Materials for developing a microbial ecology course

Do you need to develop a Microbial Ecology course? The Microbial Group at UCI has produced a syllabus template and lecture outlines to help you get started. You are welcome to use these documents as a starting point for your course. Please feel free to contact Kathleen Treseder or Steve Allison if you have any questions about the content.

Authors include (in alphabetical order): Cecilia Batmalle, Sandra Holden, Amy Zimmerman

 

II. Lecture Topic: Microbial Physiology: Metabolism, Energy/Resource Acquisition (AZ)

1. Fundamental chemistry and composition of a cell

a. Macronutrients (C,N,O,P,S,K,Mg,Ca,Na,Fe) and trace elements (discuss requirements?)

b. Macromolecules: informational and noninformational

i. Polysaccharides

ii. Lipids

iii. Nucleic acids

iv. Proteins

2. Metabolism: energy derived from light or chemicals (catabolic processes)

a. Chemoorganotrophy (energy from organic molecules)

b. Chemolithotrophy (energy from inorganic molecules)

c. Phototrophy (energy from light)

3. Basic principles of energy transformations

a. Bioenergetics

b. Oxidation/Reduction: aerobic and anaerobic

c. Electron transport

d. Respiration

4. Biosynthesis: monomers/macromolecules (anabolic processes)

5. Acquisition/Assimilation: mechanisms

a. Heterotrophy vs. autotrophy

b. Diffusion

c. Transport

i. Enzymes

 

 

III. Lecture Topic: Reproduction and Growth (RB)

1. Bacterial growth
   1. Basics : Lag/Log/stationary/lysis phases; Growth rate (X=X₀e^µt)
   2. Growing in a flask vs. Growing on Solid Media

i.     e.g. E.coli–Pseudomonas – Free lifestyle vs. “Fixed” lifestyle)

3. Mobility (How can microbes avoid stresses?)
4. Limiting factors

i.     Nutrients

ii.     Space

iii.     Toxic compounds

iv.     More?.

5. Resource allocation for growth / stresses

i.     Phenotype modification – Pseudomonas

2. Microbes as complex “single-specie” organisms
   1. The Streptomyces complex life cycle

i.     e.g. vegetative filament, spore forming units, etc

2. Fungi
3. Mixed populations (community)– Biofilms

i.     e.g. dental plaque

 

 

IV. Lecture Topic: Microbial evolution in the context of microbial ecology (RB)

[transition from organismal to population ecology…]

1. The basis of evolution: Mutation (DNA) vs. Selection (DNA-Protein)
2. Selection vs. Drift
3. “Strategies” for new gene acquisition

a.      HGT

b.     Phage

c.      Transposons

d.     More?

e.      Ramifications for evolution? For studying microbes?

4. Lab-scale evolution experiments on proteins>pathways>strains>populations
5. Evolution in a changing environment (in regard to the niche concept)
6. Struggle for life : Niche colonization & new species introduction
7. Microbial evolution « environment evolution (e.g. atmosphere, microbial corrosion)

1. The origin of life (Potential for making this lecture as long as you want)

 

 

V. Lecture Topic: Stress Tolerance (incl. extreme environments) (AZ)

1. Shelford’s Law of Tolerance (abiotic parameters control abundance of organisms)

2. Starvation Strategies

a. Biofilm formation

b. Inclusions

c. Endospore formation

3. “Longevity in Adversity”

a. Temperature

b. Salinity

c. Redox potential

d. pH

e. Radiation

f. Pressure

4. Extreme microorganisms: examples

a. Hyperthermophiles (high temperature)

b. Psychrophiles (low temperature)

c. Halophiles (high salt)

d. Acidophiles (low pH)

e. Alkaliphiles (high pH)

f. Barophile (high pressure)

VI. Lecture Topic: Microbe-microbe interactions and signaling (quorum sensing?) (RB)

1. Microorganisms in microenvironments (scale considerations)
2. “Social Ecology of bacteria” – “Social Evolution”
3. “A day in a life of a microbe”: what are the stresses that an isolated microorganisms has to face in different “social environment” (isolated cell on a plate, in an axenic colony, in a mixed colony…)
4. Interaction of microorganisms : a broad description of what is known (antagonisms, synergisms, cheating, trophic networks (spend some time on the importance of the protists/phages as regulators of the microbial communities (?))

 

 

VII. Lecture Topic: Microbial interactions with other organisms (do unto others…) (SH)

1.     Mutualisms

a.      Nodules

b.     Mycorrhizae

c.      Lichens (algal-fungal, or algal-fungal-cyanobacterial)

d.     Coral and algae

e.      Ruminants

f.      Endophytes

g.     Vibrio and squid

2.     Altruisms

a.      Slime molds

b.     Siderophores (public goods)

3.     Antagonistic

a.      Cheating

b.     Allelopathy

i.     Bacteriocins

ii.     Antibiotics

c.      Predation

i.     Protists

ii.     Bacteriophage

4.     Parasitic

a.      Viruses

b.     Bacterial infections

c.      Fungal infections

 

Suggestions from microbial group:

1.     Choose a few of the examples above and cover them as case studies using primary literature

2.     Instead of treating the above interactions as discrete groups, present them as a spectrum. Using this format, one could choose a single system as a case study, and work through how the interactions could shift from synergistic à antagonistic (emphasizing costs, benefits, and tradeoffs).

 

 

VIII. Lecture Topic: Evaluating microbial diversity (♫Who are you? Who? Who?♫) (SH)

1.     Storytime – The Global Ocean Sampling

2.     Evaluating diversity

a.      Alpha diversity, gamma diversity, beta diversity

b.     Estimating diversity

i.     Diversity indices (Shannon’s, Simpson’s, Chao1 estimation)

c.      Are communities different?

i.     Analysis of similarity

ii.     Distance decay (or just mention this and save it for biogeography lecture

3.     Culturing

a.      Physiological assays?

i.     Does it grow on medium A? Does it cause medium B to change color? etc.

b.     Pros: somewhat quick (although some are difficult to grow), inexpensive

c.      Cons: community coverage (not many environmental microbes can be cultured)

4.     DNA fingerprinting

a.      t-RFLP, ARISA

b.     Pros – better community coverage than culturing

c.      Cons – different taxa could have same length polymorphism, taxonomic resolution

5.     Sequencing

a.      Pros – better coverage and taxonomic resolution than fingerprinting, technologies are rapidly advancing

b.     Cons – technologies are rapidly advancing, more expensive (but prices are falling)

c.      Technologies – Sanger, 454, Illumina, Ion, SOLiD

6.     Phylogenetic markers

a.      Need to think about phylogenetic resolution – does this marker differentiate the groups I am interested in?

b.     Examples: 16S rRNA, 18SrRNA, functional genes, recA, rpocC

Estimating diversity exercise to go with evaluating diversity lecture (SH)

Materials:

Marbles (multiple colors)

Bags or boxes

Graph paper

By the end of this exercise, students should be able to:

1.     Explain how sampling effort influences the richness sampled

2.     Describe out estimating diversity is dependent on probabilities

3.     Calculate diversity estimates for sampled communities

 

Instructions:

You have been given a box which contains a community of marbles. Each species/taxa is represented by a color.

1.     First draw 5 marbles and count the number of unique colors, as well as the abundance of each color.

2.     Replace the marbles and draw 10. Count the number of unique colors, and the abundance of each color.

3.     Continue replacing and drawing marbles (15, 20, 25) and counting unique colors and their abundances.

4.     Graph the number of unique colors samples vs. the number of marbles sampled to create and accumulation curve.

5.     Plot a rank abundance curve of the marble colors

a.      Are there any taxa that you sampled more than the others?

b.     What can you infer about the community that you sampled?

6.     Estimate the diversity of the community using Shannon’s index, Simpson’s index, and Chao1 estimation.

7.     Check under the box lid for the actual diversity of the box.

a.      How does the actual diversity compare to your estimates?

b.     How do you think this compares to estimating the diversity of microbial communities?

 

Suggestions from microbial group:

Organize the boxes so that the study has some spatial structure, so that the class can analyze the entire metacommunity using alpha-, gamma-, and beta-diversity.

 

Learning activity resources:

ESA (Ecological Society of America): http://www.esa.org/education_diversity/educatorResources.php

MERLOT (Multimedia Educational Resource for Learning and Online Teaching): http://www.merlot.org/merlot/index.htm

IX. Lecture Topic: Biogeography – General theory and application to microbes (MM)

Core concepts:

·       Soil Microbes are influenced by geography

·       Evidence for endemism

·       Communities more dissimilar with distance

·       Island area most significant predictor of ECM richness

 

General Biogeography (for macrobes)

1.     What is biogeography?

a.      Spatial patterns of biodiversity

b.     Processes that create those patterns

2.     Microbial biogeography: Is Everything Everywhere?

a.      Highly dispersible; barriers to dispersion

b.     Large population sizes

c.      Derived from pure culture studies

3.     Everything is Everywhere (EisE)

a.      “If it were possible to expose all the individuals of a species during many generations to absolutely uniform conditions of life, there would be no variability.” –Charles Darwin, 1883

b.     “Everything is everywhere, but the environment selects.” –Lourens Bass Becking, 1934 (rephrasing M. Beijerinck, 1913)

c.      “Where the environmental conditions are closely comparable, the same types of organisms appear…we need not think in terms of local microflora and fauna.”     –Cornelius van Niel, 1949

4.     Fundamental Processes (Martiny et al. 2006)

a.      Immigration

i.     Dispersal and colonization

ii.     Transport (wind, water, physical mixing)

iii.     Competition – must be able to compete after arrival in an environment

iv.     EisE – assumes colonization rates are so great they prevent spatial differentiation and endemism

b.     Speciation

i.     Diversification due to mutation, genetic drift, and selective pressures

ii.     Microbes – short generation time allows rapid divergence

c.      Extinction

i.     Macroorganisms – endemic species with small ranges

ii.     Rare for microbes?

1.     Dormancy

2.     Large population sizes

3.     Difficult to study

 

Island Biogeography

1.     Fungal richness determined by

a.      Stochastic, neutral, processes:

i.     Immigration, extinction, birth rate, death rate

ii.     Neutral: species are equivalent within a trophic level

b.     Deterministic, niche-based processes

i.     Habitat requirements, environmental controllers, species interactions (historic, environmental, biotic filters)

ii.     Niche: The total requirements of a population or species for resources and physical conditions

c.      Equilibrium theory of Island Biogeography

i.     Small and large islands; higher extinction on small islands

ii.     Near and far islands; lower immigration on far islands

d.     Species area relationship – Ectomycorrhizal fungi & tree islands

i.     Area, rather than distance, the dominant predictor of richness

(Peay et al. 2007)

ii.     Species area relationship S ~ A^z

iii.     Lower z = more cosmopolitan distribution

iv.     Many microbial communities have low z

v.     Ectomycorrhizal fungi have a higher z than bacteria

2.     Microbial Biogeography Objectives

a.      Descriptive: define microbial habitats and distributions

i.     Do soil microbial communities exhibit endemism?

ii.     Which environmental factors best predict bacterial community structure and diversity?

b.     Test explicit spatial hypotheses

i.     Null hypothesis: Microbes are ubiquitous in a suitable habitat (EisE)

ii.     Are microbial communities more dissimilar with distance?

iii.     Is the size of a habitat or dispersion more important for determining richness in microbial communities?

iv.     Challenges: under-sampling / huge amount of diversity

v.     Habitat heterogeneity (e.g., soil)

vi.     See Fig. 1 – Lauber et al. 2009

c.      Endemism vs. cosmopolitanism –

i.     e.g., hot spring Archea

ii.     See Fig. 2. Whitaker et al., 2003;

iii.     soil Pseudomonads (Cho & Teidje, 2000)

iv.     No overlapping genotypes between sites

v.     Bacterial co-occurrence (Horner-Devine and Bohannen, 2006)

1.     Habitat preference

2.     Ability to survive in an environment

a.      Metabolic ability, traits, functional group

b.     Stress response

 

X. Lecture Topic: Biogeography – Habitats, dispersal, and connectivity (MM)

1.     Habitats that structure microbial communities

a.      Ocean

b.     Freshwater

c.      Terrestrial

d.     Sub-surface

e.      Air

2.     Scales of processes or dispersal

a.      Global

b.     Regional

c.      Local

3.     Connectivity

a.      Well mixed

i.     Air

ii.     Water

1.     Closed system – Lake

2.     Open circuit – River or estuary

b.     Heterogenous – Soil

 

XI. Lecture Topic: Biogeography – Environment and microbial communities (MM)

Environmental characteristics that structure microbial communities

1.     Structural aspects – size, shape, connectivity of pores

2.     Complexity of resources

3.     Physicochemical conditions

4.     Biological interactions

a.      Exposure to roots of different plant species

b.     Allelopathy

c.      predation

5.     Environmental parameters

a.      Temperature

b.     Moisture content

c.      Light availability

d.     Nutrient status

e.      Substrate availability

f.      Complexity

g.     Contamination with pollutants

h.     Salinity

i.       Edaphic factors

j.       pH (Figure 3)

i.     structures microbial communities at the continental scale

ii.     explains variation at the phylum or subphylum level

k.     Moisture adaptation (Figure 3)

i.     dry adapted taxa

ii.     wet adapted taxa

l.       Distance (Figure 4)

i.     Are soil rotifer communities more dissimilar with distance?

 

Figures for Biogeography Lectures: See downloadable Word file

References for Biogeography Lectures: (MM)

 

Dubinsky, E.A. 2008. Environmental Controls on Microbial Community Structure and Iron Redox Dynamics in Upland Soils. Dissertation research. UC Berkeley. Berkeley, CA

 

Lauber et al. Pyrosequencing-Based Assessment of Soil pH as a predictor of Soil Bacterial Community Structure at the Continental Scale. Applied and Environmental Microbiology (2009) vol. 75 (15) pp. 5111-5120

 

Martiny et al. Microbial biogeography: Putting microorganisms on the map. Nature Reviews Microbiology (2006) vol. 4 (2) pp. 102-112

 

O’Malley. The nineteenth century roots of ‘everything is everywhere.’ Nature Reviews Microbiology (2007) vol. 5 (8) pp. 647-51

 

Peay et al. A strong species-area relationship for eukaryotic soil microbes: Island size matters for ectomycorrhizal fungi. Ecology Letters (2007) vol. 10 (6) pp. 470-80

 

Robeson et al. Soil rotifer communities are extremely diverse globally but spatially auto-correlated locally. PNAS USA (2011) vol. 108 (11) pp. 4406-4410

 

 

 

 

 

XII. Lecture Topic: Biogeochemisty – microbial engines of the Earth system (MS)

1.     Microbial contributions to the Earth’s atmosphere (why are we interested in them?)

a.      Sheer number of microbes

b.     Producers of O₂

c.      Transformers of N₂

2.     What is a biogeochemical cycle?

a.      Earth as a closed system

b.     Redox reactions are the source of all organic compounds, all life

c.      Global change

3.     Biogeochemical cycles

a.      Oxygen cycle

i.     Oxygenic photosynthesis

ii.     Aerobic respiration

b.     Carbon cycle

i.     C reservoirs (sources and sinks)

ii.     C fluxes (turnover time)

iii.     C redox

c.      Nitrogen cycle

i.     N reservoirs

ii.     N fixation

iii.     Ammonification

iv.     Nitrification

v.     Denitrification

d.     Aerobic vs. Anaerobic

i.     Microbially driven gradient

 

Reference of note:

Falkowski PG, Fenchel T, Delong EF. 2008. The microbial engines that drive Earth’s biogeochemical cycles. Science, 320:1034-1039.

 

 

XIII. Lecture Topic: Microbial response to disturbance (MS)

1.     Natural disasters

a.      Disturbance as part of a cycle

i.     Ecological succession

2.     Anthropogenic disturbances

a.      Clearcutting

b.     Fertilization

c.      Air pollution

d.     Climate change

3.     Pulse vs. press

4.     Resistance and resilience of microbes

a.      Microbial scale

b.     Gut microbes

c.      Soil

d.     Aquatic – lake turnover

 

XIV. Lecture Topic: Effect of climate change on microbe-mediated processes (MS)

1.     Feedback loops

a.      Methane

b.     Trace gases

c.      The “main” GHGs

i.     Nitrogen excesses in fertilizer à efflux N-based gases

ii.     Warming effect on decomposition and CO₂ flux (high latitudes especially)

d.     Mitigation strategies