Mixtrophic sulfate-reducing Desulfobacterota dominate the dark carbon fixation process in marine sediments

Ubiquitous sulfate-reducing Desulfobacterota (SRD) are well-known to account for sulfate reduction and accompanying organic matter mineralization in marine sediments. However, their chemoautotrophic activities thereof are largely underestimated in both ecological and physiological studies. Here, we performed laboratory experiments whereby coastal and deep sea marine sediments were incubated in microcosms supplemented with 13C-labeled DIC (dissolved inorganic carbon). Microbial diversity based on 16S rRNA amplicon and metagenome both suggested a noticeable enrichment of Desulfobacterota after incubation. DNA-stable isotope probing (SIP) suggested that seven families of SRD assimilated 13C-DIC significantly, with Desulfovibrionaceae/Desulfocapsaceae and Desulfobacteraceae exihibiting the most remarkable activities for the coastal and deep sea sediments, respectively. Genome-resolved metagenomic analyses evidenced that the Wood-Ljungdahl pathway (WLP) and reductive glycine pathway (rGlyP) were likely responsible for the carbon fixation activities of Desulfovibrionaceae and Desulfocapsaceae/Desulfobacteraceae. Degradation of lignin-derived aromatic compounds hindered the carbon fixation activity. Combining DNA-SIP with metabolic and genomic analyses, it is inferred that mixtrophic SRD are capable of altering their trophy modes and fluxes via the bidirectional WLP or rGlyP in response to varying levels of accessible nutrients. Taken together, this study provides a deeper insight in the ecological role of SRD in marine sediments, not restricted to the well-known sulfate reducer and associated organic acid degrader, but expanded to an active participant in chemoautotrophical carbon fixation.