Introduction to Environmental Microbiology Flashcards
Anthropogenic environments?
Bioreactors, water treatment plants, waste ponds, houses…
Explain how typhoid fever and cholers led to microbiology.
At turn of 20th century the incidence of typhoid fever and
cholera were high
• tools were needed to protect public health
• disinfection and filtrations systems were develope
Old school microbiology? New?
Water Food Pollution safety safety and
bioremediation
The study of microbial fate and activity within all habitiats and the resulting impact on human health and welfare
Whats biogeochemistry?
The study of biological controls on the chemistry of the environment and geochemical regulation of ecological structure and function.
How is biogeochemist important?
Microbes play critical roles in energy transformations and biogeochemical
processes that result in the recycling of elements to living systems
What are 5 traits that make MO’s particularly good geochemical agents? Explain why for each.
- Rapid growth and cell division
• many individuals on which natural selection can act; take advantage of environments - Metabolic diversity- able to do many things
- Infallible
• have ability to go dormant in env where they won’t grow well - ubiquitous
• wide range of tolerance to various environmental conditions - Alter environment as a byproduct of metabolic activity
• O2 rich atmosphere a direct result of microbial metabolic activity
What were the first organism to perform metabolism? Seconds?
-Obligate heterotrophs – small organic molecules (CH3COOH) converted to CO2 and CH4
-S-based photosynthesis…
CO2 + 2H2S → CH2O + 2S +H2O
sunlight
- O2- producing photosynthesis… sunlight
CO2 + H2O → CH2O + O2
Whats the 1’ objective for MOs?
Survival, maintenance, generation of ATP, and sporadic growth - DIVIDE
3 microbe evolutions that changed atm?
methane spewing bacteria, O2 evolving microbes, N2 fixing microbes, and decomposition
What was the great dying?
90% of species on earth died from volcanos and methane spewing bacteria.
What was the single most significant effect of life on Earth’s geochemistry
Formation of O2 rich atmosphere
What was the great oxidation event?
-Was the biologically induced appearance of dioxygen (O2) in Earth’s atmosphere
GOE
Stage 1 of the GOE
- reducing atmosphere
- no production of O2
- prior to GOE- reducing env- mainly methane and H2
Stage 2 of the GOE
- Production of O2 by cyanobacteria
- absorption in oceans and seabed rock
- O2 oxidized iron to iron oxide in oceans and seabeds (absorbed)
- All O2 that cyano producing oxidized iron and turned into rust
Stage 3 of the GOE
- Outgassing of O2 from oceans -Absorption in lithosphere (earths crust)
- Eventually sink (amount of iron to be oxidized depleted)
Stage 4 and 5 of the GOE
-Oxidation of methane to CO2 and water= sink
-Evolution of new aerobic life forms
-Oxidative processes in all geospheres
End- Large O2 accumulation
-Once O2 was in a steady state- new aerobic life forms
-O2 source was > sinks
-Now- Source= sinks
Why did it take so long for o2 to build up in the GOE?
-Rate of O2 generation must be more than that of injection
of reduced gases by volcanoes
-Material on seafloor removes O2 from water and atmosphere, but if it is buried, it is not decomposed- O2 can’t be accessed
- Sudden buildup in burial rates allowed O2 to accumulate in atmosphere
How did nitrate help O2?
Resulted in rapid proliferation of O2- greater source
Whats the nickel famine?
- Methanogens need a lot of nickel
- 2.7 bill years old- reduced nickel
- methanogens decreases-sink decreases= O2 buildup
How was the P reserve changes? When?
So phytoplankton could use more
During the GOE
What did the presence of O2 allow for? How is the energy obtained?
- The development variety of other metabolic pathways
- Metabolic energy is obtained from flow of electrons between oxidized or reduced states
Whats oxidization? Reduction?
Oxidation- Gain H, Lose electrons,
Reduction- Lose H, gain electrons
What are three potential fates resulting from interactions with environment?
Examples?
- ecological success- ATP generation, nutrient uptake, growth, motility, photosynthesis
- ecological failure- Dormancy, sporulation
- survival/maintenance- Starvation, death, autolysis, oxidative stress, competition, predation, parasitism
What are 2 ways diversity of microbial species in an ecosystem is expressed? (2 mechanisms of looking at whats in an environment) What are these a function of?
- Species richness: the total number of different species present
- Species abundance: the proportion of each species in an ecosystem
- A function of the kinds and amounts of nutrients available in a given habitat
Whats the 1st community in a body of water?
- Community 1
Photic zone:
Oxygenic phototrophs
6CO2 6H2O C6H12O6 6 O
Whats the 2nd community in a body of water?
2. Community 2 Oxic zone: Aerobes and facultative aerobes C6H12O6 6 O2 6 CO2 6 H2O2
Whats the 3rd community in a body of water? (4 guilds)
Community 3 Anoxic sediments:
1. Guild 1: denitrifying bacteria (NO3 N2)
ferric iron-reducing bacteria (Fe3 2. Guild 2: sulfate-reducing bacteria (SO42
sulfur-reducing bacteria (S0
3. Guild 3: fermentative bacteria
4. Guild 4: methanogens (CO2 CH4) acetogens (CO2 acetate)
Fe2) H2S)
H2S)
Define: Ecosystem
• Habitat
• Guilds
• Niche
- Ecosystem: The sum total of all organisms and abiotic factors in a particular environment
- Habitat: Portion of an ecosystem where a community could reside
- Guilds: Metabolically related microbial populations
- Sets of guilds form microbial communities that interact with macroorganisms and abiotic factors in the ecosystem - Niche: Habitat shared by a guild
- Supplies nutrients as well as conditions for growth
Whats a microenvironment?
Immediate environmental surroundings of a microbial cell or group of
cells
What 4 things affect MO growth?
- Physiochemical conditions in a microenvironment are subject to rapid change, both spatially and temporally
- Resources in natural environments are highly variable and many microbes in nature face a feast-or-famine existence
- Growth rates of microbes in nature are usually well below maximum growth rates defined in the laboratory
- Competition and cooperation occur between microbes in natural systems
Whats a chemolithotroph? Chemoorganoheterotroph? Photoautotroph?
- Chemolithotroph-using inorganic chemicals for energy
- Chemoorganoheterotroph- using organic chemicals for energy
- Photoautotroph- using light for energy
How do life forms implement survival, and growth? Two main climatic determinants?
- Must exploit planetary resources- especially in relation to C and NRG sources
1. Temp
2. Precip
Aerobic respiration
general equation. Whats the terminal electron acceptor?
(C6H12O6) + 6(O2) 6(CO2) + 6(H2O)
-Oxygen
What does E harvesting come down to?
Phosphorylation and ETC
Where is amt of E obtained by MO through oxidation is reflected in?
The cell mass or yield
How to get a larger amount of E obtained in oxidation?
The more reduced the substrate
Whats pentachlorophenol?
Used to treat wood
- Very oxidized
- organisms respire this
- Can’t get much E from it
- Put on wood to prevent metabolising
Whats Octadecane?
More reduced= more E for cellular growth
Why is aerobic respiration important?
- Dominant mode of growth in oxygenated ecosystems
- Cycling of carbon (decomposition of dead biomass;
assimilation of carbon into new biomass) - Removes oxygen from groundwaters and surface sediments (allows anaerobic respiration to proceed)
- Produces simple organic carbon molecules that can be used by anaerobes and other organisms
Explain why the bottom of deep bodies of water are hypoxic. Why do fish die?
- O2 can diffuse between sediment and water
- Organisms in sediment consume O2
- If sed orgs oxidize O2 fast= hypoxia
- Fish get pushed up where the water is too hot and they can’t survive
Whats anaerobic respirations equation?
(C6H12O6) + alternate TEA  (CO2) + (CH4) + 6(H2O)
What are some alternative electron acceptors used in anaerobic respiration? Why would aerobic orgs outcompete these?
-Nitrate (NO3), ferric iron (Fe3+), sulfate (SO42),
carbonate (CO32), certain organic compounds
-Not as energetically favourable.
What are aerotolerants?
- Can live in low O2 env but does aerobic respiration
- Will be outcompeted
Whats redox? Redox potentisl?What gets the most E? Least E?
- Redox- movement of electrons from 1 molecule to the other
- Redox potential- ability of org to move electrons
- Most E- O2 to H2O
- Least E- CO2 to CH4
What decreases redox?
As orgs consume O2
What happens to redox of an env after flooding?
- No more aerobic res
- N2 respirators- use all N2
- End- little O2- Iron reducers increase
How do different redox reactions dominate?
What do low energy yields account for?
The inefficiency of anaerobic metabolism and preservation of organic matter in sediments
What redox reaction has the 2nd highest O2 yield? 3rd? 4th? 5th? 6th?
- Reduction of nitrate at 747mV (all examples are at pH7)
2NO3- + 6H+ + 6e- ↔ N2 + 3H2O - denitrification - Reduction of manganese at 526 mV
MnO2 + 4H+ + 2e- ↔ Mn+2 + 2H2O
-denitrifiers and Mn reducers are facultative anaerobes (w or w/o O2) - Reduction of iron at -47 mV Fe(OH)3 + 3H+ + e- ↔ Fe+2 + 3H2O
- all organisms metabolizing Fe, SO-2, methane are strict anaerobes (no O2)
- Mn must be depleted before Fe reduction - Reduction of sulphate at -221 mV SO4-2 + 10H+ + 8e- ↔ H2S + 4H2O
old metabolism… 2 billion years old
- SO4+2 concentrations are generally low, therefore SO4 reduction zone is very small - Once SO4 is gone, methanogens take over CH3COOH → CO2 + CH4
CO2 + 4H+ → CH4 + 2H2O
- limited by concentrations of labile organic matter • as CH4 diffuses up, it is consumed by a number of
bacteria and oxidized
- therefore, CH4 flux to atmosphere depends on the amount produced (source) compared to the amount oxidized (sink)
Why is anaerobic respiration important?
-Cycling of carbon, nitrogen, sulfur, Fe, etc., etc, etc… •various forms of Mn, As, Se, Te, Cr, V, U, Tc, Np are all
biologically reducible
- Depletes organic carbon
- Exerts control over metal (radionuclide) speciation
•solubilizes some metals, precipitates others
Explain the colours in a water column.
Red-Oxidized Fe
Grey- Reduced Fe
Black- Reduced S
Green- Photosynthetic orgs
What’s syntropy? What is it based on? Important for what?
-A process whereby two or more microbes cooperate to degrade a substance neither can degrade alone
- Most syntrophic reactions are secondary fermentations
-Most reactions are based on interspecies hydrogen
transfer (products that other produces)
•H2 production by one partner is linked to H2 consumption by the other
-Syntrophic reactions are important for the anoxic portion of the carbon cycle
What are earths microbial habitats?
soil • water • air • plants • animals
