What two studies does microbial ecology use?
- Culture-based studies
2. Molecular studies
What three types of interactions does microbial ecology study?
- Microbes - microbes
- Microbes - macroscopic organisms
- Microbes - the environment
What is microbial ecology?
The study of the interactions between microbes and their biotic and abiotic environments
What are the 7 environmental components important to microbes?
- Water (in liquid form)
- Nutritional categories (energy, electrons, carbon)
- Light
- Nutrients (C/N/P/S compounds, minerals, etc.)
- Something to oxidize and something to reduce
- Surfaces to colonize
- Temperature, pressure, pH
- What is something to oxidize?
2. What is something to reduce?
- Something to oxidize = electron donor
2. Something to reduce = electron acceptor
What is an example of an organic electron donor?
Carbohydrates (CH2O)
What are examples of inorganic electron donors?
H2O
H2
H2S
Fe2+
What is an example of an organic electron acceptor?
Organic acids
What are examples of inorganic electron acceptors?
O2
CO2
When can an electron donor serve as an energy source for chemotrophs?
When the energy is conserved in reactions that remove electrons
Where can electrons removed from a donor go?
- Move to an electron acceptor during chemotrophy or phototrophy
- Be used as a source of electrons for biosynthetic reactions
Why was it difficult to study microbes in their natural environments in the early days of microbial ecology?
The study of microbes first required their isolation/cultivation from the environment as a pure culture….but most species (95-99%) were not yet culturable.
What methods do microbial ecologists use to study complex microbial communities?
- Culture-based methods
2. Molecular biological methods
Why does it remain essential to continue to try and culture the new microbes identified via molecular techniques?
Because molecular characterization alone is not enough
even to define or name a new bacterial species
What methods do microbial ecologists use to study complex microbial communities?
- Culture-based methods
2. Molecular biological methods
Why does it remain essential to continue to try and culture the new microbes identified via molecular techniques?
Because molecular characterization alone is not enough
even to define or name a new bacterial species
What are the 4 general objectives for the study of (microbial) populations?
- Detect
- Identify
- Quantify
- Characterize
What is currently the biggest challenges in the study of microbial populations?
Characterizing the physiological and ecological functions of different members of the population.
Describe each of the 4 objectives for the study of microbial populations
- Detect - detect the cells
determine where they are!
(using microscope, PCR, metagenomic sequencing…) - Identify - identify the organisms that are present to the appropriate level (phylum, genus, species…)
Do this with or without cultivation - Quantify - quantify the relative numbers of the different groups of microbes (population sizes, fluctuations…)
Do this only via molecular methods! - Characterize - characterize the physiological and ecological functions of different members of the population.
This is currently the biggest challenge!
//Live vs. Dead, Active vs. Inactive cell differentiation //
What is the problem with molecular techniques?
What is an advantage?
Molecular techniques based on the detection or amplification of DNA cannot differentiate between living and dead cells.
Detection or amplification of RNA can be effective for investigating gene expression in ACTIVE cells.
//Live vs. Dead, Active vs. Inactive cell differentiation//
What is the problem with microscopic techniques?
They have difficulty differentiation between living/dead and active/inactive cells
What are stable isotope probing (SIP) and other techniques being developed to address?
The living/dead and active/inactive cell differentiation problems
What are stable isotope probing (SIP) and other techniques being developed to address?
The living/dead and active/inactive cell differentiation problems
Describe the Earth’s atmosphere at formation.
- High CO2
- Low O2 and N2
- Some CH4, H2S, and maybe NH3
- Reducing conditions
- High temperature
- Greenhouse effect, but offset by solar flux, allowing liquid water to exist (eventually)
