Re­search­ers cul­tiv­ate ar­chaea that break down crude oil in novel ways

How mi­croor­gan­isms deep in the seabed render crude oil harm­less

05-Jun-2023 - Germany

The sea­floor is home to around one-third of all the mi­croor­gan­isms on the Earth and is in­hab­ited even at a depth of sev­eral kilo­met­ers. Only when it be­comes too hot does the abund­ance of mi­croor­gan­isms ap­pear to de­cline. But how, and from what, do mi­croor­gan­isms in the deep sea­floor live? How do their meta­bolic cycles work and how do the in­di­vidual mem­bers of these bur­ied com­munit­ies in­ter­act? Re­search­ers at MARUM – Cen­ter for Mar­ine En­vir­on­mental Sci­ences at the Uni­versity of Bre­men and at the Max Planck In­sti­tute for Mar­ine Mi­cro­bi­o­logy at Bre­men have now been able to demon­strate in labor­at­ory cul­tures how small, li­quid com­pon­ents of crude oil are broken down through a new mech­an­ism by a group of mi­croor­gan­isms called ar­chaea. Their res­ults have now been pub­lished in the pro­fes­sional journal Nature Microbiology.

Woods Hole Ocea­no­gra­phic In­sti­tu­ti­on

In the spot­light of the U.S. deep-sea sub­mers­ible ALVIN, a small red­dish-brown vent mas­sif can be seen on the sea­floor of the Guay­mas Basin. This form­a­tion is sur­roun­ded by abund­ant hy­dro­therm­ally heated oil-rich sed­i­ments covered by white and or­ange bac­terial mats. The core from which the Can­did­atus Al­kan­o­phaga ar­chaea ul­ti­mately ori­gin­ated was col­lec­ted by the team of the manned deep-sea sub­mers­ible.

Hanna Zehnle

The microbial community was cultivated in a variety of liquid alkanes, here a hexane culture. An oil layer can be observed on the surface.

Woods Hole Ocea­no­gra­phic In­sti­tu­ti­on
Hanna Zehnle

Mi­cro­bial com­munit­ies are es­pe­cially act­ive near hy­dro­thermal seeps like those in the Guay­mas Basin in the Gulf of Cali­for­nia. The team of re­search­ers has been work­ing on un­der­stand­ing these com­munit­ies for many years. Or­ganic ma­ter­ial de­pos­ited in the Guay­mas Basin is cooked by heat sources from within the Earth, which breaks it down into crude oil and nat­ural gas. Their com­pon­ents provide the primary source of en­ergy for mi­croor­gan­isms in an oth­er­wise hos­tile en­vir­on­ment. In their latest study, the re­search­ers have demon­strated that ar­chaea use a pre­vi­ously un­known mech­an­ism to de­grade li­quid pet­ro­leum al­kanes at high tem­per­at­ures without the pres­ence of oxy­gen.

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.

The team used sed­i­ments from the 2000-meter-deep Guay­mas Basin in the Gulf of Cali­for­nia. The spe­cial geo­lo­gical con­di­tions that ex­ist here in­clude high tem­per­at­ures, li­quid crude-oil com­pon­ents, and an an­aer­obic en­vir­on­ment at shal­low sed­i­ment depths, all of which are nor­mally only found in deep-ly­ing oil reser­voirs which are dif­fi­cult for sci­ent­ists to ac­cess.

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.”

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