Ch 19 mainly self review

What is microbial ecology?

Its the study of microbes in the environment and their interactions with each other.

Define microbial communities and where theyre found

Microbial communities (microbiome) are groups of microorganisms that are living together in each ecosystem. →Found in: Soil, water, air, bodies of plants/animals, and human made environments

What molecular ("omics") techniques are used to study microorganisms in the environment?

DNA/RNA sequencing: Omics

→SSU rRNA amplification: PCR amplification of 16S rRNA

→Metagenomics: Entire nucleotide sequences

→Metatranscriptomics: RNA transcripts (RNA Seq)

→Single-cell genome sequencing

What are the 5 culture-based techniques for studying environmental microorganisms?

1. Culturing with novel substrate, antibiotic,
   under stress conditions, or for a longer time

2. Coculture with a partner organism

3. Environmental exposure: Using iChip method to culture organism in its source environment

4. Continuous culture with dilution to
   extinction: maintaining highly constant level
   of substrate and avoiding buildup of toxic
   wastes

5. Microfluidic culture: microfluidic device
   mimics the microscale structure of habitats
   such as particles of soil

What is the functional role of microbes in ecosystems

-Microbial populations fill unique niches in ecosystems and allow for the limitless variety of energy-yielding reactions.

→The microbes can digest even novel substrate like synthetic plastics. Evolution may generate microbes that can digest the indigestible.

What are the two major functional roles of microbes in ecosystems?

• Assimilation: Primary producers that acquire elements (like CO2 fixation) to build cells

• Dissimilation: Decomposers that break down organic nutrients into inorganic minerals (CO2, NO₃^-)

Which environmental factors influence microbial community structure?

1. Oxygen/electron acceptor: Aerobic respiration, anaerobic respiration, lithotrophy, hydrogenotrophy

2. Temperature: Hyperthermophiles, thermophiles, mesophiles, psychrophiles

3. Salinity and Acidity: Halophiles, halotolerant, acidophiles, alkalophiles

Define symbiosis

The intimate association of two species.

Define the following with 1 example each

• Mutualism
• Cooperation/Synergism
• Commensalism

1. Mutualism: An obligatory relationship where both partners benefit

→Zooxanthellae providing carbon to coral.

2. Cooperation/Synergism: Both species benefit but not obligatory as they grow independently.

→Prochlorococcus growing with a helper bacterium.

3. Commensalism: 1 species benefits while partner is neither helped nor harmed.

→Some plant endophytes

Define the following with 1 example each
• Amensalism

• Parasitism

• Predation

1. Ammensalism: An adverse interaction where 1 organism harms/ inhibits the growth of another.

→Pseudonocardia producing compounds to stop predatory fungi in ant colonies.

2. Parasitism: Parasite benefits at the expense of the host.

→Mycobacterium leprae in humans.

3. Predation: One organism attacks and consumes another.

→Bdellovibrio penetrating prey cell walls.

Explain the Protozoan-Termite mutualistic relationship

A mutualistic association found in the termite’s hindgut, acting as a wood-digesting microbiome.

→Termite Role: The termite provides wood particles as food for the protozoa, such as Trichonympha or Mixotricha paradoxa.

→Protozoan Role: The protozoa (w/ help of their own intracellular bacteria) digest the cellulose in the wood polysaccharides.

→Nutritional Benefit: This digestion produces short-chain fatty acids, specifically acetic acid, which the termite absorbs and uses for nutrients.

explain the Legume–rhizobium association

The Legume–Rhizobium association is a mutualistic relationship between plants like soybeans, peas, or beans (legumes) and nitrogen-fixing bacteria known as Rhizobia.

Key aspects of this relationship include:

• Nitrogen Fixation: Rhizobia fix significantly more nitrogen for the plant than it could otherwise absorb from the soil.

• Symbiosome Formation: Inside the plant's root cells, the bacteria differentiate into bacteroids. These are contained within a plant-derived membrane called a symbiosome, which facilitates the exchange of nutrients between the bacteria and the host.

• Nodule Development: The plant provides the bacteria with energy-rich nutrients in exchange for fixed nitrogen, a process that ultimately results in the formation of specialized root nodules.

Nitrogen-fixing bacteria (Rhizobia) live in plant cell "symbiosomes," fixing more nitrogen than the plant could get from soil in exchange for nutrients.

explain the Coral–microbe relationships

The Coral–microbe relationship is a mutualistic association between coral (marine invertebrates) and photosynthetic algae known as zooxanthellae (dinoflagellates).

The exchange between them works as follows:

• Zooxanthellae Role: These endosymbionts provide organic carbon to the coral host.

• Coral Role: The coral provides the algae with a protected habitat, UV radiation protection, and essential nutrients including nitrogen compounds, phosphates, and CO2​.

A breakdown of this relationship is known as coral bleaching, which occurs when temperature increases cause the coral to lose its photosynthetic pigments or expel the zooxanthellae entirely.

• Algae (Zooxanthellae) provide organic carbon; the coral provides a habitat, UV protection, and minerals.

explain the bovine rumen

The bovine rumen is one of four chambers in the bovine gut that functions as a complex digestive microbiome where feed is broken down and fermented.

Key characteristics include:

• Microbial Diversity: It contains thousands of microbial species, including bacteria like Ruminococcus and Clostridium, as well as fungi like Neocallimastix.

• Digestion: These microbes are responsible for breaking down cellulose and complex plant fibers that the animal cannot digest on its own.

• Fermentation & Methanogenesis: The fermentation process produces H2​ and CO2​ gases, which support methanogens.

• Mutualistic Benefits: Methanogens benefit the host by synthesizing essential vitamins and efficiently removing H2​, although they also produce methane as a byproduct.

• Microbes ferment plant fibers; methanogens remove H2 and synthesize vitamins for the cow.

explain the ant colonies

Attine ant colonies function through a complex multi-species interaction centered around food production:

• Fungal Cultivation: The ants cultivate a "fungal garden" using the genus Leucocoprinus as their primary food source.

• Protection via Amensalism: To protect this crop, the ants carry actinobacteria (Pseudonocardia) on their exoskeletons. These bacteria produce inhibitory compounds that prevent the growth of Escovopsis, a predatory fungus that can destroy the garden.

• Secondary Predation: Another fungus, Phialophora, may also be present to prey on "cheater" strains of the beneficial Pseudonocardia bacteria.

Attine ants cultivate a fungal garden (Leucocoprinus); they carry Pseudonocardia bacteria to produce antibiotics against parasitic fungi (Escovopsis).

Explain the lichens

Lichens are a symbiotic association, generally considered mutualistic, between a fungal partner and a photosynthetic partner.

The relationship consists of two main components:

• Mycobiont (Fungal partner): Provides a sheltered environment, water, minerals, and a firm surface (substratum) for growth.

• Phycobiont (Alga or cyanobacterial partner): Provides organic carbon and oxygen to the association.

 A mutualism where a fungus (mycobiont) provides a sheltered environment and minerals, while an alga/cyanobacteria (phycobiont) provides carbon and oxygen.

explain predation among microorganisms

Predation among microorganisms is an interaction where one organism attacks and consumes another. The sources highlight several distinct predatory strategies:

• Epibiotic Attack: Vampirococcus attaches to the surface of its prey to attack.

• Endobiotic Consumption: Daptobacter penetrates the prey to directly consume its cytoplasmic contents.

• Periplasmic Growth: Bdellovibrio penetrates the cell wall of its prey and grows outside the plasma membrane.

• Degradative Enzymes: Myxococcus cells use gliding motility to overtake prey and release enzymes that digest them.

• Viral Predation: Viruses act as major predators in marine environments, specifically attacking phytoplankton.

• Strategies include epibiotic attacks (Vampirococcus), direct cytoplasmic consumption (Daptobacter), or releasing degradative enzymes (Myxococcus).

What is microbial competition?

occurs when two organisms use the same limited resource, resulting in either competitive exclusion (one dominates) or coexistence at lower population levels.

3. Competition: Two organisms try to use same limited resource, leading to 1 dominating or both coexisting at lower levels.

What is genomic reduction?

is an outcome of long-term parasitism where the parasite loses unused genomic information because it relies on the host.