A genomic view on syntrophic versus non-syntrophic lifestyle in anaerobic fatty acid degrading communities

Abstract

In sulfate-reducing and methanogenic environments complex biopolymers are hydrolyzed and degraded by fermentative micro-organisms that produce hydrogen, carbon dioxide and short chain fatty acids. Degradation of short chain fatty acids can be coupled to methanogenesis or to sulfate-reduction. Here we study from a genome perspective why some of these micro-organisms are able to grow in syntrophy with methanogens and others are not. Bacterial strains were selected based on genome availability and upon their ability to grow on short chain fatty acids alone or in syntrophic association with methanogens. Systematic functional domain profiling allowed us to shed light on this fundamental and ecologically important question. Extra-cytoplasmic formate dehydrogenases (InterPro domain number; IPR006443), including their maturation protein FdhE (IPR024064 and IPR006452) is a typical difference between syntrophic and non-syntrophic butyrate and propionate degraders. Furthermore, two domains with a currently unknown function seem to be associated with the ability of syntrophic growth. One is putatively involved in capsule or biofilm production (IPR019079) and a second in cell division, shape-determination or sporulation (IPR018365). The sulfate-reducing bacteria Desulfobacterium autotrophicum HRM2, Desulfomonile tiedjei and Desulfosporosinus meridiei were never tested for syntrophic growth, but all crucial domains were found in their genomes, which suggests their possible ability to grow in syntrophic association with methanogens. In addition, profiling domains involved in electron transfer mechanisms revealed the important role of the Rnf-complex and the formate transporter in syntrophy, and indicate that DUF224 may have a role in electron transfer in bacteria other than Syntrophomonas wolfei as well. This article is a part of a Special Issue entitled: 18th European Bioenergetics Conference (Biochim. Biophys. Acta, Volume 1837, Issue 7, July 2014).

Microwave and ultrasound pre-treatments influence microbial community structure and digester performance in anaerobic digestion of waste activated sludge

“…Consequently, reduced particle size by the US and MW pre-treatments possibly stimulated the prevalence of this group. Clostridiales possesses diverse metabolic competences, and its members also show syntrophic capability, a mutualistic behaviour vital for complete anaerobic conversion of complex material (Worm et al 2014). At species level, a notable increase in relative abundance of S. sapovorans and S. wolfei during the later operating period of D MW further implies favouring of syntrophic bacteria by increased substrate availability.…”

Fermentative Cyclohexane Carboxylate Formation in <b><i>Syntrophus aciditrophicus</i></b>

“…The latter scenario is related to one of the most intriguing questions in syntrophy: how are the highpotential electrons derived from acyl-CoA oxidation to enoyl-CoA (E° ′ ≈ -10 mV) transferred to reduce protons to H 2 or CO 2 to formate against a huge thermodynamic barrier of ΔE ′ ≈ -250 mV (considering syntrophic concentrations of the formate/H 2 products)? The often suggested involvement of menaquinones and the membrane potential has not been experimentally demonstrated to date [Worm et al, 2014]. A gene annotated as an FeS oxidoreductase, oxr , is located next to the two encoding genes of ETF, etfAB .…”

Microbiology and Molecular Biology Tools for Biogas Process Analysis, Diagnosis and Control

“…On the molecular level, genes encoding key enzymes of important metabolic pathways in the biogas process such as methyl-coenzyme M reductase (isogenes mcr and mrt encoding coenzyme-B sulfoethylthiotransferase, EC 2.8.4.1, the key enzyme of methanogenesis, which is present in all and exclusively in methanogenic Archaea), formyl-tetrahydrofolate synthetase (or formate-tetrahydrofolate ligase, fhs, EC 6.3.4.3, key enzyme of the Wood-Ljungdahl-pathway) or certain hydrogenases (e.g. ech, hyd) and their transcripts are ideal bioindicators and targets of molecular biomarkers [4], and even more will be identified in the near future [11,99]. (RT)qPCR markers can be Fig.…”

“…Syntrophic bacteria or anaerobic fungi partners of methanogens are difficult to cultivate and to study without their product-consuming associate. Modern characterization is typically initiated by genome or metagenome analysis, possibly leading to insights about special requirements that allow cultivation of pure isolates and studying their special physiological performances [10][11][12].…”