This chapter focuses on the metabolic diversity of anaerobic and aerobic metabolism with
particular emphasis on chemolithotrophic and phototrophic microorganisms. Chemolithotrophs
use inorganic compounds and phototrophs use light for energy sources rather than organic
compounds. In addition, the significance of autotrophy – the fixation of carbon dioxide into cell
material – and nitrogen fixation – the reduction of atmospheric dinitrogen into ammonia – is
After attending lecture and reading this chapter you should be able to:
1) List the major physiological categories of microorganisms and give the source of carbon,
energy, and electrons/reductant for each classification.
2) Understand that chemoorganotrophs, chemolithotrophs, and phototrophs can all be
anaerobes or aerobes.
3) Understand the function of alternate electron transport chain components in denitrifying
and chemolithotrophic respiration.
4) Describe the function and structure of the anammoxosome.
5) Understand the significance of stacked membranes and carboxysomes in aerobic
6) Know in general why chemolithotrophy is particularly important to environmental
7) Know when NADH can be made directly or when reverse electron flow is required.
8) Understand the basics of ammonia, nitrite, sulfur, and iron oxidation and the diversity of
electron transport systems used in organisms that catalyze these reactions.
9) Know the differences between photoheterotrophy and photoautotrophy and between
oxygenic and anoxygenic photosynthesis.
10)Understand the function of cyclic electron flow and how ATP and NADH are made in
11)Understand the nitrogenase reaction, the energy required, and its sensitivity to oxgen.
12)Describe the acetylene reduction assay for measuring nitrogen fixation
I. Metabolic Classifications of Prokaryotes
Categories based on carbon source
Organotrophs (or heterotrophs)
Use reduced organic compounds as their carbon and electron source
Use carbon dioxide as their sole or principal carbon source
Categories based on energy source
1 Phototrophs obtain energy from light
Chemotrophs obtain energy from chemicals (inorganic or organic)
By combining the two sets of categorizes, microorganisms can be placed into one of four major
groups, depending on their sources of carbon, energy, and electrons:
1. Chemoorganotrophs or chemoheterotrophs (all kingdoms of life including mammals)
2. Chemolithotrophs or (mostly) chemoautotrophs: aerobic and anaerobic bacteria,
3. Photoorganotrophs or photoheterotrophs: anaerobic bacteria,
4. Photolithotrophs or photoautotrophs: aerobic cyanobacteria, anaerobic bacteria,
plants, and algae
Mixotrophic organisms combine lithotrophic and organotrophic processes, relying on an
inorganic energy sources (H is 2 common example) and an organic carbon sources because they
may lack one or more enzymes for CO fixatio2. Note that nearly all chemolithotrophs are also
autotrophs – mixotrophs are rare.
The importance of prokaryotes in the geochemical cycling of nitrogen and sulfur is very obvious
as many reactions are only catalyzed by them. These prokaryotes contribute greatly to the
chemical transformation of elements that continually occur in the ecosystem: e.g. (nitrifying
bacteria, sulfur oxidizing bacteria, iron oxidizing bacteria, hydrogen oxidizing bacteria, methane-
producing archaea). Because of the limited energy available from oxidizing inorganic fuel
sources, each bacterial cell must consume several moles of its energy source to fix one mole of
CO .2Hence, a small microbial biomass results in a massive turnover of substrate and a large
II. Anaerobic Respiration
Anaerobic microorganisms use inorganic molecules other than oxygen as terminal electron
acceptors in electron transport chains for production of proton motive force and ATP for the cell.
Anaerobic respiration usually results in less PMF and ATP than aerobic respiration due to the
smaller difference in redox potential between the fuel source and the oxidant. Anaerobic
respiration still provides more ATP than fermentation. E. coli can perform aerobic respiration,
anaerobic respiration (using nitrate as a terminal electron acceptor), and fermentation, with a
concomitant decrease in energy yield. Prokaryotes are the sole players in anaerobic
The major electron acceptors in order of greatest energy yield are nitrate/ nitrite, some metals
(Fe, Mn), sulfate, and CO . B2th chemoorganotrophs and chemolithotrophs can carry out
Bacteria able to reduce nitrate to nitrite, but no further (e.g. E. coli) are referred to as nitrate
respirers, while those able to reduce it all the way to gaseous products (NO, N O, and N2) are 2
called denitrifiers. Denitrification is widespread among microorganisms. Denitrifiers possess all
the enzymes required to reduce nitrate (NO ) to 3 with n2trite (NO ), nitric2oxide (NO) and
nitrous oxide (N O2 as intermediate products, whereas nitrate respirers only have a nitrate
2 reductase in place of the aerobic terminal oxidase.
Sulfate reducers do not translocate protons across the cytoplasmic membrane to produce PMF.
Rather, lactate is consumed in the cytoplasm, eventually producing H from p2ruvate oxidation.
This H 2s transported through the membrane to a periplasmic hydrogenase that oxidizes H to 2
protons and electrons. The protons create PMF for ATP production, while the electrons move
back through the membrane via a transmembrane protein to reduce sulfate to hydrogen sulfide.
Anammox bacteria (anaerobic ammonia oxidation) create N by oxidiz2ng ammonia and
reducing nitrite. They do not use their cytoplasmic membrane at all for PMF and ATP
production. Rather, they have a very large intracellular organelle called an “anammoxosome.”
This organelle is bounded by a lipid bilayer and creates PMF in the cytoplasmic compartment of
the cell (i.e. outside of the anammoxosome membrane). ATP production occurs inside the
anammoxosome. As an interesting side note, anammox bacteria create highly toxic and explosive
intermediates such as hydrazine, which is rocket fuel. These bacteria are also very useful for
removing nitrogen from waste water as they can get rid of both ammonia and nitrite in one step.
Methanogenesis is only carried out by methanogenic archaea. These organisms are generally
chemolithotrophs, but some chemoorganotrophs (e.g. Methanosarcina spp.) can use acetate as an
electron donor. The chemolithotrophs oxidize H and r2duce CO as their 2MF-producing
III. Aerobic chemolithotrophs
A. Specialized structures.
Invagination of cell membrane. The membrane extends inward to the cytoplasm and outward
through the periplasm. Aerobic chemolithotrophs have these structures because of the very high
O 2emand (e.g. required substrate oxidation rate) involved in their metabolism, which is about
10 times greater than that of chemoorganotrophs. The invaginations provide more surface area
and enable more rapid transport of O and2mor