title: 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).
authors: Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands. Electronic address: petra.worm@wur.nl.
authors: Petra
authors: P
authors: Worm
authors: Laboratory of Systems and Synthetic Biology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands.
authors: Jasper J
authors: JJ
authors: Koehorst
authors: Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands.
authors: Michael
authors: M
authors: Visser
authors: Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands.
authors: Vicente T
authors: VT
authors: Sedano-Núñez
authors: Laboratory of Systems and Synthetic Biology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands.
authors: Peter J
authors: PJ
authors: Schaap
authors: Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands.
authors: Caroline M
authors: CM
authors: Plugge
authors: Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands; Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal.
authors: Diana Z
authors: DZ
authors: Sousa
authors: Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands; Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal.
authors: Alfons J M
authors: AJM
authors: Stams
mesh_terms: D000693:Anaerobiosis; D001421:Bacteria, Anaerobic / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D002087:Butyrates / Q000378:metabolism; D017753:Ecosystem; D005227:Fatty Acids / Q000378:metabolism*; D016680:Genome, Bacterial / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D006859:Hydrogen / Q000378:metabolism; D008697:Methane / Q000378:metabolism; D010802:Phylogeny
chemical_list: D002087:Butyrates; D005227:Fatty Acids; D006859:Hydrogen; D008697:Methane
keywords: Acetate; Butyrate; Formate; Functional profiling; Propionate; Syntrophy