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17.03.2015 Meth­ane seeps: Oases in the deep sea

First global study of mi­cro­bial com­munit­ies at gas seeps in the deep sea shows the dis­tri­bu­tion and di­versity of meth­ane-con­sum­ing mi­croor­gan­isms. The spe­cific en­ergy source se­lects for unique mi­croor­gan­isms, which turn these eco­sys­tems into hot­spots of di­versity in the deep sea.
 
Methane seeps: Oases in the deep sea

First global study of mi­cro­bial com­munit­ies at gas seeps in the deep sea shows the dis­tri­bu­tion and di­versity of meth­ane-con­sum­ing mi­croor­gan­isms. The spe­cific en­ergy source se­lects for unique mi­croor­gan­isms, which turn these eco­sys­tems into hot­spots of di­versity in the deep sea.

Meth­ane seeps are places in the ocean, where meth­ane from deep sed­i­ment lay­ers es­capes the seabed. Spe­cific mi­croor­gan­isms use the po­ten­tial green­house gas as an en­ergy source and thus form the basis for com­plex eco­sys­tems. Now an in­ter­na­tional team of re­search­ers led by the Max Planck In­sti­tute for Mar­ine Mi­cro­bi­o­logy has in­vest­ig­ated the mi­cro­bial com­munit­ies of se­lec­ted meth­ane seeps from all oceans, and com­pared those to com­munit­ies of other mar­ine eco­sys­tems. In the cur­rent is­sue of Pro­ceed­ings of the Na­tional Academy of Sci­ences (USA), the re­search­ers re­port that meth­ane seeps con­tain many en­demic mi­croor­gan­isms and there­fore are hot­spots of biod­iversity in the deep sea. In gen­eral, the seep com­munit­ies are very dif­fer­ent from those of other eco­sys­tems. Only a few spe­cies of meth­an­o­trophs oc­cur at all seeps world­wide, but these mi­croor­gan­isms seem to greatly in­flu­ence the meth­ane budget of the ocean.

Seafloor ecosystems have unique inhabitants
Each eco­sys­tem in the deep sea is in­hab­ited by cer­tain mi­croor­gan­isms that can be as­signed to the three do­mains of the tree of life: eu­k­a­ryotes, ar­chaea and bac­teria. Eu­k­a­ryotes have a nuc­leus and in­clude all plants, fungi, an­im­als and man. Ar­chaea and bac­teria are single cells without a nuc­leus. The re­search­ers stud­ied the com­pos­i­tion and re­l­at­ive abund­ance of ar­chaea and bac­teria at 77 loc­a­tions of dif­fer­ent mar­ine eco­sys­tems, in­clud­ing coastal sed­i­ments, deep-sea sed­i­ments, black smokers and meth­ane seeps. They ex­trac­ted the DNA of these or­gan­isms from the seabed samples and ana­lyzed it us­ing mod­ern DNA se­quen­cing tech­niques and math­em­at­ical al­gorithms.

Emil Ruff, sci­ent­ist at the Max Planck In­sti­tute, sum­mar­izes: "Al­most all of the ma­jor groups of ar­chaea and bac­teria were present at all ex­amined sites. With in­creas­ing res­ol­u­tion, however, the dif­fer­ences between the eco­sys­tems be­came clearer. At the level of in­di­vidual spe­cies, which are the smal­lest branches of the tree of life, we found com­munit­ies that are char­ac­ter­istic for each eco­sys­tem and have a very spe­cific task." These char­ac­ter­istic com­munit­ies were defined as the meth­ane seep mi­cro­bi­ome. The term mi­cro­bi­ome is used to de­scribe all mi­croor­gan­isms of a par­tic­u­lar eco­sys­tem and their ge­netic di­versity. Such an eco­sys­tem may be a meth­ane seep, or soil or even the hu­man in­test­ine. The head of the re­search group, Prof. Dr. Antje Boe­t­ius, adds: "This study rep­res­ents the first global view on mi­crobes in­hab­it­ing meth­ane seeps. It was en­abled by a large in­ter­na­tional ef­fort, the In­ter­na­tional Census of Mar­ine Mi­crobes.”
Methanotrophic microorganisms of methane seep ecosystems.
Micrographs of aerobic methanotrophic bacteria (white), anaerobic methanotrophic archaea (ANME – red) and sulfate-reducing bacteria (SRB – green) visualized by fluorescence in situ hybridization. ANME and SRB perform the anaerobic oxidation of methane (AOM). AOM is a globally relevant process removing 60 million tons, the mass of ten pyramids of Giza, of the greenhouse gas methane from seafloor sediments each year. Courtesy of Katrin Knittel/Emil Ruff, MPI Bremen.
Methane seeps accommodate many specialists
Nat­ural meth­ane seeps (cold seeps) are found world­wide at con­tin­ental mar­gins. The gas is formed by de­com­pos­i­tion pro­cesses in the an­oxic lay­ers deep down in the sed­i­ment, moves up­wards and es­capes at the sea­floor. The up­per­most sed­i­ment lay­ers har­bor meth­ane ox­id­izers, which con­sume about three-quar­ters of the es­cap­ing meth­ane. This is equi­val­ent to 60 mil­lion tons of car­bon per year. At meth­ane seeps, the primary en­ergy source is com­pletely dif­fer­ent from those of the sur­round­ing seabed. Thus, like oases in the desert meth­ane sources at­tract par­tic­u­lar or­gan­isms. These in­clude groups with known func­tion, such as an­aer­obic meth­ane-ox­id­iz­ing ar­chaea (ANME) and sulfate-re­du­cing bac­teria (SRB). However, the re­search­ers also found mi­cro­bial groups on the meth­ane sources with un­known func­tion.


Emil Ruff, first au­thor of the study, said: "It was sur­pris­ing that mi­croor­gan­isms from seeps that are thou­sands of miles away in dif­fer­ent oceans, are so closely re­lated. Many meth­ane ox­id­izers and sulfate re­du­cers are sens­it­ive to oxy­gen. There­fore, it is a mys­tery how they sur­vive the great dis­tances between the meth­ane seeps." The find­ings of the re­search­ers sug­gest that only a few world­wide pop­u­la­tions are re­spons­ible for the bulk of the meth­ane con­sump­tion. The vast di­versity of spe­cies and the evol­u­tion of new spe­cies, however, is lim­ited to and can only be found at cer­tain sites. Meth­ane seeps thus con­trib­ute greatly to the biod­iversity of the deep sea.


Global dis­per­sion and local di­ver­si­fic­a­tion of the meth­ane seep mi­cro­bi­ome. Emil Ruff, Jen­nifer F. Biddle, An­dreas Teske, Kat­rin Knit­tel, Antje Boe­t­ius, Al­ban Ramette PNAS 2015.
DOI: 10.1073/​pnas.1421865112.

More information
Emil Ruff, Max Plank In­sti­tute for Mar­ine Mi­cro­bi­o­logy, Bre­men: +49 421 2028 942; eruff@mpi-bre­men.de

or from the press of­ficer

Man­fred Schlösser, Max Plank In­sti­tute for Mar­ine Mi­cro­bi­o­logy, Bre­men: +49 421 2028 704 mschloes@mpi-bre­men.de
Four methane seeps and their inhabitants

Top left: Mytilid mus­sels and Galatheid crabs in­hab­it­ing car­bon­ate pre­cip­it­a­tions of a meth­ane seep on the Kongo con­tin­ental mar­gin. Both, mus­sels and crabs can only live in this ex­treme eco­sys­tem be­cause they have sym­bi­otic bac­teria that feed their host. These sym­bionts con­vert chem­ical en­ergy into bio­mass and thus cause eco­sys­tems that are as densely pop­u­lated as trop­ical rain­forests. Cour­tesy of MARUM, Uni­versity Bre­men. ROV QUEST; MET­EOR Ex­ped­i­tion M76/​3.

Top right: Mi­cro­bial mat of or­ange and white sulf­ide-ox­id­iz­ing bac­teria on the con­tin­ental mar­gin of Costa Rica. The bac­teria grow on sulf­idic sed­i­ments and form gi­ant fil­a­ments that are vis­ible by the na­ked eye. The sulf­ide is pro­duced in the un­der­ly­ing sed­i­ment by meth­ane-ox­id­iz­ing, sulfate-re­du­cing mi­cro­bial com­munit­ies. The sed­i­ment is sampled with a “Push­core” op­er­ated by a sub­mers­ible. Cour­tesy of MARUM, Uni­versity Bre­men. dive 207: ROV QUEST; MET­EOR Ex­ped­i­tion M66/​2; Bac­terial mats

Bottom left: Mi­cro­bial reefs are found in the an­oxic part of the Black Sea. The reefs are up to sev­eral meters high and con­sist of car­bon­ate pre­cip­it­a­tions caused by mi­cro­bial activ­ity and biofilms dom­in­ated by an­aer­obic meth­an­o­trophic ar­chaea (ANME). The reefs form at the sea­floor, where meth­ane es­capes from seabed reser­voirs, form­ing streams of gas bubbles. Cour­tesy of MARUM, Uni­versity Bre­men.

Bottom right: The Guay­mas Basin in the Gulf of Cali­for­nia is a unique hy­dro­thermal eco­sys­tem where hot flu­ids formed in the sub­sur­face seep through thick sed­i­ment lay­ers. At the sed­i­ment sur­face, min­eral pre­cip­it­a­tion from the vent flu­ids form ex­tens­ive mounds and spires which are covered in or­ange and white mats of gi­ant sul­fur-ox­id­iz­ing bac­teria. The handles in the fore­ground be­long to sed­i­ment samplers that are de­ployed us­ing the sub­mers­ible ALVIN. Cour­tesy of the Woods Hole Ocean­o­graphic In­sti­tu­tion (WHOI); Guay­mas Basin cruise AT15-56, An­dreas Teske."
 
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