Genome-Guided Analysis of Clostridium ultunense and Comparative Genomics Reveal Different Strategies for Acetate Oxidation and Energy Conservation in Syntrophic Acetate-Oxidising Bacteria

Abstract

Syntrophic acetate oxidation operates close to the thermodynamic equilibrium and very little is known about the participating organisms and their metabolism. Clostridium ultunense is one of the most abundant syntrophic acetate-oxidising bacteria (SAOB) that are found in engineered biogas processes operating with high ammonia concentrations. It has been proven to oxidise acetate in cooperation with hydrogenotrophic methanogens. There is evidence that the Wood-Ljungdahl (WL) pathway plays an important role in acetate oxidation. In this study, we analysed the physiological and metabolic capacities of C. ultunense strain Esp and strain BST on genome scale and conducted a comparative study of all the known characterised SAOB, namely Syntrophaceticus schinkii, Thermacetogenium phaeum, Tepidanaerobacter acetatoxydans, and Pseudothermotoga lettingae. The results clearly indicated physiological robustness to be beneficial for anaerobic digestion environments and revealed unexpected metabolic diversity with respect to acetate oxidation and energy conservation systems. Unlike S. schinkii and Th. phaeum, C. ultunense clearly does not employ the oxidative WL pathway for acetate oxidation, as its genome (and that of P. lettingae) lack important key genes. In both of those species, a proton motive force is likely formed by chemical protons involving putative electron-bifurcating [Fe-Fe] hydrogenases rather than proton pumps. No genes encoding a respiratory Ech (energy-converting hydrogenase), as involved in energy conservation in Th. phaeum and S. schinkii, were identified in C. ultunense and P. lettingae. Moreover, two respiratory complexes sharing similarities to the proton-translocating ferredoxin:NAD+ oxidoreductase (Rnf) and the Na+ pumping NADH:quinone hydrogenase (NQR) were predicted. These might form a respiratory chain that is involved in the reduction of electron acceptors rather than protons. However, involvement of these complexes in acetate oxidation in C. ultunense and P. lettingae needs further study. This genome-based comparison provides a solid platform for future meta-proteomics and meta-transcriptomics studies and for metabolic engineering, control, and monitoring of SAOB.

The Wood–Ljungdahl pathway as a key component of metabolic versatility in candidate phylum Bipolaricaulota (Acetothermia, OP1)

“…D). This scenario is very similar to the energy conservation mechanism utilized by the syntrophic acetate oxidizer Clostridium ultunense (Manzoor et al ., ). RBG‐16‐55‐9 genomes also encode a high‐affinity acetate transporter belonging to the sodium: solute symporter family (TC: 2.A.21, pfam 00474) similar to the one identified in the acetate oxidizer Syntrophoaceticus schinkii (Manzoor et al ., ) (Fig.…”

“…(ii) An ion gradient‐driven phosphorylation, as the net ATP production by SLP during WL pathway is zero. (iii) A high affinity acetate transporter, as SAO bacteria are present in environments where acetoclastic methanogens are also prevalent and competition for acetate as a carbon source is expected (Manzoor et al ., ; ).…”

“…3D). This scenario is very similar to the energy conservation mechanism utilized by the syntrophic acetate oxidizer Clostridium ultunense (Manzoor et al, 2018). genomes also encode a high-affinity acetate transporter belonging to the sodium: solute symporter family (TC: 2.…”

“…SAO using the reversal of the WL pathway for the conversion of acetate to H 2 and CO 2 has been studied in pure culture (Schnürer et al, 1997;Hattori et al, 2005;Westerholm et al, 2011;Manzoor et al, 2016;Manzoor et al, 2018). All five SAO bacteria were from engineered biogas facilities, although multiple studies have provided evidence for the presence of SAO in other anaerobic environments (Horn et al, 2003;Chauhan and Ogram, 2006;Jones et al, 2007;Liu and Conrad, 2010;Gray et al, 2011;Rui et al, 2011;Mayumi et al, 2013).…”

Novel energy conservation strategies and behaviour of Pelotomaculum schinkii driving syntrophic propionate catabolism

“…The energy conservation strategies of Pelotomaculum and Syntrophobacter clearly differ, where Syntrophobacter seemed to have a more intricate energy conservation mechanism. A recent study has also reported contrasting energy conservation mechanisms among syntrophic acetate and aromatic compound oxidizers (Nobu et al ., ; Manzoor et al ., ), suggesting diversity in energy metabolism across syntrophic organisms.…”