Microbe Mission

Microbe Mission
Type	Life Science
Category	Lab
Description	Teams will answer questions, solve problems, and analyze data pertaining to microbes.
Event Information
Participants	2
Approx. Time	50 minutes
Allowed Resources	One notes sheet Two Class II Calculators
Rotates	Yes
Eye Protection	C
First Appearance	2011
Latest Appearance	2024
Forum Threads
2024 2018 2017 2012 2011 2010 (Trial)
Question Marathon Threads
2024 2018 2017
Official Resources
Division B Website	www.soinc.org/microbe-mission-b
Division C Website	www.soinc.org/microbe-mission-c
Division B Results
1st Daniel Wright Junior High School 2nd Paul J. Gelinas Junior High School 3rd Meads Mill Middle School
Division C Results
1st Mason High School 2nd Troy High School 3rd Harriton High School

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 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. A recommended font for Microbe Mission notes (or any other note-based event) is BenchNine or Calibri Light/Narrow, in any font size 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.

Measurements

The smallest measurement on a metric ruler is usually a millimeter (mm). One millimeter is equal to 1000 micrometers (mcm or μm). One micrometer is equal to 1000 nanometers (nm).

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 and a globular domain. Mature PrP is a 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 (PrP^C) or as a misfolded, disease-causing form that is highly resistant to degradation by proteases (PrP^Sc; named for its associated with the disease Scrapie). Additionally, some scientists have created protease-resistant isoforms of PrP in vitro that have not necessarily been shown to cause disease (PrP^Res).

Exposure to small number of prions can facilitate the conversion of the normal isoform PrP^C to the pathogenic isoform PrP^Sc, resulting in disease. In nervous tissue, PrP^Sc 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 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, leading to enlarged vacuoles that appear like "holes" when analyzing tissue. These holes are caused by vacuolation, or the development of enlarged and abundant vacuoles, 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 which are 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 are capable of self-replication within host cells, leading 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 are responsible for a variety of diseases, such as: AIDS, the common cold, hepatitis A-E, influenza, chicken pox, chikungunya, cowpox, Ebola, 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.

Some viruses, known as bacteriophages, infect bacteria. Their appearance is often compared to that of an alien landing pod. Typically, bacteriophage genomes are composed of DNA rather than RNA. Other viruses, most famously Sputnik, infect other viruses and are known as virophages.

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. HIV, which causes AIDS, is a lysogenic virus.

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, the 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. As no chromosomes are formed, 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.

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 nonmotile.

Bacterial cell shapes

Bacteria may assume many different shapes. Some of the most common morphologies are: 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.

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 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). 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.

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.

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 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.

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, the 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 animal 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 cells; protection and support
• Plasma Membrane – controls the substances exiting and entering the cell
• Cilia - 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 – between plasma membrane and nucleus; contains many organelles
• Endoplasmic reticulum (ER) - the passageway for transport of materials within the cell; synthesis of lipids – modification of newly formed polypeptide chains
• Ribosomes are the site of protein synthesis
• Golgi apparatus - final modification of proteins and lipids; packing of materials for secretion out of the cell
• Mitochondria - the site of aerobic cell respiration and ATP production
• Hydrogenosomes - sites of anaerobic cell respiration in certain protozoa. (Trichomonas, etc.)
• Lysosomes - contain enzymes to digest ingested material or damaged tissue
• Chloroplasts – store chlorophyll; site of light reactions of photosynthesis
• Vacuoles – storage; 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. In addition to these 5 phyla, 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 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 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 a 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 plats. At least 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, in some cases, photosynthetic) 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 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 and have no body cavity, meaning they are acoelomates (i.e., lack a coelom, which is 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-parasitic 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 (tapeworms), though often it is 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 "head" of tapeworms is called the scolex, which 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).

Non-parasitic flatworms

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

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 anal pore. In male nematodes, the anal pore also functions as a reproductive pore and is called the 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. They are responsible for many different diseases in humans, other animals, and plants.

Some examples of diseases caused by roundworms 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.

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, or the ability to live in conditions with high concentrations of metal cations.
• Some extremophiles exhibit radioresistance, able to withstand very high doses of ionizing and/or nuclear radiation (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 display multiple tolerances to extreme conditions.

Microbial Metabolisms

Microorganisms are often described on the basis of their metabolism. Specifically, microbial metabolisms may classified by a microbe's source of energy, source of carbon, and source of electrons.

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, some of these metabolism types have never been discovered in real organisms.

Energy Source	Electron Source	Carbon Source	Metabolism Name	Example(s), if any
Chemical energy	Organic molecules	Organic molecules	Chemoorganoheterotroph	Fungi, animals, many protozoa, many bacteria
		Inorganic molecules	Chemoorganoautotroph
	Inorganic molecules	Organic molecules	Chemolithoheterotroph
		Inorganic molecules	Chemolithoautotroph	Some chemosynthetic bacteria (e.g., Nitrosomonas)
Radiant energy (light)	Organic molecules	Organic molecules	Photoorganoheterotroph
		Inorganic molecules	Photoorganoautotroph
	Inorganic molecules	Organic molecules	Photolithoheterotroph	Purple non-sulfur and green non-sulfur bacteria
		Inorganic molecules	Photolithoautotroph	Plants, cyanobacteria, 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.

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

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, P_o = 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.

One can imagine that it is quite rare in nature and sometimes even in the lab for bacteria to divide with perfect 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 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), µ_max = the maximum possible growth rate, [S] = the concentration of the limiting nutrient, and K_S = the concentration of the limiting nutrient at which the current growth rate is half of the maximum (i.e., [S] at which μ/μ_max = 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.

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.

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 Exercises

1. Provide two differences between bacteria, viruses, and fungi.
2. Using the following key, determine (from pictures) which cell, A, B, or C is considered an alga.
3. Based on the following graph, determine which organism is best suited for growth in acid environments.
4. 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?
5. 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?
6. From the following picture, identify the organelle, provide its function, and state which type of microbe it is unique to.
7. What type of microbe is involved in the production of most breads? What type of organism is responsible for polio?
8. Based on the following graph, what will be the microbial population/ml after 3.5 hours of growth?
9. Provide two distinctive properties of viruses, then provide the name of two diseases that are caused by viruses. As a variation on this type of question, match the disease with the type of microbe that causes it.
10. Match each microbe that causes the following disease: Rubella, Schistosomiasis, Ebola, Scrapie, Malaria.

Useful links

• Microbe Mission page on soinc.org
• Has information specific to cells -- Has a lot of useful information -- Use the links on that page too!
• Has vocabulary
• Bacteriology text
• Microbiology text
• CellCraft -- a game which helps you to learn the basic organelles of a cell.
• Microbiology Online -- a great place to find in-depth information on cell organelles

See Also

• Microbe Mission disease lists for 2017-2018 and previous years
• Microbe Mission page improvement coordination
• Microscope