Professional Documents
Culture Documents
Microorganisms
WOLFGANG FRITSCHE
MARTIN HOFRICHTER
Jena, Germany
List of Abbreviations
AsO arsenic-containing organic compounds
BTX benzene, toluene, xylenes
DBDs dibenzo-p-dioxines
DBFs dibenzofurans
DCA 3,4-dichloroaniline
DCP 2,4-dichlorophenol
DDT 1,1,1-trichloro-2,2b-bis(4-chlorophenyl)ethane
DNT 2,4-dinitrotoluene
KCN potassium cyanide
LiP lignin peroxidase
MnP manganese peroxidase
PAHs polycyclic aromatic hydrocarbons
PCBs polychlorinated biphenyls
PCP pentachlorophenol
TCC tricarboxylic acid cycle
TCE trichloroethene
TNT 2,4,6-trinitrotoluene
1 Introduction:
Characteristics of Aerobic
Microorganisms Capable of
Degrading Organic
Pollutants
The most important classes of organic pollu-
tants in the environment are mineral oil con-
stituents and halogenated products of petro-
chemicals. Therefore, the capacities of aerobic
microorganisms are of particular relevance for
the biodegradation of such compounds and
are exemplarily described with reference to
the degradation of aliphatic and aromatic hy-
drocarbons as well as their chlorinated deriva-
tives. The most rapid and complete degrada-
tion of the majority of pollutants is brought
about under aerobic conditions (RISER-RO-
BERTS, 1998).
The essential characteristics of aerobic mi-
croorganisms degrading organic pollutants are Fig. 1. Main principle of aerobic degradation of hy-
(Fig. 1): drocarbons: growth associated processes.
2 Principles of Bacterial Degradation 147
(1) Metabolic processes for optimizing the ing significance for the cometabolic degrada-
contact between the microbial cells and tion of persistent organopollutants.Thus it is in
the organic pollutants. The chemicals particular the domain of basidiomycetous fun-
must be accessible to the organisms gi, which requires a deeper insight and an ex-
having biodegrading activities. For ex- tensive consideration. Therefore, this chapter
ample, hydrocarbons are water-insolu- has been divided in two sections: bacterial and
ble and their degradation requires the fungal degradation capacities.
production of biosurfactants.
(2) The initial intracellular attack of organ-
ic pollutants is an oxidative process, the
activation and incorporation of oxygen
is the enzymatic key reaction catalyzed
2 Principles of Bacterial
by oxygenases and peroxidases.
(3) Peripheral degradation pathways con-
Degradation
vert organic pollutants step by step into
intermediates of the central intermedi- 2.1 Typical Aerobic Degrading
ary metabolism, e.g., the tricarboxylic Bacteria
acid cycle.
(4) Biosynthesis of cell biomass from the The predominant degraders of organopollu-
central precursor metabolites, e.g., ace- tants in the oxic zone of contaminated areas
tyl-CoA, succinate, pyruvate. Sugars re- are chemo-organotrophic species able to use a
quired for various biosyntheses and huge number of natural and xenobiotic com-
growth must be synthesized by gluco- pounds as carbon sources and electron donors
neogenesis. for the generation of energy. Although many
bacteria are able to metabolize organic pollu-
A huge number of bacterial and fungal genera tants, a single bacterium does not possess the
possess the capability to degrade organic pol- enzymatic capability to degrade all or even
lutants. Biodegradation is defined as the bio- most of the organic compounds in a polluted
logically catalyzed reduction in complexity of soil. Mixed microbial communities have the
chemical compounds (ALEXANDER, 1994). It is most powerful biodegradative potential be-
based on two processes: growth and cometab- cause the genetic information of more than
olism. In the case of growth, organic pollutants one organism is necessary to degrade the com-
are used as sole source of carbon and energy. plex mixtures of organic compounds present in
This process results in a complete degradation contaminated areas. The genetic potential and
(mineralization) of organic pollutants as dem- certain environmental factors such as temper-
onstrated in Sect. 2.2. Cometabolism is defined ature, pH, and available nitrogen and phos-
as the metabolism of an organic compound in phorus sources, therefore, seem to determine
the presence of a growth substrate which is the rate and the extent of degradation.
used as the primary carbon and energy source. The predominant bacteria of polluted soils
The principle is explained in Sect. 2.4. belong to a spectrum of genera and species
Enzymatic key reactions of aerobic biodeg- listed in Tab. 1. The composition of this list of
radation are oxidations catalyzed by oxygen- bacteria is determined by the fact whether
ases and peroxidases. Oxygenases are oxido- they can be cultured on nutrient-rich media.
reductases that use O2 to incorporate oxygen We have to consider that the majority of bac-
into the substrate. Degradative organisms teria present in soils cannot be cultured in the
need oxygen at two metabolic sites, at the in- laboratory yet.
itial attack of the substrate and at the end of Pseudomonads, aerobic gram-negative rods
the respiratory chain (Fig. 1). Distinct higher that never show fermentative activities, seem
fungi have developed a unique oxidative to have the highest degradative potential, e.g.,
system for the degradation of lignin based on Pseudomonas putida and P. fluorescens. Fur-
extracellular ligninolytic peroxidases and lac- ther important degraders of organic pollutants
cases. This enzymatic system possesses increas- can be found within the genera Comamonas,
148 6 Aerobic Degradation by Microorganisms
Tab. 1. Predominant Bacteria in Soil Samples Pollut- reactions involved in these processes. It de-
ed with Aliphatic and Aromatic Hydrocarbons, Po- pends on the nature of the substrate and the
lycyclic Aromatic Hydrocarbons, and Chlorinated enzymatic equipment of the involved microor-
Compoundsa ganisms, what kind of enzymatic reaction is
Gram-Negative Gram-Positive
realized. n-Alkanes are the main constituents
Bacteria Bacteria of mineral oil contaminations (HINCHEE et al.,
1994). Long-chain n-alkanes (C10UC24) are
Pseudomonas spp. Nocardia spp. degraded most rapidly by mechanisms demon-
Acinetobacter spp. Mycobacterium spp. strated in Fig. 3. Short-chain alkanes (less than
Alcaligenes sp. Corynebacterium spp. C9) are toxic to many microorganisms, but
Flavobacterium/ Arthrobacter spp. they evaporate rapidly from petroleum con-
Cytophaga group taminated sites. Oxidation of alkanes is classi-
Xanthomonas spp. Bacillus spp. fied as being terminal or diterminal. The
a
The reclassification of bacteria has been based on
monoterminal oxidation is the main pathway.
phylogenetic markers resulting in changes of some It proceeds via the formation of the corre-
genera and species. This is why the names of species sponding alcohol, aldehyde, and fatty acid.
are not mentioned. b-Oxidation of the fatty acids results in the
formation of acetyl-CoA. n-Alkanes with an
uneven number of carbon atoms are degraded
to propionyl-CoA, which is in turn carboxylat-
Burkholderia, and Xanthomonas. Some spe- ed to methylmalonyl-CoA and further con-
cies utilize `100 different organic compounds verted to succinyl-CoA. Fatty acids of a phys-
as carbon sources. The immense potential of iological chain length may be directly incorpo-
the pseudomonas does not solely depend on rated into membrane lipids, but the majority of
the catabolic enzymes, but also on their capa- degradation products is introduced into the
bility of metabolic regulation (HOUGHTON and tricarboxylic acid cycle. The subterminal oxi-
SHANLEY, 1994). A second important group of dation occurs with lower (C3UC6) and longer
degrading bacteria are the gram-positive rhod- alkanes with the formation of a secondary al-
ococci and coryneform bacteria. Many species, cohol and subsequent ketone. Unsaturated 1-
now classified as Rhodococcus spp. had origi- alkenes are oxidized at the saturated end of
nally been described as Nocardia spp., Myco- the chains. A minor pathway has been shown
bacterium spp., and Corynebacterium spp. to proceed via an epoxide, which is converted
Rhodococci are aerobic actinomycetes show- to a fatty acid. Branching, in general, reduces
ing considerable morphological diversity. A the rate of biodegradation. Methyl side groups
certain group of these bacteria possess mycol- do not drastically decrease the biodegradabili-
ic acids at the external surface of the cell. ty, whereas complex branching chains, e.g., the
These compounds are unusual long-chain al- tertiary butyl group, hinder the action of the
cohols and fatty acids, esterified to the pepti- degradative enzymes.
doglycan of the cell wall. Probably, these lipo- Cyclic alkanes representing minor compo-
philic cell structures have a significance for the nents of mineral oil are relatively resistant to
affinity of rhodococci to lipophilic pollutants. microbial attack. The absence of an exposed
In general, rhodococci have high and diverse terminal methyl group complicates the pri-
metabolic activities and are able to synthesize mary attack. A few species are able to use cy-
biosurfactants. clohexane as sole carbon source; more com-
mon is its cometabolism by mixed cultures.
The mechanism of cyclohexane degradation is
2.2 Growth-Associated shown in Fig. 4. In general, alkyl side chains of
Degradation of Aliphatics cycloalkanes facilitate the degradation.
Aliphatic hydrocarbons become less water
The aerobic initial attack of aliphatic and cy- soluble with increasing chain length. Hydro-
cloaliphatic hydrocarbons requires molecular carbons with a chain length of C12 and above
oxygen. Fig. 2 shows both types of enzymatic are virtually water insoluble. Two mechanisms
2 Principles of Bacterial Degradation 149
are involved in the uptake of these lipophilic bacterial cell wall requires activated sugars
substrates: the attachment of microbial cells at synthesized by gluconeogenesis.
oil droplets and the production of biosurfac- Products of growth-associated degradation
tants (HOMMEL, 1990). The uptake mechanism are CO2, H2O, and cell biomass. The cells act as
linked to attachment of the cells is still un- the complex biocatalysts of degradation. In ad-
known, whereas the effect of biosurfactants dition, cell biomass may be mineralized after
has been studied well (Fig. 5). Biosurfactants exhaustion of the degradable pollutants in a
are molecules consisting of a hydrophilic and a contaminated site.
lipophilic moiety. They act as emulsifying
agents, by decreasing the surface tension and
by forming micelles. The microdroplets may be 2.3 Diversity of Aromatic
encapsulated in the hydrophobic microbial
cell surface. The products of hydrocarbon deg- Compounds – Unity of Catabolic
radation, introduced to the central tricarboxyl- Processes
ic acid cycle, have a dual function. They are
substrates of the energy metabolism and build- Aromatic hydrocarbons, e.g., benzene, tolu-
ing blocks for biosynthesis of cell biomass ene, ethylbenzene and xylenes (BTEX com-
and growth (Fig. 1). The synthesis of amino pounds), and naphthalene belong to the large
acids and proteins needs a nitrogen and sulfur volume petrochemicals, widely used as fuels
source, that of nucleotides and nucleic acids a and industrial solvents. Phenols and chloro-
phosphorus source. The biosynthesis of the phenols are released into the environment as
150 6 Aerobic Degradation by Microorganisms
products and waste materials from industry. Only few reports on bacteria capable of
Aromatic compounds are formed in large attacking benzene have been published
amounts by all organisms, e.g., as aromatic (SMITH, 1990). The first step of benzene oxida-
amino acids, phenols, or quinones. Thus, it is tion is a hydroxylation catalyzed by a dioxygen-
not surprising that many microorganisms have ase (Fig. 2).The product, a diol, is then convert-
evolved catabolic pathways to degrade aromat- ed to catechol by a dehydrogenase. These ini-
ic compounds. In general, man-made organic tial reactions, hydroxylation and dehydrogena-
chemicals (xenobiotics) can be degraded by tion, are also common to pathways of degrada-
microorganisms, when the respective molecu- tion of other aromatic hydrocarbons.
les are similar to natural compounds. The di- The introduction of a substituent group on-
versity of man-made aromatics shown in Fig. 6 to the benzene ring renders alternative mecha-
can be converted enzymatically to natural in- nisms possible to attack side chains or to oxid-
termediates of the degradation: catechol and ize the aromatic ring. The versatility and
protecatechuate. In general, benzene and re- adaptability of bacteria is based on the exis-
lated compounds are characterized by a higher tence of catabolic plasmids. Catabolic plasmids
thermodynamic stability than aliphatics are. have been found to encode enzymes degrading
2 Principles of Bacterial Degradation 151
Fig. 5. Involvement of
biosurfactants in the
uptake of hydrocar-
bons. The figure demon-
strates the emulsifying
effect of a rhamnolipid
produced by Pseudo-
monas spp. within the
oil–water interphase
and the formation of
micelles. Lipid phases
are printed in bold.
methane oxidation is catalyzed by methane fers, but methane has to be added as growth
monooxygenase, which attacks the inert CH4. substrate and inducer for the development of
It is an unspecific enzyme that also oxidizes methanotrophic biomass. The addition of
various other compounds, e.g., alkanes, aro- methane as substrate limits the application for
matic compounds, and trichloroethylene bioremediation.
(TCE). The proposed mechanism of TCE Cometabolism of chloroaromatics is a wide-
transformation according to HENRY and spread activity of bacteria in mixtures of in-
GRBIĆ -GALLIĆ (1994) is shown in Fig. 8.TCE is dustrial pollutants. KNACKMUSS (1997) demon-
oxidized to an epoxide excreted from the cell. strated that the cometabolic transformation of
The unstable oxidation product breaks down 2-chlorophenol gives rise to dead end metab-
to compounds, which may be used by other mi- olites, e.g., 3-chlorocatechol. This reaction
croorganisms. Methanotrophic bacteria are product may be auto-oxidized or polymerized
aerobic indigenous bacteria, in soil and aqui- in soil to humic-like structures. Irreversible
154 6 Aerobic Degradation by Microorganisms
binding of dead end metabolites may fulfill the tution of halogen as well as nitro and sulfo
function of detoxification. The accumulation groups at the aromatic ring is accomplished by
of dead end products within microbial commu- an increasing electrophilicity of the molecule.
nities under selection pressure is the basis for These compounds resist the electrophilic at-
the evolution of new catabolic traits (REIN- tack by oxygenases of aerobic bacteria. Com-
ECKE, 1994). pounds that persist under oxic conditions are,
e.g., PCBs (polychlorinated biphenyls), chlori-
nated dioxins, some pesticides, e.g., DDT.
2.4.2 Overcoming the Persistence To overcome the relatively high persistence
of halogenated xenobiotics, reductive attack of
by Cooperation of Anaerobic and anaerobic bacteria is of significance. The deg-
Aerobic Bacteria radation of environmental pollutants by an-
aerobic bacteria is the subject of Chapter 7,
As a rule, recalcitrance of organic pollutants this volume. Because of the significance of re-
increases with increasing halogenation. Substi- ductive dehalogenation for the first step in the
2 Principles of Bacterial Degradation 155