MicroBio 2/16

Post-Class Availability
- Instructor offers post-class time for discussion and questions.
- Availability throughout the week and during office hours.

Pure Cultures
- Cultures provided with sufficient nutrients and water necessary for microbial growth.
- Growth conditions are artificial compared to natural environments.
Definition of Xenic Culture
- Terms derived from Greek meaning "without strangers."
- Definition: Growth of a single species of microbe within a culture medium, free from other microbial types.
- Rarely reflects actual environmental conditions.
Normal Microbiota
- Even infections within the body contend with normal, healthy microbes, complicating our understanding of microbial diversity.

Culturable vs Non-Culturable Microbes
- Only about 5% of known microbial taxonomic groups have been identified as culturable species.
- 95% of then known bacteria cannot be grown in culture.
- Importance of recognizing the vast unknown diversity of microorganisms.
- Real-world growth typically occurs in communities, with interactions among various species.
Environmental Influences on Growth
- Environmental factors shape microbial growth; microbes can also shape their environments.
- Example: Helicobacter pylori can neutralize stomach acid by releasing invasive enzymes, thus creating a suitable microenvironment.

Claude Sobel's Contributions (1955)
- Suggested that deep sea environments had little microbial life based on failed attempts to culture microorganisms from marine sediment.
Alvin Submersible Incident (1968)
- The vessel sank and upon retrieval, a bologna sandwich intact after four years was used as evidence of little microbial life in the deep sea.
- Flaw in Logic: The cold environment and lack of known enzymes for decomposing the sandwich contradicted assumptions about microbial activity.
- Contemporary understanding recognizes abundant microbial life in deep sea environments.

Introduction
- Observations in the 1980s showed substantial discrepancies between the presence of microbial cells seen via microscopy and the number that could be cultured.
Findings
- Billions of cells detected in diverse environments, but only 1% could be cultured.
- This discrepancy is termed the great plate count anomaly, requiring rethinking growth concepts in microbiology.
Understanding Microbial Growth
- Most microbial growth does not fit into standard lab timeframes and requires new methods of analysis.
- Microbial growth can operate on much longer timescales than laboratory settings (years to decades).

Assumptions about Microbial Growth
- Assumption 1: Growth occurs when nutrients are available (temperature, pH, salt concentration, etc.).
  - Reality: Many microorganisms do not grow in lab environments even with optimal conditions.
- Assumption 2: Microorganisms can grow in isolation without interaction or assistance from other microbes.
  - Reality: Many require symbiotic relationships or contributions from other microbes for essential nutrients.
- Assumption 3: Microbes will grow rapidly when nutrient limitations are removed.
  - Reality: Various mechanisms prevent rapid growth even with sufficient nutrients.
- Assumption 4: Large batch cultures mimic natural microenvironments.
  - Reality: Culturing microbes in uniform, large environments can prevent proper growth due to lack of localized conditions that microbes need.
- Assumption 5: Laboratory growth does not introduce unknown variables affecting microbial growth.
  - Example: Variance in water quality affecting growth in E. coli due to nutritional content differences.

Factors Indicating Life vs. Death
- Cell integrity: Evaluating the integrity of the cell membrane and the chromosomes.
- Damaged membranes and fragmented DNA signify decreased viability.
Metabolic Activity
- Importance of assessing both anabolic (building) and catabolic (breaking down) metabolic processes to define life.
- Cells may exist along a continuum from actively healthy to completely non-viable.

Responses to Environmental Stress
- Microbes can reduce metabolic activities in response to stress, activating stress resistance mechanisms.
- Persistent stress can lead to growth arrest, where microbes survive but cease to divide.
- This stage can lead to a state known as VBNC (viable but non-culturable), where cells remain alive but lose the ability to reproduce.
Measuring Viability
- Tools such as live-dead staining can indicate cell viability based on membrane integrity and damage.

Types of Trophic Strategies
- Oligotrophic: Adapts to low nutrient concentrations (microorganisms can thrive in micromolar to nanomolar levels).
- Copiotrophic: Thrives in environments with high nutrient concentrations, unlike oligotrophs.
- Adaptations to nutrient environments indicate successful microbial niche occupation.
Ecological Interdependence
- Coexistence of oligotrophs and copiotrophs leads to mutual dependency for nutrient provisioning.
- Example: Microbial communities interact metabolically and through signaling, forming complex webs of interdependencies.

Holobiont Theory
- Some suggest organisms (such as humans) are effectively hybrid organisms with significant microbial contributions to physiology.
- Consideration of where one organism ends and another begins leads to a reevaluation of organism definition in biological systems.

General Overview
- A conserved stress response triggering global changes in metabolism and gene expression among bacteria.
- Response often mediated by signaling molecules such as ppGPP or pppGPP.
- Synthesis involves enzymes like the PPP GPP synthase (a.k.a. alarmone).
E. Coli Response Analysis
- Typically found in nutrient-rich environments but faces different conditions outside hosts.
- Nutrient shortages trigger stringent response mechanisms, including arresting cell division and halting ribosomal RNA production.
- Two key proteins involved:
  - RelA: Activated under amino acid starvation; causes ribosomal stalling and subsequent activation of stringent response.
  - SpoT: Monitors general nutrient levels; adjusts alarmone levels acutely to corresponding stresses.
Sequencing of Responses
- Initial responses include shutting down ribosomal RNA and halting cell division to conserve resources.
- The SOS response is activated to repair damage and restore normal processes as nutrient conditions improve.

By understanding microbial interactions, growth dynamics, and stress responses, microbiologists can better interpret ecological roles and scenarios influencing microbial communities.
Future discussions will continue exploring diverse stress response systems and their implications for microbial health and ecology.