Microbiology Exam 1

What was Carl Woese's strategy for building the RNA-based tree of life? How did his work help Norm Pace accomplish his early studies of the Earth microbiome?

-built the RNA-based tree of life by comparing the DNA sequences of 16S rDNA in many organisms. He compared them by eye. -enough for Sanger sequencing. This allowed Norm Pace to collect 16S from many different organisms in many different types of environments, without culturing the organisms.

What does current and future research in microbiology focus on?

-current research focuses on genomics; decoding our own genetic make-up will involve microorganisms. -industry; to find ways of understanding and exploiting the genetic and metabolic diversity of the microbial world. -Diversity: fewer than 0.2% of microbial species are known to science. -microbial ecology research; because microbes are the life support system of the Earth

What are the major features of bacterial biofilms?

-Biofilms are matrix-enclosed microbial consortia that adhere to biological or non-biological surfaces. -They are often resistant to stressors including biocides, such as human cells designed to kill pathogens (neutrophils). -They are also structurally complex

Conjugation HGT

-Cell-to-cell transfer of DNA. -Requires cells to be directly in contact with each other. -Can be brought together by pilus. -"Bacterial sex". -Tra genes transfer proteins

What are some key ways in which microbes changed the Earth system (through the end of the Carboniferous)?

-Cyanobacteria and other oxygen-producing microbes: expand the simple cycles of carbon, nitrogen, and other compounds to include more oxidized forms. Through oxygenation of the atmosphere, microbes drastically changed the chemistry of the oceans by allowing oxidation of various chemical species, increasing the diversity of chemicals on earth that could be metabolized by organisms to obtain energy. -The second major effect was the formation of the ozone layer. Once the ozone layer formed, UV-sensitive microorganisms could begin to move out of the ocean, where water provided some protection, and into terrestrial habitats. -A third major effect occurred somewhat later, when the cyanobacteria were incorporated by eukaryotic cells to from the chloroplasts of algae and green plants. -Lastly, microbes have shaped the kind of carbon that gets buried in the Earth's crust. During the carboniferous period, vascularlized plants evolved and began depositing large amounts of lignin onto soil as the plants senesced. Nothing could break down this lignin at the time, so lignin accumulated in soil for about 100 million years (this constitutes our modern day coal deposits). There is some phylogenetic evidence to suggest that the evolution of plant cell wall degrading enzymes in fungi (especially enzymes that degrade lignin) allowed fungi to begin decomposing and metabolizing this dead plant tissue, leading to the end of the carboniferous period.

What are the major morphological factors that distinguish bacteria from archaea?

-Different cell wall biopolymer: bacteria have peptidoglycan, while archaea do not have peptidoglycan in their cell wall. -Different cell membrane lipids: archaeal membranes are made up of terpenoid lipids, in which every several carbons extends a methyl branch. The branches strengthen the membrane because the methyl groups allow the lipid chains to physically lock into each other. -In addition, archaeal lipids replace the ester link between glycerol and fatty acid with an ether link, C-O-C. Ethers are much more stable than bacterial esters. -Finally, archaeal lipids can fuse to create a monolayer (tetraether), which is hypothesized to give archaeal cells greater stability under extreme conditions.

Outline two lines of evidence that would support Panspermia theory

-Evidence would have to come from what microbial life looks like on Mars and Earth. -For example, if life on Mars showed a completely different biochemical or metabolic basis than that of Earth -the presence of similar macromolecules in the biomass of the two microbes (i.e. cell membrane lipids like terpenoid/isoprenoid lipids or peptidoglycan).

Describe the role of peptidoglycan in the Gram stain. Make sure to discuss the differences in cell wall and cell membrane composition between Gram positive and Gram negative bacteria

-Gram positive are dark purple and Gram negative are pink. -Gram positive retain the stain because the crystal violet complex gets stuck in thick peptidoglycan layer of Gram positive cell walls. -Because there is less peptidoglycan in Gram negative cells, it is released following the washing.

If you were to create a molecule to serve as the perfect food source (i.e. resource) for a microorganism, which elements would you include and in what ratios?

Carbon, hydrogen, oxygen, nitrogen, phosphorus, sulfur are needed in high concentrations, with trace elements like manganese, copper, zinc, nickel, and molybdenum required in low concentrations. Other elements like iron, magnesium, and calcium are required in high abundance as well.: CNSFeMgCa : MnCuZnMoNi = 95:1 Alternatively, you might construct a food source that has 100% major macronutrients (carbon, hydrogen, oxygen, nitrogen, phosphorus, sulfur, iron, magnesium, calcium), as the trace elements can usually be obtained from water.

Knowing about the role of Che proteins in chemotaxis, describe the dominant direction of flagellar rotation in presence of attractant for the following E. coli strains: 1) CheB deficient and 2) CheR deficient. In your answer, explain the molecular basis for the direction chosen.

CheR deficient: No methylation = constant de-activation of CheA = no phosphorylation of CheY = CCW (run) CheB deficient: No de-methylation = activation of CheA = phosphorylation of CheY = CW (tumble)

Describe the rolls of the Che's

CheR methylates the MCP when there is no attractant binding to the MCP. This activates CheA (and CheW). CheA phosphoraltes CheY to become CheY-P. CheY-P goes to the flagella motor to turn it clock wise, thus making the cell tumble. When CheA is deactivated (there is an attractant bound to the MCP), CheZ dephorsphorloates CheY-P to create a higher concentration of CheY. The flagella motors then turn counter clockwise, resulting in a run.

What two types of enzymes are considered Penicillin Binding Proteins (PBPs)?

Transpeptidases and transglycosylases

Describe the phases of bacterial growth in batch culture. Why is it advantageous to use bacterial cultures in the exponential phase of growth for experiments?

While the number of cells produced is exponential, the rate of growth of a single cell is constant - all cellular components are synthesized at constant rates relative to each other. Therefore, the population is most uniform in terms of chemical and physical properties during this phase.

What are the specific terms used to identify taxa using DNA sequences, and what are the differences between these terms?

a. Genotype and phenotype b. Phylotype c. Operational taxonomic unit (OTU) d. Taxon

Discuss ways in which bacterial surface polysaccharides might benefit the growth of a pathogenic bacterium inside human tissues

a. physical protection from phagocytic cells (phagocytes, like your white blood cells). The capsules are uniform and slippery, making it difficult for phagocytes to lock onto the bacterial cell b. Capsules contain a great deal of water and can protect against desiccation. c. They exclude viruses and hydrophobic toxic materials such as detergents. d. They can also aid in attachment to solid surfaces - biofilms.

Phylotype

-a group of organisms classified by overall similarity in phylogenetic relatedness. -Phylotypes are often used to describe prokaryotes.

Which group of organisms are considered microorganisms?

-Bacteria and archaea are typically referred to as "microorganisms". -many people also consider fungi, algae, and protists to be microorganisms.

Bacterial genomes are unique from eukaryotic genomes in two key ways. What are they?

-Bacterial genomes tend to be way more packed with genes. -Bacteria have on average 15% of their genome as non-coding. humans have over 90% noncoding DNA. -bacterial genes tend to be organized in units called operon, where multiple genes are under the control of the same promoter.

Describe the process of binary fission, and how it differs from endospore formation

-Binary fission happens when bacterial cells split in two: DNA replicates when DNA synthesis machinery separates the parental strands in the chromosomes while simultaneously synthesizing the new, growing strands. DNA replication is semi-conservative, in that each daughter cell gets one parental strand and one newly synthesized strand of DNA. A septum forms in the center of the cell (from both membranes) and eventually splits the cell into two equal daughter cells. -Endospore formation is a type of cell differentiation technique that allows bacteria to survive stressful conditions. DNA replicates, and a septum forms from the cytoplasmic membrane near one end of the cell. Once the endospore is formed inside the mother cell, the mother cell engulfs the endospore, effectively wrapping the spore in a second membrane. The mother cell's chromosomes disintegrate, the spore gets covered in proteins, organic acids, and calcium. Then, the mother cell releases the spore to the environment, where it can germinate when conditions are right.

Describe why anemia (low iron in blood) could help you stave off infections.

-In mammals, iron is tightly bound to proteins, leading to a very low concentration of free serum iron (10-24M). This is a challenging condition for microbes to be in, so many pathogens have evolved siderophores to capture these low concentrations of iron. -The consequence of microbes having a good iron-scavenging strategy is that when iron concentrations rise in the human body, microbial pathogens can capture that iron very quickly and use it to grow. -This idea was put forth by French physician, Trousseau, who in the late 1800s (1872) alerted his medical students in Paris in a seminal lecture series to the dangers of giving iron to infected patients. His evidence was that patients to whom iron was administered in their diet as a form of 'tonic' invariably had a poorer outcome than those patients who received no additional iron and were, in fact, somewhat anemic.

How do growth strategies in bacteria differ from that in algae and fungi?

-Like bacteria, both fungi and algae will reproduce by asexual haploid reproduction However, they also reproduce via sexual reproduction -In fungi, asexual sporulation involves formation of aerial mycelium and the differentiation of the hyphal tip. -Haploid basidiospores generate primary mycelium underground, where they form gametes. -Two mating cells from hyphae of different strains of fungi can mate by fusing together. -Gametes of opposite mating types fuse their cytoplasm only, forming secondary mycelium. -The parental nuclei remain separate throughout many generations of mitosis during development of the fruiting body (mushroom). -As the mushroom matures, the basidia undergo nuclear fusion and meiosis, forming progeny basidiospores.

Describe the 2 types of Transformation HGT

-Natural: free DNA floating around. bacteria may have DNA uptake proteins that will unravel the DNA and pull a single strand into the cell. if the DNA has any complimentary pairs, it will integrate by homologous recombination -Artificial: double strand of DNA forced through cytoplasmic membrane. integration of linear fragments by homologous recombination or replication of plasmid

What is the benefit of rooting the tree of life?

-One of the big questions about the Tree of Life is figuring out which of the three major domains diverged first. This matters because when people look at groups of organisms to study parallel functions, ideally you want to use more closely related organisms. -if we don't know which is more closely related then we don't know which model is best. To figure this out, we need to root the tree of life (i.e. find an outgroup for all lineages of organisms on Earth, or an organism with a sequence from outside modern day organisms on Earth). -an unrooted tree does not indicate which of the sequences diverged earliest from the common ancestor they all shared

Describe how scientists are genetically modifying microbes to treat disease, using PKU as an example.

-Phenylketonuria (PKU) is a genetic disease that is characterized by an inability to metabolize phenylalanine (Phe). -PKU is caused by a defect in the gene encoding phenylalanine hydroxylase (PAH). -In the absence of PAH, or its function, Phe accumulates in the blood and brain to levels that can result in neurological deficits and emotional and cognitive problems. -Synthetic biologist at M.I.T. selected a harmless strain of E. coli (Nissle) and inserted genes into the bacteria's DNA so that once they arrived in the gut, they could break down phenylalanine -pathway 1: convert Phe to trans-cinnimate (TCA) by adding a gene that imports Phe into the bacterial cell, as well as a gene that encodes phenylalanine ammonia lyase (PAL), which converts Phe to TCA -pathway 2: uses L-amino acid deaminase (LAAD), a membrane-associated enzyme that converts Phe to phenylpyruvate (PP).

What were the historical obstacles to assessing microbial diversity and how did using rRNA genes to measure diversity overcome them?

-Problem #1: vastly different kinds of microbes looked more or less alike. Linnaeus thought we would never be able to clearly distinguish one from another. -Problem #2: Microbes do not readily fit the classic definition of a species—that is, a group of organisms that interbreed. For example, bacteria usually breed asexually. What the scientific world really needed was a classification system based on some trait possessed by all living organisms. In the 1970s, a scientist named Carl Woese suggested that DNA sequences of certain common genes could be used to determine the relatedness of different organisms. He chose to use the gene that encoded an RNA molecule found in ribosomes. Ribosomes are the RNA/protein complexes on which proteins are synthesized and they are found in all prokaryotes and eukaryotes.

Transduction HGT

-Process mediated by viruses. -Involves accidental packaging of host DNA. -Estimated to occur in ~1% of new phage population. -Entry into chromosome via recombination.

What are the major metabolic/ecological factors that distinguish kingdoms of eukaryotic microbes?

-Protozoa graze on other life forms. Particularly in soils and aquatic systems, protozoa can be important regulators of bacterial populations. -Other protozoa are parasites and prey on much larger organisms. -Algae, by contrast, are photosynthesizers: they form the base of many aquatic food chains, particularly in marine ecosystems. -Fungi are decomposers, acting as key recyclers of dead biomass, particularly of plant parts that bacteria can't initially breakdown

Operational taxonomic unit (OTU)

-a group of organisms that have high sequence similarity of their ribosomal DNA sequences (e.g. 16S rDNA). -Very similar (often the same as) phylotype, although this term is typically used to refer to prokaryotes (rather than fungi).

Taxon

-a unique microorganism. -This can be a single microbial species or a single strain of a species.

Compare and contrast Sanger sequencing and Illumina sequencing. What are the pros and cons of each method? Pick a method that would you use to sequence the genome of the bacteria you isolated in lab and justify it.

-Sanger sequencing: sequences a single strand of DNA at a time. -It relies on dideoxnucleotides, which can form a phosphodiester bond to a growing strand of DNA, but lack the 3' OH acceptor for a new incoming nucleotide. No new phosphodiester bond is formed. Very small amounts of dideoxynucleotides are added to Sanger samples that are actively being synthesized. Every now and then, a dideoxynucleotide will be added to the growing DNA strand and terminate the reaction. Sanger sequencing can generate a couple thousand bases per run. -Illumina: the genome to be sequenced is sonically fragmented into 100-200 bp segments and different linker oligonucleotides are ligated to each end. Strands of each fragment are separated and the mixture added and fixed to an optical flowcell. -The flowcell also has a dense lawn of oligonucelotides that are complementary to the ends of the adapters on each sequence. The fragments bend over and attach to the oligos, which serve as primers for amplification. Once amplification is complete, the double-stranded bridge is denatured and both strands remain attached to the surface. -This repeats until 1000 identical copies of a gene fragment are generated = a cluster. Sequencing is then done in a series of single-step, reversible chain termination reactions. -A fluorescently labeled nucleotide is added one at a time to the clusters. After a base is added, a snapshot is taken of the plates, illustrating the colors. Next, the fluor is removed, which reverses the chain termination, and the slide is flooded again with tagged bases.

What are the major morphological factors that distinguish kingdoms of eukaryotic microbes?

-Single cells vs. multicellularity: both protozoa and algae normally grow as single-celled organisms. On the other hand, most fungi can form large multicellular branches called hyphae. Hyphae are produced in the same way, with new cells dividing by binary fission, but instead of separating they stay together as part of the growing hyphal structure. A mass of hyphae is called mycelia. -Some fungi grow as single cells - those are the yeasts and they reproduce by budding. Most fungi grow strictly as either mycelia or yeasts, but some can switch between the two and therefore called dimorphic. Fungi that cause serious human infections are usually dimorphic fungi, living in the mycelia form outside the body and switching the yeast form when they infect.

Why is the outer membrane of a Gram negative cell not strictly considered to be a phospholipid bilayer?

-The Gram negative outer membrane has an inward-facing leaflet that includes lipoproteins and an outward-facing leaflet that contains lipopolysaccharides. -Additionally, porins are embedded in the outer cell membrane. -this gives the outer membrane a structure that contrasts with the inner membrane which is composed of two leaflets of phospholipids.

Describe the role of actin-based motility, pili, and fimbriae in bacterial cell ecology.

-The bacteria invade the host cell and the actin filaments in the cell condense around one end. The real purpose of this actin-based mobility is to infect adjacent cells. Inside mammalian cells, the bacteria are protected from the immune system, so moving from cell to cell is a way to avoid attack by immune system. - pili. shorter straight projections from the cell surface. There are some even shorter and thinner projections called fimbriae that function the same as pili. The purpose of these two types of projections is to allow the bacterium to attach to surfaces. -Pili are typically used simply for adherence, but in some cases they can also aid in bacterial movement. Some bacteria have a type of movement called a twitching mobility, which is characterized by a series of rapid movements that look similar to twitching.

Describe the difference between bacterial run and tumble. What is the role of the flagellum, and how do the bacterium use run and tumble states to generate a random walk in liquid?

-The direction of rotation determines the nature of bacterial movement. -If it rotates one way, the bacteria move forward, in what is called a run. -If it rotates the other way, or individual flagella don't rotate in synchrony, then you get the bacteria moving in a tumbling motion. -by periodically reversing the direction of flagellar rotation, the bacterium follows what is known as a "random walk". This walk, however, allows the bacterium to move up a gradient of a desired nutrient

What is a plasmid and how is it unique from bacterial chromosomes? Describe an example of a plasmid that is beneficial to bacteria and one that is detrimental to bacteria.

-The primary importance of plasmids is that they are one of the main ways bacteria share genes. -Plasmids are also a major way that disease causing bacteria become resistant to an antibiotic. Rather than mutate, they can pick up the genes needed to resist antibiotics. -Plasmids are also the way that good bacteria can go bad, by picking up virulence genes that allow them to do damage, such as genes encoding toxins that aid in pathogenesis. -Plasmid addiction systems, on the other hand, are designed to kill cells that lose the plasmid. These types of plasmids produce a toxin protein and also produce an antidote protein. They ensure their survival because if one of the daughter cells in division doesn't receive the plasmid, it still gets some of the toxin and the antidote in the cytoplasm. The catch is that the antidote protein has a shorter life than the toxic protein, so the absence of the plasmid makes it so the antidote is not being produced. -This then kills the daughter cell if the plasmid making the antidote is not in it.

Describe how transition to an obligate mutualistic symbiont of humans (i.e. a human gut symbiont) could contribute to genome contraction or expansion in a bacterium.

-Transition to a mutualistic symbiont of the human gut could cause the bacterial genome to contract, if the bacterium provides something to the host in exchange for the host providing essential nutrients or biochemical machinery for the bacterium to survive. -When bacteria don't have to create all the machinery they need to live, they will likely lose those genes, as extra genes in the genome can be expensive for the cell to maintain

Given that stromalites seem like good fossil evidence - what else could you look for in the stromalites that would further corroborate the argument that they are products of biological activity? List at least two other pieces of chemical biosignature evidence you could collect.

-We could use isotopes as a measure to see if rocks have delta C that indicates isotopic fractionation of carbon due to biological activity. -We could also look for macromolecules produced exclusively by microbial life

Compare and contrast the conditions of early Earth, under which microbes evolved, and the conditions on Earth today.

-meteorite bombardment, periods of heavy volcanic activity, and periods when entire oceans went anoxic. -Some of the impacts were so big and powerful that they could vaporize oceans, creating clouds of steam that would have sterilized the Earth's surface. -strong UV radiation, because there was no ozone layer like we have today to filter out UV radiation. -There are also microbes that can survive in very cold environments, which may have been the dominant environmental condition before we gained an atmosphere to trap heat.

What was the "Golden age" of microbiology, and what was discovered then?

-occurred from the 1850s through the 1940s, when better microscopes and culturing techniques emerged. -These advances allowed scientists like Lister and Pasteur to develop the practice of antisepsis in hospitals, and the first vaccines. -Pasteur also discovered the products produced by fermentation (e.g. alcohol). -This continued through the 1940s with the production of antibiotics like penicillin. -The Golden Age gave rise to advances in molecular biology

Horizontal Gene Transfer and the 3 types

-prokaryotes can exchange segments of DNA with other prokaryotes (and eukaryotes). -Transformation: Uptake of free DNA from the environment. -Transduction: DNA transfer mediated by bacteriophages. -Conjugation: Direct cell-to-cell transfer of DNA.

Compare and contrast taxonomic diversity measures and phylogenetic diversity measures. What is the benefit of phylogenetic diversity over taxonomic diversity estimates?

-taxonomy-based metrics of diversity assume that there is no different evolutionary relationships between species - i.e., all species are equally related. -This may not be an appropriate assumption, because 1) we know that species are evolutionarily related and 2) closely related species may be more similar in their phenotypes than distantly related species. If this is the case, then taxonomic diversity will mean something very different than phylogenetic diversity for the diversity of microbial activities in a community.

What are some differences between viruses and other microbes?

-the major difference between viruses and other microbes is that viruses are more simple in nearly every way. Viruses basically consist of a genome and set of closely associated proteins that stabilize the genome and perform essential functions during replication. -A virus infects a cell by first attaching to the surface, then releases its genome into the cell's interior. The attachment of the virus to its target is highly specific and one that attacks cells of one bacterial species will not necessarily attack any others. The second step in the infection process is the takeover of the biosynthetic machinery of the infected cell by proteins from viral genes. The virus uses that machinery to make many copies of its genome and its proteins. Finally, the components assemble into intact viruses and they exit the infected cell.

Other factors that distinguish prokaryotes and eukaryotes

1) Morphological diversity: eukaryotes have generally higher morphological diversity (shapes and sizes) than prokaryotes 2) Average cell size: prokaryotes are generally 10x smaller in diameter and 1000x smaller in volume than eukaryotes 3) Reproduction by binary fission: prokaryotes reproduce by binary fission, as opposed to mitosis like most eukaryotes 4) Few chromosomes: eukaryotes generally have high numbers of chromosomes, while prokaryotes generally have only 1 or 2 5) Presence of internal organelles: prokaryotes generally lack major intracellular organelles that eukaryotes possess (although some eukaryotes lack intracellular organelles and some lack Golgi bodies)

What are the major metabolic factors that distinguish bacteria from archaea?

1) Temperature tolerance: While bacteria can withstand extremely high temperatures (up to 90oC), archaea can persist under even higher temperatures (up to 120oC). 2) Methane production: archaea are the only known methanogens 3) Complex carbon utilization: archaea seem to be limited to the use of simple molecules as sources of carbon and energy (glucose). 4) Pathogenesis: whereas bacteria cause many diseases of animals and plants, no disease-causing archaea have been identified.

What are major defining features of microorganisms?

1) very small (often too small to be seen with the naked eye), and/or 2) simple in morphological construction, lacking highly differentiated cells and distinct tissues 3) capable of rapid rates of evolution 4) metabolically diverse for their morphological simplicity 5) taxonomically diverse, compared to other domains and kingdoms of organisms

Which specific environmental conditions on early Earth allowed the first life forms to emerge (around 3.8 GYA)?

1. Earth's crust cooled: The earth had to cool down a bit before liquid water could form 2. Appearance of water 3. Volcanic activity: volcanic activity was higher during this period than it is today. volcanoes spew out lots of carbon dioxide, which is an important greenhouse gas. This helped keep the Earth's surface from freezing 4. Water vapor from volcanoes formed the first oceans. During this period, life really began to multiply and many new environments were colonized.

categorization of microbes

1.Energy Source: Phototroph or Chemotroph (energy from external molecules) 2.Electron Source: Lithotroph (inorganic molecules) or Organotroph (organic molecules) 3.Carbon Source: Autotroph (CO2) or Heterotroph (organic)

When did people learn that microorganisms could ferment foods?

10,000 B.C

Why was there a lag in the development of microbiology as a field of research between the middle ages (1700s) until the mid-1800s?

Antony von Luewenhoek refused to share the design of his microscope with anyone. As a consequence, it took another 200 years for someone to develop a microscope with similar magnifying strength (~300x).

Which groups of microbes can be pathogens?

Bacteria and the eukaryotes (mostly protozoa and fungi) can be pathogens, as well as viruses. There are no known archaeal pathogens.

How do prokaryotes and eukaryotes differ in their approximate average generation times and optimal growth temperatures?

Fungi and protists generally grow more slowly than prokaryotes, and at lower optimal temperatures

Describe how trophic categories are distributed across taxonomic lineages of microbes and morphological groups of microbes

Generally, trophic groups match up with taxonomic and morphological groups of microbes. The prokaryotes (bacteria and archaea) generally have more diversity of nutrition types (i.e. trophic groups) compared to the eukaryotes. For example, most fungi and protists are chemoorganoheterotrophs. There are some exceptions, however. Algae are photoorganoheterotrophs, like some bacteria, and bacterial pathogens can be chemoorganoheterotrophs as well.

When and where would it be beneficial to engage in mixotrophy?

Mixotrophy is energetically expensive - a lot of energy is needed to maintain all the proteins needed for many different trophic strategies. However, mixotrophy is a benefit in low nutrient, unpredictable environments -Mixotrophy is also a benefit if you are able to disperse to many different types of habitats and need to survive in those new habitats, which could be quite different.

What are the major factors that allow us to distinguish prokaryotes and eukaryotes?

Presence of a nuclear membrane: prokaryotes lack a nuclear membrane that encloses the organism's genome, whereas eukaryotes do possess a nuclear membrane

Name the two disaccharides that are the primary components of the bacterial cell wall

The Glycan part of the peptidoglycan cell wall is composed of alternating units of N-acetylglucosamine (NAM, GlcNAc) and N-acetylmuramic acid (NAG, MurNAc).

What are the major morphological groups of microbes?

The major morphological groups of microbes include the prokaryotes, eukaryotes, and viruses

What are the major taxonomic groups of microbes?

The major taxonomic groups of microbes include the bacteria, archaea, fungi, protists, algae, and viruses

If you found an old microbial specimen in a museum that was characterized as a chemolithoautotroph that lived on rusty water pipes underground, what sorts of materials would it likely use as a carbon source, energy source, and electron source?

This organism would likely use iron as an electron source (i.e. be iron-oxidizing), maybe other inorganic molecules found in water, like sulfate or nitrate, as well. Changes in the oxidation state of iron (i.e. redox chemistry) would be used as an energy source, and CO2 would be used as a carbon source.