Bre­men re­search­ers cul­tiv­ate ar­chaea that break down crude oil in novel ways

Al­kanes are highly stable com­pounds of car­bon and hy­dro­gen. They are nat­ural com­pon­ents of nat­ural gas and crude oil. The lat­ter is re­fined by hu­mans into fuels like gas­ol­ine and ker­osene. En­vir­on­mental cata­strophes oc­cur re­peatedly due to ac­ci­dents dur­ing the ex­trac­tion of crude oil. A prime ex­ample was the ac­ci­dent on the Deep­wa­ter Ho­ri­zon drilling plat­form, which caused severe en­vir­on­mental dam­age in the Gulf of Mex­ico due to the toxic ef­fects of crude oil com­pounds like li­quid al­kanes. In the pres­ence of oxy­gen, mi­croor­gan­isms can rap­idly break down many com­pon­ents of crude oil, among oth­ers al­kanes. Without the re­act­ive oxy­gen, however, de­grad­a­tion is con­sid­er­ably more dif­fi­cult. Or­gan­isms that can per­form this task have not been ex­tens­ively re­searched. In re­cent years, however, evid­ence has been found that ar­chaea are able to em­ploy a sur­pris­ing mech­an­ism to do this. It is based on newly dis­covered vari­ants of the key en­zyme of meth­ano­gen­esis and an­aer­obic meth­ane de­grad­a­tion, methyl-coen­zyme M re­ductase (MCR). The genes that en­code these en­zymes have been found in many en­vir­on­mental samples. However, labor­at­ory cul­tures of the mi­crobes that could il­lus­trate the func­tion of these en­zymes were still lack­ing. This is where the labor­at­ory study of Hanna Zehnle and her col­leagues be­comes sig­ni­fic­ant.

In the Bre­men labor­at­or­ies the re­search­ers pre­pared cul­tures with li­quid al­kanes and al­lowed them to grow an­aer­obic­ally, i.e., without oxy­gen, at high tem­per­at­ures (70 de­grees Celsius). “After a time,” ex­plains first au­thor Hanna Zehnle, “sulf­ide forms in the cul­tures. This provides evid­ence that they are act­ive.” The com­pos­i­tion of the cul­tures is stud­ied us­ing DNA and RNA samples. “With this method we can find out what or­gan­isms are liv­ing in this sys­tem and which meta­bolic path­ways they are us­ing,” says Zehnle. These in­clude the chem­ical re­ac­tions in which sub­stances are meta­bol­ized. They found ar­chaea of the genus Candidatus Alkanophaga in the cul­tures. These ar­chaea use vari­ants of the MCR for break­ing down the al­kanes. The re­search­ers veri­fied this by tran­scrip­tome data, meas­ure­ment of the en­zyme products, and by demon­strat­ing in­activ­ity of the cul­tures when the en­zyme was in­hib­ited. But the or­gan­isms are not able to de­grade the crude oil alone. Res­pir­a­tion, in the form of sulfate re­duc­tion in this case (be­cause no oxy­gen is present), is car­ried out by bac­teria of the genus Thermodesulfobacterium, which form dense con­sor­tia with the ar­chaea.

Meth­ano­gen­esis is one of the old­est known meta­bolic pro­cesses and is a part of the global car­bon cycle. The labor­at­ory study by Hanna Zehnle and her col­leagues shows that the en­zymes in­volved in this pro­cess can also util­ize li­quid (and thus toxic) hy­dro­car­bons which high­lights the rel­ev­ance of this path­way for the global car­bon cycle.

“Thanks to their newly dis­covered cap­ab­il­it­ies, Al­kan­o­phaga and their re­l­at­ives are tar­get­ing hy­dro­car­bons in oil reser­voirs. The re­main­ing oil be­comes more and more solid and there­fore tends to re­main in the sea­floor,” ex­plains cor­res­pond­ing au­thor Gunter We­gener. “We still have not been able to in­vest­ig­ate any deep oil reser­voirs, but the ar­chaea are cer­tainly an­noy­ing the oil in­dustry with their activ­ity. But they also make an im­port­ant con­tri­bu­tion to the fact that nat­ural oil seeps are rare.”

This study is a part of the re­search within the Cluster of Ex­cel­lence “The Ocean Floor – Earth’s Un­charted In­ter­face”, which is housed at MARUM. Among other re­search areas, in­vest­ig­a­tions are be­ing con­duc­ted here to de­term­ine which mi­croor­gan­isms and en­vir­on­mental con­di­tions provide the ocean floor with the qual­it­ies re­quired to func­tion as a re­actor that has been bal­an­cing the Earth's car­bon cycle since time im­me­morial. Ques­tions re­lat­ing to what the or­gan­isms in the deep bio­sphere in higher tem­per­at­ure ranges live from is one of the core themes of the Cluster.