Diverse sulfate-reducing bacteria of the Desulfosarcina/Desulfococcus clade are the key alkane degraders at marine seeps.
Biogeochemical and microbiological data indicate that the anaerobic oxidation of non-methane hydrocarbons by sulfate-reducing bacteria (SRB) has an important role in carbon and sulfur cycling at marine seeps. Yet, little is known about the bacterial hydrocarbon degraders active in situ. Here, we provide the link between previous biogeochemical measurements and the cultivation of degraders by direct identification of SRB responsible for butane and dodecane degradation in complex on-site microbiota. Two contrasting seep sediments from Mediterranean Amon mud volcano and Guaymas Basin (Gulf of California) were incubated with (13)C-labeled butane or dodecane under sulfate-reducing conditions and analyzed via complementary stable isotope probing (SIP) techniques. Using DNA- and rRNA-SIP, we identified four specialized clades of alkane oxidizers within Desulfobacteraceae to be distinctively active in oxidation of short- and long-chain alkanes. All clades belong to the Desulfosarcina/Desulfococcus (DSS) clade, substantiating the crucial role of these bacteria in anaerobic hydrocarbon degradation at marine seeps. The identification of key enzymes of anaerobic alkane degradation, subsequent β-oxidation and the reverse Wood-Ljungdahl pathway for complete substrate oxidation by protein-SIP further corroborated the importance of the DSS clade and indicated that biochemical pathways, analog to those discovered in the laboratory, are of great relevance for natural settings. The high diversity within identified subclades together with their capability to initiate alkane degradation and growth within days to weeks after substrate amendment suggest an overlooked potential of marine benthic microbiota to react to natural changes in seepage, as well as to massive hydrocarbon input, for example, as encountered during anthropogenic oil spills.
Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany.
Sara
S
Kleindienst
Helmholtz Centre for Environmental Research (UFZ), Department of Proteomics, Leipzig, Germany.
Florian-Alexander
FA
Herbst
Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany.
Marion
M
Stagars
Helmholtz Zentrum München-German Research Center for Environmental Health, Institute for Groundwater Ecology, Neuherberg, Germany.
Frederick
F
von Netzer
Helmholtz Centre for Environmental Research (UFZ), Department of Proteomics, Leipzig, Germany.
Martin
M
von Bergen
Helmholtz Centre for Environmental Research (UFZ), Department of Proteomics, Leipzig, Germany.
Jana
J
Seifert
Ribocon GmbH, Bremen, Germany.
Jörg
J
Peplies
Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany.
Rudolf
R
Amann
Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany.
Florin
F
Musat
Helmholtz Zentrum München-German Research Center for Environmental Health, Institute for Groundwater Ecology, Neuherberg, Germany.
Tillmann
T
Lueders
Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany.
Katrin
K
Knittel
D000473:Alkanes / Q000378:metabolism*; D001419:Bacteria / Q000145:classification / Q000302:isolation & purification; D044822:Biodiversity; D002073:Butanes / Q000378:metabolism; D020564:Deltaproteobacteria / Q000145:classification / Q000302:isolation & purification / Q000378:metabolism*; D019015:Geologic Sediments / Q000382:microbiology*; D006838:Hydrocarbons / Q000378:metabolism; D010084:Oxidation-Reduction; D010802:Phylogeny; D012623:Seawater; D013431:Sulfates / Q000378:metabolism*; D013440:Sulfides / Q000378:metabolism
D000473:Alkanes; D002073:Butanes; D006838:Hydrocarbons; D013431:Sulfates; D013440:Sulfides; C007548:n-dodecane; C046888:butane