Microbial cycling of formate and other low-molecular weight aliphatic organic acids in anoxic environments

Abstract

Short-chain organic acids (SCOAs) are important intermediates in the microbial and thermogenic degradation of photosynthesis-derived organic matter, and in the abiotic synthesis of organic compounds. Despite the vast environmental importance of SCOAs, many questions remain open concerning the controls on their environmental turnover. This is true for acetate, propionate, and butyrate, which have been the subject of many past investigations, as well as for formate, which is the focus of this dissertation. To better elucidate the controls on environmental formate turnover, I therefore combined detailed analyses on natural geochemical gradients, experimental incubations, thermodynamic calculations, and a newly developed assay targeting a marker gene of formate cycling, the alpha subunit of formate hydrogenase (fdhA). In my first research chapter, I investigated formate turnover in Swiss lake sediment based on analyses of natural samples and batch incubations with added 13C-formate (Chapter 2). The batch experiments indicate rapid conversion of formate to H2 and HCO3-, and that this process is catalyzed by microbial cells rather than free enzymes. This interpretation is supported by calculations indicating that formate conversion to H2 and HCO3- is an exergonic process with free energies around the minimum that can be conserved by microorganisms. Additional incubations of marine sediments, activated sludge, anaerobic digester sludge, and river water indicate that similar mechanisms control formate cycling in other anaerobic environments, but that formate turnover operates differently in the presence of O2. Furthermore, fdhA analyses indicate the genetic potential for formate cycling to be common, with fdhA gene copy numbers in the same range as total 16S rRNA genes, and widespread among phylogenetically diverse, mostly unknown lacustrine sediment microorganisms. To follow up on the results from marine sediments, I next compared formate turnover to the turnover of acetate, propionate, butyrate in sulfate reducing and methanogenic sediment from Aarhus Bay (Chapter 3). My results indicate that formate is turned over by a similar mechanism as in lake sediment, i.e. via the conversion to H2 and HCO3-, and that the turnover rate of formate is not only vastly higher than for the other SCOAs, but also higher in methanogenic than in sulfate reducing sediment. By contrast, no significant increases in H2 or formate concentrations occurred in acetate, propionate and butyrate treatments, suggesting complete oxidation by single microorganisms and/or presence of highly efficient syntrophic consortia that leak minimal amounts of interspecies electron carriers to growth media. As in lake sediment, gene copy numbers of fdhA are in a range comparable to total 16S rRNA genes, and occur across a phylogenetically diverse number of groups. In the final research chapter, I investigated a transect of serpentinite mud volcanoes in the Mariana Convergent Margin to shed light into the origin of short-chain organic acids, H2, and methane and their potential to sustain microbial life in these mud volcanoes. My results indicate that high amounts of H2, formate, acetate, and methane are produced by and/or are an indirect outcome of serpeninitic weathering of mantle rock in the underlying subducting slab. Hereby concentrations of these compounds correlate with slab temperatures, and formate and acetate concentrations in mud fluids follow an Arrhenius-type, exponential relationship with temperature in the subducting slab. Unlike lacustrine and marine sediments, formate is at thermodynamic equilibrium with H2 and HCO3-. Thus, the elevated concentrations of formate can be explained with formate equilibration with H2 produced by serpentinization. By contrast, the drivers behind the elevated acetate and methane concentrations are uncertain. Furthermore, even though calculations indicate a wide range of microbial metabolic reactions to be thermodynamically favorable, I find no evidence of an active microbial biosphere. Overall, this thesis presents new insights into the role and microbial turnover mechanisms of formate, as well as other SCOAs, H2, and methane in seafloor and lacustrine environments. Results can be used for further research by increasing the sequencing depth of available fdhA genes form various environments and samples. This would be highly beneficial to investigate the change of relative abundance in various sediment types and redox conditions and to identify patterns in abundance to see if diversity is due to the redox state and dominating terminal respiration process, or maybe correlated with other parameters like depth and/or diagenetic status of organic matter. Confirmation of the here presented proposal of abiotic serpentinite driven acetate production mechanisms are of interest for further research on origin of life and for astrobiologists, serpentinization in ubiquitous on other planets and acetate is an important energy substrate for known catabolism.