Module 5 - Environmental Microbiology

Question 1

What are the difficulties and limitations of growing microorganisms in the laboratory?

Answer 1

Growing microorganisms in the lab is challenging due to unknown environmental conditions (like pH, temperature, and salinity), unknown nutrient requirements, and the inability to cultivate most microorganisms using traditional methods. Culture-dependent methods cannot replicate environmental conditions, and cultured microorganisms are often only minor components of the microbial ecosystem.

Question 2

How many microbial cells are estimated to exist on Earth, and why is this significant?

Answer 2

Approximately 5 × 10³⁰ microbial cells are estimated to exist, with most found in oceanic and terrestrial subsurfaces. This highlights the vastness of microbial diversity, indicating that microorganisms play critical roles in ecosystems worldwide.

Question 3

Why is the 16S rRNA gene important in microbial diversity studies?

Answer 3

The 16S rRNA gene is widely used as a marker for phylogenetic analysis due to its conserved nature and presence in all prokaryotes. It serves as a reliable tool for determining evolutionary relationships and exploring microbial diversity in various environments.

Question 4

What are some key divisions (phyla) of bacteria and archaea?

Answer 4

Important bacterial divisions include Proteobacteria, Firmicutes, Actinobacteria, and Cyanobacteria, among others. For Archaea, key phyla are Euryarchaeota and Crenarchaeota. Many groups are defined primarily from environmental sequences without any cultured representatives, emphasizing the limitations of culture-dependent methods.

Question 5

How do temperature, pH, salinity, and pressure affect microbial growth?

Answer 5

Temperature: Psychrophiles thrive in cold temperatures (<15°C), thermophiles grow optimally between 45-80°C, and hyperthermophiles thrive above 80°C.

pH: Acidophiles prefer low pH environments (<6), alkaliphiles thrive in high pH (>8), and neutrophiles grow best in neutral conditions (pH 6-8).

Salinity: Halophiles thrive at moderate salinity (1-15% NaCl), while extreme halophiles require higher concentrations (15-30% NaCl) for optimal growth.

Pressure: Barophiles thrive under high pressure; barotolerant organisms can survive high pressure but also exist in less extreme environments.

Question 6

What is the ‘Great Plate Count Anomaly’?

Answer 6

This anomaly refers to the observation that viable plate count techniques underestimate microbial diversity, revealing that less than 1% of environmental microorganisms can be cultivated in the lab.

Question 7

What methods are used to measure microbial diversity without culturing?

Answer 7

Culture-independent methods, such as DNA sequencing (especially the 16S rRNA gene), allow researchers to measure microbial diversity and determine evolutionary relationships without the need for cultivation.

Question 8

How do microorganisms adapt their membranes to survive extreme environments such as cold, heat, and high pressure?

Answer 8

Psychrophiles have higher amounts of unsaturated fatty acids in their membranes, which keeps them semi-fluid at low temperatures.

Thermophiles possess lipids rich in saturated fatty acids (Bacteria) or a lipid monolayer (Archaea), stabilizing their membranes at high temperatures.

Barophiles have a higher proportion of unsaturated fatty acids, preventing membrane gelling under high pressure.

Question 9

What is a facultative anaerobe?

Answer 9

A facultative anaerobe is an organism that can grow in both the presence and absence of oxygen. It typically grows better in the presence of oxygen but can switch to fermentation or anaerobic respiration when oxygen is not available.

Question 10

Why is O₂ used preferentially as an electron acceptor over NO₃⁻?

Answer 10

O₂ is preferred because it has a higher reduction potential, allowing for more efficient energy release during oxidation-reduction (redox) reactions. This results in a greater yield of ATP compared to using nitrate (NO₃⁻) as an electron acceptor.

Question 11

What are the names of the two phosphorylation processes for forming ATP?

Answer 11

The two phosphorylation processes are:
1. Substrate-level phosphorylation: ATP is directly synthesized from an energy-rich intermediate during metabolic reactions.
2. Oxidative phosphorylation: ATP is generated through the proton motive force created by the electron transport chain, primarily during aerobic respiration.

Question 12

Why is understanding microbial growth in relation to oxygen important?

Answer 12

Understanding microbial growth in relation to oxygen is crucial as it impacts the metabolic pathways used by microorganisms. Aerobes require oxygen for growth, while anaerobes do not and can even be killed by oxygen. The ability to adapt to different oxygen levels allows microbes to occupy various ecological niches.

Question 13

What is the significance of microbial metabolic diversity?

Answer 13

Microbial metabolic diversity allows organisms to utilize a range of substrates and energy sources, making them adaptable to various environments. This diversity is vital for ecological functions such as decomposition, nutrient cycling, and the maintenance of ecosystem stability.

Question 14

Why are oxidation-reduction (redox) reactions critical in microbial metabolism?

Answer 14

Redox reactions are fundamental for the conservation and transfer of energy within microbial cells. They involve the transfer of electrons from electron donors to electron acceptors, which is essential for processes like ATP synthesis and the metabolism of organic and inorganic compounds.

Question 15

How do aerobic respiratory pathways benefit bacteria and archaea?

Answer 15

Aerobic respiratory pathways allow bacteria and archaea to utilize O₂ as the terminal electron acceptor, leading to the efficient production of ATP through oxidative phosphorylation. This process generates more energy compared to anaerobic processes, which is crucial for energy-demanding cellular activities.

Question 16

What is the role of electron carriers in respiration?

Answer 16

Electron carriers, such as NAD⁺ and FAD, shuttle electrons during redox reactions, facilitating the transfer of energy within the cell. They help in maintaining the flow of electrons through the electron transport chain, which is vital for ATP production.

Question 17

What are some common electron acceptors used in microbial metabolism?

Answer 17

Common electron acceptors include O₂ for aerobic respiration, nitrate (NO₃⁻) for anaerobic respiration, and various organic compounds during fermentation processes.

Question 18

What are the differences between fermentation and respiration?

Answer 18

Fermentation is an anaerobic process that directly synthesizes ATP from energy-rich intermediates without using an electron transport chain. In contrast, respiration (aerobic or anaerobic) utilizes an electron transport chain to generate ATP through oxidative phosphorylation.

Question 19

What is an aerotolerant organism?

Answer 19

Can tolerate oxygen and grow in its presence even though they cannot use it.

Question 20

What are microaerophiles?

Answer 20

Can use oxygen only when it is
present at levels reduced from that in air

Question 21

What is denitrification and nitrate reduction?

Answer 21

Denitrification is the process by which nitrate (NO₃⁻) is reduced to nitrogen gas (N₂) through a series of steps involving various intermediates such as nitrite (NO₂⁻) and nitric oxide (NO). This process is critical for returning nitrogen to the atmosphere and can occur in diverse environments, especially in anaerobic conditions.

Nitrate reduction is the initial step in denitrification, where nitrate is converted to nitrite, often performed by organisms such as Escherichia coli.

Question 22

Name examples of anaerobic respiration and the organisms that carry out these processes.

Answer 22

Examples of anaerobic respiration include:

Nitrate reduction and denitrification: Carried out by bacteria such as Pseudomonas and Escherichia coli.

Manganese-oxide reduction: Conducted by specific bacteria that utilize manganese oxides as electron acceptors.

Iron reduction: Some bacteria oxidize ferrous iron (Fe²⁺) to ferric iron (Fe³⁺), including Geobacter species.

Sulfur respiration: Certain bacteria, like Desulfovibrio, can reduce sulfate (SO₄²⁻) to sulfide (H₂S).

Question 23

What are the major differences between anoxygenic and oxygenic phototrophy?

Answer 23

Anoxygenic phototrophy:
- Does not produce oxygen as a byproduct of photosynthesis.
- Utilizes electron donors such as hydrogen sulfide (H₂S), ferrous iron (Fe²⁺), or organic compounds.
- Found in several bacterial groups including Proteobacteria and Chlorobi.

Oxygenic phototrophy:
- Produces oxygen through the oxidation of water (H₂O) during photosynthesis.
- Uses light energy to convert water and CO₂ into organic compounds and oxygen.
- Primarily carried out by cyanobacteria and plants.

Question 24

What are the principles of anaerobic respiration?

Answer 24

Anaerobic respiration is a metabolic process that occurs in the absence of oxygen.
It involves the use of electron acceptors other than oxygen, such as nitrate (NO₃⁻), sulfate (SO₄²⁻), or carbon dioxide (CO₂).
Anaerobic respiration typically generates less energy compared to aerobic respiration but is crucial in environments lacking oxygen.
This process is dependent on electron transport chains to create a proton motive force, which is then used to produce ATP through ATPase activity.

Question 25

What is chemolithotrophy, and what are some examples of inorganic electron donors used by bacteria and archaea?

Answer 25

Chemolithotrophy is a form of metabolism where organisms obtain energy by oxidizing inorganic molecules. Common inorganic electron donors include: - Hydrogen sulfide (H₂S) - Hydrogen gas (H₂) - Ferrous iron (Fe²⁺) - Ammonia (NH₃) These reactions typically occur in environments such as hydrothermal vents and deep-sea ecosystems, where these electron donors are abundant.

Question 26

How do microbes carry out phototrophy?

Answer 26

Phototrophy is the process by which organisms use light energy to produce ATP and assimilate carbon. Microbial phototrophs can be divided into two main categories: - Oxygenic phototrophs (e.g., cyanobacteria) that oxidize water (H₂O) to produce oxygen during photosynthesis. - Anoxygenic phototrophs (e.g., green sulfur bacteria) that do not produce oxygen and instead use electron donors like hydrogen sulfide (H₂S) or organic compounds. Phototrophy involves the capture of light energy by pigments, such as chlorophyll and bacteriochlorophyll, which facilitate the conversion of light energy into chemical energy through processes like cyclic and non-cyclic photophosphorylation.

Question 27

What are the major steps in the nitrogen or carbon cycles and what microorganisms mediate these processes?

Answer 27

Nitrogen Cycle: Nitrogen Fixation: Conversion of atmospheric N₂ to ammonia (NH₃) by nitrogen-fixing bacteria (e.g., Azotobacter, Rhizobium). Nitrification: Conversion of ammonia to nitrite (NO₂⁻) and then to nitrate (NO₃⁻) by nitrifying bacteria (e.g., Nitrosomonas and Nitrobacter). Denitrification: Reduction of nitrate to nitrogen gas (N₂) by denitrifying bacteria (e.g., Pseudomonas). Carbon Cycle: Photosynthesis: Conversion of CO₂ into organic matter by autotrophic organisms (e.g., cyanobacteria, plants). Respiration: Decomposition of organic matter by heterotrophic microbes, releasing CO₂ back into the atmosphere. Methanogenesis: Production of methane (CH₄) by methanogenic archaea from substrates like CO₂ and H₂. Methanotrophy: Oxidation of methane back to CO₂ by methanotrophic bacteria.

Question 28

Why is nitrogen fixation by bacteria important?

Answer 28

Nitrogen fixation is crucial because it converts atmospheric nitrogen (N₂) into ammonia (NH₃), making nitrogen biologically available to plants and other organisms. This process supports the nitrogen needs of ecosystems, as most organisms cannot use atmospheric nitrogen directly. Nitrogen-fixing bacteria are essential for maintaining soil fertility and supporting plant growth.

Question 29

What substrates do methanogens use to form methane?

Answer 29

Methanogens primarily use: Carbon Dioxide (CO₂) and Hydrogen (H₂) to produce methane (CH₄) and water (H₂O). Acetic Acid (CH₃COOH) to generate methane and carbon dioxide. Alcohols (e.g., Methanol) to reduce them into methane and water.

Question 30

Why are methanogens important in anaerobic environments?

Answer 30

Methanogens are vital in anaerobic environments because they help to remove excess hydrogen and CO₂, preventing the accumulation of these gases. They play a key role in the carbon cycle by facilitating the conversion of organic matter into methane, which can be further utilized by other organisms. Additionally, methanogens are essential for processes like anaerobic digestion and wastewater treatment, where they aid in breaking down organic materials.

Question 31

What is the significance of nutrient cycling by microorganisms?

Answer 31

Nutrient cycling by microorganisms is crucial for maintaining ecosystem balance and supporting life. Microorganisms decompose organic matter, recycle nutrients, and facilitate the transformation of inorganic compounds into forms that can be utilized by plants and animals. This cycling supports soil fertility, plant growth, and the overall health of ecosystems.

Question 32

What is methanogenesis and why is it important?

Answer 32

Methanogenesis is the biological process by which methanogenic archaea convert organic matter, CO₂, and H₂ into methane (CH₄) in anaerobic environments. It is important because it helps in the decomposition of organic waste, contributes to the global carbon cycle, and provides a source of energy (biogas) that can be harnessed for human use.

Question 33

What is methanotrophy?

Answer 33

Methanotrophy is the process by which certain bacteria (methanotrophs) oxidize methane (CH₄) into carbon dioxide (CO₂) and water, often using it as their primary source of carbon and energy. This process is crucial for mitigating methane emissions, a potent greenhouse gas, and plays a significant role in the carbon cycle.

Question 34

What is anammox and its significance in the nitrogen cycle?

Answer 34

Anammox (anaerobic ammonium oxidation) is a microbial process in which ammonium (NH₄⁺) is oxidized using nitrite (NO₂⁻) as an electron acceptor, producing nitrogen gas (N₂) and water. It is significant because it provides a pathway for nitrogen removal from aquatic environments, reducing nitrogen pollution and contributing to the nitrogen cycle.

Question 35

What is the early history of Earth, including significant conditions and events?

Answer 35

Earth is approximately 4.5-4.6 billion years old. Early conditions were anoxic and hotter than today. The first cells appeared around 3.8-3.9 billion years ago, and the atmosphere was primarily composed of N₂, CO₂, and CH₄. The earliest forms of life were microbial, and the Earth was exclusively microbial until about 1 billion years ago.

Question 36

What are stromatolites, and what do they indicate about early life?

Answer 36

Stromatolites are fossilized microbial mats consisting of layers of filamentous prokaryotes (bacteria) and trapped sediment. Ancient stromatolites provide evidence of early microbial life and are found in rocks over 3.5 billion years old.

Question 37

What hypotheses exist regarding the origin of cellular life?

Answer 37

Two main hypotheses are: Surface Origin Hypothesis: Proposes that life originated from organic compounds in ponds on Earth’s surface. Subsurface Origin Hypothesis: Suggests life began at hydrothermal springs on the ocean floor, providing stable conditions and a consistent supply of energy.

Question 38

What is the significance of the Miller-Urey experiment?

Answer 38

The Miller-Urey experiment demonstrated that organic compounds, such as amino acids, could be synthesized from inorganic precursors under conditions thought to resemble those of early Earth, supporting the idea of abiotic origin of life.

Question 39

How did the evolution of oxygenic photosynthesis impact Earth?

Answer 39

Oxygenic photosynthesis, developed by cyanobacteria around 2.7-3 billion years ago, significantly increased atmospheric oxygen levels, leading to the Great Oxidation Event and the diversification of aerobic life.

Question 40

What role did microbial diversification play in Earth's biosphere?

Answer 40

Microbial diversification led to the development of new metabolic pathways that allowed organisms to exploit different environments and resources. This diversification facilitated nutrient cycling and established the foundation for complex ecosystems.

Question 41

What evidence supports the endosymbiotic origin of eukaryotes?

Answer 41

The endosymbiotic theory posits that eukaryotes arose from the symbiotic relationship between early prokaryotic cells. Mitochondria and chloroplasts in modern eukaryotes resemble prokaryotes in size, structure, and genetic material, supporting this theory.