Specialists instead of generalists oxidize alkanes in anoxic marine hydrocarbon seep sediments

The anaerobic oxidation of non-methane hydrocarbons mediated by
sulfate-reducing bacteria (SRB) is a major process of organic matter degradation at
marine hydrocarbon seeps. Several SRB have been successfully cultured, however,
knowledge about in situ active organisms is still very limited. Here, we identified
alkane-degrading key players from two contrasting seeps at the Mediterranean Amon
Mud Volcano (Amon MV) and Guaymas Basin in the Gulf of California using
complementary stable-isotope probing (SIP) techniques. Anoxic sediments were
incubated with 13C-labeled butane or dodecane under close to in situ conditions.
DNA- and RNA-based SIP in combination with 454-pyrosequencing (PYRO-SIP) allowed the
identification of four phylogenetically distinct deltaproteobacterial groups of
alkane-oxidizing SRB within the family Desulfobacteraceae. We named the groups
degrading short-chain alkanes ‘SCA-SRB1' and ‘SCA-SRB2' and those degrading
long-chain alkanes ‘LCA-SRB1' and ‘LCA-SRB2'. CARD-FISH with newly developed
specific probes revealed a high relative in situ abundance of SCA-SRB1 and SCA-SRB2
with 2% of the total community, while groups LCA-SRB1 and LCA-SRB2 were below 1% of
total cells. Protein-based SIP (Protein-SIP), which enables to trace stable isotopes
from substrate to protein, confirmed alkane-degrading key players of the family
Desulfobacteraceae. In addition, Protein-SIP indicated additional carbon sources for
13C biosynthesis besides alkanes, and gave insights into possible metabolic
pathways: (1-methylalkyl)succinylation as initial step of butane degradation and the
oxidative Wood–Ljungdahl pathway as terminal point of alkane
degradation.