Microbes and Metabolism 29It has as the ultimate electron and hydrogen sink, a variety of simple organic
compounds including acetic acid, methanol and carbon dioxide. In this case,
the end product is methane in addition to carbon dioxide or water depending
on the identity of the electron sink. These are the processes responsible for the
production of methane in an anaerobic digester which explains the necessity to
exclude air from the process.
Fermentation and respiration
The electrons derived from the catabolism of the carbon source are eventually
either donated to an organic molecule in which case the process is described as
fermentation, or donated to an inorganic acceptor by transfer along an electron
chain. This latter process is respiration and may be aerobic where the terminal
electron acceptor is oxygen, or anaerobic where the terminal electron acceptor
is other than oxygen such as nitrate, sulphate, carbon dioxide, sulphur or ferric
ion. Unfortunately, respiration is a term which has more than one definition. It
may also be used to describe a subset of the respiration processes mentioned
above to include only oxidation of organic material and where the ultimate elec-
tron acceptor is molecular oxygen. This latter definition is the basis of biological
oxygen demand (BOD), which is often used to characterise potential environmen-
tal pollutants, especially effluents, being a measure of the biodegradable material
available for oxidation by microbes.
Fermentations
In modern parlance, there are many definitions of the term ‘fermentation’. They
range from the broadest and somewhat archaic to mean any large-scale culture of
micro-organisms, to the very specific, meaning growth on an organic substance
and which is wholly dependent on substrate-level phosphorylation. This is the
synthesis of ATP by transfer of a phosphate group directly from a high energy
compound and not involving an electron transport chain. Additionally, and a
source of great confusion, is that fermentation may refer simply to any microbial
growth in the absence of oxygen but equally may be used generally to mean
microbial growth such as food spoilage where the presence or absence of oxygen
is unspecified. The definition used throughout this book, except with reference
to eutrophic fermentation discussed in Chapter 8, is that of growth dependent on
substrate-level phosphorylation.
There are very many fermentation routes but all share two requirements, the
first being the regeneration of NAD+from NADH produced during glycolysis
which is essential to maintain the overall reduction: oxidation equilibrium, and
the second being that pyruvate, or a derivative thereof, is the electron accep-
tor during the reoxidation of NADH. What this means is that all fermentation
routes start with pyruvate, the end-point of glycolysis, and proceed along a vari-
ety of pathways to an end product indicative, if not diagnostic, of the organism.