Scientists Have Cultivated a “Miracle Microbe” That Converts Oil Into Methane

By MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY DECEMBER 23, 2021


Scientists have succeeded in cultivating an archaeon that converts oil into methane. They describe how the microbe achieves the transformation and that it prefers to eat rather bulky chunks of food.

Microorganisms can convert oil into natural gas, i.e. methane. Until recently, it was thought that this conversion was only possible through the cooperation of different organisms. In 2019, Rafael Laso-Pérez and Gunter Wegener from the Max Planck Institute for Marine Microbiology suggested that a special archaeon can do this all by itself, as indicated by their genome analyses. Now, in collaboration with a team from China, the researchers have succeeded in cultivating this “miracle microbe” in the laboratory. This enabled them to describe exactly how the microbe achieves the transformation. They also discovered that it prefers to eat rather bulky chunks of food.



In an oil field like this, Gunter Wegener and his colleagues found the microorganisms that now also live in their laboratory. Genetic information shows that they are widespread and even live in the deep sea. Credit: Yoshi Canopus

Un­der­ground oil de­pos­its on land and in the sea are home to mi­croor­gan­isms that use the oil as a source of en­ergy and food, con­vert­ing it into meth­ane. Un­til re­cently, it was thought that this con­ver­sion was only pos­sible in a com­plic­ated team­work between dif­fer­ent or­gan­isms: cer­tain bac­teria and usu­ally two ar­chaeal part­ners. Now the re­search­ers have man­aged to cul­tiv­ate an ar­chaeon called Meth­an­ol­i­paria from a set­tling tank of an oil pro­duc­tion fa­cil­ity that handles this com­plex re­ac­tion all by it­self.

Enzymes just in case

This “mir­acle mi­crobe” breaks down oil into meth­ane (CH4) and car­bon di­ox­ide (CO2). “Meth­an­ol­i­paria is a kind of hy­brid creature that com­bines the prop­er­ties of an oil de­grader with those of a meth­ano­gen, i.e. a meth­ane pro­du­cer,” ex­plains study au­thor Gunter We­gener from the Max Planck In­sti­tute for Mar­ine Mi­cro­bi­o­logy and the MARUM – Cen­ter for Mar­ine En­vir­on­mental Sci­ences at the Uni­versity of Bre­men.


Image from the epifluorescence microscope: Methanoliparia cells (green) from the laboratory cultures. The oil droplet that the archaea colonized can be seen as a reddish glow. The red dots display rare bacteria in the culture. Credit: Rafael Laso-Pérez/Max Planck Institute for Marine Microbiology; from: Zhou et al., Nature, 2021

Now that the re­search­ers have suc­ceeded in cul­tiv­at­ing these mi­croor­gan­isms in the labor­at­ory, they were able to in­vest­ig­ate the un­der­ly­ing pro­cesses in de­tail. They dis­covered that its ge­netic make-up gives Meth­an­ol­i­paria unique cap­ab­il­it­ies. “In its genes it car­ries the blue­prints for en­zymes that can ac­tiv­ate and de­com­pose vari­ous hy­dro­car­bons. In ad­di­tion, it also has the com­plete gear kit of a meth­ane pro­du­cer,” says We­gener.

New pathway of methanogenesis

In their labor­at­ory cul­tures, the re­search­ers offered the mi­crobes vari­ous kinds of food and used a vari­ety of dif­fer­ent meth­ods to keep a close eye on how Meth­an­ol­i­paria deal with it. What was par­tic­u­larly sur­pris­ing to see was that this ar­chaeon ac­tiv­ated all the dif­fer­ent hy­dro­car­bons with one and the same en­zyme. “So far, we have only cul­tiv­ated ar­chaea that live on short-chain hy­dro­car­bons such as eth­ane or bu­tane. Meth­an­ol­i­paria, on the other hand, prefers heavy oil with its long-chain com­pounds,” says co-au­thor Ra­fael Laso-Pérez, who now works at Spain’s Na­tional Cen­ter for Bi­o­tech­no­logy (CNB).

“Meth­ano­genic mi­crobes that use long-chain hy­dro­car­bons dir­ectly – we did­n’t know these ex­is­ted un­til now. Even com­plic­ated hy­dro­car­bons with ring-like or aro­matic struc­tures are not too bulky for Meth­an­ol­i­paria, at least if they are bound to at least one longer car­bon chain. This means that be­sides our other ex­cit­ing res­ults we have also found a pre­vi­ously com­pletely un­known path­way of meth­ano­gen­esis.”


It doesn’t look like much, but it’s full of surprises: Bottles like these harbor the cultures of Methanoliparia. Credit: Lei Cheng

Detectable from the oil tank to the deep sea

The Meth­an­ol­i­paria cells cul­tured for the present study ori­gin­ate from one of Chin­a’s largest oil fields, the Shengli oil field. However, ge­netic ana­lyses show that these mi­crobes are dis­trib­uted all over the world, even down to the deep sea. “Our res­ults hold an en­tirely new un­der­stand­ing of oil ex­ploit­a­tion in sub­sur­face oil reser­voirs. Both the wide dis­tri­bu­tion of these or­gan­isms and the po­ten­tial in­dus­trial ap­plic­a­tions make this an ex­cit­ing field of re­search in the com­ing years,” We­gener con­cludes.

Reference: “Non-syntrophic methanogenic hydrocarbon degradation by an archaeal species” by Zhuo Zhou, Cui-jing Zhang, Peng-fei Liu, Lin Fu, Rafael Laso-Pérez, Lu Yang, Li-ping Bai, Jiang Li, Min Yang, Jun-zhang Lin, Wei-dong Wang, Gunter Wegener, Meng Li and Lei Cheng, 22 December 2021, Nature.

DOI: 10.1038/s41586-021-04235-2