Chapter 3

The physical-chemical environment of microbes

What are some important physical-chemical properties for microbes? (7)

• water

• temperature

• pH

• salt and osmotic balance

• oxygen and redox potential

• light

• pressure

What makes water an important property?

• all cells about 70% water

  • some can survive without water in resting stages

• water is good solvent due to its polarity, high dielectric constant, small size, and viscous liquid

Why is temperature one of the most important factors

changes in temp affect all chemical rxn rates

Can pro or eu-karyotes survive at higher temps

Prokaryotes (~121°C); eukaryotes only about 65°C

Why is pH an important factor

affects chemical state of key elements and adsorption of key nutrients to solid surfaces

• ex) ammonia vs ammonium (ammonia more common in high pH environments because there are no extra H+ ions to bind to ammonia to create ammonium)

Why is salt and osmotic balance important

• higher salinity lowers external water activity, so cells must raise ion conc. inside cell to retain water

Give pros/cons of inorganic vs organic solutes and state which is more common

inorganic:

• pro: energetically cheaper

• con: cell must have enzymes and proteins adapted to high salinity

Organic:

• pro: enzymes and proteins don’t need to be adapted

• con: energetically expensive to make

• more common

Gaining e- is (positive/negative) redox potential. Losing e- is (positive/negative) redox potential

1. positive

2. negative

Oxygen is a strong _____. So oxic environments have ____ redox potential and anoxic environments have ____ potential

1. oxidant

2. positive

3. negative

Oxidized compounds (like O) are common in _____ environments

oxidizing

Describe how light is important but also damaging

• light provides source of energy for auto and mixotrophs

• can cause damage to intracellular macromolecule

  • light can impact cross-linking of DNA and create oxidative species that oxidize DNA and other macromolecules

How do cells protect themselves from light damage

• “sunscreen” pigments that absorb light energy and minimize damage

• enzymes that repair UV-damaged DNA and disarm reactive oxygen species (these are not present in anaerobic organisms in anoxic environments)

What is interesting about microbes adaptations at varying pressures

• microbes adapted to both extreme high and low pressures have similar adaptations for survival

Pressure (raises/lowers) activity of microbes typically found at atmospheric pressures

lowers

What does the Reynolds number show? What kind of Reynolds number does the microbial world, and what are the consequences?

• Reynolds number is ratio of inertial forces to viscous forces

• microbial world has very low Reynolds number

  • microbial world is dominated by viscous forces

How are molecules mixed in low Reynolds environments

by diffusion (rather than turbulence)

How does diffusion vary?

• varies with phase, temp, and chemical properties

• small, uncharged molecules diffuse faster

• in gases, diffusion increase with temp and decreases with pressure

Why is diffusion important for microbes?

Sets an upper limit for how fast a compound can be taken up by a microbe

What is a consequence of low conc of microbes in aquatic environments

many microbes don’t have mechanisms to detect one another

How do some microbes find prey/nutrients

• motility via flagella, cilia, polymer secretion

  • movement also breaks down limits for diffusion

• some microbes show chemotaxis: movement up conc. gradients

Are microbes, nutrients, and other particles evenly disbursed in aquatic environments?

NO!

What makes up a biofilm?

• many microbe species

• extracellular polymer secretion (usually polysaccharides)

What is the purpose of extracellular polymer secretion?

• anchor cells

• store carbon

• prevent predation

• fend off competition

• contain extracellular enzymes

How do biofilms create uniques niches?

low oxygen within biofilms allows for anoxic niches and anaerobic microbes to occur in an otherwise oxic environment

Which one of the physical parameters listed is generally NOT a factor when considering the success of different groups of microplankton in surface waters (0 – 5 meters)?

A. pH

B. pressure

C. temperature

D. salinity

E. light

B. pressure

Which seawater parameter has a direct affect on the bioavailability of important biogenic elements such as iron (Fe)?

pH

iron solubility varies with pH

What is the name of a group of pigments, sometimes that are just used as a “sunscreen” (for absorbing light and preventing damage). Sometimes they are also used as an accessory pigment for photosynthesis.

carotenoids

All pigments absorb all wavelengths of light equally. T/F?

False

With increasing depth, all wavelengths of light are absorbed equally. T/F?

False

Why are genes for pigment-producing enzymes conserved?

Organism needs pigments to survive. If genes to make the enzymes are not conserved, the organism dies.

What are the primary pigments in cyanobacteria?

Phycocyanin and phycoerythrin

Why are cyanobacteria as a group bigger (size) than the rest of the bacteria?

Because photoautotrophy and survival in the euphotic zone requires many additional genes involved in light sensing and absorption, their genomes are larger

Why are some types of bacteria psychrophiles, and others are hyperthermophiles?

• Extemeophiles have genes that code for protein with more stable folding and so the proteins can withstand higher temperatures without denaturing

• folding is a result of specific sequences of amino acids

Despite the wide diversity of microbial metabolisms, no hyperthermophilic microbes (>80 °C) are known to be photoautotrophic. Why?

• in specific euphotic environments: Photosynthetic pigments in reaction center protein complexes are structurally unstable at high temperatures, preventing efficient light harvesting and electron transfer.

• in specific deep-sea environments: Light cannot penetrate to depths of deep-sea hydrothermal vents, so there is no selective pressure for photosynthesis

What does this figure show?

There is a difference in the effect of temperature on bulk heterotrophic processes compared to the effect of temperature on bulk photoautotrophic processes.

Why is small cell size advantageous?

• more surface area:volume

• more nutrient uptake

• less predation

• better swimming speed and diffusion time

Who would thrive in the deep ocean?

A. Thermophile

B. Piezophile

C. Halophile

D. Alkaliphile

E. Acidophile

B. Piezophile