New Microbe Produces Methane From Crude Oil

Mi­cro­scopy sug­gests that the re­cently dis­covered mi­crobe Meth­an­ol­i­paria pro­duces meth­ane from crude oil all by them­selves.

The tiny organisms cling to oil droplets and perform a great feat: As a single organism, they may produce methane from oil by a process called alkane disproportionation. Previously this was only known from symbioses between bacteria and archaea. Scientists from the Max Planck Institute for Marine Microbiology have now found cells of this microbe called Methanoliparia in oil reservoirs worldwide.

Mussels at an oil spill in the Gulf of Mexico. Credit: © MARUM – Center for Marine Environmental Sciences

Crude oil and gas nat­ur­ally es­cape from the seabed in many places known as “seeps.” There, these hy­dro­car­bons move up from source rocks through frac­tures and sed­i­ments to­wards the sur­face, where they leak out of the ground and sustain a diversity of densely populated habitats in the dark ocean. A large part of the hy­dro­car­bons, primar­ily al­kanes, is already de­graded be­fore it reaches the sed­i­ment sur­face. Even deep down in the sed­i­ment, where no oxy­gen ex­ists, it provides an im­port­ant en­ergy source for sub­sur­face mi­croor­gan­isms, amongst them some of the so-called ar­chaea.

These ar­chaea were good for many sur­prises in re­cent years (see “Fur­ther read­ing”). Now a study led by sci­ent­ists from the Max Planck In­sti­tute for Mar­ine Mi­cro­bi­o­logy in Bre­men, Ger­many, and the MARUM, Center for Mar­ine En­vir­on­mental Sci­ences, provides en­vir­on­mental in­form­a­tion, gen­omes and first im­ages of a mi­crobe that has the po­ten­tial to trans­form long-chain hy­dro­car­bons to meth­ane. Their res­ults are pub­lished in the journal mBio.

Splitting oil into methane and carbon dioxide

This mi­crobe, an ar­chaeon named Meth­an­ol­i­paria, trans­forms the hy­dro­car­bons by a pro­cess called al­kane dis­pro­por­tion­a­tion: It splits the oil into meth­ane (CH₄) and car­bon di­ox­ide (CO₂). Pre­vi­ously, this trans­form­a­tion was thought to re­quire a com­plex part­ner­ship between two kinds of or­gan­isms, ar­chaea, and bac­teria. Here the team from Max Planck In­sti­tute for Mar­ine Mi­cro­bi­o­logy and MARUM presents evid­ence for a dif­fer­ent solu­tion. “This is the first time we get to see a mi­crobe that has the po­ten­tial to de­grade oil to meth­ane all by it­self,” first-au­thor Ra­fael Laso-Pérez ex­plains.

The submersible vehicle MARUM-QUEST samples for sediment at oil seeps in the Gulf of Mexico. Credit: © MARUM – Center for Marine Environmental Sciences

Dur­ing a cruise in the Gulf of Mex­ico, the sci­ent­ists col­lec­ted sed­i­ment samples from the Chapo­pote Knoll, an oil and gas seep, 3000 m deep in the ocean. Back in the lab in Bre­men, they car­ried out ge­n­omic ana­lyses that re­vealed that Meth­an­ol­i­paria is equipped with novel en­zymes to use the quite un­re­act­ive oil without hav­ing oxy­gen at hand. “The new or­gan­ism, Meth­an­ol­i­paria, is kind of a com­pos­ite be­ing”, says Gunter We­gener, the ini­ti­ator and senior au­thor of this study. “Some of its relatives are multi-carbon hydrocarbon-degrading archaea, oth­ers are the long-known own meth­ano­gens that form meth­ane as meta­bolic product.” With the com­bined en­zymatic tools of both re­l­at­ives, Meth­an­ol­i­paria ac­tiv­ates and de­grades the oil but forms meth­ane as fi­nal product. Moreover, the visu­al­iz­a­tion of the or­gan­isms sup­ports the pro­posed mech­an­ism: “Mi­cro­scopy shows that Meth­an­ol­i­paria cells at­tach to oil droplets. We did not find any hints that it re­quires bac­teria or other ar­chaea as part­ners”, We­gener con­tin­ues.

Very frequent and globally distributed

Meth­ano­genic mi­croor­gan­isms have been im­port­ant for the earth’s cli­mate through time as their meta­bolic product, meth­ane, is an im­port­ant green­house gas that is 25 times more po­tent than car­bon di­ox­ide. Thus, Laso-Pérez and his col­leagues where also in­ter­ested to find out about how wide­spread this novel or­gan­ism is. “We scanned DNA-lib­rar­ies and found that Meth­an­ol­i­paria is fre­quently de­tec­ted in oil reser­voirs – and only in oil reser­voirs – all over the oceans. Thus, this or­gan­ism could be a key agent in the trans­form­a­tion of long-chain hy­dro­car­bons to meth­ane,” says Laso-Pérez.

Epifluorescence microscopy picture of Methanoliparia-cells attached to a droplet of oil. The white scale bar represents a length of 10 micrometers. Credit: © Max Planck Institute for Marine Microbiology

Thus, the sci­ent­ists next want to dig deeper into the secret life of this mi­crobe. “Now we have the ge­n­omic evid­ence and pic­tures about the wide dis­tri­bu­tion and sur­pris­ing po­ten­tial of Meth­an­ol­i­paria. But we can’t yet grow them in the lab. That will be the next step to take. It will en­able us to in­vest­ig­ate many more ex­cit­ing de­tails”, We­gener ex­plains. “For ex­ample, whether it is pos­sible to re­verse the pro­cess, which would ul­ti­mately al­low us to trans­form a green­house gas into fuel.”

Reference: “An­aer­obic de­grad­a­tion of non-meth­ane al­kanes by “Candidatus Methanoliparia” in hy­dro­car­bon seeps of the Gulf of Mex­ico” by Ra­fael Laso-Pérez, Cedric Hahn, Daan M. van Vliet, Halina E. Te­get­meyer, Florence Schubotz, Nad­ine T. Smit, Thomas Pape, Heiko Sah­ling, Ger­hard Bo­hr­mann, Antje Boe­t­ius, Kat­rin Knit­tel and Gunter We­gener, 20 August 2019, mBio.
DOI: 10.1128/mBio.01814-19