Natural Environment

Environment

  • Microbes found in all different places

    • Even in brain, blood-brain barrier doesn’t keep them out, some live tehre

  • Environment affects what microbes live there

  • Microbes affect their environemnt


Examples

  • Mining

  • Pollutant clean-up (bioredmediation)

  • Water treatment

  • A special application (not testable)


Mining

  • Microbial leaching → promoting microbial metabolism to extract valuable metals from low grade ores

  • Ex. copper (25% uses this method)


Copper leaching

  • Done by Acidithiobacillus ferrooxidans

  • Want to turn copper sulfide (CuS) to Cuº

  • Driven by Fe2+ oxidation

  • Work through steps in diagram


Phage Mining

  • Bioengineer their protein coat to bind to metals

  • Spread phages over land

  • Harvest them

  • Extract metals from coat by changing pH

  • Reusing phages

  • Hasn’t been tested


Bioremediation - Uranium clean up

  • Desulfovibrio

  • U6+ is soluble

  • We try to turn it to U4+ which is immobile

  • If it oxidized, which happens quickly, it can’t be moved

  • Need to introduce microbes and quickly remove the uranium


Bioremediation - Oil Spills

  • Long carbon chains in the water

  • Oil provides carbon and hydrogen, also oxygen which many bacteria use for metabolism

  • Introducing N, P, etc. speeds up process

    • Needed for proteins, etc.


Bioremediation - Xenobiotic Contamination

  • Many not degraded by microbes

    • Ex. DDT pesticide 

  • Research

    • Using microbes to break down

    • Making products that can be broken down

    • Need to be cost effective


Water Treatment

  • Aerobic bacteria prefer high nutrients and grow rapidly and take over

  • Anaerobic prefer lower nutrients and environments where less bacteria can grow, and they grow more slowly and consistently

  • FINISH NOTES HERE


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Microbes and Diverse Environments

  • Everywhere

  • Land and water

  • Carbon-rich and carbon poor

  • Oxygenated and anoxic regions


What do microbes require?

  • Energy source - organic, inorganic, light

  • Other nutrients

  • Water

  • Appropriate temp, pH, osmolarity, O2 levels

Heterotroph vs Autotroph

  • Cellular C from organic source

  • Cellular C from CO2

  • Know table from metabolism unit


Column of Water

  • Stratification and mixing

  • Layers

    • Photic zone

      • Sunlit surface water

      • Phytoplankton photosynthesis

    • Sinking organic matter

      • Bacterial decay

      • Remineralization

    • Deposition 

      • Nutrient sink

      • More bacterial decay

    • Ocean sediments

      • Net deposition

  • Water temp

    • Different seasons

  • Moving water

    • Dead zones

    • Need to move around at least top layer


Microbes live in Microenvironments

  • Clump of soil example

    • Center of soil has less oxygen and less access to outside materials

    • Outer layer of clump is different

  • May be in a less than ideal environment but if stable iits fine

  • Competition and limited nutrients


Symbiotic Relationships

  • Symbiont → organism in a symbiotic relationship

  • Symbiosis → the living together or stable close association of two dissimilar organisms

  • Mutualism

  • Commensalism

  • Parasitism


Nitrogen Fixation

  • N2 (N triple bond N)

    • Needs a lot of energy to break

  • Haber-Bosch Process

    • Main objective

    • N2 (nitrogen gas) + 3H2

    • Activation energy: +250 kJ

    • Enthalpy change: -92 kJ

    • 2NH3 (ammonium)

    • Need to heat up process which requires energy

    • Uses 2% of all energy we use

  • Ammonium acts as a fertilizer


Rhizobia and Legume Plants

  • Legumes: peas, clover, alfalfa, beans, peanuts, etc.

  • Rhizobia: nitrogen-fixing bacteria

  • Account for 25% of nitrogen fixation

  • Important in agriculture

    • Fertilizer

  • Process

    • Bacteria infect plant roots

    • Plant forms tumer-like root nodule to contain bacteria

    • Bacteria change N2 to NH3 where it can then easily be turned to different forms as needed

  • Benefit to Rhizobia?

    • Protection

    • Lack of competition

    • Provides organic C (via photosynthesis) for e- donor for N fixation

  • Need a very specific balance of oxygen

    • Nitrogenase is sensitive to damage by oxygen

    • Bacteria perform aerobic respiration, use oxygen as terminal electron acceptor

    • Plant produces leghemoglobin to keep environment microaerophilic (some O2, low level)


Termites

  • Related to cockroaches

  • Feed on dead plant material and cellulose

  • Gut microbes break down

    • Protists, bacteria, archaea

  • Strict wood diet

    • Source of nitrogen via nitrogen fixing bacteria

    • 3 organism synbiosis degrades cellulose

  • Bacteria

    • Nitrogen fixers

    • N2 → NH3

  • Protist

    • Trichonympha

    • Makes glutamine AA

    • Cellulose → glucose → acetate for host

  • Bacteria

    • Elusimicrobium

    • Converts glutamine to other AAs

    • Glucose → acetate

  • Termites provide

    • Protection

    • Nutrient supply


Bees

  • Fungus in pollen

    • Prevents spoilage

    • Important part of larval diet

  • Fungicides

    • Reduce bee population

    • Reduce growth of queen


Squids

  • Vibrio fisheri live in squids

  • Nocturnal

  • As they swim, cast shadows which give location away to predators

  • Bacteria causes them to mimic moonlight

  • Squids are not born with the bacteria

  • Bacteria in ocean diffuse into bacteria

  • Nitric oxide enocurgaes growth of A. fisheri bc they can metabolize it

  • Dangerous environmwnt for other bacteria

  • Bacteria get a place to live

  • Gauntlet for bacteria

    • Try to get to the crypt in the light organ of the squid

    • Swim past cilia beating in opposite direction

    • Get through nitric oxide

    • Get through acid

    • Swim all the way through

  • Some sort of education process to teach immune cells to not kill Vibrio fisheri

    • Immune cell will sacrafice itself to feed the bacteria




The Human Microbiome

  • More bacteria than in our own cells

  • To look at them

    • Check diff evironemnts

    • Try to maintain properties of them in process

    • Often use 16S rRNA

    • DNA sequencing

  • Where do we get out microbiome

    • Birth canal, breastmilk, everywhere

  • What can microbes do

    • Warn cells of danger

    • Teach immune cells what to attack and what to leave

    • Help with metabolism

  • Issues without microbiome

    • Asthma, obesity, other diseases