BIOL306: Microbiology: Lecture 11: Microbial Nutrition, Chemolithotrophic autotrophs, Active Transport.: Condensed Notes

Microbes are invaluable in bioremediation, degrading toxic materials into non-toxic material.

Why are microbes invaluable in metabolism?

The process of losing electrons or increasing oxidation state, often involving the reaction with oxygen.

Oxidizing

Refers to compounds that do not contain carbon-hydrogen (C-H) bonds, typically including minerals and metals

Inorganic

organisms that obtain energy by oxidizing inorganic compounds

Chemolithotrophic

organisms that produce their own food using inorganic substances, typically through photosynthesis or chemosynthesis. They can convert carbon dioxide into organic compounds

Autotrophs

single-celled organisms without a nucleus or membrane-bound organelles, including bacteria and archaea

Prokaryotes

organisms that use sunlight to convert carbon dioxide and water into organic compounds through the process of photosynthesis.

Photoautotrophs

organisms that obtain both energy and carbon by consuming organic compounds, relying on other living or dead organisms for their nutrients

Chemoheterotrophs

underwater openings on the ocean floor that emit heated, mineral-rich water, supporting unique ecosystems often fueled by chemosynthesis

Hydrothermal vents

refers to geological features or processes that involve hot water

Hydrothermal

a genus of tube-dwelling marine worms, commonly found near hydrothermal vents, that rely on symbiotic bacteria for nutrition through chemosynthesis

Riftia

a genus of marine worms, specifically polychaetes, that are often found in deep-sea environments, including areas near hydrothermal vents

Pachytilia

organisms that obtain energy by oxidizing inorganic compounds and use that energy to convert carbon dioxide into organic matter

Chemolithotrophic autotrophs

RND proteins as a protective team (like the FBI) that helps the bacteria (the president) defend itself against harmful substances (the murderers, or drugs) trying to harm it. The RND proteins work to remove these harmful substances from the bacteria, helping it survive in the presence of antibiotics

RND Family (Resistance-Nodulation-Cell Division)

MFS proteins act like grocery delivery trucks that use a proton gradient as fuel to bring essential nutrients to a family (the cell), while also functioning as garbage trucks that remove waste, ensuring the home remains clean and functional for the family's survival.

MFS (Major Facilitator Superfamily)

the difference in the amount of a substance between two areas, which causes molecules to move from where they are more concentrated to where they are less concentrated

Concentration gradient

to achieve balance or equilibrium. This process, known as diffusion, occurs naturally because molecules tend to spread out evenly in a space. Moving to lower concentration areas helps cells maintain proper function and homeostasis, as having too much of a substance can be harmful.

Why do substances move from areas of higher concentration to lower concentration?

the process by which molecules move from an area of higher concentration to an area of lower concentration, resulting in the even distribution of substances in a space. This movement occurs naturally and does not require energy

Diffusionq

SMR proteins function like a security team that quickly removes intruders (harmful substances like antibiotics) from a building (the bacterial cell) using energy from the building's power supply (proton motive force), allowing the occupants (the bacteria) to stay safe and continue functioning in a hostile environment

SMR (Small Multidrug Resistance) Family

Proton motive force

the difference in proton concentration across a membrane creates both a concentration gradient (where protons move from high to low concentration) and an electrical charge difference. This movement of protons can be harnessed as energy for the cell, driving processes like the transport of other substances and the production of ATP, which is the energy currency of the cell

Proton gradient

A proton gradient is the difference in the concentration of protons (H⁺ ions) across a membrane, where one side has a higher concentration of protons than the other. This gradient creates potential energy that can be used by cells to drive various processes

the process of protons moving from an area of higher concentration to an area of lower concentration to achieve equal distribution is similar to diffusion

Proton diffusion

MATE (Multidrug And Toxin Extrusion) Family

MATE proteins function like a HAZMAT team that actively removes dangerous substances (toxins and antibiotics) from a building (the bacterial cell), using energy from the proton gradient to ensure the safety and proper functioning of the occupants (the bacteria) in a hazardous environment

H⁺

a hydrogen ion, which is a proton that has lost its electron

Imagine two delivery trucks: one truck (carrying a substance) is leaving the building (cell) while another truck (carrying a different substance) is entering at the same time, but they are going in opposite directions. This analogy illustrates the concept of secondary active transport

Antiporters

the movement of one substance down its concentration gradient provides the energy needed to move another substance against its concentration gradient

Secondary active transport

are tiny living organisms that can only be seen with a microscope..

Microbes, or microorganisms

a type of interaction between two different species where both benefit from the relationship

Mutualistic relationship

It’s something produced during a process that can be useful to other organisms

Byproduct

One sibling (the breakdown microbe) is "eating/breaking down" the substance to gain energy and nutrients. As it breaks down the material, it produces "gas" (the byproducts) that the other sibling(s) (the other microbes) can use for their energy and nutrients. This teamwork allows all of them to benefit from the process! This teamwork allows them to share resources and support each other, making it easier for all of them to thrive in their environment. They may also help each other by creating a better environment or providing protection, all to achieve their common goal of effective digestion

Syntrophy

the use of living things, like bacteria or plants, to clean up pollution in the environment, such as oil spills or contaminated soil and water.

Bioremediation

a group of people or organizations that work together for a common purpose.a group of people or organizations that work together for a common purpose

Consortium

the chemical processes in living organisms that convert food into energy, build necessary compounds, and break down waste. They include two main types: catabolism (breaking down for energy) and anabolism (building up for growth)

Metabolic systems

a protein in red blood cells that carries oxygen from the lungs to the rest of the body and helps transport carbon dioxide back to the lungs for exhalation

Hemoglobin

specialized cells in a host's body that house beneficial bacteria, which help the insect digest food or obtain nutrients in a mutual relationship

Bacteriocytes

a type of symbiotic relationship where one organism lives inside the cells or body of another organism. In this relationship, the host and the endosymbiont (the organism living inside) often benefit from each other

Endosymbiotic

Bacteria often cannot thrive in their own waste because many of the byproducts they produce during metabolism can be toxic or prevent their own growth

Why can't bacteria live in their own waste?

the interactions and cooperative relationships between different microorganisms in a community that allow them to share metabolic processes and resources.

Metabolic association

metabolic interaction where the waste products of one species serve as nutrients for another

Cross-feeding

The breakdown of complex toxins (insecticides) may be due to the consortia of bacteria via syntrophy.

What is the breakdown of toxins due to?

Bacteria and archaea had millions of years of no eukaryotic competition. They developed remarkable biological metabolic capabilities.

How did microbes evolve advanced metabolic systems?

Most microbes in the environment cannot be grown in isolation because of syntrophy.

Why can't microbes be grown in isolation?

Many microbes are capable of breaking down organic molecules and toxins. Their product at the end of that process is still toxic to itself

What are microbes capable of?

A lot of waste products that bacteria make will inhibit the bacterium that made them. They can't live in their own waste.

Why can't bacteria live in their own waste?

Bacteria can have other bacteria in their consortium to get rid of the waste product that is toxic to them, this waste product can energize the other bacteria.

What other bacteria are in microbes consortium?

Syntrophy

metabolic association where the presence of one partner is needed for the completion of the other's metabolism. also called cross feeding. end product of bacterium A's pathway is necessary for another bacterium in the same environment.

Benzoate, an organic molecule, can be broken down by a syntrophus bacterium. Syntrophus breaks the molecule into cyclohexane carboxylate

What can Benzoate be broken down by?

This bacterium is sensitive to the accumulation of the end products, especially hydrogen gas. The entire process gets inhibited. These waste products will stop syntrophus from breaking down pollutants.

What is the syntrophus sensitive to?

There are archaea that exist in the soil with syntrophus that love these waste products, specifically hydrogen

What exists with syntrophus to prevent the pathway from stopping?

Hydrogen is a reducing agent, it has electrons. Simple organisms like archaea can oxidize hydrogen. They take the waste products of syntrophus and turn them into methane gas and carbon dioxide.

What do archea do with hydrogen?

This allows syntrophus to completely break down cyclohexane. This leaves the only waste products being methane and carbon dioxide, there is no more toxic molecule.

What do archaea allow syntrophus to do?

This is not only in bioremediation effects, this is in normal geochemical cycling.

Where else is syntrophy seen?

Microbes can be classified based on their sources of carbon, energy, and electrons.

How can microbes be classified?

Autotrophs

Carbon dioxide sole or principal biosynthetic carbon source.

Heterotrophs

Reduced, performed, organic molecules from other organisms.

Phototrophs

Light

Chemotrophs

Oxidation of organic or inorganic compounds

Lithotrophs

Reduced inorganic molecules.

Organotrophs

Organic molecules.

Hydrogen sulfide is an example of this, it is a poison gas for humans. Many microbes feed on hydrogen sulfide.

What is an example of lithotrophs?

Beggiatoa, is a filamentous bacterium that oxidizes hydrogen sulfide.

What is Beggiatoa?

Winogradsky showed that the hydrogen sulfide requirement of beggiatoa was as an energy source, Hydrogen sulfide was oxidized as humans oxidize organic sources.

What did Winogradsky discover about Beggiatoa?

This bacterium exists in salt marshes, it has crystals that refract light, which are sulfur granules.

Where does Beggiatoa exist?

Most prokaryotes are either photoautotrophs or chemoheterotrophs.

What are most prokaryotes?

Chemolithotrophy is found only among the prokaryotes.

Where is chemolithotrophy found?

Photolithotrophic Autotroph

Light energy, inorganic hydrogen/electron donor, carbon dioxide carbon source.

Photoorganotrophic Heterotrophs

Light energy, organic electron donor, organic carbon source (carbon dioxide may also be used).

Chemolithotrophic Autotrophy

Chemical energy source (inorganic), inorganic electron donor, carbon dixie carbon source.

Chemoorganotrophic Heterotroph

Chemical energy source (organic), organic electron donor, organic carbon source.

They are chemically driven, oxidize inorganic material, and use carbon as their energy source

What is chemolithtrophic autotrophy?

Chemolithotrophic autotrophs and photoorganotrophic heterotrophs are critical for global geochemical cycling (N2 to NH3 to NO3 and SO to SO4).

What is critical for geochemical cycling?

Chemolithotrophic autotrophs are the basis for some ecosystems (deep-sea hydrothermal vents).

What are Chemolithotrophic autotrophs the basis of?

Some are >3000 meters below sea surface

Where are Chemolithotrophic autotrophs?

> 300 ATM pressure

What is the pressure 3000 meters below sea level?

This was the first ecosystem discovered that did not depend on sunlight. This system is driven by chemosynthesis, not photosynthesis. These organisms are 3000 meters below the surface of the ocean.

What is the first chemosynthetic system?

They are under extreme atmospheric pressure. When people went to areas where tectonic plates were coming together or being pushed apart, this is where the superheated magma of the earth was closer to the water source

What happens where the tectonic plates meet in the first chemosynthetic system discovered?

That source of heat and pressure can take water and drive it through fissures. This basalt closer to the magma is saturated with water.

What does the source of heat and magma do?

Water is superheated in this area, it will solubilize many minerals including hydrogen sulfide from basalt, when the water rises back up and collides with cool water it will create a black smoke.

What happens when the super heated water meets cold water?

Superheated water collides with cold ocean water. The minerals come out of the solution, they are called black smokers

What happens to minerals when super heated and cold water meet?

This creates an environment around the black smokers that is very rich in materials, especially hydrogen sulfide.

What environment is created once super heated and cold water meets?

Chemolithotrophic autotrophs can exist in mutualistic relationships with multicellular creatures (Riftia pachyptila).

What can chemolithotrophic autotrophs exist with?

6 foot long tube worms. They have a gill which poses the ability to exchange oxygen, carbon dioxide, and sulfide with the bacterial cell.

What are Riftia pachyptila?

Waste products front the worm and its bacterial endosymbionts are transported and lost through the gill. The gill is respiratory and digestive.

What is transferred through the Riftia pachyptila gill?

The worm has no mouth or anus, but it functionally has a digestive system. The blood system of the worm will distribute goods through the coelom of the cell.

Does the Riftia pachyptila have a digestive system?

Within the trophosome there are bacteriocytes. These are eukaryotic worm cells

What is within the trophosome?

Within the bacteriocytes, there are endosymbiotic bacteria

What is within bacteriocytes?

Chemolithotrophic Autotrophic bacteria that want hydrogen sulfide and carbon dioxide. Within these bacteria they are oxidizing hydrogen sulfide, they are fixing carbon dioxide

What do CLA bacteria want?

The organic matter made by these bacteria are exchanged with the host cell.

What does CLA exchange?

All of these organic materials are distributed to feed the entire host worm. Some bacteria are harvested, but the population of bacteria is limited.

How are organic materials transferred within the worm?

Hydrogen sulfide is exchanged across the membrane of the gill and binds to hemoglobin. Oxygen does the same as well as nitrate. These molecules are transported to the bacteriocyte and into the endosymbiotic bacteria.

How is hydrogen sulfide exchanged across the gill?

Hydrogen sulfide is oxidized into elemental sulfur and through a process called APS ATP is created.

What is hydrogen sulfide oxidized into?

The bacteria can use ATP to drive the Calvin Benson cycle which fixes carbon. Some of that organic matter is translocated to nourish other cells in the worm, some is taken by digestion into host biomass.

What does ATP from hte worm do?

Energy-dependent. Energy must be put in.

What does active transport depend on?

Simple Transport

Driven by the energy in the proton motive force

Group translocation

Chemical modification of the transported substance driven by phosphoenolpyruvate.

ABC transporter

Periplasmic binding proteins are involved and energy comes from ATP.

There is a gated transporter proton which decreases potential energy to do work.

What is within the simple transport to decrease PE?

Expense of high energy phosphate on the cytoplasmic side to bring molecules across. The substrate is phosphorylated. This phosphate will be put on a sugar allowing the molecule to fit through the pathway.

What is the expense of group translocation?

ATP hydrolysis on the cytoplasmic side to pull a molecule across.

Where is ATP hydrolyzed in the ABC transporter?

The cargo is bound by a periplasmic or extracellular protein. Must be delivered to a membrane spanning channel.

What is cargo bound by in ABC transporter? WHere is it delivered?