A r e p ort f rom

t h e A merican Academ y
of Microbiology

Microbes &
oil spills

Downloaded from www.asmscience.org by

IP: 131.178.200.56
On: Tue, 09 Apr 2019 20:24:51
About ASM FAQs
The American Academy of
Microbiology is the honorific
branch of the American Society
for Microbiology, a non-profit
scientific society with almost
40,000 members. Fellows of
the AAM have been elected by
their peers in recognition of their
outstanding contributions to the
field of microbiology. Through its
colloquium program, the AAM
draws on the expertise of these
fellows to address critical issues
in microbiology. Steering Participants: Robert J. Steffan
Committee: Shaw Environmental,
FAQ reports are based on the Carl E. Cerniglia Inc.
deliberations of 15-20 expert Ronald M. Atlas FDA, National Center
scientists who gather for a University of Louisville for Toxicological Andreas P. Teske
day to develop science-based Research (NCTR) University of
answers to questions the public Darrell Jay Grimes North Carolina
might have about topics in University of Southern Gary M. King
microbiology. The reports are Mississippi Louisiana State Benjamin Van Mooy
reviewed by all participants, and University Woods Hole
by outside experts, and every Terry C. Hazen Oceanographic
effort is made to ensure that Lawrence Berkeley Nancy E. Kinner Institution (WHOI)
the information is accurate and Laboratory University of New
complete. However, the report Hampshire Albert D. Venosa
is not intended to advocate any Jim Spain U.S. Environmental
particular position or action. Georgia Institute Joel E. Kostka Protection Agency
of Technology Florida State University
Lawrence P. Wackett
Contents of the report may
Joseph M. Suflita Kenneth Lee University of
be distributed further so long
University of Oklahoma Department of Fisheries Minnesota
as the authorship of the AAM
and Oceans Canada
is acknowledged and this
Ann Reid Calvin H. (Herb) Ward
disclaimer is included.
American Academy Frank Loeffler Rice University
of Microbiology University of Tennessee
& Oak Ridge National Lily Young
Laboratory Rutgers University
Moderator:
Roger C. Prince Gerben J. Zylstra
Stanley Maloy ExxonMobil Biomedical Rutgers University
San Diego State Sciences Inc.
University
Patty Sobecky
University of Alabama

Copyright © 2011
American Academy
of Microbiology
1752 N Street, NW
Washington, DC 20036
www.asm.org Photos: LBNL (Lawrence Berkeley National Laboratory)
Downloaded from www.asmscience.org by
IP: 131.178.200.56
On: Tue, 09 Apr 2019 20:24:51
1. What does it mean to say that
microbes can ‘clean up’ an oil spill?
Let’s begin by defining some terms – microbes,
clean-up, and oil. First, what do we mean
by microbes? When we talk about microbes
that are able to clean up oil, we’re talking
primarily about bacteria and fungi. Bacteria
can break down oil to carbon dioxide and
water. However, no single organism can
break down all the components of crude oil
or refined fuels spilled into the environment.
The tens of thousands of different compounds
that make up oil can only be biodegraded by
communities of microorganisms acting in
concert. Some bacteria can degrade several
hydrocarbons or a class of hydrocarbons.
The combined action of the community can
degrade almost all of the components (BOX 1).

Second, what is oil? Crude oils––oils that are found in

natural reservoirs––are principally derived from ancient
algae and plant material. In other words, oil is a natural
product, generated from organisms that long ago used
sunlight as their energy source through the process of
photosynthesis. The algae were buried deep in the Earth
and heated at great pressure over millions of years. The
resulting material is oil, in which is stored the energy
generated by that ancient photosynthetic activity. There-
fore, the components of crude oil are a great source
of energy, not only as fuel to power internal combus-
tion engines, but also as food for microbes. It is not
surprising that microbes have evolved the ability to use
oil as their food source––in other words, to metabolize
or biodegrade the compounds for energy and use them
as raw material for growth.

Much of the Earth’s crude oil is trapped in underground

reservoirs, but some leaks to the surface, and has been
doing so for millions of years. It is estimated that about
half of the oil entering the world’s oceans today comes
from these natural seeps and the rest from human

FAQ: Microbes & oil spills Downloaded from www.asmscience.org by 1

IP: 131.178.200.56
On: Tue, 09 Apr 2019 20:24:51
 BOX 1: Eat, consume, metabolize, degrade, break-down…
what are the microbes doing to the oil anyway?
Photosynthetic organisms use energy from sunlight that are specific for particular degradation reactions.
to convert carbon dioxide and water into carbohy- Some of the simpler compounds can be degraded
drates, proteins, and fats, with oxygen as a byproduct. by a very wide variety of bacteria, but the ability to
Energy is stored in the newly formed chemicals. When degrade other compounds (aromatic hydrocarbons,
the organisms die and are buried in sediment, these for example) is found in fewer species. No one bacte-
chemicals are not destroyed, but rather the heat and rium can make all the different enzymes – instead,
pressure deep underground convert them into a huge each kind of bacterium specializes in a few hydrocar-
variety of different hydrocarbons – compounds that bons as preferred food sources.
contain carbon and hydrogen. The energy stored in
the chemical bonds can be released by burning (that’s Most microbial oil degradation occurs by aerobic
what happens in your car’s engine), or by a more respiration, in other words, the oil-degrading microbes
precise chemical reaction carried out by enzymes “breathe” oxygen and burn oil hydrocarbons just as
inside a living cell. These enzymes enable microorgan- humans breathe oxygen and burn food for energy.
isms to “combust” the hydrocarbons at much lower In the absence of oxygen, microbes have other
temperatures than burning. mechanisms to degrade hydrocarbons for energy.
Biodegradation of oil constituents without oxygen
The genetic machinery needed to make these (i.e., under anoxic conditions) is much slower but
oil-degrading enzymes is most commonly found anoxic processes may be relevant to the long-term
in bacteria (although many fungi and some other restoration efforts (e.g., in oil-contaminated salt marsh
organisms can also degrade oil). The bacterial cell environments).
then harnesses the energy released by degrading the
compounds to support its own life processes. The From the human point of view, what the microbes are
situation is exactly analogous to the way our bodies doing is degrading––or breaking down––the oil, which
break down the chemical energy in food to provide the results in cleaning up the environment that has been
energy and raw materials for maintenance, growth, contaminated by the spill. From the microbial point
and repair of our tissues. There are many different of view, what they are doing to the oil is “eating”––or
varieties of hydrocarbons, and over millions of years, metabolizing––or consuming it to provide the energy
bacteria have evolved catalytic machines (enzymes) and materials needed to live and grow.

activities. Oil enters waterways not only when an tiles and roads. Microbes can biodegrade up to 90% of
offshore rig blows up, a pipeline ruptures, or a tanker some light crude oil, but the largest and most complex
runs aground, but also when it is rinsed off roads and molecules––like the ones that make up road asphalt––
parking lots, spilled at marinas and discharged by are not significantly biodegradable. When refined
outboard motors, released during offshore oil opera- petroleum products are spilled, their fate depends on
tions, or washed out of ships’ ballast tanks. their composition. Gasoline, kerosene, and diesel fuel
are so volatile and easily biodegradable that they rarely
The Deepwater Horizon rig explosion and subsequent persist in marine environments, although they can
leak of the Macondo Well in the Gulf of Mexico released remain longer if buried in sediment, soils, groundwater,
light crude oil composed of a variety of compounds, or marshes where oxygen levels are very low. Heavy
with varying degrees of biodegradability (BOX 2). fuels oils, such as those spilled in the Prestige spill off
Crude oils vary from source to source, containing the coast of Spain in 2002, contain a large proportion of
different proportions of hydrocarbons ranging from heavy components that biodegrade very slowly.
methane (natural gas), to light materials similar to
gasoline, to heavy materials that resemble asphalt. Defining what we mean by ’cleaned up’ can also be
Refineries convert crude oils to products ranging from challenging. One possible measure of successful cleanup
gasoline and aviation fuel to the heavy fuel oils used might be that the oil can no longer be seen, smelled or
for ship engines and the asphalts used for roofing tasted. Human senses, however, are relatively unreli-

2 A report from the

Downloaded from www.asmscience.org by American Academy of Microbiology
IP: 131.178.200.56
On: Tue, 09 Apr 2019 20:24:51
able. Another measure might be toxicity – a spill could
be considered cleaned up when the concentrations of
its components are no longer toxic to humans, other BOX 2: A brief introduction to oil
animals, or plants. Other chemical or physical measures
of cleanliness are established by regulatory agencies.
Under the Oil Pollution Act of 1990 , after an oil spill or Crude oil (or petroleum): a liquid mixture of a variety
hazardous substance release, response agencies like the of hydrocarbon compounds derived from ancient
U.S. Environmental Protection Agency (EPA) or the U.S. algal and plant remains and found in reservoirs under
Coast Guard (USCG) oversee clean up efforts with the the Earth’s surface. Nitrogen and sulfur containing
goal of eliminating or reducing risks to human health molecules (“resins”) are common constituents of
and the environment. Cleanup efforts may not be able some crude oils.
fully to restore impaired natural resources or address
their loss for public Use. Studies are conducted through Crude oil components:
the Natural Resource Damage Assessment (NRDA)
process to identify the extent of resource injuries, the Volatile compounds - low molecular weight
best methods for restoring those resources, and the type compounds, like methane (natural gas) or propane,
and amount of restoration required. Clean-up activi- that are normally gaseous or evaporate very quickly at
ties themselves can have ecological consequences, room temperature.
and these must be balanced against the desire to
remove every vestige of contamination. Therefore a Net Saturated hydrocarbons - compounds with carbon
Ecological Benefit Analysis (NEBA) is often used—an and hydrogen atoms connected only by single bonds.
approach that was first applied to the Exxon Valdez spill Saturated hydrocarbons can be arranged in straight or
in Prince William sound. The most rigorous definition of branched chains of up to about 25 carbon atoms. Satu-
successful clean-up would be that the oil is no longer rated hydrocarbons are readily biodegraded although
detectable by any means and the area has returned to degradability decreases with chain length.
its pre-spill condition. As detection technologies become
more sophisticated, this most rigorous definition of Aromatic compounds - compounds that contain
cleanliness becomes increasingly difficult or impossible rings of carbon atoms held together with double
to achieve. Since many marine ecosystems natu- bonds between the carbon atoms. The smallest
rally contain a certain amount of crude oil because of aromatic compounds in petroleum have six carbons
seepage, and many others also include varying levels of in such a ring structure (e.g. benzene and toluene),
oil from human activities, defining when an ecosystem but other compounds contain multiple rings. These
has returned to its pre-spill state is not straightforward. A are known as polycyclic aromatic hydrocarbons,
comprehensive overview of cleanup efforts in the Gulf of often abbreviated ‘PAH’. Most aromatic molecules
Mexico after the Deepwater Horizon rig explosion can be in petroleum have multiple attached hydrocarbon
found at: http://www.gulfspillrestoration.noaa.gov/. chains. The smallest aromatic molecules (one- and
two-rings) are both volatile and readily biodegraded,
Biological mechanisms are not the only factor involved even with attached side-chains, but four-ring and
in cleaning up an oil spill. A variety of physical and larger aromatic compounds are more resistant to
chemical processes are also at work, such as: biodegradation. They are, however, susceptible to
photooxidation. Some larger PAHs are of concern
n EVAPORATION because they are potentially carcinogenic; 16 different
The volatile hydrocarbons evaporate quickly into the PAHs are designated as priority pollutants by the EPA.
atmosphere when they reach the water surface. Under The percentage of PAHs in crude oil varies, but the
controlled experimental conditions, about 50% of a ‘priority pollutants’ are present at low levels in crude
typical light crude oil evaporates within 20 hours. The oils; they are much more common as a byproduct of
characteristics of the spilled oil and environmental burning carbonaceous materials such as fuel, coal,
conditions make a big difference; light oil on a calm wood, tobacco and other materials. Asphaltenes
sea will evaporate much faster than heavier oil that has (used in making roads and roofing products) are
been churned into the water by heavy waves. Evapora- examples of high molecular weight (heavy) PAHs that
tion will also be faster at warmer temperatures. have additional chemical side chains attached to their
aromatic rings. Asphaltenes are not soluble in water
n DISSOLUTION and most organic solvents.
Some components of crude oil dissolve in water. These
compounds are the most likely to be acutely toxic to

FAQ: Microbes & oil spills Downloaded from www.asmscience.org by 3

IP: 131.178.200.56
On: Tue, 09 Apr 2019 20:24:51
sea life, but they are also among the most volatile and Dispersion can be enhanced by the addition of chemical
readily biodegradable under most conditions. Not all dispersants, which will be discussed later.
toxic compounds are lost through evaporation––some,
like heavy polycyclic aromatic hydrocarbons (PAHs), n PHOTO-OXIDATION
are poorly soluble in water and more likely to adhere to Sunlight reacts with some oil constituents, especially
particles and thus remain in the water or sediment. PAHs the polycyclic aromatic hydrocarbons (PAHs). The
can be broken down by microbes over time. However, process, known as photolysis, is important because
this process is often slow enough that these hydrocar- by breaking aromatic ring structures, it enhances the
bons can accumulate in such invertebrates as shellfish. availability of such compounds to microbes and hence
Fish and other vertebrates metabolize them rapidly. microbial degradation. On the other hand, the photo-
oxidized PAHs have been shown to be substantially
n DISPERSION more toxic to water-dwelling organisms.
Dispersion is the process by which oil is broken up into
small droplets and spread through the water. This is the The physical processes of evaporation, dissolution,
same physical process that is at work when we whisk dispersion, and photo-oxidation begin as soon as oil
oil and vinegar together to make salad dressing. Just is spilled or reaches the surface. Prompt human action
as with salad dressing, the stability of the resultant (like skimming and burning) can also physically remove
emulsion can vary. Physical dispersion can only happen some of the oil. When the danger of an oil spill reaching
in the presence of adequate mixing energy (e.g. by shorelines or other sensitive environments is imminent,
wave action or high pressure leaks)––under turbulent physical removal, via skimming or burning, can be a
conditions, dispersion can prevent oil from reaching the critically important means of minimizing damage. With
surface where it might otherwise evaporate. Dispersion the exception of burning, which comes with its own
can also drive floating oil into the water column and set of risks and limitations, these physical processes,
largely prevent it from forming surface slicks that can however, do not destroy the oil. They do not break it
threaten birds and mammals. One advantage of disper- down into harmless carbon dioxide and water. Only
sion is that oil is broken up into tiny droplets with more living organisms or high temperature combustion (i.e.,
surface area, which facilitates microbial degradation. A burning) can do that.
potential disadvantage is that it might increase expo-
sure of some inhabitants of the ecosystem to the oil.

4 A report from the

Downloaded from www.asmscience.org by American Academy of Microbiology
IP: 131.178.200.56
On: Tue, 09 Apr 2019 20:24:51
2. Where do the ‘oil-eating’ microbes come from? Are
they everywhere? Does that mean we don’t need to worry
about oil spills because microbes will always clean them
up? What are they doing when there isn’t any oil?
Microbes that use oil as their source of energy
have been around for hundreds of millions
of years—indeed, for as long as this energy-
rich substance has been available. Where
oil is naturally present, for example, on the
floor of the Gulf of Mexico, the community
of microbes that collectively feeds on all the
different compounds contained in the oil is
well established and diverse. Even where
the background levels of oil are low, a few
microbes with the capability of degrading
oil always seem to be present (BOX 3).

When there is a spill of crude or refined oil, the

bacteria capable of degrading hydrocarbons prolif-
erate quickly. Microbial cleanup can be considered in
terms of “supply and demand.” The local community of
microbes is already adapted to the background supply
of oil. It takes a certain amount of time––a lag time––
for their populations to increase in response to the
influx of new resources. The surge of oil from a leak or
spill can temporarily outpace the capacity of the local
oil-degrading microbes. The oil remains until demand
catches up to supply. Eventually, though, along with the
physical and chemical processes discussed above, the
microbes will “take care” of the problem by consuming
the oil compounds that are biodegradable.

The ability to metabolize oil is displayed by many

different types of microbes––some more versatile than
others. Certain microbes highly prefer oil hydrocar-
bons over other energy sources and their numbers
will increase faster than others in the community in
response to an oil spill. Other bacteria are capable of
using many different food sources and oil constitu-

FAQ: Microbes & oil spills Downloaded from www.asmscience.org by 5

IP: 131.178.200.56
On: Tue, 09 Apr 2019 20:24:51
 Microbes can be counted on
to biodegrade oil over time.
However, the process may
not be fast enough to prevent
ecological damage.

ents are just one of many compounds these bacteria

can utilize for growth. Such microbes can ‘turn on’
BOX 3: New ways to find the necessary metabolic machinery in the presence of
”edible” oil hydrocarbons to switch over to the newly
oil-eating microbes abundant food source.

Microbes can also evolve enhanced capabilities for

For many years, laboratory experiments have indicated degrading oil. One of the most rapid ways this can
that microbes isolated from many different environ- happen is by horizontal gene transfer (HGT). HGT is a
ments are able to biodegrade oil constituents. Recently mechanism whereby microbes can share genes with
developed techniques suggest that such microbes are each other—with HGT, a microbe that has the genetic
even more widespread in the environment than previ- instructions for producing oil-degrading enzymes can
ously suspected. The recent dramatic decline in the transfer copies of those genes to other microbes—even
cost of DNA sequencing has made it possible to detect microbes of different species previously incapable
microbes with the ability to degrade oil even when they of degrading oil components. In this way, microbes
make up only a small percentage of the initial microbial that were unable to use oil as a food source acquire
community. Scientists can now routinely extract and that capability. The ability to share genes can greatly
sequence all the DNA from an environmental sample–– promote a local microbial community’s capacity to
such as soil, seawater, or sediment––and find out exactly clean up an oil spill. Although the process is well
”who is there?” Just as the Human Genome Project established, the extent to which it takes place after an
deciphered the sequence of the entire human genome, oil spill is unknown.
this technique––known as metagenomics––determines
the collective ”genome” of a microbial community. Microbes can be counted on to biodegrade oil over
Computer programs have been designed that allow time. However, the process may not be fast enough to
scientists to search metagenomes for gene sequences prevent ecological damage. Immediate containment or
associated with the enzymes involved in oil degradation. physical removal of the oil is therefore an important first
And, indeed, everywhere we have looked, oil degraders line of defense. Even though oil-degrading microbes are
have been found. Hydrocarbons are everywhere on this found everywhere, their mere presence does not mean
planet, and not just from petroleum sources (e.g., the that environmental conditions are ideal for oil biodeg-
resins made by pine trees and the waxes made by plant radation. Environmental conditions, as well as the
leaves are also hydrocarbons). Because microbes can location, duration, and form of an oil spill strongly affect
grow rapidly and have only a single copy of DNA, muta- how quickly biodegradation will occur.
tions and gene transfer events that improve fitness have
an immediate effect. This gives microbes a profound,
innate ability to evolve the genetic machinery that lets
them use almost any form of carbon as a food and
energy source, and since hydrocarbons are present in
all environments, it is not surprising that hydrocarbon
degraders also are ubiquitous in nature.

6 A report from the

Downloaded from www.asmscience.org by American Academy of Microbiology
IP: 131.178.200.56
On: Tue, 09 Apr 2019 20:24:51
3. What do the microbes need in order to biodegrade
oil and how long does it take? What are the end-products
of microbial degradation? How is biodegradation
measured in the environment?
Microbes are able to consume oil because including nitrogen, phosphate and other nutrients.
These substances are found in nature but may be
they have the genetic instructions to produce
present in limiting quantities. When food levels are
oil-degrading enzymes. But just as crops grow high (for example, after an oil spill), the microbes
can only degrade the hydrocarbons as fast as the
faster with the right amount of light, water,
availability of other nutrients allows. If nitrogen
and fertilizer, microbes can degrade oil much and phosphate levels are very low, biodegradation
of oil constituents will take place slowly.
more quickly when environmental conditions
are optimal. Some of the important factors are: n Availability of oxygen: The enzymatic process of
breaking down oil is usually most rapid in the
presence of oxygen. Theoretically, given enough
n Physical nature of the oil: If the oil is in a single oil and other nutrients, microbial populations
large slick, there is less surface area for the microbes could grow so quickly that they exhaust the
to gain access to the oil, so degradation is slower. oxygen from the water in the vicinity of an oil
Furthermore, if the oil is heavy and viscous, the spill. In practice, oxygen has not proven to be
biodegradable components must first diffuse through as important a limiting factor as nutrients in
that thick matrix to the oil-water interface so that restricting oil degradation in the ocean, although
the microbes can access them. The lighter the oil, degradation rates could be slow if a spill occurred
the faster this diffusion, making the biodegradable in a location where oxygen levels are low.
compounds more available to the microbes.
n Water temperature: Generally, oil is degraded
n Chemical nature of the oil: Biodegradation rates more quickly in warmer waters. The problem is not
vary depending on the particular hydrocarbons that microbes cannot live in cold water–– plenty of
that make up the spilled oil. Oil is composed of oil-degrading microbes are fully adapted to life at
thousands of different compounds—some may cold temperatures––but oil metabolism proceeds
be preferred food sources and be consumed very more slowly in those habitats for the same reason
quickly, others are degraded more slowly or not at that milk spoils more slowly in a refrigerator than
all. In a marine environment like the Gulf of Mexico, on the kitchen counter. However, in environments
hydrocarbons in which carbons are arranged in that are always cold, e.g. In the arctic or deep
an unbranched chain can degrade quickly, in a ocean, cold-loving microbes have adapted so that
matter of days or weeks. Hydrocarbons that have a they can degrade oil as quickly as warm water-
branched structure, or those in which the carbons adapted microbes do in their normal habitat. But
are arranged in multiple rings (known as polycyclic colder temperatures also have physical effects on
aromatic compounds), can be far more difficult the speed of degradation––oil evaporates more
to biodegrade and therefore persist longer. The slowly, so there is more oil left in the water for the
most recalcitrant fractions of crude oil including microbes to degrade. The oil is also more viscous, so
resins and asphaltenes can last for millennia. it spreads out and disperses less readily—providing
less surface area for the microbes to access.
n Availability of nutrients: Like all living organisms,
microbes have many nutritional requirements

FAQ: Microbes & oil spills Downloaded from www.asmscience.org by 7

IP: 131.178.200.56
On: Tue, 09 Apr 2019 20:24:51
The microbes that consume When aerobic (oxygen-using) microbes completely
degrade various oil constituents, the end-products
the oil are themselves are carbon dioxide and water. Some oil constituents
are only partially degraded and the identities of these
consumed as part of the local partially degraded compounds are not always known.
Some of the intermediates may be toxic to marine
food web, and thus the carbon organisms, although they are not likely to accumulate
to levels that cause greater harm than the original oil
and energy contained in the components. The microbes that consume the oil are
themselves consumed as part of the local food web,
oil are eventually distributed and thus the carbon and energy contained in the oil are
eventually distributed through the food web.
through the food web.
There are many ways to measure clean up of an oil
spill. The ultimate goal of scientists or responders
n Pressure: The Deepwater Horizon oil spill measuring biodegradation is to document the mass
released oil at a depth of over 1500 meters, loss of hydrocarbons attributable to microbial activity.
where the temperature is low and the pressure Traditionally, such measurements have focused on the
high. These are conditions where degradation disappearance of particular oil constituents, the appear-
might have been expected to be quite slow. ance of products of biodegradation (like carbon dioxide)
However, early results show a high number and the depletion of oxygen. Decline in the amount
of oil-degrading microbial species adapted of specific oil components, or changes in the ratios
to life even in these extreme conditions. of compounds, can be taken as evidence of biodeg-
radation processes. Declining oxygen and nutrient
n pH and salinity: In most of the ocean, pH and levels are also indicative of biodegradation. Additional
salinity do not vary enough to make a big measurements include detailed chemical analyses of
difference in oil degradation rates. Some specific petroleum components, assessments of toxicity levels,
environments, like salt marsh sediments, exhibit and detection of increases in specific oil-degrading
not only high salinity, but also rapid fluctuations microbial populations. In the open ocean, it can be
in salinity, oxygen, and pH—all characteristics particularly challenging to quantify biodegradation and
that typically slow oil degradation. multiple approaches are required. Recently, such new
strategies as computational modeling and molecular
n Other microbes: Natural microbial communities tools for assessing changes in microbial communities
are diverse, with many different types of microbes have become available for evaluating the progress of
that both compete and cooperate. The complex biodegradation.
interactions that characterize healthy, natural
microbial communities are only beginning to be One question that scientists measuring oil degrada-
understood, but interdependence is the norm. tion rates want to answer is “how fast is the oil being
This is one reason why adding microbes to oil consumed?” Another is “when will the oil be gone?”
spills in the hope of speeding degradation is The two questions are linked, of course, but unlike
challenging; outsiders (i.e., artificially introduced gasoline consumption in a car’s gas tank, microbial
microbes) have a hard time breaking into the degradation does not proceed linearly over time. So,
existing community structure and competing if one-half of the oil is gone in one week, it does not
with the local species that have evolved together mean that all of the oil will be gone in two weeks.
over the millennia in a particular habitat. Generally, degradation rates slow as the oil concentra-
tions decrease, making it difficult to calculate a certain
Given all the above variables, it is not surprising that end-point. They also slow as the more readily degrad-
the rates at which oil is degraded can vary enormously. able components are used up, leaving behind the more
Examples include estimates that natural processes, recalcitrant components.
including biodegradation, removed 99.4% of the crude
oil spilled in Alaska’s Prince William Sound in 10 years
(NOAA), whereas oil spilled in the Kuwait desert is
expected to remain for centuries.

8 A report from the

Downloaded from www.asmscience.org by American Academy of Microbiology
IP: 131.178.200.56
On: Tue, 09 Apr 2019 20:24:51
4. How do dispersants and nutrients affect oil
biodegradation, and what are the ultimate fates
of these additives?
Dispersants
Dispersants work on the same principle as dishwashing
detergents––they break the oil into small droplets that
disperse in water. Dispersants help surface oil slicks
mix into the water, reducing the immediate risk to
seabirds and shorelines. At the Deepwater Horizon spill,
dispersants were added close to the broken wellhead
with the goal of dispersing the oil at its source and
preventing much of it from reaching the surface close
to the wellhead where many ships were busy trying to
stop the leak. By themselves, dispersants do nothing
to get rid of the oil––they merely change its physical
form. The decision to use dispersants involves trading
off the advantages of changing the form of the oil with
the risks of moving the oil from the surface of the water
into the water column. Generally, dispersants are used
to mitigate immediate danger to sea life and shorelines. whether there is a net benefit to dispersant use, beyond
The dispersants may themselves have harmful effects; the immediate physical impact of dispersing and
however, they are added in low concentrations relative thereby diluting the oil. In the Gulf of Mexico, the use
to the oil and are less toxic than the oil itself. of dispersants appears to have significantly reduced
the amount of oil reaching the shore, which reduced
In principle, dispersants enhance biodegradation by the immediate threat to beaches and salt marshes. The
increasing the surface area and availability of the oil effects of dispersants on the biodegradation in the deep
to the microbes. Studies of the effect of dispersants plumes are unknown.
specifically on biodegradation rates are difficult to
design and execute because conditions vary so widely Nutrients
depending on the type of spill, the local environment, Nutrients including nitrogen, phosphate, and iron
and weather conditions. are essential to any biological process and crude oils
are naturally deficient in these major nutrients. Many
Based on their chemical structures, the dispersants marine ecosystems are naturally nutrient-poor. Thus,
that have been used on oil spills should themselves be when an oil spill results in a sudden increase in avail-
fully biodegradable, but biodegradation rates have not able food (oil hydrocarbons), there may not be enough
been extensively studied. A number of bacterial species nutrients in the water to support microbial growth.
produce compounds that function as dispersants and Nutrient addition to relieve this limitation is one tool
these compounds are now produced commercially for to enhance bioremediation and various strategies
use in the food, cosmetic, crop treatment, and biore- have been employed to provide nutrients in a suit-
mediation industries. Biosurfactants, as the bacterial able form. One of the best understood examples of a
products are known, have not yet been used to treat an large scale addition of nutrients was in response to the
oil spill, but their use raises most of the same questions Exxon Valdez oil spill, where nutrient addition indeed
as that of chemically synthesized dispersants: do they enhanced oil degradation in the ecosystems of Prince
speed up biodegradation of the oil? do the microbes William Sound. Theoretically, nutrient addition could
that feed off the dispersants compete with the oil- have unintended consequences that upset the natural
consuming microbes for scarce nutrients and possibly ecosystem balance, but no such consequences have
slow down oil degradation? The question ultimately is been reported.

FAQ: Microbes & oil spills Downloaded from www.asmscience.org by 9

IP: 131.178.200.56
On: Tue, 09 Apr 2019 20:24:51
5. Does adding bacteria to the contaminated
environment speed the cleanup of an oil spill or improve
the effectiveness of biodegradation? Is it possible to
engineer microbes so they work even better?
Because bacteria that can degrade oil the oil enters the environment, local microbes begin
colonizing the oil droplets. A laboratory strain would
constituents are ubiquitous, to date there is
have to be able to displace the indigenous microbes
little convincing evidence that bioaugmentation which are well-adapted to local conditions. Designing
microbes that are both more efficient at degrading
(addition of more bacteria) significantly
oil and well adapted to the particular environmental
enhances either the rate or the extent of conditions is a daunting challenge, which has not yet
been achieved.
oil biodegradation in most environments.
Bioaugmentation has not been shown to speed It is important to remember that microbial commu-
nities, not individual microbes, are involved in
the mitigation of oil spills on marine shorelines,
degrading all the various constituents of oil. The level
freshwater wetlands, salt marshes, or soil. of metabolism in each individual microbe (which is
what theoretically could be increased in an engineered
microbe) is not what limits the rate of biodegradation.
While seemingly not useful for oil spills, addition of Even the odds of significantly increasing the rate of
oil-consuming microbes may be useful in engineered oil metabolism in individual microbes are not good.
systems (e.g., tanks of contaminated water). Bioaug- Natural selection has been acting on microbes for
mentation also has been helpful for biodegradation billions of years, honing the metabolic pathways for
of man-made organic chemicals that have entered the degradation of hydrocarbons to a highly efficient level.
biosphere recently. Chlorinated solvents and trans- Collectively, the natural communities have evolved
former fluids (PCBs) generally are not found in the remarkable capabilities to capitalize on every bit of
natural environment. There are microbes capable of energy that can be extracted from oil constituents.
degrading chlorinated solvents but their numbers are
low and they grow slowly; microbial communities Microbes might be selected or engineered to function
evolved to use these compounds as sources of food in particular habitats with extremes of pH, temperature,
and energy are not found everywhere. Bioaugmenta- salinity, or other conditions. It is possible to design
tion with competent degrading strains of bacteria can microbes that are better at degrading oil, but given
stimulate the rate and extent of biodegradation of these the ubiquity of oil-degrading microbes, the difficulty in
compounds in appropriate environments. predicting when and where the next oil spill will occur,
and, most importantly, safety and public acceptance
It is possible to engineer microbes that show enhanced considerations surrounding the release of genetically-
oil degrading capabilities in the laboratory, but such modified organisms, oil spill bioengineering is not the
microbes are unlikely to have a major impact in most promising research target.
environmental settings. First of all, from the moment

10 A report from the

Downloaded from www.asmscience.org by American Academy of Microbiology
IP: 131.178.200.56
On: Tue, 09 Apr 2019 20:24:51
6. What happens to the oil after the microbes degrade it?
Does it go up the food chain like DDT ? What happens
to all the other animals in the area while the oil-eating
microbes are at work? Does an oil spill increase the
risk of dangerous pathogen ‘blooms’?
Oil does not build up in a microbe any more
than salad oil builds up in our stomachs.
Just as our digestive tracts break food
down, microbes break oil down into simple
carbon compounds that are used to make
the sugars, fats, and proteins needed for
growth and energy production, with the
ultimate byproducts being carbon dioxide
and water. The simple carbon compounds are
incorporated into new cellular constituents––
in other words, they are used to make more
Marine animals will leave the vicinity of a spill (if
microbes! (Formally, we say that the carbon
they can). Some of the compounds in crude oil are
has been used to produce additional biomass.) toxic, others are irritating to membranes like eyes and
nostrils; they taint the water and are generally actively
The new microbes continue eating oil, unless
avoided by motile marine animals. Organisms that
they themselves are eaten by natural predators. cannot swim away could be affected if the microbial
oil degradation is using up all the available oxygen.
The important fact is that biodegradable
But there is no evidence that in open systems like the
hydrocarbons do not accumulate on or inside ocean, oxygen depletion due to oil degradation would
be so great as to affect other animals in the system.
cells and thus do not go up the food web. It
is possible that oil spills might contain some It is possible to calculate how much oxygen microbes
would need to break down all of the oil and those calcu-
recalcitrant oil components that are only poorly
lations suggest that most spills are unlikely to result in
degraded by microbes. Such compounds dangerous decreases in dissolved oxygen (DO) levels.
DO was one of the major variables monitored during
might bioconcentrate through the food chain,
the Deepwater Horizon response, and although some
but this phenomenon has not been observed small declines in DO were measured in the area where
the dispersed oil plume was found (1000- to 1300-meter
in large ecosystems like the Gulf of Mexico.
depths), levels of oxygen that would be dangerous to
marine life were never approached.

FAQ: Microbes & oil spills Downloaded from www.asmscience.org by 11

IP: 131.178.200.56
On: Tue, 09 Apr 2019 20:24:51
There are certain relatively closed ecosystems, like The microbes that degrade oil are generally not
estuaries, salt marshes, or wetlands, where oxygen human pathogens. Even oil-degrading microbes that
depletion from oil degradation is sufficient to harm are related to human pathogens do not cause disease
organisms that live there and require oxygen. Oxygen (and their disease-causing relatives cannot degrade
depletion is more likely to affect such ecosystems as oil). Even though their numbers increase significantly
the seafloor, salt marshes, or beach sands, where the after a spill, oil-degrading microbes pose no threat to
natural supply of oxygen tends to be limited. A notable human health. No evidence has been found that stress
example of an area with limited oxygen is the dead from an oil spill on organisms like oysters or shrimp
zone in the Gulf of Mexico where the Mississippi River causes them to harbor more human pathogens. No
empties into the Gulf—the zone was not caused by the case of a pathogen outbreak has been documented
oil spill but by the regular influx of nutrients from the as the result of an oil spill, even though thousands of
Mississippi, which carries agricultural fertilizer run-off spills occur annually.
from Midwestern fields and lawns into the Gulf. There
is no evidence that a one-time spill of oil––even a large
one––into the open ocean could create persistent dead
zones, although localized and temporary areas of low
oxygen are possible.

12 A report from the

Downloaded from www.asmscience.org by American Academy of Microbiology
IP: 131.178.200.56
On: Tue, 09 Apr 2019 20:24:51
7. What happens to the microbes when the oil is all gone?
Does an oil spill result in a permanent change in the mix
of microbial species that live in the area?
The microbes that degrade oil are part of the local
food web; they are consumed by other microbes
that are, in turn, consumed by larger predators.
When the oil is gone, the oil-degrading microbes,
with less food available, stop dividing so rapidly
and eventually return to pre-spill abundance.

However, determining whether the species composi-

tion is exactly as it was pre-spill is complicated at the
microbial level, because microbial communities are
dynamic systems. It is difficult to determine exactly
what the community looked like before the oil spill and
we know little about the dynamics of natural popula-
tions, even in the absence of obvious disturbances.
Further complicating matters, several kinds of bacteria
may carry out similar functions. The relative numbers
of these ‘redundant’ groups may change after an oil
spill, but the overall functionality of the community
largely remains the same. The functional stability of
microbial communities makes it difficult––and perhaps
unnecessary––to determine whether a community is
exactly the same as it was before the spill. However, no
evidence has been found that a bloom of oil-degrading
microbes crowds out other microbial species and drives
them to extinction. Even at the height of oil-degrading
activity, oil-degrading microbes make up only a small
percentage of the total microbial community.

Modern molecular methods are providing new ways of

measuring the composition and function of microbial
communities. High-throughput analytical technologies
make it possible to obtain the genetic sequence of the
entire community (see BOX 3). It is also possible to
measure change over time in the abundance of genes
that code for oil-degrading enzymes. The Deepwater
Horizon spill was one of the first where advanced high-
throughput approaches were applied comprehensively
and much is likely to be learned about what happens
within the local microbial community at the genetic
level during and after such a spill.

FAQ: Microbes & oil spills Downloaded from www.asmscience.org by 13

IP: 131.178.200.56
On: Tue, 09 Apr 2019 20:24:51
This report was designed by
Pensaré Design Group
www.pensaredesign.com
Downloaded from www.asmscience.org by
IP: 131.178.200.56
On: Tue, 09 Apr 2019 20:24:51