lakes. While many extremophiles are either archaea or bacteria, there are also some extremophilic eukaryotes. Extremophiles come in many different varieties:

  • Acidophiles and alkaliphiles prefer to live in areas with very low (usually pH < 3) or very high pH (usually pH > 9), respectively. In contrast, neutrophiles prefer environments around pH = 7 and are not considered extremophiles.
  • Capnophiles inhabit environments with very high concentrations of carbon dioxide (CO2).
  • Halophiles are highly tolerant to environments with high salt concentrations, such as salt lakes.
  • Osmophiles are organisms that live in areas with very high osmotic pressures, which result from high concentrations of solutes - especially sugars - in the surrounding environment.
  • Piezophiles (also called barophiles) live under conditions of high hydrostatic pressure.
  • Thermophiles are microorganisms prefer very high temperature environments. Usually, thermophiles are considered to live between 45-80C (sometimes the lower end of the range is states as closer to 50C), and organisms that grow best above 80C are called hyperthermophiles. Psychrophiles (also called cryophiles) are extremophilic organisms that grow at temperatures -20C to 20C, while mesophiles usually reside in moderate temperatures between 20-45C and are not considered extremophiles.
  • Xerophiles are a type of extremophile that inhabit environments with very low moisture or humidity.
  • Other extremophiles are capable of dealing with high concentrations of gases that are toxic to many other microbes.
  • Some extremophiles exhibit metallotolerance, the ability to live in conditions with high concentrations of metal cations, and are called metallophiles.
  • Some extremophiles exhibit radioresistance, the ability to withstand very high doses of ionizing and/or nuclear radiation, and are called radiophiles (e.g., Deinococcus radiodurans, and a group of microscopic animals called Tardigrades).
  • In many cases, extreme environments have more than one extreme quality and are inhabited by polyextremophiles, which are organisms that display multiple tolerances to extreme conditions.

Microbial Metabolisms

Microorganisms are often described on the basis of their metabolism.

Oxygen dependence and tolerance

One aspect of metabolism is whether microbes tolerate and/or utilize molecular oxygen (i.e., dioxygen, or O2). For example, many microbes are aerobes, which is a general term for organisms that survive and/or grow in environments with oxygen. Obligate aerobes depend on oxygen for ATP production via cellular respiration in order to survive. In contrast, obligate anaerobes do not utilize oxygen and cannot tolerate environments with high oxygen concentrations. Obligate anaerobes vary widely in their ability to tolerate oxygen, but even the most tolerant obligate anaerobes require far lower oxygen concentrations than those present in atmospheric air. The atmosphere is ~21% oxygen, and the most tolerant anaerobes may grow in ~8% oxygen, with many preferring concentrations <0.5% (note that when discussing the percentage a gas in the atmosphere, the percentage almost always refers to the molar fraction of the gas in the atmosphere, not the percentage composition by mass or by volume). Anaerobic respiration is much less efficient than aerobic respiration, producing 2 ATP per glucose molecule consumed compared to 36 ATP.

Microaerophiles are a type of aerobe that, like obligate anaerobes, only grow in environments with very low oxygen concentrations. However, microaerophiles differ in that they still depend on oxygen for metabolism, despite their inability to tolerate high oxygen concentrations. Some organisms utilize oxygen as part of their metabolism when it is available but are also capable of living anaerobically when there is no oxygen; these microbes are called facultative anaerobes. There are also aerotolerant anaerobes, which do not utilize oxygen for metabolism, but may live in environments with or without atmospheric levels of oxygen.

In the lab, both aerotolerant anaerobes and facultative anaerobes will grow regardless of oxygen concentration, but can be distinguished on the basis of the Pasteur effect, which describes how facultatively anaerobic organisms that perform fermentation in anaerobic environments switch to an aerobic metabolism (i.e., cellular respiration) once they are introduced to an environment with more oxygen. The Pasteur effect can be observed by measuring the rates at which fermentation products such as ethanol or lactate accumulate in aerobic and anaerobic environments.

Nutritional classifications

Additionally, microbial metabolisms may described by a microbe's source of energy, source of carbon, and source of electrons. The table below describes the different nutritional classifications and associated prefixes for each of these three key components of metabolism.

Things needed for metabolism Source Prefix
Energy Chemical energy, from either organic or inorganic molecules Chemo-
Radiant energy (i.e., light) Photo-
Electrons Organic molecules (e.g., sugars, amino acids, lipids, alcohols) Organo-
Inorganic molecules (e.g., water, hydrogen sulfide, molecular hydrogen, ammonium, manganous manganese, ferrous iron) Litho-
Carbon Organic molecules (e.g., sugars, amino acids, lipids, alcohols) Hetero-
Inorganic molecules (e.g., carbon dioxide) Auto-

Since there are two different possible sources for each category above, this implies the possibility of 2 x 2 x 2 = 8 different metabolism types. However, photoorganoautotrophy has never been discovered in an organism.

Energy Source Electron Source Carbon Source Metabolism Name Example(s), if any
Chemical energy Organic molecules Organic molecules Chemoorganoheterotroph Fungi, animals, many protozoa, some bacteria
Inorganic molecules Chemoorganoautotroph Anaerobic methanotrophic archaea (ANME archaea); some genetically modified bacteria and yeast
Inorganic molecules Organic molecules Chemolithoheterotroph Some bacteria (e.g., Oceanithermus profundus; see Miroshnichenko et al. 2003)
Inorganic molecules Chemolithoautotroph Some chemosynthetic bacteria (e.g., Nitrosomonas, Thiobacillus) and methanogens
Radiant energy (light) Organic molecules Organic molecules Photoorganoheterotroph Some purple sulfur bacteria (e.g., Allochromatium vinosum; see Weissberger et al. 2014) and purple non-sulfur bacteria (e.g., Rhodobacter; see Cerruti et al. 2022)
Inorganic molecules Photoorganoautotroph -
Inorganic molecules Organic molecules Photolithoheterotroph Some purple non-sulfur and green non-sulfur bacteria
Inorganic molecules Photolithoautotroph Plants, cyanobacteria, and many eukaryotic algae

Additionally, it is often common to omit the prefix describing the electron source when discussing the metabolic classification of different microbes. Bacteria may be photoautotrophic, utilizing photosynthesis to produce food and oxygen and using carbon dioxide as their source of carbon. This category includes purple and green sulfur bacteria. They may also be chemoautotrophic, making food using the energy from chemical reactions and using carbon dioxide as their source of carbon - these bacteria serve an important role in the nitrogen and sulfur cycles. The two other types are photoheterotrophs (including purple and green non-sulfur bacteria) and chemoheterotrophs (including most bacteria, animals, fungi, and protozoa).

Bacterial Culture and Growth

Types of culture

Batch culture vs. Chemostat growth

Batch culture, also called closed culture, involves growing bacteria inside a closed container using a fixed volume of medium (i.e., without adding new chemicals throughout the growth process). This is in contrast to chemostat growth, also called open or continuous culture, in which nutrients are continually added and/or removed from the medium to achieve constant environmental conditions.

Liquid vs. solid media

[This section has no information yet]

Defined vs. complex media

Defined media can be made the same way every time by following a recipe for making the media and adding measured amounts of different chemicals. In contrast, complex media (sometimes called undefined media) contains ingredients that may have a slightly different chemical composition each time they are used. For example, LB media (lysogeny broth; often incorrectly called Luria broth, Lennox broth, or Luria-Bertani media) is a complex medium because one ingredient is autolysed yeast extract. Yeast extract contains many different chemical compounds in unknown concentrations, which makes LB a complex medium.

Differential vs. selective media

[This section has no information yet]

Microbial Growth Curve

Growth curves

When bacteria are grown in closed culture, they usually follow a characteristic pattern of growth referred to as the microbial growth curve. This is usually thought to involve 4 stages:

  • Lag Phase: During the lag phase of the microbial growth cycle, cells are maturing for doubling; synthesis of RNA, enzymes, etc. Therefore, lag phase in the microbial growth curve is represented by the initial horizontal line.
  • Exponential Growth (Log) Phase: During the exponential growth, the microbial population undergoes constant doubling. The more "favorable" conditions are, the longer the slope will be, and the faster the growth, the steeper the slope. This is the phase which generation time can be calculated as well.
  • Stationary Phase: The stationary phase is another flat portion of the microbial growth curve where it appears that there is no significant increase in the number of cells; showing a stabilization of the population. This is due to the fact that the rates of cell death and cell division are nearly equal, resulting in no effective change in population size.
  • Decline or Death Phase: Unless bacteria have an infinite source of nutrients, which applies to chemostat growth but not batch culture, then living cells deplete nutrients in the media and toxic bacterial waste products accumulate. This leads to an unfavorable environment, causing death rates to be greater than the rate of cell division.
  • Long-term stationary Phase: This is a fifth phase that has been observed in the laboratory for some bacteria such as E. coli, although this phase is not usually discussed by most microbiologists. In contrast to early stationary phase, in which there is little cell division, this phase is characterized by high rates of both cell division and death. Even after the decline phase, some viable bacterial cells that can persist for various periods of time in closed culture systems. (in some, cases up to 5 years)

Bacterial growth calculations

Bacteria divide by binary fission, meaning one cell splits into two cells. Bacteria also generally have defined generation times. Accordingly, bacterial growth can be simply modeled using exponential growth equations. If the efficiency of binary fission is assumed to be 100%, then the formula for modeling bacterial growth is: [math]\displaystyle{ P = P_o * 2^{(t/g)} }[/math], where P = current population size at time t, Po = initial population size, t = time elapsed since t = 0, and g = generation time. Note that [math]\displaystyle{ t/g = n = }[/math] number of generations since t = 0. If the efficiency of binary fission were instead less than 100%, this would mean that there is a chance any given parent cell results in only one viable daughter cell. In this case, the formula we would use is: [math]\displaystyle{ P = P_o * (1+e)^{(t/g)} }[/math], where e = efficiency.

In addition to the exponential model described above, there are more complex models for bacterial growth that take into account the effect of nutrient limitation. Perhaps the most famous of these is the Monod equation, which describes a mathematical relationship between the concentration of a limiting nutrient and bacterial growth rates. Interesting, the Monod equation takes the same form as the Michaelis-Menten equation, which describes a relationship between substrate concentrations and enzymatic reaction rates (see the "Enzymes and Inhibition" section on the Cell Biology page). The Monod equation is as follows:

[math]\displaystyle{ µ = \frac{d [P]}{d t} = \frac{ µ_\max {[S]}}{K_\mathrm{S} + [S]} . }[/math] where P = population size, t = time, µ = growth rate of population (negative values indicate population is decreasing), µmax = the maximum possible growth rate, [S] = the concentration of the limiting nutrient, and KS = the concentration of the limiting nutrient at which the current growth rate is half of the maximum (i.e., [S] at which μ/μmax = 0.5).

Symbiogenesis and related evolutionary theories (Division C only)

Endosymbiotic theory

Symbiogenesis is an evolutionary theory that is often considered synonymous with the endosymbiotic theory, which describes how eukaryotes may have emerged from interactions between prokaryotic cells. Championed by Lynn Margulis in the 1960s, the endosymbiotic theory holds that mitochondria, chloroplasts, other types of plastids, and possibly other organelles present in eukaryotic cells originated from prokaryotic cells. While mitochondria are thought to be descended from an ancestor related to modern-day alphaproteobacteria (specifically a sister clade to the taxonomic order Rickettsiales), chloroplasts are suspected to be descendants of cyanobacteria.

Evidence for this theory includes that mitochondria and chloroplasts divide independently via binary fission, while the other components of eukaryotic cells divide by mitosis and cytokinesis. Additionally, these organelles are the same size as bacteria and possess their own circular DNA genomes, their own ribosomes, and two membranes. The two membranes have different chemical compositions, with the outer being biochemically similar (i.e., in terms of lipid and protein content) to the eukaryotic plasma membrane and the inner being similar to bacterial membranes. Many scientists take this as evidence that the outer layer developed when a host cell was engulfing a symbiont. Further evidence for the endosymbiotic theory is that, in some eukaryotic algae, chloroplasts still have cell walls made of peptidoglycan which is characteristic of bacteria. In addition, the chloroplasts of some eukaryotic algae may sometimes have up to 4 membranes due to secondary endosymbiotic events.

Some scientists suspect that symbiogenesis may be an even broader evolutionary phenomenon that is not limited to endosymbiosis-enabled eukaryogenesis. One observation that motivates this suspicion is that some groups of eukaryotes have secondarily lost their endosymbionts, suggesting that symbiosis can bring about significant and lasting evolutionary changes even if organisms lose their symbionts later on. This has led some scientist to wonder whether symbiosis has contributed to other major evolutionary events besides eukaryogenesis, even if not all living members affected by these events have maintained the symbiosis.

Related theories of Eukaryogenesis

While the endosymbiotic theory is the most widely accepted theory for eukaryogenesis, there are also several related theories that either expand upon the endosymbiotic theory or offer alternative ideas about the origin of eukaryotes. Some of these theories include: viral eukaryogenesis, the eocyte hypothesis, the hydrogen hypothesis, and the syntrophy hypothesis.

Microbes and pathogenic agents for 2023-2024

Viruses

SARS-CoV-2 virus

SARS-CoV-2 is a novel coronavirus identified as the human pathogen responsible for COVID-19. The virus primarily spreads between people through close contact and via respiratory droplets produced from coughs or sneezes. It enters human cells through the ACE2 receptor and uses the cell's machinery to replicate. It primarily causes respiratory illnesses which can range from mild to severe including Pneumonia and severe acute respiratory syndrome.

This virus has a genome made of single-stranded RNA, and using the Baltimore classification system, falls under Group IV (single-stranded positive-sense RNA viruses).

HIV-1

HIV-1 is the most widespread type of Human Immune-deficiency Viruses (HIVs). HIV-1 weakens your immune system by destroying important cells (T-cells or CD4 cells) that fight disease and infection, which can ultimately lead to acquired immunodeficiency syndrome (AIDS). The virus can be transmitted via contact with certain bodily fluids, most commonly during unprotected sex or through sharing needles. Due to weakened immune system, AIDS is associated with many opportunistic infections by fungi and parasites that are otherwise very rare in healthy individuals.

It is a retrovirus that contains two copies of single-stranded RNA and belongs to Group VI (ssRNA-RT viruses) according to the Baltimore classification system, as it replicates its RNA into DNA through reverse transcription.

Influenza A virus

Influenza A virus causes seasonal epidemics and occasional pandemics, affecting both humans and animals. It is a major public health threat and is the causative agent of a highly contagious respiratory infection. The virus infects the respiratory tract and causes symptoms that range from mild like fever, cough, and body aches to severe respiratory complications that require hospitalization or lead to death.

This virus is part of Group V (single-stranded negative-sense RNA viruses) according to the Baltimore classification system. Its genome is segmented and each segment or part of the virus is coded with a separate RNA molecule.

Hepatitis B virus

Hepatitis B virus (HBV) is a viral infection that attacks the liver. HBV is transmitted when blood, semen, or another body fluid from a person infected with the virus enters the body of someone who is not infected, which can happen through sexual contact, sharing needles, or from mother to child during childbirth. Chronic Hepatitis B can lead to serious health issues, like cirrhosis or liver cancer.

Despite being DNA-based, it has an intermediate phase in its replication cycle that involves RNA. Thus, it belongs to Group VII (double-stranded DNA-RT viruses) of the Baltimore classification system.

T4 phage

T4 is a bacteriophage that infects harmful E. coli bacteria. It is one of the largest phages and has a life cycle that involves the injection of its DNA into a host bacterium. T4 phage is notable for having an elongated icosahedral head and a long tail.

This virus contains double-stranded DNA and falls under Group I of the Baltimore classification system (double-stranded DNA viruses).

Canine parvovirus 2 (Division C only)

Canine Parvovirus 2 is a highly contagious viral disease that can produce a life-threatening illness in dogs, primarily puppies. The virus attacks rapidly dividing cells in a dog's body, particularly the gastrointestinal tract. It is easily transmitted between dogs through physical contact or contact with feces.

This is a non-enveloped, single-stranded DNA virus that is part of Group II (single-stranded DNA viruses) according to the Baltimore classification system.

Mimivirus (Division C only)

Mimivirus is a type of giant double-stranded DNA virus that was first discovered in 1992. Strikingly large in size compared to other viruses, mimivirus was first mistaken for a bacterium. It has a unique life cycle and has been found to cause pneumonia in humans.

As a double-stranded DNA virus, the Mimivirus is classified under Group I (double-stranded DNA viruses) according to the Baltimore classification system.

Poliovirus (Division C only)

Poliovirus is a highly infectious virus that causes poliomyelitis, which predominantly affects children under the age of 5. It is spread person to person, typically through contaminated water. The virus invades the central nervous system and can cause total paralysis in a matter of hours.

This virus carries single-stranded RNA and is part of Group IV (single-stranded positive-sense RNA viruses) according to the Baltimore classification system.

Banana bunchy top virus (Division C only)

BBTV is the most destructive viral pathogen of banana plants, causing 'bunchy top' disease. Affected banana plants show stunted growth, narrow misshapen leaf blades, and reduced fruit yield. It is transmitted by aphids and there is no known cure once a plant is infected.

BBTV is a circular single-stranded DNA virus, therefore it belongs to Group II (single-stranded DNA viruses) according to the Baltimore classification

Bacteria

Vibrio cholerae

Vibrio cholerae is a Gram-negative, comma-shaped bacterium found in environments such as brackish or saltwater where it attaches itself to copepods, small crustaceans in plankton. It causes cholera in humans, resulting in an acute, diarrheal illness. The bacterium causes disease by secreting a toxin that leads to rapid water loss in the intestines, potentially causing severe dehydration and death.

Rickettsia rickettsii

Rickettsia rickettsii is a Gram-negative, aerobic coccobacillus capable of living within the cytoplasm of eukaryotic cells and is transmitted to humans through the bite of a tick. It causes Rocky Mountain spotted fever, the symptoms of which include fever, headache, abdominal pain, rash, and muscle aches.

Streptococcus pneumoniae

Streptococcus pneumoniae, also known as pneumococcus, is a Gram-positive bacterium that is one of the leading causes of vaccine-preventable illnesses globally. The bacterium commonly resides asymptomatically in the nasopharynx of healthy individuals. However, it can also infect the lungs to cause pneumonia and may spread to other parts of the body if conditions allow. Pneumococci can spread into the bloodstream causing bacteremia and further to the brain causing meningitis. It can also spread to the inner ear and cause otitis media.

Corynebacterium diphtheriae

Corynebacterium diphtheriae is a Gram-positive bacillus responsible for causing diphtheria, a toxin-mediated disease that can cause a pseudomembrane to form over the respiratory mucosa, thereby causing difficulty in breathing and potentially stridor and suffocation.

Methicillin-resistant Staphylococcus aureus (MRSA)

Methicillin-resistant Staphylococcus aureus (MRSA) is a Gram-positive, round-shaped (cocci), cluster-forming bacterium that is resistant to many antibiotics and can cause a range of health problems, such as skin infections and pneumonia. In severe cases, it can also cause sepsis.

Mycobacterium tuberculosis

Mycobacterium tuberculosis is a small, aerobic, nonmotile bacillus. It is an acid-fast bacterium, meaning it has a thin layer of peptidoglycan and stains weakly Gram-negative or Gram-variable although the structure of the outer membrane is notably different from Gram-negative bacteria. The bacterium has a very slow metabolic rate and can remain dormant in the body for years before becoming active and causing tuberculosis. The primary target is the lungs, but it can spread and cause extrapulmonary disease as well. Infection by this bacterium is rapidly diagnosed using the Mantoux test.

Cutibacterium acnes (Division C only)

Cutibacterium acnes is preedominantly found in the oily skin regions and is a slow-growing Gram-positive bacterium linked to the skin condition of acne. It was formerly called Propionibacterium acnes. It is also associated with other medical problems such as adverse foreign body reactions and other forms of medical device-related infections.

Haemophilus influenzae (Division C only)

Haemophilus influenzae is a specis of bacteria that was first discovered in 1893 by Richard Pfeiffer during an influenza pandemic. While it does not cause the flu (which is now known to be caused by influenza viruses), it retains the species name influenzae due to the context of its discovery.

Haemophilus influenzae is a Gram-negative coccobacillus. This species includes several different strains of bacteria that can be divided into two broad groups: one group with an outer coating called a capsule and one which lacks a capsule. Encapsulated strains are further divided into six serotypes (a-f) based on the capsular antigens that are present. The serotype known as 'b' (or Hib) is the most common, particularly in children, and is known for the presence of the polysaccharide polyribosyl ribitol phosphate (PRP) in the capsule. Types a, e, and f are more uncommon, while types d and c are very rare.

The strains that lack a capsule are more varied and, because they don't have a specific 'type', we call them nontypable Haemophilus influenzae (NTHi). These nontypable strains do not cause illness and are part of the normal microbial flora present in our upper and lower respiratory tract, genitals, and even the conjunctiva of the eyes.

Encapsulated strains of Haemophilus influenzae can cause a wide range of localized and systemic infections, especially in young children and infants. This includes upper respiratory infections like pneumonia in addition to septicemia, meningitis, and epiglottitis. Although antibiotics may be used to fight infections, some strains like Hib resist certain types of antibiotics (namely beta-lactam antibiotics in the penicillin family). To protect against Hib, there is a vaccine that is usually given during early childhood (<5 years of age). There is also a combo vaccine, DTaP-IPV/Hib, which protects against multiple diseases.

Wolbachia species (Division C only)

Bacteria of the genus Wolbachia are Gram-negative and are some of the most widespread parasitic microbes. These bacteria live within the cells of a wide range of invertebrates, including insects, spiders, and crustaceans. Wolbachia can manipulate host reproduction to promote its own dissemination throughout a population. In some species, it causes pathogenic effects and confers benefits in others.

Agrobacterium tumefaciens (Division C only)

Agrobacterium tumefaciens is a Gram-negative bacterium known for its ability to transfer DNA between itself and plants. This unique DNA transferring feature of A. tumefaciens has been exploited for genetic engineering in biotechnology to insert new genes into plants. This bacterium is also known for causing crown gall disease (tumors) in plants

Fungi

Candida auris

This fungus belongs to the phylum Ascomycota. It causes serious and often fatal infections in humans. It is multi-drug resistant and is a growing global health threat especially to hospitalized, immunocompromised individuals. Infections can affect the bloodstream, wound sites, and ears, although severe cases can impact the central nervous system. The life cycle of this fungus involves the formation of yeast cells and hyphal cells.

Alternaria solani

This fungus belongs to the phylum Ascomycota. It causes early blight disease in plants of the family Solanaceae, which includes important commercial crops like potatoes, tomatoes, eggplants and peppers, leading to significant yield loss. The life cycle of the pathogen is closely tied to its host and environment. The fungus produces durable, dark spores which are dispersed by wind and can cause new infections.

Protists

Plasmodium falciparum

Giardia duodenalis

Toxoplasma gondii (Division C only)

Alexandrium catenella (Division C only)

Prions and Prion-Like Proteins

Major prion protein (PrP)

amyloid beta (amyloid-β)

tau proteins (Division C only)

α-Synuclein (Division C only)

Worms (Division C only)

Taenia solium

Ancylostoma duodenale

Viroids (Division C only)

Potato spindle tuber viroid (PSTVd)

State/National Topics for 2023-2024

On occasion, the rules will specify certain topics to only be tested at the state and national level, but not the regional level. These are listed/discussed below for the year 2023-2024.

Treatments and prevention for diseases caused by microbes and transmissible agents

[This section has no information yet]

Culture-free methods to study microbial activity

[This section has no information yet]

Metatranscriptomics

[This section has no information yet]

Proteomics

[This section has no information yet]

Metabolomics

[This section has no information yet]

Phage lambda cro repressor system

[This section has no information yet]

Research applications of lac and trp operons

[This section has no information yet]

Roles of microbes in lakes, oceans, soil, and the gut microbiome

Microbes are present in large numbers in nearly all environments. Many bacteria have a symbiotic relationship with an animal or plant host, aiding them in metabolic processes that the host would be unable to perform otherwise. Notably, bacteria are involved with the digestive systems of animal hosts. Communities of microbes, microbiomes, receive nutrients from the animal host, and in turn, produce vitamins and digestive enzymes that the host's cells cannot. A notable example is the microbial community found in the gut of termites. This microbiome includes both bacteria and protists, producing celluase enzymes that allow their detritivorous hosts to digest wood. Bacteria also are crucial to the nitrogen cycle. In this collection of processes, nitrogen-fixing bacteria convert atmospheric nitrogen (N2), into ammonia (NH3) or ammonium (NH4+). These inorganic compounds are then converted into biologically useful molecules like nitrite (NO2-) and nitrate (NO3-) by nitrifying bacteria in the process of nitrification. These molecules are subsequently incorporated into the nucleic acids and proteins of plants. Nitrogen present in organisms is decomposed by soil bacteria into ammonia or ammonium again. Denitrification occurs when other species of bacteria convert organic nitrogen compounds into molecular nitrogen, releasing N2 back into the atmosphere and completing the nitrogen cycle.

Metabolism of sulfate reducing, purple sulfur, and purple non-sulfur bacteria

[This section has no information yet]

Phylogenetic methods to detect horizontal gene transfer

[This section has no information yet]

National Topics for 2017-2018

On occasion, the rules will specify certain topics to only be tested at the national level, but not the state or regional level. These are listed/discussed below for 2017-2018.

Microbial Population Explosions

The most common example of a microbial population explosion is an algal bloom/red tide, an an aggregation of red dinoflagellates in an aquatic ecosystem. Fertilizer-rich runoff, often from a farm, is the typical cause for an algal bloom.The abundance of nutrients in the fertilizer becomes a part of the runoff and enters a nearby body of water along with it. This eutrophication fuels algal growth, allowing dinoflagellates to reproduce rapidly.

As a result, certain algae can produce potentially lethal toxins that are harmful to animals. Algal blooms are also expensive to treat, greatly impacting water treatment plants. Perhaps the most devastating consequence of all is ocean dead zones. Given a massive population of algae, many will eventually die due to lack of space, buildup of toxins, etc. Marine decomposers (i.e. bacteria) break down the organic material of the dead dinoflagellates, which requires oxygen. Oxygen in surrounding waters is depleted, causing hypoxia and eventually anoxia (the state of having no oxygen). This causes most of the marine life to die, hence the name "ocean dead zone".

Microbial population explosions can also be influenced by their behavioral preferences. For example, fungi grow best at a slightly acidic pH. One could go even further and look at the diversity of behaviors in bacteria alone. Neutrophiles are most comfortable at a neutral pH of 7, which tends to be suitable for most pathogens. Obligate anaerobes cannot tolerate any oxygen and die in its presence, making their environment anoxic. There are also xerophiles, which thrive in extremely dry surroundings. The adaptations of microbes are very broad, which allows them to rapidly multiply in almost any given environment.

Microbial Competition and Communication

Microbial communication is done through quorum sensing (qs). After attaching to a surface, qs bacteria send out autoinducers that indicate the population of nearby bacteria. If there are enough bacteria nearby, it starts creating a biofilm. Just like all organisms, microbes compete to survive. Some microbes "stab and poison" neighboring cells to kill them. Others colonize an excess amount of space to prevent other bacteria from growing there. Many methods of competition exist, though they can all be divided into two types: scramble competition and contest competition.

In scramble competition, participants use up as many available resources as possible to prevent other organisms from using them. To visualize this, imagine a ton of children are standing on a field and someone throws out a ton of quarters. The children would try to get the most quarters that they can to stop others from getting them. Contest competition is just like it sounds: direct competition between species, with the winner getting exclusive access to the resources. An analogy for this is the same scenario, except the quarters aren't thrown out and are instead reserved. All the kids are given weapons, and the last person standing gets the quarters, similar to the Hunger Games.

In every competition however, there are cheaters. The same goes for the microbial world, where "social cheaters" exist. An example of this is bacteria that mimic P. aeruginosa, which happens to produce a certain autoinducer that attracts bacteria. Once gathered, they produce a large quantity of antimicrobials to eliminate competitors. Other bacterias can analyze this behavior and replicate it without undergoing evolution.

Microbiomes

Microbiomes are defined as the microbes in a particular environment, particularly in the context of an organism's body. In the context of humans, it is simply defined as the collection of microbes that live inside and on the human body. Humans are inhabited by an estimated 3 times the number of non-human cells as human cells. The majority of microbes occupying the human microbiome are considered to have commensalistic or mutualistic relationships with their host.

The Human Microbiome Project (HMP), established in 2007, was a research project designed to study the human biome, and published its first results in 2012.

Biofilms

Biofilms are collections of microorganisms (chiefly bacteria, fungi, and protists) that grow on a surface, thus creating a "film" on that surface. The primary stages of development of a biofilm are considered to be the following:

  1. Initial attachment
  2. Irreversible attachment
  3. Maturation I
  4. Maturation II
  5. Dispersion

Sample Questions and Exercises

Complete questions

Types of microbes

  1. State whether each of the following microbes is acellular, unicellular, or multicellular: Alexandrium catenella, Alternaria Solani, Ancylostoma duodenale, Candida auris, Mycobacterium tuberculosis, T4 phage.
  2. Explain two differences between fungal mitosis and animal mitosis.
  3. Identify one similarity and one difference between viruses and prions.
  4. What type of microbe is involved in the production of most breads?
  5. List as many different groups of photosynthetic microbes as you can.
  6. Do cyanobacteria or eukaryotic algae produce more tons of O2 each year?
  7. While the promoter regions of eukaryotic genes contain a sequence called the TATA box (aka Goldberg-Hogness box), bacteria contain a promoter region called the: _________.
  8. Do archaeal gene promoters contain a TATA box, the bacterial sequence element described above, or another type of sequence element?
  9. Instead of methionine, the first amino acid that docks in the amino acid binding site of ribosomes during bacterial protein synthesis is: _________.
  10. Do archaea use methionine like eukaryotes or the same amino acid as bacteria?
  11. Describe one difference between archaeal and bacterial plasma membranes.
  12. Suppose you have a specimen in a lab that contains either Hepatitis B virus (HBV) or Potato spindle tuber viroid (PSTVd) particles suspended in an aqueous mixture. Without introducing the infectious agent into its host, identify one (bio)chemical technique or assay that could be used to distinguish whether the specimen contains a virus or viroid. Explain the result you would expect if there were a viroid or if there were a virus.

Bacteria

  1. Explain two differences between gram-positive and gram-negative bacteria.
  2. Instead of actin and myosin, bacterial cytokinesis is facilitated by a contractile ring made of a protein called: _________.
  3. What is the name of the protein that determines bacterial cell shape?
  4. Name one genus of bacteria that is capable of nitrogen fixation.
  5. Using the enzyme _________, nitrogen-fixing bacteria convert atmospheric nitrogen to the compound _________.
  6. In times of nitrogen starvation, some cells in a population of cyanobacteria differentiate into nitrogen-fixing cells called _________.
  7. The most widely used biopesticide is the bacterium: (A) Agrobacterium (B) Pseudomonas aeruginosa (C) Wolbachia melophagi (D) Bacillus thuringiensis (E) Mycobacterium avium
  8. Describe in as much detail as you can how the gene mecA facilitates drug resistance in methicillin-resistant Staphylococcus aureus (MRSA).
  9. While both are gram-_________ bacteria that contain the enzyme catalase, Staphylococcus bacteria can be distinguished from Streptococcus bacteria by the presence of the enzyme _________.
  10. Staphylococcus bacteria can also be distinguished from Streptococcus bacteria visually under a microscope. Using either 2 drawings or 2 descriptions, explain how to distinguish these bacteria based on cellular arrangement.
  11. Describe the flagellar arrangements of Cornyebacterium diptheria and Vibrio cholerae as atrichous (i.e., no flagella), monotrichous, lophotrichous, peritrichous, amphitrichous, or cephalotrichous.
  12. _________ is a prokaryotic mechanism of immune evasion against viruses that has been used to develop revolutionary gene-editing techniques for permanent excision or addition of genes from or into host genomes using guide RNA and Cas proteins.

Eukaryotic algae

  1. What group of eukaryotic algae gives corals their color? What happens to these algae during coral bleaching?
  2. Explain one difference between green algae and brown algae.
  3. Explain one difference between green algae and red algae.
  4. The chloroplasts of many eukaryotic algae and euglenids have micro-compartments called _________, which concentrate carbon dioxide around the enzyme RuBisCo to optimize photosynthetic output.
  5. The chloroplasts of brown algae have 4 membranes, while the chloroplasts in plants have 2 membranes. How are the additional membranes in brown algal chloroplasts thought to have been in acquired?
  6. Explain how eutrophication in a body of water may result in a harmful algal blooms (HAB).
  7. Especially in freshwater, HABs can catastrophically change the dissolved oxygen (DO) levels. Which best describes how and why DO levels change after HABs in freshwater lakes? (A) DO levels increase due to increased algal photosynthesis (B) DO levels increase because metabolic heat from HABs increases water temperature, which increases the partial pressure of any dissolved gasses (C) DO levels decrease because most dissolved oxygen has been incorporated into algal structural polysaccharides (D) DO levels decrease because the type of algae that cause HABs consume oxygen by cellular respiration faster than they produce oxygen by photosynthesis (E) DO levels decrease because of aerobic decomposition of dead algae
  8. In addition to freshwater lakes, sometimes HABs occur in the snow and oceans. Explain how HABs in snow and HABs in oceans each affect the albedo of the Earth’s surface.
  9. Red tide is a phenomenon that is sometimes due to non-photosynthetic ciliates that eat red algae, but most commonly it is a HAB. One of the most common algae responsible for this HAB is the dinoflagellate: (A) Oxyrrhis marina (B) Ammonia tepida (C) Blastodinium spinulosum (D) Karenia Brevis (E) Symbiodinium thermophilum
  10. Coccolithophores, diatoms, and some types of dinoflagellates have mineral outer coatings. For each of these types of algae, provide the name of the outer mineral coating and describe its chemical composition.
  11. How many flagella, if any, does Alexandrium catenella have?
  12. How many membranes do chloroplasts have in Alexandrium catenella?
  13. Is Alexandrium catenella exclusively photoautotrophic, or is it also capable of heterotrophy in some stages of its life cycle?

Fungi

  1. Describe two differences between yeasts and molds (i.e., filamentous fungi).
  2. Most of the fungi which form fruiting bodies that we call mushrooms belong to the fungal phylum: (A) Ascomycota (B) Basidiomycota (C) Chytridiomycota (D) Glomeromycota (E) Zygomycota
  3. The cap of a mushroom is called the _________ and the stem of the mushroom is called the _________.
  4. The long, branching fungal filaments seen in molds are called _________ , and the collective root-like mass of these filaments that forms the “body”of the mold is called a _________.
  5. Define plasmogamy and karyogamy in the context of fungal life cycles.

Parasitic worms

  1. Identify whether the rhabditiform and filariform of a nematode larva is the infective stage, and state which of these stages precedes the other one during development.
  2. How many times does a roundworm molt throughout its life cycle?
  3. Which of the following is NOT an important ecological role of terrestrial roundworms? (A) Bacteriophagy (B) Nitrogen mineralization (C) Soil acidification (D) Bioturbation (E) Pest suppression
  4. For each of the following characteristics, state whether it applies to flatworms, roundworms, or both. (I) Lack a complete digestive system (II) Bilateral symmetry (III) Cephalization (IV) Lack a circulatory system (V) Triploblastic (VI) Lack a true body cavity (VII) Protostomes (VIII) Obligate parasites
  5. Compare the mechanisms by which flatworms and roundworms excrete nitrogenous waste and the chemical form of nitrogenous waste.
  6. Describe 2 functions of the tegument of flatworms.
  7. Describe the functions of the mehlis gland and the yolk gland, which are found in tapeworm proglottids.
  8. Explain the difference between craspedote and acraspedote proglottids on a tapeworm.
  9. Are tapeworms obligate aerobes, microaerophiles, facultative anaerobes, aerotolerant anaerobes, or obligate anaerobes?

Prions and prion-like proteins

  1. Describe one way to sterilize an area of prions.
  2. Describe one similarity and one difference between major prion protein (PrP) and amyloid-β.
  3. True or False: Normally folded, healthy isoforms of PrP exist as a free-floating cytosolic protein.
  4. True or False: Normally folded, healthy isoforms of PrP bind to several different metal ion species.
  5. True or False: After knocking out the PrP-encoding gene in mice, the mice remain susceptible to infection by misfolded PrP.
  6. True or False: Some microbiologists have found evidence that prions or prion-like proteins have beneficial effects in yeast.

Protozoa

  1. Ciliates (members of the phylum Ciliophora) are unicellular heterotrophs that contain both a micronucleus and a macronucleus. Explain the difference in function of these two nuclei.
  2. During ciliate cell division, what happens to each nucleus?
  3. Ciliates also often have rod-like structures near their surface called _________, which may be ejected from the cell and function as a cellular defense mechanism or as a form of anchorage during feeding.
  4. Which of the following taxonomic groups does Toxoplasma belong to? (A) Apicomplexan (B) Ciliate (C) Diplomonad (D) Foram (E) Parabasalid
  5. Explain what the sporogonic, exoerythrocytic, and erythrocytic cycles are with regard to Plasmodium life cycles.
  6. Compare the mechanisms that facilitate motility in Plasmodium falciparum and Giardia duodenalis.
  7. How many total cells, nuclei, and flagella does one mature Giardia duodenalis trophozoite have?
  8. Which two eukaryotic organelles are present in most other protozoa, but are absent in diplomonads such as Giardia duodenalis (and in the poorly studied group of protozoans called retortamonads)?
  9. Identify one type of protozoan that has an outer coating called a pellicle and one type of protozoan that has an outer coating called a test, then compare the chemical compositions of pellicles and tests.

Viruses

  1. Describe the genetic material of Canine parvovirus 2 in as much detail as you can.
  2. What is viropexis?
  3. Briefly explain one way that viral infections may cause cancer.
  4. Viruses that cause cancer are called: _________. List the 7 viruses that are suspected to cause cancer.
  5. What is an arbovirus? Provide two examples of arboviruses.
  6. Explain the difference between antigenic shift and antigenic drift by defining each.
  7. The swine flu was a strain of influenza A that became very prevalent in 2009-2010. It was also called the H1N1 flu. What do "H" and "N" each stand for, and to which part of the influenza A virions do these letters refer?
  8. How many faces, sides, and vertices are on the polyhedral head of a bacteriophage?
  9. Viral vectors can facilitate horizontal transfer of genes from one bacterium to another bacterium by a process called: (A) Conjugation (B) Lysogeny (C) Transformation (D) Transduction (E) Transfection.
  10. In E. Coli, Lambda phage is a viral vector that performs a specialized version of the process described in the question above. Lambda phage is capable of transferring a controlled or restricted set of bacterial genes (i.e., not random), while the generalized version of this process occurs due to random inclusion of bacterial DNA in virions during the lytic cycle. Knowing this, explain why undergoing the lysogenic cycle is necessary for the specialized version of this process.
  11. Which 3 major viral enzymes are involved in the HIV-1 replication cycle, and what role does each one play?
  12. Many common antiviral medications like aciclovir are nucleoside analogue compounds. How might nucleoside analogues inhibit viral replication?

Microbial growth

  1. If one single bacterium reproduced every 20 minutes for 8 hours, how many bacteria would there be? Assume perfect exponential growth by binary fission and that no cells die during the interval.
  2. If a population of 100 bacteria has grown to 150 bacteria in 2 hours (t = 2), how many bacteria will there be after 4 more hours (t = 6)? Assume perfect exponential growth by binary fission and that no cells die during the interval.
  3. What would the answer to the question be if there were a 10% chance that any given binary fission event results in only 1 viable cell instead of 2? You may assume that there is a 0% chance of a binary fission event killing the diving cell, thus resulting in 0 cells, and that no other cells die during the interval.

Microbes in food production

  1. What genus and species of fungus is commonly used in alcohol production?
  2. Name two types of cheese that are made using a fungus to impart a unique flavor that is not present in cheeses made solely with bacteria.
  3. What is the difference between prebiotics and probiotics?
  4. Which common beverage is produced using a microbial community called a SCOBY, and what does SCOBY stand for?
  5. Identify two food products that are made using components of eukaryotic algae and at least one specific group of algae (i.e., diatoms, dinoflagellates, red algae, green algae, brown algae, etc.) that is used for each food.

Microbial diseases

  1. Name two viruses that cause diseases for which there is no effective vaccine.
  2. For each microbe, identify which type of microbe it is and match it to the disease it causes. There will be one correct match per category per microbe.
    1. Microbes: Alternaria Solani, Plasmodium falciparum, Rickettsia rickettsii, Taenia solium, a member of the family Filoviridae.
    2. Type of microbes: apicomplexan, bacterium, cestode, fungus, virus.
    3. Diseases: Cystericosis, Early potato blight, Ebola, Malaria, Rocky Mountain Spotted Fever
  3. Compare the geographic prevalences of HIV-1 groups M, N, and O.
  4. What do the acronyms ART, PrEP, and PEP stand for, with regard to treating and preventing HIV-1 infections?
  5. Match each clinical test to the microbe it would detect. There is one correct answer per test:
    1. Tests: Giemsa stain test, Mantoux test, Weil-Felix test
    2. Microbes: Mycobacterium tuberculosis, Plasmodium falciparum, Rickettsia rickettsii
  6. What are HA MRSA, LA MRSA, and CA MRSA?
  7. What is the name of the toxin that Alexandrium catenella produces to cause Paralytic Shellfish Poisoning?
  8. Which relatively common beverage contains a compound that is effective at treating Plasmodium falciparum infections, and what is the name of that compound?
  9. List as many diseases as you can that ae caused by the misfolding of major prion protein (PrP).
  10. Some prion diseases such as Creutzfeldt-Jakob disease (CJD) may be iatrogenic in origin. What does the word “iatrogenic” mean?
  11. If a prion disease were iatrogenic, propose a scenario explaining how it could have been contracted.

Exercises requiring more information to be completed

  1. Using a dichotomous key (must be provided), analyze the following pictures to determine which picture depicts eukaryotic algae.
  2. Based on the following graph, determine which organism is best suited for growth in acid environments.
  3. A cell is observed through a light microscope at 4x magnification. The cell takes up about half of the visual field. What is the approximate length of this organism?
  4. Students observe a Petri plate with many different colonies on it. Based on the color of the colony, how many different kinds of organisms do you detect? Which type of organism appears to be the most prevalent?
  5. From the following picture, identify the organelle, provide its function, and state which type of microbe it is unique to.
  6. Based on the following graph, what will be the microbial population/mL after 3.5 hours of growth?
  7. Streak a provided agar plate as though you were plating bacteria in a way that allows you to obtain single colonies.

Useful links

See Also