Week 1 – Overview of Microbial Metabolic Diversity
LO1: Understand the basic chemical requirements for life
LO2: Outline the diverse strategies that microbes use to obtain those basic chemical requirements
Biological Diversity, Metabolism and The Fundamental
Requirements of Life
“Life is nothing but an electron looking for a place to rest”, Albert Szent-Györgyi
What do we mean by diversity?
Morphological diversity; different sizes and shapes of organisms
Genetic (evolutionary) diversity; maps onto evolutionary diversity and living things
Metabolic diversity; the different kinds of chemistry you can use in order to sustain life
Macroorganisms (animals and plants) are morphologically very diverse, but very similar by other criteria
On a global scale, all animals are very closely related to each other, and so are plants, and all animals
are pretty closely related to all plants
o Animals do one kind of metabolism, plants another (photosynthesis)
Microbes are genetically and metabolically very diverse
Morphological diversity for them is less because they’re smaller and so all look like single celled
blobs
Genetic Diversity
Phylogenetic Tree of Life
The phylogenetic tree of life is defined in a rigorous, objective way using 16S ribosomal RNA sequencing to
look at how genetically different, different organisms are from each other
Done by comparing the sequences of a particular gene that encodes the 16S ribosomal RNA
sequence
Used because all living things have got that small ribosomal RNA
It is quantitative because the lengths of the branches correspond quantitatively to genetic differences, most
of which comes from microorganisms
See how all the large organisms are in one small box in the far right
Metabolic Diversity
Microbial metabolism controls the planet
E.g. Cyanobacteria in water and on land identified as source of methane
o Clearly microbial activity has a huge effect on methane and CO 2 []
E.g. Gulf of Mexico oil leak may give Arctic climate clues, the enormous amount of methane (a
potent greenhouse gas) released, and in areas of the Arctic trapped in the tundra and under the sea
there are loads of frozen methane which may be released due to climate change
, o Can’t think about what will happen to the released methane without considering microbes
because microbes consume the methane (this is a diverse kind of bacterial metabolism)
Microbes both consume methane which prevents excessive global warming, AND
produce methane so they matter a lot on a global scale
Metabolism from 1st Principle - What is metabolism all for?
Cyanobacteria is a photosynthetic bacterium, it assembles itself from the simple molecules CO 2 and H2O
along with a few minerals provided by the agar dish
Uses CO2 and H2O as the building blocks to make a large number of extremely complicated
molecules, which are arranged and controlled in complicated ways
The need to do that is the hallmark of life; life is all about specificity, to do that requires large complicated
specific molecules
The fundamental chemical requirements for life
Biological molecules produced by anabolic reactions
(”anabolic” - building up, “catabolic” - breaking down)
Anabolic reactions generally require:
Raw materials:
o Macronutrients: C, H, O, P, S, K, Mg, Ca, Na, Fe
All living things need to build their complicated specific molecules (e.g. proteins) by
assembling them from much smaller and simpler ingredients
o Micronutrients (trace elements): Co, Zn, Mo, Cu, Mn, Ni, Se, W
Free Energy: most anabolic reactions are energetically “uphill”
o There is an entropy “cost” from taking small simple molecules and combining them to make
something larger
Reducing power (a source of electrons); most anabolic reactions require a net output of electrons -
often supplied by reduced cofactors such as NADH, NADPH, FADH 2
o They are the “glue” that bonds molecules together, if you want to build large molecules or
glue more things together, then you need an extra source of electrons to make it happen
o Electrons are vital to do anabolic chemistry
Requirements of raw materials, energy and reducing power (electrons) for anabolic reactions
E.g. The Calvin cycle - a key anabolic metabolic pathway in plants and many bacteria (it is the MAIN
way not the ONLY way that biology fixed CO 2 from the atmosphere to produce sugars)
o Fixes CO2 to produce sugars (carbohydrates: [CH2O]n)
o Incredibly important for the biosphere - the key enzyme ribulose bisphosphate carboxylase
(Rubisco), may be the most abundant protein on the planet
Partially because its relatively inefficient under most circumstances, it requires a
large [] of that protein to complete the process
Image shows a thin section micrograph
of cyanobacteria, an organism that fixed
CO2, it has bacterial organelles called
carboxysomes which are packed with
rubisco enzyme's
The Calvin Cycle - a key anabolic pathway
LO1: Understand the basic chemical requirements for life
LO2: Outline the diverse strategies that microbes use to obtain those basic chemical requirements
Biological Diversity, Metabolism and The Fundamental
Requirements of Life
“Life is nothing but an electron looking for a place to rest”, Albert Szent-Györgyi
What do we mean by diversity?
Morphological diversity; different sizes and shapes of organisms
Genetic (evolutionary) diversity; maps onto evolutionary diversity and living things
Metabolic diversity; the different kinds of chemistry you can use in order to sustain life
Macroorganisms (animals and plants) are morphologically very diverse, but very similar by other criteria
On a global scale, all animals are very closely related to each other, and so are plants, and all animals
are pretty closely related to all plants
o Animals do one kind of metabolism, plants another (photosynthesis)
Microbes are genetically and metabolically very diverse
Morphological diversity for them is less because they’re smaller and so all look like single celled
blobs
Genetic Diversity
Phylogenetic Tree of Life
The phylogenetic tree of life is defined in a rigorous, objective way using 16S ribosomal RNA sequencing to
look at how genetically different, different organisms are from each other
Done by comparing the sequences of a particular gene that encodes the 16S ribosomal RNA
sequence
Used because all living things have got that small ribosomal RNA
It is quantitative because the lengths of the branches correspond quantitatively to genetic differences, most
of which comes from microorganisms
See how all the large organisms are in one small box in the far right
Metabolic Diversity
Microbial metabolism controls the planet
E.g. Cyanobacteria in water and on land identified as source of methane
o Clearly microbial activity has a huge effect on methane and CO 2 []
E.g. Gulf of Mexico oil leak may give Arctic climate clues, the enormous amount of methane (a
potent greenhouse gas) released, and in areas of the Arctic trapped in the tundra and under the sea
there are loads of frozen methane which may be released due to climate change
, o Can’t think about what will happen to the released methane without considering microbes
because microbes consume the methane (this is a diverse kind of bacterial metabolism)
Microbes both consume methane which prevents excessive global warming, AND
produce methane so they matter a lot on a global scale
Metabolism from 1st Principle - What is metabolism all for?
Cyanobacteria is a photosynthetic bacterium, it assembles itself from the simple molecules CO 2 and H2O
along with a few minerals provided by the agar dish
Uses CO2 and H2O as the building blocks to make a large number of extremely complicated
molecules, which are arranged and controlled in complicated ways
The need to do that is the hallmark of life; life is all about specificity, to do that requires large complicated
specific molecules
The fundamental chemical requirements for life
Biological molecules produced by anabolic reactions
(”anabolic” - building up, “catabolic” - breaking down)
Anabolic reactions generally require:
Raw materials:
o Macronutrients: C, H, O, P, S, K, Mg, Ca, Na, Fe
All living things need to build their complicated specific molecules (e.g. proteins) by
assembling them from much smaller and simpler ingredients
o Micronutrients (trace elements): Co, Zn, Mo, Cu, Mn, Ni, Se, W
Free Energy: most anabolic reactions are energetically “uphill”
o There is an entropy “cost” from taking small simple molecules and combining them to make
something larger
Reducing power (a source of electrons); most anabolic reactions require a net output of electrons -
often supplied by reduced cofactors such as NADH, NADPH, FADH 2
o They are the “glue” that bonds molecules together, if you want to build large molecules or
glue more things together, then you need an extra source of electrons to make it happen
o Electrons are vital to do anabolic chemistry
Requirements of raw materials, energy and reducing power (electrons) for anabolic reactions
E.g. The Calvin cycle - a key anabolic metabolic pathway in plants and many bacteria (it is the MAIN
way not the ONLY way that biology fixed CO 2 from the atmosphere to produce sugars)
o Fixes CO2 to produce sugars (carbohydrates: [CH2O]n)
o Incredibly important for the biosphere - the key enzyme ribulose bisphosphate carboxylase
(Rubisco), may be the most abundant protein on the planet
Partially because its relatively inefficient under most circumstances, it requires a
large [] of that protein to complete the process
Image shows a thin section micrograph
of cyanobacteria, an organism that fixed
CO2, it has bacterial organelles called
carboxysomes which are packed with
rubisco enzyme's
The Calvin Cycle - a key anabolic pathway
