Soil Biology

K5 2015
Biology Tanah Dalam
Menjaga Kualitas
Lingkungan

BB1

what organisms may do as part of their metabolism

Biodegradation, Bioremediation, Biocatalysis

what we call it when we exploit some

microbial activity for our (industrial) use
what we call it when we exploit some biodegradation
activity for clean-up purposes

BB1a

Exxon Valdez

Exxon Valdez accident

spilled 11,000,000 gallons
of crude oil in Prince
William Sound, Alaska on
March 24, 1989

tanker accidents contribute ~5% of total oil entering the seas each year
there were 16,000 accidents in 1988 - spilling four times the amount of the Exxon
Valdez oil spill into US waters
about 35% of oil entering the seas each year comes from normal ballasting and
washing operations of tankers and 36% comes from urban and industrial run-off
(borrowed from Biology 447)

BB1b

Alaskan beach contaminated by Exxon Valdez spill (1989)

BB2

Terminologi
Bioremediation is the use of
microorganisms to remove or detoxify
toxic or unwanted chemicals in an
environment
Biodegradation can be defined as the
biologically catalyzed reduction in complexity
of chemicals.
Biodegradation can be complete
(mineralization) or partial (may be termed
biotransformation).

Terminologi
Mineralization is when the biodegradation
leads to the conversion of much of the C, N,
P, S and other elements in the original
compound to inorganic products (i.e., CO2,
NH4, SO4, etc.)
Biotransformation has come to mean the
changing of a compound to another
reasonably stable molecule (often one that is
useful, or one that is less or more toxic than the
original). Often the product of
biotransformation is a simpler compound,
sometimes it is more complex (e.g.,

BB3

Principle of microbial
infallibility
(M. Alexander, 1965):
the empirical observation that no natural
organic compound is totally resistant to
biodegradation provided that
environmental conditions are
favourable

xenobiotic (completely synthetic)

chemicals not included!

Factors influencing
biodegradability, rate of
biodegradation include:
pH,
Temperature,
Organic matter content
Presence/absence of required
microbial consortium
Bioavailability of target compound

Compound degradability
may depend on:
Elemental composition
Structure of basic repeating units (in
a polymer)
Linkage between units
Degree of branching in the molecule
Arrangement and types of
substituents

BB4

CH2OH

CH2OH

CH2OH

CH2OH

CH2OH
O

O
O

CH2OH

relative biodegradability of glucose polymers

starch, glycogen
14 linkages
easy to degrade

cellulose
14 linkages
not readily degraded

BB5

2,4,5-T: also a herbicide

more recalcitrant

2,4-D: a herbicide

presence of additional Cl substituent on C5 increases

persistence of herbicide 2,4,5-T compared to related
herbicide 2,4-D
(from Fig. 19.46, Table 19.7, Madigan & Martinko)

Substance

time for 75100%

disappearance

2,4-D (2,4dichlorophenoxyacetic
acid)

~ 4 weeks

2,4,5-T (2,4,5trichlorophenoxyacetic
acid)

~20 weeks

BB6

oil-degrading bacteria congregate at the oil-water interface but not

within the droplet itself
in general, only dissolved hydrocarbon molecules are available to
the degraders

BB7

Hydrocarbon biodegradation:
hydrocarbon degraders are ubiquitous in environment
most biodegradation is aerobic because
O2 is a direct reactant oxygenases

methane: a special case

degraded by specialized C1 microorganisms (methanotrophs)
methane
monooxygenase

CH4
O2

CH3OH
H2O

CH2O

HCOO-

CO2

some generalizations:
aliphatics:
up to C9 can be toxic; biodegradable; relatively
volatileoften lost from spill
Up to C4 (i.e., methanebutane) gases
~C10 - ~C24 rapidly, readily biodegraded
Larger than C24, or branching in molecule
decreases biodegradation
Unsaturated compounds (i.e., alkynes, alkenes)
more rapidly degraded than saturated (alkanes)

alkanes aromatics alicyclics

most
less
least readily degraded

BB7a

H3C-CH2-CH2-CH2-CH2-CH3

hexane: an aliphatic hydrocarbon

benzene: an aromatic ring hydrocarbon

cyclohexane: an alicyclic ring hydrocarbon

(also aliphatic)

H2C=CH2
H3C-CH3

ethene (or ethylene), an alkene

ethane, an alkane

BB8

oxidation of n-octane (C8 aliphatic):

alkane
alcohol
- OH

aldehyde,
ketone
- CHO

-oxidation of fatty acids:

2C units (acetyl CoA)
feed into central
metabolism (TCA cycle)
+
reducing power (FADH,
NADH)
used to generate ATP, or
directly in biosynthesis

acid
- COOH

-oxidation pathway

BB9

oxidation of aromatic hydrocarbons:

monoaromatics, e.g., benzene, toluene, ethylbenzene, xylenes (BTEX)
polyaromatic hydrocarbons (PAHs), e.g., naphthalene
benzene

naphthalene

p-xylene
CH3
CH3

anthracene

Common themes in aerobic

biodegradation:
oxygenases (di- or mono-)
initial steps lead to catechols, protocatechuate (aromatic
rings with adjacent OHs)
subsequent ring cleavage between hydroxyl groups
(ortho fission), beside the hydroxyl groups (meta
fission)
eventual formation of compounds that enter central
metabolic pathways (TCA cycle)
funnelling of many different aromatic compounds
(including substituted aromatics) through a few key
intermediates (e.g., catechols) to common pathways

aerobic biodegradation of monoaromatic compounds:

BB10

ortho cleavage

succinic acid
acetyl CoA
(central metabolism)

meta cleavage

central
metabolism

BB11

anaerobic biodegradation of aromatic compounds:

ring reduction followed by ring cleavage to form fatty acid

-oxidation to acetyl-CoA units
added oxygen is from H2O not O2
BTEX compounds may be slowly biodegraded by similar pathway in
absence of oxygen

cometabolism: the metabolic transformation of a substance while a second

substance serves as primary energy or carbon source
Mycobacterium vaccae
Oxidation of primary
substrate
propane
O2

propane
monooxygenase

propanol

cometabolic
reaction
cyclohexane
cyclohexanol

Pseudomonas
propanone

production
of energy, biomass

cyclohexanone

energy +
CO2 + biomass

BB12

BB13

An example of biocatalysis:
naphthalene dioxygenase catalyzes the first step of aerobic naphthalene
degradation
the enzyme has a broad substrate range, and much potential for use in
stereospecific biocatalysis
naphthalene

indole

NH
OH

naphthalene dioxygenase
OH

OH

OH
NH

further bacterial metabolism

CO2 + H2O + new cells

spontaneous reactions

indigo
(blue jean dye)

Biodegradation of xenobiotics

BB14

examples include pesticides, polychlorinated biphenyls (PCBs), munitions, dyes,

chlorinated solvents
Losses from environmental compartments may be due to abiotic + biotic
reactions

volatilization
leaching
spontaneous chemical decomposition
biological reactions
cometabolic reactions can be important
products may sometimes be more complex/more harmful than parent
compound

reductive dechlorination of chlorinated solvents tetrachloroethene (PCE)

and trichloroethene (TCE):
Cl

H
C=C

H
Cl

Cl

Cl

C=C
Cl

Cl

C=C
Cl

TCE

Cl

C=C
Cl

PCE

trans-1,2-DCE

carcinogen?

Cl

C=C
Cl

cis-1,2-DCE
carcinogen?

H
C=C

Cl

VC

ethene

carcinogen,
mutagen

relatively
innocuous

PCE, TCE widely used as degreasers, dry cleaning fluids

common contaminants of groundwater
each dechlorination step requires electrons + H+, Cl- is released
cis-DCE is main DCE intermediate in biological reduction
this reductive dechlorination occurs in anoxic, highly reduced environments
microorganisms that conduct this most efficiently are able to halorespire (chlorinated
compound = terminal electron acceptor in respiration)

BB15

BB16

Biodegradation of 2,4,5-T by Burkholderia cepacia

O2 required
note Cl replacement by -OH
note substituted catechol formation;
subsequent ring fission
note 2,4,5-T is used as a growth substrate;
succinate, acetate feed into central metabolic
pathways

BB17

Plastics:
classically, polymers of
polyethylene, polypropylene,
PVC
examples of very recalcitrant
xenobiotic compounds
accumulate (landfills)

Consequent interest in developing

biodegradable plastics
photodegradable polymers
starch-linked polymers
plastics based on microbial storage
polymers (poly--hydroxyalkanaotes,
PHAs)
poly--hydroxybutyrate (PHB) is one you may
know

BB17a

bacterial cells with

inclusions of PHB

BB18

manipulation of growth conditions and/or genetic

modifications of PHA-producing bacteria have been used
to produce PHAs with different melting points, flexibility,
tensile strength
a copolymer of two PHAs produced
by strain of Ralstonia eutrophus
been used in European bioplastic
shampoo bottles

two advantages to natural plastics:

more readily biodegraded
technology is not petroleum-based