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Microbial physiology and cell biology

1. What do the four canonical complexes of the aerobic respiratory chain look like, what are their electron donor and acceptor, their cofactors, their contributions to the proton motive force, their number of subunits?
2. How does fermentative metabolism work? What is meant by substrate phosphorylation?
3. What are the roles of the TCA cycle in metabolism?
4. What are the roles of glycolysis in metabolism?
5. What are four examples of pathways used for carbon fixation? How does isotope fractionation work, during carbon fixation?   
6. What is the proton motive force? Of which two components is it made up? What is a typical range for the membrane potential? What is it used for?
7. What do we mean with energy conservation in cells? What mechanisms do cells use to conserve energy?
8. What are typical storage materials turned over by cells?
9. How do Bacteria, Archaea and Eukarya differ from each other?
10. What does the cell envelope look like for bacteria, archaea and eukaryotes? What is peptidoglycan? How many membranes? What is the function of the membranes?
11. What are the main classes of macromolecules that make up cells? How much is present of each type?
12. What is meant by the redox tower/ladder? How does it work?
13. How does denitrification work? Which enzymes are involved? Give a few examples of organisms that perform that pathway. Where does it sit in the redox tower?
14. How does dissimilatory nitrate reduction to ammonia work? Which enzymes are involved? Give a few examples of organisms that perform that pathway. Where does it sit in the redox tower?
15. How does anammox work? Which enzymes are involved? Give a few examples of organisms that perform that pathway. Where does it sit in the redox tower?
16. How does nitrification work? Which enzymes are involved? Give a few examples of organisms that perform that pathway. Where does it sit in the redox tower?
17. How does nitrification work? Which enzymes are involved? Give a few examples of organisms that perform that pathway. Where does it sit in the redox tower?
18. How does sulfate reduction work? Which enzymes are involved? Give a few examples of organisms that perform that pathway. Where does it sit in the redox tower?
19. How does sulfide and sulfur oxidation work? Which enzymes are involved? Give a few examples of organisms that perform that pathway. Where does it sit in the redox tower?
20. How do iron and manganese reduction work? Which enzymes are involved? Give a few examples of organisms that perform that pathway. Where does it sit in the redox tower?
21. How do iron and manganese oxidation work? Which enzymes are involved? Give a few examples of organisms that perform that pathway. Where does it sit in the redox tower?
22. How does aerobic methane oxidation work? Which enzymes are involved? Give a few examples of organisms that perform that pathway. Where does it sit in the redox tower?
23. How does methanogenesis work? Which enzymes are involved? Give a few examples of organisms that perform that pathway. Where does it sit in the redox tower?
24. How does reverse methanogenesis work? Which enzymes are involved? Give a few examples of organisms that perform that pathway. Where does it sit in the redox tower?
25. How does anoxygenic photosynthesis work? Which enzymes are involved? Give a few examples of organisms that perform that pathway. Where does it sit in the redox tower?
26. How does oxygenic photosynthesis work? Which enzymes are involved? Give a few examples of organisms that perform that pathway. Where does it sit in the redox tower?
27. What do ribosomes look like? What are their subunits? How do they work?
28. How do microbes cope with higher and lower temperatures? Give examples of adaptations.
29. How do microbes cope with low and high pH? Give examples of adaptations.
30. How do microbes cope with low and high salt strength/water activity? Give examples of adaptations.
31. What is meant by protein translocation? How does it work in Bacteria? Which molecular machines are involved? What about Eukaryotes?
32. What is meant by protein export? How does it work in Bacteria? What molecular machines are involved? What is the signal recognition particle?
33. What are outer membrane porins? What do they do?
34. How do prokaryotes move? What molecular machines are involved?
35. What are biofilms? What does extracellular polymeric substance consist of?
36. What is generation time? How does it relate to growth rate? What are typical generation times in the lab, the environment?
37. What is biomass yield? Give a few examples of biomass yields of aerobic and anaerobic bacteria in (C-mol/C-mol)?
38. How big is a bacterium? What are its dimensions? What is the volume of a bacterial cell? What is its mass? How much of its total mass is water? What are examples of very small and very large bacteria?
39. What are spores? How does sporulation work?
40. What is the efficiency of aerobic respiration? Where does the unused energy go?
41. What is the efficiency of oxygenic photosynthesis? Where does the unused energy go?
42. How do viruses work? What types of viruses do we know?
43. What nutrients do microbes need to grow?
44. How does transport of nutrients and substrates into the cell work? Give examples of different transport mechanisms.
45. How do microbes sense and respond to their environment?
46. What are Monod kinetics? What are Michaelis Menten kinetics? What is substrate affinity? What is the affinity constant? What aspects contribute to good substrate affinity?
47. What is maintenance energy? Which processes contribute to maintenance or homeostasis?
48. What is meant by K-strategy and R-strategy in microbiology?
49. How does cell division work for Bacteria, Archaea?
50. How do prokaryotes die?
51. How do cells protect themselves against oxygen?
52. Which enzymes use iron as a cofactor?
53. Which enzymes use molybdenum as a cofactor?
54. Which enzymes use copper as a cofactor?
55. Which enzymes use cobalt as a cofactor?
56. Which enzymes use calcium as a cofactor?
57. Which enzymes use selenium as a cofactor?
58. Which enzymes use manganese as a cofactor?
59. Which enzymes use tungsten as a cofactor?
60. What is the role of magnesium in the cell?
61. Why does life use only so few of the elements in the periodic system?
62. What is meant by “specificity” in biology?
63. How do chaperones work? What are examples of chaperones?
64. What is meant by “secondary metabolites”? What are examples?
65. What is life? What is cellular life?

Microbial ecology of the natural and engineered environment

1. What is symbiosis? What is syntrophy?
2. When two microbes exchange acetate, what type of metabolisms could they perform?
3. When two microbes exchange a vitamin, what benefits would that “division of labor” or specialization bring them?
4. When denitrification is performed by multiple microbes, what benefits would that arrangement bring them, compared to a single microbe performing the entire process?
5. Why is methane oxidation to CO2 or ammonium oxidation to nitrite never split over multiple microbes? 
6. What forms of symbiosis relate to iron acquisition?
7. How does the oceanic carbon pump work?
8. How do oceanic oxygen minimum zones work?
9. What are examples of microbes abundant/well known of the ocean?
10. What are examples of microbes abundant/well known of soil?
11. What are examples of microbes abundant/well known of freshwater environments?
12. What are examples of microbes abundant/well known of human microbiomes?
13. What are examples of microbes abundant/well known for their use in food/beverage production?
14. What are examples of well known viruses and phages?
15. What are examples of microbes abundant/well known for their role in causing disease?
16. How do hydrothermal vents work, what are examples of organisms which occur there?
17. How does the greenhouse effect work? What are examples of greenhouse gases?
18. What are the residence times of typical greenhouse gases in the atmosphere?
19. How do the C fluxes of photosynthesis on land/oceans, respiration on land/oceans and fossil fuel burning compare?
20. How do the N fluxes of natural nitrogen fixation, fertilizer production and ammonia deposition from fossil fuel burning compare?
21. What are the most important reservoirs/pools of the element carbon on Earth?
22. What is the “slow” carbon cycle? How does its rate compare to the “fast” carbon cycle?
23. What happened during the great oxidation event? When did it occur? What were the consequences? How do we know that?
24. How old is the Earth? When did life evolve?
25. What is meant by Snowball Earth?
26. What happened to the CO2 concentration in the atmosphere over geological time? How do we know that? What happened to the amount of incoming radiation from the sun?
27. What is the current CO2 concentration in the atmosphere? How does it relate to concentrations during the Pleistocene? Eocene?
28. What are examples of periods of extreme climate change during Earth’s geological past?
29. What are examples of geological epochs/periods?
30. When did eukaryotes originate? When did multicellular life forms first appear?
31. When did bacteria/archaea originate?
32. What is meant by sulfidic and ferruginous oceans in the context of the precambrian?
33. Did photosynthesis come first? Or respiration?
34. How does a wastewater treatment plant work?
35. What is biogas? How is it produced from sewage? What other waste streams are used for biogas production?  
36. Which foods and beverages are made using microbes? How?
37. What is stratification (in lakes)? Why does it occur?
38. What is a soda lake? How does it form? What is the required quantitative relationship between calcium/magnesium and alkalinity in the end member (source water)?
39. What is a population? What is a population bottleneck? How does a population relate to a species?
40. How many microbial species exist on Earth? How does that number relate to species of plants and insects?
41. How is the Earth’s microbial biomass distributed over the Earth’s compartments (such as deep subsurface, oceans, marine sediments, soil)? How does total microbial biomass compare to animal and plant biomass? 
42. What is meant by productivity of an ecosystem? What is the difference between net and gross productivity?
43. What do we mean by ecological diversity? What are well known metrics/measures of diversity?
44. What is meant by resilience and robustness in ecology?
45. Is there a relationship between diversity and productivity? Is there a relationship between resilience or robustness and diversity?
46. What is an ecological niche?
47. Which ecological niche and cellular process sets eukaryotes apart from bacteria?
48. What do we mean by niche and neutral theory in ecology? What are strong and weak aspects of either?
49. What are rank/abundance curves? What are collector’s curves?
50. How does microbial ecology differ from macro-ecology?
51. What is meant by microbial/cellular individuality?
52. Why have many microbes never been cultivated in the lab? What does viable but not cultivable mean?
53. What are three different mechanisms, microbes use to sense and respond to changes in their environment?
54. How does quorum sensing work? What are examples of responses regulated by quorum sensing?
55. What is ecology? What is an ecosystem? What is a habitat?
56. In microbial ecology, what is alpha diversity? Beta diversity?
57. What is meant by “panspermia”?

Microbial genomes and evolution

1. What are examples of theories about the origin of life on Earth?
2. How does evolution work?
3. Why is the species concept problematic in microbiology? How does the microbiology species definition differ from the definition in macro-ecology?
4. What is meant by reductive evolution? What are examples of microbes undergoing reductive evolution?
5. What is horizontal, or lateral, gene transfer? What is vertical gene transfer? What are mechanisms of horizontal gene transfer? What fraction of genes in a bacterial genome originate from other species?
6. What do we mean with homologous genes? Orthologues? Paralogues?
7. How does convergent evolution work? What is an example of convergent evolution in microbial ecology?
8. What is phylogeny? What is a phylogram? What is an outgroup? What is the relationship of phylogenetic analysis and visualizations to actual evolution?
9. What is meant by parsimony in the context of evolution?
10. What is meant by the molecular clock concept? How can it be used to date evolutionary events like the evolution of photosynthesis?
11. What is the size range of bacterial genomes in nucleotides? How many genes? What about eukaryotes?
12. What is the structure of DNA? RNA?
13. What are examples of structural and catalytic RNA molecules/genes? What is the importance of these features to eukaryotes and prokaryotes?
14. What are exons and introns? What is the importance of these features to eukaryotes and prokaryotes?
15. What are operons? What is the importance of these features to eukaryotes and prokaryotes?
16. What are histones? What is the importance of these features to eukaryotes and prokaryotes?
17. How do restriction enzymes work and what is their function?
18. How does CRISPR-Cas work and what is their function?
19. What are examples of proteins that interact with DNA?
20. What are examples of mobile genetic elements? What is meant by genomic islands?
21. What fraction of the mass of a bacterial cell is DNA?
22. What is a nucleoid? What is meant by polyploidy?
23. What is meant by GC skew?
24. What is meant by subsystems? What are examples of subsystems? Can you  estimate what fraction of a bacterial genome is dedicated to examples of subsystems?
25. How can new biochemical functions evolve?
26. What are theories that explain the origin of Bacteria, Archaea and Eukaryotes? What is the endosymbiosis theory?
27. What is the range for error rates of bacterial DNA replication? What are examples of proofreading and repair systems?
28. What are well known sources of damage to DNA? How does a bacterium like Deinococcus radiodurans preserve its genetic information?
29. How long does DNA preserve in geological settings? How does that compare to protein?
30. How does the fossil record contribute to the microbiology understanding of evolution?
31. What are biomarkers? How do these contribute to the microbiology understanding of evolution?
32. What are examples of phyla, the major radiations of Archaea, Bacteria and Eukaryotes? What kind of differences have been described that set phyla apart?
33. What are examples of metabolisms or other traits that only occur in very few phyla? What are examples of metabolisms or other traits that are widespread?
34. What is the central dogma and which key “molecular machines” are involved?
35. What is the genetic code? How does it work? Is it preserved across life? Why would that be? Give a few exceptions? Is it optimized? If so, to do what?
36. What is microdiversity or strain heterogeneity? What is its ecological importance?
37. What is single nucleotide polymorphism?
38. What is genome synteny?

Physics and chemistry of the microbial environment

1. How do pH buffers work? How is the pK value related to the K value of the equilibrium? What is a weak acid? What is a strong base? What are examples of acids and bases?
2. How is the carbonate buffer in the ocean important to climate change?
3. What is a solubility product?
4. Which are examples of elements or ions that are poorly soluble under most conditions?
5. What is the partial pressure of a gas? What is the composition of air?
6. How can you calculate the solubility of a gas using the Henry coefficient? Does solubility of gases increase or decrease with temperature?
7. What are examples of gases that are very or poorly soluble in water?
8. What is the solubility of oxygen in water in equilibrium with air?
9. What is the air pressure at sea level, in Calgary?
10. What is the ideal gas law? How can you use it to interconvert moles and partial pressures?
11. What are isotopes? What are stable isotopes? What are examples of isotopes of C, N, O, H? What is delta-notation for isotopic composition?
12. What is a typical elemental composition of bacterial biomass (C_uH_vO_wN_xP_yS_z)?
13. What is mass transport? Diffusion? Convection? What is a diffusion coefficient? What is a simple equation that describes mass transport? How does isotope fractionation work during diffusion?
14. How much water can air contain before it saturates with moisture? How does temperature influence that amount? What does relative humidity mean?
15. What is porosity?
16. What is viscosity? How is viscosity different at the scale of a bacterium?
17. A bacterium produces 150 ml of gas in a lab in Calgary - how much gas did it produce in moles?
18. An aerobic bacterium grows in static liquid medium with glucose - how much glucose (mol/L) can it oxidize before it depletes the oxygen in the medium?
19. A researcher takes a 1 ml medium sample into a syringe from a vessel using 30 cm of tubing - what can go wrong?
20. How does the carbon concentrating mechanism work in autotrophic bacteria?
21. What is energy?
22. What is the first law of thermodynamics? What are the consequences for cells?
23. What is the second law of thermodynamics? What are the consequences for cells?
24. What is meant by “activation energy”?

Laboratory methods

1. How does chromatography work? What is gas chromatography? What is liquid chromatography?What is it used for?
2. How does a mass spectrometer work? What is a quadrupole? What is isotope ratio mass spectrometry? What is it used for?
3. How does spectroscopy work? What is it used for? What is De Beer’s law? What is a spectrum? What is the difference between absorption and optical density?
4. How does PCR work?  What is it used for? How does Real Time PCR work?
5. How does DNA extraction work? How does RNA extraction work?
6. How does protein extraction work?
7. How does lipid extraction work?
8. What are different ways of disrupting cells?
9. How does DNA sequencing work? With Illumina machines? With nanopore machines?
10. How does amplicon sequencing work?
11. How does proteomics work? With Orbitrap MS? With TOF instruments? What are the error rates of these sequencers?
12. How does phase contrast microscopy work? Differential Interference Contrast? What are typical magnifications?
13. How does fluorescence microscopy work?
14. How does Fluorescence In Situ Hybridization (FISH) work?
15. What is FISH-micro-auto-radiography (FISH-MAR)?
16. How does nanoSIMS work? What is it used for?
17. What are in situ incubations? What are they used for?
18. How does stable isotope probing work?
19. What is density gradient centrifugation? What is it used for? 
20. How are bacteria typically isolated in pure culture? Pros and cons? Challenges?
21. How does membrane filtration of bacteria work? What is it used for?
22. What approaches are used to determine abundance of microbial cells?
23. What is meant by the great plate count anomaly?
24. What is a growth curve? What phases of the growth curve do we distinguish?
25. How does a chemostat work?
26. What components are present in a growth medium designed to grow Bacteria or Archaea?
27. How do you work with microbes that are sensitive to oxygen? What are typical approaches and machines used?
28. How does aseptic technique work?
29. How does an autoclave work? What is it used for?
30. What would an experiment look like that shows that a particular microbe, in pure culture, assimilates a certain substrate?  What if you want to show it produces a certain product? What if you want to show it turns over a certain intermediate? 
31. What would an experiment look like that shows that a particular microbe, part of a microbial community that grows in the lab, assimilates a certain substrate? What if you want to show it produces a certain product? What if you want to show it turns over a certain intermediate?
32. What would an experiment look like that shows that a particular microbe, in its natural environment, assimilates a certain substrate? What if you want to show it produces a certain product? What if you want to show it turns over a certain intermediate?
33. How does electron microscopy work? What is it used for? Negative staining? Scanning electron microscopy? Thin sections? Tomography? Cryo-electron microscopy?
34. What are protein crystal structures? Why are they important?
35. How does sediment coring work? Why is it important, what is it used for?
36. How does a pH sensor work?
37. How does an oxygen sensor work?
38. How do you calculate “x g” (“times gravity”) for a centrifugation step?
39. How is alkalinity determined?
40. What are ways to measure concentrations of dissolved ions such as sodium, chloride, etc.
41. How can the elemental composition of minerals and solids be measured?
42. How is isotopic composition measured? 
43. What is meant by sensitivity, accuracy, precision of a method?
44. How does Electrical Resistivity Tomography (ERT) work?
45. How does GPS work?
46. What is milliQ water? Demineralized water? Ultrapure water? What are some considerations for choosing which water to use for experiments?
47. How do you calculate standard deviation? What is meant by standard deviation? How do statistical tests work? What kind of factors determine what test to use? Why does the study design affect the tests? What is meant by a P value? Why is the P value sometimes controversial?
48. How does a hypothesis work? Why is it important to have a hypothesis before performing the experiment?
49. How does a laboratory journal work?
50. How often do you need to replicate an experiment?

6. Computational methods

1. How does BLAST work? What is it used for?
2. How do Hidden Markov Models work? What are they used for?
3. How does mapping of reads work? What is it used for? How do you set the threshold (minimum % identity) right? What parameters determine the speed of the mapping program? 
4. What happens during the read quality control process?
5. What is multiple sequence alignment? What is it used for?
6. What are phylogenetic trees or phylograms? What are they used for? What is bootstrapping? What do bootstrap values mean in phylogenetic trees? What are common methods in phylogeny? What is an outgroup? Why does treeing not always work well? 
7. How does assembly of short reads work? Why does assembly not always work well?
8. How does assembly of long reads work? How can we detect assembly artifacts/errors?
9. How does binning work? What is it used for? Why does binning not always work well?
10. How do we estimate the quality of a whole genome sequence or metagenome assembled genome? How do we detect binning artifacts/errors?
11. What is meant by open reading frames? How does prediction of open reading frames work?
12. How does gene annotation work?
13. How does classification work?
14. How can we predict that a given protein is a membrane protein?
15. How can we predict that a given protein is exported to the outside of the cell?
16. How can we predict that a bacterium performs a specific function? For example, fermentation of polysaccharides to acetate, antagonism to another bacterium? Metabolic dependency on other bacteria? How can these predictions go wrong?
17. How does normalization work? When we normalize relative sequence abundances, for example of genes or genomes, what do we normalize to? 
18. What are examples of use of machine learning approaches in bioinformatics? 
19. What is comparative genomics? How is orthology among genes determined? How can we detect lateral gene transfer?
20. How do we determine the “start” of a circular genome?
21. How can we estimate the growth rate of a bacterium from genomic data?
22. What are examples of databases used in microbial ecology?
23. What steps are used to process amplicon sequencing data into amplicon sequence variants?
24. What is an NMDS plot?
25. What steps are used to process transcriptomic data? 
26. What steps are used to process proteomics data?
27. Which coding languages are typically used in bioinformatics? What are the characteristics and differences in performance?
28. What is a scheduler? What is cloud computing? What type of compute is best for different stages or scope of a bioinformatics project?
29. What aspects of a server (processor, RAM, hard disk space, I/O speed of the hard disk) are important to the following operations: read quality control, mapping, assembly, blast.
30. What is a pipeline in bioinformatics?
31. What are common file formats in bioinformatics? What do they look like?
32. What are examples of data archives/repositories used in microbial ecology? How do you deposit your data in those repositories?
33. How does github work?
34. What is meant by the reproducibility crisis?
35. What are examples of ways to document/record your bioinformatics work?
36. What do the following commands do on linux/unix? cd, ls, rm, cp, mv, more, nano, top, tail, df, du, free, lsblk,  ssh, scp, chmod, grep, wget, make
37. How do you decide how much sequencing is needed to realize a given aim? For example, if I would like to obtain a metagenome assembled genome of a bacterium at 1% abundance in a particular habitat, using Illumina sequencing? How can the sequencing be tuned to improve the quality and chances of success?

The Microbial Ecology and Biogeoscience Field

1. What are the names and topics of ten principal investigators in microbial ecology/environmental microbiology/biogeoscience in Canada?
2. What are the names and topics of ten principal investigators in microbial ecology/environmental microbiology/biogeoscience in the World that inspire you?
3. What are the names and topics of ten journals relevant to our field you would like to publish in?
4. What are the names and topics of five national or international conferences you would like to present at/attend?
5. What are five current lines of inquiry that microbial ecologists are excited about, based on your reading of the recent literature? Which ones inspire you most?
6. What are three papers published last year that inspired you the most?
7. Where will the field be in five years?