Metabolism of position-labelled glucose in anoxic methanogenic paddy soil and lake sediment

Carbon flow from benthic diatoms to heterotrophic bacterial was traced in an intertidal sediment for 5 consecutive days. 13 C-labeled bicarbonate was sprayed onto the sediment surface during low tide and 13 C-label incorporation in major carbon pools, intermediate metabolites, and biomarkers were monitored. Phospholipidderived fatty acid (PLFA) and ribosomal ribonucleic acid (rRNA) were used to identify the responsible members of the microbial community at class and family phylogenetic resolution. Diatoms were the predominant primary producers, and Gammaproteobacteria, Bacteroidetes, and Deltaproteobacteria (21%, 8%, and 7% of 16S rRNAderived clone library) were major heterotrophic bacterial groups. Both 13 C-PLFA and 13 C-rRNA data suggest a fast transfer of label from diatoms (60 nmol 13 C g 21 dry weight [dry wt]) to bacteria (7 nmol 13 C g 21 dry wt) during the first 24 h, which was probably due to the exudation of low-molecular-weight organic compounds by diatoms that could be directly utilized by bacteria. After this initial fast transfer, labeling of bacteria proceeded at a slower rate to 13 nmol 13 C g 21 dry wt on the third day of the experiment, which coincided with the degradation of carbohydrates in water-extractable extracellular polymeric substances (EPS) initially produced by the diatoms. Water-extractable EPS (primarily as glucose) was a major intermediate and its turnover explained 75% of the total carbohydrate processing in the sediment. Labeling in bacteria tracked labeling in the diatoms, suggesting a closely coupled system. The heterotrophic bacterial groups benefited equally from the organic matter released by the diatoms, suggesting limited specialization in this microbial food web.

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“…The eluent was 8 mmol L 21 sulfuric acid at a flow rate of 0.4 mL min 21 (Krumbock and Conrad 1991).…”

Section: Methodsmentioning

confidence: 99%

Tracing carbon flow from microphytobenthos to major bacterial groups in an intertidal marine sediment by using an in situ ¹³C pulse‐chase method

Miyatake

Moerdijk-Poortvliet

Stal

et al. 2014

Limnology & Oceanography

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“…The pH was measured using a glass electrode. Acetate (and other fatty acids) was analyzed by high pressure liquid chromatography (HPLC) (Sykam, Gilching, Germany) equipped with both refraction index detector and UV detector (Krumböck & Conrad 1991). The δ 13 C of CH 4 and CO 2 were analyzed by gas chromatography combustion isotope ratio mass spectrometry (GC-C-IRMS), and the δ 13 C of acetate was analyzed by HPLC-C-IRMS as described before .…”

Section: Methodsmentioning

confidence: 99%

Stable carbon isotope fractionation during methanogenesis in three boreal peatland ecosystems

2010

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Abstract. The degradation of organic matter to CH 4 and CO 2 was investigated in three different boreal peatland systems in Finland, a mesotrophic fen (MES), an oligotrophic fen (OLI), and an ombrotrophic peat (OMB). MES had similar production rates of CO 2 and CH 4 , but the two nutrientpoor peatlands (OLI and OMB) produced in general more CO 2 than CH 4 . δ 13 C analysis of CH 4 and CO 2 in the presence and absence methyl fluoride (CH 3 F), an inhibitor of acetoclastic methanogenesis, showed that CH 4 was predominantly produced by hydrogenotrophic methanogenesis and that acetoclastic methanogenesis only played an important role in MES. These results, together with our observations concerning the collective inhibition of CH 4 and CO 2 production rates by CH 3 F, indicate that organic matter was degraded through different paths in the mesotrophic and the nutrient-poor peatlands. In the mesotrophic fen, the major process is canonical fermentation followed by acetoclastic and hydrogenotrophic methanogenesis, while in the nutrient-poor peat, organic matter was apparently degraded to a large extent by a different path which finally involved hydrogenotrophic methanogenesis. Our data suggest that degradation of organic substances in the oligotrophic environments was incomplete and involved the use of organic compounds as oxidants.

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“…At intervals of 3 to 4 days, the total CH 4 formed in slurries was monitored by gas chromatography (GC) (45), and 13 C/ 12 C isotope ratios of CH 4 and CO 2 were determined by GC-isotope ratio mass spectrometry (5). At intervals of ϳ10 days, 0.2 ml of slurry water was sampled for quantification of fatty acids by high-pressure liquid chromatography (25). After 2 days, 3 weeks, and 7 weeks of incubation, microcosms were opened, and soil samples stored frozen (Ϫ20°C) for subsequent nucleic acid extraction.…”

Section: Methodsmentioning

confidence: 99%

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

Lueders

Pommerenke

Friedrich

2004

Appl Environ Microbiol

186

142

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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...

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Metabolism of position-labelled glucose in anoxic methanogenic paddy soil and lake sediment

Cited by 55 publications

References 28 publications

Tracing carbon flow from microphytobenthos to major bacterial groups in an intertidal marine sediment by using an in situ ¹³C pulse‐chase method

Tracing carbon flow from microphytobenthos to major bacterial groups in an intertidal marine sediment by using an in situ ¹³C pulse‐chase method

Stable carbon isotope fractionation during methanogenesis in three boreal peatland ecosystems

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

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Metabolism of position-labelled glucose in anoxic methanogenic paddy soil and lake sediment

Cited by 55 publications

References 28 publications

Tracing carbon flow from microphytobenthos to major bacterial groups in an intertidal marine sediment by using an in situ 13C pulse‐chase method

Tracing carbon flow from microphytobenthos to major bacterial groups in an intertidal marine sediment by using an in situ 13C pulse‐chase method

Stable carbon isotope fractionation during methanogenesis in three boreal peatland ecosystems

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

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Tracing carbon flow from microphytobenthos to major bacterial groups in an intertidal marine sediment by using an in situ ¹³C pulse‐chase method

Tracing carbon flow from microphytobenthos to major bacterial groups in an intertidal marine sediment by using an in situ ¹³C pulse‐chase method