Petroleum: the connection between bacteria and the black gold

Who can imagine our life today without oil? Most of the energy we consume, and also most of the plastic products we use, originate from the same black, oily liquid that is extracted with the help of drilling facilities from the depths of the earth, and also under the seabed. How was it created and got there?

Dror Bar-Nir, "Galileo" magazine
Posted: 01.10.07, 15:38

Oil is a mixture of substances called hydrocarbons, which, as their name suggests, are long chains, and sometimes closed rings, of carbons linked to hydrogens.

We do not know for sure how oil was formed, and there are several theories that try to explain it. Here we are interested in two biogenic theories (related to life; in Greek, "bio" means "life" and "genesis" means "birth").
According to one theory, the origin of oil is the accumulation of remains of algae and plankton on the bottom of the ancient oceans, together with clay, in non-aerial conditions and without the presence of decomposer microorganisms. Under these conditions, organic sludge was formed. With the passage of time, the organic sludge was buried under sedimentary rocks and, as a result of the increase in temperatures and pressure, chemical processes took place in it that changed the organic substances into hydrocarbons.
According to the second, relatively new theory, those dead creatures, in the presence of oxygen, were decomposed by microorganisms (bacteria, algae and fungi), and the products of some of these microorganisms are the hydrocarbons that accumulated under the sedimentary rocks. Even today, we are familiar with microorganisms that secrete petroleum-like substances, all from the group of green algae. For example, the endemic algae Botryococcus braunii, which is considered a nuisance in Australian lakes and also grows on the Atlantic coast and elsewhere, secretes long hydrocarbons (30-36 carbons long) into its environment. 30 percent of the cell content of algae are these hydrocarbons.
Several research teams around the world, including Arthur Nonomura's group from the University of California at Berkeley and Margaret Mulholland's group from Old Dominion University in Virginia, are trying to grow algae and improve its hydrocarbon output. If they succeed, perhaps in the future we will use oil derived from these algae, which will grow in purified sewage water. Not only that, but the algae will also reduce the amount of the greenhouse gas carbon dioxide (CO2) in the atmosphere.
The flow of liquid oil between the rock layers and the change in geological conditions caused the oil to be trapped in pockets of soil, without contact with the external environment, for millions of years, until the drilling facilities reached it.
Humans' extensive use of oil harms the quality of the environment. The soil in the drilling and pumping areas is contaminated with oil. The crude oil is transported to and from the refineries in pipelines, trucks, trains and ships. All oil loading and unloading areas are also contaminated. The containers in which the oil and its products are kept (such as fuel storage tanks and gas stations) are not always sealed enough, and the oil seeps into the ground, reaches the groundwater and pollutes it.
And at sea: do the ships that transport the oil to long distances and unload the oil at its destination return empty? No! They fill the containers with sea water (used as ballast water, i.e. water used to balance the ship). When they return to the port of origin, they pour the ballast water, which contains oil residues, back into the sea.

Accidents cause contamination
And we haven't talked about accidents yet. More than once it happened that full oil tankers sank and ruptured in the middle of the sea, and their contents spilled into the sea and covered the area with a thick layer of oil. The oil prevents the oxygen in the air from bubbling into the sea water, and all the animals under the oil slick suffocate from lack of oxygen and die. Other animals are harmed by contact with the oil or by swallowing it, because the oil blocks the respiratory and digestive systems.
In 1967, the Tory Canyon tanker capsized off the coast of England, and all of its cargo, 120,000 cubic meters of oil, spilled into the sea. In some of the affected areas, the contamination lasted for about 10 years.
The most famous example, which served as the strongest incentive to search for solutions to the problem, occurred on March 24, 1989, when the giant tanker Exxon Valdez ran aground and split off the coast of Alaska. About 20 percent of the cargo, about 40 cubic meters of crude oil (258,000 barrels), spilled into the sea and created a huge oil slick, which polluted about 220 km of beaches.
In January 1991, in the first Gulf War, Iraq blew up Kuwait's oil wells, and as a result, the Persian Gulf was flooded with huge amounts of oil. A spot of about 600 square kilometers was created, which moved south along the coast of Saudi Arabia at a speed of about 20 km per day, destroying every living creature in its path. The area of ​​this stain was 27 times larger than the Exxon Valdez contamination.
It is important to understand that, despite the media coverage of events involving large quantities of oil, it is precisely the "chronic", prolonged infections that are the real problem. The penetration of oil, some of its components are carcinogenic, into the food chain, and contamination of the groundwater following continuous leaks, cause a decrease in the fertility of the affected creatures and long-term genetic damage.
An example of how oil can have an effect even in low concentrations: on January 17, 2001, the oil tanker "Jessica" ran aground near the island of San Cristóbal in the Galapagos Islands, and oil began to leak from it. The contamination was not serious, and they even managed to clean most of it, but by December of that year there was a 62% mortality rate (compared to a normal annual mortality of up to 7%) of the marine iguanas on the nearby island of Santa Fe - and most of those affected were actually vegetarians.
Martin Wikelski from Princeton University, who examined the contents of the digestive systems of the dead iguanas, found that they were full of algae - the usual diet of iguanas. But they could not digest it. It turned out that the oil damaged the symbiotic bacteria of the iguanas, which help them digest the plant material, which they are unable to break down on their own (as is the case with all vegetarian animals).
How are infections treated?
How can oil pollution be overcome? It turns out that certain species of bacteria can utilize different hydrocarbons as a source of carbon. The aerial decomposition processes of the hydrocarbons are much more efficient than the non-aerial decomposition processes, and sometimes different stages of the decomposition processes are carried out by different bacteria living in the same habitat. This, by the way, is the reason why the hydrocarbons in the depths of the earth are sometimes preserved for millions of years: in these oxygen-free environments, the decomposing bacteria cannot exist.
At Tel Aviv University - in the laboratories of Eugene Rosenberg, Eliora Ron and David Gutnik - they have been researching the bacteria that breaks down oil for many years. The reason for the interest is the economic possibilities inherent in these bacteria as a source of proteins, as well as the possibility of using the bacteria to get rid of the huge oil slicks that pollute the seas and beaches due to negligence, lack of adherence to procedures or accidents.
Where are oil-degrading bacteria found? The "natural" place to look for them is in a place where long-term oil pollution exists - they collect contaminated soil, or contaminated seawater, isolate bacteria from them and grow them on growth media that only contain oil as a source of carbon and energy. Since the bacteria need an aqueous environment to exist, while the oil is a water-repellent substance, "emulsion"-forming substances must be added to the mixture that will increase the accessibility of the oil to the bacteria. Several hundred species of bacteria were isolated using this method.
One of the factors limiting the activity of the oil-decomposing bacteria is the lack of nitrogen and phosphorus sources. In closed places (such as ships' ballast water tanks), or even on polluted beaches, a special fertilizer known as F-1 (developed in laboratories at Tel Aviv University), which contains the missing substances, can be spread together with decomposer bacteria - which are grown in the laboratory. In ballast water, the addition of bacteria and fertilizer to the ballast water means that the water will be free of oil and it can be poured back into the sea without polluting the environment. Also on the beaches, scattering bacteria with the special fertilizer caused an impressive increase in their activity.
But this fertilizer is not effective in open places, such as marine oil slicks, where the ingredients in the fertilizer dissolve in the seawater. One must try to find ways in which oil-degrading bacteria can efficiently break down the oil in the open sea.
We realized, therefore, that microorganisms are the source of oil. Microorganisms - and the entire food chain that depends on them, including more complex creatures - are harmed by oil. And there are also microorganisms, mainly bacteria, that break down oil. We must make more of an effort to utilize these microorganisms to prevent oil use damage and reduce it after it has occurred. It is possible that in the future, when oil reserves are depleted, microorganisms will also be used to produce oil for human needs.

Dr. Dror Bar-Nir teaches microbiology and cell biology at the Open University. Published in "Galileo" magazine