Lecture 7 - Microbial Ecology

Why may microbes be “unculturable”?

1. Microbe is slow growing

2. Microbe is present in very low abundance

3. Different microbes in the same habitat are physiologically very similar OR inhibition by other microbes in a mixed culture

4. Fastidious growth requirement

5. Cross-feeding or communication signals from other microbes are needed

6. Triggers for growth or exit from a dormant state are not present

What is a MinION?

A portable device for DNA and RNA sequencing

What are the 3 general innovative methods for the isolation and cultivation of novel microorganisms?

1. Cell sorting-based cultivation

2. Membrane diffusion-based cultivation

3. Microfluidics-based cultivation

What is membrane diffusion-based cultivation?

The use of permeable membranes that enable nutrients and metabolites to diffuse into the cultivation medium and thereby mimic more natural conditions during cultivation

What is microfluidics-based cultivation?

The ability of a method to manipulate cells in small volumes and large numbers of replicates, and can also be combined with various droplet cultivation methods

What is cell sorting-based cultivation?

The use of fluorescence in situ hybridization of love cells or reverse genomic that provides a way to target a functional or taxonomic subset of cells for isolation

How does soil work as a microbial habitat?

• Vast array of microhabitats

• Movement of water and gasses

• Optimum for microbial growth

How does teixobactin inhibit cell wall synthesis?

By binding to a highly conserved motif of lipid II and lipid III

What is the purpose of teixobactin?

An antibiotic that are efficient at killing superbugs

Is Teixobactin evolution proof?

Yes, due to the cell-wall precursors on Gram-positive bacteria

What are the 7 different microbial interaction types?

1. Mutualism

2. Cooperation

3. Commensalism

4. Amensalism

5. Predation

6. Parasitism

7. Competition

What is mutualism interaction?

A relationship in which both species benefit

What is cooperation interaction?

A cooperative behaviour benefits one party while the other performs a certain behaviour or takes a particular action

What is commensalism interaction?

A relationship between different species in which one species benefits from the while the other species is neither harmed nor benefits

What is amensalism interaction?

An interaction where one species causes harm to another without any cost or benefits to itself

What is predation interaction?

An interaction in which one organism, the predator, kills and eats another organism, its prey

What is parasitism interaction?

Am association between two different organisms wherein one benefits at the expense of the other

What is competition interaction?

An interaction between organisms or species in which both require a resource that is in limited supply

What are sulfide-based mutualism?

A tube worm-bacterial relationship that exists thousands of metres below the ocean surface

What is the function of sulfide-based mutualism?

The chemolithotrophic bacterial endosymbionts live within a specialized organs (trophosome) of host tube work and fix CO₂ with electrons provided by H₂S

What relationship do microbes and ruminants have?

A mutualistic relationship - methanogens synthesize many of the vitamins needed by their host animals, and they efficiently remove H₂

What is the microbial relationship with cows?

1. Plant material in

2. Bacterial digestion/fermentation

3. H₂ and CO₂

4. Methanogens

5. CH₄ out

What is biogeochemical cycling?

The oxidation and reduction of substances carried out by living organisms and abiotic processes that result in the cycling of elements within and between different parts of the ecosystem

What is environmental microbiology?

The study of how these cycles affect specific as well as global climate change

What is the carbon cycle?

When carbon - which can be in a variety of forms - enters a common pool of organic matter that can be oxidized back to CO₂

What does the carbon cycle begin with?

Carbon fixation, conversion of CO₂ into organic matter by microbes

What is the process of the carbon cycle where it is reduced to methane?

Inorganic carbon can be reduced anaerobically to methane by archaea

What are the effects of fertilizers being NH₄-rich and not being taken up by plants?

• The added ammonium to the soil alters the nitrogen cycle balance

• Runoff may cause eutrophication which disturbs balance of the ecosystem

• Dentrificaiton by microbes produces Nox

What are a function of alpha-proteobacteri?

Able to form nitrogen-fixing nodules (Rhizo) with legumes producing more than 100 million metric tons of fixed N reducing the need for fertilizing

When is the development of a stable micrbiome?

• Begins developing at birth and changes as we age

• We develop an adultlike community of microbes by age ~3

What are the benefits of E. coli and streptococci in the intestinal tract?

They allow the growth of anaerobes bifidobacteria and bacteroidetes due to the reducing environment

How does Bifidobacteria function in terms of early colonization?

• Found in breastfed babies

• Can synthesize all amino acids and growth factors from simple carbohydrates

• Has surface proteins that can bind to sugars - fermentation of these sugars provides the infant with calories and lowers the gut pH, limiting growth of certain pathogens

What do gut immune cells do?

• Sample gut microbes

• Produce anti-microbial molecules

What is the purpose of gut immune cells?

To limit microbial populations → immunosurveillance

What do colonocytes and immune cells recognize and respond to?

Microbes in the microbiome in addition to pathogens

What do microbiome signals influence?

Immune cell function at sites distant from the gut

What does the modulation of tissue immunity effect?

Macrophages in tissues

• Morphology

• Migration

What does PRR stimulation by microbial ligands and microbial metabolites effect?

Circulating myeloid cells

• Promotion of neutrophil aging

• Maintenance of WBC homeostasis

Bone marrow

• Maturation of myeloid cells

How does the gut microbiota affect our central nervous system?

Immune system

• LPS

• Other microbial products

Vagus nerve

• Microbes signal enteric nervous system → vagal stimulation

Blood-brain barrier

• Short chain fatty acids

What is the potential modern evolution answer in relation to diseases an microbial diversity?

Diet