Stable-Isotope Probing of Microorganisms Thriving at Thermodynamic Limits: Syntrophic Propionate Oxidation in Flooded Soil

Abstract

Propionate is an important intermediate of the degradation of organic matter in many anoxic environments. In methanogenic environments, due to thermodynamic constraints, the oxidation of propionate requires syntrophic cooperation of propionate-fermenting proton-reducing bacteria and H 2 -consuming methanogens. We have identified here microorganisms that were active in syntrophic propionate oxidation in anoxic paddy soil by rRNA-based stable-isotope probing (SIP). After 7 weeks of incubation with [ 13 C]propionate (<10 mM) and the oxidation of ϳ30 mol of 13 C-labeled substrate per g dry weight of soil, we found that archaeal nucleic acids were 13 C labeled to a larger extent than those of the bacterial partners. Nevertheless, both terminal restriction fragment length polymorphism and cloning analyses revealed Syntrophobacter spp., Smithella spp., and the novel Pelotomaculum spp. to predominate in "heavy" 13 C-labeled bacterial rRNA, clearly showing that these were active in situ in syntrophic propionate oxidation. Among the Archaea, mostly Methanobacterium and Methanosarcina spp. and also members of the yet-uncultured "rice cluster I" lineage had incorporated substantial amounts of 13 C label, suggesting that these methanogens were directly involved in syntrophic associations and/or thriving on the [13 C]acetate released by the syntrophs. With this first application of SIP in an anoxic soil environment, we were able to clearly demonstrate that even guilds of microorganisms growing under thermodynamic constraints, as well as phylogenetically diverse syntrophic associations, can be identified by using SIP. This approach holds great promise for determining the structure and function relationships of further syntrophic or other nutritional associations in natural environments and for defining metabolic functions of yet-uncultivated microorganisms.In many anoxic environments, which are low in electron acceptors such as oxygen, nitrate, sulfate, and iron or manganese oxides, complex organic matter is degraded to methane and CO 2 by the cooperation of anaerobic microorganisms of several metabolic guilds (47). An important intermediate of organic matter conversion under methanogenic conditions is propionate, which may account for up to 35% of methanogenesis in anaerobic digestors (35) and up to 30% in paddy soil (15,26). The degradation of propionate to acetate, CO 2 , and 3 H 2 is highly endergonic under standard conditions (⌬G°Ј ϭ ϩ76.1 kJ/mol), but it can be accomplished by syntrophic cooperation of propionate-oxidizing hydrogen-producing bacteria and hydrogen (or formate)-scavenging partner microorganisms (methanogens), which maintain a low hydrogen partial pressure (for a review, see reference 47). Only in such syntrophic associations does propionate degradation become feasible under methanogenic conditions. The process has been studied extensively in flooded rice field soil (26, 27, 58), in upflow anaerobic sludge blanket reactors (52), and sediments (46,49). In all environments studied, the methyl-malonyl-coenzyme...

Extracellular Quinones Affecting Methane Production and Methanogenic Community in Paddy Soil

“…Using rice paddy soil as microbial inocula, Kato et al [19] reported the syntrophic association between Geobacter and Methanosarcina in the presence of hematite and magnetite; methanogenesis was facilitated via DIET through (semi) conductive iron oxides. In this study, Methanosarcina and Methanobacterium are detected as the most abundant methanogens in the soil cultures, similar to other rice paddy soils [9,29,52]. T-RFLP results showed that the amendment of AQDS (0.5 and 5 mM) led to increased relative abundance of Methanosarcina at the expense of Methanobacterium.…”

“…The genus Geobacter has been surprisingly discovered to be capable of forming highly conductive network of pilis that facilitate long-range electron transfer [34,38,39], which is becoming an important feature of Geobacter species in anaerobic environments [17,26,27]. There is increasing evidence that Geobacter species are important syntrophic microorganisms capable of establishing syntrophic association with methanogens [19,29,45]. Recent study demonstrated the possibility of direct interspecies electron transfer (DIET) between Geobacter species and Methanosaeta concilii within upflow anaerobic sludge blanket reactor methanogenic aggregates, which were electrically conductive largely contributed by Geobacter species [32].…”

Wetland restoration and methanogenesis: the activity of microbial populations and competition for substrates at different temperatures

“…Members of RC-I are hydrogenotrophic and more active at low H 2 concentrations , which allows them to grow in syntrophy with secondary fermenters (Lueders et al, 2004). RC-I is often found in periodically oxic environments, suggesting that they are well adapted to oxic stress during periods of drought .…”

Identification of iron-reducing microorganisms in anoxic rice paddy soil by 13C-acetate probing

“…Rice field soil slurry was prepared as described earlier (Hori et al, 2007). To activate the soil microorganisms and reduce endogenous electron acceptors such as available sulfate and ferric iron oxides, the slurry was pre-incubated for 21 days in the dark at 25 1C Friedrich, 2000, 2002;Lueders et al, 2004b). Aliquots (10 ml) of the homogenized slurry were transferred into 25-ml serum vials.…”