Lectures 1-5

Question 1

What is EHEC and how does it differ from regular E. Coli

Answer 1

EHEC causes intestinal inflammation and diarrhea, whereas nonpathonogenic strands of E.Coli do not

Question 2

How do you neutralize the pathogenic character of EHEC (assume you have any technology at your disposal…)

Answer 2

Inactivating suspected genes associated with pathogenicity (Shiga)

Question 3

Shiga toxin

Answer 3

a gene that EHEC encodes for.

a bacterial toxin that inhibits protein synthesis (inhibiting this toxin reduces the bacterias ability to cause disease)

Question 4

E. Coli

Answer 4

Escherichia coli

a gram negative, motile, facultatively anaerobic bacterium

can turn into a pathogen by gaining toxin genes (weapon)

Question 5

Basic tenants of cell theory

Answer 5

1. All cells come from other cells
2. Cells are the fundamental units of organisms

Question 6

Koch’s postulates

Answer 6

1. The phenotype (sign or symptom of disease) should be associated only with pathogenic strains of a species
2. Inactivation of the suspected gene(s) associated with pathogenicity should result in a measurable loss of pathogenicity
3. Reversion of the inactive gene should restore the disease phenotype

Question 7

pure culture techniques

Answer 7

• built the field of microbiology
• disproved spontaneous generation
• identified many diseases

Question 8

Microbiome

Answer 8

a community of microorganisms that inhabit a particular environment

Question 9

how many prokaryotes in the ocean

Answer 9

1.4 x 10^29 prokaryotic cells in the ocean

Question 10

microbial ecology

Answer 10

environmental microbiology

Question 11

reductionist

Answer 11

analyzing and describing a complex phenomenon in terms of its simple or fundamental constituents.

-medical microbio often

Question 12

holistic

Answer 12

characterized by the belief that the parts of something are interconnected and can be explained only by reference to the whole

• microbial ecology more holistic

Question 13

trophic interactions

Answer 13

The transfer of energy from the bodies of individuals of one species to those of a different species

• soil food web

Question 14

succession ecology

Answer 14

the process by which the mix of species and habitat in an area changes over time.

Question 15

ecology : disturbance

Answer 15

a physical force, agent, or process, either abiotic or biotic, causing a perturbation or stress, to an ecological component or system, relative to a specified reference state and/or system.

Question 16

disturbance & succession

Answer 16

Many different kinds of disturbances, such as fire, flooding, windstorms, and human activities (e.g., logging of forests) can initiate secondary succession.

Question 17

denitrification by bacteria sent people into a panic because …

Answer 17

bad for agriculture - removes fertilizer

Question 18

chemosynthesis

Answer 18

the process by which organisms, like bacteria, produce organic compounds using chemical energy from inorganic molecules instead of sunlight, often in environments like deep-sea vents.

1891 winogradsky

Question 19

chemosynthesis-based ecosystems discovered in…

Answer 19

1977

Question 20

astrobiology

Answer 20

the study of the universe

Question 21

Microbes more critical in marine or land foodwebs?

Answer 21

marine

Question 22

Modern microbiology is the synthesis of these two historical roots…

Answer 22

agriculture (–> ecosystem –> microbial ecology)

and

medicine/ food industry (–> pure cultures –> medical/ industrial microbiology)

Question 23

biofilms

Answer 23

a complex community of microorganisms, such as bacteria, that adhere to a surface and are embedded in a protective extracellular matrix they produce. Biofilms can form on various surfaces, including medical devices and tissues, and are often resistant to antibiotics and immune responses.

• in human health context often one species… but biofilms can contain multiple

Question 24

significance of biofilms

Answer 24

protect cells from external stress

communicate and exchange dna within them

Question 25

cystic fibrosis

Answer 25

example of when body cannot remove biofilms efficiently an inherited disorder that causes severe damage to the lungs, digestive system and other organs in the body

Question 26

reynolds number

Answer 26

ratio between initial and viscous forces relates primarily to size low for small things, high for big things

Question 27

viscous forces

Answer 27

resist motion and arise from fluid friction dominate for microorganisms

Question 28

inertial forces

Answer 28

related to an object's mass and resistance to changes in motion. dominate for humans

Question 29

Why would chemical concentrations differ between the top and bottom of a biofilm?

Answer 29

Microbes at top have greater access to the nutrients and oxygen - biofilms have microscale chemical gradients

Question 30

virulence

Answer 30

a pathogen's or microorganism's ability to cause damage to a host.

Question 31

the part of the human body containing the most bacteria?

Answer 31

the gut

Question 32

obligate anaerobes

Answer 32

microbes who’s environment is very short of oxygen

Question 33

What would oxygen levels look like for microbes from the middle of the lumen to the epithelium?

Answer 33

Oxygen being received from red blood cells – most accessible on the outskirts of the gut Very minimal oxygen supply in the middle of the gut due to consumption

Question 34

how would the oxygen profile in microenvironments in marine sediment on a small scale change from day to night

Answer 34

oxygen levels typically increase during the day due to photosynthesis by microorganisms like algae, which produce oxygen. At night, when photosynthesis ceases, oxygen levels decrease as aerobic respiration continues, consuming oxygen

Question 35

sulfide levels...

Answer 35

The sulfide profile in marine sediments typically increases at night. During the day, oxygen levels are higher, allowing aerobic microorganisms to outcompete anaerobic, sulfate-reducing bacteria, which produce sulfide. At night, as oxygen decreases, sulfate-reducing bacteria become more active, leading to increased sulfide production. Therefore, sulfide levels tend to be lower during the day and higher at night.

Question 36

winogradsky column

Answer 36

a simple, self-contained microbial ecosystem used to study microbial diversity and nutrient cycling. It consists of layered sediments and organic matter in a sealed column, where different microorganisms grow in distinct zones based on their metabolic needs, such as oxygen, light, and sulfur gradients. It simulates natural microbial environments like sediments or wetlands.

Question 37

microenvironments as a unifying concept

Answer 37

shouldnt be sharp dividing lines between dif fields of microbio (medical, aquatic, terrestrial)

Question 38

Even in a single-species biofilm, chemical gradients exist across the µm scale. Why is this? What effects might this have on their growth, metabolism etc?

Answer 38

chemical gradients exist because the cells near the surface have better access to nutrients, oxygen, and other resources, while deeper layers experience limited availability These gradients can affect growth and metabolism by causing: Differential growth rates - or even entering dormant states metabolic specialisation - like becoming anaerobic survival strategies - stress responses like antiobiotic resistance

Question 39

biofilm relevance in chronic infections

Answer 39

Biofilms are involved in persistent infections, such as those on medical devices (e.g., catheters, prosthetic joints) and in conditions like cystic fibrosis. The protective matrix makes biofilm-associated bacteria more resistant to antibiotics and immune responses, making treatment difficult.

Question 40

antibiotic resistance - biofilms

Answer 40

Bacteria in biofilms can exchange genetic material, including antibiotic resistance genes, making infections harder to treat and leading to the spread of resistant strains.

Question 41

biofilms - wastewater treatment

Answer 41

Biofilms are used in biofilters and bioreactors to break down pollutants in wastewater, helping in the treatment of organic waste and improving water quality.

Question 42

biofilms - Nutrient Cycling

Answer 42

In ecosystems like soils and aquatic systems, biofilms contribute to nutrient cycling, especially nitrogen and sulfur cycling, supporting plant and microbial communities.

Question 43

Phylogenies of life

Answer 43

a diagram that depicts the lines of evolutionary descent of different species, organisms, or genes from a common ancestor

Question 44

Before microbiology how did we construct phylogenies of life

Answer 44

based on morphology, metabolism and other observable features

Question 45

ribosome

Answer 45

a cellular structure that synthesizes proteins by translating messenger RNA (mRNA) into amino acid sequences. It consists of RNA and proteins and is found in all living cells.

Question 46

rRNA

Answer 46

a type of RNA that forms the core structural and functional components of ribosomes. It helps catalyze protein synthesis by facilitating the binding of mRNA and tRNA during translation.

Question 47

shiga toxin targets...

Answer 47

eukaryotic ribosomes

Question 48

why is rRNA a good choice for phylogeny

Answer 48

conserved function : big role in protein synthesis which is an essential process in all living organisms highly conserved structure : highly conserved across different species - good for compare/ contrast universal distribution : rRNA genes present in all living organisms

Question 49

How did Woese et al profile rRNA, in general terms? Was this cultivation-dependent or cultivation-independent?

Answer 49

Woese et al. profiled rRNA by sequencing the 16S rRNA gene in prokaryotes to analyze evolutionary relationships. They compared rRNA sequences across different organisms to identify conserved and variable regions, leading to the discovery of the three domains of life (Bacteria, Archaea, Eukarya). This approach was cultivation-independent, as it allowed them to study microbes without needing to culture them in the lab.

Question 50

Why was the discovery of Archaea so significant? Why might they have been missed before? What are some examples of environments and processes that Archaea are involved in?

Answer 50

The discovery of Archaea was significant because it revealed a third domain of life. They were likely missed before due to their similarity to bacteria and difficulty to culture. Archaea thrive in extreme environments like hot springs, salt lakes, and anaerobic zones, playing key roles in processes like methane production.

Question 51

What is metabarcoding? What technologies does it use?

Answer 51

Metabarcoding is a technique used to identify and analyze biodiversity in environmental samples by sequencing specific genetic markers, usually from multiple species. It uses high-throughput sequencing technologies (like Illumina or Ion Torrent) and targets conserved regions such as the 16S rRNA gene for bacteria or ITS for fungi, allowing for rapid species identification without the need for cultivation.