Team:NU Kazakhstan/Human Practices

Bioremediation of Sour Crude Oil Waste using Cyanobacteria

Integrated Human Practices

The main goal of the iGEM NU Kazakhstan team 2018 was not only to create the cyanobacteria which can transform toxic hydrogen sulfide compound to elemental sulfur and hydrogen gas in laboratory conditions but also to investigate how to integrate this project in the real industrial situations.

Kazakhstan is commonly known to be the major producer of oil in the world; it has an enormous amount of oil resources: 30 billions of barrels, 172 oilfields, 1.8% of global oil reserves [1]. The figures speak for themselves, and Kazakhstan tries to fully use its potential. However, the major problem of an oil refinery which challenges not only our country but also other global oil exporters is the presence of hydrogen sulfide in crude oil. Decayed organic matter (kerogen), which is trapped in sedimentary rocks, serves as the main reagent of thermal conversion, in which the oil is formed as a major product. Kerogen, which is highly concentrated with sulfur, releases hydrogen sulfide during the reaction and this gas stays in crude oil.

Hydrogen sulfide is highly toxic gas, which in high concentrations can interfere with the organism’s capability of cellular respiration. The human body can block its effect by transforming it into sulfate, using hemoglobin-bound enzymes of blood or liver cells. However, when the concentration of hydrogen sulfide is too high, the organism’s ability of detoxification is overwhelmed and it eventually leads to death. Besides these health risks, the presence of H2S in the oil can lead to the corrosion of pipes and it is of the high cost to replace them periodically.

Our team decided to know more about the process of hydrogen sulfide purification and details related to the integration of the project by contacting with the variety of industrial companies in Astana, Atyrau and Almaty. Our team representatives met with one of the largest oil company directors in Atyrau, as they are located there and most of Kazakhstan’s oil reserves are from the Atyrau region. Below you can see the list of meetings and some outcomes of these meetings.


NCOC is the main offshore oil and gas developer in Kazakhstan. Their estimated oil production for 2018 is 370,000 barrels per day, which is more than their expected 75,000 barrels per day in 2016 [1]. They have five main fields on the Caspian Sea about 80km from Atyrau city. NCOC faces many safety, logistical and engineering obstacles due to its location. The oil from these fields has high hydrogen sulfide content as well as carbon dioxide. The principle system used for the sour gas treatment is the raw gas re-injection. Their shareholders (KazMunayGas, Eni, ExxonMobil, Royal Dutch Shell, Total S.A., China National Petroleum Corporation, Inpex) have been practicing raw gas re-injection in many different environments. This technique has been invented in Canada in 1989 and practiced in 39 projects in the world, including the Karachaganak and Tengiz fields in Kazakhstan. With this process, 80% of sour gas from crude oil is returned to the reservoir, while the rest 20% is generated to produce elemental sulfur. They estimated that 3800 tonnes of sulfur per day will be produced in their project [1].

Our team representatives visited the NCOC head office in Atyrau. During the meeting, we introduced them to iGEM, synthetic biology and we explained our project. They were very responsive as they were interested in our new approach to the bioremediation of sour crude oil wastewater. Even though they were hesitant about the risks of genetically modified organisms, they assured that it has good potential to turn into a commercialized project that they can apply in their wastewater treatments.

Firstly, they were interested in a specific design where our cyanobacteria can carry out the bioremediation of sour crude oil wastewater. We approached this comment by offering an approach that includes keeping the cyanobacteria in a gel-like reservoir, where the wastewater can be pumped in.

Secondly, they were concerned with what will happen to cyanobacteria after it has taken up hydrogen sulfide from the wastewater. We replied that as part of our risk management, we will be using the SuperNova, a variant of KillerRed, which uses Chromophore Assisted Light Inactivation that will lead to self-destruction of the cells at specific wavelengths of light.

For companies like NCOC, the elemental sulfur produced after the treatment of hydrogen sulfide is sold to overseas companies. We proposed a different solution. NCOC re-injects 80% of sour gas back into the reservoir. If this is treated with cyanobacteria and they are burned after they have carried out hydrogen sulfide reduction, then these can be turned into nanomaterials. The acid gas (hydrogen sulfide with carbon dioxide) re-injected back into the reservoir poses serious environmental problems in the future, as the widespread release of hydrogen sulfide due to the leakage of wellbores is a possibility to be considered [2]. According to NCOC’s report, their air quality monitoring stations registered a number of instances where the hydrogen sulfide concentrations exceeded the Maximum Permissible Concentrations in the Atyrau region due to leaks [3].

NCOC’s real-life applications questions helped to improve our project because many aspects of the project were discussed as if it was going to be applied in their production processes. This led us to examine the parts of the project that needed to be well thought out not only for laboratory conditions but also how it could be practiced in mass production at different conditions. Overall, this meeting with NCOC gave us valuable feedback and they look forward to collaborating with us, as they invited us to intern at their laboratories where they have all the samples we need to further assay the viability of our cyanobacteria. We also look forward to continuing this project with NCOC after the Giant Jamboree, because the possibility to decrease the environmental risks of hydrogen sulfide in our country is our priority.

EmbaMunayGas JSC (EMG)

In 1922, the company was developed for geological exploration, development of oil and gas fields as well as oil and gas production and treatment. The company exports oil along with selling it in the domestic market. Their produced gas is sold through the national gas supplying company. In June 2017, EMG launched a project for a treatment unit that will produce commodity gas and commercial granular sulfur [4]. EMG uses the LO-CAT Merichem technology for the production of elemental sulfur. LO-CAT Merichem is a system that converts hydrogen sulfide to elemental sulfur with the use of a chelated iron in special containers and it guarantees hydrogen sulfide removal [5]. EMG allocates funds for projects to clean historically contaminated areas for the oil sludge treatments. They use the Finnish Kalottikone Unit for the soil recycling that is later used in construction and repair of roads. The Kalottikone Unit is a thermal desorption equipment that cleans contaminated soil from oil products [6].

We organized a meeting with the executive directors of EMG in Atyrau. We got to introduce them to iGEM and explain our project. After a short presentation, we discussed with them the possibility of applying our project in their processes. They were positive about the project and offered their help for the expansion of the project in real life. However, they were a little sceptical about the genetically modified organism that would be used to treat the sour crude oil wastewater. We assured them about the safety measures we have thought about, which eased their worries about the risks of the project.

They explained the operations of their company. As their company extracts the oil from the ground, they separate the extraction into oil, gas and water. The sulfur content of the oil meets the minimum requirements and the standards of the legislature of RoK; therefore, they export or sell the oil. The extracted gas is then further produced as commodity gas that is sold for local usage. The water is pumped back into the reservoir to create the proper pressure for the oil to be pumped closer to the well in a process called water flooding [7].

Since our project is concerned about the wastewater, we tried to show that water flooding is not a reliable process even if it can increase the recovery factor and the production rate of oil extraction. We assume that their technologies (LO-CAT and Kalottikone) would not reduce the environmental factors as much as our synthetic biology approach would. Firstly, in our approach, the hydrogen sulfide reduction yields hydrogen gas and elemental sulfur, which are both potential biofuels. Secondly, the wastewater that is pumped back to create pressure can be treated with our cyanobacteria, because our process does not reduce the volume of the wastewater. Therefore, it would be producing the favorable byproducts, while creating the appropriate pressure. This solution was something new for the executive directors, but they were open to new processes.

The meeting with EMG did not only give us beneficial feedback, but they helped to clarify some oil production processes that we could not find online. They are ready to give their wastewater samples to analyze the potential of our genetically modified cyanobacteria. We look forward to collaborating with EMG, as our project can be applied as part of their oil and gas treatment processes.

Dow Chemical Company

The Dow Chemical Company (based in Midland, Michigan, USA) is one of the largest chemical manufacturers in the world. This company is involved mainly in the manufacture of plastics, chemicals and agricultural products. As the hydrogen gas is the byproduct of not only oil refinery reactions, but also different industrial processes such as paper, rayon and leather manufacture, we decided that the opinion of people specialized in chemicals production is also very important. We organized the meeting in Astana city with the representatives of this company. During this meeting, many significant conclusions were drawn:

1. The process of hydrogen sulfide conversion can be used not only in oil & gas refineries but also for sewage treatment. There is the serious problem of hydrogen sulfide remained after water treatment, which can be recognized through the strong smell present in some streets in the city of Astana. The country manager of this company also underlined that our project would find easy application namely in this case.

2. The use of cyanobacteria in hydrogen sulfide conversion would be really challenging in oil industry application. There are two reasons for this statement: light delivery and speed of flow. Under the conditions of factories, it is unknown how possible will it be to provide light for maintaining the life cycle of cyanos and what amount per hour they can really deal with.

Overall, the experts were really inspired by our project and they continue to support us by providing with essential contacts and useful advice. With their help, we contacted the ChemInvest company which promised to provide us with the oily water samples

KazMunayGas JSC

KazMunayGas is one of the major oil and gas companies in our country, so the meeting conducted with its representative specialists was probably the most challenging and important one. It was crucial to investigate the details of the oil refinery, namely the separation from the hydrogen gas; to know the possibility of integrating the project and the general aspects that we should consider. Our team members presented the project idea in Astana to the company experts who are responsible for the scientific part. The meeting was really fruitful, and it forced us to reconsider many things, such as:

1. To be realistic. The project itself is very interesting and it would be wonderful to apply such advanced principles of synthetic biology in one of the most challenging problems of the oil industry, but there are many unanswered questions such as the possible ways for storage of hydrogen gas, the capacity of H2S consumption by cyanobacteria, the disposal of cells excess and other details. They tried to explain to us that we should think more practically and consider many unexpected issues.

2. To know how to estimate the cost of the project. The company representatives told that economical aspect is essential for the project of any type and in order to integrate the project successfully, you need to know the cost of every detail participating in the process. In addition to this, they mentioned the significant price of the Claus process currently used in the desulfurization of oil and stated that finding the cheap alternative to this method would drastically decrease their expenses.

3. To know how to work with information. They strongly recommended us to search more for the information related to the amount of hydrogen sulfide found on the fields, to accurately apply the statistical methods for analyzing this data and to present it in an appropriate way.

Such meetings always play a crucial role in creating and designing projects, because it has shown us that many aspects should be considered. Also, they agreed to provide us with their samples of oily water from the fields and to coordinate us throughout the project.

MKA Engineering LLP

With the purpose of assessing the relevance of our project in the real world, meeting with “MKA Engineering” company, which specializes in the import and sale of chemical reagents for mining purposes, was organized in Almaty. Our students made a presentation about iGEM and our current project in order to receive the feedback from the general audience and to ask the company representatives several questions about the import of the chemical reagents, sulfides, in particular. As a result of this meeting, several points were made:

We learned about two main industrial methods of obtaining sulfides. In the first method, sulfide is obtained from mirabilite ore. The second method involves sodium sulfate. According to the representatives of the company, none of these were viable in Kazakhstan. For this reason, sodium sulfide is exported from other countries, mainly China. Hydrogen sulfide that is released in oil mining places is not used for further purposes. This is due to the fact that even such companies do not know the application of this byproduct. Special containers are needed to work with hydrogen sulfide gas.

Finally, we found out valuable information that could assist in the project’s development as well as collected opinions of non-experts on our presentation about iGEM, our idea and synthetic biology generally. In addition, these points led us to necessity in collaborating with oil companies.

In addition to this, as it was discovered later, the people present at the meeting were specialized namely in economics and jurisprudence, and only one geologist was present. It was difficult to explain the details of the project to people without the scientific background, and we found out that there is the significant misunderstanding of synthetic biology in Kazakhstan. Many people in our country still believe in stereotypes of the potential danger of GMO and that is why we decided to work more on the public engagement (you can see more detailed information in the section of PE).

Ecostandard LLP

Ecostandart KZ LLP improves technology for obtaining biological and technological bioremediation of oil-contaminated soils. This company produces biological products for the purification of oil-soil and water on a large scale. We had 3 meeting sessions and our collaboration was productive. On the first meeting, we presented projects to each other and discussed the current state of oil waste management problem in Kazakhstan. During the second meeting, we visited Ecostandard’s laboratory in the Technopark of the Nazarbayev University and we observed how purification of soil takes place at the initial stage. This experience was very valuable because we witnessed different methods of oil waste purification. On our 3rd meeting, we were allowed to get samples of oily water wastes from Ecostandard’s laboratory and take them into our laboratory in university. Additionally, we acquired lots of knowledge about oil water composition, its properties and optimum conditions for bacterial growth in it.

Shyndau LLP

Shyndau is a design and survey company that focuses on infrastructural support for other companies within Kazakhstan. Their work includes topographical and geotechnical investigations, development of appropriate project design with its necessary documentation and drilling of geotechnical boreholes. Our meeting with Shyndau in Atyrau was aimed to understand the geotechnical approaches of oil companies for the further development of our project design. With the help of their company, we were able to determine which type of oil is extracted from where with what type of process. Their geotechnical and geological skills assists us with our future plans to model a specific reservoir where our model organism will perform the process for bioremediation. They also suggested companies whom we may contact for further analysis of the oil fields and projects. In the future, they are happy to collaborate and sponsor our project.


[1] NCOC (2017) Sustainability Report 2017

[2] James E. Houseworth, Preston D. Jordan (2012) Comment on “Potential for environmental impact due to acid gas leakage from wellbores at EOR injection sites near Zama Lake, Alberta”, by D.M. LeNeveu

[3] NCOC (2017) Sustainability Report 2017

[4] EmbaMunaiGas (2017) Sustainable Development: Ecology

[5] Merichem Company (2017) Gast Treating: LO-CAT H2S Removal Technology

[6] Kalottikone (2018) Long Lifetime, Low Maintenance Cost

[7] Schlumberger (2018) Oilfield Glossary