Open AccessIdentification of acetate‐oxidizing bacteria in a coastal marine surface sediment by RNA ‐stable isotope probing in anoxic slurries and intact cores
Author(s) -
Vandieken Verona,
Thamdrup Bo
Publication year - 2013
Publication title -
fems microbiology ecology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.377
H-Index - 155
eISSN - 1574-6941
pISSN - 0168-6496
DOI - 10.1111/1574-6941.12069
Subject(s) - anoxic waters , biology , environmental chemistry , denitrification , bacteria , manganese , stable isotope probing , sediment , nitrate , sulfate , microbiology and biotechnology , chemistry , microorganism , ecology , nitrogen , organic chemistry , paleontology , genetics
We investigated the terminal electron‐accepting pathways and the acetate‐oxidizing bacteria in surface sediment (0–5 mm depth) of A arhus B ay, D enmark, in anoxic slurry and intact core incubations. In the intact cores, oxygen, nitrate, oxides of manganese and iron, and sulfate were all available and likely all used as electron acceptors by the microbial community, whereas microbial iron and sulfate reduction dominated in the slurries. The availability of electron acceptors clearly affected which organisms were labeled by 16 S r RNA ‐stable isotope probing ( SIP ). Members of the O ceanospirillaceae were identified as 13 C ‐acetate oxidizers in both types of incubations, but bacteria related to C olwellia and A rcobacter oxidized acetate in the intact core, while members of the D esulfuromonadales and A cidithiobacillaceae did so in the slurry incubation. D esulfuromonadales sequences also dominated 16 S r RNA gene clone libraries from the highest positive dilution of the acetate‐oxidizing most probable number cultures with manganese and iron oxides. Thus, members of D esulfuromonadales are likely important for acetate oxidation coupled to iron and manganese reduction in situ , while the identified G ammaproteobacteria and affiliates of A rcobacter may utilize oxygen, nitrate and manganese oxides. Our study further highlights some of the biases that are associated with the use of RNA ‐ SIP as well as slurry and intact core incubations.