Genome-Guided Analysis and Whole Transcriptome Profiling of the Mesophilic Syntrophic Acetate Oxidising Bacterium Syntrophaceticus schinkii

Abstract

Syntrophaceticus schinkii is a mesophilic, anaerobic bacterium capable of oxidising acetate to CO2 and H2 in intimate association with a methanogenic partner, a syntrophic relationship which operates close to the energetic limits of microbial life. Syntrophaceticus schinkii has been identified as a key organism in engineered methane-producing processes relying on syntrophic acetate oxidation as the main methane-producing pathway. However, due to strict cultivation requirements and difficulties in reconstituting the thermodynamically unfavourable acetate oxidation, the physiology of this functional group is poorly understood. Genome-guided and whole transcriptome analyses performed in the present study provide new insights into habitat adaptation, syntrophic acetate oxidation and energy conservation. The working draft genome of Syntrophaceticus schinkii indicates limited metabolic capacities, with lack of organic nutrient uptake systems, chemotactic machineries, carbon catabolite repression and incomplete biosynthesis pathways. Ech hydrogenase, [FeFe] hydrogenases, [NiFe] hydrogenases, F1F0-ATP synthase and membrane-bound and cytoplasmic formate dehydrogenases were found clearly expressed, whereas Rnf and a predicted oxidoreductase/heterodisulphide reductase complex, both found encoded in the genome, were not expressed under syntrophic growth condition. A transporter sharing similarities to the high-affinity acetate transporters of aceticlastic methanogens was also found expressed, suggesting that Syntrophaceticus schinkii can potentially compete with methanogens for acetate. Acetate oxidation seems to proceed via the Wood-Ljungdahl pathway as all genes involved in this pathway were highly expressed. This study shows that Syntrophaceticus schinkii is a highly specialised, habitat-adapted organism relying on syntrophic acetate oxidation rather than metabolic versatility. By expanding its complement of respiratory complexes, it might overcome limiting bioenergetic barriers, and drive efficient energy conservation from reactions operating close to the thermodynamic equilibrium, which might enable S. schinkii to occupy the same niche as the aceticlastic methanogens. The knowledge gained here will help specify process conditions supporting efficient and robust biogas production and will help identify mechanisms important for the syntrophic lifestyle.

Genome-Guided Analysis of the Syntrophic Acetate Oxidizer <em>C. ultunense</em> and Comparative Genomics Reveal Different Strategies for Acetate Oxidation and Energy Conservation in Syntrophic Acetate-Oxidising Bacteria

“…In the case of P. lettingae, only phage remnants were predicted (Table S2). This is within the range observed for the other SAOB (Table S2) [29,31,34]. Tepidanaerobacter acetatoxydans and Th.…”

“…Pure culture and enzymatic studies affiliate all but P. lettingae to the physiological group of acetogens, producing acetate as the main end product by employing the reductive Wood-Ljungdahl (WL) pathway when growing heterotrophically [14,23,24,[26][27][28]. Whole cell extract-based enzyme activities and mRNA expression studies indicate that the SAOB use a reversal of the WL pathway for oxidising acetate to hydrogen and carbon dioxide [14,27,29,30]. The thermophilic P. lettingae does not express acetogenic metabolism [25] and must therefore use an alternative pathway.…”

“…T. acetatoxydans might also use another metabolic route for acetate oxidation, as genome-scale analysis has revealed a lack of F0/F1-ATP synthase, which makes use of the oxidative WL pathway for acetate oxidation energetically unfeasible [31]. In contrast, transcriptomic studies of a methane-producing syntrophic co-culture have demonstrated expression of the WL pathway genes in S. schinkii [29]. Genome-based analysis, which has been thoroughly performed for T. acetatoxydans, Th.…”

“…acetatoxydans, the genome of S. schinkii harbours an Ech hydrogenase and several duplicates of [Fe-Fe] hydrogenase [29]. The genome of the thermophilic Th.…”

“…Genome-guided analyses reported for Th. phaeum [34], T. acetatoxydans [31] and S. schinkii [29] provided the basis for the comparison. In the case of P. lettingae, we analysed a publically available genome draft.…”