Ubiquitous Gammaproteobacteria dominate dark carbon fixation in coastal sediments.

Marine sediments are one of the largest carbon sinks in the world. The most dominant form of carbon fixation in the oceans is dark carbon fixation occurring in coastal sediments. Dark carbon fixation is the process of inorganic carbon fixation by chemolithoautotrophic microorganisms without the use of light energy.

The main focus of the study is to gain an insight into how inorganic carbon at the sediments surface is turned over and possibly buried. The study aims to do this by filling an important gap in our current knowledge by providing details of the microbes that drive this process.

The authors sampled sediment from 13 coastal sites across Western Europe and Australia down to a depth of up to 4.9m below the sea bed. 10 of the sediment collection sites were in tidal zones and 3 from sublittoral sandy sediments. The Authors then chose 3 different and distinct sediment layers to molecularly analyse. The molecular analysis carried out was 16S rRNA gene amplicon sequencing and CARD-FISH analysis. All sediment samples had their DNA extracted and the sequenced using the 16S rRNA gene amplicon method to provide taxonomic classifications for each sample.

From the 13 sampled sites only 3 were selected for ¹⁴C-bicarbonate incubation. There were from Calais, Courseulles-sur-Mer and Janssand. The C¹⁴ incubation was in preparation for CARD-FISH, Fluorescence activated flow sorting (FACS) and scintillography.

The results from the above mentioned analysis revealed that the most abundant clade present in all sites according to 16S rRNA gene amplicon sequencing was the Gammaproteobacteria clade making up anything from 12-45% of sequences regardless of site, sediment depth or season. This finding was supported by the CARD-FISH analysis of the Calais, Courseulles-sur-Mer and Janssand sites where 19-22% of all bacteria present were from the Gammaproteobacteria clade. The chemoautotrophs present were often associated with 1) Acidiferrobacter thiooxydans of the family Ectothiorhodospiraceae, 2) Symbiotically associated with tube worms such as Oligobrachia spp., 3) the ciliate symbiont Candidatus thiobios zoothamnicoli and 4) the BD7-8 clade which includes the g3-symbiont of Olavius algarvensis a gutless marine oligochaete. In spite of the variety of associations up to 52% of all Gammaproteobacteria sequences were found grouped with the uncultured clade JTB255. The CARD-FISH analysis of the JTB255-clade found rod-shaped cells. Although the exact environmental function of JTB255 is unknown it is thought that it carries out some kind of sulphur oxidising activity. This is important because the main chemolithoautotrophic process in marine sediments is thought to be sulfur oxidisation.

With regards to dark carbon fixation the Gammaproteobacteria had a ¹⁴C-assimilation total that was 2.5 to 5 times higher than that of the sorted Bacteria. Although Gammaproteobacteria only accounted for 19-22% of the microbial community they accounted for 70-86% of the microbial dark carbon fixation irrespective of sampling site, season and sediment depth.

This study is significant because it is starting to identify another major carbon sink on a similar level to that of the amount of carbon buried in marine vegetation habitats worldwide but more research is needed to explain this fully.

Dyksma, S., Bischof, K., Fuchs, B. M., Hoffmann, K., Meier, D., Meyerdierks, A., ... & Mußmann, M. (2016). Ubiquitous Gammaproteobacteria dominate dark carbon fixation in coastal sediments. The ISME journal.