1548 Ecological Processes | Fermentation

Fermentation
M Ciani, F Comitini, and I Mannazzu, Università Politecnica delle Marche, Ancona, Italy
ª 2008 Elsevier B.V. All rights reserved.

Metabolic Biodiversity Other Fermentation Pathways

The Fermentation Process Ecological Niches and Interactions among Fermenting
Ecological Distribution of Fermentation Processes Microorganisms
Industrial Fermentation Further Reading

Metabolic Biodiversity main product of fermentation, and it is generated by

In the biological world, the enormous assortment of
energy sources can be used in many different ways to
support the growth of organisms. The characteristics of
the different pathways that can be used to produce the
energy that arises from coupled oxidation–reduction
reactions and is needed for living processes are listed in
Table 1.
The Fermentation Process
When respiration is not possible, due to either a lack of an
external electron acceptor or an impairment of the
respiratory chain, fermentation is the catabolic pathway
that is used for the production of energy from the partial
oxidation of glucose or other carbon sources (Figure 1).
The oxidation of the substrate, which occurs
mainly through the Embden–Meyerhoff and Parnas
(EMP) or Entner–Doudoroff (ED) pathways, results in
the production of pyruvate, adenosine triphosphate
(ATP), and nicotinamide adenine dinucleotide phosphate
(NAD(P)H). In the absence of external electron accep-
tors, the pyruvate or the other organic compounds that
derive from the initial substrate reaction undergo reduc-
tion, with the regeneration of NADþ(P). This step is
essential for the fermentation process to progress and it
leads to the production of waste products (ethanol and
organic acids) that are excreted from the cell. ATP is the
phosphorylation at the substrate level. An exception to
this general rule is seen with the fermentation of car-
boxylic acids. The catabolism of these substrates
generates a gradient of Hþ or Naþ ions across the plasma
membrane, and the production of ATP involves the activ-
ity of the Hþ or Naþ membrane ATPases.
While the complete oxidation of 1 mol of glucose to
CO2 through oxidative phosphorylation (respiration)
generates up to 38 mol of ATP, fermentation produces
only a few moles of ATP (1–3) per mole of glucose. Thus,
the recovery of energy from fermentation is rather low
compared to that yielded by respiration. Moreover, it
varies depending on the initial substrate and the fermen-
tation process itself.
Ecological Distribution of Fermentation
Processes
Fermentative metabolism is widespread among living
organisms, and the ecology of fermentative processes is
particularly complicated due to the ability of different
organisms to ferment a plethora of substrates under dif-
ferent environmental conditions. Fermentation is carried
out in anoxic environments by strict anaerobic or
facultative anaerobic microorganisms, although some
microaerophilic or facultative anaerobic microorganisms
are also able to carry out fermentation in the presence of
oxygen.

Table 1 Metabolic biodiversity among living organisms

Metabolic diversity Characteristics

Phototrophy When radiant energy is absorbed by chlorophyll or other similar pigments, resulting in an excitation of the
electrons present in the complex and providing oxidation that produces oxygen (oxygenic photosynthesis)
or does not produce oxygen (nonoxygenic photosynthesis)
Aerobic respiration Molecular oxygen is the final acceptor of electrons in a redox reaction and appears in reduced form as water
Anaerobic respiration Under anaerobic conditions where molecular oxygen is absent or limited, inorganic ions (nitrate, sulphate,
carbonate) serve as final acceptors of electrons
Fermentation An organic compound that is often a metabolic intermediate coming from oxidation of an organic compound
serves as terminal oxidant, producing a more reduced organic molecule as the metabolic end product

Aminoacids
Organic
substrate Hydrolysis Sugars
Organic acids
Figure 1 Main end products of the various fermentation processes.
Microaerophilic fermenting microorganisms, such as
lactic acid bacteria, colonize habitats that are character-
ized by low oxygen concentrations or the absence of
oxygen (often c. 10% of atmospheric levels). These
microaerophilic microorganisms show a wide ecological
distribution in well-defined habitats, such as the animal
and human oral cavity, the gastro-intestinal tract, and
feces, as well as in fermented meat, beverages, vegetables
(silage, olive brine, sauerkraut), and dairy products. Lactic
acid bacteria have limited biosynthetic ability and require
pre-formed amino acids, group B vitamins, purines, and
pyrimidines. These multiple requirements restrict their
growth to habitats where the required compounds are
abundant. The fermentation activity of lactic acid bacteria
produces large amounts of lactic acid, which can cause a
drop in pH to about 4.0, and thus inhibit the growth of
most other bacteria and exert an antagonistic effect on
spoilage microorganisms and the most common human
pathogens. For these reasons, the transformation of food
and beverages by fermentation is one of the main mod-
alities for the conservation of food products and the
enhancement of their quality.
Besides microaerophilic lactic acid bacteria, anaerobic
facultative microorganisms such as yeasts are the main
group of microorganisms that are involved in the trans-
formation of fermented food. In contrast to the facultative
anaerobic bacteria, which always preferentially carry out
respiration as a metabolic pathway in the presence of
oxygen, facultative anaerobic yeast can also adopt a fer-
mentative metabolism in the presence of oxygen. This is
the case for Saccharomyces cerevisae, the most representative
yeast used in a wide varieties of industrial fermentative
processes. S. cerevisiae exhibits a specific mechanism of
respiro-fermentative regulation that is known as the
‘Crabtree effect’. At high sugar concentrations, and even
in the presence of oxygen, fermentation overrides
Ecological Processes | Fermentation 1549
Ethanol
Lactate
Glycerol
Propionate
Acetate
Fermentation 2 – 3 Butanediol
Butanol
Butyrate
Formiate
H2 + CO2
respiration. This mechanism results in a high rate of
sugar consumption and therefore the colonization of habi-
tats with high sugar content. Consequently, the ecological
niche of fermentative yeasts includes sugary fruits, flow-
ers, lymph, and tree exudates.
Anaerobic facultative bacteria represent a group of
microorganisms that is broadly diffuse in several habitats.
These microorganisms can grow in the presence of oxy-
gen, and they can use fermentative metabolism when
oxygen is not available. Anaerobic facultative bacteria
such as Enterobactericeae colonize the intestinal tract of
warmblooded animals, and some species belonging to
the genera Yersinia, Salmonella, and Shigella can cause
infectious diseases. The habitat of enteric bacteria is
very specific. Escherichia coli, the most well-known species
among the enteric bacteria, is used as indicator of fecal
contamination of water and food because of its low survi-
val in other environments. Since enteric bacteria are
anaerobic and facultative, they have important roles in
the ecology of the gut of warmblooded animals. By con-
suming the oxygen available in this habitat they maintain
the right conditions for the proliferation of other bacteria
that constitute the intestinal microflora (lactic acid bac-
teria, bifidobacteria).
Other facultative or obligate anaerobic bacteria can be
found in both soil and water environments, where they
have fundamental roles in the transformation of organic
substances under anoxygenic conditions. An example is
provided by methanogenesis, a bioprocess that occurs in
natural environments, such as the rumen, marshes, and
the industrial sites of anaerobic wastewater treatment
plants. During this process, a first group of fermenta-
tive/hydrolytic microorganisms produces low molecular
weight organic acids, alcohols, CO2, and H2. Another
bacterial group, known as the ‘syntrophic microorgan-
isms’ is very important for the conversion of organic
1550 Ecological Processes | Fermentation
compounds to CH4 during methanogenesis. In this pro-
cess, called syntrophy, methanogenic bacteria cooperate
with other fermenting microorganisms to produce the
substrates that are necessary to realize their specific eco-
logical interactions. The H2 derived from organic
molecules and produced after energetically unfavorable
fermentation is consumed by methanogenic bacteria, and
the overall reaction produces energy that is used by the
syntrophic couple.
Industrial Fermentation
As indicated above, natural fermentation is widely diffuse
in several ecological niches where the conditions of anae-
robiosis, high concentrations of carbohydrates (the
Crabtree effect), or the lack of carbohydrates (fermenta-
tion of amino acids) determine the predominant
fermenting organisms. All fermentative processes that
are today devoted to food and animal feed transformation
and preservation have ancient origins and have been
traditionally carried out by the microorganisms naturally
present in the substrates. The advent of industrialization,
the construction of appropriate equipment, and the devel-
opment of microbiology as an applied science have led
the development of the fermentation industry, transform-
ing a great number of the natural fermentation processes
into industrial-scale fermentation. These transformations
have been applied to wine, beer, distilled beverages and
bread industries where alcoholic fermentation is mainly
involved, and to the dairy and meat transformation
industries, in which lactic fermentation is the main
fermentation process. In these fermentation industries,
the use of selected starter cultures during different stages
of the fermentation processes has become progressively
diffuse. The aim of this procedure is to improve the
Table 2 Examples of industrial fermentation and their producer microorganisms
Fermented food and animal
feed Microorganisms involved
Fermented meat (salami) Lactic acid bacteria
Fermented milk Lactic acid bacteria
Fermented milk Lactic acid bacteria and yeast
Cheese Lactic acid bacteria; propionic
bacteria
Bread and bakery products Yeast and lactic acid bacteria
Beer Yeast
Wine Yeast
Olive brines Lactic acid bacteria
Silage Lactic acid bacteria
Coffee Lactic acid bacteria and yeast
Cocoa Yeast and lactic acid bacteria
management of the fermentation process through avoid-
ance of the development of spoilage and pathogenic
microorganisms, and enhancement of the quality of the
final product. Table 2 lists these main fermentation pro-
cesses that are involved in the food and animal-feed
industries.
Alcoholic Fermentation
Alcoholic fermentation is the best known of the fermenta-
tion processes, and is involved in several important
transformation, stabilization, and conservation processes
for sugar-rich substrates, such as fruit, and fruit and vege-
table juices. Alcoholic fermentation is carried out by
yeasts and some other fungi and bacteria. The first step
of the alcoholic fermentation pathway involves pyruvate,
which is formed by yeast via the EMP pathway, while it is
obtained through the ED pathway in the case of
Zymomonas (bacteria). In the following step, the pyruvate
is decarboxylated to acetaldehyde in a reaction that is
catalyzed by the enzyme pyruvate decarboxylase
(Figure 2).
The redox balance of alcoholic fermentation is
achieved by the regeneration of NADþ during the reduc-
tion of acetaldehyde to ethanol, which is catalyzed by
alcohol deydrogenase. The ATP yield of alcoholic fer-
mentation is 1 or 2 mol of ATP per mole of glucose
oxidized via the ED and EMP pathways, respectively.
Zymomonas mobilis is the most important bacterial species
that is able to perform alcoholic fermentation. The habitat
of this species is the lymph of tropical trees, such as the
palma tree from where it was originally isolated. Z. mobilis
was proposed and used as a starter for ethanol production
at the industrial level, although at present alcoholic fer-
mentation carried out by yeast is better known and has
been more thoroughly investigated. Natural alcoholic
Fermentation Undesired fermentation
Lactic
Lactic Alcoholic
Lactic and alcoholic
Lactic and sometimes Mixed-acid and butyric
propionic acid
Alcoholic and heterolactic
Alcoholic Lactic and mixed acid
Alcoholic Lactic
Lactic Butyric
Lactic Amino acids
Butyric
Mixed-acid
Alcoholic and lactic
Alcoholic and lactic

Glucose
Glucose-6P
Fructose-6P
Fructose-1,6PP
Dihydroxyacetone Glyceraldehyde-3-phosphate
+
NAD
NADH NADH
+
NAD
1,3-Diphosphoglycerate
Glycerol-3-phosphate
Pyruvate
Glycerol
Acetaldehyde
NADH
NAD+
Ethanol
Figure 2 Alcoholic fermentation and deviation from alcoholic
to glycero-pyruvic fermentation. Black line: alcoholic pathway;
red line: Glycero-pyruvic pathway; yellow box: intermediate
metabolites involved in alcoholic fermentation block.
fermentation of fruit (cacao) and fruit juices (grape must
and apple juice) is carried out by different microorgan-
isms that act sequentially. The substrate fermentation is
first achieved by apiculate yeast (Hanseniaspora), which is
followed by elliptical yeast (Saccharomyces). Other fer-
menting yeast ascribed to the genera Candida,
Kluyveromyces, Metschnikowia, Pichia, Saccharomycodes,
Torulaspora, and Zygosaccharomyces are also sometimes
found during natural alcoholic fermentation.
It is well established that the most important agent of
alcoholic fermentation is S. cerevisiae, the yeast that is used
widely in several fermentation industries (wine, beer,
cider, and bread) as a microbial starter. S. cerevisiae
becomes the dominant species during alcoholic fermenta-
tion of fruit and fruit juices because of the strongly
selective environment due to the low pH and high sugar
and ethanol concentrations, and the anaerobic conditions.
The ecological distribution of S. cerevisiae and the role of
different habitats in the evolution of this species are con-
troversial. Numerous investigations have revealed the
low diffusion of this yeast species in natural environments
such as soil, fruit surfaces, and tree exudates. On the other
hand, S. cerevisiae is found widely in wineries and other
fermentation plants since it is used to carry out the fer-
mentation processes.
In the winery, several environmental factors, including
high ethanol and sugar concentrations, the presence of
SO2, and others, can exert selective pressures on the
S. cerevisiae population. Following these considerations,
S. cerevisiae is defined as a domesticated species because
of its selection through time in man-made environments.
Ecological Processes | Fermentation 1551
Glycero-Pyruvic Fermentation
Glycero-pyruvic fermentation is always concomitant to
alcoholic fermentation, although it involves a very low
percentage of sugar (5–8%). However, under particular
fermentation conditions, some osmotolerant yeast species
(e.g., Torulopsis magnoliae, Torulopsis bombicola, and Candida
stellata) and other fermenting yeast (S. cerevisiae) can fer-
ment sugar to produce glycerol and, for example,
acetaldehyde, acetic acid, acetoin, 2,3-butanediol and
succinic acid, all compounds that can be derived from
pyruvate.
The change from alcoholic to glycero-pyruvic fermen-
tation occurs mainly because of the need to regenerate
NADþ when the reduction of acetaldehyde to ethanol is
not possible (Figure 2). This could be due to: (1) the
nonavailability of acetaldehyde, if it is bound by sulfite;
(2) the absence or low activity of pyruvate decarboxylase;
and (3) the high activity of the aldehyde dehydrogenase
enzyme (under alkaline pH) that catalyzes the reaction
from acetaldehyde to acetate.
In the past, between the two world wars, glycero-
pyruvic fermentation was exploited at an industrial level
for the production of glycerol.
Propionic Acid Fermentation
Propionic acid fermentation is carried out by several
bacteria that belong to the genus Propionibacterium and to
the species Clostridium propionicum. During propionic acid
fermentation, both sugar and lactate can be used as the
initial substrate. When sugar is available, these bacteria
use the EMP pathway to produce pyruvate; the pyruvate
is carboxylated to oxalacetate by methyl malonyl coen-
zyme-A (CoA) and then reduced to propionate via
malate, fumarate, and succinate. The other end products
of propionic fermentation are acetic acid and CO2
(Figure 3). In particular, the propionic acid fermentation
of 3 mol of glucose produces 4 mol of propionic acid,
2 mol of acetic acid, 2 mol of CO2, and 12 mol of ATP.
When lactate is the initial substrate, propionic fermenta-
tion results in the production of 2 mol of propionic acid,
1 mol of acetic acid, and 1 mol of CO2. In this process,
1 mol of ATP is generated per nine carbons, and because
of this, propionic bacteria generally grow very slowly.
The typical natural habitats of Propionibacterium are
the rumen, the intestinal tract of animals and the skin of
mammalians. Propionibacterium also colonize cheese dur-
ing maturation. While the metabolic activity of
Propionibacterium should be avoided during the matura-
tion of the vast majority of cheese, it is required for the
production of some typical products, such as Emmental
cheese. In this Swiss-type cheese, two successive fer-
mentations occur. During its manufacture, lactic acid
bacteria convert lactose into lactate, and then during
1552 Ecological Processes | Fermentation
3 mol
Glucose
3 mol
Lactate
Pyruvate
Oxalacetate
Malate
Fumarate
Succinate
Propionate
4 mol
Figure 3 Propionic fermentation and different yields of the final products coming from glucose or lactate as the initial substrate.
ripening, propionic acid bacteria convert the lactate into
propionic acid, acetic acid, and CO2. The CO2 is
responsible for ‘eye’ formation and the propionic acid
promotes the typical nutty flavor of this Swiss-type
cheese. The ability to use lactate is particularly relevant
for the ecological distribution of propionic acid ferment-
ing bacteria, which can use the final product of lactic
acid fermentation.
Amino Acid Fermentation
In the absence of electron acceptors such as oxygen,
nitrate, and sulfate, Clostridium, Fusobaterium, and a few
other anaerobes can ferment amino acids. This fermenta-
tion occurs during anaerobic and putrefaction processes.
The most important mechanism for amino acid degrada-
tion is Stickland fermentation; during Stickland
fermentation of two amino acids, one serves as the elec-
tron donor while the other serves as the acceptor. All
amino acids are classified into electron acceptors or
donors on the basis of Stickland fermentation, and only
tryptophan and tyrosine can behave both as an acceptor
and a donor. In addition to decarboxylation of various
amino acids by this mechanism, the subsequent reactions
yield a variety of products that can have unpleasant odors.
In the absence of fermentable carbohydrates and in rich
protein substrates, a large number of Clostridium species –
such as C. botulinum, C. tetani, and C. perfringens – can
generate ATP from amino acid fermentation. The ATP
yield here is 1 mol per 3 mol of amino acid used, and thus
the reaction is highly advantageous for organisms that can
grow in rich anaerobic protein environments. The main
products of the Stickland reaction are NH3, CO2, short-
chain fatty acids and H2, and the minor products are
hydrogen sulfide, methyl mercaptane, phenols, and alco-
hols, which together with fatty acids form a typical
1 mol
2 mol
Acetic acid
1 mol
CO2 2 mol
ATP 1 mol
12 mol
2 mol
putrefying odor. The favorite habitat of Clostridium is the
soil, in anaerobic scrap previously colonized by aerobic
bacteria, and Clostridium species can also colonize the
mammalian intestine. Moreover, these species can pro-
duce infectious diseases, such as botulism caused by
C. botulinum, tetanus by C. tetani, and gangrene by
C. perfringens. Clostridium sporogenes, a typical soil bacteria,
can also participate in peritoneal infection that can occur
as a result of the proliferation of food pathogens, intestinal
obstruction, or mesenteric thrombosis.
Lactic Acid Fermentation
Depending on the pathway used for glucose oxidation,
lactic acid fermentation can result in the production of
lactate (homolactic fermentation), lactate, ethanol/
acetate, and CO2 (heterolactic fermentation) or lactate
and acetate (the bifid shunt). Lactic acid fermentation is
carried out by lactic acid bacteria and bifidobacteria, and
also by some species of Bacillus, some protozoa and water
molds, and the cells of human skeletal muscle when they
are subjected to extreme work under oxygen deprivation.
Both homolactic and heterolactic fermentation are
involved in food and animal feed transformation and
preservation. In particular, lactic acid fermentation is
mainly responsible for the souring of milk products and
is used in the production of yogurt and other fermented
milk products (e.g., cheese, buttermilk, and sour cream).
However, lactic acid fermentation also occurs during the
fermentation of sauerkraut, and in other vegetable and
sourdough bread fermentation, and it has important roles
in sausage maturation, and silage fermentation and stabi-
lization. The bifid shunt occurs mainly in the human and
animal large intestine, where bifidobacteria are among the
most abundant of the microbial groups.
 Ecological Processes | Fermentation 1553

Homolactic Fermentation
Homolactic fermentation is carried out by bacteria belong-
ing to the genera Lactococcus, Enterococcus, Streptococcus, and
Pediococcus, and by some species of the genus Lactobacillus.
All of these bacteria can convert sugar to mainly lactic acid,
via glycolysis. The enzyme lactate dehydrogenase (LDH)
catalyzes the last step of this fermentation; in particular, by
transferring hydrogen from NADH to pyruvate, LDH
leads to pyruvate reduction and NADH reoxidation, with
the production of D- or L-lactate. ATP formation is
coupled to pyruvate production and the ATP yield of
homolactic fermentation is 2 mol per mole of glucose oxi-
dized (Figure 4). The homolactic behavior is not
obligatory, but depends on sugar type, rate of the glycolytic
flux, and growth conditions. Some homofermentative bac-
teria can catabolize glucose in a heterofermentative
fashion, or carry out mixed-acid fermentation when the
glycolytic flux is low, thus decreasing or increasing the
ATP yield per mole of glucose, respectively.
Heterolactic Fermentation
Heterolactic fermentation is carried out mainly by bac-
teria of the genera Leuconostoc, Oenococcus, and Weissella,
and by heterofermentative lactobacilli. Obligate hetero-
fermentative bacteria do not perform glycolysis due to the
lack of aldolase, the enzyme that breaks down fructose
1,6-bisphosphate into glyceraldehyde 3-phosphate
and dihydroxyacetone phosphate. Glucose 6-phosphate
is oxidized to 6-phosphogluconate and fermentation
is carried out through the phosphoketolase pathway
(Figure 4). The final products of this fermentation are
lactate, ethanol, and CO2 but acetate may also be pro-
duced. The ATP yield is 1 mol per mole of glucose; thus,
heterolactic metabolism yields less energy than homolac-
tic fermentation. Heterolactic fermentation can also be
carried out by facultative homofermentative bacteria.
Bifidobacterium Lactic Acid Fermentation
This type of lactic acid fermentation is exclusive to Gram-
positive bacteria belonging to the genus Bifidobacterium.
These bacteria are found mainly in the intestinal tracts
of warmblooded animals and they are recognized as pro-
biotic. In fact, they help in the maintenance of the
balanced composition of the intestinal microflora and
they exert positive effects on the health and well-being
of the host. Bifidobacteria do not have aldolase and glu-
cose-6-phosphate dehydrogenase; they thus ferment
hexose via a phosphoketolase pathway that is known as
the ‘bifid shunt’, where the final products are acetic and
lactic acids in a molar ratio of 3:2. The key enzyme in the
bifid shunt is fructose-6-phosphate phosphoketolase
(F6PPK), which converts frutose 6-phosphate into acetyl
1-phosphate and eritrose 4-phosphate (Figure 5). The
ATP yield is 5 mol per 2 mol of glucose, and it is therefore
higher than that of homolactic fermentation.
2 Glucose
2 ATP
2 ADP

2 Fructose-6P
ATP Glucose ATP
ADP ADP

Glucose-6P Glucose-6P
Fructose-6P Acetyl-P + Eritrose-4P
ADP 6P-gluconate Fructose-6P
ADP
ATP Ribulose-5P + CO2
Fructose-1,6PP
Xylulose-5P Heptose-P + Triose-P
ATP ATP
2 Glyceraldehyde-3P
4ADP ADP
Glyceraldehyde-3P + Acetyl-P 2 Acetyl-P 2 Glyceraldehyde-3P
4ATP 2 ADP ADP Acetate
4 ADP
2 ATP
Pyruvate ATP 4 ATP
Piruvate 2 ADP
2 NADH NADH NADH

NAD+ 2 Pyruvate
2 NAD+ NAD+
2 ATP 2 NADH
Lactate Lactate Ethanol
(a) (b)
2 NAD+
Figure 4 Schematic representation of homolactic (a) and 2 Acetate 2 Lactate
heterolactic (b) fermentations. Pyruvate reduction leads to the
regeneration of NADþ. Figure 5 Schematic representation of bifid shunt.
1554 Ecological Processes | Fermentation
Mixed-Acid Fermentation
Mixed-acid fermentation is characteristic of the
Enterobacteriaceae ascribed to the genera Citrobacter,
Escherichia, Proteus, Salmonella, Shigella, Yersinia, and Vibrio,
and to some species of Aeromonas; it is also carried out by
some anaerobic fungi. This metabolic group includes micro-
organisms that have a different ecology and impact on
human activities. Some of them are members of the normal
intestinal microflora of mammals and other vertebrates
(E. coli) and have a role in the colonization of lignocellulose
in the rumen (Neocallimastix). Some others are pathogens that
are responsible for human and animal diseases, and they can
be abundant in aquatic and terrestrial environments. These
microorganisms can ferment monosaccharides, disacchar-
ides, polyalcohol, and, less frequently, polysaccharides, via
the glycolytic pathway, producing lactic, formic, succinic and
acetic acids, and ethanol (Figure 6). The final amounts of
each end product vary depending on the microorganism and
the growth conditions; however, the ratio of acid to neutral
products is 4:1. Mixed-acid fermentation also results in the
production of equimolar amounts of CO2 and H2 in those
(Erwinia). Butanediol fermentation produces less acids than
mixed-acid fermentation as two molecules of pyruvate are
used to produce one molecule of 2,3-butanediol and are
therefore not available for the production of acid compounds.
Thus, the ratio of acidic to neutral products is 1:6. Moreover,
the reactions that lead to the production of 2,3-butanediol
involve a double decarboxylation step; thus, butanediol fer-
mentation produces more gas than mixed-acid fermentation,
with a ratio of carbon dioxide to hydrogen of 5:1.
Butyric Acid Fermentation
Butyric acid fermentation is characteristic of several obli-
gate anaerobic bacteria that mainly belong to the genus
Clostridium; by means of glycolysis, these are able to oxidize
sugar, and occasionally amylose and pectin, to pyruvate.
Pyruvate is in turn oxidized to acetylCoA by the pyruvate–
ferredoxin oxidoreductase enzyme system, with the pro-
duction of CO2 and H2. Part of the acetylCoA is converted
into acetic acid, with ATP production. The other part
generates acetoacetylCoA, which is reduced to
bacteria with the formate–hydrogen–lyase complex.
Pyruvate formate–lyase and LDH, the enzymes that control
entry into mixed-acid fermentation, are negatively regulated
by oxygen; thus, mixed-acid fermentation requires anaerobic
conditions to occur. That is why the natural habitat of
microorganism carrying out mixed-acid fermentation is the
gastro-enteric apparatus. The ATP yield of mixed-acid fer-
mentation is about 2.5 mol of ATP per mole of glucose.
Butanediol Fermentation
Butanediol fermentation is carried out by members of the
genera Enterobacter, Erwinia, Hafnia, Klebsiella, and Serratia.
Most of these bacteria can be found in soil and water
(Enterobacter and Serratia) and they can be plant pathogens
butyrylCoA through the production of -oxybutyrylCoA
and crotonylCoA. The transformation of butyrylCoA into
butyrate leads to further ATP production. Thus, this fer-
mentation process produces a relatively high yield of
energy, with 3 mol of ATP for each mole of glucose.
Small amounts of ethanol and isopropanol can also be
produced (Figure 7). Butyric fermentation is quite com-
mon in silage when the pH is not low enough to ensure the
exclusive activity of lactic acid bacteria. The carbon
dioxide produced during butyric fermentation also causes
an increase in the pH of the silage, thus enhancing further
butyric fermentation. Some bacteria, such as Clostridium
acetobutylicum, produce less acids and more neutral products,
thus carrying out acetone butanol fermentation. This fer-
mentation had great importance during World War I due
to the need for acetone for the production of munitions.

Glycolysis

2 ATP Pyruvate
NADH
Succinate Pyruvate
Formiate CO2 CO2
NADH
Acetyl-CoA H2 Acetolactate
Lactate
NADH CO2

Acetyl-P Acetaldehyde Acetoin

NADH NADH
ATP

Acetate Ethanol Butanediol

Figure 6 End products of mixed-acid and butanediol fermentation.

 Ecological Processes | Fermentation 1555

The main fermentation processes are summarized in controlled mechanism: if acetic acid is present in excess, a
Table 3 in terms of energy yield. considerable amount of butyric acid is formed, while if
ethanol is in excess, caproic acid is the main product.
These relationships suggest that butyric acid is an inter-
Other Fermentation Pathways mediate in the synthesis of caproic acid from acetic acid.
In homoacetic fermentation, the Acetobacterium group
The names of some other fermentation pathways derive converts fructose into acetate, and it appears that the nutri-
from the names of the final products. This is the case for tional requirements of this organism are complex. During
caproic, homoacetic, and methanogenic fermentation. For methanogenesis, methane can be formed via methanogenic
caproic fermentation, Clostridium kluyveri is the species that fermentation by Methanosaeta and Methanosarcina, which
can metabolize acetic acid and ethanol under anaerobic convert acetate and water into CH4 and carbonic acid.
conditions, producing butyric and caproic acids, in a specific In addition, there are some relatively rare fermentation
pathways that are carried out by very restricted anaerobic
Glycolysis microorganisms. In Table 4, some examples of the fermen-
ted substrates, the microorganisms and the biochemistry of
the reactions are summarized. Generally, these fermenta-
Pyruvic acid tion pathways are carried out by specialized bacteria that
use substrates that cannot be metabolized by other micro-
+ CoA + SH biological groups. Nevertheless, during the catabolic
process, all of these rare fermentation pathways produce
intermediate compounds that have high residual energies
Formic acid Acetyl-S-CoA and are commonly CoA derived, from which these micro-
organisms obtain their ATP.
The first example includes anaerobic microorganisms
+ 4H that can degrade xenobiotic industrial chemical com-
Ethanol
CO2 H2 – CoA – SH pounds through a combination of co-metabolic steps,
– CoA – SH which often yield partial degradation, or by serving as
Acetic acid +Acetyl-S-CoA growth substrates that are accompanied by mineralization
–CoA–SH of at least part of the molecule. Indeed, while aerobic
microorganisms use oxidative reactions, degradation by
Acetoacetyl-S-CoA anaerobic bacteria takes place by reduction reactions, and
they thus degrade aromatic compounds by reductive
– CO2 + 4H conversions with the central intermediates that are
Acetone Butyryl-S-CoA ready for hydrolytic ring cleavage having a 1,3-dioxo
– CoA – SH
+ 4H structure. Using an example, including aromatic, chlor-
+ 2H – CoA – SH
oaromatic, aliphatic, and chloroaliphatic compounds, one
Butyric acid Butanol case of anaerobic degradation is presented. The recently
Isopropanol
isolated fermenting bacterium Pelobacter massiliensis is
Figure 7 Different metabolic pathways of butyric acid the only strict anaerobe that is known to grow on hydro-
fermentation. xyhydroquinone (1,2,4-trihydroxybenzene) as the sole

Table 3 Summary of fermentation processes with the corresponding energy yield

Fermentation process Energy yield

Alcoholic fermentation 2 mol ATP/mol glucose

Glycero-pyruvic fermentation Net ATP production
Propionic acid fermentation (glucosea) 4 mol ATP/mol glucose
Propionic acid fermentation (lactatea) 0.3 mol ATP/ mol lactate
Amino acid fermentation 0.3 mol ATP /mol amino acid
Lactic acid fermentation (homolactic) 2 mol ATP/ mol glucose
Lactic acid fermentation (heterolactic) 1 mol ATP/ mol glucose
Bifidobacterium lactic acid fermentation 2.5 mol ATP/mol glucose
Mixed acid fermentation 2.5 mol ATP/mol glucose
Butanediol fermentation 2.5 mol ATP/mol glucose
Butyric fermentation 3 mol ATP/mol glucose
a
Carbon source.
1556 Ecological Processes | Fermentation

Table 4 Microorganisms and type of substrates metabolized in rare fermentation processes

Substrate Microorganism Reaction

Acetate Methanosaeta Acetate þ H2 O ! CH4 þ HCO3–

Ethanol and acetate Clostridium kluyveri Ethanol þ Acetate þ CO2 ! Caproate þ Butyrate þ H2
Fructose Acetobacterium spp. Fructose ! Acetate þ H2CO2 ! Acetate þ H2O
Hydroxyhydroquinone Pelobacter massiliensis, Pelobacter acidigallici C6H6O3 þ H2O ! Acetate þ Hþ
Malonate Malonomonas rubra Malonate þ H2 O ! Acetate þ HCO3–
Oxalate Oxalobacter formingenes Oxalate þ H2 O ! Formiate þ HCO3–
Putrescine Gramþ bacteria C4H12N2 þ H2O ! Acetate þ þ Butyrate þ NHþ 4 þ H2 þ H
þ

Lactic acid bacteria Propionic

and yeast bacteria and
lactic acid bacteria
Fermented milk (kefir, koumiss)
and sourdoughs
Cheese ripening

Ecological niches and

interactions among
fermenting
microorganisms Lactic acid bacteria
Bifidobacterium
Enteric bacteria

Silage
Intestinal tract of
warmblooded animals

Lactic acid bacteria

Clostridium bacteria
Enteric bacteria

Figure 8 Examples of ecological niches where different fermenting microorganisms coexist.

source of carbon and energy, converting it to stoichio-
metric amounts of acetate. Another example is seen in
Malonomonas rubra, which is a microaerotolerant ferment-
ing bacterium that can maintain its energy metabolism for
growth by decarboxylation of malonate to acetate.
M. rubra is closely related to the cluster of mesophilic
sulfur-reducing bacteria within the delta subclass of
Proteobacteria, with the fermenting bacterium Pelobacter
acidigallici and the sulfur reducers Desulfuromusa kysingii,
D. bakii, and D. succinoxidans as its closest relatives.
Ecological Niches and Interactions among
Fermenting Microorganisms
Fermentative processes are carried out by different micro-
bial groups that can interact in well-defined habitats
for the transformation of the substrate. The balance
between the different microbial groups in each specific
ecosystem depends on their initial concentrations and
on environmental conditions (e.g., temperature, O2 concen-
tration, pH, and nutrients), and the predominance of one or
the other determines the type of fermentation and the
characteristics of the final product. Some fermented milks
(Kefir, Koumiss) and sourdoughs are ecological niches colo-
nized by different fermenting microorganisms, such as lactic
acid bacteria and yeasts, which carry out contemporary
lactic acid and alcoholic fermentation. Lactic acid and pro-
pionic bacteria intervene sequentially during ‘eyed’ cheese
production. Lactic acid bacteria ferment lactose and pro-
duce lactic acid during the first stages of cheese making.
Lactic acid is then used by propionic bacteria during cheese
ripening. Another example of an ecosystem is the intestinal
tract of warmblooded animals, where enteric bacteria, lactic
acid bacteria, bifidobacteria, and clostridia coexist, all of
which are involved in the transformation of the substrate
via different fermentation pathways. In this ecological
niche, lactic acid and bifidobacteria are involved in the
maintenance of the balanced composition of the intestinal
microflora. Different fermenting microorganisms, such as
lactic acid bacteria and clostridia, are involved in silage
fermentation and maturation. Also in this case, lactic acid
bacteria should predominate to counteract the development
of clostridia and other spoilage microorganisms (Figure 8).

See also: Biological Nitrogen Fixation; Excretion.
Further Reading
Bengmark S and Martindale R (2005) Prebiotics and synbiotics in clinical
medicine. Nutrition in Clinical Practice 20: 244–261.
Bernardeau M, Guguen M, and Vernoux JP (2006) Beneficial lactobacilli
in food and feed: Long-term use, biodiversity and proposals for
specific and realistic safety assessments. FEMS Microbiology
Review 30: 487–513.
Ciani M (2002) Biodiversity and Biotechnology of Wine Yeasts, 1st edn.
Trivandrum: Research Signpost.
Fire
J E Keeley, University of California, Los Angeles, CA, USA
ª 2008 Elsevier B.V. All rights reserved.
Introduction
Fire Regimes
Fire Impacts and Recovery
Introduction
A global view of potential vegetation distribution based
on climate shows large discrepancies with actual vege-
tation distribution. Fire is often responsible for such
discrepancies and on many landscapes it is a major
determinant of vegetation distribution. Traditionally
fire has been thought of as a disturbance, much like
treefalls or floods. However, fire is a predictable eco-
system process that often plays a determining role in
community structure and function. Placing fire in its
proper role in ecological theory would treat it much
like a herbivore in the trophic pyramid, consuming
biomass and competing with biotic consumers for
resources.
Fossil evidence is clear that as an ecosystem phenom-
enon, fire dates at least to the Mesozoic over 100 Ma.
Indeed, long before our current ecosystems were in
place, fire was shaping plant traits and landscapes. For
example, tree ring patterns in Jurassic-age fossils suggest a
Mediterranean climate of mild winter rain and summer
drought, conditions conducive to wildfires and charred
fossil fragments illustrate fires were part of these ecosys-
tems. Various fossil evidence has not only shown fires
were widespread at this time but different lines of evi-
dence support a similar range of fires as found today, from
light surface burning in the understory of forests to high-
intensity crown fires in lower-stature woodlands and
shrublands.
General Ecology | Fire 1557
Madigan MT, Martinko JM, and Parker J (2003) Brock Biology of
Microorganisms, 10th edn. Edinburgh: Pearson Education.
Perry JJ, Staley JT, and Lory S (2002) Microbial life, 1st edn.
Sunderland, MA: Sinauer Associates.
Stanier RY, Ingraham JL, Wheelis ML, and Painter PR (1988) The
Microbial World, 5th edn. Englewood Cliffs, NJ: Prentice-Hall.
Waites MJ, Morgan NL, Rockey JS, and Higton G (2005) Industrial
Microbiology: An Introduction, 3rd edn. Oxford: Blackwell
Science.
Zverlov VV, Berezina O, Velikodvorskaya GA, and Schwarz WH (2006)
Bacterial acetone and butanol production by industrial fermentation
in the Soviet Union: Use of hydrolyzed agricultural waste for
biorefinery. Applied Microbiology and Biotechnology 71: 587–597.
Fire, Weather, and Climate Interactions
Human Disruptions of Natural Fire Regimes
Further Reading
However, these records do not necessarily demon-
strate fire was an important ecosystem process. The first
evidence in the geological record of major ecosystem
changes driven by fire is from the late Tertiary Period.
Massive C4 grassland expansion between 4 and 7 Ma may
be the first example of an extensive fire influence in
shaping global ecosystems. At this time in subtropical
regions there is a clear isotopic signal in soils pointing
toward a switch from woodlands to grasslands, coinciding
with marked increases in charcoal deposition. Although
this coincided with increased climatic seasonality, climate
alone cannot explain these changes since in many cases
grasslands moved from more arid environments into more
mesic ones, something likely only driven by the destruc-
tive force of fires.
In order to understand what conditions promote fire as
an important ecosystem process, we need to consider the
characteristics shared by fire-prone ecosystems today.
One way to illustrate this is with a modification of the
classical fire triangle (Figure 1a) with a triangle better
describing the ecological distribution of fire (Figure 1b).
In order for fire to be a predictable ecosystem feature
the following conditions must be met. There must be
sufficient moisture and warmth to generate primary pro-
ductivity capable of providing the fuels necessary to
spread fire from one place to another. If productivity is
very low, such as in a desert, fires are unlikely due to
insufficient biomass. However, high primary productivity
alone is insufficient because fire is unlikely unless there is